Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007964.1 Corchorus capsularis cultivar CVL-1 contig07985, 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: 49624
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:5045 original size:87 final size:87
Alignment explanation
Indices: 4899--5070 Score: 274
Period size: 87 Copynumber: 2.0 Consensus size: 87
4889 GCAAACAGCG
* * *
4899 GCAGAAAGACTAGTCTACAGCTTAGTCAAAGCCAGAAACGGCCATTTGGATCTATGGACTCCATA
1 GCAGAAAGACTAGTCCAAAGCTTAGTCAAAGCCAGAAACAGCCATTTGGATCTATGGACTCCATA
4964 CAAACATGTGAAAATGTGAGCA
66 CAAACATGTGAAAATGTGAGCA
* * *
4986 GCAGAAAGAC-AGGTCCAAAGCTTAGTGAAAGCCAGAAGCAGCCATTTGGATCTATGGACTCGAT
1 GCAGAAAGACTA-GTCCAAAGCTTAGTCAAAGCCAGAAACAGCCATTTGGATCTATGGACTCCAT
5050 ACAAACATGTGAAAATGTGAG
65 ACAAACATGTGAAAATGTGAG
5071 AATGCTTGGG
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
86 1 0.01
87 77 0.99
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.20
Consensus pattern (87 bp):
GCAGAAAGACTAGTCCAAAGCTTAGTCAAAGCCAGAAACAGCCATTTGGATCTATGGACTCCATA
CAAACATGTGAAAATGTGAGCA
Found at i:17730 original size:25 final size:25
Alignment explanation
Indices: 17702--17760 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
17692 ACTATAATGT
*
17702 TTCATCAAAAAAATAAATTTTATAA
1 TTCAACAAAAAAATAAATTTTATAA
* *
17727 TTCAAGAAAAAGATAAATTTTATAA
1 TTCAACAAAAAAATAAATTTTATAA
*
17752 TTAAACAAA
1 TTCAACAAA
17761 TGTTTTTTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.58, C:0.07, G:0.03, T:0.32
Consensus pattern (25 bp):
TTCAACAAAAAAATAAATTTTATAA
Found at i:18209 original size:16 final size:16
Alignment explanation
Indices: 18188--18219 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
18178 CAGATTGATC
18188 AACTAAATTTGAATCT
1 AACTAAATTTGAATCT
18204 AACTAAATTTGAATCT
1 AACTAAATTTGAATCT
18220 TAAATCTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (16 bp):
AACTAAATTTGAATCT
Found at i:22932 original size:1 final size:1
Alignment explanation
Indices: 22926--22966 Score: 82
Period size: 1 Copynumber: 41.0 Consensus size: 1
22916 AATTCATAGG
22926 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
22967 GACATATATC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:26300 original size:7 final size:7
Alignment explanation
Indices: 26290--26317 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
26280 TTCTTAGTTC
26290 TTACCCT
1 TTACCCT
26297 TTACCCT
1 TTACCCT
26304 TTACCCT
1 TTACCCT
26311 TTACCCT
1 TTACCCT
26318 ATCCTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.43, G:0.00, T:0.43
Consensus pattern (7 bp):
TTACCCT
Found at i:39569 original size:22 final size:23
Alignment explanation
Indices: 39539--39602 Score: 85
Period size: 22 Copynumber: 2.8 Consensus size: 23
39529 AACCAATAGG
*
39539 CAAATAAAGAAAAAAAATGTAC-
1 CAAAAAAAGAAAAAAAATGTACA
*
39561 CAAAAAAAGAAAAAATATGTACAA
1 CAAAAAAAGAAAAAAAATGTAC-A
*
39585 AAAAAAAAGAAAAAAAAT
1 CAAAAAAAGAAAAAAAAT
39603 ACATAGGTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
22 20 0.56
24 16 0.44
ACGTcount: A:0.75, C:0.06, G:0.08, T:0.11
Consensus pattern (23 bp):
CAAAAAAAGAAAAAAAATGTACA
Found at i:39605 original size:22 final size:22
Alignment explanation
Indices: 39544--39605 Score: 61
Period size: 24 Copynumber: 2.7 Consensus size: 22
39534 ATAGGCAAAT
** **
39544 AAAGAAAAAAAATGTACCAAAA
1 AAAGAAAAAAAATACAAAAAAA
*
39566 AAAGAAAAAATATGTACAAAAAAA
1 AAAGAAAAAA-A-ATACAAAAAAA
39590 AAAGAAAAAAAATACA
1 AAAGAAAAAAAATACA
39606 TAGGTGTTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
22 14 0.44
23 2 0.06
24 16 0.50
ACGTcount: A:0.76, C:0.06, G:0.08, T:0.10
Consensus pattern (22 bp):
AAAGAAAAAAAATACAAAAAAA
Found at i:40322 original size:2 final size:2
Alignment explanation
Indices: 40315--40339 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40305 TAATATTTAG
40315 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
40340 TATGTACAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42316 original size:22 final size:21
Alignment explanation
Indices: 42291--42350 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
42281 AATTGTGAGG
**
42291 TTATCACAATTTCATAGTGTGA
1 TTATCA-AATTTCATAGCATGA
*
42313 TTATCGAAATTTCTTAGCATGA
1 TTATC-AAATTTCATAGCATGA
42335 TTA-CAACATTTCATAG
1 TTATCAA-ATTTCATAG
42351 GGAGCTTATC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 2 0.06
21 9 0.28
22 20 0.62
23 1 0.03
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (21 bp):
TTATCAAATTTCATAGCATGA
Found at i:42416 original size:22 final size:22
Alignment explanation
Indices: 42333--42433 Score: 53
Period size: 22 Copynumber: 4.6 Consensus size: 22
42323 TTCTTAGCAT
* *
42333 GATTA-CAACATTTCATAGGGA
1 GATTATCAAAATTTCACAGGGA
* * * ** *
42354 GCTTATCAAAATTCCATATTGT
1 GATTATCAAAATTTCACAGGGA
* * * *
42376 GCTTACCAACATTTTACAGGGA
1 GATTATCAAAATTTCACAGGGA
*
42398 GATTATCAAAATTTCACA-GTA
1 GATTATCAAAATTTCACAGGGA
*
42419 TAATTATCAAAATTT
1 -GATTATCAAAATTT
42434 GATTGAACGG
Statistics
Matches: 58, Mismatches: 20, Indels: 3
0.72 0.25 0.04
Matches are distributed among these distances:
21 6 0.10
22 52 0.90
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.35
Consensus pattern (22 bp):
GATTATCAAAATTTCACAGGGA
Found at i:42578 original size:22 final size:22
Alignment explanation
Indices: 42553--42608 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
42543 TTATAAAAAA
42553 GTTATCAAAATTTCA-AATGGAT-
1 GTTATCAAAATTTCAGAAT--ATG
*
42575 GTTATC-GAATTTCAGAATATG
1 GTTATCAAAATTTCAGAATATG
42596 GTTATCAAAATTT
1 GTTATCAAAATTT
42609 TAATAACCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 2 0.07
21 13 0.45
22 14 0.48
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (22 bp):
GTTATCAAAATTTCAGAATATG
Found at i:44871 original size:11 final size:11
Alignment explanation
Indices: 44828--44865 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
44818 CCTATATATA
*
44828 AAATAAATTAT
1 AAATTAATTAT
44839 CAAA-TAATTAT
1 -AAATTAATTAT
44850 AAATTAATTAT
1 AAATTAATTAT
44861 AAATT
1 AAATT
44866 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:45471 original size:166 final size:166
Alignment explanation
Indices: 45197--45529 Score: 666
Period size: 166 Copynumber: 2.0 Consensus size: 166
45187 ACTGAATTTT
45197 CTTAAAAAGAATTTATAAAATAAAACAGCCGCACGCGAAGCGCGGCCGGGAAATTCTAGTTAATT
1 CTTAAAAAGAATTTATAAAATAAAACAGCCGCACGCGAAGCGCGGCCGGGAAATTCTAGTTAATT
45262 TTAATTAGATAAATATATGGAGTATTTATATTTAAACGTGTTGAGCCACGTAAAGCGATGGGGAG
66 TTAATTAGATAAATATATGGAGTATTTATATTTAAACGTGTTGAGCCACGTAAAGCGATGGGGAG
45327 AATGCGAACAAGATTAGATACTAAAAATAAAAATCA
131 AATGCGAACAAGATTAGATACTAAAAATAAAAATCA
45363 CTTAAAAAGAATTTATAAAATAAAACAGCCGCACGCGAAGCGCGGCCGGGAAATTCTAGTTAATT
1 CTTAAAAAGAATTTATAAAATAAAACAGCCGCACGCGAAGCGCGGCCGGGAAATTCTAGTTAATT
45428 TTAATTAGATAAATATATGGAGTATTTATATTTAAACGTGTTGAGCCACGTAAAGCGATGGGGAG
66 TTAATTAGATAAATATATGGAGTATTTATATTTAAACGTGTTGAGCCACGTAAAGCGATGGGGAG
45493 AATGCGAACAAGATTAGATACTAAAAATAAAAATCA
131 AATGCGAACAAGATTAGATACTAAAAATAAAAATCA
45529 C
1 C
45530 GTTGCTAGTA
Statistics
Matches: 167, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
166 167 1.00
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.25
Consensus pattern (166 bp):
CTTAAAAAGAATTTATAAAATAAAACAGCCGCACGCGAAGCGCGGCCGGGAAATTCTAGTTAATT
TTAATTAGATAAATATATGGAGTATTTATATTTAAACGTGTTGAGCCACGTAAAGCGATGGGGAG
AATGCGAACAAGATTAGATACTAAAAATAAAAATCA
Found at i:48738 original size:33 final size:34
Alignment explanation
Indices: 48692--48761 Score: 108
Period size: 33 Copynumber: 2.1 Consensus size: 34
48682 TTCTTTTTCT
48692 TTTTTTTTCTTTTGGCCA-TCAAGGAACACCTCTC
1 TTTTTTTTCTTTTGG-CATTCAAGGAACACCTCTC
*
48726 TTTTTTTT-TTTTGGCATTTAAGGAACACCTCTC
1 TTTTTTTTCTTTTGGCATTCAAGGAACACCTCTC
48759 TTT
1 TTT
48762 AACAATGACT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 2 0.06
33 24 0.71
34 8 0.24
ACGTcount: A:0.17, C:0.21, G:0.11, T:0.50
Consensus pattern (34 bp):
TTTTTTTTCTTTTGGCATTCAAGGAACACCTCTC
Found at i:49440 original size:20 final size:20
Alignment explanation
Indices: 49385--49440 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 20
49375 TTGCCTTATC
**
49385 CAATTTTTGTTTATTTGTTT
1 CAATTTTTGTTTATTTGCAT
*** *
49405 TTCTTTTT-TTTTTTTGCAT
1 CAATTTTTGTTTATTTGCAT
49424 CAATTTTTGTTTATTTG
1 CAATTTTTGTTTATTTG
49441 TTTAGTTTTC
Statistics
Matches: 25, Mismatches: 10, Indels: 2
0.68 0.27 0.05
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.12, C:0.07, G:0.09, T:0.71
Consensus pattern (20 bp):
CAATTTTTGTTTATTTGCAT
Done.