Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001468.1 Corchorus capsularis cultivar CVL-1 contig01468, 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: 4368
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Found at i:814 original size:19 final size:19
Alignment explanation
Indices: 792--828 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
782 TAAATAATAA
792 TTTAATTACTTTACTATTT
1 TTTAATTACTTTACTATTT
*
811 TTTAATTATTTTACTATT
1 TTTAATTACTTTACTATT
829 AAAATAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTAATTACTTTACTATTT
Found at i:1934 original size:22 final size:22
Alignment explanation
Indices: 1909--1984 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
1899 TAAATATTAT
*
1909 AATTTCATGAG-GAGGTTATCAA
1 AATTTCAT-AGTGAGGTTACCAA
*
1931 AATTCCATAGTGCA-GTTACCAA
1 AATTTCATAGTG-AGGTTACCAA
*
1953 AATTTCATAGTGTGGTTACCAA
1 AATTTCATAGTGAGGTTACCAA
*
1975 AATTTTATAG
1 AATTTCATAG
1985 GATCAGATTA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
21 2 0.04
22 43 0.93
23 1 0.02
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (22 bp):
AATTTCATAGTGAGGTTACCAA
Found at i:2023 original size:22 final size:22
Alignment explanation
Indices: 1992--2038 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1982 TAGGATCAGA
* *
1992 TTATTAAAATCTCTTAGGTTGG
1 TTATTAAAATCTCATAGGGTGG
* *
2014 TTATTGAAATTTCATAGGGTGG
1 TTATTAAAATCTCATAGGGTGG
2036 TTA
1 TTA
2039 ATTATCACAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.28, C:0.06, G:0.21, T:0.45
Consensus pattern (22 bp):
TTATTAAAATCTCATAGGGTGG
Found at i:2099 original size:22 final size:22
Alignment explanation
Indices: 2069--2439 Score: 224
Period size: 22 Copynumber: 16.8 Consensus size: 22
2059 AGGTTATCAA
*
2069 AGAGATTATCAAAATTTCATAG
1 AGAGGTTATCAAAATTTCATAG
*
2091 CGAGGTTAT-AAGAATTTCATAG
1 AGAGGTTATCAA-AATTTCATAG
* * *
2113 TGTGGTTAACAAAATTTCATTAG
1 AGAGGTTATCAAAATTTCA-TAG
*
2136 -GAGGTTAAT-AATATTTCATAG
1 AGAGGTT-ATCAAAATTTCATAG
* *
2157 GGAGGTTATCAAAATTTTATAG
1 AGAGGTTATCAAAATTTCATAG
* *
2179 TGTGGTTATCAAAATTTCATATG
1 AGAGGTTATCAAAATTTCATA-G
* **
2202 A-AGGTTAT-AAAAGTCTCAATTTC
1 AGAGGTTATCAAAA-TTTC-A-TAG
* *
2225 ATGA-G-TACCAAAATTTGATAG
1 A-GAGGTTATCAAAATTTCATAG
*
2246 A-AGGTTATC-AAATCTCATAG
1 AGAGGTTATCAAAATTTCATAG
* * *
2266 AGTGATTATCGAAATTT-ATAG
1 AGAGGTTATCAAAATTTCATAG
2287 AGATCGGATTATCAAAATTTCATAG
1 AGA--GG-TTATCAAAATTTCATAG
* *** *
2312 TGTTTTTATCAAAATTTCAAAG
1 AGAGGTTATCAAAATTTCATAG
* * *
2334 CGAGATTATCAAAATTACATA-
1 AGAGGTTATCAAAATTTCATAG
* * *
2355 ATATGATTATCAGAATTTCATAG
1 AGA-GGTTATCAAAATTTCATAG
* * * * *
2378 AGGGGTCAACAAAATTTTATAA
1 AGAGGTTATCAAAATTTCATAG
*
2400 AGAGGTTATCAAAATTTCATAA
1 AGAGGTTATCAAAATTTCATAG
*
2422 AGAGGTTATCAAATTTTC
1 AGAGGTTATCAAAATTTC
2440 GAAATATGAT
Statistics
Matches: 266, Mismatches: 60, Indels: 46
0.72 0.16 0.12
Matches are distributed among these distances:
19 1 0.00
20 11 0.04
21 29 0.11
22 187 0.70
23 15 0.06
24 17 0.06
25 6 0.02
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.35
Consensus pattern (22 bp):
AGAGGTTATCAAAATTTCATAG
Found at i:2209 original size:44 final size:43
Alignment explanation
Indices: 2074--3131 Score: 222
Period size: 44 Copynumber: 24.4 Consensus size: 43
2064 ATCAAAGAGA
* * **
2074 TTATCAAAATTTCATAGCGAGGTTAT-AAGAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGTGGTTATCAA-AATTTCATAG-AAGG
* * * *
2118 TTAACAAAATTTCATTAG-GAGGTTAAT-AATATTTCATAGGGAGG
1 TTATCAAAATTTCA-TAGTGTGGTT-ATCAAAATTTCATA-GAAGG
*
2162 TTATCAAAATTTTATAGTGTGGTTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATA-GAAGG
* * * * *
2206 TTAT-AAAAGTCTCA-ATTTCATGAG-TACCAAAATTTGATAGAAGG
1 TTATCAAAA-TTTCATA-GT-GTG-GTTATCAAAATTTCATAGAAGG
* * * *
2250 TTATC-AAATCTCATAGAGTGATTATCGAAATTT-ATAGAGATCGG
1 TTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGA-A--GG
** * * *
2294 ATTATCAAAATTTCATAGTGTTTTTATCAAAATTTCAAAGCGAGA
1 -TTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAG-AAGG
* * * * * *
2339 TTATCAAAATTACATAATATGATTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGA-AGG
* * * ** * *
2383 TCAACAAAATTTTATAAAGAGGTTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGA-AGG
* * * * *
2427 TTATCAAATTTTCGA-AATATGATTA-CAAAAATTTCATAG-TGG
1 TTATCAAAATTTC-ATAGTGTGGTTATC-AAAATTTCATAGAAGG
* * * * *
2469 ---T----ATTTC-TGGGGAGGTTATCAAAATTTCATTGTATGG
1 TTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAG-AAGG
* * * * * *
2505 TTA-CCAAA--T--TAG-GAAGGTTATTAAACTTTTATTATGGA-G
1 TTATCAAAATTTCATAGTG-TGGTTATCAAAATTTCA-TA-GAAGG
* * * * * * *
2544 TAATCAAAATTTC--AGGGAGGATATCAGAA-TTCA-GGGAGG
1 TTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGAAGG
* ****
2583 ATATCAAAATTTCATAAAAAGGTTATCAAAATTTCATAGTTTAA--
1 TTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAG---AAGG
* * * *
2627 TTTTCAAAATTTCATAAGAG-GGTTATCAAAATTTCATAGTATG
1 TTATCAAAATTTCAT-AGTGTGGTTATCAAAATTTCATAGAAGG
* * *** *
2670 TAGATCAAAATTTCATAGGGAAATTAACAAAATTTCATA-ATGAGG
1 T-TATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGA--AGG
* * * * * *
2715 TTATC-AAATTATCAGAATTTGTAGTTATCAATATTTCACAAGAAAG
1 TTATCAAAATT-TCA-TA-GTGTGGTTATCAAAATTTCA-TAGAAGG
* * * * *
2761 TTATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTCATAGTGTGG-TTATCAAAATTTCATA-GAAG-G
* *** * *
2807 TTTTCAAAATTTCATAGCAAGGTTATCACAATTTCATAG-TGTG
1 TTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGAAG-G
* * * *
2850 ATTATCAAAATTTCAGACTGTGATTA-CTAACAA-TTCATATGGAGG
1 -TTATCAAAATTTCATAGTGTGGTTATC-AA-AATTTCATA-GAAGG
* ** * * *
2895 TT-TTAAAATTTTCATAACGTGGTTATCAATATATCATATGGAGG
1 TTATCAAAA-TTTCATAGTGTGGTTATCAAAATTTCATA-GAAGG
** * *
2939 TTATCAGCATCTCATAGTGTTGGTTATCAAAATTTCATTGGGAA-G
1 TTATCAAAATTTCATAGTG-TGGTTATCAAAATTTCA-T-AGAAGG
* * * * *
2984 TTATCAAAATTTCATATTGAGGTCT-TCAAAATTCCTTAGGGAGG
1 TTATCAAAATTTCATAGTGTGGT-TATCAAAATTTCATA-GAAGG
* ** * ** * *
3028 TTAACAAAAATTTCATAAG-AAGATTAAAAAAATTT-ATAAAAAGA
1 TTATC-AAAATTTCAT-AGTGTGGTTATCAAAATTTCAT-AGAAGG
* * * * * *
3072 TTCTCGAAATTCCATAGTATCGTTATTAAAATTTCATAGGAAGG
1 TTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATA-GAAGG
3116 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
3132 ATGGGATCAT
Statistics
Matches: 732, Mismatches: 195, Indels: 174
0.66 0.18 0.16
Matches are distributed among these distances:
34 15 0.02
35 5 0.01
36 3 0.00
38 4 0.01
39 32 0.04
40 6 0.01
41 21 0.03
42 32 0.04
43 58 0.08
44 348 0.48
45 126 0.17
46 71 0.10
47 10 0.01
48 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.36
Consensus pattern (43 bp):
TTATCAAAATTTCATAGTGTGGTTATCAAAATTTCATAGAAGG
Found at i:2574 original size:20 final size:20
Alignment explanation
Indices: 2546--2596 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
2536 TTATGGAGTA
2546 ATCAAAATTTCAGGGAGGAT
1 ATCAAAATTTCAGGGAGGAT
*
2566 ATCAGAA-TTCAGGGAGGAT
1 ATCAAAATTTCAGGGAGGAT
2585 ATCAAAATTTCA
1 ATCAAAATTTCA
2597 TAAAAAGGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 18 0.64
20 10 0.36
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.25
Consensus pattern (20 bp):
ATCAAAATTTCAGGGAGGAT
Found at i:2609 original size:22 final size:22
Alignment explanation
Indices: 2584--3132 Score: 168
Period size: 22 Copynumber: 24.7 Consensus size: 22
2574 TCAGGGAGGA
*
2584 TATCAAAATTTCATAAAAAGGT
1 TATCAAAATTTCATAAGAAGGT
2606 TATCAAAATTTCAT-AGTTTAA--T
1 TATCAAAATTTCATAAG---AAGGT
* *
2628 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATAAGAAGGT
* *
2650 TATCAAAATTTCAT-AGTATGT
1 TATCAAAATTTCATAAGAAGGT
* * *
2671 AGATCAAAATTTCATAGGGAA-AT
1 -TATCAAAATTTCATA-AGAAGGT
*
2694 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCATAA-GAAGGT
* *
2716 TATC-AAATTATCAGAATTTGTA-GT
1 TATCAAAATT-TCATAA---GAAGGT
* * *
2740 TATCAATATTTCACAAGAAAGT
1 TATCAAAATTTCATAAGAAGGT
* * *
2762 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATAAGAAGG-T
* * *
2785 TATCAAAATTTTATAGGAAGATT
1 TATCAAAATTTCATAAGAAG-GT
*
2808 TTTCAAAATTTCAT-AGCAAGGT
1 TATCAAAATTTCATAAG-AAGGT
* *
2830 TATCACAATTTCAT-AG-TGTGAT
1 TATCAAAATTTCATAAGAAG-G-T
* * * *
2852 TATCAAAATTTCAGACTG-TGAT
1 TATCAAAATTTCATA-AGAAGGT
* *
2874 TA-CTAACAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATAAGAAGGT
* *
2896 T-TTAAAATTTTCATAACG-TGGT
1 TATCAAAA-TTTCATAA-GAAGGT
* * * *
2918 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATAAGAAGGT
** * * **
2940 TATCAGCATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-AGAAGGT
**
2963 TATCAAAATTTCATTGGGAA-GT
1 TATCAAAATTTCA-TAAGAAGGT
*
2985 TATCAAAATTTCATATTG-AGGT
1 TATCAAAATTTCATA-AGAAGGT
* * * *
3007 CT-TCAAAATTCCTTAGGGAGGT
1 -TATCAAAATTTCATAAGAAGGT
* *
3029 TAACAAAAATTTCATAAGAAGAT
1 TATC-AAAATTTCATAAGAAGGT
** * *
3052 TAAAAAAATTT-ATAAAAAGAT
1 TATCAAAATTTCATAAGAAGGT
* * * **
3073 TCTCGAAATTCCAT-AGTATCGT
1 TATCAAAATTTCATAAG-AAGGT
* *
3095 TATTAAAATTTCATAGGAAGGT
1 TATCAAAATTTCATAAGAAGGT
3117 TATCAAAATTTCATAA
1 TATCAAAATTTCATAA
3133 TGGGATCATA
Statistics
Matches: 390, Mismatches: 93, Indels: 88
0.68 0.16 0.15
Matches are distributed among these distances:
20 4 0.01
21 40 0.10
22 240 0.62
23 80 0.21
24 21 0.05
25 5 0.01
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATAAGAAGGT
Found at i:2789 original size:23 final size:23
Alignment explanation
Indices: 2739--2845 Score: 101
Period size: 23 Copynumber: 4.7 Consensus size: 23
2729 GAATTTGTAG
* * * *
2739 TTATCAATATTTCACAAGAAAG-
1 TTATCAAAATTTCATAGGAAGGT
* *
2761 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATAGGAAGGT
* *
2784 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTCATAGGAAGGT
* *
2807 TTTTCAAAATTTCATAGCAAGG-
1 TTATCAAAATTTCATAGGAAGGT
*
2829 TTATCACAATTTCATAG
1 TTATCAAAATTTCATAG
2846 TGTGATTATC
Statistics
Matches: 70, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
22 31 0.44
23 39 0.56
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.37
Consensus pattern (23 bp):
TTATCAAAATTTCATAGGAAGGT
Found at i:2999 original size:45 final size:45
Alignment explanation
Indices: 2914--2999 Score: 102
Period size: 45 Copynumber: 1.9 Consensus size: 45
2904 TTTCATAACG
* * **
2914 TGGTTATCAATATATCATATGGAGGTTATCAGCATCTCATAGTGT
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
* *
2959 TGGTTATCAAAATTTCAT-TGGGAAGTTATCAAAATTTCATA
1 TGGTTATCAAAATATCATAT-GGAAGTTATCAAAATCTCATA
3000 TTGAGGTCTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
44 1 0.03
45 33 0.97
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
Found at i:3066 original size:21 final size:23
Alignment explanation
Indices: 3028--3073 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
3018 CTTAGGGAGG
*
3028 TTAACAAAAATTTCATAAGAAGA
1 TTAACAAAAATTTCATAAAAAGA
3051 TTAA-AAAAATTT-ATAAAAAGA
1 TTAACAAAAATTTCATAAAAAGA
3072 TT
1 TT
3074 CTCGAAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.45
22 8 0.36
23 4 0.18
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (23 bp):
TTAACAAAAATTTCATAAAAAGA
Found at i:3673 original size:12 final size:12
Alignment explanation
Indices: 3652--3687 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
3642 ATTCCAATTC
*
3652 CATTTGCATTTG
1 CATTTTCATTTG
*
3664 CATTTTCATTTT
1 CATTTTCATTTG
3676 CATTTTCATTTG
1 CATTTTCATTTG
3688 TTTTTGTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.17, C:0.17, G:0.08, T:0.58
Consensus pattern (12 bp):
CATTTTCATTTG
Found at i:3679 original size:18 final size:18
Alignment explanation
Indices: 3652--3686 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3642 ATTCCAATTC
3652 CATTTGCATTTGCATTTT
1 CATTTGCATTTGCATTTT
* *
3670 CATTTTCATTTTCATTT
1 CATTTGCATTTGCATTT
3687 GTTTTTGTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.17, G:0.06, T:0.60
Consensus pattern (18 bp):
CATTTGCATTTGCATTTT
Found at i:3785 original size:42 final size:41
Alignment explanation
Indices: 3700--3817 Score: 129
Period size: 42 Copynumber: 2.9 Consensus size: 41
3690 TTTGTTTCTT
* *
3700 CATCTCCAATC-AAGGCTGCGGCATTTTCAATTG-ACTTTC
1 CATCTCCAATCTAAGGCTGTGGCATTTTCCATTGTACTTTC
* *
3739 CATCTGATCCAATCTAA-GCTGTGGCATTTTCCGTTGTA-TTTG
1 CATC---TCCAATCTAAGGCTGTGGCATTTTCCATTGTACTTTC
*
3781 CATCTCCAA-CTAAGGCTGTGGCATTTTCCTTTGTACT
1 CATCTCCAATCTAAGGCTGTGGCATTTTCCATTGTACT
3818 ATTAGCATGC
Statistics
Matches: 67, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
38 4 0.06
39 29 0.43
40 1 0.01
42 30 0.45
43 3 0.04
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.37
Consensus pattern (41 bp):
CATCTCCAATCTAAGGCTGTGGCATTTTCCATTGTACTTTC
Done.