Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013885.1 Kokia drynarioides strain JFW-HI SEQ_128913, 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: 75717
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Warning! 71 characters in sequence are not A, C, G, or T
Found at i:8488 original size:160 final size:162
Alignment explanation
Indices: 8195--8538 Score: 469
Period size: 160 Copynumber: 2.1 Consensus size: 162
8185 CCAAATTCGT
* * *
8195 CTTTCTGATAAGATACAGAGAAGCAGTTTGAAACAAATGACGCGGTCATCTTTCTGATGAGATAC
1 CTTTCTGATAAGATACAGAGAAGCAGATTGAAACAAATGACGCGATCATATTTCTGATGAG----
*
8260 TAAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGAAAATCTTCGAATCCCAGCTTCTAGAT
62 --AGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGAAAATCTTCGAACCCCAGCTTCTAGAT
* **
8325 GAGACACCGAGAAGCAGATCGAAGCAATAAATGGTTAA
125 GAGACACCAAGAAGCAGATCGAAGCAATAAACAGTTAA
* *
8363 CTTTCTGATGAGATACAGAGAAGCGGATTGAAACAAATGACGCGATCATATTTCTGATG-G-GAA
1 CTTTCTGATAAGATACAGAGAAGCAGATTGAAACAAATGACGCGATCATATTTCTGATGAGAGAA
* * *
8426 GAGGACCAAATCAAACCCACGCTGGATGTGAGCAAATCTTCGAACCCCAGCTTCCT-GATGAGAC
66 GAAGACCAAATCAAACCCACGCTCGATGTGAGAAAATCTTCGAACCCCAGCTT-CTAGATGAGAC
* *
8490 ACCAAGAAGCAGGTCGAAGCAATAAACAGTTAG
130 ACCAAGAAGCAGATCGAAGCAATAAACAGTTAA
*
8523 CTTCCTGATAAGATAC
1 CTTTCTGATAAGATAC
8539 TAAGAAGTGA
Statistics
Matches: 159, Mismatches: 16, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
160 102 0.64
161 2 0.01
167 1 0.01
168 54 0.34
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.21
Consensus pattern (162 bp):
CTTTCTGATAAGATACAGAGAAGCAGATTGAAACAAATGACGCGATCATATTTCTGATGAGAGAA
GAAGACCAAATCAAACCCACGCTCGATGTGAGAAAATCTTCGAACCCCAGCTTCTAGATGAGACA
CCAAGAAGCAGATCGAAGCAATAAACAGTTAA
Found at i:8707 original size:205 final size:204
Alignment explanation
Indices: 8363--8835 Score: 690
Period size: 205 Copynumber: 2.3 Consensus size: 204
8353 AAATGGTTAA
* * *
8363 CTTTCTGATGAGATACAGAGAAGCGGATTGAAACAAATGACGCGATCATATTTCTGAT--G----
1 CTTTCTGATGAGATACAGAGAAGCAGATTGAAACAAATGACGCGATCATCTTCCTGATGAGATAT
* * * *
8422 G-GAAGAGGACCAAATCAAACCCACGCTGGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATG
66 GAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATATTCGAACCCCAACTTCCTGATG
8486 AGACACCAAGAAGCAGGTCGAAGCAATAAACAGTTAGCTTCCTGATAAGATACTAAGAAGTGAAC
131 AGACACCAAGAAGCAGGTCGAAGCAATAAACAGTTAGCTTCCTGATAAGATACTAAGAAGTGAAC
8551 CAAATTCGT
196 CAAATTCGT
* *
8560 CTTTCTGATGAGATACAGAGAAGCAGATTGAAACAAATGATGCAATCATCTTCCTGATGAGATAT
1 CTTTCTGATGAGATACAGAGAAGCAGATTGAAACAAATGACGCGATCATCTTCCTGATGAGATA-
* *
8625 TGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATATTCGAATCCTAACTTCCTGAT
65 TGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATATTCGAACCCCAACTTCCTGAT
** * * * *
8690 GAGACGTCGAGAAGCAGGTCGAAGCAATAAACGGTTAGCTTCCTGATGAGATACTGAGAAGTGAA
130 GAGACACCAAGAAGCAGGTCGAAGCAATAAACAGTTAGCTTCCTGATAAGATACTAAGAAGTGAA
*
8755 CCAAATTCTT
195 CCAAATTCGT
* * *
8765 CTTCCTGATGAGATACAGAGAAGAAGATTGAAACAAATGGCGCGATCATCTTCCTGATGAGATAC
1 CTTTCTGATGAGATACAGAGAAGCAGATTGAAACAAATGACGCGATCATCTTCCTGATGAGATA-
8830 TGAGAA
65 TGAGAA
8836 TTGAACCAAA
Statistics
Matches: 244, Mismatches: 24, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
197 53 0.22
199 1 0.00
204 1 0.00
205 189 0.77
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (204 bp):
CTTTCTGATGAGATACAGAGAAGCAGATTGAAACAAATGACGCGATCATCTTCCTGATGAGATAT
GAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATATTCGAACCCCAACTTCCTGATG
AGACACCAAGAAGCAGGTCGAAGCAATAAACAGTTAGCTTCCTGATAAGATACTAAGAAGTGAAC
CAAATTCGT
Found at i:8778 original size:37 final size:37
Alignment explanation
Indices: 8728--8873 Score: 130
Period size: 37 Copynumber: 3.6 Consensus size: 37
8718 AAACGGTTAG
* *
8728 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCTT
1 CTTCCTGATGAGATACAGAGAAGTGAACCAAATTCAT
*
8765 CTTCCTGATGAGATACAGAGAAGAAGATTGAAACAAATGGCGCGATCAT
1 CTTCCTGATGAGATAC--AG-AGAAG--TGAACCAAAT-------TCAT
* * *
8814 CTTCCTGATGAGATACTGAGAATTGAACCAAATTCGT
1 CTTCCTGATGAGATACAGAGAAGTGAACCAAATTCAT
8851 CTTCCTGATGAGATACAGAGAAG
1 CTTCCTGATGAGATACAGAGAAG
8874 CAGATTGAAA
Statistics
Matches: 88, Mismatches: 9, Indels: 24
0.73 0.07 0.20
Matches are distributed among these distances:
37 40 0.45
39 1 0.01
40 5 0.06
42 9 0.10
44 9 0.10
46 4 0.05
47 1 0.01
49 19 0.22
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (37 bp):
CTTCCTGATGAGATACAGAGAAGTGAACCAAATTCAT
Found at i:8832 original size:86 final size:86
Alignment explanation
Indices: 8728--8922 Score: 327
Period size: 86 Copynumber: 2.3 Consensus size: 86
8718 AAACGGTTAG
*
8728 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCTTCTTCCTGATGAGATACAGAGAAGAAGAT
1 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGAAGAT
*
8793 TGAAACAAATGGCGCGATCAT
66 TGAAACAAATGACGCGATCAT
* *
8814 CTTCCTGATGAGATACTGAGAATTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGAT
1 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGAAGAT
* *
8879 TGAAATAAATGACGCGGTCAT
66 TGAAACAAATGACGCGATCAT
*
8900 CTTCCTGATAAGATACTGAGAAG
1 CTTCCTGATGAGATACTGAGAAG
8923 AAGACCAAAT
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
86 101 1.00
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.25
Consensus pattern (86 bp):
CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGAAGAT
TGAAACAAATGACGCGATCAT
Found at i:9462 original size:6 final size:6
Alignment explanation
Indices: 9451--9538 Score: 53
Period size: 6 Copynumber: 15.2 Consensus size: 6
9441 TGGGCCCAAC
* * * * *
9451 AAATTT AAATTT -ATTTT AAAATT AAGTTT -ATTTT AAATTC AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
*
9497 --ATTT GAAATTT AAGTTT --ATTAT AAATTT AAATTT AAAATTT A
1 AAATTT -AAATTT AAATTT AAATT-T AAATTT AAATTT -AAATTT A
9539 TTTATAATGT
Statistics
Matches: 62, Mismatches: 11, Indels: 18
0.68 0.12 0.20
Matches are distributed among these distances:
4 6 0.10
5 9 0.15
6 34 0.55
7 13 0.21
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (6 bp):
AAATTT
Found at i:9489 original size:34 final size:34
Alignment explanation
Indices: 9451--9531 Score: 126
Period size: 34 Copynumber: 2.4 Consensus size: 34
9441 TGGGCCCAAC
* *
9451 AAATTTAAATTTATTTTAAAATTAAGTTTATTTT
1 AAATTTAAATTTATTTGAAAATTAAGTTTATTAT
* *
9485 AAATTCAAATTTATTTGAAATTTAAGTTTATTAT
1 AAATTTAAATTTATTTGAAAATTAAGTTTATTAT
9519 AAATTTAAATTTA
1 AAATTTAAATTTA
9532 AAATTTATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (34 bp):
AAATTTAAATTTATTTGAAAATTAAGTTTATTAT
Found at i:9538 original size:24 final size:25
Alignment explanation
Indices: 9497--9545 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
9487 ATTCAAATTT
*
9497 ATTTGAAATTTAAGTTTA-TTATAA
1 ATTTGAAATTTAAATTTATTTATAA
9521 ATTT-AAATTTAAAATTTATTTATAA
1 ATTTGAAATTT-AAATTTATTTATAA
9546 TGTCCAAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 6 0.27
24 10 0.45
25 6 0.27
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (25 bp):
ATTTGAAATTTAAATTTATTTATAA
Found at i:9542 original size:17 final size:17
Alignment explanation
Indices: 9451--9531 Score: 108
Period size: 17 Copynumber: 4.8 Consensus size: 17
9441 TGGGCCCAAC
9451 AAATTTAAATTTATTTT
1 AAATTTAAATTTATTTT
* *
9468 AAAATTAAGTTTATTTT
1 AAATTTAAATTTATTTT
* *
9485 AAATTCAAATTTATTTG
1 AAATTTAAATTTATTTT
* *
9502 AAATTTAAGTTTATTAT
1 AAATTTAAATTTATTTT
9519 AAATTTAAATTTA
1 AAATTTAAATTTA
9532 AAATTTATTT
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 53 1.00
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (17 bp):
AAATTTAAATTTATTTT
Found at i:11325 original size:29 final size:29
Alignment explanation
Indices: 11293--11802 Score: 348
Period size: 30 Copynumber: 17.3 Consensus size: 29
11283 AAAAACTCTG
11293 TTTTTACCCCGAACTTCCAAAAATTCCAT
1 TTTTTACCCCGAACTTCCAAAAATTCCAT
* * *
11322 TTTTAACCTCGAAACTTCCAAAAATTCTA-
1 TTTTTACCCCG-AACTTCCAAAAATTCCAT
* *
11351 TTTTTACCCTCGAACTTGCAAAAATCCCAT
1 TTTTTACCC-CGAACTTCCAAAAATTCCAT
* *
11381 TTTTAACCCCTAAACTTCCAAAAATTCCA-
1 TTTTTACCCC-GAACTTCCAAAAATTCCAT
*
11410 -TTTTACCCCCGAACTTCCAAAAATCCCAT
1 TTTTTA-CCCCGAACTTCCAAAAATTCCAT
* * * *
11439 TTTTGACCTCGAAACTTCCAAAATTTACA-
1 TTTTTACCCCG-AACTTCCAAAAATTCCAT
*
11468 TTTTTACCCTCGAACTTCCAAAAATCCCAT
1 TTTTTACCC-CGAACTTCCAAAAATTCCAT
** * * *
11498 TTTTGGCCTCGAAACTACTAAAAATTCCA-
1 TTTTTACCCCG-AACTTCCAAAAATTCCAT
* *
11527 TTTTTACCCCCAAACTTCCAAAAATCCCAT
1 TTTTTA-CCCCGAACTTCCAAAAATTCCAT
*
11557 TTTTAACCCCGAACTTCCAAAAA-TCTCAT
1 TTTTTACCCCGAACTTCCAAAAATTC-CAT
* *
11586 TTTTGACCTCGAAACTTCC-AAAATCTCCA-
1 TTTTTACCCCG-AACTTCCAAAAAT-TCCAT
* * * *
11615 TTTTTGCCTCCAAAATTTCC-AAAATT-TAT
1 TTTTTACC-CC-GAACTTCCAAAAATTCCAT
*
11644 ATTTTTACGCCCGAACTTCCAAAAA-TCTTAT
1 -TTTTTAC-CCCGAACTTCCAAAAATTC-CAT
** * *
11675 TTTCGACCCCAAAACTTCCAAAATTTCCA-
1 TTTTTACCCC-GAACTTCCAAAAATTCCAT
* * *
11704 TTTTTACCCCCAAACTTTCAAAAAATCCCA-
1 TTTTTA-CCCCGAAC-TTCCAAAAATTCCAT
* ** * *
11734 TTTTAACCCTAAAACTCCCAAACATTCCA-
1 TTTTTACCC-CGAACTTCCAAAAATTCCAT
*
11763 TTTTTACCCCCGAACTTCTAAAAA-TCTCAT
1 TTTTTA-CCCCGAACTTCCAAAAATTC-CAT
11793 TTTTTACCCC
1 TTTTTACCCC
11803 AAAATCTCCA
Statistics
Matches: 374, Mismatches: 74, Indels: 66
0.73 0.14 0.13
Matches are distributed among these distances:
28 24 0.06
29 170 0.45
30 172 0.46
31 8 0.02
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (29 bp):
TTTTTACCCCGAACTTCCAAAAATTCCAT
Found at i:11340 original size:30 final size:30
Alignment explanation
Indices: 11274--11802 Score: 423
Period size: 29 Copynumber: 18.0 Consensus size: 30
11264 AAAGGTCCCT
* **
11274 AAACTGTCCAAAAACTCTGTTTTT-ACCCCG
1 AAACT-TCCAAAAATTCCATTTTTAACCCCG
*
11304 -AACTTCCAAAAATTCCATTTTTAACCTCG
1 AAACTTCCAAAAATTCCATTTTTAACCCCG
*
11333 AAACTTCCAAAAATTCTATTTTT-ACCCTCG
1 AAACTTCCAAAAATTCCATTTTTAACCC-CG
* * *
11363 -AACTTGCAAAAATCCCATTTTTAACCCCT
1 AAACTTCCAAAAATTCCATTTTTAACCCCG
*
11392 AAACTTCCAAAAATTCCA-TTTTACCCCCG
1 AAACTTCCAAAAATTCCATTTTTAACCCCG
* * *
11421 -AACTTCCAAAAATCCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTTAACCCCG
* *
11450 AAACTTCCAAAATTTACATTTTT-ACCCTCG
1 AAACTTCCAAAAATTCCATTTTTAACCC-CG
* ** *
11480 -AACTTCCAAAAATCCCATTTTTGGCCTCG
1 AAACTTCCAAAAATTCCATTTTTAACCCCG
* * *
11509 AAACTACTAAAAATTCCATTTTT-ACCCCC
1 AAACTTCCAAAAATTCCATTTTTAACCCCG
*
11538 AAACTTCCAAAAATCCCATTTTTAACCCCG
1 AAACTTCCAAAAATTCCATTTTTAACCCCG
* *
11568 -AACTTCCAAAAA-TCTCATTTTTGACCTCG
1 AAACTTCCAAAAATTC-CATTTTTAACCCCG
* *
11597 AAACTTCC-AAAATCTCCATTTTT-GCCTCCA
1 AAACTTCCAAAAAT-TCCATTTTTAACC-CCG
* * **
11627 AAATTTCCAAAATTTATATTTTT-ACGCCCG
1 AAACTTCCAAAAATTCCATTTTTAAC-CCCG
* ** *
11657 -AACTTCCAAAAA-TCTTATTTTCGACCCCA
1 AAACTTCCAAAAATTC-CATTTTTAACCCCG
* *
11686 AAACTTCCAAAATTTCCATTTTT-ACCCCC
1 AAACTTCCAAAAATTCCATTTTTAACCCCG
* * **
11715 AAACTTTCAAAAAATCCCA-TTTTAACCCTA
1 AAAC-TTCCAAAAATTCCATTTTTAACCCCG
* * *
11745 AAACTCCCAAACATTCCATTTTTACCCCCG
1 AAACTTCCAAAAATTCCATTTTTAACCCCG
* *
11775 -AACTTCTAAAAA-TCTCATTTTTTACCCC
1 AAACTTCCAAAAATTC-CATTTTTAACCCC
11803 AAAATCTCCA
Statistics
Matches: 398, Mismatches: 75, Indels: 53
0.76 0.14 0.10
Matches are distributed among these distances:
28 35 0.09
29 188 0.47
30 166 0.42
31 9 0.02
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (30 bp):
AAACTTCCAAAAATTCCATTTTTAACCCCG
Found at i:11373 original size:59 final size:59
Alignment explanation
Indices: 11274--11796 Score: 542
Period size: 59 Copynumber: 8.9 Consensus size: 59
11264 AAAGGTCCCT
* ** *
11274 AAACTGTCCAAAAACTCTGTTTTTA-CCCCGAACTTCCAAAAATTCCATTTTTAACCTCG
1 AAACT-TCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCG
* * * * *
11333 AAACTTCCAAAAATTCTATTTTTACCCTCGAACTTGCAAAAATCCCATTTTTAACCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCG
*
11392 AAACTTCCAAAAATTCCA-TTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCG
* * * **
11450 AAACTTCCAAAATTTACATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGGCCTCG
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCG
* * * *
11509 AAACTACTAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTTAACCCCG
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCG
* * *
11568 -AACTTCCAAAAA-TCTCATTTTTGA-CCTCGAAACTTCC-AAAATCTCCATTTTT-GCCTCCA
1 AAACTTCCAAAAATTC-CATTTTT-ACCCCCG-AACTTCCAAAAATC-CCATTTTTAACCT-CG
* * ** * ** ** * *
11627 AAATTTCCAAAATTTATATTTTTACGCCCGAACTTCCAAAAATCTTATTTTCGACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCG
* * * *
11686 AAACTTCCAAAATTTCCATTTTTACCCCCAAACTTTCAAAAAATCCCA-TTTTAACC-CTA
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAAC-TTCCAAAAATCCCATTTTTAACCTC-G
* * * *
11745 AAACTCCCAAACATTCCATTTTTACCCCCGAACTTCTAAAAATCTCATTTTT
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTT
11797 TACCCCAAAA
Statistics
Matches: 389, Mismatches: 60, Indels: 30
0.81 0.13 0.06
Matches are distributed among these distances:
57 2 0.01
58 109 0.28
59 239 0.61
60 38 0.10
61 1 0.00
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCG
Found at i:11828 original size:21 final size:20
Alignment explanation
Indices: 11783--11830 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
11773 CGAACTTCTA
* *
11783 AAAATCTCATTTTTTACCCC
1 AAAATCTCATTTTTAAACCC
11803 AAAATCTCCATTTTTAAACCC
1 AAAATCT-CATTTTTAAACCC
*
11824 TAAATCT
1 AAAATCT
11831 TCCCAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.35, C:0.27, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATCTCATTTTTAAACCC
Found at i:13671 original size:16 final size:16
Alignment explanation
Indices: 13642--13682 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
13632 TCAAGCTTTT
*
13642 TTATTTTTA-ATT-AA
1 TTATTTTTATTTTAAA
13656 TTAATTTTTATTTTAAA
1 TT-ATTTTTATTTTAAA
13673 TTATTTTTAT
1 TTATTTTTAT
13683 AAGCATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 7 0.30
16 10 0.43
17 4 0.17
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTTTTATTTTAAA
Found at i:15461 original size:42 final size:42
Alignment explanation
Indices: 15374--15480 Score: 99
Period size: 42 Copynumber: 2.6 Consensus size: 42
15364 CATTAAAGCA
* * *
15374 TTTTTTCTTGAATGAGACAAAAACACCTCCACTTGGAAGCAT
1 TTTTTTCTTGAATGAGACAAAAACACCTCCACGTAGAAACAT
* * ** * *
15416 TTTTTTGTTGAATGAGGCAAAAAGGCTTCCACGTAGAAAC-G
1 TTTTTTCTTGAATGAGACAAAAACACCTCCACGTAGAAACAT
* * *
15457 TTTTTCCTTGACTGAGATAAAAAC
1 TTTTTTCTTGAATGAGACAAAAAC
15481 GCGTTAAAAA
Statistics
Matches: 50, Mismatches: 15, Indels: 1
0.76 0.23 0.02
Matches are distributed among these distances:
41 18 0.36
42 32 0.64
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (42 bp):
TTTTTTCTTGAATGAGACAAAAACACCTCCACGTAGAAACAT
Found at i:19677 original size:22 final size:22
Alignment explanation
Indices: 19645--19693 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
19635 TTTTAATAAT
*
19645 AAAAATAGATAAATTTTTTATA
1 AAAAATAGATAAAATTTTTATA
* *
19667 AAAAATGGATAAAATTTTTATT
1 AAAAATAGATAAAATTTTTATA
19689 AAAAA
1 AAAAA
19694 GACTAATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (22 bp):
AAAAATAGATAAAATTTTTATA
Found at i:26254 original size:12 final size:10
Alignment explanation
Indices: 26228--26267 Score: 55
Period size: 10 Copynumber: 3.9 Consensus size: 10
26218 AATAAGAATT
26228 TTTAAAAAAA
1 TTTAAAAAAA
26238 -TTAAATAAAA
1 TTTAAA-AAAA
26248 TTATAAAAAAA
1 TT-TAAAAAAA
26259 TTTAAAAAA
1 TTTAAAAAA
26268 TAAAAAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 5 0.19
10 11 0.41
11 7 0.26
12 4 0.15
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
TTTAAAAAAA
Found at i:26256 original size:21 final size:20
Alignment explanation
Indices: 26230--26268 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
26220 TAAGAATTTT
26230 TAAAAAAATTAAATAAAATTA
1 TAAAAAAATTAAA-AAAATTA
*
26251 TAAAAAAATTTAAAAAAT
1 TAAAAAAATTAAAAAAAT
26269 AAAAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
TAAAAAAATTAAAAAAATTA
Found at i:26522 original size:11 final size:11
Alignment explanation
Indices: 26506--26543 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
26496 TTTATTCAAA
*
26506 TTTAAACTATT
1 TTTAAATTATT
26517 TTTAAATTA-T
1 TTTAAATTATT
*
26527 TTTAAATTGTT
1 TTTAAATTATT
26538 TTTAAA
1 TTTAAA
26544 ACATTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (11 bp):
TTTAAATTATT
Found at i:26530 original size:21 final size:21
Alignment explanation
Indices: 26506--26552 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
26496 TTTATTCAAA
**
26506 TTTAAACTATTTTTAAATTAT
1 TTTAAACTATTTTTAAAACAT
* *
26527 TTTAAATTGTTTTTAAAACAT
1 TTTAAACTATTTTTAAAACAT
26548 TTTAA
1 TTTAA
26553 TTGTCTAAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.55
Consensus pattern (21 bp):
TTTAAACTATTTTTAAAACAT
Found at i:28537 original size:87 final size:87
Alignment explanation
Indices: 28437--28607 Score: 324
Period size: 87 Copynumber: 2.0 Consensus size: 87
28427 TTGAAATTAG
* *
28437 CCACTAAACTTTGAATTTTAATTAATTTTGCCACTAAATTTGATTTTTTAAAATTAAATTTTATC
1 CCACTAAACTTTGAATTTTAATTAATTTTGCCACTAAATTTGATTTTTTAAAATTAAATCTTACC
28502 ATTAGATATTGATTTTATTTAA
66 ATTAGATATTGATTTTATTTAA
28524 CCACTAAACTTTGAATTTTAATTAATTTTGCCACTAAATTTGATTTTTTAAAATTAAATCTTACC
1 CCACTAAACTTTGAATTTTAATTAATTTTGCCACTAAATTTGATTTTTTAAAATTAAATCTTACC
28589 ATTAGATATTGATTTTATT
66 ATTAGATATTGATTTTATT
28608 GATTTGAAAA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 82 1.00
ACGTcount: A:0.35, C:0.11, G:0.06, T:0.49
Consensus pattern (87 bp):
CCACTAAACTTTGAATTTTAATTAATTTTGCCACTAAATTTGATTTTTTAAAATTAAATCTTACC
ATTAGATATTGATTTTATTTAA
Found at i:28574 original size:30 final size:29
Alignment explanation
Indices: 28436--28571 Score: 104
Period size: 30 Copynumber: 4.7 Consensus size: 29
28426 CTTGAAATTA
28436 GCCACTAAACTTTGAATTTTAATTAATTTT
1 GCCACTAAA-TTTGAATTTTAATTAATTTT
*
28466 GCCACTAAATTTGATTTTTTAAAATTAAATTTT
1 GCCACTAAATTTGA-ATTTT--AATT-AATTTT
** * * *
28499 ATCATTAGATATTG-ATTTTATTTAA----
1 GCCACTAAAT-TTGAATTTTAATTAATTTT
28524 -CCACTAAACTTTGAATTTTAATTAATTTT
1 GCCACTAAA-TTTGAATTTTAATTAATTTT
*
28553 GCCACTAAATTTGATTTTT
1 GCCACTAAATTTGAATTTT
28572 TAAAATTAAA
Statistics
Matches: 82, Mismatches: 12, Indels: 25
0.69 0.10 0.21
Matches are distributed among these distances:
24 8 0.10
25 11 0.13
29 16 0.20
30 24 0.29
32 8 0.10
33 12 0.15
34 3 0.04
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.49
Consensus pattern (29 bp):
GCCACTAAATTTGAATTTTAATTAATTTT
Found at i:28996 original size:16 final size:17
Alignment explanation
Indices: 28975--29016 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
28965 TACATGTGCA
28975 AAATAATAAAATAAA-T
1 AAATAATAAAATAAATT
*
28991 AAATAATACAATAAATT
1 AAATAATAAAATAAATT
*
29008 AAAAAATAA
1 AAATAATAA
29017 CTTTTAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAATAAAATAAATT
Found at i:40007 original size:28 final size:28
Alignment explanation
Indices: 39950--40008 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
39940 GATTTTCTTA
*
39950 TATTTTATTTTACATTCTCTTTTTACAT
1 TATTTTATTTTACATTCTATTTTTACAT
*
39978 TATTTTAATTTTA-ATTTTATTCTTTA-AT
1 TATTTT-ATTTTACATTCTATT-TTTACAT
40006 TAT
1 TAT
40009 AATCCCTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 17 0.63
29 10 0.37
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.66
Consensus pattern (28 bp):
TATTTTATTTTACATTCTATTTTTACAT
Found at i:43769 original size:145 final size:145
Alignment explanation
Indices: 43504--43939 Score: 782
Period size: 145 Copynumber: 3.0 Consensus size: 145
43494 GTTCGTTATG
*
43504 ATGTGGACGCCATTGATGTGGTCTAAGGTATATATTCTCTTTTTTTCTATTCTAGTTGATGCATT
1 ATGTGGACGCCATTGATGTGGTCTAAGGTATATATTCTCTTTTTTTCTATTCCAGTTGATGCATT
43569 GATTAATCCAAGTTCTACACATTCTGATATATATAGTACTGTGATCTTAGGTGGAGTGGTCCTAT
66 GATTAATCCAAGTTCTACACATTCTGATATATATAGTACTGTGATCTTAGGTGGAGTGGTCCTAT
43634 GGAGATGTCATATAT
131 GGAGATGTCATATAT
*
43649 ATGTGGACGCCATTGATGTGGTCTAAGGTATATATTCTCTTTTTTTCTATTCCAGCTGATGCATT
1 ATGTGGACGCCATTGATGTGGTCTAAGGTATATATTCTCTTTTTTTCTATTCCAGTTGATGCATT
* * * *
43714 GATTGATCCAATTTCTACACATTCCGATATATATAGTACTGTGATCTTAGATGGAGTGGTCCTAT
66 GATTAATCCAAGTTCTACACATTCTGATATATATAGTACTGTGATCTTAGGTGGAGTGGTCCTAT
43779 GGAGATGTCATATAT
131 GGAGATGTCATATAT
* *
43794 ATGTGGACACCATTGATGTGGTCTAAGGTATATATTCTCTTTTTTTCTATTTCAGTTGATGCATT
1 ATGTGGACGCCATTGATGTGGTCTAAGGTATATATTCTCTTTTTTTCTATTCCAGTTGATGCATT
*
43859 GATTAATCAAAGTTCTACACATTCTGATATATATAGTACTGTGATCTTAGGTGGAGTGGTCCTAT
66 GATTAATCCAAGTTCTACACATTCTGATATATATAGTACTGTGATCTTAGGTGGAGTGGTCCTAT
*
43924 GAAGATGTCATATAT
131 GGAGATGTCATATAT
43939 A
1 A
43940 ATGACTTCGA
Statistics
Matches: 276, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
145 276 1.00
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.40
Consensus pattern (145 bp):
ATGTGGACGCCATTGATGTGGTCTAAGGTATATATTCTCTTTTTTTCTATTCCAGTTGATGCATT
GATTAATCCAAGTTCTACACATTCTGATATATATAGTACTGTGATCTTAGGTGGAGTGGTCCTAT
GGAGATGTCATATAT
Found at i:51739 original size:12 final size:12
Alignment explanation
Indices: 51719--51764 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
51709 ATTCCACACA
51719 GGTTCGCATGAG
1 GGTTCGCATGAG
*
51731 GGTTGGCATTGAG
1 GGTTCGCA-TGAG
* *
51744 AGTTCGCTTGAG
1 GGTTCGCATGAG
51756 GGTTCGCAT
1 GGTTCGCAT
51765 AACAGTTTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
12 18 0.67
13 9 0.33
ACGTcount: A:0.15, C:0.15, G:0.39, T:0.30
Consensus pattern (12 bp):
GGTTCGCATGAG
Found at i:51841 original size:23 final size:23
Alignment explanation
Indices: 51815--51894 Score: 106
Period size: 23 Copynumber: 3.5 Consensus size: 23
51805 TCACATAGCA
* * *
51815 ATTCACTAAAGTGTTCGCCTAAC
1 ATTCACTAAGGGGTTCGCATAAC
*
51838 ATTCACTAAGGGGTTCACATAAC
1 ATTCACTAAGGGGTTCGCATAAC
*
51861 ATTCATTAAGGGGTTCGCATAAC
1 ATTCACTAAGGGGTTCGCATAAC
*
51884 ATTCATTAAGG
1 ATTCACTAAGG
51895 TGGTAGATCA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (23 bp):
ATTCACTAAGGGGTTCGCATAAC
Found at i:52007 original size:21 final size:21
Alignment explanation
Indices: 51969--52008 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
51959 TAAATTATCA
51969 TAAATTGTGATTGAATGTGAT
1 TAAATTGTGATTGAATGTGAT
*
51990 TAAA-TGTTATTGATATGTG
1 TAAATTGTGATTGA-ATGTG
52009 CTGAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.45
Consensus pattern (21 bp):
TAAATTGTGATTGAATGTGAT
Found at i:66035 original size:18 final size:17
Alignment explanation
Indices: 66014--66052 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
66004 AAACTTAAAA
*
66014 AATTAGTATATGCAATTT
1 AATTAGTATATACAA-TT
66032 AATTAGTATATACAATT
1 AATTAGTATATACAATT
66049 AATT
1 AATT
66053 CACGAATCGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (17 bp):
AATTAGTATATACAATT
Found at i:66728 original size:19 final size:20
Alignment explanation
Indices: 66684--66730 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
66674 AAAACTAAAA
66684 AAAAATTTTCAAAATAATTTT
1 AAAAA-TTTCAAAATAATTTT
*
66705 TAAAATTT-AAAAT-ATTTAT
1 AAAAATTTCAAAATAATTT-T
66724 AAAAATT
1 AAAAATT
66731 CCCAAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 4 0.17
19 12 0.52
20 3 0.13
21 4 0.17
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
AAAAATTTCAAAATAATTTT
Found at i:67556 original size:28 final size:28
Alignment explanation
Indices: 67503--67555 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
67493 TTTTATGTAT
* *
67503 GAAATTTAATCCTTTATTTTTATTTTAA
1 GAAATTTAATCCTTTATATATATTTTAA
*
67531 GAAATTTAGT-CTTTATATATATTTT
1 GAAATTTAATCCTTTATATATATTTT
67556 TTAATTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 13 0.59
28 9 0.41
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.57
Consensus pattern (28 bp):
GAAATTTAATCCTTTATATATATTTTAA
Found at i:67912 original size:28 final size:24
Alignment explanation
Indices: 67855--67907 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
67845 GTTAAGTAGG
*
67855 ATTAGATACATTAATAATTTTATT
1 ATTAAATACATTAATAATTTTATT
67879 ATTAAATACATTAATTTAATTTTA-T
1 ATTAAATACATTAA--TAATTTTATT
67904 ATTA
1 ATTA
67908 TTAAAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 13 0.50
25 5 0.19
26 8 0.31
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (24 bp):
ATTAAATACATTAATAATTTTATT
Found at i:71692 original size:17 final size:17
Alignment explanation
Indices: 71670--71711 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
71660 GCTTTGACGT
71670 ATTGATCTTACGTGATG
1 ATTGATCTTACGTGATG
71687 ATTGATCTTACGTGATG
1 ATTGATCTTACGTGATG
*
71704 GTTGATCT
1 ATTGATCT
71712 CATCAACGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.21, C:0.12, G:0.24, T:0.43
Consensus pattern (17 bp):
ATTGATCTTACGTGATG
Found at i:72452 original size:96 final size:96
Alignment explanation
Indices: 72281--72462 Score: 244
Period size: 96 Copynumber: 1.9 Consensus size: 96
72271 AAGGATGTTC
** *
72281 GATTATCTCGATTCGAAGAAAGGTTGCACCTAGTAAGTTAAGGCACAAATTTTCAGAATCGAAGA
1 GATTATCTCGATTCGAAGAAAAATTACACCTAGTAAGTTAAGGCACAAATTTTCAGAATCGAAGA
* *
72346 TAAGAAAATATTGCCTTGATTAAGGGTATTT
66 TAAGAAAATATTACCTCGATTAAGGGTATTT
* * *
72377 GATTATTTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCGCAAATTTTC-GAAACTCGAA
1 GATTATCTCGATTCGAAGAAAAATTACACCTAGTAAGTTAAGGCACAAATTTTCAG-AA-TCGAA
72441 -ATAA-AAGAATATTACCTCGATT
64 GATAAGAA-AATATTACCTCGATT
72463 TTAAAGTTCT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
95 3 0.04
96 67 0.89
97 5 0.07
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.30
Consensus pattern (96 bp):
GATTATCTCGATTCGAAGAAAAATTACACCTAGTAAGTTAAGGCACAAATTTTCAGAATCGAAGA
TAAGAAAATATTACCTCGATTAAGGGTATTT
Found at i:72708 original size:29 final size:29
Alignment explanation
Indices: 72676--72736 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
72666 AAAATGAGAC
*
72676 TTTTTGGATACCCG-GTGGTAAAATGGTAA
1 TTTTTGGATACCCGAG-GGCAAAATGGTAA
* *
72705 -TTTTGGATTCTCGAGGGCAAAATGGTAA
1 TTTTTGGATACCCGAGGGCAAAATGGTAA
72733 TTTT
1 TTTT
72737 GGGAAAGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
28 23 0.85
29 4 0.15
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.38
Consensus pattern (29 bp):
TTTTTGGATACCCGAGGGCAAAATGGTAA
Found at i:72765 original size:30 final size:30
Alignment explanation
Indices: 72723--72892 Score: 129
Period size: 30 Copynumber: 5.8 Consensus size: 30
72713 TCTCGAGGGC
*
72723 AAAATGGTAATTTTGGGAAAGTTTGGGGTCA
1 AAAATGG-AATTTTTGGAAAGTTTGGGGTCA
* * *
72754 AAAATGGAATTTTTAGACA-TTCGGGGGT--
1 AAAATGGAATTTTTGGAAAGTT-TGGGGTCA
* * *
72782 AAAAGGGTATTTTT-GAGAGTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAAG-TTTGGGGTCA
* * * *
72812 AAAATAGATTTTTTAG-AGGTTTTGGGGT-A
1 AAAATGGAATTTTTGGAAAG-TTTGGGGTCA
* *
72841 AAAATGGAATTTTTGG-AAGTTCGAGGTCA
1 AAAATGGAATTTTTGGAAAGTTTGGGGTCA
*
72870 AAAATGGAATTTTTGGATAGTTT
1 AAAATGGAATTTTTGGAAAGTTT
72893 AGGGACCTTT
Statistics
Matches: 109, Mismatches: 22, Indels: 17
0.74 0.15 0.11
Matches are distributed among these distances:
27 3 0.03
28 23 0.21
29 37 0.34
30 38 0.35
31 8 0.07
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.36
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAAGTTTGGGGTCA
Found at i:72794 original size:58 final size:58
Alignment explanation
Indices: 72723--72883 Score: 164
Period size: 58 Copynumber: 2.7 Consensus size: 58
72713 TCTCGAGGGC
72723 AAAATGGTAATTTTGGGAAAGTTTGGGGTCAAAAATGGAATTTTTAGACATTCGGGGGT-
1 AAAATGGT-ATTTT-GGAAAGTTTGGGGTCAAAAATGGAATTTTTAGACATTCGGGGGTA
* * * * * ** **
72782 AAAAGGGTATTTTTGAGAGTTTTGGGGTCAAAAATAGATTTTTTAGAGGTTTTGGGGTA
1 AAAATGGTATTTTGGAAAG-TTTGGGGTCAAAAATGGAATTTTTAGACATTCGGGGGTA
* * *
72841 AAAATGGAATTTTTGG-AAGTTCGAGGTCAAAAATGGAATTTTT
1 AAAATGGTA-TTTTGGAAAGTTTGGGGTCAAAAATGGAATTTTT
72884 GGATAGTTTA
Statistics
Matches: 82, Mismatches: 17, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
57 4 0.05
58 57 0.70
59 16 0.20
60 5 0.06
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (58 bp):
AAAATGGTATTTTGGAAAGTTTGGGGTCAAAAATGGAATTTTTAGACATTCGGGGGTA
Found at i:72872 original size:29 final size:30
Alignment explanation
Indices: 72723--72891 Score: 118
Period size: 29 Copynumber: 5.7 Consensus size: 30
72713 TCTCGAGGGC
* * *
72723 AAAATGGTAATTTTGGGAAAGTTTGGGGTCA
1 AAAATGG-AATTTTTGGACAGTTCGGGGTCA
*
72754 AAAATGGAATTTTTAGACA-TTCGGGGGT--
1 AAAATGGAATTTTTGGACAGTTC-GGGGTCA
* * * *
72782 AAAAGGGTATTTTT-GAGAGTTTTGGGGTCA
1 AAAATGGAATTTTTGGACAG-TTCGGGGTCA
* * * * *
72812 AAAATAGATTTTTTAGA-GGTTTTGGGGT-A
1 AAAATGGAATTTTTGGACAG-TTCGGGGTCA
*
72841 AAAATGGAATTTTTGGA-AGTTCGAGGTCA
1 AAAATGGAATTTTTGGACAGTTCGGGGTCA
*
72870 AAAATGGAATTTTTGGATAGTT
1 AAAATGGAATTTTTGGACAGTT
72892 TAGGGACCTT
Statistics
Matches: 111, Mismatches: 19, Indels: 17
0.76 0.13 0.12
Matches are distributed among these distances:
27 3 0.03
28 23 0.21
29 38 0.34
30 38 0.34
31 9 0.08
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.36
Consensus pattern (30 bp):
AAAATGGAATTTTTGGACAGTTCGGGGTCA
Found at i:74875 original size:6 final size:6
Alignment explanation
Indices: 74864--74896 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
74854 TCAAATATGA
*
74864 TTAAAT TTAAAT TTAAA- GTAAAT TTAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAA
74897 GATAAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (6 bp):
TTAAAT
Found at i:74887 original size:17 final size:17
Alignment explanation
Indices: 74865--74910 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
74855 CAAATATGAT
74865 TAAATTTAAATTTAA-A
1 TAAATTTAAATTTAAGA
74881 GTAAATTTAAATTTAAGA
1 -TAAATTTAAATTTAAGA
*
74899 TAAAATTAAATT
1 TAAATTTAAATT
74911 AAAAAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 26 0.96
18 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (17 bp):
TAAATTTAAATTTAAGA
Found at i:74908 original size:23 final size:23
Alignment explanation
Indices: 74864--74910 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
74854 TCAAATATGA
*
74864 TTAAATTTAAATTTAAAGTAAAT
1 TTAAATTTAAATTAAAAGTAAAT
*
74887 TTAAATTTAAGA-TAAAATTAAAT
1 TTAAATTTAA-ATTAAAAGTAAAT
74910 T
1 T
74911 AAAAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (23 bp):
TTAAATTTAAATTAAAAGTAAAT
Done.