Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016730.1 Corchorus olitorius cultivar O-4 contig16763, 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: 16254
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.27
Found at i:12224 original size:39 final size:38
Alignment explanation
Indices: 12181--12738 Score: 538
Period size: 39 Copynumber: 14.4 Consensus size: 38
12171 TCTCTATCTT
* *
12181 AGTAAACCTGCTTAGGTCCT-TGTTTAGAATTCCCGTTTA
1 AGTAAACCTGCTTAGGT-CTATGTTTAGAATT-TCGTTCA
* **
12220 AGTAAACCTGCTTAGGTCTATGTTTAGAATTTCATTTG
1 AGTAAACCTGCTTAGGTCTATGTTTAGAATTTCGTTCA
*
12258 AGTAAACCTGCCTAGGTCCT-TGTTTAGAATTTTCGTTCA
1 AGTAAACCTGCTTAGGT-CTATGTTTAGAA-TTTCGTTCA
* *
12297 A-TCAAACCTGCTTAGGTCTATGTTTAGAATTTCCATTTA
1 AGT-AAACCTGCTTAGGTCTATGTTTAGAATTT-CGTTCA
* * *
12336 AGTAAACCTGCTTAGGTCTATGTGTAGAATTTCATTTA
1 AGTAAACCTGCTTAGGTCTATGTTTAGAATTTCGTTCA
* *
12374 AGTAAACCTGCTTAGGTCCT-TGTTTAGAATTCCCGTTTA
1 AGTAAACCTGCTTAGGT-CTATGTTTAGAATT-TCGTTCA
* * **
12413 AGTAAACCTTCTTAGGTCTATGTTTAGAATTTCATTTG
1 AGTAAACCTGCTTAGGTCTATGTTTAGAATTTCGTTCA
*
12451 AGTAAACCTGCCTAGGTCCT-TGTTTAGAATTTTCGTTCA
1 AGTAAACCTGCTTAGGT-CTATGTTTAGAA-TTTCGTTCA
** * * *
12490 A-TCAAACCTGCTTAGGTCCCTGTGTAAAATTACCGTTCA
1 AGT-AAACCTGCTTAGGTCTATGTTTAGAATT-TCGTTCA
* * * * *
12529 AGTGAACCTGCTTAGGATCTCTGCTTAGAGTTTCGATCA
1 AGTAAACCTGCTTAGG-TCTATGTTTAGAATTTCGTTCA
* **
12568 AGTAAACCTGCTTAGGTCTATGTTTAGAATTTCATTTG
1 AGTAAACCTGCTTAGGTCTATGTTTAGAATTTCGTTCA
12606 AGTAAACCTGCTTAGGTCCT-TGTTTAGAATTTTCGTTCA
1 AGTAAACCTGCTTAGGT-CTATGTTTAGAA-TTTCGTTCA
** * * *
12645 A-TCAAACCTGCTTAGGTCCCTGTGTAAAATTACCGTTCA
1 AGT-AAACCTGCTTAGGTCTATGTTTAGAATT-TCGTTCA
* * * *
12684 AGTGAACCTGCTTAGGATCTCTGTTTAGAGTTTCGATCA
1 AGTAAACCTGCTTAGG-TCTATGTTTAGAATTTCGTTCA
12723 AGTAAACCTGCTTAGG
1 AGTAAACCTGCTTAGG
12739 CCCCCATTTT
Statistics
Matches: 436, Mismatches: 59, Indels: 48
0.80 0.11 0.09
Matches are distributed among these distances:
38 149 0.34
39 263 0.60
40 24 0.06
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (38 bp):
AGTAAACCTGCTTAGGTCTATGTTTAGAATTTCGTTCA
Found at i:12308 original size:77 final size:76
Alignment explanation
Indices: 12181--12738 Score: 499
Period size: 77 Copynumber: 7.2 Consensus size: 76
12171 TCTCTATCTT
** *
12181 AGTAAACCTGCTTAGGTCCTTGTTTAGAATTCCCGTTTAAGTAAACCTGCTTAGGTCTATGTTTA
1 AGTAAACCTGCTTAGGTCCTTGTTTAGAATTTTCGTTCAAGTAAACCTGCTTAGGTCT-TGTTTA
*
12246 GAATTTCATTTG
65 GAATTTCATTTA
*
12258 AGTAAACCTGCCTAGGTCCTTGTTTAGAATTTTCGTTCAA-TCAAACCTGCTTAGGTCTATGTTT
1 AGTAAACCTGCTTAGGTCCTTGTTTAGAATTTTCGTTCAAGT-AAACCTGCTTAGGTCT-TGTTT
12322 AGAATTTCCATTTA
64 AGAATTT-CATTTA
* * *
12336 AGTAAACCTGCTTAGGT-CTATGTGTAGAA-TTTCATTTAAGTAAACCTGCTTAGGTCCTTGTTT
1 AGTAAACCTGCTTAGGTCCT-TGTTTAGAATTTTCGTTCAAGTAAACCTGCTTAGGT-CTTGTTT
* *
12399 AGAATTCCCGTTTA
64 AGAATT-TCATTTA
* * ** *
12413 AGTAAACCTTCTTAGGT-CTATGTTTAGAA-TTTCATTTGAGTAAACCTGCCTAGGTCCTTGTTT
1 AGTAAACCTGCTTAGGTCCT-TGTTTAGAATTTTCGTTCAAGTAAACCTGCTTAGGT-CTTGTTT
* *
12476 AGAATTTTCGTTCA
64 AGAA-TTTCATTTA
* * * ** * *
12490 A-TCAAACCTGCTTAGGTCCCTGTGTAAAATTACCGTTCAAGTGAACCTGCTTAGGATCTCTGCT
1 AGT-AAACCTGCTTAGGTCCTTGTTTAGAATTTTCGTTCAAGTAAACCTGCTTAGG-TCT-TGTT
* *
12554 TAGAGTTTCGA-TCA
63 TAGAATTTC-ATTTA
* **
12568 AGTAAACCTGCTTAGGT-CTATGTTTAGAA-TTTCATTTGAGTAAACCTGCTTAGGTCCTTGTTT
1 AGTAAACCTGCTTAGGTCCT-TGTTTAGAATTTTCGTTCAAGTAAACCTGCTTAGGT-CTTGTTT
* *
12631 AGAATTTTCGTTCA
64 AGAA-TTTCATTTA
* * * ** *
12645 A-TCAAACCTGCTTAGGTCCCTGTGTAAAATTACCGTTCAAGTGAACCTGCTTAGGATCTCTGTT
1 AGT-AAACCTGCTTAGGTCCTTGTTTAGAATTTTCGTTCAAGTAAACCTGCTTAGG-TCT-TGTT
* *
12709 TAGAGTTTCGA-TCA
63 TAGAATTTC-ATTTA
12723 AGTAAACCTGCTTAGG
1 AGTAAACCTGCTTAGG
12739 CCCCCATTTT
Statistics
Matches: 402, Mismatches: 54, Indels: 49
0.80 0.11 0.10
Matches are distributed among these distances:
76 11 0.03
77 245 0.61
78 127 0.32
79 19 0.05
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (76 bp):
AGTAAACCTGCTTAGGTCCTTGTTTAGAATTTTCGTTCAAGTAAACCTGCTTAGGTCTTGTTTAG
AATTTCATTTA
Found at i:12367 original size:116 final size:116
Alignment explanation
Indices: 12181--12738 Score: 646
Period size: 116 Copynumber: 4.8 Consensus size: 116
12171 TCTCTATCTT
* *
12181 AGTAAACCTGCTTAGGTCCT-TGTTTAGAATTCCCGTTTAAGTAAACCTGCTTAGGTCTATGTTT
1 AGTAAACCTGCTTAGGT-CTATGTTTAGAATTTCCATTTAAGTAAACCTGCTTAGGTCTATGTTT
* *
12245 AGAATTTCATTTGAGTAAACCTGCCTAGGTCCTTGTTTAGAATTTTCGTTCA
65 AGAATTTCATTTGAGTAAACCTGCTTAGGTCCTTGTTTAGAATTTCCGTTCA
*
12297 A-TCAAACCTGCTTAGGTCTATGTTTAGAATTTCCATTTAAGTAAACCTGCTTAGGTCTATGTGT
1 AGT-AAACCTGCTTAGGTCTATGTTTAGAATTTCCATTTAAGTAAACCTGCTTAGGTCTATGTTT
* * *
12361 AGAATTTCATTTAAGTAAACCTGCTTAGGTCCTTGTTTAGAATTCCCGTTTA
65 AGAATTTCATTTGAGTAAACCTGCTTAGGTCCTTGTTTAGAATTTCCGTTCA
* * *
12413 AGTAAACCTTCTTAGGTCTATGTTTAGAATTT-CATTTGAGTAAACCTGCCTAGGTCCT-TGTTT
1 AGTAAACCTGCTTAGGTCTATGTTTAGAATTTCCATTTAAGTAAACCTGCTTAGGT-CTATGTTT
* * * * * * *
12476 AGAATTTTC-GTTCAATCAAACCTGCTTAGGTCCCTGTGTAAAATTACCGTTCA
65 AGAA-TTTCATTTGAGT-AAACCTGCTTAGGTCCTTGTTTAGAATTTCCGTTCA
* * * * * *
12529 AGTGAACCTGCTTAGGATCTCTGCTTAGAGTTTCGA-TCAAGTAAACCTGCTTAGGTCTATGTTT
1 AGTAAACCTGCTTAGG-TCTATGTTTAGAATTTCCATTTAAGTAAACCTGCTTAGGTCTATGTTT
*
12593 AGAATTTCATTTGAGTAAACCTGCTTAGGTCCTTGTTTAGAATTTTCGTTCA
65 AGAATTTCATTTGAGTAAACCTGCTTAGGTCCTTGTTTAGAATTTCCGTTCA
** * * * * * * *
12645 A-TCAAACCTGCTTAGGTCCCTGTGTAAAATTACCGTTCAAGTGAACCTGCTTAGGATCTCTGTT
1 AGT-AAACCTGCTTAGGTCTATGTTTAGAATTTCCATTTAAGTAAACCTGCTTAGG-TCTATGTT
* **
12709 TAGAGTTTCGA-TCAAGTAAACCTGCTTAGG
64 TAGAATTTC-ATTTGAGTAAACCTGCTTAGG
12739 CCCCCATTTT
Statistics
Matches: 377, Mismatches: 51, Indels: 27
0.83 0.11 0.06
Matches are distributed among these distances:
115 48 0.13
116 251 0.67
117 76 0.20
118 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (116 bp):
AGTAAACCTGCTTAGGTCTATGTTTAGAATTTCCATTTAAGTAAACCTGCTTAGGTCTATGTTTA
GAATTTCATTTGAGTAAACCTGCTTAGGTCCTTGTTTAGAATTTCCGTTCA
Found at i:12539 original size:193 final size:194
Alignment explanation
Indices: 12181--12637 Score: 701
Period size: 193 Copynumber: 2.4 Consensus size: 194
12171 TCTCTATCTT
12181 AGTAAACCTGCTTAGGTCCTTGTTTAGAATTCCCGTTTAAGTAAACCTGCTTAGGTCTATGTTTA
1 AGTAAACCTGCTTAGGTCCTTGTTTAGAATTCCCGTTTAAGTAAACCTGCTTAGGTCTATGTTTA
12246 GAATTTCATTTGAGTAAACCTGCCTAGGTCCTTGTTTAGAATTTTCGTTCAATCAAACCTGCTTA
66 GAATTTCATTTGAGTAAACCTGCCTAGGTCCTTGTTTAGAATTTTCGTTCAATCAAACCTGCTTA
* * * * * *
12311 GGTCTATGTTTAGAATTTCCATTTAAGTAAACCTGCTTAGG-TCTATG-TGTAGAATTTC-ATTT
131 GGTCCATGTGTAAAATTACCATTCAAGTAAACCTGCTTAGGATCTATGCT-TAGAATTTCGA-TC
12373 A
194 A
*
12374 AGTAAACCTGCTTAGGTCCTTGTTTAGAATTCCCGTTTAAGTAAACCTTCTTAGGTCTATGTTTA
1 AGTAAACCTGCTTAGGTCCTTGTTTAGAATTCCCGTTTAAGTAAACCTGCTTAGGTCTATGTTTA
12439 GAATTTCATTTGAGTAAACCTGCCTAGGTCCTTGTTTAGAATTTTCGTTCAATCAAACCTGCTTA
66 GAATTTCATTTGAGTAAACCTGCCTAGGTCCTTGTTTAGAATTTTCGTTCAATCAAACCTGCTTA
* * * * *
12504 GGTCCCTGTGTAAAATTACCGTTCAAGTGAACCTGCTTAGGATCTCTGCTTAGAGTTTCGATCA
131 GGTCCATGTGTAAAATTACCATTCAAGTAAACCTGCTTAGGATCTATGCTTAGAATTTCGATCA
* * *
12568 AGTAAACCTGCTTAGGT-CTATGTTTAGAATT-TCATTTGAGTAAACCTGCTTAGGTCCT-TGTT
1 AGTAAACCTGCTTAGGTCCT-TGTTTAGAATTCCCGTTTAAGTAAACCTGCTTAGGT-CTATGTT
12630 TAGAATTT
64 TAGAATTT
12638 TCGTTCAATC
Statistics
Matches: 243, Mismatches: 16, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
193 196 0.81
194 45 0.19
195 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (194 bp):
AGTAAACCTGCTTAGGTCCTTGTTTAGAATTCCCGTTTAAGTAAACCTGCTTAGGTCTATGTTTA
GAATTTCATTTGAGTAAACCTGCCTAGGTCCTTGTTTAGAATTTTCGTTCAATCAAACCTGCTTA
GGTCCATGTGTAAAATTACCATTCAAGTAAACCTGCTTAGGATCTATGCTTAGAATTTCGATCA
Found at i:12574 original size:155 final size:154
Alignment explanation
Indices: 12184--12738 Score: 692
Period size: 155 Copynumber: 3.6 Consensus size: 154
12174 CTATCTTAGT
* * * * * *
12184 AAACCTGCTTAGGTCCTTGTTTAGAATTCCCGTTTAAGTAAACCTGCTTAGGTCTATGTTTAGAA
1 AAACCTGCTTAGGTCCCTGTGTAAAATTACCGTTCAAGTAAACCTGCTTAGGTCTCTGTTTAGAA
** * * * *
12249 TTTC-ATTTGAGTAAACCTGCCTAGGTCCT-TGTTTAGAATTTTC-GTTCAATCAAACCTGCTTA
66 TTTCGA-TCAAGTAAACCTGCTTAGGT-CTATGTTTAGAA-TTTCATTTGAGT-AAACCTGCTTA
* * *
12311 GGT-CTATGTTTAGAATTTCCATTTAAGT-
127 GGTCCT-TGTTTAGAATTTTCGTTCAA-TC
** * * * *
12339 AAACCTGCTTAGGTCTATGTGTAGAATT-TCATTTAAGTAAACCTGCTTAGGTC-CTTGTTTAGA
1 AAACCTGCTTAGGTCCCTGTGTAAAATTACCGTTCAAGTAAACCTGCTTAGGTCTC-TGTTTAGA
* * * * *
12402 ATTCCCGTTTAAGTAAACCTTCTTAGGTCTATGTTTAGAATTTCATTTGAGTAAACCTGCCTAGG
65 ATT-TCGATCAAGTAAACCTGCTTAGGTCTATGTTTAGAATTTCATTTGAGTAAACCTGCTTAGG
12467 TCCTTGTTTAGAATTTTCGTTCAATC
129 TCCTTGTTTAGAATTTTCGTTCAATC
* *
12493 AAACCTGCTTAGGTCCCTGTGTAAAATTACCGTTCAAGTGAACCTGCTTAGGATCTCTGCTTAGA
1 AAACCTGCTTAGGTCCCTGTGTAAAATTACCGTTCAAGTAAACCTGCTTAGG-TCTCTGTTTAGA
*
12558 GTTTCGATCAAGTAAACCTGCTTAGGTCTATGTTTAGAATTTCATTTGAGTAAACCTGCTTAGGT
65 ATTTCGATCAAGTAAACCTGCTTAGGTCTATGTTTAGAATTTCATTTGAGTAAACCTGCTTAGGT
12623 CCTTGTTTAGAATTTTCGTTCAATC
130 CCTTGTTTAGAATTTTCGTTCAATC
*
12648 AAACCTGCTTAGGTCCCTGTGTAAAATTACCGTTCAAGTGAACCTGCTTAGGATCTCTGTTTAGA
1 AAACCTGCTTAGGTCCCTGTGTAAAATTACCGTTCAAGTAAACCTGCTTAGG-TCTCTGTTTAGA
*
12713 GTTTCGATCAAGTAAACCTGCTTAGG
65 ATTTCGATCAAGTAAACCTGCTTAGG
12739 CCCCCATTTT
Statistics
Matches: 357, Mismatches: 33, Indels: 20
0.87 0.08 0.05
Matches are distributed among these distances:
153 1 0.00
154 95 0.27
155 249 0.70
156 11 0.03
157 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (154 bp):
AAACCTGCTTAGGTCCCTGTGTAAAATTACCGTTCAAGTAAACCTGCTTAGGTCTCTGTTTAGAA
TTTCGATCAAGTAAACCTGCTTAGGTCTATGTTTAGAATTTCATTTGAGTAAACCTGCTTAGGTC
CTTGTTTAGAATTTTCGTTCAATC
Found at i:16193 original size:18 final size:19
Alignment explanation
Indices: 16155--16193 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
16145 TGGGCATTGT
* *
16155 ATCTTCAATTGGGTTTTTA
1 ATCTTCAATTGGGCTTCTA
16174 ATCTT-AATTGGGCTTCTA
1 ATCTTCAATTGGGCTTCTA
16192 AT
1 AT
16194 GTATATGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.23, C:0.13, G:0.15, T:0.49
Consensus pattern (19 bp):
ATCTTCAATTGGGCTTCTA
Done.