Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015463.1 Corchorus capsularis cultivar CVL-1 contig15484, 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: 26018
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:6721 original size:20 final size:20
Alignment explanation
Indices: 6698--6745 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
6688 TCTGATTTGA
*
6698 CTTTTCTTCCTTTTTTATTT
1 CTTTTCTTACTTTTTTATTT
** *
6718 CTTTAATTAGTTTTTTATTT
1 CTTTTCTTACTTTTTTATTT
6738 CTTTTCTT
1 CTTTTCTT
6746 TTGTTTTTTT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.10, C:0.15, G:0.02, T:0.73
Consensus pattern (20 bp):
CTTTTCTTACTTTTTTATTT
Found at i:6751 original size:21 final size:21
Alignment explanation
Indices: 6708--6768 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
6698 CTTTTCTTCC
** *
6708 TTTTTTATTTC-TTTAATTAG
1 TTTTTTATTTCTTTTCTTTTG
6728 TTTTTTATTTCTTTTCTTTTG
1 TTTTTTATTTCTTTTCTTTTG
*
6749 TTTTTT-TTCTTTTTTCTTTT
1 TTTTTTATT-TCTTTTCTTTT
6769 CACTTTTCTG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 13 0.37
21 22 0.63
ACGTcount: A:0.08, C:0.08, G:0.03, T:0.80
Consensus pattern (21 bp):
TTTTTTATTTCTTTTCTTTTG
Found at i:6798 original size:13 final size:13
Alignment explanation
Indices: 6780--6820 Score: 59
Period size: 11 Copynumber: 3.2 Consensus size: 13
6770 ACTTTTCTGA
6780 TTTGATGATTTTT
1 TTTGATGATTTTT
6793 TTTGATGA--TTT
1 TTTGATGATTTTT
6804 TTTGATGATTATTT
1 TTTGATGATT-TTT
6818 TTT
1 TTT
6821 TTATTAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 11 0.44
13 8 0.32
14 6 0.24
ACGTcount: A:0.17, C:0.00, G:0.15, T:0.68
Consensus pattern (13 bp):
TTTGATGATTTTT
Found at i:7743 original size:35 final size:35
Alignment explanation
Indices: 7704--7770 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 35
7694 GTTGATATTT
** *
7704 TTGTTACTATTTTATTGATGTTGTTGTTGCTGGTA
1 TTGTTACTATTTTAGGGATGTTATTGTTGCTGGTA
* * *
7739 TTGTTGCTGTTTTAGGGTTGTTATTGTTGCTG
1 TTGTTACTATTTTAGGGATGTTATTGTTGCTG
7771 TTTTAGGTCT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 26 1.00
ACGTcount: A:0.10, C:0.06, G:0.27, T:0.57
Consensus pattern (35 bp):
TTGTTACTATTTTAGGGATGTTATTGTTGCTGGTA
Found at i:7766 original size:23 final size:23
Alignment explanation
Indices: 7732--7888 Score: 208
Period size: 23 Copynumber: 6.8 Consensus size: 23
7722 TGTTGTTGTT
*
7732 GCTGGTATTGTTGCTGTTTTAGG
1 GCTGTTATTGTTGCTGTTTTAGG
*
7755 GTTGTTATTGTTGCTGTTTTAGG
1 GCTGTTATTGTTGCTGTTTTAGG
* *
7778 TCTGGTATTGTTGCTGTTTTAGG
1 GCTGTTATTGTTGCTGTTTTAGG
*
7801 GCTGGTATTGTTGCTGTTTTAGG
1 GCTGTTATTGTTGCTGTTTTAGG
* **
7824 ACTGCAATTGTTGCTGTTTTAGG
1 GCTGTTATTGTTGCTGTTTTAGG
*
7847 GCTGTAATTGTTGCTGTTTTAGG
1 GCTGTTATTGTTGCTGTTTTAGG
*
7870 GCTGATT-TTGTTGTTGTTT
1 GCTG-TTATTGTTGCTGTTT
7889 AATGGATTAA
Statistics
Matches: 120, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
23 119 0.99
24 1 0.01
ACGTcount: A:0.10, C:0.08, G:0.31, T:0.51
Consensus pattern (23 bp):
GCTGTTATTGTTGCTGTTTTAGG
Found at i:7907 original size:69 final size:69
Alignment explanation
Indices: 7732--7912 Score: 188
Period size: 69 Copynumber: 2.6 Consensus size: 69
7722 TGTTGTTGTT
* * ** ** * *
7732 GCTGGTATTGTTGCTGTTTTAGGGTTGTTATTGTTGCTGTTTTAGGTCTGGTATTGTTGCTGTTT
1 GCTGATATTGTTGCTGTTTAAGGACTGCAATTCTTGCTGTTTTAGGGCTGGTATTGTTGCTGTTT
7797 TAGG
66 TAGG
* * *
7801 GCTGGTATTGTTGCTGTTTTAGGACTGCAATTGTTGCTGTTTTAGGGCT-GTAATTGTTGCTGTT
1 GCTGATATTGTTGCTGTTTAAGGACTGCAATTCTTGCTGTTTTAGGGCTGGT-ATTGTTGCTGTT
7865 TTAGG
65 TTAGG
* * *
7870 GCTGATTTTGTTGTTGTTTAATGGA-T-TAATTTCTTGCTGTTTT
1 GCTGATATTGTTGCTGTTTAA-GGACTGCAA-TTCTTGCTGTTTT
7913 TATACTGTTT
Statistics
Matches: 98, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
68 4 0.04
69 91 0.93
70 3 0.03
ACGTcount: A:0.12, C:0.08, G:0.29, T:0.51
Consensus pattern (69 bp):
GCTGATATTGTTGCTGTTTAAGGACTGCAATTCTTGCTGTTTTAGGGCTGGTATTGTTGCTGTTT
TAGG
Found at i:7922 original size:11 final size:11
Alignment explanation
Indices: 7906--7956 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
7896 TAATTTCTTG
7906 CTGTTTTTATA
1 CTGTTTTTATA
*
7917 CTGTTTTTGATG
1 CTGTTTTT-ATA
* *
7929 TTG-TTTTATTG
1 CTGTTTTTA-TA
7940 CTGTTTTTATA
1 CTGTTTTTATA
7951 CTGTTT
1 CTGTTT
7957 GTGTGAAGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
10 1 0.03
11 23 0.70
12 9 0.27
ACGTcount: A:0.12, C:0.08, G:0.16, T:0.65
Consensus pattern (11 bp):
CTGTTTTTATA
Found at i:7975 original size:34 final size:34
Alignment explanation
Indices: 7903--7991 Score: 108
Period size: 34 Copynumber: 2.6 Consensus size: 34
7893 GATTAATTTC
* ** *
7903 TTGCTGTTTTTATACTGTTTTTGATGTTGTTTTA
1 TTGCTGTTTTTATACTGTTTGTGATGAAGTATTA
*
7937 TTGCTGTTTTTATACTGTTTGTG-TGAAGATATTG
1 TTGCTGTTTTTATACTGTTTGTGATGAAG-TATTA
*
7971 TTGCTGTTTTTATACTCTTTG
1 TTGCTGTTTTTATACTGTTTG
7992 GCTCTATGCC
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
33 3 0.06
34 45 0.94
ACGTcount: A:0.13, C:0.08, G:0.19, T:0.60
Consensus pattern (34 bp):
TTGCTGTTTTTATACTGTTTGTGATGAAGTATTA
Found at i:8855 original size:17 final size:18
Alignment explanation
Indices: 8815--8857 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
8805 GGAGAGGCCA
8815 ATATTGCATCTTAGCTTTC
1 ATATTG-ATCTTAGCTTTC
* *
8834 GTATTGAT-TTAGCTTTT
1 ATATTGATCTTAGCTTTC
8851 ATATTGA
1 ATATTGA
8858 ATCTAGCATC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 14 0.67
18 2 0.10
19 5 0.24
ACGTcount: A:0.23, C:0.12, G:0.14, T:0.51
Consensus pattern (18 bp):
ATATTGATCTTAGCTTTC
Found at i:9113 original size:2 final size:2
Alignment explanation
Indices: 9106--9135 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
9096 ACTTCGTAGA
*
9106 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9136 GCCTGCAGAT
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:11955 original size:46 final size:46
Alignment explanation
Indices: 11888--12053 Score: 172
Period size: 46 Copynumber: 3.5 Consensus size: 46
11878 TCAATTTTGT
*
11888 TTTTTACTTGCTTTTTCCCAAAATACCCTTCCTGGACGGAAGGCAC
1 TTTTTACTTGCTTTTTCCCAAAACACCCTTCCTGGACGGAAGGCAC
* * **
11934 TTTTTACTTGCTTTTCCCCAAAGCACCCTTCCCAGACGGAAGGCACTTC
1 TTTTTACTTGCTTTTTCCCAAAACACCCTTCCTGGACGGAAGGCA---C
* * * * *
11983 TTTTTACTTGCTCTTT-CTAAAACGCCCTTCCTGGACGGAGGGCGTTAA
1 TTTTTACTTGCTTTTTCCCAAAACACCCTTCCTGGACGGAAGGC---AC
*
12031 TTTTTACTTGCTTTTTCTCAAAA
1 TTTTTACTTGCTTTTTCCCAAAA
12054 TGCCCTTTCA
Statistics
Matches: 96, Mismatches: 17, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
46 40 0.42
48 36 0.38
49 19 0.20
51 1 0.01
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.37
Consensus pattern (46 bp):
TTTTTACTTGCTTTTTCCCAAAACACCCTTCCTGGACGGAAGGCAC
Found at i:12342 original size:62 final size:62
Alignment explanation
Indices: 12114--12342 Score: 261
Period size: 62 Copynumber: 3.7 Consensus size: 62
12104 AGTACTTCCG
* ** * *
12114 ATTCCCAAAAATACCCTTTCGGACAAAGGGTTGGTTTTGTCACCTTCT-TGCATTTTAGTTTACT
1 ATTCCC-AAAATACCCTTTCAGACAAAGGGTCAGTTTTGTCACATTCTCTGCA-CTTAGTTTA-T
*
12178 ATTCCCAAAATACCCTTTCAGACAAAGGGTCAGTTTCT-TCACATTC-CTGCACTTAGATTAT
1 ATTCCCAAAATACCCTTTCAGACAAAGGGTCAGTTT-TGTCACATTCTCTGCACTTAGTTTAT
*
12239 AGTTCCCAAAATACCCTTTCAGACAAAGGGTCAGTTGTGTCACATTCTCT-CA-TATAGTTTCAT
1 A-TTCCCAAAATACCCTTTCAGACAAAGGGTCAGTTTTGTCACATTCTCTGCACT-TAGTTT-AT
* * * *
12302 TTTCCCAAAATACCCTTTCGGATAAAGGGTCAATTTTGTCA
1 ATTCCCAAAATACCCTTTCAGACAAAGGGTCAGTTTTGTCA
12343 TGTTCTTGCA
Statistics
Matches: 145, Mismatches: 13, Indels: 16
0.83 0.07 0.09
Matches are distributed among these distances:
61 4 0.03
62 92 0.63
63 42 0.29
64 7 0.05
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.35
Consensus pattern (62 bp):
ATTCCCAAAATACCCTTTCAGACAAAGGGTCAGTTTTGTCACATTCTCTGCACTTAGTTTAT
Found at i:18357 original size:24 final size:24
Alignment explanation
Indices: 18329--18376 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
18319 CCCGCGCCAT
18329 GGCCCGTGCCAGCCGCTGTGCCGC
1 GGCCCGTGCCAGCCGCTGTGCCGC
18353 GGCCCGTGCCAGCCGCTGTGCCGC
1 GGCCCGTGCCAGCCGCTGTGCCGC
18377 CCAAGCCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.04, C:0.46, G:0.38, T:0.12
Consensus pattern (24 bp):
GGCCCGTGCCAGCCGCTGTGCCGC
Found at i:19884 original size:12 final size:12
Alignment explanation
Indices: 19869--19908 Score: 52
Period size: 10 Copynumber: 3.7 Consensus size: 12
19859 ATTATGCATG
19869 TTTTTATAGCTA
1 TTTTTATAGCTA
19881 TTTTTATA--TA
1 TTTTTATAGCTA
19891 TTTTT-T-GCTA
1 TTTTTATAGCTA
19901 TTTTTATA
1 TTTTTATA
19909 TGTGTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
9 1 0.04
10 14 0.58
11 1 0.04
12 8 0.33
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.68
Consensus pattern (12 bp):
TTTTTATAGCTA
Found at i:19916 original size:20 final size:20
Alignment explanation
Indices: 19877--19916 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
19867 TGTTTTTATA
*
19877 GCTATTTTTATATATTTTTT
1 GCTATTTTTATATATGTTTT
*
19897 GCTATTTTTATATGTGTTTT
1 GCTATTTTTATATATGTTTT
19917 TACCCTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.05, G:0.10, T:0.68
Consensus pattern (20 bp):
GCTATTTTTATATATGTTTT
Found at i:20172 original size:11 final size:11
Alignment explanation
Indices: 20156--20188 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
20146 AATTGAAGAC
20156 AAGCCCAGAAG
1 AAGCCCAGAAG
20167 AAGCCCAGAAG
1 AAGCCCAGAAG
*
20178 AAGCCCTGAAG
1 AAGCCCAGAAG
20189 TTGAGGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.42, C:0.27, G:0.27, T:0.03
Consensus pattern (11 bp):
AAGCCCAGAAG
Found at i:21486 original size:6 final size:6
Alignment explanation
Indices: 21475--21501 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
21465 TATAATCTGC
21475 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
21502 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:21847 original size:19 final size:20
Alignment explanation
Indices: 21819--21866 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
21809 GCTTTTAAGT
* *
21819 AATTTGTAAA-AAAAGATTG
1 AATTTTTAAATAAAAGATTA
*
21838 AATTTTTAAATGAAAGATTA
1 AATTTTTAAATAAAAGATTA
21858 AATCTTTTA
1 AAT-TTTTA
21867 TGTAATTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 9 0.38
20 10 0.42
21 5 0.21
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40
Consensus pattern (20 bp):
AATTTTTAAATAAAAGATTA
Found at i:21997 original size:52 final size:50
Alignment explanation
Indices: 21774--21999 Score: 242
Period size: 51 Copynumber: 4.5 Consensus size: 50
21764 AAAAAAGGAA
* * *
21774 TTGTGAATAGAGA-TGAATTTTTAA-TGAAAGATTAAGCTTTTAAGTAAT
1 TTGTAAATAAAGATTGAATCTTTAATTGAAAGATTAAGCTTTTAAGTAAT
* * * * *
21822 TTGTAAAAAAAGATTGAATTTTTAAATGAAAGATTAAATCTTTTATGTAAT
1 TTGTAAATAAAGATTGAATCTTTAATTGAAAGATT-AAGCTTTTAAGTAAT
* *
21873 TTGTGAATAAAGATTGAATTTTTAATTGAAAGATTAAGCTTTTAAGTAAGT
1 TTGTAAATAAAGATTGAATCTTTAATTGAAAGATTAAGCTTTTAAGTAA-T
* * * *
21924 TTGTAAATAAAAAATGTAATCTTTGATTAAAAGATTGAA-CTTTTAAGTAATTT
1 TTGTAAATAAAGATTG-AATCTTTAATTGAAAGATT-AAGCTTTTAAGTAA--T
*
21977 TTGTAAATAAAGATTAAATCTTT
1 TTGTAAATAAAGATTGAATCTTT
22000 TAAGTAAAAG
Statistics
Matches: 151, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
48 10 0.07
49 11 0.07
50 21 0.14
51 59 0.39
52 34 0.23
53 16 0.11
ACGTcount: A:0.42, C:0.03, G:0.14, T:0.41
Consensus pattern (50 bp):
TTGTAAATAAAGATTGAATCTTTAATTGAAAGATTAAGCTTTTAAGTAAT
Found at i:22551 original size:35 final size:35
Alignment explanation
Indices: 22509--23166 Score: 807
Period size: 35 Copynumber: 18.7 Consensus size: 35
22499 GAATCAGTAA
*
22509 TAATCAACTTAATTCAGGGTGATTAAGTAAGTCAG
1 TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
** *
22544 TAATCAACTTAATTCAGGCCAATTAAGTAAGT-AA
1 TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
*
22578 TAATCAACTTAATTCAAGGTAATTAAGTAAGTCAG
1 TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
* * *
22613 TAATCAATTTAATTCAGGGTGATTAAGTAAGTCGG
1 TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
* *
22648 TAATAAACTTAATTCAGGGTAATTAAGTGAGTCAGTAATTAAG
1 TAATCAACTTAATTCAGGGTAATTAAGT-A---AG----TCAG
22691 TAATAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
1 ---TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
* *
22729 CAATCAACTTAATTCAGGGTAATTAAGTGAGTCAG
1 TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
*
22764 TAATCGACTTAATTCAGGGTAATTAAGTAAGTCAG
1 TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
*
22799 TAATCAACTTTAATTCAGGGTAATTAAGTAAGTCAA
1 TAATCAAC-TTAATTCAGGGTAATTAAGTAAGTCAG
* *
22835 TAATCAACTTAATTCAGGGCAATTAAGTAAGT-AA
1 TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
22869 TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
1 TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
* * *
22904 TAATCAATTTAATTCAGGGTGATTAAGTAAGTCGG
1 TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
*
22939 TAATAAACTTAATTCAGGGTAATTAAGTAAGTCAG
1 TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
*
22974 TAATAAACTTAATTCAGGGTAA-T---TAAGTCAG
1 TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
23005 TAATCAACCTTAATTCAGGGTAA-T---TAAGTCAG
1 TAATCAA-CTTAATTCAGGGTAATTAAGTAAGTCAG
*
23037 TAATCAACTTTAATTCAGGGTAATTAAGTGAGTCAG
1 TAATCAAC-TTAATTCAGGGTAATTAAGTAAGTCAG
* * * *
23073 TAATCGACTTAAATCCAGGGTACTTAAGTAAGTCAA
1 TAATCAACTT-AATTCAGGGTAATTAAGTAAGTCAG
* * *
23109 TACAT-AACTTAATTCAGGGTAATTAAGCAGGTCAT
1 TA-ATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
* * *
23144 TGATCGACTTAATTCAGAGTAAT
1 TAATCAACTTAATTCAGGGTAAT
23167 GAAATTTAGT
Statistics
Matches: 548, Mismatches: 52, Indels: 46
0.85 0.08 0.07
Matches are distributed among these distances:
31 15 0.03
32 45 0.08
33 1 0.00
34 66 0.12
35 306 0.56
36 76 0.14
37 2 0.00
38 3 0.01
39 2 0.00
42 2 0.00
43 2 0.00
45 1 0.00
46 27 0.05
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (35 bp):
TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG
Done.