Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010301.1 Corchorus capsularis cultivar CVL-1 contig10322, 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: 41255
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:7813 original size:13 final size:13
Alignment explanation
Indices: 7768--7813 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
7758 GTATTTTTTT
7768 TTTATTTTGGTTA
1 TTTATTTTGGTTA
* *
7781 TTTTTTTTGGTGAAA
1 TTTATTTTGGT--TA
7796 TTTATTTTGGTTA
1 TTTATTTTGGTTA
7809 TTTAT
1 TTTAT
7814 CTACTATAGC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 16 0.59
15 11 0.41
ACGTcount: A:0.17, C:0.00, G:0.15, T:0.67
Consensus pattern (13 bp):
TTTATTTTGGTTA
Found at i:7847 original size:32 final size:32
Alignment explanation
Indices: 7809--7874 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
7799 ATTTTGGTTA
7809 TTTATCTACTATAGCCTATAAGATATATTTTG
1 TTTATCTACTATAGCCTATAAGATATATTTTG
7841 TTTATCTACTATAGCCTATAAGATATATTTTG
1 TTTATCTACTATAGCCTATAAGATATATTTTG
7873 TT
1 TT
7875 CAATTAGGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.48
Consensus pattern (32 bp):
TTTATCTACTATAGCCTATAAGATATATTTTG
Found at i:12521 original size:24 final size:25
Alignment explanation
Indices: 12494--12542 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
12484 CCGGTGTTTA
12494 GCCTCGTTTTTTC-GATGCAATATT
1 GCCTCGTTTTTTCTGATGCAATATT
*
12518 GCCTCTTTTTTTCTGATGCAATATT
1 GCCTCGTTTTTTCTGATGCAATATT
12543 TGATCGCCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.16, C:0.20, G:0.14, T:0.49
Consensus pattern (25 bp):
GCCTCGTTTTTTCTGATGCAATATT
Found at i:12758 original size:2 final size:2
Alignment explanation
Indices: 12751--12781 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
12741 TTTGAGATAG
12751 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12782 AACTTATTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19131 original size:20 final size:19
Alignment explanation
Indices: 19102--19152 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
19092 GGTTAAAGGC
* *
19102 TTTTTGTTTTTGTTTTTTT
1 TTTTTTTTTTTGTTTTTGT
19121 TTTTTTATTTTTGTTTTTGT
1 TTTTTT-TTTTTGTTTTTGT
*
19141 TCTTTTTTTTTG
1 TTTTTTTTTTTG
19153 CCAACAGATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.86
Consensus pattern (19 bp):
TTTTTTTTTTTGTTTTTGT
Found at i:19138 original size:26 final size:26
Alignment explanation
Indices: 19102--19151 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
19092 GGTTAAAGGC
*
19102 TTTTTGTTTTTGTTTTTTTTTTTTTA
1 TTTTTGTTTTTGTTCTTTTTTTTTTA
19128 TTTTTGTTTTTGTTCTTTTTTTTT
1 TTTTTGTTTTTGTTCTTTTTTTTT
19152 GCCAACAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.02, C:0.02, G:0.08, T:0.88
Consensus pattern (26 bp):
TTTTTGTTTTTGTTCTTTTTTTTTTA
Found at i:23035 original size:2 final size:2
Alignment explanation
Indices: 23028--23063 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
23018 AAGGTTACAT
*
23028 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23064 ATGCATCTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:23997 original size:5 final size:5
Alignment explanation
Indices: 23987--24027 Score: 82
Period size: 5 Copynumber: 8.2 Consensus size: 5
23977 TTAATTTGAA
23987 TGATT TGATT TGATT TGATT TGATT TGATT TGATT TGATT T
1 TGATT TGATT TGATT TGATT TGATT TGATT TGATT TGATT T
24028 TTGATTATAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.61
Consensus pattern (5 bp):
TGATT
Found at i:27778 original size:17 final size:17
Alignment explanation
Indices: 27751--27799 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
27741 TGTAATTTTT
*
27751 GATCACCGGTGATCTT-
1 GATCACTGGTGATCTTA
27767 GCATCACTGGTGATCTTA
1 G-ATCACTGGTGATCTTA
27785 GATCACTGGTGATCT
1 GATCACTGGTGATCT
27800 GGGGGTGATC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 1 0.03
17 28 0.93
18 1 0.03
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.33
Consensus pattern (17 bp):
GATCACTGGTGATCTTA
Found at i:32208 original size:21 final size:21
Alignment explanation
Indices: 32155--32209 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
32145 CGTGAAGTTT
32155 CTTCTTCTTCTTCTTCATCAA
1 CTTCTTCTTCTTCTTCATCAA
* *
32176 CTTCGTCATCTTCTTCATCCAA
1 CTTCTTCTTCTTCTTCAT-CAA
*
32198 -TTCTTGTTCTTC
1 CTTCTTCTTCTTC
32210 GTCGTCATCT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 25 0.89
22 3 0.11
ACGTcount: A:0.13, C:0.33, G:0.04, T:0.51
Consensus pattern (21 bp):
CTTCTTCTTCTTCTTCATCAA
Found at i:39738 original size:323 final size:322
Alignment explanation
Indices: 38859--41255 Score: 3163
Period size: 323 Copynumber: 7.4 Consensus size: 322
38849 ATGAGAAATT
* * *
38859 AATTGAG-AAAAATTTTTCGTGTCAGTTTTTTG-CGAAATCGTGTACTAACCATCACAGGTTTTT
1 AATTGAGAAAAAAATTTTCGGGTCAGTTTTTTGCCGAAATCGTGTACTAACCATCACGGGTTTTT
* * ** * *
38922 GCTAAAAACGCAATCCGATGCCCCGACTCAGTTTTATCTGATTTTTGGCGTAAAGACTCCTTGAA
66 GCTAAAAACGCAGTCCGATGCCCTGACTCAGTTTTGCCTAATTTTTGGCGTAAAGACTCCTTGAG
* * *
38987 ATACCTATATTTATCGAACCAAATCTCAACCACATTAGATTTAAGGATTTTCTTTTGT-CGAGCA
131 ATATCTATATTTATCGAACCAAATCTCAACCACATTGGATTTAAAGA-TTTCTTTT-TACGAGCA
* * *
39051 TCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCG-GAAAAAATGGGT-AACGGATATTAGAA
194 TCTGAATTTTGTTTCGGTTTAATTAGAAATTAATTCGAAAAAAAATGGGTAAAC-GATATTAGAA
* * *
39114 GCGTGAAAAACCTTTCAAATTTTTTTTGACATTGAATTATATATTTTTTCTTAGTATTGTGGCGA
258 GCGTGAAAAACCTTTC-AA-TTTTTTTGACATTGAATTATTTATTTTTTCTGAGTATTTTGGCGA
39179 AA
321 AA
** *
39181 AATTGAGAAAAAAATTTTCGGGTCAGTTTTTTGTTGAAATCGTATACTAACCATCACGGGTTTTT
1 AATTGAGAAAAAAATTTTCGGGTCAGTTTTTTGCCGAAATCGTGTACTAACCATCACGGGTTTTT
* * * *
39246 GCTAAAAA--C-GTCCAATGTCCCGGA-TTAGTTTTGCCTAATTTTTGGCGTAAAGACTCATTGA
66 GCTAAAAACGCAGTCCGATG-CCCTGACTCAGTTTTGCCTAATTTTTGGCGTAAAGACTCCTTGA
* * * * *
39307 TATATCAACATTTATCAAACTAAATCTCAACCACATTGGATTTAAAGATTTCTTTTTACGAGCAT
130 GATATCTATATTTATCGAACCAAATCTCAACCACATTGGATTTAAAGATTTCTTTTTACGAGCAT
39372 CTGAATTTTGTTTCGGTTTAATTAGAAATTAATTCGGAAAAAAAATGGGTAAACGATATTAGAAG
195 CTGAATTTTGTTTCGGTTTAATTAGAAATTAATTC-GAAAAAAAATGGGTAAACGATATTAGAAG
* * *
39437 AGTGAAAAACCTTTCAATTTTTTTGACATTGAATTATTTATTTTTTCAGAGTATTTTGGAGAAA
259 CGTGAAAAACCTTTCAATTTTTTTGACATTGAATTATTTATTTTTTCTGAGTATTTTGGCGAAA
* * *
39501 AATTGAGAAAAAAATTTTCGGGTTAGTTTTTTCCCAAAATCGTGTACTAACCATCACGGGTTTTT
1 AATTGAGAAAAAAATTTTCGGGTCAGTTTTTTGCCGAAATCGTGTACTAACCATCACGGGTTTTT
* * * * *
39566 GCTAAAAACGCAATTCGATGCCCTGGCTCAATTTTGCCTGATTTTTGGCGTAAAGACTCCTTGAG
66 GCTAAAAACGCAGTCCGATGCCCTGACTCAGTTTTGCCTAATTTTTGGCGTAAAGACTCCTTGAG
* * * * *
39631 ATATCTATATTTCTCGAGCCAAATTTTAACCACATTGGATTTAAAGATTTCTTTTTATGAGCATC
131 ATATCTATATTTATCGAACCAAATCTCAACCACATTGGATTTAAAGATTTCTTTTTACGAGCATC
*
39696 TGAATTTTGTTTCGGTTTAATTAGAAATTAATTCGAAAAAAAAATGGGTAAACGATATTAGAAGA
196 TGAATTTTGTTTCGGTTTAATTAGAAATTAATTCG-AAAAAAAATGGGTAAACGATATTAGAAGC
*
39761 GTGAAAAACCTTTCACTTTTTTTGACATTGAATTATTTATTTTTTCTGAGTATTTTGGCGAAA
260 GTGAAAAACCTTTCAATTTTTTTGACATTGAATTATTTATTTTTTCTGAGTATTTTGGCGAAA
* * * *
39824 AATTGAGAAAAAAAATTTTCGGGTCAGTTTTTTTCCCAATATCGTGTACAAACCTTCACGGGTTT
1 AATTGAG-AAAAAAATTTTCGGGTCAGTTTTTTGCCGAA-ATCGTGTACTAACCATCACGGGTTT
* * * * *
39889 TTACCAAAAACGCAGTTCGATGCCAC-GGCTCAGTTTTGCCTAATTTTTTTGCGTAAAGACTCCT
64 TTGCTAAAAACGCAGTCCGATGCC-CTGACTCAGTTTTGCCTAA-TTTTTGGCGTAAAGACTCCT
* * *
39953 TGAGATATCTATATTTATCGAACCAAATCTCAATCACATTGGATTTAGAGATTTCTTTTTATGAG
127 TGAGATATCTATATTTATCGAACCAAATCTCAACCACATTGGATTTAAAGATTTCTTTTTACGAG
* * *
40018 CATCTAAATTTTGTTTCGGTTTAATTAGAAATTAATTC-TAAAAAAATGGGTAAACGATATTAAA
192 CATCTGAATTTTGTTTCGGTTTAATTAGAAATTAATTCGAAAAAAAATGGGTAAACGATATTAGA
* * * *
40082 AGCGTGAAAAAACCTTTCAATTTTTTTTGGCATTGAATTATATATTTTTTCTGTGTATTGTGGCG
257 AGCGTG-AAAAACCTTTCAA-TTTTTTTGACATTGAATTATTTATTTTTTCTGAGTATTTTGGCG
40147 AAA
320 AAA
* ** *
40150 AATTGAGGAAAAAAA-TTTCGGGTTAGTTTTTTGTTGAAATCGTGTACTAACCATCACGGGGTTT
1 AATTGA-GAAAAAAATTTTCGGGTCAGTTTTTTGCCGAAATCGTGTACTAACCATCACGGGTTTT
* * * *
40214 TGCTAACAACGCAGTCCGATG-CCTCGACTCAGTTTTGTCTGATTTTTGGCGTAAAGACTCTTTG
65 TGCTAAAAACGCAGTCCGATGCCCT-GACTCAGTTTTGCCTAATTTTTGGCGTAAAGACTCCTTG
* * * * *
40278 AAATATCTATATTTATCGAACCAAATCTCAACCACATTGCATTTAACGATTTCTTTATATGAGCA
129 AGATATCTATATTTATCGAACCAAATCTCAACCACATTGGATTTAAAGATTTCTTTTTACGAGCA
* * * * * * *
40343 TTTGAATTTTGTTTCGGTTTAATTAGAAATTGATT-AAAAAAAAAAGGGCAAACGATACTAGATG
194 TCTGAATTTTGTTTCGGTTTAATTAGAAATTAATTCGAAAAAAAATGGGTAAACGATATTAGAAG
* * * * * *
40407 AGTGAAAAACCTTTTAA-TTTTTTGGCATTGAATTATATATATATATTT-TGATTATTTTGGTGA
259 CGTGAAAAACCTTTCAATTTTTTTGACATTGAATTAT-T-TAT-TTTTTCTGAGTATTTTGGCGA
40470 AA
321 AA
* * * *
40472 AATTGAGAAAAAAA-TTTCGGGTCA-ATTTTTGCTGAAATCGTGTATTAACCATCATGGGTTTTT
1 AATTGAGAAAAAAATTTTCGGGTCAGTTTTTTGCCGAAATCGTGTACTAACCATCACGGGTTTTT
* * * * *
40535 GCTAAAAATGCAGTCCGATACCCTGATTCAGTTTTGCCTGATTTTTATGCGTAAAGACTCCTTGA
66 GCTAAAAACGCAGTCCGATGCCCTGACTCAGTTTTGCCTAATTTTT-GGCGTAAAGACTCCTTGA
* * * * *
40600 GATATCTATATTTATTGAACCAAATCTCAACCTCATTAGAATTAAAGATTTCTTTTTACGAGCAA
130 GATATCTATATTTATCGAACCAAATCTCAACCACATTGGATTTAAAGATTTCTTTTTACGAGCAT
**
40665 CAAAATTTTGTTTCGGTTTAATTAGAAATTAATTCGGAAAAAAAAATGGGTAAACGATATTAGAA
195 CTGAATTTTGTTTCGGTTTAATTAGAAATTAATTC-G-AAAAAAAATGGGTAAACGATATTAGAA
* * *
40730 GCGTGAAAAACCTTTCAATATTTTTGACATTGAATTATTTA-TTTTACTGAGTATTTAGGCGAAA
258 GCGTGAAAAACCTTTCAATTTTTTTGACATTGAATTATTTATTTTTTCTGAGTATTTTGGCGAAA
* * *
40794 AATTGAGAAAAAAATATTCGGGTCAATTTTTTGCCGAAATCGTGTACTAACATATCACGGGTTTT
1 AATTGAGAAAAAAATTTTCGGGTCAGTTTTTTGCCGAAATCGTGTACTAAC-CATCACGGGTTTT
* * * * *
40859 TGCTAAAAATGCAGTCCGATG-CCTCGACTCAGTTTGTTGCCTAATTTTTTGTGCAAACACTCCT
65 TGCTAAAAACGCAGTCCGATGCCCT-GACTCAG-TT-TTGCCTAATTTTTGGCGTAAAGACTCCT
* *
40923 TGAGATATCTATATTTATCGAACTAAATCTCAACCACATTGAATATT-AAGATTTCTTTTTACGA
127 TGAGATATCTATATTTATCGAACCAAATCTCAACCACATTGGAT-TTAAAGATTTCTTTTTACGA
* * *
40987 GCATTTGAATTTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGGTAAACGATATTAG
191 GCATCTGAATTTTGTTTCGGTTTAATTAGAAATTAATTCGAAAAAAAATGGGTAAACGATATTAG
* *
41052 AAGCGTGAAAAACCTTTCAATTTTTTTGACATTGAATTATATATTTTTTCTGTGTATTTTGGCGA
256 AAGCGTGAAAAACCTTTCAATTTTTTTGACATTGAATTATTTATTTTTTCTGAGTATTTTGGCGA
41117 AA
321 AA
* *
41119 AATTTGAG-AAAAAATTTTCGGGTCAATTTTTTGCCGAAATCGTGTACT----ATCACAGGTTTT
1 AA-TTGAGAAAAAAATTTTCGGGTCAGTTTTTTGCCGAAATCGTGTACTAACCATCACGGGTTTT
* * *
41179 TGCTAAAAACGCAGTCCGATGCCCCGACTCAGTTTTGCCTAATTTTTTTGCGTAAACACTCCTTG
65 TGCTAAAAACGCAGTCCGATGCCCTGACTCAGTTTTGCCTAA-TTTTTGGCGTAAAGACTCCTTG
41244 AGATATCTATAT
129 AGATATCTATAT
Statistics
Matches: 1832, Mismatches: 200, Indels: 89
0.86 0.09 0.04
Matches are distributed among these distances:
318 8 0.00
319 35 0.02
320 285 0.16
321 207 0.11
322 118 0.06
323 402 0.22
324 277 0.15
325 205 0.11
326 280 0.15
327 15 0.01
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.37
Consensus pattern (322 bp):
AATTGAGAAAAAAATTTTCGGGTCAGTTTTTTGCCGAAATCGTGTACTAACCATCACGGGTTTTT
GCTAAAAACGCAGTCCGATGCCCTGACTCAGTTTTGCCTAATTTTTGGCGTAAAGACTCCTTGAG
ATATCTATATTTATCGAACCAAATCTCAACCACATTGGATTTAAAGATTTCTTTTTACGAGCATC
TGAATTTTGTTTCGGTTTAATTAGAAATTAATTCGAAAAAAAATGGGTAAACGATATTAGAAGCG
TGAAAAACCTTTCAATTTTTTTGACATTGAATTATTTATTTTTTCTGAGTATTTTGGCGAAA
Done.