Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012278.1 Corchorus capsularis cultivar CVL-1 contig12299, 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: 32654
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Found at i:4063 original size:32 final size:28
Alignment explanation
Indices: 3982--4243 Score: 133
Period size: 26 Copynumber: 9.1 Consensus size: 28
3972 TATTTTCTTC
3982 AAAAGTCCTCAAACACAAGGGCATTTAT
1 AAAAGTCCTCAAACACAAGGGCATTTAT
4010 --AAGTCC-CTAAACAC-AGAGGCATCTATACT
1 AAAAGTCCTC-AAACACAAG-GGCAT-T-TA-T
*
4039 AAAAAGTCCTCAAACACAAGGGCATTCAT
1 -AAAAGTCCTCAAACACAAGGGCATTTAT
* *
4068 --AAGTCC-CTAAACAC-AGAAGTATCTATACT
1 AAAAGTCCTC-AAACACAAG-GGCAT-T-TA-T
*
4097 AAAAAGTCCTCAAACACAAGGGCATTCAT
1 -AAAAGTCCTCAAACACAAGGGCATTTAT
*
4126 --AAGTCC-CTAAACGC-AGAGGCATCTATACT
1 AAAAGTCCTC-AAACACAAG-GGCAT-T-TA-T
*
4155 AAAAAGTCCTCAAACACAAGGGCATTCAT
1 -AAAAGTCCTCAAACACAAGGGCATTTAT
4184 --AAGTCC-CTAAACAC-AGAGGCATCTATACT
1 AAAAGTCCTC-AAACACAAG-GGCAT-T-TA-T
*
4213 AAAAAGTCCTCAAACACAAGGGCATTCAT
1 -AAAAGTCCTCAAACACAAGGGCATTTAT
4242 AA
1 AA
4244 GTCCCTAAAC
Statistics
Matches: 181, Mismatches: 13, Indels: 80
0.66 0.05 0.29
Matches are distributed among these distances:
25 12 0.07
26 65 0.36
27 4 0.02
28 7 0.04
29 8 0.04
30 4 0.02
31 4 0.02
32 65 0.36
33 12 0.07
ACGTcount: A:0.42, C:0.25, G:0.14, T:0.19
Consensus pattern (28 bp):
AAAAGTCCTCAAACACAAGGGCATTTAT
Found at i:4072 original size:58 final size:58
Alignment explanation
Indices: 3982--4268 Score: 538
Period size: 58 Copynumber: 4.9 Consensus size: 58
3972 TATTTTCTTC
*
3982 AAAAGTCCTCAAACACAAGGGCATTTATAAGTCCCTAAACACAGAGGCATCTATACTA
1 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
* *
4040 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAAGTATCTATACTA
1 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
*
4098 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACGCAGAGGCATCTATACTA
1 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
4156 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
1 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
4214 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATA
1 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATA
4269 TCAAAGTCCC
Statistics
Matches: 222, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 222 1.00
ACGTcount: A:0.41, C:0.25, G:0.14, T:0.20
Consensus pattern (58 bp):
AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
Found at i:5130 original size:35 final size:35
Alignment explanation
Indices: 5087--5186 Score: 96
Period size: 35 Copynumber: 2.9 Consensus size: 35
5077 ACATATTTCA
*
5087 TCAT-ATTCAACACTTGGGGACTCCAACAACCCCT
1 TCATCATTCAACACTTGGGGACTCCAACAACCCAT
* ** * *
5121 TCATCATTCAACAGTTGGATACTCCAGCAACTCAT
1 TCATCATTCAACACTTGGGGACTCCAACAACCCAT
* * *
5156 TC-TCCATTCAATACTTGGGGGCTTCAACAAC
1 TCAT-CATTCAACACTTGGGGACTCCAACAAC
5187 GAAAATTTCA
Statistics
Matches: 51, Mismatches: 13, Indels: 3
0.76 0.19 0.04
Matches are distributed among these distances:
34 5 0.10
35 46 0.90
ACGTcount: A:0.29, C:0.31, G:0.13, T:0.27
Consensus pattern (35 bp):
TCATCATTCAACACTTGGGGACTCCAACAACCCAT
Found at i:5658 original size:72 final size:72
Alignment explanation
Indices: 5541--5887 Score: 468
Period size: 72 Copynumber: 4.8 Consensus size: 72
5531 GTCTTCTTCT
* * *
5541 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGACAGCCCTTCGCACAATCCTTACATGATC
1 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATA
*
5606 ATCATCT
66 ATCATCA
* * * *
5613 TCATTGCGATTGTAGCCGAGACAGTTCCCACATGTGGCAGTCCTTCGCATAATCTTTACATGATA
1 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATA
*
5678 ATCTTCCA
66 ATCAT-CA
* * *
5686 T-ATTGCGGTTGTAGCCGAGGCAATTCCCACATTTGGAAGTCCTTCGCACAATCCTTACATGATA
1 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATA
*
5750 ATCTTCCA
66 ATCAT-CA
* * *** *
5758 T-ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAACCCTTATGCGATT
1 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATA
5822 AT-ATTCA
66 ATCA-TCA
5829 TCATTGCGATTGTAGCCGAGGCAGTTCCCACA-TTGGCAGTCCTTCGCACAATCCTTACA
1 TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACA
5888 ACTACCTTCC
Statistics
Matches: 244, Mismatches: 28, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
71 27 0.11
72 215 0.88
73 2 0.01
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (72 bp):
TCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATA
ATCATCA
Found at i:6315 original size:19 final size:19
Alignment explanation
Indices: 6291--6327 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6281 ACAACAAAGC
*
6291 TCGAAGCAGACTATCACAT
1 TCGAAGCACACTATCACAT
*
6310 TCGAAGCTCACTATCACA
1 TCGAAGCACACTATCACA
6328 AAATGGAAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.30, G:0.14, T:0.22
Consensus pattern (19 bp):
TCGAAGCACACTATCACAT
Found at i:6696 original size:20 final size:20
Alignment explanation
Indices: 6671--6708 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
6661 ATGAAGTGAC
*
6671 ATAGTTGCGGTAGAGACAAT
1 ATAGTTGCGGCAGAGACAAT
6691 ATAGTTGCGGCAGAGACA
1 ATAGTTGCGGCAGAGACA
6709 GAAGGATGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.13, G:0.32, T:0.21
Consensus pattern (20 bp):
ATAGTTGCGGCAGAGACAAT
Found at i:19928 original size:14 final size:13
Alignment explanation
Indices: 19903--19941 Score: 62
Period size: 14 Copynumber: 3.0 Consensus size: 13
19893 CATTTCCTTC
19903 TTTCTCTTTTTCT
1 TTTCTCTTTTTCT
19916 TTTCTCATTTTTCT
1 TTTCTC-TTTTTCT
19930 TTTCT-TTTTTCT
1 TTTCTCTTTTTCT
19942 CCATAATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 7 0.28
13 6 0.24
14 12 0.48
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTCTCTTTTTCT
Found at i:24756 original size:145 final size:145
Alignment explanation
Indices: 24493--24786 Score: 437
Period size: 145 Copynumber: 2.0 Consensus size: 145
24483 GTGTAGCATT
* * * * * *
24493 GTTGTCAGACCCAACCCGGCTCGGTAGGGTCACCCGATTAGCCCGGGACCCAGTTGTCTCTCCGG
1 GTTGTCAAACCCAACCCGGCTCGGCAGGGCCACCCGATTAGCCCGGGACCCAATGGCCTCTCCGG
* * * *
24558 GTCGGAGAGGGGTGTCATCCGGAAGTATGTTAACTCGGTCAACACTCGGAAAATCCGGTGGTTAA
66 GCCGGAGAAGGGTGTCATCCGGAAGCATGTTAACCCGGTCAACACTCGGAAAATCCGGTGGTTAA
* *
24623 CCCGGATCTGGATCG
131 CCCGGATCCGGACCG
*
24638 GTTGTCAAACCCAGCCCGGCTCGGCAGGGCCACCCGATTAGCCCGGGACCCAATGGCCAT-TCCG
1 GTTGTCAAACCCAACCCGGCTCGGCAGGGCCACCCGATTAGCCCGGGACCCAATGGCC-TCTCCG
* *
24702 GGCCGGAGAAGGGTGTCGTCCGGAAGCATGTTAGCCCGGTCAACACTCGGAAAATCCGGTGGTTA
65 GGCCGGAGAAGGGTGTCATCCGGAAGCATGTTAACCCGGTCAACACTCGGAAAATCCGGTGGTTA
24767 ACCCGGATCCGGACCG
130 ACCCGGATCCGGACCG
24783 GTTG
1 GTTG
24787 AATCGGTTTT
Statistics
Matches: 133, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
145 132 0.99
146 1 0.01
ACGTcount: A:0.20, C:0.30, G:0.32, T:0.19
Consensus pattern (145 bp):
GTTGTCAAACCCAACCCGGCTCGGCAGGGCCACCCGATTAGCCCGGGACCCAATGGCCTCTCCGG
GCCGGAGAAGGGTGTCATCCGGAAGCATGTTAACCCGGTCAACACTCGGAAAATCCGGTGGTTAA
CCCGGATCCGGACCG
Done.