Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold113
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3764034
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 4009 characters in sequence are not A, C, G, or T
File 4 of 23
Found at i:489222 original size:20 final size:20
Alignment explanation
Indices: 489197--489267 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
489187 AGACAGAATA
489197 TATCGATACATTGAAAAATG
1 TATCGATACATTGAAAAATG
* * *
489217 TATCGATACATTCATACATG
1 TATCGATACATTGAAAAATG
489237 TATCGATACATTGAAAAATG
1 TATCGATACATTGAAAAATG
489257 TATCGATACAT
1 TATCGATACAT
489268 CTGGGTAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (20 bp):
TATCGATACATTGAAAAATG
Found at i:490038 original size:32 final size:30
Alignment explanation
Indices: 489992--490693 Score: 429
Period size: 28 Copynumber: 24.3 Consensus size: 30
489982 AAAAAGGTTA
* * *
489992 CCACCAACTTGTGTGGGCTTTAGAGAAAGTTG
1 CCACTAACTTGTGTGGGCTTT-GA-AAGGATG
* *
490024 CCACTAACTTGTGTGGGCTTTAGAGAAAGTTG
1 CCACTAACTTGTGTGGGCTTT-GA-AAGGATG
** *
490056 CCACCGACTTGTGTGGGCTATGAAAGGATG
1 CCACTAACTTGTGTGGGCTTTGAAAGGATG
*
490086 CCACTGAC-T-TGTGGGCTTTGAAAGGATG
1 CCACTAACTTGTGTGGGCTTTGAAAGGATG
* * *
490114 CCACTTAC-T-TGTGGGCTTCGAAAGGGTG
1 CCACTAACTTGTGTGGGCTTTGAAAGGATG
490142 CCACTAAC-T-TGTGGGCTTTGAAAGGATG
1 CCACTAACTTGTGTGGGCTTTGAAAGGATG
* * * *
490170 TCACTGAC-T-TGTAGGCTTTG-GAGAGATG
1 CCACTAACTTGTGTGGGCTTTGAAAG-GATG
*
490198 CCACTAAC-T-TGTAGGCTTTGAAAGGATG
1 CCACTAACTTGTGTGGGCTTTGAAAGGATG
490226 CCACTAAC-T-TGTGGGCTTTGAAAGGATG
1 CCACTAACTTGTGTGGGCTTTGAAAGGATG
*
490254 CCACTGAC-T-TGTGGGCTTT-AAATGGATG
1 CCACTAACTTGTGTGGGCTTTGAAA-GGATG
*
490282 CCACTAAC-T-TGTGGGCTTTGAAAAGATG
1 CCACTAACTTGTGTGGGCTTTGAAAGGATG
* * *
490310 GCACTGAC-T-TGTAGGCTTTG-AAGAGATG
1 CCACTAACTTGTGTGGGCTTTGAAAG-GATG
* * *
490338 CCACTGAC-T-TATGGGCTTTGAAAGGCTG
1 CCACTAACTTGTGTGGGCTTTGAAAGGATG
*
490366 CCACTAACTTGTGT---CTTTGAAATGATG
1 CCACTAACTTGTGTGGGCTTTGAAAGGATG
* *
490393 CCACTAAC-T-TATGGGCTTTGAAAGTATG
1 CCACTAACTTGTGTGGGCTTTGAAAGGATG
*
490421 CCACTGAC-T-TGTGGGCTTTGAAAGGACTTTG
1 CCACTAACTTGTGTGGGCTTTGAAAGGA---TG
** * * *
490452 AAAGGGTGCCACTAACT-TATGGGCTTTGAAAGGATG
1 CCA--CT--AACT---TGTGTGGGCTTTGAAAGGATG
*
490488 CCACTGAC-T-TGTGGGCTTTG-AAGAGATG
1 CCACTAACTTGTGTGGGCTTTGAAAG-GATG
* * *
490516 CCACTGAC-T-TGTGGGATTTGAAATGATG
1 CCACTAACTTGTGTGGGCTTTGAAAGGATG
* *
490544 TCACTGAC-T-TGTGGGCTTTG-AAGAGATG
1 CCACTAACTTGTGTGGGCTTTGAAAG-GATG
* *
490572 CCACTGAC-T-TGTGGGCTTTGAAAGGGTG
1 CCACTAACTTGTGTGGGCTTTGAAAGGATG
* * **
490600 CCACTGAC-T-TATAAGCTTTGAAAGGATG
1 CCACTAACTTGTGTGGGCTTTGAAAGGATG
*
490628 CCACTGAC-T-TGTGGGCTTTG-AAGAGATG
1 CCACTAACTTGTGTGGGCTTTGAAAG-GATG
* * *
490656 CCACTGA-TT-TGTGGGTTTTGAAAGGGTG
1 CCACTAACTTGTGTGGGCTTTGAAAGGATG
*
490684 CCACTGACTT
1 CCACTAACTT
490694 ATAGGCTTTG
Statistics
Matches: 571, Mismatches: 69, Indels: 63
0.81 0.10 0.09
Matches are distributed among these distances:
25 2 0.00
26 1 0.00
27 34 0.06
28 420 0.74
29 20 0.04
30 14 0.02
31 5 0.01
32 51 0.09
33 1 0.00
34 1 0.00
35 2 0.00
36 3 0.01
39 17 0.03
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.30
Consensus pattern (30 bp):
CCACTAACTTGTGTGGGCTTTGAAAGGATG
Found at i:490107 original size:28 final size:28
Alignment explanation
Indices: 490003--490446 Score: 500
Period size: 28 Copynumber: 15.6 Consensus size: 28
489993 CACCAACTTG
* *
490003 TGTGGGCTTTAGAGAAAGTTGCCACTAACTT
1 TGTGGGCTTT-GA-AAGGATGCCACTAAC-T
* * **
490034 GTGTGGGCTTTAGAGAAAGTTGCCACCGACTT
1 -TGTGGGCTTT-GA-AAGGATGCCACTAAC-T
* *
490066 GTGTGGGCTATGAAAGGATGCCACTGACT
1 -TGTGGGCTTTGAAAGGATGCCACTAACT
*
490095 TGTGGGCTTTGAAAGGATGCCACTTACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
* *
490123 TGTGGGCTTCGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
* *
490151 TGTGGGCTTTGAAAGGATGTCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
* *
490179 TGTAGGCTTTG-GAGAGATGCCACTAACT
1 TGTGGGCTTTGAAAG-GATGCCACTAACT
*
490207 TGTAGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
*
490235 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
490263 TGTGGGCTTT-AAATGGATGCCACTAACT
1 TGTGGGCTTTGAAA-GGATGCCACTAACT
* * *
490291 TGTGGGCTTTGAAAAGATGGCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
* *
490319 TGTAGGCTTTG-AAGAGATGCCACTGACT
1 TGTGGGCTTTGAAAG-GATGCCACTAACT
* *
490347 TATGGGCTTTGAAAGGCTGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
* *
490375 TGT-GTCTTTGAAATGATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
* * *
490402 TATGGGCTTTGAAAGTATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTAACT
490430 TGTGGGCTTTGAAAGGA
1 TGTGGGCTTTGAAAGGA
490447 CTTTGAAAGG
Statistics
Matches: 361, Mismatches: 44, Indels: 18
0.85 0.10 0.04
Matches are distributed among these distances:
27 30 0.08
28 269 0.75
29 9 0.02
30 12 0.03
31 2 0.01
32 39 0.11
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTAACT
Found at i:490137 original size:56 final size:56
Alignment explanation
Indices: 490003--490705 Score: 745
Period size: 56 Copynumber: 12.2 Consensus size: 56
489993 CACCAACTTG
* * * * * *
490003 TGTGGGCTTTAGAGAAAGTTGCCACTAACTTGTGTGGGCTTTAGAGAAAGTTGCCACCGACTT
1 TGTGGGCTTT-GA-AAGGATGCCACTGAC-T-TGTGGGCTTT-GA-AAGGATGCCACTGAC-T
* *
490066 GTGTGGGCTATGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTTACT
1 -TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
490123 TGTGGGCTTCGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAGGATGTCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * * * *
490179 TGTAGGCTTTG-GAGAGATGCCACTAACTTGTAGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAG-GATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
*
490235 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTT-AAATGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAA-GGATGCCACTGACT
* * *
490291 TGTGGGCTTTGAAAAGATGGCACTGACTTGTAGGCTTTG-AAGAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAG-GATGCCACTGACT
* * * * * *
490347 TATGGGCTTTGAAAGGCTGCCACTAACTTGT-GTCTTTGAAATGATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * *
490402 TATGGGCTTTGAAAGTATGCCACTGACTTGTGGGCTTTGAAAGGACTTTGAAAGGGTGCCACTAA
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAA-G-----G--A---TGCCACTGA
490467 CT
55 CT
*
490469 TATGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG-AAGAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAG-GATGCCACTGACT
* * *
490525 TGTGGGATTTGAAATGATGTCACTGACTTGTGGGCTTTG-AAGAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAG-GATGCCACTGACT
* * **
490581 TGTGGGCTTTGAAAGGGTGCCACTGACTTATAAGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* * *
490637 TGTGGGCTTTG-AAGAGATGCCACTGATTTGTGGGTTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAG-GATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
* *
490693 TATAGGCTTTGAA
1 TGTGGGCTTTGAA
490706 GAGATGAACT
Statistics
Matches: 553, Mismatches: 65, Indels: 49
0.83 0.10 0.07
Matches are distributed among these distances:
55 55 0.10
56 388 0.70
57 7 0.01
58 11 0.02
59 3 0.01
60 10 0.02
61 2 0.00
62 13 0.02
63 2 0.00
64 10 0.02
65 1 0.00
66 2 0.00
67 49 0.09
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (56 bp):
TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:490165 original size:84 final size:84
Alignment explanation
Indices: 490003--490705 Score: 772
Period size: 84 Copynumber: 8.2 Consensus size: 84
489993 CACCAACTTG
* * * * *
490003 TGTGGGCTTTAGAGAAAGTTGCCACTAACTTGTGTGGGCTTTAGAGAAAGTTGCCACCGACTTGT
1 TGTGGGCTTT-GA-AAGGATGCCACTAAC-T-TGTGGGCTTT-GA-AAGGATGCCACTGAC-T-T
*
490068 GTGGGCTATGAAAGGATGCCACTGACT
58 GTGGGCTTTGAAAGGATGCCACTGACT
* * * *
490095 TGTGGGCTTTGAAAGGATGCCACTTACTTGTGGGCTTCGAAAGGGTGCCACTAACTTGTGGGCTT
1 TGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTT
*
490160 TGAAAGGATGTCACTGACT
66 TGAAAGGATGCCACTGACT
* * * *
490179 TGTAGGCTTTG-GAGAGATGCCACTAACTTGTAGGCTTTGAAAGGATGCCACTAACTTGTGGGCT
1 TGTGGGCTTTGAAAG-GATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCT
490243 TTGAAAGGATGCCACTGACT
65 TTGAAAGGATGCCACTGACT
* * *
490263 TGTGGGCTTT-AAATGGATGCCACTAACTTGTGGGCTTTGAAAAGATGGCACTGACTTGTAGGCT
1 TGTGGGCTTTGAAA-GGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCT
490327 TTG-AAGAGATGCCACTGACT
65 TTGAAAG-GATGCCACTGACT
* * * * * *
490347 TATGGGCTTTGAAAGGCTGCCACTAACTTGT-GTCTTTGAAATGATGCCACTAACTTATGGGCTT
1 TGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTT
*
490411 TGAAAGTATGCCACTGACT
66 TGAAAGGATGCCACTGACT
*
490430 TGTGGGCTTTGAAAGGACTTTGAAAGGGTGCCACTAACTTATGGGCTTTGAAAGGATGCCACTGA
1 TGTGGGCTTTGAAA-G-----G--A---TGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGA
490495 CTTGTGGGCTTTG-AAGAGATGCCACTGACT
55 CTTGTGGGCTTTGAAAG-GATGCCACTGACT
* * * *
490525 TGTGGGATTTGAAATGATGTCACTGACTTGTGGGCTTTG-AAGAGATGCCACTGACTTGTGGGCT
1 TGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAG-GATGCCACTGACTTGTGGGCT
*
490589 TTGAAAGGGTGCCACTGACT
65 TTGAAAGGATGCCACTGACT
* ** * * *
490609 TATAAGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG-AAGAGATGCCACTGATTTGTGGGTT
1 TGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAG-GATGCCACTGACTTGTGGGCT
*
490673 TTGAAAGGGTGCCACTGACT
65 TTGAAAGGATGCCACTGACT
* *
490693 TATAGGCTTTGAA
1 TGTGGGCTTTGAA
490706 GAGATGAACT
Statistics
Matches: 534, Mismatches: 56, Indels: 50
0.83 0.09 0.08
Matches are distributed among these distances:
83 62 0.12
84 342 0.64
85 8 0.01
86 11 0.02
87 3 0.01
88 9 0.02
89 3 0.01
90 12 0.02
91 2 0.00
92 10 0.02
94 16 0.03
95 56 0.10
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (84 bp):
TGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTT
TGAAAGGATGCCACTGACT
Found at i:490462 original size:39 final size:39
Alignment explanation
Indices: 490408--490485 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
490398 AACTTATGGG
* * *
490408 CTTTGAAAGTATGCCACTGACTTGTGGGCTTTGAAAGGA
1 CTTTGAAAGGATGCCACTAACTTATGGGCTTTGAAAGGA
*
490447 CTTTGAAAGGGTGCCACTAACTTATGGGCTTTGAAAGGA
1 CTTTGAAAGGATGCCACTAACTTATGGGCTTTGAAAGGA
490486 TGCCACTGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (39 bp):
CTTTGAAAGGATGCCACTAACTTATGGGCTTTGAAAGGA
Found at i:490489 original size:67 final size:67
Alignment explanation
Indices: 490380--490509 Score: 233
Period size: 67 Copynumber: 1.9 Consensus size: 67
490370 TAACTTGTGT
* *
490380 CTTTGAAATGATGCCACTAACTTATGGGCTTTGAAAGTATGCCACTGACTTGTGGGCTTTGAAAG
1 CTTTGAAAGGATGCCACTAACTTATGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAG
490445 GA
66 GA
*
490447 CTTTGAAAGGGTGCCACTAACTTATGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAA
1 CTTTGAAAGGATGCCACTAACTTATGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAA
490510 GAGATGCCAC
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (67 bp):
CTTTGAAAGGATGCCACTAACTTATGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAG
GA
Found at i:491934 original size:13 final size:12
Alignment explanation
Indices: 491915--491948 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
491905 TAGACCCTTC
491915 TTTTTGTTTGTT
1 TTTTTGTTTGTT
491927 TGTTTTGTTTGTT
1 T-TTTTGTTTGTT
491940 TTTTT-TTTG
1 TTTTTGTTTG
491949 GTACGAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.19
12 5 0.24
13 12 0.57
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (12 bp):
TTTTTGTTTGTT
Found at i:493993 original size:42 final size:41
Alignment explanation
Indices: 493941--494187 Score: 209
Period size: 42 Copynumber: 5.9 Consensus size: 41
493931 TCAAAGATAA
* * *
493941 TGCCACCAATTGCTGTAGGTTTTAAAACGAAAAAAGAAAGGG
1 TGCCACCAATTG-TGTGGGCTTTAAAAAGAAAAAAGAAAGGG
* * * *
493983 TGCCATCAATTGTGTGGGCTTAAAGAAAG-AAAAAGGAGGGG
1 TGCCACCAATTGTGTGGGCTTTAA-AAAGAAAAAAGAAAGGG
*
494024 ATGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAA-AAA-GG
1 -TGCCACCAA-TTGTGTGGGCTTTAAAAAGAAAAAAGAAAGGG
* *
494065 TGCCACCAATTGTGTGGGCTTAAAGAAAGAAAAAA-AAAGGA
1 TGCCACCAATTGTGTGGGCTTTAA-AAAGAAAAAAGAAAGGG
* * * *
494106 TGACATCAACTTGTGTGGGCTTTTGAAAGGAAAAAAAGAAAGGGG
1 TGCCACCAA-TTGTGTGGGC-TTTAAAAAG-AAAAAAGAAA-GGG
* * *
494151 TGCCACCAACTCGTGTGGACTTT-GAAAG-AAAAAGAAA
1 TGCCACCAA-TTGTGTGGGCTTTAAAAAGAAAAAAGAAA
494188 ATCGTCCTGC
Statistics
Matches: 168, Mismatches: 26, Indels: 23
0.77 0.12 0.11
Matches are distributed among these distances:
39 14 0.08
40 21 0.12
41 38 0.23
42 40 0.24
43 31 0.18
44 6 0.04
45 18 0.11
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (41 bp):
TGCCACCAATTGTGTGGGCTTTAAAAAGAAAAAAGAAAGGG
Found at i:494045 original size:43 final size:42
Alignment explanation
Indices: 493971--494188 Score: 200
Period size: 41 Copynumber: 5.2 Consensus size: 42
493961 TTTAAAACGA
* *
493971 AAAAAGAAAGGGTGCCATCAA-TTGTGTGGGCTTAAAGAAAG
1 AAAAAGAAAAGGTGCCACCAACTTGTGTGGGCTTAAAGAAAG
* ** *
494012 AAAAAGGAGGGGATGCCACCAACTTGTGTGGGCTTTAA-AAAG
1 AAAAAGAAAAGG-TGCCACCAACTTGTGTGGGCTTAAAGAAAG
*
494054 GAAAA-AAAAGGTGCCACCAA-TTGTGTGGGCTTAAAGAAAG
1 AAAAAGAAAAGGTGCCACCAACTTGTGTGGGCTTAAAGAAAG
* * *
494094 AAAAA-AAAAGGATGACATCAACTTGTGTGGGCTTTTGAAAGGAA-
1 AAAAAGAAAAGG-TGCCACCAACTTGTGTGGGC--TT-AAAGAAAG
* * * *
494138 AAAAAGAAAGGGGTGCCACCAACTCGTGTGGACTT--TGAAAG
1 AAAAAGAAA-AGGTGCCACCAACTTGTGTGGGCTTAAAGAAAG
494179 AAAAAGAAAA
1 AAAAAGAAAA
494189 TCGTCCTGCT
Statistics
Matches: 145, Mismatches: 21, Indels: 23
0.77 0.11 0.12
Matches are distributed among these distances:
39 14 0.10
40 26 0.18
41 29 0.20
42 26 0.18
43 16 0.11
44 7 0.05
45 25 0.17
46 2 0.01
ACGTcount: A:0.42, C:0.12, G:0.28, T:0.18
Consensus pattern (42 bp):
AAAAAGAAAAGGTGCCACCAACTTGTGTGGGCTTAAAGAAAG
Found at i:494085 original size:82 final size:82
Alignment explanation
Indices: 493940--494142 Score: 257
Period size: 81 Copynumber: 2.5 Consensus size: 82
493930 CTCAAAGATA
* * * * *
493940 ATGCCACCAA-TTGCTGTAGGTTTTAAAACGAAAAAAGAAAGGGTGCCATCAATTGTGTGGGCTT
1 ATGCCACCAACTTG-TGTGGGCTTTAAAAAGGAAAAA-AAAGGGTGCCACCAATTGTGTGGGCTT
* **
494004 AAAGAAAGAAAAAGGAGGGG
64 AAAGAAAGAAAAA-AAAAGG
494024 ATGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAAAAA-GGTGCCACCAATTGTGTGGGCTTAA
1 ATGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAAAAAGGGTGCCACCAATTGTGTGGGCTTAA
494088 AGAAAGAAAAAAAAAGG
66 AGAAAGAAAAAAAAAGG
* * **
494105 ATGACATCAACTTGTGTGGGCTTTTGAAAGGAAAAAAA
1 ATGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAAAA
494143 GAAAGGGGTG
Statistics
Matches: 106, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
81 37 0.35
82 35 0.33
83 3 0.03
84 28 0.26
85 3 0.03
ACGTcount: A:0.41, C:0.12, G:0.26, T:0.21
Consensus pattern (82 bp):
ATGCCACCAACTTGTGTGGGCTTTAAAAAGGAAAAAAAAGGGTGCCACCAATTGTGTGGGCTTAA
AGAAAGAAAAAAAAAGG
Found at i:494286 original size:63 final size:61
Alignment explanation
Indices: 494149--494431 Score: 293
Period size: 60 Copynumber: 4.6 Consensus size: 61
494139 AAAAGAAAGG
* * * * *
494149 GGTGCCACCAACTCGTGTGGACTTTGAAAGAAAAAGAAAATCGTCCTGCTCCTTAAGTACTAAAA
1 GGTGCCACCAACTCGTGTGGACTTTAAAAGAAAAAG---AT-GCCCTACTCTTTAAGGACTAAAA
* *
494214 GGTGCCACTAACTCGTGTGGACTTTATAAAGAAAATAGATGCCCTACTCTTTGAGGACTAAAA
1 GGTGCCACCAACTCGTGTGGACTTTA-AAAGAAAA-AGATGCCCTACTCTTTAAGGACTAAAA
* * * *
494277 GGTGCCACTAACTCGTGTAGG-CTTTATAAAGAAAAAGGTGCCTTACTCTTTAAGGATTAAAA
1 GGTGCCACCAACTCGTGT-GGACTTTA-AAAGAAAAAGATGCCCTACTCTTTAAGGACTAAAA
* * * * * * * *
494339 GGTGCCACCGACTCGTGTGGGCTCTAAAA-AAAAAGGTGTCCTGCTCTTTGACGACTAAAA
1 GGTGCCACCAACTCGTGTGGACTTTAAAAGAAAAAGATGCCCTACTCTTTAAGGACTAAAA
*
494399 GGTGCCACCAACTCGTGTGGGCTTTAAAA-AAAA
1 GGTGCCACCAACTCGTGTGGACTTTAAAAGAAAA
494432 GGTGTCCTGC
Statistics
Matches: 192, Mismatches: 22, Indels: 13
0.85 0.10 0.06
Matches are distributed among these distances:
60 56 0.29
61 5 0.03
62 43 0.22
63 50 0.26
64 4 0.02
65 24 0.12
66 8 0.04
67 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (61 bp):
GGTGCCACCAACTCGTGTGGACTTTAAAAGAAAAAGATGCCCTACTCTTTAAGGACTAAAA
Found at i:494399 original size:60 final size:62
Alignment explanation
Indices: 494149--494439 Score: 308
Period size: 63 Copynumber: 4.7 Consensus size: 62
494139 AAAAGAAAGG
* * * * * * *
494149 GGTGCCACCAACTCGTGTGGACTTT-GAAAGAAAAAGAAAATCGTCCTGCTCCTTAAGTACTAAA
1 GGTGCCACCAACTCGTGTGGGCTTTATAAAGAAAAAG---GT-GTCCTACTCTTTGAGGACTAAA
494213 A
62 A
* * * *
494214 GGTGCCACTAACTCGTGTGGACTTTATAAAGAAAATAGATGCCCTACTCTTTGAGGACTAAAA
1 GGTGCCACCAACTCGTGTGGGCTTTATAAAGAAAA-AGGTGTCCTACTCTTTGAGGACTAAAA
* * * *
494277 GGTGCCACTAACTCGTGTAGGCTTTATAAAGAAAAAGGTG-CCTTACTCTTTAAGGATTAAAA
1 GGTGCCACCAACTCGTGTGGGCTTTATAAAGAAAAAGGTGTCC-TACTCTTTGAGGACTAAAA
* * * *
494339 GGTGCCACCGACTCGTGTGGGCTCTA-AAA-AAAAAGGTGTCCTGCTCTTTGACGACTAAAA
1 GGTGCCACCAACTCGTGTGGGCTTTATAAAGAAAAAGGTGTCCTACTCTTTGAGGACTAAAA
494399 GGTGCCACCAACTCGTGTGGGC-TT-TAAA-AAAAAGGTGTCCT
1 GGTGCCACCAACTCGTGTGGGCTTTATAAAGAAAAAGGTGTCCT
494440 GCTTTTTGGG
Statistics
Matches: 199, Mismatches: 22, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
59 17 0.09
60 45 0.23
61 7 0.04
62 43 0.22
63 51 0.26
64 2 0.01
65 24 0.12
66 8 0.04
67 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.25
Consensus pattern (62 bp):
GGTGCCACCAACTCGTGTGGGCTTTATAAAGAAAAAGGTGTCCTACTCTTTGAGGACTAAAA
Found at i:494461 original size:122 final size:125
Alignment explanation
Indices: 494209--494435 Score: 322
Period size: 122 Copynumber: 1.9 Consensus size: 125
494199 CCTTAAGTAC
* * *
494209 TAAAAGGTGCCACTAACTCGTGTGGACTTTATAAAGAAAATAGATGCCCTACTCTTTGAGGACTA
1 TAAAAGGTGCCACCAACTCGTGTGGACTCTATAAAGAAAATAGATGCCCTACTCTTTGACGACTA
*
494274 AAAGGTGCCACTAACTCGTGTAGGCTTTATAAAGAAAAAGGTGCCTTACTCTTTAAGGAT
66 AAAGGTGCCACCAACTCGTGTAGGCTTTATAAAGAAAAAGGTGCCTTACTCTTTAAGGAT
* * * * *
494334 TAAAAGGTGCCACCGACTCGTGTGGGCTCTA-AAA-AAAA-AGGTGTCCTGCTCTTTGACGACTA
1 TAAAAGGTGCCACCAACTCGTGTGGACTCTATAAAGAAAATAGATGCCCTACTCTTTGACGACTA
*
494396 AAAGGTGCCACCAACTCGTGTGGGC-TT-TAAA-AAAAAGGTG
66 AAAGGTGCCACCAACTCGTGTAGGCTTTATAAAGAAAAAGGTG
494436 TCCTGCTTTT
Statistics
Matches: 92, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
119 9 0.10
120 4 0.04
121 2 0.02
122 43 0.47
123 4 0.04
124 3 0.03
125 27 0.29
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.26
Consensus pattern (125 bp):
TAAAAGGTGCCACCAACTCGTGTGGACTCTATAAAGAAAATAGATGCCCTACTCTTTGACGACTA
AAAGGTGCCACCAACTCGTGTAGGCTTTATAAAGAAAAAGGTGCCTTACTCTTTAAGGAT
Found at i:494583 original size:61 final size:61
Alignment explanation
Indices: 494450--495219 Score: 897
Period size: 61 Copynumber: 12.6 Consensus size: 61
494440 GCTTTTTGGG
* * * ** *
494450 GGCTTTAAAAAGAAAAAGACATCCTCCTTTTTGAGGACTAAAAGGTGCCACCATTTCGTGTG
1 GGCTTTAAAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAA-GTGCCACCAACTCGTGTA
* ** * *
494512 GGCTTTAAAATGAAAAAGGGGTCCTGCTCTCTGAGGACTAAAAGTGCCACCAACTCATGTA
1 GGCTTTAAAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAGTGCCACCAACTCGTGTA
* * * *
494573 GGCTTTAAAATGAAAAAGGCATCCTGTTCTTTGAGAACTAAAAGTGCCACAAACTCGTGTA
1 GGCTTTAAAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAGTGCCACCAACTCGTGTA
* * * * * *
494634 GGATTTAAAAAGAAAAATGCATCATGCTCTTTGCGGACTAAAAGGTACCACCAACTCATGTA
1 GGCTTTAAAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAA-GTGCCACCAACTCGTGTA
*
494696 GGCTTTAAAAAGAAAAAGGCATCCTGCTCTTTAAGGACTAAAAGTTGCCACCAACTCGTGT-
1 GGCTTTAAAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAG-TGCCACCAACTCGTGTA
* * *
494757 GGACTTTAAAAAGAAAAAGGCATCCTACTCTTTGAGGATTAAAAATGCCACCAACTCGTGTA
1 GG-CTTTAAAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAGTGCCACCAACTCGTGTA
* * * *
494819 GGCTTTAAAAAGAAAAAGGCATCTTGCTCTTTGAGGACTAAAAGTGCCGCCAACTCATGTG
1 GGCTTTAAAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAGTGCCACCAACTCGTGTA
* * ** * * * * * *
494880 GGCTATAAAAAGAAAAAGGCGTATTGCTTTTTGTGGAGTAAAAAGTGCCACTAACTCCTGTG
1 GGCTTTAAAAAGAAAAAGGCATCCTGCTCTTTGAGGACT-AAAAGTGCCACCAACTCGTGTA
* * * **
494942 GGCTTTAAAAAG-AAAAGGCATCTTGCTCTTTGAGGACTAAAAGGTTCCCCCAACTTATGT-
1 GGCTTTAAAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAA-GTGCCACCAACTCGTGTA
* * * *
495002 GAGCTTTAAAAAGAAAAAGGCATCCTACTTTTTGAGGACTAAAAATGCCACCAACTCGTGTG
1 G-GCTTTAAAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAGTGCCACCAACTCGTGTA
* * *
495064 GGCTTTAAAAAG-AAAAGGCATCCTGCTCTTTGAGGACTAAAAGGTTCCAACAACTCGTGTG
1 GGCTTTAAAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAA-GTGCCACCAACTCGTGTA
* * * *
495125 GGCTTTAAAAAGAAAAAGGCATCTTGCTCTTTGAGAACTAAAAGTGCCACCAACTAGTAT-
1 GGCTTTAAAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAGTGCCACCAACTCGTGTA
* *
495185 GGCTTTAGAAAGAAAAA-G-AGTCCTACTCTTTGAGG
1 GGCTTTAAAAAGAAAAAGGCA-TCCTGCTCTTTGAGG
495220 GCTTAAAGGA
Statistics
Matches: 607, Mismatches: 89, Indels: 27
0.84 0.12 0.04
Matches are distributed among these distances:
58 1 0.00
59 13 0.02
60 49 0.08
61 315 0.52
62 229 0.38
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (61 bp):
GGCTTTAAAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAGTGCCACCAACTCGTGTA
Found at i:494896 original size:184 final size:183
Alignment explanation
Indices: 494450--495228 Score: 931
Period size: 184 Copynumber: 4.2 Consensus size: 183
494440 GCTTTTTGGG
* * * ** *
494450 GGCTTTAAAAAGAAAAAGACATCCTCCTTTTTGAGGACTAAAAGGTGCCACCATTTCGTGTGGGC
1 GGCTTTAAAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGGC
* ** * * *
494515 TTTAAAATGAAAAAGGGGTCCTGCTCTCTGAGGACTAAAAGTGCCACCAACTCATGTAGGCTTTA
66 TTTAAAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAGTGCCACCAACTCGTGTGGGCTTTA
* * *
494580 AAATGAAAAAGGCATCCTGTTCTTTGAGAACTAAAAGTGCCACAAACTCGTGT
131 AAAAGAAAAAGGCATCCTGCTCTTTGAGAACTAAAAGTGCCACCAACTCGTGT
* * * * * *
494633 AGGATTTAAAAAGAAAAATGCATCATGCTCTTTGCGGACTAAAAGGTACCACCAACTCATGTAGG
1 -GGCTTTAAAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGG
* *
494698 CTTTAAAAAGAAAAAGGCATCCTGCTCTTTAAGGACTAAAAGTTGCCACCAACTCGTGTGGACTT
65 CTTTAAAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAG-TGCCACCAACTCGTGTGGGCTT
* * * *
494763 TAAAAAGAAAAAGGCATCCTACTCTTTGAGGATTAAAAATGCCACCAACTCGTGT
129 TAAAAAGAAAAAGGCATCCTGCTCTTTGAGAACTAAAAGTGCCACCAACTCGTGT
* *
494818 AGGCTTTAAAAAGAAAAAGGCATCTTGCTCTTTGAGGACTAAAA-GTGCCGCCAACTCATGTGGG
1 -GGCTTTAAAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGG
* * ** * * * * *
494882 CTATAAAAAGAAAAAGGCGTATTGCTTTTTGTGGAGTAAAAAGTGCCACTAACTCCTGTGGGCTT
65 CTTTAAAAAGAAAAAGGCATCCTGCTCTTTGAGGACT-AAAAGTGCCACCAACTCGTGTGGGCTT
* * * * **
494947 TAAAAAG-AAAAGGCATCTTGCTCTTTGAGGACTAAAAGGTTCCCCCAACTTATGT
129 TAAAAAGAAAAAGGCATCCTGCTCTTTGAGAACTAAAA-GTGCCACCAACTCGTGT
* * * *
495002 GAGCTTTAAAAAGAAAAAGGCATCCTACTTTTTGAGGACTAAAA-ATGCCACCAACTCGTGTGGG
1 G-GCTTTAAAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGG
* *
495066 CTTTAAAAAG-AAAAGGCATCCTGCTCTTTGAGGACTAAAAGGTTCCAACAACTCGTGTGGGCTT
65 CTTTAAAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAA-GTGCCACCAACTCGTGTGGGCTT
* * *
495130 TAAAAAGAAAAAGGCATCTTGCTCTTTGAGAACTAAAAGTGCCACCAACTAGTAT
129 TAAAAAGAAAAAGGCATCCTGCTCTTTGAGAACTAAAAGTGCCACCAACTCGTGT
* * * *
495185 GGCTTTAGAAAGAAAAA-G-AGTCCTACTCTTTGAGGGCTTAAAGG
1 GGCTTTAAAAAGAAAAAGGCA-TCCTGCTCTTTGAGGACTAAAAGG
495229 ATAAAAGGGG
Statistics
Matches: 506, Mismatches: 81, Indels: 18
0.84 0.13 0.03
Matches are distributed among these distances:
180 1 0.00
181 20 0.04
182 19 0.04
183 87 0.17
184 267 0.53
185 112 0.22
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (183 bp):
GGCTTTAAAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCATGTGGGC
TTTAAAAAGAAAAAGGCATCCTGCTCTTTGAGGACTAAAAGTGCCACCAACTCGTGTGGGCTTTA
AAAAGAAAAAGGCATCCTGCTCTTTGAGAACTAAAAGTGCCACCAACTCGTGT
Found at i:502803 original size:19 final size:20
Alignment explanation
Indices: 502759--502811 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
502749 CTGCAAGTTT
**
502759 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
*
502779 CATGTATCGATATAA-TGAA
1 CATGTATCGATACAATTGAA
502798 CATGTATCGATACA
1 CATGTATCGATACA
502812 TTATATCGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:504486 original size:21 final size:21
Alignment explanation
Indices: 504446--504494 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
504436 TTTGTTGATG
504446 ATTTTG-ATGAAAAATGAAGA
1 ATTTTGAATGAAAAATGAAGA
504466 ATTTTGAAGTGAAAAAT-AAGA
1 ATTTTGAA-TGAAAAATGAAGA
504487 ATTTTGAA
1 ATTTTGAA
504495 CAAGATTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.22
21 13 0.48
22 8 0.30
ACGTcount: A:0.49, C:0.00, G:0.18, T:0.33
Consensus pattern (21 bp):
ATTTTGAATGAAAAATGAAGA
Found at i:505307 original size:13 final size:13
Alignment explanation
Indices: 505289--505315 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
505279 ATACTTGTGC
505289 ACAACAACTTCCT
1 ACAACAACTTCCT
505302 ACAACAACTTCCT
1 ACAACAACTTCCT
505315 A
1 A
505316 TGGATATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.37, G:0.00, T:0.22
Consensus pattern (13 bp):
ACAACAACTTCCT
Found at i:509167 original size:12 final size:12
Alignment explanation
Indices: 509152--509177 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
509142 TTCATCCGAG
509152 TCACCATCATCA
1 TCACCATCATCA
509164 TCACCATCATCA
1 TCACCATCATCA
509176 TC
1 TC
509178 TTCATAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.42, G:0.00, T:0.27
Consensus pattern (12 bp):
TCACCATCATCA
Found at i:510798 original size:20 final size:20
Alignment explanation
Indices: 510773--510826 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
510763 GTTTGAAGCA
*
510773 ATGTATCGATACAAT-TAATC
1 ATGTATCGATACAATGT-ACC
*
510793 ATGTATCGATACAATGTGCC
1 ATGTATCGATACAATGTACC
510813 ATGTATCGATACAA
1 ATGTATCGATACAA
510827 ACAGTAGTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:510880 original size:20 final size:20
Alignment explanation
Indices: 510855--510912 Score: 84
Period size: 19 Copynumber: 3.0 Consensus size: 20
510845 CTGCCAGTTT
*
510855 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGTA
*
510875 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGTA
510894 CATGTATCGATAC-ATTGTA
1 CATGTATCGATACAATTGTA
510913 TCGATATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 1 0.03
19 18 0.53
20 15 0.44
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGTA
Found at i:513258 original size:78 final size:79
Alignment explanation
Indices: 513079--513469 Score: 477
Period size: 79 Copynumber: 4.9 Consensus size: 79
513069 TCATTGATGT
* ** *
513079 TTTTATTTCCAAAATAT-GATTTTTCCACCATCGACGATACTACAA-CCTCGTTA-TTTCTGAGG
1 TTTTATTTCTAAAATATCGA-TTTTCCACCATCGGGGATACTCCAACCCT-GTTATTTTC-GAGG
* *
513141 AGATACTCTAACCCCGA
63 GGATACTCCAACCCCGA
* * * *
513158 TTTTATTTTTAAAATATCGATTTTCCACCATTGGGGATACTCCAAGCCTATTA-TTTCGAGGGGA
1 TTTTATTTCTAAAATATCGATTTTCCACCATCGGGGATACTCCAACCCTGTTATTTTCGAGGGGA
*
513222 TACTCCAACCCTGA
66 TACTCCAACCCCGA
* ** *
513236 TTTTATTTCTAAAATATTGATTTTCCACCATCGGGGATACTTTAACCCCGTTATTTTCGAGGGGA
1 TTTTATTTCTAAAATATCGATTTTCCACCATCGGGGATACTCCAACCCTGTTATTTTCGAGGGGA
*
513301 TA-TGTCAACCCCGA
66 TACT-CCAACCCCGA
*
513315 TTTTATTTCTAAAATATCGATTTTTCACCATCGGGGATACTCCAACCCTGTTATTTTCGAGGGGA
1 TTTTATTTCTAAAATATCGATTTTCCACCATCGGGGATACTCCAACCCTGTTATTTTCGAGGGGA
*
513380 TACTCCAACCCCAA
66 TACTCCAACCCCGA
* * * * * * *
513394 TTTTATTTCCAAAATATCGATTTTTACACCATCGGGAATACTCCAACCCCGTTGTTTTCAAAGGG
1 TTTTATTTCTAAAATATCGA-TTTTCCACCATCGGGGATACTCCAACCCTGTTATTTTCGAGGGG
513459 ATACTCCAACC
65 ATACTCCAACC
513470 ATGTTTTTAT
Statistics
Matches: 272, Mismatches: 34, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
78 64 0.24
79 153 0.56
80 55 0.20
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (79 bp):
TTTTATTTCTAAAATATCGATTTTCCACCATCGGGGATACTCCAACCCTGTTATTTTCGAGGGGA
TACTCCAACCCCGA
Found at i:513369 original size:157 final size:159
Alignment explanation
Indices: 513079--513469 Score: 522
Period size: 157 Copynumber: 2.5 Consensus size: 159
513069 TCATTGATGT
** * *
513079 TTTTATTTCCAAAATA-TGATTTTTCCACCATCGACGATACTACAACCTCGTTA-TTTCTGAGGA
1 TTTTATTTCCAAAATATTGATTTTTCCACCATCGGGGATACTACAACCCCGTTATTTTC-GAGGG
* * *
513142 GATACTCTAACCCCGATTTTATTTTTAAAATATCGATTTTCCACCATTGGGGATACTCCAAGCCT
65 GATACTCTAACCCCGATTTTATTTCTAAAATATCGATTTTCCACCATCGGGGATACTCCAACCCT
**
513207 ATTA-TTTCGAGGGGATACTCCAACCCTGA
130 ATTATTTTCGAGGGGATACTCCAACCCCAA
* **
513236 TTTTATTTCTAAAATATTGA-TTTTCCACCATCGGGGATACTTTAACCCCGTTATTTTCGAGGGG
1 TTTTATTTCCAAAATATTGATTTTTCCACCATCGGGGATACTACAACCCCGTTATTTTCGAGGGG
* *
513300 ATA-TGTCAACCCCGATTTTATTTCTAAAATATCGATTTTTCACCATCGGGGATACTCCAACCCT
66 ATACTCT-AACCCCGATTTTATTTCTAAAATATCGATTTTCCACCATCGGGGATACTCCAACCCT
*
513364 GTTATTTTCGAGGGGATACTCCAACCCCAA
130 ATTATTTTCGAGGGGATACTCCAACCCCAA
* * * * * * *
513394 TTTTATTTCCAAAATATCGATTTTTACACCATCGGGAATACTCCAACCCCGTTGTTTTCAAAGGG
1 TTTTATTTCCAAAATATTGATTTTTCCACCATCGGGGATACTACAACCCCGTTATTTTCGAGGGG
*
513459 ATACTCCAACC
66 ATACTCTAACC
513470 ATGTTTTTAT
Statistics
Matches: 202, Mismatches: 26, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
156 2 0.01
157 107 0.53
158 48 0.24
159 44 0.22
160 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (159 bp):
TTTTATTTCCAAAATATTGATTTTTCCACCATCGGGGATACTACAACCCCGTTATTTTCGAGGGG
ATACTCTAACCCCGATTTTATTTCTAAAATATCGATTTTCCACCATCGGGGATACTCCAACCCTA
TTATTTTCGAGGGGATACTCCAACCCCAA
Found at i:516021 original size:79 final size:78
Alignment explanation
Indices: 515938--516320 Score: 324
Period size: 79 Copynumber: 4.9 Consensus size: 78
515928 ATAGAAACCA
** * * *
515938 GGGTTGGAGTATCGTCTCAGAAATAACGGGGTGAGAATATCCCCGAGATCAAAAATTTAATA-TT
1 GGGTTGGAGTATCCCCTCAGAAATAACGGGGTG-GAGTATCCTCGAGATGAAAAATTTAATATTT
516002 TTGAAAATAAAAATG
65 TTG-AAATAAAAATG
* * * * * * **
516017 GGGTTAGAGTATTCCCTCAAAAATAACGGAGTTGGAGTATCCTCGCGATGAAGAATTTAACGTTT
1 GGGTTGGAGTATCCCCTCAGAAATAACGG-GGTGGAGTATCCTCGAGATGAAAAATTTAATATTT
* **
516082 TGGAAATAAAAACA
65 TTGAAATAAAAATG
* * * * * * * *
516096 AGGTTGGAGTATCCCCTCGGAATTGATGGGGTTGGAGTATCCTCAAGATGAAAATTTTGATATTT
1 GGGTTGGAGTATCCCCTCAGAAATAACGGGG-TGGAGTATCCTCGAGATGAAAAATTTAATATTT
516161 TTGAAATAAAAATG
65 TTGAAATAAAAATG
* * * * * * *
516175 GGGTTGAAGTATCCCCTCA-AAATTGATGGGATTGCAGTATCCTTGAGATGAAAATTTTAATATT
1 GGGTTGGAGTATCCCCTCAGAAA-TAACGGG-GTGGAGTATCCTCGAGATGAAAAATTTAATATT
516239 TTTGAAATAAAAATG
64 TTTGAAATAAAAATG
* ** * * * *
516254 GGGTTGGAGTATCCTCTTTGAATTAATGAGGTTGGAGTATCCCTC-AGATGAAAAA-TCAATATT
1 GGGTTGGAGTATCCCCTCAGAAATAACG-GGGTGGAGTAT-CCTCGAGATGAAAAATTTAATATT
516317 TTTG
64 TTTG
516321 GAAGGGAAAA
Statistics
Matches: 242, Mismatches: 54, Indels: 17
0.77 0.17 0.05
Matches are distributed among these distances:
78 14 0.06
79 214 0.88
80 14 0.06
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.31
Consensus pattern (78 bp):
GGGTTGGAGTATCCCCTCAGAAATAACGGGGTGGAGTATCCTCGAGATGAAAAATTTAATATTTT
TGAAATAAAAATG
Found at i:517697 original size:32 final size:33
Alignment explanation
Indices: 517633--517697 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
517623 GCACACCTAG
* *
517633 ATGTATTGATACATATTGCTTAGTATCAATACA
1 ATGTATCGATACATATTGCATAGTATCAATACA
* *
517666 ATGTATCGATACATGTT-CATAGTATCGATACA
1 ATGTATCGATACATATTGCATAGTATCAATACA
517698 CCTTGAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (33 bp):
ATGTATCGATACATATTGCATAGTATCAATACA
Found at i:517789 original size:17 final size:18
Alignment explanation
Indices: 517747--517815 Score: 52
Period size: 20 Copynumber: 3.8 Consensus size: 18
517737 AACTCACTCA
*
517747 GTATCGATACATTGTATC
1 GTATCGATACATTGAATC
* *
517765 G-ATAGATAC-TTGAATT
1 GTATCGATACATTGAATC
** *
517781 GTATCGATACATAGTCCATT
1 GTATCGATACAT--TGAATC
517801 GTATCGATACATTGA
1 GTATCGATACATTGA
517816 GCCTAACGAC
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
16 6 0.15
17 14 0.36
18 3 0.08
20 16 0.41
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.36
Consensus pattern (18 bp):
GTATCGATACATTGAATC
Found at i:518250 original size:23 final size:23
Alignment explanation
Indices: 518207--518250 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
518197 GCATTCAACC
*
518207 TTGGGGTACAATCTTTTAAGAAT
1 TTGGGGTACAATCTTTGAAGAAT
*
518230 TTGGGGTATAAT-TCTTGAAGA
1 TTGGGGTACAATCT-TTGAAGA
518251 GATTGAGAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 1 0.06
23 17 0.94
ACGTcount: A:0.30, C:0.07, G:0.25, T:0.39
Consensus pattern (23 bp):
TTGGGGTACAATCTTTGAAGAAT
Found at i:519399 original size:3 final size:3
Alignment explanation
Indices: 519391--519421 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
519381 TTAACCATCA
*
519391 ATG ATG ATG AAG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
519422 AGAAGTTGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.29
Consensus pattern (3 bp):
ATG
Found at i:525969 original size:30 final size:30
Alignment explanation
Indices: 525935--525992 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
525925 CTAATATTAG
525935 TATCAATGAACATTTCGGGACTTTATTAAA
1 TATCAATGAACATTTCGGGACTTTATTAAA
525965 TATCAATGAACATTTCGGGACTTTATTA
1 TATCAATGAACATTTCGGGACTTTATTA
525993 TGAGTTATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (30 bp):
TATCAATGAACATTTCGGGACTTTATTAAA
Found at i:527542 original size:78 final size:79
Alignment explanation
Indices: 527212--527590 Score: 403
Period size: 79 Copynumber: 4.8 Consensus size: 79
527202 ATAACAACGA
* * * * *
527212 GGTTGGAGTATCCCCGATTAT-AAAAAT-TAGTGTTCTAGAAAT-ACAGTCGGGGTTGGAGTATC
1 GGTTGGAGTATCCCCGATTGTGAAAAATCGA-TGTTTTAGAAATAAAACT-GGGGTTGGAGTATC
527274 CCCTCGAAAATAACAG
64 CCCTCGAAAATAACAG
* * * * *
527290 GGTTGGAGCATCCCTGATTAT-AGAAAATCGATG-TCTAGAAAATAAAATTGGGGTTGGAGTATC
1 GGTTGGAGTATCCCCGATTGTGA-AAAATCGATGTTTTAG-AAATAAAACTGGGGTTGGAGTATC
* * **
527353 CTCTCAAAAATAATGG
64 CCCTCGAAAATAACAG
* * *
527369 GGTTGGAGTATCCCCGATTGTGGAAAATCGATGCTTTAGAAATAAGACCTGGGGTTGGAGTATCC
1 GGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTTAGAAATAA-AACTGGGGTTGGAGTATCC
*
527434 TCTCGAAAATAAC-G
65 CCTCGAAAATAACAG
* * * *
527448 GGTTGGAATATGCCCGATTGTGAAAAATTGATGTTTTAGAAATAAAACTGGGGTTTGAGTATCCC
1 GGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTTAGAAATAAAACTGGGGTTGGAGTATCCC
*
527513 CTCGGAAA-AACAG
66 CTCGAAAATAACAG
* * * * **
527526 GGTTAGAGTATCCCCGATGGTGGAAAATCGATGTTTTGGAAATAAAACCAGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTTAGAAATAAAACTGGGGTTGGAGTATCCC
527591 TGATTATGGA
Statistics
Matches: 256, Mismatches: 37, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
77 3 0.01
78 105 0.41
79 112 0.44
80 36 0.14
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (79 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATCGATGTTTTAGAAATAAAACTGGGGTTGGAGTATCCC
CTCGAAAATAACAG
Found at i:527588 original size:51 final size:51
Alignment explanation
Indices: 527518--527640 Score: 149
Period size: 51 Copynumber: 2.4 Consensus size: 51
527508 ATCCCCTCGG
* * *
527518 AAAAACAGGGTTAGAGTATCCCCGATGGTGGAAAATCGATGTTTTGGAAAT
1 AAAAACAGGGTTGGAGTATCCCCGATGATGGAAAATCGATGTTTTAGAAAT
* * * *
527569 AAAACCAGGGTTGGAGTATCCCTGATTATGGAAAATTGATGTTTTAGAAAT
1 AAAAACAGGGTTGGAGTATCCCCGATGATGGAAAATCGATGTTTTAGAAAT
* *
527620 AAAATC-GGAGTTGTAGTATCC
1 AAAAACAGG-GTTGGAGTATCC
527641 TCTCGGAAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
50 2 0.03
51 60 0.97
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.28
Consensus pattern (51 bp):
AAAAACAGGGTTGGAGTATCCCCGATGATGGAAAATCGATGTTTTAGAAAT
Found at i:527613 original size:129 final size:130
Alignment explanation
Indices: 527447--527702 Score: 335
Period size: 129 Copynumber: 2.0 Consensus size: 130
527437 CGAAAATAAC
* *
527447 GGGTTGGAATATGCCCGATTGTGAAAAATTGATGTTTTAGAAATAAAA-CTGGGGTT-TGAGTAT
1 GGGTTGGAATATGCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATC-GGAGTTGT-AGTAT
**
527510 CCCCTCGGAAA-AAC-AGGGTTAGAGTATCCCCGATGGTGGAAAATCGA-TGTTTTGGAAATAAA
64 CCCCTCGGAAATAACGA-GGTTAGAGTATCCCCGATGGTAAAAAAT-GAGTGTTTTGGAAATAAA
527572 ACCA
127 ACCA
* *
527576 GGGTTGGAGTAT-CCCTGATTATGGAAAATTGATGTTTTAGAAATAAAATCGGAGTTGTAGTATC
1 GGGTTGGAATATGCCC-GATTATGAAAAATTGATGTTTTAGAAATAAAATCGGAGTTGTAGTATC
* * * *
527640 CTCTCGGAAATAACGAGGTTGGAGTATCCCCGATTGTAAAAAATTAGTGTTTTGGAAATAAAA
65 CCCTCGGAAATAACGAGGTTAGAGTATCCCCGATGGTAAAAAATGAGTGTTTTGGAAATAAAA
527703 ACATGAATGA
Statistics
Matches: 111, Mismatches: 10, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
128 3 0.03
129 62 0.56
130 45 0.41
131 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (130 bp):
GGGTTGGAATATGCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCGGAGTTGTAGTATCC
CCTCGGAAATAACGAGGTTAGAGTATCCCCGATGGTAAAAAATGAGTGTTTTGGAAATAAAACCA
Found at i:530167 original size:20 final size:20
Alignment explanation
Indices: 530142--530194 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
530132 TATCACTATT
530142 TGTATCGATACATG-GGATAA
1 TGTATCGATACATGCGGA-AA
*
530162 TGTATCGATACATGCTGAAA
1 TGTATCGATACATGCGGAAA
530182 TGTATCGATACAT
1 TGTATCGATACAT
530195 AGCTTGTAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 29 0.94
21 2 0.06
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (20 bp):
TGTATCGATACATGCGGAAA
Found at i:530253 original size:19 final size:20
Alignment explanation
Indices: 530229--530266 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
530219 ATAATTTCAA
530229 ATGAA-TGTATCGATACATT
1 ATGAATTGTATCGATACATT
530248 ATGAATTGTATCGATACAT
1 ATGAATTGTATCGATACAT
530267 GGCTGCAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (20 bp):
ATGAATTGTATCGATACATT
Found at i:538887 original size:20 final size:19
Alignment explanation
Indices: 538841--538897 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
538831 TTGTATCGAT
*
538841 ACATTATATCGATACATGC
1 ACATTGTATCGATACATGC
* *
538860 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGC
538879 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
538898 AGATTGGCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:538968 original size:33 final size:33
Alignment explanation
Indices: 538926--538992 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
538916 CTATCACTAT
*
538926 TTGTATCGATACATG-GGACAATGTATCGATACA
1 TTGTATCGATAAATGCGGA-AATGTATCGATACA
*
538959 TTGTATCGATAAATGCTGAAATGTATCGATACA
1 TTGTATCGATAAATGCGGAAATGTATCGATACA
538992 T
1 T
538993 AGCTTGTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 29 0.94
34 2 0.06
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.33
Consensus pattern (33 bp):
TTGTATCGATAAATGCGGAAATGTATCGATACA
Found at i:539051 original size:19 final size:20
Alignment explanation
Indices: 539027--539064 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
539017 ATAATTTCAA
539027 ATGAA-TGTATCGATACATT
1 ATGAATTGTATCGATACATT
539046 ATGAATTGTATCGATACAT
1 ATGAATTGTATCGATACAT
539065 GGCTACGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (20 bp):
ATGAATTGTATCGATACATT
Found at i:539620 original size:20 final size:20
Alignment explanation
Indices: 539595--539651 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
539585 ATGTATCGAT
539595 ACAATGTATCGATACAATGA
1 ACAATGTATCGATACAATGA
*
539615 ACAATGTATCAATACAATGA
1 ACAATGTATCGATACAATGA
539635 ACAATGTATCGATACAA
1 ACAATGTATCGATACAA
539652 ATTATAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.25
Consensus pattern (20 bp):
ACAATGTATCGATACAATGA
Found at i:539633 original size:13 final size:13
Alignment explanation
Indices: 539584--539613 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
539574 GTAAACCCAG
539584 AATGTATCGATAC
1 AATGTATCGATAC
539597 AATGTATCGATAC
1 AATGTATCGATAC
539610 AATG
1 AATG
539614 AACAATGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:540392 original size:62 final size:60
Alignment explanation
Indices: 540314--541699 Score: 1560
Period size: 62 Copynumber: 22.5 Consensus size: 60
540304 AGGAGAGACG
* *
540314 GAAAAGGCGTCCTGCTCTTTGAGGACTAAAACAGTGCCACCAACTCGTGTGGGCTTTGAAAA
1 GAAAAGGCGTCCTGCTCTTTGAGGACTAAAA-GGTGCCACCAACTTGTGTGGGCTTT-AAAA
* ** * *
540376 GAAAAGGCGTCTTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAG
1 GAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAA
* *
540437 GAAAAGGCATCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
1 GAAAAGGCGTCCTGCTCTTTGAGGACTA-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAA
* * *
540498 GGAAAAGGCATCCTGCTCTTTGAAGACTAAAAGGTGCCACCAACTTATGTGGGCTTTAAAA
1 -GAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA
* *
540559 GGAAAATGCGTCCTGCTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGACTTTAAAAA
1 -GAAAAGGCGTCCTGCTCTTTGAGGACTA-AAAGGTGCCACCAACTTGTGTGGGCTTT-AAAA
* *
540622 GAAAAGGCATCCTGTTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA
1 GAAAAGGCGTCCTGCTCTTTGAGGACTA-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAA
* ** * * *
540683 GGAAAAGGCATCCTATTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGAGCTTTGAAAG
1 -GAAAAGGCGTCCTGCTCTTTGAGGACTA-AAAGGTGCCACCAACTTGTGTGGGCTTT-AAAA
* * * *
540746 GAAAAGGCATCCTACTCTTTGAGGACT-GAAGGTGCCACCAGCTTGTGTGGGCTTTAAAA
1 GAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA
* * *
540805 GGAAAAAGCGTCCTGCTCTTTGAGGACTAGAAGAGTGCCACCAACATGTGTGGGCTTTGAAAA
1 -GAAAAGGCGTCCTGCTCTTTGAGGACTAAAAG-GTGCCACCAACTTGTGTGGGCTTT-AAAA
* *
540868 GGAAAAGGCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAA
1 -GAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA
* * * * * *
540929 GGGAAAGGCGTCCTACTCTTTGTGGACAAGAAAGGTGCCACCAACTTGTATGGACTTTAAAAA
1 -GAAAAGGCGTCCTGCTCTTTGAGGACTA-AAAGGTGCCACCAACTTGTGTGGGCTTT-AAAA
* * * *
540992 GAAAAGGTGTCCTACAT-TTTGAGGACCAGAAAGATGCCACCAACTTGTGTGGGCTTTAAAA
1 GAAAAGGCGTCCTGC-TCTTTGAGGACTA-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAA
* * * *
541053 GGAAAAGGCATCCTGCTCTTTGAGGAATAGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAG
1 -GAAAAGGCGTCCTGCTCTTTGAGGACTA-AAAGGTGCCACCAACTTGTGTGGGCTTT-AAAA
* * * *
541116 GAAAAGGCATCCTACTCTTTGAGGACT-GAAGGTGCCACCAGCTTGTGTGGGCTTTAAAA
1 GAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA
* * * * * *
541175 GGAAAAGACATCATACTCTTTGAGGACTAGAAGGGTGCCACCAACATGTGTGGGCTTTGAAAA
1 -GAAAAGGCGTCCTGCTCTTTGAGGACTA-AAAGGTGCCACCAACTTGTGTGGGCTTT-AAAA
* * *
541238 GGAAAAGGCATCCTGCTCTTTGAGGACT-GAAGGTGCCACCTAGCTTGTGTGGGCTTTAAAA
1 -GAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACC-AACTTGTGTGGGCTTTAAAA
* * *
541299 GGAAAAAGCGTTCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAA
1 -GAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA
* * * *
541360 GAAAAGGCGTCCTGCTCTTTAAGGACT-GAAGGTGCCACCAGCTTGTGTGGCCTTTAAAAA
1 GAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAA
* * * * **
541420 GAAAAAAGGCATCTTGTTCTTTGAGGACTAAAAAAGTGCCACCAACTCATGTGGGCTTTGAAAA
1 G--AAAAGGCGTCCTGCTCTTTGAGGACT-AAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAA
* * * *
541484 GAAAAAGACGTCCTGCTCTTTGAGGACTAGAAGGGTGCCACCAACTCGTGTGGGCTTTGCAAA
1 G-AAAAGGCGTCCTGCTCTTTGAGGACTA-AAAGGTGCCACCAACTTGTGTGGGCTTT-AAAA
* * * * * *
541547 GAAAAAGACGTCCTACTCTTTGAGGACTAAAGGGTGCCACCAACTCGCGTGGGCTTTGAAAG
1 G-AAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAA
* * **
541609 GAAAAGGTGTCCTACTCTTTGAGGACT-AAAGGTGCCACCAACTCATGTGGGCTTTAAAAA
1 GAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAA
** *
541669 GAAAAATACGTCCTACTCTTTGAGGACTAAA
1 G-AAAAGGCGTCCTGCTCTTTGAGGACTAAA
541700 GGGCTAAAAG
Statistics
Matches: 1166, Mismatches: 128, Indels: 60
0.86 0.09 0.04
Matches are distributed among these distances:
59 32 0.03
60 156 0.13
61 255 0.22
62 537 0.46
63 159 0.14
64 27 0.02
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.24
Consensus pattern (60 bp):
GAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA
Found at i:540643 original size:246 final size:245
Alignment explanation
Indices: 540313--541697 Score: 1816
Period size: 246 Copynumber: 5.6 Consensus size: 245
540303 AAGGAGAGAC
* * *
540313 GGAAAAGGCGTCCTGCTCTTTGAGGACTA-AAACAGTGCCACCAACTCGTGTGGGCTTTGAAAAG
1 GGAAAAAGCGTCCTGCTCTTTGAGGACTAGAAA-GGTGCCACCAACTTGTGTGGGCTTTGAAAAG
* * **
540377 AAAAGGCGTCTTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAGGAAAA
65 AAAAGGCATCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA
*
540442 GGCATCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
129 GGCATCCTACTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
* *
540507 ATCCTGCTCTTTGAAGACTAAAAGGTGCCACCAACTTATGTGGGCTTTAAAA
194 ATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA
* * *
540559 GGAAAATGCGTCCTGCTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGACTTTAAAAAGA
1 GGAAAAAGCGTCCTGCTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGA
*
540624 AAAGGCATCCTGTTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA
66 AAAGGCATCCTGCTCTTTGAGGACT-G-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA
* * *
540689 GGCATCCTATTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGAGCTTTGAAAGGAAAAGGC
129 GGCATCCTACTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGC
* * *
540754 ATCCTACTCTTTGAGGACT-GAAGGTGCCACCAGCTTGTGTGGGCTTTAAAA
194 ATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA
*
540805 GGAAAAAGCGTCCTGCTCTTTGAGGACTAG-AAGAGTGCCACCAACATGTGTGGGCTTTGAAAAG
1 GGAAAAAGCGTCCTGCTCTTTGAGGACTAGAAAG-GTGCCACCAACTTGTGTGGGCTTTGAAAA-
*
540869 GAAAAGGCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGGAA
64 GAAAAGGCATCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAA
* * * * * * *
540934 AGGCGTCCTACTCTTTGTGGACAAGAAAGGTGCCACCAACTTGTATGGACTTTAAAAAGAAAAGG
128 AGGCATCCTACTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
** * * *
540999 TGTCCTACAT-TTTGAGGACCAGAAAGATGCCACCAACTTGTGTGGGCTTTAAAA
193 CATCCTGC-TCTTTGAGGACTA-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAA
* * * * *
541053 GGAAAAGGCATCCTGCTCTTTGAGGAATAGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGA
1 GGAAAAAGCGTCCTGCTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGA
* * *
541118 AAAGGCATCCTACTCTTTGAGGACTGAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGGAAAAGA
66 AAAGGCATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
* ** *
541183 CATCATACTCTTTGAGGACTAGAAGGGTGCCACCAACATGTGTGGGCTTTGAAAAGGAAAAGGCA
131 CATCCTACTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGGCA
* *
541248 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCTAGCTTGTGTGGGCTTTAAAA
195 TCCTGCTCTTTGAGGACTAAAAGGTGCCACC-AACTTGTGTGGGCTTTAAAA
*
541299 GGAAAAAGCGTTCTGCTCTTTGAGGACTAG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGA
1 GGAAAAAGCGTCCTGCTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGA
* * * * *
541362 AAAGGCGTCCTGCTCTTTAAGGACTGAAGGTGCCACCAGCTTGTGTGGCCTTTAAAAAGAAAAAA
66 AAAGGCATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAG-GAAAA
* ** * ** * *
541427 GGCATCTTGTTCTTTGAGGACTAAAAAAGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGA
129 GGCATCCTACTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGG
* * * *
541492 CGTCCTGCTCTTTGAGGACTAGAAGGGTGCCACCAACTCGTGTGGGCTTTGCAAA
193 CATCCTGCTCTTTGAGGACTA-AAAGGTGCCACCAACTTGTGTGGGCTTT-AAAA
* * * * *
541547 -GAAAAAGACGTCCTACTCTTTGAGGACTA-AAGGGTGCCACCAACTCGCGTGGGCTTTGAAAGG
1 GGAAAAAG-CGTCCTGCTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAG
** * * ** *
541610 AAAAGGTGTCCTACTCTTTGAGGACTAAAGGTGCCACCAACTCATGTGGGCTTTAAAAAGAAAAA
65 AAAAGGCATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAA
** *
541675 TACGTCCTACTCTTTGAGGACTA
129 GGCATCCTACTCTTTGAGGACTA
541698 AAGGGCTAAA
Statistics
Matches: 1003, Mismatches: 117, Indels: 36
0.87 0.10 0.03
Matches are distributed among these distances:
244 54 0.05
245 44 0.04
246 469 0.47
247 217 0.22
248 161 0.16
249 58 0.06
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.24
Consensus pattern (245 bp):
GGAAAAAGCGTCCTGCTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGA
AAAGGCATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGG
CATCCTACTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCAT
CCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA
Found at i:540994 original size:370 final size:372
Alignment explanation
Indices: 540313--541697 Score: 1933
Period size: 370 Copynumber: 3.7 Consensus size: 372
540303 AAGGAGAGAC
* *
540313 GGAAAAGGCGTCCTGCTCTTTGAGGACTA-AAACAGTGCCACCAACTCGTGTGGGCTTTGAAAAG
1 GGAAAAGGCATCCTGCTCTTTGAGGACTAGAAA-AGTGCCACCAACTCGTGTGGGCTTTGAAAGG
* * * * **
540377 AAAAGGCGTCTTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAGG-AAA
65 AAAAGGCATCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAA
* * * *
540441 AGGCATCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAG
130 AGACATCCTACTCTTTGAGGACTAGAAGAGTGCCACCAACATGTGTGGGCTTTGAAAAGGAAAAG
* *
540505 GCATCCTGCTCTTTGAAGACTAAAAGGTGCCACCAACTTATGTGGGCTTTAAAAGGAAAATGCGT
195 GCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTATGTGGGCTTTAAAAGGAAAATGCGT
* *
540570 CCTGCTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGACTTTAAAAAGAAAAGGCATCCT
260 CCTACTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGACTTTAAAAAGAAAAGGCGTCCT
*
540635 GTTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA
325 GATCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA
** * *
540683 GGAAAAGGCATCCTATTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGAGCTTTGAAAGGA
1 GGAAAAGGCATCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGA
*
540748 AAAGGCATCCTACTCTTTGAGGACT-GAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGGAAAAA
66 AAAGGCATCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAA
* *
540812 G-CGTCCTGCTCTTTGAGGACTAGAAGAGTGCCACCAACATGTGTGGGCTTTGAAAAGGAAAAGG
131 GACATCCTACTCTTTGAGGACTAGAAGAGTGCCACCAACATGTGTGGGCTTTGAAAAGGAAAAGG
* * *
540876 CATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGGAAAGGCGTC
196 CATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTATGTGGGCTTTAAAAGGAAAATGCGTC
* * * *
540941 CTACTCTTTGTGGACAAGAAAGGTGCCACCAACTTGTATGGACTTTAAAAAGAAAAGGTGTCCTA
261 CTACTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGACTTTAAAAAGAAAAGGCGTCCT-
* * *
541006 CAT-TTTGAGGACCAGAAAGATGCCACCAACTTGTGTGGGCTTTAAAA
325 GATCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA
* *
541053 GGAAAAGGCATCCTGCTCTTTGAGGAATAGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGA
1 GGAAAAGGCATCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGA
*
541118 AAAGGCATCCTACTCTTTGAGGACT-GAAGGTGCCACCAGCTTGTGTGGGCTTTAAAAGG-AAAA
66 AAAGGCATCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAA
* *
541181 GACATCATACTCTTTGAGGACTAGAAGGGTGCCACCAACATGTGTGGGCTTTGAAAAGGAAAAGG
131 GACATCCTACTCTTTGAGGACTAGAAGAGTGCCACCAACATGTGTGGGCTTTGAAAAGGAAAAGG
* * *
541246 CATCCTGCTCTTTGAGGACT-GAAGGTGCCACCTAGCTTGTGTGGGCTTTAAAAGGAAAAAGCGT
196 CATCCTGCTCTTTGAGGACTAGAAGGTGCCACC-AACTTATGTGGGCTTTAAAAGGAAAATGCGT
* * *
541310 TCTGCTCTTTGAGGACTAG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCGTCCT
260 CCTACTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGACTTTAAAAAGAAAAGGCGTCCT
* * * *
541373 GCTCTTTAAGGACT-G-AAGGTGCCACCAGCTTGTGTGGCCTTTAAAAA
325 GATCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAA
* * * * *
541420 GAAAAAAGGCATCTTGTTCTTTGAGGACTAAAAAAGTGCCACCAACTCATGTGGGCTTTGAAAAG
1 G-GAAAAGGCATCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTCGTGTGGGCTTTG-AAAG
* * * * * *
541485 AAAAAGACGTCCTGCTCTTTGAGGACTAGAAGGGTGCCACCAACTCGTGTGGGCTTTGCAAA-GA
64 GAAAAGGCATCCTACTCTTTGAGGACTAGAA-GGTGCCACCAACTTGTGTGGGCTTT-AAAAGGA
* * *
541549 AAAAGACGTCCTACTCTTTGAGGACTA-AAGGGTGCCACCAAC-TCGCGTGGGCTTTG-AAAGGA
127 AAAAGACATCCTACTCTTTGAGGACTAGAAGAGTGCCACCAACAT-GTGTGGGCTTTGAAAAGGA
** * * *
541611 AAAGGTGTCCTACTCTTTGAGGACTA-AAGGTGCCACCAACTCATGTGGGCTTTAAAAAGAAAAA
191 AAAGGCATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTATGTGGGCTTT-AAAAGGAAAA
*
541675 TACGTCCTACTCTTTGAGGACTA
255 TGCGTCCTACTCTTTGAGGACTA
541698 AAGGGCTAAA
Statistics
Matches: 915, Mismatches: 83, Indels: 34
0.89 0.08 0.03
Matches are distributed among these distances:
366 24 0.03
367 7 0.01
368 75 0.08
369 160 0.17
370 567 0.62
371 54 0.06
372 28 0.03
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.24
Consensus pattern (372 bp):
GGAAAAGGCATCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGA
AAAGGCATCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAA
GACATCCTACTCTTTGAGGACTAGAAGAGTGCCACCAACATGTGTGGGCTTTGAAAAGGAAAAGG
CATCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTATGTGGGCTTTAAAAGGAAAATGCGTC
CTACTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGACTTTAAAAAGAAAAGGCGTCCTG
ATCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAA
Found at i:548001 original size:79 final size:79
Alignment explanation
Indices: 547857--548239 Score: 416
Period size: 79 Copynumber: 4.8 Consensus size: 79
547847 TGTGGATAAC
* * * * * * *
547857 AACGGGGCTGGAGTATCCCCGATTATAAAAAATTGGTATTTTAGAAATAAAGTCGGGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAATCGATGTCTTAGAAATAAAATCGGGGTTGGAGT
547922 ATCCCCTCGGAAAT
66 ATCCCCTCGGAAAT
** * * * *
547936 AACAAGGTTGGAATATCCCTGATTAT-AGAAAATC-AGTGTCTTAAAAATAAAATCGGGATTGGA
1 AACGGGGTTGGAGTATCCCCGATTATGA-AAAATCGA-TGTCTTAGAAATAAAATCGGGGTTGGA
*
547999 GTATCCCCTCGAAAAT
64 GTATCCCCTCGGAAAT
* * *
548015 AATGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATG-CTTTAGAAATAAGA-CTGGGGTTGGA
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAATCGATGTC-TTAGAAATAAAATC-GGGGTTGGA
*
548078 GTATCCCCTCAGAAAT
64 GTATCCCCTCGGAAAT
* * * * *
548094 AACGGGGTTGGAGTATCCTCGATTGTGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGT
1 AACGGGGTTGGAGTATCCCCGATTATGAAAAATCGATGTCTTAGAAATAAAATCGGGGTTGGAGT
*
548159 ATCCCCTTGGAAAT
66 ATCCCCTCGGAAAT
* * * * * *
548173 AACGGGGTTAGAGTATCCCCTATGT-TGGAAAATCGATGTTTTGGAAATAAAATCGGGGTTGCAG
1 AACGGGGTTGGAGTATCCCCGAT-TATGAAAAATCGATGTCTTAGAAATAAAATCGGGGTTGGAG
548237 TAT
65 TAT
548240 TCCCGATTGT
Statistics
Matches: 256, Mismatches: 39, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
78 3 0.01
79 249 0.97
80 4 0.02
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (79 bp):
AACGGGGTTGGAGTATCCCCGATTATGAAAAATCGATGTCTTAGAAATAAAATCGGGGTTGGAGT
ATCCCCTCGGAAAT
Found at i:548239 original size:51 final size:49
Alignment explanation
Indices: 548173--548295 Score: 140
Period size: 51 Copynumber: 2.4 Consensus size: 49
548163 CCTTGGAAAT
*
548173 AACGGGGTTAGAGTATCCCCTA-TGTTGGAAAATCGATGTTTTGGAAATAA
1 AACGGGGTT-GAGTATCCCCTATTG-TGGAAAATCGATGTTTTAGAAATAA
* * *
548223 AATCGGGGTTGCAGTATTCCCGATTGTGGAAAATTGATGTTTTAGAAATAA
1 AA-CGGGGTTG-AGTATCCCCTATTGTGGAAAATCGATGTTTTAGAAATAA
*
548274 AACTGGAGTTGAAGTATCCCCT
1 AAC-GGGGTTG-AGTATCCCCT
548296 CGAAAATAAC
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
50 4 0.07
51 55 0.90
52 2 0.03
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (49 bp):
AACGGGGTTGAGTATCCCCTATTGTGGAAAATCGATGTTTTAGAAATAA
Found at i:548247 original size:130 final size:130
Alignment explanation
Indices: 548096--548354 Score: 369
Period size: 130 Copynumber: 2.0 Consensus size: 130
548086 TCAGAAATAA
* * *
548096 CGGGGTTGGAGTATCCTCGATTGTGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT
1 CGGGGTTGCAGTATCCTCGATTGTGAAAAATTGATGTTTTAGAAATAAAACCGGAGTTGAAGTAT
* * * **
548161 CCCCTTGGAAATAACGGGGTTAGAGTATCCCCTA-TGTTGGAAAATCGATGTTTTGGAAATAAAA
66 CCCCTCGAAAATAACGGGGTTAGAGTATCCCCGATTG-TAAAAAATCGATGTTTTGGAAATAAAA
548225 T
130 T
* *
548226 CGGGGTTGCAGTATTCC-CGATTGTGGAAAATTGATGTTTTAGAAATAAAACTGGAGTTGAAGTA
1 CGGGGTTGCAGTA-TCCTCGATTGTGAAAAATTGATGTTTTAGAAATAAAACCGGAGTTGAAGTA
* * *
548290 TCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTAAAAAATTGGTGTTTTGGAAATAAAA
65 TCCCCTCGAAAATAACGGGGTTAGAGTATCCCCGATTGTAAAAAATCGATGTTTTGGAAATAAAA
548355 ACATGAATGA
Statistics
Matches: 114, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
130 109 0.96
131 5 0.04
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (130 bp):
CGGGGTTGCAGTATCCTCGATTGTGAAAAATTGATGTTTTAGAAATAAAACCGGAGTTGAAGTAT
CCCCTCGAAAATAACGGGGTTAGAGTATCCCCGATTGTAAAAAATCGATGTTTTGGAAATAAAAT
Found at i:552278 original size:310 final size:309
Alignment explanation
Indices: 551710--552324 Score: 944
Period size: 310 Copynumber: 2.0 Consensus size: 309
551700 CATGAGCATG
*
551710 TGAGTTAATCATGCTCATTATACAATGAATGCTCTATAATTAATTGAAAAATTCACACTCAAGTT
1 TGAGTTAATCATGCTCACTATACAATGAATGCTCTATAATTAATTGAAAAATTCACACTCAAGTT
* * * * * * *
551775 GTTCCTAACTATCTATCGCCCCACACTCAAGATTAGTGTACTAACTGAAGGCATTGCCTTTTAAT
66 GTTCCCAACTATCTATCACCCCACACTAAAGATCAATGTACCAACTAAAGGCATTGCCTTTTAAT
* * *
551840 GATCAAACAAATTGCTTCATCATTAGATCTCCATCAATGCTAGCATTATTACAAGTTTCCACAAA
131 GATCAAACAAATGGCTTCATCATGAGATCTCCATCAATGCCAGCATTATTACAAGTTTCCACAAA
* *
551905 ATGTGCAATATGTGGGCATAGATTTCCTTTGCCATTAAACTACTGGAACTTTAGAGAGTGATAAT
196 ATGTGCAATATGTGGGCATAGATTTCCTTTGCCATCAAACTACTGGAACTTTAAAGAGTGATAAT
551970 TCT-CAAGCATCTTCAAATTATTGATCATTTGAGAATATGGTTTAGTATA
261 T-TACAAGCATCTTCAAATTATTGATCATTTGAGAATATGGTTTAGTATA
** * * * **
552019 TGAGTTCAATCATGCTCACTATATGATGACTGGTCTATAATTGATTGAAAAATTCATGCTCAAGT
1 TGAGTT-AATCATGCTCACTATACAATGAATGCTCTATAATTAATTGAAAAATTCACACTCAAGT
552084 TGTTCCCAACTATCTATCACCCCACACTAAAGATCAATGTACCAACTAAAGGCATTGCCTTTTAA
65 TGTTCCCAACTATCTATCACCCCACACTAAAGATCAATGTACCAACTAAAGGCATTGCCTTTTAA
** * * *
552149 TGATTGAACGAATGGCTTCATCATGAGATCTCCATCAGTGCCAGCATTATTATAAGTTTCCACAA
130 TGATCAAACAAATGGCTTCATCATGAGATCTCCATCAATGCCAGCATTATTACAAGTTTCCACAA
* * *
552214 AATGTGCAATATGTTGGCATAGATTTCCTTTGCCATCAAACTATTGGAACTTTAAAGGGTGATAA
195 AATGTGCAATATGTGGGCATAGATTTCCTTTGCCATCAAACTACTGGAACTTTAAAGAGTGATAA
*
552279 TTTACAAGCATCTTCAAATTATTGATTATTTGAGAATATGGTTTAG
260 TTTACAAGCATCTTCAAATTATTGATCATTTGAGAATATGGTTTAG
552325 CAAATGTATA
Statistics
Matches: 275, Mismatches: 29, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
309 7 0.03
310 268 0.97
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (309 bp):
TGAGTTAATCATGCTCACTATACAATGAATGCTCTATAATTAATTGAAAAATTCACACTCAAGTT
GTTCCCAACTATCTATCACCCCACACTAAAGATCAATGTACCAACTAAAGGCATTGCCTTTTAAT
GATCAAACAAATGGCTTCATCATGAGATCTCCATCAATGCCAGCATTATTACAAGTTTCCACAAA
ATGTGCAATATGTGGGCATAGATTTCCTTTGCCATCAAACTACTGGAACTTTAAAGAGTGATAAT
TTACAAGCATCTTCAAATTATTGATCATTTGAGAATATGGTTTAGTATA
Found at i:553361 original size:44 final size:44
Alignment explanation
Indices: 553312--553485 Score: 210
Period size: 44 Copynumber: 3.9 Consensus size: 44
553302 CTTATCTTTC
*
553312 TTATTTATCTCTTAATTAATTTAATTTAATTTA-ACAT-AATTGTT
1 TTATTTATCTCTTAATTAATTTAATTTAA-TTAGAGATAAATT-TT
* *
553356 TTATTTATCTCTTAATTAACTTAATTTAATTAGAGATAAAATTTC
1 TTATTTATCTCTTAATTAATTTAATTTAATTAGAGAT-AAATTTT
* *
553401 TCATTTATCTC-CAATTAATTTAATTTAATTAGAGATAAAATTTCT
1 TTATTTATCTCTTAATTAATTTAATTTAATTAGAGAT-AAATTT-T
* * *
553446 TGATTTATCTATTAATTAATTTAATTTAATTAGATATAAA
1 TTATTTATCTCTTAATTAATTTAATTTAATTAGAGATAAA
553486 AATGATTCTC
Statistics
Matches: 114, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
43 3 0.03
44 61 0.54
45 23 0.20
46 27 0.24
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.51
Consensus pattern (44 bp):
TTATTTATCTCTTAATTAATTTAATTTAATTAGAGATAAATTTT
Found at i:553470 original size:90 final size:89
Alignment explanation
Indices: 553308--553486 Score: 238
Period size: 90 Copynumber: 2.0 Consensus size: 89
553298 AAAACTTATC
* * * *
553308 TTTCTTATTTATCTCTTAATTAATTTAATTTAATTTAACATAATTGTTTTATTTATCTCTTAATT
1 TTTCTCATTTATCTCTCAATTAATTTAATTTAATTTAACATAATTGTTTGATTTATCTATTAATT
553373 AACTTAATTTAATTAGAGATAAAA
66 AACTTAATTTAATTAGAGATAAAA
*
553397 TTTCTCATTTATCTC-CAATTAATTTAATTTAA-TTAGAGATAAAATT-TCTTGATTTATCTATT
1 TTTCTCATTTATCTCTCAATTAATTTAATTTAATTTA-ACAT--AATTGT-TTGATTTATCTATT
* *
553459 AATTAATTTAATTTAATTAGATATAAAA
62 AATTAACTTAATTTAATTAGAGATAAAA
553487 ATGATTCTCA
Statistics
Matches: 79, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
87 3 0.04
88 19 0.24
89 15 0.19
90 42 0.53
ACGTcount: A:0.37, C:0.08, G:0.04, T:0.51
Consensus pattern (89 bp):
TTTCTCATTTATCTCTCAATTAATTTAATTTAATTTAACATAATTGTTTGATTTATCTATTAATT
AACTTAATTTAATTAGAGATAAAA
Found at i:558388 original size:43 final size:43
Alignment explanation
Indices: 558156--558778 Score: 556
Period size: 43 Copynumber: 14.1 Consensus size: 43
558146 CTTAAAGATG
* *
558156 AAGGTGCCAATGTGCTAATTCAAGGCCAGCGATATTGGGCTT-
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGTCTTA
* * * *
558198 ---GTGCCAATGTGTTGAGTCAAGGCCAACGACATTGGTCTTAAAGATA
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGTC-T-----TA
*
558244 AAGGTGCC-A--TGCTGATTCAAGGCCAGCGATATTGGACTT-
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGTCTTA
*
558283 ---GTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTTGTGA
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGTC-T-T-A
* *
558326 CAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTA
1 -AAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGTCTTA
* *
558370 AAGGTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAAAGA
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGTCTT----A
* * * * *
558417 TGAAGGTGCCAATATGCTTATTCAATGCCTGCGATATTGGACTTA
1 --AAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGTCTTA
*
558462 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGTCTT----A
* * *
558509 TGAAGGTGCCAATATGCTGATTCAAGGCTAGCGATATTGGACTTA
1 --AAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGTCTTA
*
558554 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTA
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGTCTTA
* *
558597 AAGATAAAGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT-
1 AAG-----GTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGTCTTA
* * *
558644 -A--TGCCGATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGACA
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGTCTT------A
* * *
558690 AAGGTGCCAATATACTGATTCAAGGCCAGCGATATTGGACTTA
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGTCTTA
* *
558733 AAGGTGTCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTA
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGTCTTA
558776 AAG
1 AAG
558779 ATGAAAGGAG
Statistics
Matches: 476, Mismatches: 57, Indels: 95
0.76 0.09 0.15
Matches are distributed among these distances:
36 5 0.01
37 1 0.00
39 91 0.19
40 3 0.01
41 1 0.00
43 158 0.33
44 1 0.00
45 5 0.01
46 25 0.05
47 39 0.08
48 37 0.08
49 110 0.23
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (43 bp):
AAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGTCTTA
Found at i:558456 original size:92 final size:92
Alignment explanation
Indices: 558104--558830 Score: 970
Period size: 92 Copynumber: 8.1 Consensus size: 92
558094 CTTAGAAATG
* * * * * * * *
558104 TTAAAGATGCCAATATGCTGAGTCAAGGCCAATC-ATATCGGACTTAAAGATGAAGGTGCCAATG
1 TTAAAGGTGCCAATGTGCTGATTCAAGGCC-AGCGACATTGGTCTTAAAGATGAAGGTGCCAATA
* *
558168 TGCTAATTCAAGGCCAGCGATATTGGGC
65 TGCTGATTCAAGGCCAGCGATATTGGAC
* * * *
558196 TT----GTGCCAATGTGTTGAGTCAAGGCCAACGACATTGGTCTTAAAGATAAAGGTGCC---AT
1 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATAT
558254 GCTGATTCAAGGCCAGCGATATTGGAC
66 GCTGATTCAAGGCCAGCGATATTGGAC
* * ** *
558281 TT----GTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTT-GTGA-CAAGGTGCCAATAT
1 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATAT
*
558340 GCTGATTCAAGGCCAGCGATATTGGGC
66 GCTGATTCAAGGCCAGCGATATTGGAC
*
558367 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAAAGATGAAGGTGCCAATAT
1 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATAT
* * *
558432 GCTTATTCAATGCCTGCGATATTGGAC
66 GCTGATTCAAGGCCAGCGATATTGGAC
558459 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATAT
1 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATAT
*
558524 GCTGATTCAAGGCTAGCGATATTGGAC
66 GCTGATTCAAGGCCAGCGATATTGGAC
*
558551 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAT-AAAGTGCCAATAT
1 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATAT
*
558615 GCTGATTCAAGGCCAGCGATATTGGGC
66 GCTGATTCAAGGCCAGCGATATTGGAC
* * **
558642 TT--A--TGCCGATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATAT
1 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATAT
*
558703 ACTGATTCAAGGCCAGCGATATTGGAC
66 GCTGATTCAAGGCCAGCGATATTGGAC
* *
558730 TTAAAGGTGTCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAAGGAGCCAATA
1 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATG-AAGGTGCCAATA
* *
558795 TGCTGATTCAAGGCCAGCGACATTGGGC
65 TGCTGATTCAAGGCCAGCGATATTGGAC
558823 TTAGAAGG
1 TTA-AAGG
558831 GTTGCCACCG
Statistics
Matches: 565, Mismatches: 53, Indels: 32
0.87 0.08 0.05
Matches are distributed among these distances:
83 8 0.01
84 2 0.00
85 62 0.11
86 30 0.05
87 43 0.08
88 82 0.15
89 1 0.00
90 37 0.07
91 41 0.07
92 216 0.38
93 39 0.07
94 4 0.01
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (92 bp):
TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATAT
GCTGATTCAAGGCCAGCGATATTGGAC
Found at i:558578 original size:21 final size:20
Alignment explanation
Indices: 558511--558578 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 20
558501 CTTAAAGATG
558511 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAAT-TGCTGATTC
* *
558532 AAGGCTAGCGATATTG--GACTTA
1 AAGG-T-GCCA-ATTGCTGA-TTC
558554 AAGGTGCCAATGTGCTGATTC
1 AAGGTGCCAAT-TGCTGATTC
558575 AAGG
1 AAGG
558579 CCAGCGACAT
Statistics
Matches: 36, Mismatches: 4, Indels: 14
0.67 0.07 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.14
21 13 0.36
22 9 0.25
23 5 0.14
24 2 0.06
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.26
Consensus pattern (20 bp):
AAGGTGCCAATTGCTGATTC
Found at i:558723 original size:179 final size:181
Alignment explanation
Indices: 558110--558825 Score: 983
Period size: 179 Copynumber: 4.0 Consensus size: 181
558100 AATGTTAAAG
* * * * * * * * *
558110 ATGCCAATATGCTGAGTCAAGGCCAATC-ATATCGGACTTAAAGATGAAGGTGCCAATGTGCTAA
1 ATGCCAATGTGCTGATTCAAGGCC-AGCGACATTGGTCTTAAAGACGAAGGTGCCAATATGCTGA
* * * *
558174 TTCAAGGCCAGCGATATTGGGCTT----GTGCCAATGTGTTGAGTCAAGGCCAACGACATTGGTC
65 TTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTC
558235 TTAAAGAT-AAAGGTGCC---ATGCTGATTCAAGGCCAGCGATATTGGACTT
130 TTAAAGATGAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
* * * **
558283 GTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGGCTT-GTGAC-AAGGTGCCAATATGCTGAT
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACGAAGGTGCCAATATGCTGAT
* *
558346 TCAAGGCCAGCGATATTGGGCTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTCT
66 TCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCT
* * *
558411 TAAAGATG-AAGGTGCCAATATGCTTATTCAATGCCTGCGATATTGGACTT
131 TAAAGATGAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
*
558461 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATATGC
1 --A--TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACGAAGGTGCCAATATGC
*
558526 TGATTCAAGGCTAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTG
62 TGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTG
*
558591 GTCTTAAAGAT-AAA-GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT
127 GTCTTAAAGATGAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
* * * *
558644 ATGCCGATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATATACTGAT
1 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACGAAGGTGCCAATATGCTGAT
*
558709 TCAAGGCCAGCGATATTGGACTTAAAGGTGTCAATGTGCTGATTCAAGGCCAGCGACATTGGTCT
66 TCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCT
* * *
558774 TAAAGATGAAAGGAGCCAATATGCTGATTCAAGGCCAGCGACATTGGGCTT
131 TAAAGATGAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
558825 A
1 A
558826 GAAGGGTTGC
Statistics
Matches: 485, Mismatches: 40, Indels: 28
0.88 0.07 0.05
Matches are distributed among these distances:
171 40 0.08
172 4 0.01
173 30 0.06
175 49 0.10
178 28 0.06
179 129 0.27
180 3 0.01
181 39 0.08
182 36 0.07
183 37 0.08
184 90 0.19
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.26
Consensus pattern (181 bp):
ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACGAAGGTGCCAATATGCTGAT
TCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCT
TAAAGATGAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
Found at i:558869 original size:33 final size:33
Alignment explanation
Indices: 558830--558892 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
558820 GGCTTAGAAG
558830 GGTTGCCACCGACTTGTGTGGGCTTTAGAAAAT
1 GGTTGCCACCGACTTGTGTGGGCTTTAGAAAAT
558863 GGTTGCCACCGACTTGTGTGGGCTTTAGAA
1 GGTTGCCACCGACTTGTGTGGGCTTTAGAA
558893 GGGGGTGCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.19, C:0.19, G:0.32, T:0.30
Consensus pattern (33 bp):
GGTTGCCACCGACTTGTGTGGGCTTTAGAAAAT
Found at i:558912 original size:32 final size:31
Alignment explanation
Indices: 558818--558895 Score: 122
Period size: 33 Copynumber: 2.5 Consensus size: 31
558808 CCAGCGACAT
558818 TGGGC-TTAGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAAGGGTTGCCACCGACTTGTG
*
558848 TGGGCTTTAGAAAATGGTTGCCACCGACTTGTG
1 TGGGCTTTAG--AAGGGTTGCCACCGACTTGTG
558881 TGGGCTTTAGAAGGG
1 TGGGCTTTAGAAGGG
558896 GGTGCCACGG
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
30 5 0.12
31 8 0.19
33 30 0.70
ACGTcount: A:0.19, C:0.17, G:0.36, T:0.28
Consensus pattern (31 bp):
TGGGCTTTAGAAGGGTTGCCACCGACTTGTG
Found at i:558971 original size:33 final size:32
Alignment explanation
Indices: 558897--559300 Score: 232
Period size: 33 Copynumber: 12.7 Consensus size: 32
558887 TTAGAAGGGG
* *
558897 GTGCCACGGAGTTGTGGACTTAAAAG-AAAAG
1 GTGCCACGGAGTTGTGGACTTAAAGGAAAAAA
558928 GTGCCACGGAGTTGTGGACTTAACAGGAAAAAA
1 GTGCCACGGAGTTGTGGACTTAA-AGGAAAAAA
*
558961 CTGCCACGGAGTTGTGGACTTAACAGGAAAAAA
1 GTGCCACGGAGTTGTGGACTTAA-AGGAAAAAA
*
558994 GTGCCACGGAGTTGTGGGCTTAAA-GAAAAAA
1 GTGCCACGGAGTTGTGGACTTAAAGGAAAAAA
** * * * *
559025 -TGCCACTAAGTCGTGGATTTTGAA-GAAAAGA
1 GTGCCACGGAGTTGTGGA-CTTAAAGGAAAAAA
* *
559056 -TGCCACTGAGTCGTGGACTT---GGAAGAAAA
1 GTGCCACGGAGTTGTGGACTTAAAGGAA-AAAA
* * *
559085 GGATGCCACTGAGTCGTGGACTT--A-GAAAAGA
1 -G-TGCCACGGAGTTGTGGACTTAAAGGAAAAAA
* * *
559116 GATGCCACTGAGTTGTGGACTTTGAA-GACAAAA
1 G-TGCCACGGAGTTGTGGAC-TTAAAGGAAAAAA
* * *
559149 GATGCCACTGAGTCGTGGACTTGGAA-G-AAAAA
1 G-TGCCACGGAGTTGTGGACTT-AAAGGAAAAAA
* * * *
559181 GATGCCACTGAATCGTGGACTTTGAA-GAAAAAA
1 G-TGCCACGGAGTTGTGGAC-TTAAAGGAAAAAA
* * *
559214 GATGCCACTGAGTCGTGGACTTGGAA-GAAAAAA
1 G-TGCCACGGAGTTGTGGACTT-AAAGGAAAAAA
* * * *
559247 GATGCCACTGAGTCGTGGACTT--GGGAGAAAAG
1 G-TGCCACGGAGTTGTGGACTTAAAGGA-AAAAA
*
559279 GATGCCACTGAGTTGTGGACTT
1 G-TGCCACGGAGTTGTGGACTT
559301 TGAGAAGAGA
Statistics
Matches: 329, Mismatches: 26, Indels: 35
0.84 0.07 0.09
Matches are distributed among these distances:
28 3 0.01
29 3 0.01
30 34 0.10
31 63 0.19
32 82 0.25
33 144 0.44
ACGTcount: A:0.34, C:0.15, G:0.30, T:0.21
Consensus pattern (32 bp):
GTGCCACGGAGTTGTGGACTTAAAGGAAAAAA
Found at i:559204 original size:65 final size:64
Alignment explanation
Indices: 558898--559300 Score: 405
Period size: 65 Copynumber: 6.3 Consensus size: 64
558888 TAGAAGGGGG
* * ** * * * *
558898 TGCCACGGAGTTGTGGACTTAAAAG-AAAAGGTGCCACGGAGTTGTGGACTT-AACAGGAAAAA-
1 TGCCACTGAGTCGTGGACTTGGAAGAAAAAGATGCCACTGAGTCGTGGACTTGGA-A-GAAAAAG
558960 A
64 A
* * * * * * *
558961 CTGCCACGGAGTTGTGGACTT-AACAGGAAAAA-AGTGCCACGGAGTTGTGGGCTT-AAAGAAAA
1 -TGCCACTGAGTCGTGGACTTGGA-A-GAAAAAGA-TGCCACTGAGTCGTGGACTTGGAAGAAAA
559023 A-A
62 AGA
* * * *
559025 TGCCACTAAGTCGTGGATTTTGAAG-AAAAGATGCCACTGAGTCGTGGACTTGGAAGAAAAGGA
1 TGCCACTGAGTCGTGGACTTGGAAGAAAAAGATGCCACTGAGTCGTGGACTTGGAAGAAAAAGA
* *
559088 TGCCACTGAGTCGTGGACTT---AGAAAAGAGATGCCACTGAGTTGTGGACTTTGAAGACAAAAG
1 TGCCACTGAGTCGTGGACTTGGAAGAAAA-AGATGCCACTGAGTCGTGGACTTGGAAGA-AAAAG
559150 A
64 A
* *
559151 TGCCACTGAGTCGTGGACTTGGAAGAAAAAGATGCCACTGAATCGTGGACTTTGAAGAAAAAAGA
1 TGCCACTGAGTCGTGGACTTGGAAGAAAAAGATGCCACTGAGTCGTGGACTTGGAAG-AAAAAGA
* *
559216 TGCCACTGAGTCGTGGACTTGGAAGAAAAAAGATGCCACTGAGTCGTGGACTTGGGAGAAAAGGA
1 TGCCACTGAGTCGTGGACTTGGAAG-AAAAAGATGCCACTGAGTCGTGGACTTGGAAGAAAAAGA
*
559281 TGCCACTGAGTTGTGGACTT
1 TGCCACTGAGTCGTGGACTT
559301 TGAGAAGAGA
Statistics
Matches: 299, Mismatches: 24, Indels: 31
0.84 0.07 0.09
Matches are distributed among these distances:
60 2 0.01
61 24 0.08
62 36 0.12
63 63 0.21
64 29 0.10
65 84 0.28
66 61 0.20
ACGTcount: A:0.34, C:0.15, G:0.30, T:0.21
Consensus pattern (64 bp):
TGCCACTGAGTCGTGGACTTGGAAGAAAAAGATGCCACTGAGTCGTGGACTTGGAAGAAAAAGA
Found at i:559265 original size:98 final size:97
Alignment explanation
Indices: 559019--559303 Score: 436
Period size: 98 Copynumber: 3.0 Consensus size: 97
559009 GGGCTTAAAG
* *
559019 AAAAA-ATGCCACTAAGTCGTGGATTTTGAAG-AAAAGATGCCACTGAGTCGTGGACTTGGAAGA
1 AAAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAAGATGCCACTGAGTCGTGGACTTGGAAGA
559082 AAAGGATGCCACTGAGTCGTGGAC-TT--AGA
66 AAAGGATGCCACTGAGTCGTGGACTTTGAAGA
* *
559111 AAAGAGATGCCACTGAGTTGTGGACTTTGAAGACAAAAGATGCCACTGAGTCGTGGACTTGGAAG
1 AAAAAGATGCCACTGAGTCGTGGACTTTGAAGA-AAAAGATGCCACTGAGTCGTGGACTTGGAAG
* *
559176 AAAAAGATGCCACTGAATCGTGGACTTTGAAGA
65 AAAAGGATGCCACTGAGTCGTGGACTTTGAAGA
* *
559209 AAAAAGATGCCACTGAGTCGTGGACTTGGAAGAAAAAAGATGCCACTGAGTCGTGGACTTGGGAG
1 AAAAAGATGCCACTGAGTCGTGGACTTTGAAG-AAAAAGATGCCACTGAGTCGTGGACTTGGAAG
*
559274 AAAAGGATGCCACTGAGTTGTGGACTTTGA
65 AAAAGGATGCCACTGAGTCGTGGACTTTGA
559304 GAAGAGATTT
Statistics
Matches: 173, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
92 4 0.02
93 23 0.13
95 54 0.31
96 2 0.01
98 89 0.51
99 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.29, T:0.21
Consensus pattern (97 bp):
AAAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAAGATGCCACTGAGTCGTGGACTTGGAAGA
AAAGGATGCCACTGAGTCGTGGACTTTGAAGA
Found at i:560219 original size:19 final size:18
Alignment explanation
Indices: 560193--560231 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
560183 GTTTTTCCTC
*
560193 TTTTTTTTTGTTTGTTTG
1 TTTTTTTTTGTTTGTGTG
*
560211 TTTTGTTTTTTTTTGTGTG
1 TTTT-TTTTTGTTTGTGTG
560230 TT
1 TT
560232 GGAAAAGAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (18 bp):
TTTTTTTTTGTTTGTGTG
Found at i:560506 original size:6 final size:6
Alignment explanation
Indices: 560495--560553 Score: 59
Period size: 6 Copynumber: 10.0 Consensus size: 6
560485 TTGTGTGTAT
* * *
560495 TTTTTG TTTTTG TTTTTG -TTTT- TTTGTG TTGTTG TTTTTTG TTTTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG -TTTTTG TTTTTG
*
560542 TTTTTG TGTTTG
1 TTTTTG TTTTTG
560554 CACTTTTGAG
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
5 7 0.16
6 31 0.72
7 5 0.12
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (6 bp):
TTTTTG
Found at i:560511 original size:29 final size:28
Alignment explanation
Indices: 560479--560551 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 28
560469 CTTTCTTCTC
* *
560479 TTTTTTTTGTGTGTATTTTTTGTTTTTGTT
1 TTTTTTTTGTGTGT-TGTTGT-TTTTTGTT
*
560509 TTTGTTTTTTTGTGTTGTTGTTTTTTGTT
1 TTT-TTTTTGTGTGTTGTTGTTTTTTGTT
560538 TTTTTTTT-TGTGTT
1 TTTTTTTTGTGTGTT
560552 TGCACTTTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
27 6 0.15
28 5 0.13
29 11 0.28
30 7 0.18
31 10 0.26
ACGTcount: A:0.01, C:0.00, G:0.18, T:0.81
Consensus pattern (28 bp):
TTTTTTTTGTGTGTTGTTGTTTTTTGTT
Found at i:560524 original size:22 final size:22
Alignment explanation
Indices: 560494--560552 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
560484 TTTGTGTGTA
*
560494 TTTTTTGTTTTTG-TTTTTGTT
1 TTTTTTGTTGTTGTTTTTTGTT
560515 TTTTTGTGTTGTTGTTTTTTGTT
1 TTTTT-TGTTGTTGTTTTTTGTT
*
560538 TTTTTTTTTG-TGTTT
1 TTTTTTGTTGTTGTTT
560553 GCACTTTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.29
22 11 0.32
23 13 0.38
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (22 bp):
TTTTTTGTTGTTGTTTTTTGTT
Found at i:560529 original size:16 final size:16
Alignment explanation
Indices: 560480--560534 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
560470 TTTCTTCTCT
*
560480 TTTTTTTGTG-TGTATT
1 TTTTTTTGTGTTGT-TG
* *
560496 TTTTGTTTTTGTTTTTG
1 TTTT-TTTGTGTTGTTG
560513 TTTTTTTGTGTTGTTG
1 TTTTTTTGTGTTGTTG
560529 TTTTTT
1 TTTTTT
560535 GTTTTTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
16 20 0.62
17 10 0.31
18 2 0.06
ACGTcount: A:0.02, C:0.00, G:0.18, T:0.80
Consensus pattern (16 bp):
TTTTTTTGTGTTGTTG
Found at i:560533 original size:35 final size:33
Alignment explanation
Indices: 560480--560548 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 33
560470 TTTCTTCTCT
560480 TTTTTTTGTGTGTATTTTTTGTTTTTGTTTTTG
1 TTTTTTTGTGTGTATTTTTTGTTTTTGTTTTTG
* *
560513 TTTTTTTGTGTTGTTGTTTTTTGTTTTTTTTTTTG
1 TTTTTTTGTG-TG-TATTTTTTGTTTTTGTTTTTG
560548 T
1 T
560549 GTTTGCACTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 10 0.31
34 2 0.06
35 20 0.62
ACGTcount: A:0.01, C:0.00, G:0.17, T:0.81
Consensus pattern (33 bp):
TTTTTTTGTGTGTATTTTTTGTTTTTGTTTTTG
Found at i:567565 original size:13 final size:13
Alignment explanation
Indices: 567547--567572 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
567537 ACAAAGATCC
567547 ATGTATCGATACA
1 ATGTATCGATACA
567560 ATGTATCGATACA
1 ATGTATCGATACA
567573 TTGAGTAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:568601 original size:49 final size:45
Alignment explanation
Indices: 568533--569235 Score: 551
Period size: 49 Copynumber: 15.5 Consensus size: 45
568523 ATATTAAAGA
* ** * *
568533 TGCCAATATGCTGAGTCAAGGCCAATGATATCGAACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT---GAT-AAGG
* * *
568582 TGCCAATGTGCTGATTCAAGGCCAACGATATTGG-CCT--T---G
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTGATAAGG
* * * *
568621 TGCCAATGTGCTGAGTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT---GAT-AAGG
568670 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTG---A--
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTGATAAGG
* *
568710 -GCCAATGTGCTGATTCAAGGCTAGCGATATT-GAGCTTGTGATAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGA-C-T-TGATAAGG
* *
568756 TGCCAATATGCTGATTCAAGGCCAGTGATATTGGGCTT-A-AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTGATAAGG
* * *
568799 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT---GAT-AAGG
*
568848 TGCCAATATGCTTATTCAAGGCCAGCGATATTGGACTT-A-AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTGATAAGG
* * * *
568891 TGCCAATGTGCTGATTCAAGGCCAGTGACATTGGTCTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT---GAT-AAGG
*
568940 TGCCAATATGCTGATTCAAGGCCAACGATATTGGACTT-A-AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTGATAAGG
* * * * * * *
568983 TGCCAATGTGCTAATTTAAGGCCAACGACATTGGTCTTAAAGATAAAG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT---GATAAGG
*
569031 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGGC-T--T---G
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTGATAAGG
* * * * *
569070 TGCCGATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT---GA-TAAGG
569119 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-A-AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTGATAAGG
* * * *
569162 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAATG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT---GAT--AAGG
*
569212 AGCCAATATGCTGATTCAAGGCCA
1 TGCCAATATGCTGATTCAAGGCCA
569236 ATGACATTGG
Statistics
Matches: 535, Mismatches: 65, Indels: 107
0.76 0.09 0.15
Matches are distributed among these distances:
38 2 0.00
39 95 0.18
40 4 0.01
41 2 0.00
42 2 0.00
43 152 0.28
44 2 0.00
45 5 0.01
46 2 0.00
47 34 0.06
48 36 0.07
49 174 0.33
50 25 0.05
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (45 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTGATAAGG
Found at i:568813 original size:43 final size:43
Alignment explanation
Indices: 568578--569203 Score: 576
Period size: 43 Copynumber: 14.1 Consensus size: 43
568568 CTTAAAGATG
* *
568578 AAGGTGCCAATGTGCTGATTCAAGGCCAACGATATTGGCCTT-
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGTCTTA
* *
568620 ---GTGCCAATGTGCTGAGTCAAGGCCAGCGACATTGGTCTTAAAGATA
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGTC-T-----TA
* *
568666 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGTCTTA
* *
568708 ---GAGCCAATGTGCTGATTCAAGGCTAGCGATATTGAG-CTTGTGA
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTG-GTC-T-T-A
* * *
568751 TAAGGTGCCAATATGCTGATTCAAGGCCAGTGATATTGGGCTTA
1 -AAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGTCTTA
*
568795 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATA
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGTC-T-----TA
* * *
568844 AAGGTGCCAATATGCTTATTCAAGGCCAGCGATATTGGACTTA
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGTCTTA
* *
568887 AAGGTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGTCTTAAAGA
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGTCTT----A
* * *
568934 TGAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTA
1 --AAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGTCTTA
* * * *
568979 AAGGTGCCAATGTGCTAATTTAAGGCCAACGACATTGGTCTTA
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGTCTTA
* *
569022 AAGATAAAGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTT-
1 AAG-----GTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGTCTTA
* *
569069 ---GTGCCGATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACA
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGTCTT------A
* *
569115 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGTCTTA
*
569158 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTA
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGTCTTA
569201 AAG
1 AAG
569204 ATGAAATGAG
Statistics
Matches: 482, Mismatches: 55, Indels: 93
0.77 0.09 0.15
Matches are distributed among these distances:
39 100 0.21
40 3 0.01
41 1 0.00
43 161 0.33
44 2 0.00
45 3 0.01
46 2 0.00
47 32 0.07
48 35 0.07
49 143 0.30
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.26
Consensus pattern (43 bp):
AAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGTCTTA
Found at i:568870 original size:92 final size:92
Alignment explanation
Indices: 568526--569235 Score: 993
Period size: 92 Copynumber: 7.9 Consensus size: 92
568516 CTTAGGAATA
* * * ** * * ** * *
568526 TTAAAGATGCCAATATGCTGAGTCAAGGCCAATGATATCGAACTTAAAGATGAAGGTGCCAATGT
1 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGCCAATAT
* *
568591 GCTGATTCAAGGCCAACGATATTGGCC
66 GCTGATTCAAGGCCAGCGATATTGGAC
*
568618 TT----GTGCCAATGTGCTGAGTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGCCAATAT
1 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGCCAATAT
568679 GCTGATTCAAGGCCAGCGATATTGGAC
66 GCTGATTCAAGGCCAGCGATATTGGAC
* * * **
568706 TT----GAGCCAATGTGCTGATTCAAGGCTAGCGATATTGAG-CTT-GTGAT-AAGGTGCCAATA
1 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTG-GTCTTAAAGATAAAGGTGCCAATA
* *
568764 TGCTGATTCAAGGCCAGTGATATTGGGC
65 TGCTGATTCAAGGCCAGCGATATTGGAC
568792 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGCCAATAT
1 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGCCAATAT
*
568857 GCTTATTCAAGGCCAGCGATATTGGAC
66 GCTGATTCAAGGCCAGCGATATTGGAC
* *
568884 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGTCTTAAAGATGAAGGTGCCAATAT
1 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGCCAATAT
*
568949 GCTGATTCAAGGCCAACGATATTGGAC
66 GCTGATTCAAGGCCAGCGATATTGGAC
* * *
568976 TTAAAGGTGCCAATGTGCTAATTTAAGGCCAACGACATTGGTCTTAAAGATAAA-GTGCCAATAT
1 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGCCAATAT
*
569040 GCTGATTCAAGGCCAGCGATATTGGGC
66 GCTGATTCAAGGCCAGCGATATTGGAC
* *
569067 TT----GTGCCGATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCCAATAT
1 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGCCAATAT
569128 GCTGATTCAAGGCCAGCGATATTGGAC
66 GCTGATTCAAGGCCAGCGATATTGGAC
* *
569155 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAATGAGCCAATA
1 TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAT-AAAGGTGCCAATA
569220 TGCTGATTCAAGGCCA
65 TGCTGATTCAAGGCCA
569236 ATGACATTGG
Statistics
Matches: 555, Mismatches: 49, Indels: 27
0.88 0.08 0.04
Matches are distributed among these distances:
86 40 0.07
87 46 0.08
88 147 0.26
89 2 0.00
90 34 0.06
91 40 0.07
92 219 0.39
93 27 0.05
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (92 bp):
TTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGCCAATAT
GCTGATTCAAGGCCAGCGATATTGGAC
Found at i:569294 original size:33 final size:33
Alignment explanation
Indices: 569255--569317 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
569245 GGCTTAGAAG
569255 GGTTGCCACCAACTTGTGTGGGCTTTAGAAAAT
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAAAAT
*
569288 GGTTGCCACCGACTTGTGTGGGCTTTAGAA
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAA
569318 GGGGGTGCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (33 bp):
GGTTGCCACCAACTTGTGTGGGCTTTAGAAAAT
Found at i:569337 original size:32 final size:31
Alignment explanation
Indices: 569243--569337 Score: 104
Period size: 33 Copynumber: 3.0 Consensus size: 31
569233 CCAATGACAT
569243 TGGGC-TTAGAAGGGTTGCCACCA-ACTTGTG
1 TGGGCTTTAGAAGGGTTGCCA-CAGACTTGTG
* *
569273 TGGGCTTTAGAAAATGGTTGCCACCGACTTGTG
1 TGGGCTTTAG--AAGGGTTGCCACAGACTTGTG
* *
569306 TGGGCTTTAGAAGGGGGTGCCACAGAGTTGTG
1 TGGGCTTTAGAA-GGGTTGCCACAGACTTGTG
569338 GACTTAAAAG
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
30 5 0.09
31 6 0.11
32 16 0.30
33 27 0.50
ACGTcount: A:0.20, C:0.17, G:0.36, T:0.27
Consensus pattern (31 bp):
TGGGCTTTAGAAGGGTTGCCACAGACTTGTG
Found at i:569400 original size:33 final size:33
Alignment explanation
Indices: 569322--569661 Score: 181
Period size: 33 Copynumber: 10.6 Consensus size: 33
569312 TTAGAAGGGG
* * **
569322 GTGCCACAGAGTTGTGGACTTAA-AAGGAAATG
1 GTGCCACGGAGTTGTGGACTTAACAAGAAAAAA
569354 GTGCCACGGAGTTGTGGACTTAACAAGAAAAAA
1 GTGCCACGGAGTTGTGGACTTAACAAGAAAAAA
* *
569387 GTGTCACGGAGTTGTGGACTTAACAGGAAAAAA
1 GTGCCACGGAGTTGTGGACTTAACAAGAAAAAA
* *
569420 GTGCCACGGAGTTGTGGGCTT-A-AAGAAGAAA
1 GTGCCACGGAGTTGTGGACTTAACAAGAAAAAA
** * *** *
569451 -TGCCACTAAGTCGTGGA-TTTTGAAGAAAAGA
1 GTGCCACGGAGTTGTGGACTTAACAAGAAAAAA
* * * ** *
569482 -TGCCACTGAGTCGTAGACTT-GGAAG-AAAAT
1 GTGCCACGGAGTTGTGGACTTAACAAGAAAAAA
* * *
569512 GATGCCACTGAGTCGTGGACTT----AGAAAAGA
1 G-TGCCACGGAGTTGTGGACTTAACAAGAAAAAA
* **
569542 GATGCCACTGAGTTGTGGACTT-GGAAG-AAAAA
1 G-TGCCACGGAGTTGTGGACTTAACAAGAAAAAA
* * * **
569574 GATGCCACTGAATCGTGGACTT-TGAAGAAAAAA
1 G-TGCCACGGAGTTGTGGACTTAACAAGAAAAAA
* * **
569607 GATGCCACTGAGTCGTGGACTT-GGAAGAAAAAA
1 G-TGCCACGGAGTTGTGGACTTAACAAGAAAAAA
* *
569640 GATGCCACTGAGTCGTGGACTT
1 G-TGCCACGGAGTTGTGGACTT
569662 GGGAGAAAAG
Statistics
Matches: 265, Mismatches: 32, Indels: 21
0.83 0.10 0.07
Matches are distributed among these distances:
29 4 0.02
30 40 0.15
31 33 0.12
32 72 0.27
33 116 0.44
ACGTcount: A:0.34, C:0.15, G:0.29, T:0.21
Consensus pattern (33 bp):
GTGCCACGGAGTTGTGGACTTAACAAGAAAAAA
Found at i:569634 original size:65 final size:65
Alignment explanation
Indices: 569413--569693 Score: 339
Period size: 62 Copynumber: 4.4 Consensus size: 65
569403 GACTTAACAG
* * * * *
569413 GAAAAAAG-TGCCACGGAGTTGTGGGCTT-AAAGAAGAA-ATGCCACT-AAGTCGTGGATTTTGA
1 GAAAAAAGATGCCACTGAGTTGTGGACTTGGAAGAAAAAGATGCCACTGAA-TCGTGGACTTTGA
569474 A
65 A
* * * *
569475 G--AAAAGATGCCACTGAGTCGTAGACTTGGAAGAAAATGATGCCACTGAGTCGTGGAC-TT--A
1 GAAAAAAGATGCCACTGAGTTGTGGACTTGGAAGAAAAAGATGCCACTGAATCGTGGACTTTGAA
*
569535 GAAAAGAGATGCCACTGAGTTGTGGACTTGGAAGAAAAAGATGCCACTGAATCGTGGACTTTGAA
1 GAAAAAAGATGCCACTGAGTTGTGGACTTGGAAGAAAAAGATGCCACTGAATCGTGGACTTTGAA
* * * *
569600 GAAAAAAGATGCCACTGAGTCGTGGACTTGGAAGAAAAAAGATGCCACTGAGTCGTGGACTTGGG
1 GAAAAAAGATGCCACTGAGTTGTGGACTTGGAAG-AAAAAGATGCCACTGAATCGTGGACTTTGA
569665 A
65 A
*
569666 G-AAAAGGATGCCACTGAGTTGTGGACTT
1 GAAAAAAGATGCCACTGAGTTGTGGACTT
569694 TGAGAAGAGA
Statistics
Matches: 188, Mismatches: 21, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
60 7 0.04
61 16 0.09
62 60 0.32
63 17 0.09
64 1 0.01
65 58 0.31
66 29 0.15
ACGTcount: A:0.34, C:0.15, G:0.30, T:0.21
Consensus pattern (65 bp):
GAAAAAAGATGCCACTGAGTTGTGGACTTGGAAGAAAAAGATGCCACTGAATCGTGGACTTTGAA
Found at i:569662 original size:33 final size:32
Alignment explanation
Indices: 569415--569693 Score: 338
Period size: 32 Copynumber: 8.8 Consensus size: 32
569405 CTTAACAGGA
* * * *
569415 AAAAAG-TGCCACGGAGTTGTGGGCTT-AAAG
1 AAAAAGATGCCACTGAGTCGTGGACTTGGAAG
* * * *
569445 AAGAA-ATGCCACTAAGTCGTGGATTTTGAAG
1 AAAAAGATGCCACTGAGTCGTGGACTTGGAAG
*
569476 -AAAAGATGCCACTGAGTCGTAGACTTGGAAG
1 AAAAAGATGCCACTGAGTCGTGGACTTGGAAG
*
569507 AAAATGATGCCACTGAGTCGTGGACTT---AG
1 AAAAAGATGCCACTGAGTCGTGGACTTGGAAG
*
569536 AAAAGAGATGCCACTGAGTTGTGGACTTGGAAG
1 AAAA-AGATGCCACTGAGTCGTGGACTTGGAAG
* *
569569 AAAAAGATGCCACTGAATCGTGGACTTTGAAG
1 AAAAAGATGCCACTGAGTCGTGGACTTGGAAG
569601 AAAAAAGATGCCACTGAGTCGTGGACTTGGAAG
1 -AAAAAGATGCCACTGAGTCGTGGACTTGGAAG
*
569634 AAAAAAGATGCCACTGAGTCGTGGACTTGGGAG
1 -AAAAAGATGCCACTGAGTCGTGGACTTGGAAG
* *
569667 AAAAGGATGCCACTGAGTTGTGGACTT
1 AAAAAGATGCCACTGAGTCGTGGACTT
569694 TGAGAAGAGA
Statistics
Matches: 216, Mismatches: 24, Indels: 16
0.84 0.09 0.06
Matches are distributed among these distances:
29 6 0.03
30 43 0.20
31 25 0.12
32 74 0.34
33 68 0.31
ACGTcount: A:0.34, C:0.15, G:0.30, T:0.22
Consensus pattern (32 bp):
AAAAAGATGCCACTGAGTCGTGGACTTGGAAG
Found at i:570898 original size:6 final size:6
Alignment explanation
Indices: 570889--570940 Score: 54
Period size: 6 Copynumber: 9.0 Consensus size: 6
570879 TTGTGTGTAT
* * *
570889 TTTTTG TTTTTG TTTTTA TTTTTT TTTTTG TTGTT- TTTTT- TTTTTG
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
*
570935 TGTTTG
1 TTTTTG
570941 CACTTTTGAG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
5 9 0.23
6 30 0.77
ACGTcount: A:0.02, C:0.00, G:0.13, T:0.85
Consensus pattern (6 bp):
TTTTTG
Found at i:570898 original size:18 final size:18
Alignment explanation
Indices: 570871--570937 Score: 93
Period size: 19 Copynumber: 3.8 Consensus size: 18
570861 TTTCATCTTC
570871 TTTTTTTTTTGTGTGTAT
1 TTTTTTTTTTGTGTGTAT
* *
570889 TTTTTGTTTTTGTTTTTAT
1 TTTTT-TTTTTGTGTGTAT
570908 TTTTTTTTTTGT-TGT-T
1 TTTTTTTTTTGTGTGTAT
570924 TTTTTTTTTTGTGT
1 TTTTTTTTTTGTGT
570938 TTGCACTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
16 13 0.30
17 3 0.07
18 12 0.27
19 16 0.36
ACGTcount: A:0.03, C:0.00, G:0.13, T:0.84
Consensus pattern (18 bp):
TTTTTTTTTTGTGTGTAT
Found at i:570938 original size:18 final size:18
Alignment explanation
Indices: 570871--570938 Score: 81
Period size: 17 Copynumber: 3.8 Consensus size: 18
570861 TTTCATCTTC
570871 TTTTTTTTTTGTG-TGTAT
1 TTTTTTTTTTGTGTTGT-T
570889 TTTTTGTTTTTGT-TT-TT
1 TTTTT-TTTTTGTGTTGTT
570906 ATTTTTTTTTT-TGTTGTT
1 -TTTTTTTTTTGTGTTGTT
570924 TTTTTTTTTTGTGTT
1 TTTTTTTTTTGTGTT
570939 TGCACTTTTG
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
16 1 0.02
17 18 0.41
18 17 0.39
19 8 0.18
ACGTcount: A:0.03, C:0.00, G:0.13, T:0.84
Consensus pattern (18 bp):
TTTTTTTTTTGTGTTGTT
Found at i:580430 original size:35 final size:34
Alignment explanation
Indices: 580336--580433 Score: 126
Period size: 34 Copynumber: 2.9 Consensus size: 34
580326 AACCTTATAA
*
580336 CCCTATCTTTTCATAA-GCTAAAATAGAACATTTT
1 CCCTATCTTTTCA-AAGGCTAAGATAGAACATTTT
* * * *
580370 CCTTATCTTTTGATAGGCTAAGATAGAACTTTTT
1 CCCTATCTTTTCAAAGGCTAAGATAGAACATTTT
580404 CCCTATCTTTTTCAAAGGCTAAGATAGAAC
1 CCCTATC-TTTTCAAAGGCTAAGATAGAAC
580434 CTCTTAATCA
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
33 1 0.02
34 33 0.61
35 20 0.37
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (34 bp):
CCCTATCTTTTCAAAGGCTAAGATAGAACATTTT
Found at i:581190 original size:22 final size:22
Alignment explanation
Indices: 581143--581190 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
581133 TATTTATTTA
**
581143 AAAAACATTAATTCTTTGCTTG
1 AAAAACATTAATTCTTTGCTCC
*
581165 AAAAACATTTATT-TTTGTCTCC
1 AAAAACATTAATTCTTTG-CTCC
581187 AAAA
1 AAAA
581191 CATCTTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.40
Consensus pattern (22 bp):
AAAAACATTAATTCTTTGCTCC
Found at i:581728 original size:17 final size:17
Alignment explanation
Indices: 581706--581791 Score: 136
Period size: 17 Copynumber: 5.1 Consensus size: 17
581696 CTTGAGTTTA
581706 TAACACTTCTCCCTCTT
1 TAACACTTCTCCCTCTT
* *
581723 TAACACTTCTCCTTCTA
1 TAACACTTCTCCCTCTT
*
581740 TAACACTTCTCCCTCTG
1 TAACACTTCTCCCTCTT
*
581757 TAACACTTCTCCCCCTT
1 TAACACTTCTCCCTCTT
581774 TAACACTTCTCCCTCTT
1 TAACACTTCTCCCTCTT
581791 T
1 T
581792 TTTCCATAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 62 1.00
ACGTcount: A:0.19, C:0.41, G:0.01, T:0.40
Consensus pattern (17 bp):
TAACACTTCTCCCTCTT
Found at i:586546 original size:35 final size:34
Alignment explanation
Indices: 586459--586558 Score: 157
Period size: 34 Copynumber: 2.9 Consensus size: 34
586449 AACCTTACAA
586459 CCCTATCTTTTCACAGGCTAAGATAGAACCTTCT
1 CCCTATCTTTTCACAGGCTAAGATAGAACCTTCT
586493 CCCTATCTTTTCACAGGCTAAGATAGAACCTAT-T
1 CCCTATCTTTTCACAGGCTAAGATAGAACCT-TCT
* *
586527 CCCTATCTTTTTCAAAGGCTAACATAGAACCT
1 CCCTATC-TTTTCACAGGCTAAGATAGAACCT
586559 CTCAAGCACT
Statistics
Matches: 62, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
34 39 0.63
35 23 0.37
ACGTcount: A:0.29, C:0.28, G:0.11, T:0.32
Consensus pattern (34 bp):
CCCTATCTTTTCACAGGCTAAGATAGAACCTTCT
Found at i:587738 original size:13 final size:13
Alignment explanation
Indices: 587720--587745 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
587710 AAACAATAAA
587720 TGTATCGATACAT
1 TGTATCGATACAT
587733 TGTATCGATACAT
1 TGTATCGATACAT
587746 GCCTAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:587846 original size:21 final size:21
Alignment explanation
Indices: 587820--587867 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
587810 AAATGAATTA
587820 ATACATTTACT-ATTTGTATCG
1 ATACATTTACTCA-TTGTATCG
*
587841 ATACA-TTATTCATTGTATCG
1 ATACATTTACTCATTGTATCG
587861 ATACATT
1 ATACATT
587868 CTGAGTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (21 bp):
ATACATTTACTCATTGTATCG
Found at i:592161 original size:23 final size:22
Alignment explanation
Indices: 592122--592174 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 22
592112 TCATCATCCT
592122 AAACACACCCCCAAAACACCTTC
1 AAACAC-CCCCCAAAACACCTTC
*
592145 AAACACCCTCCCGAAACACCTTC
1 AAACACCC-CCCAAAACACCTTC
592168 AAACACC
1 AAACACC
592175 AGAAAAATCT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 2 0.07
23 26 0.93
ACGTcount: A:0.42, C:0.47, G:0.02, T:0.09
Consensus pattern (22 bp):
AAACACCCCCCAAAACACCTTC
Found at i:605307 original size:13 final size:13
Alignment explanation
Indices: 605289--605313 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
605279 TAGCTCATTA
605289 TGTATCGATACAT
1 TGTATCGATACAT
605302 TGTATCGATACA
1 TGTATCGATACA
605314 ACATTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:609729 original size:16 final size:16
Alignment explanation
Indices: 609692--609730 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
609682 ACTATGCCTT
* **
609692 AAAAAAATAAAATTTA
1 AAAAAAACAAAATAAA
609708 AAAAAAACAAAATAAA
1 AAAAAAACAAAATAAA
609724 AAAAAAA
1 AAAAAAA
609731 GTGTTCCAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.13
Consensus pattern (16 bp):
AAAAAAACAAAATAAA
Found at i:610954 original size:40 final size:41
Alignment explanation
Indices: 610885--610975 Score: 121
Period size: 40 Copynumber: 2.2 Consensus size: 41
610875 TTATTTTCTT
*
610885 TTTGTCCTCAAGAAGCAAGACTCACTTCA-TCTCCTCTTCC
1 TTTGTCCTCAAGAAGCAAGACCCACTTCATTCTCCTCTTCC
* * * *
610925 TTTGTCCTCAAGGAGCAGGACCCATTTCATTCTCCTTTTCC
1 TTTGTCCTCAAGAAGCAAGACCCACTTCATTCTCCTCTTCC
*
610966 TTTATCCTCA
1 TTTGTCCTCA
610976 GATAGCATGG
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 25 0.57
41 19 0.43
ACGTcount: A:0.20, C:0.33, G:0.11, T:0.36
Consensus pattern (41 bp):
TTTGTCCTCAAGAAGCAAGACCCACTTCATTCTCCTCTTCC
Found at i:611039 original size:31 final size:31
Alignment explanation
Indices: 611001--611122 Score: 138
Period size: 31 Copynumber: 3.9 Consensus size: 31
610991 ACTCTTTTTT
* *
611001 AAGCCCGCACGAGTTGGTGGCACCCT-AGTCA
1 AAGCCCGCACAAGTTGGCGGCA-CCTAAGTCA
* ** * *
611032 AAGCCCGCACAAGCTAACGGCACCTGAGTCT
1 AAGCCCGCACAAGTTGGCGGCACCTAAGTCA
*
611063 AAGCCCGCACAAGTTGGCAGCACCTAAGTCA
1 AAGCCCGCACAAGTTGGCGGCACCTAAGTCA
* *
611094 AAGCCCACACAAGTTGGTGGCACCTAAGT
1 AAGCCCGCACAAGTTGGCGGCACCTAAGT
611123 TAGAGTCAAG
Statistics
Matches: 75, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
30 3 0.04
31 72 0.96
ACGTcount: A:0.29, C:0.32, G:0.25, T:0.15
Consensus pattern (31 bp):
AAGCCCGCACAAGTTGGCGGCACCTAAGTCA
Found at i:611198 original size:87 final size:87
Alignment explanation
Indices: 611090--611622 Score: 307
Period size: 87 Copynumber: 6.0 Consensus size: 87
611080 CAGCACCTAA
611090 GTCAAAGCCCACACAAGTTGGTGGCACCTAAGTTAGAGTCAAGCCCAAATTAGTTGGCACCTATC
1 GTCAAAGCCCACACAAGTTGGTGGCACCTAAGTTAGAGTCAAGCCCAAATTAGTTGGCACCTATC
611155 TAAGGAGGTCAAGCCTTAGAAT
66 TAAGGAGGTCAAGCCTTAGAAT
* * * * ** ** ** ** *
611177 GCCAAAGCCCACACGAGTTGGTGGCACCCT-AGTCAAAG-CCCGCATAAGCT-GGCGGCACCCGA
1 GTCAAAGCCCACACAAGTTGGTGGCA-CCTAAGTTAGAGTCAAGCCCAAATTAGTTGGCA-CCTA
*** * * *
611239 GTCTAAGCCCGTACGAG-TTGGTAGCACCTAA
64 -TCTAAGGAGGT-CAAGCCT--TAG-A---AT
* * * * * ** * *
611270 GTTAAAGCCCACACAAGCTGGTGGCACCTTAGTTCGAGTTAAGTTCATATTAGTTGGCACCTGTC
1 GTCAAAGCCCACACAAGTTGGTGGCACCTAAGTTAGAGTCAAGCCCAAATTAGTTGGCACCTATC
*
611335 TAAGGAGGTTAAGCCTTAGAAT
66 TAAGGAGGTCAAGCCTTAGAAT
* * * * * ** **
611357 GTCAAAGCCCACACGAGTTGGTGGCACCCTAA-TCAAAGTCCA-CACAAGCT-GACGGCACCTGA
1 GTCAAAGCCCACACAAGTTGGTGGCA-CCTAAGTTAGAGTCAAGCCCAAATTAGTTGGCACCT-A
* **
611419 GTCTAAGCCTACACGAGTTGGCGTGCC-T-G-A-
64 -TCTAAG-------GAG--GTCAAGCCTTAGAAT
* * * * *
611449 GTCAAAGTCCACACAAGTTGGTGGCACCTAAGTTCGAGTCAAGTCCACATTAGTTGGCACCTGTC
1 GTCAAAGCCCACACAAGTTGGTGGCACCTAAGTTAGAGTCAAGCCCAAATTAGTTGGCACCTATC
* *
611514 TAAGGAGATCAAGACTTAGAAT
66 TAAGGAGGTCAAGCCTTAGAAT
* * * *
611536 GTCAAAGCCCACGCAAGCTGGTGGCACCTAAGTCT-GAGTCAAGTCCACATTAGTTGGCACCTAT
1 GTCAAAGCCCACACAAGTTGGTGGCACCTAAGT-TAGAGTCAAGCCCAAATTAGTTGGCACCTAT
611600 CTAAGGAGGTCAAGCCTTAGAAT
65 CTAAGGAGGTCAAGCCTTAGAAT
611623 ACCAAAACCC
Statistics
Matches: 320, Mismatches: 92, Indels: 68
0.67 0.19 0.14
Matches are distributed among these distances:
83 3 0.01
84 1 0.00
85 17 0.05
86 13 0.04
87 153 0.48
88 11 0.03
89 3 0.01
90 2 0.01
91 8 0.03
92 41 0.13
93 41 0.13
94 17 0.05
95 6 0.02
96 4 0.01
ACGTcount: A:0.29, C:0.26, G:0.24, T:0.21
Consensus pattern (87 bp):
GTCAAAGCCCACACAAGTTGGTGGCACCTAAGTTAGAGTCAAGCCCAAATTAGTTGGCACCTATC
TAAGGAGGTCAAGCCTTAGAAT
Found at i:611217 original size:31 final size:31
Alignment explanation
Indices: 611179--611302 Score: 106
Period size: 31 Copynumber: 4.0 Consensus size: 31
611169 CTTAGAATGC
* *
611179 CAAAGCCCACACGAGTTGGTGGCACCCTAGT
1 CAAAGCCCACACAAGCTGGTGGCACCCTAGT
* * * *
611210 CAAAGCCCGCATAAGCTGGCGGCACCCGAGT
1 CAAAGCCCACACAAGCTGGTGGCACCCTAGT
* ** * * *
611241 CTAAGCCCGTACGAGTTGGTAGCA-CCTAAGT
1 CAAAGCCCACACAAGCTGGTGGCACCCT-AGT
* *
611272 TAAAGCCCACACAAGCTGGTGGCACCTTAGT
1 CAAAGCCCACACAAGCTGGTGGCACCCTAGT
611303 TCGAGTTAAG
Statistics
Matches: 69, Mismatches: 22, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
30 2 0.03
31 65 0.94
32 2 0.03
ACGTcount: A:0.27, C:0.31, G:0.26, T:0.17
Consensus pattern (31 bp):
CAAAGCCCACACAAGCTGGTGGCACCCTAGT
Found at i:611324 original size:180 final size:179
Alignment explanation
Indices: 611001--611563 Score: 802
Period size: 180 Copynumber: 3.1 Consensus size: 179
610991 ACTCTTTTTT
* *
611001 AAGCCCGCACGAGTTGGTGGCACCCTAGTCAAAGCCCGCACAAGCTAACGGCACCTGAGTCTAAG
1 AAGCCCACACGAGTTGGTGGCACCCTAGTCAAAGCCCGCACAAGCTGACGGCACCTGAGTCTAAG
* *
611066 CCCGCACAAGTTGGCAGCACCTAAGTCAAAGCCCACACAAGTTGGTGGCACCTAAGTTAGAGTCA
66 CCCGCACGAGTTGG-AGCACCTAAGTCAAAGCCCACACAAGTTGGTGGCACCTAAGTTCGAGTCA
* * *
611131 AGCCCAAATTAGTTGGCACCTATCTAAGGAGGTCAAGCCTTAGAATGCCA
130 AGTCCAAATTAGTTGGCACCTGTCTAAGGAGGTCAAGCCTTAGAATGTCA
* * *
611181 AAGCCCACACGAGTTGGTGGCACCCTAGTCAAAGCCCGCATAAGCTGGCGGCACCCGAGTCTAAG
1 AAGCCCACACGAGTTGGTGGCACCCTAGTCAAAGCCCGCACAAGCTGACGGCACCTGAGTCTAAG
* * * * *
611246 CCCGTACGAGTTGGTAGCACCTAAGTTAAAGCCCACACAAGCTGGTGGCACCTTAGTTCGAGTTA
66 CCCGCACGAGTTGG-AGCACCTAAGTCAAAGCCCACACAAGTTGGTGGCACCTAAGTTCGAGTCA
* * *
611311 AGTTCATATTAGTTGGCACCTGTCTAAGGAGGTTAAGCCTTAGAATGTCA
130 AGTCCAAATTAGTTGGCACCTGTCTAAGGAGGTCAAGCCTTAGAATGTCA
* * *
611361 AAGCCCACACGAGTTGGTGGCACCCTAATCAAAGTCCACACAAGCTGACGGCACCTGAGTCTAAG
1 AAGCCCACACGAGTTGGTGGCACCCTAGTCAAAGCCCGCACAAGCTGACGGCACCTGAGTCTAAG
** * ** * *
611426 CCTACACGAGTTGGCGTGCCTGAGTCAAAGTCCACACAAGTTGGTGGCACCTAAGTTCGAGTCAA
66 CCCGCACGAGTTGGAGCACCTAAGTCAAAGCCCACACAAGTTGGTGGCACCTAAGTTCGAGTCAA
* * *
611491 GTCCACATTAGTTGGCACCTGTCTAAGGAGATCAAGACTTAGAATGTCA
131 GTCCAAATTAGTTGGCACCTGTCTAAGGAGGTCAAGCCTTAGAATGTCA
* * *
611540 AAGCCCACGCAAGCTGGTGGCACC
1 AAGCCCACACGAGTTGGTGGCACC
611564 TAAGTCTGAG
Statistics
Matches: 338, Mismatches: 45, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
179 107 0.32
180 231 0.68
ACGTcount: A:0.28, C:0.27, G:0.25, T:0.20
Consensus pattern (179 bp):
AAGCCCACACGAGTTGGTGGCACCCTAGTCAAAGCCCGCACAAGCTGACGGCACCTGAGTCTAAG
CCCGCACGAGTTGGAGCACCTAAGTCAAAGCCCACACAAGTTGGTGGCACCTAAGTTCGAGTCAA
GTCCAAATTAGTTGGCACCTGTCTAAGGAGGTCAAGCCTTAGAATGTCA
Found at i:618009 original size:55 final size:55
Alignment explanation
Indices: 617930--618041 Score: 215
Period size: 55 Copynumber: 2.0 Consensus size: 55
617920 CCTTCTTTCA
617930 TCATCTTCTCTAAAAAAAAATCCTTTTCCACACCCTTTGAGCCTAACAAAATCAT
1 TCATCTTCTCTAAAAAAAAATCCTTTTCCACACCCTTTGAGCCTAACAAAATCAT
*
617985 TCATCTTCTCTCAAAAAAAATCCTTTTCCACACCCTTTGAGCCTAACAAAATCAT
1 TCATCTTCTCTAAAAAAAAATCCTTTTCCACACCCTTTGAGCCTAACAAAATCAT
618040 TC
1 TC
618042 TTTTGAAACC
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.35, C:0.30, G:0.04, T:0.31
Consensus pattern (55 bp):
TCATCTTCTCTAAAAAAAAATCCTTTTCCACACCCTTTGAGCCTAACAAAATCAT
Found at i:619594 original size:30 final size:29
Alignment explanation
Indices: 619505--619595 Score: 87
Period size: 30 Copynumber: 3.0 Consensus size: 29
619495 TCTTTTTCCA
*
619505 AAAGCCCACGACTCTGTGGCACCCTTCTT-
1 AAAGCCCACAACTCTGTGGCACCCTT-TTC
* *
619534 GAAGCCCATACAAGTC-GATGGCAACCCTTTTC
1 AAAGCCC--ACAACTCTG-TGGC-ACCCTTTTC
619566 AAAGCCCACAACTCTGTGGCACCTCTTTTC
1 AAAGCCCACAACTCTGTGGCACC-CTTTTC
619596 TCTTCTAAAG
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
29 9 0.18
30 17 0.34
31 12 0.24
32 12 0.24
ACGTcount: A:0.24, C:0.35, G:0.16, T:0.24
Consensus pattern (29 bp):
AAAGCCCACAACTCTGTGGCACCCTTTTC
Found at i:619708 original size:34 final size:33
Alignment explanation
Indices: 619575--619727 Score: 166
Period size: 32 Copynumber: 4.5 Consensus size: 33
619565 CAAAGCCCAC
* *
619575 AACTCTGTGGCACCTCTTTTCTCTTCTAAAGTCCAC
1 AACTCTGTGGCACCT-TTTTCT-TT-TTAAGTCCAT
* * *
619611 AACTCCGTTGCA-CTTTTTCCTTTTAAGTCCAT
1 AACTCTGTGGCACCTTTTTCTTTTTAAGTCCAT
* *
619643 AACTCTATGGCACC-TTTTCTTTTTAATTCCAT
1 AACTCTGTGGCACCTTTTTCTTTTTAAGTCCAT
619675 AACTCTGTGGCACCTTTTTCTTTTTTAAGTCCAT
1 AACTCTGTGGCACCTTTTTC-TTTTTAAGTCCAT
* *
619709 AACTCCGTGACAGCCTTTT
1 AACTCTGTGGCA-CCTTTT
619728 AAGTCCACAA
Statistics
Matches: 99, Mismatches: 14, Indels: 9
0.81 0.11 0.07
Matches are distributed among these distances:
32 46 0.46
33 8 0.08
34 27 0.27
35 8 0.08
36 10 0.10
ACGTcount: A:0.20, C:0.28, G:0.10, T:0.42
Consensus pattern (33 bp):
AACTCTGTGGCACCTTTTTCTTTTTAAGTCCAT
Found at i:619748 original size:93 final size:98
Alignment explanation
Indices: 619575--619751 Score: 247
Period size: 93 Copynumber: 1.8 Consensus size: 98
619565 CAAAGCCCAC
**
619575 AACTCTGTGGCACCTCTTTTCTCTTCTAAAGTCCACAACTCCGTTGCACTTTTTCCTTTTAAGTC
1 AACTCTGTGGCACCTCTTTTCTCTTCTAAAGTCCACAACTCCGTTGCAC--TAGCCTTTTAAGTC
*
619640 CATAACTCTATGGCACCTTTTCTTTTTAATTCCAT
64 CACAACTCTATGGCACCTTTTCTTTTTAATTCCAT
* * *
619675 AACTCTGTGGCACCT-TTTTCT-TTTTTAAGTCCATAACTCCG-TG-AC-AGCCTTTTAAGTCCA
1 AACTCTGTGGCACCTCTTTTCTCTTCTAAAGTCCACAACTCCGTTGCACTAGCCTTTTAAGTCCA
619735 CAACTCTATGGCACCTT
66 CAACTCTATGGCACCTT
619752 ACCCTTCTCA
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
93 29 0.41
96 2 0.03
97 2 0.03
98 17 0.24
99 6 0.08
100 15 0.21
ACGTcount: A:0.21, C:0.29, G:0.11, T:0.40
Consensus pattern (98 bp):
AACTCTGTGGCACCTCTTTTCTCTTCTAAAGTCCACAACTCCGTTGCACTAGCCTTTTAAGTCCA
CAACTCTATGGCACCTTTTCTTTTTAATTCCAT
Found at i:619852 original size:33 final size:33
Alignment explanation
Indices: 619752--620238 Score: 497
Period size: 32 Copynumber: 15.2 Consensus size: 33
619742 ATGGCACCTT
**
619752 ACCCTTCTC-AAAGCCCACACAAGTTAGTGGCA
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
* * * * *
619784 ACCCTTCT-TAAAGCCCATATAAGTTGATGGGA
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
619816 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
619849 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
** **
619882 ACATTTCT-TAAAGCCTGCACAAGTCGGTGGCA
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
*
619914 ACCCTT-TCTCAAAGCCCACATAA----GT--C-
1 ACCCTTCTCT-AAAGCCCACACAAGTCGGTGGCA
* * *
619940 ATCCTTCTCTAAAGCCCACATAAGTCGTTGGCA
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
*** *
619973 ACCCGTT-T-TAAAGCCCACACAAGTTAATGCCA
1 ACCC-TTCTCTAAAGCCCACACAAGTCGGTGGCA
* **
620005 ACCTTTCT-TAAAGCCCACACAAGTTAGTGGCA
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
* *
620037 ACCTTTATC-AAAGCCCACACAAGTCGGTGGCA
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
* * *
620069 ACCTTTCTC-AAAGCCCCCACAAGTCGGTAGCA
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
* * **
620101 ACCCTTCTTTAAAGCCCACAGAAGTTAGTGGCA
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
** **
620134 ACCCTTC-CGGAAGCCCACACAAGTCAATGGCA
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
620166 ACCCTTCT-TAAAGCCCACACAAGTCGGTGGCA
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
* *
620198 ACCCTTCTCTAAAGCCCACACAAGTCAGTAGCA
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
620231 ACCCTTCT
1 ACCCTTCT
620239 TAACCCAATG
Statistics
Matches: 382, Mismatches: 55, Indels: 35
0.81 0.12 0.07
Matches are distributed among these distances:
26 18 0.05
27 4 0.01
29 2 0.01
30 1 0.00
31 3 0.01
32 225 0.59
33 127 0.33
34 2 0.01
ACGTcount: A:0.30, C:0.33, G:0.16, T:0.21
Consensus pattern (33 bp):
ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
Found at i:619855 original size:65 final size:65
Alignment explanation
Indices: 619752--620241 Score: 497
Period size: 65 Copynumber: 7.7 Consensus size: 65
619742 ATGGCACCTT
* * * *
619752 ACCCTTCTC-AAAGCCCACACAAGTTAGTGGCAACCCTTCTTAAAGCCCATATAAGTTGATGGGA
1 ACCCTTCTCTAAAGCCCACACAAGTCAGTGGCAACCCTTCTTAAAGCCCACACAAGTTGATGGCA
* * *
619816 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGC
1 ACCCTTCTCTAAAGCCCACACAAGTCAGTGGCAACCCTTCT-TAAAGCCCACACAAGTTGATGGC
619881 A
65 A
** ** * * *
619882 ACATTTCT-TAAAGCCTGCACAAGTCGGTGGCAACCCTTTCTCAAAGCCCACATAA---G-T--C
1 ACCCTTCTCTAAAGCCCACACAAGTCAGTGGCAACCC-TTCTTAAAGCCCACACAAGTTGATGGC
619940 -
65 A
* * * *
619940 ATCCTTCTCTAAAGCCCACATAAGTC-GTTGGCAACCCGTT-TTAAAGCCCACACAAGTTAATGC
1 ACCCTTCTCTAAAGCCCACACAAGTCAG-TGGCAACCC-TTCTTAAAGCCCACACAAGTTGATGG
620003 CA
64 CA
* * * * * * *
620005 ACCTTTCT-TAAAGCCCACACAAGTTAGTGGCAACCTTTATCAAAGCCCACACAAGTCGGTGGCA
1 ACCCTTCTCTAAAGCCCACACAAGTCAGTGGCAACCCTTCTTAAAGCCCACACAAGTTGATGGCA
* * * * *
620069 ACCTTTCTC-AAAGCCCCCACAAGTCGGTAGCAACCCTTCTTTAAAGCCCACAGAAGTT-AGTGG
1 ACCCTTCTCTAAAGCCCACACAAGTCAGTGGCAACCCTTC-TTAAAGCCCACACAAGTTGA-TGG
620132 CA
64 CA
** * * *
620134 ACCCTTC-CGGAAGCCCACACAAGTCAATGGCAACCCTTCTTAAAGCCCACACAAGTCGGTGGCA
1 ACCCTTCTCTAAAGCCCACACAAGTCAGTGGCAACCCTTCTTAAAGCCCACACAAGTTGATGGCA
*
620198 ACCCTTCTCTAAAGCCCACACAAGTCAGTAGCAACCCTTCTTAA
1 ACCCTTCTCTAAAGCCCACACAAGTCAGTGGCAACCCTTCTTAA
620242 CCCAATGTCT
Statistics
Matches: 350, Mismatches: 56, Indels: 39
0.79 0.13 0.09
Matches are distributed among these distances:
58 19 0.05
59 26 0.07
61 1 0.00
62 2 0.01
63 2 0.01
64 114 0.33
65 157 0.45
66 29 0.08
ACGTcount: A:0.30, C:0.32, G:0.16, T:0.21
Consensus pattern (65 bp):
ACCCTTCTCTAAAGCCCACACAAGTCAGTGGCAACCCTTCTTAAAGCCCACACAAGTTGATGGCA
Found at i:620007 original size:91 final size:90
Alignment explanation
Indices: 619851--620224 Score: 243
Period size: 97 Copynumber: 4.0 Consensus size: 90
619841 CGGTGGCAAC
* ** ** *
619851 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAACATTTCTTAAAGCCTGCACAAGTCGGTGGCAAC
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAACAGTTCTTAAAGCCCACACAAGTCAATGCCAA-
*
619916 CCTTTCTCAAAGCCCACATAAGTCAT
65 CCTTTCTCAAAGCCCACACAAGTCAT
* * * *
619942 CCTTCTCTAAAGCCCACATAAGTCGTTGGCAACCCGTT-TTAAAGCCCACACAAGTTAATGCCAA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAA-CAGTTCTTAAAGCCCACACAAGTCAATGCCAA
* *
620006 CCTTTCTTAAAGCCCACACAAGTTAGTGGCAA
65 CCTTTCTCAAAGCCCACAC-A---AGT--CAT
* ** * * **
620038 CCTT-TATCAAAGCCCACACAAGTCGGTGGCAACCTTTCTCAAAGCCCCCACAAGTCGGTAG-CA
1 CCTTCTCT-AAAGCCCACACAAGTCGGTGGCAACAGTTCTTAAAGCCCACACAAGTCAAT-GCCA
* * * *
620101 ACCCTTCTTTAAAGCCCACAGAAGTTAGTGGCAAC
64 ACCTTTC-TCAAAGCCCACA-CA---AGT--C-AT
** ** ** ** *
620136 CCTTC-CGGAAGCCCACACAAGTCAATGGCAACCCTTCTTAAAGCCCACACAAGTCGGTGGCAAC
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAACAGTTCTTAAAGCCCACACAAGTCAATGCCAAC
*
620200 CCTTCTCTAAAGCCCACACAAGTCA
66 CTTTCTC-AAAGCCCACACAAGTCA
620225 GTAGCAACCC
Statistics
Matches: 232, Mismatches: 35, Indels: 33
0.77 0.12 0.11
Matches are distributed among these distances:
90 18 0.08
91 52 0.22
92 3 0.01
93 3 0.01
94 3 0.01
95 6 0.03
96 55 0.24
97 87 0.38
98 5 0.02
ACGTcount: A:0.30, C:0.33, G:0.16, T:0.21
Consensus pattern (90 bp):
CCTTCTCTAAAGCCCACACAAGTCGGTGGCAACAGTTCTTAAAGCCCACACAAGTCAATGCCAAC
CTTTCTCAAAGCCCACACAAGTCAT
Found at i:620309 original size:52 final size:51
Alignment explanation
Indices: 620253--621197 Score: 488
Period size: 52 Copynumber: 17.7 Consensus size: 51
620243 CCAATGTCTT
* *
620253 TGGCCTTGAATCAGCACATTGGCACATTTTTCTTTCTTAAGTCCAATATCGC
1 TGGCCTTGAATCAGCACATTGGCACCTTTTTC-ATCTTAAGTCCAATATCGC
* * ** *
620305 TGGCCTTGAATCAGCATATTAGCATTTTTTTCATCTCTAAGTCCAATGTCGC
1 TGGCCTTGAATCAGCACATTGGCACCTTTTTCATCT-TAAGTCCAATATCGC
** * * * * **
620357 TAACCTTGAATCAGCACATTGGCATCC-TTATCATCTTTAAGTCTAGTGTCAT
1 TGGCCTTGAATCAGCACATTGGCA-CCTTTTTCATC-TTAAGTCCAATATCGC
* *
620409 TGGCCTTAAATCAGCACATTGGCACCTTTTTCTTTCTTAAGTCCAATATCGC
1 TGGCCTTGAATCAGCACATTGGCACCTTTTTC-ATCTTAAGTCCAATATCGC
* * * * * *
620461 TGGCCTTAAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCGT
1 TGGCCTTGAATCAGCACATTGGCACCTTTTTCATC-TTAAGTCCAATATCGC
** * * *
620513 TGGCCTTGAATCAATACATTGGCACCTTTTTCTTTCTTAAGTCTAATATCAC
1 TGGCCTTGAATCAGCACATTGGCACCTTTTTC-ATCTTAAGTCCAATATCGC
* * * * **
620565 TGGCTTTGAATCAGTATATTAGCA-CTTTTGTCATCTTTAAGTCTGATATCGC
1 TGGCCTTGAATCAGCACATTGGCACCTTTT-TCATC-TTAAGTCCAATATCGC
* * * ** * * * *
620617 TAGCCTTAAATCAGCATATTGGCATCC-TTAACATTCTTAAGCCCAATGTTGT
1 TGGCCTTGAATCAGCACATTGGCA-CCTTTTTCA-TCTTAAGTCCAATATCGC
* * * *
620669 TGGCCTTGAATCAGTACATTAGCA--TTCTTCTCATCTTCAAGTCTAATGTCGC
1 TGGCCTTGAATCAGCACATTGGCACCTT-TT-TCATCTT-AAGTCCAATATCGC
* *
620721 TAGCCTTGAATCAGCACATTGGCACCTTTGTCATCTTTAAG-CCTAATATCGC
1 TGGCCTTGAATCAGCACATTGGCACCTTTTTCATC-TTAAGTCC-AATATCGC
* * * * * *
620773 TGGCCTTGAATCACCATATTGACACCTTTATCATTCTTCTCATCTTCAAGCCCGATATCAC
1 TGGCCTTGAATCAGCACATTGGCA-C-----C-TT-TT-TCATCTT-AAGTCCAATATCGC
* * * * * * *
620834 TGGCCGTGAATCAGCATATCGGTACTTTTATCATTCTTTGCATATTTAAGTCCGATATCGT
1 TGGCCTTGAATCAGCACATTGG--C----A-CCTT-TTT-CAT-CTTAAGTCCAATATCGC
* * * ** * *
620895 TGGCCTTGAATTAGCATATTGGCATCTTTAACATTCCTAAG-CCTAATGTCGC
1 TGGCCTTGAATCAGCACATTGGCACCTTTTTCA-TCTTAAGTCC-AATATCGC
* * * * *
620947 TAGCCTTGAATAAGCACATTGGCA--TTATTCTCATCTTTAAGTCTAATGTCGT
1 TGGCCTTGAATCAGCACATTGGCACCTT-TT-TCATC-TTAAGTCCAATATCGC
* * * ** *
620999 TGGCTTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCTGATAGCGC
1 TGGCCTTGAATCAGCACATTGGCACCTTTTTCATC-TTAAGTCCAATATCGC
* * * * * *
621051 TGGCTTTGAATCAGCATATTGACACCTTTATCATTCTTCTCATCTTCAAGTCCAATGTTGT
1 TGGCCTTGAATCAGCACATTGGCA-C-----C-TT-TT-TCATCTT-AAGTCCAATATCGC
* ***
621112 TGGCCTTGAATCAGCACATTGGCACCTTTGTCATCTTTAAG-CCTAATATTAT
1 TGGCCTTGAATCAGCACATTGGCACCTTTTTCATC-TTAAGTCC-AATATCGC
* * * *
621164 TGGCCTTCAATTAGCATATTGGCACCTTTATCAT
1 TGGCCTTGAATCAGCACATTGGCACCTTTTTCAT
621198 TTTTTTCATC
Statistics
Matches: 689, Mismatches: 145, Indels: 118
0.72 0.15 0.12
Matches are distributed among these distances:
50 3 0.00
51 27 0.04
52 501 0.73
53 21 0.03
54 9 0.01
55 2 0.00
58 2 0.00
59 5 0.01
60 8 0.01
61 104 0.15
62 4 0.01
63 1 0.00
67 2 0.00
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.37
Consensus pattern (51 bp):
TGGCCTTGAATCAGCACATTGGCACCTTTTTCATCTTAAGTCCAATATCGC
Found at i:620536 original size:156 final size:156
Alignment explanation
Indices: 620253--620806 Score: 602
Period size: 156 Copynumber: 3.6 Consensus size: 156
620243 CCAATGTCTT
* * *
620253 TGGCCTTGAATCAGCACATTGGCACATTTTTC-TTTCTTAAGTCCAATATCGCTGGCCTTGAATC
1 TGGCCTTGAATCAGCACATTGGCACCTTTTTCATCT-TTAAGTCCAATATCGCTGGCCTTAAATC
* ** * * * ** *
620317 AGCATATTAGCATTTTTTTCATCTCTAAGTCCAATGTCGCTAACCTTGAATCAGCACATTGGCAT
65 AGCATATTGGCACCTTTATCATCTTTAAGTCCAATGTCGTTGGCCTTGAATCAGTACATTGGCAT
* *
620382 CCTTATCATCTTTAAGTCTAGTGTCAT
130 CCTTATCATCTTTAAGTCTAATGTCAC
* *
620409 TGGCCTTAAATCAGCACATTGGCACCTTTTTC-TTTCTTAAGTCCAATATCGCTGGCCTTAAATC
1 TGGCCTTGAATCAGCACATTGGCACCTTTTTCATCT-TTAAGTCCAATATCGCTGGCCTTAAATC
* * *
620473 AGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCGTTGGCCTTGAATCAATACATTGGCA-
65 AGCATATTGGCACCTTTATCATCTTTAAGTCCAATGTCGTTGGCCTTGAATCAGTACATTGGCAT
* * *
620537 CCTTTTTC-TTTCTTAAGTCTAATATCAC
130 CC-TTATCATCT-TTAAGTCTAATGTCAC
* * * * ** *
620565 TGGCTTTGAATCAGTATATTAGCA-CTTTTGTCATCTTTAAGTCTGATATCGCTAGCCTTAAATC
1 TGGCCTTGAATCAGCACATTGGCACCTTTT-TCATCTTTAAGTCCAATATCGCTGGCCTTAAATC
* * * *
620629 AGCATATTGGCATCC-TTAACAT-TCTTAAGCCCAATGTTGTTGGCCTTGAATCAGTACATTAGC
65 AGCATATTGGCA-CCTTTATCATCT-TTAAGTCCAATGTCGTTGGCCTTGAATCAGTACATTGGC
* * * *
620692 ATTCTTCTCATCTTCAAGTCTAATGTCGC
128 ATCCTTATCATCTTTAAGTCTAATGTCAC
* * *
620721 TAGCCTTGAATCAGCACATTGGCACCTTTGTCATCTTTAAG-CCTAATATCGCTGGCCTTGAATC
1 TGGCCTTGAATCAGCACATTGGCACCTTTTTCATCTTTAAGTCC-AATATCGCTGGCCTTAAATC
* *
620785 ACCATATTGACACCTTTATCAT
65 AGCATATTGGCACCTTTATCAT
620807 TCTTCTCATC
Statistics
Matches: 333, Mismatches: 54, Indels: 22
0.81 0.13 0.05
Matches are distributed among these distances:
155 13 0.04
156 309 0.93
157 11 0.03
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (156 bp):
TGGCCTTGAATCAGCACATTGGCACCTTTTTCATCTTTAAGTCCAATATCGCTGGCCTTAAATCA
GCATATTGGCACCTTTATCATCTTTAAGTCCAATGTCGTTGGCCTTGAATCAGTACATTGGCATC
CTTATCATCTTTAAGTCTAATGTCAC
Found at i:620846 original size:61 final size:60
Alignment explanation
Indices: 620751--621310 Score: 268
Period size: 61 Copynumber: 9.8 Consensus size: 60
620741 GGCACCTTTG
** * *
620751 TCATCTTTAAGCCTAATATCGCTGGCCTTGAATCACCATATTGACACCTTTATCATTCTT
1 TCATCTTTAAGCCCGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATTCTT
* * * * * *
620811 CTCATCTTCAAGCCCGATATCACTGGCCGTGAATCAGCATATCGGTACTTTTATCATTCTT
1 -TCATCTTTAAGCCCGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATTCTT
* * * * * *
620872 TGCATATTTAAGTCCGATATCGTTGGCCTTGAATTAGCATATTGGCATCTTTA--A--CAT
1 T-CATCTTTAAGCCCGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATTCTT
** * * * *
620929 TC--C--TAAGCCTAATGTCGCTAGCCTTGAATAAGCACATTGGCA----T-T-ATTC--
1 TCATCTTTAAGCCCGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATTCTT
* ** * * * *
620977 TCATCTTTAAGTCTAATGTCGTTGGCTTTGAATCAGCATATTGGCA-C-----C-TT-TG
1 TCATCTTTAAGCCCGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATTCTT
* * * * *
621029 TCATCTTTAAGTCTGATAGCGCTGGCTTTGAATCAGCATATTGACACCTTTATCATTCTT
1 TCATCTTTAAGCCCGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATTCTT
* * * * * * * *
621089 CTCATCTTCAAGTCCAATGTTGTTGGCCTTGAATCAGCACATTGGCA-C-----C-TT-TG
1 -TCATCTTTAAGCCCGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATTCTT
** *** * * *
621142 TCATCTTTAAGCCTAATATTATTGGCCTTCAATTAGCATATTGGCACCTTTATCATTTTTT
1 TCATCTTTAAGCCCGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCA-TTCTT
** * ** *
621203 TCATCTTT-AGACCCGATATCATTGGCCGTGAATCAGCATATTGGCATTTTTATCGTTCTT
1 TCATCTTTAAG-CCCGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATTCTT
* ** * * * *
621263 TGCATCTTTAAGTCTAATGTCGCTGACCTTGAATCAGCACATTAGCAC
1 T-CATCTTTAAGCCCGATATCGCTGGCCTTGAATCAGCATATTGGCAC
621311 TCTTCTCATC
Statistics
Matches: 382, Mismatches: 84, Indels: 66
0.72 0.16 0.12
Matches are distributed among these distances:
48 4 0.01
50 2 0.01
51 2 0.01
52 143 0.37
53 3 0.01
54 2 0.01
55 1 0.00
56 1 0.00
57 3 0.01
58 2 0.01
59 3 0.01
60 12 0.03
61 202 0.53
62 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.38
Consensus pattern (60 bp):
TCATCTTTAAGCCCGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATTCTT
Found at i:621097 original size:278 final size:279
Alignment explanation
Indices: 620591--621100 Score: 779
Period size: 278 Copynumber: 1.8 Consensus size: 279
620581 TATTAGCACT
* * *
620591 TTTGTCATCTTTAAGTCTGATATCGCTAGCCTTAAATCAGCATATTGGCATCCTTAACATTCTTA
1 TTTGTCATATTTAAGTCCGATATCGCTAGCCTTAAATCAGCATATTGGCATCCTTAACATTCCTA
* * * * * *
620656 AGCCCAATGTTGTTGGCCTTGAATCAGTACATTAGCATTCTTCTCATCTTCAAGTCTAATGTCGC
66 AGCCCAATGTCGCTAGCCTTGAATAAGCACATTAGCATTATTCTCATCTTCAAGTCTAATGTCGC
*
620721 TAGCCTTGAATCAGCACATTGGCACCTTTGTCATCTTTAAGCCTAATATCGCTGGCCTTGAATCA
131 TAGCCTTGAATCAGCACATTGGCACCTTTGTCATCTTTAAGCCTAATAGCGCTGGCCTTGAATCA
620786 CCATATTGACACCTTTATCATTCTTCTCATCTTCAAGCCCGATATCACTGGCCGTGAATCAGCAT
196 CCATATTGACACCTTTATCATTCTTCTCATCTTCAAGCCCGATATCACTGGCCGTGAATCAGCAT
620851 ATCGGTACTTTTATCATTC
261 ATCGGTACTTTTATCATTC
* * * * *
620870 TTTG-CATATTTAAGTCCGATATCGTTGGCCTTGAATTAGCATATTGGCATCTTTAACATTCCTA
1 TTTGTCATATTTAAGTCCGATATCGCTAGCCTTAAATCAGCATATTGGCATCCTTAACATTCCTA
* * * *
620934 AGCCTAATGTCGCTAGCCTTGAATAAGCACATTGGCATTATTCTCATCTTTAAGTCTAATGTCGT
66 AGCCCAATGTCGCTAGCCTTGAATAAGCACATTAGCATTATTCTCATCTTCAAGTCTAATGTCGC
* * * * * *
620999 TGGCTTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCTGATAGCGCTGGCTTTGAATCA
131 TAGCCTTGAATCAGCACATTGGCACCTTTGTCATCTTTAAGCCTAATAGCGCTGGCCTTGAATCA
*
621064 GCATATTGACACCTTTATCATTCTTCTCATCTTCAAG
196 CCATATTGACACCTTTATCATTCTTCTCATCTTCAAG
621101 TCCAATGTTG
Statistics
Matches: 205, Mismatches: 26, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
278 201 0.98
279 4 0.02
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (279 bp):
TTTGTCATATTTAAGTCCGATATCGCTAGCCTTAAATCAGCATATTGGCATCCTTAACATTCCTA
AGCCCAATGTCGCTAGCCTTGAATAAGCACATTAGCATTATTCTCATCTTCAAGTCTAATGTCGC
TAGCCTTGAATCAGCACATTGGCACCTTTGTCATCTTTAAGCCTAATAGCGCTGGCCTTGAATCA
CCATATTGACACCTTTATCATTCTTCTCATCTTCAAGCCCGATATCACTGGCCGTGAATCAGCAT
ATCGGTACTTTTATCATTC
Found at i:621121 original size:113 final size:113
Alignment explanation
Indices: 620969--621209 Score: 320
Period size: 113 Copynumber: 2.1 Consensus size: 113
620959 AGCACATTGG
* * * *
620969 CATTATTCTCATCTTTAAGTCTAATGTCGTTGGCTTTGAATCAGCATATTGGCACCTTTGTCATC
1 CATTATTCTCATCTTCAAGTCCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTTGTCATC
* * * * *
621034 TTTAAGTCTGATAGCGCTGGCTTTGAATCAGCATATTGACACCTTTAT
66 TTTAAGCCTAATAGCACTGGCCTTCAATCAGCATATTGACACCTTTAT
* *
621082 CATTCTTCTCATCTTCAAGTCCAATGTTGTTGGCCTTGAATCAGCACATTGGCACCTTTGTCATC
1 CATTATTCTCATCTTCAAGTCCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTTGTCATC
** * * *
621147 TTTAAGCCTAATATTATTGGCCTTCAATTAGCATATTGGCACCTTTAT
66 TTTAAGCCTAATAGCACTGGCCTTCAATCAGCATATTGACACCTTTAT
* *
621195 CATTTTTTTCATCTT
1 CATTATTCTCATCTT
621210 TAGACCCGAT
Statistics
Matches: 110, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
113 110 1.00
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (113 bp):
CATTATTCTCATCTTCAAGTCCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTTGTCATC
TTTAAGCCTAATAGCACTGGCCTTCAATCAGCATATTGACACCTTTAT
Found at i:621228 original size:113 final size:113
Alignment explanation
Indices: 620969--621248 Score: 301
Period size: 113 Copynumber: 2.5 Consensus size: 113
620959 AGCACATTGG
* * * * * * *
620969 CATTATTCTCATCTTTAAGTCTAATGTCGTTGGCTTTGAATCAGCATATTGGCACCTTTGTCATC
1 CATTCTTCTCATCTTCAAGCCCAATATCATTGGCCTTGAATCAGCATATTGGCACCTTTGTCATC
* * * * *
621034 TTTAAGTCTGATAGCGCTGGCTTTGAATCAGCATATTGACACCTTTAT
66 TTTAAGCCTAATAGCACTGGCCTTCAATCAGCATATTGACACCTTTAT
* * ** *
621082 CATTCTTCTCATCTTCAAGTCCAATGTTGTTGGCCTTGAATCAGCACATTGGCACCTTTGTCATC
1 CATTCTTCTCATCTTCAAGCCCAATATCATTGGCCTTGAATCAGCATATTGGCACCTTTGTCATC
** * * *
621147 TTTAAGCCTAATATTATTGGCCTTCAATTAGCATATTGGCACCTTTAT
66 TTTAAGCCTAATAGCACTGGCCTTCAATCAGCATATTGACACCTTTAT
* * * * *
621195 CATTTTTTTCATCTT-TAGACCCGATATCATTGGCCGTGAATCAGCATATTGGCA
1 CATTCTTCTCATCTTCAAG-CCCAATATCATTGGCCTTGAATCAGCATATTGGCA
621249 TTTTTATCGT
Statistics
Matches: 140, Mismatches: 26, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
112 2 0.01
113 138 0.99
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (113 bp):
CATTCTTCTCATCTTCAAGCCCAATATCATTGGCCTTGAATCAGCATATTGGCACCTTTGTCATC
TTTAAGCCTAATAGCACTGGCCTTCAATCAGCATATTGACACCTTTAT
Found at i:621250 original size:278 final size:272
Alignment explanation
Indices: 620405--621198 Score: 680
Period size: 278 Copynumber: 3.0 Consensus size: 272
620395 AAGTCTAGTG
* * * * * *
620405 TCATTGGCCTTAAATCAGCACATTGGCACCTTTTTCT-TTCTT-AAGTCCAATATCGCTGGCCTT
1 TCATTGGCCTTGAATCAGCACATTGGCA--TTATTCTCATCTTCAAGTCTAATGTCGCTAGCCTT
* * * * ** *
620468 AAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCC-AAT-GTCGTTGGCCTTGAATCAATACA
64 GAATCAGCACATTGGCACCTTTGTCATCTTTAAG-CCTAATAG-CGCTGGCCTTGAATCACCATA
* * * ** * * **
620531 TTGGCACC-TT-T--TTC-T-T--TCTT-AAGTCTAATATCACTGGCTTTGAATCAGTATATTAG
127 TTGACACCTTTATCATTCTTCTCATCTTCAAGCCCAATATCACTGGCCGTGAATCAGCACATCGG
* ** ** * * *
620587 -C-A-CT-TTTGTCATCTTTAAGTCTGATATCGCTAGCCTTAAATCAGCATATTGGCATCC-TTA
192 ACTATCTCTTTG-CATATTTAAGTCCAATATCATTGGCCTTCAATTAGCATATTGGCA-CCTTTA
* *
620647 ACATTCTTAAGCCCAATG
255 ACATTCCTAAGCCCAATA
** * * *
620665 TTGTTGGCCTTGAATCAGTACATTAGCATTCTTCTCATCTTCAAGTCTAATGTCGCTAGCCTTGA
1 TCATTGGCCTTGAATCAGCACATTGGCATTATTCTCATCTTCAAGTCTAATGTCGCTAGCCTTGA
*
620730 ATCAGCACATTGGCACCTTTGTCATCTTTAAGCCTAATATCGCTGGCCTTGAATCACCATATTGA
66 ATCAGCACATTGGCACCTTTGTCATCTTTAAGCCTAATAGCGCTGGCCTTGAATCACCATATTGA
* *
620795 CACCTTTATCATTCTTCTCATCTTCAAGCCCGATATCACTGGCCGTGAATCAGCATATCGGTACT
131 CACCTTTATCATTCTTCTCATCTTCAAGCCCAATATCACTGGCCGTGAATCAGCACATCGG-AC-
* * * *
620860 TTTATCATTCTTTGCATATTTAAGTCCGATATCGTTGGCCTTGAATTAGCATATTGGCATCTTTA
194 --TATC--TCTTTGCATATTTAAGTCCAATATCATTGGCCTTCAATTAGCATATTGGCACCTTTA
* *
620925 ACATTCCTAAGCCTAATG
255 ACATTCCTAAGCCCAATA
** * * * * * *
620943 TCGCTAGCCTTGAATAAGCACATTGGCATTATTCTCATCTTTAAGTCTAATGTCGTTGGCTTTGA
1 TCATTGGCCTTGAATCAGCACATTGGCATTATTCTCATCTTCAAGTCTAATGTCGCTAGCCTTGA
* * * * *
621008 ATCAGCATATTGGCACCTTTGTCATCTTTAAGTCTGATAGCGCTGGCTTTGAATCAGCATATTGA
66 ATCAGCACATTGGCACCTTTGTCATCTTTAAGCCTAATAGCGCTGGCCTTGAATCACCATATTGA
* * *** * *
621073 CACCTTTATCATTCTTCTCATCTTCAAGTCCAATGTTGTTGGCCTTGAATCAGCACATTGG-C-A
131 CACCTTTATCATTCTTCTCATCTTCAAGCCCAATATCACTGGCCGTGAATCAGCACATCGGACTA
* * *
621136 -C-CTTTGTCATCTTTAAG-CCTAATATTATTGGCCTTCAATTAGCATATTGGCACCTTTATCAT
196 TCTCTTTG-CATATTTAAGTCC-AATATCATTGGCCTTCAATTAGCATATTGGCACCTTTAACAT
621198 T
259 T
621199 TTTTTCATCT
Statistics
Matches: 439, Mismatches: 69, Indels: 43
0.80 0.13 0.08
Matches are distributed among these distances:
258 6 0.01
259 6 0.01
260 99 0.23
261 2 0.00
262 1 0.00
264 3 0.01
265 1 0.00
266 1 0.00
268 11 0.03
269 74 0.17
271 2 0.00
272 1 0.00
275 1 0.00
276 2 0.00
277 1 0.00
278 224 0.51
279 4 0.01
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.37
Consensus pattern (272 bp):
TCATTGGCCTTGAATCAGCACATTGGCATTATTCTCATCTTCAAGTCTAATGTCGCTAGCCTTGA
ATCAGCACATTGGCACCTTTGTCATCTTTAAGCCTAATAGCGCTGGCCTTGAATCACCATATTGA
CACCTTTATCATTCTTCTCATCTTCAAGCCCAATATCACTGGCCGTGAATCAGCACATCGGACTA
TCTCTTTGCATATTTAAGTCCAATATCATTGGCCTTCAATTAGCATATTGGCACCTTTAACATTC
CTAAGCCCAATA
Found at i:625981 original size:52 final size:51
Alignment explanation
Indices: 625825--626169 Score: 302
Period size: 52 Copynumber: 6.9 Consensus size: 51
625815 GAGAAGAGTG
* * * * **
625825 AGAAAGGTGCCAATATGCTGATTCAAGGCCAGTGATATTGGGTTTAAAGAT
1 AGAAAGATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT
* * * * * *
625876 ATAAAGAATGTCAATGTGCTGATTCACGGTCAGCGACCA-TAGACTTGAAGAT
1 AGAAAG-ATGCCAATGTGCTGATTCAAGGCCAGCGA-CATTGGACTTAAAGAT
* * *
625928 GAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCGACATTGCACTTAAGGAT
1 -AGAAAGATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT
* * * * *
625980 GACAAAGGTACCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT
1 -AGAAAGATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT
* * *
626032 -G-AAGGTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGGT
1 AGAAAGATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT
* * *
626081 -G-AAGATGCCAATGTGTTGATTCAAGGCCAGCAACATTAGACTT--A-A-
1 AGAAAGATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT
* * *
626126 AG---G-TGCCAATATGCTGATTCATGGCCAGCGATATTGGACTTAAA
1 AGAAAGATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAA
626170 AGAAGATGCC
Statistics
Matches: 242, Mismatches: 45, Indels: 20
0.79 0.15 0.07
Matches are distributed among these distances:
43 32 0.13
44 1 0.00
45 1 0.00
46 1 0.00
47 1 0.00
49 83 0.34
51 7 0.03
52 111 0.46
53 5 0.02
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (51 bp):
AGAAAGATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT
Found at i:626217 original size:30 final size:27
Alignment explanation
Indices: 626176--626231 Score: 76
Period size: 30 Copynumber: 2.0 Consensus size: 27
626166 TAAAAGAAGA
626176 TGCCACCAACTTGTGTGGGCTTTTGAAAGT
1 TGCCACCAAC-T-TGTGGGC-TTTGAAAGT
*
626206 TGCCACTAACTTGTGGGCTTTGAAAG
1 TGCCACCAACTTGTGGGCTTTGAAAG
626232 ATGTTAGGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 8 0.32
28 7 0.28
29 1 0.04
30 9 0.36
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (27 bp):
TGCCACCAACTTGTGGGCTTTGAAAGT
Found at i:636592 original size:13 final size:13
Alignment explanation
Indices: 636574--636632 Score: 67
Period size: 13 Copynumber: 4.9 Consensus size: 13
636564 CAAAGATCAG
636574 TGTATCGATACAA
1 TGTATCGATACAA
636587 TGTATCGATAC-A
1 TGTATCGATACAA
636599 T-T-T-GAGT--AA
1 TGTATCGA-TACAA
636608 TGTATCGATACAA
1 TGTATCGATACAA
636621 TGTATCGATACA
1 TGTATCGATACA
636633 TTTGAGTAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
9 4 0.10
10 3 0.08
11 3 0.08
12 4 0.10
13 25 0.64
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:636617 original size:34 final size:34
Alignment explanation
Indices: 636574--636653 Score: 160
Period size: 34 Copynumber: 2.4 Consensus size: 34
636564 CAAAGATCAG
636574 TGTATCGATACAATGTATCGATACATTTGAGTAA
1 TGTATCGATACAATGTATCGATACATTTGAGTAA
636608 TGTATCGATACAATGTATCGATACATTTGAGTAA
1 TGTATCGATACAATGTATCGATACATTTGAGTAA
636642 TGTATCGATACA
1 TGTATCGATACA
636654 TTTTCTTGGC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (34 bp):
TGTATCGATACAATGTATCGATACATTTGAGTAA
Found at i:636709 original size:19 final size:19
Alignment explanation
Indices: 636685--636749 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
636675 AACTGTACAT
636685 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
636704 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
636717 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
636736 TGTATCGATACAAA
1 TGTATCGATACAAA
636750 TCGTTGAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
16 2 0.05
18 1 0.03
19 24 0.62
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:636721 original size:32 final size:32
Alignment explanation
Indices: 636680--636747 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
636670 TTCGTAACTG
636680 TACATTGTATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATACAAAACTTATGTATCGA
*
636712 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAAAACTTATGTATCGA
636744 TACA
1 TACA
636748 AATCGTTGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.34
Consensus pattern (32 bp):
TACATTGTATCGATACAAAACTTATGTATCGA
Found at i:636722 original size:13 final size:13
Alignment explanation
Indices: 636704--636728 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
636694 ACAAAACTTA
636704 TGTATCGATACAT
1 TGTATCGATACAT
636717 TGTATCGATACA
1 TGTATCGATACA
636729 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:637489 original size:97 final size:97
Alignment explanation
Indices: 637338--637525 Score: 243
Period size: 97 Copynumber: 1.9 Consensus size: 97
637328 TGTCCCCACA
* * *
637338 GAGGAATGGGGTTGGAGTATCCCCTACGATGATAACTTAAGCGAAAATAAGATTTAAACCTTAAC
1 GAGGAATAGGGTTGGAGTATCCCCGAAGATGATAACTTAAGCGAAAATAAGATTTAAACCTTAAC
*
637403 AAGTT-TAAAAACGGGGTTGGAGTATCCCTTTG
66 AAGTTCTAAAAA-GGGGTTAGAGTATCCCTTTG
* * * ** * * * *
637435 GAGGAATAGGGTTGGAGTGTCCCCGAATATGATAATTTGGGTGAAATTAAGATTTAAATCTTGAC
1 GAGGAATAGGGTTGGAGTATCCCCGAAGATGATAACTTAAGCGAAAATAAGATTTAAACCTTAAC
637500 AAGTTCTAAAAAGGGGTTAGAGTATC
66 AAGTTCTAAAAAGGGGTTAGAGTATC
637526 TCTAAAATTA
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
97 71 0.92
98 6 0.08
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (97 bp):
GAGGAATAGGGTTGGAGTATCCCCGAAGATGATAACTTAAGCGAAAATAAGATTTAAACCTTAAC
AAGTTCTAAAAAGGGGTTAGAGTATCCCTTTG
Found at i:637556 original size:52 final size:52
Alignment explanation
Indices: 637478--637577 Score: 166
Period size: 52 Copynumber: 1.9 Consensus size: 52
637468 AATTTGGGTG
*
637478 AAATTAAGATTTAAATCTTGACAAGTTCTAAAAA-GGGGTTAGAGTATCTCTA
1 AAATTAAGATTTAAATCTTAACAAGTT-TAAAAACGGGGTTAGAGTATCTCTA
*
637530 AAATTAAGATTTAAATCTTAACAAGTTTAAAAACGGGGTTGGAGTATC
1 AAATTAAGATTTAAATCTTAACAAGTTTAAAAACGGGGTTAGAGTATC
637578 CCTTTGGAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
51 6 0.13
52 39 0.87
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (52 bp):
AAATTAAGATTTAAATCTTAACAAGTTTAAAAACGGGGTTAGAGTATCTCTA
Found at i:637655 original size:149 final size:148
Alignment explanation
Indices: 637381--637677 Score: 558
Period size: 149 Copynumber: 2.0 Consensus size: 148
637371 AACTTAAGCG
**
637381 AAAATAAGATTTAAACCTTAACAAGTTTAAAAACGGGGTTGGAGTATCCCTTTGGAGGAATAGGG
1 AAAATAAGATTTAAACCTTAACAAGTTTAAAAACGGGGTTGGAGTATCCCTTTGGAAAAATAGGG
637446 TTGGAGTGTCCCCGAATATGATAATTTGGGTGAAATTAAGATTTAAATCTTGACAAGTTCTAAAA
66 TTGGAGTGTCCCCGAATATGATAATTTGGGTGAAATTAAGATTTAAATCTTGACAAGTTCTAAAA
637511 AGGGGTTAGAGTATCTCT
131 AGGGGTTAGAGTATCTCT
*
637529 AAAATTAAGATTTAAATCTTAACAAGTTTAAAAACGGGGTTGGAGTATCCCTTTGGAAAAATAGG
1 AAAA-TAAGATTTAAACCTTAACAAGTTTAAAAACGGGGTTGGAGTATCCCTTTGGAAAAATAGG
637594 GTTGGAGTGTCCCCGAATATGATAATTTGGGTGAAATTAAGATTTAAATCTTGACAAGTTCTAAA
65 GTTGGAGTGTCCCCGAATATGATAATTTGGGTGAAATTAAGATTTAAATCTTGACAAGTTCTAAA
637659 AAGGGGTTAGAGTATCTCT
130 AAGGGGTTAGAGTATCTCT
637678 GATGATGATA
Statistics
Matches: 145, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
148 4 0.03
149 141 0.97
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (148 bp):
AAAATAAGATTTAAACCTTAACAAGTTTAAAAACGGGGTTGGAGTATCCCTTTGGAAAAATAGGG
TTGGAGTGTCCCCGAATATGATAATTTGGGTGAAATTAAGATTTAAATCTTGACAAGTTCTAAAA
AGGGGTTAGAGTATCTCT
Found at i:639670 original size:13 final size:13
Alignment explanation
Indices: 639652--639677 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
639642 ATTTTTTTGG
639652 TGTATCGATACAT
1 TGTATCGATACAT
639665 TGTATCGATACAT
1 TGTATCGATACAT
639678 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:639692 original size:32 final size:34
Alignment explanation
Indices: 639631--639695 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 34
639621 TACAAGCCAA
**
639631 TGTATCGATACATTTTTTTGGTGTATCGATACAT
1 TGTATCGATACATTACTTTGGTGTATCGATACAT
639665 TGTATCGATACA-TACTTT-GTGTATCGATACA
1 TGTATCGATACATTACTTTGGTGTATCGATACA
639696 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 13 0.45
33 4 0.14
34 12 0.41
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.43
Consensus pattern (34 bp):
TGTATCGATACATTACTTTGGTGTATCGATACAT
Found at i:642250 original size:13 final size:13
Alignment explanation
Indices: 642232--642270 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
642222 ATAATCCCAC
*
642232 TGTATCGATACAG
1 TGTATCGATACAA
642245 TGTATCGATACAA
1 TGTATCGATACAA
642258 TGTATCGATACAA
1 TGTATCGATACAA
642271 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:648471 original size:13 final size:13
Alignment explanation
Indices: 648453--648478 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
648443 ATTTTTTTGG
648453 TGTATCGATACAT
1 TGTATCGATACAT
648466 TGTATCGATACAT
1 TGTATCGATACAT
648479 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:648493 original size:32 final size:34
Alignment explanation
Indices: 648432--648496 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 34
648422 TACAAGCCAA
**
648432 TGTATCGATACATTTTTTTGGTGTATCGATACAT
1 TGTATCGATACATTACTTTGGTGTATCGATACAT
648466 TGTATCGATACA-TACTTT-GTGTATCGATACA
1 TGTATCGATACATTACTTTGGTGTATCGATACA
648497 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 13 0.45
33 4 0.14
34 12 0.41
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.43
Consensus pattern (34 bp):
TGTATCGATACATTACTTTGGTGTATCGATACAT
Found at i:650214 original size:51 final size:51
Alignment explanation
Indices: 650136--650324 Score: 228
Period size: 51 Copynumber: 3.8 Consensus size: 51
650126 TTAAATTTAA
*
650136 CTAG-ATGTATCGATACAATGAAGAATGTATCGATACATTTGGGTCAAAAC
1 CTAGAATGTATCGATACAATGAAAAATGTATCGATACATTTGGGTCAAAAC
* *
650186 CTAGAATGTATCGATACAATGAATAATGTATCGATACATTTAGGTCAAAA-
1 CTAGAATGTATCGATACAATGAAAAATGTATCGATACATTTGGGTCAAAAC
* * * * *
650236 CTCAGAATATATCGATATAATGAAAAATGTATCAATACATTTGGATC-AATC
1 CT-AGAATGTATCGATACAATGAAAAATGTATCGATACATTTGGGTCAAAAC
* * *
650287 C-AGAATGTATGGATATAA--AAAAATGTATAGATACATTT
1 CTAGAATGTATCGATACAATGAAAAATGTATCGATACATTT
650325 TCTTTCTAGA
Statistics
Matches: 123, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
47 18 0.15
49 15 0.12
50 8 0.07
51 82 0.67
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (51 bp):
CTAGAATGTATCGATACAATGAAAAATGTATCGATACATTTGGGTCAAAAC
Done.