Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012521.1 Corchorus olitorius cultivar O-4 contig12554, 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: 19477
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.31
Found at i:1053 original size:6 final size:6
Alignment explanation
Indices: 1042--1074 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
1032 CAAAATAAGA
1042 ATTAGC ATTAGC ATTAGC ATTAGC ATTAGC ATT
1 ATTAGC ATTAGC ATTAGC ATTAGC ATTAGC ATT
1075 CTCATCTCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (6 bp):
ATTAGC
Found at i:1832 original size:76 final size:76
Alignment explanation
Indices: 1702--1901 Score: 364
Period size: 76 Copynumber: 2.6 Consensus size: 76
1692 GAACCACTAG
*
1702 TTGCTTTTGATAATGGAGAGTTTAATCCATTGCGCATTGACAGCAATAGCCAAATTTTTTATCTG
1 TTGCTTTTGATAATGGAGAGTTTAATCCATTGCGCATTGACAGCAACAGCCAAATTTTTTATCTG
1767 AACTGGATCCA
66 AACTGGATCCA
* *
1778 TTGTTTTTGATAATCGAGAGTTTAATCCATTGCGCATTGACAGCAACAGCCAAATTTTTTATCTG
1 TTGCTTTTGATAATGGAGAGTTTAATCCATTGCGCATTGACAGCAACAGCCAAATTTTTTATCTG
*
1843 AACTGGATCCT
66 AACTGGATCCA
1854 TTGCTTTTGATAATGGAGAGTTTAATCCATTGCGCATTGACAGCAACA
1 TTGCTTTTGATAATGGAGAGTTTAATCCATTGCGCATTGACAGCAACA
1902 ATATTCTGTT
Statistics
Matches: 118, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 118 1.00
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.35
Consensus pattern (76 bp):
TTGCTTTTGATAATGGAGAGTTTAATCCATTGCGCATTGACAGCAACAGCCAAATTTTTTATCTG
AACTGGATCCA
Found at i:4893 original size:21 final size:21
Alignment explanation
Indices: 4863--4954 Score: 150
Period size: 21 Copynumber: 4.4 Consensus size: 21
4853 TGCTAGGAGT
*
4863 TCATTAGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
4884 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
*
4905 TCATTCGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
4926 TCATTGGAG-AAGGTTCCAAGC
1 TCATTGGAGCAA-GTTCCAAGC
4947 TCATTGGA
1 TCATTGGA
4955 ATTGCCTAAG
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
20 2 0.03
21 65 0.97
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (21 bp):
TCATTGGAGCAAGTTCCAAGC
Found at i:8705 original size:25 final size:24
Alignment explanation
Indices: 8668--8714 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
8658 CTAGAAAATT
8668 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAACTTTGAT-GAT-AGATGGA
8694 TGAAAAAC-TTGATGATAGATG
1 TGAAAAACTTTGATGATAGATG
8715 AATAGAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (24 bp):
TGAAAAACTTTGATGATAGATGGA
Found at i:9010 original size:70 final size:70
Alignment explanation
Indices: 8897--9036 Score: 280
Period size: 70 Copynumber: 2.0 Consensus size: 70
8887 TCTTCCGTCG
8897 GCCTTAAACCTCCAATTAGACCTGCAATTGAACACCTAAGATCATAAGATTCACAAGCAATCAAG
1 GCCTTAAACCTCCAATTAGACCTGCAATTGAACACCTAAGATCATAAGATTCACAAGCAATCAAG
8962 TATCA
66 TATCA
8967 GCCTTAAACCTCCAATTAGACCTGCAATTGAACACCTAAGATCATAAGATTCACAAGCAATCAAG
1 GCCTTAAACCTCCAATTAGACCTGCAATTGAACACCTAAGATCATAAGATTCACAAGCAATCAAG
9032 TATCA
66 TATCA
9037 CAACTTAATT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.40, C:0.26, G:0.11, T:0.23
Consensus pattern (70 bp):
GCCTTAAACCTCCAATTAGACCTGCAATTGAACACCTAAGATCATAAGATTCACAAGCAATCAAG
TATCA
Found at i:9682 original size:21 final size:21
Alignment explanation
Indices: 9658--9728 Score: 126
Period size: 21 Copynumber: 3.4 Consensus size: 21
9648 CTTAGGCAAT
9658 TCCAATGAGCTTGGAACCTT-C
1 TCCAATGAGCTTGGAA-CTTGC
9679 TCCAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
9700 TCCAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGGAACTTGC
9721 TCCAATGA
1 TCCAATGA
9729 ACTCCTAGCA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
20 3 0.06
21 46 0.94
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACTTGC
Found at i:15269 original size:29 final size:29
Alignment explanation
Indices: 15237--15488 Score: 258
Period size: 29 Copynumber: 8.7 Consensus size: 29
15227 TCTGCGCTCA
* * *
15237 GGGGAATTTTGGTCATTTTTGCATATATG
1 GGGGCATTTTGGTCATTTTCGCATATCTG
* *
15266 GGGGCATTTTGGTCATTTCCACATATCTG
1 GGGGCATTTTGGTCATTTTCGCATATCTG
* *
15295 GGGGCATTCTGGTCATTTTCGCATATTCGG
1 GGGGCATTTTGGTCATTTTCGCATA-TCTG
* *
15325 GGGGCATTTTGGTCATTTCCACATATCTG
1 GGGGCATTTTGGTCATTTTCGCATATCTG
* *
15354 GGGGCATTCTGGTCATTTTCGCATATCCG
1 GGGGCATTTTGGTCATTTTCGCATATCTG
* * *
15383 GGGGCATTTTGGTCATTTTTGCACATCTA
1 GGGGCATTTTGGTCATTTTCGCATATCTG
* **
15412 GGAGCATTTTGGTCATTCTT-GCATATCCA
1 GGGGCATTTTGGTCATT-TTCGCATATCTG
* *
15441 GGGGCATTTCGGTCATCTTTACACAT-TCT-
1 GGGGCATTTTGGTCAT-TTT-CGCATATCTG
* *
15470 GGGGCAGTTTGGTTATTTT
1 GGGGCATTTTGGTCATTTT
15489 TTGCATACTC
Statistics
Matches: 186, Mismatches: 32, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
28 3 0.02
29 150 0.81
30 30 0.16
31 3 0.02
ACGTcount: A:0.17, C:0.18, G:0.26, T:0.39
Consensus pattern (29 bp):
GGGGCATTTTGGTCATTTTCGCATATCTG
Found at i:15396 original size:88 final size:87
Alignment explanation
Indices: 15236--15428 Score: 242
Period size: 88 Copynumber: 2.2 Consensus size: 87
15226 TTCTGCGCTC
* *** * *
15236 AGGGGAATTTTGGTCATTTTTGCATATATGGGGGCATTTTGGTCATTTCCACATATCTGGGGGCA
1 AGGGGCATTTTGGTCATTTCCACATATATGGGGGCATTCTGGTCATTTCCACATATCCGGGGGCA
*
15301 TTCTGGTCATTTTCGCATATTCG
66 TTCTGGTCATTTTCGCACA-TCG
* * * *
15324 GGGGGCATTTTGGTCATTTCCACATATCTGGGGGCATTCTGGTCATTTTCGCATATCCGGGGGCA
1 AGGGGCATTTTGGTCATTTCCACATATATGGGGGCATTCTGGTCATTTCCACATATCCGGGGGCA
* * *
15389 TTTTGGTCATTTTTGCACATCT
66 TTCTGGTCATTTTCGCACATCG
*
15411 AGGAGCATTTTGGTCATT
1 AGGGGCATTTTGGTCATT
15429 CTTGCATATC
Statistics
Matches: 89, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
87 18 0.20
88 71 0.80
ACGTcount: A:0.17, C:0.18, G:0.26, T:0.39
Consensus pattern (87 bp):
AGGGGCATTTTGGTCATTTCCACATATATGGGGGCATTCTGGTCATTTCCACATATCCGGGGGCA
TTCTGGTCATTTTCGCACATCG
Done.