Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015095.1 Corchorus capsularis cultivar CVL-1 contig15116, 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: 25637
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Found at i:1648 original size:22 final size:22
Alignment explanation
Indices: 1558--1730 Score: 120
Period size: 22 Copynumber: 7.9 Consensus size: 22
1548 TCATAGTGTT
**
1558 GGTTATCAAAATTTCATTGGAA
1 GGTTATCAAAATTTCATAAGAA
* *
1580 AGTTATCAAAATTTCATATTG-A
1 GGTTATCAAAATTTCATA-AGAA
* * * *
1602 GGTCT-TCAAAATTCCTTAGGGA
1 GGT-TATCAAAATTTCATAAGAA
*
1624 GGTTAACAAAATTTCATAAGAA
1 GGTTATCAAAATTTCATAAGAA
** *
1646 GGTTAAAAAGAATTT-ATAAAAA
1 GGTTATCAA-AATTTCATAAGAA
* *
1668 GGTTCTCGAAATTTCATAA-AA
1 GGTTATCAAAATTTCATAAGAA
* * * *
1689 TCGTTATTAAAATTTTATAGGAA
1 -GGTTATCAAAATTTCATAAGAA
1712 GGTTATCAAAATTTCATAA
1 GGTTATCAAAATTTCATAA
1731 TGAGATCATA
Statistics
Matches: 115, Mismatches: 28, Indels: 16
0.72 0.18 0.10
Matches are distributed among these distances:
21 9 0.08
22 97 0.84
23 9 0.08
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAAGAA
Found at i:1882 original size:15 final size:16
Alignment explanation
Indices: 1862--1891 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1852 CGGTCCAAAG
1862 AAAAGAAAAA-AAAAA
1 AAAAGAAAAACAAAAA
1877 AAAAGAAAAACAAAA
1 AAAAGAAAAACAAAA
1892 CTACTACCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.90, C:0.03, G:0.07, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAACAAAAA
Found at i:3875 original size:20 final size:20
Alignment explanation
Indices: 3843--3881 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3833 GTTAATTAGC
*
3843 TGATTATAGTATTATTATTA
1 TGATTATAGTATTAATATTA
3863 TGATATATA-TATTAATATT
1 TGAT-TATAGTATTAATATT
3882 GTCGTACTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (20 bp):
TGATTATAGTATTAATATTA
Found at i:11305 original size:333 final size:331
Alignment explanation
Indices: 10700--11356 Score: 977
Period size: 333 Copynumber: 2.0 Consensus size: 331
10690 TTGCTCGTTT
** * * *
10700 TAAGAAGCTTCTGCAGCTAGTGACTGTGCGATTGCTCCTCTTTTTATTTGATAGTATTATCTGAA
1 TAAGAAGCTTCTGCAGCTAGCAACTGTACGATTGCACCTCTTTTTATATGATAGTATTATCTGAA
* *
10765 AGATTTTCTTCTTCATTGCCATTTTTGTTATCTGTCATTCTAAAACTTTTTTTTTCCTGAAAAAT
66 AGATTTTCTACTTCATTGCCATATTTGTTATCTGTCATTCTAAAACTTTTTTTTTCCTGAAAAAT
* * * * *
10830 TACCCACAAACTCTAAACTTTTCTTTGTCTAATGCAGGCAGAATGTCAGTTATACGGGTTGGTCC
131 TACCCACAAACCCTAAACTTGTCTGTGTCTAATGCAGGCAGAATGCCAGTTATACAGGTTGG-CC
10895 TCCTTATGGTACCAATACTAGGGGAATTGCTCCTTACAACCACCGTGTGTCCGGTGTTCCTGGTA
195 TCCTTATGGTACCAATACTAGGGGAATTGCTCCTTACAACCACCGTGTGTCCGGTGTTCCTGGTA
*
10960 TCTCTCTGCCTTTGTGTTTCAATACTTTTGTTTCTGCCATTGGAATTGTTTTCCCTTTAATCTTT
260 TCTCTCTGCCTTTGTGCTTCAATACTTTTGTTTCTGCCATTGGAATTGTTTTCCCTTTAATCTTT
11025 ATATCAA
325 ATATCAA
*
11032 TAAGAAGCTTCTGCAGCTAGCAACTGTATGATTGCACCTCTTTTTATATGATAGTATTATCTGAA
1 TAAGAAGCTTCTGCAGCTAGCAACTGTACGATTGCACCTCTTTTTATATGATAGTATTATCTGAA
*
11097 AGATTTTCTACTTCATTTTGCCA-ATTTGTTAAT-TGTCATTCTAAAACTTTTTTTTTTTTTTTC
66 AGATTTTCTACTTCA--TTGCCATATTTGTT-ATCTGTCATTCTAAAAC-----TTTTTTTTTCC
* * * * *
11160 TG-AAAGTT-TCCTCAAACCCTAAACTTGTCTGTGTCTAATGCAGTCAGAATGCCAGTTCTACAG
123 TGAAAAATTACCCACAAACCCTAAACTTGTCTGTGTCTAATGCAGGCAGAATGCCAGTTATACAG
*
11223 GTT-G-CTCCTTATGGTACCAATACTAGGGGAATTGCTCCTTACCACCACCGTGTG-CCTGGTGT
188 GTTGGCCTCCTTATGGTACCAATACTAGGGGAATTGCTCCTTACAACCACCGTGTGTCC-GGTGT
*
11285 TCCTGGTATCTCTCTGCCTTTGTGCTTCAGTACTTTTGTTTCTGCCATTGGAATTGTTTTCCCTT
252 TCCTGGTATCTCTCTGCCTTTGTGCTTCAATACTTTTGTTTCTGCCATTGGAATTGTTTTCCCTT
11350 TAATCTT
317 TAATCTT
11357 CTAATTCTCT
Statistics
Matches: 294, Mismatches: 22, Indels: 17
0.88 0.07 0.05
Matches are distributed among these distances:
332 75 0.26
333 144 0.49
334 8 0.03
335 1 0.00
336 49 0.17
337 5 0.02
338 12 0.04
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.42
Consensus pattern (331 bp):
TAAGAAGCTTCTGCAGCTAGCAACTGTACGATTGCACCTCTTTTTATATGATAGTATTATCTGAA
AGATTTTCTACTTCATTGCCATATTTGTTATCTGTCATTCTAAAACTTTTTTTTTCCTGAAAAAT
TACCCACAAACCCTAAACTTGTCTGTGTCTAATGCAGGCAGAATGCCAGTTATACAGGTTGGCCT
CCTTATGGTACCAATACTAGGGGAATTGCTCCTTACAACCACCGTGTGTCCGGTGTTCCTGGTAT
CTCTCTGCCTTTGTGCTTCAATACTTTTGTTTCTGCCATTGGAATTGTTTTCCCTTTAATCTTTA
TATCAA
Found at i:11589 original size:33 final size:33
Alignment explanation
Indices: 11544--11611 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
11534 CCTCGTCAAG
11544 GAGGTGGAGAAGGAGGAATCCCTTGTGAAACTT
1 GAGGTGGAGAAGGAGGAATCCCTTGTGAAACTT
*
11577 GAGGTGGTGAAGGAGGAATCCCTTGTGAAACTT
1 GAGGTGGAGAAGGAGGAATCCCTTGTGAAACTT
11610 GA
1 GA
11612 TTCTAATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.29, C:0.12, G:0.37, T:0.22
Consensus pattern (33 bp):
GAGGTGGAGAAGGAGGAATCCCTTGTGAAACTT
Found at i:12103 original size:21 final size:22
Alignment explanation
Indices: 12054--12103 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
12044 TGAGCGTTGA
*
12054 TGGTATATATCAAGTAAAGAGC
1 TGGTATAAATCAAGTAAAGAGC
* *
12076 AGTGTATAAATCAAGTGAAGAG-
1 TG-GTATAAATCAAGTAAAGAGC
12098 TGGTAT
1 TGGTAT
12104 TTAACAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 4 0.17
22 2 0.09
23 17 0.74
ACGTcount: A:0.40, C:0.06, G:0.26, T:0.28
Consensus pattern (22 bp):
TGGTATAAATCAAGTAAAGAGC
Found at i:18187 original size:45 final size:44
Alignment explanation
Indices: 18057--18191 Score: 162
Period size: 45 Copynumber: 3.0 Consensus size: 44
18047 TGATTCATTC
* * * * *
18057 ACATCAGCAGCCACAGGAGTTTGAGGGTCATTGGCCCCATCATTG
1 ACATCAGCAGCCACAGGAATTTG-GGGTCATTGACCCCATTAGTA
* * *
18102 ACATCAGCAGCCACTGGATTTTGGGGGTTATTGACCCCATTAGTA
1 ACATCAGCAGCCACAGGAATTT-GGGGTCATTGACCCCATTAGTA
*
18147 ACATCAGCAGCCACCGGAATTTGGGAGTCATTGACCCCATTAGTA
1 ACATCAGCAGCCACAGGAATTTGGG-GTCATTGACCCCATTAGTA
18192 GAATTACACA
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
44 3 0.04
45 74 0.95
46 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.24
Consensus pattern (44 bp):
ACATCAGCAGCCACAGGAATTTGGGGTCATTGACCCCATTAGTA
Found at i:22020 original size:16 final size:16
Alignment explanation
Indices: 21999--22044 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
21989 TAGATATTTT
21999 TCTCGGGTTATTCGGG
1 TCTCGGGTTATTCGGG
* *
22015 TCTCGGGTCATTTGGG
1 TCTCGGGTTATTCGGG
22031 T-TCGGGTTATTCGG
1 TCTCGGGTTATTCGG
22045 ATTTCGGGTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
15 11 0.42
16 15 0.58
ACGTcount: A:0.07, C:0.17, G:0.37, T:0.39
Consensus pattern (16 bp):
TCTCGGGTTATTCGGG
Found at i:22037 original size:15 final size:16
Alignment explanation
Indices: 21999--22054 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 16
21989 TAGATATTTT
*
21999 TCTCGGGTTATTCGGG
1 TCTCGGGTCATTCGGG
*
22015 TCTCGGGTCATTTGGG
1 TCTCGGGTCATTCGGG
* *
22031 T-TCGGGTTATTCGGA
1 TCTCGGGTCATTCGGG
*
22046 TTTCGGGTC
1 TCTCGGGTC
22055 TCGAGTCATA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
15 12 0.36
16 21 0.64
ACGTcount: A:0.07, C:0.18, G:0.36, T:0.39
Consensus pattern (16 bp):
TCTCGGGTCATTCGGG
Found at i:22406 original size:42 final size:42
Alignment explanation
Indices: 22342--22423 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
22332 TAGATATTAA
22342 TTTTAAATATTAAATACATAATTGA-TTATCAGGTGAGGTAGG
1 TTTTAAATATTAAATACATAATT-ATTTATCAGGTGAGGTAGG
* * *
22384 TTTTGAATATTAAATATATAATTATTTATTAGGTGAGGTA
1 TTTTAAATATTAAATACATAATTATTTATCAGGTGAGGTA
22424 TGTGTCAACA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 1 0.03
42 35 0.97
ACGTcount: A:0.38, C:0.02, G:0.17, T:0.43
Consensus pattern (42 bp):
TTTTAAATATTAAATACATAATTATTTATCAGGTGAGGTAGG
Found at i:23068 original size:16 final size:16
Alignment explanation
Indices: 23049--23132 Score: 84
Period size: 16 Copynumber: 5.2 Consensus size: 16
23039 GGATCACTCA
23049 GGTTACGGGTCATTCG
1 GGTTACGGGTCATTCG
*
23065 GGTTTCGGGTCA-TCTG
1 GGTTACGGGTCATTC-G
*
23081 GGTAACGGGTCATTCG
1 GGTTACGGGTCATTCG
23097 GGTCT-CGGGTCA-TCTG
1 GGT-TACGGGTCATTC-G
* *
23113 GGTTGCGGGTCATTCA
1 GGTTACGGGTCATTCG
23129 GGTT
1 GGTT
23133 CGTGGGGTCT
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
15 5 0.09
16 48 0.84
17 4 0.07
ACGTcount: A:0.11, C:0.19, G:0.38, T:0.32
Consensus pattern (16 bp):
GGTTACGGGTCATTCG
Found at i:23094 original size:32 final size:32
Alignment explanation
Indices: 23053--23132 Score: 124
Period size: 32 Copynumber: 2.5 Consensus size: 32
23043 CACTCAGGTT
23053 ACGGGTCATTCGGGTTTCGGGTCATCTGGGTA
1 ACGGGTCATTCGGGTTTCGGGTCATCTGGGTA
* *
23085 ACGGGTCATTCGGGTCTCGGGTCATCTGGGTT
1 ACGGGTCATTCGGGTTTCGGGTCATCTGGGTA
* *
23117 GCGGGTCATTCAGGTT
1 ACGGGTCATTCGGGTT
23133 CGTGGGGTCT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.11, C:0.20, G:0.38, T:0.31
Consensus pattern (32 bp):
ACGGGTCATTCGGGTTTCGGGTCATCTGGGTA
Found at i:24502 original size:13 final size:13
Alignment explanation
Indices: 24464--24502 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
24454 TCTCCAGATA
* *
24464 ATCTTCAGTTGAA
1 ATCTTCTGTTGAT
*
24477 ATCTTCTGATGAT
1 ATCTTCTGTTGAT
24490 ATCTTCTGTTGAT
1 ATCTTCTGTTGAT
24503 TCTCTGGAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (13 bp):
ATCTTCTGTTGAT
Done.