Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017650.1 Corchorus olitorius cultivar O-4 contig17683, 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: 54895
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1109 original size:21 final size:22
Alignment explanation
Indices: 1073--1114 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1063 AAATATTAAA
* *
1073 AAAATTTATAAAATTTGAATTC
1 AAAATATATAAAATTTAAATTC
1095 AAAATATAT-AAATTTAAATT
1 AAAATATATAAAATTTAAATT
1115 TATTTTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
AAAATATATAAAATTTAAATTC
Found at i:5046 original size:2 final size:2
Alignment explanation
Indices: 5041--5077 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
5031 TAAAAAATAC
* *
5041 AT AT AT AT AT AT AT AT AG AT AT AT AT AT AT AG AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5078 CTAGTATCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.43
Consensus pattern (2 bp):
AT
Found at i:5064 original size:14 final size:14
Alignment explanation
Indices: 5045--5077 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
5035 AAATACATAT
5045 ATATATATATATAG
1 ATATATATATATAG
5059 ATATATATATATAG
1 ATATATATATATAG
5073 ATATA
1 ATATA
5078 CTAGTATCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (14 bp):
ATATATATATATAG
Found at i:7400 original size:17 final size:17
Alignment explanation
Indices: 7378--7414 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
7368 TTTTCTGACC
7378 ATTATTATGAAATAATT
1 ATTATTATGAAATAATT
**
7395 ATTATTATTCAATAATT
1 ATTATTATGAAATAATT
7412 ATT
1 ATT
7415 CCTTAATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (17 bp):
ATTATTATGAAATAATT
Found at i:8956 original size:104 final size:104
Alignment explanation
Indices: 8709--9064 Score: 592
Period size: 104 Copynumber: 3.4 Consensus size: 104
8699 CTTAATTTCG
* *
8709 CTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATTAATAATTT
1 CTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATTAATAA--T
* *
8774 ATTGTTATAGGGTTTTAGAAATAAAATACAAAACTAATTTCA
64 ATTGTTATAGGGTTTTAGAAATAAAATATACAACTAA-TTCA
*
8816 ATAAGTTTAGCCCCAAATTAAAATTTTA--TTT-TTTTAAGGGTAAATTCCATAATTAATAATAT
1 CTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATTAATAATAT
8878 TGTTATAGGGTTTTAGAAATAAAATATACAACTAATTCA
66 TGTTATAGGGTTTTAGAAATAAAATATACAACTAATTCA
8917 CTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATTAATAATAT
1 CTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATTAATAATAT
8982 TGTTATAGGGTTTTAGAAATAAAATATACAACTAATTCA
66 TGTTATAGGGTTTTAGAAATAAAATATACAACTAATTCA
** *
9021 CTAAGTTTAGCCCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 CTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
9065 TAGAAAAATT
Statistics
Matches: 237, Mismatches: 9, Indels: 9
0.93 0.04 0.04
Matches are distributed among these distances:
101 31 0.13
102 36 0.15
103 3 0.01
104 137 0.58
105 3 0.01
107 27 0.11
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.40
Consensus pattern (104 bp):
CTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATTAATAATAT
TGTTATAGGGTTTTAGAAATAAAATATACAACTAATTCA
Found at i:9688 original size:28 final size:28
Alignment explanation
Indices: 9645--9703 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
9635 CAAATCAACT
*
9645 CTTATTAATTGCCTTAATTTACTTTTAA
1 CTTATTAATTGCCTTAATTCACTTTTAA
* *
9673 CTTATTATTTGTCTTAATTCACTTTTAA
1 CTTATTAATTGCCTTAATTCACTTTTAA
9701 CTT
1 CTT
9704 TAGTTAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.15, G:0.03, T:0.56
Consensus pattern (28 bp):
CTTATTAATTGCCTTAATTCACTTTTAA
Found at i:29325 original size:2 final size:2
Alignment explanation
Indices: 29282--29310 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29272 TTGTGAAATT
29282 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29311 TTGAAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31381 original size:7 final size:7
Alignment explanation
Indices: 31359--31403 Score: 58
Period size: 7 Copynumber: 6.4 Consensus size: 7
31349 CTTAGGGTTT
31359 TAATATA
1 TAATATA
31366 TATATATA
1 TA-ATATA
31374 TAATATA
1 TAATATA
31381 TAATATA
1 TAATATA
31388 TAA-ATA
1 TAATATA
31394 CTAA-ATA
1 -TAATATA
31401 TAA
1 TAA
31404 AAAATATTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
6 6 0.17
7 23 0.64
8 7 0.19
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (7 bp):
TAATATA
Found at i:31387 original size:22 final size:22
Alignment explanation
Indices: 31359--31402 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
31349 CTTAGGGTTT
*
31359 TAATATATATATA-TATAATATA
1 TAATATATAAATACTA-AATATA
31381 TAATATATAAATACTAAATATA
1 TAATATATAAATACTAAATATA
31403 AAAAATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
TAATATATAAATACTAAATATA
Found at i:31388 original size:20 final size:20
Alignment explanation
Indices: 31363--31403 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
31353 GGGTTTTAAT
*
31363 ATATATATATA-TAATATATA
1 ATATATAAATACTAA-ATATA
31383 ATATATAAATACTAAATATA
1 ATATATAAATACTAAATATA
31403 A
1 A
31404 AAAATATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
ATATATAAATACTAAATATA
Found at i:33144 original size:129 final size:129
Alignment explanation
Indices: 32986--33221 Score: 445
Period size: 129 Copynumber: 1.8 Consensus size: 129
32976 ATGTTAAAAT
*
32986 TCCGATTAAGATGATAAAGATATTGAATCGACATATCAAATGTAAATTTTACAAATTATGAAAAT
1 TCCGATTAAGATGATAAAGATATTAAATCGACATATCAAATGTAAATTTTACAAATTATGAAAAT
33051 GTGTGAAATAAATATAATGTACACAAAATGAAAGTGGATCTCTACCCAAAACACACACACACAC
66 GTGTGAAATAAATATAATGTACACAAAATGAAAGTGGATCTCTACCCAAAACACACACACACAC
33115 TCCGATTAAGATGATAAAGATATTAAATCGACATATCAAATGTAAATTTTACAAATTATGAAAAT
1 TCCGATTAAGATGATAAAGATATTAAATCGACATATCAAATGTAAATTTTACAAATTATGAAAAT
* *
33180 GTGTGAAATAGATATAATGTACACAAAATGTAAGTGGATCTC
66 GTGTGAAATAAATATAATGTACACAAAATGAAAGTGGATCTC
33222 ACAAATTATG
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
129 104 1.00
ACGTcount: A:0.46, C:0.13, G:0.14, T:0.28
Consensus pattern (129 bp):
TCCGATTAAGATGATAAAGATATTAAATCGACATATCAAATGTAAATTTTACAAATTATGAAAAT
GTGTGAAATAAATATAATGTACACAAAATGAAAGTGGATCTCTACCCAAAACACACACACACAC
Found at i:33657 original size:85 final size:85
Alignment explanation
Indices: 33514--33685 Score: 308
Period size: 85 Copynumber: 2.0 Consensus size: 85
33504 GAAAGTCTTT
* *
33514 AAAATTTGAGGGTGTAAGAGAAAAGTCAAGATAAAAATAGCAAAACTTTTCTAGGAAAGTTAACT
1 AAAATTTGAGGGTATAAGAGAAAAGTCAAGATAAAAATAGCAAAACTTTCCTAGGAAAGTTAACT
* *
33579 TTCTCATCCTTTTAGGTGGG
66 TTCCCATCATTTTAGGTGGG
33599 AAAATTTGAGGGTATAAGAGAAAAGTCAAGATAAAAATAGCAAAACTTTCCTAGGAAAGTTAACT
1 AAAATTTGAGGGTATAAGAGAAAAGTCAAGATAAAAATAGCAAAACTTTCCTAGGAAAGTTAACT
33664 TTCCCATCATTTTAGGTGGG
66 TTCCCATCATTTTAGGTGGG
33684 AA
1 AA
33686 TGACATTCCC
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 83 1.00
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.28
Consensus pattern (85 bp):
AAAATTTGAGGGTATAAGAGAAAAGTCAAGATAAAAATAGCAAAACTTTCCTAGGAAAGTTAACT
TTCCCATCATTTTAGGTGGG
Found at i:34393 original size:3 final size:3
Alignment explanation
Indices: 34385--34418 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
34375 CATTACTTTG
* *
34385 TAA TAA TAA TAT TAT TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
34419 TGATGTGAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:35679 original size:13 final size:13
Alignment explanation
Indices: 35661--35686 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35651 TCTTTAATTT
35661 TACAATCCTCCCA
1 TACAATCCTCCCA
35674 TACAATCCTCCCA
1 TACAATCCTCCCA
35687 AATGGGAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.46, G:0.00, T:0.23
Consensus pattern (13 bp):
TACAATCCTCCCA
Found at i:38146 original size:2 final size:2
Alignment explanation
Indices: 38135--38164 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
38125 AAATTATAAT
38135 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38165 TTGTATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40653 original size:99 final size:99
Alignment explanation
Indices: 40539--40736 Score: 378
Period size: 99 Copynumber: 2.0 Consensus size: 99
40529 CTCACGGAAT
*
40539 GTGAGTTTGTTTGTAATTTGTTTGTTTATTTGGTAGGTAGGTAGTTTATTTATGGTATAGTTTCT
1 GTGAGTTTGTTTGTAATTTGTTTGTTTATTTGGTAGATAGGTAGTTTATTTATGGTATAGTTTCT
40604 AGTTTGGGTTAAATTCTCGTTTAAATGTTTGGGC
66 AGTTTGGGTTAAATTCTCGTTTAAATGTTTGGGC
40638 GTGAGTTTGTTTGTAATTTGTTTGTTTATTTGGTAGATAGGTAGTTTATTTATGGTATAGTTTCT
1 GTGAGTTTGTTTGTAATTTGTTTGTTTATTTGGTAGATAGGTAGTTTATTTATGGTATAGTTTCT
*
40703 AGTTTGGGTTGAATTCTCGTTTAAATGTTTGGGC
66 AGTTTGGGTTAAATTCTCGTTTAAATGTTTGGGC
40737 ATAGAGATTT
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
99 97 1.00
ACGTcount: A:0.18, C:0.04, G:0.26, T:0.52
Consensus pattern (99 bp):
GTGAGTTTGTTTGTAATTTGTTTGTTTATTTGGTAGATAGGTAGTTTATTTATGGTATAGTTTCT
AGTTTGGGTTAAATTCTCGTTTAAATGTTTGGGC
Found at i:41132 original size:228 final size:225
Alignment explanation
Indices: 40690--41143 Score: 820
Period size: 228 Copynumber: 2.0 Consensus size: 225
40680 AGTTTATTTA
*
40690 TGGTATAGTTTCTAGTTTGGGTTGAATTCTCGTTTAAATGTTTGGGCATAGAGATTTATTTGAAT
1 TGGTATAGTTTCTAGTTTGGGTTGAATTCTCGTTTAAATGTTTGGGCATAAAGATTTATTTGAAT
*
40755 TGTAATAAGATTACACTGGGTTTGTTGGCTCATAGATTAACGTTTCAGTAATGCCAACTAATCAT
66 TGTAATAAGATTACACTGGGTTTGTTGGCTCATAAATTAACGTTTCAGTAATGCCAACTAATCAT
40820 GTAGCGGTGTACGGATCTTTGTGTACGCGTTTGTAATCCCAATCTCTTCAAAAAATGAAAAAAAA
131 GTAGCGGTGTACGGATCTTTGTGTACGCGTTTGTAATCCCAATCTCTTCAAAAAATGAAAAAAAA
*
40885 TTTAATACGATCTGACCCATAAACACCTCT
196 TTTAATACGATCCGACCCATAAACACCTCT
40915 TGGTATAGTTTCTAGTTTGGGTTGAATTCTCGTTTAAATGTTTGGGCATAAAGATTTATTTGAAT
1 TGGTATAGTTTCTAGTTTGGGTTGAATTCTCGTTTAAATGTTTGGGCATAAAGATTTATTTGAAT
* *
40980 TGTAATGAGATTACACTGGGTTTGTTTGTTGGCTCATAAATTAACGTTTCGGTAATG-CAACTAA
66 TGTAATAAGATTACACT-GG---GTTTGTTGGCTCATAAATTAACGTTTCAGTAATGCCAACTAA
41044 TCATGTAGCGGTGTACGGATCTTTGTGTACGCGTTTGTAATCCCAATCTCTTCAAAAAATGAAAA
127 TCATGTAGCGGTGTACGGATCTTTGTGTACGCGTTTGTAATCCCAATCTCTTCAAAAAATGAAAA
41109 AAAATTTAATACGATCCGACCCATAAACACCTCT
192 AAAATTTAATACGATCCGACCCATAAACACCTCT
41143 T
1 T
41144 CCAACTCATC
Statistics
Matches: 220, Mismatches: 5, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
225 80 0.36
226 2 0.01
228 106 0.48
229 32 0.15
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (225 bp):
TGGTATAGTTTCTAGTTTGGGTTGAATTCTCGTTTAAATGTTTGGGCATAAAGATTTATTTGAAT
TGTAATAAGATTACACTGGGTTTGTTGGCTCATAAATTAACGTTTCAGTAATGCCAACTAATCAT
GTAGCGGTGTACGGATCTTTGTGTACGCGTTTGTAATCCCAATCTCTTCAAAAAATGAAAAAAAA
TTTAATACGATCCGACCCATAAACACCTCT
Found at i:42793 original size:39 final size:39
Alignment explanation
Indices: 42715--42795 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 39
42705 ACATAATTAT
** * *
42715 TCATAAAGTTATGTCTATATGGGAAGAGATATGTATTGA
1 TCATAAAGTTATGTCTATATGAAAAGACATATATATTGA
*
42754 TCATAAAGTTATGTCTATATGAAAAGACATATATGTTGA
1 TCATAAAGTTATGTCTATATGAAAAGACATATATATTGA
42793 TCA
1 TCA
42796 AGTATATATA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.38, C:0.07, G:0.19, T:0.36
Consensus pattern (39 bp):
TCATAAAGTTATGTCTATATGAAAAGACATATATATTGA
Found at i:43019 original size:10 final size:10
Alignment explanation
Indices: 43004--43028 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
42994 AAATTCATTT
43004 GACCCGGCCC
1 GACCCGGCCC
43014 GACCCGGCCC
1 GACCCGGCCC
43024 GACCC
1 GACCC
43029 AACCCAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.60, G:0.28, T:0.00
Consensus pattern (10 bp):
GACCCGGCCC
Found at i:43861 original size:23 final size:23
Alignment explanation
Indices: 43835--43908 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
43825 AATAATTAAA
*
43835 TAAAAATAGAGTTTTTATTTGAG
1 TAAAAATAGAGTTTTTAATTGAG
* * * * *
43858 TAAAGATATTAG-ATTTAATTAAA
1 TAAAAATA-GAGTTTTTAATTGAG
* *
43881 TAAAAATAGAATTTTTAGTTGAG
1 TAAAAATAGAGTTTTTAATTGAG
43904 TAAAA
1 TAAAA
43909 CTATAAAAGT
Statistics
Matches: 36, Mismatches: 13, Indels: 4
0.68 0.25 0.08
Matches are distributed among these distances:
22 1 0.03
23 33 0.92
24 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39
Consensus pattern (23 bp):
TAAAAATAGAGTTTTTAATTGAG
Found at i:43887 original size:46 final size:48
Alignment explanation
Indices: 43813--43907 Score: 149
Period size: 46 Copynumber: 2.0 Consensus size: 48
43803 TAGTTCAAAG
* *
43813 GATATTAGATTTAATAATTAAATAAAAATAGAGTTTTTATTTGAGTAAA
1 GATATTAGATTT-ATAATTAAATAAAAATAGAATTTTTAGTTGAGTAAA
43862 GATATTAGA-TT-TAATTAAATAAAAATAGAATTTTTAGTTGAGTAAA
1 GATATTAGATTTATAATTAAATAAAAATAGAATTTTTAGTTGAGTAAA
43908 ACTATAAAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
46 33 0.75
48 2 0.05
49 9 0.20
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (48 bp):
GATATTAGATTTATAATTAAATAAAAATAGAATTTTTAGTTGAGTAAA
Found at i:52792 original size:29 final size:29
Alignment explanation
Indices: 52758--52835 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
52748 ACTTGTAGCA
* *
52758 TTTGGACGTTTTGTCCCCTAAATTTCAAT
1 TTTGGACATTTTGTCCCCTAAACTTCAAT
* *
52787 TTTGGACATTTTGTCCTCTGAACTTCAAT
1 TTTGGACATTTTGTCCCCTAAACTTCAAT
* *
52816 TTTGGGATATTTTGCCCCCT
1 TTT-GGACATTTTGTCCCCT
52836 CAGGTTAACG
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 28 0.68
30 13 0.32
ACGTcount: A:0.18, C:0.22, G:0.15, T:0.45
Consensus pattern (29 bp):
TTTGGACATTTTGTCCCCTAAACTTCAAT
Found at i:54487 original size:131 final size:129
Alignment explanation
Indices: 54351--54599 Score: 356
Period size: 131 Copynumber: 1.9 Consensus size: 129
54341 ATTGTTTAAA
* * *
54351 CTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTACTTAAATCTAATATCCTTATAACT
1 CTTTTATAGTTTTACTCAACTAAAAACTCCATTTTTATTGAATTAAATCTAATAT--TTATAACT
* * *
54416 ATTTAATTTTTACCATTGTACTATTTTAATTTAAAAA-CTTATATATATTAGAATTTTTTAAATA
64 ATTTAATTTTTACCATTGTACTAATTTAA-TTAAAAATCTTAGATATATTAAAATTTTTTAAATA
54480 TG
128 TG
* *
54482 CTTTTATAGTTTTACTCAACTAAAAGCTCCATTTTTATTGAATTAAATCTAATATTTATACCTAT
1 CTTTTATAGTTTTACTCAACTAAAAACTCCATTTTTATTGAATTAAATCTAATATTTATAACTAT
* * * *
54547 TTTATTTTTACCATTTTATTAATTTAATTAAAAATTTTAGATATATTAAAATT
66 TTAATTTTTACCATTGTACTAATTTAATTAAAAATCTTAGATATATTAAAATT
54600 CTTAAAAATA
Statistics
Matches: 105, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
128 7 0.07
129 47 0.45
131 51 0.49
ACGTcount: A:0.36, C:0.11, G:0.03, T:0.50
Consensus pattern (129 bp):
CTTTTATAGTTTTACTCAACTAAAAACTCCATTTTTATTGAATTAAATCTAATATTTATAACTAT
TTAATTTTTACCATTGTACTAATTTAATTAAAAATCTTAGATATATTAAAATTTTTTAAATATG
Found at i:54564 original size:14 final size:15
Alignment explanation
Indices: 54534--54566 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
54524 TTAAATCTAA
54534 TATTTATACCTATTT
1 TATTTATACCTATTT
*
54549 TATTTTTACC-ATTT
1 TATTTATACCTATTT
54563 TATT
1 TATT
54567 AATTTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (15 bp):
TATTTATACCTATTT
Done.