Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014689.1 Corchorus capsularis cultivar CVL-1 contig14710, 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: 100278
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:6653 original size:29 final size:29
Alignment explanation
Indices: 6621--6690 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
6611 ACTTGTAGCA
*
6621 TTTGGACGTTTTGTCC-CATAAATTTCAAT
1 TTTGGACGTTTTG-CCTCATAAACTTCAAT
* * *
6650 TTTGGACATTTTGCCTTATGAACTTCAAT
1 TTTGGACGTTTTGCCTCATAAACTTCAAT
6679 TTTGGGACGTTT
1 TTT-GGACGTTT
6691 GCCCCCTCAG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 2 0.06
29 25 0.74
30 7 0.21
ACGTcount: A:0.21, C:0.16, G:0.17, T:0.46
Consensus pattern (29 bp):
TTTGGACGTTTTGCCTCATAAACTTCAAT
Found at i:10021 original size:17 final size:17
Alignment explanation
Indices: 9999--10035 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
9989 ACGTGTCTTC
9999 TTTCTTCTTTTT-TTTTT
1 TTTCTT-TTTTTATTTTT
10016 TTTCTTTTTTTATTTTT
1 TTTCTTTTTTTATTTTT
10033 TTT
1 TTT
10036 ATTAAGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.03, C:0.08, G:0.00, T:0.89
Consensus pattern (17 bp):
TTTCTTTTTTTATTTTT
Found at i:10022 original size:14 final size:15
Alignment explanation
Indices: 10003--10033 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
9993 GTCTTCTTTC
10003 TTCTTTTTTT-TTTT
1 TTCTTTTTTTATTTT
10017 TTCTTTTTTTATTTT
1 TTCTTTTTTTATTTT
10032 TT
1 TT
10034 TTATTAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.03, C:0.06, G:0.00, T:0.90
Consensus pattern (15 bp):
TTCTTTTTTTATTTT
Found at i:10222 original size:107 final size:107
Alignment explanation
Indices: 10050--10314 Score: 478
Period size: 107 Copynumber: 2.5 Consensus size: 107
10040 AGTTTAGCCT
* **
10050 TAATTTCACTAAGTTTAGCTCCAAATTAAAAAATT-TTTTTATTTTAAGGGTAAATTTAAAAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTAAAAATT
*
10114 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
66 AATAATTTATTGTTATAGGATTTTAGAAATAAAATACAAAAC
*
10156 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTAAAAATT
10221 AATAATTTATTGTTATAGGATTTTAGAAATAAAATACAAAAC
66 AATAATTTATTGTTATAGGATTTTAGAAATAAAATACAAAAC
10263 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
10315 TAGAAAAATT
Statistics
Matches: 153, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
106 32 0.21
107 121 0.79
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (107 bp):
TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTAAAAATT
AATAATTTATTGTTATAGGATTTTAGAAATAAAATACAAAAC
Found at i:14196 original size:2 final size:2
Alignment explanation
Indices: 14189--14217 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
14179 TTACCTAGGC
14189 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
14218 GCTCCAGTCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24125 original size:13 final size:13
Alignment explanation
Indices: 24107--24131 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24097 AATTACACTT
24107 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
24120 TTTTTCTTTTTT
1 TTTTTCTTTTTT
24132 AAATTTTGGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:24554 original size:18 final size:17
Alignment explanation
Indices: 24526--24572 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
24516 TAATAAAAAT
24526 ATTAA-ATTTATAATTA
1 ATTAATATTTATAATTA
*
24542 ATTAAATATTTATTGATTA
1 ATT-AATATTTA-TAATTA
*
24561 CTTAATATTTAT
1 ATTAATATTTAT
24573 TTTTATTACT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 3 0.12
17 3 0.12
18 13 0.50
19 7 0.27
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (17 bp):
ATTAATATTTATAATTA
Found at i:31017 original size:2 final size:2
Alignment explanation
Indices: 31012--31041 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
31002 TTATATGTGT
*
31012 TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31042 CACACACATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:32200 original size:33 final size:32
Alignment explanation
Indices: 32150--32227 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 32
32140 ATGACCTTGG
* *
32150 AGGAGGATGGTTGTGGGAAGAAATCGATCTTAA
1 AGGAGGA-GGATGTGGGAAGAAATCAATCTTAA
*
32183 AGGAGGAGGATGATGGGAAGAAATCAATCTTAG
1 AGGAGGAGGATG-TGGGAAGAAATCAATCTTAA
32216 AGGAGGAGGATG
1 AGGAGGAGGATG
32228 GGAGGTCTAC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 4 0.10
33 37 0.90
ACGTcount: A:0.36, C:0.05, G:0.40, T:0.19
Consensus pattern (32 bp):
AGGAGGAGGATGTGGGAAGAAATCAATCTTAA
Found at i:39980 original size:23 final size:23
Alignment explanation
Indices: 39950--39998 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
39940 TATGTCTTCG
39950 ATCACATCATTGGGTACTCCATT
1 ATCACATCATTGGGTACTCCATT
*
39973 ATCACATCATTGGGTACTTCATT
1 ATCACATCATTGGGTACTCCATT
39996 ATC
1 ATC
39999 TATTTCTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (23 bp):
ATCACATCATTGGGTACTCCATT
Found at i:43722 original size:11 final size:11
Alignment explanation
Indices: 43692--43725 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
43682 TAAAGTAAAC
**
43692 AAAACAGAACA
1 AAAACAGAGGA
43703 AAAACAGAGGA
1 AAAACAGAGGA
43714 AAAACAGAGGA
1 AAAACAGAGGA
43725 A
1 A
43726 CCAAAAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.68, C:0.12, G:0.21, T:0.00
Consensus pattern (11 bp):
AAAACAGAGGA
Found at i:44983 original size:22 final size:22
Alignment explanation
Indices: 44942--44984 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
44932 ATTCATATGA
* *
44942 AATTATGATAATCCCTCTATTG
1 AATTATGATAATCACACTATTG
*
44964 AATTATGATAATTACACTATT
1 AATTATGATAATCACACTATT
44985 ATGATCTCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (22 bp):
AATTATGATAATCACACTATTG
Found at i:45079 original size:22 final size:23
Alignment explanation
Indices: 45053--45098 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
45043 GAATTTCGAT
* *
45053 AACCTTTTTAT-AAATTTTTTTA
1 AACCTTCTTATGAAATTTTGTTA
45075 AACCTTCTTATGAAATTTTGTTA
1 AACCTTCTTATGAAATTTTGTTA
45098 A
1 A
45099 CCTCTGTAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.33, C:0.11, G:0.04, T:0.52
Consensus pattern (23 bp):
AACCTTCTTATGAAATTTTGTTA
Found at i:45100 original size:22 final size:21
Alignment explanation
Indices: 45052--45101 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
45042 GGAATTTCGA
* *
45052 TAACCTTTTTATAAATTTTTT
1 TAACCTTCTTATAAATTTTGT
45073 TAAACCTTCTTATGAAATTTTGT
1 T-AACCTTCTTAT-AAATTTTGT
45096 TAACCT
1 TAACCT
45102 CTGTAAGGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 15 0.60
23 9 0.36
ACGTcount: A:0.30, C:0.14, G:0.04, T:0.52
Consensus pattern (21 bp):
TAACCTTCTTATAAATTTTGT
Found at i:45267 original size:22 final size:22
Alignment explanation
Indices: 45229--45288 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
45219 AAAACTTCCA
* *
45229 TATGAA-TTGTTAGTAATCGCAC
1 TATGAATTTGTGA-TAATCACAC
*
45251 TCTGAAATTT-TGATAATCACAC
1 TATG-AATTTGTGATAATCACAC
45273 TATGAATTTGTGATAA
1 TATGAATTTGTGATAA
45289 CCTCGTTATG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
21 5 0.16
22 20 0.65
23 4 0.13
24 2 0.06
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (22 bp):
TATGAATTTGTGATAATCACAC
Found at i:45325 original size:23 final size:23
Alignment explanation
Indices: 45299--45378 Score: 99
Period size: 23 Copynumber: 3.5 Consensus size: 23
45289 CCTCGTTATG
45299 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAATCTTCCTATA
* *
45322 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAATCTTCCTATA
* * *
45345 AAATTTTGATAACT-TTCTTATG
1 AAATTTTGATAAATCTTCCTATA
*
45367 AAATCTTGATAA
1 AAATTTTGATAA
45379 CTACAAATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 16 0.33
23 33 0.67
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.41
Consensus pattern (23 bp):
AAATTTTGATAAATCTTCCTATA
Found at i:45349 original size:46 final size:45
Alignment explanation
Indices: 45277--45378 Score: 116
Period size: 46 Copynumber: 2.2 Consensus size: 45
45267 TCACACTATG
** *
45277 AATTTGTGAT-AACCTCGTTATGAAATTTTGATAAATCTTCCTATAA
1 AATTT-TGATAAACCTCCCTATAAAATTTTGATAAAT-TTCCTATAA
* * *
45323 AATTTTGATAAACCTCCCTATAAAATTTTGATAACTTTCTTATGA
1 AATTTTGATAAACCTCCCTATAAAATTTTGATAAATTTCCTATAA
*
45368 AATCTTGATAA
1 AATTTTGATAA
45379 CTACAAATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
45 21 0.44
46 27 0.56
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (45 bp):
AATTTTGATAAACCTCCCTATAAAATTTTGATAAATTTCCTATAA
Found at i:45455 original size:22 final size:22
Alignment explanation
Indices: 45253--45523 Score: 145
Period size: 22 Copynumber: 12.5 Consensus size: 22
45243 AATCGCACTC
* * *
45253 TGAAATTTTGATAATCACACTA
1 TGAAATTTTGATAACCTCCCTA
**
45275 TG-AATTTGTGATAACCTCGTTA
1 TGAAATTT-TGATAACCTCCCTA
* *
45297 TGAAATTTTGATAAATCTTCCTA
1 TGAAATTTTGAT-AACCTCCCTA
*
45320 TAAAATTTTGATAAACCTCCCTA
1 TGAAATTTTGAT-AACCTCCCTA
* * * *
45343 TAAAATTTTGATAACTTTCTTA
1 TGAAATTTTGATAACCTCCCTA
*
45365 TGAAATCTTGATAA-----CTA
1 TGAAATTTTGATAACCTCCCTA
*
45382 -CAAATTTTGATAACCTCCCTA
1 TGAAATTTTGATAACCTCCCTA
** **
45403 TGATTTTTTGATAACCTCATTA
1 TGAAATTTTGATAACCTCCCTA
* *
45425 TGGAAATTTTGTTAATCTCCCTA
1 T-GAAATTTTGATAACCTCCCTA
*
45448 TGAAA-TTT--TAACCTACGTACTA
1 TGAAATTTTGATAACCT-C--CCTA
* **
45470 TGAAATTTTGA-AAACTAAACTA
1 TGAAATTTTGATAACCT-CCCTA
* *
45492 TGAAATTTTAATATCCTCCC--
1 TGAAATTTTGATAACCTCCCTA
45512 TGAAATTTTGAT
1 TGAAATTTTGAT
45524 TACTCTATAA
Statistics
Matches: 192, Mismatches: 40, Indels: 36
0.72 0.15 0.13
Matches are distributed among these distances:
16 11 0.06
17 2 0.01
19 5 0.03
20 12 0.06
21 11 0.06
22 81 0.42
23 65 0.34
24 5 0.03
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCCCTA
Found at i:46169 original size:37 final size:37
Alignment explanation
Indices: 46082--46176 Score: 111
Period size: 38 Copynumber: 2.5 Consensus size: 37
46072 TCTAAATCCA
**
46082 AATAGGACGTTGGAGGCAAAGACAAAAAGCAAAATTG
1 AATAGGACGTTGGAAACAAAGACAAAAAGCAAAATTG
** * *
46119 AATACAACGGTTGGAAATAAAGACAAAAGGCAAAATT-
1 AATAGGAC-GTTGGAAACAAAGACAAAAAGCAAAATTG
46156 AAGTAGGACGTTGGAAACAAA
1 AA-TAGGACGTTGGAAACAAA
46177 AAGTCAAATT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
37 19 0.40
38 28 0.60
ACGTcount: A:0.51, C:0.11, G:0.24, T:0.15
Consensus pattern (37 bp):
AATAGGACGTTGGAAACAAAGACAAAAAGCAAAATTG
Found at i:46737 original size:31 final size:31
Alignment explanation
Indices: 46702--46767 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
46692 TGGCAATTTA
* *
46702 GAAATATGTTTTAAAAA-AAGGGGTACAATTG
1 GAAATATGTTTTAAAAATAA-AGGTACAATCG
46733 GAAATATGTTTTAAAAATAAAGGTACAATCG
1 GAAATATGTTTTAAAAATAAAGGTACAATCG
46764 GAAA
1 GAAA
46768 ACATCAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 30 0.94
32 2 0.06
ACGTcount: A:0.48, C:0.05, G:0.20, T:0.27
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAAGGTACAATCG
Found at i:49239 original size:40 final size:40
Alignment explanation
Indices: 49194--49271 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
49184 TTTATAATTT
*
49194 GGGGCTAAACCTGAATTTAATTTCTTACCTTAATTATTCG
1 GGGGCTAAACCTGAATTTAATTTATTACCTTAATTATTCG
* *
49234 GGGGCTAAACCTGGATTTAATTTATTTCCTTAATTATT
1 GGGGCTAAACCTGAATTTAATTTATTACCTTAATTATT
49272 ATGAGGGTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (40 bp):
GGGGCTAAACCTGAATTTAATTTATTACCTTAATTATTCG
Found at i:78381 original size:111 final size:111
Alignment explanation
Indices: 78198--78475 Score: 369
Period size: 111 Copynumber: 2.5 Consensus size: 111
78188 GTGACTTGAG
* * *
78198 TTAGTCTTTCATGTAGACTTCATGAATAACTCTTCATAGCCCCTTGTAGGTTGCATGTTCACATG
1 TTAGCCTTTCATGTAGACTTCATGAGTAACTCTTCATAGCCCCTTGTAGATTGCATGTTCACATG
* * * *
78263 TTGTGTTTCACCATTGATTATCATTTCTCATCGTTCGTGACTCAAG
66 TTATGTTTCACCATTAATGATCATTTCTCATCGTTCGTGACTCAAA
* * **
78309 TTTGCCTTTTATGTAGACTTCATGAGTAACTCTTCATAGCCCCTTGTAGATTGCATGTTTC-TTT
1 TTAGCCTTTCATGTAGACTTCATGAGTAACTCTTCATAGCCCCTTGTAGATTGCATG-TTCACAT
** * * *
78373 GTTATGTTTCACCATTAATGATCATTTCTTGTTGTTTGTGACTTAAA
65 GTTATGTTTCACCATTAATGATCATTTCTCATCGTTCGTGACTCAAA
* * *
78420 TTAGCCTTTCATGTAGAGTTAATGAGTAACTCTTCATAGCCCCTTGTATATTGCAT
1 TTAGCCTTTCATGTAGACTTCATGAGTAACTCTTCATAGCCCCTTGTAGATTGCAT
78476 TTTTTTTTTT
Statistics
Matches: 145, Mismatches: 21, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
111 142 0.98
112 3 0.02
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.43
Consensus pattern (111 bp):
TTAGCCTTTCATGTAGACTTCATGAGTAACTCTTCATAGCCCCTTGTAGATTGCATGTTCACATG
TTATGTTTCACCATTAATGATCATTTCTCATCGTTCGTGACTCAAA
Found at i:80872 original size:7 final size:7
Alignment explanation
Indices: 80862--80887 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
80852 GTTCAAAGGG
80862 CCAAAAC
1 CCAAAAC
80869 CCAAAAC
1 CCAAAAC
80876 CCAAAAC
1 CCAAAAC
80883 CCAAA
1 CCAAA
80888 TCCATAACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.42, G:0.00, T:0.00
Consensus pattern (7 bp):
CCAAAAC
Done.