Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008907.1 Corchorus capsularis cultivar CVL-1 contig08928, 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: 41685
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:83 original size:15 final size:14
Alignment explanation
Indices: 32--124 Score: 58
Period size: 11 Copynumber: 7.1 Consensus size: 14
22 TTATGATTAG
*
32 TTTTAATTAGTTAA
1 TTTTAATTAGTTTA
** *
46 TTAAAATTA-CTTA
1 TTTTAATTAGTTTA
*
59 GTTT-ATTAGTTTA
1 TTTTAATTAGTTTA
72 TGTTTAATTAG--TA
1 T-TTTAATTAGTTTA
*
85 -TATAATTAGTTTA
1 TTTTAATTAGTTTA
98 TTATTAATTAG--TA
1 TT-TTAATTAGTTTA
111 -TTTAATTAGTTTA
1 TTTTAATTAGTTTA
124 T
1 T
125 GATTAAAATG
Statistics
Matches: 58, Mismatches: 11, Indels: 20
0.65 0.12 0.22
Matches are distributed among these distances:
11 16 0.28
12 5 0.09
13 14 0.24
14 11 0.19
15 12 0.21
ACGTcount: A:0.34, C:0.01, G:0.09, T:0.56
Consensus pattern (14 bp):
TTTTAATTAGTTTA
Found at i:92 original size:26 final size:26
Alignment explanation
Indices: 63--130 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
53 TACTTAGTTT
63 ATTAGTTTATGTTTAATTAGTATATA
1 ATTAGTTTATGTTTAATTAGTATATA
*
89 ATTAGTTTAT-TATTAATTAGTATTTA
1 ATTAGTTTATGT-TTAATTAGTATATA
*
115 ATTAGTTTATGATTAA
1 ATTAGTTTATGTTTAA
131 AATGAAGGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 1 0.03
26 37 0.97
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.54
Consensus pattern (26 bp):
ATTAGTTTATGTTTAATTAGTATATA
Found at i:130 original size:15 final size:14
Alignment explanation
Indices: 63--130 Score: 58
Period size: 15 Copynumber: 5.1 Consensus size: 14
53 TACTTAGTTT
*
63 ATTAGTTTATGTTTA
1 ATTAGTTTAT-ATTA
78 ATTAG--TATA-TA
1 ATTAGTTTATATTA
89 ATTAGTTTATTATTA
1 ATTAGTTTA-TATTA
104 ATTAG--TAT-TTA
1 ATTAGTTTATATTA
115 ATTAGTTTATGATTA
1 ATTAGTTTAT-ATTA
130 A
1 A
131 AATGAAGGAA
Statistics
Matches: 44, Mismatches: 1, Indels: 16
0.72 0.02 0.26
Matches are distributed among these distances:
11 15 0.34
12 1 0.02
13 10 0.23
14 2 0.05
15 16 0.36
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.54
Consensus pattern (14 bp):
ATTAGTTTATATTA
Found at i:178 original size:24 final size:25
Alignment explanation
Indices: 139--198 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
129 AAAATGAAGG
*
139 AAAATGAA-TTTGAAG-ATTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
162 AAAATGAAGTTTGAAGAAGTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
*
187 GAAATGAAGTTT
1 AAAATGAAGTTT
199 AGGGTTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
23 8 0.24
24 7 0.21
25 18 0.55
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (25 bp):
AAAATGAAGTTTGAAGAAGTTGTTA
Found at i:1539 original size:438 final size:437
Alignment explanation
Indices: 655--1659 Score: 1238
Period size: 438 Copynumber: 2.3 Consensus size: 437
645 ACATCTGGAT
* * ** * * *
655 AAAAAATAATATGAAATTAAATAGATTATCAATCAAAATCACAAAATTTCAAAAGTATTTTTTAG
1 AAAAAATTATATGATATTAAATAGACCAACAATCAAAA-CACAAAATTTAAAAAGCATTTTTTAG
* * * * * ** *
720 AATTGAAATATGAAAATTAT-CTTTTTAGTCTTTCATGAAAGTTGTAGATCACAAAATTACATTT
65 AATTAAAACATAAAAATT-TGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAATTACCTTT
* * * * *
784 TAACAGACACCTGAATTACCTTAAATGGAAAAATATAACAAAGAAAATAAAAAAAAATAAGCGTT
129 CAACAGACACATGAATCAACTTAAATGGAAAAATAAAACAAAG-AAATAAAAAAAAATAAGCGTT
* *
849 AAATCAAATAAGATAGAATTTGTAAATGACTAAGTAGCATAAAATAGAAAAGTATGAGGGTCATT
193 AAATCAAATAAGATAGAATTTGTAAAGGACTAAGTAGCATAAAATAGAAAAATATGAGGGTCATT
* * * *
914 TGATAACTAATTCAAATAAGAAAATATTTCGTAATGGATATCTTGAAACATAAAAATTCGCTTTT
258 TGATAAATAATACAAATAAGAAAATATTTCGTAATAGAGATCTTGAAACATAAAAATTCGCTTTT
*
979 GAACCCTTCATGAAACTCGTAGATCAAATTAACTTTCGGGTTCTTCATGAAAGTCGTAGATCATA
323 GAACCCTTCATGAAACTCGTAGATCAAATTAACTTTCGGGTTCTTCATGAAAGTCGTAAATCATA
* * *
1044 CAATAACCTTTTAACCGACACTTAAATAACTTTAATCGGACATGTGGATC
388 CAATAACCTTTTAACCAACACTTAAATAACTTCAATCGGACATGTGGAAC
* * * *
1094 -GAAAATTATATGGTATTAAATAGACCAACAATCAAAACGACAAAATTTAAAAAGCCTTTTTTTG
1 AAAAAATTATATGATATTAAATAGACCAACAATCAAAAC-ACAAAATTTAAAAAGCATTTTTTAG
1158 AATTAAAACATAAAAATTTGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAATTACCTTTC
65 AATTAAAACATAAAAATTTGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAATTACCTTTC
* * * * * *
1223 AATAGACACATGAATCAATTTAATTGGACAAATAAAACAAAG-AATAAAAAAATA-AATC-TTAA
130 AACAGACACATGAATCAACTTAAATGGAAAAATAAAACAAAGAAATAAAAAAAAATAAGCGTTAA
* *
1285 A-CATTAGATTAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAGTAGAAAAATATGAGGGTCA
195 ATCA--A-A-TAAGATAGAATTTGTAAAGGACTAAGTAGCATAAAATAGAAAAATATGAGGGTCA
* * *
1349 TTTGATAAATAATACAAATAAGAAAATGTTT-GTTAATAGAGATCTTGAAGCATAAAAATTCTCT
256 TTTGATAAATAATACAAATAAGAAAATATTTCG-TAATAGAGATCTTGAAACATAAAAATTCGCT
* *
1413 TTTGAACCCTTCATGAAACTCGTAGATCAAATTTAGCTTTCGGG-TCTTTCATGAAAGTTGTAAA
320 TTTGAACCCTTCATGAAACTCGTAGATCAAA-TTAACTTTCGGGTTC-TTCATGAAAGTCGTAAA
* * *
1477 TTATGCAATAACCTTTT-ACCTAACACTTCAATAACTTCAATCGGACATGT-GAAC
383 TCATACAATAACCTTTTAACC-AACACTTAAATAACTTCAATCGGACATGTGGAAC
* * * ** * ***
1531 AAAAAATTATACGATATTAAATTGGCCGGCAATCAAATCCACAAAATTTTGGAAGCATTTTTTAG
1 AAAAAATTATATGATATTAAATAGACCAACAATCAAA-ACACAAAATTTAAAAAGCATTTTTTAG
* * * * * *
1596 AATCAAAACATTAAAATTGGCTTTTGAGTTCTTCATGAAAATTGTAGATAATGAAATTACCTTT
65 AATTAAAACATAAAAATTTGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAATTACCTTT
1660 TAGTACAATT
Statistics
Matches: 485, Mismatches: 69, Indels: 25
0.84 0.12 0.04
Matches are distributed among these distances:
433 2 0.00
434 5 0.01
435 4 0.01
436 13 0.03
437 147 0.30
438 313 0.65
439 1 0.00
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.31
Consensus pattern (437 bp):
AAAAAATTATATGATATTAAATAGACCAACAATCAAAACACAAAATTTAAAAAGCATTTTTTAGA
ATTAAAACATAAAAATTTGCTTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAATTACCTTTCA
ACAGACACATGAATCAACTTAAATGGAAAAATAAAACAAAGAAATAAAAAAAAATAAGCGTTAAA
TCAAATAAGATAGAATTTGTAAAGGACTAAGTAGCATAAAATAGAAAAATATGAGGGTCATTTGA
TAAATAATACAAATAAGAAAATATTTCGTAATAGAGATCTTGAAACATAAAAATTCGCTTTTGAA
CCCTTCATGAAACTCGTAGATCAAATTAACTTTCGGGTTCTTCATGAAAGTCGTAAATCATACAA
TAACCTTTTAACCAACACTTAAATAACTTCAATCGGACATGTGGAAC
Found at i:3341 original size:38 final size:38
Alignment explanation
Indices: 3290--3365 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
3280 TTTTGACGAA
3290 AAATAAATGACTAATTCAAATTGATGAACAAAAGAGAC
1 AAATAAATGACTAATTCAAATTGATGAACAAAAGAGAC
3328 AAATAAATGACTAATTCAAATTGATGAACAAAAGAGAC
1 AAATAAATGACTAATTCAAATTGATGAACAAAAGAGAC
3366 GGTCATCAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.55, C:0.11, G:0.13, T:0.21
Consensus pattern (38 bp):
AAATAAATGACTAATTCAAATTGATGAACAAAAGAGAC
Found at i:9097 original size:108 final size:111
Alignment explanation
Indices: 8905--9124 Score: 356
Period size: 108 Copynumber: 2.0 Consensus size: 111
8895 TCGAATTTGC
* *
8905 TAACCACCTACCCACATATATTATAAGAACCGAGAGAGAAAAAAAAACTTTATAACTAAAATGAT
1 TAACCACCTACCCACATATATGATAAGAACCGAGAGAGAAAAAAAAACTTTAAAACTAAAATGAT
** *
8970 TTGCTGGCCACACATCAAGAATGCTCGACGCGCCAGCGCGAGCCGA
66 TTGCAAGCCACAAATCAAGAATGCTCGACGCGCCAGCGCGAGCCGA
*
9016 TAACCACCTACTCACATATATGATAAGAACC-A-AGAG-AAAAAAAACTTTAAAACTAAAATGAT
1 TAACCACCTACCCACATATATGATAAGAACCGAGAGAGAAAAAAAAACTTTAAAACTAAAATGAT
*
9078 TTGCAAGCCACAAATCAAGAATGCTCGACGCGCCAGCGTGAGCCGA
66 TTGCAAGCCACAAATCAAGAATGCTCGACGCGCCAGCGCGAGCCGA
9124 T
1 T
9125 CAACTTGTTT
Statistics
Matches: 102, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
108 68 0.67
109 4 0.04
110 1 0.01
111 29 0.28
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.18
Consensus pattern (111 bp):
TAACCACCTACCCACATATATGATAAGAACCGAGAGAGAAAAAAAAACTTTAAAACTAAAATGAT
TTGCAAGCCACAAATCAAGAATGCTCGACGCGCCAGCGCGAGCCGA
Found at i:10415 original size:31 final size:32
Alignment explanation
Indices: 10380--10451 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 32
10370 TAAATTATTT
*
10380 CAAATTAAAAAAAAT-TAAG-CATTAAATTAAA
1 CAAATTAAAAAAAATGAAAGTC-TTAAATTAAA
* **
10411 CAAA-TCATTAAAATGAAAGTCTTAAATTAAA
1 CAAATTAAAAAAAATGAAAGTCTTAAATTAAA
10442 CAAATTAAAA
1 CAAATTAAAA
10452 GCTGATAGAC
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
30 7 0.23
31 21 0.68
32 3 0.10
ACGTcount: A:0.61, C:0.08, G:0.04, T:0.26
Consensus pattern (32 bp):
CAAATTAAAAAAAATGAAAGTCTTAAATTAAA
Found at i:14177 original size:10 final size:10
Alignment explanation
Indices: 14162--14200 Score: 69
Period size: 10 Copynumber: 3.9 Consensus size: 10
14152 AGATTTTGGG
14162 TGTGAGAGAT
1 TGTGAGAGAT
14172 TGTGAGAGAT
1 TGTGAGAGAT
*
14182 TGTGTGAGAT
1 TGTGAGAGAT
14192 TGTGAGAGA
1 TGTGAGAGA
14201 AAAAAAGCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.41, T:0.31
Consensus pattern (10 bp):
TGTGAGAGAT
Found at i:14518 original size:18 final size:19
Alignment explanation
Indices: 14495--14536 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
14485 ATGTATTAAA
*
14495 AAGTAAGGAAAA-TTAGCT
1 AAGTAAAGAAAATTTAGCT
*
14513 AAGTAAAGAAAATTTTGCT
1 AAGTAAAGAAAATTTAGCT
14532 AAGTA
1 AAGTA
14537 TTGACAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.50, C:0.05, G:0.19, T:0.26
Consensus pattern (19 bp):
AAGTAAAGAAAATTTAGCT
Found at i:21684 original size:75 final size:75
Alignment explanation
Indices: 21605--21777 Score: 183
Period size: 75 Copynumber: 2.3 Consensus size: 75
21595 GATGCTCAAA
* *
21605 ATTTGAATTTGAATCAGAAACCTAATAA-AGTGAATCA-GCTTCAAGATGTTG-CAAATCATCAT
1 ATTTGAATTTGAATCAGAAACCTAATAAGA-TGAACCATG-TTCAAGATGTTGTCAAA-CACCAT
21667 CAGAAAACTTAGT
63 CAGAAAACTTAGT
* * * * *
21680 ATTTGAATTTAAAACAGGAAA-CTAATCAGATGAACCATGTTCAAGATTTTGTCTAACACCATCA
1 ATTTGAATTTGAATCA-GAAACCTAATAAGATGAACCATGTTCAAGATGTTGTCAAACACCATCA
*
21744 GAAAACTTATT
65 GAAAACTTAGT
* * *
21755 ATTTGAATTCGAATTAGCAACCT
1 ATTTGAATTTGAATCAGAAACCT
21778 GAGAAGGAGA
Statistics
Matches: 80, Mismatches: 13, Indels: 10
0.78 0.13 0.10
Matches are distributed among these distances:
74 3 0.04
75 68 0.85
76 9 0.11
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (75 bp):
ATTTGAATTTGAATCAGAAACCTAATAAGATGAACCATGTTCAAGATGTTGTCAAACACCATCAG
AAAACTTAGT
Found at i:30693 original size:27 final size:27
Alignment explanation
Indices: 30628--30685 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 27
30618 TTGATTACCA
*
30628 ATTACCAT-GTTTTACTCTTTGTACTG
1 ATTACCATATTTTTACTCTTTGTACTG
*
30654 ATTACCATATTTTTACTCTTTTTTACTG
1 ATTACCATATTTTTACTC-TTTGTACTG
30682 ATTA
1 ATTA
30686 TCTCTTTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 8 0.29
27 8 0.29
28 12 0.43
ACGTcount: A:0.22, C:0.17, G:0.07, T:0.53
Consensus pattern (27 bp):
ATTACCATATTTTTACTCTTTGTACTG
Found at i:30757 original size:26 final size:27
Alignment explanation
Indices: 30687--30790 Score: 142
Period size: 27 Copynumber: 3.9 Consensus size: 27
30677 TACTGATTAT
*
30687 CTCTTTTCTTACTGAAT-ACCACATT-TTA
1 CTCTTTT-TTACTG-ATCACCA-TTTCTTA
30715 CTCTTTTTTACTGATCACCATTTCTTA
1 CTCTTTTTTACTGATCACCATTTCTTA
*
30742 CTC-TTTTTACTAATCACCATTTCTTA
1 CTCTTTTTTACTGATCACCATTTCTTA
30768 CTCTTTTTTACTGATCACCATTT
1 CTCTTTTTTACTGATCACCATTT
30791 TTTTGCTCAT
Statistics
Matches: 70, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
26 29 0.41
27 34 0.49
28 7 0.10
ACGTcount: A:0.21, C:0.26, G:0.03, T:0.50
Consensus pattern (27 bp):
CTCTTTTTTACTGATCACCATTTCTTA
Found at i:30814 original size:65 final size:66
Alignment explanation
Indices: 30733--30859 Score: 184
Period size: 66 Copynumber: 1.9 Consensus size: 66
30723 TACTGATCAC
* *
30733 CATTTCTTACTCTTTTTACTAATCAC-CATTTCTTACTCTTTTTTACTGATCACCATTTTTTTGC
1 CATTTCTTACTCTTTTTACTAATCACTCATTTCTTACTCTTTTTTACTAATCACCACTTTTTTGC
30797 T
66 T
* * * * *
30798 CATTTCTTACTTTTTTTACTGATTACTCTTTTCTTACTCTTTTTTACTAATTACCACTTTTT
1 CATTTCTTACTCTTTTTACTAATCACTCATTTCTTACTCTTTTTTACTAATCACCACTTTTT
30860 ACTCTTCTTC
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
65 23 0.43
66 31 0.57
ACGTcount: A:0.18, C:0.23, G:0.02, T:0.57
Consensus pattern (66 bp):
CATTTCTTACTCTTTTTACTAATCACTCATTTCTTACTCTTTTTTACTAATCACCACTTTTTTGC
T
Found at i:30828 original size:18 final size:18
Alignment explanation
Indices: 30765--30835 Score: 56
Period size: 18 Copynumber: 3.9 Consensus size: 18
30755 TCACCATTTC
30765 TTACTC-TTTTTTACTGA
1 TTACTCTTTTTTTACTGA
* * *
30782 TCAC-CATTTTTTTGCTCA
1 TTACTC-TTTTTTTACTGA
*
30800 TTTCTTACTTTTTTTACTGA
1 TTAC-T-CTTTTTTTACTGA
*
30820 TTACTCTTTTCTTACT
1 TTACTCTTTTTTTACT
30836 CTTTTTTACT
Statistics
Matches: 40, Mismatches: 9, Indels: 9
0.69 0.16 0.16
Matches are distributed among these distances:
16 1 0.03
17 3 0.08
18 21 0.52
19 1 0.03
20 13 0.32
21 1 0.03
ACGTcount: A:0.15, C:0.21, G:0.04, T:0.59
Consensus pattern (18 bp):
TTACTCTTTTTTTACTGA
Found at i:30861 original size:27 final size:28
Alignment explanation
Indices: 30800--30865 Score: 84
Period size: 27 Copynumber: 2.4 Consensus size: 28
30790 TTTTTGCTCA
* *
30800 TTTCTTACT-TTTTTTACTGATTACTCT
1 TTTCTTACTCTTTTTTACTAATTACTCC
30827 TTTCTTACTCTTTTTTACTAATTAC-CAC
1 TTTCTTACTCTTTTTTACTAATTACTC-C
30855 TTT-TTACTCTT
1 TTTCTTACTCTT
30866 CTTCTTTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 18 0.51
28 17 0.49
ACGTcount: A:0.17, C:0.21, G:0.02, T:0.61
Consensus pattern (28 bp):
TTTCTTACTCTTTTTTACTAATTACTCC
Found at i:30871 original size:66 final size:65
Alignment explanation
Indices: 30733--30863 Score: 174
Period size: 65 Copynumber: 2.0 Consensus size: 65
30723 TACTGATCAC
* * *
30733 CATTTCTTACTCTTTTTACTAATCACCATTTCTTACTCTTTTTTACTGATCACCATTTTTTTGCT
1 CATTTCTTACTCTTTTTACTAATCACCATTTCTTACTCTTTTTTACTAATCACCATCTTTTTACT
* * * * *
30798 CATTTCTTACTTTTTTTACTGATTACTCTTTTCTTACTCTTTTTTACTAATTACCA-CTTTTTAC
1 CATTTCTTACTCTTTTTACTAATCAC-CATTTCTTACTCTTTTTTACTAATCACCATCTTTTTAC
30862 T
65 T
30863 C
1 C
30864 TTCTTCTTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
65 31 0.54
66 26 0.46
ACGTcount: A:0.18, C:0.24, G:0.02, T:0.56
Consensus pattern (65 bp):
CATTTCTTACTCTTTTTACTAATCACCATTTCTTACTCTTTTTTACTAATCACCATCTTTTTACT
Found at i:31064 original size:20 final size:20
Alignment explanation
Indices: 31023--31078 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
31013 ATTACCCTTT
*
31023 TTACTT-TTACTGTTTACAA
1 TTACTTCTTACTGATTACAA
31042 TTACTTCTTACTGATTA-ATA
1 TTACTTCTTACTGATTACA-A
31062 TTAC-TCTTTACTGATTA
1 TTACTTC-TTACTGATTA
31079 TCACTTTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 9 0.27
20 24 0.73
ACGTcount: A:0.27, C:0.16, G:0.05, T:0.52
Consensus pattern (20 bp):
TTACTTCTTACTGATTACAA
Found at i:31148 original size:22 final size:22
Alignment explanation
Indices: 31097--31157 Score: 79
Period size: 21 Copynumber: 2.8 Consensus size: 22
31087 ATCTTTTCTA
* **
31097 ATTACCATTTTACCCTTTACAG
1 ATTACCTTTTTACTTTTTACAG
*
31119 A-TACCTTTTTACTTTTTACCG
1 ATTACCTTTTTACTTTTTACAG
31140 ATTACCTTTTTACTTTTT
1 ATTACCTTTTTACTTTTT
31158 TACTGTTTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 17 0.50
22 17 0.50
ACGTcount: A:0.21, C:0.23, G:0.03, T:0.52
Consensus pattern (22 bp):
ATTACCTTTTTACTTTTTACAG
Found at i:31180 original size:128 final size:127
Alignment explanation
Indices: 31007--31244 Score: 370
Period size: 128 Copynumber: 1.9 Consensus size: 127
30997 TTGAACTGGA
* *
31007 TTACTGATTACCCTTTTTACTTTTACTGTTTACAATTACTTCTTACTGATTAATATTACTCTTTA
1 TTACCGATTACCCTTTTTACTTTTACTGTTTACAATTACCTCTTACTGATTAATATTACTCTTTA
*
31072 CTGATTATCACTTTAATCTTTTCTAATTACCATTTTACCCTTTACAGATACCTTTTTACTTT
66 CTGATTATCACTTTAATCTTTACTAATTACCATTTTACCCTTTACAGATACCTTTTTACTTT
* **
31134 TTACCGATTA-CCTTTTTACTTTTTTACTGTTTACTATTACCTCTTACTGATTTCTATTACTCTT
1 TTACCGATTACCCTTTTTAC--TTTTACTGTTTACAATTACCTCTTACTGATTAATATTACTCTT
* * *
31198 TACTGATTATTACTTTACTCTTTACTAATTACCATTTTACCTTTTAC
64 TACTGATTATCACTTTAATCTTTACTAATTACCATTTTACCCTTTAC
31245 TGATTTCTAT
Statistics
Matches: 100, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
126 9 0.09
127 9 0.09
128 82 0.82
ACGTcount: A:0.23, C:0.21, G:0.04, T:0.52
Consensus pattern (127 bp):
TTACCGATTACCCTTTTTACTTTTACTGTTTACAATTACCTCTTACTGATTAATATTACTCTTTA
CTGATTATCACTTTAATCTTTACTAATTACCATTTTACCCTTTACAGATACCTTTTTACTTT
Found at i:31182 original size:20 final size:20
Alignment explanation
Indices: 31156--31275 Score: 86
Period size: 20 Copynumber: 5.8 Consensus size: 20
31146 TTTTTACTTT
31156 TTTACTG-TTTACTATTAC-C
1 TTTACTGATTT-CTATTACTC
31175 TCTTACTGATTTCTATTACTC
1 T-TTACTGATTTCTATTACTC
31196 TTTACTGATTAT-TACTTTACTC
1 TTTACTGATT-TCTA--TTACTC
* * *
31218 TTTACTAATTACCATTTTAC-C
1 TTTACTGATT-TC-TATTACTC
* *
31239 TTTTACTGATTTCTATTATTT
1 -TTTACTGATTTCTATTACTC
*
31260 TTTACTGATTACTATT
1 TTTACTGATTTCTATT
31276 TTACTATTTG
Statistics
Matches: 82, Mismatches: 9, Indels: 19
0.75 0.08 0.17
Matches are distributed among these distances:
19 1 0.01
20 43 0.52
21 8 0.10
22 29 0.35
24 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.04, T:0.55
Consensus pattern (20 bp):
TTTACTGATTTCTATTACTC
Found at i:31236 original size:22 final size:22
Alignment explanation
Indices: 31007--31280 Score: 139
Period size: 22 Copynumber: 12.9 Consensus size: 22
30997 TTGAACTGGA
*
31007 TTACTGATTACCCTTTTTACT-T
1 TTACTGATTA-CCATTTTACTCT
* *
31029 TTACTGTTTA-CA-ATTACT-T
1 TTACTGATTACCATTTTACTCT
*
31048 CTTACTGATTA--ATATTACTCT
1 -TTACTGATTACCATTTTACTCT
* * *
31069 TTACTGATTATCACTTTAATCT
1 TTACTGATTACCATTTTACTCT
* * *
31091 TTTCTAATTACCATTTTACCCT
1 TTACTGATTACCATTTTACTCT
* * *
31113 TTACAGA-TACCTTTTTACTTT
1 TTACTGATTACCATTTTACTCT
* * *
31134 TTACCGATTACCTTTTTACTTTT
1 TTACTGATTACCATTTTAC-TCT
* *
31157 TTACTGTTTA-C-TATTAC-CT
1 TTACTGATTACCATTTTACTCT
* *
31176 CTTACTGATT-TC-TATTACTCT
1 -TTACTGATTACCATTTTACTCT
** *
31197 TTACTGATTATTACTTTACTCT
1 TTACTGATTACCATTTTACTCT
*
31219 TTACTAATTACCATTTTAC-CTT
1 TTACTGATTACCATTTTACTC-T
* *
31241 TTACTGATTTCTATTATT--T-T
1 TTACTGATTACCATT-TTACTCT
*
31261 TTACTGATTACTATTTTACT
1 TTACTGATTACCATTTTACT
31281 ATTTGAATTT
Statistics
Matches: 199, Mismatches: 36, Indels: 35
0.74 0.13 0.13
Matches are distributed among these distances:
19 10 0.05
20 65 0.33
21 28 0.14
22 83 0.42
23 13 0.07
ACGTcount: A:0.23, C:0.20, G:0.04, T:0.53
Consensus pattern (22 bp):
TTACTGATTACCATTTTACTCT
Found at i:31399 original size:36 final size:33
Alignment explanation
Indices: 31326--31406 Score: 81
Period size: 36 Copynumber: 2.4 Consensus size: 33
31316 TTACTGATTG
* * *
31326 CTTTTTCCTTATTGAACTTAATCAATGATTAAT
1 CTTTTTACTTTTTGAACTTAATCAATGATTAAC
* *
31359 CTTTTTACTTTTTGGAACTTAATCACTCTGATTACC
1 CTTTTTACTTTTT-GAACTTAATCA--ATGATTAAC
*
31395 CTTTTGACTTTT
1 CTTTTTACTTTT
31407 CTGACTGACC
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
33 11 0.28
34 11 0.28
36 17 0.44
ACGTcount: A:0.23, C:0.19, G:0.07, T:0.51
Consensus pattern (33 bp):
CTTTTTACTTTTTGAACTTAATCAATGATTAAC
Found at i:36039 original size:26 final size:25
Alignment explanation
Indices: 36010--36059 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
36000 TATGATTAAA
36010 ATGCAAC-AATACTAAGCTAAATGAAG
1 ATGCAACTAATA-TAA-CTAAATGAAG
*
36036 ATGCAACTAATATTACTAAATGAA
1 ATGCAACTAATATAACTAAATGAA
36060 AATATGCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 9 0.41
26 9 0.41
27 4 0.18
ACGTcount: A:0.50, C:0.14, G:0.12, T:0.24
Consensus pattern (25 bp):
ATGCAACTAATATAACTAAATGAAG
Found at i:36195 original size:28 final size:29
Alignment explanation
Indices: 36163--36226 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
36153 GTAGATTAAG
36163 AATGACCAAAAT-ACCCCCTAAATGCAAA
1 AATGACCAAAATGACCCCCTAAATGCAAA
* * **
36191 AATGACCAAAATGCCCCCCTAGATGTGAA
1 AATGACCAAAATGACCCCCTAAATGCAAA
36220 AATGACC
1 AATGACC
36227 TTAATGCTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 12 0.39
29 19 0.61
ACGTcount: A:0.44, C:0.28, G:0.12, T:0.16
Consensus pattern (29 bp):
AATGACCAAAATGACCCCCTAAATGCAAA
Found at i:36542 original size:46 final size:46
Alignment explanation
Indices: 36442--36553 Score: 143
Period size: 46 Copynumber: 2.4 Consensus size: 46
36432 TGCCATGAAC
* **
36442 AAATCTGATTCCTCGAATCAAACTTTGAAGAAATACTGCAACGCGGT
1 AAAT-TGATTCATCGAATCAAACTTTGAAGAAATACTGCAACGCACT
* * *
36489 AAGTTGATTCATCGAATCAAACTTTGAAGAAATAGTGCACCGCACT
1 AAATTGATTCATCGAATCAAACTTTGAAGAAATACTGCAACGCACT
* *
36535 AAATTGATCCACCGAATCA
1 AAATTGATTCATCGAATCA
36554 CTCTGAACTG
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
46 53 0.95
47 3 0.05
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (46 bp):
AAATTGATTCATCGAATCAAACTTTGAAGAAATACTGCAACGCACT
Found at i:36640 original size:92 final size:90
Alignment explanation
Indices: 36501--36773 Score: 358
Period size: 92 Copynumber: 3.0 Consensus size: 90
36491 GTTGATTCAT
* * *
36501 CGAATCAAACTTTGAAGAAAT-AGTGCACCGCAC-TAAATTGATCCACCGAATCA-CTCTGAACT
1 CGAATCCAACTTTGAAGAAATAAG-GCACCGC-CTTAACTTGATTCACCGAATCATC-CTGAACT
* * * *
36563 GTCTGAAAATGTGCTGTACCAAGCTCAC
63 GTTTGAAAATTTGCTGCACCGAGCTCAC
* *
36591 CGACTTCCAATCTTTGAAGAAAATAAGGCACCGCCTTAACTT-ATTCACCGAATCATCCTTAACT
1 CGA-ATCCAA-CTTTGAAG-AAATAAGGCACCGCCTTAACTTGATTCACCGAATCATCCTGAACT
36655 GTTTGAAAATTTGCTGCACCGAGCTCAC
63 GTTTGAAAATTTGCTGCACCGAGCTCAC
36683 CGAATCCAAC-TTGAAGAAATAAGGCACCGCCTTAACTTGATTCACCGAATCATCCTTGAACTGT
1 CGAATCCAACTTTGAAGAAATAAGGCACCGCCTTAACTTGATTCACCGAATCATCC-TGAACTGT
*
36747 TTGAAAATTTGCTACACCGAGCTCAC
65 TTGAAAATTTGCTGCACCGAGCTCAC
36773 C
1 C
36774 TGGTTCACCG
Statistics
Matches: 163, Mismatches: 12, Indels: 16
0.85 0.06 0.08
Matches are distributed among these distances:
88 22 0.13
89 22 0.13
90 37 0.23
91 9 0.06
92 54 0.33
93 17 0.10
94 2 0.01
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.26
Consensus pattern (90 bp):
CGAATCCAACTTTGAAGAAATAAGGCACCGCCTTAACTTGATTCACCGAATCATCCTGAACTGTT
TGAAAATTTGCTGCACCGAGCTCAC
Found at i:37019 original size:54 final size:54
Alignment explanation
Indices: 36881--37075 Score: 219
Period size: 54 Copynumber: 3.6 Consensus size: 54
36871 AAGGTATACC
* * * * * * *
36881 TAAATCACTGAAAACTTCCTTGACTGACCACACTGGTTCATTTAAAGATAAACT
1 TAAACCACTGCAAACTTTCTTGACTGACCGCACTGGATCACTTGAAGATAAACT
* * * * * *
36935 TAATACCACTGGACACTTTCGTAACTGACCGCATTGGATCACTTGAAGATGAACT
1 TAA-ACCACTGCAAACTTTCTTGACTGACCGCACTGGATCACTTGAAGATAAACT
* * *
36990 TAAACCACTACAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGTTAAACT
1 TAAACCACTGCAAACTTTCTTGACTGACCGCACTGGATCACTTGAAGATAAACT
* *
37044 TAAACCACTGTAAACTTTCTTGATTGACCGCA
1 TAAACCACTGCAAACTTTCTTGACTGACCGCA
37076 GTGGCTAATG
Statistics
Matches: 117, Mismatches: 23, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
54 75 0.64
55 42 0.36
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (54 bp):
TAAACCACTGCAAACTTTCTTGACTGACCGCACTGGATCACTTGAAGATAAACT
Found at i:41447 original size:26 final size:28
Alignment explanation
Indices: 41418--41477 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
41408 TTGATTACCA
41418 ATTACCAT-GTTTTACT-TTTTGTACTG
1 ATTACCATAGTTTTACTCTTTTGTACTG
* *
41444 ATTACCATATTTTTACTCTTTTTTACTG
1 ATTACCATAGTTTTACTCTTTTGTACTG
41472 ATTACC
1 ATTACC
41478 TCTTTTCTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 8 0.27
27 7 0.23
28 15 0.50
ACGTcount: A:0.22, C:0.18, G:0.07, T:0.53
Consensus pattern (28 bp):
ATTACCATAGTTTTACTCTTTTGTACTG
Found at i:41483 original size:27 final size:27
Alignment explanation
Indices: 41418--41584 Score: 90
Period size: 26 Copynumber: 6.5 Consensus size: 27
41408 TTGATTACCA
*
41418 ATTACCAT-GTTTTACTTTTTGTACTG
1 ATTACCATATTTTTACTTTTTGTACTG
*
41444 ATTACCATATTTTTACTCTTTTTTACTG
1 ATTACCATATTTTTACT-TTTTGTACTG
*
41472 ATTACC-T-CTTTT-C----T-TACTG
1 ATTACCATATTTTTACTTTTTGTACTG
* * *
41491 AATACCACATTTTTACTCTTTTTTACTG
1 ATTACCATATTTTTACT-TTTTGTACTG
* * *
41519 ATCACCAT-TTCTTACTCTTTT-TACTA
1 ATTACCATATTTTTACT-TTTTGTACTG
* *
41545 ATCACCAT-TTCTTACTCTTTT-TACTG
1 ATTACCATATTTTTACT-TTTTGTACTG
* *
41571 ATCACCATTTTTTT
1 ATTACCATATTTTT
41585 GCTTCATTTC
Statistics
Matches: 116, Mismatches: 13, Indels: 23
0.76 0.09 0.15
Matches are distributed among these distances:
19 10 0.09
20 1 0.01
21 4 0.03
22 1 0.01
25 1 0.01
26 49 0.42
27 25 0.22
28 25 0.22
ACGTcount: A:0.21, C:0.22, G:0.04, T:0.53
Consensus pattern (27 bp):
ATTACCATATTTTTACTTTTTGTACTG
Found at i:41490 original size:19 final size:18
Alignment explanation
Indices: 41459--41507 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
41449 CATATTTTTA
*
41459 CTCTTTTTTACTGATTAC
1 CTCTTTTTTACTGAATAC
41477 CTCTTTTCTTACTGAATAC
1 CTCTTTT-TTACTGAATAC
* *
41496 CACATTTTTACT
1 CTCTTTTTTACT
41508 CTTTTTTACT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 12 0.44
19 15 0.56
ACGTcount: A:0.20, C:0.24, G:0.04, T:0.51
Consensus pattern (18 bp):
CTCTTTTTTACTGAATAC
Found at i:41539 original size:26 final size:26
Alignment explanation
Indices: 41498--41580 Score: 141
Period size: 26 Copynumber: 3.2 Consensus size: 26
41488 CTGAATACCA
41498 CATTT-TTACTCTTTTTTACTGATCAC
1 CATTTCTTACTC-TTTTTACTGATCAC
*
41524 CATTTCTTACTCTTTTTACTAATCAC
1 CATTTCTTACTCTTTTTACTGATCAC
41550 CATTTCTTACTCTTTTTACTGATCAC
1 CATTTCTTACTCTTTTTACTGATCAC
41576 CATTT
1 CATTT
41581 TTTTGCTTCA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
26 48 0.89
27 6 0.11
ACGTcount: A:0.20, C:0.25, G:0.02, T:0.52
Consensus pattern (26 bp):
CATTTCTTACTCTTTTTACTGATCAC
Done.