Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007219.1 Corchorus capsularis cultivar CVL-1 contig07240, 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: 39019
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:2679 original size:19 final size:18
Alignment explanation
Indices: 2646--2681 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2636 TTGAAATAAT
2646 TCTTCAATAATCTTCAAA
1 TCTTCAATAATCTTCAAA
*
2664 TCTTCAAATTATCTTCAA
1 TCTTC-AATAATCTTCAA
2682 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.36, C:0.22, G:0.00, T:0.42
Consensus pattern (18 bp):
TCTTCAATAATCTTCAAA
Found at i:9824 original size:73 final size:73
Alignment explanation
Indices: 9718--9864 Score: 285
Period size: 73 Copynumber: 2.0 Consensus size: 73
9708 CATTGGTCTG
9718 TTTATTGAGTTAATGTACCGGCCCAAAATGCAAAATTGGCTTAAGAGAAACTACTCACTGTATCA
1 TTTATTGAGTTAATGTACCGGCCCAAAATGCAAAATTGGCTTAAGAGAAACTACTCACTGTATCA
9783 ACATGCAA
66 ACATGCAA
*
9791 TTTATTGAGTTAATGTACCGGCCCAAAATGCAAAATTGGCTTAAGAGAAACTACTTACTGTATCA
1 TTTATTGAGTTAATGTACCGGCCCAAAATGCAAAATTGGCTTAAGAGAAACTACTCACTGTATCA
9856 ACATGCAA
66 ACATGCAA
9864 T
1 T
9865 CATATTTCAA
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (73 bp):
TTTATTGAGTTAATGTACCGGCCCAAAATGCAAAATTGGCTTAAGAGAAACTACTCACTGTATCA
ACATGCAA
Found at i:14248 original size:21 final size:21
Alignment explanation
Indices: 14222--14270 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
14212 GCACTGGAGT
* * *
14222 ACATGGGTCGCGAGGCAAACC
1 ACATGGGGCGCCAAGCAAACC
14243 ACATGGGGCGCCAAGCAAACC
1 ACATGGGGCGCCAAGCAAACC
14264 ACATGGG
1 ACATGGG
14271 CGTCCAGCGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.31, C:0.29, G:0.33, T:0.08
Consensus pattern (21 bp):
ACATGGGGCGCCAAGCAAACC
Found at i:17164 original size:21 final size:21
Alignment explanation
Indices: 17125--17173 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
17115 TCAATGCTTT
**
17125 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCAATTTCAA
*
17147 AGGAAGCAAGAGCAATTTCCA
1 AGGAAGCAAGAGCAATTTCAA
17168 A-GAAGC
1 AGGAAGC
17174 TGCAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.43, C:0.14, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCAATTTCAA
Found at i:27125 original size:31 final size:31
Alignment explanation
Indices: 27087--27193 Score: 112
Period size: 31 Copynumber: 3.5 Consensus size: 31
27077 CAAGGCTAAT
27087 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
* * * * **
27118 TGCTCAAATAAGGACCCGATC-TTT--TAATT
1 TGCTCAAATAAGG-GCCTAACGTTTGCCAAAA
* *
27147 TGGTCAAATAAGGGCCTAAAGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
27178 TGCTCAAATAAGGGCC
1 TGCTCAAATAAGGGCC
27194 CCATCTTTGA
Statistics
Matches: 57, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
28 3 0.05
29 17 0.30
31 33 0.58
32 4 0.07
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.25
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
Found at i:27228 original size:49 final size:53
Alignment explanation
Indices: 27092--27242 Score: 184
Period size: 60 Copynumber: 2.8 Consensus size: 53
27082 CTAATTGCTC
* *
27092 AAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGACCCGATCTTTTAATTTGG
1 AAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATC---T--TTTGG
*
27150 TCAAATAAGGGCCTAAAGTTTGCCAAAATGCTCAAATAAGGGCCCCATC-TTT-G
1 --AAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTTGG
27203 -AA-AAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
1 AAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
27243 TGTCGCACGC
Statistics
Matches: 87, Mismatches: 4, Indels: 11
0.85 0.04 0.11
Matches are distributed among these distances:
49 37 0.43
50 2 0.02
53 1 0.01
54 3 0.03
60 44 0.51
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (53 bp):
AAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTTGG
Found at i:27309 original size:31 final size:30
Alignment explanation
Indices: 27271--27469 Score: 158
Period size: 31 Copynumber: 6.6 Consensus size: 30
27261 AATTGACATC
27271 AGGCCCTTATTTGAGCATTTTCGATAACGTT
1 AGGCCCTTATTTGAGCATTTTCGA-AACGTT
27302 AGGCCCTTATTTGAGCATTTTCGATAACGTT
1 AGGCCCTTATTTGAGCATTTTCGA-AACGTT
* ** * *
27333 AGGTCCTTATTTG-GCCAAATT--AAAAGATC
1 AGGCCCTTATTTGAG-CATTTTCGAAACG-TT
* *
27362 AGACCCTTATTTGAGCATTTTCGATAATGTT
1 AGGCCCTTATTTGAGCATTTTCGA-AACGTT
* ** * *
27393 AGGTCCTTATTTG-GCCAAATT--AAAAGAT
1 AGGCCCTTATTTGAG-CATTTTCGAAACGTT
* *
27421 CGGACCCTTATTTGAGCATTTTGGCAAACGTT
1 AGG-CCCTTATTTGAGCATTTTCG-AAACGTT
27453 AGGCCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
27470 ATTAGCCTTA
Statistics
Matches: 132, Mismatches: 24, Indels: 24
0.73 0.13 0.13
Matches are distributed among these distances:
28 9 0.07
29 31 0.23
30 4 0.03
31 78 0.59
32 10 0.08
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (30 bp):
AGGCCCTTATTTGAGCATTTTCGAAACGTT
Found at i:27374 original size:29 final size:29
Alignment explanation
Indices: 27337--27434 Score: 83
Period size: 29 Copynumber: 3.3 Consensus size: 29
27327 AACGTTAGGT
27337 CCTTATTTGGCCAAATTAAAAGATCAGAC
1 CCTTATTTGGCCAAATTAAAAGATCAGAC
** * * **
27366 CCTTATTTGAG-CATTTTCGATAATG-TTAGGT
1 CCTTATTTG-GCCAAATT--A-AAAGATCAGAC
*
27397 CCTTATTTGGCCAAATTAAAAGATCGGAC
1 CCTTATTTGGCCAAATTAAAAGATCAGAC
27426 CCTTATTTG
1 CCTTATTTG
27435 AGCATTTTGG
Statistics
Matches: 50, Mismatches: 13, Indels: 12
0.67 0.17 0.16
Matches are distributed among these distances:
28 3 0.06
29 25 0.50
30 2 0.04
31 17 0.34
32 3 0.06
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (29 bp):
CCTTATTTGGCCAAATTAAAAGATCAGAC
Found at i:27374 original size:60 final size:60
Alignment explanation
Indices: 27305--27465 Score: 270
Period size: 60 Copynumber: 2.7 Consensus size: 60
27295 TAACGTTAGG
27305 CCCTTATTTGAGCATTTTCGATAACGTTAGGTCCTTATTTGGCCAAATTAAAAGATCAGA
1 CCCTTATTTGAGCATTTTCGATAACGTTAGGTCCTTATTTGGCCAAATTAAAAGATCAGA
* *
27365 CCCTTATTTGAGCATTTTCGATAATGTTAGGTCCTTATTTGGCCAAATTAAAAGATCGGA
1 CCCTTATTTGAGCATTTTCGATAACGTTAGGTCCTTATTTGGCCAAATTAAAAGATCAGA
* *
27425 CCCTTATTTGAGCATTTTGGCA-AACGTTAGGCCCTTATTTG
1 CCCTTATTTGAGCATTTTCG-ATAACGTTAGGTCCTTATTTG
27466 AGCAATTAGC
Statistics
Matches: 95, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
60 94 0.99
61 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.37
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTCGATAACGTTAGGTCCTTATTTGGCCAAATTAAAAGATCAGA
Found at i:28621 original size:31 final size:29
Alignment explanation
Indices: 28551--28622 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 29
28541 ATTTTTAGCC
* * *
28551 GCCAATTTAAGGCTAAATCTTTCAAAGTT
1 GCCAATTTGAGGCTAAATCTTTAAAAATT
*
28580 GCTCAATTTGAGTCTAAATCTTTTAAAAATT
1 GC-CAATTTGAGGCTAAATC-TTTAAAAATT
28611 GACCAATTTGAG
1 G-CCAATTTGAG
28623 CATTAAAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 2 0.06
30 15 0.42
31 18 0.50
32 1 0.03
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (29 bp):
GCCAATTTGAGGCTAAATCTTTAAAAATT
Found at i:29321 original size:16 final size:16
Alignment explanation
Indices: 29302--29340 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
29292 TTTTTTATTG
*
29302 AAAAAATATTTTTTAA
1 AAAAAATATATTTTAA
*
29318 AAAATATATATTTTAA
1 AAAAAATATATTTTAA
*
29334 AGAAAAT
1 AAAAAAT
29341 GGGTGAGGGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
AAAAAATATATTTTAA
Found at i:30047 original size:12 final size:12
Alignment explanation
Indices: 30030--30057 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
30020 ACACGTTTAT
30030 ACGACACGAAAC
1 ACGACACGAAAC
30042 ACGACACGAAAC
1 ACGACACGAAAC
30054 ACGA
1 ACGA
30058 ATTGCCAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.32, G:0.18, T:0.00
Consensus pattern (12 bp):
ACGACACGAAAC
Found at i:30435 original size:19 final size:19
Alignment explanation
Indices: 30395--30431 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
30385 AATTTTTAGG
30395 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
*
30414 TAAAAATTTAATAT-TAAA
1 TAAAAATATAATATATAAA
30432 ATAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:34287 original size:16 final size:16
Alignment explanation
Indices: 34248--34358 Score: 91
Period size: 16 Copynumber: 6.9 Consensus size: 16
34238 GACCTAGGAT
* *
34248 CCGAATGACTCGTAAC
1 CCGAATGACCCGAAAC
* *
34264 CC-AGATGATCCGAGAC
1 CCGA-ATGACCCGAAAC
*
34280 CCGAATGACTCGAAAC
1 CCGAATGACCCGAAAC
* * *
34296 TCGAAGGACCCGTAAC
1 CCGAATGACCCGAAAC
* *
34312 CCGAGTGACCCGAGAC
1 CCGAATGACCCGAAAC
34328 CC-ATATGACCCGAAAC
1 CCGA-ATGACCCGAAAC
*
34344 CCGAATAACCCGAAA
1 CCGAATGACCCGAAA
34359 AGTTAACCCG
Statistics
Matches: 72, Mismatches: 19, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
15 2 0.03
16 68 0.94
17 2 0.03
ACGTcount: A:0.34, C:0.33, G:0.21, T:0.12
Consensus pattern (16 bp):
CCGAATGACCCGAAAC
Found at i:34355 original size:48 final size:48
Alignment explanation
Indices: 34248--34355 Score: 130
Period size: 48 Copynumber: 2.2 Consensus size: 48
34238 GACCTAGGAT
* * *
34248 CCGAATGACTCGTAACCCAGATGATCCGAGACCCGAATGACTCGAAAC
1 CCGAATGACCCGTAACCCAGATGACCCGAGACCCGAATGACCCGAAAC
* *
34296 TCGAAGGACCCGTAACCC-GAGTGACCCGAGACCC-ATATGACCCGAAAC
1 CCGAATGACCCGTAACCCAGA-TGACCCGAGACCCGA-ATGACCCGAAAC
*
34344 CCGAATAACCCG
1 CCGAATGACCCG
34356 AAAAGTTAAC
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
47 3 0.06
48 47 0.94
ACGTcount: A:0.32, C:0.34, G:0.21, T:0.12
Consensus pattern (48 bp):
CCGAATGACCCGTAACCCAGATGACCCGAGACCCGAATGACCCGAAAC
Found at i:34887 original size:42 final size:42
Alignment explanation
Indices: 34835--34917 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
34825 TGTTGATACA
*
34835 TACCCCACCTGATAATTAATTATGTATTTAATATTCAAAATC
1 TACCCCACCTGATAATCAATTATGTATTTAATATTCAAAATC
*
34877 TACCTCACCTGATAATCAATTATGTATTTAATATTCAAAAT
1 TACCCCACCTGATAATCAATTATGTATTTAATATTCAAAAT
34918 TGATATATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.39
Consensus pattern (42 bp):
TACCCCACCTGATAATCAATTATGTATTTAATATTCAAAATC
Found at i:35176 original size:16 final size:16
Alignment explanation
Indices: 35144--35244 Score: 93
Period size: 16 Copynumber: 6.4 Consensus size: 16
35134 CCCGTCCAAT
*
35144 CCGAGACCCG-GTAGAC
1 CCGAGACCCGAAT-GAC
*
35160 CTGAGACCCGAATGAC
1 CCGAGACCCGAATGAC
35176 CCG-GAACCCGAATGAC
1 CCGAG-ACCCGAATGAC
*
35192 CTGAGACCCGAATGAC
1 CCGAGACCCGAATGAC
* *
35208 CCAAAACCC-ATATGAC
1 CCGAGACCCGA-ATGAC
*
35224 CCGAAACCCGAATGA-
1 CCGAGACCCGAATGAC
35239 CCGAGA
1 CCGAGA
35245 AAACAACCTG
Statistics
Matches: 71, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
15 7 0.10
16 61 0.86
17 3 0.04
ACGTcount: A:0.34, C:0.35, G:0.23, T:0.09
Consensus pattern (16 bp):
CCGAGACCCGAATGAC
Found at i:35185 original size:32 final size:32
Alignment explanation
Indices: 35149--35240 Score: 114
Period size: 32 Copynumber: 2.9 Consensus size: 32
35139 CCAATCCGAG
**
35149 ACCCGGTA-GACCTGAGACCCGAATGACCCGGA
1 ACCC-GTATGACCTGAGACCCGAATGACCCAAA
*
35181 ACCCGAATGACCTGAGACCCGAATGACCCAAA
1 ACCCGTATGACCTGAGACCCGAATGACCCAAA
* * *
35213 ACCCATATGACCCGAAACCCGAATGACC
1 ACCCGTATGACCTGAGACCCGAATGACC
35241 GAGAAAACAA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
31 2 0.04
32 50 0.96
ACGTcount: A:0.34, C:0.36, G:0.21, T:0.10
Consensus pattern (32 bp):
ACCCGTATGACCTGAGACCCGAATGACCCAAA
Done.