Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009436.1 Kokia drynarioides strain JFW-HI SEQ_124143, whole genome shotgun sequence
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: 156619
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 223 characters in sequence are not A, C, G, or T
Found at i:4228 original size:142 final size:142
Alignment explanation
Indices: 3972--4255 Score: 568
Period size: 142 Copynumber: 2.0 Consensus size: 142
3962 TGCTGACTTG
3972 AACAAACTGCTTTTCATACTCAGCCACAGACTTGTTTCCTTGCTTCAGTTCAAGGAACTCTTTCT
1 AACAAACTGCTTTTCATACTCAGCCACAGACTTGTTTCCTTGCTTCAGTTCAAGGAACTCTTTCT
4037 TCTTCCTCTCTAAATACCTATTGTTCTCATACTTCTTACGAAACTCGGTTTAATAGAACTCCCAG
66 TCTTCCTCTCTAAATACCTATTGTTCTCATACTTCTTACGAAACTCGGTTTAATAGAACTCCCAG
4102 TTGACCCTTGCT
131 TTGACCCTTGCT
4114 AACAAACTGCTTTTCATACTCAGCCACAGACTTGTTTCCTTGCTTCAGTTCAAGGAACTCTTTCT
1 AACAAACTGCTTTTCATACTCAGCCACAGACTTGTTTCCTTGCTTCAGTTCAAGGAACTCTTTCT
4179 TCTTCCTCTCTAAATACCTATTGTTCTCATACTTCTTACGAAACTCGGTTTAATAGAACTCCCAG
66 TCTTCCTCTCTAAATACCTATTGTTCTCATACTTCTTACGAAACTCGGTTTAATAGAACTCCCAG
4244 TTGACCCTTGCT
131 TTGACCCTTGCT
4256 TTCAGTACCA
Statistics
Matches: 142, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
142 142 1.00
ACGTcount: A:0.24, C:0.28, G:0.11, T:0.37
Consensus pattern (142 bp):
AACAAACTGCTTTTCATACTCAGCCACAGACTTGTTTCCTTGCTTCAGTTCAAGGAACTCTTTCT
TCTTCCTCTCTAAATACCTATTGTTCTCATACTTCTTACGAAACTCGGTTTAATAGAACTCCCAG
TTGACCCTTGCT
Found at i:4862 original size:37 final size:37
Alignment explanation
Indices: 4807--5027 Score: 192
Period size: 37 Copynumber: 5.9 Consensus size: 37
4797 CTTCTTGATT
* * *
4807 CACCAGCACAAAGTCTACTAGGCACAAAGCTTGAATA
1 CACCGGCACAAAGCCTACTAGGCACAAAGCCTGAATA
* ** *
4844 CATCGGCATGAAGCCTACTAGGCACAAAGCCTGATTA
1 CACCGGCACAAAGCCTACTAGGCACAAAGCCTGAATA
* * * *
4881 CACCGGCACAAAGCCTACTAGACACACAGTCTGAATC
1 CACCGGCACAAAGCCTACTAGGCACAAAGCCTGAATA
* * * *
4918 CACCAGCACAAATCCTAGTAGGCACAAAGCCCTAAATA
1 CACCGGCACAAAGCCTACTAGGCACAAAG-CCTGAATA
* * ** * *
4956 CACCGGCACAAAACCTAGTAAACACACAA-TCTGAATT
1 CACCGGCACAAAGCCTACTAGGCACA-AAGCCTGAATA
** * *
4993 CACCGGCATGAAGCCTATTAGGCACATAGCCTGAA
1 CACCGGCACAAAGCCTACTAGGCACAAAGCCTGAA
5028 CATTTAAATG
Statistics
Matches: 143, Mismatches: 38, Indels: 6
0.76 0.20 0.03
Matches are distributed among these distances:
36 1 0.01
37 113 0.79
38 27 0.19
39 2 0.01
ACGTcount: A:0.38, C:0.30, G:0.17, T:0.16
Consensus pattern (37 bp):
CACCGGCACAAAGCCTACTAGGCACAAAGCCTGAATA
Found at i:4981 original size:75 final size:75
Alignment explanation
Indices: 4854--5023 Score: 207
Period size: 75 Copynumber: 2.3 Consensus size: 75
4844 CATCGGCATG
* * * * *
4854 AAGCCTACTAGGCACAAAG-CCTGATTACACCGGCACAAAGCCTACTAGACACACAGTCTGAATC
1 AAGCCTACTAGGCACAAAGCCCTAAATACACCGGCACAAAACCTACTAAACACACAATCTGAATC
4918 CACCAGCACA
66 CACCAGCACA
* * * *
4928 AATCCTAGTAGGCACAAAGCCCTAAATACACCGGCACAAAACCTAGTAAACACACAATCTGAATT
1 AAGCCTACTAGGCACAAAGCCCTAAATACACCGGCACAAAACCTACTAAACACACAATCTGAATC
* **
4993 CACCGGCATG
66 CACCAGCACA
* *
5003 AAGCCTATTAGGCACATAGCC
1 AAGCCTACTAGGCACAAAGCC
5024 TGAACATTTA
Statistics
Matches: 80, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
74 17 0.21
75 63 0.79
ACGTcount: A:0.38, C:0.31, G:0.16, T:0.15
Consensus pattern (75 bp):
AAGCCTACTAGGCACAAAGCCCTAAATACACCGGCACAAAACCTACTAAACACACAATCTGAATC
CACCAGCACA
Found at i:10592 original size:24 final size:24
Alignment explanation
Indices: 10565--10641 Score: 91
Period size: 24 Copynumber: 3.2 Consensus size: 24
10555 GATGCACCTC
*
10565 CGGTTCCACCTCTGGATTACCCTG
1 CGGTTCCACCTCTGGATTACCCTA
* *
10589 CGGTTCCACTTTTGGATTACCCTA
1 CGGTTCCACCTCTGGATTACCCTA
* * * *
10613 CTGTTCCACCTCCGGATTATCCTT
1 CGGTTCCACCTCTGGATTACCCTA
10637 CGGTT
1 CGGTT
10642 GTATGACCCG
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.13, C:0.34, G:0.18, T:0.35
Consensus pattern (24 bp):
CGGTTCCACCTCTGGATTACCCTA
Found at i:13146 original size:31 final size:33
Alignment explanation
Indices: 13108--13178 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
13098 TAAATTAAAG
*
13108 CCAAATATTTTT-GTTTTTATCATTTATCTTA-
1 CCAAATATTTTTAGTTTTTACCATTTATCTTAT
* *
13139 CCAAATATTTTTAATTTTTTACCTTTTATCTTAT
1 CCAAATATTTTT-AGTTTTTACCATTTATCTTAT
13173 CCAAAT
1 CCAAAT
13179 GATGTTTACT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 12 0.35
33 16 0.47
34 6 0.18
ACGTcount: A:0.28, C:0.15, G:0.01, T:0.55
Consensus pattern (33 bp):
CCAAATATTTTTAGTTTTTACCATTTATCTTAT
Found at i:13970 original size:22 final size:22
Alignment explanation
Indices: 13945--13986 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
13935 TCTAAACATT
*
13945 AAAAAATG-TTAAGATGATTAA
1 AAAAAAAGATTAAGATGATTAA
13966 AAAAAAAGATTAAGATGATTA
1 AAAAAAAGATTAAGATGATTA
13987 TATACAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.60, C:0.00, G:0.14, T:0.26
Consensus pattern (22 bp):
AAAAAAAGATTAAGATGATTAA
Found at i:23248 original size:58 final size:58
Alignment explanation
Indices: 23186--23371 Score: 216
Period size: 58 Copynumber: 3.2 Consensus size: 58
23176 AAAAACGTAA
*
23186 TTTTGGAAGTTCGGGATAATAATGTAATTTTTGAGAAGTGCAGGGTCAAAAATGTGAT
1 TTTTGGAAGTTCGGGATAATAATGTAATTTTTGAGAAGTTCAGGGTCAAAAATGTGAT
* * *
23244 TTTTGGAAGTTCGAGATAATGATGTAATTTTTGAGAAGTTCAAGAGT-AAAAATGTGAT
1 TTTTGGAAGTTCGGGATAATAATGTAATTTTTGAGAAGTTC-AGGGTCAAAAATGTGAT
* * * * * * *
23302 TTTTGGAAGTTTAGGGGTAAAAATGTGATTTTTG-GAAGTTTAGGGGCAAAATTGT-ATT
1 TTTTGGAAG-TTCGGGATAATAATGTAATTTTTGAGAAGTTCAGGGTCAAAAATGTGA-T
23360 TTTTGAGAAGTT
1 TTTTG-GAAGTT
23372 TAGGGGTCAA
Statistics
Matches: 109, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
57 4 0.04
58 79 0.72
59 26 0.24
ACGTcount: A:0.32, C:0.03, G:0.27, T:0.38
Consensus pattern (58 bp):
TTTTGGAAGTTCGGGATAATAATGTAATTTTTGAGAAGTTCAGGGTCAAAAATGTGAT
Found at i:23325 original size:87 final size:83
Alignment explanation
Indices: 23119--23341 Score: 223
Period size: 85 Copynumber: 2.6 Consensus size: 83
23109 GTTTGGGTTT
* * * * *
23119 AAAATATAA-TTTTGGAAAGTTTTAAGGGTAAAAATGTCATTTTGGGAAATTCAAGGTAAAAACG
1 AAAATGTAATTTTTGG-AAG-TTT-AGGGTAAAAATGTGATTTTTGGAAGTTCAAGATAAAAACG
**
23183 TAATTTTGGAAGTTCGGGATA
63 TAATTTTGGAAGTTCAAGATA
* ** * ** *
23204 ATAATGTAATTTTTGAGAAGTGCAGGGTCAAAAATGTGATTTTTGGAAGTTCGAGATAATGATGT
1 AAAATGTAATTTTTG-GAAGTTTAGGGT-AAAAATGTGATTTTTGGAAGTTCAAGATAAAAACGT
23269 AATTTTTGAGAAGTTCAAGAGTA
64 AA-TTTTG-GAAGTTCAAGA-TA
*
23292 AAAATGTGATTTTTGGAAGTTTAGGGGTAAAAATGTGATTTTTGGAAGTT
1 AAAATGTAATTTTTGGAAGTTTA-GGGTAAAAATGTGATTTTTGGAAGTT
23342 TAGGGGCAAA
Statistics
Matches: 113, Mismatches: 18, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
84 5 0.04
85 38 0.34
86 13 0.12
87 38 0.34
88 19 0.17
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (83 bp):
AAAATGTAATTTTTGGAAGTTTAGGGTAAAAATGTGATTTTTGGAAGTTCAAGATAAAAACGTAA
TTTTGGAAGTTCAAGATA
Found at i:23342 original size:29 final size:29
Alignment explanation
Indices: 23128--23451 Score: 196
Period size: 29 Copynumber: 11.1 Consensus size: 29
23118 TAAAATATAA
* *
23128 TTTTGGAAAGTTTTAAGGGTAAAAATGTCAT
1 TTTTGG-AAG-TTTAGGGGTAAAAATGTGAT
* * * * * *
23159 TTTGGGAAATTCA-AGGTAAAAACGT-AA
1 TTTTGGAAGTTTAGGGGTAAAAATGTGAT
* * * *
23186 TTTTGGAAG-TTCGGGATAATAATGTAAT
1 TTTTGGAAGTTTAGGGGTAAAAATGTGAT
**
23214 TTTTGAGAAGTGCA-GGGTCAAAAATGTGAT
1 TTTTG-GAAGTTTAGGGGT-AAAAATGTGAT
* * * ** *
23244 TTTTGGAAG-TTCGAGATAATGATGTAAT
1 TTTTGGAAGTTTAGGGGTAAAAATGTGAT
* * *
23272 TTTTGAGAAGTTCAAGAGTAAAAATGTGAT
1 TTTTG-GAAGTTTAGGGGTAAAAATGTGAT
23302 TTTTGGAAGTTTAGGGGTAAAAATGTGAT
1 TTTTGGAAGTTTAGGGGTAAAAATGTGAT
* *
23331 TTTTGGAAGTTTAGGGGCAAAATTGT-ATT
1 TTTTGGAAGTTTAGGGGTAAAAATGTGA-T
* *
23360 TTTTGAGAAGTTTAGGGGT-CAAATATGAT
1 TTTTG-GAAGTTTAGGGGTAAAAATGTGAT
** * * *
23389 TTTTAAAAGTTTAGAGGTAAAAATATAAT
1 TTTTGGAAGTTTAGGGGTAAAAATGTGAT
* * *
23418 TTTTAAGAAGTTT-GAGGGTCAAAATATGAT
1 TTTT-GGAAGTTTAG-GGGTAAAAATGTGAT
23448 TTTT
1 TTTT
23452 TGACAGTTCA
Statistics
Matches: 223, Mismatches: 56, Indels: 29
0.72 0.18 0.09
Matches are distributed among these distances:
26 1 0.00
27 16 0.07
28 41 0.18
29 93 0.42
30 67 0.30
31 5 0.02
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.37
Consensus pattern (29 bp):
TTTTGGAAGTTTAGGGGTAAAAATGTGAT
Found at i:23361 original size:87 final size:88
Alignment explanation
Indices: 23128--23451 Score: 229
Period size: 87 Copynumber: 3.7 Consensus size: 88
23118 TAAAATATAA
* * * * * * * * *
23128 TTTTGGAAAGTTTTAAGGGTAAAAATGTCATTTTGGGAAATTCA-AGGTAAAA-ACGTAATTTTG
1 TTTTGG-AAG-TTTAGGGGTAAAAATGTGATTTTTGGAAGTTTAGGGGCAAAATATGTATTTTTG
* * *
23191 -GAAGTTCGGGA-TAATAATGTAAT
64 AGAAGTTCAGGAGTAAAAATGTGAT
** * * *
23214 TTTTGAGAAGTGCA-GGGTCAAAAATGTGATTTTTGGAAG-TT-CGAG-ATAATGATGTAATTTT
1 TTTTG-GAAGTTTAGGGGT-AAAAATGTGATTTTTGGAAGTTTAGGGGCAAAAT-ATGT-ATTTT
*
23275 TGAGAAGTTCAAGAGTAAAAATGTGAT
62 TGAGAAGTTCAGGAGTAAAAATGTGAT
23302 TTTTGGAAGTTTAGGGGTAAAAATGTGATTTTTGGAAGTTTAGGGGCAAAAT-TGTATTTTTTGA
1 TTTTGGAAGTTTAGGGGTAAAAATGTGATTTTTGGAAGTTTAGGGGCAAAATATGTA-TTTTTGA
* * * *
23366 GAAGTTTAGGGGT-CAAATATGAT
65 GAAGTTCAGGAGTAAAAATGTGAT
** * * * * *
23389 TTTTAAAAGTTTAGAGGTAAAAATATAATTTTTAAGAAGTTTGAGGGTCAAAATATG-ATTTTT
1 TTTTGGAAGTTTAGGGGTAAAAATGTGATTTTT-GGAAGTTT-AGGGGCAAAATATGTATTTTT
23452 TGACAGTTCA
Statistics
Matches: 190, Mismatches: 32, Indels: 30
0.75 0.13 0.12
Matches are distributed among these distances:
83 3 0.02
84 6 0.03
85 22 0.12
86 14 0.07
87 73 0.38
88 53 0.28
89 13 0.07
90 6 0.03
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.37
Consensus pattern (88 bp):
TTTTGGAAGTTTAGGGGTAAAAATGTGATTTTTGGAAGTTTAGGGGCAAAATATGTATTTTTGAG
AAGTTCAGGAGTAAAAATGTGAT
Found at i:25105 original size:19 final size:18
Alignment explanation
Indices: 25081--25119 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
25071 ATTACAATGG
*
25081 CGGTGGTGCAACTTGGTGA
1 CGGTGGGGCAAC-TGGTGA
*
25100 CGGTGGGGCAGCTGGTGA
1 CGGTGGGGCAACTGGTGA
25118 CG
1 CG
25120 TGAGAACATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.13, C:0.18, G:0.49, T:0.21
Consensus pattern (18 bp):
CGGTGGGGCAACTGGTGA
Found at i:25259 original size:7 final size:7
Alignment explanation
Indices: 25247--25284 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
25237 TTGGGTCTAA
25247 GTTTAGT
1 GTTTAGT
25254 GTTTAGT
1 GTTTAGT
25261 GTTTAGT
1 GTTTAGT
25268 GTTTAGT
1 GTTTAGT
25275 GTTTAG-
1 GTTTAGT
25281 GTTT
1 GTTT
25285 TGGGTTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 4 0.13
7 27 0.87
ACGTcount: A:0.13, C:0.00, G:0.29, T:0.58
Consensus pattern (7 bp):
GTTTAGT
Found at i:26438 original size:20 final size:19
Alignment explanation
Indices: 26376--26435 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
26366 TTTATGAGTT
*
26376 TTTTAATAAATTTTATA-A
1 TTTTAATAATTTTTATATA
*
26394 GTTTATATCAA-TTTTA-ATA
1 TTTTA-AT-AATTTTTATATA
26413 TTTTAATAATTTTTATATA
1 TTTTAATAATTTTTATATA
26432 TTTT
1 TTTT
26436 TAAAAATTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
17 2 0.06
18 12 0.34
19 19 0.54
20 2 0.06
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTTAATAATTTTTATATA
Found at i:26443 original size:20 final size:18
Alignment explanation
Indices: 26405--26477 Score: 58
Period size: 19 Copynumber: 3.8 Consensus size: 18
26395 TTTATATCAA
*
26405 TTTTAATATTTTAATAAT
1 TTTTAATATTTTAAAAAT
26423 TTTTATATATTTTTAAAAA-
1 TTTTA-ATA-TTTTAAAAAT
*
26442 TTCTAATACATTTTATAAAAT
1 TTTTAAT--ATTTTA-AAAAT
* *
26463 ATTAAATATTTTAAA
1 TTTTAATATTTTAAA
26478 TATGTTTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
18 9 0.20
19 18 0.41
20 13 0.30
21 4 0.09
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTTAATATTTTAAAAAT
Found at i:26449 original size:37 final size:37
Alignment explanation
Indices: 26376--26449 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 37
26366 TTTATGAGTT
** *
26376 TTTTAATAAATTTTATAAGTTTATATCAATTTTAATA
1 TTTTAATAAATTTTATAAGTTTATAAAAATTCTAATA
* *
26413 TTTTAATAATTTTTATATA-TTTTTAAAAATTCTAATA
1 TTTTAATAAATTTTATA-AGTTTATAAAAATTCTAATA
26450 CATTTTATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 30 0.97
38 1 0.03
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (37 bp):
TTTTAATAAATTTTATAAGTTTATAAAAATTCTAATA
Found at i:34676 original size:15 final size:15
Alignment explanation
Indices: 34656--34684 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
34646 TCTTTACCCC
34656 TTAATAATAATAATA
1 TTAATAATAATAATA
34671 TTAATAATAATAAT
1 TTAATAATAATAAT
34685 TCATATGGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TTAATAATAATAATA
Found at i:40047 original size:21 final size:21
Alignment explanation
Indices: 40008--40047 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
39998 ATAAATTACC
* *
40008 TGAATTTTTATAGGGAAAACT
1 TGAATTTATACAGGGAAAACT
*
40029 TGAATTTATACAGGTAAAA
1 TGAATTTATACAGGGAAAA
40048 AAATATTTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.05, G:0.17, T:0.35
Consensus pattern (21 bp):
TGAATTTATACAGGGAAAACT
Found at i:41344 original size:17 final size:18
Alignment explanation
Indices: 41275--41346 Score: 55
Period size: 17 Copynumber: 4.2 Consensus size: 18
41265 AAAATTTTAG
*
41275 ATTT-TAAATCTT-AATTC
1 ATTTGTAAAT-TTAAATTT
*
41292 ATTT-TAATTTTAAATTT
1 ATTTGTAAATTTAAATTT
**
41309 A-TTGTAAATTTAAGCTT
1 ATTTGTAAATTTAAATTT
*
41326 ATTTG-AAGTTTAAATTT
1 ATTTGTAAATTTAAATTT
41343 ATTT
1 ATTT
41347 TGAAATAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
16 4 0.09
17 37 0.84
18 3 0.07
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.56
Consensus pattern (18 bp):
ATTTGTAAATTTAAATTT
Found at i:43108 original size:30 final size:30
Alignment explanation
Indices: 43082--43499 Score: 257
Period size: 30 Copynumber: 14.3 Consensus size: 30
43072 CGAAAATCAT
* *
43082 ATTTTGACCCCTAAACTTTCTAAAAATCAC
1 ATTTTGACCCCTAAACTTTCCAAAAATTAC
* *
43112 ATTTTAACCCTTAAA-TTTCCAAAAATTAC
1 ATTTTGACCCCTAAACTTTCCAAAAATTAC
* * * *
43141 A-TTTCAACTCTCAAACTTTCTAAAAATTAC
1 ATTTTGACCCCT-AAACTTTCCAAAAATTAC
* * *
43171 ATTTTAATCTCTAAACTTTCCAAAAATTAC
1 ATTTTGACCCCTAAACTTTCCAAAAATTAC
*
43201 ATTTTGACACCTAAACTTTCCAAAAATTAC
1 ATTTTGACCCCTAAACTTTCCAAAAATTAC
*
43231 A-TTTGACCCTTAAACTTTCCAAAAATTAC
1 ATTTTGACCCCTAAACTTTCCAAAAATTAC
*
43260 ATTTTGACCCTTAAAC-TTCCAAAAATTACC
1 ATTTTGACCCCTAAACTTTCCAAAAATTA-C
* * *
43290 ATTTT-A-CCCTCGAAC-ATCC-AAAA--CC
1 ATTTTGACCCCT-AAACTTTCCAAAAATTAC
* * ** *
43315 ATTTTTATCCC-GGA-TGTCCAAAAATTAC
1 ATTTTGACCCCTAAACTTTCCAAAAATTAC
* **
43343 ATTTTTGA-CCTTAATTTTTCCAAAAATTACC
1 A-TTTTGACCCCTAAACTTTCCAAAAATTA-C
* * * * *
43374 ATTTT-ACCCTTGAA-TGTCTAAAAATTCC
1 ATTTTGACCCCTAAACTTTCCAAAAATTAC
* *
43402 ATTTTTGA-CCTTGAAC-TTCCAAAAATTAC
1 A-TTTTGACCCCTAAACTTTCCAAAAATTAC
* * *
43431 ATTTTTGACCTC-GAACTTTTCAAAAATTACC
1 A-TTTTGACCCCTAAACTTTCCAAAAATTA-C
* ** *
43462 ATGTT-A-CCCTCGGA-TGTCCAAAAATTAC
1 ATTTTGACCCCT-AAACTTTCCAAAAATTAC
43490 ATTTTGACCC
1 ATTTTGACCC
43500 TCGAGTGTCT
Statistics
Matches: 313, Mismatches: 48, Indels: 54
0.75 0.12 0.13
Matches are distributed among these distances:
25 11 0.04
26 5 0.02
27 3 0.01
28 26 0.08
29 124 0.40
30 132 0.42
31 12 0.04
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.36
Consensus pattern (30 bp):
ATTTTGACCCCTAAACTTTCCAAAAATTAC
Found at i:43130 original size:29 final size:30
Alignment explanation
Indices: 43082--43500 Score: 304
Period size: 29 Copynumber: 14.4 Consensus size: 30
43072 CGAAAATCAT
* * *
43082 ATTTTGACCCCTAAACTTTCTAAAAATCAC
1 ATTTTGACCCTTAAACTTTCCAAAAATTAC
*
43112 ATTTTAACCCTTAAA-TTTCCAAAAATTAC
1 ATTTTGACCCTTAAACTTTCCAAAAATTAC
** * * *
43141 ATTTCAACTCTCAAACTTTCTAAAAATTAC
1 ATTTTGACCCTTAAACTTTCCAAAAATTAC
**
43171 ATTTT-AATCTCTAAACTTTCCAAAAATTAC
1 ATTTTGACCCT-TAAACTTTCCAAAAATTAC
43201 ATTTTGACACC-TAAACTTTCCAAAAATTAC
1 ATTTTGAC-CCTTAAACTTTCCAAAAATTAC
43231 A-TTTGACCCTTAAACTTTCCAAAAATTAC
1 ATTTTGACCCTTAAACTTTCCAAAAATTAC
43260 ATTTTGACCCTTAAAC-TTCCAAAAATTACC
1 ATTTTGACCCTTAAACTTTCCAAAAATTA-C
** * *
43290 ATTTT-ACCCTCGAAC-ATCC-AAAA--CC
1 ATTTTGACCCTTAAACTTTCCAAAAATTAC
* ** *
43315 ATTTTTATCCC--GGA-TGTCCAAAAATTAC
1 ATTTTGA-CCCTTAAACTTTCCAAAAATTAC
**
43343 ATTTTTGA-CCTTAATTTTTCCAAAAATTACC
1 A-TTTTGACCCTTAAACTTTCCAAAAATTA-C
* * * *
43374 ATTTT-ACCCTTGAA-TGTCTAAAAATTCC
1 ATTTTGACCCTTAAACTTTCCAAAAATTAC
*
43402 ATTTTTGA-CCTTGAAC-TTCCAAAAATTAC
1 A-TTTTGACCCTTAAACTTTCCAAAAATTAC
** *
43431 ATTTTTGA-CCTCGAACTTTTCAAAAATTACC
1 A-TTTTGACCCTTAAACTTTCCAAAAATTA-C
* *** *
43462 ATGTT-ACCCTCGGA-TGTCCAAAAATTAC
1 ATTTTGACCCTTAAACTTTCCAAAAATTAC
43490 ATTTTGACCCT
1 ATTTTGACCCT
43501 CGAGTGTCTA
Statistics
Matches: 322, Mismatches: 41, Indels: 53
0.77 0.10 0.13
Matches are distributed among these distances:
25 11 0.03
26 5 0.02
27 5 0.02
28 15 0.05
29 146 0.45
30 134 0.42
31 5 0.02
32 1 0.00
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.36
Consensus pattern (30 bp):
ATTTTGACCCTTAAACTTTCCAAAAATTAC
Found at i:43456 original size:59 final size:57
Alignment explanation
Indices: 43082--43501 Score: 247
Period size: 59 Copynumber: 7.2 Consensus size: 57
43072 CGAAAATCAT
* * * *
43082 ATTTTGACCC-CTAAACTTTCTAAAAATCACATTTTAACCCTTAAATTTCCAAAAATTAC
1 ATTTTGACCCTC-AAAC-TTCCAAAAATTACATTTTGA-CCTTAAACTTCCAAAAATTAC
** * * * *
43141 ATTTCAACTCTCAAACTTTCTAAAAATTACATTTTAATCTCTAAACTTTCCAAAAATTAC
1 ATTTTGACCCTCAAAC-TTCCAAAAATTACATTTTGACCT-TAAAC-TTCCAAAAATTAC
43201 ATTTTGACACCT-AAACTTTCCAAAAATTACA-TTTGACCCTTAAACTTTCCAAAAATTAC
1 ATTTTGAC-CCTCAAAC-TTCCAAAAATTACATTTTGA-CCTTAAAC-TTCCAAAAATTAC
* ** * *
43260 ATTTTGACCCTTAAACTTCCAAAAATTACCATTTT-ACCCTCGAACATCC-AAAA--CC
1 ATTTTGACCCTCAAACTTCCAAAAATTA-CATTTTGA-CCTTAAACTTCCAAAAATTAC
* * ** **
43315 ATTTTTATCC-CGGA-TGTCCAAAAATTACATTTTTGACCTTAATTTTTCCAAAAATTACC
1 ATTTTGACCCTCAAACT-TCCAAAAATTACA-TTTTGACCTTAA-ACTTCCAAAAATTA-C
** * * *
43374 ATTTT-ACCCTTGAA-TGTCTAAAAATTCCATTTTTGACCTTGAACTTCCAAAAATTAC
1 ATTTTGACCCTCAAACT-TCCAAAAATTACA-TTTTGACCTTAAACTTCCAAAAATTAC
* * * ***
43431 ATTTTTGA-CCTCGAACTTTTCAAAAATTACCATGTT-ACCCTCGGA-TGTCCAAAAATTAC
1 A-TTTTGACCCTCAAAC-TTCCAAAAATTA-CATTTTGA-CCTTAAACT-TCCAAAAATTAC
43490 ATTTTGACCCTC
1 ATTTTGACCCTC
43502 GAGTGTCTAA
Statistics
Matches: 294, Mismatches: 42, Indels: 50
0.76 0.11 0.13
Matches are distributed among these distances:
53 3 0.01
54 20 0.07
55 13 0.04
56 4 0.01
57 6 0.02
58 53 0.18
59 147 0.50
60 46 0.16
61 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.36
Consensus pattern (57 bp):
ATTTTGACCCTCAAACTTCCAAAAATTACATTTTGACCTTAAACTTCCAAAAATTAC
Found at i:43501 original size:29 final size:30
Alignment explanation
Indices: 43103--43587 Score: 259
Period size: 29 Copynumber: 16.6 Consensus size: 30
43093 TAAACTTTCT
* * * * *
43103 AAAAATCACATTTTAACCCT-TAAATTTCC
1 AAAAATTACATTTTGACCCTCGAACTGTCC
** * * * *
43132 AAAAATTACATTTCAACTCTCAAACTTTCT
1 AAAAATTACATTTTGACCCTCGAACTGTCC
** * *
43162 AAAAATTACATTTT-AATCTCTAAACTTTCC
1 AAAAATTACATTTTGACCCTC-GAACTGTCC
* *
43192 AAAAATTACATTTTGACACCT-AAACTTTCC
1 AAAAATTACATTTTGAC-CCTCGAACTGTCC
** *
43222 AAAAATTACA-TTTGACCCTTAAACTTTCC
1 AAAAATTACATTTTGACCCTCGAACTGTCC
**
43251 AAAAATTACATTTTGACCCTTAAACT-TCC
1 AAAAATTACATTTTGACCCTCGAACTGTCC
*
43280 AAAAATTACCATTTT-ACCCTCGAAC-ATCC
1 AAAAATTA-CATTTTGACCCTCGAACTGTCC
* * * *
43309 -AAAA--CCATTTTTATCC-CGGA-TGTCC
1 AAAAATTACATTTTGACCCTCGAACTGTCC
* * *
43334 AAAAATTACATTTTTGA-CCT-TAATTTTTCC
1 AAAAATTACA-TTTTGACCCTCGAA-CTGTCC
* *
43364 AAAAATTACCATTTT-ACCCTTGAA-TGTCT
1 AAAAATTA-CATTTTGACCCTCGAACTGTCC
* *
43393 AAAAATTCCATTTTTGA-CCTTGAACT-TCC
1 AAAAATTACA-TTTTGACCCTCGAACTGTCC
* *
43422 AAAAATTACATTTTTGA-CCTCGAACTTTTC
1 AAAAATTACA-TTTTGACCCTCGAACTGTCC
* *
43452 AAAAATTACCATGTT-ACCCTCGGA-TGTCC
1 AAAAATTA-CATTTTGACCCTCGAACTGTCC
* *
43481 AAAAATTACATTTTGACCCTCG-AGTGTCT
1 AAAAATTACATTTTGACCCTCGAACTGTCC
* *
43510 AAAAATTACCATTTTG-CCCCCGAAGTGTCC
1 AAAAATTA-CATTTTGACCCTCGAACTGTCC
* *
43540 -AAAATTATCGTTTT-ACCCTCGAGA--ATCC
1 AAAAATTA-CATTTTGACCCTCGA-ACTGTCC
*
43568 AAAAATCACATTTTTGACCC
1 AAAAATTACA-TTTTGACCC
43588 CTTTTATTTT
Statistics
Matches: 377, Mismatches: 44, Indels: 69
0.77 0.09 0.14
Matches are distributed among these distances:
25 12 0.03
26 7 0.02
28 24 0.06
29 186 0.49
30 139 0.37
31 7 0.02
32 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.35
Consensus pattern (30 bp):
AAAAATTACATTTTGACCCTCGAACTGTCC
Found at i:50104 original size:98 final size:98
Alignment explanation
Indices: 49933--50848 Score: 1155
Period size: 98 Copynumber: 9.3 Consensus size: 98
49923 TTACAGGATT
* **
49933 CAGTACCATGAAGATATTAAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCA
1 CAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCA
49998 TAAAGGGAAAGATTTAAGCCGCAACGGCGAATC
66 TAAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * *
50031 CGGTACCATGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGA-GAACCTTGAACCTCAGAAGC
1 CAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAAC-GACGAACCTTGTACCTCAGAAGC
50095 ATAAAGGGAAAGATTTAAGCCGCAACGGCGAATC
65 ATAAAGGGAAAGATTTAAGCCGCAACGGCGAATC
*
50129 CAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAATGACGAACCTTGTACCTCAGAAGCA
1 CAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCA
* * * * **
50194 TGAAGGGAGAGATTTAAGCTGTAACGGAAAATC
66 TAAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* *
50227 CAGTACCACGAAGATATGGAGGGAAAGAAGGTTTAAGTCACAAC-AGCGAACCTTGAACCTCAGA
1 CAGTACCACGAAGATATGGAGGG--A-AAGGTTTAAGTCGCAACGA-CGAACCTTGTACCTCAGA
* * * *
50291 AGCATAAAGAGCAAGATTTAAGCCGCAACAGTGAATC
62 AGCATAAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * * * *
50328 CGGTACCACGAAGATTTGAAGGGAAAGGTTTAAGTCGCAATGACGAACCTTGTACCTCAAAAGCA
1 CAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCA
* * * * *
50393 TAAACGAAAAGATTTAAGCTGTAACGGCGAATT
66 TAAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * * * * * *
50426 CGGTACCATGAAGATTTGAAGGGAAAGGTTTTAGTCGCAACGACGAATCTTGCACCTCAGAAGCA
1 CAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCA
*
50491 TGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
66 TAAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * *
50524 CAATACCACGAAGATATGGAGGGAAAGGTTTAAGTCGTAACGACGAACCTTGTACCTCAAAAGCA
1 CAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCA
* * * *
50589 TGAAGGGAGAGATTTAAGCTGCAACGGCAAATC
66 TAAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * * **
50622 CAGTACCAC-AAGGATATGGAGAGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTTGGAAGC
1 CAGTACCACGAA-GATATGGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGC
*
50686 ATGAAA-GGAAAGATTTAAGCCGCAACGTCGAATC
65 AT-AAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* ** * *
50720 TAGTACCAC-AAGGATATAAAGGGGAAAGGTTTAAGTCGTAAC-AGCGAACCTTGTAACTC-GAA
1 CAGTACCACGAA-GATATGGA-GGGAAAGGTTTAAGTCGCAACGA-CGAACCTTGTACCTCAG-A
*
50782 AGCATGAAA-GGAAAGATTTAAGCCGCAACGACGAATC
62 AGCAT-AAAGGGAAAGATTTAAGCCGCAACGGCGAATC
*
50819 CAATACCACGAAGATATGGAGGGAAAGGTT
1 CAGTACCACGAAGATATGGAGGGAAAGGTT
50849 ACAACCACAA
Statistics
Matches: 711, Mismatches: 94, Indels: 26
0.86 0.11 0.03
Matches are distributed among these distances:
97 4 0.01
98 536 0.75
99 87 0.12
100 4 0.01
101 80 0.11
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.18
Consensus pattern (98 bp):
CAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCA
TAAAGGGAAAGATTTAAGCCGCAACGGCGAATC
Found at i:50844 original size:49 final size:49
Alignment explanation
Indices: 49935--50845 Score: 476
Period size: 49 Copynumber: 18.5 Consensus size: 49
49925 ACAGGATTCA
* * * *
49935 GTACCATGAAGATATTAAGGGAAAGGTTTAAGTCGCAACGACGAA-CCTT
1 GTACCACGAAGATATGAAGGGAAAGATTTAAGCCGCAACGACGAATCC-T
* * *
49984 GTACCTCAGAAGCATA--AAGGGAAAGATTTAAGCCGCAACGGCGAATCCG
1 GTACCAC-GAAG-ATATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCT
* * * *
50033 GTACCATGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGA-GAA-CCTT
1 GTACCACGAAGATATGAAGGGAAAGATTTAAGCCGCAAC-GACGAATCC-T
* * * *
50082 GAACCTCAGAAGCATA--AAGGGAAAGATTTAAGCCGCAACGGCGAATCCA
1 GTACCAC-GAAG-ATATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCT
* * * *
50131 GTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAATGACGAA-CCTT
1 GTACCACGAAGATATGAAGGGAAAGATTTAAGCCGCAACGACGAATCC-T
* * * * * * *
50180 GTACCTCAGAAG-CATGAAGGGAGAGATTTAAGCTGTAACGGA-AAATCCA
1 GTACCAC-GAAGATATGAAGGGAAAGATTTAAGCCGCAAC-GACGAATCCT
* * *
50229 GTACCACGAAGATATGGAGGGAAAGAAGGTTTAAGTCACAAC-AGCGAA-CCTT
1 GTACCACGAAGATATGAAGGGAAAG-A--TTTAAGCCGCAACGA-CGAATCC-T
* * * * * *
50281 GAACCTCAGAAGCATA--AAGAGCAAGATTTAAGCCGCAAC-AGTGAATCCG
1 GTACCAC-GAAG-ATATGAAGGGAAAGATTTAAGCCGCAACGA-CGAATCCT
* * * *
50330 GTACCACGAAGATTTGAAGGGAAAGGTTTAAGTCGCAATGACGAA-CCTT
1 GTACCACGAAGATATGAAGGGAAAGATTTAAGCCGCAACGACGAATCC-T
* * * * * * * * *
50379 GTACCTCAAAAGCATA--AACGAAAAGATTTAAGCTGTAACGGCGAATTCG
1 GTACCAC-GAAG-ATATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCT
* * * * * *
50428 GTACCATGAAGATTTGAAGGGAAAGGTTTTAGTCGCAACGACGAATCTT
1 GTACCACGAAGATATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCT
* * * * *
50477 GCACCTCAGAAG-CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCA
1 GTACCAC-GAAGATATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCT
* * * * *
50526 ATACCACGAAGATATGGAGGGAAAGGTTTAAGTCGTAACGACGAA-CCTT
1 GTACCACGAAGATATGAAGGGAAAGATTTAAGCCGCAACGACGAATCC-T
* * * * * * * *
50575 GTACCTC-AAAAGCATGAAGGGAGAGATTTAAGCTGCAACGGCAAATCCA
1 GTACCACGAAGA-TATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCT
* * * * * *
50624 GTACCAC-AAGGATATGGAGAGAAAGGTTTAAGTCGCAATGGCGAA-CCTT
1 GTACCACGAA-GATATGAAGGGAAAGATTTAAGCCGCAACGACGAATCC-T
** * * *
50673 GTACCTTGGAAG-CATGAAAGGAAAGATTTAAGCCGCAACGTCGAAT-CT
1 GTACC-ACGAAGATATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCT
* * * *
50721 AGTACCAC-AAGGATATAAAGGGGAAAGGTTTAAGTCGTAAC-AGCGAA-CCTT
1 -GTACCACGAA-GATATGAA-GGGAAAGATTTAAGCCGCAACGA-CGAATCC-T
* * * * *
50772 GTAACTCGAA-AGCATGAAAGGAAAGATTTAAGCCGCAACGACGAATCCA
1 GTACCACGAAGA-TATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCT
* *
50821 ATACCACGAAGATATGGAGGGAAAG
1 GTACCACGAAGATATGAAGGGAAAG
50846 GTTACAACCA
Statistics
Matches: 627, Mismatches: 177, Indels: 116
0.68 0.19 0.13
Matches are distributed among these distances:
47 12 0.02
48 39 0.06
49 458 0.73
50 73 0.12
51 16 0.03
52 22 0.04
53 4 0.01
54 3 0.00
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.18
Consensus pattern (49 bp):
GTACCACGAAGATATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCT
Found at i:51168 original size:39 final size:39
Alignment explanation
Indices: 51122--51388 Score: 217
Period size: 39 Copynumber: 6.8 Consensus size: 39
51112 CATCATCAAC
* *
51122 CAATCTCTTACCCCAAGCTTGGGGCAGATTGCAACCATT
1 CAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCATT
*
51161 CAATCTCTTACCCCGAGCCTGGGGTAGA-T-C-ACCATT
1 CAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCATT
* *
51197 AGCCAATCTCCTACCCCGAGCTTGGGGCAGATTGCAACCATT
1 ---CAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCATT
*** * * * *
51239 TGGTCTCTTACCTCAAGCCTGAGGCAGA-T-C-ACTATT
1 CAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCATT
* **
51275 AGCCAATCTCTTACCCCGAGCCTGGGGCAAATTGCAGTCATT
1 ---CAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCATT
* * **
51317 CGATCTCTTACCCCGAGCCTGGGGCAGA-T-CATCATCAAC
1 CAATCTCTTACCCCGAGCCTGGGGCAGATTGCA--ACCATT
* *
51356 CAATCTCCTACCCCGAGTCTGGGGCAGATTGCA
1 CAATCTCTTACCCCGAGCCTGGGGCAGATTGCA
51389 GTTATCCAAA
Statistics
Matches: 179, Mismatches: 33, Indels: 30
0.74 0.14 0.12
Matches are distributed among these distances:
36 11 0.06
37 4 0.02
38 3 0.02
39 145 0.81
40 3 0.02
41 4 0.02
42 9 0.05
ACGTcount: A:0.23, C:0.32, G:0.21, T:0.24
Consensus pattern (39 bp):
CAATCTCTTACCCCGAGCCTGGGGCAGATTGCAACCATT
Found at i:51250 original size:78 final size:78
Alignment explanation
Indices: 51121--51388 Score: 358
Period size: 78 Copynumber: 3.4 Consensus size: 78
51111 TCATCATCAA
* * * *
51121 CCAATCTCTTACCCCAAGCTTGGGGCAGATTGCAACCATTCAATCTCTTACCCCGAGCCTGGGGT
1 CCAATCTCCTACCCCGAGCTTGGGGCAGATTGCAACCATTCGATCTCTTACCCCGAGCCTGGGGC
51186 AGATCACCATTAG
66 AGATCACCATTAG
* * * * *
51199 CCAATCTCCTACCCCGAGCTTGGGGCAGATTGCAACCATTTGGTCTCTTACCTCAAGCCTGAGGC
1 CCAATCTCCTACCCCGAGCTTGGGGCAGATTGCAACCATTCGATCTCTTACCCCGAGCCTGGGGC
*
51264 AGATCACTATTAG
66 AGATCACCATTAG
* * * **
51277 CCAATCTCTTACCCCGAGCCTGGGGCAAATTGCAGTCATTCGATCTCTTACCCCGAGCCTGGGGC
1 CCAATCTCCTACCCCGAGCTTGGGGCAGATTGCAACCATTCGATCTCTTACCCCGAGCCTGGGGC
* * *
51342 AGATCATCATCAA
66 AGATCACCATTAG
51355 CCAATCTCCTACCCCGAG-TCTGGGGCAGATTGCA
1 CCAATCTCCTACCCCGAGCT-TGGGGCAGATTGCA
51389 GTTATCCAAA
Statistics
Matches: 162, Mismatches: 27, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
78 162 1.00
ACGTcount: A:0.23, C:0.32, G:0.21, T:0.24
Consensus pattern (78 bp):
CCAATCTCCTACCCCGAGCTTGGGGCAGATTGCAACCATTCGATCTCTTACCCCGAGCCTGGGGC
AGATCACCATTAG
Found at i:52057 original size:17 final size:17
Alignment explanation
Indices: 51968--52062 Score: 84
Period size: 17 Copynumber: 5.5 Consensus size: 17
51958 AAAATTTTAG
*
51968 ATTTTAAATCTT-AATTC
1 ATTTTAAAT-TTAAATTT
* *
51985 CTTTTAATTTTAAATTT
1 ATTTTAAATTTAAATTT
* **
52002 ATTGTAAATTTAAGCTT
1 ATTTTAAATTTAAATTT
** *
52019 ATTTGGAGTTTAAATTT
1 ATTTTAAATTTAAATTT
52036 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
52053 ATTTTGAAAT
1 ATTTT-AAAT
52063 AAAAATTTAA
Statistics
Matches: 59, Mismatches: 17, Indels: 3
0.75 0.22 0.04
Matches are distributed among these distances:
16 2 0.03
17 53 0.90
18 4 0.07
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.55
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:52068 original size:18 final size:17
Alignment explanation
Indices: 52030--52071 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
52020 TTTGGAGTTT
**
52030 AAATTTATTTTAAATTT
1 AAATTTATTTTAAATAA
52047 AAATTTATTTTGAAATAA
1 AAATTTATTTT-AAATAA
52065 AAATTTA
1 AAATTTA
52072 AATTTAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
AAATTTATTTTAAATAA
Found at i:53804 original size:29 final size:30
Alignment explanation
Indices: 53776--54012 Score: 226
Period size: 29 Copynumber: 8.1 Consensus size: 30
53766 TATGTCTTGA
* *
53776 CCTTAAGCTTTCCAAAAATTACATTTTGAC
1 CCTTAAACTTTCCAAAAATTACATTTTAAC
53806 CCTTAAAC-TTCCAAAAATTACATTTTAACC
1 CCTTAAACTTTCCAAAAATTACATTTTAA-C
*
53836 CCTT-AACTTTCTAAAAATTACATTTTAAC
1 CCTTAAACTTTCCAAAAATTACATTTTAAC
*
53865 CCCTAAACTTTCCAAAAATTACA-TTTAAC
1 CCTTAAACTTTCCAAAAATTACATTTTAAC
*
53894 CCCTAAACTTTCCAAAAATTACCATTTT-AC
1 CCTTAAACTTTCCAAAAATTA-CATTTTAAC
** * *
53924 CCTCGAAC-ATCCAAAAATTACCATTTTCATC
1 CCTTAAACTTTCCAAAAATTA-CATTTT-AAC
* *
53955 CC--GAA-TGTCCAAAAATTACATTTTAA-
1 CCTTAAACTTTCCAAAAATTACATTTTAAC
** *
53981 CC-TCGATTTTCCAAAAATTACCATTTT-AC
1 CCTTAAACTTTCCAAAAATTA-CATTTTAAC
54010 CCT
1 CCT
54013 CGGATGTCTA
Statistics
Matches: 179, Mismatches: 15, Indels: 26
0.81 0.07 0.12
Matches are distributed among these distances:
26 2 0.01
27 2 0.01
28 19 0.11
29 93 0.52
30 57 0.32
31 6 0.03
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.34
Consensus pattern (30 bp):
CCTTAAACTTTCCAAAAATTACATTTTAAC
Found at i:53853 original size:59 final size:58
Alignment explanation
Indices: 53783--54071 Score: 268
Period size: 59 Copynumber: 4.9 Consensus size: 58
53773 TGACCTTAAG
** *
53783 CTTTCCAAAAATTACATTTTGACCCTTAAACTTCCAAAAATTACATTTTAACCCCTTAA
1 CTTTCCAAAAATTACATTTT-ACCCTCGAACTTCCAAAAATTACATTTTAACCCCTGAA
* * *
53842 CTTTCTAAAAATTACATTTTAACCC-CTAAACTTTCCAAAAATTACA-TTTAACCCCTAAA
1 CTTTCCAAAAATTACATTTT-ACCCTC-GAAC-TTCCAAAAATTACATTTTAACCCCTGAA
* * *
53901 CTTTCCAAAAATTACCATTTTACCCTCGAACATCCAAAAATTACCATTTTCATCCC-GAA
1 CTTTCCAAAAATTA-CATTTTACCCTCGAACTTCCAAAAATTA-CATTTTAACCCCTGAA
* * ** *
53960 -TGTCCAAAAATTACATTTTAACCTCGATTTTCCAAAAATTACCATTTT-A-CCCTCGGA
1 CTTTCCAAAAATTACATTTTACCCTCGAACTTCCAAAAATTA-CATTTTAACCCCT-GAA
* * * **
54017 -TGTCTAAAAATTTCATTTTTGGCCTCGAACTTCCAAAAATTACATTTTTAACCCC
1 CTTTCCAAAAATTACA-TTTTACCCTCGAACTTCCAAAAATTACA-TTTTAACCCC
54072 AAAACTATGC
Statistics
Matches: 196, Mismatches: 22, Indels: 23
0.81 0.09 0.10
Matches are distributed among these distances:
55 3 0.02
56 1 0.01
57 48 0.24
58 49 0.25
59 64 0.33
60 31 0.16
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.35
Consensus pattern (58 bp):
CTTTCCAAAAATTACATTTTACCCTCGAACTTCCAAAAATTACATTTTAACCCCTGAA
Found at i:54000 original size:57 final size:57
Alignment explanation
Indices: 53786--54064 Score: 228
Period size: 57 Copynumber: 4.8 Consensus size: 57
53776 CCTTAAGCTT
* ** * *
53786 TCCAAAAATTACATTTTGACCCTTAAACTTCCAAAAATTA-CATTTTAACCC-CTTAACTT
1 TCCAAAAATTACATTTT-AACCTCGAACTTCCAAAAATTACCATTTT-ACCCTC-GAA-TG
* * * * * *
53845 TCTAAAAATTACATTTTAACCCCTAAACTTTCCAAAAATTA-CATTTAACCC-CTAAACTT
1 TCCAAAAATTACATTTTAACCTC-GAAC-TTCCAAAAATTACCATTTTACCCTC-GAA-TG
* * *
53904 TCCAAAAATTACCATTTTACCCTCGAACATCCAAAAATTACCATTTTCATCC-CGAATG
1 TCCAAAAATTA-CATTTTAACCTCGAACTTCCAAAAATTACCATTTT-ACCCTCGAATG
** *
53962 TCCAAAAATTACATTTTAACCTCGATTTTCCAAAAATTACCATTTTACCCTCGGATG
1 TCCAAAAATTACATTTTAACCTCGAACTTCCAAAAATTACCATTTTACCCTCGAATG
* * **
54019 TCTAAAAATTTCATTTTTGGCCTCGAACTTCCAAAAATTA-CATTTT
1 TCCAAAAATTACA-TTTTAACCTCGAACTTCCAAAAATTACCATTTT
54065 TAACCCCAAA
Statistics
Matches: 186, Mismatches: 27, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
56 3 0.02
57 53 0.28
58 48 0.26
59 51 0.27
60 31 0.17
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.35
Consensus pattern (57 bp):
TCCAAAAATTACATTTTAACCTCGAACTTCCAAAAATTACCATTTTACCCTCGAATG
Found at i:54013 original size:29 final size:29
Alignment explanation
Indices: 53784--54074 Score: 220
Period size: 29 Copynumber: 10.0 Consensus size: 29
53774 GACCTTAAGC
* *
53784 TTTCCAAAAATTACATTTTGACCCTTAAA
1 TTTCCAAAAATTACATTTTAACCCTCAAA
* * *
53813 CTTCCAAAAATTACATTTTAACCCCTTAAC
1 TTTCCAAAAATTACATTTTAA-CCCTCAAA
*
53843 TTTCTAAAAATTACATTTTAACCC-CTAAA
1 TTTCCAAAAATTACATTTTAACCCTC-AAA
53872 CTTTCCAAAAATTACA-TTTAACCC-CTAAA
1 -TTTCCAAAAATTACATTTTAACCCTC-AAA
*
53901 CTTTCCAAAAATTACCATTTT-ACCCTCGAA
1 -TTTCCAAAAATTA-CATTTTAACCCTCAAA
** * * *
53931 CATCCAAAAATTACCATTTTCATCC-CGAA
1 TTTCCAAAAATTA-CATTTTAACCCTCAAA
* * *
53960 TGTCCAAAAATTACATTTTAA-CCTCGAT
1 TTTCCAAAAATTACATTTTAACCCTCAAA
**
53988 TTTCCAAAAATTACCATTTT-ACCCTCGGA
1 TTTCCAAAAATTA-CATTTTAACCCTCAAA
* * * *** *
54017 TGTCTAAAAATTTCATTTTTGGCCTCGAA
1 TTTCCAAAAATTACATTTTAACCCTCAAA
*
54046 CTTCCAAAAATTACATTTTTAACCC-CAAA
1 TTTCCAAAAATTACA-TTTTAACCCTCAAA
54075 ACTATGCAAA
Statistics
Matches: 217, Mismatches: 33, Indels: 24
0.79 0.12 0.09
Matches are distributed among these distances:
27 2 0.01
28 29 0.13
29 125 0.58
30 57 0.26
31 4 0.02
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.34
Consensus pattern (29 bp):
TTTCCAAAAATTACATTTTAACCCTCAAA
Found at i:54026 original size:86 final size:86
Alignment explanation
Indices: 53785--54105 Score: 242
Period size: 89 Copynumber: 3.7 Consensus size: 86
53775 ACCTTAAGCT
* * *
53785 TTCCAAAAATTACATTTTGACCCTTAAAC-TTCCAAAAATTA-CATTTTAACCC-CTTAACTTTC
1 TTCCAAAAATTACATTTT-AACC-TAAACTTTCCAAAAATTACCATTTT-ACCCTC-GAAC-ATC
* * * * *
53847 TAAAAATTACATTTT-AACCCCTAAAC
61 CAAAAATTCCATTTTCAGCCTC-GAAC
53873 TTTCCAAAAATTACA-TTTAACCCCTAAACTTTCCAAAAATTACCATTTTACCCTCGAACATCCA
1 -TTCCAAAAATTACATTTTAA--CCTAAACTTTCCAAAAATTACCATTTTACCCTCGAACATCCA
*
53937 AAAATTACCATTTTCATCC-CGAA-
63 AAAATT-CCATTTTCAGCCTCGAAC
** * * ** *
53960 TGTCCAAAAATTACATTTTAACCTCGATTTTCCAAAAATTACCATTTTACCCTCGGATGTCTAAA
1 T-TCCAAAAATTACATTTTAACCTAAACTTTCCAAAAATTACCATTTTACCCTCGAACATCCAAA
* **
54025 AATTTCATTTTTGGCCTCGAAC
65 AATTCCATTTTCAGCCTCGAAC
* * * * * *
54047 TTCCAAAAATTACATTTTTAACCCCAAAACTATGCAAAAAATACCATGTTACCCCCGAA
1 TTCCAAAAATTACA-TTTTAA--CCTAAACTTTCCAAAAATTACCATTTTACCCTCGAA
54106 TGCCCAAAAA
Statistics
Matches: 190, Mismatches: 28, Indels: 28
0.77 0.11 0.11
Matches are distributed among these distances:
85 8 0.04
86 59 0.31
87 21 0.11
88 24 0.13
89 68 0.36
90 10 0.05
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (86 bp):
TTCCAAAAATTACATTTTAACCTAAACTTTCCAAAAATTACCATTTTACCCTCGAACATCCAAAA
ATTCCATTTTCAGCCTCGAAC
Found at i:57068 original size:180 final size:180
Alignment explanation
Indices: 56764--57123 Score: 675
Period size: 180 Copynumber: 2.0 Consensus size: 180
56754 CAATTTAACC
56764 ATTCCTTCTTAGGTAGCCACCACTGTTTGGCCATCAAGGAGTCCTATACGGAATATGCTACAACA
1 ATTCCTTCTTAGGTAGCCACCACTGTTTGGCCATCAAGGAGTCCTATACGGAATATGCTACAACA
*
56829 TCTCTTACATTTTCCAAACACAAAAAATCACCTGTAACATGATTAGGATACTATATATCAATAAT
66 TCTCTCACATTTTCCAAACACAAAAAATCACCTGTAACATGATTAGGATACTATATATCAATAAT
*
56894 CCAATTATTTTTGGACTTACCATTCAACCAATTGGAAGTTGATTGTTTAT
131 CCAATTATTTTTGGACTTACCATTCAACCAAGTGGAAGTTGATTGTTTAT
56944 ATTCCTTCTTAGGTAGCCACCACTGTTTGGCCATCAAGGAGTCCTATACGGAATATGCTACAACA
1 ATTCCTTCTTAGGTAGCCACCACTGTTTGGCCATCAAGGAGTCCTATACGGAATATGCTACAACA
* * *
57009 TCTCTCACATTTTCCAAACACAGAAAATCACCTGTAACATGATTAGGATACTCTATATCAATAGT
66 TCTCTCACATTTTCCAAACACAAAAAATCACCTGTAACATGATTAGGATACTATATATCAATAAT
57074 CCAATTATTTTTGGACTTACCATTCAACCAAGTGGAAGTTGATTGTTTAT
131 CCAATTATTTTTGGACTTACCATTCAACCAAGTGGAAGTTGATTGTTTAT
57124 TACCGAACAC
Statistics
Matches: 175, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
180 175 1.00
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.33
Consensus pattern (180 bp):
ATTCCTTCTTAGGTAGCCACCACTGTTTGGCCATCAAGGAGTCCTATACGGAATATGCTACAACA
TCTCTCACATTTTCCAAACACAAAAAATCACCTGTAACATGATTAGGATACTATATATCAATAAT
CCAATTATTTTTGGACTTACCATTCAACCAAGTGGAAGTTGATTGTTTAT
Found at i:62252 original size:23 final size:24
Alignment explanation
Indices: 62210--62254 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
62200 ATATATTTAT
*
62210 TTTTATAATAAATAACTTAAAAGC
1 TTTTATAATAAAAAACTTAAAAGC
*
62234 TTTTA-AATAAAAAATTTAAAA
1 TTTTATAATAAAAAACTTAAAA
62255 TAAATGACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (24 bp):
TTTTATAATAAAAAACTTAAAAGC
Found at i:62476 original size:26 final size:27
Alignment explanation
Indices: 62439--62502 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
62429 ACTAAGTCCC
62439 CACTTTGATACTTGTA-TATTTTTATT
1 CACTTTGATACTTGTATTATTTTTATT
* *
62465 CACTTTGGTACTTGTATTTTTTTTATT
1 CACTTTGATACTTGTATTATTTTTATT
*
62492 CACTTTAATAC
1 CACTTTGATAC
62503 ATGAATTTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
26 15 0.45
27 18 0.55
ACGTcount: A:0.22, C:0.14, G:0.08, T:0.56
Consensus pattern (27 bp):
CACTTTGATACTTGTATTATTTTTATT
Found at i:62510 original size:27 final size:27
Alignment explanation
Indices: 62457--62510 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
62447 TACTTGTATA
** * *
62457 TTTTTATTCACTTTGGTACTTGTATTT
1 TTTTTATTCACTTTAATACATGAATTT
62484 TTTTTATTCACTTTAATACATGAATTT
1 TTTTTATTCACTTTAATACATGAATTT
62511 GATAACTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.22, C:0.11, G:0.07, T:0.59
Consensus pattern (27 bp):
TTTTTATTCACTTTAATACATGAATTT
Found at i:62742 original size:22 final size:22
Alignment explanation
Indices: 62715--62761 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
62705 ATTTTTATCG
62715 ATTTCGAGCATTTTCCGATTCA
1 ATTTCGAGCATTTTCCGATTCA
62737 ATTTCGAGCATTTTCCGATTCA
1 ATTTCGAGCATTTTCCGATTCA
62759 ATT
1 ATT
62762 GGTTCAACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.43
Consensus pattern (22 bp):
ATTTCGAGCATTTTCCGATTCA
Found at i:64305 original size:77 final size:77
Alignment explanation
Indices: 64217--64367 Score: 207
Period size: 77 Copynumber: 2.0 Consensus size: 77
64207 TTTCTTTTCA
* ** *
64217 TTTTAATATCGTACATATTGCATGTGTTATTATTAAT-TAATTTCAAATTATACATTACAATATT
1 TTTTAATATCGTACATATTGCATATGTTATTATTAATCT-ATTTCAAACCATAAATTACAATA-T
64281 TATTGTATGTTTTT
64 TATTGTATGTTTTT
* * *
64295 TTTTAA-ATCGTATATATTTCATATGTTATTATTAATCTATTTCAAACCATAAATTACATTATTA
1 TTTTAATATCGTACATATTGCATATGTTATTATTAATCTATTTCAAACCATAAATTACAATATTA
64359 TTGTATGTT
66 TTGTATGTT
64368 ACTTTCAAAC
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
76 12 0.18
77 46 0.71
78 7 0.11
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.52
Consensus pattern (77 bp):
TTTTAATATCGTACATATTGCATATGTTATTATTAATCTATTTCAAACCATAAATTACAATATTA
TTGTATGTTTTT
Found at i:64628 original size:9 final size:9
Alignment explanation
Indices: 64616--64644 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
64606 TTTCTATTGT
64616 AAAAA-AAA
1 AAAAAGAAA
64624 AAAAAGAAA
1 AAAAAGAAA
64633 AAAAAGAAA
1 AAAAAGAAA
64642 AAA
1 AAA
64645 GAATGTACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 5 0.25
9 15 0.75
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:64637 original size:16 final size:16
Alignment explanation
Indices: 64616--64647 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
64606 TTTCTATTGT
64616 AAAAAAAAAAAAAGAA
1 AAAAAAAAAAAAAGAA
*
64632 AAAAAAGAAAAAAGAA
1 AAAAAAAAAAAAAGAA
64648 TGTACCAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAGAA
Found at i:68261 original size:14 final size:15
Alignment explanation
Indices: 68236--68265 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
68226 CCCCCTGTAT
68236 GTGAAGCCCCTACAA
1 GTGAAGCCCCTACAA
68251 GTGAA-CCCCTACAA
1 GTGAAGCCCCTACAA
68265 G
1 G
68266 CATGCCCATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.33, C:0.33, G:0.20, T:0.13
Consensus pattern (15 bp):
GTGAAGCCCCTACAA
Found at i:68282 original size:28 final size:28
Alignment explanation
Indices: 68251--68349 Score: 128
Period size: 28 Copynumber: 3.5 Consensus size: 28
68241 GCCCCTACAA
*
68251 GTGAACCCCTACAAGC-ATGCCCATGTAT
1 GTGAACCCCTATAAGCGA-GCCCATGTAT
*
68279 GTGAACCCCCTATAAGCGAGCCCCTGTAT
1 GTGAA-CCCCTATAAGCGAGCCCATGTAT
** *
68308 GCAAACCCCTATAGGCGAGCCCATGTAT
1 GTGAACCCCTATAAGCGAGCCCATGTAT
68336 GTGAACCCCTATAA
1 GTGAACCCCTATAA
68350 ACAAACCCAA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
28 37 0.62
29 22 0.37
30 1 0.02
ACGTcount: A:0.28, C:0.32, G:0.19, T:0.20
Consensus pattern (28 bp):
GTGAACCCCTATAAGCGAGCCCATGTAT
Found at i:68358 original size:28 final size:28
Alignment explanation
Indices: 68251--68375 Score: 117
Period size: 28 Copynumber: 4.5 Consensus size: 28
68241 GCCCCTACAA
* *
68251 GTGAACCCCTACAAGCATGCCCATGTAT
1 GTGAACCCCTATAAGCAAGCCCATGTAT
* *
68279 GTGAACCCCCTATAAGCGAGCCCCTGTAT
1 GTGAA-CCCCTATAAGCAAGCCCATGTAT
** * *
68308 GCAAACCCCTATAGGCGAGCCCATGTAT
1 GTGAACCCCTATAAGCAAGCCCATGTAT
* * * *
68336 GTGAACCCCTATAAACAAACCCA-ATAC
1 GTGAACCCCTATAAGCAAGCCCATGTAT
*
68363 ATGAACCCCTATA
1 GTGAACCCCTATA
68376 GGCTAACCTA
Statistics
Matches: 79, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
27 14 0.18
28 43 0.54
29 22 0.28
ACGTcount: A:0.32, C:0.33, G:0.16, T:0.19
Consensus pattern (28 bp):
GTGAACCCCTATAAGCAAGCCCATGTAT
Found at i:68403 original size:27 final size:27
Alignment explanation
Indices: 68338--68405 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
68328 CCATGTATGT
** *
68338 GAACCCCTATAAACAAACCCAATACAT
1 GAACCCCTATAGGCAAACCCAATACAC
* * *
68365 GAACCCCTATAGGCTAACCTAATACGC
1 GAACCCCTATAGGCAAACCCAATACAC
68392 GAACCCCTATAGGC
1 GAACCCCTATAGGC
68406 GAATCTCCAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.38, C:0.34, G:0.12, T:0.16
Consensus pattern (27 bp):
GAACCCCTATAGGCAAACCCAATACAC
Found at i:68748 original size:15 final size:15
Alignment explanation
Indices: 68706--68766 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 15
68696 TGAATCATCA
** *
68706 TGCAAACCCCCTAGG
1 TGCAAACCCTATATG
*
68721 TGCGAACCC-ATATG
1 TGCAAACCCTATATG
68735 TGCAAACCCTATATG
1 TGCAAACCCTATATG
* * *
68750 AGCAAATCCTACATG
1 TGCAAACCCTATATG
68765 TG
1 TG
68767 GGAACCTTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
14 11 0.30
15 26 0.70
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (15 bp):
TGCAAACCCTATATG
Found at i:68864 original size:58 final size:58
Alignment explanation
Indices: 68713--68866 Score: 148
Period size: 58 Copynumber: 2.7 Consensus size: 58
68703 TCATGCAAAC
* * *
68713 CCCCTAGGTGCGAACCCATATGTGCAAACCCTATATGAGCAAATCCTACATGTGGGAA
1 CCCCTAAGTGCGAACCCATATGTGCAAACTCTATATGTGCAAATCCTACATGTGGGAA
** * * * * * ** * *
68771 CCTTTAAATGCAAACCCATATGTGCGAGCTTTATATGTGTGAA-CTTCACATGTGTGAA
1 CCCCTAAGTGCGAACCCATATGTGCAAACTCTATATGTGCAAATCCT-ACATGTGGGAA
* *
68829 CCCCTAAGTGCGAACTCATATGTGCAAAATCTATATGT
1 CCCCTAAGTGCGAACCCATATGTGCAAACTCTATATGT
68867 ACGAACCTTG
Statistics
Matches: 72, Mismatches: 23, Indels: 2
0.74 0.24 0.02
Matches are distributed among these distances:
57 2 0.03
58 70 0.97
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (58 bp):
CCCCTAAGTGCGAACCCATATGTGCAAACTCTATATGTGCAAATCCTACATGTGGGAA
Found at i:70714 original size:77 final size:77
Alignment explanation
Indices: 70625--70783 Score: 237
Period size: 77 Copynumber: 2.1 Consensus size: 77
70615 TTCTAGTTAG
* * * *
70625 GATAAAAAGATATGGAATTCTATTTCTATTTGAATTTTTGAAGAAGGACAATATATGATTTCAAA
1 GATAAAAAGATATGAAATTCTATTTCTATTTGAATTTTTAAAGAAGGACAATAAATAATTTCAAA
70690 TTAGGATAAGAA
66 TTAGGATAAGAA
* * * * *
70702 GATAAAAAGATATGAAATTTTATTTTTGTTTGAATTTTTAAAGAGGGATAATAAATAATTTCAAA
1 GATAAAAAGATATGAAATTCTATTTCTATTTGAATTTTTAAAGAAGGACAATAAATAATTTCAAA
70767 TTAGGATAAGAA
66 TTAGGATAAGAA
70779 GATAA
1 GATAA
70784 TAAATAATTT
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
77 73 1.00
ACGTcount: A:0.45, C:0.03, G:0.16, T:0.36
Consensus pattern (77 bp):
GATAAAAAGATATGAAATTCTATTTCTATTTGAATTTTTAAAGAAGGACAATAAATAATTTCAAA
TTAGGATAAGAA
Found at i:83572 original size:31 final size:31
Alignment explanation
Indices: 83514--83573 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
83504 ATACATATCT
* *
83514 TTTTTACATTGTATATTTTATACATATATTG
1 TTTTTACATTATATATTATATACATATATTG
*
83545 TTTTTACA-TATATATTGATATATATATAT
1 TTTTTACATTATATATT-ATATACATATAT
83574 AGATTGTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (31 bp):
TTTTTACATTATATATTATATACATATATTG
Found at i:90342 original size:3 final size:3
Alignment explanation
Indices: 90334--90363 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
90324 ATTAATAGAC
90334 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
90364 GTTTGAGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:94245 original size:7 final size:7
Alignment explanation
Indices: 94233--94267 Score: 61
Period size: 7 Copynumber: 4.9 Consensus size: 7
94223 TGGATGTGAA
94233 ATAAAAT
1 ATAAAAT
94240 ATAAAAT
1 ATAAAAT
94247 ATAAAAT
1 ATAAAAT
94254 ATAAAAT
1 ATAAAAT
94261 ATTAAAA
1 A-TAAAA
94268 AAGAGTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 22 0.81
8 5 0.19
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
ATAAAAT
Found at i:94285 original size:6 final size:6
Alignment explanation
Indices: 94274--94317 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
94264 AAAAAAGAGT
* * * *
94274 AATAAG AATAAG AATAGG AATAGG AATACG AATAGG AATGGG AA
1 AATAGG AATAGG AATAGG AATAGG AATAGG AATAGG AATAGG AA
94318 GAATTTTAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.55, C:0.02, G:0.27, T:0.16
Consensus pattern (6 bp):
AATAGG
Found at i:94300 original size:18 final size:18
Alignment explanation
Indices: 94274--94317 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
94264 AAAAAAGAGT
*
94274 AATAAGAATAAGAATAGG
1 AATAGGAATAAGAATAGG
*
94292 AATAGGAATACGAATAGG
1 AATAGGAATAAGAATAGG
*
94310 AATGGGAA
1 AATAGGAA
94318 GAATTTTAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.55, C:0.02, G:0.27, T:0.16
Consensus pattern (18 bp):
AATAGGAATAAGAATAGG
Found at i:99870 original size:24 final size:21
Alignment explanation
Indices: 99804--99859 Score: 71
Period size: 19 Copynumber: 2.7 Consensus size: 21
99794 TAGAAACGTT
* *
99804 TTTAATATAT-ATTAACAT-A
1 TTTATTATATCATTATCATAA
99823 TTTATTATATCATTATCATAA
1 TTTATTATATCATTATCATAA
99844 TTTATTATTATCATTA
1 TTTATTA-TATCATTA
99860 ATTTTGAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 9 0.28
20 7 0.22
21 8 0.25
22 8 0.25
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTATTATATCATTATCATAA
Found at i:100980 original size:30 final size:29
Alignment explanation
Indices: 100932--101199 Score: 169
Period size: 30 Copynumber: 9.0 Consensus size: 29
100922 TAAAAATCAT
*
100932 ATTTTGACTCCTTAAATTTTTTTAAAATTAC
1 ATTTTGA--CCTTAAATTTTTCTAAAATTAC
100963 ATTTTGACCTCTAAATTTTTCTAAAATTAC
1 ATTTTGACCT-TAAATTTTTCTAAAATTAC
*
100993 ATTTTGACCTTAAACTTTTCTAAAATTAC
1 ATTTTGACCTTAAATTTTTCTAAAATTAC
* * ** * * *
101022 ATTTTAATCCCTAAACATTCCCAAAATCAC
1 ATTTTGA-CCTTAAATTTTTCTAAAATTAC
* * * * *
101052 ATTTTAACCCTCAAACTTTTCCAAAATTTC
1 ATTTTGA-CCTTAAATTTTTCTAAAATTAC
* * ** * *
101082 ATTTTAACATCCGAACTTTTCTAAAATTGC
1 ATTTTGACCT-TAAATTTTTCTAAAATTAC
* ** * *
101112 ATTTTGATCCTTAAA-CTTTCCCAAATCAT
1 ATTTTGA-CCTTAAATTTTTCTAAAATTAC
* * *
101141 ATTTTGACCCCTAAACTTTCCTAAAATTAC
1 ATTTTGA-CCTTAAATTTTTCTAAAATTAC
* * *
101171 ATTTTGATCCCTAAATTTTCCAAAAATTA
1 ATTTTGA-CCTTAAATTTTTCTAAAATTA
101200 TGTTTTAACC
Statistics
Matches: 192, Mismatches: 40, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
29 50 0.26
30 133 0.69
31 9 0.05
ACGTcount: A:0.34, C:0.21, G:0.03, T:0.41
Consensus pattern (29 bp):
ATTTTGACCTTAAATTTTTCTAAAATTAC
Found at i:101018 original size:59 final size:60
Alignment explanation
Indices: 100932--101214 Score: 261
Period size: 59 Copynumber: 4.8 Consensus size: 60
100922 TAAAAATCAT
* ** * * *
100932 ATTTTGACTCCTTAAATTTTTTTAAAATTACATTTTGACCTCTAAATTTTTCTAAAATTAC
1 ATTTTGA-TCCTTAAACTTTTCCAAAATTACATTTTAACCTCTAAACTTTCCTAAAATTAC
* * * *
100993 ATTTTGA-CCTTAAACTTTTCTAAAATTACATTTTAATCC-CTAAACATTCCCAAAATCAC
1 ATTTTGATCCTTAAACTTTTCCAAAATTACATTTTAA-CCTCTAAACTTTCCTAAAATTAC
* * * * * ** * *
101052 ATTTTAACCCTCAAACTTTTCCAAAATTTCATTTTAACATCCGAACTTTTCTAAAATTGC
1 ATTTTGATCCTTAAACTTTTCCAAAATTACATTTTAACCTCTAAACTTTCCTAAAATTAC
* * * * *
101112 ATTTTGATCCTTAAAC-TTTCCCAAATCATATTTTGACCCCTAAACTTTCCTAAAATTAC
1 ATTTTGATCCTTAAACTTTTCCAAAATTACATTTTAACCTCTAAACTTTCCTAAAATTAC
* **
101171 ATTTTGATCCCTAAA-TTTTCCAAAAATTATGTTTTAACC-CTAAA
1 ATTTTGATCCTTAAACTTTTCC-AAAATTACATTTTAACCTCTAAA
101215 TTCTTCGAAA
Statistics
Matches: 178, Mismatches: 39, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
59 104 0.58
60 67 0.38
61 7 0.04
ACGTcount: A:0.34, C:0.21, G:0.03, T:0.41
Consensus pattern (60 bp):
ATTTTGATCCTTAAACTTTTCCAAAATTACATTTTAACCTCTAAACTTTCCTAAAATTAC
Found at i:101208 original size:119 final size:119
Alignment explanation
Indices: 100979--101195 Score: 296
Period size: 119 Copynumber: 1.8 Consensus size: 119
100969 ACCTCTAAAT
* * *
100979 TTTTCTAAAATTACATTTTGACCTTAAACTTTTCTAAAATTACATTTTAATCCCTAAACATTCCC
1 TTTTCTAAAATTACATTTTGACCTTAAACTTTTCCAAAATCACATTTTAACCCCTAAACATTCCC
101044 AAAATCACATTTTAACCCTCAAACTTTTCCAAAATTTCATTTTAACATCCGAAC
66 AAAATCACATTTTAACCCTCAAACTTTTCCAAAATTTCATTTTAACATCCGAAC
* * * * *
101098 TTTTCTAAAATTGCATTTTGATCCTTAAAC-TTTCCCAAATCATATTTTGACCCCTAAACTTTCC
1 TTTTCTAAAATTACATTTTGA-CCTTAAACTTTTCCAAAATCACATTTTAACCCCTAAACATTCC
* * *
101162 TAAAATTACATTTTGATCCCT-AAA-TTTTCCAAAA
65 CAAAATCACATTTT-AACCCTCAAACTTTTCCAAAA
101196 ATTATGTTTT
Statistics
Matches: 85, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
118 10 0.12
119 62 0.73
120 13 0.15
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.40
Consensus pattern (119 bp):
TTTTCTAAAATTACATTTTGACCTTAAACTTTTCCAAAATCACATTTTAACCCCTAAACATTCCC
AAAATCACATTTTAACCCTCAAACTTTTCCAAAATTTCATTTTAACATCCGAAC
Found at i:111263 original size:42 final size:43
Alignment explanation
Indices: 111197--111281 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 43
111187 ATATTTTGCC
** *
111197 TAAAAAAAAGGATTGAGATGAAAACCCGCAAAAGGCATCTTGA
1 TAAAAAAAAGGATCAAGATAAAAACCCGCAAAAGGCATCTTGA
* *
111240 TAAAAAAAA-GATCAAGATAAAAACCCGCAAAGGGCTTCTTGA
1 TAAAAAAAAGGATCAAGATAAAAACCCGCAAAAGGCATCTTGA
111282 AACCAAAAGG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 28 0.76
43 9 0.24
ACGTcount: A:0.49, C:0.15, G:0.19, T:0.16
Consensus pattern (43 bp):
TAAAAAAAAGGATCAAGATAAAAACCCGCAAAAGGCATCTTGA
Found at i:112544 original size:161 final size:161
Alignment explanation
Indices: 112271--112620 Score: 425
Period size: 161 Copynumber: 2.2 Consensus size: 161
112261 CTTCAAAAGG
* * ** *
112271 TCATCTTCCCGATGAAATACAGAGAAACAGACCAAAACAATGAAGCGAAGCTCAAAGTGAGTGAA
1 TCATCTTCCTGATGAGATACAGAGAAGTAGACCAAAACAATAAAGCGAAGCTCAAAGTGAGTGAA
* * * * * * *
112336 ACCTCAAACCCCCATCTTCTTGATGAGATACAGAGAATTGGGTCAAAGCAATAAAGTGGTTATCT
66 ACCTCAAACCCCCATCTTCCTAATGAGATACAAAGAAGTGAGTCAAAGCAATAAAGAGGTCATCT
* * * *
112401 TCTTGACGAGATGCATAAAAGTGAATC-AAAT
131 TCCTAACAAGATGCAGAAAAGTGAA-CAAAAT
** * *
112432 TCATCTTCCTGATGAGATACAGAGAAGTAGACCAATTCAATAAAGCGAAGCTTAATGTGAGTGAA
1 TCATCTTCCTGATGAGATACAGAGAAGTAGACCAAAACAATAAAGCGAAGCTCAAAGTGAGTGAA
* *
112497 ACTTCTAAA-CTCCATCTTCCTAATGAGATACAAAGAAGTGAGTCAAAGCAATAAAGAGGTCATC
66 ACCTC-AAACCCCCATCTTCCTAATGAGATACAAAGAAGTGAGTCAAAGCAATAAAGAGGTCATC
* *
112561 TTCCTAACAAGATGTAGAGAAGTGAACAAAAT
130 TTCCTAACAAGATGCAGAAAAGTGAACAAAAT
* * *
112593 CCGTCTTCCTAATGAGATACAGAGAAGT
1 TCATCTTCCTGATGAGATACAGAGAAGT
112621 GGATTAAATC
Statistics
Matches: 160, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
160 1 0.01
161 156 0.98
162 3 0.02
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.23
Consensus pattern (161 bp):
TCATCTTCCTGATGAGATACAGAGAAGTAGACCAAAACAATAAAGCGAAGCTCAAAGTGAGTGAA
ACCTCAAACCCCCATCTTCCTAATGAGATACAAAGAAGTGAGTCAAAGCAATAAAGAGGTCATCT
TCCTAACAAGATGCAGAAAAGTGAACAAAAT
Found at i:112678 original size:85 final size:85
Alignment explanation
Indices: 112511--112668 Score: 210
Period size: 85 Copynumber: 1.9 Consensus size: 85
112501 CTAAACTCCA
*
112511 TCTTCCTAATGAGATACAAAGAAGTGAGTCAAAGCAATAAAGAGGTCATCTTCCTAACAAGATGT
1 TCTTCCTAATGAGATACAAAGAAGTGAGTCAAAGCAATAAAGAGGTCATCTTCCTAACAAGATAT
112576 AGAGAAGTGAACAAAATCCG
66 AGAGAAGTGAACAAAATCCG
* * * * ** * **
112596 TCTTCCTAATGAGATACAGAGAAGTG-GATTAAATCAATGAAGCTGTCATCTTCCTGATGAGATA
1 TCTTCCTAATGAGATACAAAGAAGTGAG-TCAAAGCAATAAAGAGGTCATCTTCCTAACAAGATA
112660 TAGAGAAGT
65 TAGAGAAGT
112669 AGACCAAATC
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
84 1 0.02
85 61 0.98
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (85 bp):
TCTTCCTAATGAGATACAAAGAAGTGAGTCAAAGCAATAAAGAGGTCATCTTCCTAACAAGATAT
AGAGAAGTGAACAAAATCCG
Found at i:114760 original size:29 final size:30
Alignment explanation
Indices: 114592--114962 Score: 308
Period size: 30 Copynumber: 12.5 Consensus size: 30
114582 TTTTTTTTCT
**
114592 AAAATTACATTTTAA-CCCTCAAACTTTTTC
1 AAAATTACATTTTAACCCCT-AAACTTTCCC
* * *
114622 AAAAATGCATTTTAACCCTTAAACTTTCCC
1 AAAATTACATTTTAACCCCTAAACTTTCCC
* * *
114652 ATAATCACATTTTAACCCCTAAACTTTTCC
1 AAAATTACATTTTAACCCCTAAACTTTCCC
** * *
114682 AAAATTGTATTTTAATCCCTAAACTTTTCC
1 AAAATTACATTTTAACCCCTAAACTTTCCC
* *
114712 AAAATTGCATTTCAATCCCCT-AACTTTCCC
1 AAAATTACATTTTAA-CCCCTAAACTTTCCC
* *
114742 AAAATCACATTTTAACCCCTAAACTTTTCC
1 AAAATTACATTTTAACCCCTAAACTTTCCC
** *
114772 AAAATTACATTTTAA-TACTAAATTTTCCC
1 AAAATTACATTTTAACCCCTAAACTTTCCC
* * * *
114801 AAAATCACATTTTGA-CCCTCGAACTTTTCC
1 AAAATTACATTTTAACCCCT-AAACTTTCCC
* * **
114831 AAAAGTACATTTTGA-CCCTAAACTTTCTT
1 AAAATTACATTTTAACCCCTAAACTTTCCC
* * **
114860 AAAATTACATTTTGACTCC-AAACTTTCAT
1 AAAATTACATTTTAACCCCTAAACTTTCCC
* * **
114889 AAAATCACATTTTGACCCC-AAACTTTCTT
1 AAAATTACATTTTAACCCCTAAACTTTCCC
* * * *
114918 AAAATTACATTTTGATCCCT-AATTTTTCC
1 AAAATTACATTTTAACCCCTAAACTTTCCC
114947 AAAATTACATTTTAAC
1 AAAATTACATTTTAAC
114963 ATTAAATTCT
Statistics
Matches: 279, Mismatches: 56, Indels: 13
0.80 0.16 0.04
Matches are distributed among these distances:
29 121 0.43
30 151 0.54
31 7 0.03
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (30 bp):
AAAATTACATTTTAACCCCTAAACTTTCCC
Found at i:116237 original size:24 final size:23
Alignment explanation
Indices: 116180--116242 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
116170 TTCATTTAAC
*
116180 TTAATTGAACATATTCACGAACA
1 TTAATTGAACATGTTCACGAACA
** * *
116203 TTAAACGAACATGTTCATGAATA
1 TTAATTGAACATGTTCACGAACA
116226 TATAATTGAACATGTTC
1 T-TAATTGAACATGTTC
116243 TCCAACAATG
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 19 0.59
24 13 0.41
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.33
Consensus pattern (23 bp):
TTAATTGAACATGTTCACGAACA
Found at i:126040 original size:152 final size:150
Alignment explanation
Indices: 125766--126070 Score: 556
Period size: 152 Copynumber: 2.0 Consensus size: 150
125756 GTAGCCTTCA
*
125766 TTCTCTCCTTTTCAATTTCACATCCAAAATCTAAAGTAAATCTAAAAAAAAAAAAACCCTCCATT
1 TTCTCTCCTTTTCAATTTCACATCCAAAATCTAAAGTAAATCTAAAAAAAAAAAAACCCTCCACT
*
125831 ATGGTTCTACAAAAATCAACATTGTCGCGAGAAATTTTCAATTGAGCCCATTCATCCTTGAATAT
66 ATGATTCTACAAAAATCAACATTGTCGCGAGAAATTTTCAATTGAGCCCATTCATCCTTGAATAT
125896 TTATGTACTCTTAATTTATT
131 TTATGTACTCTTAATTTATT
125916 TTCTCTCCTTTTCAATTTCACATCCAAAATCTAAAGTAAATCTAAAAAAAAAAAAAAACCCTCCA
1 TTCTCTCCTTTTCAATTTCACATCCAAAATCTAAAGTAAATCT--AAAAAAAAAAAAACCCTCCA
* *
125981 CTGTGATTCTACAAAAATCAACATTGTCGCGAGAAATTTTCAATTGAGGCCATTCATCCTTGAAT
64 CTATGATTCTACAAAAATCAACATTGTCGCGAGAAATTTTCAATTGAGCCCATTCATCCTTGAAT
126046 ATTTATGTACTCTTAATTTATT
129 ATTTATGTACTCTTAATTTATT
126068 TTC
1 TTC
126071 AATTTACTTG
Statistics
Matches: 149, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
150 43 0.29
152 106 0.71
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.35
Consensus pattern (150 bp):
TTCTCTCCTTTTCAATTTCACATCCAAAATCTAAAGTAAATCTAAAAAAAAAAAAACCCTCCACT
ATGATTCTACAAAAATCAACATTGTCGCGAGAAATTTTCAATTGAGCCCATTCATCCTTGAATAT
TTATGTACTCTTAATTTATT
Found at i:136665 original size:26 final size:25
Alignment explanation
Indices: 136617--136665 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
136607 TCCTTCTAAA
*
136617 AATCAGTATTTAAGAAGATAATAAT
1 AATCAGTATTTAAGAAGAAAATAAT
136642 AATCAGTAGTTTAA-AATGAAAATA
1 AATCAGTA-TTTAAGAA-GAAAATA
136666 TTGAAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.53, C:0.04, G:0.12, T:0.31
Consensus pattern (25 bp):
AATCAGTATTTAAGAAGAAAATAAT
Found at i:145435 original size:28 final size:28
Alignment explanation
Indices: 145376--145442 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
145366 TGATGGGAAA
* * *
145376 GCCTTTGTGGCTATCTTTATTTAAGGAT
1 GCCTTTATGGCTATCTTTATTTAAGAAC
* *
145404 GCCTTTATGGTTATCTTTGTTTAAGAAC
1 GCCTTTATGGCTATCTTTATTTAAGAAC
*
145432 GCCTCTATGGC
1 GCCTTTATGGC
145443 GATTCTTCGA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.43
Consensus pattern (28 bp):
GCCTTTATGGCTATCTTTATTTAAGAAC
Found at i:149184 original size:24 final size:23
Alignment explanation
Indices: 149156--149219 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
149146 GGAAAAATCT
149156 AAAAAAATTTAAAATATAAAAATG
1 AAAAAAATTTAAAATAT-AAAATG
* * * *
149180 CAAAAAA-TTATAAATATACATTT
1 AAAAAAATTTA-AAATATAAAATG
149203 AAAAAAATTTAAAATAT
1 AAAAAAATTTAAAATAT
149220 GTTATAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
23 18 0.55
24 15 0.45
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.30
Consensus pattern (23 bp):
AAAAAAATTTAAAATATAAAATG
Found at i:156202 original size:11 final size:11
Alignment explanation
Indices: 156188--156214 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
156178 TTAAAGGATT
156188 TTTTAATTTTA
1 TTTTAATTTTA
156199 TTTTAATTTTA
1 TTTTAATTTTA
156210 TTTTA
1 TTTTA
156215 GTTTAATAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTAATTTTA
Found at i:156214 original size:16 final size:17
Alignment explanation
Indices: 156188--156221 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
156178 TTAAAGGATT
*
156188 TTTTAATTTTATTTTAA
1 TTTTAATTTTAGTTTAA
156205 TTTT-ATTTTAGTTTAA
1 TTTTAATTTTAGTTTAA
156221 T
1 T
156222 AAGTGTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTTAATTTTAGTTTAA
Done.