Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016102.1 Corchorus olitorius cultivar O-4 contig16135, 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: 66805
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:985 original size:33 final size:33
Alignment explanation
Indices: 948--1059 Score: 120
Period size: 33 Copynumber: 3.4 Consensus size: 33
938 ATTAGCATCC
*
948 AAAACAGAATTT-GTTTCATCACAAACAACACCT
1 AAAACAG-ATTTAGTGTCATCACAAACAACACCT
981 AAAACAGATTTAGTGTCATCACAAACAACA-CT
1 AAAACAGATTTAGTGTCATCACAAACAACACCT
** * * * * *
1013 CAAATTAGGTTTAGTATTATCGCAAACAACATCT
1 -AAAACAGATTTAGTGTCATCACAAACAACACCT
1047 AAAACAGATTTAG
1 AAAACAGATTTAG
1060 AATTACTCTT
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
32 6 0.09
33 58 0.88
34 2 0.03
ACGTcount: A:0.45, C:0.20, G:0.10, T:0.26
Consensus pattern (33 bp):
AAAACAGATTTAGTGTCATCACAAACAACACCT
Found at i:9550 original size:117 final size:117
Alignment explanation
Indices: 9273--9618 Score: 638
Period size: 117 Copynumber: 2.9 Consensus size: 117
9263 TCGACAATTA
* * *
9273 CTAACTACTATAACCCGTTAGCAGGGCCTTAAGCTAACTACTATAACCCGTTAGTAGGGCCATTT
1 CTAACTACTATAACCCGTTAGCAGGGCCTTAAGCTAACTACTATAACCCGTTAGCATGGCCGTTT
* *
9338 TCCAGTTACCATAACCCAACTGGCCAGGGCCGATAGAACATGTTCTCAATTTG
66 TCCAGTTACTATAACCC-ACTAGCCAGGGCCGATAGAACATGTTCTCAATTTG
9391 CTAACTACTATAACCCGTTAGCAGGGCCTTAAGCTAACTACTATAACCCGTTAGCATGGCCGTTT
1 CTAACTACTATAACCCGTTAGCAGGGCCTTAAGCTAACTACTATAACCCGTTAGCATGGCCGTTT
9456 TCCAGTTACTATAACCCACTAGCCAGGGCCGATAGAACATGTTCTCAATTTG
66 TCCAGTTACTATAACCCACTAGCCAGGGCCGATAGAACATGTTCTCAATTTG
9508 CTAACTACTATAACCCGTTAGCAGGGCCTTAAGCTAACTACTATAACCCGTTAGCATGGCCGTTT
1 CTAACTACTATAACCCGTTAGCAGGGCCTTAAGCTAACTACTATAACCCGTTAGCATGGCCGTTT
9573 TCCAGTTACTATAACCCACTAGCCAGGGCCGATAGAACATGTTCTC
66 TCCAGTTACTATAACCCACTAGCCAGGGCCGATAGAACATGTTCTC
9619 TGTCGATCAT
Statistics
Matches: 223, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
117 145 0.65
118 78 0.35
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (117 bp):
CTAACTACTATAACCCGTTAGCAGGGCCTTAAGCTAACTACTATAACCCGTTAGCATGGCCGTTT
TCCAGTTACTATAACCCACTAGCCAGGGCCGATAGAACATGTTCTCAATTTG
Found at i:14812 original size:17 final size:17
Alignment explanation
Indices: 14792--14846 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
14782 TTTTTCCATT
14792 TTCTTTCTCTCATTCTC
1 TTCTTTCTCTCATTCTC
14809 TTCTTTCT-TC-TTCT-
1 TTCTTTCTCTCATTCTC
* *
14823 TCTCTTTTTCTAATTCTC
1 T-TCTTTCTCTCATTCTC
14841 TTCTTT
1 TTCTTT
14847 TCCTAATCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
14 1 0.03
15 10 0.31
16 3 0.09
17 17 0.53
18 1 0.03
ACGTcount: A:0.05, C:0.29, G:0.00, T:0.65
Consensus pattern (17 bp):
TTCTTTCTCTCATTCTC
Found at i:14847 original size:17 final size:17
Alignment explanation
Indices: 14792--14853 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 17
14782 TTTTTCCATT
* *
14792 TTCTTTCTCTCATTCTC
1 TTCTTTTTCTAATTCTC
14809 TTCTTTCTTC---TTCT-
1 TTCTTT-TTCTAATTCTC
14823 TCTCTTTTTCTAATTCTC
1 T-TCTTTTTCTAATTCTC
*
14841 TTCTTTTCCTAAT
1 TTCTTTTTCTAAT
14854 CTCCTCCGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
14 4 0.11
15 9 0.24
17 21 0.57
18 3 0.08
ACGTcount: A:0.08, C:0.29, G:0.00, T:0.63
Consensus pattern (17 bp):
TTCTTTTTCTAATTCTC
Found at i:15385 original size:48 final size:49
Alignment explanation
Indices: 15324--15428 Score: 185
Period size: 48 Copynumber: 2.1 Consensus size: 49
15314 TAATATGATC
15324 TATAATTAGGTAATTGTATGTAATATTC-TTCTTCTTTAAAATTTGTCA
1 TATAATTAGGTAATTGTATGTAATATTCTTTCTTCTTTAAAATTTGTCA
*
15372 TATAGTTAGGTAATTGTATGTAATATTCTTTCTTCTTTAAAATTTGTCA
1 TATAATTAGGTAATTGTATGTAATATTCTTTCTTCTTTAAAATTTGTCA
15421 TATTAATT
1 TA-TAATT
15429 GTCTTATATA
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
48 27 0.51
49 22 0.42
50 4 0.08
ACGTcount: A:0.30, C:0.08, G:0.10, T:0.51
Consensus pattern (49 bp):
TATAATTAGGTAATTGTATGTAATATTCTTTCTTCTTTAAAATTTGTCA
Found at i:16110 original size:67 final size:67
Alignment explanation
Indices: 16002--16135 Score: 268
Period size: 67 Copynumber: 2.0 Consensus size: 67
15992 TTTACTCTAA
16002 AGAAAATTTTAAAATAAAAATAGTTAATTAAAGCTGGAAGTCTTTCTTGTCTTAGCTGTTTGTTT
1 AGAAAATTTTAAAATAAAAATAGTTAATTAAAGCTGGAAGTCTTTCTTGTCTTAGCTGTTTGTTT
16067 GG
66 GG
16069 AGAAAATTTTAAAATAAAAATAGTTAATTAAAGCTGGAAGTCTTTCTTGTCTTAGCTGTTTGTTT
1 AGAAAATTTTAAAATAAAAATAGTTAATTAAAGCTGGAAGTCTTTCTTGTCTTAGCTGTTTGTTT
16134 GG
66 GG
16136 TATTCAACAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.40
Consensus pattern (67 bp):
AGAAAATTTTAAAATAAAAATAGTTAATTAAAGCTGGAAGTCTTTCTTGTCTTAGCTGTTTGTTT
GG
Found at i:21696 original size:11 final size:11
Alignment explanation
Indices: 21680--21714 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
21670 TTCAATGTAC
21680 CATTATATTTT
1 CATTATATTTT
21691 CATTATATTTT
1 CATTATATTTT
*
21702 TATTATAGTTTT
1 CATTATA-TTTT
21714 C
1 C
21715 CTTAATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.26, C:0.09, G:0.03, T:0.63
Consensus pattern (11 bp):
CATTATATTTT
Found at i:21806 original size:13 final size:13
Alignment explanation
Indices: 21788--21812 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21778 TCATTTTATT
21788 ATTTTAATTAAAA
1 ATTTTAATTAAAA
21801 ATTTTAATTAAA
1 ATTTTAATTAAA
21813 TCTAATCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTAATTAAAA
Found at i:22881 original size:21 final size:21
Alignment explanation
Indices: 22847--22887 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
22837 AAATACAAGA
* *
22847 CAACTTCGGTCCAGATGTTGT
1 CAACTTCGGCCCAGAAGTTGT
*
22868 CAACTTCTGCCCAGAAGTTG
1 CAACTTCGGCCCAGAAGTTG
22888 GCCTGTCGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (21 bp):
CAACTTCGGCCCAGAAGTTGT
Found at i:22955 original size:22 final size:22
Alignment explanation
Indices: 22919--22962 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
22909 TTGCGCAGGA
*
22919 CAACTTCGGCCCAGAACTTGTT
1 CAACTTCGGCACAGAACTTGTT
* *
22941 CAACTTCGGGACAGAAGTTGTT
1 CAACTTCGGCACAGAACTTGTT
22963 GCGCAGGACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (22 bp):
CAACTTCGGCACAGAACTTGTT
Found at i:22967 original size:52 final size:52
Alignment explanation
Indices: 22901--23017 Score: 225
Period size: 52 Copynumber: 2.2 Consensus size: 52
22891 TGTCGAAAAG
*
22901 AGAAGTTGTTGCGCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGAC
1 AGAAGTTGTTGCGCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCAGGAC
22953 AGAAGTTGTTGCGCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCAGGAC
1 AGAAGTTGTTGCGCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCAGGAC
23005 AGAAGTTGTTGCG
1 AGAAGTTGTTGCG
23018 GAAAGAAAAA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 64 1.00
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (52 bp):
AGAAGTTGTTGCGCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCAGGAC
Found at i:29304 original size:21 final size:21
Alignment explanation
Indices: 29270--29310 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
29260 AAATACAAGA
* *
29270 CAACTTCGGTCCAGATGTTGT
1 CAACTTCGGCCCAGAAGTTGT
*
29291 CAACTTCTGCCCAGAAGTTG
1 CAACTTCGGCCCAGAAGTTG
29311 GCCTGTCGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (21 bp):
CAACTTCGGCCCAGAAGTTGT
Found at i:29378 original size:22 final size:22
Alignment explanation
Indices: 29342--29385 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
29332 TTGCGCAGGA
*
29342 CAACTTCGGCCCAGAACTTGTT
1 CAACTTCGGCACAGAACTTGTT
* *
29364 CAACTTCGGGACAGAAGTTGTT
1 CAACTTCGGCACAGAACTTGTT
29386 GCGGAAAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (22 bp):
CAACTTCGGCACAGAACTTGTT
Found at i:32816 original size:22 final size:23
Alignment explanation
Indices: 32791--32833 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
32781 TTTGGGATTT
*
32791 GGTTTTTT-TTTTTTTTTTTTAG
1 GGTTTTTTATTCTTTTTTTTTAG
32813 GGTTTTTTATTCTTTTTTTTT
1 GGTTTTTTATTCTTTTTTTTT
32834 GTAATATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.05, C:0.02, G:0.12, T:0.81
Consensus pattern (23 bp):
GGTTTTTTATTCTTTTTTTTTAG
Found at i:42335 original size:27 final size:27
Alignment explanation
Indices: 42305--42369 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
42295 AAGGTCATTT
*
42305 AGGGGCATTTTAGTCATTTGCACGTCC
1 AGGGGCATTTTAGTCATTTGCACCTCC
** ** *
42332 AGGGATATTTCGGTCATTTGCACCTTC
1 AGGGGCATTTTAGTCATTTGCACCTCC
*
42359 AGGGGCGTTTT
1 AGGGGCATTTT
42370 GGTAATTTTA
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.17, C:0.20, G:0.28, T:0.35
Consensus pattern (27 bp):
AGGGGCATTTTAGTCATTTGCACCTCC
Found at i:43756 original size:27 final size:27
Alignment explanation
Indices: 43712--43765 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 27
43702 TTCTATCTTT
43712 GTTCTATTTTGTTAAAA-TTGCATTTA
1 GTTCTATTTTGTTAAAATTTGCATTTA
43738 GTTCTATTTT-TACTAAAATTTGCATTTA
1 GTTCTATTTTGT--TAAAATTTGCATTTA
43766 AATAGGTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 1 0.04
26 10 0.40
27 5 0.20
28 9 0.36
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.54
Consensus pattern (27 bp):
GTTCTATTTTGTTAAAATTTGCATTTA
Found at i:43975 original size:23 final size:24
Alignment explanation
Indices: 43949--43994 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
43939 TTTTTAAAAC
*
43949 CTTTACTTGGGCCA-TTTTATTTT
1 CTTTACCTGGGCCATTTTTATTTT
*
43972 CTTTACCTGGTCCATTTTTATTT
1 CTTTACCTGGGCCATTTTTATTT
43995 ATTTGGTCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.13, C:0.20, G:0.11, T:0.57
Consensus pattern (24 bp):
CTTTACCTGGGCCATTTTTATTTT
Found at i:43995 original size:19 final size:19
Alignment explanation
Indices: 43968--44007 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
43958 GGCCATTTTA
*
43968 TTTTCTTTACCTGGTCCAT
1 TTTTATTTACCTGGTCCAT
**
43987 TTTTATTTATTTGGTCCAT
1 TTTTATTTACCTGGTCCAT
44006 TT
1 TT
44008 ACTTGGTCCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.12, C:0.17, G:0.10, T:0.60
Consensus pattern (19 bp):
TTTTATTTACCTGGTCCAT
Found at i:60433 original size:39 final size:39
Alignment explanation
Indices: 60388--60703 Score: 142
Period size: 39 Copynumber: 8.4 Consensus size: 39
60378 CATTTAAGTG
60388 AACCTGCTTAGGTCCTTGTCTAGAATTTCCGTTTAAACA
1 AACCTGCTTAGGTCCTTGTCTAGAATTTCCGTTTAAACA
* *
60427 AACCTGCTTAGGT-C-T-TC--G---TTCCATTCAAGTA-A
1 AACCTGCTTAGGTCCTTGTCTAGAATTTCCGTTTAA--ACA
* **
60459 AACCTGCTTAGGTCCCTT-TCTAGAA-TTCTCGTTCAAGTA
1 AACCTGCTTAGGT-CCTTGTCTAGAATTTC-CGTTTAAACA
* * *
60498 AACCTGCTTAGGT-CTTCATTTAGAAGTTT-CGTTTAAATCG
1 AACCTGCTTAGGTCCTT-GTCTAGAA-TTTCCGTTTAAA-CA
* * *
60538 AACCTGCTTACGTCCTTGTGTAGAATTTCC------ATA
1 AACCTGCTTAGGTCCTTGTCTAGAATTTCCGTTTAAACA
* * ** *
60571 AACCTGCATAGG-CGCCTG-CTTAGAGCTT-CGTTTAATCA
1 AACCTGCTTAGGTC-CTTGTC-TAGAATTTCCGTTTAAACA
**
60609 AACCTGCTTAGGTCCTT-TCTTTAGAACTTT-CGTTTAATTA
1 AACCTGCTTAGGTCCTTGTC--TAGAA-TTTCCGTTTAAACA
* * * * *
60649 AACCTGCTTAGGCCCCTGTTTAGAATTTTCGTTTAAGCA
1 AACCTGCTTAGGTCCTTGTCTAGAATTTCCGTTTAAACA
60688 AACCTGCTTAGG-CCTT
1 AACCTGCTTAGGTCCTT
60704 CATTTCGTTT
Statistics
Matches: 212, Mismatches: 33, Indels: 65
0.68 0.11 0.21
Matches are distributed among these distances:
31 8 0.04
32 16 0.08
33 20 0.09
34 3 0.01
35 3 0.01
36 2 0.01
37 5 0.02
38 22 0.10
39 76 0.36
40 51 0.24
41 6 0.03
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.36
Consensus pattern (39 bp):
AACCTGCTTAGGTCCTTGTCTAGAATTTCCGTTTAAACA
Found at i:60644 original size:40 final size:39
Alignment explanation
Indices: 60597--60703 Score: 151
Period size: 39 Copynumber: 2.7 Consensus size: 39
60587 TGCTTAGAGC
60597 TTCGTTTAATCAAACCTGCTTAGGTCCTTTCTTTAGAACT
1 TTCGTTTAATCAAACCTGCTTAGG-CCTTTCTTTAGAACT
* ** * *
60637 TTCGTTTAATTAAACCTGCTTAGGCCCCTGTTTAGAATT
1 TTCGTTTAATCAAACCTGCTTAGGCCTTTCTTTAGAACT
*
60676 TTCGTTTAAGCAAACCTGCTTAGGCCTT
1 TTCGTTTAATCAAACCTGCTTAGGCCTT
60704 CATTTCGTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
39 35 0.60
40 23 0.40
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.40
Consensus pattern (39 bp):
TTCGTTTAATCAAACCTGCTTAGGCCTTTCTTTAGAACT
Found at i:61340 original size:26 final size:27
Alignment explanation
Indices: 61311--61364 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
61301 TCTATCTTTG
61311 TTCTATTTTGT-TAAAA-TTGCATTTAA
1 TTCTATTTT-TATAAAATTTGCATTTAA
61337 TTCTATTTTTACTAAAATTTGCATTTAA
1 TTCTATTTTTA-TAAAATTTGCATTTAA
61365 ATAGGTATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 1 0.04
26 9 0.36
27 5 0.20
28 10 0.40
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.54
Consensus pattern (27 bp):
TTCTATTTTTATAAAATTTGCATTTAA
Found at i:61573 original size:23 final size:24
Alignment explanation
Indices: 61547--61592 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
61537 TTTTTAAAAC
*
61547 CTTTACTTGGGCCA-TTTTATTTT
1 CTTTACCTGGGCCATTTTTATTTT
*
61570 CTTTACCTGGTCCATTTTTATTT
1 CTTTACCTGGGCCATTTTTATTT
61593 ACTTGGTCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.13, C:0.20, G:0.11, T:0.57
Consensus pattern (24 bp):
CTTTACCTGGGCCATTTTTATTTT
Found at i:61612 original size:21 final size:19
Alignment explanation
Indices: 61566--61603 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
61556 GGCCATTTTA
*
61566 TTTTCTTTACCTGGTCCAT
1 TTTTATTTACCTGGTCCAT
*
61585 TTTTATTTACTTGGTCCAT
1 TTTTATTTACCTGGTCCAT
61604 CTCTTTATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.13, C:0.21, G:0.11, T:0.55
Consensus pattern (19 bp):
TTTTATTTACCTGGTCCAT
Done.