Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016142.1 Corchorus capsularis cultivar CVL-1 contig16163, 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: 18506
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Found at i:2077 original size:38 final size:38
Alignment explanation
Indices: 2045--2417 Score: 638
Period size: 38 Copynumber: 9.8 Consensus size: 38
2035 AATTAAGGAC
*
2045 CAAAGTAATAGTAAACAGTAAAATTGATAATTAAGAGT
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
*
2083 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGG
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
*
2121 CAAAGTAATAGTAAACAGTAAAATTGATAATTAAGAGT
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
*
2159 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGG
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
* *
2197 CAAAGTAATAGTAAACAGTAAAATTTATAATTAAGAGT
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
*
2235 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGC
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
* *
2273 CAAAGTAATAGTAAACAATAAAATTGATAATTAAGAGT
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
*
2311 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGG
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
*
2349 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGC
1 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
*
2387 CAAAGTAATAGCAATCAGTAAAATTGATAAT
1 CAAAGTAATAGTAATCAGTAAAATTGATAAT
2418 CAAGGATCAA
Statistics
Matches: 315, Mismatches: 20, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 315 1.00
ACGTcount: A:0.51, C:0.06, G:0.16, T:0.27
Consensus pattern (38 bp):
CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
Found at i:2526 original size:31 final size:31
Alignment explanation
Indices: 2504--2571 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
2494 AGGGAGAGAG
*
2504 TAAAAGAGTAATCAGTAATTAAGAAAGGAAA
1 TAAAAAAGTAATCAGTAATTAAGAAAGGAAA
* *
2535 TAAAAAATTAATCAGTAATTAAGAAAGGAAG
1 TAAAAAAGTAATCAGTAATTAAGAAAGGAAA
2566 TAAAAA
1 TAAAAA
2572 GGATTAGTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.60, C:0.03, G:0.16, T:0.21
Consensus pattern (31 bp):
TAAAAAAGTAATCAGTAATTAAGAAAGGAAA
Found at i:2613 original size:30 final size:31
Alignment explanation
Indices: 2572--2630 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
2562 GAAGTAAAAA
*
2572 GGATTAGTCAGT-AAATTAGTAATTAAGAAG
1 GGATTAATCAGTAAAATTAGTAATTAAGAAG
*
2602 GGATTAATCAGTAAAATTGGTAATTAAGA
1 GGATTAATCAGTAAAATTAGTAATTAAGA
2631 GTCAAAGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.31
Consensus pattern (31 bp):
GGATTAATCAGTAAAATTAGTAATTAAGAAG
Found at i:2857 original size:14 final size:13
Alignment explanation
Indices: 2835--2934 Score: 69
Period size: 14 Copynumber: 7.3 Consensus size: 13
2825 CAGTAAAAAT
2835 GTAAAAGTAATCA
1 GTAAAAGTAATCA
2848 GTAAAGAGTAATCA
1 GTAAA-AGTAATCA
**
2862 GTAAAAAGTAAAAA
1 GT-AAAAGTAATCA
* *
2876 TGGCAAAGAGTAGT-A
1 --GTAAA-AGTAATCA
*
2891 -AAAAAGTAATCA
1 GTAAAAGTAATCA
*
2903 GGCAAAAGTAATCA
1 -GTAAAAGTAATCA
2917 GTAAGAAGTAATCA
1 GTAA-AAGTAATCA
2931 GTAA
1 GTAA
2935 GAAGGTAAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
11 5 0.07
12 4 0.06
13 8 0.12
14 40 0.58
15 7 0.10
16 5 0.07
ACGTcount: A:0.54, C:0.07, G:0.20, T:0.19
Consensus pattern (13 bp):
GTAAAAGTAATCA
Found at i:3024 original size:25 final size:25
Alignment explanation
Indices: 2996--3046 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
2986 AAAATGGTGT
2996 AGAGTAAAAAATGGTATTAAGTAAA
1 AGAGTAAAAAATGGTATTAAGTAAA
* *
3021 AGAGTAAAGAATGGTATTAATTAAA
1 AGAGTAAAAAATGGTATTAAGTAAA
3046 A
1 A
3047 AATGGTGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.20, T:0.25
Consensus pattern (25 bp):
AGAGTAAAAAATGGTATTAAGTAAA
Found at i:3050 original size:17 final size:17
Alignment explanation
Indices: 3023--3063 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
3013 TAAGTAAAAG
*
3023 AGTAAAGAATGGTATTA
1 AGTAAAAAATGGTATTA
* *
3040 ATTAAAAAATGGTGTTA
1 AGTAAAAAATGGTATTA
3057 AGTAAAA
1 AGTAAAA
3064 GGGTCAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.20, T:0.29
Consensus pattern (17 bp):
AGTAAAAAATGGTATTA
Found at i:3144 original size:58 final size:57
Alignment explanation
Indices: 3027--3144 Score: 132
Period size: 58 Copynumber: 2.0 Consensus size: 57
3017 TAAAAGAGTA
* * * **
3027 AAGAATGGTATTAATTAAAAAATGGTGTTAAGTAAAAGGGTCAAAAATGCTATCCAGT
1 AAGAATGGTATTAA-TAAAAAATGGTATTAAGTAAAAGAGTAAAAAATGCTATAAAGT
*
3085 AAGAGATGGTATTAA-ACAAAAATGGTATTAAGTAAAAGAGTAAAAAAATGGTA-AAAGT
1 AAGA-ATGGTATTAATA-AAAAATGGTATTAAGTAAAAGAGT-AAAAAATGCTATAAAGT
3143 AA
1 AA
3145 AAACGATAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
57 1 0.02
58 31 0.61
59 19 0.37
ACGTcount: A:0.51, C:0.04, G:0.20, T:0.25
Consensus pattern (57 bp):
AAGAATGGTATTAATAAAAAATGGTATTAAGTAAAAGAGTAAAAAATGCTATAAAGT
Found at i:3147 original size:26 final size:26
Alignment explanation
Indices: 3102--3155 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
3092 GGTATTAAAC
*
3102 AAAAATGGTATTAAGTAAAA-GAGTAA
1 AAAAATGGTATAAAGTAAAACGA-TAA
3128 AAAAATGGTA-AAAGTAAAAACGATAA
1 AAAAATGGTATAAAGT-AAAACGATAA
3154 AA
1 AA
3156 GTAGCAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 4 0.16
26 19 0.76
27 2 0.08
ACGTcount: A:0.63, C:0.02, G:0.17, T:0.19
Consensus pattern (26 bp):
AAAAATGGTATAAAGTAAAACGATAA
Found at i:4794 original size:16 final size:17
Alignment explanation
Indices: 4775--4812 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
4765 AGGCCCAGTT
4775 TTTTTTCCTTTTC-TTC
1 TTTTTTCCTTTTCTTTC
*
4791 TTTTTTCTTTTTCTTTC
1 TTTTTTCCTTTTCTTTC
4808 TTTTT
1 TTTTT
4813 GCGACCTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTCCTTTTCTTTC
Found at i:12567 original size:63 final size:62
Alignment explanation
Indices: 12492--12727 Score: 231
Period size: 63 Copynumber: 3.7 Consensus size: 62
12482 TGACATCCAT
** * * * *
12492 AATTAAATACATAGTCCAGACACATCATACACTGCTGAATAATACCATAAATTCCGAGTACA
1 AATTAAATACATAGTCTGGAAACACCATCCACTGCTGAATAATACCATAAACTCCGAGTACA
* * * * * *
12554 CAATTAAACACATAGTCTGGAAATAGCATCCACTGCTGAATAATACCATGAACTCCAAATACA
1 -AATTAAATACATAGTCTGGAAACACCATCCACTGCTGAATAATACCATAAACTCCGAGTACA
*
12617 AGCATTGAATAATAACATAGTCTGGAAACACCATCCCCTGCTGAATAATACCATAAACTCCGAGT
1 A--ATT--A-AAT-ACATAGTCTGGAAACACCATCCACTGCTGAATAATACCATAAACTCCGAGT
12682 ACA
60 ACA
* * * *
12685 TAATTAAATATATAGTCTGAAAATACCA-CCAACTACTGAATAA
1 -AATTAAATACATAGTCTGGAAACACCATCC-ACTGCTGAATAA
12728 CACATTGTCT
Statistics
Matches: 142, Mismatches: 23, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
62 3 0.02
63 77 0.54
64 6 0.04
65 1 0.01
66 1 0.01
67 5 0.04
68 48 0.34
69 1 0.01
ACGTcount: A:0.43, C:0.22, G:0.11, T:0.24
Consensus pattern (62 bp):
AATTAAATACATAGTCTGGAAACACCATCCACTGCTGAATAATACCATAAACTCCGAGTACA
Found at i:16316 original size:22 final size:23
Alignment explanation
Indices: 16260--16340 Score: 87
Period size: 22 Copynumber: 3.6 Consensus size: 23
16250 TCATTCTTTA
* *
16260 CTTTGTACTGATTACTATTTTACT
1 CTTT-TACTGATTACCATCTTACT
* *
16284 CTTGT--TGATTACCCTCTTACT
1 CTTTTACTGATTACCATCTTACT
*
16305 -TTTTACTGATTACCATTTTACT
1 CTTTTACTGATTACCATCTTACT
16327 CTTTTACTGATTAC
1 CTTTTACTGATTAC
16341 TATTTTCTGC
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
20 3 0.06
21 13 0.28
22 14 0.30
23 14 0.30
24 3 0.06
ACGTcount: A:0.20, C:0.21, G:0.07, T:0.52
Consensus pattern (23 bp):
CTTTTACTGATTACCATCTTACT
Found at i:16385 original size:22 final size:20
Alignment explanation
Indices: 16352--16420 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 20
16342 ATTTTCTGCT
16352 CTTTTTTTTTTACTGATTAC
1 CTTTTTTTTTTACTGATTAC
*
16372 TCTTTTATTTTTTACTGATTGC
1 -CTTTT-TTTTTTACTGATTAC
*
16394 CTTTTGCTTTTTACTGATTAC
1 CTTTT-TTTTTTACTGATTAC
16415 CTTTTT
1 CTTTTT
16421 ACTTCTTGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
21 28 0.67
22 14 0.33
ACGTcount: A:0.13, C:0.16, G:0.07, T:0.64
Consensus pattern (20 bp):
CTTTTTTTTTTACTGATTAC
Found at i:16421 original size:43 final size:44
Alignment explanation
Indices: 16358--16641 Score: 176
Period size: 43 Copynumber: 6.7 Consensus size: 44
16348 TGCTCTTTTT
* * *
16358 TTTTTACTGATTA-CTCTTTTATTTTTTACTGATT-GCCTTTTGC
1 TTTTTACTGATTACCT-TTTTACTTCTTACTGATTAGCCTTTTAC
** *
16401 TTTTTACTGATTACCTTTTTACTTCTTGTTGATTAGCTTTTTAC
1 TTTTTACTGATTACCTTTTTACTTCTTACTGATTAGCCTTTTAC
* *
16445 TCTTTACTGATCACCTTTTTAC-TCTTACT-A--A----TTT-C
1 TTTTTACTGATTACCTTTTTACTTCTTACTGATTAGCCTTTTAC
* * * *
16480 CTTTTACTTATTACCATTTTAC-TCTTACTGATTA--CTATTTGC
1 TTTTTACTGATTACCTTTTTACTTCTTACTGATTAGCCT-TTTAC
* * **
16522 TTTTTACTGACTA-CTATTTTTC-TCTTGTTGATTA-CCTTCTTAC
1 TTTTTACTGATTACCT-TTTTACTTCTTACTGATTAGCCTT-TTAC
*
16565 TTTTTACTGATTA-CTCTTTTAC-TCTTTACTAATTA-CCATTTTACC
1 TTTTTACTGATTACCT-TTTTACTTC-TTACTGATTAGCC-TTTTA-C
** *
16610 CCTTTACTGATTACCTTTTTACTTTTTACTGA
1 TTTTTACTGATTACCTTTTTACTTCTTACTGA
16642 CTGCATGCTA
Statistics
Matches: 191, Mismatches: 33, Indels: 32
0.75 0.13 0.12
Matches are distributed among these distances:
35 25 0.13
36 4 0.02
38 1 0.01
40 1 0.01
41 4 0.02
42 28 0.15
43 58 0.30
44 41 0.21
45 26 0.14
46 3 0.02
ACGTcount: A:0.18, C:0.20, G:0.06, T:0.55
Consensus pattern (44 bp):
TTTTTACTGATTACCTTTTTACTTCTTACTGATTAGCCTTTTAC
Found at i:16493 original size:21 final size:21
Alignment explanation
Indices: 16461--16525 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
16451 CTGATCACCT
* *
16461 TTTTAC-TCTTACTAATTTCC
1 TTTTACTTATTACTAATTTAC
* *
16481 TTTTACTTATTACCATTTTAC
1 TTTTACTTATTACTAATTTAC
* * *
16502 TCTTACTGATTACT-ATTTGC
1 TTTTACTTATTACTAATTTAC
16522 TTTT
1 TTTT
16526 TACTGACTAC
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 13 0.38
21 21 0.62
ACGTcount: A:0.20, C:0.20, G:0.03, T:0.57
Consensus pattern (21 bp):
TTTTACTTATTACTAATTTAC
Found at i:16578 original size:22 final size:21
Alignment explanation
Indices: 16360--16641 Score: 169
Period size: 22 Copynumber: 13.4 Consensus size: 21
16350 CTCTTTTTTT
* *
16360 TTTACTGATTACTCTTTTATTT
1 TTTACTGATTAC-CTTTTACTC
* * *
16382 TTTACTGATTGCCTTTTGCTT
1 TTTACTGATTACCTTTTACTC
16403 TTTACTGATTACCTTTTTACTTC
1 TTTACTGATTACC-TTTTAC-TC
*
16426 TTGT--TGATTAGCTTTTTACTC
1 TT-TACTGATTA-CCTTTTACTC
*
16447 TTTACTGATCACCTTTTTACTC
1 TTTACTGATTACC-TTTTACTC
* *
16469 -TTACTAATTTCCTTTTA--C
1 TTTACTGATTACCTTTTACTC
16487 --T--T-ATTACCATTTTACTC
1 TTTACTGATTACC-TTTTACTC
* *
16504 -TTACTGATTA-CTATTTGCTT
1 TTTACTGATTACCT-TTTACTC
* * *
16524 TTTACTGACTACTATTTTTCTC
1 TTTACTGATTAC-CTTTTACTC
*
16546 TTGT--TGATTACCTTCTTACTT
1 TT-TACTGATTACCTT-TTACTC
16567 TTTACTGATTACTCTTTTACTC
1 TTTACTGATTAC-CTTTTACTC
* *
16589 TTTACTAATTACCATTTTACCCC
1 TTTACTGATTACC-TTTTA-CTC
*
16612 TTTACTGATTACCTTTTTACTT
1 TTTACTGATTACC-TTTTACTC
16634 TTTACTGA
1 TTTACTGA
16642 CTGCATGCTA
Statistics
Matches: 205, Mismatches: 30, Indels: 50
0.72 0.11 0.18
Matches are distributed among these distances:
14 5 0.02
15 6 0.03
17 2 0.01
18 2 0.01
19 1 0.00
20 16 0.08
21 59 0.29
22 85 0.41
23 28 0.14
24 1 0.00
ACGTcount: A:0.18, C:0.21, G:0.06, T:0.55
Consensus pattern (21 bp):
TTTACTGATTACCTTTTACTC
Found at i:16629 original size:23 final size:23
Alignment explanation
Indices: 16567--16631 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
16557 CTTCTTACTT
* *
16567 TTTACTGATTACTC-TTTTA-CTC
1 TTTACTAATTAC-CATTTTACCCC
16589 TTTACTAATTACCATTTTACCCC
1 TTTACTAATTACCATTTTACCCC
* *
16612 TTTACTGATTACCTTTTTAC
1 TTTACTAATTACCATTTTAC
16632 TTTTTACTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 1 0.03
22 16 0.43
23 20 0.54
ACGTcount: A:0.22, C:0.25, G:0.03, T:0.51
Consensus pattern (23 bp):
TTTACTAATTACCATTTTACCCC
Found at i:16974 original size:55 final size:55
Alignment explanation
Indices: 16903--17041 Score: 224
Period size: 55 Copynumber: 2.5 Consensus size: 55
16893 CTAATTACTA
* *
16903 TCTTTTTACCTGATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATC
1 TCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATC
* *
16958 TCTTTTTACTTAATTACTGATTTACTGATTACTATTACTTTGTCTCTGATTAATC
1 TCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATC
* *
17013 TCTTTTTACTTAATTGCCGATTTACTGAT
1 TCTTTTTACTTAATTACTGATTTACTGAT
17042 CGAGCCAAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 78 1.00
ACGTcount: A:0.23, C:0.18, G:0.09, T:0.50
Consensus pattern (55 bp):
TCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATC
Found at i:17006 original size:29 final size:29
Alignment explanation
Indices: 16919--17008 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
16909 TACCTGATTA
* *
16919 CTGATTTACTGATTACTATTACCTTGACT
1 CTGATTTACTGATTACTATTACTTTGTCT
* * **
16948 CTGATTAATCT-CTT--T-TTACTTAAT-T
1 CTGATTTA-CTGATTACTATTACTTTGTCT
16973 ACTGATTTACTGATTACTATTACTTTGTCT
1 -CTGATTTACTGATTACTATTACTTTGTCT
17003 CTGATT
1 CTGATT
17009 AATCTCTTTT
Statistics
Matches: 44, Mismatches: 10, Indels: 14
0.65 0.15 0.21
Matches are distributed among these distances:
25 3 0.07
26 14 0.32
27 1 0.02
28 1 0.02
29 22 0.50
30 3 0.07
ACGTcount: A:0.23, C:0.18, G:0.09, T:0.50
Consensus pattern (29 bp):
CTGATTTACTGATTACTATTACTTTGTCT
Found at i:17280 original size:11 final size:11
Alignment explanation
Indices: 17264--17295 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
17254 GAAGTTCGTG
17264 TTTGAAGATTA
1 TTTGAAGATTA
*
17275 TTTGAAGATAA
1 TTTGAAGATTA
17286 TTTGAAGATT
1 TTTGAAGATT
17296 TGAAGACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (11 bp):
TTTGAAGATTA
Found at i:17298 original size:19 final size:18
Alignment explanation
Indices: 17274--17311 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
17264 TTTGAAGATT
*
17274 ATTTGAAGATAATTTGAAG
1 ATTTGAAGACAA-TTGAAG
17293 ATTTGAAGACAATTGAAG
1 ATTTGAAGACAATTGAAG
17311 A
1 A
17312 ATTAATTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32
Consensus pattern (18 bp):
ATTTGAAGACAATTGAAG
Done.