Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012675.1 Corchorus olitorius cultivar O-4 contig12708, 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: 37826
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1104 original size:22 final size:22
Alignment explanation
Indices: 1076--1129 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
1066 ATTATATTAT
* * *
1076 TTTTGATGACTTTCTTATGAAA
1 TTTTGATAACCTTCTTATAAAA
1098 TTTTGATAACCTTCTTATAAAA
1 TTTTGATAACCTTCTTATAAAA
*
1120 TTTTAATAAC
1 TTTTGATAAC
1130 GATACTATGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.48
Consensus pattern (22 bp):
TTTTGATAACCTTCTTATAAAA
Found at i:1185 original size:22 final size:22
Alignment explanation
Indices: 1160--1201 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1150 ACCTTTTTTA
* *
1160 AACCTTCTTATGAAATTTTGTT
1 AACCTCCTTAAGAAATTTTGTT
*
1182 AACCTCCTTAAGGAATTTTG
1 AACCTCCTTAAGAAATTTTG
1202 AAGATCTCAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.43
Consensus pattern (22 bp):
AACCTCCTTAAGAAATTTTGTT
Found at i:1359 original size:22 final size:23
Alignment explanation
Indices: 1332--1386 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 23
1322 AAATCCTCCA
1332 TATG-AATTGTTAATAATCACAC
1 TATGAAATTGTTAATAATCACAC
* *
1354 TCTGAAATT-TTGATAATCACAC
1 TATGAAATTGTTAATAATCACAC
1376 TATGAAATTGT
1 TATGAAATTGT
1387 GATAACCTCG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 23 0.82
23 5 0.18
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (23 bp):
TATGAAATTGTTAATAATCACAC
Found at i:1389 original size:22 final size:22
Alignment explanation
Indices: 1344--1411 Score: 91
Period size: 22 Copynumber: 3.1 Consensus size: 22
1334 TGAATTGTTA
*
1344 ATAATCACACTCTGAAATTTTG
1 ATAATCACACTATGAAATTTTG
*
1366 ATAATCACACTATGAAATTGTG
1 ATAATCACACTATGAAATTTTG
* * *
1388 ATAACCTCGCTATGAAATTTTG
1 ATAATCACACTATGAAATTTTG
1410 AT
1 AT
1412 TCACCTTCCT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (22 bp):
ATAATCACACTATGAAATTTTG
Found at i:1478 original size:22 final size:21
Alignment explanation
Indices: 1356--1734 Score: 189
Period size: 22 Copynumber: 17.9 Consensus size: 21
1346 AATCACACTC
* *
1356 TGAAATTTTGATAATCACACTA
1 TGAAATTTTGATAACCTC-CTA
*
1378 TGAAATTGTGATAACCTCGCTA
1 TGAAATTTTGATAACCTC-CTA
*
1400 TGAAATTTTGATTCACCTTCCTA
1 TGAAATTTTGA-TAACC-TCCTA
*
1423 TAAAATTTTGATAAACCTCCCTA
1 TGAAATTTTGAT-AACCT-CCTA
1446 T--AA-TTTGATAACCTCCTTA
1 TGAAATTTTGATAACCTCC-TA
*
1465 TGAAATCTTGATAA----CTA
1 TGAAATTTTGATAACCTCCTA
* *
1482 -CAAATTTTGATAACCGCCCTA
1 TGAAATTTTGATAACC-TCCTA
* * *
1503 TG-ATTCTTTTATAACCTCATTA
1 TGAAAT-TTTGATAACCTC-CTA
* *
1525 TGAAATTTTGTTAATCTCCCTA
1 TGAAATTTTGATAACCT-CCTA
* * *
1547 TGAAATTTTGATCCACATACTA
1 TGAAATTTTGAT-AACCTCCTA
*
1569 TGAAATTTTGATAACCCTCTTA
1 TGAAATTTTGATAA-CCTCCTA
* *
1591 TGAAATTTTGA-AAACTAAACTA
1 TGAAATTTTGATAACCT--CCTA
* *
1613 TGAAATTTTCATAACCTTCATA
1 TGAAATTTTGATAACC-TCCTA
* ** *
1635 TGAATTTTTGATGTCCTCC-C
1 TGAAATTTTGATAACCTCCTA
*
1655 TGAAATTTTGATTA-CTCCATAA
1 TGAAATTTTGATAACCTCC-T-A
* *
1677 TAAAATTTTAATAACCTTCC--
1 TGAAATTTTGATAACC-TCCTA
* *
1697 T--AA-TTTGGTAACCATACTA
1 TGAAATTTTGATAACC-TCCTA
1716 TGAAATTTTGATAACCTCC
1 TGAAATTTTGATAACCTCC
1735 CCAGAAATAC
Statistics
Matches: 267, Mismatches: 56, Indels: 69
0.68 0.14 0.18
Matches are distributed among these distances:
16 11 0.04
17 12 0.04
18 5 0.02
19 13 0.05
20 20 0.07
21 19 0.07
22 147 0.55
23 34 0.13
24 6 0.02
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (21 bp):
TGAAATTTTGATAACCTCCTA
Found at i:1861 original size:66 final size:66
Alignment explanation
Indices: 1772--1919 Score: 152
Period size: 66 Copynumber: 2.2 Consensus size: 66
1762 AATCACATTT
* * * * * * * * ** *
1772 TGAAAATTTGATAACCTCTTTATGAAATTTTCATAACCTCTCTATAAAATTTTGTTGACCCCTCT
1 TGAAATTTTGATAATCACATTATGAAATATTCATAACCTCGCTATAAAATTTTGATAACAACACT
1837 A
66 A
* * * *
1838 TGAAATTTTGATAATCACATTATGTAATATTGATAACCTCGCTTTGAAATTTTGATAACAACACT
1 TGAAATTTTGATAATCACATTATGAAATATTCATAACCTCGCTATAAAATTTTGATAACAACACT
1903 A
66 A
*
1904 CGAAATTTTGATAATC
1 TGAAATTTTGATAATC
1920 TTCCTATAAA
Statistics
Matches: 66, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.39
Consensus pattern (66 bp):
TGAAATTTTGATAATCACATTATGAAATATTCATAACCTCGCTATAAAATTTTGATAACAACACT
A
Found at i:1932 original size:21 final size:22
Alignment explanation
Indices: 1748--2001 Score: 109
Period size: 22 Copynumber: 11.5 Consensus size: 22
1738 GAAATACCAG
*
1748 TATGAAATTTTGGTAATCACATT-
1 TATGAAATTTTGATAAT--CATTC
*
1771 T-TGAAAATTTGATAACCTC-TT-
1 TATGAAATTTTGATAA--TCATTC
* *
1792 TATGAAATTTTCATAA-CCTCTC
1 TATGAAATTTTGATAATCAT-TC
* * * * **
1814 TATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAATCATTC
*
1836 TATGAAATTTTGATAATCACAT-
1 TATGAAATTTTGATAATCA-TTC
* * * *
1858 TATGTAATATTGATAA-CCTCGC
1 TATGAAATTTTGATAATCAT-TC
* **
1880 TTTGAAATTTTGATAA-CAACAC
1 TATGAAATTTTGATAATC-ATTC
*
1902 TACGAAATTTTGATAATC-TTCC
1 TATGAAATTTTGATAATCATT-C
1924 TAT-AAATTTTGATAATCCGATCTC
1 TATGAAATTTTGATAAT-C-AT-TC
*
1948 TATGAAATTTCGATAATCATTC
1 TATGAAATTTTGATAATCATTC
* *
1970 TATGAGA-TTTGATAA-CCTTC
1 TATGAAATTTTGATAATCATTC
*
1990 TATCAAATTTTG
1 TATGAAATTTTG
2002 GTACTCCTTA
Statistics
Matches: 175, Mismatches: 37, Indels: 40
0.69 0.15 0.16
Matches are distributed among these distances:
19 1 0.01
20 10 0.06
21 29 0.17
22 108 0.62
23 7 0.04
24 7 0.04
25 13 0.07
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAATCATTC
Found at i:2053 original size:22 final size:22
Alignment explanation
Indices: 2039--2372 Score: 125
Period size: 22 Copynumber: 15.0 Consensus size: 22
2029 TAACCTTCAC
*
2039 ATGAAATTTTGATAACCACCCT
1 ATGAAATTTTGATAACCACACT
* * * * *
2061 ATAAAATTTTGATCACCTCCCC
1 ATGAAATTTTGATAACCACACT
* *
2083 ATGAAATATT-AGTAACCTC-CTT
1 ATGAAATTTTGA-TAACCACAC-T
*
2105 ATGAAATTTTGTTAACCACACT
1 ATGAAATTTTGATAACCACACT
* *
2127 ATGAAATTCTT-ATAACCTCGCT
1 ATGAAATT-TTGATAACCACACT
* * *
2149 ATGACATTTTGATAA--TCTCT
1 ATGAAATTTTGATAACCACACT
* * *
2169 TTGATAACCTTTCTATATAACCACATT
1 ATGA-AA--TTT-T-GATAACCACACT
** *
2196 ATGAAATTTCAATAACCTTC-CT
1 ATGAAATTTTGATAACC-ACACT
* * **
2218 AAGAAATTTTAATAATTTGATC-CT
1 ATGAAATTTTGATAA--CCA-CACT
* *
2242 ATGAAATTTTGATAACCTTC-CC
1 ATGAAATTTTGATAACC-ACACT
*
2264 ATGAAATTTTGATAATTTC-CA-T
1 ATGAAATTTTGATAA--CCACACT
*
2286 ATGAAATTTTGGTAACCACACT
1 ATGAAATTTTGATAACCACACT
*
2308 ATGAAATTTTGATAACCTC-CT
1 ATGAAATTTTGATAACCACACT
*** * *
2329 CATGAAATTAAAATAAGCATC-TT
1 -ATGAAATTTTGATAACCA-CACT
2352 ATGAAATTTTGATAACCACAC
1 ATGAAATTTTGATAACCACAC
2373 AGAGACAAGA
Statistics
Matches: 231, Mismatches: 55, Indels: 52
0.68 0.16 0.15
Matches are distributed among these distances:
20 8 0.03
21 10 0.04
22 172 0.74
23 9 0.04
24 21 0.09
25 4 0.02
26 2 0.01
27 5 0.02
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.37
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACACT
Found at i:2262 original size:46 final size:44
Alignment explanation
Indices: 2195--2302 Score: 128
Period size: 46 Copynumber: 2.4 Consensus size: 44
2185 ATAACCACAT
** *
2195 TATGAAATTTCAATAACCTTCCTAAGAAATTTTAATAATTTGATCC-
1 TATGAAATTTTGATAACCTTCCCAAGAAATTTTAATAA-TT--TCCA
* *
2241 TATGAAATTTTGATAACCTTCCCATGAAATTTTGATAATTTCCA
1 TATGAAATTTTGATAACCTTCCCAAGAAATTTTAATAATTTCCA
*
2285 TATGAAATTTTGGTAACC
1 TATGAAATTTTGATAACC
2303 ACACTATGAA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
43 3 0.05
44 17 0.31
45 2 0.04
46 33 0.60
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (44 bp):
TATGAAATTTTGATAACCTTCCCAAGAAATTTTAATAATTTCCA
Found at i:2334 original size:44 final size:43
Alignment explanation
Indices: 1748--2368 Score: 260
Period size: 44 Copynumber: 13.9 Consensus size: 43
1738 GAAATACCAG
* * * * * *
1748 TATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTC-C
* * * * * * *
1792 TATGAAATTTTCATAACCTCTCTATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTC-C
* * * *
1836 TATGAAATTTTGATAATCACATTATGTAATATTGATAACCTCGC
1 TATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTC-C
* * * *
1880 TTTGAAATTTTGATAACAACACTACGAAATTTTGATAATCTTCC
1 TATGAAATTTTGATAACCACACTATGAAATTTTGATAA-CCTCC
* * * *
1924 TAT-AAATTTTGATAATCCGATCTCTATGAAATTTCGATAATCATTC
1 TATGAAATTTTGATAA-CC-A-CACTATGAAATTTTGATAA-CCTCC
* ** * *
1970 TATGAGA-TTTGATAACC-TTCTATCAAATTTTGGT-A-CTCC
1 TATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCC
* * *
2009 TTATGAAATTGAGACTTTTATAACCTTCAC-ATGAAATTTTGATAACCACCC
1 -TATGAAA-T-----TTTGATAACC-ACACTATGAAATTTTGATAACC-TCC
* * * * * *
2060 TATAAAATTTTGATCACCTCCCCATGAAATATT-AGTAACCTCC
1 TATGAAATTTTGATAACCACACTATGAAATTTTGA-TAACCTCC
*
2103 TTATGAAATTTTGTTAACCACACTATGAAATTCTT-ATAACCTCGC
1 -TATGAAATTTTGATAACCACACTATGAAATT-TTGATAACCTC-C
* * * * * * *
2148 TATGACATTTTGATAA--TCTCTTTGATAACCTTTCTATATAACCACAT
1 TATGAAATTTTGATAACCACACTATGA-AA--TTT-T-GATAACCTC-C
** * * * **
2195 TATGAAATTTCAATAACCTTC-CTAAGAAATTTTAATAATTTGATCC
1 TATGAAATTTTGATAACC-ACACTATGAAATTTTGATAA---CCTCC
* * **
2241 TATGAAATTTTGATAACCTTC-CCATGAAATTTTGATAATTTCC
1 TATGAAATTTTGATAACC-ACACTATGAAATTTTGATAACCTCC
*
2284 ATATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTCC
1 -TATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCC
*** * *
2328 TCATGAAATTAAAATAAGCATC-TTATGAAATTTTGATAACC
1 T-ATGAAATTTTGATAACCA-CACTATGAAATTTTGATAACC
2369 ACACAGAGAC
Statistics
Matches: 435, Mismatches: 103, Indels: 78
0.71 0.17 0.13
Matches are distributed among these distances:
39 2 0.00
40 6 0.01
41 1 0.00
42 19 0.04
43 25 0.06
44 237 0.54
45 15 0.03
46 67 0.15
47 32 0.07
48 13 0.03
49 7 0.02
50 9 0.02
51 2 0.00
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (43 bp):
TATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTCC
Found at i:2355 original size:66 final size:66
Alignment explanation
Indices: 2240--2372 Score: 171
Period size: 66 Copynumber: 2.0 Consensus size: 66
2230 TAATTTGATC
*** ** *
2240 CTATGAAATTTTGATAACCTTCCCATGAAATTTTGATAATTTCCATATGAAATTTTGGTAACCAC
1 CTATGAAATTTTGATAACCTTCCCATGAAATTAAAATAACATCCATATGAAATTTTGATAACCAC
2305 A
66 A
*
2306 CTATGAAATTTTGATAACC-TCCTCATGAAATTAAAATAAGCAT-CTTATGAAATTTTGATAACC
1 CTATGAAATTTTGATAACCTTCC-CATGAAATTAAAATAA-CATCCATATGAAATTTTGATAACC
2369 ACA
64 ACA
2372 C
1 C
2373 AGAGACAAGA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
65 3 0.05
66 54 0.93
67 1 0.02
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (66 bp):
CTATGAAATTTTGATAACCTTCCCATGAAATTAAAATAACATCCATATGAAATTTTGATAACCAC
A
Found at i:2765 original size:20 final size:20
Alignment explanation
Indices: 2737--2775 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2727 TATTGACATT
2737 TAAAATATTGAAA-TTAAAAG
1 TAAAATATT-AAATTTAAAAG
*
2757 TAAACTATTAAATTTAAAA
1 TAAAATATTAAATTTAAAA
2776 AATAATAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (20 bp):
TAAAATATTAAATTTAAAAG
Found at i:3994 original size:19 final size:20
Alignment explanation
Indices: 3976--4011 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
3966 AATTAATTAT
3976 TTTA-ATATTA-ATTTTTTA
1 TTTATATATTATATTTTTTA
3994 TTTATATATTATATTTTT
1 TTTATATATTATATTTTT
4012 ACTTAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.25
19 6 0.38
20 6 0.38
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTATATATTATATTTTTTA
Found at i:4021 original size:19 final size:19
Alignment explanation
Indices: 3979--4023 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
3969 TAATTATTTT
*
3979 AATATTAATTTTTTATTTA
1 AATATTAATTTTTTACTTA
*
3998 TATATT-ATATTTTTACTTA
1 AATATTAAT-TTTTTACTTA
4017 AATATTA
1 AATATTA
4024 CTCCTAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
AATATTAATTTTTTACTTA
Found at i:4900 original size:11 final size:11
Alignment explanation
Indices: 4884--4997 Score: 67
Period size: 11 Copynumber: 10.8 Consensus size: 11
4874 AAAAAATTTG
4884 TTATATATATT
1 TTATATATATT
*
4895 TTATATATATC
1 TTATATATATT
* * *
4906 ATAAATATA-A
1 TTATATATATT
4916 TT-TATATATT
1 TTATATATATT
* *
4926 TTACATGTATT
1 TTATATATATT
4937 TTATATATA--
1 TTATATATATT
* * *
4946 TCATAAATA-A
1 TTATATATATT
*
4956 TTAAATATATT
1 TTATATATATT
*
4967 TTATATATATC
1 TTATATATATT
* *
4978 ATAAATATATT
1 TTATATATATT
*
4989 TGATATATA
1 TTATATATA
4998 ATAGCATAAT
Statistics
Matches: 74, Mismatches: 25, Indels: 8
0.69 0.23 0.07
Matches are distributed among these distances:
9 12 0.16
10 9 0.12
11 53 0.72
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (11 bp):
TTATATATATT
Found at i:32937 original size:64 final size:64
Alignment explanation
Indices: 32859--32988 Score: 233
Period size: 64 Copynumber: 2.0 Consensus size: 64
32849 GTCAAGAATG
* *
32859 TTGAAGATAGAATAAGATATTGCATCCACTCACAACATTTTCTCATTTAGTTACTATTACCTTT
1 TTGAAGATAGAATAAGATATTGCATCCACTCACAACATTTTCCCATTTAGTTACTATTAACTTT
*
32923 TTGAAGATAGAATAAGATATTGCATCCATTCACAACATTTTCCCATTTAGTTACTATTAACTTT
1 TTGAAGATAGAATAAGATATTGCATCCACTCACAACATTTTCCCATTTAGTTACTATTAACTTT
32987 TT
1 TT
32989 TCTACTTCCC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.40
Consensus pattern (64 bp):
TTGAAGATAGAATAAGATATTGCATCCACTCACAACATTTTCCCATTTAGTTACTATTAACTTT
Found at i:35496 original size:2 final size:2
Alignment explanation
Indices: 35489--35517 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35479 TATTAGATAG
35489 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
35518 AATTAATACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.