Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016283.1 Corchorus olitorius cultivar O-4 contig16316, 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: 15291
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:1687 original size:38 final size:38
Alignment explanation
Indices: 1637--1730 Score: 140
Period size: 38 Copynumber: 2.5 Consensus size: 38
1627 TGTGTATAAG
1637 AATAT-TATGTGTACAATAAATATAT-A-TATATATTGTA
1 AATATATATGTGTACAATAAATATATAATTA-AT-TTGTA
*
1674 AATATATATGTGTACAATACATATATAATTAATTTGTA
1 AATATATATGTGTACAATAAATATATAATTAATTTGTA
1712 AATATATATGTGTACAATA
1 AATATATATGTGTACAATA
1731 GGTATAAGAA
Statistics
Matches: 53, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
37 5 0.09
38 43 0.81
39 3 0.06
40 2 0.04
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (38 bp):
AATATATATGTGTACAATAAATATATAATTAATTTGTA
Found at i:1692 original size:15 final size:13
Alignment explanation
Indices: 1662--1730 Score: 54
Period size: 13 Copynumber: 5.2 Consensus size: 13
1652 ATAAATATAT
1662 ATATATATTGTAA
1 ATATATATTGTAA
1675 ATATATATGTGTACA
1 ATATATAT-TGTA-A
* *
1690 ATACATA-TATAA
1 ATATATATTGTAA
*
1702 TTA-AT-TTGTAA
1 ATATATATTGTAA
1713 ATATATATGTGTACA
1 ATATATAT-TGTA-A
1728 ATA
1 ATA
1731 GGTATAAGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
11 8 0.18
12 5 0.11
13 12 0.27
14 8 0.18
15 11 0.25
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (13 bp):
ATATATATTGTAA
Found at i:1697 original size:19 final size:19
Alignment explanation
Indices: 1637--1700 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
1627 TGTGTATAAG
1637 AATAT-TATGTGTACAATA
1 AATATATATGTGTACAATA
* * ***
1655 AATATATATATATATTGTA
1 AATATATATGTGTACAATA
1674 AATATATATGTGTACAATA
1 AATATATATGTGTACAATA
*
1693 CATATATA
1 AATATATA
1701 ATTAATTTGT
Statistics
Matches: 34, Mismatches: 11, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
18 5 0.15
19 29 0.85
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.41
Consensus pattern (19 bp):
AATATATATGTGTACAATA
Found at i:5878 original size:2 final size:2
Alignment explanation
Indices: 5871--5901 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5861 AATACAAATT
*
5871 TA TA TA TA TA TA TA TA TC TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5902 TAGTATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6922 original size:41 final size:39
Alignment explanation
Indices: 6817--6923 Score: 117
Period size: 41 Copynumber: 2.6 Consensus size: 39
6807 TTATAAAACT
*
6817 AATAAAAATA-ATTTATTATATATATTTTATATATATCATA
1 AATATAAATATATTT-TT-TATATATTTTATATATATCATA
* **
6857 AATATAATTTATATATTTACATATATTTTATATATATCATA
1 AATATAA-ATATAT-TTTTTATATATTTTATATATATCATA
6898 AATAATTAAATATATTTTTTATATAT
1 AAT-A-TAAATATATTTTTTATATAT
6924 CATAAATATA
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
40 6 0.11
41 35 0.64
42 9 0.16
43 5 0.09
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (39 bp):
AATATAAATATATTTTTTATATATTTTATATATATCATA
Found at i:7805 original size:32 final size:32
Alignment explanation
Indices: 7755--7824 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
7745 TTGAGTCAGG
* *
7755 TCGGGTTAAATTTAGGTCAGGTTGATTCG-GAT
1 TCGGGTCAAATTTAGGTCAGGTTAATTCGTG-T
* *
7787 TCGGGTCAATTTTGGGTCAGGTTAATTCGTGT
1 TCGGGTCAAATTTAGGTCAGGTTAATTCGTGT
7819 TCGGGT
1 TCGGGT
7825 TCGGGCTGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 32 0.97
33 1 0.03
ACGTcount: A:0.17, C:0.11, G:0.33, T:0.39
Consensus pattern (32 bp):
TCGGGTCAAATTTAGGTCAGGTTAATTCGTGT
Found at i:8044 original size:17 final size:17
Alignment explanation
Indices: 8024--8056 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
8014 TTTTTTCAGG
8024 TTCGGGTTCAGGTTTTT
1 TTCGGGTTCAGGTTTTT
*
8041 TTCGGGTTCGGGTTTT
1 TTCGGGTTCAGGTTTT
8057 GGTTTTTTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.03, C:0.12, G:0.33, T:0.52
Consensus pattern (17 bp):
TTCGGGTTCAGGTTTTT
Found at i:8062 original size:22 final size:23
Alignment explanation
Indices: 8011--8070 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
8001 ATTGAATTTG
*
8011 GGTTTTTTTCAGGTTCGGGTTCA
1 GGTTTTTTTCGGGTTCGGGTTCA
**
8034 GGTTTTTTTCGGGTTCGGGTTTT
1 GGTTTTTTTCGGGTTCGGGTTCA
8057 GG-TTTTTTCGGGTT
1 GGTTTTTTTCGGGTT
8071 TGAGCTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
22 12 0.35
23 22 0.65
ACGTcount: A:0.03, C:0.10, G:0.33, T:0.53
Consensus pattern (23 bp):
GGTTTTTTTCGGGTTCGGGTTCA
Found at i:9703 original size:3 final size:3
Alignment explanation
Indices: 9697--9725 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
9687 TAAAAAAAAT
9697 TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
9726 CTGGTATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:10119 original size:22 final size:22
Alignment explanation
Indices: 10094--10170 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
10084 TATTTTTATG
*
10094 AAATTTTGATAATCACCCTATT
1 AAATTTTGATAATCACCCTATA
* * * *
10116 AAATTTTGTTAACCACCATATG
1 AAATTTTGATAATCACCCTATA
*
10138 AAATTTTGATAATTA-CCTATA
1 AAATTTTGATAATCACCCTATA
*
10159 AAATTATGATAA
1 AAATTTTGATAA
10171 ACTCCATAAG
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
21 15 0.33
22 30 0.67
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (22 bp):
AAATTTTGATAATCACCCTATA
Found at i:10178 original size:43 final size:44
Alignment explanation
Indices: 10090--10192 Score: 127
Period size: 43 Copynumber: 2.4 Consensus size: 44
10080 TGAATATTTT
* * * *
10090 TATGAAATTTTGATAATCACCCTATTAAATTTTGTTAACCACCA
1 TATGAAATTTTGATAATCACCCTATAAAATTATGATAAACACCA
* *
10134 TATGAAATTTTGATAATTA-CCTATAAAATTATGATAAACTCCA
1 TATGAAATTTTGATAATCACCCTATAAAATTATGATAAACACCA
* *
10177 TAAGAAACTTTGATAA
1 TATGAAATTTTGATAA
10193 CCTAATTTAT
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
43 33 0.65
44 18 0.35
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.37
Consensus pattern (44 bp):
TATGAAATTTTGATAATCACCCTATAAAATTATGATAAACACCA
Found at i:13209 original size:22 final size:22
Alignment explanation
Indices: 13160--13258 Score: 96
Period size: 22 Copynumber: 4.5 Consensus size: 22
13150 TGAATATTTT
*
13160 TATGAAATTTTGAT-AA-TTACC
1 TATGAAATTTTGATAAACTT-CA
**
13181 TATGAAATTGCGATAAACTTCA
1 TATGAAATTTTGATAAACTTCA
* *
13203 TATGAAATTTTGAT-AACCTAA
1 TATGAAATTTTGATAAACTTCA
*
13224 CTATGAAATTTTAATAAACCTTCA
1 -TATGAAATTTTGATAAA-CTTCA
13248 TATGAAATTTT
1 TATGAAATTTT
13259 TTAACCTTCC
Statistics
Matches: 63, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
21 17 0.27
22 28 0.44
23 15 0.24
24 3 0.05
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAAACTTCA
Found at i:13242 original size:44 final size:45
Alignment explanation
Indices: 13160--13283 Score: 148
Period size: 44 Copynumber: 2.8 Consensus size: 45
13150 TGAATATTTT
* ***
13160 TATGAAATTTTGATAA-TTACCTATGAAATTGCGATAAA-CTTCA
1 TATGAAATTTTGATAACCTACCTATGAAATTTTAATAAACCTTCA
*
13203 TATGAAATTTTGATAACCTAACTATGAAATTTTAATAAACCTTCA
1 TATGAAATTTTGATAACCTACCTATGAAATTTTAATAAACCTTCA
* * *
13248 TATGAAATTTT-TTAACCTTCCTATG-ATTTTTAATAA
1 TATGAAATTTTGATAACCTACCTATGAAATTTTAATAA
13284 CCTACCCATA
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
43 26 0.37
44 28 0.40
45 16 0.23
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (45 bp):
TATGAAATTTTGATAACCTACCTATGAAATTTTAATAAACCTTCA
Found at i:13284 original size:21 final size:22
Alignment explanation
Indices: 13193--13286 Score: 79
Period size: 21 Copynumber: 4.3 Consensus size: 22
13183 TGAAATTGCG
* * *
13193 ATAAACTTCATATGAAATTTTG
1 ATAACCTTCATATGAATTTTTA
* *
13215 ATAACC-TAACTATGAAATTTTA
1 ATAACCTTCA-TATGAATTTTTA
13237 ATAAACCTTCATATGAAATTTTT-
1 AT-AACCTTCATATG-AATTTTTA
*
13260 -TAACCTTCCTATG-ATTTTTA
1 ATAACCTTCATATGAATTTTTA
13280 ATAACCT
1 ATAACCT
13287 ACCCATAAGA
Statistics
Matches: 60, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
19 6 0.10
21 19 0.32
22 19 0.32
23 8 0.13
24 8 0.13
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.41
Consensus pattern (22 bp):
ATAACCTTCATATGAATTTTTA
Found at i:14107 original size:12 final size:12
Alignment explanation
Indices: 14090--14117 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
14080 GGGTTGGCAA
14090 ATAATAATATAT
1 ATAATAATATAT
14102 ATAATAATATAT
1 ATAATAATATAT
14114 ATAA
1 ATAA
14118 AACATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
ATAATAATATAT
Found at i:14998 original size:75 final size:75
Alignment explanation
Indices: 14875--15026 Score: 295
Period size: 75 Copynumber: 2.0 Consensus size: 75
14865 GAGATTTCAC
*
14875 TGAGTTTGTTTGTTAGGGAAGGGGTTTGTTGGCTCATAGATTAGCATTTCGGTATTGTAGCTAAT
1 TGAGTTTGTTTGTTAGGGAAGGGATTTGTTGGCTCATAGATTAGCATTTCGGTATTGTAGCTAAT
14940 CATGTAGCGG
66 CATGTAGCGG
14950 TGAGTTTGTTTGTTAGGGAAGGGATTTGTTGGCTCATAGATTAGCATTTCGGTATTGTAGCTAAT
1 TGAGTTTGTTTGTTAGGGAAGGGATTTGTTGGCTCATAGATTAGCATTTCGGTATTGTAGCTAAT
15015 CATGTAGCGG
66 CATGTAGCGG
15025 TG
1 TG
15027 TACGGGTCTT
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 76 1.00
ACGTcount: A:0.20, C:0.09, G:0.32, T:0.39
Consensus pattern (75 bp):
TGAGTTTGTTTGTTAGGGAAGGGATTTGTTGGCTCATAGATTAGCATTTCGGTATTGTAGCTAAT
CATGTAGCGG
Found at i:15206 original size:24 final size:23
Alignment explanation
Indices: 15163--15208 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 23
15153 CCATTATTTT
15163 AATAATGGAATAATTAAAATATTA
1 AATAATGGAAT-ATTAAAATATTA
15187 AATAATGGCAAT-TTAGAAATAT
1 AATAATGG-AATATTA-AAATAT
15209 ATTTGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 3 0.15
24 14 0.70
25 3 0.15
ACGTcount: A:0.54, C:0.02, G:0.11, T:0.33
Consensus pattern (23 bp):
AATAATGGAATATTAAAATATTA
Done.