Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012560.1 Corchorus capsularis cultivar CVL-1 contig12581, 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: 20849
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:530 original size:28 final size:28
Alignment explanation
Indices: 490--557 Score: 127
Period size: 28 Copynumber: 2.4 Consensus size: 28
480 TGAACAATGC
*
490 ATGAAGCTATGATTCTATTAATGACTAA
1 ATGAAACTATGATTCTATTAATGACTAA
518 ATGAAACTATGATTCTATTAATGACTAA
1 ATGAAACTATGATTCTATTAATGACTAA
546 ATGAAACTATGA
1 ATGAAACTATGA
558 AGTGTATGTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (28 bp):
ATGAAACTATGATTCTATTAATGACTAA
Found at i:8421 original size:23 final size:22
Alignment explanation
Indices: 8395--8439 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
8385 TTTTCAAGTG
8395 TTTAAATAGTGCGATT-AGGGTTT
1 TTTAAATA-T-CGATTAAGGGTTT
*
8418 TTTAATTATCGATTAAGGGTTT
1 TTTAAATATCGATTAAGGGTTT
8440 AAAGTGTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 8 0.40
23 7 0.35
ACGTcount: A:0.27, C:0.04, G:0.22, T:0.47
Consensus pattern (22 bp):
TTTAAATATCGATTAAGGGTTT
Found at i:9506 original size:81 final size:81
Alignment explanation
Indices: 9371--9548 Score: 252
Period size: 81 Copynumber: 2.2 Consensus size: 81
9361 GGTCATGTTG
* * * * *
9371 GGGCTGATGAGGAG-TTAAATGAGGAAGTTAATGTGGAAGAAGTGGTTGGTGATGTTTTTTCTGA
1 GGGCTGGTGAGG-GTTTAAATGAGGAAGTAAATGTGCAAGAAGGGGTGGGTGATGTTTTTTCTGA
*
9435 GCATATTGAAGA-TGTAC
65 CCATATTGAAGAGT-TAC
*
9452 GGGCTGGTGAGGGTTTAAATGAGGAAGTAAATGTGCAAGAAGGGGTGGGTGATGTTTTTTCTGTC
1 GGGCTGGTGAGGGTTTAAATGAGGAAGTAAATGTGCAAGAAGGGGTGGGTGATGTTTTTTCTGAC
9517 CATATTGAAGAGTTAC
66 CATATTGAAGAGTTAC
9533 GGGCTGGTGAAGGGTT
1 GGGCTGGTG-AGGGTT
9549 GCATGATGGT
Statistics
Matches: 87, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
80 1 0.01
81 79 0.91
82 7 0.08
ACGTcount: A:0.26, C:0.06, G:0.37, T:0.31
Consensus pattern (81 bp):
GGGCTGGTGAGGGTTTAAATGAGGAAGTAAATGTGCAAGAAGGGGTGGGTGATGTTTTTTCTGAC
CATATTGAAGAGTTAC
Found at i:13525 original size:16 final size:17
Alignment explanation
Indices: 13504--13547 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
13494 AGATTAGATC
13504 TCCTTTTATTTC-GATT
1 TCCTTTTATTTCTGATT
*
13520 TCCTTTTTTTTCTGATT
1 TCCTTTTATTTCTGATT
*
13537 TCTTTTTATTT
1 TCCTTTTATTT
13548 GGGCGGGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.09, C:0.16, G:0.05, T:0.70
Consensus pattern (17 bp):
TCCTTTTATTTCTGATT
Found at i:13536 original size:17 final size:16
Alignment explanation
Indices: 13504--13543 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
13494 AGATTAGATC
*
13504 TCCTTTTATTTCGATT
1 TCCTTTTTTTTCGATT
13520 TCCTTTTTTTTCTGATT
1 TCCTTTTTTTTC-GATT
13537 T-CTTTTT
1 TCCTTTTT
13544 ATTTGGGCGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.07, C:0.17, G:0.05, T:0.70
Consensus pattern (16 bp):
TCCTTTTTTTTCGATT
Found at i:17448 original size:58 final size:60
Alignment explanation
Indices: 17378--17496 Score: 199
Period size: 58 Copynumber: 2.0 Consensus size: 60
17368 CTATTTGTCC
17378 TTTAACATTTGTTCATATATAAATATACT-GTTAAATGTT-G-TGTGTGTGTGTGTGTGTG
1 TTTAACATTTGTTCATATATAAATATA-TAGTTAAATGTTGGCTGTGTGTGTGTGTGTGTG
*
17436 TTTAACATTTGTTCATATATAAATATATAGTTAAATGTTGGCTTTGTGTGTGTGTGTGTG
1 TTTAACATTTGTTCATATATAAATATATAGTTAAATGTTGGCTGTGTGTGTGTGTGTGTG
17496 T
1 T
17497 GTGTGTGTGT
Statistics
Matches: 57, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
57 1 0.02
58 37 0.65
59 1 0.02
60 18 0.32
ACGTcount: A:0.24, C:0.05, G:0.22, T:0.49
Consensus pattern (60 bp):
TTTAACATTTGTTCATATATAAATATATAGTTAAATGTTGGCTGTGTGTGTGTGTGTGTG
Found at i:17487 original size:2 final size:2
Alignment explanation
Indices: 17480--17520 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
17470 ATGTTGGCTT
17480 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
17521 TTAACATTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:17551 original size:84 final size:84
Alignment explanation
Indices: 17416--17588 Score: 346
Period size: 84 Copynumber: 2.1 Consensus size: 84
17406 TGTTAAATGT
17416 TGTGTGTGTGTGTGTGTGTGTTTAACATTTGTTCATATATAAATATATAGTTAAATGTTGGCTTT
1 TGTGTGTGTGTGTGTGTGTGTTTAACATTTGTTCATATATAAATATATAGTTAAATGTTGGCTTT
17481 GTGTGTGTGTGTGTGTGTG
66 GTGTGTGTGTGTGTGTGTG
17500 TGTGTGTGTGTGTGTGTGTGTTTAACATTTGTTCATATATAAATATATAGTTAAATGTTGGCTTT
1 TGTGTGTGTGTGTGTGTGTGTTTAACATTTGTTCATATATAAATATATAGTTAAATGTTGGCTTT
17565 GTGTGTGTGTGTGTGTGTG
66 GTGTGTGTGTGTGTGTGTG
17584 TGTGT
1 TGTGT
17589 TTGAAACTAA
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 89 1.00
ACGTcount: A:0.17, C:0.03, G:0.30, T:0.49
Consensus pattern (84 bp):
TGTGTGTGTGTGTGTGTGTGTTTAACATTTGTTCATATATAAATATATAGTTAAATGTTGGCTTT
GTGTGTGTGTGTGTGTGTG
Found at i:17571 original size:2 final size:2
Alignment explanation
Indices: 17564--17588 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17554 ATGTTGGCTT
17564 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
17589 TTGAAACTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:17676 original size:12 final size:13
Alignment explanation
Indices: 17657--17690 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
17647 GATCGATACC
17657 TCGATATATCC-A
1 TCGATATATCCGA
*
17669 TTGATATATCCGA
1 TCGATATATCCGA
17682 TCGATATAT
1 TCGATATAT
17691 GTATCGATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (13 bp):
TCGATATATCCGA
Done.