Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005865.1 Hibiscus syriacus cultivar Beakdansim tig00013788_pilon, 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: 92730
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:4596 original size:24 final size:24
Alignment explanation
Indices: 4569--4615 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
4559 GTTAGAAGGT
4569 CTTTACACC-GAATATGTTGCAAGC
1 CTTTACACCTGAAT-TGTTGCAAGC
* *
4593 CTTTTCACCTGAATTGTTTCAAG
1 CTTTACACCTGAATTGTTGCAAG
4616 TCGTCGGCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (24 bp):
CTTTACACCTGAATTGTTGCAAGC
Found at i:11930 original size:6 final size:6
Alignment explanation
Indices: 11919--11953 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
11909 ATCATATGCT
11919 CTCTCG CTCTCG CTCTCG CTCTCG CTCTCG CTCTC
1 CTCTCG CTCTCG CTCTCG CTCTCG CTCTCG CTCTC
11954 TGATCTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.51, G:0.14, T:0.34
Consensus pattern (6 bp):
CTCTCG
Found at i:14785 original size:29 final size:29
Alignment explanation
Indices: 14738--14799 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
14728 TGTTAGATGG
* *
14738 CGAACTTGAACTTACAAAATTTCAGGGGA
1 CGAACTTAAACTTACAAAATTTCAAGGGA
* * *
14767 CGAACTTAAATTTATAAAATTTTAAGGGA
1 CGAACTTAAACTTACAAAATTTCAAGGGA
14796 CGAA
1 CGAA
14800 AACAAATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (29 bp):
CGAACTTAAACTTACAAAATTTCAAGGGA
Found at i:29060 original size:20 final size:20
Alignment explanation
Indices: 29037--29087 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
29027 GCTCTAAATC
29037 ATTTTTCAAAACTTC-ATTTT
1 ATTTTTCAAAAC-TCAATTTT
29057 ATTTTTCAAAA-TCAATTTT
1 ATTTTTCAAAACTCAATTTT
29076 -TTCTTTCAAAAC
1 ATT-TTTCAAAAC
29088 CAAATCCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 4 0.14
19 13 0.46
20 11 0.39
ACGTcount: A:0.33, C:0.16, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTTTCAAAACTCAATTTT
Found at i:32017 original size:12 final size:12
Alignment explanation
Indices: 32000--32031 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
31990 CTTATTTTCT
*
32000 TCATTCTTCTTG
1 TCATTCTTCTTA
32012 TCATTCTTCTTA
1 TCATTCTTCTTA
32024 TCATTCTT
1 TCATTCTT
32032 TTCTTCATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.12, C:0.25, G:0.03, T:0.59
Consensus pattern (12 bp):
TCATTCTTCTTA
Found at i:32039 original size:12 final size:12
Alignment explanation
Indices: 31999--32040 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
31989 TCTTATTTTC
31999 TTCATTCTTCTT
1 TTCATTCTTCTT
*
32011 GTCATTCTTCTT
1 TTCATTCTTCTT
*
32023 ATCATTCTT-TT
1 TTCATTCTTCTT
32034 CTTCATT
1 -TTCATT
32041 AGTTTCCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 2 0.08
12 24 0.92
ACGTcount: A:0.12, C:0.24, G:0.02, T:0.62
Consensus pattern (12 bp):
TTCATTCTTCTT
Found at i:34547 original size:23 final size:24
Alignment explanation
Indices: 34502--34567 Score: 73
Period size: 25 Copynumber: 2.8 Consensus size: 24
34492 TTATAATATT
34502 TTTTATATATTAACTTAAAAAATA
1 TTTTATATATTAACTTAAAAAATA
*
34526 TTTT-TATATTAACTTATTAAATATA
1 TTTTATATATTAACTTA--AAAAATA
* *
34551 TTTCAT-TATTAAATTAA
1 TTTTATATATTAACTTAA
34568 TTTAAAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
23 13 0.36
24 4 0.11
25 18 0.50
26 1 0.03
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.52
Consensus pattern (24 bp):
TTTTATATATTAACTTAAAAAATA
Found at i:34684 original size:17 final size:17
Alignment explanation
Indices: 34637--34685 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
34627 TTAAGATAAA
*
34637 AATAAAATATATTTAAT
1 AATACAATATATTTAAT
*
34654 AAT-C--TA-AATTAAT
1 AATACAATATATTTAAT
34667 AATACAATATATTTAAT
1 AATACAATATATTTAAT
34684 AA
1 AA
34686 ATTAAGATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 8
0.69 0.08 0.22
Matches are distributed among these distances:
13 9 0.36
14 3 0.12
16 2 0.08
17 11 0.44
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (17 bp):
AATACAATATATTTAAT
Found at i:34745 original size:57 final size:59
Alignment explanation
Indices: 34616--34766 Score: 159
Period size: 57 Copynumber: 2.6 Consensus size: 59
34606 TTATGTTAAA
* * *
34616 ATATTTTAAAGTTAAGATAAAAATAAAATATATTTAATAATCTAAATTAATAATACAAT
1 ATATTTTAAAATTAAGATAAAAATAAAATATATTTAAAAATCTAAATTAATAATAAAAT
* *
34675 ATATTTAATAAATTAAGAT-AAAAT-ATATA-ATTTGAAAAAT-TATAA-TAATAATAAAAT
1 ATATTTTA-AAATTAAGATAAAAATAAAATATATTT-AAAAATCTA-AATTAATAATAAAAT
* *
34732 ATATTTTTAAAATTTTAGATAAGAATAAAATATAT
1 ATA-TTTTAAAA-TTAAGATAAAAATAAAATATAT
34767 ATTTTTAAAT
Statistics
Matches: 75, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
57 23 0.31
58 21 0.28
59 16 0.21
60 13 0.17
61 2 0.03
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.38
Consensus pattern (59 bp):
ATATTTTAAAATTAAGATAAAAATAAAATATATTTAAAAATCTAAATTAATAATAAAAT
Found at i:34759 original size:31 final size:31
Alignment explanation
Indices: 34688--34784 Score: 108
Period size: 31 Copynumber: 3.1 Consensus size: 31
34678 TTTAATAAAT
*
34688 TAAG-ATAAAATATATAATTTGAAAAATTATAA
1 TAAGAATAAAATATAT-ATTT-TAAAATTATAA
* *
34720 TAATAATAAAATATAT-TTTTAAAATTTTAGA
1 TAAGAATAAAATATATATTTTAAAATTATA-A
* *
34751 TAAGAATAAAATATATATTTTTAAATTAAAA
1 TAAGAATAAAATATATATTTTAAAATTATAA
34782 TAA
1 TAA
34785 AAAATATTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
30 8 0.15
31 23 0.42
32 13 0.24
33 11 0.20
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (31 bp):
TAAGAATAAAATATATATTTTAAAATTATAA
Found at i:34799 original size:23 final size:24
Alignment explanation
Indices: 34750--34808 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 24
34740 AAAATTTTAG
34750 ATAAGAATAAAATATATATTTTTAAA
1 ATAA-AATAAAATATATA-TTTTAAA
*
34776 TTAAAATAAAA-A-ATATTTTAAA
1 ATAAAATAAAATATATATTTTAAA
34798 ATAAAA-AAAAT
1 ATAAAATAAAAT
34809 TTAAATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
21 4 0.13
22 12 0.40
23 3 0.10
24 1 0.03
25 7 0.23
26 3 0.10
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (24 bp):
ATAAAATAAAATATATATTTTAAA
Found at i:34811 original size:16 final size:17
Alignment explanation
Indices: 34776--34826 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 17
34766 TATTTTTAAA
*
34776 TTAAAATAAAAAATATT
1 TTAAAATAAAAAATAAT
34793 TTAAAATAAAAAA-AAT
1 TTAAAATAAAAAATAAT
*
34809 TTAAATTAAATAAATAAT
1 TTAAAATAAA-AAATAAT
34827 AAATGAAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
16 11 0.37
17 16 0.53
18 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TTAAAATAAAAAATAAT
Found at i:35019 original size:7 final size:7
Alignment explanation
Indices: 35007--35036 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
34997 AATTAATGAA
35007 AATAAAT
1 AATAAAT
35014 AATAAAT
1 AATAAAT
35021 AATAAAT
1 AATAAAT
*
35028 ACTAAAT
1 AATAAAT
35035 AA
1 AA
35037 ATATAAGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (7 bp):
AATAAAT
Found at i:35399 original size:57 final size:58
Alignment explanation
Indices: 35309--35418 Score: 159
Period size: 57 Copynumber: 1.9 Consensus size: 58
35299 TTCTCTTAGT
* * *
35309 TTCTAAAGAATAAAAAAAAAACAATCTGAAAGTATGACGGTTAAGACTCAATTATCGG
1 TTCTAAAGAATAAAAAAAAAACAATCTAAAAGTATGAAGATTAAGACTCAATTATCGG
* * *
35367 TTCTAAAGAAT-CAAAAAATACAATTTAAAAGTATGAAGATTAAGACTCAATT
1 TTCTAAAGAATAAAAAAAAAACAATCTAAAAGTATGAAGATTAAGACTCAATT
35419 CTCACGATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
57 35 0.76
58 11 0.24
ACGTcount: A:0.50, C:0.11, G:0.13, T:0.26
Consensus pattern (58 bp):
TTCTAAAGAATAAAAAAAAAACAATCTAAAAGTATGAAGATTAAGACTCAATTATCGG
Found at i:35522 original size:13 final size:12
Alignment explanation
Indices: 35503--35538 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 12
35493 TTAATATTGT
35503 AAAAAGAAAATA
1 AAAAAGAAAATA
35515 ATAAAAGAAAATA
1 A-AAAAGAAAATA
35528 AAGAAAGAAAA
1 AA-AAAGAAAA
35539 ACAGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 2 0.09
13 20 0.91
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATA
Found at i:35709 original size:3 final size:3
Alignment explanation
Indices: 35701--35732 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
35691 CCAATTCCTA
35701 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
35733 AGTAATCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:38292 original size:13 final size:13
Alignment explanation
Indices: 38274--38302 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
38264 CCACCGTACT
38274 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
38287 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
38300 CCG
1 CCG
38303 TAACGGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:39060 original size:3 final size:3
Alignment explanation
Indices: 39052--39179 Score: 132
Period size: 3 Copynumber: 41.7 Consensus size: 3
39042 TTATTCATTA
*
39052 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
* * * * * * *
39099 TAT TAT TAT TAT TAT AAT AAT AAT AAT ACT AAT AAT AAT ATTT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT
*
39145 AAT AAT AAT AAT AAT AA- ATTT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AA
39180 ATTTAAATGA
Statistics
Matches: 110, Mismatches: 10, Indels: 10
0.85 0.08 0.08
Matches are distributed among these distances:
2 1 0.01
3 100 0.91
4 9 0.08
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (3 bp):
AAT
Found at i:39436 original size:76 final size:76
Alignment explanation
Indices: 39305--40023 Score: 1341
Period size: 76 Copynumber: 9.5 Consensus size: 76
39295 GATGGAAATG
* *
39305 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
39370 CCCGAAGGCTT
66 CCCGAAGGCTT
*
39381 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
39446 CCCGAAGGCTT
66 CCCGAAGGCTT
*
39457 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
*
39522 CCTGAAGGCTTT
66 CCCGAAGGC-TT
39534 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
39599 CCCGAAGGCTT
66 CCCGAAGGCTT
*
39610 TTTGGAAACATCATGCACTGGAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
39675 CCCGAAGGCTT
66 CCCGAAGGCTT
39686 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
39751 CCCGAAGGCTT
66 CCCGAAGGCTT
*
39762 TTTGGAAACATCATGCACTGGAGGACTTACAGATGACCCGAAGGATTTGAAAACATC-AAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
39826 CCCGAAGGCTT
66 CCCGAAGGCTT
*
39837 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGTT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
39902 CCCGAAGGCTT
66 CCCGAAGGCTT
*
39913 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGTT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
39978 CCCGAAGGCTT
66 CCCGAAGGCTT
39989 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
40024 TGGGAAATAG
Statistics
Matches: 630, Mismatches: 11, Indels: 4
0.98 0.02 0.01
Matches are distributed among these distances:
75 74 0.12
76 482 0.77
77 74 0.12
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:39711 original size:229 final size:228
Alignment explanation
Indices: 39305--40023 Score: 1341
Period size: 229 Copynumber: 3.2 Consensus size: 228
39295 GATGGAAATG
* *
39305 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
*
39370 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAAC
39435 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
131 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
* *
39500 GCTTTGAAAACATCAAAAAGCTCCTGAAGGCTTT
196 GATTTGAAAACATCAAAAAGCTCCCGAAGGC-TT
39534 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
*
39599 CCCGAAGGCTTTTTGGAAACATCATGCACTGGAGGACTTACAGATGACCCGAAGGATTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAAC
39664 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
131 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
39729 GATTTGAAAACATCAAAAAGCTCCCGAAGGCTT
196 GATTTGAAAACATCAAAAAGCTCCCGAAGGCTT
*
39762 TTTGGAAACATCATGCACTGGAGGACTTACAGATGACCCGAAGGATTTGAAAACATC-AAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
39826 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAAC
*
39891 ATCAAAAAGTTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
131 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
*
39956 GATTTGAAAACATCAAAAAGTTCCCGAAGGCTT
196 GATTTGAAAACATCAAAAAGCTCCCGAAGGCTT
39989 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
40024 TGGGAAATAG
Statistics
Matches: 479, Mismatches: 11, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
227 201 0.42
228 58 0.12
229 220 0.46
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (228 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAAC
ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
GATTTGAAAACATCAAAAAGCTCCCGAAGGCTT
Found at i:40713 original size:22 final size:22
Alignment explanation
Indices: 40688--40742 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
40678 GATAAAGCTT
40688 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
40710 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
40732 TCATCTTTGAA
1 TCATCTTTGAA
40743 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:41187 original size:54 final size:52
Alignment explanation
Indices: 41105--41213 Score: 146
Period size: 54 Copynumber: 2.1 Consensus size: 52
41095 AGAATAGCAG
*** *
41105 GTTCGTAAAACATTTGACAGTGCATTCATCTTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCAT-TTTT-CTGTGGCTTCTACTCAGAT
* *
41159 GTTCGTAAAACATTTGACAACACATTCATTTTTTTTTGGCTTCTACTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATTTTTCTGTGGCTTCTACTCAGAT
41211 GTT
1 GTT
41214 ATCAAACATT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
52 19 0.39
53 4 0.08
54 26 0.53
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (52 bp):
GTTCGTAAAACATTTGACAACACATTCATTTTTCTGTGGCTTCTACTCAGAT
Found at i:42145 original size:74 final size:75
Alignment explanation
Indices: 42004--42181 Score: 234
Period size: 74 Copynumber: 2.4 Consensus size: 75
41994 ATTGTGGGCC
* * * *
42004 TTCAGCATGCCCCAACATTGGCTAATACAAGTGTTCAAAATGCATCAACAGTTCTGATTCTGATT
1 TTCAGCATGCCCCAACATTTGCTGATACAAGTATTCAAAATACATCAACAGTTCTGATTCTGATT
*
42069 GAAATGGGTT
66 GAAAAGGGTT
* ** * *
42079 TTCAGCATGCCCCAACATTTTGCTGATA-AA-TATTCAGAATATTTCAACATTTCTGATTCTGTT
1 TTCAGCATGCCCCAACA-TTTGCTGATACAAGTATTCAAAATACATCAACAGTTCTGATTCTGAT
42142 TGAAAAGGGTT
65 TGAAAAGGGTT
*
42153 TTCAGCATGCCCCAATATTTGCTGATACA
1 TTCAGCATGCCCCAACATTTGCTGATACA
42182 GATGTTAAAA
Statistics
Matches: 90, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
73 10 0.11
74 53 0.59
75 19 0.21
76 8 0.09
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (75 bp):
TTCAGCATGCCCCAACATTTGCTGATACAAGTATTCAAAATACATCAACAGTTCTGATTCTGATT
GAAAAGGGTT
Found at i:51070 original size:111 final size:111
Alignment explanation
Indices: 50846--51046 Score: 300
Period size: 111 Copynumber: 1.8 Consensus size: 111
50836 TATACATAAA
* * * *
50846 TAAGATATTTACTTATTTAGAAATATCAGAAAAGGGCTTCTAGGTGCTTTAAGACAGCTCTTTTC
1 TAAGATATTTACTTATTCAAAAATATCAGAAAAGAGCTTCTAGGTGCTTTAAGACAACTCTTTTC
*
50911 TTTAATATTTAAAAATAAATATCAAAAACCTTTTATTTTAATATAG
66 TTTAATATTTAAAAATAAATATCAAAAACATTTTATTTTAATATAG
* *
50957 TAAGATATTTATTTATTCAAAAATATCAGAAAAGAGCTTCTAGGT-ATCTTAAGACAACT-TTTT
1 TAAGATATTTACTTATTCAAAAATATCAGAAAAGAGCTTCTAGGTGCT-TTAAGACAACTCTTTT
*
51020 CTTTGATA-TTAAAAATAAATATCAAAA
65 CTTTAATATTTAAAAATAAATATCAAAA
51047 TATGATTATT
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
109 19 0.23
110 12 0.15
111 51 0.62
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.38
Consensus pattern (111 bp):
TAAGATATTTACTTATTCAAAAATATCAGAAAAGAGCTTCTAGGTGCTTTAAGACAACTCTTTTC
TTTAATATTTAAAAATAAATATCAAAAACATTTTATTTTAATATAG
Found at i:51885 original size:13 final size:13
Alignment explanation
Indices: 51867--51895 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
51857 CCACCGTACT
51867 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
51880 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
51893 CCG
1 CCG
51896 TAACGGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:52651 original size:3 final size:3
Alignment explanation
Indices: 52643--52770 Score: 141
Period size: 3 Copynumber: 41.7 Consensus size: 3
52633 TTATTCATTA
*
52643 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
* * * * * *
52690 AAT TAT TAT TAT TAT AAT AAT AAT AAT ACT AAT AAT AAT ATTT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT
*
52736 AAT AAT AAT AAT AAT AA- ATTT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AA
52771 ATTTAAATGA
Statistics
Matches: 110, Mismatches: 10, Indels: 10
0.85 0.08 0.08
Matches are distributed among these distances:
2 1 0.01
3 100 0.91
4 9 0.08
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:64835 original size:31 final size:32
Alignment explanation
Indices: 64758--64842 Score: 95
Period size: 31 Copynumber: 2.7 Consensus size: 32
64748 TTTTAAAAAC
*
64758 AAACTCAACTC-AACTCAAAAACTTAAAAATTATC
1 AAACTCAACTCAAACTC-AAAAC-T-AAAATTATA
* *
64792 AATCT-AACTCAAACTCAAAAC-AAAATTTTA
1 AAACTCAACTCAAACTCAAAACTAAAATTATA
64822 AAACTCAACTCAAACTCAAAA
1 AAACTCAACTCAAACTCAAAA
64843 AAACTTAAAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
30 11 0.24
31 15 0.33
33 10 0.22
34 9 0.20
ACGTcount: A:0.54, C:0.24, G:0.00, T:0.22
Consensus pattern (32 bp):
AAACTCAACTCAAACTCAAAACTAAAATTATA
Found at i:64852 original size:16 final size:16
Alignment explanation
Indices: 64828--64908 Score: 81
Period size: 16 Copynumber: 5.1 Consensus size: 16
64818 TTTAAAACTC
64828 AACTCAAACTCAAAAA
1 AACTCAAACTCAAAAA
*
64844 AACTTAAACTCAAAAA
1 AACTCAAACTCAAAAA
* **
64860 AACTCAAATTCATCAA
1 AACTCAAACTCAAAAA
* * * *
64876 TATTTAAATTCAAAAA
1 AACTCAAACTCAAAAA
*
64892 ATCTCAAACTCAAAAA
1 AACTCAAACTCAAAAA
64908 A
1 A
64909 TTTCAAAAAT
Statistics
Matches: 50, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.58, C:0.20, G:0.00, T:0.22
Consensus pattern (16 bp):
AACTCAAACTCAAAAA
Found at i:64909 original size:16 final size:16
Alignment explanation
Indices: 64830--64940 Score: 76
Period size: 16 Copynumber: 7.4 Consensus size: 16
64820 TAAAACTCAA
*
64830 CTCAAACTCAAAAAAA
1 CTCAAACTCAAAAAAT
* *
64846 CTTAAACTCAAAAAAA
1 CTCAAACTCAAAAAAT
* * *
64862 CTCAAATTCATCAATAT
1 CTCAAACTCA-AAAAAT
* *
64879 -TTAAATTCAAAAAAT
1 CTCAAACTCAAAAAAT
64894 CTCAAACTCAAAAAAT
1 CTCAAACTCAAAAAAT
64910 -T-----TC-AAAAAT
1 CTCAAACTCAAAAAAT
64919 CTCAAACTCAAAAAAT
1 CTCAAACTCAAAAAAT
*
64935 TTCAAA
1 CTCAAA
64941 AACTCTATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
9 6 0.08
10 3 0.04
15 7 0.09
16 55 0.74
17 3 0.04
ACGTcount: A:0.56, C:0.20, G:0.00, T:0.24
Consensus pattern (16 bp):
CTCAAACTCAAAAAAT
Found at i:64909 original size:25 final size:26
Alignment explanation
Indices: 64884--64942 Score: 111
Period size: 25 Copynumber: 2.3 Consensus size: 26
64874 AATATTTAAA
64884 TTCAAAAAATCTCAAACTCAAAAAAT
1 TTCAAAAAATCTCAAACTCAAAAAAT
64910 TTC-AAAAATCTCAAACTCAAAAAAT
1 TTCAAAAAATCTCAAACTCAAAAAAT
64935 TTCAAAAA
1 TTCAAAAA
64943 CTCTATTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 25 0.78
26 7 0.22
ACGTcount: A:0.58, C:0.19, G:0.00, T:0.24
Consensus pattern (26 bp):
TTCAAAAAATCTCAAACTCAAAAAAT
Found at i:66640 original size:7 final size:7
Alignment explanation
Indices: 66628--66664 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
66618 TCACATAATT
66628 GGGTTTA
1 GGGTTTA
66635 GGGTTTA
1 GGGTTTA
66642 GGGTTTA
1 GGGTTTA
*
66649 GAGTTTA
1 GGGTTTA
66656 GGGTTTA
1 GGGTTTA
66663 GG
1 GG
66665 ATTCATTACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.16, C:0.00, G:0.43, T:0.41
Consensus pattern (7 bp):
GGGTTTA
Found at i:70404 original size:147 final size:149
Alignment explanation
Indices: 70015--70476 Score: 824
Period size: 149 Copynumber: 3.1 Consensus size: 149
70005 TATAATTGCA
* *
70015 CCGAAGTG-CCGCGTAGAATTGCACCGTAATGCCATATAATAATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
70079 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
70144 CCACAGAATATATATATATC
130 CCACAGAATATATATATATC
70164 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
70229 TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
70294 CACAG-A-ATATATATATC
131 CACAGAATATATATATATC
70311 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
** *
70376 TCCTTAAGAATCATATACATATGCTAGGGATCATA-TATGTGTCTCACCAGACTTCACACATGTT
66 TCCTTAAGAATCATATACATATGCTAGGGATCA-AGTATGTGTCTTTCAAGACTTCACACATGTT
*
70440 CCAAAGAATATATATATATC
130 CCACAGAATATATATATATC
70460 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
70477 CCCTCGACTC
Statistics
Matches: 303, Mismatches: 6, Indels: 8
0.96 0.02 0.03
Matches are distributed among these distances:
147 140 0.46
148 4 0.01
149 159 0.52
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CACAGAATATATATATATC
Found at i:71391 original size:18 final size:18
Alignment explanation
Indices: 71370--71404 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
71360 TCCCATCTAG
71370 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
71388 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
71405 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:72011 original size:21 final size:21
Alignment explanation
Indices: 71987--72031 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
71977 TGTTGTTCGT
* *
71987 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
72008 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
72029 TTG
1 TTG
72032 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:75317 original size:23 final size:23
Alignment explanation
Indices: 75286--75330 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
75276 CGTATAATTA
*
75286 CGTATAATTACACCGAAGTGCCG
1 CGTAGAATTACACCGAAGTGCCG
*
75309 CGTAGAATTACACCGTAGTGCC
1 CGTAGAATTACACCGAAGTGCC
75331 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (23 bp):
CGTAGAATTACACCGAAGTGCCG
Found at i:75568 original size:149 final size:147
Alignment explanation
Indices: 75298--75748 Score: 751
Period size: 149 Copynumber: 3.1 Consensus size: 147
75288 TATAATTACA
* *
75298 CCGAAGTG-CCGCGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
75362 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
75427 CCACAGAATATATATATATC
130 CCACAG-A-ATATATATATC
75447 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
75512 TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
75577 CACAGAATATATATATC
131 CACAGAATATATATATC
75594 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
** *
75659 TCC-TAAGAATCATATACATATGCT----A-C-A-TATGTGTCTCACCAGACTTCACACATGTT-
66 TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
*
75715 CAAAGAATATATATATC
131 CACAGAATATATATATC
75732 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
75749 CCCTCGATCT
Statistics
Matches: 295, Mismatches: 6, Indels: 13
0.94 0.02 0.04
Matches are distributed among these distances:
138 33 0.11
139 26 0.09
140 1 0.00
141 1 0.00
142 1 0.00
146 21 0.07
147 79 0.27
148 2 0.01
149 131 0.44
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (147 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CACAGAATATATATATC
Found at i:76648 original size:18 final size:18
Alignment explanation
Indices: 76627--76661 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
76617 TCCCATCTAG
76627 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
76645 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
76662 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:77269 original size:21 final size:21
Alignment explanation
Indices: 77245--77289 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
77235 TGTTGTTCGT
*
77245 TTGAAGGGGTACCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
* *
77266 TTGAATGGGTACTGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
77287 TTG
1 TTG
77290 CCCAAAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:79026 original size:24 final size:24
Alignment explanation
Indices: 78999--79056 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
78989 TAGTTAATGC
* *
78999 ATCGATGCACATATTACTGAGTGT
1 ATCGATGCACATACTACAGAGTGT
79023 ATCGATGCACATACTACAGAGTGT
1 ATCGATGCACATACTACAGAGTGT
*
79047 ACCGATGCAC
1 ATCGATGCAC
79057 TTCAAAGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (24 bp):
ATCGATGCACATACTACAGAGTGT
Found at i:89287 original size:18 final size:19
Alignment explanation
Indices: 89251--89289 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
89241 AAGTAAACTT
*
89251 TATATTATTTTTATTATAAA
1 TATAATATTTTTA-TATAAA
89271 TATAATATTTTTA-ATAAA
1 TATAATATTTTTATATAAA
89289 T
1 T
89290 TATCAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
20 12 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TATAATATTTTTATATAAA
Found at i:89399 original size:15 final size:15
Alignment explanation
Indices: 89379--89481 Score: 53
Period size: 16 Copynumber: 6.5 Consensus size: 15
89369 TGCTTTTGGG
89379 TCGGGTTAATTCGGT
1 TCGGGTTAATTCGGT
* *
89394 TCGGGTTACTTCGGA
1 TCGGGTTAATTCGGT
*
89409 TCGAGTTAAAATTCGGT
1 TCGGGTT--AATTCGGT
* * **
89426 TTGAGTTTCTTTCGGT
1 TCG-GGTTAATTCGGT
* *
89442 TCAGGTTAATTTCAGT
1 TCGGGTTAA-TTCGGT
* **
89458 TTGGGTTGCTTTCGGT
1 TCGGGTT-AATTCGGT
89474 TCGGGTTA
1 TCGGGTTA
89482 TTTTTAGTTT
Statistics
Matches: 60, Mismatches: 23, Indels: 10
0.65 0.25 0.11
Matches are distributed among these distances:
15 22 0.37
16 28 0.47
17 8 0.13
18 2 0.03
ACGTcount: A:0.15, C:0.14, G:0.29, T:0.43
Consensus pattern (15 bp):
TCGGGTTAATTCGGT
Found at i:89464 original size:16 final size:16
Alignment explanation
Indices: 89445--89496 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
89435 TTTCGGTTCA
89445 GGTTAATTTCAGTTTG
1 GGTTAATTTCAGTTTG
** * *
89461 GGTTGCTTTCGGTTCG
1 GGTTAATTTCAGTTTG
* *
89477 GGTTATTTTTAGTTTG
1 GGTTAATTTCAGTTTG
89493 GGTT
1 GGTT
89497 GCTTTTGGTT
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.10, C:0.08, G:0.31, T:0.52
Consensus pattern (16 bp):
GGTTAATTTCAGTTTG
Found at i:89470 original size:32 final size:31
Alignment explanation
Indices: 89424--89523 Score: 128
Period size: 32 Copynumber: 3.1 Consensus size: 31
89414 TTAAAATTCG
* *
89424 GTTTGAGTTTCTTTCGGTTCAGGTTAATTTCA
1 GTTTGGGTTGCTTTCGGTTC-GGTTAATTTCA
* *
89456 GTTTGGGTTGCTTTCGGTTCGGGTTATTTTTA
1 GTTTGGGTTGCTTTCGGTTC-GGTTAATTTCA
*
89488 GTTTGGGTTGCTTTTGGTTCGAGTTAATTTCA
1 GTTTGGGTTGCTTTCGGTTCG-GTTAATTTCA
89520 GTTT
1 GTTT
89524 CGATTCGAGT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
31 1 0.02
32 58 0.98
ACGTcount: A:0.11, C:0.10, G:0.27, T:0.52
Consensus pattern (31 bp):
GTTTGGGTTGCTTTCGGTTCGGTTAATTTCA
Found at i:89502 original size:16 final size:16
Alignment explanation
Indices: 89455--89502 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
89445 GGTTAATTTC
*
89455 AGTTTGGGTTGCTTTC
1 AGTTTGGGTTGCTTTT
* * **
89471 GGTTCGGGTTATTTTT
1 AGTTTGGGTTGCTTTT
89487 AGTTTGGGTTGCTTTT
1 AGTTTGGGTTGCTTTT
89503 GGTTCGAGTT
Statistics
Matches: 23, Mismatches: 9, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.06, C:0.08, G:0.31, T:0.54
Consensus pattern (16 bp):
AGTTTGGGTTGCTTTT
Done.