Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007751.1 Hibiscus syriacus cultivar Beakdansim tig00110017_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: 1434969
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 6 of 6
Found at i:1360131 original size:75 final size:76
Alignment explanation
Indices: 1360046--1360195 Score: 223
Period size: 76 Copynumber: 2.0 Consensus size: 76
1360036 AGATGATTTG
* * * *
1360046 CCATTTTTCAGGAATTGGGTA-TTGTTTATGATTTTTGGTATCTGAACATTTGA-ATTGAAATGA
1 CCATTTTTCAGGAATTGGGTATTTGTTTACGATCTTTGGTATCTAAACATTTGATA-TAAAATGA
1360109 AGTTCCATGATT
65 AGTTCCATGATT
* *
1360121 CCATTTTTCAGGAATTGGGTATTTGTTTACGATCTTTGTTATCTAAAGATTTGATATAAAATGAA
1 CCATTTTTCAGGAATTGGGTATTTGTTTACGATCTTTGGTATCTAAACATTTGATATAAAATGAA
1360186 GTTCCATGAT
66 GTTCCATGAT
1360196 AACCGGATGA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
75 21 0.31
76 45 0.67
77 1 0.01
ACGTcount: A:0.28, C:0.10, G:0.19, T:0.43
Consensus pattern (76 bp):
CCATTTTTCAGGAATTGGGTATTTGTTTACGATCTTTGGTATCTAAACATTTGATATAAAATGAA
GTTCCATGATT
Found at i:1360252 original size:189 final size:190
Alignment explanation
Indices: 1359932--1360309 Score: 749
Period size: 189 Copynumber: 2.0 Consensus size: 190
1359922 AGATGATTTG
1359932 CCATTTTTCAGGAATTGGGTATTTGTTTACGATCTTTGTTATCTAAAGATTTGATATAAAATGAA
1 CCATTTTTCAGGAATTGGGTATTTGTTTACGATCTTTGTTATCTAAAGATTTGATATAAAATGAA
1359997 GTTCCATGATAACCGGATGACTTGAACTTGAGCTCTTTAAGATGATTTGCCATTTTTCAGGAATT
66 GTTCCATGATAACCGGATGACTTGAACTTGAGCTCTTTAAGATGATTTGCCATTTTTCAGGAATT
1360062 GGGTA-TTGTTTATGATTTTTGGTATCTGAACATTTGAATTGAAATGAAGTTCCATGATT
131 GGGTATTTGTTTATGATTTTTGGTATCTGAACATTTGAATTGAAATGAAGTTCCATGATT
1360121 CCATTTTTCAGGAATTGGGTATTTGTTTACGATCTTTGTTATCTAAAGATTTGATATAAAATGAA
1 CCATTTTTCAGGAATTGGGTATTTGTTTACGATCTTTGTTATCTAAAGATTTGATATAAAATGAA
1360186 GTTCCATGATAACCGGATGACTTGAACTTGAGCTCTTTAAGATGATTTGCCATTTTTCAGGAATT
66 GTTCCATGATAACCGGATGACTTGAACTTGAGCTCTTTAAGATGATTTGCCATTTTTCAGGAATT
1360251 GGGTATTTGTTTATGATTTTTGGTATCTGAACATTTGAATTGAAATGAAGTTCCATGAT
131 GGGTATTTGTTTATGATTTTTGGTATCTGAACATTTGAATTGAAATGAAGTTCCATGAT
1360310 AACTGGATGA
Statistics
Matches: 188, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
189 135 0.72
190 53 0.28
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (190 bp):
CCATTTTTCAGGAATTGGGTATTTGTTTACGATCTTTGTTATCTAAAGATTTGATATAAAATGAA
GTTCCATGATAACCGGATGACTTGAACTTGAGCTCTTTAAGATGATTTGCCATTTTTCAGGAATT
GGGTATTTGTTTATGATTTTTGGTATCTGAACATTTGAATTGAAATGAAGTTCCATGATT
Found at i:1360402 original size:110 final size:110
Alignment explanation
Indices: 1360121--1360435 Score: 454
Period size: 114 Copynumber: 2.8 Consensus size: 110
1360111 TTCCATGATT
* * *
1360121 CCATTTTTCAGGAATTGGGTATTTGTTTACGATCTTTGTTATCTAAAGATTTG-ATATAAAATGA
1 CCATTTTTCAGGAATTGGGTATTTGTTTACGATCTTTGGTATCTGAAGATTTGAAT-TGAAATGA
*
1360185 AGTTCCATGATAACCGGATGACTTGAACTTGAGCTCTTTAAGATGATTTG
65 AGTTCCATGATAACTGGATGACTTGAAC----GCTCTTTAAGATGATTTG
* * *
1360235 CCATTTTTCAGGAATTGGGTATTTGTTTATGATTTTTGGTATCTGAACATTTGAATTGAAATGAA
1 CCATTTTTCAGGAATTGGGTATTTGTTTACGATCTTTGGTATCTGAAGATTTGAATTGAAATGAA
*
1360300 GTTCCATGATAACTGGATGAGTTGAAC-CTCTTTAAGATGATTTG
66 GTTCCATGATAACTGGATGACTTGAACGCTCTTTAAGATGATTTG
* *
1360344 TCATTTTTCAGGAATTTGGGTATTTGTTAACGATCTTTGGTATCTGAAGATTTGAATTGAAATGA
1 CCATTTTTCAGGAA-TTGGGTATTTGTTTACGATCTTTGGTATCTGAAGATTTGAATTGAAATGA
* *
1360409 AGTTTCATGATAGCTGGATGACTTGAA
65 AGTTCCATGATAACTGGATGACTTGAA
1360436 AGATCTCATC
Statistics
Matches: 183, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
109 30 0.16
110 70 0.38
114 81 0.44
115 2 0.01
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.40
Consensus pattern (110 bp):
CCATTTTTCAGGAATTGGGTATTTGTTTACGATCTTTGGTATCTGAAGATTTGAATTGAAATGAA
GTTCCATGATAACTGGATGACTTGAACGCTCTTTAAGATGATTTG
Found at i:1360604 original size:16 final size:16
Alignment explanation
Indices: 1360583--1360614 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1360573 ATATACACAC
*
1360583 ATATATGTATGTATGT
1 ATATATATATGTATGT
1360599 ATATATATATGTATGT
1 ATATATATATGTATGT
1360615 GCGTGTATAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (16 bp):
ATATATATATGTATGT
Found at i:1361580 original size:21 final size:21
Alignment explanation
Indices: 1361556--1361595 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1361546 TTATCACTAC
*
1361556 ATAATATG-TGATTATATCATT
1 ATAATA-GATGATTACATCATT
1361577 ATAATAGATGATTACATCA
1 ATAATAGATGATTACATCA
1361596 ATATTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.40
Consensus pattern (21 bp):
ATAATAGATGATTACATCATT
Found at i:1362756 original size:195 final size:196
Alignment explanation
Indices: 1362424--1362815 Score: 761
Period size: 195 Copynumber: 2.0 Consensus size: 196
1362414 ATACTGTTAA
1362424 ATTGGTTGGATACAACTTTTAAACATTTGAGTCACGACGCCTCTGAGGAACATATTAAAATGTAT
1 ATTGGTTGGATACAACTTTTAAACATTTGAGTCACGACGCCTCTGAGGAACATATTAAAATGTAT
1362489 GAATGAGCTTGCATATTACAACTCATAGGAGGGATTCTTGATGCCCACAAATCAAGCAACCAAGT
66 GAATGAGCTTGCATATTACAACTCATAGGAGGGATTCTTGATGCCCACAAATCAAGCAACCAAGT
1362554 TTAATGTATGTGGTTGCATCACCTCACAGCTTTTCACGTTGCC-GCGCACTCAGTTGGGGCTCTG
131 TTAATGTATGTGGTTGCATCACCTCACAGCTTTTCACGTTGCCGGCGCACTCAGTTGGGGCTCTG
1362618 C
196 C
1362619 ATTGGTTGGATACAACTTTTAAACATTTGAGTCACGACGCCTCTGAGGAACATATTAAAATGTAT
1 ATTGGTTGGATACAACTTTTAAACATTTGAGTCACGACGCCTCTGAGGAACATATTAAAATGTAT
1362684 GAATGAGCTTGCATATTACAACTCATAGGAGGGA-TCTTGATGCCCGACAAATCAAGCAACCAAG
66 GAATGAGCTTGCATATTACAACTCATAGGAGGGATTCTTGATGCCC-ACAAATCAAGCAACCAAG
1362748 TTTAATGTATGTGGTTGCATCACCTCACAGCTTTTCACGTTGCCGGCGCACTCAGTTGGGGCTCT
130 TTTAATGTATGTGGTTGCATCACCTCACAGCTTTTCACGTTGCCGGCGCACTCAGTTGGGGCTCT
1362813 GC
195 GC
1362815 A
1 A
1362816 GTTTTGGCAT
Statistics
Matches: 195, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
194 11 0.06
195 161 0.83
196 23 0.12
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.29
Consensus pattern (196 bp):
ATTGGTTGGATACAACTTTTAAACATTTGAGTCACGACGCCTCTGAGGAACATATTAAAATGTAT
GAATGAGCTTGCATATTACAACTCATAGGAGGGATTCTTGATGCCCACAAATCAAGCAACCAAGT
TTAATGTATGTGGTTGCATCACCTCACAGCTTTTCACGTTGCCGGCGCACTCAGTTGGGGCTCTG
C
Found at i:1364329 original size:19 final size:18
Alignment explanation
Indices: 1364307--1364348 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1364297 GTTTACTAGC
1364307 AATTTTAAAGTTTTTATTT
1 AATTTTAAA-TTTTTATTT
* *
1364326 AATTATGAATTTTTATTT
1 AATTTTAAATTTTTATTT
1364344 -ATTTT
1 AATTTT
1364349 GTTTGTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 4 0.20
18 9 0.45
19 7 0.35
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (18 bp):
AATTTTAAATTTTTATTT
Found at i:1366825 original size:60 final size:60
Alignment explanation
Indices: 1366728--1366844 Score: 171
Period size: 60 Copynumber: 1.9 Consensus size: 60
1366718 CACGATGTCG
* * * * * *
1366728 ACATTTAGGTCGAACAAGTTGGTAGTTGAATGTCTTCCCCTTAAACTTGAAGGCATCTCA
1 ACATTGAGGTCGAACAAGCTCGCAGTTGAATGCCTTCCCCTAAAACTTGAAGGCATCTCA
*
1366788 ACATTGAGGTCGAAGAAGCTCGCAGTTGAATGCCTTCCCCTAAAACTTGAAGGCATC
1 ACATTGAGGTCGAACAAGCTCGCAGTTGAATGCCTTCCCCTAAAACTTGAAGGCATC
1366845 GTGTCAAATG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.27
Consensus pattern (60 bp):
ACATTGAGGTCGAACAAGCTCGCAGTTGAATGCCTTCCCCTAAAACTTGAAGGCATCTCA
Found at i:1367742 original size:11 final size:11
Alignment explanation
Indices: 1367696--1367765 Score: 65
Period size: 11 Copynumber: 6.5 Consensus size: 11
1367686 ACAACAACAA
1367696 AAAAT-AATAT
1 AAAATAAATAT
*
1367706 AAAATAATTAGT
1 AAAATAAATA-T
* *
1367718 ACAATAAATGT
1 AAAATAAATAT
*
1367729 AAATTAAATAT
1 AAAATAAATAT
1367740 AAAATAAATAT
1 AAAATAAATAT
*
1367751 AATAT-AATA-
1 AAAATAAATAT
1367760 AAAATA
1 AAAATA
1367766 TTAGTAAAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
9 4 0.09
10 9 0.19
11 26 0.55
12 8 0.17
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (11 bp):
AAAATAAATAT
Found at i:1367777 original size:53 final size:57
Alignment explanation
Indices: 1367699--1367827 Score: 149
Period size: 58 Copynumber: 2.3 Consensus size: 57
1367689 ACAACAAAAA
*
1367699 ATAATATAAAATAATTAGTACAATAA-ATGT-A-AATTAAATATAAAATAAATATAAT
1 ATAATA-AAAATAATTAGTAAAATAATATGTAATAATTAAATATAAAATAAATATAAT
* * * *
1367754 ATAATAAAAAT-ATTAGTAAAATAATTTTTTAAATAATTAAATATAAACTAATTATAAT
1 ATAATAAAAATAATTAGTAAAATAA-TATGT-AATAATTAAATATAAAATAAATATAAT
1367812 ATAATAAAAAATAATT
1 ATAAT-AAAAATAATT
1367828 TTACATTATA
Statistics
Matches: 62, Mismatches: 5, Indels: 9
0.82 0.07 0.12
Matches are distributed among these distances:
53 12 0.19
54 5 0.08
55 8 0.13
57 1 0.02
58 27 0.44
59 6 0.10
60 3 0.05
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (57 bp):
ATAATAAAAATAATTAGTAAAATAATATGTAATAATTAAATATAAAATAAATATAAT
Found at i:1367807 original size:15 final size:15
Alignment explanation
Indices: 1367783--1367815 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
1367773 AATAATTTTT
1367783 TAAATAATTA-AATA
1 TAAATAATTATAATA
1367797 TAAACTAATTATAATA
1 TAAA-TAATTATAATA
1367813 TAA
1 TAA
1367816 TAAAAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 6 0.35
16 7 0.41
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (15 bp):
TAAATAATTATAATA
Found at i:1371127 original size:18 final size:19
Alignment explanation
Indices: 1371093--1371129 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1371083 TTCTGATAAT
*
1371093 TTTAAAATTTTTATTTAAA
1 TTTAAAATTTATATTTAAA
1371112 TTTAAAA-TTATATTTAAA
1 TTTAAAATTTATATTTAAA
1371130 AACATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTAAAATTTATATTTAAA
Found at i:1378523 original size:16 final size:16
Alignment explanation
Indices: 1378502--1378534 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1378492 TAATAAATAA
1378502 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1378518 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1378534 A
1 A
1378535 AAAATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1378625 original size:16 final size:16
Alignment explanation
Indices: 1378604--1378664 Score: 113
Period size: 16 Copynumber: 3.8 Consensus size: 16
1378594 TAATAAATAA
1378604 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1378620 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1378636 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
1378652 ACGAACATAAACG
1 ACGAACATAAACG
1378665 TTGGAGACCC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.56, C:0.23, G:0.13, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1379708 original size:24 final size:24
Alignment explanation
Indices: 1379681--1379755 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
1379671 TATTGGGTTA
* *
1379681 AACATAAATGAATGAACATAAACG
1 AACATAACTGAACGAACATAAACG
1379705 AACATAACTGAACGAACATAAACG
1 AACATAACTGAACGAACATAAACG
* *
1379729 AACATAACCGAACGAACATAACCG
1 AACATAACTGAACGAACATAAACG
1379753 AAC
1 AAC
1379756 GTTCACGAAC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.55, C:0.21, G:0.12, T:0.12
Consensus pattern (24 bp):
AACATAACTGAACGAACATAAACG
Found at i:1379718 original size:14 final size:14
Alignment explanation
Indices: 1379701--1379756 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
1379691 AATGAACATA
*
1379701 AACGAACATAACTG
1 AACGAACATAACCG
1379715 AACGAACAT-A---
1 AACGAACATAACCG
1379725 AACGAACATAACCG
1 AACGAACATAACCG
1379739 AACGAACATAACCG
1 AACGAACATAACCG
1379753 AACG
1 AACG
1379757 TTCACGAACG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 27 0.71
ACGTcount: A:0.52, C:0.25, G:0.14, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:1379755 original size:10 final size:10
Alignment explanation
Indices: 1379694--1379741 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
1379684 ATAAATGAAT
1379694 GAACATAAAC
1 GAACATAAAC
1379704 GAACATAACTGAAC
1 GAACAT-A---AAC
1379718 GAACATAAAC
1 GAACATAAAC
*
1379728 GAACATAACC
1 GAACATAAAC
1379738 GAAC
1 GAAC
1379742 GAACATAACC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Found at i:1390546 original size:13 final size:13
Alignment explanation
Indices: 1390528--1390552 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1390518 TGAAGCAAAC
1390528 CCATCAGTAAGTG
1 CCATCAGTAAGTG
1390541 CCATCAGTAAGT
1 CCATCAGTAAGT
1390553 CTTTCGAGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:1390580 original size:22 final size:21
Alignment explanation
Indices: 1390548--1390622 Score: 64
Period size: 22 Copynumber: 3.5 Consensus size: 21
1390538 GTGCCATCAG
*
1390548 TAAGTCTTTCGAGCATGATGA
1 TAAGTCCTTCGAGCATGATGA
* *
1390569 TGAAGTCCTTCGGGCCATCA-G-
1 T-AAGTCCTTCGAG-CATGATGA
*
1390590 TAAGTCTTTCGAGCATGATGA
1 TAAGTCCTTCGAGCATGATGA
*
1390611 TTAAATCCTTCG
1 -TAAGTCCTTCG
1390623 GGTAATTTGT
Statistics
Matches: 41, Mismatches: 8, Indels: 9
0.71 0.14 0.16
Matches are distributed among these distances:
19 4 0.10
20 11 0.27
21 2 0.05
22 20 0.49
23 4 0.10
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (21 bp):
TAAGTCCTTCGAGCATGATGA
Found at i:1390599 original size:42 final size:42
Alignment explanation
Indices: 1390540--1390922 Score: 210
Period size: 42 Copynumber: 9.0 Consensus size: 42
1390530 ATCAGTAAGT
*
1390540 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGG
*
1390582 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGG
** ** * * * * *
1390624 GTAATTTGTAAGCCTTCACCGAAGAAT-AGTGAAGCAAATCCATCAGTAAG
1 GCCATCAGTAAGTCTT--TCG-AGCATGA-TGATG-AAATCCTTC-G---G
*
1390674 TGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
1 -GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGG
** ** * * * * **
1390717 GTAATTTGTAAG-CCTTC-ACCGAAGA-GTAGTG-AAGCAAAT---
1 GCCATCAGTAAGTCTTTCGAGC-ATGATG-A-TGAAATC-CTTCGG
* *
1390756 -CCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGA
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGG
* * * *
1390797 GTCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCAG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGG
* * * * *
1390839 GCCATAAGTAAGTCTTTCGAGGATGATGATTAAATCATTCAG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGG
* *** * * *
1390881 GTCATTTTTGAGTCTTTCGAGCAAGATAAT-AAATCCTTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGG
1390922 G
1 G
1390923 TTATCCATAA
Statistics
Matches: 255, Mismatches: 63, Indels: 47
0.70 0.17 0.13
Matches are distributed among these distances:
38 10 0.04
39 10 0.04
40 6 0.02
41 21 0.08
42 157 0.62
43 1 0.00
44 3 0.01
45 7 0.03
46 9 0.04
47 9 0.04
48 7 0.03
49 3 0.01
50 1 0.00
51 11 0.04
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (42 bp):
GCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGG
Found at i:1390600 original size:20 final size:20
Alignment explanation
Indices: 1390540--1390603 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
1390530 ATCAGTAAGT
1390540 GCCATCAGTAAGTCTTTCGA
1 GCCATCAGTAAGTCTTTCGA
* * *
1390560 G-CATGATGATGAAGTCCTTCGG
1 GCCATCA-G-T-AAGTCTTTCGA
1390582 GCCATCAGTAAGTCTTTCGA
1 GCCATCAGTAAGTCTTTCGA
1390602 GC
1 GC
1390604 ATGATGATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
19 4 0.12
20 13 0.38
21 2 0.06
22 11 0.32
23 4 0.12
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.28
Consensus pattern (20 bp):
GCCATCAGTAAGTCTTTCGA
Found at i:1390627 original size:135 final size:135
Alignment explanation
Indices: 1390436--1390717 Score: 474
Period size: 135 Copynumber: 2.1 Consensus size: 135
1390426 TAAACAATCT
* * *
1390436 AAGTCCTTTGGGCCATCAGTAAGGCTTTCGAGCATGATGATTAAGTCTTTCAGGTAATTTGTAAG
1 AAGTCCTTCGGGCCATCAGTAAGGCTTTCGAGCATGATGATTAAATCCTTCAGGTAATTTGTAAG
* *
1390501 CCTTCATCGAAGAGTAGTGAAGCAAACCCATCAGTAAGTGCCATCAGTAAGTCTTTCGAGCATGA
66 CCTTCACCGAAGAATAGTGAAGCAAACCCATCAGTAAGTGCCATCAGTAAGTCTTTCGAGCATGA
1390566 TGATG
131 TGATG
* *
1390571 AAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAG
1 AAGTCCTTCGGGCCATCAGTAAGGCTTTCGAGCATGATGATTAAATCCTTCAGGTAATTTGTAAG
*
1390636 CCTTCACCGAAGAATAGTGAAGCAAATCCATCAGTAAGTGCCATCAGTAAGTCTTTCGAGCATGA
66 CCTTCACCGAAGAATAGTGAAGCAAACCCATCAGTAAGTGCCATCAGTAAGTCTTTCGAGCATGA
*
1390701 TGATT
131 TGATG
*
1390706 AAATCCTTCGGG
1 AAGTCCTTCGGG
1390718 TAATTTGTAA
Statistics
Matches: 137, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
135 137 1.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.29
Consensus pattern (135 bp):
AAGTCCTTCGGGCCATCAGTAAGGCTTTCGAGCATGATGATTAAATCCTTCAGGTAATTTGTAAG
CCTTCACCGAAGAATAGTGAAGCAAACCCATCAGTAAGTGCCATCAGTAAGTCTTTCGAGCATGA
TGATG
Found at i:1390681 original size:13 final size:13
Alignment explanation
Indices: 1390663--1390687 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1390653 TGAAGCAAAT
1390663 CCATCAGTAAGTG
1 CCATCAGTAAGTG
1390676 CCATCAGTAAGT
1 CCATCAGTAAGT
1390688 CTTTCGAGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:1390741 original size:93 final size:93
Alignment explanation
Indices: 1390582--1390767 Score: 363
Period size: 93 Copynumber: 2.0 Consensus size: 93
1390572 AGTCCTTCGG
1390582 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAA
1 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAA
1390647 GAATAGTGAAGCAAATCCATCAGTAAGT
66 GAATAGTGAAGCAAATCCATCAGTAAGT
1390675 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAA
1 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAA
*
1390740 GAGTAGTGAAGCAAATCCATCAGTAAGT
66 GAATAGTGAAGCAAATCCATCAGTAAGT
1390768 CTTTCGAGCA
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (93 bp):
GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAA
GAATAGTGAAGCAAATCCATCAGTAAGT
Found at i:1390789 original size:22 final size:21
Alignment explanation
Indices: 1390763--1390868 Score: 78
Period size: 20 Copynumber: 5.0 Consensus size: 21
1390753 AATCCATCAG
1390763 TAAGTCTTTCGAGCATGATGA
1 TAAGTCTTTCGAGCATGATGA
* *
1390784 TGAAGTCCTTCGAGTCATCA-G-
1 T-AAGTCTTTCGAG-CATGATGA
1390805 TAAGTCTTTCGAGCATGATGA
1 TAAGTCTTTCGAGCATGATGA
* * *
1390826 TTAAATCATTC-AGGCCAT-AAG-
1 -TAAGTCTTTCGA-G-CATGATGA
*
1390847 TAAGTCTTTCGAGGATGATGA
1 TAAGTCTTTCGAGCATGATGA
1390868 T
1 T
1390869 TAAATCATTC
Statistics
Matches: 64, Mismatches: 11, Indels: 20
0.67 0.12 0.21
Matches are distributed among these distances:
19 6 0.09
20 23 0.36
21 5 0.08
22 23 0.36
23 7 0.11
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (21 bp):
TAAGTCTTTCGAGCATGATGA
Found at i:1391441 original size:53 final size:53
Alignment explanation
Indices: 1391364--1391567 Score: 293
Period size: 53 Copynumber: 3.8 Consensus size: 53
1391354 ATCACACCAT
* *
1391364 AAGATTGTTCAAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGACAT
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGACAG
* *
1391417 AAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGACAG
* *
1391470 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTTGGTC-G
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCG-TAGACAG
* * * * *
1391523 AAGTTTGTTCGAGTTCTACTTCTTGAAGCAATAGGGAGCAAACCC
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCC
1391568 TTTTTTTAGA
Statistics
Matches: 138, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
53 135 0.98
54 3 0.02
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.23
Consensus pattern (53 bp):
AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGACAG
Found at i:1409700 original size:14 final size:14
Alignment explanation
Indices: 1409681--1409708 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1409671 AGAACACAAT
1409681 TATGTTATGGCACA
1 TATGTTATGGCACA
1409695 TATGTTATGGCACA
1 TATGTTATGGCACA
1409709 GTAGACTAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (14 bp):
TATGTTATGGCACA
Found at i:1419714 original size:6 final size:6
Alignment explanation
Indices: 1419656--1419710 Score: 92
Period size: 6 Copynumber: 9.2 Consensus size: 6
1419646 AATTATTCAA
*
1419656 AGAGGG AGAGTG AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG
1 AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG
*
1419704 ATAGGG A
1 AGAGGG A
1419711 TAGGAAACGC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.35, C:0.00, G:0.62, T:0.04
Consensus pattern (6 bp):
AGAGGG
Found at i:1427533 original size:84 final size:84
Alignment explanation
Indices: 1427392--1427559 Score: 318
Period size: 84 Copynumber: 2.0 Consensus size: 84
1427382 AATCAAATAA
*
1427392 ATGTTTTTTCTTGTGCTTATAAGATTTCATTTTGATTATTTTGAACCGGCTCGTATCGCACACTT
1 ATGTTTTTTCTTGTGCTTATAAGATTTCATTTTGATTATTTTAAACCGGCTCGTATCGCACACTT
*
1427457 GATTTTGATTGGTGAATTT
66 GATTTTGATAGGTGAATTT
1427476 ATGTTTTTTCTTGTGCTTATAAGATTTCATTTTGATTATTTTAAACCGGCTCGTATCGCACACTT
1 ATGTTTTTTCTTGTGCTTATAAGATTTCATTTTGATTATTTTAAACCGGCTCGTATCGCACACTT
1427541 GATTTTGATAGGTGAATTT
66 GATTTTGATAGGTGAATTT
1427560 TTTTAGGAAT
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 82 1.00
ACGTcount: A:0.21, C:0.13, G:0.17, T:0.48
Consensus pattern (84 bp):
ATGTTTTTTCTTGTGCTTATAAGATTTCATTTTGATTATTTTAAACCGGCTCGTATCGCACACTT
GATTTTGATAGGTGAATTT
Found at i:1429093 original size:38 final size:36
Alignment explanation
Indices: 1429022--1429266 Score: 219
Period size: 38 Copynumber: 6.4 Consensus size: 36
1429012 TATATTTTCG
*
1429022 AAAACATTTTG--AAAATATATAATATATAGTTTTT
1 AAAACATTTTGAAAAAATATATAATATATAATTTTT
* *
1429056 AAAACATTTTGAAAACATTTATATATTATATAATTTTTTTT
1 AAAACATTTTGAAAA-A-ATATATAATATATAA---TTTTT
* * * *
1429097 AAAAAATGTTTTTACAAAAAAATATAATATATAATTTTC
1 AAAACA--TTTTGA-AAAAATATATAATATATAATTTTT
*
1429136 AAAACATTTTTGAAAAAATATATATATTATATAGTTTTT
1 AAAACA-TTTTGAAAAAATATATA-A-TATATAATTTTT
1429175 AAAACATTTTGAAAATAAATATATAATATATAATTTTTT
1 AAAACATTTTG-AAA-AAATATATAATATATAA-TTTTT
1429214 GAAAAAACATTTTG--AAAATATATAATATATAATTTTT
1 ---AAAACATTTTGAAAAAATATATAATATATAATTTTT
*
1429251 AAAATATTTTTGAAAA
1 AAAACA-TTTTGAAAA
1429267 TTATATGGTT
Statistics
Matches: 173, Mismatches: 17, Indels: 39
0.76 0.07 0.17
Matches are distributed among these distances:
34 16 0.09
35 5 0.03
36 2 0.01
37 18 0.10
38 46 0.27
39 35 0.20
40 9 0.05
41 10 0.06
42 23 0.13
43 6 0.03
44 3 0.02
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (36 bp):
AAAACATTTTGAAAAAATATATAATATATAATTTTT
Found at i:1429157 original size:115 final size:114
Alignment explanation
Indices: 1429010--1429272 Score: 329
Period size: 115 Copynumber: 2.3 Consensus size: 114
1429000 TTTTTTTATT
1429010 TATAT-ATTTTCGAAAACA-TTTTG-AAAATATATA-A-TATATAGTTTTTAAAACATTTTGAAA
1 TATATAATTTTC-AAAACATTTTTGAAAAATATATATATTATATAGTTTTTAAAACATTTTGAAA
** * * **
1429070 ACATTTATATATTATATAATTTTTTTTAAAAAATGTTTTTACAAAAAAATATAA
65 ACAAATATATAATATATAA-TTTTTTGAAAAAA-CATTTT--AAAAAAATATAA
1429124 TATATAATTTTCAAAACATTTTTGAAAAAATATATATATTATATAGTTTTTAAAACATTTTGAAA
1 TATATAATTTTCAAAACATTTTTG-AAAAATATATATATTATATAGTTTTTAAAACATTTTGAAA
* * *
1429189 ATAAATATATAATATATAATTTTTTGAAAAAACATTTTGAAAATATATAA
65 ACAAATATATAATATATAATTTTTTGAAAAAACATTTTAAAAAAATATAA
* * *
1429239 TATATAATTTTTAAAATATTTTTGAAAATTATAT
1 TATATAATTTTCAAAACATTTTTGAAAAATATAT
1429273 GGTTTTAAAA
Statistics
Matches: 131, Mismatches: 12, Indels: 12
0.85 0.08 0.08
Matches are distributed among these distances:
114 20 0.15
115 43 0.33
117 14 0.11
118 13 0.10
119 41 0.31
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (114 bp):
TATATAATTTTCAAAACATTTTTGAAAAATATATATATTATATAGTTTTTAAAACATTTTGAAAA
CAAATATATAATATATAATTTTTTGAAAAAACATTTTAAAAAAATATAA
Found at i:1429306 original size:17 final size:16
Alignment explanation
Indices: 1429254--1429316 Score: 56
Period size: 17 Copynumber: 3.8 Consensus size: 16
1429244 AATTTTTAAA
1429254 ATATTTTTGAAAATTAT
1 ATATTTTT-AAAATTAT
** * *
1429271 ATGGTTTTAAAA-AAA
1 ATATTTTTAAAATTAT
1429286 ATATTTTTGAAAATTAT
1 ATATTTTT-AAAATTAT
1429303 ATATATTTTAAAAT
1 ATAT-TTTTAAAAT
1429317 ATTTTTGGAA
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
15 7 0.20
16 8 0.23
17 16 0.46
18 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (16 bp):
ATATTTTTAAAATTAT
Found at i:1429335 original size:30 final size:31
Alignment explanation
Indices: 1429238--1429347 Score: 120
Period size: 32 Copynumber: 3.5 Consensus size: 31
1429228 AAAATATATA
1429238 ATATATAATTTTTAAAATATTTTTGAAAATT
1 ATATATAATTTTTAAAATATTTTTGAAAATT
* **
1429269 ATATGGT--TTTAAAAAAAATATTTTTGAAAATT
1 ATAT-ATAATTT--TTAAAATATTTTTGAAAATT
*
1429301 ATATAT-A-TTTTAAAATATTTTTGGAAATTT
1 ATATATAATTTTTAAAATATTTTT-GAAAATT
1429331 ATATATAATTTTTAAAA
1 ATATATAATTTTTAAAA
1429348 GAAACGGTTT
Statistics
Matches: 65, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
29 11 0.17
30 15 0.23
31 8 0.12
32 31 0.48
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.49
Consensus pattern (31 bp):
ATATATAATTTTTAAAATATTTTTGAAAATT
Found at i:1429397 original size:3 final size:3
Alignment explanation
Indices: 1429389--1429439 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
1429379 TTTATATTTG
* * *
1429389 TTA TTA TTA TTA TTTA TTA TCA CTA TTA TTA TTA ATA TT- TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1429434 CTTA TT
1 -TTA TT
1429440 TTTTGTTAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
2 2 0.05
3 31 0.79
4 6 0.15
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1429710 original size:16 final size:15
Alignment explanation
Indices: 1429689--1429718 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1429679 CCGGTCGAAA
1429689 ATCTCGGGACTGACCC
1 ATCTCGGGA-TGACCC
1429705 ATCTCGGGATGACC
1 ATCTCGGGATGACC
1429719 GGCCTCAACG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.33, G:0.27, T:0.20
Consensus pattern (15 bp):
ATCTCGGGATGACCC
Found at i:1431041 original size:14 final size:14
Alignment explanation
Indices: 1431024--1431090 Score: 50
Period size: 14 Copynumber: 4.8 Consensus size: 14
1431014 TTTACTAAAT
1431024 TTTATTTATATTTA
1 TTTATTTATATTTA
*
1431038 TTTATCTAT-TTATA
1 TTTATTTATATT-TA
* * *
1431052 TTATATTAATTTTTC
1 TT-TATTTATATTTA
1431067 TTT-TTTCATATTTA
1 TTTATTT-ATATTTA
1431081 TTT-TTTATAT
1 TTTATTTATAT
1431091 ATTCTAACAA
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
13 8 0.19
14 24 0.57
15 8 0.19
16 2 0.05
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTATTTATATTTA
Done.