Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020568.1 Corchorus olitorius cultivar O-4 contig20601, 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: 46084
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:405 original size:2 final size:2
Alignment explanation
Indices: 394--439 Score: 67
Period size: 2 Copynumber: 23.0 Consensus size: 2
384 AGTTTAGACT
*
394 TA TA TA -A TA TA TA GA TA TA TA TA TA TA TA TA TA TA CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
436 TA TA
1 TA TA
440 CTAAATATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 1 0.03
2 37 0.93
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:15870 original size:123 final size:127
Alignment explanation
Indices: 15723--15974 Score: 386
Period size: 131 Copynumber: 2.0 Consensus size: 127
15713 CATTGTTTAA
* *
15723 ACTTTTATAGTTTCACTAAACTAAAAACTCTATTTTTATTTAATTAAATCTAATAT-CTT-TA-T
1 ACTTTTACAGTTTCACTAAACTAAAAACTCTATTTTTATTTAATTAAAACTAATATCCTTATACT
*
15785 A-ATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
66 ATATTTTTACCATTTTAATATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
* * *
15846 ACTTTTACAGTTTTACTCAACTAAAAATTCTATTTTTATTTAATTAAAACTAATATCCTTATACC
1 ACTTTTACAGTTTCACTAAACTAAAAACTCTATTTTTATTTAATTAAAACTAATATCCTTATA-C
15911 TATTTTATTTTTACCATTTTAATATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAAT
65 TA---TATTTTTACCATTTTAATATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAAT
15975 TTATTTCTTA
Statistics
Matches: 115, Mismatches: 6, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
123 51 0.44
124 3 0.03
125 2 0.02
127 2 0.02
131 57 0.50
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (127 bp):
ACTTTTACAGTTTCACTAAACTAAAAACTCTATTTTTATTTAATTAAAACTAATATCCTTATACT
ATATTTTTACCATTTTAATATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:19366 original size:131 final size:123
Alignment explanation
Indices: 19219--19470 Score: 387
Period size: 123 Copynumber: 2.0 Consensus size: 123
19209 TAAGAAATAA
* *
19219 ATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATATTAAAATGGTAAAAATAAAATAG
1 ATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATAGTAAAAAT----TA-
*
19284 GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAAGTA
61 -TA-AA-GATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTA
19349 T
123 T
*
19350 ATTTAAAATATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATAGTAAAAATTATAAAG
1 ATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATAGTAAAAATTATAAAG
*
19415 ATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTGAAACTATAAAAGT
66 ATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGT
19471 TTAAACAATG
Statistics
Matches: 116, Mismatches: 5, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
123 55 0.47
124 2 0.02
125 2 0.02
127 2 0.02
131 55 0.47
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.38
Consensus pattern (123 bp):
ATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATAGTAAAAATTATAAAG
ATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTAT
Found at i:22609 original size:30 final size:31
Alignment explanation
Indices: 22573--22630 Score: 109
Period size: 30 Copynumber: 1.9 Consensus size: 31
22563 GTTAATAAGC
22573 CATTAAAATTTGAGGGTATAAG-AGAAAAAT
1 CATTAAAATTTGAGGGTATAAGAAGAAAAAT
22603 CATTAAAATTTGAGGGTATAAGAAGAAA
1 CATTAAAATTTGAGGGTATAAGAAGAAA
22631 GTCAAGATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.50, C:0.03, G:0.21, T:0.26
Consensus pattern (31 bp):
CATTAAAATTTGAGGGTATAAGAAGAAAAAT
Found at i:22932 original size:28 final size:28
Alignment explanation
Indices: 22877--22932 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
22867 TAGTTAAATG
* *
22877 GAAAAACAAAAGAGAGAAATGTACAAAA
1 GAAAAACAAAAAAGAGAAATCTACAAAA
*
22905 GAAAAACAAAAAAGAGAAATCTAGAAAA
1 GAAAAACAAAAAAGAGAAATCTACAAAA
22933 CGGATGACCC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.70, C:0.07, G:0.16, T:0.07
Consensus pattern (28 bp):
GAAAAACAAAAAAGAGAAATCTACAAAA
Found at i:27508 original size:55 final size:55
Alignment explanation
Indices: 27419--27530 Score: 206
Period size: 55 Copynumber: 2.0 Consensus size: 55
27409 CATCCGTTTC
*
27419 CTTTCACACAATAAATGTTAGAATAAATCTTATCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTAGAATAAATCATATCCCCTATCTCTACTTAATTATT
*
27474 CTTTCACACAATAAATGTTATAATAAATCATATCCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTAGAATAAATCATATCCCCTATCTCTACTTAATTATT
27529 CT
1 CT
27531 ACAAAATAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.40
Consensus pattern (55 bp):
CTTTCACACAATAAATGTTAGAATAAATCATATCCCCTATCTCTACTTAATTATT
Found at i:27621 original size:21 final size:21
Alignment explanation
Indices: 27597--27663 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
27587 AAGGATCAGG
*
27597 ATTTGAGTTGAGTATTTCTTA
1 ATTTGAGATGAGTATTTCTTA
* * *
27618 ATTT-ACAATGAAT-TTTCTATG
1 ATTTGA-GATGAGTATTTCT-TA
*
27639 ATTTGAGCTGAGTATTTCTTA
1 ATTTGAGATGAGTATTTCTTA
27660 ATTT
1 ATTT
27664 ACAGAGAATT
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
20 6 0.18
21 22 0.65
22 6 0.18
ACGTcount: A:0.27, C:0.07, G:0.15, T:0.51
Consensus pattern (21 bp):
ATTTGAGATGAGTATTTCTTA
Found at i:27655 original size:42 final size:42
Alignment explanation
Indices: 27596--27676 Score: 137
Period size: 42 Copynumber: 1.9 Consensus size: 42
27586 TAAGGATCAG
*
27596 GATTTGAGTTGAGTATTTCTTAATTTACA-ATGAATTTTCTAT
1 GATTTGAGCTGAGTATTTCTTAATTTACAGA-GAATTTTCTAT
27638 GATTTGAGCTGAGTATTTCTTAATTTACAGAGAATTTTC
1 GATTTGAGCTGAGTATTTCTTAATTTACAGAGAATTTTC
27677 AAGACTTAGC
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
42 36 0.97
43 1 0.03
ACGTcount: A:0.28, C:0.09, G:0.16, T:0.47
Consensus pattern (42 bp):
GATTTGAGCTGAGTATTTCTTAATTTACAGAGAATTTTCTAT
Found at i:37140 original size:16 final size:16
Alignment explanation
Indices: 37116--37146 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
37106 ACACGTTAAA
37116 AATACGAATGAAATTC
1 AATACGAATGAAATTC
*
37132 AATATGAATGAAATT
1 AATACGAATGAAATT
37147 GAACAAAATT
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:0.52, C:0.06, G:0.13, T:0.29
Consensus pattern (16 bp):
AATACGAATGAAATTC
Found at i:43150 original size:27 final size:27
Alignment explanation
Indices: 43112--43165 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
43102 ACGTTTTACC
43112 AAAGGATTGGCTCAGATTAGATTGCTT
1 AAAGGATTGGCTCAGATTAGATTGCTT
43139 AAAGGATTGGCTCAGATTAGATTGCTT
1 AAAGGATTGGCTCAGATTAGATTGCTT
43166 TCTAAAGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.33
Consensus pattern (27 bp):
AAAGGATTGGCTCAGATTAGATTGCTT
Found at i:44882 original size:6 final size:6
Alignment explanation
Indices: 44871--44918 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
44861 TGAAAAAAAA
44871 TGTTTT TGTTTT T-TGTTT TG-TTT TGTTTT TGTTTT T-TTTGT T-TTTT
1 TGTTTT TGTTTT TGT-TTT TGTTTT TGTTTT TGTTTT TGTTT-T TGTTTT
44917 TG
1 TG
44919 GGAACTTTCC
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
5 11 0.30
6 26 0.70
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (6 bp):
TGTTTT
Found at i:44889 original size:5 final size:5
Alignment explanation
Indices: 44881--44914 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
44871 TGTTTTTGTT
44881 TTTTG TTTTG TTTTG TTTTTG TTTT- TTTTG TTTT
1 TTTTG TTTTG TTTTG -TTTTG TTTTG TTTTG TTTT
44915 TTTGGGAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 18 0.67
6 5 0.19
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (5 bp):
TTTTG
Found at i:45002 original size:35 final size:35
Alignment explanation
Indices: 44954--45128 Score: 219
Period size: 34 Copynumber: 4.9 Consensus size: 35
44944 AGCTGAAAAT
*
44954 GATGGGAACTTTCCCTAAATTGAAAAC-TAAAACCC
1 GATGGGAACTTTCCC-AATTTGAAAACTTAAAACCC
* *
44989 GGTGGGAACTTTCCCAATTTGAAAACTTAAAAACTC
1 GATGGGAACTTTCCCAATTTGAAAACTT-AAAACCC
* *
45025 GATGGGAACTTTCCCAATTTGAAAGC-TAAAACCT
1 GATGGGAACTTTCCCAATTTGAAAACTTAAAACCC
*
45059 GATGGGAACTTTCCCAATTTGAAAACTTAAAAAAAACTC
1 GATGGGAACTTTCCCAATTTGAAAACTT----AAAACCC
*
45098 AATGGGAACTTTCCCAATTTGAAAACTTAAA
1 GATGGGAACTTTCCCAATTTGAAAACTTAAA
45129 CCTGACGAAA
Statistics
Matches: 122, Mismatches: 11, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
34 40 0.33
35 20 0.16
36 30 0.25
39 32 0.26
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.26
Consensus pattern (35 bp):
GATGGGAACTTTCCCAATTTGAAAACTTAAAACCC
Found at i:45063 original size:34 final size:34
Alignment explanation
Indices: 44917--45133 Score: 218
Period size: 39 Copynumber: 6.0 Consensus size: 34
44907 TTTGTTTTTT
* **
44917 TGGGAACTTTCCCACTTTGAAAACTAAAGCTGAAAATGA
1 TGGGAACTTTCCCAATTTGAAAACT-AA----AACCTGA
* * *
44956 TGGGAACTTTCCCTAAATTGAAAACTAAAACCCGG
1 TGGGAACTTTCCC-AATTTGAAAACTAAAACCTGA
*
44991 TGGGAACTTTCCCAATTTGAAAACTTAAAAACTCGA
1 TGGGAACTTTCCCAATTTGAAAAC-TAAAACCT-GA
*
45027 TGGGAACTTTCCCAATTTGAAAGCTAAAACCTGA
1 TGGGAACTTTCCCAATTTGAAAACTAAAACCTGA
* *
45061 TGGGAACTTTCCCAATTTGAAAACTTAAAAAAAACTCAA
1 TGGGAACTTTCCCAATTTGAAAAC-T---AAAACCT-GA
*
45100 TGGGAACTTTCCCAATTTGAAAACTTAAACCTGA
1 TGGGAACTTTCCCAATTTGAAAACTAAAACCTGA
45134 CGAAATAATT
Statistics
Matches: 152, Mismatches: 18, Indels: 21
0.80 0.09 0.11
Matches are distributed among these distances:
34 36 0.24
35 35 0.23
36 24 0.16
38 7 0.05
39 40 0.26
40 10 0.07
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (34 bp):
TGGGAACTTTCCCAATTTGAAAACTAAAACCTGA
Found at i:45070 original size:70 final size:70
Alignment explanation
Indices: 44917--45133 Score: 274
Period size: 70 Copynumber: 3.0 Consensus size: 70
44907 TTTGTTTTTT
* * * *
44917 TGGGAACTTTCCCACTTTGAAAACTAAAGCTGAAAAT-GATGGGAACTTTCCCTAAATTGAAAAC
1 TGGGAACTTTCCCAATTTGAAAACTTAA----AAACTCGATGGGAACTTTCCC-AATTTGAAAAC
* *
44981 TAAAACCCGG
61 TAAAACCTGA
*
44991 TGGGAACTTTCCCAATTTGAAAACTTAAAAACTCGATGGGAACTTTCCCAATTTGAAAGCTAAAA
1 TGGGAACTTTCCCAATTTGAAAACTTAAAAACTCGATGGGAACTTTCCCAATTTGAAAACTAAAA
45056 CCTGA
66 CCTGA
* *
45061 TGGGAACTTTCCCAATTTGAAAACTTAAAAAAAACTCAATGGGAACTTTCCCAATTTGAAAACTT
1 TGGGAACTTTCCCAATTTGAAAACTT---AAAAACTCGATGGGAACTTTCCCAATTTGAAAACTA
45126 AAACCTGA
63 AAACCTGA
45134 CGAAATAATT
Statistics
Matches: 129, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
70 47 0.36
71 15 0.12
73 41 0.32
74 26 0.20
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (70 bp):
TGGGAACTTTCCCAATTTGAAAACTTAAAAACTCGATGGGAACTTTCCCAATTTGAAAACTAAAA
CCTGA
Done.