Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024432.1 Corchorus olitorius cultivar O-4 contig24465, 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: 79162
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2427 original size:41 final size:41
Alignment explanation
Indices: 2368--2664 Score: 405
Period size: 41 Copynumber: 7.2 Consensus size: 41
2358 TTTTCGTTTG
* *
2368 TTCAAGATCAAGTCATCGAGACCCTTGAACTAAATTATCAA
1 TTCAAGATTAAGTCATCGAGACCCTTGAATTAAATTATCAA
* *
2409 TACAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATTAAGTCATCGAGACCCTTGAATTAAATTATCAA
* * *
2450 TTCAAGATTGAGTCATCGGGAGCCTTGAATTAAATTATCAA
1 TTCAAGATTAAGTCATCGAGACCCTTGAATTAAATTATCAA
*
2491 TTCAAGATTTAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATTAAGTCATCGAGACCCTTGAATTAAATTATCAA
2532 TTCAAGATTAAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATTAAGTCATCGAGACCCTTGAATTAAATTATCAA
** *
2573 TTCAAGAGCAAGTCATCGAGACCCTTGAATCGAATTATTATCAA
1 TTCAAGATTAAGTCATCGAGACCCTTGAAT-TAA--ATTATCAA
** * * * **
2617 TTCAAGACCAAGTCGTCAAGACCCTTGAATTAGATCGTCAA
1 TTCAAGATTAAGTCATCGAGACCCTTGAATTAAATTATCAA
2658 TTCAAGA
1 TTCAAGA
2665 CCAAGTAATC
Statistics
Matches: 232, Mismatches: 21, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
41 194 0.84
42 2 0.01
43 1 0.00
44 35 0.15
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (41 bp):
TTCAAGATTAAGTCATCGAGACCCTTGAATTAAATTATCAA
Found at i:11300 original size:29 final size:30
Alignment explanation
Indices: 11261--11326 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
11251 TAAAATTGAT
*
11261 TTTTTACTCCCTAAACTT-TAATATGAGAC
1 TTTTTACTCCCTAAACTTACAATATGAGAC
*
11290 TTTTTGCTCCCTAAACTTACAATATGAGGAC
1 TTTTTACTCCCTAAACTTACAATATGA-GAC
*
11321 ATTTTA
1 TTTTTA
11327 GTCCATCTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 17 0.55
30 7 0.23
31 7 0.23
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (30 bp):
TTTTTACTCCCTAAACTTACAATATGAGAC
Found at i:16426 original size:2 final size:2
Alignment explanation
Indices: 16370--16409 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
16360 ACATTTCATA
*
16370 AT AT AT AT AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16410 GCAAAATGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:21142 original size:16 final size:16
Alignment explanation
Indices: 21107--21148 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
21097 CCTGAGGCCA
21107 AAACCCGA-ACATGCC
1 AAACCCGAGACATGCC
* *
21122 TAACCCGAGACATGGC
1 AAACCCGAGACATGCC
21138 AAACCCGAGAC
1 AAACCCGAGAC
21149 CCGAATAACC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.38, C:0.36, G:0.19, T:0.07
Consensus pattern (16 bp):
AAACCCGAGACATGCC
Found at i:21158 original size:16 final size:16
Alignment explanation
Indices: 21139--21190 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
21129 AGACATGGCA
21139 AACCCGAGACCCGAAT
1 AACCCGAGACCCGAAT
*
21155 AACCTG-GAACCCGCAAT
1 AACCCGAG-ACCCG-AAT
21172 -ACCCGAGACCCGAAT
1 AACCCGAGACCCGAAT
21187 AACC
1 AACC
21191 TGGAACCCGC
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
15 4 0.13
16 22 0.73
17 4 0.13
ACGTcount: A:0.37, C:0.38, G:0.17, T:0.08
Consensus pattern (16 bp):
AACCCGAGACCCGAAT
Found at i:21176 original size:32 final size:32
Alignment explanation
Indices: 21136--21219 Score: 143
Period size: 32 Copynumber: 2.6 Consensus size: 32
21126 CCGAGACATG
21136 GCAA-ACCCGAGACCCGAATAACCTGGAACCC
1 GCAATACCCGAGACCCGAATAACCTGGAACCC
21167 GCAATACCCGAGACCCGAATAACCTGGAACCC
1 GCAATACCCGAGACCCGAATAACCTGGAACCC
21199 GCAATACCCGAATGACCCGAA
1 GCAATACCCG-A-GACCCGAA
21220 ACCCGAATGG
Statistics
Matches: 50, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
31 4 0.08
32 37 0.74
33 1 0.02
34 8 0.16
ACGTcount: A:0.36, C:0.37, G:0.19, T:0.08
Consensus pattern (32 bp):
GCAATACCCGAGACCCGAATAACCTGGAACCC
Found at i:21198 original size:16 final size:17
Alignment explanation
Indices: 21147--21204 Score: 70
Period size: 16 Copynumber: 3.6 Consensus size: 17
21137 CAAACCCGAG
21147 ACCCG-AATAACCTGGA
1 ACCCGCAATAACCTGGA
*
21163 ACCCGCAAT-ACC-CGA
1 ACCCGCAATAACCTGGA
21178 GACCCG-AATAACCTGGA
1 -ACCCGCAATAACCTGGA
21195 ACCCGCAATA
1 ACCCGCAATA
21205 CCCGAATGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
15 5 0.14
16 21 0.60
17 9 0.26
ACGTcount: A:0.36, C:0.36, G:0.17, T:0.10
Consensus pattern (17 bp):
ACCCGCAATAACCTGGA
Found at i:21225 original size:16 final size:16
Alignment explanation
Indices: 21204--21281 Score: 61
Period size: 16 Copynumber: 4.9 Consensus size: 16
21194 AACCCGCAAT
21204 ACCCGAATGACCCGAA
1 ACCCGAATGACCCGAA
* *
21220 ACCCGAATGGCCCAAA
1 ACCCGAATGACCCGAA
* * *
21236 ACCCAAATAACCTG-A
1 ACCCGAATGACCCGAA
* * *
21251 A-CCTAGATCACCCAAA
1 ACCCGA-ATGACCCGAA
21267 ACCCGAATGACCCGA
1 ACCCGAATGACCCGA
21282 GAAACTTGCC
Statistics
Matches: 45, Mismatches: 14, Indels: 6
0.69 0.22 0.09
Matches are distributed among these distances:
14 3 0.07
15 7 0.16
16 32 0.71
17 3 0.07
ACGTcount: A:0.40, C:0.37, G:0.14, T:0.09
Consensus pattern (16 bp):
ACCCGAATGACCCGAA
Found at i:22549 original size:11 final size:11
Alignment explanation
Indices: 22533--22557 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
22523 CTCATTCCTC
22533 TTTCAATTTGA
1 TTTCAATTTGA
22544 TTTCAATTTGA
1 TTTCAATTTGA
22555 TTT
1 TTT
22558 TTCTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.60
Consensus pattern (11 bp):
TTTCAATTTGA
Found at i:22627 original size:45 final size:42
Alignment explanation
Indices: 22575--22672 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 42
22565 TTTACCAGTT
* *
22575 TTCAATTTGATATGACATTACGGTAACTTCTCACTTTTCTTTGAA
1 TTCAATTTGACAT-A-ATTAAGGTAA-TTCTCACTTTTCTTTGAA
* **
22620 TTCAATTTGACATATTTAATTTAATTCTCACTTTTCTTTGAA
1 TTCAATTTGACATAATTAAGGTAATTCTCACTTTTCTTTGAA
**
22662 TTTGATTTGAC
1 TTCAATTTGAC
22673 GTTTCTAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
42 27 0.59
43 6 0.13
44 1 0.02
45 12 0.26
ACGTcount: A:0.27, C:0.15, G:0.09, T:0.49
Consensus pattern (42 bp):
TTCAATTTGACATAATTAAGGTAATTCTCACTTTTCTTTGAA
Found at i:32956 original size:33 final size:33
Alignment explanation
Indices: 32912--32986 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 33
32902 ATAGTTTTTT
*
32912 TTCTTTCTTTTTAAG-GACTTTATTTTTTTGACG
1 TTCTTTCTTTTTAAGTGAC-TTATTTTTTTGAAG
* **
32945 TTCTTTTTTTTTGGGTGACTTATTTTTTTGAAG
1 TTCTTTCTTTTTAAGTGACTTATTTTTTTGAAG
32978 TTGCTTTCT
1 TT-CTTTCT
32987 CTACATTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
33 27 0.77
34 8 0.23
ACGTcount: A:0.12, C:0.11, G:0.15, T:0.63
Consensus pattern (33 bp):
TTCTTTCTTTTTAAGTGACTTATTTTTTTGAAG
Found at i:40488 original size:2 final size:2
Alignment explanation
Indices: 40481--40511 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
40471 CTCCTTTATG
40481 TA TA TA 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 TA TA TA T
40512 CAAGTTTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42871 original size:101 final size:102
Alignment explanation
Indices: 42696--42899 Score: 295
Period size: 101 Copynumber: 2.0 Consensus size: 102
42686 ATATCAAAGA
* * * * **
42696 CCTACACTTGAAGAAACTCATTTCGGAGTAACATAAACCCTGAATAGATCTAATTCAAAATGATT
1 CCTACACTTGAAGAAACTCATTTCCGAGTAACATAAACCATGAATAAATCTAACTCAAAACCATT
*
42761 CGAACCTAGGCCATG-TAAGAACTAATTAATAAATAC
66 CGAACCTAGGCCATGATAAGAACTAATCAATAAATAC
* *
42797 CCTACACTTGAAGAAACTCATTTCCGAGTAGCTTAAA-CATGGAATAAATCTAACTCAAAACCAT
1 CCTACACTTGAAGAAACTCATTTCCGAGTAACATAAACCAT-GAATAAATCTAACTCAAAACCAT
42861 TCGAACCTAGGCCATGTATAAGAACTAATCAATAAATAC
65 TCGAACCTAGGCCATG-ATAAGAACTAATCAATAAATAC
42900 TTGATCTTGA
Statistics
Matches: 91, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
100 2 0.02
101 69 0.76
103 20 0.22
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.25
Consensus pattern (102 bp):
CCTACACTTGAAGAAACTCATTTCCGAGTAACATAAACCATGAATAAATCTAACTCAAAACCATT
CGAACCTAGGCCATGATAAGAACTAATCAATAAATAC
Found at i:43621 original size:88 final size:90
Alignment explanation
Indices: 43466--43642 Score: 261
Period size: 89 Copynumber: 2.0 Consensus size: 90
43456 TTGTTTAAAG
* *
43466 TTTTATAGTTTTACTCAATTAAAAACTCTATTTTTTATTTAATTAAGTTTAATATCATTATAACT
1 TTTTATAGTTTTACTCAATTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCATTATAACT
*
43531 A-TTTTATTTTTAGCAGTTTACTAT
66 ATTTTTATTTTTACCAGTTTACTAT
** *
43555 TTTTATAGTTTTACTCAATTAAAAACTCTA-TTTTTATCTT-ATTAAATCTAATATTTTTATACC
1 TTTTATAGTTTTACTCAATTAAAAACTCTATTTTTTAT-TTAATTAAATCTAATATCATTATAAC
*
43618 TATTTTTATTTTTACCATTTTACTA
65 TATTTTTATTTTTACCAGTTTACTA
43643 ATTTAATTAA
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
88 27 0.34
89 52 0.66
ACGTcount: A:0.32, C:0.11, G:0.03, T:0.55
Consensus pattern (90 bp):
TTTTATAGTTTTACTCAATTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCATTATAACT
ATTTTTATTTTTACCAGTTTACTAT
Found at i:51313 original size:17 final size:17
Alignment explanation
Indices: 51291--51327 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
51281 CGTGTAGGAT
*
51291 GAGAGAAGAGAGGTAAG
1 GAGAGAAGAGACGTAAG
51308 GAGAGAAGAGACGTAAG
1 GAGAGAAGAGACGTAAG
51325 GAG
1 GAG
51328 TTTCCGGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.03, G:0.46, T:0.05
Consensus pattern (17 bp):
GAGAGAAGAGACGTAAG
Found at i:54087 original size:96 final size:95
Alignment explanation
Indices: 53919--54095 Score: 277
Period size: 96 Copynumber: 1.9 Consensus size: 95
53909 AAATAAGTCG
53919 GAAGAAAATTCAAAACCCAAAGCCCAGTTGATGCACAATGTCCAAAACCTGAGCCCAAAATGACT
1 GAAGAAAATTCAAAACCCAAAGCCCAGTTGATGCACAATGTCCAAAACCTGAGCCCAAAATGACT
53984 CCGATGTAAGTTGCCTTAAACCTCAAACCT
66 CCGATGTAAGTTGCCTTAAACCTCAAACCT
* * **
54014 GAAGAAAATTC-AAACCCAAAGCCCATTTGATGCACAAAATGTCTAAAACCTGAGCCTGAAATGA
1 GAAGAAAATTCAAAACCCAAAGCCCAGTTGATGCAC--AATGTCCAAAACCTGAGCCCAAAATGA
54078 CTTCC-ATGTAAGTTGCCT
64 C-TCCGATGTAAGTTGCCT
54096 AACCTAATTA
Statistics
Matches: 75, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
94 23 0.31
95 11 0.15
96 38 0.51
97 3 0.04
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.21
Consensus pattern (95 bp):
GAAGAAAATTCAAAACCCAAAGCCCAGTTGATGCACAATGTCCAAAACCTGAGCCCAAAATGACT
CCGATGTAAGTTGCCTTAAACCTCAAACCT
Found at i:60615 original size:10 final size:10
Alignment explanation
Indices: 60573--60617 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
60563 TAAGGTTAAG
60573 GTTAATTAGT
1 GTTAATTAGT
60583 GTTAATTAGT
1 GTTAATTAGT
*
60593 -TTATTTTAGT
1 GTTA-ATTAGT
*
60603 GTTAATTACT
1 GTTAATTAGT
60613 GTTAA
1 GTTAA
60618 ATAACTAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 3 0.10
10 24 0.80
11 3 0.10
ACGTcount: A:0.29, C:0.02, G:0.16, T:0.53
Consensus pattern (10 bp):
GTTAATTAGT
Found at i:60728 original size:54 final size:55
Alignment explanation
Indices: 60670--60776 Score: 173
Period size: 54 Copynumber: 2.0 Consensus size: 55
60660 ATTTTACAAT
*
60670 AATTCATAA-TACTAATACTAAATAATACTAAT-TATTAATAATAACACTAATATC
1 AATTC-TAATTACTAATAATAAATAATACTAATATATTAATAATAACACTAATATC
*
60724 AATTCTAATTAGTAATAATAAATAATACTAATATATTAATAATAACACTAATA
1 AATTCTAATTACTAATAATAAATAATACTAATATATTAATAATAACACTAATA
60777 ATTATTATAT
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
53 3 0.06
54 26 0.53
55 20 0.41
ACGTcount: A:0.53, C:0.10, G:0.01, T:0.36
Consensus pattern (55 bp):
AATTCTAATTACTAATAATAAATAATACTAATATATTAATAATAACACTAATATC
Found at i:60773 original size:20 final size:20
Alignment explanation
Indices: 60739--60780 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
60729 TAATTAGTAA
*
60739 TAATAAATAATACTAATATAT
1 TAATAAATAACACTAATA-AT
60760 TAAT-AATAACACTAATAAT
1 TAATAAATAACACTAATAAT
60779 TA
1 TA
60781 TTATATTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 12 0.60
21 4 0.20
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (20 bp):
TAATAAATAACACTAATAAT
Found at i:61986 original size:16 final size:16
Alignment explanation
Indices: 61965--61997 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
61955 ATGAACTACC
61965 TAATAGTTGAGAGTGT
1 TAATAGTTGAGAGTGT
61981 TAATAGTTGAGAGTGT
1 TAATAGTTGAGAGTGT
61997 T
1 T
61998 CTACTTAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.30, T:0.39
Consensus pattern (16 bp):
TAATAGTTGAGAGTGT
Found at i:62942 original size:19 final size:20
Alignment explanation
Indices: 62904--62960 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 20
62894 TAACATTCTC
62904 ATCTGTACAGTACCTAATCTA
1 ATCTGTACAGTA-CTAATCTA
* *
62925 ATCTGTACAGT-GTAATCTC
1 ATCTGTACAGTACTAATCTA
*
62944 ATCTGCACAGTTACTAA
1 ATCTGTACAG-TACTAA
62961 ACAGTATCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 15 0.50
20 1 0.03
21 14 0.47
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (20 bp):
ATCTGTACAGTACTAATCTA
Found at i:68475 original size:28 final size:28
Alignment explanation
Indices: 68401--68475 Score: 100
Period size: 28 Copynumber: 2.7 Consensus size: 28
68391 TATAGGCATA
*
68401 AAATTACCGTTTTACCCTAAGAATGAGT
1 AAATTACCGTTTTACCCTTAGAATGAGT
68429 AAATTACCGTTTTACCCTTAGAA-G-GTT
1 AAATTACCGTTTTACCCTTAGAATGAG-T
*
68456 AAATTTACAGTTTTACCCTT
1 AAA-TTACCGTTTTACCCTT
68476 TTAACCTTGT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
26 1 0.02
27 5 0.12
28 37 0.86
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (28 bp):
AAATTACCGTTTTACCCTTAGAATGAGT
Done.