Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012537.1 Corchorus olitorius cultivar O-4 contig12570, 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: 32356
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:6805 original size:5 final size:5
Alignment explanation
Indices: 6780--6842 Score: 51
Period size: 5 Copynumber: 12.6 Consensus size: 5
6770 ATATAGAAAG
* * *
6780 AAAAA AAAAT AAAGAA AAAAT GAAAT AAAAT AAAAT AGAAGA- AAAAT
1 AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT AAAAT A-AA-AT AAAAT
6827 -AAAT AAAAT -AAAT AAA
1 AAAAT AAAAT AAAAT AAA
6843 GAGTTAAATG
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
4 9 0.19
5 30 0.64
6 7 0.15
7 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.14
Consensus pattern (5 bp):
AAAAT
Found at i:6851 original size:25 final size:26
Alignment explanation
Indices: 6775--6838 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
6765 ATGTTATATA
* *
6775 GAAAGAAAAAAAAATA-AAGAAAAAAT
1 GAAATAAAATAAAATAGAAG-AAAAAT
6801 GAAATAAAATAAAATAGAAGAAAAAT
1 GAAATAAAATAAAATAGAAGAAAAAT
6827 -AAATAAAATAAA
1 GAAATAAAATAAA
6839 TAAAGAGTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
25 12 0.34
26 20 0.57
27 3 0.09
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.12
Consensus pattern (26 bp):
GAAATAAAATAAAATAGAAGAAAAAT
Found at i:9781 original size:14 final size:14
Alignment explanation
Indices: 9762--9789 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
9752 TAATAGGTTG
9762 TTATGATTGCTACA
1 TTATGATTGCTACA
9776 TTATGATTGCTACA
1 TTATGATTGCTACA
9790 ATGTTTATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (14 bp):
TTATGATTGCTACA
Found at i:12089 original size:22 final size:22
Alignment explanation
Indices: 12061--12615 Score: 194
Period size: 22 Copynumber: 25.6 Consensus size: 22
12051 TCAGGGAGGA
12061 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
12083 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
12105 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
12127 TATCGAAATTTCATA--ATATGT
1 TATCAAAATTTCATATGA-AGGT
* * * *
12148 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
*
12171 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
*** * *
12193 TATCAAAAAACCATAGGGAGGT
1 TATCAAAATTTCATATGAAGGT
*
12215 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
12231 TATCAAGATTTCATAAGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * *
12253 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
*
12276 TAT-AAAATTTTATA-GAAAGGTT
1 TATCAAAATTTCATATG-AAGG-T
12298 TATCAAAATTTCATAGTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
*** * *
12320 TATTGCAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
12342 TATCAAAATTTTAAAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
*
12364 TA-CTAACAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATATGAAGGT
* * * * *
12386 TTTTAAATTTTCATAACG-TGGT
1 TATCAAAATTTCAT-ATGAAGGT
* * *
12408 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
** * **
12430 TATCAACGTCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
*
12453 TATCAAAATTTCAT-TGGAAAGT
1 TATCAAAATTTCATAT-GAAGGT
*
12475 TATCAAAATTTCATAGTG-AGAT
1 TATCAAAATTTCATA-TGAAGGT
*
12497 CT-TCAAAATTTCATATGGAGGT
1 -TATCAAAATTTCATATGAAGGT
* *
12519 CAACAAAATTTC--AT-AAGGT
1 TATCAAAATTTCATATGAAGGT
** *
12538 TAAAAAAATTT-ATA-AAATGGT
1 TATCAAAATTTCATATGAA-GGT
**
12559 T-TCCAAAATTTCATA-GTATTGT
1 TAT-CAAAATTTCATATG-AAGGT
* *
12581 TATTAAAATTTCATAGGAAGGT
1 TATCAAAATTTCATATGAAGGT
12603 TATCAAAATTTCA
1 TATCAAAATTTCA
12616 AAAGGAGGTC
Statistics
Matches: 401, Mismatches: 90, Indels: 84
0.70 0.16 0.15
Matches are distributed among these distances:
16 9 0.02
17 2 0.00
18 2 0.00
19 13 0.03
20 7 0.02
21 27 0.07
22 291 0.73
23 48 0.12
24 1 0.00
25 1 0.00
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:12118 original size:44 final size:43
Alignment explanation
Indices: 12061--12615 Score: 243
Period size: 44 Copynumber: 12.8 Consensus size: 43
12051 TCAGGGAGGA
12061 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAGT
1 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAG-TTAGT
* * * * *
12105 TTTCAAAATTTCATAAGAGGGTTATCGAAATTTCATA-ATATGT
1 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTA-GT
* * * * * * *
12148 AGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGGT
1 -TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTA-GT
*** * *
12193 TATCAAAAAACCATAGGGAGGTTATCAAAA-TT--T-G-TAGT
1 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTAGT
* * * * **
12231 TATCAAGATTTCATAAGGAGGTTATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTA-G-T
* *
12276 TAT-AAAATTTTATA-GAAAGGTTTATCAAAATTTCATAGTGAGGT
1 TATCAAAATTTCATATG-AAGG-TTATCAAAATTTCATAGTTA-GT
*** * * * *
12320 TATTGCAATTTCATAGTG-TGATTATCAAAATTTTAAAGTGT-GAT
1 TATCAAAATTTCATA-TGAAGGTTATCAAAATTTCATAGT-TAG-T
* * * * *
12364 TA-CTAACAA-TTCATATGGAGGTTTTTAAATTTTCATAACG-TGGT
1 TATC-AA-AATTTCATATGAAGGTTATCAAAATTTCAT-A-GTTAGT
* * * ** * *
12408 TATCAATATATCATATGGAGGTTATCAACGTCTCATAGTGTTGGT
1 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATA--GTTAGT
* *
12453 TATCAAAATTTCAT-TGGAAAGTTATCAAAATTTCATAGTGAGAT
1 TATCAAAATTTCATAT-GAAGGTTATCAAAATTTCATAGTTAG-T
* * *
12497 CT-TCAAAATTTCATATGGAGGTCAACAAAATTTCATA---AGGT
1 -TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTA-GT
** * *
12538 TAAAAAAATTT-ATA-AAATGGTT-TCCAAAATTTCATAGTATTGT
1 TATCAAAATTTCATATGAA-GGTTAT-CAAAATTTCATAGT-TAGT
* *
12581 TATTAAAATTTCATAGGAAGGTTATCAAAATTTCA
1 TATCAAAATTTCATATGAAGGTTATCAAAATTTCA
12616 AAAGGAGGTC
Statistics
Matches: 385, Mismatches: 84, Indels: 84
0.70 0.15 0.15
Matches are distributed among these distances:
38 27 0.07
39 4 0.01
40 19 0.05
41 11 0.03
42 4 0.01
43 25 0.06
44 215 0.56
45 78 0.20
46 1 0.00
47 1 0.00
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.37
Consensus pattern (43 bp):
TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTAGT
Found at i:12537 original size:19 final size:19
Alignment explanation
Indices: 12500--12552 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
12490 GTGAGATCTT
12500 CAAAATTTCATATGGAGGTCAA
1 CAAAATTTCATA---AGGTCAA
*
12522 CAAAATTTCATAAGGTTAA
1 CAAAATTTCATAAGGTCAA
*
12541 AAAAATTT-ATAA
1 CAAAATTTCATAA
12553 AATGGTTTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 4 0.14
19 13 0.45
22 12 0.41
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.30
Consensus pattern (19 bp):
CAAAATTTCATAAGGTCAA
Found at i:12624 original size:22 final size:22
Alignment explanation
Indices: 12579--12632 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
12569 TCATAGTATT
* *
12579 GTTATTAAAATTTCATAGGAAG
1 GTTATCAAAATTTCAAAGGAAG
12601 GTTATCAAAATTTCAAAAGG-AG
1 GTTATCAAAATTTC-AAAGGAAG
*
12623 GTCATCAAAA
1 GTTATCAAAA
12633 ATAGTGTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 24 0.86
23 4 0.14
ACGTcount: A:0.44, C:0.09, G:0.17, T:0.30
Consensus pattern (22 bp):
GTTATCAAAATTTCAAAGGAAG
Found at i:12996 original size:15 final size:16
Alignment explanation
Indices: 12971--13000 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12961 GATCTCTTCG
12971 TAATATAATTAATTAT
1 TAATATAATTAATTAT
12987 TAAT-TAATTAATTA
1 TAATATAATTAATTA
13001 GTACTAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TAATATAATTAATTAT
Found at i:13439 original size:6 final size:6
Alignment explanation
Indices: 13426--13487 Score: 72
Period size: 6 Copynumber: 10.3 Consensus size: 6
13416 AGAAGATGAA
* * **
13426 CAAGAG CCAGAG CCAGAG CAAGAG CAAGAG CAAGAG CAAGAG CCGGAG
1 CAAGAG CAAGAG CAAGAG CAAGAG CAAGAG CAAGAG CAAGAG CAAGAG
13474 CAAGAAG -AAGAG CA
1 CAAG-AG CAAGAG CA
13488 GCATAAGGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
5 2 0.04
6 44 0.92
7 2 0.04
ACGTcount: A:0.45, C:0.21, G:0.34, T:0.00
Consensus pattern (6 bp):
CAAGAG
Found at i:13560 original size:9 final size:9
Alignment explanation
Indices: 13546--13579 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
13536 AGTCGACGAC
*
13546 GAAGATGAT
1 GAAGATGAG
13555 GAAGATGAG
1 GAAGATGAG
13564 GAAGATGAG
1 GAAGATGAG
13573 GAAGATG
1 GAAGATG
13580 GTAACGTTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.44, C:0.00, G:0.41, T:0.15
Consensus pattern (9 bp):
GAAGATGAG
Found at i:25305 original size:16 final size:17
Alignment explanation
Indices: 25284--25327 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
25274 ATGCGCATCG
25284 TTTTTATATTTTC-TTC
1 TTTTTATATTTTCTTTC
25300 TTTTTAT-TTTTCTTTC
1 TTTTTATATTTTCTTTC
**
25316 CCTTTATATTTT
1 TTTTTATATTTT
25328 TCCCCTCTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.21
16 15 0.62
17 4 0.17
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTATATTTTCTTTC
Found at i:25614 original size:23 final size:23
Alignment explanation
Indices: 25584--25631 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
25574 ATCAGATGAG
25584 AATTTACAAAGACAAAACCCACA
1 AATTTACAAAGACAAAACCCACA
25607 AATTTACAAAGACAAAACCCACA
1 AATTTACAAAGACAAAACCCACA
25630 AA
1 AA
25632 GAGACACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.58, C:0.25, G:0.04, T:0.12
Consensus pattern (23 bp):
AATTTACAAAGACAAAACCCACA
Found at i:27009 original size:15 final size:15
Alignment explanation
Indices: 26989--27018 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
26979 TAAAATACTC
26989 ATATGTGAAGTATTT
1 ATATGTGAAGTATTT
27004 ATATGTGAAGTATTT
1 ATATGTGAAGTATTT
27019 GATGTGTGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (15 bp):
ATATGTGAAGTATTT
Found at i:28803 original size:18 final size:19
Alignment explanation
Indices: 28780--28816 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
28770 CACCCTAGCC
28780 CTAAAACTAGAAGA-AAAA
1 CTAAAACTAGAAGAGAAAA
28798 CTAAAACTAGAAGAGAAAA
1 CTAAAACTAGAAGAGAAAA
28817 AGAAGAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.65, C:0.11, G:0.14, T:0.11
Consensus pattern (19 bp):
CTAAAACTAGAAGAGAAAA
Found at i:29459 original size:19 final size:18
Alignment explanation
Indices: 29426--29461 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
29416 TGGAAATAAT
29426 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
29444 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
29462 TAAGTATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:30031 original size:26 final size:26
Alignment explanation
Indices: 29995--30091 Score: 158
Period size: 26 Copynumber: 3.7 Consensus size: 26
29985 TGTTACATTT
*
29995 GCATTCACATTAGTAATTAGGTAATG
1 GCATTCACATTAGTAATTAGGTAATA
30021 GCATTCACATTAGTAATTAGGTAATA
1 GCATTCACATTAGTAATTAGGTAATA
* * *
30047 GCATCCACATTAGTAATTAGGCATTA
1 GCATTCACATTAGTAATTAGGTAATA
30073 GCATTCACATTAGTAATTA
1 GCATTCACATTAGTAATTA
30092 TTAGTAATTA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 66 1.00
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.34
Consensus pattern (26 bp):
GCATTCACATTAGTAATTAGGTAATA
Found at i:30099 original size:36 final size:36
Alignment explanation
Indices: 30055--30127 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
30045 TAGCATCCAC
30055 ATTAGTAATTAGGCATTAGCATTCACATTAGTAATT
1 ATTAGTAATTAGGCATTAGCATTCACATTAGTAATT
*
30091 ATTAGTAATTAGGCATTAGCATTCACATTTGTAATT
1 ATTAGTAATTAGGCATTAGCATTCACATTAGTAATT
30127 A
1 A
30128 GGCATTAACA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.40
Consensus pattern (36 bp):
ATTAGTAATTAGGCATTAGCATTCACATTAGTAATT
Found at i:31463 original size:8 final size:8
Alignment explanation
Indices: 31450--31475 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
31440 AGATGTGAAA
31450 TTGATAAT
1 TTGATAAT
31458 TTGATAAT
1 TTGATAAT
31466 TTGATAAT
1 TTGATAAT
31474 TT
1 TT
31476 TCACTACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.54
Consensus pattern (8 bp):
TTGATAAT
Found at i:31600 original size:19 final size:18
Alignment explanation
Indices: 31576--31611 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
31566 TGAAGACTTA
31576 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
31595 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
31612 ATTATCTCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Done.