Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1389
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: 31965
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Found at i:13091 original size:22 final size:22
Alignment explanation
Indices: 13060--13109 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
13050 TACCTTTTAA
* *
13060 TATTTTAGTTGTTCATGCTTTT
1 TATTTAAGTTGTTCATGATTTT
* * *
13082 TATTTAAGTTTTTCTTTATTTT
1 TATTTAAGTTGTTCATGATTTT
13104 TATTTA
1 TATTTA
13110 TTAAATAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.18, C:0.06, G:0.08, T:0.68
Consensus pattern (22 bp):
TATTTAAGTTGTTCATGATTTT
Found at i:14052 original size:23 final size:21
Alignment explanation
Indices: 14002--14054 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
13992 TGTAGTTAAC
* *
14002 TTTATTTTAATATTTAGTTTA
1 TTTATTTTGATATTAAGTTTA
*
14023 TAT-TTTTGATAATTAAGGTTTA
1 TTTATTTTGAT-ATTAA-GTTTA
14045 TTTATTTTGA
1 TTTATTTTGA
14055 CTCCATATCT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 6 0.24
21 6 0.24
22 7 0.28
23 6 0.24
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.62
Consensus pattern (21 bp):
TTTATTTTGATATTAAGTTTA
Found at i:19939 original size:31 final size:32
Alignment explanation
Indices: 19897--19956 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
19887 TGAGAGATAA
* *
19897 TTAATTAAATTAGATAGTATTTA-TATTAAGT
1 TTAACTAAATTAGATAATATTTATTATTAAGT
*
19928 TTAACTAAATTATATAATATTTATTATTA
1 TTAACTAAATTAGATAATATTTATTATTA
19957 TTTATTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 20 0.80
32 5 0.20
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (32 bp):
TTAACTAAATTAGATAATATTTATTATTAAGT
Found at i:21179 original size:27 final size:26
Alignment explanation
Indices: 21116--21194 Score: 74
Period size: 27 Copynumber: 3.0 Consensus size: 26
21106 AATTTTTTTT
*
21116 ATTTTTATATA-TTTAT-AATTTTTAC
1 ATTTTTATA-AGTTTATGAATTTTTAA
*
21141 ATTATTTGTAAGTTTATGAATTTTTAA
1 ATT-TTTATAAGTTTATGAATTTTTAA
21168 ATCTTTTATAAGATTT-TGAATGTTTTA
1 AT-TTTTATAAG-TTTATGAAT-TTTTA
21195 TTAATTTATA
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
25 4 0.09
26 10 0.22
27 22 0.49
28 9 0.20
ACGTcount: A:0.32, C:0.03, G:0.08, T:0.58
Consensus pattern (26 bp):
ATTTTTATAAGTTTATGAATTTTTAA
Found at i:25819 original size:23 final size:23
Alignment explanation
Indices: 25784--25828 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
25774 CCTTATTTAA
**
25784 TTCAAATTGATTAT-AATATTATT
1 TTCAAATAAATTATCAA-ATTATT
25807 TTCAAATAAATTATCAAATTAT
1 TTCAAATAAATTATCAAATTAT
25829 AAAATGACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (23 bp):
TTCAAATAAATTATCAAATTATT
Found at i:29014 original size:89 final size:89
Alignment explanation
Indices: 28907--29105 Score: 237
Period size: 89 Copynumber: 2.2 Consensus size: 89
28897 TTTTAGTAAG
* * *
28907 TTCATATAAGAAATTTTATTATTAAGAATTTTATG-AA-TT-ATATATGACTATTAAATTATAT-
1 TTCATATAAGAAAATTTATTATCAAGAA-TTTATGAAATTTAATAT-TAACTATTAAATTATATG
*
28968 TTAATATTATTTATTTTAAATTGTA-AAA
64 TTAA-ATTA-TTATTTTAAA-TATACAAA
*
28996 TTCATATAAGAAAATTTATTATCAAGAATTTATGAAATTTAATATTAATTATTAAATTATATGTT
1 TTCATATAAGAAAATTTATTATCAAGAATTTATGAAATTTAATATTAACTATTAAATTATATGTT
*
29061 TAATTATTATTTTAAATATACAAA
66 AAATTATTATTTTAAATATACAAA
* * *
29085 TTCATAAAATATAATTTATTA
1 TTCATATAAGAAAATTTATTA
29106 GTTATAATTA
Statistics
Matches: 96, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
88 9 0.09
89 59 0.61
90 21 0.22
91 7 0.07
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.48
Consensus pattern (89 bp):
TTCATATAAGAAAATTTATTATCAAGAATTTATGAAATTTAATATTAACTATTAAATTATATGTT
AAATTATTATTTTAAATATACAAA
Found at i:29243 original size:17 final size:18
Alignment explanation
Indices: 29223--29269 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
29213 CATATAAGAA
*
29223 TATTATTATTATA-ATTT
1 TATTATAATTATATATTT
29240 TATTA-AATTATATATTT
1 TATTATAATTATATATTT
29257 TATTATAA-TATAT
1 TATTATAATTATAT
29270 TTAATAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 6 0.22
17 19 0.70
18 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTATAATTATATATTT
Found at i:29281 original size:115 final size:119
Alignment explanation
Indices: 29135--29523 Score: 618
Period size: 118 Copynumber: 3.3 Consensus size: 119
29125 ATTTTAAATC
* * *
29135 ATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAATTTTTA-TTTATAGTATCATATA-T
1 ATATTTTAATTATAATATATTTAATAATAATTATGTT-AATTTTTATTTTACAGTATCATATATT
*
29197 ATGATTTGAGTAAATTCATATAAGAATATTATTATT-ATAATTTTATTAAATTAT
65 ATGATTTGAGTAAATTCATATAAGAATATTATTATTAAGAATTTTATTAAATTAT
*
29251 ATATTTT-ATTATAATATATTTAATAATAATTATGTTAATTTATATTTTACCAGTATCATATATT
1 ATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTTTATTTTA-CAGTATCATATATT
29315 ATGATTTGAGTAAATTCATATAAGAATATT-TTATTAAGAATTTTTATTAAATTAT
65 ATGATTTGAGTAAATTCATATAAGAATATTATTATTAAGAA-TTTTATTAAATTAT
29370 ATATTTTAATTATAATATATTTAATAATAATTATGTTAA-TTTTATTTTACAGTATCATATATTA
1 ATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTTTATTTTACAGTATCATATATTA
29434 TGATTTGAGTAAATTCATA-AAGAATATTAATTATTAAGAATTTTATT-AATTAT
66 TGATTTGAGTAAATTCATATAAGAATATT-ATTATTAAGAATTTTATTAAATTAT
29487 ATATTTTAATTATAATATAATTTAATAAT-ATTATGTT
1 ATATTTTAATTATAATAT-ATTTAATAATAATTATGTT
29524 TAAATTGATT
Statistics
Matches: 257, Mismatches: 6, Indels: 19
0.91 0.02 0.07
Matches are distributed among these distances:
115 31 0.12
116 13 0.05
117 57 0.22
118 85 0.33
119 40 0.16
120 31 0.12
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (119 bp):
ATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTTTATTTTACAGTATCATATATTA
TGATTTGAGTAAATTCATATAAGAATATTATTATTAAGAATTTTATTAAATTAT
Found at i:29361 original size:13 final size:14
Alignment explanation
Indices: 29335--29364 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
29325 TAAATTCATA
29335 TAAGAATATTTTAT
1 TAAGAATATTTTAT
29349 TAAGAAT-TTTTAT
1 TAAGAATATTTTAT
29362 TAA
1 TAA
29365 ATTATATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
TAAGAATATTTTAT
Found at i:29394 original size:15 final size:15
Alignment explanation
Indices: 29359--29410 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
29349 TAAGAATTTT
*
29359 TATTAAATTAT-ATA
1 TATTTAATTATAATA
29373 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
29387 TATTTAATAATAAT-
1 TATTTAATTATAATA
29401 TATGTTAATT
1 TAT-TTAATT
29411 TTATTTTACA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:29639 original size:18 final size:19
Alignment explanation
Indices: 29618--29660 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
29608 AATTTCTGCT
29618 AATTATAAAATTTT-ATTA
1 AATTATAAAATTTTAATTA
*
29636 AATTAT-ATATTTTAATTA
1 AATTATAAAATTTTAATTA
*
29654 AAATATA
1 AATTATA
29661 TTTAATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AATTATAAAATTTTAATTA
Found at i:29715 original size:157 final size:153
Alignment explanation
Indices: 29461--29773 Score: 488
Period size: 154 Copynumber: 2.0 Consensus size: 153
29451 TAAAGAATAT
*
29461 TAATTATTAAGAATTTTATTAATTATATATTTTAATTATAATATAATTTAATAATATTATGTTTA
1 TAATTATTAAGAATTTTATTAATTATATATTTTAATTAAAATATAATTTAATAATATTATGTTTA
* * *
29526 AATTGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAAAT
66 AATTGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAA-TTAAATAAC-ATAAC-AAT
*
29591 AATAATTTACCAAAACAAATTTCTGC
128 AATAATTTACCAAAACAAATTTATGC
29617 TAATTA-TAA-AATTTTATTAAATTATATATTTTAATTAAAATAT-ATTTAATAATAATTATGGT
1 TAATTATTAAGAATTTTATT-AATTATATATTTTAATTAAAATATAATTTAATAAT-ATTAT-GT
29679 TTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTAAATAACATAACAA
63 TTAAAT-TGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTAAATAACATAACAA
*
29744 TAATCATTTACCAAAACAAATTTATGC
127 TAATAATTTACCAAAACAAATTTATGC
29771 TAA
1 TAA
29774 GGGTATTCTA
Statistics
Matches: 147, Mismatches: 6, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
154 49 0.33
155 36 0.24
156 23 0.16
157 39 0.27
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (153 bp):
TAATTATTAAGAATTTTATTAATTATATATTTTAATTAAAATATAATTTAATAATATTATGTTTA
AATTGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTAAATAACATAACAATAAT
AATTTACCAAAACAAATTTATGC
Done.