Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013391.1 Corchorus capsularis cultivar CVL-1 contig13412, 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: 46207
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Found at i:7408 original size:33 final size:33
Alignment explanation
Indices: 7362--7427 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
7352 CAAAAGAAAA
7362 AAACCTTCAAAGTATCCTGATTGATTGACAAAT
1 AAACCTTCAAAGTATCCTGATTGATTGACAAAT
* *
7395 AAACCTTCGAAGTATCCTGATTTATTGACAAAT
1 AAACCTTCAAAGTATCCTGATTGATTGACAAAT
7428 CTAATTTGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (33 bp):
AAACCTTCAAAGTATCCTGATTGATTGACAAAT
Found at i:7601 original size:16 final size:16
Alignment explanation
Indices: 7580--7610 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
7570 AACAAGTTGA
*
7580 GCACGTGATTTCTATT
1 GCACGTGATCTCTATT
7596 GCACGTGATCTCTAT
1 GCACGTGATCTCTAT
7611 AACTTCAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (16 bp):
GCACGTGATCTCTATT
Found at i:12194 original size:13 final size:13
Alignment explanation
Indices: 12176--12210 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
12166 AATCTAAATC
*
12176 TAAAGCAGATTAA
1 TAAAGCAAATTAA
12189 TAAAGCAAATTAA
1 TAAAGCAAATTAA
12202 TAAAGCAAA
1 TAAAGCAAA
12211 CAATAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.60, C:0.09, G:0.11, T:0.20
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:17450 original size:76 final size:76
Alignment explanation
Indices: 17324--17465 Score: 257
Period size: 76 Copynumber: 1.9 Consensus size: 76
17314 ATCACCACTT
* *
17324 AGAAAGTCAAAATATGAAAGGCTTCAAATTATAAGATGGTTAGATTGATCATTCCGATTTCTCCT
1 AGAAACTCAAAATATGAAAGGCTTCAAATTATAAGATGGTTAGATTGATCATTCCAATTTCTCCT
17389 CCAACCACTAA
66 CCAACCACTAA
*
17400 AGAAACTCAAAATATGAAGGGCTTCAAATTATAAGATGGTTAGATTGATCATTCCAATTTCTCCT
1 AGAAACTCAAAATATGAAAGGCTTCAAATTATAAGATGGTTAGATTGATCATTCCAATTTCTCCT
17465 C
66 C
17466 GAAATCTGGA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 63 1.00
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (76 bp):
AGAAACTCAAAATATGAAAGGCTTCAAATTATAAGATGGTTAGATTGATCATTCCAATTTCTCCT
CCAACCACTAA
Found at i:28515 original size:3 final size:3
Alignment explanation
Indices: 28507--28536 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
28497 TGCTACTTAA
28507 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
28537 CTGTTTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:28725 original size:19 final size:19
Alignment explanation
Indices: 28701--28738 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
28691 CAATGATTTA
28701 AAACATATAAAGGAAGTTG
1 AAACATATAAAGGAAGTTG
28720 AAACATATAAAGGAAGTTG
1 AAACATATAAAGGAAGTTG
28739 TGCCAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (19 bp):
AAACATATAAAGGAAGTTG
Found at i:45910 original size:21 final size:21
Alignment explanation
Indices: 45884--45927 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
45874 CTTAACCGAA
45884 TTGCTAAAT-AACGCCCCATTT
1 TTGCT-AATCAACGCCCCATTT
* *
45905 TTGCTATTCATCGCCCCATTT
1 TTGCTAATCAACGCCCCATTT
45926 TT
1 TT
45928 TACGTTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.20, C:0.30, G:0.09, T:0.41
Consensus pattern (21 bp):
TTGCTAATCAACGCCCCATTT
Found at i:46203 original size:33 final size:33
Alignment explanation
Indices: 46132--46207 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 33
46122 CCATGTCTCA
*
46132 AGCCGCCCCACTGGGGAGGCTCAACCACGGCGG
1 AGCCGCCCCACTGGGGAGGCTCAACCACGGCAG
* *
46165 AGCCGCCCCACTGGGGTGGCTTC-ACCATGGGCAG
1 AGCCGCCCCACTGGGGAGGC-TCAACCA-CGGCAG
46199 -GCCGCCCCA
1 AGCCGCCCCA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 32 0.84
34 6 0.16
ACGTcount: A:0.16, C:0.41, G:0.34, T:0.09
Consensus pattern (33 bp):
AGCCGCCCCACTGGGGAGGCTCAACCACGGCAG
Done.