Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018644.1 Corchorus olitorius cultivar O-4 contig18677, 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: 37066
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:828 original size:25 final size:25
Alignment explanation
Indices: 790--837 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
780 CGAGAATCCG
790 AATATATATTTTATTATAA-ATATTA
1 AATATATATTTTATT-TAAGATATTA
815 AATATAT-TTATTATTTAAGATAT
1 AATATATATT-TTATTTAAGATAT
838 ATTATATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
AATATATATTTTATTTAAGATATTA
Found at i:1184 original size:23 final size:23
Alignment explanation
Indices: 1158--1203 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
1148 ACCCTAACCC
1158 GAAAATCCCCAATCCCCAATCCT
1 GAAAATCCCCAATCCCCAATCCT
*
1181 GAAAATCCCCAATCCTCAATCCT
1 GAAAATCCCCAATCCCCAATCCT
1204 TTTAAATTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.41, G:0.04, T:0.20
Consensus pattern (23 bp):
GAAAATCCCCAATCCCCAATCCT
Found at i:2111 original size:13 final size:13
Alignment explanation
Indices: 2093--2117 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2083 ATATTTTTGT
2093 TTTGCTTATATGC
1 TTTGCTTATATGC
2106 TTTGCTTATATG
1 TTTGCTTATATG
2118 ATATTAGATT
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:0.16, C:0.12, G:0.16, T:0.56
Consensus pattern (13 bp):
TTTGCTTATATGC
Found at i:4246 original size:3 final size:3
Alignment explanation
Indices: 4240--4265 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4230 GAATGGGGCT
4240 TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TG
4266 TCATGAATGA
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:0.31, C:0.00, G:0.35, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:4899 original size:14 final size:14
Alignment explanation
Indices: 4882--4941 Score: 61
Period size: 14 Copynumber: 4.4 Consensus size: 14
4872 AAGTTCCTGA
4882 TTTTT-AGTGGCTG
1 TTTTTGAGTGGCTG
**
4895 TTTTTGAGTTTCTG
1 TTTTTGAGTGGCTG
4909 TTTTT-AGTGGCTG
1 TTTTTGAGTGGCTG
* **
4922 ATTTTGAGTTCCTG
1 TTTTTGAGTGGCTG
4936 TTTTTG
1 TTTTTG
4942 TGTTTTGCAC
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
13 15 0.41
14 22 0.59
ACGTcount: A:0.08, C:0.08, G:0.25, T:0.58
Consensus pattern (14 bp):
TTTTTGAGTGGCTG
Found at i:4920 original size:27 final size:27
Alignment explanation
Indices: 4867--4940 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
4857 TGATTTCCTG
*
4867 TTTTGAAGTTCCTGATTTTTAGTGGCTGT
1 TTTTG-AGTTCCTG-TTTTTAGTGGCTGA
*
4896 TTTTGAGTTTCTGTTTTTAGTGGCTGA
1 TTTTGAGTTCCTGTTTTTAGTGGCTGA
4923 TTTTGAGTTCCTGTTTTT
1 TTTTGAGTTCCTGTTTTT
4941 GTGTTTTGCA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
27 30 0.71
28 7 0.17
29 5 0.12
ACGTcount: A:0.11, C:0.09, G:0.23, T:0.57
Consensus pattern (27 bp):
TTTTGAGTTCCTGTTTTTAGTGGCTGA
Found at i:5021 original size:22 final size:21
Alignment explanation
Indices: 4979--5019 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4969 GATGTAGATC
*
4979 CTGTTTTCAATTTCTTTTTTA
1 CTGTTTTCAAGTTCTTTTTTA
*
5000 CTGTTTTGAAGTTCTTTTTT
1 CTGTTTTCAAGTTCTTTTTT
5020 TAGTGGCTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.10, T:0.66
Consensus pattern (21 bp):
CTGTTTTCAAGTTCTTTTTTA
Found at i:5055 original size:28 final size:28
Alignment explanation
Indices: 5002--5075 Score: 98
Period size: 28 Copynumber: 2.7 Consensus size: 28
4992 CTTTTTTACT
5002 GTTTTGAAG-TTCT-TTTTTTAGTGGCTG
1 GTTTTG-AGTTTCTGTTTTTTAGTGGCTG
5029 GTTTTGAGTTTCTGTTTTTTAGTGGCTG
1 GTTTTGAGTTTCTGTTTTTTAGTGGCTG
* * *
5057 ATTTTTAGTTCCTGTTTTT
1 GTTTTGAGTTTCTGTTTTT
5076 GTGTTTTGCA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
26 2 0.05
27 10 0.24
28 30 0.71
ACGTcount: A:0.09, C:0.08, G:0.23, T:0.59
Consensus pattern (28 bp):
GTTTTGAGTTTCTGTTTTTTAGTGGCTG
Found at i:5075 original size:14 final size:14
Alignment explanation
Indices: 5015--5075 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 14
5005 TTGAAGTTCT
5015 TTTTTTAGTGGCTG
1 TTTTTTAGTGGCTG
* * **
5029 GTTTTGAGTTTCTG
1 TTTTTTAGTGGCTG
5043 TTTTTTAGTGGCTG
1 TTTTTTAGTGGCTG
* **
5057 ATTTTTAGTTCCTG
1 TTTTTTAGTGGCTG
5071 TTTTT
1 TTTTT
5076 GTGTTTTGCA
Statistics
Matches: 35, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.08, C:0.08, G:0.23, T:0.61
Consensus pattern (14 bp):
TTTTTTAGTGGCTG
Found at i:5107 original size:135 final size:137
Alignment explanation
Indices: 4864--5167 Score: 463
Period size: 135 Copynumber: 2.2 Consensus size: 137
4854 TTTTGATTTC
*
4864 CTGTTTTGAAGTTCCTGATTTTTAGTGGCTGTTTTTGAGTTTCTGTTTTTAGTGGCTGATTTTGA
1 CTGTTTTGAAGTTCCTGATTTTTAGTGGCTGGTTTTGAGTTTCTGTTTTTAGTGGCTGATTTTGA
* *
4929 GTTCCTGTTTTTGTGTTTTGCACTTTCTGTTTTTTGGGTTGATGTAGATCCTG-TTTTCAATTTC
66 GTTCCTGTTTTTGTGTTTTGCAATTTCTGTTTTTTGGGTTGATGTACATCCTGTTTTTCAATTTC
*
4993 TTTTTTA
131 TGTTTTA
* *
5000 CTGTTTTGAAGTT-CT-TTTTTTAGTGGCTGGTTTTGAGTTTCTGTTTTTTAGTGGCTGATTTTT
1 CTGTTTTGAAGTTCCTGATTTTTAGTGGCTGGTTTTGAGTTTCTG-TTTTTAGTGGCTGATTTTG
*
5063 AGTTCCTGTTTTTGTGTTTTGCAATTTTTGTTTTTTGGGTTGATGTACATCCTGTTTTTCAATTT
65 AGTTCCTGTTTTTGTGTTTTGCAATTTCTGTTTTTTGGGTTGATGTACATCCTGTTTTTCAATTT
5128 CTGTTTTA
130 CTGTTTTA
* ** *
5136 TTGTTTTCCAGTTCCTG-TTTTTGAGTTGCTGG
1 CTGTTTTGAAGTTCCTGATTTTT-AGTGGCTGG
5168 CTGTTTTCTT
Statistics
Matches: 152, Mismatches: 11, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
134 26 0.17
135 71 0.47
136 40 0.26
137 7 0.05
138 8 0.05
ACGTcount: A:0.11, C:0.11, G:0.21, T:0.57
Consensus pattern (137 bp):
CTGTTTTGAAGTTCCTGATTTTTAGTGGCTGGTTTTGAGTTTCTGTTTTTAGTGGCTGATTTTGA
GTTCCTGTTTTTGTGTTTTGCAATTTCTGTTTTTTGGGTTGATGTACATCCTGTTTTTCAATTTC
TGTTTTA
Found at i:5140 original size:22 final size:22
Alignment explanation
Indices: 5115--5156 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5105 ATGTACATCC
* *
5115 TGTTTTTCAATTTCTGTTTTAT
1 TGTTTTCCAATTCCTGTTTTAT
*
5137 TGTTTTCCAGTTCCTGTTTT
1 TGTTTTCCAATTCCTGTTTT
5157 TGAGTTGCTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.10, C:0.14, G:0.12, T:0.64
Consensus pattern (22 bp):
TGTTTTCCAATTCCTGTTTTAT
Found at i:6627 original size:30 final size:30
Alignment explanation
Indices: 6593--6653 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
6583 ATCAATTGGC
*
6593 TTCAATCATCAATCTCAAATTGATACTGAT
1 TTCAACCATCAATCTCAAATTGATACTGAT
6623 TTCAACCATCAATCTCAAATTGATACTGAT
1 TTCAACCATCAATCTCAAATTGATACTGAT
6653 T
1 T
6654 AACAATTGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (30 bp):
TTCAACCATCAATCTCAAATTGATACTGAT
Found at i:13039 original size:64 final size:65
Alignment explanation
Indices: 12938--13068 Score: 228
Period size: 64 Copynumber: 2.0 Consensus size: 65
12928 ACCTGAAGGG
* *
12938 TGACATGTGTCCTTTAGGGATTAAATTGAAATAGTTAAAAC-TTAGTTAATTCAAAAAATGGACA
1 TGACATGTGTCCTCTAGGGATTAAATTGAAATAGTTAAAACTTTAGTTAATTAAAAAAATGGACA
*
13002 TGACATGTGTCCTCTAGGGATTAGATTGAAATAGTTAAAACTTTAGTTAATTAAAAAAATGGACA
1 TGACATGTGTCCTCTAGGGATTAAATTGAAATAGTTAAAACTTTAGTTAATTAAAAAAATGGACA
13067 TG
1 TG
13069 TGTCAACTCC
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
64 39 0.62
65 24 0.38
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.33
Consensus pattern (65 bp):
TGACATGTGTCCTCTAGGGATTAAATTGAAATAGTTAAAACTTTAGTTAATTAAAAAAATGGACA
Found at i:16012 original size:11 final size:11
Alignment explanation
Indices: 15988--16029 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
15978 TTGACAGCGC
15988 AACAAAAACAA
1 AACAAAAACAA
* *
15999 AACGAAAACGA
1 AACAAAAACAA
16010 AACAAAAACAAA
1 AACAAAAAC-AA
16022 AACAAAAA
1 AACAAAAA
16030 ACAGAAAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.79, C:0.17, G:0.05, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:16022 original size:5 final size:6
Alignment explanation
Indices: 15988--16029 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
15978 TTGACAGCGC
* *
15988 AACAAA AAC-AA AACGAA AAC-GA AACAAA AACAAA AACAAA AA
1 AACAAA AACAAA AACAAA AACAAA AACAAA AACAAA AACAAA AA
16030 ACAGAAAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 9 0.28
6 23 0.72
ACGTcount: A:0.79, C:0.17, G:0.05, T:0.00
Consensus pattern (6 bp):
AACAAA
Found at i:16260 original size:31 final size:30
Alignment explanation
Indices: 16210--16314 Score: 112
Period size: 29 Copynumber: 3.5 Consensus size: 30
16200 AGGGCTAAAT
16210 GCTCAATTTGGT--TAAACCTTTGAGTGAGC
1 GCTCAATTTGGTCCTAAACCTTTGAG-GAGC
*
16239 GCTCAATTTGGTCCTAAACCTTTGA--ACGT
1 GCTCAATTTGGTCCTAAACCTTTGAGGA-GC
*
16268 GCTCAATTTGGTCCTAAATCTTTGAGCG-GTC
1 GCTCAATTTGGTCCTAAACCTTTGAG-GAG-C
*
16299 GCTCAATTTAGTCCTA
1 GCTCAATTTGGTCCTA
16315 TTTCAGACGG
Statistics
Matches: 65, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
28 1 0.02
29 37 0.57
30 1 0.02
31 26 0.40
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (30 bp):
GCTCAATTTGGTCCTAAACCTTTGAGGAGC
Found at i:19122 original size:26 final size:27
Alignment explanation
Indices: 19069--19123 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
19059 AAGAAGAGAT
**
19069 AAATAGCATTAGTGGTCTTTATATATA
1 AAATAGCATTAGTGGTCTAAATATATA
19096 AAATAGCATTAGTGGTCTAAATA-ATA
1 AAATAGCATTAGTGGTCTAAATATATA
19122 AA
1 AA
19124 TATTGTTGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.35
Consensus pattern (27 bp):
AAATAGCATTAGTGGTCTAAATATATA
Found at i:22189 original size:44 final size:42
Alignment explanation
Indices: 22107--22191 Score: 116
Period size: 44 Copynumber: 2.0 Consensus size: 42
22097 TATCATTATG
*
22107 CATGTGGCTTTTTTTTACTTTAGAAATAGCCACGTGGCTATC
1 CATGTGGCTTTTTTTTACTTTAAAAATAGCCACGTGGCTATC
* * *
22149 CATGTGGTTTTTTTTTACTTTATAAAAATTGCCATGTGGCTAT
1 CATGTGGCTTTTTTTTAC-TT-TAAAAATAGCCACGTGGCTAT
22192 TTTATTGAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 17 0.46
43 2 0.05
44 18 0.49
ACGTcount: A:0.22, C:0.15, G:0.18, T:0.45
Consensus pattern (42 bp):
CATGTGGCTTTTTTTTACTTTAAAAATAGCCACGTGGCTATC
Found at i:22306 original size:31 final size:31
Alignment explanation
Indices: 22271--22369 Score: 150
Period size: 31 Copynumber: 3.3 Consensus size: 31
22261 AATAGGACTG
22271 AATTGAGCGACTGCTCAAAGGTTTAGGACCA
1 AATTGAGCGACTGCTCAAAGGTTTAGGACCA
*
22302 AATTGAGC-AC-GTTCAAAGGTTTAGGACCA
1 AATTGAGCGACTGCTCAAAGGTTTAGGACCA
*
22331 AATTGAGTG-CTCGCTCAAAGGTTTAGGACCA
1 AATTGAGCGACT-GCTCAAAGGTTTAGGACCA
22362 AATTGAGC
1 AATTGAGC
22370 ATTTAGCCAA
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
29 26 0.43
30 2 0.03
31 33 0.54
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.24
Consensus pattern (31 bp):
AATTGAGCGACTGCTCAAAGGTTTAGGACCA
Found at i:36432 original size:3 final size:3
Alignment explanation
Indices: 36424--36465 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
36414 TTTTATTTAT
36424 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
36466 AGAGATGAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:36710 original size:48 final size:48
Alignment explanation
Indices: 36635--36776 Score: 157
Period size: 49 Copynumber: 3.0 Consensus size: 48
36625 GAGCGTGCCA
* * *
36635 ATCAATTTTG-TCAAAAAATTGATAAAAAGTGCGA-TGAAAATTAAAAG
1 ATCAATTTTGTTCAAAAAATTGAGAAAAAGTGCAAGT-AAAAATAAAAG
**
36682 ATCAATTTTGTTTTAAAAATTGAGAAAAAGATGCAAGTAAAAATAAAAG
1 ATCAATTTTGTTCAAAAAATTGAGAAAAAG-TGCAAGTAAAAATAAAAG
* *
36731 TTCAATTTTGTAGC-AAAAATTGAGAAAAAGTGC-AGTAAAAAGTAAA
1 ATCAATTTTGT-TCAAAAAATTGAGAAAAAGTGCAAGTAAAAA-TAAA
36777 TGATTGCTTT
Statistics
Matches: 82, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
47 18 0.22
48 23 0.28
49 40 0.49
50 1 0.01
ACGTcount: A:0.51, C:0.06, G:0.15, T:0.27
Consensus pattern (48 bp):
ATCAATTTTGTTCAAAAAATTGAGAAAAAGTGCAAGTAAAAATAAAAG
Done.