Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012845.1 Corchorus olitorius cultivar O-4 contig12878, 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: 29684
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:1593 original size:20 final size:22
Alignment explanation
Indices: 1568--1613 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
1558 TTTTGCATTA
1568 TAATTAAAAT-AA-TAATAAAT
1 TAATTAAAATAAACTAATAAAT
1588 TAATTAAAATCAAACTAATAAAT
1 TAATTAAAAT-AAACTAATAAAT
1611 TAA
1 TAA
1614 AATTAACTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.43
22 2 0.09
23 11 0.48
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (22 bp):
TAATTAAAATAAACTAATAAAT
Found at i:3113 original size:17 final size:17
Alignment explanation
Indices: 3091--3162 Score: 92
Period size: 17 Copynumber: 4.2 Consensus size: 17
3081 ATCACCCCCC
*
3091 AGATCACTAGTGATCTA
1 AGATCACCAGTGATCTA
*
3108 AGATCACTAGTGATCTA
1 AGATCACCAGTGATCTA
3125 AGATCACCAGTGATGC-A
1 AGATCACCAGTGAT-CTA
* *
3142 AGATCACCGGTGATCAA
1 AGATCACCAGTGATCTA
3159 AGAT
1 AGAT
3163 TACATGGGTT
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
16 1 0.02
17 49 0.96
18 1 0.02
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (17 bp):
AGATCACCAGTGATCTA
Found at i:5205 original size:14 final size:14
Alignment explanation
Indices: 5186--5213 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5176 GAAAGTCAGT
5186 CCTTGGATATGAGC
1 CCTTGGATATGAGC
5200 CCTTGGATATGAGC
1 CCTTGGATATGAGC
5214 AAAGCTAAAG
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:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (14 bp):
CCTTGGATATGAGC
Found at i:5256 original size:14 final size:14
Alignment explanation
Indices: 5237--5264 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5227 GTCTGAGCGG
5237 CCTTGGATATGAGC
1 CCTTGGATATGAGC
5251 CCTTGGATATGAGC
1 CCTTGGATATGAGC
5265 AAAGCTAAAG
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:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (14 bp):
CCTTGGATATGAGC
Found at i:5333 original size:40 final size:40
Alignment explanation
Indices: 5279--5355 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
5269 CTAAAGAAAA
5279 TCAGTCCTCATATCCAAGGATATGAGCCCTTGGATATTAG
1 TCAGTCCTCATATCCAAGGATATGAGCCCTTGGATATTAG
** **
5319 TCAGTCCTTGTATCCTTGGATATGAGCCCTTGGATAT
1 TCAGTCCTCATATCCAAGGATATGAGCCCTTGGATAT
5356 GAGCCTTCCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (40 bp):
TCAGTCCTCATATCCAAGGATATGAGCCCTTGGATATTAG
Found at i:5351 original size:14 final size:14
Alignment explanation
Indices: 5332--5360 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5322 GTCCTTGTAT
5332 CCTTGGATATGAGC
1 CCTTGGATATGAGC
5346 CCTTGGATATGAGC
1 CCTTGGATATGAGC
5360 C
1 C
5361 TTCCTTGGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.28
Consensus pattern (14 bp):
CCTTGGATATGAGC
Found at i:5368 original size:17 final size:15
Alignment explanation
Indices: 5331--5371 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
5321 AGTCCTTGTA
5331 TCCTTGGATATGAGC
1 TCCTTGGATATGAGC
5346 -CCTTGGATATGAGCC
1 TCCTTGGATATGAG-C
5361 TTCCTTGGATA
1 -TCCTTGGATA
5372 CACTCCCAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 13 0.57
15 1 0.04
17 9 0.39
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.34
Consensus pattern (15 bp):
TCCTTGGATATGAGC
Found at i:5467 original size:26 final size:24
Alignment explanation
Indices: 5402--5474 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 24
5392 TAAATAATAC
5402 CTCATAATTATAAGCTTCTCTCATAT
1 CTCAT-ATTA-AAGCTTCTCTCATAT
5428 CTCATA-T-AAGCTTCTCTCATAT
1 CTCATATTAAAGCTTCTCTCATAT
5450 CTCATAGTTAAAAGCTTCTCTCATA
1 CTCATA-TT-AAAGCTTCTCTCATA
5475 CCTCGAACTC
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
22 21 0.49
24 2 0.05
25 1 0.02
26 19 0.44
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.40
Consensus pattern (24 bp):
CTCATATTAAAGCTTCTCTCATAT
Found at i:9780 original size:48 final size:48
Alignment explanation
Indices: 9709--9807 Score: 153
Period size: 48 Copynumber: 2.1 Consensus size: 48
9699 CCATCTTTCT
* * *
9709 TCGCCTTCCACTCTTTTTAATTGCCTTTTTATTCATCAGAACCACAGC
1 TCGCCTTCCACTCTCTTTAATTGCCTTTATAATCATCAGAACCACAGC
* *
9757 TCGCCTTCCACTCTCTTTGATTGCCTTTATAATCATCAGAACCACATC
1 TCGCCTTCCACTCTCTTTAATTGCCTTTATAATCATCAGAACCACAGC
9805 TCG
1 TCG
9808 TTGGCTGCGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.21, C:0.32, G:0.09, T:0.37
Consensus pattern (48 bp):
TCGCCTTCCACTCTCTTTAATTGCCTTTATAATCATCAGAACCACAGC
Found at i:10115 original size:2 final size:2
Alignment explanation
Indices: 10110--10149 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
10100 TCTTTTATTT
10110 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA T
10150 GTGTGTGATA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14312 original size:21 final size:20
Alignment explanation
Indices: 14273--14311 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
14263 AAAAATGTAT
14273 AAATTGGGGGAATAAAAAAG
1 AAATTGGGGGAATAAAAAAG
14293 AAATTGGGGGAATAAAAAA
1 AAATTGGGGGAATAAAAAA
14312 AAGGGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.28, T:0.15
Consensus pattern (20 bp):
AAATTGGGGGAATAAAAAAG
Found at i:15205 original size:36 final size:36
Alignment explanation
Indices: 15158--15229 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
15148 TGTCCATTTT
15158 CTGAATTAATTAAATTTTAAATATTTCAATCTAATC
1 CTGAATTAATTAAATTTTAAATATTTCAATCTAATC
15194 CTGAATTAATTAAATTTTAAATATTTCAATCTAATC
1 CTGAATTAATTAAATTTTAAATATTTCAATCTAATC
15230 ACTAGGGGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.44
Consensus pattern (36 bp):
CTGAATTAATTAAATTTTAAATATTTCAATCTAATC
Found at i:15698 original size:84 final size:84
Alignment explanation
Indices: 15591--15835 Score: 348
Period size: 84 Copynumber: 2.9 Consensus size: 84
15581 CCTATATTTC
* * ** *
15591 AAAGTCCTCAAACACATTTATAACACAAAAACATCTATA-TCAAAGTCCCTAAACACAATTATAA
1 AAAGTCATCAAACACATTTATAACACAGAGGCATCCATACT-AAAGTCCCTAAACACAATTATAA
*
15655 CACATGAGCAATTCTCTCTA
65 CACAAGAGCAATTCTCTCTA
*
15675 AAAGTCATCAAACACATTTATAACACAGAGGCATCCATACTAAAGTCCCCAAACACAATTATAAC
1 AAAGTCATCAAACACATTTATAACACAGAGGCATCCATACTAAAGTCCCTAAACACAATTATAAC
* * *
15740 ATAGGGGCAATTCTCTCTA
66 ACAAGAGCAATTCTCTCTA
* * *
15759 AAAGTCTTCAAACACATTTATAACACAGAGGCATCCATACTAAAGTTCCTAAACACAATTATATC
1 AAAGTCATCAAACACATTTATAACACAGAGGCATCCATACTAAAGTCCCTAAACACAATTATAAC
*
15824 ACAAGAACAATT
66 ACAAGAGCAATT
15836 TCTATATGGC
Statistics
Matches: 143, Mismatches: 17, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
84 142 0.99
85 1 0.01
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (84 bp):
AAAGTCATCAAACACATTTATAACACAGAGGCATCCATACTAAAGTCCCTAAACACAATTATAAC
ACAAGAGCAATTCTCTCTA
Found at i:15737 original size:41 final size:42
Alignment explanation
Indices: 15551--15826 Score: 214
Period size: 43 Copynumber: 6.6 Consensus size: 42
15541 AATAATTAAC
* * * *
15551 GTCCTCAAACACAATTATAATACTGAGGCA-CCTATATTTCAAA
1 GTCCTCAAACACAATTATAACACAGAGGCATCC-ATA-CTAAAA
* * ** * *
15594 GTCCTCAAACACATTTATAACACAAAAACATCTATA-TCAAA
1 GTCCTCAAACACAATTATAACACAGAGGCATCCATACTAAAA
15635 GTCC-CTAAACACAATTATAACACATGA-GCAATTCTC-T-CTAAAA
1 GTCCTC-AAACACAATTATAACACA-GAGGC-A-TC-CATACTAAAA
* *
15678 GTCATCAAACACATTTATAACACAGAGGCATCCATACT-AAA
1 GTCCTCAAACACAATTATAACACAGAGGCATCCATACTAAAA
* * *
15719 GTCCCCAAACACAATTATAACATAGGGGCAATTCTC-T-CTAAAA
1 GTCCTCAAACACAATTATAACACAGAGGC-A-TC-CATACTAAAA
* *
15762 GTCTTCAAACACATTTATAACACAGAGGCATCCATACT-AAA
1 GTCCTCAAACACAATTATAACACAGAGGCATCCATACTAAAA
*
15803 GTTCCT-AAACACAATTATATCACA
1 G-TCCTCAAACACAATTATAACACA
15827 AGAACAATTT
Statistics
Matches: 188, Mismatches: 27, Indels: 38
0.74 0.11 0.15
Matches are distributed among these distances:
40 3 0.02
41 80 0.43
42 16 0.09
43 86 0.46
44 3 0.02
ACGTcount: A:0.42, C:0.25, G:0.08, T:0.25
Consensus pattern (42 bp):
GTCCTCAAACACAATTATAACACAGAGGCATCCATACTAAAA
Found at i:19942 original size:24 final size:24
Alignment explanation
Indices: 19904--19950 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
19894 CCACGATTCC
*
19904 TCCTCATCTCGTTCATCTTCGTCG
1 TCCTCATCTCGTTCATCATCGTCG
19928 TCCTCATCCTC-TTCATCATCGTC
1 TCCTCAT-CTCGTTCATCATCGTC
19951 ATCGGCTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.11, C:0.40, G:0.09, T:0.40
Consensus pattern (24 bp):
TCCTCATCTCGTTCATCATCGTCG
Found at i:22320 original size:13 final size:13
Alignment explanation
Indices: 22304--22332 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
22294 AACCTTCTCC
22304 TTCTTTTTTCTTT
1 TTCTTTTTTCTTT
22317 TTCTTTTTTCTTT
1 TTCTTTTTTCTTT
22330 TTC
1 TTC
22333 ACCCTTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTCTTTTTTCTTT
Found at i:22350 original size:9 final size:10
Alignment explanation
Indices: 22326--22352 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
22316 TTTCTTTTTT
22326 CTTTTTCACC
1 CTTTTTCACC
22336 CTTTTTCACC
1 CTTTTTCACC
22346 CTTTTTC
1 CTTTTTC
22353 CTTTGGGTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.07, C:0.37, G:0.00, T:0.56
Consensus pattern (10 bp):
CTTTTTCACC
Found at i:25880 original size:24 final size:24
Alignment explanation
Indices: 25848--25893 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
25838 AATCATCAAC
*
25848 AAGAAGAAGAGGAGGAGGAGGAAG
1 AAGAAGAAGAGGAAGAGGAGGAAG
*
25872 AAGAAGAAGAGGAAGATGAGGA
1 AAGAAGAAGAGGAAGAGGAGGA
25894 TGAAATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.52, C:0.00, G:0.46, T:0.02
Consensus pattern (24 bp):
AAGAAGAAGAGGAAGAGGAGGAAG
Found at i:27491 original size:14 final size:14
Alignment explanation
Indices: 27472--27499 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
27462 TTGTTGGAAT
27472 AACTTTCATTCTCA
1 AACTTTCATTCTCA
27486 AACTTTCATTCTCA
1 AACTTTCATTCTCA
27500 GAAAGGTGGA
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:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (14 bp):
AACTTTCATTCTCA
Found at i:29662 original size:2 final size:2
Alignment explanation
Indices: 29655--29683 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29645 GCCTACATTT
29655 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
29684 G
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Done.