Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014342.1 Corchorus olitorius cultivar O-4 contig14375, 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: 29245
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.31
Found at i:161 original size:14 final size:15
Alignment explanation
Indices: 142--171 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
132 AACTAGGAAA
142 AATAAAT-AACAAGG
1 AATAAATAAACAAGG
156 AATAAATAAACAAGG
1 AATAAATAAACAAGG
171 A
1 A
172 TTGGACTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.67, C:0.07, G:0.13, T:0.13
Consensus pattern (15 bp):
AATAAATAAACAAGG
Found at i:6427 original size:23 final size:20
Alignment explanation
Indices: 6380--6430 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 20
6370 AATATATACA
*
6380 TGAAAAATCAAAAAGAATTT
1 TGAAAAATCAAAAAAAATTT
6400 TGAAAAATCTACAAAAAAATTT
1 TGAAAAATC-A-AAAAAAATTT
6422 TCGAAAAAT
1 T-GAAAAAT
6431 TTTCTTCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 9 0.33
21 1 0.04
22 10 0.37
23 7 0.26
ACGTcount: A:0.59, C:0.08, G:0.08, T:0.25
Consensus pattern (20 bp):
TGAAAAATCAAAAAAAATTT
Found at i:8253 original size:19 final size:18
Alignment explanation
Indices: 8229--8267 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
8219 AAATATTTCC
*
8229 AATTAGGGCTAATTGCACA
1 AATTAGAGC-AATTGCACA
*
8248 AATTAGATCAATTGCACA
1 AATTAGAGCAATTGCACA
8266 AA
1 AA
8268 AACAAGAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (18 bp):
AATTAGAGCAATTGCACA
Found at i:15175 original size:54 final size:53
Alignment explanation
Indices: 15092--15206 Score: 178
Period size: 54 Copynumber: 2.2 Consensus size: 53
15082 CCTTCTAACT
* *
15092 GTCTTCC-AATCATTCTGATGAAATTGTCTTCCGAACTATTTCTGATGAGATC
1 GTCTTCCGAACCATTCTGATGAAATCGTCTTCCGAACTATTTCTGATGAGATC
* *
15144 GTCTTCCGAACCATTTCTGATGAGATCGTCTTCTGAACTATTTCTGATGAGATC
1 GTCTTCCGAACCA-TTCTGATGAAATCGTCTTCCGAACTATTTCTGATGAGATC
15198 GTCTTCCGA
1 GTCTTCCGA
15207 GTTACTTCTG
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
52 7 0.12
53 4 0.07
54 46 0.81
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (53 bp):
GTCTTCCGAACCATTCTGATGAAATCGTCTTCCGAACTATTTCTGATGAGATC
Found at i:15217 original size:27 final size:27
Alignment explanation
Indices: 15104--15206 Score: 170
Period size: 27 Copynumber: 3.8 Consensus size: 27
15094 CTTCCAATCA
* *
15104 TTCTGATGAAATTGTCTTCCGAACTAT
1 TTCTGATGAGATCGTCTTCCGAACTAT
*
15131 TTCTGATGAGATCGTCTTCCGAACCAT
1 TTCTGATGAGATCGTCTTCCGAACTAT
*
15158 TTCTGATGAGATCGTCTTCTGAACTAT
1 TTCTGATGAGATCGTCTTCCGAACTAT
15185 TTCTGATGAGATCGTCTTCCGA
1 TTCTGATGAGATCGTCTTCCGA
15207 GTTACTTCTG
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 70 1.00
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.38
Consensus pattern (27 bp):
TTCTGATGAGATCGTCTTCCGAACTAT
Found at i:16541 original size:13 final size:13
Alignment explanation
Indices: 16523--16548 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16513 GGAATGCAAT
16523 TCATTTTCAAAAC
1 TCATTTTCAAAAC
16536 TCATTTTCAAAAC
1 TCATTTTCAAAAC
16549 ATTCTCAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38
Consensus pattern (13 bp):
TCATTTTCAAAAC
Found at i:24731 original size:72 final size:72
Alignment explanation
Indices: 24645--25274 Score: 863
Period size: 72 Copynumber: 8.8 Consensus size: 72
24635 CCTCTTCTTC
* *
24645 ATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTTGCACAATCCTTACATGATAAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATAAT
*
24710 CTCCCAT
66 CTTCCAT
** * *
24717 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCATT-GCACAATCCTTATGTCATTA
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCC-TTCGCACAATCCTTACATGATAA
*
24781 TCTTCCTT
65 TCTTCCAT
* * * * *
24789 GTTGCGATTATAGCCAAGGCAGTTCCCACATTTGGCAGTCCTTCGCAAAATCCTTACATGATAAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATAAT
24854 CTTCCAT
66 CTTCCAT
* * ** *
24861 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCACACATTCCTTATGTGATTAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATAAT
*
24926 CTTCCTT
66 CTTCCAT
* * * * *
24933 ATTGCGGTTGTAGTCGGGGCAGTTCCCACATTTGGTAGTCATTCCCACAATCCTTACATGATAAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATAAT
*
24998 CTCCCAT
66 CTTCCAT
* * * ** *
25005 ATTGCAGTTATA-CCGGAGGCAGTTCCCACATTTGGCAGTTCTTCGCACAATCCTTATGTGATTA
1 ATTGCGGTTGTAGCC-GAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATAA
*
25069 TCTTCCTT
65 TCTTCCAT
25077 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATAAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATAAT
25142 CTTCCAT
66 CTTCCAT
* ** *
25149 ATTGCGGTTGTAGCCGAGGTAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTATGTGATTAT
1 ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATAAT
*
25214 C-TCCGT
66 CTTCCAT
*
25220 CATTGCGATTGTAGCCGAGGCAGTTCCCACA-TTGGCAGTCCTTCGCACAATCCTT
1 -ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTT
25275 GCTACTAATC
Statistics
Matches: 487, Mismatches: 66, Indels: 11
0.86 0.12 0.02
Matches are distributed among these distances:
71 31 0.06
72 452 0.93
73 4 0.01
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (72 bp):
ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTACATGATAAT
CTTCCAT
Found at i:24831 original size:144 final size:144
Alignment explanation
Indices: 24637--25274 Score: 1007
Period size: 144 Copynumber: 4.4 Consensus size: 144
24627 CACATGGTCC
*
24637 TCTT-CTTCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTTGCACAATCCTTA
1 TCTTCCTT-ATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTA
24701 CATGATAATCTCCCATATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCATT-GCAC
65 CATGATAATCTCCCATATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCC-TTCGCAC
*
24765 AATCCTTATGTCATTA
129 AATCCTTATGTGATTA
* * * *
24781 TCTTCCTTGTTGCGATTATAGCCAAGGCAGTTCCCACATTTGGCAGTCCTTCGCAAAATCCTTAC
1 TCTTCCTTATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
* * *
24846 ATGATAATCTTCCATATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCACACAT
66 ATGATAATCTCCCATATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAA
24911 TCCTTATGTGATTA
131 TCCTTATGTGATTA
* * * * * *
24925 TCTTCCTTATTGCGGTTGTAGTCGGGGCAGTTCCCACATTTGGTAGTCATTCCCACAATCCTTAC
1 TCTTCCTTATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
* * *
24990 ATGATAATCTCCCATATTGCAGTTATA-CCGGAGGCAGTTCCCACATTTGGCAGTTCTTCGCACA
66 ATGATAATCTCCCATATTGCGGTTGTAGCC-GAGGCAGTTCCCACATTTGGCAGTCCTTCGCACA
25054 ATCCTTATGTGATTA
130 ATCCTTATGTGATTA
*
25069 TCTTCCTTATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
1 TCTTCCTTATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
* *
25134 ATGATAATCTTCCATATTGCGGTTGTAGCCGAGGTAGTTCCCACATTTGGCAGTCCTTCGCACAA
66 ATGATAATCTCCCATATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAA
25199 TCCTTATGTGATTA
131 TCCTTATGTGATTA
*
25213 TC-TCCGTCATTGCGATTGTAGCCGAGGCAGTTCCCACA-TTGGCAGTCCTTCGCACAATCCTT
1 TCTTCC-TTATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTT
25275 GCTACTAATC
Statistics
Matches: 452, Mismatches: 37, Indels: 11
0.90 0.07 0.02
Matches are distributed among these distances:
143 31 0.07
144 416 0.92
145 5 0.01
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (144 bp):
TCTTCCTTATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTAC
ATGATAATCTCCCATATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAA
TCCTTATGTGATTA
Found at i:28936 original size:29 final size:29
Alignment explanation
Indices: 28889--28977 Score: 97
Period size: 29 Copynumber: 3.1 Consensus size: 29
28879 ATTTAAGTCA
** * *
28889 TTTGCACATTCGGGGGCATTTTGGTCATT
1 TTTGCACATTTTGGAGCATCTTGGTCATT
*
28918 TTTGCACATTTTGGAGCATCTTGGTCTTT
1 TTTGCACATTTTGGAGCATCTTGGTCATT
** * *
28947 TTTGTGCATTTTAGAGCATCTTGGTCGTT
1 TTTGCACATTTTGGAGCATCTTGGTCATT
28976 TT
1 TT
28978 GAATGCTCTA
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.13, C:0.16, G:0.24, T:0.47
Consensus pattern (29 bp):
TTTGCACATTTTGGAGCATCTTGGTCATT
Done.