Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010918.1 Corchorus capsularis cultivar CVL-1 contig10939, 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: 20913
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:148 original size:16 final size:16
Alignment explanation
Indices: 127--169 Score: 70
Period size: 16 Copynumber: 2.7 Consensus size: 16
117 TTAAGTCTTA
127 TTTTCATTTTCTCA-TT
1 TTTTCATTTT-TCATTT
143 TTTTCATTTTTCATTT
1 TTTTCATTTTTCATTT
159 TTTTCATTTTT
1 TTTTCATTTTT
170 TAAAATCTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 3 0.12
16 23 0.88
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTCATTTTTCATTT
Found at i:161 original size:8 final size:8
Alignment explanation
Indices: 127--170 Score: 63
Period size: 8 Copynumber: 5.5 Consensus size: 8
117 TTAAGTCTTA
127 TTTTCATT
1 TTTTCATT
*
135 TTCTCATT
1 TTTTCATT
143 TTTTCA-T
1 TTTTCATT
150 TTTTCATTT
1 TTTTCA-TT
159 TTTTCATT
1 TTTTCATT
167 TTTT
1 TTTT
171 AAAATCTCGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 7 0.22
8 18 0.56
9 7 0.22
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTCATT
Found at i:169 original size:7 final size:7
Alignment explanation
Indices: 127--160 Score: 50
Period size: 7 Copynumber: 4.6 Consensus size: 7
117 TTAAGTCTTA
127 TTTTCAT
1 TTTTCAT
134 TTTCTCATT
1 TTT-TCA-T
143 TTTTCAT
1 TTTTCAT
150 TTTTCAT
1 TTTTCAT
157 TTTT
1 TTTT
161 TTCATTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 15 0.60
8 6 0.24
9 4 0.16
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTCAT
Found at i:2507 original size:156 final size:156
Alignment explanation
Indices: 2123--2507 Score: 419
Period size: 156 Copynumber: 2.5 Consensus size: 156
2113 CATCTAGGTG
* ** * *
2123 AAATTTCATCTCAAACAGACTTAGCATGAAAAACTTATGCTAGTTTTTCAGTTAAGGACAGTTTG
1 AAATTTCAGCTCATTCAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTG
** * * * *
2188 AGGAGTCAAACCACTTCTCTATGCTAGAGAGTTCGGTTTTACTTAGAATTTTTCCCATAGCTTTA
66 AGGAGAGAAACCACTTCACCATGCAAGAGAGCTCGGTTTTACTTAGAATTTTTCCCATAGCTTTA
*
2253 TGGGGATAATCTAAGTCTACTGGTGGA
131 TGAGGATAATCTAAGTCTACT-GTGGA
* ** **
2280 AAA-TT-AG-TCTTGTTGGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACCA-CC
1 AAATTTCAGCTCAT-TCAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGA-CAGTT
* * * *
2341 TGGGGAGAGAAACCTAGTTCACCAT-CAAGGGGAGCTCGGTTTTACTTAGAATTTTTTCCATAG-
64 TGAGGAGAGAAACC-ACTTCACCATGCAA-GAGAGCTCGGTTTTACTTAGAATTTTTCCCATAGC
*
2404 TCTTATGAGGAT-ATGCTAAG-CTCCT-TGGCA
127 T-TTATGAGGATAAT-CTAAGTCTACTGTGG-A
*
2434 AAATTTCAGCTCATTCAGACTTAGAATGAAAAACTTATGTTAGTTTTTCATTTAAGGACAGTTTG
1 AAATTTCAGCTCATTCAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTG
*
2499 AGGTGAGAA
66 AGGAGAGAA
2508 GCTCGGTTTA
Statistics
Matches: 187, Mismatches: 30, Indels: 23
0.78 0.12 0.10
Matches are distributed among these distances:
153 3 0.02
154 6 0.03
155 64 0.34
156 108 0.58
157 6 0.03
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (156 bp):
AAATTTCAGCTCATTCAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTG
AGGAGAGAAACCACTTCACCATGCAAGAGAGCTCGGTTTTACTTAGAATTTTTCCCATAGCTTTA
TGAGGATAATCTAAGTCTACTGTGGA
Found at i:2873 original size:17 final size:17
Alignment explanation
Indices: 2853--2885 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2843 GTAGCCTATC
2853 ACCTCATACTACCTAGT
1 ACCTCATACTACCTAGT
2870 ACCTCATACTACCTAG
1 ACCTCATACTACCTAG
2886 GTACTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.36, G:0.06, T:0.27
Consensus pattern (17 bp):
ACCTCATACTACCTAGT
Found at i:12799 original size:14 final size:15
Alignment explanation
Indices: 12780--12809 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12770 AACAAAATTA
12780 ACAAA-TTTGTTAAT
1 ACAAATTTTGTTAAT
12794 ACAAATTTTGTTAAT
1 ACAAATTTTGTTAAT
12809 A
1 A
12810 AGTTGGTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (15 bp):
ACAAATTTTGTTAAT
Found at i:17994 original size:31 final size:31
Alignment explanation
Indices: 17959--18127 Score: 124
Period size: 31 Copynumber: 5.4 Consensus size: 31
17949 ACGGTGTTCG
* * *
17959 ACGTGGCATGCCACGTGGATCAAAAAGTAAC
1 ACGTGGCACGCCACGTGGACCAAAAAGTGAC
** * * * *
17990 ACGTGATACACCATGTGGATCAAAAAGTGAT
1 ACGTGGCACGCCACGTGGACCAAAAAGTGAC
*
18021 ACGTTGCACGCCACGTGTG-CCAAAAATGTGAC
1 ACGTGGCACGCCACGTG-GACCAAAAA-GTGAC
** * * * * *
18053 ATTTGGCATGTCACATGTACCAAAAAGTGAT
1 ACGTGGCACGCCACGTGGACCAAAAAGTGAC
* * *
18084 ATGTGGTACGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGGACCAAAAAGTGAC
*
18115 ACGTGGCATGCCA
1 ACGTGGCACGCCA
18128 AGTGCACTAA
Statistics
Matches: 104, Mismatches: 31, Indels: 6
0.74 0.22 0.04
Matches are distributed among these distances:
31 81 0.78
32 23 0.22
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (31 bp):
ACGTGGCACGCCACGTGGACCAAAAAGTGAC
Found at i:19667 original size:2 final size:2
Alignment explanation
Indices: 19660--19711 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
19650 AATTTGAACC
19660 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
19702 CT CT CT CT CT
1 CT CT CT CT CT
19712 AGAAACAAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:20776 original size:60 final size:60
Alignment explanation
Indices: 20710--20869 Score: 252
Period size: 60 Copynumber: 2.7 Consensus size: 60
20700 GCTAATTGCT
* *
20710 CAAATAAGGGTCTAACGTT-TGCCAAAATGCTCAAATAAGGG-TCCGATTTTTTAATTTGGC
1 CAAATAAGGGTCTAACGTTAT-CGAAAATGCTCAAATAAGGGCT-CGATCTTTTAATTTGGC
*
20770 CAAATAAGGGTCTAACCTTATCGAAAATGCTCAAATAAGGGCTCGATCTTTTAATTTGGC
1 CAAATAAGGGTCTAACGTTATCGAAAATGCTCAAATAAGGGCTCGATCTTTTAATTTGGC
*
20830 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGG
1 CAAATAAGGGTCTAACGTTATCGAAAATGCTCAAATAAGG
20870 ACCTAACGTT
Statistics
Matches: 93, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
60 91 0.98
61 2 0.02
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.28
Consensus pattern (60 bp):
CAAATAAGGGTCTAACGTTATCGAAAATGCTCAAATAAGGGCTCGATCTTTTAATTTGGC
Found at i:20808 original size:31 final size:31
Alignment explanation
Indices: 20706--20901 Score: 131
Period size: 31 Copynumber: 6.5 Consensus size: 31
20696 TTTGGCTAAT
*
20706 TGCTCAAATAAGGGTCTAACGTT-TGCCAAAA
1 TGCTCAAATAAGGGTCTAACGTTAT-CGAAAA
* ** **
20737 TGCTCAAATAAGGGTC---CGATTTTTTAATT
1 TGCTCAAATAAGGGTCTAACG-TTATCGAAAA
*
20766 TGGC-CAAATAAGGGTCTAACCTTATCGAAAA
1 T-GCTCAAATAAGGGTCTAACGTTATCGAAAA
* * * **
20797 TGCTCAAATAAGGGCTCGATC-TT-T-TAATT
1 TGCTCAAATAAGGG-TCTAACGTTATCGAAAA
*
20826 TGGC-CAAATAAGGGCCTAACGTTATCGAAAA
1 T-GCTCAAATAAGGGTCTAACGTTATCGAAAA
** **
20857 TGCTCAAATAAGGACCTAACGTTATAAAAAA
1 TGCTCAAATAAGGGTCTAACGTTATCGAAAA
20888 TGCTCAAATAAGGG
1 TGCTCAAATAAGGG
20902 CCTGTTGTCA
Statistics
Matches: 127, Mismatches: 25, Indels: 26
0.71 0.14 0.15
Matches are distributed among these distances:
28 5 0.04
29 32 0.25
30 11 0.09
31 74 0.58
32 5 0.04
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (31 bp):
TGCTCAAATAAGGGTCTAACGTTATCGAAAA
Found at i:20840 original size:29 final size:28
Alignment explanation
Indices: 20741--20839 Score: 83
Period size: 29 Copynumber: 3.4 Consensus size: 28
20731 CCAAAATGCT
*
20741 CAAATAAGGGTCCGATTTTTTAATTTGGC
1 CAAATAAGGGT-CGATCTTTTAATTTGGC
* * * **
20770 CAAATAAGGGTCTAACCTTATCGAAAAT-GC
1 CAAATAAGGGTC-GATCTT-T-TAATTTGGC
20800 TCAAATAAGGGCTCGATCTTTTAATTTGGC
1 -CAAATAAGGG-TCGATCTTTTAATTTGGC
20830 CAAATAAGGG
1 CAAATAAGGG
20840 CCTAACGTTA
Statistics
Matches: 53, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
28 1 0.02
29 27 0.51
30 6 0.11
31 17 0.32
32 2 0.04
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.30
Consensus pattern (28 bp):
CAAATAAGGGTCGATCTTTTAATTTGGC
Done.