Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024814.1 Corchorus olitorius cultivar O-4 contig24847, 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: 30022
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:1252 original size:69 final size:70
Alignment explanation
Indices: 1157--1317 Score: 243
Period size: 69 Copynumber: 2.3 Consensus size: 70
1147 ATTTCCCGCA
* * *
1157 ACAACTCCTGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTA-ATTTGCGCTCTTCA
1 ACAAGTCCTGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATATTTGCACTCCTCA
1221 ACAGC
66 ACAGC
* * *
1226 ACAAGTCCGGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATTTTTGCATTCCTCA
1 ACAAGTCCTGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATATTTGCACTCCTCA
1291 ACAGC
66 ACAGC
* *
1296 CCAAGTCTTGGACAGGACTTGG
1 ACAAGTCCTGGACAGGACTTGG
1318 CCAAGATCTG
Statistics
Matches: 82, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
69 48 0.59
70 34 0.41
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (70 bp):
ACAAGTCCTGGACAGGACTTGGGTAACTCCTGCCCAGGTCTTGTCCTGTATATTTGCACTCCTCA
ACAGC
Found at i:1329 original size:22 final size:22
Alignment explanation
Indices: 1296--1357 Score: 108
Period size: 22 Copynumber: 2.8 Consensus size: 22
1286 CCTCAACAGC
1296 CCAAG-TCTTGGACAGGACTTGG
1 CCAAGATC-TGGACAGGACTTGG
1318 CCAAGATCTGGACAGGACTTGG
1 CCAAGATCTGGACAGGACTTGG
1340 CCAAGATCTGGACAGGAC
1 CCAAGATCTGGACAGGAC
1358 GTGTTCTGCA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
22 37 0.95
23 2 0.05
ACGTcount: A:0.27, C:0.24, G:0.31, T:0.18
Consensus pattern (22 bp):
CCAAGATCTGGACAGGACTTGG
Found at i:9292 original size:16 final size:15
Alignment explanation
Indices: 9255--9292 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
9245 CAGATTTTTC
*
9255 TGATTAGCCTTCCTT
1 TGATTATCCTTCCTT
9270 T-ATTATCCTCTCCTT
1 TGATTATCCT-TCCTT
9285 TGATTATC
1 TGATTATC
9293 TATTTTTCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 7 0.35
15 7 0.35
16 6 0.30
ACGTcount: A:0.16, C:0.26, G:0.08, T:0.50
Consensus pattern (15 bp):
TGATTATCCTTCCTT
Found at i:15768 original size:22 final size:22
Alignment explanation
Indices: 15703--15760 Score: 116
Period size: 22 Copynumber: 2.6 Consensus size: 22
15693 GGTTTTTCAT
15703 GGCTAATGAAGTATCTGTGATC
1 GGCTAATGAAGTATCTGTGATC
15725 GGCTAATGAAGTATCTGTGATC
1 GGCTAATGAAGTATCTGTGATC
15747 GGCTAATGAAGTAT
1 GGCTAATGAAGTAT
15761 TTGCGATCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.29, C:0.12, G:0.28, T:0.31
Consensus pattern (22 bp):
GGCTAATGAAGTATCTGTGATC
Found at i:15783 original size:22 final size:22
Alignment explanation
Indices: 15758--15801 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
15748 GCTAATGAAG
*
15758 TATTTGCGATCATTCTGATTGT
1 TATTTGCGATAATTCTGATTGT
15780 TATTTGCGATAATTCTGATTGT
1 TATTTGCGATAATTCTGATTGT
15802 GATCGGCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.11, G:0.18, T:0.50
Consensus pattern (22 bp):
TATTTGCGATAATTCTGATTGT
Found at i:19722 original size:42 final size:43
Alignment explanation
Indices: 19671--19764 Score: 129
Period size: 45 Copynumber: 2.2 Consensus size: 43
19661 AGTGCATTAC
* *
19671 CTAA-ATTCTA-CTCCATCTTTAGGTAATTCATCAAAATAAAA
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
*
19712 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAA
19757 CTAATATT
1 CTAATATT
19765 AATTGTTGCT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 36 0.78
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAA
Found at i:20712 original size:2 final size:2
Alignment explanation
Indices: 20699--20748 Score: 82
Period size: 2 Copynumber: 24.0 Consensus size: 2
20689 ACTAAAAATA
20699 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
20743 AT AT AT
1 AT AT AT
20749 GTGTATCTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 42 0.91
3 4 0.09
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21461 original size:207 final size:203
Alignment explanation
Indices: 21083--21479 Score: 686
Period size: 207 Copynumber: 1.9 Consensus size: 203
21073 TCGATAATGG
* *
21083 ATGTTATTAATTTTTTAAGTCTAATATTACTATCAAAGTTGTAGTGAATAAGATACAACACATTA
1 ATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAACACATTA
* * *
21148 TTATTATATATATAAAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTGATTTATTAAATT
66 CTATTATATATATAAAACTACACAAAAAAAAATTAGTTGAACATTAGTGGTTGATTTATTAAATT
*
21213 AAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCTGATTTATATAT
131 AAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGATCCGATTTATATAT
21278 CAATGGTGA
195 CAATGGTGA
*
21287 ATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATCCAACACATTA
1 ATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAACACATTA
*
21352 CTATTATATATATAGAACTACACAAAAAAAAAAAATTAGTTGAACATTAGTGGTTGATTTATTAA
66 CTATTATATATATAAAACTACAC---AAAAAAAAATTAGTTGAACATTAGTGGTTGATTTATTAA
21417 ATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCCGATTTAT
128 ATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCCGATTTAT
21480 TTATTATTAA
Statistics
Matches: 182, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
204 82 0.45
206 13 0.07
207 87 0.48
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.36
Consensus pattern (203 bp):
ATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAGATACAACACATTA
CTATTATATATATAAAACTACACAAAAAAAAATTAGTTGAACATTAGTGGTTGATTTATTAAATT
AAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAGATCCGATTTATATATC
AATGGTGA
Found at i:21567 original size:25 final size:24
Alignment explanation
Indices: 21533--21579 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
21523 AACAATACAC
21533 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
21558 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
21580 TGTAAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (24 bp):
AAATACCTAAGAATTTAATTAAAA
Found at i:21590 original size:17 final size:17
Alignment explanation
Indices: 21565--21629 Score: 51
Period size: 17 Copynumber: 3.5 Consensus size: 17
21555 AAAAAATACC
*
21565 TAAGAATTTAATTAATG
1 TAAGTATTTAATTAATG
21582 TAAGTATTTCAATTATTATAG
1 TAAGTATTT-AATTA--AT-G
*
21603 TATTA-CATTTAATTAATG
1 TA--AGTATTTAATTAATG
21621 TAAGTATTT
1 TAAGTATTT
21630 TAGCTATTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 14
0.69 0.05 0.25
Matches are distributed among these distances:
16 1 0.03
17 12 0.32
18 8 0.21
19 2 0.05
20 2 0.05
21 8 0.21
22 4 0.11
23 1 0.03
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.48
Consensus pattern (17 bp):
TAAGTATTTAATTAATG
Found at i:21631 original size:18 final size:18
Alignment explanation
Indices: 21571--21631 Score: 54
Period size: 18 Copynumber: 3.2 Consensus size: 18
21561 TACCTAAGAA
21571 TTTAATTAATGTAAGTAT
1 TTTAATTAATGTAAGTAT
*
21589 TTCAATT-AT-TATAGTATT
1 TTTAATTAATGTA-AGTA-T
21607 ACATTTAATTAATGTAAGTAT
1 ---TTTAATTAATGTAAGTAT
21628 TTTA
1 TTTA
21632 GCTATTATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 14
0.68 0.04 0.28
Matches are distributed among these distances:
16 2 0.06
17 6 0.18
18 11 0.32
21 7 0.21
22 6 0.18
23 2 0.06
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (18 bp):
TTTAATTAATGTAAGTAT
Found at i:21638 original size:39 final size:40
Alignment explanation
Indices: 21570--21650 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 40
21560 ATACCTAAGA
* *
21570 ATTTAATTAATGTAAGTATTTCAATTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAACTATTATATATATTAC
* *
21609 ATTTAATTAATGTAAGTATTTTAGCTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAACTATTATATATATTAC
21649 AT
1 AT
21651 AGGAATTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 29 0.78
40 8 0.22
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.49
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAACTATTATATATATTAC
Found at i:23771 original size:13 final size:13
Alignment explanation
Indices: 23753--23779 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
23743 ATAGCATTGT
23753 AGGATCCAAGAAA
1 AGGATCCAAGAAA
23766 AGGATCCAAGAAA
1 AGGATCCAAGAAA
23779 A
1 A
23780 CATAGGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.15, G:0.22, T:0.07
Consensus pattern (13 bp):
AGGATCCAAGAAA
Found at i:25365 original size:20 final size:20
Alignment explanation
Indices: 25314--25369 Score: 51
Period size: 20 Copynumber: 2.9 Consensus size: 20
25304 TAGAGAAGGC
*
25314 TTTTTCAAAACAATTTTTAA
1 TTTTTCAAAAAAATTTTTAA
** * * *
25334 AATTTGACAAAAATTTTTGA
1 TTTTTCAAAAAAATTTTTAA
25354 TTTTTC-AAAAAATTTT
1 TTTTTCAAAAAAATTTT
25370 GCTTCTCTAG
Statistics
Matches: 26, Mismatches: 10, Indels: 1
0.70 0.27 0.03
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (20 bp):
TTTTTCAAAAAAATTTTTAA
Found at i:28141 original size:27 final size:28
Alignment explanation
Indices: 28091--28143 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
28081 AAATCAATTA
*
28091 GAAATCATAAAAACATAAAGATAAATCT
1 GAAATCATAAAAACACAAAGATAAATCT
28119 GAAATCATAAAATAC-CAAA-ATAAAT
1 GAAATCATAAAA-ACACAAAGATAAAT
28144 AATCAGATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 6 0.26
28 15 0.65
29 2 0.09
ACGTcount: A:0.62, C:0.11, G:0.06, T:0.21
Consensus pattern (28 bp):
GAAATCATAAAAACACAAAGATAAATCT
Done.