Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016292.1 Corchorus olitorius cultivar O-4 contig16325, 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: 81220
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:1588 original size:17 final size:17
Alignment explanation
Indices: 1566--1601 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1556 ACAAGTAGAA
1566 GCAGGTGATAACTTCTC
1 GCAGGTGATAACTTCTC
1583 GCAGGTGATAACTTCTC
1 GCAGGTGATAACTTCTC
1600 GC
1 GC
1602 TTGTATCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.28
Consensus pattern (17 bp):
GCAGGTGATAACTTCTC
Found at i:4424 original size:16 final size:17
Alignment explanation
Indices: 4393--4426 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
4383 AATCTATCCA
4393 TCTCCACCATTTCTTCT
1 TCTCCACCATTTCTTCT
*
4410 TCTCCATCA-TTCTTCT
1 TCTCCACCATTTCTTCT
4426 T
1 T
4427 AGCCTTCTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.12, C:0.38, G:0.00, T:0.50
Consensus pattern (17 bp):
TCTCCACCATTTCTTCT
Found at i:12305 original size:14 final size:12
Alignment explanation
Indices: 12268--12309 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
12258 AAAGAGATTG
12268 AGAAGAA-ACAGT
1 AGAAGAAGA-AGT
12280 AGAAGAAGAAGT
1 AGAAGAAGAAGT
12292 AGAAGCAGAGAAGT
1 AGAAG-A-AGAAGT
12306 AGAA
1 AGAA
12310 AAGCTATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 15 0.56
13 2 0.07
14 10 0.37
ACGTcount: A:0.57, C:0.05, G:0.31, T:0.07
Consensus pattern (12 bp):
AGAAGAAGAAGT
Found at i:16301 original size:2 final size:2
Alignment explanation
Indices: 16294--16322 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
16284 TACACTCAAT
16294 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 T
16323 ATAGTTAATT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:21806 original size:6 final size:6
Alignment explanation
Indices: 21795--21819 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
21785 ATTAATCAAT
21795 CAGTTA CAGTTA CAGTTA CAGTTA C
1 CAGTTA CAGTTA CAGTTA CAGTTA C
21820 TAGCTTATAT
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:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (6 bp):
CAGTTA
Found at i:26421 original size:7 final size:7
Alignment explanation
Indices: 26409--26453 Score: 90
Period size: 7 Copynumber: 6.4 Consensus size: 7
26399 CTATCCCAAT
26409 AGTTGAG
1 AGTTGAG
26416 AGTTGAG
1 AGTTGAG
26423 AGTTGAG
1 AGTTGAG
26430 AGTTGAG
1 AGTTGAG
26437 AGTTGAG
1 AGTTGAG
26444 AGTTGAG
1 AGTTGAG
26451 AGT
1 AGT
26454 GTTTATTGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.29, C:0.00, G:0.42, T:0.29
Consensus pattern (7 bp):
AGTTGAG
Found at i:42096 original size:19 final size:19
Alignment explanation
Indices: 42072--42109 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
42062 GCATGAAATG
42072 GCACAATACCTACATACAA
1 GCACAATACCTACATACAA
42091 GCACAATACCTACATACAA
1 GCACAATACCTACATACAA
42110 TCTATATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.32, G:0.05, T:0.16
Consensus pattern (19 bp):
GCACAATACCTACATACAA
Found at i:42372 original size:23 final size:22
Alignment explanation
Indices: 42342--42403 Score: 80
Period size: 23 Copynumber: 3.0 Consensus size: 22
42332 TTTTTCATTT
42342 ATCTTTCTCTTATATTCTCAAAA
1 ATCTTTCTCTTATATT-TCAAAA
42365 ATCTTTCTCTTATATTTC--AA
1 ATCTTTCTCTTATATTTCAAAA
42385 A---TTCTCTTATATTTCAAAA
1 ATCTTTCTCTTATATTTCAAAA
42404 TTTAATAACT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
17 14 0.38
19 2 0.05
20 3 0.08
22 2 0.05
23 16 0.43
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (22 bp):
ATCTTTCTCTTATATTTCAAAA
Found at i:42391 original size:17 final size:17
Alignment explanation
Indices: 42369--42436 Score: 86
Period size: 17 Copynumber: 4.0 Consensus size: 17
42359 TCAAAAATCT
42369 TTCTCTTATATTTCAAA
1 TTCTCTTATATTTCAAA
42386 TTCTCTTATATTTCAAA
1 TTCTCTTATATTTCAAA
* *
42403 AT-T-TAATAACTTTCAAA
1 TTCTCTTAT-A-TTTCAAA
42420 TTCTCTTATATTTCAAA
1 TTCTCTTATATTTCAAA
42437 ATTTAATAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
15 3 0.07
16 2 0.05
17 33 0.77
18 2 0.05
19 3 0.07
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (17 bp):
TTCTCTTATATTTCAAA
Found at i:42418 original size:34 final size:34
Alignment explanation
Indices: 42379--42451 Score: 146
Period size: 34 Copynumber: 2.1 Consensus size: 34
42369 TTCTCTTATA
42379 TTTCAAATTCTCTTATATTTCAAAATTTAATAAC
1 TTTCAAATTCTCTTATATTTCAAAATTTAATAAC
42413 TTTCAAATTCTCTTATATTTCAAAATTTAATAAC
1 TTTCAAATTCTCTTATATTTCAAAATTTAATAAC
42447 TTTCA
1 TTTCA
42452 CGTCAACCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.37, C:0.15, G:0.00, T:0.48
Consensus pattern (34 bp):
TTTCAAATTCTCTTATATTTCAAAATTTAATAAC
Found at i:42450 original size:17 final size:17
Alignment explanation
Indices: 42396--42451 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
42386 TTCTCTTATA
42396 TTTCAAAATTTAATAAC
1 TTTCAAAATTTAATAAC
**
42413 TTTC-AAATTCTCTTATA-
1 TTTCAAAATT-TAATA-AC
42430 TTTCAAAATTTAATAAC
1 TTTCAAAATTTAATAAC
42447 TTTCA
1 TTTCA
42452 CGTCAACCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
16 6 0.19
17 19 0.61
18 6 0.19
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTCAAAATTTAATAAC
Found at i:42528 original size:50 final size:50
Alignment explanation
Indices: 42474--42576 Score: 188
Period size: 50 Copynumber: 2.1 Consensus size: 50
42464 ATGGTAATCT
*
42474 TATTCCCATAAAAATAAAAAAACTATATTTTCCCACTAAAATAACATTGC
1 TATTCCCATAAAAATAAAAAAACTATATTTTCCCACTAAAATAACATTCC
*
42524 TATTCCCATAAAAATAAAAAAATTATATTTTCCCACTAAAATAACATTCC
1 TATTCCCATAAAAATAAAAAAACTATATTTTCCCACTAAAATAACATTCC
42574 TAT
1 TAT
42577 GAAAGTAGTG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.48, C:0.19, G:0.01, T:0.32
Consensus pattern (50 bp):
TATTCCCATAAAAATAAAAAAACTATATTTTCCCACTAAAATAACATTCC
Found at i:42567 original size:27 final size:27
Alignment explanation
Indices: 42476--42564 Score: 82
Period size: 27 Copynumber: 3.4 Consensus size: 27
42466 GGTAATCTTA
*
42476 TTCCCATAAAAATAAAAAAACTATATT
1 TTCCCATAAAAATAAAAAAATTATATT
* *
42503 TTCCCACT-AAAAT---AACATTGCTA--
1 TTCCCA-TAAAAATAAAAAAATT-ATATT
42526 TTCCCATAAAAATAAAAAAATTATATT
1 TTCCCATAAAAATAAAAAAATTATATT
42553 TTCCCACTAAAA
1 TTCCCA-TAAAA
42565 TAACATTCCT
Statistics
Matches: 48, Mismatches: 5, Indels: 17
0.69 0.07 0.24
Matches are distributed among these distances:
22 1 0.02
23 11 0.23
24 4 0.08
25 4 0.08
26 5 0.10
27 17 0.35
28 6 0.12
ACGTcount: A:0.49, C:0.19, G:0.01, T:0.30
Consensus pattern (27 bp):
TTCCCATAAAAATAAAAAAATTATATT
Found at i:45237 original size:81 final size:81
Alignment explanation
Indices: 45135--45305 Score: 324
Period size: 81 Copynumber: 2.1 Consensus size: 81
45125 TTTATGCTGC
*
45135 AGGAATCAATGTTATGCGAAGGAGCTTGTTTCATTATGGAGATTCAGGAGTTTAATTGCTCTTAC
1 AGGAATCAATGTTATGCGAAGGAGCTTGTTTCATTATGGAGATCCAGGAGTTTAATTGCTCTTAC
45200 AGATCAACAAGAAGTA
66 AGATCAACAAGAAGTA
*
45216 AGGAATCAATGTTATGCGAAGGAGCTTGTTTCATTATGGAGATCCGGGAGTTTAATTGCTCTTAC
1 AGGAATCAATGTTATGCGAAGGAGCTTGTTTCATTATGGAGATCCAGGAGTTTAATTGCTCTTAC
45281 AGATCAACAAGAAGTA
66 AGATCAACAAGAAGTA
45297 AGGAATCAA
1 AGGAATCAA
45306 GGAATCAATT
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 88 1.00
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (81 bp):
AGGAATCAATGTTATGCGAAGGAGCTTGTTTCATTATGGAGATCCAGGAGTTTAATTGCTCTTAC
AGATCAACAAGAAGTA
Found at i:63958 original size:62 final size:62
Alignment explanation
Indices: 63887--64008 Score: 217
Period size: 62 Copynumber: 2.0 Consensus size: 62
63877 AGATTTATAG
*
63887 TTTTACTCAACAAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTTA
1 TTTTACTCAACAAAAAACTATATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTTA
* *
63949 TTTTACTCAACTAAAAACTATATTTTTATTTAATTAAATTTAATATCTTTATAACTATTT
1 TTTTACTCAACAAAAAACTATATTTTTATTTAATTAAATCTAATATCTTTATAACTATTT
64009 CAGTTTACCA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (62 bp):
TTTTACTCAACAAAAAACTATATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTTA
Found at i:64783 original size:2 final size:2
Alignment explanation
Indices: 64776--64800 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
64766 GTGAAGACTA
64776 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
64801 ATAAAATTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:65600 original size:21 final size:22
Alignment explanation
Indices: 65561--65601 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
65551 AGGAAAATCT
* *
65561 AAAAAAAAAACCTTTAAAGAAG
1 AAAAAAAAAACCATGAAAGAAG
65583 AAAAAAAAAA-CATGAAAGA
1 AAAAAAAAAACCATGAAAGA
65602 GGTGGGTCGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.73, C:0.07, G:0.10, T:0.10
Consensus pattern (22 bp):
AAAAAAAAAACCATGAAAGAAG
Found at i:67818 original size:29 final size:30
Alignment explanation
Indices: 67759--67829 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
67749 TGACATCAAA
*
67759 TTGTAAGTAGAGGAACCAAATTGACAGTTT
1 TTGTAAGTAGAGGAACCAAATTGACACTTT
* *
67789 TTGT-AGTAGAGGGACTAAATTGATC-CTTT
1 TTGTAAGTAGAGGAACCAAATTGA-CACTTT
67818 TCTGTAAGTAGA
1 T-TGTAAGTAGA
67830 CGGTATTTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 21 0.60
30 8 0.23
31 6 0.17
ACGTcount: A:0.32, C:0.10, G:0.24, T:0.34
Consensus pattern (30 bp):
TTGTAAGTAGAGGAACCAAATTGACACTTT
Found at i:68807 original size:42 final size:43
Alignment explanation
Indices: 68756--68849 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 43
68746 AGTACATTAT
* *
68756 CTAA-ATTCTA-CTCCATCTCTGGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
68797 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
68842 CTAATATT
1 CTAATATT
68850 AATTGTTGCT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 37 0.79
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:76008 original size:24 final size:22
Alignment explanation
Indices: 75970--76017 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 22
75960 ACTCGTGATC
75970 TATTTCAAATCCTTTTCTTCTCTT
1 TATTTCAAATCCTTTT-TTCT-TT
* *
75994 TATTTCACATTCTTTTTTCTTT
1 TATTTCAAATCCTTTTTTCTTT
76016 TA
1 TA
76018 ATCATGTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 4 0.18
23 4 0.18
24 14 0.64
ACGTcount: A:0.17, C:0.21, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTCAAATCCTTTTTTCTTT
Done.