Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015170.1 Corchorus olitorius cultivar O-4 contig15203, 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: 35948
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Found at i:1070 original size:49 final size:49
Alignment explanation
Indices: 993--1122 Score: 156
Period size: 49 Copynumber: 2.7 Consensus size: 49
983 CAAGCAATCC
* * **
993 TTTACTTTTCACTGCACTTTTTATCAATTTTT-ACTACAAAATTGAACT
1 TTTAATTTTCATTGCACTTTTTATCAATTTTTAAAGACAAAATTGAACT
* * *
1041 TTT-ATTTTTACTTGCATCTTTTTCTCAATTTTTAAAGACAAAATTGATCT
1 TTTAATTTTCA-TTGCA-CTTTTTATCAATTTTTAAAGACAAAATTGAACT
*
1091 TTTAATTTTCATCGCACTTTTTATCAATTTTT
1 TTTAATTTTCATTGCACTTTTTATCAATTTTT
1123 TGACACAATT
Statistics
Matches: 68, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
47 5 0.07
48 7 0.10
49 30 0.44
50 20 0.29
51 6 0.09
ACGTcount: A:0.27, C:0.16, G:0.05, T:0.52
Consensus pattern (49 bp):
TTTAATTTTCATTGCACTTTTTATCAATTTTTAAAGACAAAATTGAACT
Found at i:1644 original size:84 final size:84
Alignment explanation
Indices: 1546--1705 Score: 284
Period size: 84 Copynumber: 1.9 Consensus size: 84
1536 GGTGTGTCCT
*
1546 AAATAAATGAAAGTATATGCAAAATGTCAATTTTCAAAAGGTAAGAATGCAAAAGGTTTAAGCCG
1 AAATAAATGAAAGTATATGCAAAATGTCAATTTTCAAAAGGTAAGAATGCAAAAGGTCTAAGCCG
*
1611 AAAATTTTATATATATGCA
66 AAAATTATATATATATGCA
* *
1630 AAATAAATGAAAGTATATGCAAAATGTCCATTTTCAAAAGGTAAGGATGCAAAAGGTCTAAGCCG
1 AAATAAATGAAAGTATATGCAAAATGTCAATTTTCAAAAGGTAAGAATGCAAAAGGTCTAAGCCG
1695 AAAATTATATA
66 AAAATTATATA
1706 CATGCTCCTC
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 72 1.00
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.27
Consensus pattern (84 bp):
AAATAAATGAAAGTATATGCAAAATGTCAATTTTCAAAAGGTAAGAATGCAAAAGGTCTAAGCCG
AAAATTATATATATATGCA
Found at i:2340 original size:19 final size:20
Alignment explanation
Indices: 2295--2357 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
2285 GCTGCTCTAA
*
2295 TAATCTCATATGTACAGTGCC
1 TAATCTCATCTGTACAGTG-C
*
2316 TAATCTAATCTGTACAGTG-
1 TAATCTCATCTGTACAGTGC
2335 TAATCTCATCTG-ACAGTTGC
1 TAATCTCATCTGTACAG-TGC
2355 TAA
1 TAA
2358 ACAGTGTCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
18 4 0.11
19 13 0.35
20 3 0.08
21 17 0.46
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (20 bp):
TAATCTCATCTGTACAGTGC
Found at i:9651 original size:14 final size:14
Alignment explanation
Indices: 9610--9651 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
9600 GAAAAATACG
9610 TACAAGTAGCTATA
1 TACAAGTAGCTATA
*
9624 TACTA-TA-C-ATA
1 TACAAGTAGCTATA
9635 TACAAGTAGCTATA
1 TACAAGTAGCTATA
9649 TAC
1 TAC
9652 CATGAACCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
11 7 0.30
12 3 0.13
13 3 0.13
14 10 0.43
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.31
Consensus pattern (14 bp):
TACAAGTAGCTATA
Found at i:15406 original size:20 final size:21
Alignment explanation
Indices: 15381--15420 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
15371 TAAAAACCAC
15381 AAGAACTCCG-AATGGAGTAT
1 AAGAACTCCGCAATGGAGTAT
*
15401 AAGAACTCCGCGATGGAGTA
1 AAGAACTCCGCAATGGAGTA
15421 AAAACCATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.38, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
AAGAACTCCGCAATGGAGTAT
Found at i:19907 original size:2 final size:2
Alignment explanation
Indices: 19898--19933 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
19888 CATATAAAAA
19898 AT AT -T 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 A
19934 CCATTCCACT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21608 original size:17 final size:19
Alignment explanation
Indices: 21583--21622 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
21573 TTAGTAGAAT
21583 AAAACTGTAAA-A-ATTTA
1 AAAACTGTAAATATATTTA
*
21600 AAAATTGTAAATATATTTA
1 AAAACTGTAAATATATTTA
21619 AAAA
1 AAAA
21623 ATTCAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 10 0.50
18 1 0.05
19 9 0.45
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.33
Consensus pattern (19 bp):
AAAACTGTAAATATATTTA
Found at i:21630 original size:19 final size:19
Alignment explanation
Indices: 21595--21634 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
21585 AACTGTAAAA
*
21595 ATTTAAAAATTGTAAATAT
1 ATTTAAAAATTGCAAATAT
21614 ATTTAAAAAATT-CAAATAT
1 ATTT-AAAAATTGCAAATAT
21633 AT
1 AT
21635 CTAAGGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (19 bp):
ATTTAAAAATTGCAAATAT
Found at i:21707 original size:132 final size:133
Alignment explanation
Indices: 21558--21827 Score: 289
Period size: 140 Copynumber: 2.0 Consensus size: 133
21548 TTAAATTTAA
* * *
21558 TTAAATAAAAATATTTTAGTAGAAT-AAAACTGTAAAAATTTAAA-AATTG-T-AAATATATTTA
1 TTAAATAAAAAAATTTTAGTAG-ATCAAAACTATAAAAATTTAAACAATTGTTAAAATATATTCA
* *
21619 AAAAATTCAAATATATCTAAG-GTTTTTAATTAAAATAATCAAATGGTAAAAAATAAAATAGTTA
65 AAAAATTAAAATATATCTAAGTGTTTTTAATTAAAATAATAAAATGGTAAAAAA-AAAATAGTTA
21683 TAAAG
129 TAAAG
* **
21688 TTAAATAAAATAAAGTTTTAGTTGATCAAAACTATAAATGTTTAAACAATTGCATTTCAGAAATA
1 TTAAATAAAA-AAA-TTTTAGTAGATCAAAACTATAAAAATTTAAACAATTG---TT-A-AAATA
** * * * * *
21753 TATTCGGAATATTAAAATATATTTAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAATAAAAAT
59 TATTCAAAAAATTAAAATATATCTAAGTGTTTTTAATTAAAATAATAAAATGGTAAAAAAAAAAT
21818 AGTTATAAAG
124 AGTTATAAAG
21828 ATATTAGATT
Statistics
Matches: 113, Mismatches: 15, Indels: 14
0.80 0.11 0.10
Matches are distributed among these distances:
130 10 0.09
131 4 0.04
132 24 0.21
133 5 0.04
137 1 0.01
140 41 0.36
141 28 0.25
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (133 bp):
TTAAATAAAAAAATTTTAGTAGATCAAAACTATAAAAATTTAAACAATTGTTAAAATATATTCAA
AAAATTAAAATATATCTAAGTGTTTTTAATTAAAATAATAAAATGGTAAAAAAAAAATAGTTATA
AAG
Found at i:21896 original size:23 final size:24
Alignment explanation
Indices: 21836--21896 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
21826 AGATATTAGA
* *
21836 TTTAATTAAATAAAAATAGAGTTT
1 TTTAATTGAGTAAAAATAGAGTTT
* *
21860 TTTCAGTG-GATAAAAATAGAG-TT
1 TTTAATTGAG-TAAAAATAGAGTTT
21883 TTTAATTGAGTAAA
1 TTTAATTGAGTAAA
21897 TTATAAAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
23 12 0.41
24 17 0.59
ACGTcount: A:0.44, C:0.02, G:0.15, T:0.39
Consensus pattern (24 bp):
TTTAATTGAGTAAAAATAGAGTTT
Found at i:22420 original size:17 final size:16
Alignment explanation
Indices: 22390--22426 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
22380 AATGAACAAA
22390 ATAT-TATATAATTAT
1 ATATATATATAATTAT
22405 ATATATATATATATTAT
1 ATATATATATA-ATTAT
22422 ATATA
1 ATATA
22427 ATAATTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 4 0.20
16 6 0.30
17 10 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATATATATATAATTAT
Found at i:22506 original size:16 final size:16
Alignment explanation
Indices: 22485--22516 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
22475 TTTATAATTT
22485 TTATTAATAATATATA
1 TTATTAATAATATATA
*
22501 TTATTATTAATATATA
1 TTATTAATAATATATA
22517 AATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATTAATAATATATA
Found at i:22530 original size:19 final size:18
Alignment explanation
Indices: 22485--22531 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
22475 TTTATAATTT
* *
22485 TTATTAATAATATATATTA
1 TTATTAAT-ATATAAATAA
22504 TTATTAATATATAAATAA
1 TTATTAATATATAAATAA
22522 TTATATAATA
1 TTAT-TAATA
22532 AATGAACGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 12 0.48
19 13 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTATTAATATATAAATAA
Found at i:22601 original size:35 final size:35
Alignment explanation
Indices: 22562--22630 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
22552 ATAAACGAAC
*
22562 ACTTAAATGAACAATAAACGAGCCTATTCGTGAAT
1 ACTTAAATGAACAATAAACGAGCATATTCGTGAAT
* *
22597 ACTTAAATGAATAATAAACGAGCATGTTCGTGAA
1 ACTTAAATGAACAATAAACGAGCATATTCGTGAA
22631 CATAAACGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.26
Consensus pattern (35 bp):
ACTTAAATGAACAATAAACGAGCATATTCGTGAAT
Found at i:23605 original size:18 final size:18
Alignment explanation
Indices: 23582--23616 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
23572 ATTTGAGTGT
23582 AATTTAATTACCTAATGC
1 AATTTAATTACCTAATGC
23600 AATTTAATTACCTAATG
1 AATTTAATTACCTAATG
23617 GTCTAGAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.40
Consensus pattern (18 bp):
AATTTAATTACCTAATGC
Found at i:24627 original size:22 final size:21
Alignment explanation
Indices: 24602--24677 Score: 82
Period size: 22 Copynumber: 3.6 Consensus size: 21
24592 TATTTTTATA
24602 AAATTTTGATAATTATCCTATT
1 AAATTTTGATAATTA-CCTATT
**
24624 AAATTTTGATAACCACCCTATT
1 AAATTTTGATAATTA-CCTATT
* *
24646 AAA-TTTGATAATTACCCATG
1 AAATTTTGATAATTACCTATT
*
24666 AAATTATGATAA
1 AAATTTTGATAA
24678 ACTCCACATG
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
20 7 0.16
21 16 0.36
22 22 0.49
ACGTcount: A:0.41, C:0.13, G:0.07, T:0.39
Consensus pattern (21 bp):
AAATTTTGATAATTACCTATT
Found at i:24662 original size:21 final size:21
Alignment explanation
Indices: 24606--24677 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
24596 TTTATAAAAT
*
24606 TTTGATAATTATCCTATTAAA
1 TTTGATAATTACCCTATTAAA
**
24627 TTTTGATAACCACCCTATTAAA
1 -TTTGATAATTACCCTATTAAA
*
24649 TTTGATAATTACCC-ATGAAA
1 TTTGATAATTACCCTATTAAA
24669 TTATGATAA
1 TT-TGATAA
24678 ACTCCACATG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
20 7 0.16
21 18 0.42
22 18 0.42
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.40
Consensus pattern (21 bp):
TTTGATAATTACCCTATTAAA
Found at i:24766 original size:21 final size:22
Alignment explanation
Indices: 24685--24767 Score: 80
Period size: 23 Copynumber: 3.8 Consensus size: 22
24675 TAAACTCCAC
* **
24685 ATGAAACTTTTGATAACCTAACT
1 ATGAAA-TTTTAATAACCTTCCT
24708 ATGAAATTTTAATAAACCTTCCT
1 ATGAAATTTTAAT-AACCTTCCT
* *
24731 ATGAAATCTT-GTAACCTTCCT
1 ATGAAATTTTAATAACCTTCCT
*
24752 ATG-ATTTTTAATAACC
1 ATGAAATTTTAATAACC
24768 CCTCTGTGAG
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
20 4 0.08
21 17 0.34
22 7 0.14
23 22 0.44
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.39
Consensus pattern (22 bp):
ATGAAATTTTAATAACCTTCCT
Found at i:25835 original size:3 final size:3
Alignment explanation
Indices: 25827--25861 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
25817 TTTAGTATAT
* *
25827 ATA ATA ATA ATA ATA ATT ATT ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
25862 TCTTGCCCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
ATA
Found at i:31765 original size:18 final size:19
Alignment explanation
Indices: 31738--31776 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
31728 CCTTCCTTTT
31738 TTTTTGTTTTTGGCCATAA
1 TTTTTGTTTTTGGCCATAA
*
31757 TTTTT-TTTTTGGGCATAA
1 TTTTTGTTTTTGGCCATAA
31775 TT
1 TT
31777 AATGAACACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.15, C:0.08, G:0.15, T:0.62
Consensus pattern (19 bp):
TTTTTGTTTTTGGCCATAA
Found at i:32785 original size:2 final size:2
Alignment explanation
Indices: 32773--32801 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
32763 TAACTTGTAA
32773 AT AT A- 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
32802 TATTTGTCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35373 original size:2 final size:2
Alignment explanation
Indices: 35366--35397 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
35356 GTATTTAATT
35366 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35398 GATGATCATC
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):
TA
Done.