Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008597.1 Corchorus capsularis cultivar CVL-1 contig08618, 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: 15495
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Found at i:87 original size:22 final size:21
Alignment explanation
Indices: 53--445 Score: 107
Period size: 22 Copynumber: 17.6 Consensus size: 21
43 CTAATCCCTG
*
53 TGAAACTTTGATACCCACACTA
1 TGAAA-TTTGATAACCACACTA
***
75 TGAAATTTCGATAACCGTGCTA
1 TGAAATTT-GATAACCACACTA
* *
97 TTAAATTTTGATTACCACACTA
1 TGAAA-TTTGATAACCACACTA
119 TGAAACTTTGATAACCACACTA
1 TGAAA-TTTGATAACCACACTA
* * *
141 TAAAATAGTGATAACCTCTAC-A
1 TGAAAT-TTGATAACCAC-ACTA
* *
163 TGAAATTAATTTTGCTAA-CTCACTA
1 TG--A--AA-TTTGATAACCACACTA
* *
188 TAAAATTTTGATAACCACAATAA
1 TGAAA-TTTGATAACCACACT-A
* ****
211 TTTGAAAAGGTTGATTTGGTACACTA
1 --TG-AAA-TTTGA-TAACCACACTA
*
237 TGAAATTTGGATAACCATACTA
1 TGAAATTT-GATAACCACACTA
*
259 TGAAATTTTGATAACCTC-CTA
1 TGAAA-TTTGATAACCACACTA
* ** *
280 -GGAATATTGATAACTTCCCTA
1 TGAAAT-TTGATAACCACACTA
* * * * *
301 TAGAATTTTGTTAATCTCACCA
1 T-GAAATTTGATAACCACACTA
*
323 TGAAATTTTGATAAGCACAAC-A
1 TGAAA-TTTGATAACCAC-ACTA
* * **
345 TCAAATTTTGATTACC-TTCTA
1 TGAAA-TTTGATAACCACACTA
* *
366 TGAAATTTTTG-TAACTACATTA
1 TGAAA--TTTGATAACCACACTA
* *
388 TGAAATTTGGATAATCACATTA
1 TGAAATTT-GATAACCACACTA
**
410 TGAAATTTTGATAGTCACACTA
1 TGAAA-TTTGATAACCACACTA
432 TGAAATTTTGATAA
1 TGAAA-TTTGATAA
446 TCTGCAAAGT
Statistics
Matches: 274, Mismatches: 67, Indels: 60
0.68 0.17 0.15
Matches are distributed among these distances:
19 1 0.00
20 17 0.06
21 32 0.12
22 169 0.62
23 23 0.08
24 5 0.02
25 6 0.02
26 15 0.05
27 6 0.02
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.36
Consensus pattern (21 bp):
TGAAATTTGATAACCACACTA
Found at i:196 original size:21 final size:20
Alignment explanation
Indices: 170--210 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
160 ACATGAAATT
* *
170 AATTTTGCTAACTCACTATAA
1 AATTTTGATAAC-CACAATAA
191 AATTTTGATAACCACAATAA
1 AATTTTGATAACCACAATAA
211 TTTGAAAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.34
Consensus pattern (20 bp):
AATTTTGATAACCACAATAA
Found at i:934 original size:31 final size:31
Alignment explanation
Indices: 882--977 Score: 176
Period size: 31 Copynumber: 3.1 Consensus size: 31
872 TGGCAATTTA
*
882 GAAATATGTTTTAAAAA-AAGGGTACAATTG
1 GAAATATATTTTAAAAATAAGGGTACAATTG
912 GAAATATATTTTAAAAATAAGGGTACAATTG
1 GAAATATATTTTAAAAATAAGGGTACAATTG
943 GAAATATATTTTAAAAATAAGGGTACAATTG
1 GAAATATATTTTAAAAATAAGGGTACAATTG
974 GAAA
1 GAAA
978 ACATAAAGTT
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
30 16 0.25
31 48 0.75
ACGTcount: A:0.49, C:0.03, G:0.18, T:0.30
Consensus pattern (31 bp):
GAAATATATTTTAAAAATAAGGGTACAATTG
Found at i:1032 original size:27 final size:27
Alignment explanation
Indices: 994--1048 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
984 AGTTTCCTCT
994 TATTCGTACTTTTATATATAGTATAGA
1 TATTCGTACTTTTATATATAGTATAGA
1021 TATTCGTACTTTTATATATAGTATAGA
1 TATTCGTACTTTTATATATAGTATAGA
1048 T
1 T
1049 TAGTTTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.07, G:0.11, T:0.49
Consensus pattern (27 bp):
TATTCGTACTTTTATATATAGTATAGA
Found at i:5160 original size:109 final size:109
Alignment explanation
Indices: 5028--5375 Score: 637
Period size: 109 Copynumber: 3.2 Consensus size: 109
5018 AAAAAAATTA
*
5028 TATAAA-ATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
1 TATAAAGATATTAG-ATTTAATTAAATGAAAATAAAGTTTTTAGTAGAATAAAATTGTATATTAG
*
5091 AAAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
65 AAAAAATTTTAGTATATCCAAATTTTTTGGTAAAAATAAAGTAAT
5136 TATAAAGATATTAGATTTAATTAAATGAAAATAAAGTTTTTAGTAGAATAAAATTGTATATTAGA
1 TATAAAGATATTAGATTTAATTAAATGAAAATAAAGTTTTTAGTAGAATAAAATTGTATATTAGA
5201 AAAAATTTTAGTATATCCAAATTTTTTGGTAAAAATAAAGTAAT
66 AAAAATTTTAGTATATCCAAATTTTTTGGTAAAAATAAAGTAAT
5245 TATAAAGATATTAGATTTAATTAAATGAAAATAAAGTTTTTAGTAGAATAAAATTGTATATTAGA
1 TATAAAGATATTAGATTTAATTAAATGAAAATAAAGTTTTTAGTAGAATAAAATTGTATATTAGA
* *
5310 AAAAATTTTAGTATATCTAAATATTTTGGTAAAAATAAAGTAAT
66 AAAAATTTTAGTATATCCAAATTTTTTGGTAAAAATAAAGTAAT
5354 TATAAAGATATTAGATTTAATT
1 TATAAAGATATTAGATTTAATT
5376 TAATTGAATA
Statistics
Matches: 234, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
108 6 0.03
109 227 0.97
110 1 0.00
ACGTcount: A:0.49, C:0.01, G:0.11, T:0.39
Consensus pattern (109 bp):
TATAAAGATATTAGATTTAATTAAATGAAAATAAAGTTTTTAGTAGAATAAAATTGTATATTAGA
AAAAATTTTAGTATATCCAAATTTTTTGGTAAAAATAAAGTAAT
Found at i:5611 original size:42 final size:42
Alignment explanation
Indices: 5552--5635 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
5542 AAACTTGTTT
5552 GAGGCAGGTTGGTCCATTATGGGATAAAACTCTCCTAAGTAC
1 GAGGCAGGTTGGTCCATTATGGGATAAAACTCTCCTAAGTAC
*
5594 GAGGCAGGTTGGTCCATTTTGGGATAAAACTCTCCTAAGTAC
1 GAGGCAGGTTGGTCCATTATGGGATAAAACTCTCCTAAGTAC
5636 CAATAATAGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.27
Consensus pattern (42 bp):
GAGGCAGGTTGGTCCATTATGGGATAAAACTCTCCTAAGTAC
Found at i:5702 original size:34 final size:34
Alignment explanation
Indices: 5659--5729 Score: 115
Period size: 34 Copynumber: 2.1 Consensus size: 34
5649 CTCCATTCAT
* *
5659 AAGACTCGAATCAGATACCTTGCTTAAGGGGATC
1 AAGACTCGAACCAGATACCTTACTTAAGGGGATC
*
5693 AAGACTCGAACCAGATACTTTACTTAAGGGGATC
1 AAGACTCGAACCAGATACCTTACTTAAGGGGATC
5727 AAG
1 AAG
5730 TGTCAAACCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.23
Consensus pattern (34 bp):
AAGACTCGAACCAGATACCTTACTTAAGGGGATC
Found at i:5739 original size:34 final size:34
Alignment explanation
Indices: 5659--5739 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 34
5649 CTCCATTCAT
* * *
5659 AAGACTCGAATCAGATACCTTGCTTAAGGGGATC
1 AAGACTCAAACCAGATACCTTACTTAAGGGGATC
* *
5693 AAGACTCGAACCAGATACTTTACTTAAGGGGATC
1 AAGACTCAAACCAGATACCTTACTTAAGGGGATC
**
5727 AAGTGTCAAACCA
1 AAGACTCAAACCA
5740 CTTGAACCAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (34 bp):
AAGACTCAAACCAGATACCTTACTTAAGGGGATC
Found at i:5806 original size:26 final size:26
Alignment explanation
Indices: 5754--5807 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
5744 AACCAACCAC
**
5754 TTAGTGGTGAAGTAAGCTGTGGTTTG
1 TTAGTGGTGAAGTAAGCTGTGAATTG
* *
5780 TTAGTGGTGAAGTAAGCTTTTAATTG
1 TTAGTGGTGAAGTAAGCTGTGAATTG
5806 TT
1 TT
5808 GACTCGTTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.22, C:0.04, G:0.31, T:0.43
Consensus pattern (26 bp):
TTAGTGGTGAAGTAAGCTGTGAATTG
Found at i:6102 original size:22 final size:22
Alignment explanation
Indices: 6074--6118 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
6064 CAGACCATAC
6074 GATTGAATCACATAATTTATCT
1 GATTGAATCACATAATTTATCT
6096 GATTGAATCACATAATTTATCT
1 GATTGAATCACATAATTTATCT
6118 G
1 G
6119 TTTACCTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (22 bp):
GATTGAATCACATAATTTATCT
Found at i:7310 original size:2 final size:2
Alignment explanation
Indices: 7303--7334 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
7293 ACAGCAACAA
7303 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7335 CAAGTTTCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9704 original size:21 final size:21
Alignment explanation
Indices: 9678--9720 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
9668 ATCTGCTAAA
9678 ACAAACACGTTCTAGTTGACC
1 ACAAACACGTTCTAGTTGACC
9699 ACAAACACGTTCTAGTTGACC
1 ACAAACACGTTCTAGTTGACC
9720 A
1 A
9721 TTCACCATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.28, G:0.14, T:0.23
Consensus pattern (21 bp):
ACAAACACGTTCTAGTTGACC
Found at i:10486 original size:3 final size:3
Alignment explanation
Indices: 10478--10567 Score: 108
Period size: 3 Copynumber: 30.0 Consensus size: 3
10468 ACTGTCATGG
* * * * * * *
10478 TCA TCA TCA CCA CCA CCA TCA TCA TCA TCA CCA CCA CCA CCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
*
10526 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TTA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
10568 GCGTCTTCGT
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 81 1.00
ACGTcount: A:0.33, C:0.40, G:0.00, T:0.27
Consensus pattern (3 bp):
TCA
Found at i:12629 original size:32 final size:32
Alignment explanation
Indices: 12593--12665 Score: 128
Period size: 32 Copynumber: 2.3 Consensus size: 32
12583 AAAAGTAGTG
*
12593 GTGCCGCCCTCCTAGGGCGGCAAGCCATGGTT
1 GTGCCGCCCTCCTAAGGCGGCAAGCCATGGTT
12625 GTGCCGCCCTCCTAAGGCGGCAAGCCATGGTT
1 GTGCCGCCCTCCTAAGGCGGCAAGCCATGGTT
*
12657 GTACCGCCC
1 GTGCCGCCC
12666 CACGCTGGGC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.14, C:0.37, G:0.32, T:0.18
Consensus pattern (32 bp):
GTGCCGCCCTCCTAAGGCGGCAAGCCATGGTT
Found at i:13146 original size:11 final size:11
Alignment explanation
Indices: 13130--13155 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
13120 ATCAAAAACC
13130 TTTTTTTTCTT
1 TTTTTTTTCTT
13141 TTTTTTTTCTT
1 TTTTTTTTCTT
13152 TTTT
1 TTTT
13156 GTAAAATCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:13851 original size:2 final size:2
Alignment explanation
Indices: 13844--13876 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
13834 TATGTAGTAG
13844 TA TA 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 TA TA T
13877 CTCCCTCTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14240 original size:15 final size:15
Alignment explanation
Indices: 14220--14268 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
14210 TACTTAGTTT
14220 ATTAGTTTAT-ATTTA
1 ATTAGTTTATGA-TTA
14235 ATTAGTTTATGATTA
1 ATTAGTTTATGATTA
* *
14250 ATTAATTCATGATTA
1 ATTAGTTTATGATTA
14265 ATTA
1 ATTA
14269 AATACTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
15 30 0.97
16 1 0.03
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.53
Consensus pattern (15 bp):
ATTAGTTTATGATTA
Found at i:14277 original size:11 final size:11
Alignment explanation
Indices: 14263--14333 Score: 61
Period size: 11 Copynumber: 5.7 Consensus size: 11
14253 AATTCATGAT
14263 TAATTAAATAC
1 TAATTAAATAC
14274 TAATTAATCATAAAC
1 TAATTAA--AT--AC
14289 TAATTAAATAC
1 TAATTAAATAC
*
14300 CAATTAATCATAAAC
1 TAATTAA--AT--AC
14315 TAATTAAATAC
1 TAATTAAATAC
14326 TAATTAAA
1 TAATTAAA
14334 CATAAACTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 16
0.74 0.03 0.24
Matches are distributed among these distances:
11 25 0.50
13 8 0.16
15 17 0.34
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (11 bp):
TAATTAAATAC
Found at i:14277 original size:26 final size:26
Alignment explanation
Indices: 14263--14344 Score: 146
Period size: 26 Copynumber: 3.2 Consensus size: 26
14253 AATTCATGAT
14263 TAATTAAATACTAATTAATCATAAAC
1 TAATTAAATACTAATTAATCATAAAC
*
14289 TAATTAAATACCAATTAATCATAAAC
1 TAATTAAATACTAATTAATCATAAAC
*
14315 TAATTAAATACTAATTAAACATAAAC
1 TAATTAAATACTAATTAATCATAAAC
14341 TAAT
1 TAAT
14345 AAACTAAGTA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (26 bp):
TAATTAAATACTAATTAATCATAAAC
Found at i:14279 original size:15 final size:15
Alignment explanation
Indices: 14272--14344 Score: 72
Period size: 15 Copynumber: 5.4 Consensus size: 15
14262 TTAATTAAAT
14272 ACTAATTAATCATAA
1 ACTAATTAATCATAA
14287 ACTAATTAA--AT--
1 ACTAATTAATCATAA
*
14298 ACCAATTAATCATAA
1 ACTAATTAATCATAA
14313 ACTAATTAA--AT--
1 ACTAATTAATCATAA
*
14324 ACTAATTAAACATAA
1 ACTAATTAATCATAA
14339 ACTAAT
1 ACTAAT
14345 AAACTAAGTA
Statistics
Matches: 48, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
11 17 0.35
13 8 0.17
15 23 0.48
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.32
Consensus pattern (15 bp):
ACTAATTAATCATAA
Found at i:14379 original size:18 final size:18
Alignment explanation
Indices: 14341--14380 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
14331 AAACATAAAC
* **
14341 TAATAAACTAAGTAATTT
1 TAATAAACTAACTAAAAT
14359 TAATAAACTAACTAAAAT
1 TAATAAACTAACTAAAAT
14377 TAAT
1 TAAT
14381 CATAAACATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.35
Consensus pattern (18 bp):
TAATAAACTAACTAAAAT
Found at i:15070 original size:19 final size:19
Alignment explanation
Indices: 15028--15070 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
15018 CCTAAGTGGC
* *
15028 ATTTGCTTAATTTTCTTTG
1 ATTTTCTTAATTTTCTTTA
* *
15047 TTTTTCTTAATTTTTTTTA
1 ATTTTCTTAATTTTCTTTA
15066 ATTTT
1 ATTTT
15071 GAATTCTAAA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.07, G:0.05, T:0.72
Consensus pattern (19 bp):
ATTTTCTTAATTTTCTTTA
Done.