Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014040.1 Corchorus olitorius cultivar O-4 contig14073, 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: 35541
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:861 original size:22 final size:22
Alignment explanation
Indices: 826--867 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
816 TATAAGTTTT
*
826 CAAAATAACAAAATCAAACTTA
1 CAAAATAACAAAATAAAACTTA
**
848 CAAAATAATTAAATAAAACT
1 CAAAATAACAAAATAAAACT
868 AAACTAAAGA
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:0.64, C:0.14, G:0.00, T:0.21
Consensus pattern (22 bp):
CAAAATAACAAAATAAAACTTA
Found at i:3282 original size:28 final size:27
Alignment explanation
Indices: 3238--3290 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
3228 ATGATTTAGG
3238 GGTTACTAAATCCCTTTTTTTCTTTTGA
1 GGTTACTAAATCCCTTTTTTT-TTTTGA
*
3266 GGTTACTAACA-CTCTTTTTTTTTTT
1 GGTTACTAA-ATCCCTTTTTTTTTTT
3291 CAGAGGGACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
28 18 0.78
29 1 0.04
ACGTcount: A:0.17, C:0.17, G:0.09, T:0.57
Consensus pattern (27 bp):
GGTTACTAAATCCCTTTTTTTTTTTGA
Found at i:10581 original size:6 final size:6
Alignment explanation
Indices: 10570--10603 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
10560 TTGTGAATTA
*
10570 TTTTTC TTTTTC ATTTTC -TTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
10604 TATTTGCACT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:10603 original size:17 final size:17
Alignment explanation
Indices: 10571--10602 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
10561 TGTGAATTAT
10571 TTTTCTTTTTCATTTTC
1 TTTTCTTTTTCATTTTC
10588 TTTTCTTTTTC-TTTT
1 TTTTCTTTTTCATTTT
10603 TTATTTGCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTCTTTTTCATTTTC
Found at i:15188 original size:29 final size:29
Alignment explanation
Indices: 15127--15375 Score: 215
Period size: 29 Copynumber: 8.7 Consensus size: 29
15117 GATCACCTAG
*
15127 GGGCATTTTGGTTATTTTT-CACATTC-A
1 GGGCATTTTGGTCATTTTTGCACATTCAA
* *
15154 GTGGCATTATGGTCATTTTTGCACCTTCAA
1 G-GGCATTTTGGTCATTTTTGCACATTCAA
* * * *
15184 GGGCATTTTGGGCCA-TTTT-CAAAATCCA
1 GGGCATTTT-GGTCATTTTTGCACATTCAA
* **
15212 GTGGCATTTTGGTCATTTTTGCACACTCGG
1 G-GGCATTTTGGTCATTTTTGCACATTCAA
* *
15242 GGGCATTTTGGTCATTTTTGCACCTTCAG
1 GGGCATTTTGGTCATTTTTGCACATTCAA
* * * *
15271 GGGCATTTTGGGCCA-TTTT-CAAAATCCA
1 GGGCATTTT-GGTCATTTTTGCACATTCAA
* **
15299 GTGGCATTTTGGTCATTTTTGCACACTCTG
1 G-GGCATTTTGGTCATTTTTGCACATTCAA
*
15329 GGGCATTTTGGTCA-TTTTGCACATTCAG
1 GGGCATTTTGGTCATTTTTGCACATTCAA
*
15357 GGGTATTTTGGTCATTTTT
1 GGGCATTTTGGTCATTTTT
15376 AAGTTCACAT
Statistics
Matches: 179, Mismatches: 31, Indels: 22
0.77 0.13 0.09
Matches are distributed among these distances:
27 1 0.01
28 60 0.34
29 96 0.54
30 22 0.12
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.41
Consensus pattern (29 bp):
GGGCATTTTGGTCATTTTTGCACATTCAA
Found at i:15265 original size:87 final size:87
Alignment explanation
Indices: 15128--15367 Score: 385
Period size: 87 Copynumber: 2.8 Consensus size: 87
15118 ATCACCTAGG
* * * * *
15128 GGCATTTTGGTTATTTTT-CACATTCAGTGGCATTATGGTCATTTTTGCACCTTCAAGGGCATTT
1 GGCATTTTGGTCATTTTTGCACACTCAGGGGCATTTTGGTCATTTTTGCACCTTCAGGGGCATTT
15192 TGGGCCATTTTCAAAATCCAGT
66 TGGGCCATTTTCAAAATCCAGT
*
15214 GGCATTTTGGTCATTTTTGCACACTCGGGGGCATTTTGGTCATTTTTGCACCTTCAGGGGCATTT
1 GGCATTTTGGTCATTTTTGCACACTCAGGGGCATTTTGGTCATTTTTGCACCTTCAGGGGCATTT
15279 TGGGCCATTTTCAAAATCCAGT
66 TGGGCCATTTTCAAAATCCAGT
* * *
15301 GGCATTTTGGTCATTTTTGCACACTCTGGGGCATTTTGGTCA-TTTTGCACATTCAGGGGTATTT
1 GGCATTTTGGTCATTTTTGCACACTCAGGGGCATTTTGGTCATTTTTGCACCTTCAGGGGCATTT
15365 TGG
66 TGG
15368 TCATTTTTAA
Statistics
Matches: 144, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
86 40 0.28
87 104 0.72
ACGTcount: A:0.18, C:0.19, G:0.23, T:0.40
Consensus pattern (87 bp):
GGCATTTTGGTCATTTTTGCACACTCAGGGGCATTTTGGTCATTTTTGCACCTTCAGGGGCATTT
TGGGCCATTTTCAAAATCCAGT
Found at i:15276 original size:58 final size:56
Alignment explanation
Indices: 15125--15375 Score: 238
Period size: 58 Copynumber: 4.4 Consensus size: 56
15115 TGGATCACCT
* * *
15125 AGGGGCATTTTGGTTATTTTTCACATTCAGTGGCATTATGGTCATTTTTGCAC-CTTC
1 AGGGGCATTTTGGTCATTTTTCACATTCAGGGGCATTTTGGTCA-TTTTGCACAC-TC
* * * * *
15182 AAGGGCATTTTGGGCCA-TTTTCAAAATCCAGTGGCATTTTGGTCATTTTTGCACACTC
1 AGGGGCATTTT-GGTCATTTTTC-ACATTCAGGGGCATTTTGGTCA-TTTTGCACACTC
* * * * *
15240 GGGGGCATTTTGGTCATTTTTGCACCTTCAGGGGCATTTTGGGCCATTTT-CAAAATCC
1 AGGGGCATTTTGGTCATTTTT-CACATTCAGGGGCATTTT-GGTCATTTTGCACACT-C
* * * *
15298 AGTGGCATTTTGGTCATTTTTGCACACTCTGGGGCATTTTGGTCATTTTGCACATTC
1 AGGGGCATTTTGGTCATTTTT-CACATTCAGGGGCATTTTGGTCATTTTGCACACTC
*
15355 AGGGGTATTTTGGTCATTTTT
1 AGGGGCATTTTGGTCATTTTT
15376 AAGTTCACAT
Statistics
Matches: 160, Mismatches: 26, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
57 51 0.32
58 103 0.64
59 6 0.04
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.41
Consensus pattern (56 bp):
AGGGGCATTTTGGTCATTTTTCACATTCAGGGGCATTTTGGTCATTTTGCACACTC
Found at i:16018 original size:9 final size:9
Alignment explanation
Indices: 15993--16037 Score: 63
Period size: 9 Copynumber: 4.8 Consensus size: 9
15983 CAAAAAAGTC
15993 AAATCAAAA
1 AAATCAAAA
16002 CCAAATCAAAA
1 --AAATCAAAA
16013 AAATCAAAA
1 AAATCAAAA
*
16022 AAATAAAAA
1 AAATCAAAA
16031 AAATCAA
1 AAATCAA
16038 TTAAATTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
9 23 0.72
11 9 0.28
ACGTcount: A:0.76, C:0.13, G:0.00, T:0.11
Consensus pattern (9 bp):
AAATCAAAA
Found at i:16731 original size:50 final size:50
Alignment explanation
Indices: 16656--16805 Score: 237
Period size: 50 Copynumber: 3.0 Consensus size: 50
16646 AGTTTTACAA
* *
16656 TAAAATTGCTTTCCATTTATGAGTTCAAGATCAAAATTCACTTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
* *
16706 TAAAATTGCTTTCCATTTGTAAGTTCAAGATCAAAATTTGCTTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
* * *
16756 TAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAG
1 TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
16806 GACAGTGAAG
Statistics
Matches: 91, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 91 1.00
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (50 bp):
TAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
Found at i:17537 original size:50 final size:50
Alignment explanation
Indices: 17475--17749 Score: 514
Period size: 50 Copynumber: 5.5 Consensus size: 50
17465 TCCGAATGAT
*
17475 TAGGCTTTTCCACAAGCCGAACTCGTTTCCATACGAGTCAATTATCAACA
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
17525 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
*
17575 TAGGCTTTTCCACAATCCAAACTCGTTTCCATACGAGTCAATTATCAACA
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
17625 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
* *
17675 TGGGCTTTTCCACAAGCCAAGCTCGTTTCCATACGAGTCAATTATCAACA
1 TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
17725 TAGGCTTTTCCACAAGCCAAACTCG
1 TAGGCTTTTCCACAAGCCAAACTCG
17750 AGGATCTCTT
Statistics
Matches: 218, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 218 1.00
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (50 bp):
TAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACA
Found at i:18018 original size:29 final size:29
Alignment explanation
Indices: 17960--18123 Score: 183
Period size: 29 Copynumber: 5.7 Consensus size: 29
17950 AGGATCACCT
17960 AGGGGCATTTTGGTCATTTTT-CACATTC
1 AGGGGCATTTTGGTCATTTTTGCACATTC
* * *
17988 AGTGGCATTATGGTCATTTTTGCACCTTC
1 AGGGGCATTTTGGTCATTTTTGCACATTC
* * *
18017 AGGGGCATTTTGGCCCA-TTTT-CAAAATCC
1 AGGGGCATTTTGG-TCATTTTTGC-ACATTC
* *
18046 AGTGGCATTTTGGTCATTTTTGCACACTC
1 AGGGGCATTTTGGTCATTTTTGCACATTC
*
18075 GGGGGCATTTTGGTCA-TTTTGCACATTC
1 AGGGGCATTTTGGTCATTTTTGCACATTC
* *
18103 AGGGGTATTTTGGTCAATTTT
1 AGGGGCATTTTGGTCATTTTT
18124 AATTTCACAT
Statistics
Matches: 111, Mismatches: 19, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
28 47 0.42
29 61 0.55
30 3 0.03
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.40
Consensus pattern (29 bp):
AGGGGCATTTTGGTCATTTTTGCACATTC
Found at i:18123 original size:58 final size:56
Alignment explanation
Indices: 17960--18123 Score: 204
Period size: 57 Copynumber: 2.9 Consensus size: 56
17950 AGGATCACCT
*
17960 AGGGGCATTTTGGTCATTTTTCACATTCAGTGGCATTATGGTCATTTTTGCACCTTC
1 AGGGGCATTTTGGTCA-TTTTCACATTCAGTGGCATTTTGGTCATTTTTGCACCTTC
* * *
18017 AGGGGCATTTTGGCCCATTTTCAAAATCCAGTGGCATTTTGGTCATTTTTGCACAC-TC
1 AGGGGCATTTTGG-TCATTTTC-ACATTCAGTGGCATTTTGGTCATTTTTGCAC-CTTC
* * * *
18075 GGGGGCATTTTGGTCATTTTGCACATTCAGGGGTATTTTGGTCAATTTT
1 AGGGGCATTTTGGTCATTTT-CACATTCAGTGGCATTTTGGTCATTTTT
18124 AATTTCACAT
Statistics
Matches: 92, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
57 46 0.50
58 45 0.49
59 1 0.01
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.40
Consensus pattern (56 bp):
AGGGGCATTTTGGTCATTTTCACATTCAGTGGCATTTTGGTCATTTTTGCACCTTC
Found at i:30606 original size:59 final size:59
Alignment explanation
Indices: 30537--30741 Score: 331
Period size: 59 Copynumber: 3.5 Consensus size: 59
30527 TTTTAAATTT
*
30537 TGCTCGAGGTCTCTGGTAGAGAGATTTT-AATTCAAAATCTTGTCTTGTTTTTAAAATCC
1 TGCTCGAGGTCTCTGATAGAGAG-TTTTCAATTCAAAATCTTGTCTTGTTTTTAAAATCC
*
30596 TGCTCGAGGTCTCTGATAGAGAGTTTTCAATTCAAAATCTTGTCCTGTTTTTAAAATCC
1 TGCTCGAGGTCTCTGATAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAATCC
*
30655 TGCTCGAGGTCTCTGATAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAATCT
1 TGCTCGAGGTCTCTGATAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAATCC
* ** *
30714 TGTTTAAGGTCTCTGATAGAAAGTTTTC
1 TGCTCGAGGTCTCTGATAGAGAGTTTTC
30742 TGCTTTAAAA
Statistics
Matches: 137, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
58 4 0.03
59 133 0.97
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (59 bp):
TGCTCGAGGTCTCTGATAGAGAGTTTTCAATTCAAAATCTTGTCTTGTTTTTAAAATCC
Found at i:33664 original size:21 final size:21
Alignment explanation
Indices: 33635--33679 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
33625 GTGACACGGC
* *
33635 CCACTTGGGTTCTC-AGGCAAA
1 CCACATGGGTGCTCAAGG-AAA
33656 CCACATGGGTGCTCAAGGAAA
1 CCACATGGGTGCTCAAGGAAA
33677 CCA
1 CCA
33680 TGTGGGCACC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.18
Consensus pattern (21 bp):
CCACATGGGTGCTCAAGGAAA
Found at i:35290 original size:11 final size:10
Alignment explanation
Indices: 35276--35327 Score: 54
Period size: 11 Copynumber: 5.2 Consensus size: 10
35266 CCCTTATCTT
35276 TTTATTTTTC
1 TTTATTTTTC
35286 GTTTATTTTTC
1 -TTTATTTTTC
*
35297 TTT-TTCTT-
1 TTTATTTTTC
*
35305 TTTATTTTTGT
1 TTTATTTTT-C
35316 TTTATTTTTC
1 TTTATTTTTC
35326 TT
1 TT
35328 AGTTTACTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
8 3 0.09
9 8 0.23
10 5 0.14
11 19 0.54
ACGTcount: A:0.08, C:0.08, G:0.04, T:0.81
Consensus pattern (10 bp):
TTTATTTTTC
Found at i:35319 original size:29 final size:29
Alignment explanation
Indices: 35272--35327 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
35262 CTTACCCTTA
35272 TCTTTTTATTTTTCGTTTATTTTTCTTTT
1 TCTTTTTATTTTTCGTTTATTTTTCTTTT
35301 TCTTTTTATTTTT-GTTTTATTTTTCTT
1 TCTTTTTATTTTTCG-TTTATTTTTCTT
35328 AGTTTACTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 1 0.04
29 25 0.96
ACGTcount: A:0.07, C:0.09, G:0.04, T:0.80
Consensus pattern (29 bp):
TCTTTTTATTTTTCGTTTATTTTTCTTTT
Found at i:35324 original size:18 final size:18
Alignment explanation
Indices: 35274--35318 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
35264 TACCCTTATC
* *
35274 TTTTTATTTTTC-GTTTA
1 TTTTTCTTTTTCTTTTTA
35291 TTTTTCTTTTTCTTTTTA
1 TTTTTCTTTTTCTTTTTA
*
35309 TTTTTGTTTT
1 TTTTTCTTTT
35319 ATTTTTCTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.07, C:0.07, G:0.04, T:0.82
Consensus pattern (18 bp):
TTTTTCTTTTTCTTTTTA
Done.