Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007224.1 Corchorus capsularis cultivar CVL-1 contig07245, 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: 66419
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:18694 original size:20 final size:20
Alignment explanation
Indices: 18669--18706 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
18659 TTTTAAGTTG
18669 AATTAATCAAAATTTAATGT
1 AATTAATCAAAATTTAATGT
**
18689 AATTAATCGGAATTTAAT
1 AATTAATCAAAATTTAAT
18707 TTAACTATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.39
Consensus pattern (20 bp):
AATTAATCAAAATTTAATGT
Found at i:25921 original size:3 final size:3
Alignment explanation
Indices: 25913--25956 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
25903 TTGATACATA
*
25913 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
25957 ATAAAAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:39204 original size:22 final size:22
Alignment explanation
Indices: 39179--39326 Score: 68
Period size: 22 Copynumber: 6.8 Consensus size: 22
39169 ATGACCCCAT
39179 TATGAAATTTTGATAACCTTTC
1 TATGAAATTTTGATAACCTTTC
* *** *
39201 TATGAAATTTTAATAATGATAC
1 TATGAAATTTTGATAACCTTTC
* * * *
39223 TATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTTC
* ** *
39245 TAT-AATTTTTTTTAATC-TTC
1 TATGAAATTTTGATAACCTTTC
* * **
39265 TTATGATATTTTGTTAACCTCCC
1 -TATGAAATTTTGATAACCTTTC
* ***
39288 TAAGAAATTTTGA-AGACCTCAA
1 TATGAAATTTTGATA-ACCTTTC
39310 TATGAAATTTTGATAAC
1 TATGAAATTTTGATAAC
39327 TTCCCAGCAT
Statistics
Matches: 87, Mismatches: 34, Indels: 10
0.66 0.26 0.08
Matches are distributed among these distances:
20 2 0.02
21 11 0.13
22 72 0.83
23 2 0.02
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTTC
Found at i:39456 original size:22 final size:22
Alignment explanation
Indices: 39431--39716 Score: 110
Period size: 22 Copynumber: 13.1 Consensus size: 22
39421 GAATTATTAG
*
39431 TAATCACACTCTGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
*
39453 TAATCACACTATGAAATTGTGA
1 TAATCACACTATGAAATTTTGA
* * *
39475 TAACCTCGCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* *
39497 TAAATCTTC-CTATAAAATTTTGATA
1 T-AATC-ACACTATGAAATTTTG--A
* * * *
39522 TAAACCTCCCTATAAAATTTTGA
1 T-AATCACACTATGAAATTTTGA
** * *
39545 TAACTTTC-TTATGAAATCTTGA
1 TAA-TCACACTATGAAATTTTGA
*
39567 TAAGT---AC----AAATTTTAA
1 TAA-TCACACTATGAAATTTTGA
* * * **
39583 AAACCACCCTATGATTTTTTGA
1 TAATCACACTATGAAATTTTGA
* * * *
39605 TAACCTCATTATGAAATTTTGT
1 TAATCACACTATGAAATTTTGA
* * *
39627 TGATCTCCCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* *
39649 TTTAT-ATACTATGAAATTTTGA
1 -TAATCACACTATGAAATTTTGA
39671 TAATC-CACTTATGAAATTTTGA
1 TAATCACAC-TATGAAATTTTGA
* *
39693 AAAGT-AAACTATGAAATTTTGA
1 TAA-TCACACTATGAAATTTTGA
39715 TA
1 TA
39717 TCCTCCCTGA
Statistics
Matches: 200, Mismatches: 45, Indels: 38
0.71 0.16 0.13
Matches are distributed among these distances:
16 9 0.05
18 1 0.00
21 5 0.03
22 137 0.69
23 25 0.12
24 4 0.02
25 19 0.09
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (22 bp):
TAATCACACTATGAAATTTTGA
Found at i:39514 original size:23 final size:23
Alignment explanation
Indices: 39483--39569 Score: 86
Period size: 25 Copynumber: 3.7 Consensus size: 23
39473 GATAACCTCG
*
39483 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAATCTTC
* *
39506 CTATAAAATTTTGATATAAACCTCC
1 CTATAAAATTTTG--ATAAATCTTC
*
39531 CTATAAAATTTTGATAACT-TTC
1 CTATAAAATTTTGATAAATCTTC
* * *
39553 TTATGAAATCTTGATAA
1 CTATAAAATTTTGATAA
39570 GTACAAATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
22 16 0.30
23 16 0.30
25 21 0.40
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (23 bp):
CTATAAAATTTTGATAAATCTTC
Found at i:39533 original size:25 final size:25
Alignment explanation
Indices: 39476--39546 Score: 92
Period size: 25 Copynumber: 2.9 Consensus size: 25
39466 AAATTGTGAT
* *
39476 AACCTCGCTATGAAATTTTG--ATA
1 AACCTCCCTATAAAATTTTGATATA
* *
39499 AATCTTCCTATAAAATTTTGATATA
1 AACCTCCCTATAAAATTTTGATATA
39524 AACCTCCCTATAAAATTTTGATA
1 AACCTCCCTATAAAATTTTGATA
39547 ACTTTCTTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
23 16 0.40
25 24 0.60
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.38
Consensus pattern (25 bp):
AACCTCCCTATAAAATTTTGATATA
Found at i:39662 original size:44 final size:44
Alignment explanation
Indices: 39614--39737 Score: 132
Period size: 44 Copynumber: 2.8 Consensus size: 44
39604 ATAACCTCAT
* * *
39614 TATGAAATTTTGTTGATCTCCCTATGAAATTTTGATTTA-TATAC
1 TATGAAATTTTGAT-ATCTCCCTATGAAATTTTGATTAAGTAAAC
* *
39658 TATGAAATTTTGATAATC-CACTTATGAAATTTTGA-AAAGTAAAC
1 TATGAAATTTTGAT-ATCTC-CCTATGAAATTTTGATTAAGTAAAC
39702 TATGAAATTTTGATATCCTCCC--TGAAATTTTGATTA
1 TATGAAATTTTGATAT-CTCCCTATGAAATTTTGATTA
39738 CTCCATAATA
Statistics
Matches: 67, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
42 11 0.16
43 5 0.07
44 50 0.75
45 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (44 bp):
TATGAAATTTTGATATCTCCCTATGAAATTTTGATTAAGTAAAC
Found at i:39866 original size:22 final size:22
Alignment explanation
Indices: 39841--39946 Score: 81
Period size: 22 Copynumber: 4.8 Consensus size: 22
39831 GATCACATTT
39841 TGAAAATTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
* *
39863 TGAAATTTTGATAACCTCTGTA
1 TGAAAATTTGATAACCTCTTTA
* * * *
39885 T-AAAATTTTATTGACCCCTCTA
1 TGAAAATTTGA-TAACCTCTTTA
* * *
39907 TG-AAATTCTGATAATCACATTA
1 TGAAAATT-TGATAACCTCTTTA
* *
39929 TGTAATTTTGATAACCTC
1 TGAAAATTTGATAACCTC
39947 GCTTTGAAAT
Statistics
Matches: 64, Mismatches: 16, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
21 7 0.11
22 51 0.80
23 6 0.09
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTTTA
Found at i:39957 original size:22 final size:22
Alignment explanation
Indices: 39839--39965 Score: 66
Period size: 22 Copynumber: 5.8 Consensus size: 22
39829 GTGATCACAT
* *
39839 TTTGAAAATTTGATAACCTC-T
1 TTTGAAATTTTGATAACCTCGC
39860 TTATGAAATTTTGATAACCTCTG-
1 TT-TGAAATTTTGATAACCTC-GC
* * * * *
39883 TATAAAATTTT-ATTGACCCCTC
1 TTTGAAATTTTGA-TAACCTCGC
* * *
39905 TATGAAATTCTGATAA--TCAC
1 TTTGAAATTTTGATAACCTCGC
*
39925 ATTATGTAATTTTGATAACCTCGC
1 -TT-TGAAATTTTGATAACCTCGC
*
39949 TTTGAAATTTCGATAAC
1 TTTGAAATTTTGATAAC
39966 AAAACTATGA
Statistics
Matches: 79, Mismatches: 17, Indels: 19
0.69 0.15 0.17
Matches are distributed among these distances:
20 2 0.03
21 4 0.05
22 66 0.84
23 4 0.05
24 3 0.04
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (22 bp):
TTTGAAATTTTGATAACCTCGC
Found at i:39964 original size:44 final size:46
Alignment explanation
Indices: 39904--40015 Score: 124
Period size: 44 Copynumber: 2.5 Consensus size: 46
39894 ATTGACCCCT
* * *
39904 CTATGAAA-TTCTGATAATCACATTATGTAATTTTGATAA-C-CTCG
1 CTATGAAATTTC-GATAATCACACTATGAAATTTTGATAATCGATCG
* *
39948 CTTTGAAATTTCGATAA-CAAAACTATGAAATTTTGATAATCTGATCG
1 CTATGAAATTTCGATAATC-ACACTATGAAATTTTGATAATC-GATCG
39995 CTATGAAATTTCGATAATCAC
1 CTATGAAATTTCGATAATCAC
40016 TCTGAGATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
43 1 0.02
44 29 0.53
45 4 0.07
47 20 0.36
48 1 0.02
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (46 bp):
CTATGAAATTTCGATAATCACACTATGAAATTTTGATAATCGATCG
Found at i:40275 original size:31 final size:31
Alignment explanation
Indices: 40224--40284 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
40214 CAATTTAGAA
*
40224 ATATGTTTAAAAAAAAGGTACAATTGGAAAT
1 ATATGTTTAAAAAAAAGGTACAATCGGAAAT
* * *
40255 ATATTTTTAAAATAAGGGTACAATCGGAAA
1 ATATGTTTAAAAAAAAGGTACAATCGGAAA
40285 ACATAAAGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.49, C:0.05, G:0.16, T:0.30
Consensus pattern (31 bp):
ATATGTTTAAAAAAAAGGTACAATCGGAAAT
Found at i:40571 original size:29 final size:31
Alignment explanation
Indices: 40526--40589 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
40516 TGGTAATTTA
* * *
40526 GAAATATGTTTT-TAAA-AAGGGTACAATTG
1 GAAATATATTTTAAAAATAAGGGTACAATCG
40555 GAAATATATTTTAAAAATAAGGGTACAATCG
1 GAAATATATTTTAAAAATAAGGGTACAATCG
40586 GAAA
1 GAAA
40590 ACATAAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 11 0.37
30 3 0.10
31 16 0.53
ACGTcount: A:0.47, C:0.05, G:0.19, T:0.30
Consensus pattern (31 bp):
GAAATATATTTTAAAAATAAGGGTACAATCG
Found at i:63953 original size:43 final size:45
Alignment explanation
Indices: 63860--63964 Score: 115
Period size: 43 Copynumber: 2.4 Consensus size: 45
63850 TGAATATTTT
* * * * *
63860 TATGAAATTTTGATAACTGTGCTATTTAAATTTTGATAATCACCC
1 TATGAAATTTTGATAACTATGCTATTGAAATTGTGATAAACACCA
* * *
63905 GATGAAATTTTGATAATTAT-CTA-TGAAATTGTGATAAACGCCA
1 TATGAAATTTTGATAACTATGCTATTGAAATTGTGATAAACACCA
*
63948 TATGAAACTTTGATAAC
1 TATGAAATTTTGATAAC
63965 CTAATTATGA
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
43 29 0.59
44 3 0.06
45 17 0.35
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.38
Consensus pattern (45 bp):
TATGAAATTTTGATAACTATGCTATTGAAATTGTGATAAACACCA
Found at i:65141 original size:3 final size:3
Alignment explanation
Indices: 65133--65167 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
65123 AATTTATAGC
*
65133 AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
65168 TATCATAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:65541 original size:21 final size:21
Alignment explanation
Indices: 65498--65541 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
65488 TTTTAGGGGG
* *
65498 TTGCTAAATACCGTCCTAGTT
1 TTGCTAAATACCGCCCCAGTT
*
65519 TTGCTAAATACCGCCCCATTT
1 TTGCTAAATACCGCCCCAGTT
65540 TT
1 TT
65542 TACACTTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.27, G:0.11, T:0.39
Consensus pattern (21 bp):
TTGCTAAATACCGCCCCAGTT
Found at i:65777 original size:42 final size:42
Alignment explanation
Indices: 65718--65804 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
65708 CGGGGTATAA
65718 ACGTGTATAATTTAGGAGTATATGGCCAAACACGAACACGAC
1 ACGTGTATAATTTAGGAGTATATGGCCAAACACGAACACGAC
65760 ACGTGTATAATTTAGGAGTATATGGCCAAACACGAACACGAC
1 ACGTGTATAATTTAGGAGTATATGGCCAAACACGAACACGAC
65802 ACG
1 ACG
65805 AATAATTAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.21
Consensus pattern (42 bp):
ACGTGTATAATTTAGGAGTATATGGCCAAACACGAACACGAC
Done.