Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr10
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: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31
Warning! 2980117 characters in sequence are not A, C, G, or T
File 2 of 284
Found at i:338545 original size:31 final size:31
Alignment explanation
Indices: 338487--338545 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
338477 GTTACCAATC
*
338487 CAGTGACTAGAATGAAAATCTTTAAATAGTT
1 CAGTGACTAGAATGAAAAGCTTTAAATAGTT
338518 CAGTGACATA-AATG-AAAGCTTTCAAATA
1 CAGTGAC-TAGAATGAAAAGCTTT-AAATA
338546 ATTTAATAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 7 0.28
31 16 0.64
32 2 0.08
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (31 bp):
CAGTGACTAGAATGAAAAGCTTTAAATAGTT
Found at i:346603 original size:14 final size:14
Alignment explanation
Indices: 346584--346614 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
346574 TAAAAATAAT
346584 AGAGTCAGATAAAC
1 AGAGTCAGATAAAC
*
346598 AGAGTCAGATAATC
1 AGAGTCAGATAAAC
346612 AGA
1 AGA
346615 ATCCTACCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.23, T:0.16
Consensus pattern (14 bp):
AGAGTCAGATAAAC
Found at i:349025 original size:20 final size:19
Alignment explanation
Indices: 348989--349039 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
348979 AAGGGCTATT
*
348989 TTGTAAA-GTTGTAAAATAA
1 TTGTAAATG-TGTGAAATAA
349008 GTTGTAAATGTGTGAAATAA
1 -TTGTAAATGTGTGAAATAA
349028 TTG-AAAT-TGTGA
1 TTGTAAATGTGTGA
349040 GTTTCTATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.17
18 4 0.14
19 3 0.10
20 16 0.55
21 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (19 bp):
TTGTAAATGTGTGAAATAA
Found at i:349949 original size:142 final size:138
Alignment explanation
Indices: 349689--349952 Score: 341
Period size: 142 Copynumber: 1.9 Consensus size: 138
349679 TACGTGTGCT
* * *
349689 AGTGTAAGACATGTCTGGGACATACATCGGCCACATTATGAGAGCCAGTGTAAGACATGTTTGGG
1 AGTGTAAGACATGTCTGGGACATACATCGACCACATTATGAGAGCCAATGTAAGACATGTCTGGG
*
349754 ACATGCATCAGCCTTGAGATATGCAAGCCAGTGTAAGACCTGTCTAGGACATGGCATCGGCTTGA
66 ACATGCATCAGCCTCGAGATATGCAAGCCAGTGTAAGACCTGTCTAGGACATGGCATCGGCTTGA
349819 CATGTGTC
131 CATGTGTC
* * * *
349827 AGTGTAAGACCTGTCTGGGACATGGCATCGA-CACCGATATATGAGAGCTAATGTAAGACCTGTC
1 AGTGTAAGACATGTCTGGGACAT-ACATCGACCA-C-AT-TATGAGAGCCAATGTAAGACATGTC
** * * * * *
349891 TGGGACATGACATTGGCCTCGATATATGGAAGTCAGTGTAAGACCTGTCTGGGGCATGGCAT
62 TGGGACATG-CATCAGCCTCGAGATATGCAAGCCAGTGTAAGACCTGTCTAGGACATGGCAT
349953 TGACTTAGAT
Statistics
Matches: 106, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
138 24 0.23
139 6 0.06
140 2 0.02
141 30 0.28
142 44 0.42
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (138 bp):
AGTGTAAGACATGTCTGGGACATACATCGACCACATTATGAGAGCCAATGTAAGACATGTCTGGG
ACATGCATCAGCCTCGAGATATGCAAGCCAGTGTAAGACCTGTCTAGGACATGGCATCGGCTTGA
CATGTGTC
Found at i:349954 original size:49 final size:48
Alignment explanation
Indices: 349689--349952 Score: 233
Period size: 49 Copynumber: 5.6 Consensus size: 48
349679 TACGTGTGCT
* * * *
349689 AGTGTAAGACATGTCTGGGACAT-ACATCGGCCAC-AT-TATGAGAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGATATATGA-AGTC
* * * * * *
349735 AGTGTAAGACATGTTTGGGACAT-GCATCAGCCTTGAGATATGCAAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGATATATG-AAGTC
* * * *
349783 AGTGTAAGACCTGTCTAGGACATGGCATCGG-CTTG--ACATG-TGTC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGATATATGAAGTC
*
349827 AGTGTAAGACCTGTCTGGGACATGGCATCGACAC-CGATATATGAGAG-C
1 AGTGTAAGACCTGTCTGGGACATGGCATCGGC-CTCGATATATGA-AGTC
* * *
349875 TAATGTAAGACCTGTCTGGGACATGACATTGGCCTCGATATATGGAAGTC
1 -AGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGATATAT-GAAGTC
*
349925 AGTGTAAGACCTGTCTGGGGCATGGCAT
1 AGTGTAAGACCTGTCTGGGACATGGCAT
349953 TGACTTAGAT
Statistics
Matches: 179, Mismatches: 25, Indels: 25
0.78 0.11 0.11
Matches are distributed among these distances:
44 31 0.17
45 1 0.01
46 34 0.19
47 5 0.03
48 34 0.19
49 71 0.40
50 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (48 bp):
AGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGATATATGAAGTC
Found at i:352499 original size:24 final size:23
Alignment explanation
Indices: 352468--352513 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
352458 TATTACTTTC
352468 AAAACATACCAATTCAACCATTTA
1 AAAACATACCAA-TCAACCATTTA
*
352492 AAAACATATCAATCAACCATTT
1 AAAACATACCAATCAACCATTT
352514 CTTTCCTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (23 bp):
AAAACATACCAATCAACCATTTA
Found at i:353440 original size:18 final size:18
Alignment explanation
Indices: 353414--353454 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
353404 GGTCATGGGG
*
353414 CATTATCGAACAAAAACA
1 CATTTTCGAACAAAAACA
**
353432 CATTTTCGAACAACCACA
1 CATTTTCGAACAAAAACA
353450 CATTT
1 CATTT
353455 ATACAAGTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.44, C:0.27, G:0.05, T:0.24
Consensus pattern (18 bp):
CATTTTCGAACAAAAACA
Found at i:355103 original size:56 final size:56
Alignment explanation
Indices: 355043--355167 Score: 196
Period size: 56 Copynumber: 2.2 Consensus size: 56
355033 TCTTCCTCTG
* * * *
355043 ACACATATATCGGAGTCACATATCGATGCCAACGTATAAAACGTGGTGTTACTCGT
1 ACACATATATCGAAGTCACATATAGATGCCAACGTATAAAACGTGGTCTTACTCGC
* *
355099 ACACATATATCGAAGTCACATATAGATGCCAATGTATAAAATGTGGTCTTACTCGC
1 ACACATATATCGAAGTCACATATAGATGCCAACGTATAAAACGTGGTCTTACTCGC
355155 ACACATATATCGA
1 ACACATATATCGA
355168 TGCCATGGTC
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (56 bp):
ACACATATATCGAAGTCACATATAGATGCCAACGTATAAAACGTGGTCTTACTCGC
Found at i:367196 original size:20 final size:22
Alignment explanation
Indices: 367156--367203 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 22
367146 TCAGAAGAGC
367156 ACCAAAAAGGAGCAAAAAACGA
1 ACCAAAAAGGAGCAAAAAACGA
* *
367178 ACCAAAAAGG-G-ACAAAACGG
1 ACCAAAAAGGAGCAAAAAACGA
367198 ACCAAA
1 ACCAAA
367204 TTAAGAAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 13 0.54
21 1 0.04
22 10 0.42
ACGTcount: A:0.60, C:0.21, G:0.19, T:0.00
Consensus pattern (22 bp):
ACCAAAAAGGAGCAAAAAACGA
Found at i:367686 original size:26 final size:27
Alignment explanation
Indices: 367579--367695 Score: 146
Period size: 27 Copynumber: 4.4 Consensus size: 27
367569 GGATAAGTTC
*
367579 TAGAATTACCGAAATACCCCTGTAGGA
1 TAGAATTACCGAAATACCCCTGTAGGG
* **
367606 TAGAATTACCGAAATAACATTGTAGGG
1 TAGAATTACCGAAATACCCCTGTAGGG
* *
367633 TAGAAATACTGAAATACCCCTGTAGGG
1 TAGAATTACCGAAATACCCCTGTAGGG
* *
367660 TAGAATTACCG-AATACCCTTGTGGGG
1 TAGAATTACCGAAATACCCCTGTAGGG
*
367686 TAAAATTACC
1 TAGAATTACC
367696 ATTTTGCCCC
Statistics
Matches: 76, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
26 22 0.29
27 54 0.71
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.25
Consensus pattern (27 bp):
TAGAATTACCGAAATACCCCTGTAGGG
Found at i:375135 original size:27 final size:27
Alignment explanation
Indices: 375093--375192 Score: 141
Period size: 27 Copynumber: 3.7 Consensus size: 27
375083 TGGATAAGTT
375093 GTAGAATTACTGAAATACCCCTGTAGG
1 GTAGAATTACTGAAATACCCCTGTAGG
* **
375120 ATAGAATTACCAAAATA-CCCTAGTAGG
1 GTAGAATTACTGAAATACCCCT-GTAGG
*
375147 GTAGAAATACTGAAATACCCCTGTAGG
1 GTAGAATTACTGAAATACCCCTGTAGG
375174 GTAGAATTACTG-AATACCC
1 GTAGAATTACTGAAATACCC
375193 TTTATGTTTG
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
26 11 0.17
27 48 0.76
28 4 0.06
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (27 bp):
GTAGAATTACTGAAATACCCCTGTAGG
Found at i:385675 original size:40 final size:40
Alignment explanation
Indices: 385630--385804 Score: 287
Period size: 40 Copynumber: 4.4 Consensus size: 40
385620 TATGTGCACA
* *
385630 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCAAAG
1 GCATTCGTGCGGGTTATTATAACCGGGCTAAGTCCCGAAG
385670 GCATTCGTGCGGGTTATTATAACCGGGCTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGCTAAGTCCCGAAG
385710 GCATTCGTGCGGGTTATTATAACCGGGCTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGCTAAGTCCCGAAG
* * * *
385750 GCATTCGTGCGAGTTATTATTACCGGGTTAAGTCCTGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGCTAAGTCCCGAAG
*
385790 GCATTCGTGCTGGTT
1 GCATTCGTGCGGGTT
385805 GTTACATCCG
Statistics
Matches: 127, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 127 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (40 bp):
GCATTCGTGCGGGTTATTATAACCGGGCTAAGTCCCGAAG
Found at i:388256 original size:40 final size:40
Alignment explanation
Indices: 388201--388343 Score: 207
Period size: 40 Copynumber: 3.6 Consensus size: 40
388191 GGATGATAAC
*
388201 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTTT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTTA
*
388241 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTTC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTTA
* * **
388281 CGGGCTAAGTCTCGAAGGCATTTGTGCGAGCTACTA-AAA
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTTA
*
388320 CTGGGCTAAGTCCTGAAGGCATTT
1 C-GGGCTAAGTCCCGAAGGCATTT
388344 AAGCGAGTAG
Statistics
Matches: 94, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
39 1 0.01
40 93 0.99
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTTA
Found at i:401628 original size:40 final size:40
Alignment explanation
Indices: 401584--401769 Score: 243
Period size: 40 Copynumber: 4.7 Consensus size: 40
401574 GCTACTCATT
*
401584 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
401624 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
401664 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
401704 CCAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
401745 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
401770 CATCATTCAA
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
39 3 0.02
40 116 0.89
41 12 0.09
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:404494 original size:10 final size:10
Alignment explanation
Indices: 404479--404507 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
404469 TTAAGTGCCG
404479 AATTGAGCTA
1 AATTGAGCTA
404489 AATTGAGCTA
1 AATTGAGCTA
404499 AATTGAGCT
1 AATTGAGCT
404508 GACACAAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (10 bp):
AATTGAGCTA
Found at i:407546 original size:15 final size:15
Alignment explanation
Indices: 407526--407580 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
407516 ACTCTCCTCA
*
407526 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
407541 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
407556 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
407570 TTCTTTT-TCTC
1 TTCTTTTCTCTC
407581 GCTCAATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
14 16 0.46
15 19 0.54
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:409672 original size:12 final size:11
Alignment explanation
Indices: 409655--409696 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
409645 AAATACAAAC
409655 TTTTTTTTTGAA
1 TTTTTTTTT-AA
409667 TTTTTTTTTCAA
1 TTTTTTTTT-AA
*
409679 ATTTTTTTT-A
1 TTTTTTTTTAA
409689 TTTTTTTT
1 TTTTTTTT
409697 ACAATCTCGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 8 0.30
12 19 0.70
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.81
Consensus pattern (11 bp):
TTTTTTTTTAA
Found at i:409673 original size:13 final size:13
Alignment explanation
Indices: 409650--409687 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
409640 AAATTAAATA
409650 CAAACTTTTTTTTT
1 CAAA-TTTTTTTTT
*
409664 -GAATTTTTTTTT
1 CAAATTTTTTTTT
409676 CAAATTTTTTTT
1 CAAATTTTTTTT
409688 ATTTTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.21, C:0.08, G:0.03, T:0.68
Consensus pattern (13 bp):
CAAATTTTTTTTT
Found at i:413999 original size:13 final size:13
Alignment explanation
Indices: 413969--414019 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
413959 TAGTTTCTCG
* *
413969 AAAAAACAAACTC
1 AAAAAAAAAATTC
*
413982 GAAAAAAAAATTC
1 AAAAAAAAAATTC
*
413995 AAAAAAAAATTTC
1 AAAAAAAAAATTC
*
414008 GAAAAAAAAATT
1 AAAAAAAAAATT
414020 TGGTTTCCAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.71, C:0.10, G:0.04, T:0.16
Consensus pattern (13 bp):
AAAAAAAAAATTC
Found at i:414020 original size:14 final size:13
Alignment explanation
Indices: 413966--414019 Score: 74
Period size: 14 Copynumber: 4.1 Consensus size: 13
413956 TAGTAGTTTC
*
413966 TCGAAAAAACAAAC
1 TCGAAAAAA-AAAT
413980 TCGAAAAAAAAAT
1 TCGAAAAAAAAAT
413993 TC-AAAAAAAAATT
1 TCGAAAAAAAAA-T
414006 TCGAAAAAAAAAT
1 TCGAAAAAAAAAT
414019 T
1 T
414020 TGGTTTCCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
12 9 0.24
13 10 0.27
14 18 0.49
ACGTcount: A:0.67, C:0.11, G:0.06, T:0.17
Consensus pattern (13 bp):
TCGAAAAAAAAAT
Found at i:414080 original size:16 final size:16
Alignment explanation
Indices: 414059--414112 Score: 85
Period size: 15 Copynumber: 3.5 Consensus size: 16
414049 TATCAAGTTG
414059 AAAAAAAAATTCGTG-
1 AAAAAAAAATTCGTGA
414074 AAAAAAAAA-TCGTGA
1 AAAAAAAAATTCGTGA
*
414089 AAAAAAAATTTCGTGA
1 AAAAAAAAATTCGTGA
414105 AAAAAAAA
1 AAAAAAAA
414113 GAAGAAGCTA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
14 5 0.14
15 17 0.47
16 14 0.39
ACGTcount: A:0.67, C:0.06, G:0.11, T:0.17
Consensus pattern (16 bp):
AAAAAAAAATTCGTGA
Found at i:425725 original size:28 final size:28
Alignment explanation
Indices: 425694--425747 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
425684 GGTACGAAGT
*
425694 AAAAAAAATTCAA-AAAAAAGAAGTGAGC
1 AAAAAAAAATCAAGAAAAAA-AAGTGAGC
*
425722 AAAAAAAAATCAAGTAAAAAAAGTGA
1 AAAAAAAAATCAAGAAAAAAAAGTGA
425748 AAAGTCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.70, C:0.06, G:0.13, T:0.11
Consensus pattern (28 bp):
AAAAAAAAATCAAGAAAAAAAAGTGAGC
Found at i:426221 original size:18 final size:18
Alignment explanation
Indices: 426198--426233 Score: 56
Period size: 17 Copynumber: 2.0 Consensus size: 18
426188 GTTGTAAAGT
426198 TTTATTTTTATTTA-TTTA
1 TTTA-TTTTATTTAGTTTA
426216 TTTATTTTATTTAGTTTA
1 TTTATTTTATTTAGTTTA
426234 AATTTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (18 bp):
TTTATTTTATTTAGTTTA
Found at i:433416 original size:19 final size:19
Alignment explanation
Indices: 433392--433434 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
433382 AATGTTCAAA
* *
433392 ATTTTAATACAATTTAATT
1 ATTTTAATAAAAATTAATT
433411 ATTTT-ATAAAAATTAATT
1 ATTTTAATAAAAATTAATT
433429 ATTTTA
1 ATTTTA
433435 TGACAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTTAATAAAAATTAATT
Found at i:434888 original size:18 final size:18
Alignment explanation
Indices: 434867--434927 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
434857 GGTTGAAAAG
*
434867 GAAGGTGATGCTGAAGAA
1 GAAGGTGTTGCTGAAGAA
* *
434885 GAAGAAGTTGTTGCAGAAGAG
1 GAAG--G-TGTTGCTGAAGAA
*
434906 GAAGTTGTTGCTGAAGAA
1 GAAGGTGTTGCTGAAGAA
434924 GAAG
1 GAAG
434928 TTGCTGAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 19 0.56
20 1 0.03
21 14 0.41
ACGTcount: A:0.38, C:0.05, G:0.38, T:0.20
Consensus pattern (18 bp):
GAAGGTGTTGCTGAAGAA
Found at i:434928 original size:18 final size:18
Alignment explanation
Indices: 434881--434930 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
434871 GTGATGCTGA
434881 AGAAGAAGAAGTTGTTGC
1 AGAAGAAGAAGTTGTTGC
*
434899 AGAAGAGGAAGTTGTTGC
1 AGAAGAAGAAGTTGTTGC
*
434917 TGAAGAAGAAGTTG
1 AGAAGAAGAAGTTG
434931 CTGAAAACAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.38, C:0.04, G:0.36, T:0.22
Consensus pattern (18 bp):
AGAAGAAGAAGTTGTTGC
Found at i:435407 original size:17 final size:17
Alignment explanation
Indices: 435385--435417 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
435375 AGTATACATA
*
435385 GTCATTGCATTTTCATT
1 GTCATTACATTTTCATT
435402 GTCATTACATTTTCAT
1 GTCATTACATTTTCAT
435418 GTTAGTGCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.18, G:0.09, T:0.52
Consensus pattern (17 bp):
GTCATTACATTTTCATT
Found at i:435995 original size:21 final size:21
Alignment explanation
Indices: 435971--436016 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
435961 ATATGTATAT
*
435971 AAATAGTTAGTATTGTACAAA
1 AAATACTTAGTATTGTACAAA
*
435992 AAATACTTAGTATTGTACAAT
1 AAATACTTAGTATTGTACAAA
436013 AAAT
1 AAAT
436017 GCTGTAATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.35
Consensus pattern (21 bp):
AAATACTTAGTATTGTACAAA
Found at i:438672 original size:17 final size:17
Alignment explanation
Indices: 438634--438672 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
438624 TCAACCTGGG
* *
438634 AAAAGATCCTGAAATAT
1 AAAATATCCTGAAATAC
*
438651 GAAATATCCTGAAATAC
1 AAAATATCCTGAAATAC
438668 AAAAT
1 AAAAT
438673 CAAGAATTAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.13, G:0.10, T:0.23
Consensus pattern (17 bp):
AAAATATCCTGAAATAC
Found at i:439576 original size:41 final size:41
Alignment explanation
Indices: 439519--439600 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
439509 GCAACCTTCA
439519 TGAGATACATGACCGCGATCTTTGCTGATATGCTAGAAGAG
1 TGAGATACATGACCGCGATCTTTGCTGATATGCTAGAAGAG
* *
439560 TGAGATACATGACCGCGATCTTTGCTGATTTGCTAGTAGAG
1 TGAGATACATGACCGCGATCTTTGCTGATATGCTAGAAGAG
439601 CGGTTAGATG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (41 bp):
TGAGATACATGACCGCGATCTTTGCTGATATGCTAGAAGAG
Found at i:445848 original size:30 final size:30
Alignment explanation
Indices: 445813--445873 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
445803 AGGGTGATGT
445813 AAATCTATTTTTAGGATTAGGGATACATAC
1 AAATCTATTTTTAGGATTAGGGATACATAC
445843 AAATCTATTTTTAGGATTAGGGATACATAC
1 AAATCTATTTTTAGGATTAGGGATACATAC
445873 A
1 A
445874 TACATAATTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (30 bp):
AAATCTATTTTTAGGATTAGGGATACATAC
Found at i:454557 original size:26 final size:26
Alignment explanation
Indices: 454518--454579 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
454508 ACATATTTTT
*
454518 TCAAAATTTGACTAGGGGTAAAATCA
1 TCAAAATTTTACTAGGGGTAAAATCA
* *
454544 TCAAAATTTTACTAGGGGTAAATTCG
1 TCAAAATTTTACTAGGGGTAAAATCA
454570 TCAAAATTTT
1 TCAAAATTTT
454580 GTAAGAGGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (26 bp):
TCAAAATTTTACTAGGGGTAAAATCA
Found at i:454589 original size:26 final size:26
Alignment explanation
Indices: 454518--454593 Score: 82
Period size: 26 Copynumber: 2.9 Consensus size: 26
454508 ACATATTTTT
* *
454518 TCAAAATTTGACTAGGGGTAAAATCA
1 TCAAAATTTTACTAGAGGTAAAATCA
* * *
454544 TCAAAATTTTACTAGGGGTAAATTCG
1 TCAAAATTTTACTAGAGGTAAAATCA
*
454570 TCAAAATTTT-GTAAGAGGTAAAAT
1 TCAAAATTTTACT-AGAGGTAAAAT
454594 AAGGATGAGA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
25 1 0.02
26 42 0.98
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (26 bp):
TCAAAATTTTACTAGAGGTAAAATCA
Found at i:460798 original size:27 final size:27
Alignment explanation
Indices: 460694--460787 Score: 145
Period size: 27 Copynumber: 3.5 Consensus size: 27
460684 AATAACCTTG
460694 AAGGGTAAAATGACTGAAATACCCTCA
1 AAGGGTAAAATGACTGAAATACCCTCA
* *
460721 AAAGGTAAAATGAAC-GAAATACCCTCG
1 AAGGGTAAAATG-ACTGAAATACCCTCA
*
460748 AAGGGTAAAATGACTGAAATACCCCCA
1 AAGGGTAAAATGACTGAAATACCCTCA
460775 AAGGGTAAAATGA
1 AAGGGTAAAATGA
460788 TTGTTATACC
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
26 2 0.03
27 56 0.93
28 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.16
Consensus pattern (27 bp):
AAGGGTAAAATGACTGAAATACCCTCA
Found at i:460799 original size:54 final size:54
Alignment explanation
Indices: 460672--460787 Score: 178
Period size: 54 Copynumber: 2.1 Consensus size: 54
460662 GTAATGGGCC
** * * *
460672 TAAAATGGCCGAAATAACCTTGAAGGGTAAAATGACTGAAATACCCTCAAAAGG
1 TAAAATGAACGAAATACCCTCGAAGGGTAAAATGACTGAAATACCCCCAAAAGG
*
460726 TAAAATGAACGAAATACCCTCGAAGGGTAAAATGACTGAAATACCCCCAAAGGG
1 TAAAATGAACGAAATACCCTCGAAGGGTAAAATGACTGAAATACCCCCAAAAGG
460780 TAAAATGA
1 TAAAATGA
460788 TTGTTATACC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (54 bp):
TAAAATGAACGAAATACCCTCGAAGGGTAAAATGACTGAAATACCCCCAAAAGG
Found at i:460992 original size:26 final size:26
Alignment explanation
Indices: 460963--461039 Score: 118
Period size: 26 Copynumber: 3.0 Consensus size: 26
460953 TTGCCACATA
*
460963 TACTGTTACTGGCAGCTTTGCTGCGT
1 TACTATTACTGGCAGCTTTGCTGCGT
* *
460989 TACTATTACTGGTAGCGTTGCTGCGT
1 TACTATTACTGGCAGCTTTGCTGCGT
*
461015 TACTATTATTGGCAGCTTTGCTGCG
1 TACTATTACTGGCAGCTTTGCTGCG
461040 ATATTGGTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.14, C:0.21, G:0.26, T:0.39
Consensus pattern (26 bp):
TACTATTACTGGCAGCTTTGCTGCGT
Found at i:461183 original size:30 final size:30
Alignment explanation
Indices: 461147--461204 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
461137 TACATTGTAC
* *
461147 TGTTACTGTATTGGGCTAAGGCCCACACAT
1 TGTTACTGTAATGGGATAAGGCCCACACAT
461177 TGTTACTGTAATGGGATAAGGCCCACAC
1 TGTTACTGTAATGGGATAAGGCCCACAC
461205 CGTACTGCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (30 bp):
TGTTACTGTAATGGGATAAGGCCCACACAT
Found at i:461560 original size:30 final size:32
Alignment explanation
Indices: 461487--461554 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
461477 ATTTTTCCTT
461487 GAATATTTTAAACTGCTAGATTAGGAGATGAA
1 GAATATTTTAAACTGCTAGATTAGGAGATGAA
*
461519 GAATATTTTAAACTGCTAGATTAGGAGATGAC
1 GAATATTTTAAACTGCTAGATTAGGAGATGAA
461551 GAAT
1 GAAT
461555 TTTAAAATAA
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:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (32 bp):
GAATATTTTAAACTGCTAGATTAGGAGATGAA
Found at i:470926 original size:24 final size:22
Alignment explanation
Indices: 470890--470936 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 22
470880 ATTAGCACAT
470890 ATATAATCACATACAT-ATCAAA
1 ATATAATCACATA-ATAATCAAA
470912 ATATCAATCATCATAATAATCAAA
1 ATAT-AATCA-CATAATAATCAAA
470936 A
1 A
470937 GTTCTAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 4 0.18
23 7 0.32
24 11 0.50
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (22 bp):
ATATAATCACATAATAATCAAA
Found at i:488803 original size:17 final size:17
Alignment explanation
Indices: 488759--488810 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
488749 CTACCTATCA
*
488759 TTTTCACAGTCTATAG-
1 TTTTCATAGTCTATAGT
* * *
488775 TTGTCCTAGTCTTTAGT
1 TTTTCATAGTCTATAGT
488792 TTTTCATAGTCTATAGT
1 TTTTCATAGTCTATAGT
488809 TT
1 TT
488811 CAAAGCTAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
16 12 0.43
17 16 0.57
ACGTcount: A:0.19, C:0.15, G:0.13, T:0.52
Consensus pattern (17 bp):
TTTTCATAGTCTATAGT
Found at i:489843 original size:22 final size:22
Alignment explanation
Indices: 489817--489861 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
489807 AGATCAACAC
489817 AAATAT-AATCACATACATATCA
1 AAATATCAATCACA-ACATATCA
*
489839 AAATATCAATCTCAACATATCA
1 AAATATCAATCACAACATATCA
489861 A
1 A
489862 TCATCATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.53, C:0.20, G:0.00, T:0.27
Consensus pattern (22 bp):
AAATATCAATCACAACATATCA
Found at i:494781 original size:47 final size:47
Alignment explanation
Indices: 494712--494803 Score: 184
Period size: 47 Copynumber: 2.0 Consensus size: 47
494702 ATTTAATAAT
494712 ATCAAAAGATCATCTAAAATAAATGAATAATAAATAAATAAAATTAA
1 ATCAAAAGATCATCTAAAATAAATGAATAATAAATAAATAAAATTAA
494759 ATCAAAAGATCATCTAAAATAAATGAATAATAAATAAATAAAATT
1 ATCAAAAGATCATCTAAAATAAATGAATAATAAATAAATAAAATT
494804 CAGGCGACCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.63, C:0.07, G:0.04, T:0.26
Consensus pattern (47 bp):
ATCAAAAGATCATCTAAAATAAATGAATAATAAATAAATAAAATTAA
Found at i:495781 original size:13 final size:13
Alignment explanation
Indices: 495759--495796 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
495749 TTCCTGGCTT
495759 TATA-CACCCTAG
1 TATATCACCCTAG
495771 TATATCACCCTAG
1 TATATCACCCTAG
495784 TATATCACCCTAG
1 TATATCACCCTAG
495797 GGGGCTCCGG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 4 0.16
13 21 0.84
ACGTcount: A:0.32, C:0.32, G:0.08, T:0.29
Consensus pattern (13 bp):
TATATCACCCTAG
Found at i:497204 original size:20 final size:21
Alignment explanation
Indices: 497169--497207 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
497159 CACCTCGTTG
497169 AGCTCAATTCAGCTCATTTCC
1 AGCTCAATTCAGCTCATTTCC
*
497190 AGCTC-ATTGAGCTCATTT
1 AGCTCAATTCAGCTCATTT
497208 GCTTGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.36
Consensus pattern (21 bp):
AGCTCAATTCAGCTCATTTCC
Found at i:497614 original size:13 final size:13
Alignment explanation
Indices: 497596--497621 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
497586 TGTGTCCTAA
497596 TATGAATTAAATT
1 TATGAATTAAATT
497609 TATGAATTAAATT
1 TATGAATTAAATT
497622 GCTTTCAGGT
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:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TATGAATTAAATT
Found at i:498520 original size:9 final size:9
Alignment explanation
Indices: 498506--498553 Score: 60
Period size: 9 Copynumber: 5.1 Consensus size: 9
498496 GGAGTAAGTG
498506 ATTAAAAAA
1 ATTAAAAAA
498515 ATTAAAAAAA
1 ATT-AAAAAA
498525 ATTGAAAAAA
1 ATT-AAAAAA
*
498535 ATAAAAAAA
1 ATTAAAAAA
*
498544 AGTAAAAAA
1 ATTAAAAAA
498553 A
1 A
498554 AAATTCGTGG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
9 17 0.50
10 17 0.50
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (9 bp):
ATTAAAAAA
Found at i:498524 original size:10 final size:10
Alignment explanation
Indices: 498509--498554 Score: 67
Period size: 10 Copynumber: 4.7 Consensus size: 10
498499 GTAAGTGATT
498509 AAAAAAATTA
1 AAAAAAATTA
*
498519 AAAAAAATTG
1 AAAAAAATTA
498529 AAAAAAA-TA
1 AAAAAAATTA
*
498538 AAAAAAAGTA
1 AAAAAAATTA
498548 AAAAAAA
1 AAAAAAA
498555 AATTCGTGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
9 8 0.24
10 25 0.76
ACGTcount: A:0.83, C:0.00, G:0.04, T:0.13
Consensus pattern (10 bp):
AAAAAAATTA
Found at i:498555 original size:20 final size:19
Alignment explanation
Indices: 498508--498554 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
498498 AGTAAGTGAT
* *
498508 TAAAAAAATTAAAAAAAAT
1 TAAAAAAAATAAAAAAAAA
* *
498527 TGAAAAAAATAAAAAAAAG
1 TAAAAAAAATAAAAAAAAA
498546 TAAAAAAAA
1 TAAAAAAAA
498555 AATTCGTGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (19 bp):
TAAAAAAAATAAAAAAAAA
Found at i:499658 original size:21 final size:20
Alignment explanation
Indices: 499633--499688 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
499623 AAAAGAAAAC
*
499633 AAAAAAGAAAATGAAAATGA
1 AAAAAAGAAAATGAAAAAGA
*
499653 AGAAAAGAAAATTGAAAAAGA
1 AAAAAAGAAAA-TGAAAAAGA
*
499674 AAAATATGAAAATGA
1 AAAA-AAGAAAATGA
499689 GATTTCAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 10 0.33
21 14 0.47
22 6 0.20
ACGTcount: A:0.71, C:0.00, G:0.16, T:0.12
Consensus pattern (20 bp):
AAAAAAGAAAATGAAAAAGA
Found at i:499669 original size:27 final size:27
Alignment explanation
Indices: 499625--499676 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
499615 GAAGAAGAAA
*
499625 AAGAAAACAAAAAAGAAAATGAAAATG
1 AAGAAAACAAAAAAGAAAAAGAAAATG
* **
499652 AAGAAAAGAAAATTGAAAAAGAAAA
1 AAGAAAACAAAAAAGAAAAAGAAAA
499677 ATATGAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.75, C:0.02, G:0.15, T:0.08
Consensus pattern (27 bp):
AAGAAAACAAAAAAGAAAAAGAAAATG
Found at i:499688 original size:6 final size:6
Alignment explanation
Indices: 499603--499677 Score: 53
Period size: 6 Copynumber: 12.0 Consensus size: 6
499593 TAATGAATTC
** * * *
499603 GAAAAA GAAAGT GAAGAA GAAAAA GAAAACA -AAAAA GAAAAT GAAAAT
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAA-A GAAAAA GAAAAA GAAAAA
*
499651 GAAGAAAA GAAAATT GAAAAA GAAAAA
1 G-A-AAAA GAAAA-A GAAAAA GAAAAA
499678 TATGAAAATG
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
5 1 0.02
6 41 0.76
7 8 0.15
8 4 0.07
ACGTcount: A:0.73, C:0.01, G:0.19, T:0.07
Consensus pattern (6 bp):
GAAAAA
Found at i:499720 original size:17 final size:18
Alignment explanation
Indices: 499695--499734 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
499685 ATGAGATTTC
499695 AAAAACAAAA-GAGAGTG
1 AAAAACAAAATGAGAGTG
* *
499712 AAAAGCAAAATGAGATTG
1 AAAAACAAAATGAGAGTG
499730 AAAAA
1 AAAAA
499735 GAAAGAGAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.65, C:0.05, G:0.20, T:0.10
Consensus pattern (18 bp):
AAAAACAAAATGAGAGTG
Found at i:499726 original size:18 final size:17
Alignment explanation
Indices: 499695--499744 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
499685 ATGAGATTTC
499695 AAAAACAAAAGAGAGTG
1 AAAAACAAAAGAGAGTG
* *
499712 AAAAGCAAAATGAGATTG
1 AAAAACAAAA-GAGAGTG
*
499730 AAAAA-GAAAGAGAGT
1 AAAAACAAAAGAGAGT
499745 TTGAAAAGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
16 5 0.19
17 12 0.44
18 10 0.37
ACGTcount: A:0.62, C:0.04, G:0.24, T:0.10
Consensus pattern (17 bp):
AAAAACAAAAGAGAGTG
Found at i:499750 original size:36 final size:34
Alignment explanation
Indices: 499681--499776 Score: 92
Period size: 36 Copynumber: 2.8 Consensus size: 34
499671 AGAAAAATAT
* *
499681 GAAAATGAGATTTCAAAAACAAAAGAGAG-TGAAAA
1 GAAAATGAGA-TTGAAAAA-GAAAGAGAGTTGAAAA
499716 GCAAAATGAGATTGAAAAAGAAAGAGAGTTTGAAAA
1 G-AAAATGAGATTGAAAAAGAAAGAGAG-TTGAAAA
* *
499752 GAAAACGAG--TGAAGAAG-AAGAGAGT
1 GAAAATGAGATTGAAAAAGAAAGAGAGT
499777 GCTCAAACAC
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
31 1 0.02
32 7 0.13
33 7 0.13
34 8 0.15
35 15 0.28
36 16 0.30
ACGTcount: A:0.56, C:0.04, G:0.26, T:0.14
Consensus pattern (34 bp):
GAAAATGAGATTGAAAAAGAAAGAGAGTTGAAAA
Found at i:499753 original size:17 final size:16
Alignment explanation
Indices: 499702--499776 Score: 52
Period size: 16 Copynumber: 4.6 Consensus size: 16
499692 TTCAAAAACA
499702 AAAGAGAG-TGAAAAG
1 AAAGAGAGTTGAAAAG
499717 CAAA-ATGAGATTGAAAAAG
1 -AAAGA-GAG-TTG-AAAAG
499736 AAAGAGAGTTTGAAAAG
1 AAAGAGAG-TTGAAAAG
499753 AAA-ACGAG-TGAAGAAG
1 AAAGA-GAGTTGAA-AAG
499769 -AAGAGAGT
1 AAAGAGAGT
499777 GCTCAAACAC
Statistics
Matches: 49, Mismatches: 1, Indels: 18
0.72 0.01 0.26
Matches are distributed among these distances:
15 10 0.20
16 11 0.22
17 11 0.22
18 11 0.22
19 6 0.12
ACGTcount: A:0.56, C:0.03, G:0.29, T:0.12
Consensus pattern (16 bp):
AAAGAGAGTTGAAAAG
Found at i:501044 original size:20 final size:21
Alignment explanation
Indices: 501009--501047 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
500999 CAGCTCGTTG
501009 AGCTCAATTCAGCTCATTTCC
1 AGCTCAATTCAGCTCATTTCC
*
501030 AGCTC-ATTGAGCTCATTT
1 AGCTCAATTCAGCTCATTT
501048 GTTTGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.36
Consensus pattern (21 bp):
AGCTCAATTCAGCTCATTTCC
Found at i:501454 original size:13 final size:13
Alignment explanation
Indices: 501436--501461 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
501426 TGTGTCCTAA
501436 TATGAATTAAATT
1 TATGAATTAAATT
501449 TATGAATTAAATT
1 TATGAATTAAATT
501462 GCTTTCAGGT
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:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TATGAATTAAATT
Found at i:510505 original size:30 final size:30
Alignment explanation
Indices: 510469--510530 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
510459 TGAATTATTT
* * *
510469 TTAAAAATTTGGTTACTCTTTTTGTAAATA
1 TTAAAAATTAGATGACTCTTTTTGTAAATA
*
510499 TTAAAAATTAGATGCCTCTTTTTGTAAATA
1 TTAAAAATTAGATGACTCTTTTTGTAAATA
510529 TT
1 TT
510531 TTCAAAAAGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.34, C:0.08, G:0.10, T:0.48
Consensus pattern (30 bp):
TTAAAAATTAGATGACTCTTTTTGTAAATA
Found at i:511240 original size:25 final size:25
Alignment explanation
Indices: 511180--511240 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
511170 CTCCTAAATT
*
511180 TTAATTTAATTATCTAATTTTTCAA
1 TTAATTAAATTATCTAATTTTTCAA
* *
511205 TTTATTGAATTAT-TAATATTTT-ATA
1 TTAATTAAATTATCTAAT-TTTTCA-A
511230 TTAATTAAATT
1 TTAATTAAATT
511241 TTTGAGGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
24 5 0.17
25 25 0.83
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (25 bp):
TTAATTAAATTATCTAATTTTTCAA
Found at i:521113 original size:145 final size:145
Alignment explanation
Indices: 520846--521149 Score: 592
Period size: 145 Copynumber: 2.1 Consensus size: 145
520836 CCCGAATCAT
*
520846 ATTT-TTTCAAAATTACCATTTTACCTTTATACTTTTAATTCTTTACAATTTAGTCCCTAGCACA
1 ATTTATTTCACAATTACCATTTTACCTTTATACTTTTAATTCTTTACAATTTAGTCCCTAGCACA
520910 TAAAAATGGAAATTTATGCAATTTCACCACAATCCACTATGGCCGAATATCAACTAAATCCTTAG
66 TAAAAATGGAAATTTATGCAATTTCACCACAATCCACTATGGCCGAATATCAACTAAATCCTTAG
520975 AAAGCCCTATATTTC
131 AAAGCCCTATATTTC
520990 ATTTATTTCACAATTACCATTTTACCTTTATACTTTTAATTCTTTACAATTTAGTCCCTAGCACA
1 ATTTATTTCACAATTACCATTTTACCTTTATACTTTTAATTCTTTACAATTTAGTCCCTAGCACA
521055 TAAAAATGGAAATTTATGCAATTTCACCACAATCCACTATGGCCGAATATCAACTAAATCCTTAG
66 TAAAAATGGAAATTTATGCAATTTCACCACAATCCACTATGGCCGAATATCAACTAAATCCTTAG
521120 AAAGCCCTATATTTC
131 AAAGCCCTATATTTC
521135 ATTTATTTCACAATT
1 ATTTATTTCACAATT
521150 TCACCACATA
Statistics
Matches: 158, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
144 4 0.03
145 154 0.97
ACGTcount: A:0.35, C:0.21, G:0.07, T:0.38
Consensus pattern (145 bp):
ATTTATTTCACAATTACCATTTTACCTTTATACTTTTAATTCTTTACAATTTAGTCCCTAGCACA
TAAAAATGGAAATTTATGCAATTTCACCACAATCCACTATGGCCGAATATCAACTAAATCCTTAG
AAAGCCCTATATTTC
Found at i:524151 original size:43 final size:43
Alignment explanation
Indices: 524081--524183 Score: 143
Period size: 43 Copynumber: 2.4 Consensus size: 43
524071 TGTCCCAGAC
* *** * *
524081 ATGGTCTTACATGAAAATCTTGCATCGATGTCAATAGCCTAGCT
1 ATGGTCTTACACG-AAATCTCAAATCGATGCCAATAGCCCAGCT
524125 ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCCCAGCT
1 ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCCCAGCT
524168 ATGGTCTTACACGAAA
1 ATGGTCTTACACGAAA
524184 CCACACCTCA
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 41 0.77
44 12 0.23
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.27
Consensus pattern (43 bp):
ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCCCAGCT
Found at i:524353 original size:31 final size:31
Alignment explanation
Indices: 524303--524386 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 31
524293 ATCCAATGCT
* *
524303 CAAATC-AATTTGACAATGTATATCCATAAA
1 CAAATCAAATTCGGCAATGTATATCCATAAA
* ** * *
524333 CAATTCAAATTCGGTGATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCCATAAA
524364 CAAATCAAATTCGGCAATGTATA
1 CAAATCAAATTCGGCAATGTATA
524387 AAACATATAC
Statistics
Matches: 43, Mismatches: 10, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
30 5 0.12
31 38 0.88
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (31 bp):
CAAATCAAATTCGGCAATGTATATCCATAAA
Found at i:533554 original size:62 final size:59
Alignment explanation
Indices: 533439--533555 Score: 144
Period size: 62 Copynumber: 1.9 Consensus size: 59
533429 ATCAATTTAA
* * * * *
533439 TATTAAATTAATATAATATTTATCAAGATAATTACTAGATTAAATTTAGTATTAATTCT
1 TATTAAATTAATAGAATATTTATCAAGATAAATACTACAATAAATTTAATATTAATTCT
* *
533498 TATTTAATTAATAGAATATTTATCTACAAGATAAATATTACAATAAATTTAATATTAA
1 TATTAAATTAATAGAATATTTA--T-CAAGATAAATACTACAATAAATTTAATATTAA
533556 GATAATCACT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
59 20 0.42
61 1 0.02
62 27 0.56
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (59 bp):
TATTAAATTAATAGAATATTTATCAAGATAAATACTACAATAAATTTAATATTAATTCT
Found at i:533560 original size:17 final size:18
Alignment explanation
Indices: 533531--533577 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
533521 CTACAAGATA
533531 AATATTACAATAA-A-TTT
1 AATATTA-AATAACACTTT
533548 AATATTAAGATAATCACTTT
1 AATATTAA-ATAA-CACTTT
533568 AATATTAAAT
1 AATATTAAAT
533578 TAGTAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 1 0.04
17 11 0.42
19 3 0.12
20 11 0.42
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.40
Consensus pattern (18 bp):
AATATTAAATAACACTTT
Found at i:535053 original size:20 final size:20
Alignment explanation
Indices: 535028--535066 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
535018 TATTTTCTTC
535028 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
535048 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
535067 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:535402 original size:50 final size:49
Alignment explanation
Indices: 535269--535413 Score: 159
Period size: 50 Copynumber: 2.9 Consensus size: 49
535259 GATAATAACA
* * *
535269 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTT-TCCTGTAC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATATAC
* * *
535318 TGCCAATGTCATATCCCAGATATGGTCTTACATGGGAGTTCTCATAT-C
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATAC
* * **
535366 GGTGCCCATGCCATGTCCCAGACATGGTCTTCCATGGGACCTCTCATA
1 --TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATA
535414 ACCTCAATAA
Statistics
Matches: 80, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
48 4 0.05
49 37 0.46
50 39 0.49
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (49 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATAC
Found at i:544040 original size:15 final size:14
Alignment explanation
Indices: 544017--544064 Score: 69
Period size: 15 Copynumber: 3.3 Consensus size: 14
544007 AAATTGAGAG
544017 AAGAAAAAAAGAAA
1 AAGAAAAAAAGAAA
*
544031 TAAGAGAAAAAGAAA
1 -AAGAAAAAAAGAAA
544046 AAGAAATAAAAGAAA
1 AAGAAA-AAAAGAAA
544061 AAGA
1 AAGA
544065 TGAAAATGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 5 0.17
15 25 0.83
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (14 bp):
AAGAAAAAAAGAAA
Found at i:544046 original size:21 final size:21
Alignment explanation
Indices: 544013--544064 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
544003 AATGAAATTG
*
544013 AGAGAAGAA-AAAAAGAAATA
1 AGAGAAAAAGAAAAAGAAATA
544033 AGAGAAAAAGAAAAAGAAATA
1 AGAGAAAAAGAAAAAGAAATA
*
544054 AAAGAAAAAGA
1 AGAGAAAAAGA
544065 TGAAAATGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 8 0.28
21 21 0.72
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (21 bp):
AGAGAAAAAGAAAAAGAAATA
Found at i:546492 original size:13 final size:13
Alignment explanation
Indices: 546474--546498 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
546464 GTATTGATCA
546474 TGTGTTCACACCT
1 TGTGTTCACACCT
546487 TGTGTTCACACC
1 TGTGTTCACACC
546499 ATGATGACCA
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:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:551253 original size:21 final size:21
Alignment explanation
Indices: 551227--551266 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
551217 AGAATATAAA
551227 TTACAACTTTCAATTATTTCT
1 TTACAACTTTCAATTATTTCT
* *
551248 TTACAATTTTTAATTATTT
1 TTACAACTTTCAATTATTT
551267 TCCAAAGTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.00, T:0.57
Consensus pattern (21 bp):
TTACAACTTTCAATTATTTCT
Found at i:551753 original size:41 final size:40
Alignment explanation
Indices: 551696--551885 Score: 209
Period size: 41 Copynumber: 4.6 Consensus size: 40
551686 GATCCCGGTA
551696 GAATCAACACTTAGCAACCACCTTATAATCAATGATACGGG
1 GAATCAACACTTAGCAACC-CCTTATAATCAATGATACGGG
* * * **
551737 GAATCAACACATAGCAACCCCTTTCACAATCAAGGATACAATG
1 GAATCAACACTTAGCAACCCC-TT-ATAATCAATGATAC-GGG
* *
551780 GAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGA
1 GAATCAACACTTAGCAACC-CCTTATAATCAATGATACGGG
* * * *
551821 GAATCAACACATAGCAACCCCTATTTGATCAATGATTCGGG
1 GAATCAACACTTAGCAACCCCT-TATAATCAATGATACGGG
**
551862 GAATCTGCACTTAGCAACCCCTTA
1 GAATCAACACTTAGCAACCCCTTA
551886 CATTCAAAGA
Statistics
Matches: 122, Mismatches: 22, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
40 6 0.05
41 70 0.57
42 24 0.20
43 20 0.16
44 2 0.02
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.22
Consensus pattern (40 bp):
GAATCAACACTTAGCAACCCCTTATAATCAATGATACGGG
Found at i:551877 original size:125 final size:128
Alignment explanation
Indices: 551650--551884 Score: 316
Period size: 125 Copynumber: 1.9 Consensus size: 128
551640 CATTACACGG
* ** * *
551650 TGGAATTAGCACTTAGCAACCACCTCATGTTCAAAGGATCCCGGTAGAATCAACACTTAGCAACC
1 TGGAATCAGCACTTAGCAACCACCTCATAATCAAAGGATCACGGTAGAATCAACACATAGCAACC
551715 ACCTTATAATCAATGATACGGGGAATCAACACATAGCAACCCCTTTCACAATCAAGGATACAA
66 ACCTTATAATCAATGATACGGGGAATCAACACATAGCAACCCCTTTCACAATCAAGGATACAA
* *
551778 TGGAATCAGCACTTAGCAACCACCTTATAATC-AATGAT-ACGG-AGAATCAACACATAGCAACC
1 TGGAATCAGCACTTAGCAACCACCTCATAATCAAAGGATCACGGTAGAATCAACACATAGCAACC
* * * ** *
551840 -CCTATTTGATCAATGATTCGGGGAATCTGCACTTAGCAACCCCTT
66 ACCT-TATAATCAATGATACGGGGAATCAACACATAGCAACCCCTT
551885 ACATTCAAAG
Statistics
Matches: 93, Mismatches: 13, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
124 3 0.03
125 54 0.58
126 3 0.03
127 5 0.05
128 28 0.30
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (128 bp):
TGGAATCAGCACTTAGCAACCACCTCATAATCAAAGGATCACGGTAGAATCAACACATAGCAACC
ACCTTATAATCAATGATACGGGGAATCAACACATAGCAACCCCTTTCACAATCAAGGATACAA
Found at i:560322 original size:18 final size:18
Alignment explanation
Indices: 560301--560379 Score: 86
Period size: 18 Copynumber: 4.4 Consensus size: 18
560291 CACGGCCTAA
*
560301 GACACGGGCACGGACTGG
1 GACACGGGCACAGACTGG
* *
560319 GACACGGCCACAGATTGG
1 GACACGGGCACAGACTGG
* *
560337 AAAACGGGCACAGACTGG
1 GACACGGGCACAGACTGG
* *
560355 GACACAGGCACAGATTGG
1 GACACGGGCACAGACTGG
*
560373 CACACGG
1 GACACGG
560380 CCTAGCAAGT
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.30, C:0.27, G:0.35, T:0.08
Consensus pattern (18 bp):
GACACGGGCACAGACTGG
Found at i:560353 original size:36 final size:36
Alignment explanation
Indices: 560304--560372 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
560294 GGCCTAAGAC
*
560304 ACGGGCACGGACTGGGACAC-GGCCACAGATTGGAAA
1 ACGGGCACAGACTGGGACACAGG-CACAGATTGGAAA
560340 ACGGGCACAGACTGGGACACAGGCACAGATTGG
1 ACGGGCACAGACTGGGACACAGGCACAGATTGG
560373 CACACGGCCT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
36 29 0.94
37 2 0.06
ACGTcount: A:0.30, C:0.25, G:0.36, T:0.09
Consensus pattern (36 bp):
ACGGGCACAGACTGGGACACAGGCACAGATTGGAAA
Found at i:564391 original size:21 final size:21
Alignment explanation
Indices: 564365--564427 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
564355 TTGGTATTTG
564365 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
564386 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
564407 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
564428 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:588819 original size:14 final size:14
Alignment explanation
Indices: 588800--588828 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
588790 GTGTTCAATA
588800 TGAACTAAGACATG
1 TGAACTAAGACATG
588814 TGAACTAAGACATG
1 TGAACTAAGACATG
588828 T
1 T
588829 AAGCATGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (14 bp):
TGAACTAAGACATG
Found at i:592609 original size:12 final size:12
Alignment explanation
Indices: 592592--592621 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
592582 TCATGGTGTT
*
592592 ACACGGCCTAGC
1 ACACGGCCCAGC
592604 ACACGGCCCAGC
1 ACACGGCCCAGC
592616 ACACGG
1 ACACGG
592622 GCGTGTGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.43, G:0.27, T:0.03
Consensus pattern (12 bp):
ACACGGCCCAGC
Found at i:596087 original size:40 final size:40
Alignment explanation
Indices: 595981--596155 Score: 205
Period size: 40 Copynumber: 4.4 Consensus size: 40
595971 GATGATAACT
* * *
595981 GGGCTAAGTGCCGAAGGCATTTGTGCTAGTGACTA-ATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCC
*
596021 GGGCCAAG-CCCGAAGGCATTTGTGCGAGTTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
* * *
596060 GGGCTAAGTACCGAAGGCATTTTTGCGAGTTACTATAACC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
* *
596100 GGGCTAAGTCCCGAAGGCATTTGAGCAAG-TAGCTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCC
* *
596140 -GGCTAAATTCCGAAGG
1 GGGCTAAGTCCCGAAGG
596156 TACTTGGTTT
Statistics
Matches: 117, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
39 49 0.42
40 68 0.58
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
Found at i:596144 original size:79 final size:79
Alignment explanation
Indices: 595981--596155 Score: 212
Period size: 79 Copynumber: 2.2 Consensus size: 79
595971 GATGATAACT
* * * *
595981 GGGCTAAGTGCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCCAAGCCCGAAGGCATTTGTGC
1 GGGCTAAGTACCGAAGGCATTTGTGCGAGTGACTAATACCGGGCCAAGCCCGAAGGCATTTGAGC
*
596046 GAGTTACTATATCC
66 AAGTTACTATATCC
* * *
596060 GGGCTAAGTACCGAAGGCATTTTTGCGAGTTACT-ATAACCGGGCTAAGTCCCGAAGGCATTTGA
1 GGGCTAAGTACCGAAGGCATTTGTGCGAGTGACTAAT-ACCGGGCCAAG-CCCGAAGGCATTTGA
596124 GCAAG-TAGCTATATCC
64 GCAAGTTA-CTATATCC
* *
596140 -GGCTAAATTCCGAAGG
1 GGGCTAAGTACCGAAGG
596156 TACTTGGTTT
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
78 2 0.02
79 55 0.66
80 26 0.31
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (79 bp):
GGGCTAAGTACCGAAGGCATTTGTGCGAGTGACTAATACCGGGCCAAGCCCGAAGGCATTTGAGC
AAGTTACTATATCC
Found at i:597265 original size:326 final size:327
Alignment explanation
Indices: 596671--597322 Score: 1270
Period size: 326 Copynumber: 2.0 Consensus size: 327
596661 TAGCCATGCG
596671 AAAATGGCTTATATATATACTTTGAGCATAGCATTATAATCGTTTTGTATGTTGTTCATTGAGAG
1 AAAATGGCTTATATATATACTTTGAGCATAGCATTATAATCGTTTTGTATGTTGTTCATTGAGAG
* *
596736 GTATGGAAATGTTTGGTAATGATTAGCCATTGGAATGGTTAATCATGATCATTTTGGTGCTTTGT
66 GTATGGAAATGTTTGATAACGATTAGCCATTGGAATGGTTAATCATGATCATTTTGGTGCTTTGT
596801 ATGACAAGTTCTAGTTGATTCATGGAAAACCATGAAATAGGTAAAGTTTACCTTAAAAACAGATG
131 ATGACAAGTTCTAGTTGATTCATGGAAAACCATGAAATAGGTAAAGTTTACCTTAAAAACAGATG
596866 CTGACAGTAGCAGTAGTGTGGATTTGAAAAATCACTAAAAATAGTAGGAATGGAATTAAATAGTG
196 CTGACAGTAGCAGTAGTGTGGATTTGAAAAATCACTAAAAATAGTAGGAATGGAATTAAATAGTG
596931 AATAAATTATGTTATATAACCTTGATGAATCTACTTTCATATGGAAGAAACGAAACGATCATATG
261 AATAAATTATGTTATATAACCTTGATGAATCTACTTTCATATGGAAGAAACGAAACGATCATATG
596996 AA
326 AA
*
596998 AAAATGGCTTTTATATATACTTTGAGCATAGCATTATAATCGTTTTGTATGTTGTTCATTGAGAG
1 AAAATGGCTTATATATATACTTTGAGCATAGCATTATAATCGTTTTGTATGTTGTTCATTGAGAG
597063 GTATGGAAATGTTTGATAACGATTAGCCATT-GAATGGTTAATCATGATCATTTTGGTGCTTTGT
66 GTATGGAAATGTTTGATAACGATTAGCCATTGGAATGGTTAATCATGATCATTTTGGTGCTTTGT
597127 ATGACAAGTTCTAGTTGATTCATGGAAAACCATGAAATAGGTAAAGTTTACCTTAAAAACAGATG
131 ATGACAAGTTCTAGTTGATTCATGGAAAACCATGAAATAGGTAAAGTTTACCTTAAAAACAGATG
597192 CTGACAGTAGCAGTAGTGTGGATTTGAAAAATCACTAAAAATAGTAGGAATGGAATTAAATAGTG
196 CTGACAGTAGCAGTAGTGTGGATTTGAAAAATCACTAAAAATAGTAGGAATGGAATTAAATAGTG
597257 AATAAATTATGTTATATAACCTTGATGAATCTACTTTCATATGGAAGAAACGAAACGATCATATG
261 AATAAATTATGTTATATAACCTTGATGAATCTACTTTCATATGGAAGAAACGAAACGATCATATG
597322 A
326 A
597323 GTCGTATTTT
Statistics
Matches: 322, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
326 229 0.71
327 93 0.29
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34
Consensus pattern (327 bp):
AAAATGGCTTATATATATACTTTGAGCATAGCATTATAATCGTTTTGTATGTTGTTCATTGAGAG
GTATGGAAATGTTTGATAACGATTAGCCATTGGAATGGTTAATCATGATCATTTTGGTGCTTTGT
ATGACAAGTTCTAGTTGATTCATGGAAAACCATGAAATAGGTAAAGTTTACCTTAAAAACAGATG
CTGACAGTAGCAGTAGTGTGGATTTGAAAAATCACTAAAAATAGTAGGAATGGAATTAAATAGTG
AATAAATTATGTTATATAACCTTGATGAATCTACTTTCATATGGAAGAAACGAAACGATCATATG
AA
Found at i:599017 original size:12 final size:12
Alignment explanation
Indices: 599000--599024 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
598990 ATTCGGGGAG
599000 TTGTAGATTCCA
1 TTGTAGATTCCA
599012 TTGTAGATTCCA
1 TTGTAGATTCCA
599024 T
1 T
599025 GACCACTCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (12 bp):
TTGTAGATTCCA
Found at i:603969 original size:40 final size:39
Alignment explanation
Indices: 603866--604025 Score: 216
Period size: 40 Copynumber: 4.0 Consensus size: 39
603856 GATGATAACT
* *
603866 GGGCTAAGTCCCGAAGCCATTTGTGCTAGTGACTA-ATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGT-ACTATA-TCC
603906 GGGCTAAG-CCCGAAGGCATTTGTGCGAGCTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATATCC
*
603945 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATATCC
* *
603985 GGGCTAAGTCCCGAAGGCATTTGAGCAAGTAGCTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTA-CTATATCC
604025 G
1 G
604026 ACTAAATCCT
Statistics
Matches: 109, Mismatches: 7, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
39 35 0.32
40 74 0.68
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (39 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATATCC
Found at i:604040 original size:79 final size:79
Alignment explanation
Indices: 603869--604040 Score: 215
Period size: 79 Copynumber: 2.2 Consensus size: 79
603859 GATAACTGGG
* * * * *
603869 CTAAGTCCCGAAGCCATTTGTGCTAGTGACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAG
1 CTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCATTTGAGCAAG
*
603934 CTACTATATCCGGG
66 CTACTATATCCGGA
*
603948 CTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCA
1 CTAAGTCCCGAAGGCATTTGTGCGAGTGACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAGCA
604012 AG-TAGCTATATCC-GA
64 AGCTA-CTATATCCGGA
* *
604027 CTAAATCCTGAAGG
1 CTAAGTCCCGAAGG
604041 TACTTGGTTT
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
78 2 0.02
79 53 0.65
80 26 0.32
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (79 bp):
CTAAGTCCCGAAGGCATTTGTGCGAGTGACTAATACCGGGCTAAGCCCGAAGGCATTTGAGCAAG
CTACTATATCCGGA
Found at i:610564 original size:40 final size:40
Alignment explanation
Indices: 610501--610684 Score: 235
Period size: 40 Copynumber: 4.6 Consensus size: 40
610491 TATTCGAATG
* * *
610501 ATATCTGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
* * * * *
610541 ATATCCGGACTAAGATCCAAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGACT
* * *
610581 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
* *
610621 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
610661 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
610685 CTTGTGCGAG
Statistics
Matches: 123, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
39 1 0.01
40 120 0.98
41 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGACT
Found at i:613823 original size:26 final size:26
Alignment explanation
Indices: 613794--613848 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
613784 ATAAAAAAAG
613794 TATTTATTACCTAAAAATTTCCTAAT
1 TATTTATTACCTAAAAATTTCCTAAT
613820 TATTTATTACCTAAAAATTTCCTAAT
1 TATTTATTACCTAAAAATTTCCTAAT
613846 TAT
1 TAT
613849 ACTTTTCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.47
Consensus pattern (26 bp):
TATTTATTACCTAAAAATTTCCTAAT
Found at i:614222 original size:26 final size:26
Alignment explanation
Indices: 614188--614245 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
614178 AAAGTATCAT
*
614188 AAAA-GAAATAAACTTCAAGAGATTG
1 AAAAGGAAATAAACTTCAAGAGATAG
614213 AAAAGGAAATAAACTTCAAGAGATAG
1 AAAAGGAAATAAACTTCAAGAGATAG
614239 AAAAGGA
1 AAAAGGA
614246 GAATGAATCA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 4 0.13
26 27 0.87
ACGTcount: A:0.59, C:0.07, G:0.19, T:0.16
Consensus pattern (26 bp):
AAAAGGAAATAAACTTCAAGAGATAG
Found at i:616075 original size:19 final size:20
Alignment explanation
Indices: 616051--616089 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
616041 ACAAAGTATC
616051 ATAATTATTCAA-TAGATAT
1 ATAATTATTCAAGTAGATAT
616070 ATAATTATTCAAGTAGATAT
1 ATAATTATTCAAGTAGATAT
616090 CTATTGAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (20 bp):
ATAATTATTCAAGTAGATAT
Found at i:617351 original size:18 final size:18
Alignment explanation
Indices: 617316--617354 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
617306 TTTAATAAAA
*
617316 TTATTTAATATTAGAATT
1 TTATTTAATAATAGAATT
617334 TTATTCTAATAATA-AATT
1 TTATT-TAATAATAGAATT
617352 TTA
1 TTA
617355 ACATTAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (18 bp):
TTATTTAATAATAGAATT
Found at i:621089 original size:23 final size:23
Alignment explanation
Indices: 621059--621104 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
621049 AGTTATTCGA
*
621059 ATCAACTCAAATAAAAAATTAAG
1 ATCAACTCAAATAAAAAAATAAG
*
621082 ATCAACTCGAATAAAAAAATAAG
1 ATCAACTCAAATAAAAAAATAAG
621105 TTTTTTTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.61, C:0.13, G:0.07, T:0.20
Consensus pattern (23 bp):
ATCAACTCAAATAAAAAAATAAG
Found at i:624246 original size:18 final size:18
Alignment explanation
Indices: 624223--624262 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
624213 GTCAGACATG
* *
624223 GAGGAAAGGGATATAATT
1 GAGGAAAAGGATATAATC
624241 GAGGAAAAGGATATAATC
1 GAGGAAAAGGATATAATC
624259 GAGG
1 GAGG
624263 GTGATACTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.03, G:0.35, T:0.17
Consensus pattern (18 bp):
GAGGAAAAGGATATAATC
Found at i:626914 original size:19 final size:21
Alignment explanation
Indices: 626871--626914 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
626861 TATAATATTA
626871 TAAT-ATTATTTTACATGAAT
1 TAATAATTATTTTACATGAAT
626891 T-ATAATTA-TTTA-ATGAAT
1 TAATAATTATTTTACATGAAT
626909 TAATAA
1 TAATAA
626915 ATACATGCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 7 0.32
19 10 0.45
20 5 0.23
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (21 bp):
TAATAATTATTTTACATGAAT
Found at i:628625 original size:12 final size:12
Alignment explanation
Indices: 628608--628640 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
628598 TGGCCTGTCC
628608 ATATTAATTTTT
1 ATATTAATTTTT
628620 ATATT-ATTTTT
1 ATATTAATTTTT
628631 ATA-TAATTTT
1 ATATTAATTTT
628641 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:630587 original size:20 final size:20
Alignment explanation
Indices: 630562--630612 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
630552 AAAATTACAA
630562 AAAAATCAAAAATAAATTTC
1 AAAAATCAAAAATAAATTTC
** * *
630582 AAAAATTGAAAATAATTTTT
1 AAAAATCAAAAATAAATTTC
*
630602 AAAATTCAAAA
1 AAAAATCAAAA
630613 TATTTATAAA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (20 bp):
AAAAATCAAAAATAAATTTC
Found at i:630598 original size:19 final size:19
Alignment explanation
Indices: 630570--630633 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
630560 AAAAAAATCA
*
630570 AAAATAAATTTCAAAAATTG
1 AAAAT-AATTTCAAAAATTC
**
630590 AAAATAATTTTTAAAATTC
1 AAAATAATTTCAAAAATTC
*
630609 AAAAT-ATTTATAAAAATTC
1 AAAATAATTT-CAAAAATTC
630628 TAAAAT
1 -AAAAT
630634 TTTTATTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
18 4 0.11
19 24 0.63
20 10 0.26
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.36
Consensus pattern (19 bp):
AAAATAATTTCAAAAATTC
Found at i:630638 original size:20 final size:19
Alignment explanation
Indices: 630582--630639 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
630572 AATAAATTTC
*
630582 AAAAATTGAAAATAATTT-T
1 AAAAATTCAAAAT-ATTTAT
*
630601 TAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
*
630620 AAAAATTCTAAAATTTTTAT
1 AAAAATTC-AAAATATTTAT
630640 TTTTTTTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 4 0.12
19 19 0.58
20 10 0.30
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:630679 original size:19 final size:18
Alignment explanation
Indices: 630647--630696 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
630637 TATTTTTTTT
* *
630647 AAAAAATTATAAAATCTA
1 AAAAAATTAAAAAATATA
630665 AAAAAATCTAAAAAATATA
1 AAAAAAT-TAAAAAATATA
*
630684 TAAAAATTTAAAA
1 -AAAAAATTAAAA
630697 TTTAAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 7 0.26
19 14 0.52
20 6 0.22
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAAAATTAAAAAATATA
Found at i:630785 original size:3 final size:3
Alignment explanation
Indices: 630777--630808 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
630767 CTAAAATATC
630777 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
630809 TTGCTTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:635067 original size:32 final size:32
Alignment explanation
Indices: 635025--635089 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
635015 TTCATTTTTT
635025 TTAACCCTTAACTTCCATTATTTGTCAAATCA
1 TTAACCCTTAACTTCCATTATTTGTCAAATCA
* * * * *
635057 TTAACTCTTAATTTGCATTGTTTGTTAAATCA
1 TTAACCCTTAACTTCCATTATTTGTCAAATCA
635089 T
1 T
635090 ATCTACAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.46
Consensus pattern (32 bp):
TTAACCCTTAACTTCCATTATTTGTCAAATCA
Found at i:640602 original size:20 final size:18
Alignment explanation
Indices: 640565--640607 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
640555 CTATATAAAC
640565 TCACAATTT-CAATTATT
1 TCACAATTTACAATTATT
640582 TCACACATTTACAACTTATT
1 TCACA-ATTTACAA-TTATT
*
640602 TTACAA
1 TCACAA
640608 ACTTTACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 5 0.23
18 4 0.18
19 4 0.18
20 9 0.41
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (18 bp):
TCACAATTTACAATTATT
Found at i:643531 original size:5 final size:5
Alignment explanation
Indices: 643521--643550 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
643511 TTCTTCCCTA
643521 TTTCT TTTCT TTTCT TTTCAT TTTCT TTTC
1 TTTCT TTTCT TTTCT TTTC-T TTTCT TTTC
643551 ATCATATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTCT
Found at i:643544 original size:11 final size:11
Alignment explanation
Indices: 643521--643552 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
643511 TTCTTCCCTA
643521 TTTCTTTTC-T
1 TTTCTTTTCAT
643531 TTTCTTTTCAT
1 TTTCTTTTCAT
643542 TTTCTTTTCAT
1 TTTCTTTTCAT
643553 CATATTTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTCTTTTCAT
Found at i:644177 original size:21 final size:21
Alignment explanation
Indices: 644151--644191 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
644141 CAAGGCTTGG
*
644151 CCACATGGTCATGTAACCCTT
1 CCACATGGCCATGTAACCCTT
*
644172 CCACATGGCCATGTGACCCT
1 CCACATGGCCATGTAACCCT
644192 GTTTTATAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.37, G:0.17, T:0.24
Consensus pattern (21 bp):
CCACATGGCCATGTAACCCTT
Found at i:645744 original size:16 final size:15
Alignment explanation
Indices: 645720--645753 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
645710 ATATTTTCTA
*
645720 TTTTCATTTTTAATTT
1 TTTTAATTTTT-ATTT
645736 TTTTAATTTTTATTT
1 TTTTAATTTTTATTT
645751 TTT
1 TTT
645754 ACTTTTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTAATTTTTATTT
Found at i:645957 original size:34 final size:33
Alignment explanation
Indices: 645880--645957 Score: 84
Period size: 35 Copynumber: 2.3 Consensus size: 33
645870 GAAGGTTAAT
* * *
645880 TAGACCTCAATTTTTTTTTAAAAAAGTTCTCAT
1 TAGACCTTAATTTTTTTTTAAAAAAATTCTCAC
* * *
645913 TAAACTCTTAATTTTTTTTTTAAAAAAATTTTTAC
1 TAGAC-CTTAA-TTTTTTTTTAAAAAAATTCTCAC
645948 TAGACCTTAA
1 TAGACCTTAA
645958 AACATAATTC
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
33 4 0.11
34 9 0.25
35 23 0.64
ACGTcount: A:0.36, C:0.13, G:0.04, T:0.47
Consensus pattern (33 bp):
TAGACCTTAATTTTTTTTTAAAAAAATTCTCAC
Found at i:648550 original size:7 final size:7
Alignment explanation
Indices: 648538--648567 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
648528 TTATTATTAA
648538 TTGAATT
1 TTGAATT
648545 TTGAATT
1 TTGAATT
648552 TTGAATT
1 TTGAATT
*
648559 TTAAATT
1 TTGAATT
648566 TT
1 TT
648568 AAATAAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (7 bp):
TTGAATT
Found at i:663830 original size:21 final size:20
Alignment explanation
Indices: 663797--663835 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
663787 TTAAGATGAC
*
663797 CACACGGGCGTGTTGCCCTTG
1 CACACGAGCGTG-TGCCCTTG
*
663818 CACACGAGTGTGTGCCCT
1 CACACGAGCGTGTGCCCT
663836 GTTTCAAGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.13, C:0.33, G:0.31, T:0.23
Consensus pattern (20 bp):
CACACGAGCGTGTGCCCTTG
Found at i:664596 original size:17 final size:17
Alignment explanation
Indices: 664574--664606 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
664564 TAAAATCAAA
664574 CAGAGCACACAACCGTG
1 CAGAGCACACAACCGTG
*
664591 CAGAGCACACAGCCGT
1 CAGAGCACACAACCGT
664607 ATGGTAAACG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.36, G:0.24, T:0.06
Consensus pattern (17 bp):
CAGAGCACACAACCGTG
Found at i:671762 original size:20 final size:20
Alignment explanation
Indices: 671737--671776 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
671727 TGAAAAATAT
671737 CGATACCATTGAACTAGTAC
1 CGATACCATTGAACTAGTAC
671757 CGATACCATTGAACTAGTAC
1 CGATACCATTGAACTAGTAC
671777 AAATACCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (20 bp):
CGATACCATTGAACTAGTAC
Found at i:671782 original size:20 final size:20
Alignment explanation
Indices: 671739--671783 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
671729 AAAAATATCG
**
671739 ATACCATTGAACTAGTACCG
1 ATACCATTGAACTAGTACAA
671759 ATACCATTGAACTAGTACAA
1 ATACCATTGAACTAGTACAA
671779 ATACC
1 ATACC
671784 TATGTAACCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.40, C:0.24, G:0.11, T:0.24
Consensus pattern (20 bp):
ATACCATTGAACTAGTACAA
Found at i:674067 original size:25 final size:25
Alignment explanation
Indices: 674039--674096 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
674029 GGCAATAATA
* *
674039 CTCACACAAGCTATAATTGTAATTG
1 CTCACACAAGCTATAACTGTAAATG
* * *
674064 CTCACACGAGTTGTAACTGTAAATG
1 CTCACACAAGCTATAACTGTAAATG
674089 CTCACACA
1 CTCACACA
674097 GGCTGTGAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (25 bp):
CTCACACAAGCTATAACTGTAAATG
Found at i:675911 original size:46 final size:46
Alignment explanation
Indices: 675844--676139 Score: 221
Period size: 46 Copynumber: 6.4 Consensus size: 46
675834 AGTACTAGTG
*
675844 TAAGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCCAGTA
1 TAAGACATGTCTGGGACATGCATCAGCCTCGAGACGTAAGCCAGTA
* * * * * * *
675890 TAAGACATGTTTGGAACATGCATC-GGCTATGAGATGT--GTCAGTG
1 TAAGACATGTCTGGGACATGCATCAGCCT-CGAGACGTAAGCCAGTA
* * * * * * *
675934 TAAGACCATCTCTGGGACATGGCATCGGCATTGAGACG-AGTGCTAGTG
1 TAAGA-CATGTCTGGGACAT-GCATCAGCCTCGAGACGTA-AGCCAGTA
* * *
675982 TATGACATGTCTGGGACATGCATCAGCCTCGGGACGTAAGCTAGTA
1 TAAGACATGTCTGGGACATGCATCAGCCTCGAGACGTAAGCCAGTA
* * * *
676028 TAAGACATGTCTGGGACATGCATC-GGCTACGAGATGT--GTCAGTG
1 TAAGACATGTCTGGGACATGCATCAGCCT-CGAGACGTAAGCCAGTA
* * *
676072 TAAGACCATGTCTGGGACATGGCATCGGCCTCGAAGATG-ATAGCCAGTG
1 TAAGA-CATGTCTGGGACAT-GCATCAGCCTCG-AGACGTA-AGCCAGTA
676121 TAAGACCATGTCTGGGACA
1 TAAGA-CATGTCTGGGACA
676140 CGGCATCGAC
Statistics
Matches: 201, Mismatches: 33, Indels: 29
0.76 0.13 0.11
Matches are distributed among these distances:
44 19 0.09
45 31 0.15
46 93 0.46
47 24 0.12
48 9 0.04
49 25 0.12
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (46 bp):
TAAGACATGTCTGGGACATGCATCAGCCTCGAGACGTAAGCCAGTA
Found at i:676047 original size:138 final size:138
Alignment explanation
Indices: 675791--676139 Score: 538
Period size: 138 Copynumber: 2.5 Consensus size: 138
675781 TTATGAGAGC
* * *
675791 CAGTGTAAGACCATGTCTGGGACTTGGCAACGGCATTGAGATGAGTACTAGTGTAAGACATGTCT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAGTACTAGTGTAAGACATGTCT
* *
675856 GGGACATGCATCAGCCTCGGGACGTAAGCCAGTATAAGACATGTTTGGAACATGCATCGGCTATG
66 GGGACATGCATCAGCCTCGGGACGTAAGCCAGTATAAGACATGTCTGGAACATGCATCGGCTACG
675921 AGATGTGT
131 AGATGTGT
* * *
675929 CAGTGTAAGACCATCTCTGGGACATGGCATCGGCATTGAGACGAGTGCTAGTGTATGACATGTCT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAGTACTAGTGTAAGACATGTCT
* *
675994 GGGACATGCATCAGCCTCGGGACGTAAGCTAGTATAAGACATGTCTGGGACATGCATCGGCTACG
66 GGGACATGCATCAGCCTCGGGACGTAAGCCAGTATAAGACATGTCTGGAACATGCATCGGCTACG
676059 AGATGTGT
131 AGATGTGT
* * * *
676067 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAAGATGA-TAGCCAGTGTAAGACCATG
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTG-AGACGAGTA-CTAGTGTAAGA-CATG
676131 TCTGGGACA
63 TCTGGGACA
676140 CGGCATCGAC
Statistics
Matches: 191, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
138 164 0.86
139 14 0.07
140 13 0.07
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (138 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAGTACTAGTGTAAGACATGTCT
GGGACATGCATCAGCCTCGGGACGTAAGCCAGTATAAGACATGTCTGGAACATGCATCGGCTACG
AGATGTGT
Found at i:679565 original size:45 final size:45
Alignment explanation
Indices: 679433--679567 Score: 227
Period size: 45 Copynumber: 3.0 Consensus size: 45
679423 CGATATCCTT
* *
679433 TCACCGGCATTATAGCCTGCTAGGCTCGAAA-GCCCGAATAGTATC
1 TCACCGGCATTATAGCCTACTAGGCTC-AAAGGCCCGAATAGTGTC
*
679478 TCACCGGCATTGTAGCCTACTAGGCTCAAAGGCCCGAATAGTGTC
1 TCACCGGCATTATAGCCTACTAGGCTCAAAGGCCCGAATAGTGTC
679523 TCACCGGCATTATAGCCTACTAGGCTCAAAGGCCCGAATAGTGTC
1 TCACCGGCATTATAGCCTACTAGGCTCAAAGGCCCGAATAGTGTC
679568 GTACGATAAT
Statistics
Matches: 85, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
44 3 0.04
45 82 0.96
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.22
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTACTAGGCTCAAAGGCCCGAATAGTGTC
Found at i:687040 original size:43 final size:42
Alignment explanation
Indices: 686992--687102 Score: 118
Period size: 43 Copynumber: 2.6 Consensus size: 42
686982 TTTTATCAAA
* *
686992 TCACCGGCATTTAGCCTGCTAGGTTTTAAAAACCCGA-ATTCAT
1 TCACCGGCATTTAGCCTGCTAGG-CTT-AAAACCCGATATCCAT
* ** *
687035 TCACCGGCATTTCA-CCTGCTAGGCTTGAGGCCCGATATCCTT
1 TCACCGGCATTT-AGCCTGCTAGGCTTAAAACCCGATATCCAT
687077 TCACCGGCATTATAGCCTGCTAGGCT
1 TCACCGGCATT-TAGCCTGCTAGGCT
687103 CGAAAGCATG
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
41 6 0.10
42 18 0.31
43 33 0.57
44 1 0.02
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.29
Consensus pattern (42 bp):
TCACCGGCATTTAGCCTGCTAGGCTTAAAACCCGATATCCAT
Found at i:687143 original size:13 final size:13
Alignment explanation
Indices: 687125--687151 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
687115 TAGTATCTCA
687125 CCGGCATTGTAGC
1 CCGGCATTGTAGC
687138 CCGGCATTGTAGC
1 CCGGCATTGTAGC
687151 C
1 C
687152 TGCTAGGCTC
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:0.15, C:0.33, G:0.30, T:0.22
Consensus pattern (13 bp):
CCGGCATTGTAGC
Found at i:687174 original size:58 final size:58
Alignment explanation
Indices: 687080--687196 Score: 164
Period size: 58 Copynumber: 2.0 Consensus size: 58
687070 TATCCTTTCA
* * *
687080 CCGGCATTATAGCCTGCTAGGCTCGAAAGCATGAATAGTATCTCACCGGCATTGTAGC
1 CCGGCATTATAGCCTGCTAGGCTCGAAAGCACGAATAATATCTCACCGGCATTATAGC
* * *
687138 CCGGCATTGTAGCCTGCTAGGCTC-AAAGGCCCGAATAATGTCTCACCGGCATTATAGC
1 CCGGCATTATAGCCTGCTAGGCTCGAAA-GCACGAATAATATCTCACCGGCATTATAGC
687196 C
1 C
687197 TGCTAGGCTC
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
57 3 0.06
58 49 0.94
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (58 bp):
CCGGCATTATAGCCTGCTAGGCTCGAAAGCACGAATAATATCTCACCGGCATTATAGC
Found at i:687202 original size:45 final size:45
Alignment explanation
Indices: 687138--687224 Score: 156
Period size: 45 Copynumber: 1.9 Consensus size: 45
687128 GCATTGTAGC
*
687138 CCGGCATTGTAGCCTGCTAGGCTCAAAGGCCCGAATAATGTCTCA
1 CCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATGTCTCA
*
687183 CCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTGTC
1 CCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATGTC
687225 GTACGATAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.24, C:0.29, G:0.25, T:0.22
Consensus pattern (45 bp):
CCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATGTCTCA
Found at i:688224 original size:18 final size:17
Alignment explanation
Indices: 688198--688234 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
688188 TTATAAAAAT
*
688198 AGAATAGGGGATCTAGA
1 AGAACAGGGGATCTAGA
688215 NAGAACAGGGGATCTAGA
1 -AGAACAGGGGATCTAGA
688233 AG
1 AG
688235 TCATTTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.41, C:0.08, G:0.35, T:0.14
Consensus pattern (17 bp):
AGAACAGGGGATCTAGA
Found at i:693398 original size:7 final size:7
Alignment explanation
Indices: 693386--693416 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
693376 AATTTTGACT
693386 AAAATAG
1 AAAATAG
693393 AAAATAG
1 AAAATAG
693400 AAAATAG
1 AAAATAG
*
693407 AAAATGG
1 AAAATAG
693414 AAA
1 AAA
693417 TGATATTACC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.71, C:0.00, G:0.16, T:0.13
Consensus pattern (7 bp):
AAAATAG
Found at i:694457 original size:94 final size:92
Alignment explanation
Indices: 694258--694535 Score: 301
Period size: 94 Copynumber: 2.9 Consensus size: 92
694248 TTGGGCCATT
* * * *
694258 TGTGAAAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATGAGAGCCAATGTAAG
1 TGTGAAAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCTACGA-GAT--GTGCCAGTGTAAG
*
694322 ACCATGCCTGGGACATGGCATCGGCATTGA
63 ACCATGTCTGGGACATGGCATCGGCATTGA
** *
694352 -GATGACTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGTGTCAGTGTAAGAC
1 TG-TGAAAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGTGCCAGTGTAAGAC
* * *
694416 TATGTCTGGCACATGGCATCGGCATGGTTA
65 CATGTCTGGGACATGGCATCGGCAT--TGA
* *
694446 TGTGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCT-CGAAGTTGATAGCCAGTGT
1 TGTGAAAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGG-CTACG-AGATG-T-GCCAGTGT
*
694510 AAGACCATGTCTGGGACATGGTATCG
60 AAGACCATGTCTGGGACATGGCATCG
694536 ACACTTTACC
Statistics
Matches: 155, Mismatches: 18, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
92 34 0.22
93 1 0.01
94 58 0.37
95 16 0.10
96 9 0.06
97 6 0.04
98 1 0.01
99 30 0.19
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (92 bp):
TGTGAAAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGTGCCAGTGTAAGACC
ATGTCTGGGACATGGCATCGGCATTGA
Done.