Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012412.1 Corchorus capsularis cultivar CVL-1 contig12433, 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: 17747
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:556 original size:29 final size:30
Alignment explanation
Indices: 519--605 Score: 122
Period size: 29 Copynumber: 2.9 Consensus size: 30
509 ACAGATCCTA
*
519 AAAGGTTTAGTATCAAATTGAGCATTT-TT
1 AAAGGTTTAGTATCAAATTGAGCATTTCTC
*
548 GAAGGTTTAGTATCAAATTGAGCATTTCGTC
1 AAAGGTTTAGTATCAAATTGAGCATTTC-TC
* *
579 AAAGGTTTGGTACCAAATTGAGCATTT
1 AAAGGTTTAGTATCAAATTGAGCATTT
606 AGCCCTCTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
29 26 0.51
31 25 0.49
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.37
Consensus pattern (30 bp):
AAAGGTTTAGTATCAAATTGAGCATTTCTC
Found at i:3686 original size:2 final size:2
Alignment explanation
Indices: 3679--3727 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
3669 CTTCATTACA
* * *
3679 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT TT AT AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3721 AT -T AT AT
1 AT AT AT AT
3728 GTCCTCTCTC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:3752 original size:14 final size:14
Alignment explanation
Indices: 3733--3765 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
3723 TATATGTCCT
3733 CTCTCCCCTTCTCC
1 CTCTCCCCTTCTCC
3747 CTCTCCCCTTCTCC
1 CTCTCCCCTTCTCC
*
3761 TTCTC
1 CTCTC
3766 TAGTTCTCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (14 bp):
CTCTCCCCTTCTCC
Found at i:4722 original size:26 final size:26
Alignment explanation
Indices: 4693--4745 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
4683 CTCAAAAACA
4693 TTAGTTATAGCATTAATCCTCATGAT
1 TTAGTTATAGCATTAATCCTCATGAT
4719 TTAGTTATAGCATTAATCCTCATGAT
1 TTAGTTATAGCATTAATCCTCATGAT
4745 T
1 T
4746 AGGGTTTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.43
Consensus pattern (26 bp):
TTAGTTATAGCATTAATCCTCATGAT
Found at i:6530 original size:12 final size:12
Alignment explanation
Indices: 6513--6549 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
6503 ATAAGTAGTA
*
6513 ATTTATACCTAT
1 ATTTATATCTAT
6525 ATTTATATCTAT
1 ATTTATATCTAT
*
6537 ATCTATATCTAT
1 ATTTATATCTAT
6549 A
1 A
6550 CTGTATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.35, C:0.14, G:0.00, T:0.51
Consensus pattern (12 bp):
ATTTATATCTAT
Found at i:6531 original size:6 final size:6
Alignment explanation
Indices: 6516--6549 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
6506 AGTAGTAATT
* *
6516 TATACC TATATT TATATC TATATC TATATC TATA
1 TATATC TATATC TATATC TATATC TATATC TATA
6550 CTGTATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (6 bp):
TATATC
Found at i:7441 original size:4 final size:4
Alignment explanation
Indices: 7432--7461 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
7422 GTTGACGAAG
7432 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA
7462 ATAGCATCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:16452 original size:2 final size:2
Alignment explanation
Indices: 16445--16483 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
16435 ATGCGTGGAA
16445 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16484 CTAGTTTTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16819 original size:22 final size:22
Alignment explanation
Indices: 16595--16831 Score: 80
Period size: 22 Copynumber: 10.7 Consensus size: 22
16585 TTTAACCTTC
* *
16595 TTATGAAATTTTGTTAACCTCCA
1 TTATGAAATTTTGATAACC-ACA
* * *
16618 -TAAGGAATTTTGA-AGACCTCA
1 TTATGAAATTTTGATA-ACCACA
* * *
16639 ATATAAAATTTTGATAACTTCCCA
1 TTATGAAATTTTGATAAC--CACA
16663 --ATGAAATTTTGATAACCA-A
1 TTATGAAATTTTGATAACCACA
* * *
16682 TACTATGAGATGTTGATAACCTTCA
1 T--TATGAAATTTTGATAACC-ACA
* * *
16707 -TATGATATATTGATAACCACG
1 TTATGAAATTTTGATAACCACA
* * * *
16728 TTATAAAAATTTAAAAATCTC-CA
1 TTATGAAATTTTGATAA-C-CACA
*
16751 -TAT-AAATTGTT-AGTAATCACA
1 TTATGAAATT-TTGA-TAACCACA
* * *
16772 CTCTGAAATTTTGATAATCACA
1 TTATGAAATTTTGATAACCACA
* * *
16794 TTATGAAATTGTGATAACCTCG
1 TTATGAAATTTTGATAACCACA
16816 TTATGAAATTTTGATA
1 TTATGAAATTTTGATA
16832 TATCTTCCTA
Statistics
Matches: 159, Mismatches: 35, Indels: 41
0.68 0.15 0.17
Matches are distributed among these distances:
19 1 0.01
20 2 0.01
21 11 0.07
22 116 0.73
23 24 0.15
24 4 0.03
25 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.37
Consensus pattern (22 bp):
TTATGAAATTTTGATAACCACA
Found at i:16851 original size:23 final size:23
Alignment explanation
Indices: 16821--16878 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
16811 CCTCGTTATG
* * *
16821 AAATTTTGATATATCTTCCTATA
1 AAATTTTGATAAATCTCCCCATA
*
16844 AAGTTTTGATAAATCTCCCCATA
1 AAATTTTGATAAATCTCCCCATA
16867 AAATTTTGATAA
1 AAATTTTGATAA
16879 CTTTCTTATG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (23 bp):
AAATTTTGATAAATCTCCCCATA
Found at i:17108 original size:22 final size:21
Alignment explanation
Indices: 16775--17376 Score: 176
Period size: 22 Copynumber: 27.9 Consensus size: 21
16765 AATCACACTC
* *
16775 TGAAATTTTGATAATCACATTA
1 TGAAATTTTGATAACCTC-TTA
*
16797 TGAAATTGTGATAACCTCGTTA
1 TGAAATTTTGATAACCTC-TTA
* *
16819 TGAAATTTTGATATATCTTCCTA
1 TGAAATTTTGATA-A-CCTCTTA
* **
16842 T-AAAGTTTTGATAAATCTCCCCA
1 TGAAA-TTTTGAT-AACCT-CTTA
* *
16865 TAAAATTTTGATAACTTTCTTA
1 TGAAATTTTGATAAC-CTCTTA
*
16887 TGAAATCTTGATAA---C-TA
1 TGAAATTTTGATAACCTCTTA
* *
16904 -CAAATTTTGATAACCTCCCTA
1 TGAAATTTTGATAACCT-CTTA
*
16925 TG-ATTTTCTGATAACCTCATTA
1 TGAAATTT-TGATAACCTC-TTA
* **
16947 TGAAATTTTGTTATTCTCCTTA
1 TGAAATTTTGATAACCT-CTTA
* *
16969 TGAAATTTTGATCTACATAC-TA
1 TGAAATTTTGAT-AACCT-CTTA
*
16991 TGAAATTTGGATAACCCTCTTA
1 TGAAATTTTGATAA-CCTCTTA
* * *
17013 TCAAAATTTGA-AAACTAAAC-TA
1 TGAAATTTTGATAACCT---CTTA
* *
17035 TGAAATTTTGATATCCTCCCTA
1 TGAAATTTTGATAACCT-CTTA
* * *
17057 --AAATTTTTG-TAATCACATTT
1 TGAAA-TTTTGATAACCTC-TTA
*
17077 TGAAAATTTGATAACCTCTTCA
1 TGAAATTTTGATAACCTCTT-A
17099 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTC-TTA
* * * *
17121 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCT-TA
* *
17143 TGAAATTCTGGTAA--TC--A
1 TGAAATTTTGATAACCTCTTA
17160 T---ATTTTGATAACCTAGCTT-
1 TGAAATTTTGATAACCT--CTTA
**
17179 TGAAATTTTGATAACAACATTA
1 TGAAATTTTGATAACCTC-TTA
* * *
17201 TGAAATTTTGATATTCTTCCTA
1 TGAAATTTTGATA-ACCTCTTA
* *
17223 T-AAATTTTGATGATCTGATCTCTA
1 TGAAATTTTGAT-AAC--CTCT-TA
* * *
17247 TGAAATTTCGATAATCACTATA
1 TGAAATTTTGATAACCTCT-TA
17269 TGAAA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCT-TA
* *
17289 TCAAATTTTGGT-A-CTCCTTA
1 TGAAATTTTGATAACCT-CTTA
* *
17309 TGAAATTGAGACTTGTATAACATTCATA
1 TGAAATT-----TTG-ATAAC-CTCTTA
*
17337 TGAAATTTTGATAACCACATTA
1 TGAAATTTTGATAACCTC-TTA
*
17359 TAAAATTTTGATAACCTC
1 TGAAATTTTGATAACCTC
17377 CCCATAAAAT
Statistics
Matches: 424, Mismatches: 93, Indels: 126
0.66 0.14 0.20
Matches are distributed among these distances:
14 8 0.02
16 12 0.03
17 4 0.01
18 2 0.00
19 4 0.01
20 28 0.07
21 53 0.12
22 233 0.55
23 44 0.10
24 11 0.03
25 12 0.03
26 1 0.00
27 1 0.00
28 10 0.02
29 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (21 bp):
TGAAATTTTGATAACCTCTTA
Found at i:17430 original size:22 final size:22
Alignment explanation
Indices: 17339--17440 Score: 84
Period size: 22 Copynumber: 4.6 Consensus size: 22
17329 CATTCATATG
*
17339 AAATTTTGATAACCACATTATA
1 AAATTTTGATAACCACACTATA
* * *
17361 AAATTTTGATAACCTCCCCATA
1 AAATTTTGATAACCACACTATA
* *
17383 AAATATT-AGTAACCTC-CTAATA
1 AAATTTTGA-TAACCACACT-ATA
* *
17405 AAATTTTGTTAACCACACTATG
1 AAATTTTGATAACCACACTATA
17427 AAATTCTT-ATAACC
1 AAATT-TTGATAACC
17441 TCGCGATGAC
Statistics
Matches: 64, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
21 2 0.03
22 58 0.91
23 4 0.06
ACGTcount: A:0.41, C:0.20, G:0.05, T:0.34
Consensus pattern (22 bp):
AAATTTTGATAACCACACTATA
Found at i:17440 original size:44 final size:43
Alignment explanation
Indices: 17335--17442 Score: 108
Period size: 44 Copynumber: 2.4 Consensus size: 43
17325 ATAACATTCA
* * * *
17335 TATGAAATTTTGATAACCACATTATAAAATTTTGATAACCTCCC
1 TATGAAATTTT-ATAACCTCATAATAAAATTTTGATAACCACAC
* * * * *
17379 CATAAAATATTAGTAACCTCCTAATAAAATTTTGTTAACCACAC
1 TATGAAATTTTA-TAACCTCATAATAAAATTTTGATAACCACAC
17423 TATGAAATTCTTATAACCTC
1 TATGAAATT-TTATAACCTC
17443 GCGATGACAT
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
43 1 0.02
44 46 0.92
45 3 0.06
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.35
Consensus pattern (43 bp):
TATGAAATTTTATAACCTCATAATAAAATTTTGATAACCACAC
Done.