Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020553.1 Corchorus olitorius cultivar O-4 contig20586, 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: 15063
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:246 original size:22 final size:22
Alignment explanation
Indices: 218--279 Score: 108
Period size: 22 Copynumber: 2.8 Consensus size: 22
208 TGCAGAACAC
218 GTCCTGTCCAGATCTTGGCCAA
1 GTCCTGTCCAGATCTTGGCCAA
240 GTCCTGTCCAGATCTTGGCCAA
1 GTCCTGTCCAGATCTTGGCCAA
262 GTCCTGTCCAAGA-CTTGG
1 GTCCTGTCC-AGATCTTGG
280 GCTGTTGAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
22 36 0.92
23 3 0.08
ACGTcount: A:0.18, C:0.31, G:0.24, T:0.27
Consensus pattern (22 bp):
GTCCTGTCCAGATCTTGGCCAA
Found at i:403 original size:69 final size:70
Alignment explanation
Indices: 258--418 Score: 252
Period size: 69 Copynumber: 2.3 Consensus size: 70
248 CAGATCTTGG
* * *
258 CCAAGTCCTGTCCAAGACTTGGGCTGTTGAGGAATGCAAAAATACAGGACAAGACCTGGGCAGGA
1 CCAAGTCCTGTCCAGGACTTGTGCTGTTGAGGAACGCAAAAATACAGGACAAGACCTGGGCAGGA
323 GTTAC
66 GTTAC
* * *
328 CCAAGTCCTGTCCCGGACTTGTGCTGTTGAGGAGCGC-AAATTACAGGACAAGACCTGGGCAGGA
1 CCAAGTCCTGTCCAGGACTTGTGCTGTTGAGGAACGCAAAAATACAGGACAAGACCTGGGCAGGA
392 GTTAC
66 GTTAC
*
397 CCAAGTCCTGTCCAGGAGTTGT
1 CCAAGTCCTGTCCAGGACTTGT
419 TGCGGGAAAT
Statistics
Matches: 83, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
69 51 0.61
70 32 0.39
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (70 bp):
CCAAGTCCTGTCCAGGACTTGTGCTGTTGAGGAACGCAAAAATACAGGACAAGACCTGGGCAGGA
GTTAC
Found at i:9443 original size:2 final size:2
Alignment explanation
Indices: 9436--9469 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
9426 AGATAGTAAG
9436 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9470 TCCTTACATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11788 original size:2 final size:2
Alignment explanation
Indices: 11772--11822 Score: 59
Period size: 2 Copynumber: 25.5 Consensus size: 2
11762 AATTATAAAG
* * *
11772 AT AT -T AT AA AT AT AT AT AT AT AT AT AT AT AT CT AT AT CT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11813 AT ACT AT AT A
1 AT A-T AT AT A
11823 AGTCTAAACT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
1 1 0.02
2 38 0.93
3 2 0.05
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12093 original size:39 final size:40
Alignment explanation
Indices: 12039--12116 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 40
12029 TTAATTCCTA
*
12039 TGTAATATATATAATAACTAAAATACTTGCATTAATTAAG
1 TGTAATATATATAATAACTAAAATACTTACATTAATTAAG
* *
12079 TGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 TGTAATATATATAATAACTAAAATACTTACATTAATTAA
12117 ATTCTTAGGT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 28 0.80
40 7 0.20
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.37
Consensus pattern (40 bp):
TGTAATATATATAATAACTAAAATACTTACATTAATTAAG
Found at i:12578 original size:203 final size:203
Alignment explanation
Indices: 12229--12639 Score: 714
Period size: 203 Copynumber: 2.0 Consensus size: 203
12219 TTCCTTAATA
* *
12229 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTAATCTAATTT
1 ATAAATAAATCGGATCTTTAACATCTTTTATAATTTTGAAATTTTATTTGACATTAATCTAATTT
* *
12294 AATTTAATAAATCAACCACTAATGTTCAACTACCTTTTTTTTGGTATAGTTCTATATATAATAGT
66 AATATAATAAATCAACCACTAATGTTCAACTACCTTTTTTTTGGTATAGTTCTATATATAATAAT
*
12359 AATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATT
131 AATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAAACTTAAAAAATTAATAACATT
12424 CACCATTG
196 CACCATTG
* *
12432 ATAAATAAATCGGATCTTTAACATTTTTTATAATTTTGAAATTTTATTTGACATTGATCTAATTT
1 ATAAATAAATCGGATCTTTAACATCTTTTATAATTTTGAAATTTTATTTGACATTAATCTAATTT
* ** *
12497 AATATAATAATTCAACCACTAATGTTCAACTATTTTTTTTTTGGTATAGTTTTATATATAATAAT
66 AATATAATAAATCAACCACTAATGTTCAACTACCTTTTTTTTGGTATAGTTCTATATATAATAAT
*
12562 AATGTGTTGTATCTTATTCACTGCAACTTTGTTAGTAATCTTAAACTTAAAAAATTAATAACATT
131 AATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAAACTTAAAAAATTAATAACATT
12627 CACCATTG
196 CACCATTG
12635 ATAAA
1 ATAAA
12640 GTTATTAAGC
Statistics
Matches: 196, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
203 196 1.00
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.44
Consensus pattern (203 bp):
ATAAATAAATCGGATCTTTAACATCTTTTATAATTTTGAAATTTTATTTGACATTAATCTAATTT
AATATAATAAATCAACCACTAATGTTCAACTACCTTTTTTTTGGTATAGTTCTATATATAATAAT
AATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAAACTTAAAAAATTAATAACATT
CACCATTG
Found at i:12668 original size:13 final size:13
Alignment explanation
Indices: 12650--12676 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12640 GTTATTAAGC
12650 ATGTAAGGTTGCT
1 ATGTAAGGTTGCT
12663 ATGTAAGGTTGCT
1 ATGTAAGGTTGCT
12676 A
1 A
12677 CATTTCTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.07, G:0.30, T:0.37
Consensus pattern (13 bp):
ATGTAAGGTTGCT
Done.