Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013546.1 Corchorus capsularis cultivar CVL-1 contig13567, 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: 42376
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Found at i:1811 original size:38 final size:38
Alignment explanation
Indices: 1769--1948 Score: 281
Period size: 38 Copynumber: 4.7 Consensus size: 38
1759 GGCTGTGCAT
1769 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATGGTAAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATGGTAAG
* ** *
1807 AGTGGATCCGTGCCTCAGGGGGTTAAACT-ATAAATTAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGAT-GGTAAG
1845 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATGGTAAG
1 AGTGGACCCGTGCCTCAGGGGGTTAAACTGATGGTAAG
*
1883 AGTGGACCCATGTGCCTCAGGGGGTTAAACTGTTGGTAAG
1 AGTGGACCC--GTGCCTCAGGGGGTTAAACTGATGGTAAG
1923 AGTGGACCCGTGCCTCAGGGGGTTAA
1 AGTGGACCCGTGCCTCAGGGGGTTAA
1949 CTGTTGGCTA
Statistics
Matches: 129, Mismatches: 9, Indels: 8
0.88 0.06 0.05
Matches are distributed among these distances:
37 2 0.02
38 88 0.68
39 2 0.02
40 37 0.29
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.23
Consensus pattern (38 bp):
AGTGGACCCGTGCCTCAGGGGGTTAAACTGATGGTAAG
Found at i:13546 original size:9 final size:9
Alignment explanation
Indices: 13532--13607 Score: 61
Period size: 9 Copynumber: 8.3 Consensus size: 9
13522 CAGTTTATAC
13532 TTTATTTAT
1 TTTATTTAT
13541 TTTATTTTAT
1 TTTA-TTTAT
13551 TATTATTT-T
1 T-TTATTTAT
*
13560 TATTATTTTT
1 T-TTATTTAT
13570 TTTA-TTAT
1 TTTATTTAT
13578 TTTA-TTAT
1 TTTATTTAT
13586 TATTA-TTAT
1 T-TTATTTAT
*
13595 TTTTTTTCAT
1 TTTATTT-AT
13605 TTT
1 TTT
13608 CAAAAAAAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
8 14 0.24
9 26 0.44
10 16 0.27
11 3 0.05
ACGTcount: A:0.21, C:0.01, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTATTTAT
Found at i:13555 original size:3 final size:3
Alignment explanation
Indices: 13537--13595 Score: 70
Period size: 3 Copynumber: 20.7 Consensus size: 3
13527 TATACTTTAT
* * *
13537 TTA TT- TTA TT- TTA TTA TTA TTT TTA TTA TTT TTT TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
13582 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
13596 TTTTTTCATT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 6 0.12
3 43 0.88
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (3 bp):
TTA
Found at i:13567 original size:29 final size:28
Alignment explanation
Indices: 13533--13607 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 28
13523 AGTTTATACT
* *
13533 TTATTTATTTTATTTTATTATTATTTTTA
1 TTATTTTTTTTATTTT-TTATTATTATTA
13562 TTATTTTTTTTATTATTTTATTATTATTA
1 TTATTTTTTTTATT-TTTTATTATTATTA
13591 TTATTTTTTTTCATTTT
1 TTATTTTTTTT-ATTTT
13608 CAAAAAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
29 37 0.88
30 5 0.12
ACGTcount: A:0.21, C:0.01, G:0.00, T:0.77
Consensus pattern (28 bp):
TTATTTTTTTTATTTTTTATTATTATTA
Found at i:13583 original size:32 final size:31
Alignment explanation
Indices: 13542--13601 Score: 102
Period size: 32 Copynumber: 1.9 Consensus size: 31
13532 TTTATTTATT
*
13542 TTATTTTATTATTATTTTTATTATTTTTTTTA
1 TTATTTTATTATTATTATTATT-TTTTTTTTA
13574 TTATTTTATTATTATTATTATTTTTTTT
1 TTATTTTATTATTATTATTATTTTTTTT
13602 CATTTTCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 6 0.22
32 21 0.78
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (31 bp):
TTATTTTATTATTATTATTATTTTTTTTTTA
Found at i:15726 original size:5 final size:5
Alignment explanation
Indices: 15710--15788 Score: 76
Period size: 5 Copynumber: 16.4 Consensus size: 5
15700 AGTATCTTTC
* *
15710 TTATT TTTTT TTATTT TTATT TT-TT TTA-- TTATT TTATT TGATT TTATT
1 TTATT TTATT TTA-TT TTATT TTATT TTATT TTATT TTATT TTATT TTATT
* * *
15758 TGATT TTATT TGATT TGATT TTATT TT-TT TT
1 TTATT TTATT TTATT TTATT TTATT TTATT TT
15789 TTGTAGTTTG
Statistics
Matches: 62, Mismatches: 8, Indels: 9
0.78 0.10 0.11
Matches are distributed among these distances:
3 3 0.05
4 8 0.13
5 46 0.74
6 5 0.08
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.78
Consensus pattern (5 bp):
TTATT
Found at i:15736 original size:18 final size:17
Alignment explanation
Indices: 15713--15768 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 17
15703 ATCTTTCTTA
15713 TTTTTTT-TTATTTTTAT
1 TTTTTTTATTA-TTTTAT
15730 TTTTTTTATTATTTTAT
1 TTTTTTTATTATTTTAT
*
15747 TTGATTTTATTTGATTTTAT
1 TT-TTTTTA-TT-ATTTTAT
15767 TT
1 TT
15769 GATTTGATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
17 15 0.44
18 8 0.24
19 2 0.06
20 9 0.26
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (17 bp):
TTTTTTTATTATTTTAT
Found at i:30537 original size:21 final size:20
Alignment explanation
Indices: 30499--30538 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
30489 CAATAATATG
30499 AATAAAAAAACTAAGAAAAT
1 AATAAAAAAACTAAGAAAAT
30519 AATAAAACAAA-TCAAGAAAA
1 AATAAAA-AAACT-AAGAAAA
30539 ATGATGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.75, C:0.07, G:0.05, T:0.12
Consensus pattern (20 bp):
AATAAAAAAACTAAGAAAAT
Found at i:33711 original size:33 final size:35
Alignment explanation
Indices: 33643--33713 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 35
33633 TAAATACCAC
33643 GGTATTAGCATGTCTGTCTTTTTAGGAAGTATAGTTT
1 GGTATTAGCATGTC-GTCTTTTTAGGAAG-ATAGTTT
33680 GGTATTAGCATGTC-TCTTTTTAGGAAG-TAGTTT
1 GGTATTAGCATGTCGTCTTTTTAGGAAGATAGTTT
33713 G
1 G
33714 TGAACATATG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 7 0.21
35 13 0.38
37 14 0.41
ACGTcount: A:0.21, C:0.08, G:0.25, T:0.45
Consensus pattern (35 bp):
GGTATTAGCATGTCGTCTTTTTAGGAAGATAGTTT
Found at i:36092 original size:27 final size:28
Alignment explanation
Indices: 36049--36106 Score: 91
Period size: 29 Copynumber: 2.1 Consensus size: 28
36039 CGATGTAATT
*
36049 TTTTTTTTTAT-ATATATTGGAGAAAAC
1 TTTTTTTTGATAATATATTGGAGAAAAC
36076 TTTTTTTTGATCAATATATTGGAGAAAAC
1 TTTTTTTTGAT-AATATATTGGAGAAAAC
36105 TT
1 TT
36107 AATGAAGTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
27 10 0.36
29 18 0.64
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.50
Consensus pattern (28 bp):
TTTTTTTTGATAATATATTGGAGAAAAC
Done.