Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014567.1 Corchorus olitorius cultivar O-4 contig14600, 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: 62030
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:16117 original size:1 final size:1
Alignment explanation
Indices: 16111--16145 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
16101 TTAATCTGGG
16111 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
16146 CAACAACAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:16150 original size:3 final size:3
Alignment explanation
Indices: 16144--16169 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
16134 AAAAAAAAAA
16144 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
16170 TATGCTGCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:19006 original size:19 final size:18
Alignment explanation
Indices: 18973--19031 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 18
18963 TTTAAATTAT
18973 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
18991 TCTTCAAATTGTCTTCAATAA
1 TCTTC-AATGGTCTTC-A-AA
*
19012 GTCTTCAATAAGTCTTCAAA
1 -TCTTCAAT-GGTCTTCAAA
19032 CACGAACTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
18 5 0.15
19 9 0.26
20 3 0.09
21 6 0.18
22 11 0.32
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.39
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:19015 original size:11 final size:11
Alignment explanation
Indices: 19001--19030 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
18991 TCTTCAAATT
19001 GTCTTCAATAA
1 GTCTTCAATAA
19012 GTCTTCAATAA
1 GTCTTCAATAA
19023 GTCTTCAA
1 GTCTTCAA
19031 ACACGAACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (11 bp):
GTCTTCAATAA
Found at i:21559 original size:17 final size:17
Alignment explanation
Indices: 21537--21572 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
21527 CCACATGTAC
* *
21537 CAAAAAATGACACGTGG
1 CAAAAAAGGACACATGG
21554 CAAAAAAGGACACATGG
1 CAAAAAAGGACACATGG
21571 CA
1 CA
21573 CGTCATGTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.50, C:0.19, G:0.22, T:0.08
Consensus pattern (17 bp):
CAAAAAAGGACACATGG
Found at i:22794 original size:18 final size:17
Alignment explanation
Indices: 22771--22808 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
22761 GGGACATTGA
22771 TTCTTTCTTCTTCTTCTT
1 TTCTTTCTTCTTCTT-TT
*
22789 TTCTTTCTTTTTCTTTT
1 TTCTTTCTTCTTCTTTT
22806 TTC
1 TTC
22809 ATTTTTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (17 bp):
TTCTTTCTTCTTCTTTT
Found at i:26389 original size:94 final size:94
Alignment explanation
Indices: 26228--26420 Score: 377
Period size: 94 Copynumber: 2.1 Consensus size: 94
26218 AAAACGTATC
*
26228 CTTTGTAACGAGTATAAAAAGAGTTAGTCTACGACCATTAAGGCCGGGAATAATACCCTTAATTA
1 CTTTGTAACGAGTATAAAAAGAATTAGTCTACGACCATTAAGGCCGGGAATAATACCCTTAATTA
26293 CACTATGTCCAACCTCAACTAGAGAAAGA
66 CACTATGTCCAACCTCAACTAGAGAAAGA
26322 CTTTGTAACGAGTATAAAAAGAATTAGTCTACGACCATTAAGGCCGGGAATAATACCCTTAATTA
1 CTTTGTAACGAGTATAAAAAGAATTAGTCTACGACCATTAAGGCCGGGAATAATACCCTTAATTA
26387 CACTATGTCCAACCTCAACTAGAGAAAGA
66 CACTATGTCCAACCTCAACTAGAGAAAGA
26416 CTTTG
1 CTTTG
26421 GTAGTGTCAA
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 98 1.00
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (94 bp):
CTTTGTAACGAGTATAAAAAGAATTAGTCTACGACCATTAAGGCCGGGAATAATACCCTTAATTA
CACTATGTCCAACCTCAACTAGAGAAAGA
Found at i:28395 original size:32 final size:32
Alignment explanation
Indices: 28359--28437 Score: 77
Period size: 32 Copynumber: 2.5 Consensus size: 32
28349 CAAAAAACCC
* *
28359 AAACCCGAACCCGAAGAAGCTCAAACTCGAAA
1 AAACCCGAACCCGAAAAAGCTCAAACCCGAAA
* * * * * *
28391 AAACCAGAATCTGAAAAATCTTAAACCCGATA
1 AAACCCGAACCCGAAAAAGCTCAAACCCGAAA
*
28423 AAACTCGAACCCGAA
1 AAACCCGAACCCGAA
28438 CCTGAAAAAC
Statistics
Matches: 35, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.48, C:0.28, G:0.13, T:0.11
Consensus pattern (32 bp):
AAACCCGAACCCGAAAAAGCTCAAACCCGAAA
Found at i:34588 original size:141 final size:141
Alignment explanation
Indices: 34334--34615 Score: 492
Period size: 141 Copynumber: 2.0 Consensus size: 141
34324 TAGTTTCAAT
* *
34334 TGGTGAAGCAGTTTCATCTAAGCTGCATTGCAGCATTGCCCATTTGGCTTAAATGAATAATGTAA
1 TGGTGAAGCAGTTTCATCTAAGCTGCATTGCAGCATTGCCCATTTGGCATAAATGAATAACGTAA
** *
34399 TGATTTCATTTTGAGCATCCTTGCTGTGGAGAAAGGCAGGTAAGATCCCCTTCATAACTCCTATG
66 TGATTTCATTTTGAGCATCCTTGCTGCAGAGAAAGGCAGGTAAGATCCCCTTCACAACTCCTATG
34464 TATGACAACAA
131 TATGACAACAA
*
34475 TGGTGAGGCAGTTTCATCTAAGCTGCATTGCAGCATTGCCCATTTGGCATAAATGAATAACGTAA
1 TGGTGAAGCAGTTTCATCTAAGCTGCATTGCAGCATTGCCCATTTGGCATAAATGAATAACGTAA
* *
34540 TGATTTCATTTTGAGCATCCTTGCTGCAGAGATAGGCAGGTAAGATCCCCTTCACAATTCCTATG
66 TGATTTCATTTTGAGCATCCTTGCTGCAGAGAAAGGCAGGTAAGATCCCCTTCACAACTCCTATG
34605 TATGACAACAA
131 TATGACAACAA
34616 ACTTTGGATT
Statistics
Matches: 133, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
141 133 1.00
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (141 bp):
TGGTGAAGCAGTTTCATCTAAGCTGCATTGCAGCATTGCCCATTTGGCATAAATGAATAACGTAA
TGATTTCATTTTGAGCATCCTTGCTGCAGAGAAAGGCAGGTAAGATCCCCTTCACAACTCCTATG
TATGACAACAA
Found at i:36431 original size:3 final size:3
Alignment explanation
Indices: 36423--36455 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
36413 AAATGTTTTG
*
36423 TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
36456 CATCATCATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:36456 original size:12 final size:12
Alignment explanation
Indices: 36423--36458 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
36413 AAATGTTTTG
*
36423 TATTATTATTAT
1 TATTATTATCAT
36435 TATTATTATCAT
1 TATTATTATCAT
36447 TATTATTATCAT
1 TATTATTATCAT
36459 CATCATCATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (12 bp):
TATTATTATCAT
Found at i:46414 original size:31 final size:29
Alignment explanation
Indices: 46376--46451 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
46366 TACCGTACAG
46376 GTCCCTCTACTTACAGAAAAGGATCAATTTA
1 GTCCCTCTACTTACA-AAAAGG-TCAATTTA
** *
46407 GTCCCTCTACTATA-AAAATTGTCAATTTG
1 GTCCCTCTACT-TACAAAAAGGTCAATTTA
*
46436 GTCTCTCTACTTACAA
1 GTCCCTCTACTTACAA
46452 TTTGGTGTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 2 0.05
29 19 0.49
30 4 0.10
31 12 0.31
32 2 0.05
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.34
Consensus pattern (29 bp):
GTCCCTCTACTTACAAAAAGGTCAATTTA
Found at i:46775 original size:31 final size:31
Alignment explanation
Indices: 46740--46829 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 31
46730 AGAGAGATTC
**
46740 AATTGACACCAAATTGTAAGTAGAGGGACCA
1 AATTGACACCATTTTGTAAGTAGAGGGACCA
46771 AATTGACA--ATTTTTGT-AGTAGAGGGACCA
1 AATTGACACCA-TTTTGTAAGTAGAGGGACCA
* *
46800 AATGGATC-CCTTTTTGTAAGTAGAGGGACC
1 AATTGA-CACCATTTTGTAAGTAGAGGGACC
46830 TGTACGGTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
29 19 0.38
30 11 0.22
31 20 0.40
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.27
Consensus pattern (31 bp):
AATTGACACCATTTTGTAAGTAGAGGGACCA
Found at i:46791 original size:29 final size:31
Alignment explanation
Indices: 46753--46829 Score: 113
Period size: 29 Copynumber: 2.5 Consensus size: 31
46743 TGACACCAAA
*
46753 TTGTAAGTAGAGGGACCAAATTGA-CAATTT
1 TTGTAAGTAGAGGGACCAAATGGATCAATTT
**
46783 TTGT-AGTAGAGGGACCAAATGGATCCCTTT
1 TTGTAAGTAGAGGGACCAAATGGATCAATTT
46813 TTGTAAGTAGAGGGACC
1 TTGTAAGTAGAGGGACC
46830 TGTACGGTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
29 18 0.43
30 12 0.29
31 12 0.29
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (31 bp):
TTGTAAGTAGAGGGACCAAATGGATCAATTT
Found at i:47306 original size:21 final size:21
Alignment explanation
Indices: 47281--47331 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
47271 TATCTTAGAT
47281 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
47302 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
47323 ATAAATAAT
1 AT-AATAAT
47332 GAGTTCAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 11 0.41
22 9 0.33
23 7 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:47314 original size:25 final size:25
Alignment explanation
Indices: 47283--47331 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
47273 TCTTAGATAT
*
47283 AATATATATT-ATTAAATAAATAATA
1 AATATATATTAAAT-AATAAATAATA
*
47308 AATATATTTTAAATAATAAATAAT
1 AATATATATTAAATAATAAATAAT
47332 GAGTTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATATATATTAAATAATAAATAATA
Found at i:50356 original size:51 final size:51
Alignment explanation
Indices: 50241--50387 Score: 240
Period size: 51 Copynumber: 2.8 Consensus size: 51
50231 TTGATAATTT
* **
50241 CCATAATTATCTCTAATAATATAAAAAGATAATATGGTTAATAAATATAATCA
1 CCATAATTATCTCTAAT-ATATATATGGATAATATGGTTAAT-AATATAATCA
50294 CCATAATTATCTCTAATATATATATGGATAATATGGTTAATAATATAATCA
1 CCATAATTATCTCTAATATATATATGGATAATATGGTTAATAATATAATCA
*
50345 CCATAATTATCTCTAATATATTTATGGATAATATGGTTAATAA
1 CCATAATTATCTCTAATATATATATGGATAATATGGTTAATAA
50388 AGGTAATGGG
Statistics
Matches: 90, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
51 52 0.58
52 21 0.23
53 17 0.19
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (51 bp):
CCATAATTATCTCTAATATATATATGGATAATATGGTTAATAATATAATCA
Found at i:53291 original size:3 final size:3
Alignment explanation
Indices: 53283--53336 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
53273 TAGTATATAT
53283 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
53331 ATA ATA
1 ATA ATA
53337 TATTATTATT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:53343 original size:3 final size:3
Alignment explanation
Indices: 53337--53368 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
53327 AATAATAATA
53337 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
53369 AGGCTATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:57939 original size:63 final size:61
Alignment explanation
Indices: 57838--57954 Score: 198
Period size: 63 Copynumber: 1.9 Consensus size: 61
57828 GCTATAGCTA
*
57838 ATTAATCAAATGGTTTTGTGTAATTGAATATGTCATTATATACATATATATATATATATATAT
1 ATTAATCAAATGGTTTTGTGTAATTGAATATGTAATTATAT-C-TATATATATATATATATAT
*
57901 ATTAATCAAATGGTTTTGTGTAATTGAATATGTAATTATATCTATATCTATATA
1 ATTAATCAAATGGTTTTGTGTAATTGAATATGTAATTATATCTATATATATATA
57955 CAATATAAGT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
61 11 0.21
62 1 0.02
63 40 0.77
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.46
Consensus pattern (61 bp):
ATTAATCAAATGGTTTTGTGTAATTGAATATGTAATTATATCTATATATATATATATATAT
Found at i:58278 original size:18 final size:20
Alignment explanation
Indices: 58235--58283 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
58225 CGTTAAACCT
58235 CTTATTATTATAATTATTAA
1 CTTATTATTATAATTATTAA
*
58255 GCTTATTATTATTA-TATTAA
1 -CTTATTATTATAATTATTAA
58275 -TTATTATTA
1 CTTATTATTA
58284 GTGGTAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 9 0.33
20 6 0.22
21 12 0.44
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (20 bp):
CTTATTATTATAATTATTAA
Done.