Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011057.1 Kokia drynarioides strain JFW-HI SEQ_126028, 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: 153329
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:4155 original size:96 final size:96
Alignment explanation
Indices: 4033--4217 Score: 316
Period size: 96 Copynumber: 1.9 Consensus size: 96
4023 TCTTCTTTAG
* * *
4033 TTGGATATTTAATTGGACATTAGAAACCTTTATGATCTTTTGAACTACACCAATAACATTGCGCA
1 TTGGATATTTAATTGGACATTAGAAACCCTTATGACCTTTTGAACTACACCAATAACATTGCACA
* *
4098 AAAGGTGATATCTCAATTGTATTCTCTCTAT
66 AAAGGTGATAGCTCAATCGTATTCTCTCTAT
*
4129 TTGGATATTTAATTGGACATTGGAAACCCTTATGACCTTTTGAACTACACCAATAACATTGCACA
1 TTGGATATTTAATTGGACATTAGAAACCCTTATGACCTTTTGAACTACACCAATAACATTGCACA
4194 AAAGGTGATAGCTCAATCGTATTC
66 AAAGGTGATAGCTCAATCGTATTC
4218 CTCCTTTCGT
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
96 83 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.35
Consensus pattern (96 bp):
TTGGATATTTAATTGGACATTAGAAACCCTTATGACCTTTTGAACTACACCAATAACATTGCACA
AAAGGTGATAGCTCAATCGTATTCTCTCTAT
Found at i:6161 original size:5 final size:5
Alignment explanation
Indices: 6151--6175 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
6141 TATGACAACT
6151 AATAA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA
6176 CAAAATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:9751 original size:22 final size:22
Alignment explanation
Indices: 9723--9775 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
9713 AAAAAAATAT
*
9723 TCAATTATATTGGCGTAATCAA
1 TCAATTATATTGGCGCAATCAA
9745 TCAATTATATTGGCGCAATCAA
1 TCAATTATATTGGCGCAATCAA
9767 TCAATTATA
1 TCAATTATA
9776 CTGTTATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (22 bp):
TCAATTATATTGGCGCAATCAA
Found at i:21613 original size:37 final size:37
Alignment explanation
Indices: 21509--21605 Score: 149
Period size: 37 Copynumber: 2.6 Consensus size: 37
21499 AATACATCAA
*
21509 CACAAAGCCTGAAAACACCGGCATGAAGTCTACTAGG
1 CACAAAGCCTGAAAACACCGGCATGAAGCCTACTAGG
* * *
21546 CACATAGCTTGAAAACACCGACATGAAGCCTACTAGG
1 CACAAAGCCTGAAAACACCGGCATGAAGCCTACTAGG
*
21583 CACAAAGCCTAAAAACACCGGCA
1 CACAAAGCCTGAAAACACCGGCA
21606 CAAAGCCTGA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.40, C:0.29, G:0.19, T:0.12
Consensus pattern (37 bp):
CACAAAGCCTGAAAACACCGGCATGAAGCCTACTAGG
Found at i:28721 original size:37 final size:37
Alignment explanation
Indices: 28669--28836 Score: 221
Period size: 37 Copynumber: 4.5 Consensus size: 37
28659 CATTGGCATA
* * * * *
28669 AAGCCTGCTAAGCACATAG-CTCAAATACACTGACACG
1 AAGCCTACTAGGCACAAAGCCTGAAA-ACACCGACACG
*
28706 AAGCCTACTAGGCACATAGCCTGAAAACACCGACACG
1 AAGCCTACTAGGCACAAAGCCTGAAAACACCGACACG
* *
28743 AAGCCTACTAGGCACAAAGCCTGAAAACACCGGCACA
1 AAGCCTACTAGGCACAAAGCCTGAAAACACCGACACG
* * *
28780 AAGCTTACTAGGGACAAAGACTGAAAACACCGACACG
1 AAGCCTACTAGGCACAAAGCCTGAAAACACCGACACG
28817 AAGCCTACTAGGCACAAAGC
1 AAGCCTACTAGGCACAAAGC
28837 TTGACTTTTT
Statistics
Matches: 115, Mismatches: 15, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
37 110 0.96
38 5 0.04
ACGTcount: A:0.40, C:0.30, G:0.19, T:0.11
Consensus pattern (37 bp):
AAGCCTACTAGGCACAAAGCCTGAAAACACCGACACG
Found at i:32634 original size:3 final size:3
Alignment explanation
Indices: 32626--32679 Score: 101
Period size: 3 Copynumber: 18.3 Consensus size: 3
32616 AGTAAAATTG
32626 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
32674 A-T ATT A
1 ATT ATT A
32680 CACACATAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:35564 original size:19 final size:20
Alignment explanation
Indices: 35534--35575 Score: 61
Period size: 18 Copynumber: 2.1 Consensus size: 20
35524 CATAAAATTA
35534 ATTTTTCTAAAAATATT-TTT
1 ATTTTTCT-AAAATATTATTT
35554 ATTTTTC-AAAATATTATTT
1 ATTTTTCTAAAATATTATTT
35573 ATT
1 ATT
35576 GATTTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 6 0.29
20 7 0.33
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTTTCTAAAATATTATTT
Found at i:38108 original size:13 final size:15
Alignment explanation
Indices: 38059--38109 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 15
38049 TTCATAAATA
* *
38059 AATTAATATTTTA-T
1 AATTAAAATATTATT
38073 AATTAAAAT-TTATT
1 AATTAAAATATTATT
38087 AATTAAAATATT-TT
1 AATTAAAATATTATT
38101 AA-TAAAATA
1 AATTAAAATA
38110 AACTATGCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
13 10 0.29
14 22 0.65
15 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTAAAATATTATT
Found at i:44306 original size:31 final size:30
Alignment explanation
Indices: 44242--44335 Score: 102
Period size: 31 Copynumber: 3.1 Consensus size: 30
44232 TAATGATATC
* *
44242 TAAAATAT-TTTAAA-AACTTAAATATAATAA
1 TAAAATATATTTAAATAATTTAAATA-AA-GA
44272 TAAAATATATTTAAATAATTTAACATAAAGA
1 TAAAATATATTTAAATAATTTAA-ATAAAGA
* *
44303 TAAATTATATTTAAATAATTTAATATAATGA
1 TAAAATATATTTAAATAATTTAA-ATAAAGA
44334 TA
1 TA
44336 CATGAAATAT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
30 8 0.14
31 37 0.66
32 8 0.14
33 3 0.05
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (30 bp):
TAAAATATATTTAAATAATTTAAATAAAGA
Found at i:44360 original size:34 final size:34
Alignment explanation
Indices: 44309--44392 Score: 111
Period size: 34 Copynumber: 2.6 Consensus size: 34
44299 AAGATAAATT
* *
44309 ATATTTAA-ATAATTTAATATAATGATACATGAA
1 ATATGTAATATAATTTAATATAATGATACATAAA
*
44342 ATATGTAATATAATTTAATATAATGATATATAAA
1 ATATGTAATATAATTTAATATAATGATACATAAA
*
44376 ATATG-AAT-TAATCTAAT
1 ATATGTAATATAATTTAAT
44393 TTTTATATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
32 8 0.17
33 10 0.22
34 28 0.61
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.40
Consensus pattern (34 bp):
ATATGTAATATAATTTAATATAATGATACATAAA
Found at i:45684 original size:64 final size:64
Alignment explanation
Indices: 45586--45717 Score: 246
Period size: 64 Copynumber: 2.1 Consensus size: 64
45576 AATTAAGAAT
45586 AAAAAAATAGAACCAAAATTAGTTATCTTACTTTCAATAGGAAAGTAAATATCTCTCTTATATA
1 AAAAAAATAGAACCAAAATTAGTTATCTTACTTTCAATAGGAAAGTAAATATCTCTCTTATATA
* *
45650 AAAAAAATAGAACCAAAATTAGTTATCTTACTTTCAGTAGGAAAGTAAATCTCTCTCTTATATA
1 AAAAAAATAGAACCAAAATTAGTTATCTTACTTTCAATAGGAAAGTAAATATCTCTCTTATATA
45714 AAAA
1 AAAA
45718 CCGGTAGAAT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32
Consensus pattern (64 bp):
AAAAAAATAGAACCAAAATTAGTTATCTTACTTTCAATAGGAAAGTAAATATCTCTCTTATATA
Found at i:45750 original size:22 final size:20
Alignment explanation
Indices: 45725--45769 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
45715 AAACCGGTAG
*
45725 AATTGTTATTCTTGGAAAATA
1 AATT-TTATACTTGGAAAATA
45746 TAA-TTTATACTTGGAAAATA
1 -AATTTTATACTTGGAAAATA
45766 AATT
1 AATT
45770 CTCACTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 2 0.10
20 16 0.76
21 1 0.05
22 2 0.10
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.42
Consensus pattern (20 bp):
AATTTTATACTTGGAAAATA
Found at i:45758 original size:20 final size:19
Alignment explanation
Indices: 45730--45769 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
45720 GGTAGAATTG
*
45730 TTATTCTTGGAAAATATAAT
1 TTATACTTGGAAAATA-AAT
45750 TTATACTTGGAAAATAAAT
1 TTATACTTGGAAAATAAAT
45769 T
1 T
45770 CTCACTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.42
Consensus pattern (19 bp):
TTATACTTGGAAAATAAAT
Found at i:47676 original size:26 final size:26
Alignment explanation
Indices: 47647--47712 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 26
47637 TAGCTTAAAT
*
47647 GAGCCTAAACAGAGTTTAGCTCTTAC
1 GAGCCTAGACAGAGTTTAGCTCTTAC
* * **
47673 GAGCCCAGACAGATTTTCTCTCTTAC
1 GAGCCTAGACAGAGTTTAGCTCTTAC
47699 GAG-CTAGACAGAGT
1 GAGCCTAGACAGAGT
47713 ATCGATCTTA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
25 9 0.27
26 24 0.73
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (26 bp):
GAGCCTAGACAGAGTTTAGCTCTTAC
Found at i:49724 original size:80 final size:80
Alignment explanation
Indices: 49591--49752 Score: 324
Period size: 80 Copynumber: 2.0 Consensus size: 80
49581 AATATGTCAT
49591 CTATCACGTCCAAATTAGGAAGATGATTTGTCTTAAGCATTAGAGTGGATGACTTCCAGAAGATA
1 CTATCACGTCCAAATTAGGAAGATGATTTGTCTTAAGCATTAGAGTGGATGACTTCCAGAAGATA
49656 GAGGCATAAATGTGA
66 GAGGCATAAATGTGA
49671 CTATCACGTCCAAATTAGGAAGATGATTTGTCTTAAGCATTAGAGTGGATGACTTCCAGAAGATA
1 CTATCACGTCCAAATTAGGAAGATGATTTGTCTTAAGCATTAGAGTGGATGACTTCCAGAAGATA
49736 GAGGCATAAATGTGA
66 GAGGCATAAATGTGA
49751 CT
1 CT
49753 GACTTGACTG
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 82 1.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (80 bp):
CTATCACGTCCAAATTAGGAAGATGATTTGTCTTAAGCATTAGAGTGGATGACTTCCAGAAGATA
GAGGCATAAATGTGA
Found at i:50734 original size:19 final size:17
Alignment explanation
Indices: 50698--50738 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
50688 TCAAAAAATT
50698 ATTTAATTAGAAATTTA
1 ATTTAATTAGAAATTTA
*
50715 ATTTAATATATAATATTTA
1 ATTTAAT-TAGAA-ATTTA
50734 ATTTA
1 ATTTA
50739 GAAATAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
18 4 0.19
19 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
ATTTAATTAGAAATTTA
Found at i:54164 original size:21 final size:21
Alignment explanation
Indices: 54133--54206 Score: 98
Period size: 21 Copynumber: 3.5 Consensus size: 21
54123 GGAGTTTTTG
*
54133 GTATTGGTAGATGCATGACTT
1 GTATCGGTAGATGCATGACTT
*
54154 GTATCGATAGATGCATGACTT
1 GTATCGGTAGATGCATGACTT
54175 GTATCGGTAGAAAT-CAT-ACTT
1 GTATCGGTAG--ATGCATGACTT
54196 GTATCGGTAGA
1 GTATCGGTAGA
54207 GCTAGCACAA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.02
21 42 0.88
22 3 0.06
23 2 0.04
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.34
Consensus pattern (21 bp):
GTATCGGTAGATGCATGACTT
Found at i:55877 original size:56 final size:56
Alignment explanation
Indices: 55685--56026 Score: 494
Period size: 56 Copynumber: 6.2 Consensus size: 56
55675 AAGGATATTT
* **
55685 TGTAAAGGTTATATACGTAAGGATATTATGAAAA--GATGTCCGAAAGGATAT-TT
1 TGTAAAGGTTATATCCGTAAGGATATTATGAAAAGGGATGTCCGAAAGGATATCAA
* **
55738 TGTAAAGGTTATATTCGTAAGGATATTATGAAAAGGGATGTCCGAAAGGATAT-TT
1 TGTAAAGGTTATATCCGTAAGGATATTATGAAAAGGGATGTCCGAAAGGATATCAA
* * *
55793 TGTAAAGGTTACATCCGTAAGGATATTATGGAAAGGGATTTCCGAAAGGATATCAA
1 TGTAAAGGTTATATCCGTAAGGATATTATGAAAAGGGATGTCCGAAAGGATATCAA
55849 TGTAAAGGTTATATCCGTAAGGATATTATGAAAAGGGATGTCCGAAAGGATATCAA
1 TGTAAAGGTTATATCCGTAAGGATATTATGAAAAGGGATGTCCGAAAGGATATCAA
* * *
55905 TGTAAAGGTTATATCCATAAGGATATTATGAAAAGGGGTGTCCGAAAGGATATCAG
1 TGTAAAGGTTATATCCGTAAGGATATTATGAAAAGGGATGTCCGAAAGGATATCAA
* * * **
55961 TGTAAAGGTTATATGCGTAAGGATATTATCAAAAGGGATATTTGAAAGGATATCAA
1 TGTAAAGGTTATATCCGTAAGGATATTATGAAAAGGGATGTCCGAAAGGATATCAA
*
56017 CGTAAAGGTT
1 TGTAAAGGTT
56027 TAAAAATATT
Statistics
Matches: 264, Mismatches: 22, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
53 33 0.12
55 68 0.26
56 163 0.62
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.29
Consensus pattern (56 bp):
TGTAAAGGTTATATCCGTAAGGATATTATGAAAAGGGATGTCCGAAAGGATATCAA
Found at i:56545 original size:25 final size:25
Alignment explanation
Indices: 56511--56561 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
56501 ATAGTTTCGA
56511 TAGAAGTGCAGGGGAGGCTAAACTT
1 TAGAAGTGCAGGGGAGGCTAAACTT
56536 TAGAAGTGCAGGGGAGGCTAAACTT
1 TAGAAGTGCAGGGGAGGCTAAACTT
56561 T
1 T
56562 GGCTACTGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.35, T:0.22
Consensus pattern (25 bp):
TAGAAGTGCAGGGGAGGCTAAACTT
Found at i:64832 original size:10 final size:9
Alignment explanation
Indices: 64818--64882 Score: 51
Period size: 10 Copynumber: 6.7 Consensus size: 9
64808 TTTTCATGCA
64818 TTTTATAAT
1 TTTTATAAT
64827 TATTTATAAT
1 T-TTTATAAT
64837 TTTTATAAAATAT
1 TTTTAT---A-AT
*
64850 TTTTCTAAT
1 TTTTATAAT
*
64859 TTTTAATAAA
1 TTTT-ATAAT
64869 TTTTAT-AT
1 TTTTATAAT
64877 TTTTAT
1 TTTTAT
64883 TAAAATTTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
8 7 0.15
9 14 0.30
10 17 0.37
12 1 0.02
13 7 0.15
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (9 bp):
TTTTATAAT
Found at i:64878 original size:18 final size:18
Alignment explanation
Indices: 64857--64913 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 18
64847 TATTTTTCTA
64857 ATTTTTAATAAATTTTAT
1 ATTTTTAATAAATTTTAT
*
64875 ATTTTTATTAAAATTTAATAT
1 ATTTTTAAT-AAATTT--TAT
* *
64896 TTTTTTTATAAATTTTAT
1 ATTTTTAATAAATTTTAT
64914 TGTTTTTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
18 11 0.34
19 6 0.19
20 6 0.19
21 9 0.28
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTTTAATAAATTTTAT
Found at i:64921 original size:19 final size:18
Alignment explanation
Indices: 64858--64923 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 18
64848 ATTTTTCTAA
*
64858 TTTTTAATAAATTTTATAT
1 TTTTTTATAAATTTTAT-T
64877 TTTTATTA-AAATTTAATATT
1 TTTT-TTATAAATTT--TATT
64897 TTTTTTATAAATTTTATT
1 TTTTTTATAAATTTTATT
64915 GTTTTTTAT
1 -TTTTTTAT
64924 TTTTTATATT
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
18 4 0.10
19 21 0.51
20 13 0.32
21 3 0.07
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTTTTATAAATTTTATT
Found at i:67638 original size:47 final size:47
Alignment explanation
Indices: 67547--67643 Score: 115
Period size: 47 Copynumber: 2.1 Consensus size: 47
67537 CAATCAAAAT
* *
67547 AACCCTAAATCAAAAATGAAAATCCAAATCCAAATTAAAATCGAATA
1 AACCCTAAATCAAAAATCAAAATCCAAATCCAAATCAAAATCGAATA
* * * * *
67594 AACCCTAAATTAAAAATCACAAT-CAATATCGACATCAAATTCGAATA
1 AACCCTAAATCAAAAATCAAAATCCAA-ATCCAAATCAAAATCGAATA
67641 AAC
1 AAC
67644 ACGAAATAAC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
46 3 0.07
47 39 0.93
ACGTcount: A:0.55, C:0.21, G:0.04, T:0.21
Consensus pattern (47 bp):
AACCCTAAATCAAAAATCAAAATCCAAATCCAAATCAAAATCGAATA
Found at i:68258 original size:24 final size:25
Alignment explanation
Indices: 68231--68283 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
68221 ACCCTTAAAG
* * *
68231 TTATGGAAATTGAGACTAATAAT-T
1 TTATGGAAACTAAGACTAAAAATGT
68255 TTATGGAAACTAAGACTAAAAATGT
1 TTATGGAAACTAAGACTAAAAATGT
68280 TTAT
1 TTAT
68284 AATTATCAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.43, C:0.06, G:0.15, T:0.36
Consensus pattern (25 bp):
TTATGGAAACTAAGACTAAAAATGT
Found at i:69820 original size:9 final size:9
Alignment explanation
Indices: 69806--69988 Score: 63
Period size: 9 Copynumber: 20.0 Consensus size: 9
69796 TTTTAAATTG
69806 TTATGTATA
1 TTATGTATA
*
69815 TTATGTATG
1 TTATGTATA
*
69824 TTATGCATA
1 TTATGTATA
*
69833 TTATGTATG
1 TTATGTATA
* *
69842 CTATGTTTA
1 TTATGTATA
* * *
69851 CTGT-TATG
1 TTATGTATA
69859 TT-TGTATA
1 TTATGTATA
69867 TT-TGTAT-
1 TTATGTATA
* *
69874 GTATGTAATG
1 TTATGT-ATA
*
69884 TTATGTACTG
1 TTATGTA-TA
69894 TTATGTATA
1 TTATGTATA
69903 TTATG-A-A
1 TTATGTATA
* *
69910 TGTATGTTTG
1 T-TATGTATA
*
69920 TTATGTTACTG
1 TTATG-TA-TA
*
69931 TTATGTGTA
1 TTATGTATA
* *
69940 TGACTGTTTA
1 TTA-TGTATA
*
69950 TTTAATGTTTA
1 -TT-ATGTATA
69961 TGTATGTATA
1 T-TATGTATA
* *
69971 TTTTGTATG
1 TTATGTATA
69980 TTATGTATA
1 TTATGTATA
69989 ATATTGTTTA
Statistics
Matches: 131, Mismatches: 29, Indels: 28
0.70 0.15 0.15
Matches are distributed among these distances:
7 4 0.03
8 21 0.16
9 60 0.46
10 30 0.23
11 15 0.11
12 1 0.01
ACGTcount: A:0.24, C:0.03, G:0.18, T:0.55
Consensus pattern (9 bp):
TTATGTATA
Found at i:69876 original size:37 final size:37
Alignment explanation
Indices: 69807--69936 Score: 118
Period size: 36 Copynumber: 3.7 Consensus size: 37
69797 TTTAAATTGT
* *
69807 TATGT-ATATTATGTA-TGTTATGCATATTATGTATG
1 TATGTAATGTTATGTACTGTTATGTATATTATGTATG
69842 CTATG---T-TTACTGTTA-TGTT-TGTATATT-TGTATG
1 -TATGTAATGTTA-TG-TACTGTTATGTATATTATGTATG
*
69875 TATGTAATGTTATGTACTGTTATGTATATTATGAATG
1 TATGTAATGTTATGTACTGTTATGTATATTATGTATG
*
69912 TATGT-TTGTTATGTTACTGTTATGT
1 TATGTAATGTTATG-TACTGTTATGT
69937 GTATGACTGT
Statistics
Matches: 81, Mismatches: 3, Indels: 19
0.79 0.03 0.18
Matches are distributed among these distances:
32 4 0.05
33 9 0.11
34 12 0.15
35 13 0.16
36 22 0.27
37 21 0.26
ACGTcount: A:0.24, C:0.04, G:0.18, T:0.54
Consensus pattern (37 bp):
TATGTAATGTTATGTACTGTTATGTATATTATGTATG
Found at i:69921 original size:4 final size:5
Alignment explanation
Indices: 69804--69941 Score: 64
Period size: 5 Copynumber: 28.4 Consensus size: 5
69794 GTTTTTAAAT
* * * *
69804 TGTTA TG-TA TATTA TG-TA TGTTA TG-CA TATTA TG-TA TGCTA TGTTTA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TG-TTA
* *
69851 CTGTTA TGTT- TGTATA TTTGTA TG-TA TGTAA TGTTA TG-TA CTGTTA
1 -TGTTA TGTTA TGT-TA TGT-TA TGTTA TGTTA TGTTA TGTTA -TGTTA
* *
69897 TG-TA TATTA TG-AA TG-TA TGTT- TGTTA TGTTA CTGTTA TGTGTA TG
1 TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA TGTTA -TGTTA TGT-TA TG
69942 ACTGTTTATT
Statistics
Matches: 101, Mismatches: 16, Indels: 31
0.68 0.11 0.21
Matches are distributed among these distances:
4 35 0.35
5 43 0.43
6 21 0.21
7 2 0.02
ACGTcount: A:0.23, C:0.04, G:0.20, T:0.54
Consensus pattern (5 bp):
TGTTA
Found at i:75439 original size:23 final size:23
Alignment explanation
Indices: 75353--75450 Score: 76
Period size: 23 Copynumber: 4.2 Consensus size: 23
75343 ACTTTAGCGC
*
75353 GCTCTCTGTTTAGCACTAT-GTGT
1 GCTCTCTGATTAGCACT-TCGTGT
* * *
75376 GCTCTC-CATTTAGCACGTC-TCAT
1 GCTCTCTGA-TTAGCACTTCGT-GT
*
75399 GCTCTCCGTTATTAGCACTTCGTGT
1 GCTCT-C-TGATTAGCACTTCGTGT
*
75424 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTCGTGT
75447 GCTC
1 GCTC
75451 AGTACTTTGT
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
22 2 0.03
23 38 0.64
24 2 0.03
25 15 0.25
26 2 0.03
ACGTcount: A:0.13, C:0.28, G:0.19, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTTCGTGT
Found at i:75479 original size:39 final size:39
Alignment explanation
Indices: 75415--75489 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
75405 CGTTATTAGC
* *
75415 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTGTGTGTGCTCAGT
* *
75454 ACTTTGTGTACTCTCTGGTTAGCACTGTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTGTGTGTGCTC
75490 TCTATTTAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.12, C:0.23, G:0.24, T:0.41
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTGTGTGTGCTCAGT
Found at i:76277 original size:21 final size:21
Alignment explanation
Indices: 76253--76300 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
76243 GAAAATTATT
76253 GATACCATTTGAGATGGTATC
1 GATACCATTTGAGATGGTATC
76274 GATACCATTTGAGATGGTATC
1 GATACCATTTGAGATGGTATC
76295 GATACC
1 GATACC
76301 CAATCGACAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (21 bp):
GATACCATTTGAGATGGTATC
Found at i:78001 original size:21 final size:20
Alignment explanation
Indices: 77971--78012 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
77961 TTTAATGTAT
77971 TAATAATAATTAAATATTAA
1 TAATAATAATTAAATATTAA
**
77991 TAATAAATAATTTTATATTAA
1 TAAT-AATAATTAAATATTAA
78012 T
1 T
78013 TATTAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TAATAATAATTAAATATTAA
Found at i:79779 original size:31 final size:31
Alignment explanation
Indices: 79741--79843 Score: 111
Period size: 30 Copynumber: 3.4 Consensus size: 31
79731 TTTTTTTTGA
79741 CCTAATTTGGTATTTGAACTTGACACTTTTT
1 CCTAATTTGGTATTTGAACTTGACACTTTTT
* * *** ***
79772 CCTAATTTGGTACTTAAACTT-TTTCTTGAA
1 CCTAATTTGGTATTTGAACTTGACACTTTTT
*
79802 CCTAATTTGGTATCTGAACTTGACA-TTTTT
1 CCTAATTTGGTATTTGAACTTGACACTTTTT
79832 CCTAATTTGGTA
1 CCTAATTTGGTA
79844 CCTAAGCTTT
Statistics
Matches: 54, Mismatches: 17, Indels: 3
0.73 0.23 0.04
Matches are distributed among these distances:
30 35 0.65
31 19 0.35
ACGTcount: A:0.24, C:0.17, G:0.13, T:0.47
Consensus pattern (31 bp):
CCTAATTTGGTATTTGAACTTGACACTTTTT
Found at i:79822 original size:30 final size:29
Alignment explanation
Indices: 79716--79822 Score: 76
Period size: 31 Copynumber: 3.7 Consensus size: 29
79706 ACATTTTTTT
* *
79716 TAATTTGGTATC-CAA-TTTTTTTTGACC
1 TAATTTGGTATCTGAACTTTTTCTTGACC
* *** **
79743 TAATTTGGTATTTGAACTTGACACTTTTTCC
1 TAATTTGGTATCTGAACTT-TTTC-TTGACC
*
79774 TAATTTGGTA-CTTAAACTTTTTCTTGAACC
1 TAATTTGGTATC-TGAACTTTTTCTTG-ACC
79804 TAATTTGGTATCTGAACTT
1 TAATTTGGTATCTGAACTT
79823 GACATTTTTC
Statistics
Matches: 57, Mismatches: 16, Indels: 11
0.68 0.19 0.13
Matches are distributed among these distances:
27 11 0.19
28 2 0.04
29 4 0.07
30 19 0.33
31 21 0.37
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.49
Consensus pattern (29 bp):
TAATTTGGTATCTGAACTTTTTCTTGACC
Found at i:79856 original size:61 final size:58
Alignment explanation
Indices: 79688--79858 Score: 220
Period size: 60 Copynumber: 2.9 Consensus size: 58
79678 TTAATATAAC
* **
79688 ATTTGGTATATGAATTTGACATTTTTTTTAATTTGGTATCC-AA-TTTTTTTTGACCTA
1 ATTTGGTATATGAACTTGACATTTTTCCTAATTTGGTA-CCTAACTTTTTTTTGACCTA
* * *
79745 ATTTGGTATTTGAACTTGACACTTTTTCCTAATTTGGTACTTAAACTTTTTCTTGAACCTA
1 ATTTGGTATATGAACTTGACA-TTTTTCCTAATTTGGTACCT-AACTTTTTTTTG-ACCTA
*
79806 ATTTGGTATCTGAACTTGACATTTTTCCTAATTTGGTACCTAAGCTTTTTTTT
1 ATTTGGTATATGAACTTGACATTTTTCCTAATTTGGTACCTAA-CTTTTTTTT
79859 TTAGATTCAA
Statistics
Matches: 99, Mismatches: 9, Indels: 9
0.85 0.08 0.08
Matches are distributed among these distances:
57 20 0.20
58 15 0.15
59 4 0.04
60 35 0.35
61 25 0.25
ACGTcount: A:0.23, C:0.13, G:0.12, T:0.51
Consensus pattern (58 bp):
ATTTGGTATATGAACTTGACATTTTTCCTAATTTGGTACCTAACTTTTTTTTGACCTA
Found at i:87926 original size:134 final size:132
Alignment explanation
Indices: 87677--87944 Score: 317
Period size: 134 Copynumber: 2.0 Consensus size: 132
87667 TTTGAGTGCG
**
87677 TTGAAGCACATATTCTTTTATTTTAAGGTTGAAGACGGGTTATGAATAATTTTAAATATTATATA
1 TTGAAGCACATATTCTTTTATTTTAAGGTTGAAGACGAATTATGAATAATTTTAAATATTATATA
* * *
87742 AAAATAACATATATGATAAGAATTTCATATATACAAAATAAAAAAAAAATTGGA-AGTTGGGTGT
66 AAAAGAACAGATATGATAAGAATTTCATATATACAAAAT--AAAAAAAATT-GATAGTTGGGTGC
87806 AATAA
128 AATAA
* ** * * *
87811 TTGAAGCGCATATT-TTTTATTTTAAGGTTGAAGACGAATTATGGGTAGTTTTAGATATTGTATT
1 TTGAAGCACATATTCTTTTATTTTAAGGTTGAAGACGAATTATGAATAATTTTAAATATTATA-T
** * *
87875 AAAAAGAGTAGATATGATAAGAATTTTATTATATATTCAAAAT-AAAAAAATTGATTGTTGGGTG
65 AAAAAGAACAGATATGATAAGAATTTCA-TATATA--CAAAATAAAAAAAATTGATAGTTGGGTG
87939 CAATAA
127 CAATAA
87945 CTGACTTGTG
Statistics
Matches: 114, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
133 43 0.38
134 59 0.52
135 6 0.05
137 6 0.05
ACGTcount: A:0.42, C:0.04, G:0.16, T:0.37
Consensus pattern (132 bp):
TTGAAGCACATATTCTTTTATTTTAAGGTTGAAGACGAATTATGAATAATTTTAAATATTATATA
AAAAGAACAGATATGATAAGAATTTCATATATACAAAATAAAAAAAATTGATAGTTGGGTGCAAT
AA
Found at i:88149 original size:17 final size:16
Alignment explanation
Indices: 88116--88149 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
88106 AAATATGTAG
88116 TTTAATATATTTATTT
1 TTTAATATATTTATTT
88132 TTTAATA-ATATTATTT
1 TTTAATATAT-TTATTT
88148 TT
1 TT
88150 ATTTTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 15 0.88
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTAATATATTTATTT
Found at i:88160 original size:21 final size:19
Alignment explanation
Indices: 88118--88156 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
88108 ATATGTAGTT
88118 TAATATATTTATTTTTTAA
1 TAATATATTTATTTTTTAA
88137 TAATATTATTT-TTATTTTAA
1 TAATA-TATTTATT-TTTTAA
88157 ATAAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TAATATATTTATTTTTTAA
Found at i:112624 original size:18 final size:18
Alignment explanation
Indices: 112589--112627 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
112579 TTAATGGATT
112589 TTTATATTTTGTATTTTA
1 TTTATATTTTGTATTTTA
*
112607 TTTATTATTTTTTA-TTTA
1 TTTA-TATTTTGTATTTTA
112625 TTT
1 TTT
112628 TTGGGTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (18 bp):
TTTATATTTTGTATTTTA
Found at i:114505 original size:62 final size:62
Alignment explanation
Indices: 114408--114532 Score: 250
Period size: 62 Copynumber: 2.0 Consensus size: 62
114398 AGCATTGAAT
114408 GTAGTCCAAAGGCATCCCTCCCCAGTAGCTGCTTCTCGATGGACACCCCCTCCACCAACTTA
1 GTAGTCCAAAGGCATCCCTCCCCAGTAGCTGCTTCTCGATGGACACCCCCTCCACCAACTTA
114470 GTAGTCCAAAGGCATCCCTCCCCAGTAGCTGCTTCTCGATGGACACCCCCTCCACCAACTTA
1 GTAGTCCAAAGGCATCCCTCCCCAGTAGCTGCTTCTCGATGGACACCCCCTCCACCAACTTA
114532 G
1 G
114533 GTCAATATAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.22, C:0.40, G:0.17, T:0.21
Consensus pattern (62 bp):
GTAGTCCAAAGGCATCCCTCCCCAGTAGCTGCTTCTCGATGGACACCCCCTCCACCAACTTA
Found at i:116464 original size:5 final size:5
Alignment explanation
Indices: 116454--116510 Score: 60
Period size: 5 Copynumber: 11.4 Consensus size: 5
116444 GTAGGACATT
*** * * *
116454 ATATG ATATG ATCCA ATATG ACATG ATATG ATCTG ATATG TTATG ATATG
1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG
116504 ATATG AT
1 ATATG AT
116511 CCGATACATT
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
5 40 1.00
ACGTcount: A:0.37, C:0.07, G:0.18, T:0.39
Consensus pattern (5 bp):
ATATG
Found at i:116522 original size:25 final size:25
Alignment explanation
Indices: 116470--116526 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
116460 TATGATCCAA
* * **
116470 TATGACATGATATGATCTGATATGT
1 TATGATATGATATGATCCGATACAT
116495 TATGATATGATATGATCCGATACAT
1 TATGATATGATATGATCCGATACAT
116520 TATGATA
1 TATGATA
116527 AGTTATGTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.39
Consensus pattern (25 bp):
TATGATATGATATGATCCGATACAT
Found at i:116533 original size:25 final size:25
Alignment explanation
Indices: 116478--116533 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
116468 AATATGACAT
* ** *
116478 GATATGATCTGATATGTTATGATAT
1 GATATGATCCGATACATTATGATAA
116503 GATATGATCCGATACATTATGATAA
1 GATATGATCCGATACATTATGATAA
*
116528 GTTATG
1 GATATG
116534 TTCTGGTATA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (25 bp):
GATATGATCCGATACATTATGATAA
Found at i:121742 original size:23 final size:22
Alignment explanation
Indices: 121706--121749 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
121696 TAAATATTTC
*
121706 ATTAAATAATTTGGGTTGAATTA
1 ATTAAATAAATTGGGTT-AATTA
*
121729 ATTAATTAAATTGGGTTAATT
1 ATTAAATAAATTGGGTTAATT
121750 TTATTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (22 bp):
ATTAAATAAATTGGGTTAATTA
Found at i:136845 original size:39 final size:40
Alignment explanation
Indices: 136802--136941 Score: 129
Period size: 40 Copynumber: 3.5 Consensus size: 40
136792 GAAAACGCCT
* * * *
136802 CAAAATGTAAAGCAATGGTGGCGTTTTTT-ATAAACCCCG
1 CAAAAGGTAAAGCAATAGCGGCGTTTTTTCATAAACCCCA
* * * **
136841 CAAAAGGTAAAACAATAGCGTCATTTTTTCATAAACGTCA
1 CAAAAGGTAAAGCAATAGCGGCGTTTTTTCATAAACCCCA
** ** *
136881 CAAAAGGTAAAGCAATAGCGGCGTTTTCCCATAAATGCCG
1 CAAAAGGTAAAGCAATAGCGGCGTTTTTTCATAAACCCCA
*
136921 CAAAAGGTAAGAGCATTAGCG
1 CAAAAGGTAA-AGCAATAGCG
136942 ATGTTTATAA
Statistics
Matches: 81, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
39 23 0.28
40 49 0.60
41 9 0.11
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.24
Consensus pattern (40 bp):
CAAAAGGTAAAGCAATAGCGGCGTTTTTTCATAAACCCCA
Found at i:136914 original size:40 final size:39
Alignment explanation
Indices: 136841--137000 Score: 113
Period size: 40 Copynumber: 4.0 Consensus size: 39
136831 ATAAACCCCG
* * **
136841 CAAAAGGTAAAACAATAGCGTCATTTTTTCATAAACGTCA
1 CAAAAGGTAAAGCAATAGCGGCATTTTCCCATAAACG-CA
* * *
136881 CAAAAGGTAAAGCAATAGCGGCGTTTTCCCATAAATGCCG
1 CAAAAGGTAAAGCAATAGCGGCATTTTCCCATAAACG-CA
* *** *** *
136921 CAAAAGGTAAGAGCATTAGCGATGTTTATAAGAAAAACGCTA
1 CAAAAGGTAA-AGCAATAGCGGCATTT-TCCCATAAACGC-A
* * *
136963 CTAAAGATTAAGCAATAGCGGCATTTTCCCATAAACGC
1 CAAAAGGTAAAGCAATAGCGGCATTTTCCCATAAACGC
137001 CGCGAATTTA
Statistics
Matches: 89, Mismatches: 28, Indels: 6
0.72 0.23 0.05
Matches are distributed among these distances:
40 50 0.56
41 26 0.29
42 13 0.15
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (39 bp):
CAAAAGGTAAAGCAATAGCGGCATTTTCCCATAAACGCA
Found at i:137983 original size:23 final size:23
Alignment explanation
Indices: 137957--138000 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
137947 AATTTAGCTA
137957 TCAATGTTCAC-ATTTTTTTTTGG
1 TCAAT-TTCACTATTTTTTTTTGG
*
137980 TCAATTTGACTATTTTTTTTT
1 TCAATTTCACTATTTTTTTTT
138001 AACTAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.61
Consensus pattern (23 bp):
TCAATTTCACTATTTTTTTTTGG
Found at i:143399 original size:43 final size:43
Alignment explanation
Indices: 143255--143415 Score: 193
Period size: 43 Copynumber: 3.8 Consensus size: 43
143245 CTGTTAATGT
* * *
143255 TAGCGGCGTTTGTGGAAAAAAG-GCCACTAAAGAACATGTTCTA
1 TAGCGGCGTTTGTGG-GAAAAGCACCGCTAAAGAACATGTTCTA
** *
143298 TAGCGGCGTTTGTGGGAAAAATACCGCTAAAGATCATGTTCTA
1 TAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGAACATGTTCTA
* * * *
143341 TAACGACATTTGTGGGAAAAGCA-CGACTAAAGACCATGTTCTA
1 TAGCGGCGTTTGTGGGAAAAGCACCG-CTAAAGAACATGTTCTA
143384 TAGCGGCGTTTGTGGG-AAAGCACCGCTAAAGA
1 TAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGA
143416 TGGTAGTAAA
Statistics
Matches: 101, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
42 19 0.19
43 82 0.81
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGAACATGTTCTA
Found at i:143689 original size:10 final size:10
Alignment explanation
Indices: 143661--143701 Score: 50
Period size: 9 Copynumber: 4.3 Consensus size: 10
143651 AAATTGTTAT
*
143661 TTTCTTATT-
1 TTTCTTTTTA
*
143670 TTTGTTTTTA
1 TTTCTTTTTA
143680 TTTCTTTTTA
1 TTTCTTTTTA
143690 TTTC-TTTTA
1 TTTCTTTTTA
143699 TTT
1 TTT
143702 TATAAGTTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
9 15 0.54
10 13 0.46
ACGTcount: A:0.10, C:0.07, G:0.02, T:0.80
Consensus pattern (10 bp):
TTTCTTTTTA
Done.