Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021959.1 Corchorus olitorius cultivar O-4 contig21992, 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: 37070
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:809 original size:104 final size:104
Alignment explanation
Indices: 655--852 Score: 292
Period size: 104 Copynumber: 1.9 Consensus size: 104
645 GTTTTTTTAA
* * * *
655 TAAAATTAGTAAAACGATAAAAATAAAATAGGTATAAGGATATTATATTTAATTAAATAAAAGTA
1 TAAAATTAGTAAAACGATAAAAATAAAATACGTATAAGGATATTAGATTTAATCAAATAAAAATA
*
720 GAG-TTTTTAGTTGAGTAAAACTATAAAAGTATTTTCAT
66 GAGTTTTTTAGTTAAGTAAAACTATAAAAGTATTTTCAT
* * *
758 TAAAA-TAGTAAAATGGTAAAAATAAATAGTACTTATAAGGATATTAGATTTAATCAAATAAAAA
1 TAAAATTAGTAAAACGATAAAAATAAA-A-TACGTATAAGGATATTAGATTTAATCAAATAAAAA
822 TAGAGTTTTTTAGTTAAGTAAAACTATAAAA
64 TAGAGTTTTTTAGTTAAGTAAAACTATAAAA
853 ATTTAAGCAA
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
102 19 0.23
103 6 0.07
104 35 0.42
105 24 0.29
ACGTcount: A:0.51, C:0.03, G:0.12, T:0.34
Consensus pattern (104 bp):
TAAAATTAGTAAAACGATAAAAATAAAATACGTATAAGGATATTAGATTTAATCAAATAAAAATA
GAGTTTTTTAGTTAAGTAAAACTATAAAAGTATTTTCAT
Found at i:1150 original size:6 final size:6
Alignment explanation
Indices: 1141--1165 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1131 CTTTAATAAT
1141 AATATA AATATA AATATA AATATA A
1 AATATA AATATA AATATA AATATA A
1166 TATGGGGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AATATA
Found at i:4499 original size:26 final size:23
Alignment explanation
Indices: 4466--4516 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
4456 TTGACATCGT
*
4466 TTTCGTTTTTCTGTTTTTTGTTTTTG
1 TTTCG-TTTT-TGTTTTGT-TTTTTG
4492 TTTCGTTTTTGTTTTGTTTTTTG
1 TTTCGTTTTTGTTTTGTTTTTTG
4515 TT
1 TT
4517 GCATTGTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 8 0.33
24 7 0.29
25 4 0.17
26 5 0.21
ACGTcount: A:0.00, C:0.06, G:0.16, T:0.78
Consensus pattern (23 bp):
TTTCGTTTTTGTTTTGTTTTTTG
Found at i:6466 original size:14 final size:14
Alignment explanation
Indices: 6449--6502 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 14
6439 GTTGGTTCCT
6449 TCTTGTTGATCTCC
1 TCTTGTTGATCTCC
*
6463 TCTTG--GTTC-CC
1 TCTTGTTGATCTCC
6474 TTCTTGTTGATCTCC
1 -TCTTGTTGATCTCC
6489 TCCTT-TTGATCTCC
1 T-CTTGTTGATCTCC
6503 ATGAGAGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
11 2 0.06
12 8 0.24
14 18 0.55
15 5 0.15
ACGTcount: A:0.06, C:0.31, G:0.13, T:0.50
Consensus pattern (14 bp):
TCTTGTTGATCTCC
Found at i:6479 original size:26 final size:25
Alignment explanation
Indices: 6440--6490 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 25
6430 CAGGCATTCG
6440 TTGGTTCCTTCTTGTTGATCTCCTC
1 TTGGTTCCTTCTTGTTGATCTCCTC
6465 TTGGTTCCCTTCTTGTTGATCTCCTC
1 TTGGTT-CCTTCTTGTTGATCTCCTC
6491 CTTTTGATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.04, C:0.29, G:0.16, T:0.51
Consensus pattern (25 bp):
TTGGTTCCTTCTTGTTGATCTCCTC
Found at i:10403 original size:14 final size:16
Alignment explanation
Indices: 10369--10405 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
10359 TTAAAGGTTT
10369 TCTTTTTACTTTTACC
1 TCTTTTTACTTTTACC
*
10385 TCTTTTTA-TTTT-TC
1 TCTTTTTACTTTTACC
10399 TCTTTTT
1 TCTTTTT
10406 TGAAAGGTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 8 0.40
15 4 0.20
16 8 0.40
ACGTcount: A:0.08, C:0.19, G:0.00, T:0.73
Consensus pattern (16 bp):
TCTTTTTACTTTTACC
Found at i:20919 original size:19 final size:19
Alignment explanation
Indices: 20895--20952 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
20885 CTGTTTAACA
20895 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* *
20914 ACTGTACAGATTAGATTAGAT
1 ACTGTACAGATGAGATT--AC
*
20935 ACTGTACATATGAGATTA
1 ACTGTACAGATGAGATTA
20953 TTAGAGCAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:27902 original size:14 final size:14
Alignment explanation
Indices: 27883--27916 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
27873 TTTTATAATT
27883 ATTTTATTTTTACC
1 ATTTTATTTTTACC
*
27897 ATTTTATTTTTACT
1 ATTTTATTTTTACC
27911 ATTTTA
1 ATTTTA
27917 ATTTAAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTATTTTTACC
Found at i:27964 original size:15 final size:15
Alignment explanation
Indices: 27944--27974 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
27934 GATTAACCTG
27944 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
27959 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
27974 T
1 T
27975 AATGTATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (15 bp):
TTTCTATTTGATAGT
Found at i:29369 original size:34 final size:34
Alignment explanation
Indices: 29331--29398 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
29321 CTTACCCTTT
29331 GTTTTGATTTTAATTACAAAATTACCATATTAGC
1 GTTTTGATTTTAATTACAAAATTACCATATTAGC
*
29365 GTTTTGATTTTAGTTACAAAATTACCATATTAGC
1 GTTTTGATTTTAATTACAAAATTACCATATTAGC
29399 ACAAATAACA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (34 bp):
GTTTTGATTTTAATTACAAAATTACCATATTAGC
Found at i:32432 original size:15 final size:14
Alignment explanation
Indices: 32397--32424 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
32387 TTAATTATAA
32397 AAATTTTAAAAAAT
1 AAATTTTAAAAAAT
32411 AAATTTTAAAAAAT
1 AAATTTTAAAAAAT
32425 TATATTTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AAATTTTAAAAAAT
Found at i:33057 original size:31 final size:31
Alignment explanation
Indices: 32961--33068 Score: 146
Period size: 31 Copynumber: 3.5 Consensus size: 31
32951 TCCTTTTGTG
32961 CACGTGGCATGCCACATGTCACTTTTTGGTA
1 CACGTGGCATGCCACATGTCACTTTTTGGTA
* ** *
32992 CACATGG-AGTGATACGTGTCACTTTTTGGTA
1 CACGTGGCA-TGCCACATGTCACTTTTTGGTA
* *
33023 CACGTGGCGTGCCACATGTCGCTTTTTGGTA
1 CACGTGGCATGCCACATGTCACTTTTTGGTA
33054 CACGTGGCATGCCAC
1 CACGTGGCATGCCAC
33069 GTCAAACACC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
30 1 0.02
31 63 0.98
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.31
Consensus pattern (31 bp):
CACGTGGCATGCCACATGTCACTTTTTGGTA
Found at i:33804 original size:17 final size:16
Alignment explanation
Indices: 33782--33841 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 16
33772 AAGATTATCA
33782 GTGATCTTGCATCACTG
1 GTGATCTTG-ATCACTG
*
33799 GTGATCTAAGATCACTG
1 GTGATCT-TGATCACTG
*
33816 GTGAT-TTAAGATCAATG
1 GTGATCTT--GATCACTG
33833 GTGATCTTG
1 GTGATCTTG
33842 GGGGGTGATC
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
16 2 0.06
17 31 0.86
18 3 0.08
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (16 bp):
GTGATCTTGATCACTG
Found at i:34165 original size:36 final size:36
Alignment explanation
Indices: 34114--34185 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
34104 GAACAACGTT
*
34114 GAAATTTTTGACTAACTCCAAGATCTCCATAATTAA
1 GAAAATTTTGACTAACTCCAAGATCTCCATAATTAA
* *
34150 GAAAATTTTGGCTAACTCCAGGATCTCCATAATTAA
1 GAAAATTTTGACTAACTCCAAGATCTCCATAATTAA
34186 ACAAGCTACT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (36 bp):
GAAAATTTTGACTAACTCCAAGATCTCCATAATTAA
Found at i:34818 original size:15 final size:15
Alignment explanation
Indices: 34798--34829 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
34788 GATTTTTTAC
34798 GACGGTCGCAAATGA
1 GACGGTCGCAAATGA
34813 GACGGTCGCAAATGA
1 GACGGTCGCAAATGA
34828 GA
1 GA
34830 GTATTGACGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.19, G:0.34, T:0.12
Consensus pattern (15 bp):
GACGGTCGCAAATGA
Done.