Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016635.1 Corchorus olitorius cultivar O-4 contig16668, 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: 104609
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:887 original size:1 final size:1
Alignment explanation
Indices: 881--915 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
871 CAAAATTTTC
881 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
916 CCCACGTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:6191 original size:30 final size:30
Alignment explanation
Indices: 6118--6194 Score: 120
Period size: 30 Copynumber: 2.5 Consensus size: 30
6108 GAGTATGACG
*
6118 AGGAGGAAGATTCCGATCTCTTTGTTTGTGA
1 AGGA-GAAGATTCTGATCTCTTTGTTTGTGA
6149 AGGAGAAGATTCTGATCTCTTTGTTTGTGA
1 AGGAGAAGATTCTGATCTCTTTGTTTGTGA
6179 AGGAG-AGAATTCTGAT
1 AGGAGAAG-ATTCTGAT
6195 TTTGTCATTA
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
29 2 0.05
30 38 0.86
31 4 0.09
ACGTcount: A:0.26, C:0.10, G:0.29, T:0.35
Consensus pattern (30 bp):
AGGAGAAGATTCTGATCTCTTTGTTTGTGA
Found at i:6663 original size:31 final size:31
Alignment explanation
Indices: 6625--6688 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
6615 AGAGTTTGTC
*
6625 TTTATTTTCTTA-TTTAGATTATTATTAGGCT
1 TTTATTTTCTTATTTTAG-TTAGTATTAGGCT
*
6656 TTTATTTTCTTATTTTAGTTAGTATTGGGCT
1 TTTATTTTCTTATTTTAGTTAGTATTAGGCT
6687 TT
1 TT
6689 ATTGGCTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 25 0.83
32 5 0.17
ACGTcount: A:0.19, C:0.06, G:0.12, T:0.62
Consensus pattern (31 bp):
TTTATTTTCTTATTTTAGTTAGTATTAGGCT
Found at i:9814 original size:35 final size:35
Alignment explanation
Indices: 9775--9846 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
9765 GGATTTTTCC
9775 TTTCTTCTGTTCTGATTGATTCCTGATAATATGTT
1 TTTCTTCTGTTCTGATTGATTCCTGATAATATGTT
9810 TTTCTTCTGTTCTGATTGATTCCTGATAATATGTT
1 TTTCTTCTGTTCTGATTGATTCCTGATAATATGTT
9845 TT
1 TT
9847 CATTTTTCGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.17, C:0.14, G:0.14, T:0.56
Consensus pattern (35 bp):
TTTCTTCTGTTCTGATTGATTCCTGATAATATGTT
Found at i:11493 original size:12 final size:12
Alignment explanation
Indices: 11476--11514 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
11466 CTATCTTAAA
11476 TTGTCCCTATAG
1 TTGTCCCTATAG
*
11488 TTGTCCCTATAA
1 TTGTCCCTATAG
11500 TTGTCCCTATAG
1 TTGTCCCTATAG
11512 TTG
1 TTG
11515 CTTCTTCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.18, C:0.23, G:0.15, T:0.44
Consensus pattern (12 bp):
TTGTCCCTATAG
Found at i:11700 original size:12 final size:12
Alignment explanation
Indices: 11683--11708 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11673 CAAAGAGATG
11683 AAAAAAAAAAGA
1 AAAAAAAAAAGA
11695 AAAAAAAAAAGA
1 AAAAAAAAAAGA
11707 AA
1 AA
11709 GGGGCTAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:18701 original size:30 final size:30
Alignment explanation
Indices: 18658--18776 Score: 184
Period size: 30 Copynumber: 4.0 Consensus size: 30
18648 GCACTCTGGA
* **
18658 GAAGGAGGAAGTTCCTGTGAAGTTGAGCGG
1 GAAGGAAGAAGTTCCTGTGAAGTTGAGCTT
* *
18688 GAAGAAAGAAGTTCCTGTGAAGTCGAGCTT
1 GAAGGAAGAAGTTCCTGTGAAGTTGAGCTT
*
18718 GAAGGAAGAAGTTCCTGTGAGGTTGAGCTT
1 GAAGGAAGAAGTTCCTGTGAAGTTGAGCTT
18748 GAAGGAAGAAGTTCCTGTGAAGTTGAGCT
1 GAAGGAAGAAGTTCCTGTGAAGTTGAGCT
18777 GCTAGATTCT
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 80 1.00
ACGTcount: A:0.29, C:0.11, G:0.36, T:0.24
Consensus pattern (30 bp):
GAAGGAAGAAGTTCCTGTGAAGTTGAGCTT
Found at i:21117 original size:19 final size:19
Alignment explanation
Indices: 21067--21126 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
21057 TCTTTTGCAG
*
21067 TTTTGCTTTCTCTTT-TCTT
1 TTTTGCTTTGTCTTTGT-TT
**
21086 TTTTTTTTCTGTCTTTGTTT
1 TTTTGCTT-TGTCTTTGTTT
*
21106 TTTTGCTTTGTCTCTGTTT
1 TTTTGCTTTGTCTTTGTTT
21125 TT
1 TT
21127 AAGATGTCTG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 18 0.55
20 14 0.42
21 1 0.03
ACGTcount: A:0.00, C:0.15, G:0.10, T:0.75
Consensus pattern (19 bp):
TTTTGCTTTGTCTTTGTTT
Found at i:46486 original size:34 final size:34
Alignment explanation
Indices: 46448--46512 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
46438 CAATGCAGGT
*
46448 TTCCAGAGATAGGTTCTCTTTCATTAGTATTATA
1 TTCCAGAGATAGGTTCTCTTTCAGTAGTATTATA
* *
46482 TTCCAGAGATGGGTTGTCTTTCAGTAGTATT
1 TTCCAGAGATAGGTTCTCTTTCAGTAGTATT
46513 TAAGTATTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.43
Consensus pattern (34 bp):
TTCCAGAGATAGGTTCTCTTTCAGTAGTATTATA
Found at i:58965 original size:15 final size:16
Alignment explanation
Indices: 58945--58978 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
58935 CATATAAATG
58945 AAATGAAATGA-AACA
1 AAATGAAATGATAACA
58960 AAATGAAATGATAACA
1 AAATGAAATGATAACA
58976 AAA
1 AAA
58979 CTGCAATTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.68, C:0.06, G:0.12, T:0.15
Consensus pattern (16 bp):
AAATGAAATGATAACA
Found at i:59133 original size:26 final size:26
Alignment explanation
Indices: 59097--59148 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
59087 TATTATAATA
59097 AACTAGAAATGAGTTCAACAGAATGT
1 AACTAGAAATGAGTTCAACAGAATGT
59123 AACTAGAAATGAGTTCAACAGAATGT
1 AACTAGAAATGAGTTCAACAGAATGT
59149 TTTTCAGAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.12, G:0.19, T:0.23
Consensus pattern (26 bp):
AACTAGAAATGAGTTCAACAGAATGT
Found at i:78427 original size:40 final size:40
Alignment explanation
Indices: 78370--78448 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
78360 TTTATAACTA
* *
78370 GGGGCTAAACCTGGATTTAATTTCTTACCTTAATTATTAG
1 GGGGCTAAACCTAGATTTAATTTATTACCTTAATTATTAG
*
78410 GGGGCTAAACCTAGATTTAATTTATTTCCTTAATTATTA
1 GGGGCTAAACCTAGATTTAATTTATTACCTTAATTATTA
78449 AGAGGGTGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (40 bp):
GGGGCTAAACCTAGATTTAATTTATTACCTTAATTATTAG
Found at i:78969 original size:10 final size:11
Alignment explanation
Indices: 78954--78990 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
78944 AACACACAGA
78954 CTTTTT-TCTT
1 CTTTTTCTCTT
78964 CTTTTTCTCTT
1 CTTTTTCTCTT
*
78975 -TTTTTCTTTT
1 CTTTTTCTCTT
78985 CTTTTT
1 CTTTTT
78991 AGGATCTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (11 bp):
CTTTTTCTCTT
Found at i:85487 original size:6 final size:6
Alignment explanation
Indices: 85465--85512 Score: 62
Period size: 6 Copynumber: 8.0 Consensus size: 6
85455 TTTTAGCATC
* *
85465 AATGGA AATGAGG -ATGGG AATGGG GATGGG AATGGG AATGGG AATGGG
1 AATGGG AATG-GG AATGGG AATGGG AATGGG AATGGG AATGGG AATGGG
85513 GGTGAATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
5 2 0.05
6 34 0.92
7 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.50, T:0.17
Consensus pattern (6 bp):
AATGGG
Found at i:87553 original size:2 final size:2
Alignment explanation
Indices: 87546--87577 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
87536 TTGAGACTTT
87546 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
87578 CTAGTTAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:89154 original size:58 final size:58
Alignment explanation
Indices: 89058--89167 Score: 168
Period size: 58 Copynumber: 1.9 Consensus size: 58
89048 ATTAATCAAA
*
89058 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTCGGACCAAGGCT
1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGGCT
* * *
89116 TATCGAGTGACATGTTTTTTTATTAGATGCCT-AAAAAAGACGTTTTAGGACC
1 TATCAAGTGACATG-TTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACC
89168 GATGCATGAT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
58 32 0.68
59 15 0.32
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.34
Consensus pattern (58 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGGCT
Found at i:89729 original size:36 final size:36
Alignment explanation
Indices: 89675--89744 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
89665 TTCAATAACC
* *
89675 TTACATCTTTTATGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTATAATTTTGATTATCATATTTCTTA
* *
89711 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTATAATTTTGATTATCATATTTCT
89745 CCAAAATCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.23, C:0.10, G:0.07, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTATAATTTTGATTATCATATTTCTTA
Found at i:90647 original size:204 final size:204
Alignment explanation
Indices: 90257--90674 Score: 705
Period size: 204 Copynumber: 2.0 Consensus size: 204
90247 GCTTAATAAC
*
90257 TTTATCAATGGTGAATATTATTAATTTTTTAAGTTTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATATTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
*
90322 GATACAACACATTATTATTATTATTATTATATATAAAACTATACAAAAAAAAGTAGTTGAACATT
66 GATACAACAC-----TATTACTATTATTATATATAAAACTATACAAAAAAAAGTAGTTGAACATT
*
90387 AGTGGTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATAT
126 AGTGGTTGATTTATTAAATTAAATTAGATCAATGCCAAACAAAATTTCAAAATTATAAAAGATAT
90452 TAAAGATCCGATTTA
191 T-AAGATCCGATTTA
*
90467 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATATTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
* *
90532 GATACAACAC-ATTACTATTA-TATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTG
66 GATACAACACTATTACTATTATTATATATAAAACTATA-CAAAAAAAAGTAGTTGAACATTAGTG
90595 GTTGATTTATTAAATTAAATTAGATCAATGCCAAACAAAATTTCAAAATTATAAAAGATATTAAG
130 GTTGATTTATTAAATTAAATTAGATCAATGCCAAACAAAATTTCAAAATTATAAAAGATATTAAG
90660 ATCCGATTTA
195 ATCCGATTTA
90670 TTTAT
1 TTTAT
90675 TATTAAGGAC
Statistics
Matches: 201, Mismatches: 6, Indels: 9
0.93 0.03 0.04
Matches are distributed among these distances:
203 33 0.16
204 95 0.47
210 73 0.36
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (204 bp):
TTTATCAATGGTGAATATTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAACACTATTACTATTATTATATATAAAACTATACAAAAAAAAGTAGTTGAACATTAGTGG
TTGATTTATTAAATTAAATTAGATCAATGCCAAACAAAATTTCAAAATTATAAAAGATATTAAGA
TCCGATTTA
Found at i:90780 original size:25 final size:24
Alignment explanation
Indices: 90746--90792 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
90736 ACGTTTGCAC
90746 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
*
90771 AAATATCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
90793 TGTAAGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.32
Consensus pattern (24 bp):
AAATACCTAAGAATTTAATTAAAA
Found at i:90837 original size:39 final size:40
Alignment explanation
Indices: 90783--90863 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
90773 ATATCTAAGA
*
90783 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
90822 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
90862 AT
1 AT
90864 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:91091 original size:2 final size:2
Alignment explanation
Indices: 91079--91126 Score: 71
Period size: 2 Copynumber: 24.0 Consensus size: 2
91069 AGTTTAGACT
*
91079 TA TA TA GTA TA TA GA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
91121 TA TA TA
1 TA TA TA
91127 GAAGGAGAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 1 0.02
2 39 0.93
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:96176 original size:80 final size:77
Alignment explanation
Indices: 96036--96273 Score: 388
Period size: 76 Copynumber: 3.1 Consensus size: 77
96026 GAGGGTCAGA
*
96036 AAAGATGATGAGTTCTTTCCACCAAACCTAACAAAGTGTCGATTTTCTAATATCCATCTTGTTTT
1 AAAGA-GATGAGTTCTTTCCACCAAACCTAACAAAGTGTCGATTTTCTAATTTCCATCTTGTTTT
*
96101 GAAATTAAGACTT
65 GAACTTAAGACTT
* * *
96114 AAAGAGATTAGTTCTTTCCACCACCAAACCTAACAAAGTGTTGATTTTCTGATTTCCATCTTGTT
1 AAAGAGATGAGTTCTTT---CCACCAAACCTAACAAAGTGTCGATTTTCTAATTTCCATCTTGTT
96179 TTGAACTTAAGACTT
63 TTGAACTTAAGACTT
96194 -AAGAGATGAGTTCTTTCCACCAAACCTAACAAAGTGTCGATTTTCTAATTTCCATCTTGTTTTG
1 AAAGAGATGAGTTCTTTCCACCAAACCTAACAAAGTGTCGATTTTCTAATTTCCATCTTGTTTTG
96258 AACTTAAGACTT
66 AACTTAAGACTT
96270 AAAG
1 AAAG
96274 GTGCATTTGC
Statistics
Matches: 148, Mismatches: 8, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
76 58 0.39
77 14 0.09
78 5 0.03
79 15 0.10
80 56 0.38
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (77 bp):
AAAGAGATGAGTTCTTTCCACCAAACCTAACAAAGTGTCGATTTTCTAATTTCCATCTTGTTTTG
AACTTAAGACTT
Found at i:102704 original size:65 final size:65
Alignment explanation
Indices: 102600--102737 Score: 267
Period size: 65 Copynumber: 2.1 Consensus size: 65
102590 GCTATTGGAT
*
102600 AAACATATTTAATACTATTTCCAAAAAATAGGAAAGCCCCATAATACTACAAAAATGGGAGCAAC
1 AAACAAATTTAATACTATTTCCAAAAAATAGGAAAGCCCCATAATACTACAAAAATGGGAGCAAC
102665 AAACAAATTTAATACTATTTCCAAAAAATAGGAAAGCCCCATAATACTACAAAAATGGGAGCAAC
1 AAACAAATTTAATACTATTTCCAAAAAATAGGAAAGCCCCATAATACTACAAAAATGGGAGCAAC
102730 AAACAAAT
1 AAACAAAT
102738 GAGAGGGAAG
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 72 1.00
ACGTcount: A:0.51, C:0.18, G:0.10, T:0.20
Consensus pattern (65 bp):
AAACAAATTTAATACTATTTCCAAAAAATAGGAAAGCCCCATAATACTACAAAAATGGGAGCAAC
Found at i:103018 original size:84 final size:85
Alignment explanation
Indices: 102859--103021 Score: 249
Period size: 84 Copynumber: 1.9 Consensus size: 85
102849 TAATAATACC
* * *
102859 CTAAAATAATTTCATTTAATGAAAAACATATATATTCTATAACGTTAAAATATCAAACATAATGA
1 CTAAAATAATTCCATTTAATAAAAAACATATATATTCTATAACGTTAAAAAATCAAACATAATGA
* *
102924 TTTATATAGAATTTGTAAAA
66 TTGAAATAGAATTTGTAAAA
*
102944 CTAAATTAATTCCATTTAATAAAAAACATA-A-ATTCTATAACGTTACAAAAATCAAACATAATG
1 CTAAAATAATTCCATTTAATAAAAAACATATATATTCTATAACGTTA-AAAAATCAAACATAATG
103007 ATTGAAATAGAATTT
65 ATTGAAATAGAATTT
103022 ATAGGATGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
83 14 0.20
84 30 0.42
85 27 0.38
ACGTcount: A:0.50, C:0.10, G:0.06, T:0.34
Consensus pattern (85 bp):
CTAAAATAATTCCATTTAATAAAAAACATATATATTCTATAACGTTAAAAAATCAAACATAATGA
TTGAAATAGAATTTGTAAAA
Found at i:104505 original size:31 final size:31
Alignment explanation
Indices: 104470--104584 Score: 105
Period size: 31 Copynumber: 3.8 Consensus size: 31
104460 AAAGGCTAAT
* *
104470 TGCTCAAATAAGGGCTTAATGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAATCTTTGCCAAAA
* * **
104501 TGCTCAAA-AAGGGGCAC-GATCTTT--TAATT
1 TGCTCAAATAA-GGGC-CTAATCTTTGCCAAAA
*
104530 TGGC-CAAATAAGGGCCTAATTTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAATCTTTGCCAAAA
104561 TGCTCAAATAAGGGCCTAATCTTT
1 TGCTCAAATAAGGGCCTAATCTTT
104585 TAATTTGGCC
Statistics
Matches: 64, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
28 1 0.02
29 16 0.25
30 8 0.12
31 39 0.61
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAATCTTTGCCAAAA
Found at i:104567 original size:60 final size:60
Alignment explanation
Indices: 104474--104609 Score: 213
Period size: 60 Copynumber: 2.3 Consensus size: 60
104464 GCTAATTGCT
* *
104474 CAAATAAGGGCTTAATGTTTGCCAAAATGCTCAAA-AAGGGGCAC-GATCTTTTAATTTGGC
1 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAA-GGGC-CTAATCTTTTAATTTGGC
*
104534 CAAATAAGGGCCTAATTTTTGCCAAAATGCTCAAATAAGGGCCTAATCTTTTAATTTGGC
1 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCCTAATCTTTTAATTTGGC
104594 CAAATAAGGGCCTAAT
1 CAAATAAGGGCCTAAT
Statistics
Matches: 71, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
59 1 0.01
60 68 0.96
61 2 0.03
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29
Consensus pattern (60 bp):
CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCCTAATCTTTTAATTTGGC
Found at i:104607 original size:29 final size:29
Alignment explanation
Indices: 104519--104609 Score: 114
Period size: 29 Copynumber: 3.1 Consensus size: 29
104509 AAGGGGCACG
104519 ATCTTTTAATTTGGCCAAATAAGGGCCTA
1 ATCTTTTAATTTGGCCAAATAAGGGCCTA
**
104548 AT-TTTTGCCAAAAT-GCTCAAATAAGGGCCTA
1 ATCTTTT---AATTTGGC-CAAATAAGGGCCTA
104579 ATCTTTTAATTTGGCCAAATAAGGGCCTA
1 ATCTTTTAATTTGGCCAAATAAGGGCCTA
104608 AT
1 AT
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
28 4 0.08
29 21 0.40
30 4 0.08
31 19 0.37
32 4 0.08
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (29 bp):
ATCTTTTAATTTGGCCAAATAAGGGCCTA
Done.