Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008045.1 Corchorus capsularis cultivar CVL-1 contig08066, 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: 6700
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.32
Found at i:5042 original size:16 final size:17
Alignment explanation
Indices: 5003--5120 Score: 105
Period size: 17 Copynumber: 7.1 Consensus size: 17
4993 TGGTGACCTC
5003 ACCAGGTGAGTAT-TGT
1 ACCAGGTGAGTATCTGT
** *
5019 ACTGGGTGAGTATCT-C
1 ACCAGGTGAGTATCTGT
* *
5035 ACCAGGTGAGTGTTTGT
1 ACCAGGTGAGTATCTGT
*
5052 ACCAGGTGAGTATTTGT
1 ACCAGGTGAGTATCTGT
* *
5069 ACCAGGTGAGTGTTTGT
1 ACCAGGTGAGTATCTGT
* * * *
5086 ACCAGATGAGTGTTTAT
1 ACCAGGTGAGTATCTGT
*
5103 ACCAGGTGAGTATTTGT
1 ACCAGGTGAGTATCTGT
5120 A
1 A
5121 TTGGGTGAGT
Statistics
Matches: 85, Mismatches: 15, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
16 22 0.26
17 63 0.74
ACGTcount: A:0.23, C:0.13, G:0.31, T:0.34
Consensus pattern (17 bp):
ACCAGGTGAGTATCTGT
Found at i:5057 original size:17 final size:17
Alignment explanation
Indices: 5035--5120 Score: 136
Period size: 17 Copynumber: 5.1 Consensus size: 17
5025 TGAGTATCTC
5035 ACCAGGTGAGTGTTTGT
1 ACCAGGTGAGTGTTTGT
*
5052 ACCAGGTGAGTATTTGT
1 ACCAGGTGAGTGTTTGT
5069 ACCAGGTGAGTGTTTGT
1 ACCAGGTGAGTGTTTGT
* *
5086 ACCAGATGAGTGTTTAT
1 ACCAGGTGAGTGTTTGT
*
5103 ACCAGGTGAGTATTTGT
1 ACCAGGTGAGTGTTTGT
5120 A
1 A
5121 TTGGGTGAGT
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 62 1.00
ACGTcount: A:0.23, C:0.12, G:0.30, T:0.35
Consensus pattern (17 bp):
ACCAGGTGAGTGTTTGT
Found at i:5128 original size:51 final size:50
Alignment explanation
Indices: 5003--5131 Score: 170
Period size: 51 Copynumber: 2.6 Consensus size: 50
4993 TGGTGACCTC
* *
5003 ACCAGGTGAGTA-TTGTACTGGGTGAGTATCTCACCAGGTGAGTGTTTGT
1 ACCAGGTGAGTATTTGTACTGGGTGAGTATCTCACCAGATGAGTGTTTAT
** * * *
5052 ACCAGGTGAGTATTTGTACCAGGTGAGTGTTTGTACCAGATGAGTGTTTAT
1 ACCAGGTGAGTATTTGTACTGGGTGAGTATCT-CACCAGATGAGTGTTTAT
*
5103 ACCAGGTGAGTATTTGTATTGGGTGAGTA
1 ACCAGGTGAGTATTTGTACTGGGTGAGTA
5132 GGGTAGGAAC
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
49 12 0.18
50 15 0.22
51 40 0.60
ACGTcount: A:0.22, C:0.12, G:0.32, T:0.34
Consensus pattern (50 bp):
ACCAGGTGAGTATTTGTACTGGGTGAGTATCTCACCAGATGAGTGTTTAT
Found at i:5130 original size:34 final size:33
Alignment explanation
Indices: 5003--5120 Score: 139
Period size: 34 Copynumber: 3.5 Consensus size: 33
4993 TGGTGACCTC
** * *
5003 ACCAGGTGAGTA-TTGTACTGGGTGAGTATCTC
1 ACCAGGTGAGTATTTGTACCAGGTGAGTATTTT
*
5035 ACCAGGTGAGTGTTTGTACCAGGTGAGTATTTGT
1 ACCAGGTGAGTATTTGTACCAGGTGAGTATTT-T
* * *
5069 ACCAGGTGAGTGTTTGTACCAGATGAGTGTTTAT
1 ACCAGGTGAGTATTTGTACCAGGTGAGTATTT-T
5103 ACCAGGTGAGTATTTGTA
1 ACCAGGTGAGTATTTGTA
5121 TTGGGTGAGT
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
32 11 0.15
33 16 0.21
34 48 0.64
ACGTcount: A:0.23, C:0.13, G:0.31, T:0.34
Consensus pattern (33 bp):
ACCAGGTGAGTATTTGTACCAGGTGAGTATTTT
Found at i:5965 original size:12 final size:12
Alignment explanation
Indices: 5932--5965 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5922 CTTTTATGCT
5932 TTTTTTTTATAAC
1 TTTTTTTT-TAAC
*
5945 TTTTGTTTTAAC
1 TTTTTTTTTAAC
5957 TTTTTTTTT
1 TTTTTTTTT
5966 TTAAGAGAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76
Consensus pattern (12 bp):
TTTTTTTTTAAC
Found at i:6082 original size:40 final size:40
Alignment explanation
Indices: 6014--6112 Score: 157
Period size: 40 Copynumber: 2.5 Consensus size: 40
6004 CTAGCACATA
6014 TCAGGGGAGTCTCCCCTAGAGCAGAGCAAGAGAGTCTCCC
1 TCAGGGGAGTCTCCCCTAGAGCAGAGCAAGAGAGTCTCCC
*
6054 TCAGGGGAGTCTCCGCTA-ACGC-GCAGCAAGAGAGTCTCCC
1 TCAGGGGAGTCTCCCCTAGA-GCAG-AGCAAGAGAGTCTCCC
6094 TCAGGGGAGTCTCCCCTAG
1 TCAGGGGAGTCTCCCCTAG
6113 CGCACAACCA
Statistics
Matches: 54, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
39 2 0.04
40 52 0.96
ACGTcount: A:0.22, C:0.31, G:0.30, T:0.16
Consensus pattern (40 bp):
TCAGGGGAGTCTCCCCTAGAGCAGAGCAAGAGAGTCTCCC
Found at i:6409 original size:33 final size:33
Alignment explanation
Indices: 6362--6517 Score: 192
Period size: 33 Copynumber: 4.8 Consensus size: 33
6352 TAGCACGTAG
* * *
6362 CAAGCGAGTCTCCCCTGAGGGAGTCTTGCGTAA
1 CAAGGGAGTCTCCCCTGAGGGAGTCTCGCATAA
* * * *
6395 TACGGGAGTCTCCCCTGAGGGAGTCTC-CCT-T
1 CAAGGGAGTCTCCCCTGAGGGAGTCTCGCATAA
* *
6426 GAA-GGAGTCTCCCCTGAGGGAGTCTCGCATAG
1 CAAGGGAGTCTCCCCTGAGGGAGTCTCGCATAA
* *
6458 CAAGGGAGTCTCCCTTGAGGGAGTATCGCATAA
1 CAAGGGAGTCTCCCCTGAGGGAGTCTCGCATAA
6491 CAAGGGAGTCTCCCCTGAGGGAGTCTC
1 CAAGGGAGTCTCCCCTGAGGGAGTCTC
6518 CCCTGAAGGA
Statistics
Matches: 104, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
30 23 0.22
31 3 0.03
32 4 0.04
33 74 0.71
ACGTcount: A:0.21, C:0.27, G:0.31, T:0.21
Consensus pattern (33 bp):
CAAGGGAGTCTCCCCTGAGGGAGTCTCGCATAA
Found at i:6418 original size:15 final size:15
Alignment explanation
Indices: 6398--6532 Score: 126
Period size: 15 Copynumber: 8.6 Consensus size: 15
6388 TGCGTAATAC
6398 GGGAGTCTCCCCTGA
1 GGGAGTCTCCCCTGA
*
6413 GGGAGTCTCCCTTGA
1 GGGAGTCTCCCCTGA
*
6428 AGGAGTCTCCCCTGA
1 GGGAGTCTCCCCTGA
* *
6443 GGGAGTCTCGCATAGCAA
1 GGGAGTCTCCCCT-G--A
*
6461 GGGAGTCTCCCTTGA
1 GGGAGTCTCCCCTGA
* * * *
6476 GGGAGTATCGCATAACAA
1 GGGAGTCTCCCCT---GA
6494 GGGAGTCTCCCCTGA
1 GGGAGTCTCCCCTGA
6509 GGGAGTCTCCCCTGA
1 GGGAGTCTCCCCTGA
*
6524 AGGAGTCTC
1 GGGAGTCTC
6533 GCATAGCAAG
Statistics
Matches: 97, Mismatches: 17, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
15 72 0.74
16 1 0.01
17 1 0.01
18 23 0.24
ACGTcount: A:0.20, C:0.27, G:0.32, T:0.21
Consensus pattern (15 bp):
GGGAGTCTCCCCTGA
Found at i:6498 original size:96 final size:96
Alignment explanation
Indices: 6359--6532 Score: 276
Period size: 96 Copynumber: 1.8 Consensus size: 96
6349 ACCTAGCACG
* * * * *
6359 TAGCAAGCGAGTCTCCCCTGAGGGAGTCTTGCGTAATACGGGAGTCTCCCCTGAGGGAGTCTCCC
1 TAGCAAGCGAGTCTCCCCTGAGGGAGTATCGCATAACAAGGGAGTCTCCCCTGAGGGAGTCTCCC
*
6424 TTGAAGGAGTCTCCCCTGAGGGAGTCTCGCA
66 CTGAAGGAGTCTCCCCTGAGGGAGTCTCGCA
* *
6455 TAGCAAGGGAGTCTCCCTTGAGGGAGTATCGCATAACAAGGGAGTCTCCCCTGAGGGAGTCTCCC
1 TAGCAAGCGAGTCTCCCCTGAGGGAGTATCGCATAACAAGGGAGTCTCCCCTGAGGGAGTCTCCC
6520 CTGAAGGAGTCTC
66 CTGAAGGAGTCTC
6533 GCATAGCAAG
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
96 70 1.00
ACGTcount: A:0.21, C:0.27, G:0.31, T:0.21
Consensus pattern (96 bp):
TAGCAAGCGAGTCTCCCCTGAGGGAGTATCGCATAACAAGGGAGTCTCCCCTGAGGGAGTCTCCC
CTGAAGGAGTCTCCCCTGAGGGAGTCTCGCA
Found at i:6535 original size:48 final size:48
Alignment explanation
Indices: 6367--6551 Score: 187
Period size: 48 Copynumber: 3.9 Consensus size: 48
6357 CGTAGCAAGC
* * * * *
6367 GAGTCTCCCCTGAGGGAGTCTTGCGTAATACGGGAGTCTCCCCTGAGG
1 GAGTCTCCCCTGAAGGAGTCTCGCATAACAAGGGAGTCTCCCCTGAGG
* * * * * *
6415 GAGTCTCCCTTGAAGGAGTCTCCCCT---GAGGGAGTCTCGCATAGCAAGG
1 GAGTCTCCCCTGAAGGAGTCTCGCATAACAAGGGAGTCTCCCCT-G--AGG
* * *
6463 GAGTCTCCCTTGAGGGAGTATCGCATAACAAGGGAGTCTCCCCTGAGG
1 GAGTCTCCCCTGAAGGAGTCTCGCATAACAAGGGAGTCTCCCCTGAGG
*
6511 GAGTCTCCCCTGAAGGAGTCTCGCATAGCAAGGGAGTCTCC
1 GAGTCTCCCCTGAAGGAGTCTCGCATAACAAGGGAGTCTCC
6552 TTTAAGAGAA
Statistics
Matches: 111, Mismatches: 20, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
45 11 0.10
46 1 0.01
48 86 0.77
50 1 0.01
51 12 0.11
ACGTcount: A:0.21, C:0.27, G:0.31, T:0.21
Consensus pattern (48 bp):
GAGTCTCCCCTGAAGGAGTCTCGCATAACAAGGGAGTCTCCCCTGAGG
Found at i:6545 original size:33 final size:33
Alignment explanation
Indices: 6508--6617 Score: 141
Period size: 33 Copynumber: 3.3 Consensus size: 33
6498 GTCTCCCCTG
6508 AGGGAGTCTCCCCTGAAGGAGTCTCGCATAGCA
1 AGGGAGTCTCCCCTGAAGGAGTCTCGCATAGCA
* * * *** *
6541 AGGGAGTCT-CCTTTAAGAGAATCTTATATAGTA
1 AGGGAGTCTCCCCTGAAG-GAGTCTCGCATAGCA
6574 AGGGAGTCTCCCCTGAAGGAGTCTCGCATAGCA
1 AGGGAGTCTCCCCTGAAGGAGTCTCGCATAGCA
6607 AGGGAGTCTCC
1 AGGGAGTCTCC
6618 TTTAAGAGAA
Statistics
Matches: 61, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
32 6 0.10
33 49 0.80
34 6 0.10
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (33 bp):
AGGGAGTCTCCCCTGAAGGAGTCTCGCATAGCA
Found at i:6545 original size:66 final size:63
Alignment explanation
Indices: 6429--6618 Score: 152
Period size: 66 Copynumber: 2.9 Consensus size: 63
6419 CTCCCTTGAA
* * * *
6429 GGAGTCTCCCCTGAGGGAGTCTCGCATAGCAAGGGAGTCTC-CCTTG--AGGGAGTATCGCATAA
1 GGAGTCTCCCCTGAGGGAGTCTCCCCT-G-AA-GGAGTCTCGCATAGCAAGGGAGTATC-C-T-A
6491 CAAG
60 CAAG
* **
6495 GGAGTCTCCCCTGAGGGAGTCTCCCCTGAAGGAGTCTCGCATAGCAAGGGAGTCTCCTTTAAG
1 GGAGTCTCCCCTGAGGGAGTCTCCCCTGAAGGAGTCTCGCATAGCAAGGGAGTATCCTACAAG
* * **** *
6558 AGAATCTTATATAGTAAGGGAGTCTCCCCTGAAGGAGTCTCGCATAGCAAGGGAGTCTCCT
1 GGAGTCTCCCCT-G--AGGGAGTCTCCCCTGAAGGAGTCTCGCATAGCAAGGGAGTATCCT
6619 TTAAGAGAAT
Statistics
Matches: 105, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
63 17 0.16
64 7 0.07
65 2 0.02
66 79 0.75
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.22
Consensus pattern (63 bp):
GGAGTCTCCCCTGAGGGAGTCTCCCCTGAAGGAGTCTCGCATAGCAAGGGAGTATCCTACAAG
Found at i:6577 original size:81 final size:81
Alignment explanation
Indices: 6412--6598 Score: 261
Period size: 81 Copynumber: 2.3 Consensus size: 81
6402 GTCTCCCCTG
* *
6412 AGGGAGTCTCCCTTGAAGGAGTCTCCCCTGAGGGAGTCTCGCATAGCAAGGGAGTCTCCCTTGAG
1 AGGGAGTCTCCCCTGAAGGAGTCTCCCCTGAAGGAGTCTCGCATAGCAAGGGAGTCTCCCTTGAG
* *
6477 GGAGTATCGCATAACA
66 AGAGAATCGCATAACA
* *
6493 AGGGAGTCTCCCCTGAGGGAGTCTCCCCTGAAGGAGTCTCGCATAGCAAGGGAGTCT-CCTTTA-
1 AGGGAGTCTCCCCTGAAGGAGTCTCCCCTGAAGGAGTCTCGCATAGCAAGGGAGTCTCCCTTGAG
** *
6556 AGAGAATCTTATATAGTA
66 AGAGAATCGCATA-A-CA
6574 AGGGAGTCTCCCCTGAAGGAGTCTC
1 AGGGAGTCTCCCCTGAAGGAGTCTC
6599 GCATAGCAAG
Statistics
Matches: 94, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
79 9 0.10
80 6 0.06
81 79 0.84
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.22
Consensus pattern (81 bp):
AGGGAGTCTCCCCTGAAGGAGTCTCCCCTGAAGGAGTCTCGCATAGCAAGGGAGTCTCCCTTGAG
AGAGAATCGCATAACA
Found at i:6619 original size:66 final size:66
Alignment explanation
Indices: 6508--6651 Score: 288
Period size: 66 Copynumber: 2.2 Consensus size: 66
6498 GTCTCCCCTG
6508 AGGGAGTCTCCCCTGAAGGAGTCTCGCATAGCAAGGGAGTCTCCTTTAAGAGAATCTTATATAGT
1 AGGGAGTCTCCCCTGAAGGAGTCTCGCATAGCAAGGGAGTCTCCTTTAAGAGAATCTTATATAGT
6573 A
66 A
6574 AGGGAGTCTCCCCTGAAGGAGTCTCGCATAGCAAGGGAGTCTCCTTTAAGAGAATCTTATATAGT
1 AGGGAGTCTCCCCTGAAGGAGTCTCGCATAGCAAGGGAGTCTCCTTTAAGAGAATCTTATATAGT
6639 A
66 A
6640 AGGGAGTCTCCC
1 AGGGAGTCTCCC
6652 TGAGGAATTT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 78 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (66 bp):
AGGGAGTCTCCCCTGAAGGAGTCTCGCATAGCAAGGGAGTCTCCTTTAAGAGAATCTTATATAGT
A
Found at i:6643 original size:33 final size:33
Alignment explanation
Indices: 6535--6650 Score: 144
Period size: 33 Copynumber: 3.5 Consensus size: 33
6525 GGAGTCTCGC
6535 ATAGCAAGGGAGTCTCCTTTAAGAGAATCTTAT
1 ATAGCAAGGGAGTCTCCTTTAAGAGAATCTTAT
* * * * ***
6568 ATAGTAAGGGAGTCTCCCCTGAAG-GAGTCTCGC
1 ATAGCAAGGGAGTCT-CCTTTAAGAGAATCTTAT
6601 ATAGCAAGGGAGTCTCCTTTAAGAGAATCTTAT
1 ATAGCAAGGGAGTCTCCTTTAAGAGAATCTTAT
*
6634 ATAGTAAGGGAGTCTCC
1 ATAGCAAGGGAGTCTCC
6651 CTGAGGAATT
Statistics
Matches: 66, Mismatches: 15, Indels: 4
0.78 0.18 0.05
Matches are distributed among these distances:
32 6 0.09
33 54 0.82
34 6 0.09
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (33 bp):
ATAGCAAGGGAGTCTCCTTTAAGAGAATCTTAT
Done.