Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014144.1 Corchorus capsularis cultivar CVL-1 contig14165, 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: 36403
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:680 original size:18 final size:17
Alignment explanation
Indices: 636--690 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 17
626 GAAATTCTTA
636 ATTTTAATTTAGATTAATT
1 ATTTTAA-TTAG-TTAATT
*
655 ATTATTAATTAGTTTATT
1 ATT-TTAATTAGTTAATT
673 AGTTTTAATTAGTTAATT
1 A-TTTTAATTAGTTAATT
691 TATGATTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 19 0.59
19 9 0.28
20 4 0.12
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (17 bp):
ATTTTAATTAGTTAATT
Found at i:770 original size:18 final size:18
Alignment explanation
Indices: 749--810 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
739 TTAATTATTG
*
749 TTAAATAGTTTATTAGGA
1 TTAATTAGTTTATTAGGA
* **
767 TTAATTATTTTATTAGTT
1 TTAATTAGTTTATTAGGA
*
785 TTAATTAGTTTATTTACGA
1 TTAATTAGTTTA-TTAGGA
804 TTAATTA
1 TTAATTA
811 CTGTTAATTA
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
18 25 0.71
19 10 0.29
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.55
Consensus pattern (18 bp):
TTAATTAGTTTATTAGGA
Found at i:791 original size:28 final size:29
Alignment explanation
Indices: 728--792 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
718 AATTTTGAAA
*
728 TTTAATTAAGATTAATTATTGTTAAATAG
1 TTTAATTAGGATTAATTATTGTTAAATAG
*
757 TTT-ATTAGGATTAATTATT-TT-ATTAG
1 TTTAATTAGGATTAATTATTGTTAAATAG
783 TTTTAATTAG
1 -TTTAATTAG
793 TTTATTTACG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 4 0.12
27 5 0.16
28 20 0.62
29 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (29 bp):
TTTAATTAGGATTAATTATTGTTAAATAG
Found at i:1226 original size:22 final size:20
Alignment explanation
Indices: 1196--1255 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 20
1186 TTTGTTACAA
*
1196 ATTTAATTATTAATTTTATATT
1 ATTT-ATTATTAATTTAAT-TT
*
1218 ATTTGATTAGTAATTTAATTT
1 ATTT-ATTATTAATTTAATTT
*
1239 AGTTATTAATTAATTTA
1 ATTTATT-ATTAATTTA
1256 TTAATTTTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 3 0.09
21 13 0.41
22 16 0.50
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (20 bp):
ATTTATTATTAATTTAATTT
Found at i:7190 original size:34 final size:35
Alignment explanation
Indices: 7135--7201 Score: 86
Period size: 34 Copynumber: 1.9 Consensus size: 35
7125 ATCTTTGCGT
7135 TAAAAAAAATTGAATTTTTATTTTTGC-GTTTTTTC
1 TAAAAAAAATTGAATTTTTATTTTT-CTGTTTTTTC
*
7170 TAAAAAAAA-T-ATTTTCTTATTTTTCTGTTTTT
1 TAAAAAAAATTGAATTT-TTATTTTTCTGTTTTT
7202 AATTTTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
33 5 0.17
34 15 0.52
35 9 0.31
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (35 bp):
TAAAAAAAATTGAATTTTTATTTTTCTGTTTTTTC
Found at i:11448 original size:17 final size:17
Alignment explanation
Indices: 11426--11459 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
11416 CAATATCATG
11426 ATAAAATGCAAAACATA
1 ATAAAATGCAAAACATA
11443 ATAAAATGCAAAACATA
1 ATAAAATGCAAAACATA
11460 TGTCATCCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.65, C:0.12, G:0.06, T:0.18
Consensus pattern (17 bp):
ATAAAATGCAAAACATA
Found at i:15521 original size:21 final size:21
Alignment explanation
Indices: 15488--15536 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
15478 AAGAATTGTA
*
15488 GCTT-CTTGGAAATGACTCTT
1 GCTTCCTTGGAAATCACTCTT
* *
15508 GCTTCCTTTGAAATCCCTCTT
1 GCTTCCTTGGAAATCACTCTT
15529 GCATTCCT
1 GC-TTCCT
15537 AAAGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.16, C:0.29, G:0.14, T:0.41
Consensus pattern (21 bp):
GCTTCCTTGGAAATCACTCTT
Found at i:19230 original size:8 final size:8
Alignment explanation
Indices: 19219--19248 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
19209 GAAAAATATC
19219 AAAAAATA
1 AAAAAATA
19227 AAAAAAT-
1 AAAAAATA
19234 AAAAAATA
1 AAAAAATA
19242 AAAAAAT
1 AAAAAAT
19249 TTTCGTCCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (8 bp):
AAAAAATA
Found at i:19237 original size:15 final size:15
Alignment explanation
Indices: 19219--19248 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
19209 GAAAAATATC
19219 AAAAAATAAAAAAAT
1 AAAAAATAAAAAAAT
19234 AAAAAATAAAAAAAT
1 AAAAAATAAAAAAAT
19249 TTTCGTCCAG
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:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (15 bp):
AAAAAATAAAAAAAT
Found at i:20951 original size:33 final size:33
Alignment explanation
Indices: 20873--20977 Score: 113
Period size: 33 Copynumber: 3.2 Consensus size: 33
20863 TTGCAAAGAG
* * * *
20873 TGTTTTAGATGTTGTTTGCAATGATACTAAACC
1 TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC
** *
20906 TAATTT-GAGTGTTGTTTGCGATGACACTAAATC
1 TGTTTTAG-GTGTTGTTTGCGATGAAACTAAATC
* *
20939 TGTTTTAGGTGTTGTTTGTGATGAAACAAAATC
1 TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC
20972 TGTTTT
1 TGTTTT
20978 GGTTGATCAT
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
32 1 0.02
33 57 0.97
34 1 0.02
ACGTcount: A:0.26, C:0.10, G:0.21, T:0.44
Consensus pattern (33 bp):
TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC
Found at i:21420 original size:30 final size:29
Alignment explanation
Indices: 21384--21476 Score: 141
Period size: 30 Copynumber: 3.1 Consensus size: 29
21374 TCTTCAAGGG
21384 GGAGGGAATGATGCGCCCAAGGCTTATCAT
1 GGAGGGAATGATGCG-CCAAGGCTTATCAT
*
21414 GGAGGGAATGATGCACCAAGGACTTATCAT
1 GGAGGGAATGATGCGCCAAGG-CTTATCAT
*
21444 GGAGGGAATGATGCGCCAAGAACTTATCAT
1 GGAGGGAATGATGCGCCAAG-GCTTATCAT
21474 GGA
1 GGA
21477 CTTGAAGATG
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
29 6 0.10
30 52 0.90
ACGTcount: A:0.31, C:0.17, G:0.32, T:0.19
Consensus pattern (29 bp):
GGAGGGAATGATGCGCCAAGGCTTATCAT
Found at i:21543 original size:18 final size:19
Alignment explanation
Indices: 21520--21557 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
21510 GTGCATGGGC
*
21520 TGCATGGAG-GCATGAAGA
1 TGCATGGAGACCATGAAGA
21538 TGCATGGAGACCATGAAGA
1 TGCATGGAGACCATGAAGA
21557 T
1 T
21558 AATGGACTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.34, C:0.13, G:0.34, T:0.18
Consensus pattern (19 bp):
TGCATGGAGACCATGAAGA
Found at i:26505 original size:45 final size:43
Alignment explanation
Indices: 26450--26540 Score: 137
Period size: 45 Copynumber: 2.1 Consensus size: 43
26440 AAGATTACTT
*
26450 CACCAACTCATCATTAATCCTGGGTAGGGATCTTTTAGTAATTC
1 CACCAACTCATCATTAATCCGGGGTAGGGATC-TTTAGTAATTC
* *
26494 CACCTAACTCATCATTTATTCGGGGTAGGGATCTTTAGTAATTC
1 CACC-AACTCATCATTAATCCGGGGTAGGGATCTTTAGTAATTC
26538 CAC
1 CAC
26541 TACTCTATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 18 0.42
45 25 0.58
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.34
Consensus pattern (43 bp):
CACCAACTCATCATTAATCCGGGGTAGGGATCTTTAGTAATTC
Found at i:26743 original size:210 final size:208
Alignment explanation
Indices: 26353--26944 Score: 753
Period size: 210 Copynumber: 2.8 Consensus size: 208
26343 CTTTTTGTAA
* * * * * *
26353 AAATGACCTAAAAGTTTAGATATTTAATCCCCTCAAGAAT-AAAAGGTTAGGACATTTAAGTAAT
1 AAATGACCAAAAAGTCTAGTTATTTAATCACCTCTAGAATCAAAA-GTTAGGGCATTTAAGTAAT
**** * * * * *
26417 TTACCAAGTAGGTAAAGACGAAAAAGATTACTTCAC-CAACTCATCATTAATCCTGGGTAGGGAT
65 CGGTCAAGTAGGAAAAGACGAAAAAAATTAATTCTCTC-ACTCCTCATTAATCC-GGGTAGGGAT
** * ** * **
26481 CTTTTAGTAA-TTCCACCTA-ACTCA-TCATTTATTCGGGGTAGGGATCTTTAGTAATTCCACTA
128 CTTTTAGTAATTTCCA--TATGTTTATTCAAATAAT--ATGTAGGGATCTTTAGTAATTCCACTA
*
26543 CTCTATTAAAGTCATTTGAG
189 CTCTATTAAAGTAATTTGAG
26563 AAATGACCAAAAAGTCTAGTTATTTAATCACCTCTAGAATCAAAAGTTAGGGCATTTAAGTAATC
1 AAATGACCAAAAAGTCTAGTTATTTAATCACCTCTAGAATCAAAAGTTAGGGCATTTAAGTAATC
26628 GGTCAAGTAGGAAAAGACGAAAAAAATTAATTCTCTCACTCCTCATTAATCCAGGGTAGGGATCT
66 GGTCAAGTAGGAAAAGACGAAAAAAATTAATTCTCTCACTCCTCATTAATCC-GGGTAGGGATCT
*
26693 TTTAGTAATTTTCATATGTTTATTCAAATAATATGTAGGGATCTTTTAGTAATTCCACTACTCTA
130 TTTAGTAATTTCCATATGTTTATTCAAATAATATGTAGGGATC-TTTAGTAATTCCACTACTCTA
26758 TTAAAGTAATTTGAG
194 TTAAAGTAATTTGAG
*
26773 AAATGAACAAAAATTAAGTCTAGTTATTTAATCACCTCTAGAATCAAAAGTTAGGGCATTTAAGT
1 AAATG-AC-CAAA--AAGTCTAGTTATTTAATCACCTCTAGAATCAAAAGTTAGGGCATTTAAGT
* * * *
26838 AATCGGTCAAGTGGGAAAAGACGAAAAAAATTAGTTTTCTCGCTCCTCATTAATCCGGGATAGGG
62 AATCGGTCAAGTAGGAAAAGACGAAAAAAATTAATTCTCTCACTCCTCATTAATCCGGG-TAGGG
26903 ATCTTTTAGTAATTTCCATATGTTTATTCAAATAATATGTAG
126 ATCTTTTAGTAATTTCCATATGTTTATTCAAATAATATGTAG
26945 TATATATCAG
Statistics
Matches: 339, Mismatches: 32, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
209 11 0.03
210 157 0.46
211 17 0.05
212 3 0.01
213 3 0.01
214 148 0.44
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (208 bp):
AAATGACCAAAAAGTCTAGTTATTTAATCACCTCTAGAATCAAAAGTTAGGGCATTTAAGTAATC
GGTCAAGTAGGAAAAGACGAAAAAAATTAATTCTCTCACTCCTCATTAATCCGGGTAGGGATCTT
TTAGTAATTTCCATATGTTTATTCAAATAATATGTAGGGATCTTTAGTAATTCCACTACTCTATT
AAAGTAATTTGAG
Found at i:27383 original size:36 final size:34
Alignment explanation
Indices: 27317--27383 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
27307 TAAATCAATC
**
27317 AATTTAGAGACAAATATTTTTGCCTTTAATTCTT
1 AATTTAGAGACAAATATTTTTGCCACTAATTCTT
27351 AATTTAGAGACAAATTATTATTTGCCACTAATT
1 AATTTAGAGACAAA-TATT-TTTGCCACTAATT
27384 AGTCGCTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 14 0.48
35 4 0.14
36 11 0.38
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (34 bp):
AATTTAGAGACAAATATTTTTGCCACTAATTCTT
Found at i:28261 original size:14 final size:14
Alignment explanation
Indices: 28244--28275 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
28234 TTTGTTTTCT
28244 TAGTTTTTCTACAC
1 TAGTTTTTCTACAC
28258 TAG-TTTTCTACAC
1 TAGTTTTTCTACAC
28271 T-GTTT
1 TAGTTT
28276 GCAAAATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 1 0.06
13 13 0.76
14 3 0.18
ACGTcount: A:0.19, C:0.19, G:0.09, T:0.53
Consensus pattern (14 bp):
TAGTTTTTCTACAC
Found at i:34526 original size:35 final size:32
Alignment explanation
Indices: 34467--34532 Score: 96
Period size: 35 Copynumber: 2.0 Consensus size: 32
34457 AGGGGAGGAC
34467 GGCACCACCATGGCGTGCCATCCTGACAGGGT
1 GGCACCACCATGGCGTGCCATCCTGACAGGGT
*
34499 GGCACCACCCATGGGGCGTGCCGTCCTGACAGGG
1 GGCACCA-CCAT--GGCGTGCCATCCTGACAGGG
34533 CGACATCGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 7 0.23
33 4 0.13
35 19 0.63
ACGTcount: A:0.17, C:0.35, G:0.35, T:0.14
Consensus pattern (32 bp):
GGCACCACCATGGCGTGCCATCCTGACAGGGT
Found at i:34674 original size:10 final size:10
Alignment explanation
Indices: 34659--34683 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
34649 ATAGCTTGAA
34659 GATTTCAGAG
1 GATTTCAGAG
34669 GATTTCAGAG
1 GATTTCAGAG
34679 GATTT
1 GATTT
34684 GAATTGTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.08, G:0.28, T:0.36
Consensus pattern (10 bp):
GATTTCAGAG
Found at i:35578 original size:32 final size:32
Alignment explanation
Indices: 35536--35604 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
35526 AAGGGGAGGA
* *
35536 CGGCACCACCATGGCGTGCCGTCCTGACAGGG
1 CGGCACCACCATGGCGAGCCGTCCTCACAGGG
*
35568 TGGCACCACCATGGCGAGCCGTCCTCACAGGG
1 CGGCACCACCATGGCGAGCCGTCCTCACAGGG
35600 CGGCA
1 CGGCA
35605 TCGTCATATC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.17, C:0.38, G:0.33, T:0.12
Consensus pattern (32 bp):
CGGCACCACCATGGCGAGCCGTCCTCACAGGG
Found at i:35738 original size:10 final size:10
Alignment explanation
Indices: 35723--35750 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
35713 GTGATAGCTT
35723 GAGGATTTCA
1 GAGGATTTCA
35733 GAGGATTTCA
1 GAGGATTTCA
35743 GAGGATTT
1 GAGGATTT
35751 GAATTGTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.29, C:0.07, G:0.32, T:0.32
Consensus pattern (10 bp):
GAGGATTTCA
Found at i:35814 original size:22 final size:21
Alignment explanation
Indices: 35787--35831 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
35777 GCAAGAGTGT
* *
35787 CAAAAGGGGGGCGATAAGTAG
1 CAAAAAGGGGGCGATAAATAG
*
35808 CAAAAAGGGGGCGGTAAATAG
1 CAAAAAGGGGGCGATAAATAG
35829 CAA
1 CAA
35832 CACCCTTTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.11, G:0.38, T:0.09
Consensus pattern (21 bp):
CAAAAAGGGGGCGATAAATAG
Done.