Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012796.1 Corchorus capsularis cultivar CVL-1 contig12817, 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: 17632
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:368 original size:17 final size:17
Alignment explanation
Indices: 343--375 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
333 AAAAGTGAAC
343 CCGAACCCGAACCCGAT
1 CCGAACCCGAACCCGAT
*
360 CCGAGCCCGAACCCGA
1 CCGAACCCGAACCCGA
376 AAATACCCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.48, G:0.21, T:0.03
Consensus pattern (17 bp):
CCGAACCCGAACCCGAT
Found at i:386 original size:16 final size:16
Alignment explanation
Indices: 365--471 Score: 171
Period size: 16 Copynumber: 6.8 Consensus size: 16
355 CCGATCCGAG
365 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
*
381 CCCGAACCCGAAAAAA
1 CCCGAACCCGAAAATA
* *
397 CCCGAACTCGAAAGTA
1 CCCGAACCCGAAAATA
413 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
429 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
*
445 CCCGAACCCG-AAGTA
1 CCCGAACCCGAAAATA
460 CCCGAACCCGAA
1 CCCGAACCCGAA
472 CCCGCCCGAA
Statistics
Matches: 83, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
15 14 0.17
16 69 0.83
ACGTcount: A:0.41, C:0.38, G:0.15, T:0.06
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:392 original size:6 final size:6
Alignment explanation
Indices: 339--376 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
329 TATCAAAAGT
* *
339 GAACCC GAACCC GAACCC G-ATCC GAGCCC GAACCC GAA
1 GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAA
377 AATACCCGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.32, C:0.45, G:0.21, T:0.03
Consensus pattern (6 bp):
GAACCC
Found at i:480 original size:31 final size:32
Alignment explanation
Indices: 365--485 Score: 145
Period size: 32 Copynumber: 3.8 Consensus size: 32
355 CCGATCCGAG
* *
365 CCCGAACCCGAAAATACCCGAACCCGAAAAAA
1 CCCGAACCCGAAAACACCCGAACCCGAAAATA
* **
397 CCCGAACTCGAAAGTACCCGAACCCGAAAATA
1 CCCGAACCCGAAAACACCCGAACCCGAAAATA
* *
429 CCCGAACCCGAAAATACCCGAACCCG-AAGTA
1 CCCGAACCCGAAAACACCCGAACCCGAAAATA
** *
460 CCCGAACCCGAACCCGCCCGAACCCG
1 CCCGAACCCGAAAACACCCGAACCCG
486 CCCAATTGCC
Statistics
Matches: 79, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
31 26 0.33
32 53 0.67
ACGTcount: A:0.38, C:0.41, G:0.16, T:0.05
Consensus pattern (32 bp):
CCCGAACCCGAAAACACCCGAACCCGAAAATA
Found at i:663 original size:2 final size:2
Alignment explanation
Indices: 656--688 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
646 CATGGCCTAA
656 AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
689 TTGTACTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1305 original size:15 final size:16
Alignment explanation
Indices: 1285--1314 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1275 GCCATTACCG
1285 AATTAATCAC-TAATT
1 AATTAATCACATAATT
1300 AATTAATCACATAAT
1 AATTAATCACATAAT
1315 GGAACTTGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (16 bp):
AATTAATCACATAATT
Found at i:5465 original size:15 final size:15
Alignment explanation
Indices: 5427--5495 Score: 77
Period size: 15 Copynumber: 4.6 Consensus size: 15
5417 ACTCTCCTTG
* *
5427 CTGGGCCTACAGTTG
1 CTGGGCCTGCAGTTT
*
5442 CTGGGCCTGTAGTTT
1 CTGGGCCTGCAGTTT
*
5457 CTGGGCCTGCATTTT
1 CTGGGCCTGCAGTTT
*
5472 CT-GGCACTGCATTTT
1 CTGGGC-CTGCAGTTT
5487 CTGGGCCTG
1 CTGGGCCTG
5496 GATTATCTTC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
14 3 0.06
15 41 0.87
16 3 0.06
ACGTcount: A:0.09, C:0.26, G:0.30, T:0.35
Consensus pattern (15 bp):
CTGGGCCTGCAGTTT
Found at i:6350 original size:26 final size:26
Alignment explanation
Indices: 6308--6372 Score: 103
Period size: 26 Copynumber: 2.4 Consensus size: 26
6298 TTAATTCTTC
6308 TTTATTACTCACTTACTATACGAATTAA
1 TTTATTA-T-ACTTACTATACGAATTAA
*
6336 TTTATTATACTTACTATACTAATTAA
1 TTTATTATACTTACTATACGAATTAA
6362 TTTATTATACT
1 TTTATTATACT
6373 GTTTTTGCTT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
26 28 0.78
27 1 0.03
28 7 0.19
ACGTcount: A:0.35, C:0.14, G:0.02, T:0.49
Consensus pattern (26 bp):
TTTATTATACTTACTATACGAATTAA
Found at i:10026 original size:3 final size:3
Alignment explanation
Indices: 10014--10059 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
10004 TCTGACATTC
10014 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
10060 ATATAATATA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:10137 original size:15 final size:15
Alignment explanation
Indices: 10117--10152 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
10107 TTTTAGGTCT
10117 TTTGCATTTCTTTTA
1 TTTGCATTTCTTTTA
10132 TTTGCATTTCTTTTA
1 TTTGCATTTCTTTTA
10147 TTTGCA
1 TTTGCA
10153 AGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.08, T:0.64
Consensus pattern (15 bp):
TTTGCATTTCTTTTA
Found at i:16785 original size:5 final size:5
Alignment explanation
Indices: 16777--16810 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
16767 TATTTTCTCC
*
16777 TTTTA TTTT- TTCTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
16811 CTAATCCTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
4 3 0.12
5 23 0.88
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:16789 original size:15 final size:14
Alignment explanation
Indices: 16763--16810 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
16753 GGGCCTAGAA
*
16763 ATTTTATTTTCTC-
1 ATTTTATTTTTTCT
*
16776 CTTTTATTTTTTCT
1 ATTTTATTTTTTCT
*
16790 ATTTTATTTTATTTT
1 ATTTTATTTT-TTCT
16805 ATTTTA
1 ATTTTA
16811 CTAATCCTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 11 0.38
14 9 0.31
15 9 0.31
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (14 bp):
ATTTTATTTTTTCT
Done.