Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006941.1 Corchorus capsularis cultivar CVL-1 contig06962, 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: 40135
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:849 original size:11 final size:11
Alignment explanation
Indices: 801--855 Score: 60
Period size: 11 Copynumber: 5.1 Consensus size: 11
791 AACATTTTTC
*
801 TATATAAATAT
1 TATAAAAATAT
*
812 TA-AAATAAAAT
1 TATAAA-AATAT
*
823 TATGAAAATA-
1 TATAAAAATAT
833 TATAAAAATAT
1 TATAAAAATAT
844 TATAAAAATAT
1 TATAAAAATAT
855 T
1 T
856 TTAATATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
10 11 0.31
11 23 0.64
12 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (11 bp):
TATAAAAATAT
Found at i:2664 original size:33 final size:33
Alignment explanation
Indices: 2627--2694 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
2617 GTACAATGGC
2627 ATTTTAGAAATATATTTGACAAGTAAGGGTATA
1 ATTTTAGAAATATATTTGACAAGTAAGGGTATA
2660 ATTTTAGAAATATATTTGACAAGTAAGGGTATA
1 ATTTTAGAAATATATTTGACAAGTAAGGGTATA
2693 AT
1 AT
2695 GGGCGATTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.43, C:0.03, G:0.18, T:0.37
Consensus pattern (33 bp):
ATTTTAGAAATATATTTGACAAGTAAGGGTATA
Found at i:2769 original size:60 final size:60
Alignment explanation
Indices: 2676--2796 Score: 215
Period size: 60 Copynumber: 2.0 Consensus size: 60
2666 GAAATATATT
*
2676 TGACAAGTAAGGGTATAATGGGCGATTCAAAAGTTTTACAGGTGAACGTAGTTTTTAATA
1 TGACAAGTAAGGGTATAATGGACGATTCAAAAGTTTTACAGGTGAACGTAGTTTTTAATA
* *
2736 TGACATGTAAGGGTATAATGGACGATTCAAAAGTTTTACAGGTGAACGTATTTTTTAATA
1 TGACAAGTAAGGGTATAATGGACGATTCAAAAGTTTTACAGGTGAACGTAGTTTTTAATA
2796 T
1 T
2797 AGTATAGATA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.34
Consensus pattern (60 bp):
TGACAAGTAAGGGTATAATGGACGATTCAAAAGTTTTACAGGTGAACGTAGTTTTTAATA
Found at i:7743 original size:64 final size:66
Alignment explanation
Indices: 7642--7773 Score: 214
Period size: 64 Copynumber: 2.0 Consensus size: 66
7632 GTCTAGATAA
* *
7642 GGTCTTCATCAGTGTGCTTCTCGGGAGATCGAAATTATGTTCTCACC-T-TTGTTGGGATAAAAG
1 GGTCTTCATCAGTATGCTTCTCAGGAGATCGAAATTATGTTCTCACCTTGTTGTTGGGATAAAAG
7705 C
66 C
*
7706 GGTCTTCATCAGTATGTTTCTCAGGAGATCGAAATTATGTTCTCACCTTTGTTGTTGGGATAAAA
1 GGTCTTCATCAGTATGCTTCTCAGGAGATCGAAATTATGTTCTCACC-TTGTTGTTGGGATAAAA
7771 GC
65 GC
7773 G
1 G
7774 CTACGCCTAC
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
64 44 0.71
66 1 0.02
67 17 0.27
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (66 bp):
GGTCTTCATCAGTATGCTTCTCAGGAGATCGAAATTATGTTCTCACCTTGTTGTTGGGATAAAAG
C
Found at i:12185 original size:31 final size:32
Alignment explanation
Indices: 12147--12208 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 32
12137 CAAAAATGAT
* *
12147 ACAAAATCCATTTGAATA-GAGAACTTCTAGC
1 ACAAAATCCATTTAAAAATGAGAACTTCTAGC
12178 ACAAAATCCATTTAAAAATGAGAACTTCTAG
1 ACAAAATCCATTTAAAAATGAGAACTTCTAG
12209 ATGGACAGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 16 0.57
32 12 0.43
ACGTcount: A:0.45, C:0.18, G:0.11, T:0.26
Consensus pattern (32 bp):
ACAAAATCCATTTAAAAATGAGAACTTCTAGC
Found at i:24393 original size:16 final size:16
Alignment explanation
Indices: 24372--24447 Score: 70
Period size: 16 Copynumber: 4.9 Consensus size: 16
24362 CGTAATTTCA
*
24372 TATATAGTATATATAG
1 TATATAGTATAGATAG
24388 TATATAGTATAGATAG
1 TATATAGTATAGATAG
*
24404 ATAGATAG-ATAGATAG
1 -TATATAGTATAGATAG
*
24420 ATAGATAG-ATAGATAG
1 -TATATAGTATAGATAG
*
24436 -ATAGA-TATAGAT
1 TATATAGTATAGAT
24448 GAATGAGGAA
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
14 9 0.17
16 39 0.72
17 6 0.11
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (16 bp):
TATATAGTATAGATAG
Found at i:24403 original size:4 final size:4
Alignment explanation
Indices: 24391--24442 Score: 95
Period size: 4 Copynumber: 12.8 Consensus size: 4
24381 TATATAGTAT
24391 ATAG TATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG -ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
24440 ATA
1 ATA
24443 TAGATGAATG
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
4 43 0.91
5 4 0.09
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (4 bp):
ATAG
Found at i:26692 original size:36 final size:36
Alignment explanation
Indices: 26618--26692 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 36
26608 AATAAAAATT
* *
26618 AAAAAAATCAATTTTCCTTTTTTTTCCTTTTTTCAA
1 AAAAAAAACAATTTTCCTTTTTTTTACTTTTTTCAA
* * *
26654 AAAAAAAACGATTTT-CTTTTTTTTATTTGTTTTGAA
1 AAAAAAAACAATTTTCCTTTTTTTTACTT-TTTTCAA
26690 AAA
1 AAA
26693 TATTTAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
35 11 0.33
36 22 0.67
ACGTcount: A:0.35, C:0.11, G:0.04, T:0.51
Consensus pattern (36 bp):
AAAAAAAACAATTTTCCTTTTTTTTACTTTTTTCAA
Found at i:28799 original size:9 final size:7
Alignment explanation
Indices: 28765--28792 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
28755 ATTATACACC
28765 GAGAGAG
1 GAGAGAG
28772 GAGAGAG
1 GAGAGAG
28779 GAGAGAG
1 GAGAGAG
28786 GAGAGAG
1 GAGAGAG
28793 TCGAGAGTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (7 bp):
GAGAGAG
Found at i:30508 original size:3 final size:3
Alignment explanation
Indices: 30496--30525 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
30486 TTTTTACTTT
30496 TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
30526 AATATAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:30606 original size:7 final size:7
Alignment explanation
Indices: 30594--30621 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
30584 CTTATGTCAA
30594 TGGCAAT
1 TGGCAAT
30601 TGGCAAT
1 TGGCAAT
30608 TGGCAAT
1 TGGCAAT
30615 TGGCAAT
1 TGGCAAT
30622 GCCCCCTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (7 bp):
TGGCAAT
Found at i:31417 original size:3 final size:3
Alignment explanation
Indices: 31409--31439 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
31399 ATAAGACTTG
31409 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
31440 ACTCTATACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:39777 original size:11 final size:11
Alignment explanation
Indices: 39761--39803 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
39751 TATACTATAT
39761 CTAATTAATAG
1 CTAATTAATAG
*
39772 CTAATTAATAT
1 CTAATTAATAG
39783 CTAATTAATAG
1 CTAATTAATAG
*
39794 TTAATTAATA
1 CTAATTAATA
39804 ATGAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:39785 original size:22 final size:22
Alignment explanation
Indices: 39757--39803 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
39747 CTATTATACT
39757 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAGCTAATTA
*
39779 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGCTAATTA
39801 ATA
1 ATA
39804 ATGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAATTA
Done.