Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016299.1 Corchorus capsularis cultivar CVL-1 contig16320, 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: 32603
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2153 original size:34 final size:34
Alignment explanation
Indices: 2114--2183 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
2104 TTATATATAT
2114 ATATAAATAAGATGTATAGTCAATAGTTAGAATA
1 ATATAAATAAGATGTATAGTCAATAGTTAGAATA
2148 ATATAAATAAGATGTATAGTCAATAGTTAGAATA
1 ATATAAATAAGATGTATAGTCAATAGTTAGAATA
2182 AT
1 AT
2184 TTACTTTTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.14, T:0.33
Consensus pattern (34 bp):
ATATAAATAAGATGTATAGTCAATAGTTAGAATA
Found at i:4129 original size:23 final size:23
Alignment explanation
Indices: 4098--4143 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
4088 ACAAAATCAG
*
4098 AAAGCTACACTATATAAGATACA
1 AAAGATACACTATATAAGATACA
*
4121 AAAGATACACTATATAAGCTACA
1 AAAGATACACTATATAAGATACA
4144 CTAAATTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.52, C:0.17, G:0.09, T:0.22
Consensus pattern (23 bp):
AAAGATACACTATATAAGATACA
Found at i:11360 original size:143 final size:145
Alignment explanation
Indices: 11079--11361 Score: 482
Period size: 145 Copynumber: 2.0 Consensus size: 145
11069 TAATTAAAAG
11079 CCTTAAACATTAATTAAAAACAATTAAGGAAGGGAAATGTGTAATTACAAAAAAAGGATAGAAGG
1 CCTTAAACATTAATTAAAAACAATTAAGGAAGGGAAATGTGTAATTACAAAAAAAGGATAGAAGG
* * *
11144 AACATGAATTGGGGAAACTCATAGAGGGGCGTTTTAGTCATCCGAAAAGTGAGAAAATACCAAAA
66 AAAAGGAATTGGGGAAACTCATAGAGGGGCGTTTTAGTCATCCGAAAAGTGAGAAAAGACCAAAA
11209 ATAGCCAAAAGGTAA
131 ATAGCCAAAAGGTAA
*
11224 CCTTAAACATTAATTAAAAACAATTAAGGAAGGGAAATGTGTAATTACAAAAAATGG-TAGAAGG
1 CCTTAAACATTAATTAAAAACAATTAAGGAAGGGAAATGTGTAATTACAAAAAAAGGATAGAAGG
* *
11288 AAAAGGAA-TGGGGAAAACTCATAGA-GGGCTTTTTAGTCATCTGAAAAGTGAGAAAAGACCAAA
66 AAAAGGAATTGGGG-AAACTCATAGAGGGGCGTTTTAGTCATCCGAAAAGTGAGAAAAGACCAAA
11351 AATAGCCAAAA
130 AATAGCCAAAA
11362 ACTAGTACCA
Statistics
Matches: 131, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
143 51 0.39
144 24 0.18
145 56 0.43
ACGTcount: A:0.48, C:0.11, G:0.21, T:0.20
Consensus pattern (145 bp):
CCTTAAACATTAATTAAAAACAATTAAGGAAGGGAAATGTGTAATTACAAAAAAAGGATAGAAGG
AAAAGGAATTGGGGAAACTCATAGAGGGGCGTTTTAGTCATCCGAAAAGTGAGAAAAGACCAAAA
ATAGCCAAAAGGTAA
Found at i:17369 original size:19 final size:18
Alignment explanation
Indices: 17337--17373 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
17327 TTGAAATAAT
*
17337 TCTTCAATTGTCTTCAAA
1 TCTTCAATTATCTTCAAA
17355 TCTTCAAATTATCTTCAAA
1 TCTTC-AATTATCTTCAAA
17374 ACACGAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.32, C:0.22, G:0.03, T:0.43
Consensus pattern (18 bp):
TCTTCAATTATCTTCAAA
Found at i:20460 original size:12 final size:12
Alignment explanation
Indices: 20445--20494 Score: 59
Period size: 11 Copynumber: 4.3 Consensus size: 12
20435 ATATTTTGGT
20445 TATTATTATATA
1 TATTATTATATA
20457 TATTATTATATA
1 TATTATTATATA
*
20469 TA-TAATATATA
1 TATTATTATATA
* *
20480 TAAT-TTATATT
1 TATTATTATATA
20491 TATT
1 TATT
20495 TAAAAAAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
11 18 0.55
12 15 0.45
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TATTATTATATA
Found at i:20932 original size:22 final size:22
Alignment explanation
Indices: 20907--20982 Score: 77
Period size: 21 Copynumber: 3.5 Consensus size: 22
20897 AATTTATATT
* *
20907 AAATTTTGATAATTACACCATA
1 AAATTTTGATAATTACACTATG
* *
20929 AAATTTTAATACGTT-CA-TATG
1 AAATTTTGATA-ATTACACTATG
*
20950 AAATTTTGATAATCACACTATG
1 AAATTTTGATAATTACACTATG
20972 AAA-TTTGATAA
1 AAATTTTGATAA
20983 CAACATCAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.02
21 22 0.50
22 19 0.43
23 2 0.05
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.38
Consensus pattern (22 bp):
AAATTTTGATAATTACACTATG
Found at i:21240 original size:44 final size:44
Alignment explanation
Indices: 21213--21311 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
21203 CTCCATGTGG
* * * *
21213 AATGTTGGTAAGCACATTACGAAATTTTGATCACCTTCCTATAA
1 AATGTCGGTAAGCACACTACGAAATTTTAATAACCTTCCTATAA
* * *
21257 AATGTCGGTAAGCACACTACGAAATTTTGATCACTTTCCTATAA
1 AATGTCGGTAAGCACACTACGAAATTTTAATAACCTTCCTATAA
*
21301 AATGTTGGTAA
1 AATGTCGGTAA
21312 TCACTATCAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 51 1.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Consensus pattern (44 bp):
AATGTCGGTAAGCACACTACGAAATTTTAATAACCTTCCTATAA
Found at i:21355 original size:23 final size:22
Alignment explanation
Indices: 21328--21397 Score: 86
Period size: 23 Copynumber: 3.1 Consensus size: 22
21318 TCAAATTGTG
*
21328 AAACCTCATAATAAAATTTTGAT
1 AAACCTC-TTATAAAATTTTGAT
*
21351 AAACCTCTTTGTAAAATTTTGAT
1 AAACCTC-TTATAAAATTTTGAT
* *
21374 AACCCTCTTTTAAAATTTTGAT
1 AAACCTCTTATAAAATTTTGAT
21396 AA
1 AA
21398 TCTCATGAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 16 0.38
23 26 0.62
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.40
Consensus pattern (22 bp):
AAACCTCTTATAAAATTTTGAT
Found at i:21387 original size:22 final size:23
Alignment explanation
Indices: 21339--21397 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
21329 AACCTCATAA
21339 TAAAATTTTGATAAACCTCTTTG
1 TAAAATTTTGATAAACCTCTTTG
*
21362 TAAAATTTTGATAACCCTCTTT-
1 TAAAATTTTGATAAACCTCTTTG
21384 TAAAATTTTGATAA
1 TAAAATTTTGATAA
21398 TCTCATGAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 14 0.40
23 21 0.60
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (23 bp):
TAAAATTTTGATAAACCTCTTTG
Found at i:21595 original size:22 final size:23
Alignment explanation
Indices: 21428--21595 Score: 88
Period size: 22 Copynumber: 7.6 Consensus size: 23
21418 CACCTCAAGA
21428 AATTTTGATAA-CTACC-CTATGT
1 AATTTTGATAACCT-CCACTATGT
* *
21450 AATTTTGATAACCTGC-CTCTG-
1 AATTTTGATAACCTCCACTATGT
* * *
21471 AATTTTTTATAACATCC-CTTATGA
1 AA-TTTTGATAACCTCCAC-TATGT
** * *
21495 AATTTTCTTAACCTCC-CTACGA
1 AATTTTGATAACCTCCACTATGT
*
21517 AATTTTGAAAACCAT--ACTAT-T
1 AATTTTGATAACC-TCCACTATGT
21538 AAATTTTGATAA-CTCCACTATGT
1 -AATTTTGATAACCTCCACTATGT
** * *
21561 AATTACGATAACCTCC-CTGTTT
1 AATTTTGATAACCTCCACTATGT
21583 AATTTTGATAACC
1 AATTTTGATAACC
21596 AAACTATCAA
Statistics
Matches: 113, Mismatches: 22, Indels: 22
0.72 0.14 0.14
Matches are distributed among these distances:
20 1 0.01
21 3 0.03
22 84 0.74
23 23 0.20
24 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.39
Consensus pattern (23 bp):
AATTTTGATAACCTCCACTATGT
Found at i:21724 original size:22 final size:22
Alignment explanation
Indices: 21666--21707 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
21656 ATAACATCCC
*
21666 TCTTAAAAACCACACTATGAAA
1 TCTTAATAACCACACTATGAAA
21688 TCTTAATAACCACACTATGA
1 TCTTAATAACCACACTATGA
21708 TATTTTGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.24, G:0.05, T:0.26
Consensus pattern (22 bp):
TCTTAATAACCACACTATGAAA
Found at i:22633 original size:32 final size:32
Alignment explanation
Indices: 22597--22663 Score: 109
Period size: 31 Copynumber: 2.1 Consensus size: 32
22587 TTAATAATGT
*
22597 CAATTTAGAAATATATATGAAAATAAAGGGTA
1 CAATTTAGAAATATATACGAAAATAAAGGGTA
*
22629 CAA-TTGGAAATATATACGAAAATAAAGGGTA
1 CAATTTAGAAATATATACGAAAATAAAGGGTA
22660 CAAT
1 CAAT
22664 CGGAAAACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 29 0.91
32 3 0.09
ACGTcount: A:0.52, C:0.06, G:0.16, T:0.25
Consensus pattern (32 bp):
CAATTTAGAAATATATACGAAAATAAAGGGTA
Found at i:22642 original size:31 final size:31
Alignment explanation
Indices: 22604--22669 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
22594 TGTCAATTTA
* *
22604 GAAATATATATGAAAATAAAGGGTACAATTG
1 GAAATATATACGAAAATAAAGGGTACAATCG
22635 GAAATATATACGAAAATAAAGGGTACAATCG
1 GAAATATATACGAAAATAAAGGGTACAATCG
22666 GAAA
1 GAAA
22670 ACATAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.53, C:0.06, G:0.20, T:0.21
Consensus pattern (31 bp):
GAAATATATACGAAAATAAAGGGTACAATCG
Found at i:22811 original size:22 final size:22
Alignment explanation
Indices: 22769--22813 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
22759 TATTCATATG
* *
22769 AAATTATGATAACTCCTCTATT
1 AAATTATGATAACTACACTATT
*
22791 AAATTATGATAATTACACTATT
1 AAATTATGATAACTACACTATT
22813 A
1 A
22814 TGATCTCATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.13, G:0.04, T:0.40
Consensus pattern (22 bp):
AAATTATGATAACTACACTATT
Found at i:22907 original size:22 final size:22
Alignment explanation
Indices: 22881--22929 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
22871 GAATTTCGAG
* *
22881 AACCTTTTTAT-AAATTTTTTTT
1 AACCTTCTTATGAAA-TTTTGTT
22903 AACCTTCTTATGAAATTTTGTT
1 AACCTTCTTATGAAATTTTGTT
22925 AACCT
1 AACCT
22930 CTCTAAGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.29, C:0.14, G:0.04, T:0.53
Consensus pattern (22 bp):
AACCTTCTTATGAAATTTTGTT
Found at i:23122 original size:22 final size:22
Alignment explanation
Indices: 22911--23192 Score: 87
Period size: 22 Copynumber: 12.7 Consensus size: 22
22901 TTAACCTTCT
* * *
22911 TATGAAATTTTGTTAACCTCTC
1 TATGAAATTTTGATAACCACAC
* * *
22933 TAAGGAATTTTGA-AGACCTCA-
1 TATGAAATTTTGATA-ACCACAC
* ** *
22954 AATGAAATTTTGATAACTTCCC
1 TATGAAATTTTGATAACCACAC
* * *
22976 AATTAAATTTTGATAACCAACAA
1 TATGAAATTTTGATAACC-ACAC
* * *
22999 TATGAGATGTTGATAACCTTCA-
1 TATGAAATTTTGATAACC-ACAC
* * * *
23021 TATGATATATTGATAACCATAT
1 TATGAAATTTTGATAACCACAC
* *
23043 TATGAAAATTTT-AAAACCTC-C
1 TATG-AAATTTTGATAACCACAC
* *
23064 ATATG-AATTGTT-AGTAATCGCAC
1 -TATGAAATT-TTGA-TAACCACAC
** *
23087 TCCGAAATTTTGATAATCACAC
1 TATGAAATTTTGATAACCACAC
* *
23109 TATG-AATTTGTGATAACCTCCC
1 TATGAAATTT-TGATAACCACAC
**
23131 TATGAAATTTTGATAAATCTTC-C
1 TATGAAATTTTGAT-AA-CCACAC
* * *
23154 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCACAC
*
23177 TATAAAATTTTGATAA
1 TATGAAATTTTGATAA
23193 TTTTCTTATG
Statistics
Matches: 199, Mismatches: 44, Indels: 34
0.72 0.16 0.12
Matches are distributed among these distances:
20 4 0.02
21 24 0.12
22 101 0.51
23 67 0.34
24 3 0.02
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAC
Found at i:23155 original size:23 final size:22
Alignment explanation
Indices: 23090--23214 Score: 117
Period size: 23 Copynumber: 5.6 Consensus size: 22
23080 ATCGCACTCC
* *
23090 GAAATTTTGATAATCACACTAT
1 GAAATTTTGATAATCTCCCTAT
*
23112 G-AATTTGTGATAACCTCCCTAT
1 GAAATTT-TGATAATCTCCCTAT
*
23134 GAAATTTTGATAAATCTTCCTAT
1 GAAATTTTGAT-AATCTCCCTAT
* *
23157 AAAATTTTGATAAACCTCCCTAT
1 GAAATTTTGAT-AATCTCCCTAT
* * * *
23180 AAAATTTTGATAATTTTCTTAT
1 GAAATTTTGATAATCTCCCTAT
*
23202 GAAATCTTGATAA
1 GAAATTTTGATAA
23215 CTACAAATTT
Statistics
Matches: 86, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
21 5 0.06
22 36 0.42
23 45 0.52
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (22 bp):
GAAATTTTGATAATCTCCCTAT
Found at i:23176 original size:46 final size:45
Alignment explanation
Indices: 23091--23214 Score: 137
Period size: 45 Copynumber: 2.8 Consensus size: 45
23081 TCGCACTCCG
* * *
23091 AAATTTTGATAATC-ACACTAT-GAATTTGTGAT-AACCTCCCTATG
1 AAATTTTGATAATCTTC-CTATAAAATTT-TGATAAACCTCCCTATA
23135 AAATTTTGATAAATCTTCCTATAAAATTTTGATAAACCTCCCTATA
1 AAATTTTGAT-AATCTTCCTATAAAATTTTGATAAACCTCCCTATA
* * * *
23181 AAATTTTGATAATTTTCTTATGAAATCTTGATAA
1 AAATTTTGATAATCTTCCTATAAAATTTTGATAA
23215 CTACAAATTT
Statistics
Matches: 69, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
44 10 0.14
45 32 0.46
46 27 0.39
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (45 bp):
AAATTTTGATAATCTTCCTATAAAATTTTGATAAACCTCCCTATA
Found at i:27794 original size:21 final size:21
Alignment explanation
Indices: 27768--27809 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
27758 CTGTGTAATT
27768 TAATCAACAGAAAACTTTCAA
1 TAATCAACAGAAAACTTTCAA
*
27789 TAATCAATAGAAAACTTTCAA
1 TAATCAACAGAAAACTTTCAA
27810 AAGCGACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.17, G:0.05, T:0.26
Consensus pattern (21 bp):
TAATCAACAGAAAACTTTCAA
Done.