Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019225.1 Corchorus olitorius cultivar O-4 contig19258, 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: 112178
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:9824 original size:25 final size:27
Alignment explanation
Indices: 9767--9824 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
9757 TCCAAAGTAT
9767 AAATTAGTAATACAGATTATCTCAAAA
1 AAATTAGTAATACAGATTATCTCAAAA
*
9794 AAATTAGTAATACAGA-TA-CTGAAAA
1 AAATTAGTAATACAGATTATCTCAAAA
9819 AAATTA
1 AAATTA
9825 AAGAGAAGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 12 0.40
26 2 0.07
27 16 0.53
ACGTcount: A:0.55, C:0.09, G:0.09, T:0.28
Consensus pattern (27 bp):
AAATTAGTAATACAGATTATCTCAAAA
Found at i:16048 original size:33 final size:33
Alignment explanation
Indices: 16006--16071 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
15996 AAGTGATTTA
16006 ATATTTGTTTCCGTTAAATAAGATCTCGAATTC
1 ATATTTGTTTCCGTTAAATAAGATCTCGAATTC
*
16039 ATATTTGTTTCCGTTAAATAAGATCTTGAATTC
1 ATATTTGTTTCCGTTAAATAAGATCTCGAATTC
16072 GAGCCATCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (33 bp):
ATATTTGTTTCCGTTAAATAAGATCTCGAATTC
Found at i:26199 original size:15 final size:15
Alignment explanation
Indices: 26164--26209 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
26154 TTTTTAAACA
* *
26164 AAAATAAAATTTCAAT
1 AAAATAAAATAT-ATT
26180 AAAATAAAATATATT
1 AAAATAAAATATATT
*
26195 AAAATAAAAAATATT
1 AAAATAAAATATATT
26210 TAATTTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 16 0.59
16 11 0.41
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAATAAAATATATT
Found at i:26599 original size:19 final size:18
Alignment explanation
Indices: 26570--26611 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
26560 CAAGTAGTTT
* *
26570 TTAAGTAAAAATGTAATA
1 TTAAATAAAAATATAATA
26588 TATAAATAAAAATATAATA
1 T-TAAATAAAAATATAATA
26607 TTAAA
1 TTAAA
26612 ATAATTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (18 bp):
TTAAATAAAAATATAATA
Found at i:26615 original size:19 final size:19
Alignment explanation
Indices: 26575--26611 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
26565 AGTTTTTAAG
*
26575 TAAAAATGTAATATATAAA
1 TAAAAATATAATATATAAA
26594 TAAAAATATAATAT-TAAA
1 TAAAAATATAATATATAAA
26612 ATAATTAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:29839 original size:6 final size:6
Alignment explanation
Indices: 29818--29852 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
29808 TATGGAGTAT
*
29818 AATTTA AACCTTA AATTTA AATTTA AATTTA AATT
1 AATTTA AA-TTTA AATTTA AATTTA AATTTA AATT
29853 AATTAAGGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (6 bp):
AATTTA
Found at i:36841 original size:2 final size:2
Alignment explanation
Indices: 36834--36867 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
36824 TTCCTTTATT
36834 TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36868 CATTGCTGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40316 original size:2 final size:2
Alignment explanation
Indices: 40309--40351 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
40299 TATTCAACAA
*
40309 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40351 A
1 A
40352 ACGAAATAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:48544 original size:30 final size:29
Alignment explanation
Indices: 48471--48547 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
48461 AGTATTCCTA
*
48471 ACACGTGGCATGCCACGTGCCCTTTCTGT
1 ACACGTGGCATGCCACGTGCCATTTCTGT
* * * *
48500 ACATGTGGCGTGCCACGTGTCATTTTTAGT
1 ACACGTGGCATGCCACGTGCCATTTCT-GT
*
48530 GCACGTGGCATGCCACGT
1 ACACGTGGCATGCCACGT
48548 CAGTCGCCGT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 22 0.56
30 17 0.44
ACGTcount: A:0.16, C:0.29, G:0.27, T:0.29
Consensus pattern (29 bp):
ACACGTGGCATGCCACGTGCCATTTCTGT
Found at i:51123 original size:24 final size:24
Alignment explanation
Indices: 51070--51125 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
51060 TTTCGCCCAG
* **
51070 AAAAAAAAAAGAAAAAAATTTGTG
1 AAAAAAAAAAGAAAAAAAATTGAA
*
51094 AGAAAAAAAAGAAAACAAAATT-AA
1 AAAAAAAAAAGAAAA-AAAATTGAA
51118 AAAAAAAA
1 AAAAAAAA
51126 TACTAATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 21 0.81
25 5 0.19
ACGTcount: A:0.79, C:0.02, G:0.09, T:0.11
Consensus pattern (24 bp):
AAAAAAAAAAGAAAAAAAATTGAA
Found at i:54488 original size:60 final size:60
Alignment explanation
Indices: 54395--54514 Score: 188
Period size: 60 Copynumber: 2.0 Consensus size: 60
54385 TATGTTCCTT
*
54395 CTTTTGCTTGGAGCTGAAATCCTCCATGCTTGTGAAGATTATTT-GATAAAATGCTATCCA
1 CTTTTGCTTGGAGCTGAAATCCTCCATGCTTGTGAAAATT-TTTCGATAAAATGCTATCCA
* * *
54455 CTTTTGGTTGGAGCTGAAATCCTCCGTGCTTGTGAAAATTTTTCGATAAATTGCTATCCA
1 CTTTTGCTTGGAGCTGAAATCCTCCATGCTTGTGAAAATTTTTCGATAAAATGCTATCCA
54515 GCATAAGCTG
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
59 3 0.05
60 52 0.95
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (60 bp):
CTTTTGCTTGGAGCTGAAATCCTCCATGCTTGTGAAAATTTTTCGATAAAATGCTATCCA
Found at i:54527 original size:60 final size:60
Alignment explanation
Indices: 54403--54529 Score: 159
Period size: 60 Copynumber: 2.1 Consensus size: 60
54393 TTCTTTTGCT
* * ** *
54403 TGGAGCTGAAATCCTCCATGCTTGTGAAGATTATTTGATAAAATGCTATCCACTTTTGGT
1 TGGAGCTGAAATCCTCCATGCTTGTGAAAATTATTTGATAAAATGCTATCCACTATAAGC
* *
54463 TGGAGCTGAAATCCTCCGTGCTTGTGAAAATT-TTTCGATAAATTGCTATCCAGC-ATAAGC
1 TGGAGCTGAAATCCTCCATGCTTGTGAAAATTATTT-GATAAAATGCTATCCA-CTATAAGC
54523 TGGAGCT
1 TGGAGCT
54530 TTTAAATTGT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
59 3 0.05
60 54 0.93
61 1 0.02
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (60 bp):
TGGAGCTGAAATCCTCCATGCTTGTGAAAATTATTTGATAAAATGCTATCCACTATAAGC
Found at i:57078 original size:19 final size:20
Alignment explanation
Indices: 57054--57094 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
57044 CCTTGGGACA
57054 GTTCC-ATATCTGAATAGGT
1 GTTCCAATATCTGAATAGGT
57073 GTTCCATATATCTGAATAGGT
1 GTTCCA-ATATCTGAATAGGT
57094 G
1 G
57095 CTTTCTTGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.25
21 15 0.75
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.37
Consensus pattern (20 bp):
GTTCCAATATCTGAATAGGT
Found at i:59054 original size:2 final size:2
Alignment explanation
Indices: 59047--59077 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
59037 AGTGTTCTTT
59047 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
59078 ATTTAAGAGT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:61293 original size:17 final size:18
Alignment explanation
Indices: 61271--61306 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
61261 TTCAAATATG
61271 ATTTCGA-CAAAAAAAGA
1 ATTTCGACCAAAAAAAGA
61288 ATTTCGACCAAAAAAAGA
1 ATTTCGACCAAAAAAAGA
61306 A
1 A
61307 AAAGAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.58, C:0.14, G:0.11, T:0.17
Consensus pattern (18 bp):
ATTTCGACCAAAAAAAGA
Found at i:65091 original size:4 final size:4
Alignment explanation
Indices: 65082--65108 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
65072 GTCTAGTATT
65082 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
65109 TTGCTAGCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:77406 original size:123 final size:127
Alignment explanation
Indices: 77176--77427 Score: 386
Period size: 131 Copynumber: 2.0 Consensus size: 127
77166 TAAGAAATAA
*
77176 ATTTAAAAAATTCTAATATATATAAGTTTTGTAATTAAAATATTAAAATGGTAAAAATAAAATAG
1 ATTTAAAAAATTCTAATATATATAAGTTTTGTAATTAAAATAGTAAAATGGTAAAAAT---ATA-
* *
77241 GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAAGTA
62 GTATAAGGATATTAAATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTA
77306 T
127 T
* *
77307 ATTTAAAAAATTCTAATATATATAAGTTTTTTGATTAAAATAGTAAAATGGTAAAAAT-TA-TA-
1 ATTTAAAAAATTCTAATATATATAAGTTTTGTAATTAAAATAGTAAAATGGTAAAAATATAGTAT
*
77369 AA-GATATTAAATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTGAAACTATAAAAGT
66 AAGGATATTAAATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGT
77428 TTAAATAATG
Statistics
Matches: 115, Mismatches: 6, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
123 54 0.47
124 2 0.02
125 2 0.02
127 2 0.02
131 55 0.48
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.37
Consensus pattern (127 bp):
ATTTAAAAAATTCTAATATATATAAGTTTTGTAATTAAAATAGTAAAATGGTAAAAATATAGTAT
AAGGATATTAAATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTAT
Found at i:83620 original size:29 final size:31
Alignment explanation
Indices: 83576--83640 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 31
83566 TCAGTGGGGC
*
83576 TAAAATGGTTCCAAATTGCAAGTTTAGGAAG
1 TAAAATGGTTCCAAATTGAAAGTTTAGGAAG
* *
83607 TAAAAT-G-TCCAAATTTAAAGTTTAGGAGG
1 TAAAATGGTTCCAAATTGAAAGTTTAGGAAG
83636 TAAAA
1 TAAAA
83641 CATGTACAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 24 0.77
30 1 0.03
31 6 0.19
ACGTcount: A:0.43, C:0.08, G:0.20, T:0.29
Consensus pattern (31 bp):
TAAAATGGTTCCAAATTGAAAGTTTAGGAAG
Found at i:86272 original size:32 final size:32
Alignment explanation
Indices: 86226--86301 Score: 129
Period size: 30 Copynumber: 2.4 Consensus size: 32
86216 ATTGAACCCA
*
86226 ACTAATCTAGAGTTTTTTTTTTTGGCACCACG
1 ACTAATCTAAAGTTTTTTTTTTTGGCACCACG
86258 ACTAATCTAAAG--TTTTTTTTTGGCACCACG
1 ACTAATCTAAAGTTTTTTTTTTTGGCACCACG
86288 ACTAATCTAAAGTT
1 ACTAATCTAAAGTT
86302 CAGCTTGAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
30 30 0.73
32 11 0.27
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (32 bp):
ACTAATCTAAAGTTTTTTTTTTTGGCACCACG
Done.