Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010446.1 Corchorus capsularis cultivar CVL-1 contig10467, 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: 18346
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Found at i:961 original size:2 final size:2
Alignment explanation
Indices: 956--981 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
946 TGTTGTTAGG
956 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
982 GAAACTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1873 original size:22 final size:22
Alignment explanation
Indices: 1845--2004 Score: 148
Period size: 22 Copynumber: 7.3 Consensus size: 22
1835 TGTCTCTATG
*
1845 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* * *
1867 TGGTTATTATAATTTCTTGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
1890 -GGTTATCAAAATTTCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
*
1911 TGGTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-GGA
*
1934 -AGTTATCAAAATTTCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
* * *
1955 TGGTTACCAAAATTTCTTAGGC
1 TGGTTATCAAAATTTCATAGGA
** *
1977 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAGGA
1999 TGGTTA
1 TGGTTA
2005 ATTTTCACAA
Statistics
Matches: 112, Mismatches: 18, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
21 4 0.04
22 104 0.93
23 4 0.04
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.39
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:1915 original size:44 final size:43
Alignment explanation
Indices: 1846--2004 Score: 185
Period size: 44 Copynumber: 3.6 Consensus size: 43
1836 GTCTCTATGT
* ** *
1846 GGTTATCAAAATTTCATAAG-ATGGTTATTATAATTTCTTGAGGA
1 GGTTATCAAAATTTCAT-AGTGTGGTTACCAAAATTTCTT-AGGA
*
1890 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCTTA-GGA
* *
1934 AGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCTTAGGCT
1 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCTTAGG-A
** *
1978 GGTTATTGAAATTTCATAGGGTGGTTA
1 GGTTATCAAAATTTCATAGTGTGGTTA
2005 ATTTTCACAA
Statistics
Matches: 100, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
43 5 0.05
44 95 0.95
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.39
Consensus pattern (43 bp):
GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCTTAGGA
Found at i:2065 original size:22 final size:22
Alignment explanation
Indices: 2040--2523 Score: 139
Period size: 22 Copynumber: 21.7 Consensus size: 22
2030 ATCAAAGAGA
*
2040 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGCGAGG
* *
2062 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGCGAGG
* *
2084 TTAACAAAATTTCATTAGGAGAGG
1 TTATCAAAATTTCA-TA-GCGAGG
* * * *
2108 TTA-CTAATATTTCATGGGGAGA
1 TTATC-AAAATTTCATAGCGAGG
* * * *
2130 TTACCAAAATTTTATAGTGTGG
1 TTATCAAAATTTCATAGCGAGG
*
2152 TTATCAAAA-TTCAATATG-AAGG
1 TTATCAAAATTTC-ATA-GCGAGG
* **
2174 TTATAAAAGTCTCAATTTCATAAGGA-G
1 TTAT-CAA-----AATTTCATAGCGAGG
* * *
2201 -TACCAAAATTTGATAG-AAGG
1 TTATCAAAATTTCATAGCGAGG
* * * * *
2221 TTAT-TAAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGCGAGG
* * *
2242 TTATCGAAATTTCATAGAGATCAGA
1 TTATCAAAATTTCATAGCG---AGG
*
2267 TTATCAAAATTT-ATAG-GAAGA
1 TTATCAAAATTTCATAGCG-AGG
* **
2288 TTATCAAAA-TTCTATAGTGTTG
1 TTATCAAAATTTC-ATAGCGAGG
*
2310 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAGCGAGG
*
2332 TTATCAAAATTACATAATGCGA--
1 TTATCAAAATTTCAT-A-GCGAGG
* * *
2354 TTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAGCGAGG
* * * ***
2376 TCAACAAAATTTTATAAATAGG
1 TTATCAAAATTTCATAGCGAGG
**
2398 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGCGAGG
* * ** ***
2420 TTATCAAATTTTCAGAATGTTT
1 TTATCAAAATTTCATAGCGAGG
* * *
2442 TTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAGCGAGG
* * * **
2464 TCAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTCATAGCGAGG
**
2486 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGCGAGG
*
2508 TTATCAAATTTTCATA
1 TTATCAAAATTTCATA
2524 ATGTGATTAC
Statistics
Matches: 343, Mismatches: 88, Indels: 62
0.70 0.18 0.13
Matches are distributed among these distances:
19 1 0.00
20 22 0.06
21 24 0.07
22 230 0.67
23 16 0.05
24 23 0.07
25 15 0.04
26 2 0.01
27 1 0.00
28 6 0.02
29 3 0.01
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (22 bp):
TTATCAAAATTTCATAGCGAGG
Found at i:2358 original size:44 final size:44
Alignment explanation
Indices: 2265--2896 Score: 238
Period size: 44 Copynumber: 14.4 Consensus size: 44
2255 ATAGAGATCA
* * *
2265 GATTATCAAAATTT-ATAG-GAAGATTATCAAAA-TTCTATAGTGTT
1 GATTATCAAAATTTCAAAGAG-AGGTTATCAAAATTTC-ATAATG-T
* * *
2309 G-TTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATGC
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
* * * * * *
2352 GATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAATAG-
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCAT-AAT-GT
* *
2397 G-TTATCAAAATTTCATAA-AGAGGTTATCAAATTTTCAGAATGT
1 GATTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAATGT
** * * * * * * * *
2440 TTTTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGA
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
* *
2484 GGTTATCAAAATTTCATAA-AGAGGTTATCAAATTTTCATAATGT
1 GATTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAATGT
* *
2528 GATTA-CAAAAATTTCATAGTGGTATTTCTGAGGAGGTTATCAAAATTTCATAGTAT
1 GATTATC-AAAATTTCA-A-----A-----GA-GAGGTTATCAAAATTTCATAATGT
* * * * * * *
2584 GGTTA-CCAAA-TT--AGGA-AGGTTATTAAACTTTTATTATG-
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
* * * * * *
2622 GAGTAATCAAAATTTC--AGGGAGGATATCAAAATTTTATAGTTT
1 GA-TTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
* * * *
2665 AATTTTCAAAATTTCATAAGAG-GGTTATCAAAATTTCATAGTAT
1 GATTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAATGT
* * * * * *
2709 GCA-GATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGA
1 G-ATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
* * * *
2753 GGTTATCAAAATTT----G-TA-GTTATCAAGATTTCATAA-GA
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
* * * * * * *
2790 AAGTTATCAAAATTTTATAGGGAGGTTTATCAAAATTTTAT-AGGAA
1 GA-TTATCAAAATTTCAAAGAGAGG-TTATCAAAATTTCATAATG-T
* * * *
2836 GATTTATCAAAATTTCATAGCGAGGTTATCACAATTTCATAGTGT
1 GA-TTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
2881 GATTATCAAAATTTCA
1 GATTATCAAAATTTCA
2897 GAGTGTGATT
Statistics
Matches: 437, Mismatches: 104, Indels: 94
0.69 0.16 0.15
Matches are distributed among these distances:
37 2 0.00
38 28 0.06
39 19 0.04
40 5 0.01
41 5 0.01
42 29 0.07
43 23 0.05
44 226 0.52
45 42 0.10
46 24 0.05
49 1 0.00
51 1 0.00
54 2 0.00
55 4 0.01
56 26 0.06
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (44 bp):
GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
Found at i:2385 original size:88 final size:86
Alignment explanation
Indices: 2309--2546 Score: 327
Period size: 88 Copynumber: 2.7 Consensus size: 86
2299 CTATAGTGTT
* * * *
2309 GTTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATGCGATTATCAGAATTTCATAGAG
1 GTTATCAAAATTTCATAA-AGAGGTTATCAAATTTTCATAATGTGATTATCAGAATTTCATAGAG
2373 GGGTCAACAAAATTTTATAAATAG
65 GGGTCAACAAAATTTTAT-AAT-G
* **
2397 GTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAGAATGTTTTTATCAGAATTTCATAGAGG
1 GTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCATAATGTGATTATCAGAATTTCATAGAGG
*
2462 GGTCAACAAAATTTTATAAAGAG
66 GGTCAACAAAATTTTAT-AA-TG
*
2485 GTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCATAATGTGATTA-CAAAAATTTCATAG
1 GTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCATAATGTGATTATC-AGAATTTCATAG
2547 TGGTATTTCT
Statistics
Matches: 135, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
87 1 0.01
88 132 0.98
89 2 0.01
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (86 bp):
GTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCATAATGTGATTATCAGAATTTCATAGAGG
GGTCAACAAAATTTTATAATG
Found at i:2524 original size:22 final size:22
Alignment explanation
Indices: 2309--2524 Score: 191
Period size: 22 Copynumber: 9.8 Consensus size: 22
2299 CTATAGTGTT
*
2309 GTTATCAAAATTTCA-AAGCGAG
1 GTTATCAAAATTTCATAA-AGAG
* * *
2331 GTTATCAAAATTACATAATGCG
1 GTTATCAAAATTTCATAAAGAG
* * * *
2353 ATTATCAGAATTTCATAGAGGG
1 GTTATCAAAATTTCATAAAGAG
* * * *
2375 GTCAACAAAATTTTATAAATAG
1 GTTATCAAAATTTCATAAAGAG
2397 GTTATCAAAATTTCATAAAGAG
1 GTTATCAAAATTTCATAAAGAG
* * * **
2419 GTTATCAAATTTTCAGAATGTT
1 GTTATCAAAATTTCATAAAGAG
* * * *
2441 TTTATCAGAATTTCATAGAGGG
1 GTTATCAAAATTTCATAAAGAG
* * *
2463 GTCAACAAAATTTTATAAAGAG
1 GTTATCAAAATTTCATAAAGAG
2485 GTTATCAAAATTTCATAAAGAG
1 GTTATCAAAATTTCATAAAGAG
*
2507 GTTATCAAATTTTCATAA
1 GTTATCAAAATTTCATAA
2525 TGTGATTACA
Statistics
Matches: 148, Mismatches: 45, Indels: 2
0.76 0.23 0.01
Matches are distributed among these distances:
22 146 0.99
23 2 0.01
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (22 bp):
GTTATCAAAATTTCATAAAGAG
Found at i:2542 original size:22 final size:22
Alignment explanation
Indices: 2226--2545 Score: 148
Period size: 22 Copynumber: 14.5 Consensus size: 22
2216 GAAGGTTATT
* * * *
2226 AAATCTCATAGAGTGATTATCG
1 AAATTTCATAAAGAGATTATCA
*
2248 AAATTTCATAGAGATCAGATTATCA
1 AAATTTCATA-A-A-GAGATTATCA
*
2273 AAATTT-AT-AGGAAGATTATCA
1 AAATTTCATAAAG-AGATTATCA
* * *
2294 AAA-TTC-TATAGTGTTGTTATCA
1 AAATTTCATAAAGAG--ATTATCA
* *
2316 AAATTTCA-AAGCGAGGTTATCA
1 AAATTTCATAA-AGAGATTATCA
* * *
2338 AAATTACATAATGCGATTATCA
1 AAATTTCATAAAGAGATTATCA
* * * * * *
2360 GAATTTCATAGAGGGGTCAACA
1 AAATTTCATAAAGAGATTATCA
* * *
2382 AAATTTTATAAATAGGTTATCA
1 AAATTTCATAAAGAGATTATCA
*
2404 AAATTTCATAAAGAGGTTATCA
1 AAATTTCATAAAGAGATTATCA
* * * ***
2426 AATTTTCAGAATGTTTTTATCA
1 AAATTTCATAAAGAGATTATCA
* * * * * *
2448 GAATTTCATAGAGGGGTCAACA
1 AAATTTCATAAAGAGATTATCA
* *
2470 AAATTTTATAAAGAGGTTATCA
1 AAATTTCATAAAGAGATTATCA
*
2492 AAATTTCATAAAGAGGTTATCA
1 AAATTTCATAAAGAGATTATCA
* * *
2514 AATTTTCATAATGTGATTA-CAA
1 AAATTTCATAAAGAGATTATC-A
2536 AAATTTCATA
1 AAATTTCATA
2546 GTGGTATTTC
Statistics
Matches: 222, Mismatches: 63, Indels: 26
0.71 0.20 0.08
Matches are distributed among these distances:
20 4 0.02
21 14 0.06
22 180 0.81
23 6 0.03
24 5 0.02
25 13 0.06
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.34
Consensus pattern (22 bp):
AAATTTCATAAAGAGATTATCA
Found at i:2985 original size:22 final size:22
Alignment explanation
Indices: 2670--3048 Score: 177
Period size: 22 Copynumber: 17.4 Consensus size: 22
2660 AGTTTAATTT
*
2670 TCAAAATTTCATA-AGAGGGTTA
1 TCAAAATTTCATATGGA-GGTTA
* ***
2692 TCAAAATTTCATA-GTATGCAGA
1 TCAAAATTTCATATGGA-GGTTA
* *
2714 TCAAAATTTCATAGGGAGATTA
1 TCAAAATTTCATATGGAGGTTA
*
2736 ACAAAATTTCATAAT-GAGGTTA
1 TCAAAATTTCAT-ATGGAGGTTA
*
2758 TCAAAA--T--T-TGTA-GTTA
1 TCAAAATTTCATATGGAGGTTA
* * * *
2774 TCAAGATTTCATAAGAAAGTTA
1 TCAAAATTTCATATGGAGGTTA
* *
2796 TCAAAATTTTATAGGGAGGTTTA
1 TCAAAATTTCATATGGAGG-TTA
* *
2819 TCAAAATTTTATA-GGAAGATTTA
1 TCAAAATTTCATATGG-AG-GTTA
2842 TCAAAATTTCATA-GCGAGGTTA
1 TCAAAATTTCATATG-GAGGTTA
*
2864 TCACAATTTCATAGTGTGA--TTA
1 TCAAAATTTCATA-TG-GAGGTTA
*
2886 TCAAAATTTCAGAGTGTGA--TTA
1 TCAAAATTTCATA-TG-GAGGTTA
*
2908 -CTAACAA-TTCATATGGAGGTTT
1 TC-AA-AATTTCATATGGAGGTTA
* * *
2930 TTAAATTTTCATAATGTA-GTTA
1 TCAAAATTTCAT-ATGGAGGTTA
* * *
2952 CCAATATATCATATGGAGGTTA
1 TCAAAATTTCATATGGAGGTTA
* * **
2974 TCAACATCTCATAGTGTTGGTTA
1 TCAAAATTTCATA-TGGAGGTTA
*
2997 TCAAAATTTCAT-TGGGAAGTTA
1 TCAAAATTTCATAT-GGAGGTTA
*
3019 TCAAAATTTCATATTGAGGTCT-
1 TCAAAATTTCATATGGAGGT-TA
3041 TCAAAATT
1 TCAAAATT
3049 CCTTAGACAG
Statistics
Matches: 276, Mismatches: 54, Indels: 54
0.72 0.14 0.14
Matches are distributed among these distances:
16 10 0.04
17 1 0.00
18 2 0.01
20 4 0.01
21 11 0.04
22 180 0.65
23 64 0.23
24 4 0.01
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (22 bp):
TCAAAATTTCATATGGAGGTTA
Found at i:3283 original size:2 final size:2
Alignment explanation
Indices: 3276--3308 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3266 GCTAAAACTA
3276 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3309 AAAGAGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6294 original size:106 final size:107
Alignment explanation
Indices: 6053--6328 Score: 500
Period size: 106 Copynumber: 2.6 Consensus size: 107
6043 AACATAAAAA
*
6053 CCGGTTCAAATCCGATCCAATTGCCCAGTCCAACCGGTTTTATCCGGCTGTTGACCAAAGGCACA
1 CCGGTTCAAATCCGATCCAATTGCCCGGTCCAACCGGTTTTATCCGGCTGTTGACCAAAGGCACA
6118 AATTTTTTTTAAACAATTTCCAAACATAAAAACCGGTTCAAT
66 AATTTTTTTTAAACAATTTCCAAACATAAAAACCGGTTCAAT
*
6160 CCGGTTCAAATCCGATCCAATTGTCCGGTCCAACCGGTTTTATCCGGCTGTTGACCAAAGGCACA
1 CCGGTTCAAATCCGATCCAATTGCCCGGTCCAACCGGTTTTATCCGGCTGTTGACCAAAGGCACA
6225 AA-TTTTTTTAAACAATTTCCAAACATAAAAACCGGTTCAAT
66 AATTTTTTTTAAACAATTTCCAAACATAAAAACCGGTTCAAT
** *
6266 CTTGTTCAAATCCTATCCAATTGCCCGGTCCAACCGGTTTTATCCGGCTGTTGACCAAAGGCA
1 CCGGTTCAAATCCGATCCAATTGCCCGGTCCAACCGGTTTTATCCGGCTGTTGACCAAAGGCA
6329 AAACCTGGAA
Statistics
Matches: 163, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
106 98 0.60
107 65 0.40
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (107 bp):
CCGGTTCAAATCCGATCCAATTGCCCGGTCCAACCGGTTTTATCCGGCTGTTGACCAAAGGCACA
AATTTTTTTTAAACAATTTCCAAACATAAAAACCGGTTCAAT
Found at i:7924 original size:11 final size:11
Alignment explanation
Indices: 7886--7918 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
7876 ATATATAATA
7886 AATTATCAAA-T
1 AATTAT-AAATT
7897 AATTATAAATT
1 AATTATAAATT
7908 AATTATAAATT
1 AATTATAAATT
7919 TGTTATGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 3 0.14
11 18 0.86
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (11 bp):
AATTATAAATT
Found at i:9752 original size:23 final size:25
Alignment explanation
Indices: 9711--9763 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
9701 AAGTTCAATT
9711 TTCTC-CAAACAAATAATACTTGTA
1 TTCTCACAAACAAATAATACTTGTA
*
9735 TTCTCACAAA-AAA-AATACTTTTA
1 TTCTCACAAACAAATAATACTTGTA
9758 TTCTCA
1 TTCTCA
9764 TATTTACCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 15 0.56
24 8 0.30
25 4 0.15
ACGTcount: A:0.42, C:0.21, G:0.02, T:0.36
Consensus pattern (25 bp):
TTCTCACAAACAAATAATACTTGTA
Done.