Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008908.1 Corchorus capsularis cultivar CVL-1 contig08929, 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: 17757
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3426 original size:22 final size:22
Alignment explanation
Indices: 3398--3439 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
3388 ATCCTTCAAT
3398 GAGAATGTGAACCTCTTTGATG
1 GAGAATGTGAACCTCTTTGATG
*
3420 GAGAATGTGAGCCTCTTTGA
1 GAGAATGTGAACCTCTTTGA
3440 GCTCATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (22 bp):
GAGAATGTGAACCTCTTTGATG
Found at i:4051 original size:28 final size:28
Alignment explanation
Indices: 3983--4054 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
3973 GTAGATTAAG
*
3983 AATGACCAAAATACCCCCTAAATGCAAA
1 AATGACCAAAATGCCCCCTAAATGCAAA
* * **
4011 AATGAGCAAAATGCCCCCTAGATGTGAA
1 AATGACCAAAATGCCCCCTAAATGCAAA
4039 AATGACCAAAATGCCC
1 AATGACCAAAATGCCC
4055 ATGGATGACC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.44, C:0.26, G:0.14, T:0.15
Consensus pattern (28 bp):
AATGACCAAAATGCCCCCTAAATGCAAA
Found at i:6707 original size:26 final size:26
Alignment explanation
Indices: 6652--6699 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
6642 GGGTCTCTTA
* *
6652 GTGTGAATAAAATAATGGACCCTTGT
1 GTGTGAATAAAATAATGGACCATTGG
6678 GTGTGAATAAAAT-ATGG-CCATT
1 GTGTGAATAAAATAATGGACCATT
6700 AAGGGTGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.19
25 4 0.19
26 13 0.62
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.31
Consensus pattern (26 bp):
GTGTGAATAAAATAATGGACCATTGG
Found at i:11297 original size:14 final size:13
Alignment explanation
Indices: 11231--11511 Score: 78
Period size: 14 Copynumber: 19.9 Consensus size: 13
11221 AGTCAGCAAG
11231 AGTAAAATAGTAATT
1 AGTAAAA-AGTAA-T
11246 AGTAAAAAGTAA-
1 AGTAAAAAGTAAT
** *
11258 AGGTAATCAGTAAG
1 A-GTAAAAAGTAAT
*
11272 AGTAAGAGAGTAATT
1 AGTAA-AAAGTAA-T
*
11287 AGTAAAAAGTAAA
1 AGTAAAAAGTAAT
*** *
11300 AGGTAGTCAGTAAG
1 A-GTAAAAAGTAAT
*
11314 AGTAAGAGAGTAATT
1 AGTAA-AAAGTAA-T
*
11329 AGTAAAAAGTAAA
1 AGTAAAAAGTAAT
*** *
11342 AGGTAGTCAGTAAG
1 A-GTAAAAAGTAAT
*
11356 AGTAAGAGAGTAATT
1 AGTAA-AAAGTAA-T
*
11371 AGTAAAGAAGTAAAA
1 AGTAAA-AAGT-AAT
** *
11386 AGTAATCAGTAAG
1 AGTAAAAAGTAAT
*
11399 AGTAAGAGAGTAATT
1 AGTAA-AAAGTAA-T
*
11414 AGTAAAGAAGTAAA
1 AGTAAA-AAGTAAT
** *
11428 AGGTAATCAGTAAG
1 A-GTAAAAAGTAAT
11442 AGTAAAATAGTAAT
1 AGTAAAA-AGTAAT
* *
11456 CAGTAAAAAATAAA
1 -AGTAAAAAGTAAT
** *
11470 AGGTAGTAAGTAAG
1 A-GTAAAAAGTAAT
11484 AGTAAAATAGTAAT
1 AGTAAAA-AGTAAT
11498 CAGTAAAAAAGTAA
1 -AGT-AAAAAGTAA
11512 AAGGTAGTCA
Statistics
Matches: 194, Mismatches: 50, Indels: 44
0.67 0.17 0.15
Matches are distributed among these distances:
12 1 0.01
13 37 0.19
14 91 0.47
15 59 0.30
16 6 0.03
ACGTcount: A:0.53, C:0.02, G:0.22, T:0.22
Consensus pattern (13 bp):
AGTAAAAAGTAAT
Found at i:11382 original size:15 final size:14
Alignment explanation
Indices: 11356--11426 Score: 54
Period size: 15 Copynumber: 4.9 Consensus size: 14
11346 AGTCAGTAAG
11356 AGTAAGAGAGTAATT
1 AGTAAGA-AGTAATT
**
11371 AGTAAAGAAGTAAAA
1 AGT-AAGAAGTAATT
** *
11386 AGTAATCAGTAA-G
1 AGTAAGAAGTAATT
11399 AGTAAGAGAGTAATT
1 AGTAAGA-AGTAATT
11414 AGTAAAGAAGTAA
1 AGT-AAGAAGTAA
11427 AAGGTAATCA
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
13 5 0.11
14 12 0.27
15 19 0.43
16 8 0.18
ACGTcount: A:0.54, C:0.01, G:0.24, T:0.21
Consensus pattern (14 bp):
AGTAAGAAGTAATT
Found at i:11396 original size:43 final size:42
Alignment explanation
Indices: 11195--11679 Score: 541
Period size: 43 Copynumber: 11.3 Consensus size: 42
11185 GTTGGTAATC
* * * *
11195 AGTAATCAGTAAAAAAGGTAAAAGGTAGTCAGCAAGAGTAAAAT
1 AGTAATTAGT-AAAAA-GTAAAAGGTAATCAGTAAGAGTAAAAG
*
11239 AGTAATTAGTAAAAAGT-AAAGGTAATCAGTAAGAGTAAGAG
1 AGTAATTAGTAAAAAGTAAAAGGTAATCAGTAAGAGTAAAAG
* *
11280 AGTAATTAGTAAAAAGTAAAAGGTAGTCAGTAAGAGTAAGAG
1 AGTAATTAGTAAAAAGTAAAAGGTAATCAGTAAGAGTAAAAG
* *
11322 AGTAATTAGTAAAAAGTAAAAGGTAGTCAGTAAGAGTAAGAG
1 AGTAATTAGTAAAAAGTAAAAGGTAATCAGTAAGAGTAAAAG
* *
11364 AGTAATTAGTAAAGAAGTAAAAAGTAATCAGTAAGAGTAAGAG
1 AGTAATTAGTAAA-AAGTAAAAGGTAATCAGTAAGAGTAAAAG
*
11407 AGTAATTAGTAAAGAAGTAAAAGGTAATCAGTAAGAGTAAAAT
1 AGTAATTAGTAAA-AAGTAAAAGGTAATCAGTAAGAGTAAAAG
* * * * *
11450 AGTAATCAGTAAAAAATAAAAGGTAGTAAGTAAGAGTAAAAT
1 AGTAATTAGTAAAAAGTAAAAGGTAATCAGTAAGAGTAAAAG
* * *
11492 AGTAATCAGTAAAAAAGTAAAAGGTAGTCAGTAAGAGTAAGAG
1 AGTAATTAGT-AAAAAGTAAAAGGTAATCAGTAAGAGTAAAAG
* *
11535 AGTAATTAGTAAAGAAGTAAAACGTAATCAGTAAGAGTAAAAC
1 AGTAATTAGTAAA-AAGTAAAAGGTAATCAGTAAGAGTAAAAG
* *
11578 AGT-ATTCAGTACAAAAAGGTAATA-GTAATCAGTAAGAAGCAATAA-
1 AGTAATT-AGT--AAAAA-GTAAAAGGTAATCAGTAAG-AGTAA-AAG
* *
11623 A--AATCAGTAAAAAGTAAAAAGGTAATCAGTAAAAAGTAAAAAAG
1 AGTAATTAGTAAAAAGT-AAAAGGTAATCAGT-AAGAGT--AAAAG
*
11667 AGTAATCAGTAAA
1 AGTAATTAGTAAA
11680 GAAAAAATGG
Statistics
Matches: 392, Mismatches: 30, Indels: 36
0.86 0.07 0.08
Matches are distributed among these distances:
40 2 0.01
41 45 0.11
42 133 0.34
43 159 0.41
44 28 0.07
45 13 0.03
46 12 0.03
ACGTcount: A:0.53, C:0.04, G:0.22, T:0.21
Consensus pattern (42 bp):
AGTAATTAGTAAAAAGTAAAAGGTAATCAGTAAGAGTAAAAG
Found at i:11463 original size:128 final size:129
Alignment explanation
Indices: 11194--11682 Score: 629
Period size: 128 Copynumber: 3.8 Consensus size: 129
11184 AGTTGGTAAT
* *
11194 CAGTAATCAGTAAAAAAGGTAAAAGGTAGTCAGCAAGAGTAAAATAGTAATTAGTAAAAAGT-AA
1 CAGTAATCAGTAAAAAAGGTAAAAGGTAGTCAGTAAGAGTAAAATAGTAATCAGTAAAAAGTAAA
* * *
11258 AGGTAATCAGTAAGAGTAAGAGAGTAATTAGTAAA-AAGTAAAAGGTAGTCAGTAAGAGTAAGA
66 AAGTAATCAGTAAGAGTAAGAGAGTAATTAGTAAAGAAGTAAAAGGTAATCAGTAAGAGTAAAA
* * * * *
11321 GAGTAATTAGT-AAAAA-GTAAAAGGTAGTCAGTAAGAGTAAGAGAGTAATTAGTAAAGAAGTAA
1 CAGTAATCAGTAAAAAAGGTAAAAGGTAGTCAGTAAGAGTAAAATAGTAATCAGTAAA-AAGTAA
11384 AAAGTAATCAGTAAGAGTAAGAGAGTAATTAGTAAAGAAGTAAAAGGTAATCAGTAAGAGTAAAA
65 AAAGTAATCAGTAAGAGTAAGAGAGTAATTAGTAAAGAAGTAAAAGGTAATCAGTAAGAGTAAAA
* *
11449 TAGTAATCAGTAAAAAA--TAAAAGGTAGTAAGTAAGAGTAAAATAGTAATCAGTAAAAAAGTAA
1 CAGTAATCAGTAAAAAAGGTAAAAGGTAGTCAGTAAGAGTAAAATAGTAATCAGT-AAAAAGTAA
* * *
11512 AAGGTAGTCAGTAAGAGTAAGAGAGTAATTAGTAAAGAAGTAAAACGTAATCAGTAAGAGTAAAA
65 AAAGTAATCAGTAAGAGTAAGAGAGTAATTAGTAAAGAAGTAAAAGGTAATCAGTAAGAGTAAAA
* * * *
11577 CAGTATTCAGTACAAAAAGGTAATA-GTAATCAGTAAGAAGCAATAA-A--AATCAGTAAAAAGT
1 CAGTAATCAGTA-AAAAAGGTAAAAGGTAGTCAGTAAG-AGTAA-AATAGTAATCAGTAAAAAGT
* * *
11638 AAAAAGGTAATCAGTAAAAAGTAAAAAAGAGTAATCAGTAAAGAA
63 AAAAA-GTAATCAGT-AAGAGT--AAGAGAGTAATTAGTAAAGAA
11683 AAAATGGTAA
Statistics
Matches: 320, Mismatches: 28, Indels: 23
0.86 0.08 0.06
Matches are distributed among these distances:
125 37 0.12
126 9 0.03
127 45 0.14
128 156 0.49
129 28 0.09
130 15 0.05
131 9 0.03
132 21 0.07
ACGTcount: A:0.53, C:0.04, G:0.22, T:0.20
Consensus pattern (129 bp):
CAGTAATCAGTAAAAAAGGTAAAAGGTAGTCAGTAAGAGTAAAATAGTAATCAGTAAAAAGTAAA
AAGTAATCAGTAAGAGTAAGAGAGTAATTAGTAAAGAAGTAAAAGGTAATCAGTAAGAGTAAAA
Found at i:11671 original size:24 final size:22
Alignment explanation
Indices: 11196--11679 Score: 251
Period size: 21 Copynumber: 22.5 Consensus size: 22
11186 TTGGTAATCA
11196 GTAATCAGTAAAAAAGGT-AAAAG
1 GTAATCAGT-AAAAA-GTAAAAAG
* * *
11219 GTAGTCAG-CAAGAGTAAAATA-
1 GTAATCAGTAAAAAGTAAAA-AG
*
11240 GTAATTAGTAAAAAGT--AAAG
1 GTAATCAGTAAAAAGTAAAAAG
* *
11260 GTAATCAGT-AAGAGT-AAGAG
1 GTAATCAGTAAAAAGTAAAAAG
*
11280 AGTAATTAGTAAAAAGT-AAAAG
1 -GTAATCAGTAAAAAGTAAAAAG
* * *
11302 GTAGTCAGT-AAGAGT-AAGAG
1 GTAATCAGTAAAAAGTAAAAAG
*
11322 AGTAATTAGTAAAAAGT-AAAAG
1 -GTAATCAGTAAAAAGTAAAAAG
* * *
11344 GTAGTCAGT-AAGAGT-AAGAG
1 GTAATCAGTAAAAAGTAAAAAG
*
11364 AGTAATTAGTAAAGAAGTAAAAA-
1 -GTAATCAGTAAA-AAGTAAAAAG
* *
11387 GTAATCAGT-AAGAGT-AAGAG
1 GTAATCAGTAAAAAGTAAAAAG
*
11407 AGTAATTAGTAAAGAAGT-AAAAG
1 -GTAATCAGTAAA-AAGTAAAAAG
*
11430 GTAATCAGT-AAGAGTAAAATA-
1 GTAATCAGTAAAAAGTAAAA-AG
*
11451 GTAATCAGTAAAAAAT-AAAAG
1 GTAATCAGTAAAAAGTAAAAAG
* * *
11472 GTAGTAAGT-AAGAGTAAAATA-
1 GTAATCAGTAAAAAGTAAAA-AG
11493 GTAATCAGTAAAAAAGT-AAAAG
1 GTAATCAGT-AAAAAGTAAAAAG
* * *
11515 GTAGTCAGT-AAGAGT-AAGAG
1 GTAATCAGTAAAAAGTAAAAAG
* *
11535 AGTAATTAGTAAAGAAGT-AAAAC
1 -GTAATCAGTAAA-AAGTAAAAAG
*
11558 GTAATCAGT-AAGAGTAAAACA-
1 GTAATCAGTAAAAAGTAAAA-AG
* *
11579 GTATTCAGTACAAAAAGGT-AATA-
1 GTAATCAGT--AAAAA-GTAAAAAG
* *
11602 GTAATCAGTAAGAAGCAATAAA-
1 GTAATCAGTAAAAAGTAA-AAAG
11624 --AATCAGTAAAAAGTAAAAAG
1 GTAATCAGTAAAAAGTAAAAAG
11644 GTAATCAGTAAAAAGTAAAAAAG
1 GTAATCAGTAAAAAGT-AAAAAG
11667 AGTAATCAGTAAA
1 -GTAATCAGTAAA
11680 GAAAAAATGG
Statistics
Matches: 354, Mismatches: 65, Indels: 83
0.71 0.13 0.17
Matches are distributed among these distances:
19 12 0.03
20 71 0.20
21 118 0.33
22 88 0.25
23 43 0.12
24 20 0.06
25 2 0.01
ACGTcount: A:0.53, C:0.04, G:0.22, T:0.21
Consensus pattern (22 bp):
GTAATCAGTAAAAAGTAAAAAG
Found at i:11741 original size:53 final size:55
Alignment explanation
Indices: 11668--11789 Score: 167
Period size: 53 Copynumber: 2.3 Consensus size: 55
11658 GTAAAAAAGA
*
11668 GTAATCAGTAAAGAAAAAATGGTAAAGAGTAAAGAGTAATCAGCAAAGGA-AATG
1 GTAATCAGTAAAGAAAAAATGGTAAAGAGTAAAGAGTAATCAGCAAAGAATAATG
* * * *
11722 GTAATTAGTAGAG-AAAAATGGTAAAGAGTAATGAGTAATCAGTAAAGAATAATG
1 GTAATCAGTAAAGAAAAAATGGTAAAGAGTAAAGAGTAATCAGCAAAGAATAATG
**
11776 GTAAAGAGTAAAGA
1 GTAATCAGTAAAGA
11790 GTAATCAGTA
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
53 33 0.57
54 25 0.43
ACGTcount: A:0.52, C:0.03, G:0.25, T:0.20
Consensus pattern (55 bp):
GTAATCAGTAAAGAAAAAATGGTAAAGAGTAAAGAGTAATCAGCAAAGAATAATG
Found at i:11776 original size:34 final size:34
Alignment explanation
Indices: 11718--11845 Score: 147
Period size: 34 Copynumber: 3.8 Consensus size: 34
11708 CAGCAAAGGA
* * *
11718 AATG-GTAATTAGTAGAGAAAAATGGTAAAGAGT
1 AATGAGTAATCAGTAAAGAATAATGGTAAAGAGT
11751 AATGAGTAATCAGTAAAGAATAATGGTAAAGAGT
1 AATGAGTAATCAGTAAAGAATAATGGTAAAGAGT
*
11785 AAAGAGTAATCAGTAAAGGAA-AATGGTAAAGAGT
1 AATGAGTAATCAGTAAA-GAATAATGGTAAAGAGT
*
11819 AAAAT-ATTAATCAGTAAA-AAGTAATGG
1 --AATGAGTAATCAGTAAAGAA-TAATGG
11846 CAATCAGTAA
Statistics
Matches: 83, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
33 6 0.07
34 55 0.66
35 20 0.24
36 2 0.02
ACGTcount: A:0.52, C:0.02, G:0.23, T:0.23
Consensus pattern (34 bp):
AATGAGTAATCAGTAAAGAATAATGGTAAAGAGT
Done.