Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012460.1 Corchorus capsularis cultivar CVL-1 contig12481, 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: 64173
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:9 original size:2 final size:2
Alignment explanation
Indices: 3--28 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1 AT
3 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
29 CATTTTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:355 original size:2 final size:2
Alignment explanation
Indices: 348--374 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
338 TATCATGCAG
348 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 A
375 AATTATTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:419 original size:35 final size:35
Alignment explanation
Indices: 373--445 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
363 TATATATATA
373 TAAATTATTTACAATTAGTTAAATAAAATATTTTT
1 TAAATTATTTACAATTAGTTAAATAAAATATTTTT
408 TAAATTATTTACAATTAGTTAAATAAAATATTTTT
1 TAAATTATTTACAATTAGTTAAATAAAATATTTTT
443 TAA
1 TAA
446 GGTAAAGTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (35 bp):
TAAATTATTTACAATTAGTTAAATAAAATATTTTT
Found at i:431 original size:19 final size:19
Alignment explanation
Indices: 373--431 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
363 TATATATATA
373 TAAATTATTTACAATTAGT
1 TAAATTATTTACAATTAGT
* **
392 TAAA-TA---AAATATTTTT
1 TAAATTATTTACA-ATTAGT
408 TAAATTATTTACAATTAGT
1 TAAATTATTTACAATTAGT
427 TAAAT
1 TAAAT
432 AAAATATTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 10
0.64 0.13 0.22
Matches are distributed among these distances:
15 2 0.07
16 8 0.28
17 2 0.07
18 2 0.07
19 13 0.45
20 2 0.07
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.47
Consensus pattern (19 bp):
TAAATTATTTACAATTAGT
Found at i:5680 original size:11 final size:12
Alignment explanation
Indices: 5649--5681 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
5639 AATCATTATT
5649 ATTATTGCAATA
1 ATTATTGCAATA
*
5661 ATAATTGCAA-A
1 ATTATTGCAATA
5672 ATTATTGCAA
1 ATTATTGCAA
5682 GATCCAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (12 bp):
ATTATTGCAATA
Found at i:8279 original size:16 final size:16
Alignment explanation
Indices: 8258--8291 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
8248 TAAAAATCAT
8258 CACTGGGAAATTTGCA
1 CACTGGGAAATTTGCA
8274 CACTGGGAAATTTGCA
1 CACTGGGAAATTTGCA
8290 CA
1 CA
8292 ATATCGTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (16 bp):
CACTGGGAAATTTGCA
Found at i:9335 original size:2 final size:2
Alignment explanation
Indices: 9328--9357 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
9318 TTAAAGTGTA
9328 AT AT AT 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
9358 TTGAGTATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11593 original size:11 final size:11
Alignment explanation
Indices: 11569--11603 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
11559 TTGGCAGCGC
11569 AACAAAAACAA
1 AACAAAAACAA
* *
11580 AACGAAAACGA
1 AACAAAAACAA
11591 AACAAAAACAA
1 AACAAAAACAA
11602 AA
1 AA
11604 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:29616 original size:14 final size:14
Alignment explanation
Indices: 29597--29625 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
29587 CTCTTGTTGG
29597 ATATATTTGATTGT
1 ATATATTTGATTGT
29611 ATATATTTGATTGT
1 ATATATTTGATTGT
29625 A
1 A
29626 ATTAGATATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (14 bp):
ATATATTTGATTGT
Found at i:29758 original size:30 final size:29
Alignment explanation
Indices: 29695--29764 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
29685 ACTGAACCGT
****
29695 CAAATAAGCCCCTGAACTATTATTTCAGC
1 CAAATAAGCCCCTGAACTATTAAAAAAGC
*
29724 CAAATAAGCCCCTGAACTCTTAAAAAATGC
1 CAAATAAGCCCCTGAACTATTAAAAAA-GC
29754 CAAATAAGCCC
1 CAAATAAGCCC
29765 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 22 0.63
30 13 0.37
ACGTcount: A:0.40, C:0.29, G:0.10, T:0.21
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTATTAAAAAAGC
Found at i:46667 original size:688 final size:687
Alignment explanation
Indices: 45351--46728 Score: 2738
Period size: 688 Copynumber: 2.0 Consensus size: 687
45341 TATAAAATAA
45351 AATTTATTTATAATTAATTAATTAGAAAAGAGAAAAATCACCATATAATCATATATTTTTCAATA
1 AATTTATTTATAATTAATTAATTAGAAAAGAGAAAAATCACCATATAATCATATATTTTTCAATA
45416 AGGTTTCATTTAGTTTCCTTTTGGTCCCAAAAGGACATCTCAGTGATTAAAATTTGAGATTTTTT
66 AGGTTTCATTTAGTTTCCTTTTGGTCCCAAAAGGACATCTCAGTGATTAAAATTTGAGATTTTTT
45481 GTGAAAAGTTTCGGATTCGAATCCTGAAATGGATGGCATGGAATGATGGGAAAGGAGATGATCAT
131 GTGAAAAGTTTCGGATTCGAATCCTGAAATGGATGGCATGGAATGATGGGAAAGGAGATGATCAT
45546 CTCTTATTGTATAACCCATTTGATCAAAATGCATGCTTAAAATAAAAATAACACGGAGAAAATTA
196 CTCTTATTGTATAACCCATTTGATCAAAATGCATGCTTAAAATAAAAATAACACGGAGAAAATTA
45611 TTATAAAACTAGGAGAGGAATATATAAACTCTCATGATATGTAATATAGTATAGTAATTATATAT
261 TTATAAAACTAGGAGAGGAATATATAAACTCTCATGATATGTAATATAGTATAGTAATTATATAT
45676 GGACTTTAGCCCTTTGCTAATTTGATGATATTGAGATAGGTCGTCATAGCCGTCATGGTTTAAGT
326 GGACTTTAGCCCTTTGCTAATTTGATGATATTGAGATAGGTCGTCATAGCCGTCATGGTTTAAGT
45741 CAAATTATTATCACTAATAATATATCTACCATGGGCTAATAATTAATCAACATAATTAACGACAG
391 CAAATTATTATCACTAATAATATATCTACCATGGGCTAATAATTAATCAACATAATTAACGACAG
45806 CCATATATAAAATGCCAATGTTAGATAACAAGAATAGAAAATCTACAATTTGACATGACTTGACA
456 CCATATATAAAATGCCAATGTTAGATAACAAGAATAGAAAATCTACAATTTGACATGACTTGACA
45871 AATTAAATTGTTTCTTCCACACCCTCTTTGGCCGCCTCCTATATACATCAATTTCAAAGGCTGGA
521 AATTAAATTGTTTCTTCCACACCCTCTTTGGCCGCCTCCTATATACATCAATTTCAAAGGCTGGA
*
45936 GGATAATTTGAAAGAACTTTTTTTTTTTTAATTTTTGGTGGAAAATTAAAGAACTTTATTTTTCA
586 GGATAATTTGAAAGAACTTTTTTTTTTTAAATTTTTGGTGGAAAATTAAAGAACTTTA-TTTTCA
46001 CCATGGTCCATGAAGGCTTCTTTTTCTAGCTATCATGC
650 CCATGGTCCATGAAGGCTTCTTTTTCTAGCTATCATGC
46039 AATTTATTTATAATTAATTAATTAGAAAAGAGAAAAATCACCATATAATCATATATTTTTCAATA
1 AATTTATTTATAATTAATTAATTAGAAAAGAGAAAAATCACCATATAATCATATATTTTTCAATA
46104 AGGTTTCATTTAGTTTCCTTTTGGTCCCAAAAGGACATCTCAGTGATTAAAATTTGAGATTTTTT
66 AGGTTTCATTTAGTTTCCTTTTGGTCCCAAAAGGACATCTCAGTGATTAAAATTTGAGATTTTTT
46169 GTGAAAAGTTTCGGATTCGAATCCTGAAATGGATGGCATGGAATGATGGGAAAGGAGATGATCAT
131 GTGAAAAGTTTCGGATTCGAATCCTGAAATGGATGGCATGGAATGATGGGAAAGGAGATGATCAT
46234 CTCTTATTGTATAACCCATTTGATCAAAATGCATGCTTAAAATAAAAATAACACGGAGAAAATTA
196 CTCTTATTGTATAACCCATTTGATCAAAATGCATGCTTAAAATAAAAATAACACGGAGAAAATTA
46299 TTATAAAACTAGGAGAGGAATATATAAACTCTCATGATATGTAATATAGTATAGTAATTATATAT
261 TTATAAAACTAGGAGAGGAATATATAAACTCTCATGATATGTAATATAGTATAGTAATTATATAT
46364 GGACTTTAGCCCTTTGCTAATTTGATGATATTGAGATAGGTCGTCATAGCCGTCATGGTTTAAGT
326 GGACTTTAGCCCTTTGCTAATTTGATGATATTGAGATAGGTCGTCATAGCCGTCATGGTTTAAGT
46429 CAAATTATTATCACTAATAATATATCTACCATGGGCTAATAATTAATCAACATAATTAACGACAG
391 CAAATTATTATCACTAATAATATATCTACCATGGGCTAATAATTAATCAACATAATTAACGACAG
46494 CCATATATAAAATGCCAATGTTAGATAACAAGAATAGAAAATCTACAATTTGACATGACTTGACA
456 CCATATATAAAATGCCAATGTTAGATAACAAGAATAGAAAATCTACAATTTGACATGACTTGACA
46559 AATTAAATTGTTTCTTCCACACCCTCTTTGGCCGCCTCCTATATACATCAATTTCAAAGGCTGGA
521 AATTAAATTGTTTCTTCCACACCCTCTTTGGCCGCCTCCTATATACATCAATTTCAAAGGCTGGA
46624 GGATAATTTGAAAGAACTTTTTTTTTTTAAATTTTTGGTGGAAAATTAAAGAACTTTATTTTCAC
586 GGATAATTTGAAAGAACTTTTTTTTTTTAAATTTTTGGTGGAAAATTAAAGAACTTTATTTTCAC
46689 CATGGTCCATGAAGGCTTCTTTTTCTAGCTATCATGC
651 CATGGTCCATGAAGGCTTCTTTTTCTAGCTATCATGC
46726 AAT
1 AAT
46729 GTGTGGGGGA
Statistics
Matches: 689, Mismatches: 1, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
687 47 0.07
688 642 0.93
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (687 bp):
AATTTATTTATAATTAATTAATTAGAAAAGAGAAAAATCACCATATAATCATATATTTTTCAATA
AGGTTTCATTTAGTTTCCTTTTGGTCCCAAAAGGACATCTCAGTGATTAAAATTTGAGATTTTTT
GTGAAAAGTTTCGGATTCGAATCCTGAAATGGATGGCATGGAATGATGGGAAAGGAGATGATCAT
CTCTTATTGTATAACCCATTTGATCAAAATGCATGCTTAAAATAAAAATAACACGGAGAAAATTA
TTATAAAACTAGGAGAGGAATATATAAACTCTCATGATATGTAATATAGTATAGTAATTATATAT
GGACTTTAGCCCTTTGCTAATTTGATGATATTGAGATAGGTCGTCATAGCCGTCATGGTTTAAGT
CAAATTATTATCACTAATAATATATCTACCATGGGCTAATAATTAATCAACATAATTAACGACAG
CCATATATAAAATGCCAATGTTAGATAACAAGAATAGAAAATCTACAATTTGACATGACTTGACA
AATTAAATTGTTTCTTCCACACCCTCTTTGGCCGCCTCCTATATACATCAATTTCAAAGGCTGGA
GGATAATTTGAAAGAACTTTTTTTTTTTAAATTTTTGGTGGAAAATTAAAGAACTTTATTTTCAC
CATGGTCCATGAAGGCTTCTTTTTCTAGCTATCATGC
Found at i:53937 original size:2 final size:2
Alignment explanation
Indices: 53930--53956 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
53920 TTCACAACAA
53930 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 A
53957 AGATTGATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.