Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020212.1 Corchorus olitorius cultivar O-4 contig20245, 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: 53923
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:11037 original size:31 final size:31
Alignment explanation
Indices: 11002--11063 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
10992 TGTTTCAAAA
11002 GTGCTTTTGGACATTAAATGACTAAAATCTC
1 GTGCTTTTGGACATTAAATGACTAAAATCTC
*
11033 GTGCTTTTGGACATTAAATGACTATAATCTC
1 GTGCTTTTGGACATTAAATGACTAAAATCTC
11064 CTAATTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (31 bp):
GTGCTTTTGGACATTAAATGACTAAAATCTC
Found at i:18728 original size:96 final size:96
Alignment explanation
Indices: 18564--18756 Score: 350
Period size: 96 Copynumber: 2.0 Consensus size: 96
18554 AAACGCAATG
18564 AAACCATGGACTTTGAAATCAATTACTATGGATTCCCCAAGTTCCCAACTACCCCAGCCAGGTTA
1 AAACCATGGACTTTGAAATCAATTACTATGGATTCCCCAAGTTCCCAACTACCCCAGCCAGGTTA
18629 ATTGACTCCAAAATCAATTTGAGTAATAGTT
66 ATTGACTCCAAAATCAATTTGAGTAATAGTT
* * *
18660 AAACCCTGGACTTTGAAATCAATTACTATGGATTCCCCAAGTTCCCAACTGCTCCAGCCAGGTTA
1 AAACCATGGACTTTGAAATCAATTACTATGGATTCCCCAAGTTCCCAACTACCCCAGCCAGGTTA
*
18725 ATTGACTCCAAAATCAATTTGAGTAATTGTT
66 ATTGACTCCAAAATCAATTTGAGTAATAGTT
18756 A
1 A
18757 TGTAATGTTT
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
96 93 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (96 bp):
AAACCATGGACTTTGAAATCAATTACTATGGATTCCCCAAGTTCCCAACTACCCCAGCCAGGTTA
ATTGACTCCAAAATCAATTTGAGTAATAGTT
Found at i:26098 original size:15 final size:15
Alignment explanation
Indices: 26075--26104 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
26065 TTTTTGGCAA
26075 AAAAAAAAAGAAAAT
1 AAAAAAAAAGAAAAT
*
26090 AAAAGAAAAGAAAAT
1 AAAAAAAAAGAAAAT
26105 CACAAAAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (15 bp):
AAAAAAAAAGAAAAT
Found at i:26239 original size:9 final size:9
Alignment explanation
Indices: 26225--26253 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
26215 CAAAGCAAAG
26225 CTTCTCTCT
1 CTTCTCTCT
26234 CTTCTCTCT
1 CTTCTCTCT
26243 CTTCTC-CT
1 CTTCTCTCT
26251 CTT
1 CTT
26254 AAACCCTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 5 0.25
9 15 0.75
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (9 bp):
CTTCTCTCT
Found at i:32181 original size:53 final size:53
Alignment explanation
Indices: 32123--32233 Score: 213
Period size: 53 Copynumber: 2.1 Consensus size: 53
32113 ACCCTTCCAT
32123 TGTGCTGCTTCATTTCTTTCTTATATACCACTAAAATAAACCTTTTAGATATC
1 TGTGCTGCTTCATTTCTTTCTTATATACCACTAAAATAAACCTTTTAGATATC
32176 TGTGCTGCTTCATTTCTTTCTTATATACCACTAAAATAAACCTTTTAGATATC
1 TGTGCTGCTTCATTTCTTTCTTATATACCACTAAAATAAACCTTTTAGATATC
*
32229 CGTGC
1 TGTGC
32234 ATGTGGGATA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 57 1.00
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.42
Consensus pattern (53 bp):
TGTGCTGCTTCATTTCTTTCTTATATACCACTAAAATAAACCTTTTAGATATC
Found at i:32562 original size:2 final size:2
Alignment explanation
Indices: 32555--32598 Score: 54
Period size: 2 Copynumber: 22.0 Consensus size: 2
32545 GTTGATTTTA
* *
32555 TC TC TC TC TC TC TC TC TC TC TC TC TT TC T- TGC TC TC TG TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T-C TC TC TC TC TC
32597 TC
1 TC
32599 CCTTTTTCTG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
1 1 0.03
2 34 0.94
3 1 0.03
ACGTcount: A:0.00, C:0.43, G:0.05, T:0.52
Consensus pattern (2 bp):
TC
Found at i:33920 original size:26 final size:26
Alignment explanation
Indices: 33890--33941 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
33880 TAGGTGACAC
33890 TATGATTTCAATTTTCCCAAATGCTA
1 TATGATTTCAATTTTCCCAAATGCTA
*
33916 TATGATTTCACTTTTCCCAAATGCTA
1 TATGATTTCAATTTTCCCAAATGCTA
33942 AAAGATAAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.42
Consensus pattern (26 bp):
TATGATTTCAATTTTCCCAAATGCTA
Found at i:35860 original size:13 final size:13
Alignment explanation
Indices: 35844--35869 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35834 AACAAACAGC
35844 AAAAAATAAAAAT
1 AAAAAATAAAAAT
35857 AAAAAATAAAAAT
1 AAAAAATAAAAAT
35870 TGAATTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:36380 original size:2 final size:2
Alignment explanation
Indices: 36369--36400 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
36359 TCTATATGAT
36369 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36401 TTCTCTTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41570 original size:148 final size:148
Alignment explanation
Indices: 41302--41597 Score: 565
Period size: 148 Copynumber: 2.0 Consensus size: 148
41292 TTACAAAAAA
41302 GGGCTCAAGGGCAAAAACTGGCTAGAATCTAACCTAGGGTCTTCTTAGTAATTTGGCAAGTGAGA
1 GGGCTCAAGGGCAAAAACTGGCTAGAATCTAACCTAGGGTCTTCTTAGTAATTTGGCAAGTGAGA
41367 AAAGACAGAAAAGGACAAAAGAAGTTCAAATGGAACCTCCTCATCAATCCTCAAAAGGGGCTTTT
66 AAAGACAGAAAAGGACAAAAGAAGTTCAAATGGAACCTCCTCATCAATCCTCAAAAGGGGCTTTT
* *
41432 GGTAAATTTTCTGGGTCT
131 GATAAATTTCCTGGGTCT
41450 GGGCTCAAGGGCAAAAACTGGCTAGAATCTAACCTAGGGTCTTCTTAGTAATTTGGCAAGTGAGA
1 GGGCTCAAGGGCAAAAACTGGCTAGAATCTAACCTAGGGTCTTCTTAGTAATTTGGCAAGTGAGA
*
41515 AAAGACAGAAAAGGACAAAAGAAGTTCAAATGGAGCCTCCTCATCAATCCTCAAAAGGGGCTTTT
66 AAAGACAGAAAAGGACAAAAGAAGTTCAAATGGAACCTCCTCATCAATCCTCAAAAGGGGCTTTT
41580 GATAAATTTCCTGGGTCT
131 GATAAATTTCCTGGGTCT
41598 TTCAAATACT
Statistics
Matches: 145, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
148 145 1.00
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (148 bp):
GGGCTCAAGGGCAAAAACTGGCTAGAATCTAACCTAGGGTCTTCTTAGTAATTTGGCAAGTGAGA
AAAGACAGAAAAGGACAAAAGAAGTTCAAATGGAACCTCCTCATCAATCCTCAAAAGGGGCTTTT
GATAAATTTCCTGGGTCT
Found at i:45183 original size:42 final size:45
Alignment explanation
Indices: 45132--45225 Score: 151
Period size: 45 Copynumber: 2.2 Consensus size: 45
45122 AGTGCATTAC
*
45132 CTAA-ATTCTACT-C-C-ATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCCTCTATCTCTAGATAATTCATCAAAATAAAG
45173 CTAATATTCTACTCCTCTATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTACTCCTCTATCTCTAGATAATTCATCAAAATAAAG
45218 CTAATATT
1 CTAATATT
45226 AATTGTTGCT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
41 4 0.08
42 8 0.17
43 1 0.02
44 1 0.02
45 34 0.71
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.35
Consensus pattern (45 bp):
CTAATATTCTACTCCTCTATCTCTAGATAATTCATCAAAATAAAG
Found at i:46999 original size:25 final size:24
Alignment explanation
Indices: 46965--47011 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
46955 ACGTTTGCAC
46965 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
46990 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
47012 TGTAAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (24 bp):
AAATACCTAAGAATTTAATTAAAA
Found at i:53790 original size:28 final size:29
Alignment explanation
Indices: 53758--53813 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
53748 TTCTTCAAGC
*
53758 TTTCTAAT-TTCAAGAACGCTCAAGAACA
1 TTTCTAATCTTCAAGAACGCTAAAGAACA
*
53786 TTTCTAATCTTTAAGAACGCTAAAGAAC
1 TTTCTAATCTTCAAGAACGCTAAAGAAC
53814 GTGGAATAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (29 bp):
TTTCTAATCTTCAAGAACGCTAAAGAACA
Done.