Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005972.1 Corchorus capsularis cultivar CVL-1 contig05990, 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: 11552
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Found at i:163 original size:75 final size:75
Alignment explanation
Indices: 84--260 Score: 291
Period size: 75 Copynumber: 2.4 Consensus size: 75
74 CCCATCCACA
*
84 TCCATACCACTATAAATCACCTCCTCCTCCCCGTTATTACAAGTCCCCAGTACCTCCATCGCACC
1 TCCATACCACTATAAATCACCTCCTCCTCCCCGTCATTACAAGTCCCCAGTACCTCCATCGCACC
*
149 ATGCACATCC
66 ATGCACACCC
* * * *
159 TCCATACCGCTATAAATCACCTCCTCCTCCTCGTCATTACAAGTCTCCAGTACCTCCATCTCACC
1 TCCATACCACTATAAATCACCTCCTCCTCCCCGTCATTACAAGTCCCCAGTACCTCCATCGCACC
224 ATGCACACCC
66 ATGCACACCC
*
234 TCCATACCTCTATAAATCACCTCCTCC
1 TCCATACCACTATAAATCACCTCCTCC
261 ACCATCCTAC
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 95 1.00
ACGTcount: A:0.25, C:0.44, G:0.06, T:0.25
Consensus pattern (75 bp):
TCCATACCACTATAAATCACCTCCTCCTCCCCGTCATTACAAGTCCCCAGTACCTCCATCGCACC
ATGCACACCC
Found at i:266 original size:48 final size:48
Alignment explanation
Indices: 221--315 Score: 154
Period size: 48 Copynumber: 2.0 Consensus size: 48
211 CCTCCATCTC
*
221 ACCATGCACACCCTCCATACCTCTATAAATCACCTCCTCCACCATCCT
1 ACCATGCACACCCTCCATACCTCTACAAATCACCTCCTCCACCATCCT
* * *
269 ACCATGCACATCCTCCATACGTCTACAAGTCACCTCCTCCACCATCC
1 ACCATGCACACCCTCCATACCTCTACAAATCACCTCCTCCACCATCC
316 AAGTCTCCTC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.26, C:0.47, G:0.04, T:0.22
Consensus pattern (48 bp):
ACCATGCACACCCTCCATACCTCTACAAATCACCTCCTCCACCATCCT
Found at i:1305 original size:18 final size:18
Alignment explanation
Indices: 1282--1325 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1272 TTAAGGCCGA
*
1282 AATTATTAAATAAATAAT
1 AATTATTAAAGAAATAAT
***
1300 AATTATTTTCGAAATAAT
1 AATTATTAAAGAAATAAT
1318 AATTATTA
1 AATTATTA
1326 TTTTCCATAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (18 bp):
AATTATTAAAGAAATAAT
Found at i:1320 original size:21 final size:22
Alignment explanation
Indices: 1289--1330 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1279 CGAAATTATT
1289 AAATAAATAATAATTATTTTCG
1 AAATAAATAATAATTATTTTCG
*
1311 AAAT-AATAATTATTATTTTC
1 AAATAAATAATAATTATTTTC
1331 CATAAATGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (22 bp):
AAATAAATAATAATTATTTTCG
Found at i:3427 original size:20 final size:20
Alignment explanation
Indices: 3402--3440 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3392 AGTGCTTCAA
*
3402 ACACGCTTCTACAGCTACAC
1 ACACGCTTCTACAACTACAC
3422 ACACGCTTCTACAACTACA
1 ACACGCTTCTACAACTACA
3441 AACTTGCTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.38, G:0.08, T:0.21
Consensus pattern (20 bp):
ACACGCTTCTACAACTACAC
Found at i:7203 original size:22 final size:22
Alignment explanation
Indices: 7164--7216 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
7154 CATAAGAAGG
* *
7164 AAAATTTCAAATGGAGGTTCTC
1 AAAATTTCAAATGAAGGTTATC
*
7186 AAAATTTCAAA-GCAAGGTTATT
1 AAAATTTCAAATG-AAGGTTATC
7208 AAAATTTCA
1 AAAATTTCA
7217 GAGCGTGATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 1 0.04
22 26 0.96
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.32
Consensus pattern (22 bp):
AAAATTTCAAATGAAGGTTATC
Found at i:7283 original size:48 final size:47
Alignment explanation
Indices: 7220--7313 Score: 118
Period size: 48 Copynumber: 2.0 Consensus size: 47
7210 AATTTCAGAG
*
7220 CGTGATTATCCAAATTTCATA-GTGAGCTTATCAAAATTTCACAGTGTA
1 CGTGATTATCAAAATTTCATATG-GAGCTTA-CAAAATTTCACAGTGTA
* * * *
7268 CGTGGTTATCAAAATTTCATATGGAGTTTACAAGATTTCATAGTGT
1 CGTGATTATCAAAATTTCATATGGAGCTTACAAAATTTCACAGTGT
7314 GATCATCAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
47 14 0.35
48 25 0.62
49 1 0.03
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (47 bp):
CGTGATTATCAAAATTTCATATGGAGCTTACAAAATTTCACAGTGTA
Found at i:7330 original size:22 final size:22
Alignment explanation
Indices: 7203--7417 Score: 107
Period size: 22 Copynumber: 9.5 Consensus size: 22
7193 CAAAGCAAGG
* * *
7203 TTATTAAAATTTCAGAGCGTGA
1 TTATCAAAATTTCATAGTGTGA
* * *
7225 TTATCCAAATTTCATAGTGAGC
1 TTATCAAAATTTCATAGTGTGA
* *
7247 TTATCAAAATTTCACAGTGTACGTGG
1 TTATCAAAATTTCATA--GT--GTGA
7273 TTATCAAAATTTCATA-TG-GA
1 TTATCAAAATTTCATAGTGTGA
*
7293 GTT-TACAAGATTTCATAGTGTGA
1 -TTAT-CAAAATTTCATAGTGTGA
*
7316 TCATCAAAATTTCAT--TGTGA
1 TTATCAAAATTTCATAGTGTGA
* * ** ** * *
7336 CGTTAACAAACTTTTGTAAAGAGG
1 --TTATCAAAATTTCATAGTGTGA
* *
7360 TTATCAAAATTTCATAAGGAGCTAAA
1 TTATCAAAATTTCAT-A-GTG-T-GA
7386 TTATCAAAATTTCATAGTGTGA
1 TTATCAAAATTTCATAGTGTGA
7408 TTATCAAAAT
1 TTATCAAAAT
7418 CTTAGAGTGT
Statistics
Matches: 143, Mismatches: 33, Indels: 34
0.68 0.16 0.16
Matches are distributed among these distances:
20 7 0.05
21 14 0.10
22 75 0.52
23 6 0.04
24 8 0.06
25 1 0.01
26 32 0.22
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGA
Found at i:7426 original size:22 final size:22
Alignment explanation
Indices: 7385--7428 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
7375 AAGGAGCTAA
*
7385 ATTATCAAAATTTCATAGTGTG
1 ATTATCAAAATTTCAGAGTGTG
7407 ATTATCAAAATCTT-AGAGTGTG
1 ATTATCAAAAT-TTCAGAGTGTG
7429 GTATGTTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (22 bp):
ATTATCAAAATTTCAGAGTGTG
Found at i:7598 original size:44 final size:44
Alignment explanation
Indices: 7505--7756 Score: 159
Period size: 44 Copynumber: 5.8 Consensus size: 44
7495 TTGTAGAGTA
* * **
7505 ATCAAAATTTCAT-TGGAAGGTTATTAAAATTTCAT-GTGAAAGTT
1 ATCAAAATTTCATATGG-AGATTATCAAAATTTCATAGT-TTAGTT
*
7549 ATCAAAATTTCATATGGAGATTATCAAAATTTCATAGTTTATTT
1 ATCAAAATTTCATATGGAGATTATCAAAATTTCATAGTTTAGTT
* * *
7593 TTCAAAATTTCATATGGGAAATTATCAAAATTTCATAGTTT-GTAG
1 ATCAAAATTTCATAT-GGAGATTATCAAAATTTCATAGTTTAGT-T
* * * *
7638 ATCGAAATTTCAT-TGGGAGGTTAAT-AAAATTTCATA-ATGAGGTT
1 ATCAAAATTTCATAT-GGAGATT-ATCAAAATTTCATAGTTTA-GTT
* ** * * *
7682 ATGAAAAAATCATAGGGAGGTTATCAAAA-TTC---G-TGA-TT
1 ATCAAAATTTCATATGGAGATTATCAAAATTTCATAGTTTAGTT
* * * *
7720 ATTAAAATTTCATAAGGAGGTTATCAAAATTTTATAG
1 ATCAAAATTTCATATGGAGATTATCAAAATTTCATAG
7757 GGAGCTTTAT
Statistics
Matches: 168, Mismatches: 26, Indels: 30
0.75 0.12 0.13
Matches are distributed among these distances:
38 27 0.16
39 2 0.01
40 3 0.02
42 1 0.01
43 6 0.04
44 85 0.51
45 44 0.26
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (44 bp):
ATCAAAATTTCATATGGAGATTATCAAAATTTCATAGTTTAGTT
Found at i:7646 original size:45 final size:45
Alignment explanation
Indices: 7505--7673 Score: 161
Period size: 44 Copynumber: 3.8 Consensus size: 45
7495 TTGTAGAGTA
* * * * *
7505 ATCAAAATTTCAT-TGGAAGGTTATTAAAATTTCAT-G-TGAAAG
1 ATCAAAATTTCATATGGGAGATTATCAAAATTTCATAGTTTATAG
**
7547 TTATCAAAATTTCATAT-GGAGATTATCAAAATTTCATAGTTTATTT
1 --ATCAAAATTTCATATGGGAGATTATCAAAATTTCATAGTTTATAG
* * *
7593 TTCAAAATTTCATATGGGAAATTATCAAAATTTCATAGTTTGTAG
1 ATCAAAATTTCATATGGGAGATTATCAAAATTTCATAGTTTATAG
* *
7638 ATCGAAATTTCAT-TGGGAGGTTAAT-AAAATTTCATA
1 ATCAAAATTTCATATGGGAGATT-ATCAAAATTTCATA
7674 ATGAGGTTAT
Statistics
Matches: 104, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
44 62 0.60
45 40 0.38
46 2 0.02
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (45 bp):
ATCAAAATTTCATATGGGAGATTATCAAAATTTCATAGTTTATAG
Found at i:7688 original size:22 final size:22
Alignment explanation
Indices: 7505--7796 Score: 122
Period size: 22 Copynumber: 13.4 Consensus size: 22
7495 TTGTAGAGTA
*
7505 ATCAAAATTTCAT-TGGAAGGTT
1 ATCAAAATTTCATAAGG-AGGTT
* ** * *
7527 ATTAAAATTTCATGTGAAAGTT
1 ATCAAAATTTCATAAGGAGGTT
* *
7549 ATCAAAATTTCATATGGAGATT
1 ATCAAAATTTCATAAGGAGGTT
* *
7571 ATCAAAATTTCAT-AGTTTA-TTT
1 ATCAAAATTTCATAAG--GAGGTT
* * **
7593 TTCAAAATTTCATATGGGAAATT
1 ATCAAAATTTCATA-AGGAGGTT
*** *
7616 ATCAAAATTTCAT-AGTTTGTAG
1 ATCAAAATTTCATAAGGAGGT-T
* **
7638 ATCGAAATTTCATTGGGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
*
7660 AAT-AAAATTTCATAATGAGGTT
1 -ATCAAAATTTCATAAGGAGGTT
* ** *
7682 ATGAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
*
7704 ATCAAAA-TTCGT---GA--TT
1 ATCAAAATTTCATAAGGAGGTT
*
7720 ATTAAAATTTCATAAGGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
* * *
7742 ATCAAAATTTTATAGGGAGCTTT
1 ATCAAAATTTCATAAGGAG-GTT
* *
7765 ATCAATATTTTAT-AGGAAGGTTT
1 ATCAAAATTTCATAAGG-AGG-TT
7788 ATCAAAATT
1 ATCAAAATT
7797 AAAAATTTCT
Statistics
Matches: 202, Mismatches: 49, Indels: 37
0.70 0.17 0.13
Matches are distributed among these distances:
16 8 0.04
17 4 0.02
18 2 0.01
20 2 0.01
21 8 0.04
22 129 0.64
23 48 0.24
24 1 0.00
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.38
Consensus pattern (22 bp):
ATCAAAATTTCATAAGGAGGTT
Found at i:7774 original size:23 final size:23
Alignment explanation
Indices: 7740--7796 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
7730 CATAAGGAGG
*
7740 TTATCAAAATTTTATAGGGAGCT
1 TTATCAAAATTTTATAGGAAGCT
* *
7763 TTATCAATATTTTATAGGAAGGT
1 TTATCAAAATTTTATAGGAAGCT
7786 TTATCAAAATT
1 TTATCAAAATT
7797 AAAAATTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGCT
Found at i:7943 original size:22 final size:22
Alignment explanation
Indices: 7916--7984 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
7906 GCTTGCCAAC
*
7916 ATTTCACAGGAAGGTTATCAAA
1 ATTTCACAGGATGGTTATCAAA
* *
7938 ATTTCATTATG-TGGTTATC-AA
1 ATTTCA-CAGGATGGTTATCAAA
*
7959 ATTTCACTGGATGGTTATCAAA
1 ATTTCACAGGATGGTTATCAAA
7981 ATTT
1 ATTT
7985 AATATTGAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.03
21 16 0.42
22 19 0.50
23 2 0.05
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (22 bp):
ATTTCACAGGATGGTTATCAAA
Found at i:7973 original size:21 final size:21
Alignment explanation
Indices: 7916--7980 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
7906 GCTTGCCAAC
* *
7916 ATTTCACAGGAAGGTTATCAAA
1 ATTTCACTGGATGGTTATC-AA
* *
7938 ATTTCATTATG-TGGTTATCAA
1 ATTTCACT-GGATGGTTATCAA
7959 ATTTCACTGGATGGTTATCAA
1 ATTTCACTGGATGGTTATCAA
7980 A
1 A
7981 ATTTAATATT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
20 1 0.03
21 20 0.57
22 13 0.37
23 1 0.03
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (21 bp):
ATTTCACTGGATGGTTATCAA
Found at i:7996 original size:22 final size:21
Alignment explanation
Indices: 7927--7996 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 21
7917 TTTCACAGGA
7927 AGGTTATCAAAATTTCATTATG
1 AGGTTATCAAAATTTCATT-TG
* * *
7949 TGGTTATC-AAATTTCACTGG
1 AGGTTATCAAAATTTCATTTG
*
7969 ATGGTTATCAAAATTTAATATTG
1 A-GGTTATCAAAATTTCAT-TTG
7992 AGGTT
1 AGGTT
7997 TTGAAATTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
20 1 0.03
21 16 0.42
22 18 0.47
23 3 0.08
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (21 bp):
AGGTTATCAAAATTTCATTTG
Found at i:8004 original size:43 final size:43
Alignment explanation
Indices: 7916--8028 Score: 111
Period size: 43 Copynumber: 2.6 Consensus size: 43
7906 GCTTGCCAAC
* *
7916 ATTTCACAGGAAGGTTATCAAAATTTCATTATGTGGTTATCAA
1 ATTTCACAGGAAGGTTATCAAAATTTAATTATGAGGTTATCAA
* * * *
7959 ATTTCACTGGATGGTTATCAAAATTTAA-TATTGAGGTTTTGAA
1 ATTTCACAGGAAGGTTATCAAAATTTAATTA-TGAGGTTATCAA
* * * *
8002 ATTTTCATAGGGATGTTAACAAAATTT
1 A-TTTCACAGGAAGGTTATCAAAATTT
8029 TATAGGAAGG
Statistics
Matches: 56, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
42 2 0.04
43 35 0.62
44 19 0.34
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.40
Consensus pattern (43 bp):
ATTTCACAGGAAGGTTATCAAAATTTAATTATGAGGTTATCAA
Found at i:8041 original size:22 final size:23
Alignment explanation
Indices: 8000--8054 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
7990 TGAGGTTTTG
* *
8000 AAATTTTCATAGGGATGTTAACA
1 AAATTTTCATAGGAAGGTTAACA
*
8023 AAATTTT-ATAGGAAGGTTAACG
1 AAATTTTCATAGGAAGGTTAACA
8045 AAA-TTTCATA
1 AAATTTTCATA
8055 CAAAATGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.11
22 18 0.64
23 7 0.25
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.35
Consensus pattern (23 bp):
AAATTTTCATAGGAAGGTTAACA
Found at i:8112 original size:22 final size:22
Alignment explanation
Indices: 8087--8142 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 22
8077 GGGGAGCTTC
8087 TCAAAATTTCATAAGAAGATTA
1 TCAAAATTTCATAAGAAGATTA
* * *
8109 TCAAATTTTTAT-ATAAGATTA
1 TCAAAATTTCATAAGAAGATTA
8130 TCAAAATTTCATA
1 TCAAAATTTCATA
8143 GTTATATAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.39
Consensus pattern (22 bp):
TCAAAATTTCATAAGAAGATTA
Found at i:10987 original size:108 final size:109
Alignment explanation
Indices: 10837--11130 Score: 423
Period size: 108 Copynumber: 2.7 Consensus size: 109
10827 TAAATTAAAA
* *
10837 TGGTAAAAATAAAAAAAATTATATAAAATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGT
1 TGGTAAAAAT-AAAGAAATTATA-AAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGT
10901 AGAATAAAATTGTATATTAG-AAAAATTTTAATATATCCAAATTTTT
63 AGAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
* *
10947 TGGTAGAAATAAAGAAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTATA
1 TGGTAAAAATAAAGAAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
*
11012 ATAAAATTGTATATTAGAAAAAATTTTAGTATATCCAAATTTTT
66 ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
* * *
11056 T-GTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTA
1 TGGTAAAAATAAAGAAATTATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTA
11120 GTAGAATAAAA
61 GTAGAATAAAA
11131 CTATAATAGT
Statistics
Matches: 167, Mismatches: 10, Indels: 11
0.89 0.05 0.06
Matches are distributed among these distances:
108 90 0.54
109 40 0.24
110 10 0.06
113 27 0.16
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (109 bp):
TGGTAAAAATAAAGAAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
Done.