Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016025.1 Corchorus capsularis cultivar CVL-1 contig16046, 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: 24604
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:2493 original size:23 final size:23
Alignment explanation
Indices: 2463--2508 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
2453 AATTTGATTG
*
2463 AAGGCTCCAGAATAGCTAGTATT
1 AAGGCTCCAGAAGAGCTAGTATT
*
2486 AAGGCTCCGGAAGAGCTAGTATT
1 AAGGCTCCAGAAGAGCTAGTATT
2509 GTTTTATCTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (23 bp):
AAGGCTCCAGAAGAGCTAGTATT
Found at i:12589 original size:31 final size:32
Alignment explanation
Indices: 12554--12620 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
12544 AACTTTATGT
* *
12554 TTTCCGATTATA-CCCTTATTTTTAAAATATA
1 TTTCCAATTATATCCCTTATTTTTAAAACATA
* * *
12585 TTTCCAATTGTATCCTTTTTTTTTAAAACATA
1 TTTCCAATTATATCCCTTATTTTTAAAACATA
12617 TTTC
1 TTTC
12621 TAAATTGCCA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 10 0.33
32 20 0.67
ACGTcount: A:0.28, C:0.16, G:0.03, T:0.52
Consensus pattern (32 bp):
TTTCCAATTATATCCCTTATTTTTAAAACATA
Found at i:13027 original size:19 final size:20
Alignment explanation
Indices: 13000--13037 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
12990 AACTATTATT
13000 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
13020 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
13038 ACTGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:13273 original size:44 final size:43
Alignment explanation
Indices: 13204--13773 Score: 172
Period size: 44 Copynumber: 13.0 Consensus size: 43
13194 GTCTCTATGT
* * ** *
13204 GGTTATGAAAATTTCATAAG-ATGGTTATTATAATTTCATGAGGA
1 GGTTATCAAAATTTCAT-AGTGTGGTTACCAAAATTTCAT-AGGA
13248 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATA-GGA
* * * *
13292 AGTTTTCAAAATTTCATAGTGTGGTTACCAAAATTGCATAGTGT
1 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAG-GA
* ** * *
13336 GGTTACCAAAATTTCATAG-GATCAGGTTAATTAAAATTTCTTAGGTT
1 GGTTATCAAAATTTCATAGTG-T--GGTT-ACCAAAATTTCATAGG-A
** * * * * *
13383 GGTTATTGAAATTTCATAGGGTGGTTAATTATCACAATTTTATAGAAA
1 GGTTATCAAAATTTCATAGTGTGG----TTACCAAAATTTCATAG-GA
* * * *
13431 GGTTATC-AAA---GATA------TTATCAAAATGTCATCGCGA
1 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAG-GA
*
13465 GGTTAT-AAGAATTTCATAGTGTGGTTAACAAAATTTCATTAGGA
1 GGTTATCAA-AATTTCATAGTGTGGTTACCAAAATTTCA-TAGGA
* * * * * * *
13509 GGTTA-CTAATATTTCATGGGGGGGTTATCAAAATTTTATAGTA
1 GGTTATC-AAAATTTCATAGTGTGGTTACCAAAATTTCATAGGA
* ** *
13552 TGGTTATCAAAATTTCATA-TGAAGGTTATAAAAGTCTCAATTTCATAAGA
1 -GGTTATCAAAATTTCATAGTG-TGGTTA-CCAA-----AATTTCATAGGA
* * * ** * *
13602 AG-TACCAAAATTTGATAG-AAGGTTATC-AAATCTCATA-GA
1 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGA
* * * *
13641 GTGATTATCGAAATTTCATAGAGATCAGATTATCAAAATTT-ATAGGAA
1 G-G-TTATCAAAATTTCATAGTG-T--GGTTACCAAAATTTCATAGG-A
** * * *
13689 TATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCAAAGTGA
1 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAG-GA
* * * * * *
13733 GGTTATCAAAATTACATAATGTGATTATCAGAATTACATAG
1 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAG
13774 AGGGGGTCAA
Statistics
Matches: 392, Mismatches: 84, Indels: 100
0.68 0.15 0.17
Matches are distributed among these distances:
34 21 0.05
35 2 0.01
38 3 0.01
39 2 0.01
40 9 0.02
42 13 0.03
43 22 0.06
44 189 0.48
45 12 0.03
46 31 0.08
47 44 0.11
48 32 0.08
49 3 0.01
50 9 0.02
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.36
Consensus pattern (43 bp):
GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGA
Found at i:13372 original size:25 final size:22
Alignment explanation
Indices: 13204--13402 Score: 124
Period size: 22 Copynumber: 8.9 Consensus size: 22
13194 GTCTCTATGT
* *
13204 GGTTATGAAAATTTCATAAG-A
1 GGTTATTAAAATTTCATAGGTA
*
13225 TGGTTATTATAATTTCATGAGG-A
1 -GGTTATTAAAATTTCAT-AGGTA
*
13248 GGTTATCAAAATTTCATAGTGT-
1 GGTTATTAAAATTTCATAG-GTA
**
13270 GGTTACCAAAATTTCATATGG-A
1 GGTTATTAAAATTTCATA-GGTA
*
13292 AGTT-TTCAAAATTTCATAGTGT-
1 GGTTATT-AAAATTTCATAG-GTA
** *
13314 GGTTACCAAAATTGCATAGTGT-
1 GGTTATTAAAATTTCATAG-GTA
**
13336 GGTTACCAAAATTTCATAGGATCA
1 GGTTATTAAAATTTCATAGG-T-A
* *
13360 GGTTAATTAAAATTTCTTAGGTT
1 GGTT-ATTAAAATTTCATAGGTA
*
13383 GGTTATTGAAATTTCATAGG
1 GGTTATTAAAATTTCATAGG
13403 GTGGTTAATT
Statistics
Matches: 144, Mismatches: 20, Indels: 26
0.76 0.11 0.14
Matches are distributed among these distances:
21 4 0.03
22 114 0.79
23 8 0.06
24 5 0.03
25 13 0.09
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (22 bp):
GGTTATTAAAATTTCATAGGTA
Found at i:13490 original size:22 final size:21
Alignment explanation
Indices: 13465--13584 Score: 82
Period size: 22 Copynumber: 5.5 Consensus size: 21
13455 GTCATCGCGA
13465 GGTTATAAGAATTTCATAGTGT
1 GGTTATAA-AATTTCATAGTGT
* *
13487 GGTTAACAAAATTTCATTAG-GA
1 GGTT-ATAAAATTTCA-TAGTGT
* * * *
13509 GGTTACTAATATTTCATGGGGG
1 GGTTA-TAAAATTTCATAGTGT
* *
13531 GGTTATCAAAATTTTATAGTAT
1 GGTTAT-AAAATTTCATAGTGT
*
13553 GGTTATCAAAATTTCATA-TGAA
1 GGTTAT-AAAATTTCATAGTG-T
13575 GGTTATAAAA
1 GGTTATAAAA
13585 GTCTCAATTT
Statistics
Matches: 77, Mismatches: 15, Indels: 13
0.73 0.14 0.12
Matches are distributed among these distances:
21 9 0.12
22 62 0.81
23 6 0.08
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.38
Consensus pattern (21 bp):
GGTTATAAAATTTCATAGTGT
Found at i:13659 original size:22 final size:22
Alignment explanation
Indices: 13607--14208 Score: 131
Period size: 22 Copynumber: 28.0 Consensus size: 22
13597 TAAGAAGTAC
*
13607 CAAAATTTGATAGAAG-G-TTAT
1 CAAAATTTCATAG-AGTGATTAT
*
13628 C-AAATCTCATAGAGTGATTAT
1 CAAAATTTCATAGAGTGATTAT
*
13649 CGAAATTTCATAGAGATCAGATTAT
1 CAAAATTTCATAGAG-T--GATTAT
*
13674 CAAAATTT-ATAGGAAT-ATTAT
1 CAAAATTTCATA-GAGTGATTAT
*
13695 CAAAATTTCATAGTGTTG-TTAT
1 CAAAATTTCATAGAG-TGATTAT
13717 CAAAATTTCA-A-AGTGAGGTTAT
1 CAAAATTTCATAGAGTGA--TTAT
*
13739 CAAAATTACATA-ATGTGATTAT
1 CAAAATTTCATAGA-GTGATTAT
* * * * * *
13761 CAGAATTACATAGAGGGGGTCAA
1 CAAAATTTCATAGA-GTGATTAT
* * * *
13784 CAAAATTTTATAAAGAGGTTAT
1 CAAAATTTCATAGAGTGATTAT
* * *
13806 CAAATTTTC-TAAATGTGCTTA-
1 CAAAATTTCATAGA-GTGATTAT
*
13827 CAAAAATTTCATAGTA-TGGTTA-
1 C-AAAATTTCATAG-AGTGATTAT
* *
13849 CCAAA-TT-A-GGAAG-G-TTAT
1 CAAAATTTCATAG-AGTGATTAT
* * *
13867 TAAACTTTTATTACGGAGT-A--AT
1 CAAAATTTCA-TA--GAGTGATTAT
13889 CAAAATTTCA-AGGAGT-A-TAT
1 CAAAATTTCATA-GAGTGATTAT
**
13909 CAAAATTTCAGGGAG-GA-TAT
1 CAAAATTTCATAGAGTGATTAT
* * * *
13929 CACAATTTCATAG-TTTAGTTTT
1 CAAAATTTCATAGAGTGA-TTAT
*
13951 CAAAATTTCATAAGAG-GGTTAT
1 CAAAATTTCAT-AGAGTGATTAT
*
13973 CAAAATTTCATAGTA-TGCA-GAT
1 CAAAATTTCATAG-AGTG-ATTAT
*
13995 CAAAATTTCATATG-GAGATTA-
1 CAAAATTTCATA-GAGTGATTAT
* *
14016 AAAAATTTCATA-A-TAAGGTTAT
1 CAAAATTTCATAGAGT--GATTAT
** * * *
14038 CAAAAAATCATAGGGAGGTTAT
1 CAAAATTTCATAGAGTGATTAT
*
14060 CAAAATTT-GT--A--G-TTAT
1 CAAAATTTCATAGAGTGATTAT
* **
14076 CAAGATTTCATA-AGAAAGTTAT
1 CAAAATTTCATAGAGTGA-TTAT
* *
14098 CAAAATTTTATAGGGAG-GTTTAT
1 CAAAATTTCATA--GAGTGATTAT
*
14121 CAAAATCTT-ATAG-GAAGATTTAT
1 CAAAAT-TTCATAGAG-TGA-TTAT
* *
14144 CAAAATTTCATAGCGAGATTAT
1 CAAAATTTCATAGAGTGATTAT
* *
14166 CACAATTTCATAGTGTGATTAT
1 CAAAATTTCATAGAGTGATTAT
* *
14188 CAAAATTTCAGAGTGTGATTA
1 CAAAATTTCATAGAGTGATTA
14209 CTAACAATTC
Statistics
Matches: 436, Mismatches: 80, Indels: 129
0.68 0.12 0.20
Matches are distributed among these distances:
16 11 0.03
17 5 0.01
18 6 0.01
19 13 0.03
20 46 0.11
21 49 0.11
22 221 0.51
23 55 0.13
24 13 0.03
25 17 0.04
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAGAGTGATTAT
Found at i:13912 original size:20 final size:20
Alignment explanation
Indices: 13881--13938 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
13871 CTTTTATTAC
13881 GGAGTA-ATCAAAATTTCAA
1 GGAGTATATCAAAATTTCAA
*
13900 GGAGTATATCAAAATTTCAG
1 GGAGTATATCAAAATTTCAA
* *
13920 GGAGGATATCACAATTTCA
1 GGAGTATATCAAAATTTCA
13939 TAGTTTAGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
19 6 0.17
20 29 0.83
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (20 bp):
GGAGTATATCAAAATTTCAA
Found at i:14166 original size:45 final size:45
Alignment explanation
Indices: 14072--14197 Score: 116
Period size: 45 Copynumber: 2.8 Consensus size: 45
14062 AAATTTGTAG
* * * * * *
14072 TTATCAAGATTTCATA-AGAAAGTTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATAGTGAGA-TTATCAAAATTTCATAGCGAGGA
14117 TTATCAAAATCTT-ATAG-GAAGATTTATCAAAATTTCATAGCGA-GA
1 TTATCAAAAT-TTCATAGTG-AGA-TTATCAAAATTTCATAGCGAGGA
* *
14162 TTATCACAATTTCATAGTGTGATTATCAAAATTTCA
1 TTATCAAAATTTCATAGTGAGATTATCAAAATTTCA
14198 GAGTGTGATT
Statistics
Matches: 68, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
44 16 0.24
45 29 0.43
46 23 0.34
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (45 bp):
TTATCAAAATTTCATAGTGAGATTATCAAAATTTCATAGCGAGGA
Found at i:14219 original size:22 final size:23
Alignment explanation
Indices: 14140--14217 Score: 83
Period size: 22 Copynumber: 3.5 Consensus size: 23
14130 ATAGGAAGAT
* * *
14140 TTATCAA-AATTTCATAGCGAGA
1 TTATCAACAATTTCAGAGTGTGA
*
14162 TTATC-ACAATTTCATAGTGTGA
1 TTATCAACAATTTCAGAGTGTGA
14184 TTATCAA-AATTTCAGAGTGTGA
1 TTATCAACAATTTCAGAGTGTGA
14206 TTA-CTAACAATT
1 TTATC-AACAATT
14218 CATATGAAGG
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
21 2 0.04
22 42 0.86
23 5 0.10
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (23 bp):
TTATCAACAATTTCAGAGTGTGA
Found at i:14403 original size:21 final size:22
Alignment explanation
Indices: 14358--14405 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
14348 TTCCTTAGAG
* *
14358 AGGTTAACAAAATTTCACAAGA
1 AGGTTAAAAAAATTTCACAAAA
*
14380 AGGTTAAAAAAATTT-ATAAAA
1 AGGTTAAAAAAATTTCACAAAA
14401 AGGTT
1 AGGTT
14406 CTCGAAATTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.52, C:0.06, G:0.15, T:0.27
Consensus pattern (22 bp):
AGGTTAAAAAAATTTCACAAAA
Found at i:14713 original size:19 final size:19
Alignment explanation
Indices: 14689--14727 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
14679 GATCCGTCCC
14689 TGTTTGGTATGTTTAGTGT
1 TGTTTGGTATGTTTAGTGT
14708 TGTTTGGTATGTTTAGTGT
1 TGTTTGGTATGTTTAGTGT
14727 T
1 T
14728 TGTAAATGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.10, C:0.00, G:0.31, T:0.59
Consensus pattern (19 bp):
TGTTTGGTATGTTTAGTGT
Found at i:18538 original size:61 final size:61
Alignment explanation
Indices: 18442--18560 Score: 220
Period size: 61 Copynumber: 2.0 Consensus size: 61
18432 CTGATGCAAT
18442 TAAGAATCAGAAGGCAATTCACTGCCGTAACGAACAGCTTTATACCGAAAGCTCTGACTTA
1 TAAGAATCAGAAGGCAATTCACTGCCGTAACGAACAGCTTTATACCGAAAGCTCTGACTTA
* *
18503 TAAGAATCAGAAGGCACTTCACTGCCGTAAGGAACAGCTTTATACCGAAAGCTCTGAC
1 TAAGAATCAGAAGGCAATTCACTGCCGTAACGAACAGCTTTATACCGAAAGCTCTGAC
18561 GTTTATAAAG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 56 1.00
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (61 bp):
TAAGAATCAGAAGGCAATTCACTGCCGTAACGAACAGCTTTATACCGAAAGCTCTGACTTA
Found at i:24026 original size:26 final size:26
Alignment explanation
Indices: 23983--24047 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
23973 CCATTGGAAG
*
23983 TCACGTGTGGAGTTGTAC-TTCGGAGA
1 TCACGTGTGGAGTCGTACGTT-GGAGA
* *
24009 TCACGTGTGGGGTCGTACGTTGGAGG
1 TCACGTGTGGAGTCGTACGTTGGAGA
24035 TCACGTGTGGAGT
1 TCACGTGTGGAGT
24048 GCCAGCTGGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 32 0.94
27 2 0.06
ACGTcount: A:0.15, C:0.15, G:0.40, T:0.29
Consensus pattern (26 bp):
TCACGTGTGGAGTCGTACGTTGGAGA
Done.