Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010861.1 Corchorus capsularis cultivar CVL-1 contig10882, 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: 135095
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:711 original size:46 final size:46
Alignment explanation
Indices: 644--735 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
634 CAGATTAACG
644 CCCTTAGTTCCTTTACCTGGGGGAAAGGCGCTAGTTTAAAGTCGGC
1 CCCTTAGTTCCTTTACCTGGGGGAAAGGCGCTAGTTTAAAGTCGGC
690 CCCTTAGTTCCTTTACCTGGGGGAAAGGCGCTAGTTTAAAGTCGGC
1 CCCTTAGTTCCTTTACCTGGGGGAAAGGCGCTAGTTTAAAGTCGGC
736 TGGTCGTGTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.28
Consensus pattern (46 bp):
CCCTTAGTTCCTTTACCTGGGGGAAAGGCGCTAGTTTAAAGTCGGC
Found at i:2336 original size:5 final size:5
Alignment explanation
Indices: 2326--2354 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
2316 AGATTCTCTT
2326 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
2355 TTTAATCAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:15205 original size:75 final size:75
Alignment explanation
Indices: 15069--15207 Score: 224
Period size: 75 Copynumber: 1.9 Consensus size: 75
15059 TCAAACTCAA
*
15069 ACTCTGGTTCGTCTGATCAGATGGTGGAGTTCGTTTGGCTTTGAAAACTATCGGCTCCGCCATGA
1 ACTCTGGTTCGTCTGATCAGATGGTGGAGTTCGTTTGGCTTTGAAAACCATCGGCTCCGCCATGA
15134 TTGGACTTCC
66 TTGGACTTCC
* ** * *
15144 ACTCTGGTTCGTCTGATCAGATGGTGGAGTTCGTTTGGGTTTGGGAACCATTGGCTTCGCCATG
1 ACTCTGGTTCGTCTGATCAGATGGTGGAGTTCGTTTGGCTTTGAAAACCATCGGCTCCGCCATG
15208 GTTATGGTTG
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 58 1.00
ACGTcount: A:0.16, C:0.21, G:0.29, T:0.34
Consensus pattern (75 bp):
ACTCTGGTTCGTCTGATCAGATGGTGGAGTTCGTTTGGCTTTGAAAACCATCGGCTCCGCCATGA
TTGGACTTCC
Found at i:24812 original size:16 final size:16
Alignment explanation
Indices: 24791--24822 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
24781 TCATATTCAA
24791 CATCTAATTCACAACC
1 CATCTAATTCACAACC
24807 CATCTAATTCACAACC
1 CATCTAATTCACAACC
24823 TATAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
CATCTAATTCACAACC
Found at i:28636 original size:14 final size:15
Alignment explanation
Indices: 28617--28646 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
28607 AGTGATGAAG
28617 AAAAAAAAAAG-GAA
1 AAAAAAAAAAGAGAA
28631 AAAAAAAAAAGAGAA
1 AAAAAAAAAAGAGAA
28646 A
1 A
28647 GGATAATTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAGAGAA
Found at i:34316 original size:54 final size:54
Alignment explanation
Indices: 34241--34356 Score: 187
Period size: 54 Copynumber: 2.1 Consensus size: 54
34231 TTGTGCATTA
* * * *
34241 ATAGCTCAATTGCTTCAATTACATAACCTTTTCCATGCAATTACATCTGCATCT
1 ATAGCTCAATTGCTTCAATTACATAACCTTTTACAAGCAATCACATCCGCATCT
*
34295 ATAGCTCAATTGCTTCAATTACATAACCTTTTACAAGCAATCATATCCGCATCT
1 ATAGCTCAATTGCTTCAATTACATAACCTTTTACAAGCAATCACATCCGCATCT
34349 ATAGCTCA
1 ATAGCTCA
34357 CATGCATACA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.32, C:0.26, G:0.08, T:0.34
Consensus pattern (54 bp):
ATAGCTCAATTGCTTCAATTACATAACCTTTTACAAGCAATCACATCCGCATCT
Found at i:40967 original size:19 final size:21
Alignment explanation
Indices: 40943--40987 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
40933 ACTTATAAGC
40943 AGCAAA-TATTTTCT-AACGA
1 AGCAAATTATTTTCTCAACGA
* *
40962 AGCAAATTTTTTTCTCAACGC
1 AGCAAATTATTTTCTCAACGA
40983 AGCAA
1 AGCAA
40988 TCTTTTCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.27
20 7 0.32
21 9 0.41
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (21 bp):
AGCAAATTATTTTCTCAACGA
Found at i:40993 original size:20 final size:20
Alignment explanation
Indices: 40951--40993 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
40941 GCAGCAAATA
*
40951 TTTTCTAACGAAGCAAATTT
1 TTTTCTAACGAAGCAAATCT
*
40971 TTTTCTCAACGCAGC-AATCT
1 TTTTCT-AACGAAGCAAATCT
40991 TTT
1 TTT
40994 CTTTCTTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.42
Consensus pattern (20 bp):
TTTTCTAACGAAGCAAATCT
Found at i:43626 original size:17 final size:17
Alignment explanation
Indices: 43597--43630 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
43587 GATCATGATG
43597 AAATCAATGGCAGAGAT
1 AAATCAATGGCAGAGAT
43614 AAATCTAAT-GCAGAGAT
1 AAATC-AATGGCAGAGAT
43631 CAATAACGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.47, C:0.12, G:0.21, T:0.21
Consensus pattern (17 bp):
AAATCAATGGCAGAGAT
Found at i:46228 original size:52 final size:52
Alignment explanation
Indices: 46171--46274 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
46161 AAATGATAGG
46171 AAAGTCCATCTTCATATATAGAACAAGAATTTACAAGGTAAAAATACTCTAC
1 AAAGTCCATCTTCATATATAGAACAAGAATTTACAAGGTAAAAATACTCTAC
46223 AAAGTCCATCTTCATATATAGAACAAGAATTTACAAGGTAAAAATACTCTAC
1 AAAGTCCATCTTCATATATAGAACAAGAATTTACAAGGTAAAAATACTCTAC
46275 TTCAAACTTG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.46, C:0.17, G:0.10, T:0.27
Consensus pattern (52 bp):
AAAGTCCATCTTCATATATAGAACAAGAATTTACAAGGTAAAAATACTCTAC
Found at i:68093 original size:183 final size:183
Alignment explanation
Indices: 67783--68124 Score: 560
Period size: 183 Copynumber: 1.9 Consensus size: 183
67773 ATTCTCGTCC
* *
67783 ACCGCCACTTCCCTCGAGGCTCCACCGCCACAAGAAACGAAACCGGCCACTGAATTGACAAAAAA
1 ACCGCCACTTCCCTCGAGGCTCCACCGCCACAAGAAACAAAACCGGCCACTGAACTGACAAAAAA
* *
67848 GTTGGCCGATATAGAAGATGGAGTTGCGGAAGAGAAAGGCGTGGCAGAACTCGACATTGGAAGTC
66 GTCGGCCGATATAGAAGATGGAGTTGCGGAAGAGAAAGGCGTGGCAGAAATCGACATTGGAAGTC
*
67913 TTGCGATCGATGAGAACAATAAGATCAACCCAGAAAATTCGAATATTAAAGGA
131 TTGCGATCGATGAGAACAAAAAGATCAACCCAGAAAATTCGAATATTAAAGGA
* * * **
67966 ACCGCCACTTCCGTCGAGGCTCCACCGCCACTAGAAACAAAACCGGCCACTGAACTGCCAAAAGG
1 ACCGCCACTTCCCTCGAGGCTCCACCGCCACAAGAAACAAAACCGGCCACTGAACTGACAAAAAA
*
68031 GTCGGCCGATATAGAAGATGGAGTTGCGGAAGAGAAAGGCGTGG-AGGAAATCGACTTTGGAAGT
66 GTCGGCCGATATAGAAGATGGAGTTGCGGAAGAGAAAGGCGTGGCA-GAAATCGACATTGGAAGT
*
68095 CTTTCGATCGATGAGAACAAAAAGATCAAC
130 CTTGCGATCGATGAGAACAAAAAGATCAAC
68125 AAGTTCCTCG
Statistics
Matches: 146, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
182 1 0.01
183 145 0.99
ACGTcount: A:0.35, C:0.23, G:0.26, T:0.16
Consensus pattern (183 bp):
ACCGCCACTTCCCTCGAGGCTCCACCGCCACAAGAAACAAAACCGGCCACTGAACTGACAAAAAA
GTCGGCCGATATAGAAGATGGAGTTGCGGAAGAGAAAGGCGTGGCAGAAATCGACATTGGAAGTC
TTGCGATCGATGAGAACAAAAAGATCAACCCAGAAAATTCGAATATTAAAGGA
Found at i:80421 original size:18 final size:18
Alignment explanation
Indices: 80398--80436 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
80388 TATTAATGTT
80398 ACAAATACCATAATTACC
1 ACAAATACCATAATTACC
* *
80416 ACAAATTCCATAATTATC
1 ACAAATACCATAATTACC
80434 ACA
1 ACA
80437 TCTATCTCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (18 bp):
ACAAATACCATAATTACC
Found at i:93851 original size:2 final size:2
Alignment explanation
Indices: 93844--93870 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
93834 GAAGTTGTTC
93844 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 A
93871 CTCACATGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:95445 original size:16 final size:17
Alignment explanation
Indices: 95413--95446 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
95403 GGAAATGAAC
*
95413 CTTTTTATTTATTTATT
1 CTTTTTATTTATCTATT
95430 CTTTTTATTT-TCTATT
1 CTTTTTATTTATCTATT
95446 C
1 C
95447 CCTAACTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.74
Consensus pattern (17 bp):
CTTTTTATTTATCTATT
Found at i:118820 original size:17 final size:16
Alignment explanation
Indices: 118788--118823 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
118778 GTCAGGGCCG
118788 ATAAAAATATAGATAT
1 ATAAAAATATAGATAT
*
118804 ATAAAATATATATATAT
1 ATAAAA-ATATAGATAT
118821 ATA
1 ATA
118824 TATAGAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
ATAAAAATATAGATAT
Found at i:133346 original size:21 final size:21
Alignment explanation
Indices: 133320--133360 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
133310 GCAGGTCTGT
133320 TGGCATGTTTGGAGGGTTTGC
1 TGGCATGTTTGGAGGGTTTGC
*
133341 TGGCATGTTTGTAGGGTTTG
1 TGGCATGTTTGGAGGGTTTG
133361 TTTCAGCTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.07, G:0.41, T:0.41
Consensus pattern (21 bp):
TGGCATGTTTGGAGGGTTTGC
Done.