Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015765.1 Corchorus olitorius cultivar O-4 contig15798, 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: 69256
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:1859 original size:33 final size:31
Alignment explanation
Indices: 1786--1890 Score: 120
Period size: 33 Copynumber: 3.2 Consensus size: 31
1776 GCTATGATCA
** *
1786 ACCAAAACAGATTTGTTTTCATCACAATTAGC
1 ACCAAAACAGATTTG-TTTCATCACAAACAAC
1818 ATCCAAAACAGAATTTGTTTCATCACAAACAAC
1 A-CCAAAACAG-ATTTGTTTCATCACAAACAAC
*
1851 ACCTAAAACAGATTTAGTGTCATCACAAACAAC
1 ACC-AAAACAGATTT-GTTTCATCACAAACAAC
1884 ACTCAAA
1 AC-CAAA
1891 TTAGGTTTAA
Statistics
Matches: 64, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
32 7 0.11
33 51 0.80
34 6 0.09
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.25
Consensus pattern (31 bp):
ACCAAAACAGATTTGTTTCATCACAAACAAC
Found at i:4415 original size:21 final size:21
Alignment explanation
Indices: 4389--4430 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
4379 GCATCTTAGG
4389 CAACTCCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
4410 CAACTCCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
4431 TTCTTCCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.29, G:0.19, T:0.19
Consensus pattern (21 bp):
CAACTCCGATGAGCTTGAAAC
Found at i:8089 original size:2 final size:2
Alignment explanation
Indices: 8082--8108 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8072 ATTAAAATTA
8082 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
8109 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:11380 original size:17 final size:17
Alignment explanation
Indices: 11358--11399 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
11348 ATCAACACCC
*
11358 AGATCACTAGTGAT-CTA
1 AGATCACCAGTGATGC-A
11375 AGATCACCAGTGATGCA
1 AGATCACCAGTGATGCA
11392 AGATCACC
1 AGATCACC
11400 GGTAATCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 22 0.96
18 1 0.04
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (17 bp):
AGATCACCAGTGATGCA
Found at i:30465 original size:24 final size:24
Alignment explanation
Indices: 30438--30511 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 24
30428 AAAAGTCATA
30438 CTGGTCATGGCAAAATGCCACAAG
1 CTGGTCATGGCAAAATGCCACAAG
* * *
30462 CTGGTCGTTAGG--AATTGCCATAAG
1 CTGGTC-AT-GGCAAAATGCCACAAG
* *
30486 CTGGTCGTGGCAAAAAGCCACAAG
1 CTGGTCATGGCAAAATGCCACAAG
30510 CT
1 CT
30512 AGTCGTTAGA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
22 2 0.05
23 1 0.03
24 33 0.85
25 1 0.03
26 2 0.05
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.20
Consensus pattern (24 bp):
CTGGTCATGGCAAAATGCCACAAG
Found at i:30524 original size:24 final size:24
Alignment explanation
Indices: 30449--30525 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
30439 TGGTCATGGC
*
30449 AAAATGCCACAAGCTGGTCGTTAG
1 AAAAAGCCACAAGCTGGTCGTTAG
* ** * *
30473 GAATTGCCATAAGCTGGTCG-TGG
1 AAAAAGCCACAAGCTGGTCGTTAG
*
30496 CAAAAAGCCACAAGCTAGTCGTTAG
1 -AAAAAGCCACAAGCTGGTCGTTAG
30521 AAAAA
1 AAAAA
30526 CCATGTTGAC
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
23 2 0.05
24 37 0.90
25 2 0.05
ACGTcount: A:0.36, C:0.19, G:0.25, T:0.19
Consensus pattern (24 bp):
AAAAAGCCACAAGCTGGTCGTTAG
Found at i:33966 original size:12 final size:12
Alignment explanation
Indices: 33949--33973 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33939 CTTTTGATTC
33949 ACTTTGATTTGA
1 ACTTTGATTTGA
33961 ACTTTGATTTGA
1 ACTTTGATTTGA
33973 A
1 A
33974 TTACTTAACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.08, G:0.16, T:0.48
Consensus pattern (12 bp):
ACTTTGATTTGA
Found at i:34297 original size:13 final size:14
Alignment explanation
Indices: 34268--34306 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
34258 ACCCAAAAAC
34268 TTTTGAAAACCTAT
1 TTTTGAAAACCTAT
* *
34282 TTTTGAAAGCCTTT
1 TTTTGAAAACCTAT
34296 TTCTTGAAAAC
1 TT-TTGAAAAC
34307 AATTTTCTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (14 bp):
TTTTGAAAACCTAT
Found at i:34304 original size:15 final size:15
Alignment explanation
Indices: 34270--34320 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
34260 CCAAAAACTT
*
34270 TTGAAAACCTATTT-
1 TTGAAAACCTTTTTC
*
34284 TTGAAAGCCTTTTTC
1 TTGAAAACCTTTTTC
**
34299 TTGAAAACAATTTTC
1 TTGAAAACCTTTTTC
34314 TTGAAAA
1 TTGAAAA
34321 ACGTCCCTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
14 12 0.39
15 19 0.61
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (15 bp):
TTGAAAACCTTTTTC
Found at i:35441 original size:42 final size:43
Alignment explanation
Indices: 35394--35475 Score: 112
Period size: 42 Copynumber: 1.9 Consensus size: 43
35384 AGTAATGAAC
*
35394 GGATAATGCATGACCTATGCATGAACATA-TATACAAAGGGAT
1 GGATAATGCATGACCAATGCATGAACATAGTATACAAAGGGAT
** *
35436 GGATAATGCATGATGAATGTATGAACATATGTATACAAAG
1 GGATAATGCATGACCAATGCATGAACATA-GTATACAAAG
35476 ACATGGACCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 25 0.74
44 9 0.26
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.26
Consensus pattern (43 bp):
GGATAATGCATGACCAATGCATGAACATAGTATACAAAGGGAT
Found at i:35489 original size:44 final size:42
Alignment explanation
Indices: 35414--35503 Score: 117
Period size: 44 Copynumber: 2.1 Consensus size: 42
35404 TGACCTATGC
** * *
35414 ATGAACATATATACAAAGGGATGGATAATGCATGATGAATGT
1 ATGAACATATATACAAAGACATGGACAATGCATGAAGAATGT
*
35456 ATGAACATATGTATACAAAGACATGGACCATGCATGAAGAATGT
1 ATGAACATA--TATACAAAGACATGGACAATGCATGAAGAATGT
35500 ATGA
1 ATGA
35504 CAAATATCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
42 9 0.22
44 32 0.78
ACGTcount: A:0.43, C:0.10, G:0.22, T:0.24
Consensus pattern (42 bp):
ATGAACATATATACAAAGACATGGACAATGCATGAAGAATGT
Found at i:37084 original size:32 final size:35
Alignment explanation
Indices: 37048--37136 Score: 105
Period size: 37 Copynumber: 2.6 Consensus size: 35
37038 ATTTTATTAA
37048 TTTCCAAAATCTTCTTTTGGGAACTA-T-C-TTAT
1 TTTCCAAAATCTTCTTTTGGGAACTATTACTTTAT
* *
37080 TTTCCAAAACCTTCTTTT-GGAATTATTAAACTTTTAT
1 TTTCCAAAATCTTCTTTTGGGAACTATT--AC-TTTAT
37117 TTTCCAAAATCTTCTTTTGG
1 TTTCCAAAATCTTCTTTTGG
37137 AGTTTACTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
31 6 0.13
32 18 0.38
35 1 0.02
37 21 0.45
38 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.48
Consensus pattern (35 bp):
TTTCCAAAATCTTCTTTTGGGAACTATTACTTTAT
Found at i:37292 original size:21 final size:20
Alignment explanation
Indices: 37267--37317 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
37257 CTTTTATTGC
37267 ATCTTTTTTACTTCTTGATTTT
1 ATCTTTTTT--TTCTTGATTTT
*
37289 -TCTTTTTTTTTTTGATTTT
1 ATCTTTTTTTTCTTGATTTT
37308 GATCTTTTTT
1 -ATCTTTTTT
37318 CTATCTCTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 10 0.38
21 16 0.62
ACGTcount: A:0.10, C:0.10, G:0.06, T:0.75
Consensus pattern (20 bp):
ATCTTTTTTTTCTTGATTTT
Found at i:44863 original size:2 final size:2
Alignment explanation
Indices: 44858--44910 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
44848 TATATATATC
44858 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
44900 TG TG TG TG TG T
1 TG TG TG TG TG T
44911 TAAATAAAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:52053 original size:49 final size:49
Alignment explanation
Indices: 51981--52091 Score: 222
Period size: 49 Copynumber: 2.3 Consensus size: 49
51971 AGAATCAGAT
51981 TACTAAAGATTCATCCTATCTCAATCTATATCAAAGATAATTAAATTGC
1 TACTAAAGATTCATCCTATCTCAATCTATATCAAAGATAATTAAATTGC
52030 TACTAAAGATTCATCCTATCTCAATCTATATCAAAGATAATTAAATTGC
1 TACTAAAGATTCATCCTATCTCAATCTATATCAAAGATAATTAAATTGC
52079 TACTAAAGATTCA
1 TACTAAAGATTCA
52092 CAACTTAACC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 62 1.00
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.34
Consensus pattern (49 bp):
TACTAAAGATTCATCCTATCTCAATCTATATCAAAGATAATTAAATTGC
Found at i:60734 original size:351 final size:349
Alignment explanation
Indices: 60023--60722 Score: 1185
Period size: 351 Copynumber: 2.0 Consensus size: 349
60013 ACCGACGGTT
60023 TGGACTTTTTTAATTTAAACCATTATTTAATTTTATTCAAATTGAAAAAGTTTGTCCTTTTAAAG
1 TGGA-TTTTTTAATTTAAACCATTATTTAATTTTATTCAAATTGAAAAAGTTTGTCCTTTTAAAG
*
60088 AGAAAACCGAATAACTACCGGTTCTGGGTTTATCGGTCAAACCGATTCTCAAGTGGTTCATAGGA
65 AGAAAACCGAATAACTACCGGTTCTGGGTTTACCGGTCAAACCGATTCTCAAGTGGTTCATAGGA
* * *
60153 ACCGCGATTAATGTCTTTGATAGAACAGTATTGACTGCTGAATCCTGGTCGAACCGTTCAATTCA
130 ACCGCGATTAATGTCTTTGATAGAACAGTATTAACTGCTGAATCCTGATCGAACCGTTCAATCCA
60218 GTCCGGTTTTCAAAAACTATGATTATGAATGCCATATCTTGCTGATAAAAAAATAAACAAACAGT
195 GTCCGGTTTTCAAAAACTATGATTATGAATGCCATATCTTGCTGATAAAAAAATAAACAAACAGT
*
60283 TAGTTTTTTTTTTGAGATAATAAACAGTTACTTATTGAACATTGATTTTTATGAGTAATGGATTG
260 TAG-ATTTTTTTTGAGATAATAAACAGTTACTTATTGAACATTGATTTTTATGAGTAATGGATTG
* * *
60348 TCCAAGAACATTTTTTTTGTCCTTAA
324 TCCAAGAACATTTTTTTAGTACTAAA
60374 TGGATTTTTTTAATTTAAACCATTATTTAATTTTATTCAAATTGAAAAAGTTTGTCCTTTTAAAG
1 TGGA-TTTTTTAATTTAAACCATTATTTAATTTTATTCAAATTGAAAAAGTTTGTCCTTTTAAAG
*
60439 AGAAAACCGGATAACTACCGGTT-TCGGGTTTACCGGTCAAACC-AGTTCTCAAGTGGTTCATAG
65 AGAAAACCGAATAACTACCGGTTCT-GGGTTTACCGGTCAAACCGA-TTCTCAAGTGGTTCATAG
* *
60502 GAACCGCGATTAATGTCTTTGATAGGACAGTATTAACTGCTGAATCCTGATCGAACTGTTCAATC
128 GAACCGCGATTAATGTCTTTGATAGAACAGTATTAACTGCTGAATCCTGATCGAACCGTTCAATC
* *
60567 CAGTCCGGTTTTCGAAAACTATGGTTATGAATGCCATATCTTGCTGATAAAAAAATAAACAAACA
193 CAGTCCGGTTTTCAAAAACTATGATTATGAATGCCATATCTTGCTGATAAAAAAATAAACAAACA
*
60632 GTTA-ATTTTTTTT-AGATAATAAACAGTTACTTGTTGAACATTGATTTTTATGAGTAATGGATT
258 GTTAGATTTTTTTTGAGATAATAAACAGTTACTTATTGAACATTGATTTTTATGAGTAATGGATT
60695 GTCCAAGAACATTTTTTTAAGTAC-AAA
323 GTCCAAGAACATTTTTTT-AGTACTAAA
60722 T
1 T
60723 TGTTTATTTT
Statistics
Matches: 331, Mismatches: 15, Indels: 9
0.93 0.04 0.03
Matches are distributed among these distances:
348 70 0.21
349 11 0.03
350 2 0.01
351 248 0.75
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (349 bp):
TGGATTTTTTAATTTAAACCATTATTTAATTTTATTCAAATTGAAAAAGTTTGTCCTTTTAAAGA
GAAAACCGAATAACTACCGGTTCTGGGTTTACCGGTCAAACCGATTCTCAAGTGGTTCATAGGAA
CCGCGATTAATGTCTTTGATAGAACAGTATTAACTGCTGAATCCTGATCGAACCGTTCAATCCAG
TCCGGTTTTCAAAAACTATGATTATGAATGCCATATCTTGCTGATAAAAAAATAAACAAACAGTT
AGATTTTTTTTGAGATAATAAACAGTTACTTATTGAACATTGATTTTTATGAGTAATGGATTGTC
CAAGAACATTTTTTTAGTACTAAA
Found at i:65940 original size:23 final size:22
Alignment explanation
Indices: 65906--65948 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
65896 AAGAACATTT
65906 TTATAAATTTTTTATTAACCTTC
1 TTATAAA-TTTTTATTAACCTTC
*
65929 TTATGAAA-TTTTGTTAACCT
1 TTAT-AAATTTTTATTAACCT
65949 CCCTAAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 11 0.61
23 4 0.22
24 3 0.17
ACGTcount: A:0.30, C:0.12, G:0.05, T:0.53
Consensus pattern (22 bp):
TTATAAATTTTTATTAACCTTC
Found at i:66058 original size:22 final size:21
Alignment explanation
Indices: 66024--66096 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 21
66014 AACACTATAC
*
66024 TATGAGATGTTGATAACCTCCA
1 TATGA-ATATTGATAACCTCCA
* **
66046 TATGATATATTGATAACCACGT
1 TATGA-ATATTGATAACCTCCA
* *
66068 TATGAAAATTTATAAACCTCCA
1 TATGAATATTGAT-AACCTCCA
66090 TATGAAT
1 TATGAAT
66097 TGTTAGTAAT
Statistics
Matches: 39, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
21 6 0.15
22 33 0.85
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.34
Consensus pattern (21 bp):
TATGAATATTGATAACCTCCA
Found at i:66296 original size:22 final size:21
Alignment explanation
Indices: 66227--66307 Score: 72
Period size: 22 Copynumber: 3.7 Consensus size: 21
66217 ATCTGCATAC
* *
66227 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGAT-ACCTTCA
* * **
66249 TATGAAATTTTGAAAACTAAA
1 TATGAAATTTTGATACCTTCA
66270 CTATGAAATTTTGATACCATTCA
1 -TATGAAATTTTGATACC-TTCA
*
66293 TATGAAAGTTTGATA
1 TATGAAATTTTGATA
66308 TCCTCCCTGA
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
21 2 0.04
22 42 0.91
23 2 0.04
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (21 bp):
TATGAAATTTTGATACCTTCA
Found at i:66991 original size:17 final size:17
Alignment explanation
Indices: 66969--67004 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
66959 TTATTGATTC
*
66969 TTTTCCGTTTTTTCATT
1 TTTTCCATTTTTTCATT
66986 TTTTCCATTTTTTCATT
1 TTTTCCATTTTTTCATT
67003 TT
1 TT
67005 CATTTATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.08, C:0.17, G:0.03, T:0.72
Consensus pattern (17 bp):
TTTTCCATTTTTTCATT
Done.