Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001274.1 Corchorus capsularis cultivar CVL-1 contig01274, 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: 8807
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32
Found at i:2638 original size:19 final size:20
Alignment explanation
Indices: 2616--2672 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 20
2606 CTAAATAATA
2616 TTTTAATTATTCCATTATTT
1 TTTTAATTATTCCATTATTT
* **
2636 TTTTAATCA-TAAATTATTT
1 TTTTAATTATTCCATTATTT
2655 TTTTAATTATTCC-TTATT
1 TTTTAATTATTCCATTATT
2673 AAATTTTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 21 0.70
20 9 0.30
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTAATTATTCCATTATTT
Found at i:2664 original size:12 final size:12
Alignment explanation
Indices: 2645--2698 Score: 56
Period size: 12 Copynumber: 4.2 Consensus size: 12
2635 TTTTTAATCA
2645 TAAATTATTTTT
1 TAAATTATTTTT
*
2657 TTAATTATTCCTTAT
1 TAAATTATT--TT-T
2672 TAAATT-TTTTT
1 TAAATTATTTTT
2683 TAAAATTATTTTT
1 T-AAATTATTTTT
2696 TAA
1 TAA
2699 TCATAATTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
11 2 0.06
12 17 0.49
13 6 0.17
14 4 0.11
15 6 0.17
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (12 bp):
TAAATTATTTTT
Found at i:2774 original size:22 final size:22
Alignment explanation
Indices: 2746--2851 Score: 90
Period size: 22 Copynumber: 4.7 Consensus size: 22
2736 TGTCTCTATG
2746 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
2768 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* *
2791 -GGTTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
2812 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAAGA
*
2834 TCAGGTTATTAAAATTTC
1 T--GGTTATCAAAATTTC
2852 TTAGGTTGAT
Statistics
Matches: 64, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
20 1 0.02
22 46 0.72
23 4 0.06
24 13 0.20
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:2826 original size:44 final size:43
Alignment explanation
Indices: 2747--2833 Score: 104
Period size: 44 Copynumber: 2.0 Consensus size: 43
2737 GTCTCTATGT
* ** *
2747 GGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGGA
1 GGTTATCAAAATTCCATAAGATGGTTACCAAAATTTCAT-AGGA
*
2791 GGTTATCAAAATTCCAT-AGTGTGGTTACCAAAATTTCATAGGA
1 GGTTATCAAAATTCCATAAG-ATGGTTACCAAAATTTCATAGGA
2834 TCAGGTTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
43 6 0.16
44 31 0.84
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (43 bp):
GGTTATCAAAATTCCATAAGATGGTTACCAAAATTTCATAGGA
Found at i:2945 original size:22 final size:21
Alignment explanation
Indices: 2917--3290 Score: 127
Period size: 22 Copynumber: 16.9 Consensus size: 21
2907 TGTTATCAAA
*
2917 GAGGTTATCAAAATGTCATAG
1 GAGGTTATCAAAATTTCATAG
2938 CGAGGTTAT-AAGAATTTCATAG
1 -GAGGTTATCAA-AATTTCATAG
* *
2960 TGTGGTTAACAAAATTTCATTAG
1 -GAGGTTATCAAAATTTCA-TAG
* * *
2983 AAGGTTA-CTAATATTTCATGGG
1 GAGGTTATC-AAAATTTCAT-AG
3005 GAGGTTATCAAAATTTCATATG
1 GAGGTTATCAAAATTTCATA-G
* *
3027 AAGGTTATAAAAGTCTCAATTTCATA-
1 GAGGTTAT-CAA-----AATTTCATAG
* * *
3053 -AGGAGTACCAAAATTTGATAG
1 GAGG-TTATCAAAATTTCATAG
* * *
3074 AAGGTTAT-TAAATCTCATA-
1 GAGGTTATCAAAATTTCATAG
*
3093 GAGTGATTATCGAAATTTCATAG
1 GAG-G-TTATCAAAATTTCATAG
* * *
3116 AAATCAGATTATCGAAATTT-ATAG
1 ----GAGGTTATCAAAATTTCATAG
*
3140 GAAGATTATCAAAATTTCATAG
1 G-AGGTTATCAAAATTTCATAG
** *
3162 CGTTGTTATCAAAATTTCAAAG
1 -GAGGTTATCAAAATTTCATAG
* *
3184 CGAGGTTATCAAAATTACATAAT
1 -GAGGTTATCAAAATTTCAT-AG
* *
3207 GTGATTAT-AAGAATTTCATAAAG
1 GAGGTTATCAA-AATTTCAT--AG
* * * *
3230 G-GGTCAACAAAATTTGATAAA
1 GAGGTTATCAAAATTTCAT-AG
*
3251 GAGGTTATCAAAATTTCATAAA
1 GAGGTTATCAAAATTTCAT-AG
* *
3273 GAGGTTGTCAAATTTTCA
1 GAGGTTATCAAAATTTCA
3291 AAATGTGATT
Statistics
Matches: 268, Mismatches: 52, Indels: 64
0.70 0.14 0.17
Matches are distributed among these distances:
19 2 0.01
20 17 0.06
21 29 0.11
22 171 0.64
23 15 0.06
24 4 0.01
25 17 0.06
26 2 0.01
27 2 0.01
28 9 0.03
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (21 bp):
GAGGTTATCAAAATTTCATAG
Found at i:3130 original size:25 final size:22
Alignment explanation
Indices: 3083--3161 Score: 79
Period size: 21 Copynumber: 3.5 Consensus size: 22
3073 GAAGGTTATT
* **
3083 AAATCTCATAGAGTGATTATCG
1 AAATTTCATAGAAAGATTATCG
3105 AAATTTCATAGAAATCAGATTATCG
1 AAATTTCATAG-AA--AGATTATCG
* *
3130 AAATTT-ATAGGAAGATTATCA
1 AAATTTCATAGAAAGATTATCG
3151 AAATTTCATAG
1 AAATTTCATAG
3162 CGTTGTTATC
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
21 14 0.29
22 14 0.29
23 2 0.04
24 4 0.08
25 14 0.29
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (22 bp):
AAATTTCATAGAAAGATTATCG
Found at i:3241 original size:44 final size:43
Alignment explanation
Indices: 3149--3314 Score: 111
Period size: 44 Copynumber: 3.8 Consensus size: 43
3139 GGAAGATTAT
** * * *
3149 CAAAATTTCATAGCGTTG-TTATCAAAATTTCA-AAGCGAGGTTAT
1 CAAAATTTCATAATG-TGATTAT-AAAATTTCATAA-AGAGGTCAA
* *
3193 CAAAATTACATAATGTGATTATAAGAATTTCATAAAGGGGTCAA
1 CAAAATTTCATAATGTGATTATAA-AATTTCATAAAGAGGTCAA
* * * * ***
3237 CAAAATTTGATAAAGAGGTTATCAAAATTTCATAAAGAGGTTGT
1 CAAAATTTCATAATGTGATTAT-AAAATTTCATAAAGAGGTCAA
* * *
3281 CAAATTTTCAAAATGTGATTACAAAAATTTCATA
1 CAAAATTTCATAATGTGATTA-TAAAATTTCATA
3315 GTGGTATTTC
Statistics
Matches: 94, Mismatches: 23, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
43 4 0.04
44 86 0.91
45 4 0.04
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (43 bp):
CAAAATTTCATAATGTGATTATAAAATTTCATAAAGAGGTCAA
Found at i:3488 original size:44 final size:45
Alignment explanation
Indices: 3396--3625 Score: 146
Period size: 44 Copynumber: 5.3 Consensus size: 45
3386 TTATGAAGTA
** * * * * *
3396 ATCAAAATTTCATA-AGAGGGCTATCACAATTTCATAGT-ATGTAG
1 ATCAAAATTTCATAGAGAAAGTTATCAAAAATTCATAGTGAGGT-T
* *
3440 ATCAAAATTTCATAGAGAAA-TTAACAAAAATTCATAATGAGGTT
1 ATCAAAATTTCATAGAGAAAGTTATCAAAAATTCATAGTGAGGTT
** * *
3484 ATCAAAAAATCATAG-GGAGGTTATC-AAAATT--T-GT-A-GTT
1 ATCAAAATTTCATAGAGAAAGTTATCAAAAATTCATAGTGAGGTT
* * *
3522 AT-AAAGATTTCATA-AGAAAGTTATCAAAATTTTATAGGGAGGTTT
1 ATCAAA-ATTTCATAGAGAAAGTTATCAAAAATTCATAGTGAGG-TT
* * *
3567 ATCAAAATTT-ATAG-GAAGATTTATCAAAATTTCATAGTGATGTT
1 ATCAAAATTTCATAGAGAA-AGTTATCAAAAATTCATAGTGAGGTT
*
3611 ATCACAATTTCATAG
1 ATCAAAATTTCATAG
3626 TGTGGTTATC
Statistics
Matches: 144, Mismatches: 26, Indels: 31
0.72 0.13 0.15
Matches are distributed among these distances:
37 3 0.02
38 19 0.13
39 6 0.04
40 1 0.01
41 2 0.01
42 1 0.01
43 9 0.06
44 62 0.43
45 38 0.26
46 3 0.02
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (45 bp):
ATCAAAATTTCATAGAGAAAGTTATCAAAAATTCATAGTGAGGTT
Found at i:3553 original size:22 final size:22
Alignment explanation
Indices: 3391--3624 Score: 87
Period size: 22 Copynumber: 10.9 Consensus size: 22
3381 TTTTATTATG
*
3391 AAGTAATCAAAATTTCATAAGA
1 AAGTTATCAAAATTTCATAAGA
** * * *
3413 GGGCTATCACAATTTCAT-AGT
1 AAGTTATCAAAATTTCATAAGA
* *
3434 ATGTAGATCAAAATTTCATAGAGA
1 AAGT-TATCAAAATTTCATA-AGA
* *
3458 AA-TTAACAAAAATTCATAATG-
1 AAGTTATCAAAATTTCATAA-GA
* ** * *
3479 AGGTTATCAAAAAATCATAGGG
1 AAGTTATCAAAATTTCATAAGA
*
3501 AGGTTATCAAAA-TT--T--G-
1 AAGTTATCAAAATTTCATAAGA
*
3517 TAGTTAT-AAAGATTTCATAAGA
1 AAGTTATCAAA-ATTTCATAAGA
* * *
3539 AAGTTATCAAAATTTTATAGGG
1 AAGTTATCAAAATTTCATAAGA
* *
3561 AGGTTTATCAAAATTT-ATAGGA
1 AAG-TTATCAAAATTTCATAAGA
* *
3583 AGATTTATCAAAATTTCAT-AGTG
1 A-AGTTATCAAAATTTCATAAG-A
* *
3606 ATGTTATCACAATTTCATA
1 AAGTTATCAAAATTTCATA
3625 GTGTGGTTAT
Statistics
Matches: 157, Mismatches: 36, Indels: 37
0.68 0.16 0.16
Matches are distributed among these distances:
15 3 0.02
16 6 0.04
17 3 0.02
19 2 0.01
21 8 0.05
22 113 0.72
23 19 0.12
24 3 0.02
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (22 bp):
AAGTTATCAAAATTTCATAAGA
Found at i:3581 original size:82 final size:83
Alignment explanation
Indices: 3446--3598 Score: 186
Period size: 82 Copynumber: 1.9 Consensus size: 83
3436 GTAGATCAAA
* *
3446 ATTTCATAGAGAAATTAACAAAAATTCATAATGAGGTTATCAAAAAATCATAGGGAG-GTTATCA
1 ATTTCATAGAGAAATTAACAAAAATTCATAAGGAGGTTATCAAAAAATCATAGGAAGAGTTATCA
3510 AAATTTGTAGTTATAAAG
66 AAATTTGTAGTTATAAAG
* * * * * * *
3528 ATTTCATA-AGAAAGTTATCAAAATTTTATAGGGAGGTTTATC-AAAATTTATAGGAAGATTTAT
1 ATTTCATAGAGAAA-TTAACAAAAATTCATAAGGAGG-TTATCAAAAAATCATAGGAAGAGTTAT
3591 CAAAATTT
64 CAAAATTT
3599 CATAGTGATG
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
81 5 0.08
82 37 0.63
83 17 0.29
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.34
Consensus pattern (83 bp):
ATTTCATAGAGAAATTAACAAAAATTCATAAGGAGGTTATCAAAAAATCATAGGAAGAGTTATCA
AAATTTGTAGTTATAAAG
Found at i:3625 original size:22 final size:22
Alignment explanation
Indices: 3541--3802 Score: 108
Period size: 22 Copynumber: 11.8 Consensus size: 22
3531 TCATAAGAAA
* * *
3541 GTTATCAAAATTTTATAGGGAG
1 GTTATCAAAATTTCATAGTGTG
*
3563 GTTTATCAAAATTT-ATAG-GAAG
1 G-TTATCAAAATTTCATAGTG-TG
*
3585 ATTTATCAAAATTTCATAGTGAT-
1 -GTTATCAAAATTTCATAGTG-TG
*
3608 GTTATCACAATTTCATAGTGTG
1 GTTATCAAAATTTCATAGTGTG
*
3630 GTTATCAAAATTTCAAAGTGTG
1 GTTATCAAAATTTCATAGTGTG
* *
3652 ATT-TACTAACAA-TTCATA-TGGAG
1 GTTAT-C-AA-AATTTCATAGT-GTG
* * * ***
3675 GTTTTTAAATTTTCATAACCTG
1 GTTATCAAAATTTCATAGTGTG
* * *
3697 GTTATCAATATATCATA-TGGAG
1 GTTATCAAAATTTCATAGT-GTG
* *
3719 GTTATCAACATCTCATAGTGTTG
1 GTTATCAAAATTTCATAGTG-TG
* * * *
3742 GTTATTAAAATTTTATATTGAG
1 GTTATCAAAATTTCATAGTGTG
* * * *
3764 GTCT-TCAAAATTGCTTAGGGAG
1 GT-TATCAAAATTTCATAGTGTG
*
3786 GTTAACAAAATTTCATA
1 GTTATCAAAATTTCATA
3803 AAAAAGATTA
Statistics
Matches: 181, Mismatches: 41, Indels: 36
0.70 0.16 0.14
Matches are distributed among these distances:
21 5 0.03
22 126 0.70
23 45 0.25
24 5 0.03
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGTGTG
Found at i:3835 original size:12 final size:12
Alignment explanation
Indices: 3800--3840 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
3790 ACAAAATTTC
3800 ATAAAAAAGATT
1 ATAAAAAAGATT
3812 A-AAAAAA-ATT
1 ATAAAAAAGATT
*
3822 ATAAAAAAGGTT
1 ATAAAAAAGATT
3834 ATCAAAA
1 AT-AAAA
3841 TTCCATAGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
10 4 0.16
11 12 0.48
12 5 0.20
13 4 0.16
ACGTcount: A:0.68, C:0.02, G:0.07, T:0.22
Consensus pattern (12 bp):
ATAAAAAAGATT
Found at i:3840 original size:22 final size:23
Alignment explanation
Indices: 3784--3840 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
3774 TTGCTTAGGG
*
3784 AGGTTAACAAAATTTCATAAAAA
1 AGGTTAACAAAAATTCATAAAAA
* *
3807 AGATTAAAAAAAATT-ATAAAAA
1 AGGTTAACAAAAATTCATAAAAA
*
3829 AGGTTATCAAAA
1 AGGTTAACAAAA
3841 TTCCATAGCA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 16 0.57
23 12 0.43
ACGTcount: A:0.61, C:0.05, G:0.09, T:0.25
Consensus pattern (23 bp):
AGGTTAACAAAAATTCATAAAAA
Found at i:3884 original size:22 final size:22
Alignment explanation
Indices: 3828--3891 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
3818 AATTATAAAA
*
3828 AAGGTTATCAAAATTCCATAGC
1 AAGGTTATCAAAATTTCATAGC
** * * *
3850 ATCGTTGTTAAAATTTCATAGG
1 AAGGTTATCAAAATTTCATAGC
3872 AAGGTTATCAAAATTTCATA
1 AAGGTTATCAAAATTTCATA
3892 ATAGGATCAT
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.34
Consensus pattern (22 bp):
AAGGTTATCAAAATTTCATAGC
Found at i:6867 original size:27 final size:29
Alignment explanation
Indices: 6816--6878 Score: 94
Period size: 27 Copynumber: 2.2 Consensus size: 29
6806 ACTACGTGAC
* *
6816 TTTTTAAATAATTTTTTTATTATTTTTTA
1 TTTTTAAATAACTTTTTTATTATTTTTAA
6845 TTTTTAAA-AACTTTTTTA-TATTTTTAA
1 TTTTTAAATAACTTTTTTATTATTTTTAA
6872 TTTTTAA
1 TTTTTAA
6879 TATTTTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 15 0.47
28 9 0.28
29 8 0.25
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (29 bp):
TTTTTAAATAACTTTTTTATTATTTTTAA
Found at i:6875 original size:16 final size:16
Alignment explanation
Indices: 6856--6887 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
6846 TTTTAAAAAC
*
6856 TTTTTTATATTTTTAA
1 TTTTTAATATTTTTAA
6872 TTTTTAATATTTTTAA
1 TTTTTAATATTTTTAA
6888 ACCCGCTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTAATATTTTTAA
Found at i:6930 original size:31 final size:31
Alignment explanation
Indices: 6892--6952 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
6882 TTTTAAACCC
6892 GCTCAAATAGGTACTAAACGTTTCAAAATTG
1 GCTCAAATAGGTACTAAACGTTTCAAAATTG
6923 GCTCAAATAGGTACTAAACGTTTCAAAATT
1 GCTCAAATAGGTACTAAACGTTTCAAAATT
6953 AGATCAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (31 bp):
GCTCAAATAGGTACTAAACGTTTCAAAATTG
Done.