Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022191.1 Corchorus olitorius cultivar O-4 contig22224, 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: 26078
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Found at i:3244 original size:25 final size:24
Alignment explanation
Indices: 3204--3250 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
3194 AATGCTTACA
*
3204 TTAATTAAATTCTTAGGTATTTTT
1 TTAATTAAATTATTAGGTATTTTT
3228 TTAATTCAAATTATTAGGTATTT
1 TTAATT-AAATTATTAGGTATTT
3251 GTGCAAAGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.32, C:0.04, G:0.09, T:0.55
Consensus pattern (24 bp):
TTAATTAAATTATTAGGTATTTTT
Found at i:3440 original size:15 final size:15
Alignment explanation
Indices: 3420--3450 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3410 GTTCAACTAA
3420 TTTTTTTGGTATAGT
1 TTTTTTTGGTATAGT
3435 TTTTTTTGGTATAGT
1 TTTTTTTGGTATAGT
3450 T
1 T
3451 CTATATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.00, G:0.19, T:0.68
Consensus pattern (15 bp):
TTTTTTTGGTATAGT
Found at i:3658 original size:15 final size:15
Alignment explanation
Indices: 3638--3668 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3628 GTTCAACTAC
3638 TTTTTTT-GGTATAG
1 TTTTTTTGGGTATAG
3652 TTTTTTTGGGTATAG
1 TTTTTTTGGGTATAG
3667 TT
1 TT
3669 CTATATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.13, C:0.00, G:0.23, T:0.65
Consensus pattern (15 bp):
TTTTTTTGGGTATAG
Found at i:3700 original size:218 final size:217
Alignment explanation
Indices: 3323--3968 Score: 1100
Period size: 218 Copynumber: 3.0 Consensus size: 217
3313 TCCCTTAATA
*
3323 ATAAATAAATCGGATC-TTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATATAATTT
1 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
* *
3387 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTGGTATAGTTTTTTTTGGTATAGTTC
66 AATTTAATAAATTAACCACTAATGTTCAACTACTTTTTTTGGTATAG-TTTTTTTGGTATAGTTC
*
3452 TATATATATAATAGTAATGTTTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTCGACTTAA
130 TATATATATAATAGTAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTCGACTTAA
*
3517 AAAATTAAAAACATTCACCATTG
195 AAAATTAATAACATTCACCATTG
*
3540 ATAAATAAATCGGATCTTTAATGTCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
3605 AATTTAATAAATTAACCACTAATGTTCAACTACTTTTTTTGGTATAGTTTTTTTGGGTATAGTTC
66 AATTTAATAAATTAACCACTAATGTTCAACTACTTTTTTTGGTATAGTTTTTTT-GGTATAGTTC
3670 TATATATATAATAGTAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTCGACTTAA
130 TATATATATAATAGTAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTCGACTTAA
3735 AAAATTAATAACATTCACCATTG
195 AAAATTAATAACATTCACCATTG
3758 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
*
3823 AATTTAATAAATTAACCACTAATGTTCAACTACTTTTTTTGGTATA----ATTT--TATA----T
66 AATTTAATAAATTAACCACTAATGTTCAACTACTTTTTTTGGTATAGTTTTTTTGGTATAGTTCT
* * *
3878 AT-TATATAATAATAATGTGTTGTATCTTATTTACTACAACTTTGTTAGTAATCTTAGACTTAAA
131 ATATATATAATAGTAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTCGACTTAAA
3942 AAATTAATAACATTCACCATTG
196 AAATTAATAACATTCACCATTG
3964 ATAAA
1 ATAAA
3969 GTTATTAAGC
Statistics
Matches: 416, Mismatches: 11, Indels: 15
0.94 0.02 0.03
Matches are distributed among these distances:
206 86 0.21
207 3 0.01
211 4 0.01
214 3 0.01
217 23 0.06
218 297 0.71
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.45
Consensus pattern (217 bp):
ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
AATTTAATAAATTAACCACTAATGTTCAACTACTTTTTTTGGTATAGTTTTTTTGGTATAGTTCT
ATATATATAATAGTAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTCGACTTAAA
AAATTAATAACATTCACCATTG
Found at i:17309 original size:12 final size:12
Alignment explanation
Indices: 17292--17316 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17282 TCAATCTATA
17292 CCTGAAGAAATT
1 CCTGAAGAAATT
17304 CCTGAAGAAATT
1 CCTGAAGAAATT
17316 C
1 C
17317 TGCTGCTCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (12 bp):
CCTGAAGAAATT
Found at i:19154 original size:21 final size:22
Alignment explanation
Indices: 19129--19169 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
19119 ACTCTATTAG
19129 GCAGATACATGAA-TATTAATA
1 GCAGATACATGAATTATTAATA
**
19150 GCAGATTTATGAATTATTAA
1 GCAGATACATGAATTATTAA
19170 CTTGTTCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.34
Consensus pattern (22 bp):
GCAGATACATGAATTATTAATA
Found at i:22294 original size:41 final size:41
Alignment explanation
Indices: 22192--22285 Score: 136
Period size: 41 Copynumber: 2.3 Consensus size: 41
22182 AGTAAAATCT
* * *
22192 TAAATCA-GGAGCGAAATTGAATCAATAAATAAATATTATCC
1 TAAATCAGGGA-CAAAATTGAATCAATAAACAAATATTACCC
*
22233 TAAATCAGGGACAAAATTGAATCAATCAACAAATATTACCC
1 TAAATCAGGGACAAAATTGAATCAATAAACAAATATTACCC
22274 TAAATCAGGGAC
1 TAAATCAGGGAC
22286 TGTATTGAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 45 0.94
42 3 0.06
ACGTcount: A:0.48, C:0.16, G:0.13, T:0.23
Consensus pattern (41 bp):
TAAATCAGGGACAAAATTGAATCAATAAACAAATATTACCC
Found at i:23555 original size:31 final size:31
Alignment explanation
Indices: 23520--23587 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
23510 TAAATCCTTT
*
23520 ATTTTATGAGGA-TCAATGTAATAAAACTTCA
1 ATTTTA-GAGGAGTCAATATAATAAAACTTCA
* *
23551 ATTTTAGTGGAGTCAATATGATAAAACTTCA
1 ATTTTAGAGGAGTCAATATAATAAAACTTCA
23582 ATTTTA
1 ATTTTA
23588 ATGGGGTCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (31 bp):
ATTTTAGAGGAGTCAATATAATAAAACTTCA
Found at i:23597 original size:31 final size:31
Alignment explanation
Indices: 23540--23598 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
23530 GATCAATGTA
*
23540 ATAAAACTTCAATTTTAGTGGAGTCAATATG
1 ATAAAACTTCAATTTTAATGGAGTCAATATG
*
23571 ATAAAACTTCAATTTTAATGGGGTCAAT
1 ATAAAACTTCAATTTTAATGGAGTCAAT
23599 TGGTAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (31 bp):
ATAAAACTTCAATTTTAATGGAGTCAATATG
Found at i:25827 original size:27 final size:27
Alignment explanation
Indices: 25760--25819 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
25750 ATGTGAACTT
*
25760 AAAATGACCAAAATGCCCCTGAATATG
1 AAAATGACCAAAATGCCCCTGAATATA
* *
25787 CAAATGACCAAAATGCCCCTGAATGTA
1 AAAATGACCAAAATGCCCCTGAATATA
25814 AAAATG
1 AAAATG
25820 TCTAAAATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.45, C:0.22, G:0.15, T:0.18
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGAATATA
Done.