Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011260.1 Corchorus capsularis cultivar CVL-1 contig11281, 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: 33227
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1362 original size:12 final size:12
Alignment explanation
Indices: 1345--1370 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1335 TTAACTAAAC
1345 TATATATATAAT
1 TATATATATAAT
1357 TATATATATAAT
1 TATATATATAAT
1369 TA
1 TA
1371 AAGATAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TATATATATAAT
Found at i:1603 original size:42 final size:43
Alignment explanation
Indices: 1542--1622 Score: 121
Period size: 42 Copynumber: 1.9 Consensus size: 43
1532 TAAACATGTT
*
1542 AATCGTGTCTTGACACGATT-ACGACACGAAACACGATAATCTC
1 AATCGTGTCTCGACACGATTCA-GACACGAAACACGATAATCTC
*
1585 AATCGTGTC-CGACACGATTCAGACACGAGACACGATAA
1 AATCGTGTCTCGACACGATTCAGACACGAAACACGATAA
1623 GCCAAACACA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
42 25 0.71
43 10 0.29
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.20
Consensus pattern (43 bp):
AATCGTGTCTCGACACGATTCAGACACGAAACACGATAATCTC
Found at i:9180 original size:2 final size:2
Alignment explanation
Indices: 9168--9227 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
9158 TCTATNTCTG
*
9168 TC TC T- TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC GC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
9209 TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC T
9228 ATATATATAT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.00, C:0.48, G:0.02, T:0.50
Consensus pattern (2 bp):
TC
Found at i:16357 original size:17 final size:17
Alignment explanation
Indices: 16320--16383 Score: 58
Period size: 17 Copynumber: 3.7 Consensus size: 17
16310 AAATACTTAA
** *
16320 AAATATTAAGAAATAAA
1 AAATATTAATTAATAAT
16337 AAATATTCAATTAA-AAT
1 AAATATT-AATTAATAAT
*
16354 AAATATTTAAATAATAAT
1 AAATA-TTAATTAATAAT
*
16372 GAATATTAATTA
1 AAATATTAATTA
16384 GAAGTGTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 25 0.66
18 13 0.34
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (17 bp):
AAATATTAATTAATAAT
Found at i:17282 original size:39 final size:39
Alignment explanation
Indices: 17225--17301 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
17215 TAATCAAATT
* * *
17225 GAATTCTTTTAGTGCAATTCCAATTATGTATTACGGGTA
1 GAATTCTTTTAGTACAATTCAAATTATATATTACGGGTA
*
17264 GAATT-TTATTAGTACAATTCAAATTATATTTTACGGGT
1 GAATTCTT-TTAGTACAATTCAAATTATATATTACGGGT
17302 TCTCTGACTC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 2 0.06
39 31 0.94
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (39 bp):
GAATTCTTTTAGTACAATTCAAATTATATATTACGGGTA
Found at i:17457 original size:28 final size:26
Alignment explanation
Indices: 17398--17459 Score: 74
Period size: 24 Copynumber: 2.4 Consensus size: 26
17388 AAGTAACCTT
* *
17398 GAAGAGATTGGTTGAGATTAAAATTG
1 GAAGAGTTTGGTTGAGATTAAAAATG
17424 G--GAGTTTGGTTGAGATTAAAAATG
1 GAAGAGTTTGGTTGAGATTAAAAATG
17448 GTTAAGAGTTTG
1 G--AAGAGTTTG
17460 TCTAAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
24 22 0.73
26 1 0.03
28 7 0.23
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (26 bp):
GAAGAGTTTGGTTGAGATTAAAAATG
Found at i:17493 original size:13 final size:13
Alignment explanation
Indices: 17477--17504 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
17467 TAAAAAGATT
17477 ATATAACATATTA
1 ATATAACATATTA
17490 ATATAACATATTA
1 ATATAACATATTA
17503 AT
1 AT
17505 TAATGAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (13 bp):
ATATAACATATTA
Found at i:17688 original size:6 final size:6
Alignment explanation
Indices: 17672--17710 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
17662 TAATATGTTT
17672 AAATT- AAATTA AAATTA AAATTA AAATTA AAATTA AAAT
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAAT
17711 CTTAAGTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.15
6 28 0.85
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AAATTA
Found at i:19570 original size:11 final size:11
Alignment explanation
Indices: 19556--19593 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
19546 ATTCATAACA
19556 AATTTATAATT
1 AATTTATAATT
19567 AATTTATAATT
1 AATTTATAATT
19578 -ATTTGATAATT
1 AATTT-ATAATT
*
19589 TATTT
1 AATTT
19594 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:25639 original size:25 final size:25
Alignment explanation
Indices: 25593--25642 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
25583 AATAAAATCC
**
25593 ATCGCCTCATAACAGATTGAACAAA
1 ATCGCCTCATAACAGAAAGAACAAA
*
25618 ATCGCCTCATAATAGAAAGAACAAA
1 ATCGCCTCATAACAGAAAGAACAAA
25643 GAGAAAAGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.48, C:0.22, G:0.12, T:0.18
Consensus pattern (25 bp):
ATCGCCTCATAACAGAAAGAACAAA
Found at i:29855 original size:30 final size:27
Alignment explanation
Indices: 29816--29887 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 27
29806 GAGTTTTTTA
29816 CCAAACTATAACATTTCAAAAACTTATTTC
1 CCAAACTATAACATTT---AAACTTATTTC
*
29846 CCAATCTATAACACATTTAAACTTATTTC
1 CCAAACTAT-A-ACATTTAAACTTATTTC
*
29875 TCAAACTATAACA
1 CCAAACTATAACA
29888 AATCATGCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
27 3 0.08
28 1 0.03
29 18 0.49
30 8 0.22
31 1 0.03
32 6 0.16
ACGTcount: A:0.43, C:0.24, G:0.00, T:0.33
Consensus pattern (27 bp):
CCAAACTATAACATTTAAACTTATTTC
Done.