Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019047.1 Corchorus olitorius cultivar O-4 contig19080, 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: 13212
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Found at i:12226 original size:35 final size:35
Alignment explanation
Indices: 12177--12632 Score: 408
Period size: 35 Copynumber: 12.6 Consensus size: 35
12167 ATTTCAGATG
*
12177 CTTCAGTTCATTTCAGTTGACCCAGGGCGGTCTTT
1 CTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTT
* * *
12212 ATCCAGTTTATTTCAGCTGACCCAGGGCGGTCTTT
1 CTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTT
* * * *
12247 CTTCAGTTTATTTCAGTTGATCTAGGGCGATCCTT
1 CTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTT
* * * * * *
12282 ATTCAATTCATTTCAATTGACTCAGGGTGGTCCTATTT
1 CTTCAGTTTATTTCAGTTGACCCAGGGCGGT-C--TTT
* * *
12320 CAGTTTATTTCAGTTTATTTCAGTTTGATCCAGGGTGATCCTTT
1 C-------TTCAGTTTATTTCAG-TTGACCCAGGGCGGT-CTTT
* **
12364 CTTCGGTTTTATTTCAGTTGACCCAGGGTAGTCTTT
1 CTTCAG-TTTATTTCAGTTGACCCAGGGCGGTCTTT
* *
12400 CTTTAGTTTATTTCAGTTGACGCAGGGCGGTCTTT
1 CTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTT
* * *
12435 CTTCAGTTTATTTCAGTTGATCTAGGGCGATCCTTT
1 CTTCAGTTTATTTCAGTTGACCCAGGGCGGT-CTTT
*
12471 CTTCAGTTTATTTCAGTTGACCCAGGGCTGTCTTT
1 CTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTT
* *
12506 CTTTAATTTATTTCAGTTGACCCAGGGCGGTCTTT
1 CTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTT
* * * *
12541 ATTCAGTTTATTTCAGTTGATCCAGGGAGATCTTT
1 CTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTT
* * * * * * *
12576 CTTCAATTTACTTCAGTAGATCTAAGGCGATCTTCT
1 CTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTT-T
* *
12612 CTGCAGTTTATTTCAATTGAC
1 CTTCAGTTTATTTCAGTTGAC
12633 TGCAAAATGG
Statistics
Matches: 339, Mismatches: 68, Indels: 27
0.78 0.16 0.06
Matches are distributed among these distances:
35 225 0.66
36 56 0.17
37 16 0.05
38 12 0.04
44 4 0.01
45 12 0.04
46 14 0.04
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.42
Consensus pattern (35 bp):
CTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTT
Found at i:12330 original size:10 final size:10
Alignment explanation
Indices: 12315--12345 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
12305 AGGGTGGTCC
12315 TATTTCAGTT
1 TATTTCAGTT
12325 TATTTCAGTT
1 TATTTCAGTT
12335 TATTTCAGTT
1 TATTTCAGTT
12345 T
1 T
12346 GATCCAGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.19, C:0.10, G:0.10, T:0.61
Consensus pattern (10 bp):
TATTTCAGTT
Found at i:12392 original size:83 final size:80
Alignment explanation
Indices: 12248--12417 Score: 198
Period size: 83 Copynumber: 2.1 Consensus size: 80
12238 GCGGTCTTTC
* * *
12248 TTCAGTTTATTTCAGTTGATCTAGGGCGATCCTTATTCAATTCATTTCAATTGACTCAGGGTGGT
1 TTCAGTTTATTTCAGTTGATCCAGGGCGATCCTTATTCAATTCATTTCAATTGACCCAGGGTAGT
12313 CCTAT-TTCAGTTTAT
66 -CTATCTTCAGTTTAT
* * ** * *
12328 TTCAGTTTATTTCAGTTTGATCCAGGGTGATCCTTTCTTCGGTTTTATTTCAGTTGACCCAGGGT
1 TTCAGTTTATTTCAG-TTGATCCAGGGCGATCC-TTATTC-AATTCATTTCAATTGACCCAGGGT
* *
12393 AGTCTTTCTTTAGTTTAT
63 AGTCTATCTTCAGTTTAT
12411 TTCAGTT
1 TTCAGTT
12418 GACGCAGGGC
Statistics
Matches: 75, Mismatches: 11, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
80 15 0.20
81 15 0.20
82 8 0.11
83 37 0.49
ACGTcount: A:0.18, C:0.17, G:0.18, T:0.46
Consensus pattern (80 bp):
TTCAGTTTATTTCAGTTGATCCAGGGCGATCCTTATTCAATTCATTTCAATTGACCCAGGGTAGT
CTATCTTCAGTTTAT
Found at i:12516 original size:106 final size:106
Alignment explanation
Indices: 12323--12592 Score: 409
Period size: 106 Copynumber: 2.5 Consensus size: 106
12313 CCTATTTCAG
* *
12323 TTTATTTCAGTTTATTTCAGTTTGATCCAGGGTGATCCTTTCTTCGGTTTTATTTCAGTTGACCC
1 TTTA-TTCAGTTTATTTCAG-TTGATCCAGGGAGATCCTTTCTTCAG-TTTATTTCAGTTGACCC
* *
12388 AGGGTAGTCTTTCTTTAGTTTATTTCAGTTGACGCAGGGCGGTC
63 AGGGTAGTCTTTCTTTAATTTATTTCAGTTGACCCAGGGCGGTC
* * *
12432 TTTCTTCAGTTTATTTCAGTTGATCTAGGGCGATCCTTTCTTCAGTTTATTTCAGTTGACCCAGG
1 TTTATTCAGTTTATTTCAGTTGATCCAGGGAGATCCTTTCTTCAGTTTATTTCAGTTGACCCAGG
12497 GCT-GTCTTTCTTTAATTTATTTCAGTTGACCCAGGGCGGTC
66 G-TAGTCTTTCTTTAATTTATTTCAGTTGACCCAGGGCGGTC
* *
12538 TTTATTCAGTTTATTTCAGTTGATCCAGGGAGAT-CTTTCTTCAATTTACTTCAGT
1 TTTATTCAGTTTATTTCAGTTGATCCAGGGAGATCCTTTCTTCAGTTTATTTCAGT
12593 AGATCTAAGG
Statistics
Matches: 149, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
105 19 0.13
106 88 0.59
107 24 0.16
108 15 0.10
109 3 0.02
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.45
Consensus pattern (106 bp):
TTTATTCAGTTTATTTCAGTTGATCCAGGGAGATCCTTTCTTCAGTTTATTTCAGTTGACCCAGG
GTAGTCTTTCTTTAATTTATTTCAGTTGACCCAGGGCGGTC
Found at i:12622 original size:106 final size:105
Alignment explanation
Indices: 12323--12632 Score: 365
Period size: 106 Copynumber: 2.9 Consensus size: 105
12313 CCTATTTCAG
* ** *
12323 TTTATTTCAGTTTATTTCAGTTTGATCCAGGGTGATCCTTTCTTCGGTTTTATTTCAGTTGACCC
1 TTTA-TTCAGTTTATTTCAG-TTGATCCAGGGAGATCCTTTCTTC-AATTTATTTCAGTTGACCA
*
12388 AGG-GTAGTCTTTCTTTAGTTTATTTCAGTTGACGCAGGGCGGTC
63 AGGCG-A-TCTTTCTTTAGTTTATTTCAGTTGACCCAGGGCGGTC
* * * * *
12432 TTTCTTCAGTTTATTTCAGTTGATCTAGGGCGATCCTTTCTTCAGTTTATTTCAGTTGACCCAGG
1 TTTATTCAGTTTATTTCAGTTGATCCAGGGAGATCCTTTCTTCAATTTATTTCAGTTGA-CCAAG
*
12497 GCTG-TCTTTCTTTAATTTATTTCAGTTGACCCAGGGCGGTC
65 GC-GATCTTTCTTTAGTTTATTTCAGTTGACCCAGGGCGGTC
* * *
12538 TTTATTCAGTTTATTTCAGTTGATCCAGGGAGAT-CTTTCTTCAATTTACTTCAGTAGATCTAAG
1 TTTATTCAGTTTATTTCAGTTGATCCAGGGAGATCCTTTCTTCAATTTATTTCAGTTGA-CCAAG
** *
12602 GCGATCTTCTCTGCAGTTTATTTCAATTGAC
65 GCGATCTT-TCTTTAGTTTATTTCAGTTGAC
12633 TGCAAAATGG
Statistics
Matches: 174, Mismatches: 22, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
104 1 0.01
105 30 0.17
106 98 0.56
107 26 0.15
108 15 0.09
109 4 0.02
ACGTcount: A:0.18, C:0.19, G:0.19, T:0.44
Consensus pattern (105 bp):
TTTATTCAGTTTATTTCAGTTGATCCAGGGAGATCCTTTCTTCAATTTATTTCAGTTGACCAAGG
CGATCTTTCTTTAGTTTATTTCAGTTGACCCAGGGCGGTC
Found at i:12625 original size:141 final size:143
Alignment explanation
Indices: 12330--12632 Score: 391
Period size: 141 Copynumber: 2.1 Consensus size: 143
12320 CAGTTTATTT
* ** *
12330 CAGTTTATTTCAGTTTGATCCAGGGTGATCCTTTCTTCGGTTTTATTTCAGTTGACCCAGGGTAG
1 CAGTTTATTTCAG-TTGACCCAGGGTGATCCTTTCTTCGAATTTATTTCAGTTGACCCAGGGCAG
* * * * * * * *
12395 TCTTTCTTTAGTTTATTTCAGTTGACGCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGATCTAG
65 TCTTTATTCAGTTTATTTCAGTTGACGCAGGGAGATCTTTCTTCAATTTACTTCAGTAGATCTAA
*
12460 GGCGATCCTTTCTT
130 GGCGATCCTTTCTG
* *
12474 CAGTTTATTTCAGTTGACCCAGGGCTG-T-CTTTCTT-TAATTTATTTCAGTTGACCCAGGGCGG
1 CAGTTTATTTCAGTTGACCCAGGG-TGATCCTTTCTTCGAATTTATTTCAGTTGACCCAGGGCAG
12536 TCTTTATTCAGTTTATTTCAGTTGATC-CAGGGAGATCTTTCTTCAATTTACTTCAGTAGATCTA
65 TCTTTATTCAGTTTATTTCAGTTGA-CGCAGGGAGATCTTTCTTCAATTTACTTCAGTAGATCTA
12600 AGGCGAT-CTTCTCTG
129 AGGCGATCCTT-TCTG
*
12615 CAGTTTATTTCAATTGAC
1 CAGTTTATTTCAGTTGAC
12633 TGCAAAATGG
Statistics
Matches: 140, Mismatches: 16, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
140 3 0.02
141 103 0.74
142 8 0.06
143 11 0.08
144 15 0.11
ACGTcount: A:0.18, C:0.19, G:0.20, T:0.43
Consensus pattern (143 bp):
CAGTTTATTTCAGTTGACCCAGGGTGATCCTTTCTTCGAATTTATTTCAGTTGACCCAGGGCAGT
CTTTATTCAGTTTATTTCAGTTGACGCAGGGAGATCTTTCTTCAATTTACTTCAGTAGATCTAAG
GCGATCCTTTCTG
Found at i:12937 original size:30 final size:30
Alignment explanation
Indices: 12903--13212 Score: 513
Period size: 30 Copynumber: 10.5 Consensus size: 30
12893 GTTCACTTTG
* *
12903 ATCCTGGTTGAGGATCATTGCTTTATTTTA
1 ATCCTGTTTGAGGATCATTGCTTTATGTTA
12933 ATCCTG-TTGAGGATCATTGCTTTATGTTA
1 ATCCTGTTTGAGGATCATTGCTTTATGTTA
12962 ATCCTGTTTGAGGATCATTGCTTTATGTTA
1 ATCCTGTTTGAGGATCATTGCTTTATGTTA
*
12992 ATCCTGTTTGAGGATCATTGCTTTATTTTA
1 ATCCTGTTTGAGGATCATTGCTTTATGTTA
13022 ATCCTGTTTGAGGATCATTGCTTTATGTTA
1 ATCCTGTTTGAGGATCATTGCTTTATGTTA
13052 ATCCTGTTTGAGGATCATTGC-TTATGTTA
1 ATCCTGTTTGAGGATCATTGCTTTATGTTA
13081 ATCCTGTTTGAGGATCATTGCTTTATGTTA
1 ATCCTGTTTGAGGATCATTGCTTTATGTTA
13111 ATCCTGTTTGA-G--CATTGCTTTATGTTA
1 ATCCTGTTTGAGGATCATTGCTTTATGTTA
* *
13138 ATCCTGGTTGAGGATCATTGCTTTATATTA
1 ATCCTGTTTGAGGATCATTGCTTTATGTTA
** *
13168 ATCCTGTTTGAGGAGAACTGCTTTATGTTA
1 ATCCTGTTTGAGGATCATTGCTTTATGTTA
13198 ATCCTGTTTGAGGAT
1 ATCCTGTTTGAGGAT
Statistics
Matches: 264, Mismatches: 11, Indels: 10
0.93 0.04 0.04
Matches are distributed among these distances:
27 25 0.09
28 1 0.00
29 58 0.22
30 180 0.68
ACGTcount: A:0.21, C:0.14, G:0.20, T:0.45
Consensus pattern (30 bp):
ATCCTGTTTGAGGATCATTGCTTTATGTTA
Found at i:13181 original size:146 final size:148
Alignment explanation
Indices: 12903--13212 Score: 518
Period size: 146 Copynumber: 2.1 Consensus size: 148
12893 GTTCACTTTG
* *
12903 ATCCTGGTTGAGGATCATTGCTTTATTTTAATCCTGTTGAGGATCATTGCTTTATGTTAATCCTG
1 ATCCTGTTTGAGGATCATTGCTTTATGTTAATCCTGTTGAGGATCATTGCTTTATGTTAATCCTG
* *
12968 TTTGAGGATCATTGCTTTATGTTAATCCTGTTTGAGGATCATTGCTTTATTTTAATCCTGTTTGA
66 TTTGAGGA-CATTGCTTTATGTTAATCCTGGTTGAGGATCATTGCTTTATATTAATCCTGTTTGA
** *
13033 GGATCATTGCTTTATGTTA
130 GGAGAACTGCTTTATGTTA
13052 ATCCTGTTTGAGGATCATTGC-TTATGTTAATCCTGTTTGAGGATCATTGCTTTATGTTAATCCT
1 ATCCTGTTTGAGGATCATTGCTTTATGTTAATCCTG-TTGAGGATCATTGCTTTATGTTAATCCT
13116 GTTTGA-G-CATTGCTTTATGTTAATCCTGGTTGAGGATCATTGCTTTATATTAATCCTGTTTGA
65 GTTTGAGGACATTGCTTTATGTTAATCCTGGTTGAGGATCATTGCTTTATATTAATCCTGTTTGA
13179 GGAGAACTGCTTTATGTTA
130 GGAGAACTGCTTTATGTTA
13198 ATCCTGTTTGAGGAT
1 ATCCTGTTTGAGGAT
Statistics
Matches: 153, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
146 85 0.56
148 14 0.09
149 54 0.35
ACGTcount: A:0.21, C:0.14, G:0.20, T:0.45
Consensus pattern (148 bp):
ATCCTGTTTGAGGATCATTGCTTTATGTTAATCCTGTTGAGGATCATTGCTTTATGTTAATCCTG
TTTGAGGACATTGCTTTATGTTAATCCTGGTTGAGGATCATTGCTTTATATTAATCCTGTTTGAG
GAGAACTGCTTTATGTTA
Done.