Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022496.1 Corchorus olitorius cultivar O-4 contig22529, 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: 33199
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:1527 original size:199 final size:200
Alignment explanation
Indices: 1159--1563 Score: 708
Period size: 199 Copynumber: 2.0 Consensus size: 200
1149 GCTTAATAAC
*
1159 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTGTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
*
1224 GATACAACACATTATTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
66 GATACAACACATTACTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
1289 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAG-A-T-AGATCCG
131 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGAATTAAGATCCG
1351 ATTTA
196 ATTTA
1356 TTTATCAATGGTGAATGTTATTAATTTTGTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTGTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
** *
1421 GATACAACAGTTTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGT
66 GATACAACACATTACTATTATATATA-A-AACTATACCAAAAAAAAGTAGTTGAACATTAGTGGT
*
1486 TGGTTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGAT
129 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGA-ATTAAGAT
1551 CCGATTTA
193 CCGATTTA
1559 TTTAT
1 TTTAT
1564 TATTAAGGAA
Statistics
Matches: 196, Mismatches: 6, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
197 87 0.44
198 1 0.01
199 89 0.45
201 1 0.01
202 1 0.01
203 17 0.09
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.36
Consensus pattern (200 bp):
TTTATCAATGGTGAATGTTATTAATTTTGTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAACACATTACTATTATATATAAAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTTG
ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGAATTAAGATCCG
ATTTA
Found at i:2090 original size:21 final size:21
Alignment explanation
Indices: 2066--2111 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
2056 ATTACATTAT
*
2066 TTTTGATGACC-CCTTATGAAA
1 TTTTGATAACCTCC-TATGAAA
2087 TTTTGATAACCTTCCTATGAAA
1 TTTTGATAACC-TCCTATGAAA
2109 TTT
1 TTT
2112 CAATAACGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 10 0.45
22 10 0.45
23 2 0.09
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.43
Consensus pattern (21 bp):
TTTTGATAACCTCCTATGAAA
Found at i:2231 original size:22 final size:21
Alignment explanation
Indices: 2160--2232 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 21
2150 AATTTTTTTT
*
2160 TAACCTTCTTATGAAATTTTGT
1 TAACC-TCTTATGAAATTTTGA
* * *
2182 TAACCTCCCTAAGGAATTTTGA
1 TAACCT-CTTATGAAATTTTGA
2204 -AGACCTCATTATGAAATTTTGA
1 TA-ACCTC-TTATGAAATTTTGA
2226 TAACCTC
1 TAACCTC
2233 CTGTTGCGCC
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
21 3 0.08
22 36 0.90
23 1 0.03
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (21 bp):
TAACCTCTTATGAAATTTTGA
Found at i:4313 original size:22 final size:22
Alignment explanation
Indices: 4285--4331 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
4275 GACTTGTTAG
* *
4285 TAATCACACTCTAAAATTTTGA
1 TAATCACACTATAAAATTGTGA
*
4307 TAATCACACTATTAAATTGTGA
1 TAATCACACTATAAAATTGTGA
4329 TAA
1 TAA
4332 CCTCGCTATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.36
Consensus pattern (22 bp):
TAATCACACTATAAAATTGTGA
Found at i:4340 original size:22 final size:22
Alignment explanation
Indices: 4315--4567 Score: 116
Period size: 22 Copynumber: 11.7 Consensus size: 22
4305 GATAATCACA
* *
4315 CTATTAAATTGTGAT-AACCTC
1 CTATAAAATTTTGATAAACCTC
* *
4336 GCTATGAAATTTTCATAAACCTTC
1 -CTATAAAATTTTGATAAACC-TC
4360 CTATAAAATTTTGATAAACCTC
1 CTATAAAATTTTGATAAACCTC
*
4382 ATTATAAAATTTTGAT-AACCTC
1 -CTATAAAATTTTGATAAACCTC
* *
4404 CTTATAAAATTTTAAT-AA-CTG
1 C-TATAAAATTTTGATAAACCTC
4425 C-AT---ATTTTGAT-AACCTCC
1 CTATAAAATTTTGATAAACCT-C
**
4443 CTATAATTTTTTGAT-AACCTC
1 CTATAAAATTTTGATAAACCTC
* ** * *
4464 ATTATGGAATTTTG-TTAATCTC
1 -CTATAAAATTTTGATAAACCTC
* ** * *
4486 TCTATGAAATTTTGATTTACATA
1 -CTATAAAATTTTGATAAACCTC
***
4509 CTATGTGATTTTGATAAACCTC
1 CTATAAAATTTTGATAAACCTC
* *
4531 TTATGAAATTTTGAT-AACCTTC
1 CTATAAAATTTTGATAAACC-TC
* *
4553 ATATGAAATTTTGAT
1 CTATAAAATTTTGAT
4568 TACTATCTAT
Statistics
Matches: 182, Mismatches: 35, Indels: 28
0.74 0.14 0.11
Matches are distributed among these distances:
16 9 0.05
17 2 0.01
18 1 0.01
19 4 0.02
21 9 0.05
22 115 0.63
23 40 0.22
24 2 0.01
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.43
Consensus pattern (22 bp):
CTATAAAATTTTGATAAACCTC
Found at i:4363 original size:23 final size:23
Alignment explanation
Indices: 4337--4421 Score: 86
Period size: 23 Copynumber: 3.7 Consensus size: 23
4327 GATAACCTCG
*
4337 CTATGAAATTTTCATAAACCTTC
1 CTATAAAATTTTCATAAACCTTC
*
4360 CTATAAAATTTTGATAAACC-TC
1 CTATAAAATTTTCATAAACCTTC
* *
4382 ATTATAAAATTTTGAT-AACC-TC
1 -CTATAAAATTTTCATAAACCTTC
*
4404 CTTATAAAATTTTAATAA
1 C-TATAAAATTTTCATAA
4422 CTGCATATTT
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
22 21 0.39
23 33 0.61
ACGTcount: A:0.41, C:0.15, G:0.04, T:0.40
Consensus pattern (23 bp):
CTATAAAATTTTCATAAACCTTC
Found at i:4499 original size:44 final size:43
Alignment explanation
Indices: 4320--4567 Score: 133
Period size: 44 Copynumber: 5.7 Consensus size: 43
4310 TCACACTATT
* * * * * *
4320 AAATTGTGATAACCTCGCTATGAAATTTTCATAAACCTTCCTATA
1 AAATTTTGATAACCTC-ATATGGAATTTTGATAAACC-TCTTATG
** *
4365 AAATTTTGATAAACCTCATTATAAAATTTTGAT-AACCTCCTTATA
1 AAATTTTGAT-AACCTCA-TATGGAATTTTGATAAACCT-CTTATG
* *
4410 AAATTTTAATAA-CTGC--AT---ATTTTGAT-AACCTCCCTAT-
1 AAATTTTGATAACCT-CATATGGAATTTTGATAAACCT-CTTATG
* * *
4447 AATTTTTTGATAACCTCATTATGGAATTTTG-TTAATCTCTCTATG
1 AA-ATTTTGATAACCTCA-TATGGAATTTTGATAAACCTCT-TATG
* *
4492 AAATTTTGATTTACAT-ACTATGTG-ATTTTGATAAACCTCTTATG
1 AAATTTTGA-TAACCTCA-TATG-GAATTTTGATAAACCTCTTATG
*
4536 AAATTTTGATAACCTTCATATGAAATTTTGAT
1 AAATTTTGATAACC-TCATATGGAATTTTGAT
4568 TACTATCTAT
Statistics
Matches: 162, Mismatches: 20, Indels: 43
0.72 0.09 0.19
Matches are distributed among these distances:
37 2 0.01
38 27 0.17
39 2 0.01
41 4 0.02
43 7 0.04
44 60 0.37
45 42 0.26
46 18 0.11
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.42
Consensus pattern (43 bp):
AAATTTTGATAACCTCATATGGAATTTTGATAAACCTCTTATG
Found at i:13182 original size:23 final size:24
Alignment explanation
Indices: 13139--13184 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
13129 AGCTTCCAAA
*
13139 TTCTTCAAAAAGATCTACTGCAAT
1 TTCTTCAAAAAGATCAACTGCAAT
13163 TTCTTC-AAAAG-TCAAGCTGCAA
1 TTCTTCAAAAAGATCAA-CTGCAA
13185 ATTTAGCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 11 0.55
24 6 0.30
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (24 bp):
TTCTTCAAAAAGATCAACTGCAAT
Found at i:13187 original size:24 final size:25
Alignment explanation
Indices: 13135--13188 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
13125 TGATAGCTTC
*
13135 CAAA-TTCTTCAAAAAGATCTACTG
1 CAAATTTCTTCAAAAAGATCAACTG
13159 C-AATTTCTTC-AAAAG-TCAAGCTG
1 CAAATTTCTTCAAAAAGATCAA-CTG
13182 CAAATTT
1 CAAATTT
13189 AGCCAAACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 3 0.12
23 11 0.42
24 12 0.46
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.31
Consensus pattern (25 bp):
CAAATTTCTTCAAAAAGATCAACTG
Found at i:14505 original size:63 final size:63
Alignment explanation
Indices: 14406--14529 Score: 212
Period size: 63 Copynumber: 2.0 Consensus size: 63
14396 CTTTGATAAG
* * *
14406 ATTTTCGGATGTTAAAACTAATATATGGCTTAAATTTAGTGAATCTACAGGTTTTTCTCTTAA
1 ATTTTCAGATGTTAAAACTAATATATGGATTAAATTTAGTGAATCTACAGGTTTGTCTCTTAA
*
14469 ATTTTCAGATGTTAAAACTAATTTATGGATTAAATTTAGTGAATCTACAGGTTTGTCTCTT
1 ATTTTCAGATGTTAAAACTAATATATGGATTAAATTTAGTGAATCTACAGGTTTGTCTCTT
14530 GTTTGGTTGA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (63 bp):
ATTTTCAGATGTTAAAACTAATATATGGATTAAATTTAGTGAATCTACAGGTTTGTCTCTTAA
Found at i:15472 original size:5 final size:5
Alignment explanation
Indices: 15462--15530 Score: 82
Period size: 5 Copynumber: 15.4 Consensus size: 5
15452 GTAATATATA
15462 TATCT TATCT TATCT TA-C- TATCT TA-C- TATCT TATCT TA-C- TATCT
1 TATCT TATCT TATCT TATCT TATCT TATCT TATCT TATCT TATCT TATCT
15506 TATCT TATCT TA-C- TATCT TATCT TA
1 TATCT TATCT TATCT TATCT TATCT TA
15531 CTATATATAT
Statistics
Matches: 56, Mismatches: 0, Indels: 16
0.78 0.00 0.22
Matches are distributed among these distances:
3 8 0.14
4 8 0.14
5 40 0.71
ACGTcount: A:0.23, C:0.22, G:0.00, T:0.55
Consensus pattern (5 bp):
TATCT
Found at i:15485 original size:13 final size:13
Alignment explanation
Indices: 15467--15534 Score: 72
Period size: 13 Copynumber: 5.2 Consensus size: 13
15457 ATATATATCT
15467 TATCTTATCTTAC
1 TATCTTATCTTAC
15480 TATCTTA-C-TATC
1 TATCTTATCTTA-C
15492 TTATCTTA-C-TATC
1 -TATCTTATCTTA-C
15505 TTATCTTATCTTAC
1 -TATCTTATCTTAC
15519 TATCTTATCTTAC
1 TATCTTATCTTAC
15532 TAT
1 TAT
15535 ATATATATAT
Statistics
Matches: 51, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.04
12 2 0.04
13 43 0.84
14 2 0.04
15 2 0.04
ACGTcount: A:0.24, C:0.22, G:0.00, T:0.54
Consensus pattern (13 bp):
TATCTTATCTTAC
Found at i:15485 original size:18 final size:18
Alignment explanation
Indices: 15462--15530 Score: 111
Period size: 18 Copynumber: 3.7 Consensus size: 18
15452 GTAATATATA
15462 TATCTTATCTTATCTTAC
1 TATCTTATCTTATCTTAC
15480 TATCTTACTATCTTATCTTAC
1 TATC-T--TATCTTATCTTAC
15501 TATCTTATCTTATCTTAC
1 TATCTTATCTTATCTTAC
15519 TATCTTATCTTA
1 TATCTTATCTTA
15531 CTATATATAT
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
18 29 0.60
19 1 0.02
20 1 0.02
21 17 0.35
ACGTcount: A:0.23, C:0.22, G:0.00, T:0.55
Consensus pattern (18 bp):
TATCTTATCTTATCTTAC
Found at i:15539 original size:2 final size:2
Alignment explanation
Indices: 15532--15567 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
15522 CTTATCTTAC
15532 TA TA 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 TA TA
15568 AAATCACGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16674 original size:23 final size:23
Alignment explanation
Indices: 16644--16687 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
16634 AGAACTCGCT
16644 TGTCTGGAAAGCCATCGACAATG
1 TGTCTGGAAAGCCATCGACAATG
16667 TGTCTGGAAAGCCATCGACAA
1 TGTCTGGAAAGCCATCGACAA
16688 GTTCTTTCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (23 bp):
TGTCTGGAAAGCCATCGACAATG
Found at i:26033 original size:25 final size:25
Alignment explanation
Indices: 26005--26057 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
25995 CTTTTGATTG
* *
26005 ATCATAGATGAA-CTCTGTGAGGATA
1 ATCATACATGAATC-CTGTGAAGATA
26030 ATCATACATGAATCCTGTGAAGATA
1 ATCATACATGAATCCTGTGAAGATA
26055 ATC
1 ATC
26058 CCTGAGTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 24 0.96
26 1 0.04
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (25 bp):
ATCATACATGAATCCTGTGAAGATA
Found at i:32561 original size:5 final size:5
Alignment explanation
Indices: 32546--32576 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
32536 TATCTCGTTC
*
32546 CGTGT CATGT CGTGT CGTGT CGTGT CGTGT C
1 CGTGT CGTGT CGTGT CGTGT CGTGT CGTGT C
32577 AAGACCCGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.03, C:0.23, G:0.35, T:0.39
Consensus pattern (5 bp):
CGTGT
Done.