Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold391
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: 290649
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
File 3 of 3
Found at i:227438 original size:34 final size:34
Alignment explanation
Indices: 227369--227466 Score: 103
Period size: 33 Copynumber: 2.9 Consensus size: 34
227359 TTATTTTTTA
*
227369 AAATTATTTATTTATAATTAATATTTATATTTATAT
1 AAATT-TTTATTTAT-ATTAATATTTATATATATAT
* *
227405 AAATTTTAATTTATATTAA-ATTTTTATA-ATAT
1 AAATTTTTATTTATATTAATATTTATATATATAT
* *
227437 ATAATTTTTATTTTTATTCATA-TTATATAT
1 A-AATTTTTATTTATATTAATATTTATATAT
227467 TTACATTTGA
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
32 5 0.10
33 28 0.54
34 6 0.12
35 8 0.15
36 5 0.10
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (34 bp):
AAATTTTTATTTATATTAATATTTATATATATAT
Found at i:227712 original size:18 final size:18
Alignment explanation
Indices: 227649--227712 Score: 51
Period size: 18 Copynumber: 3.5 Consensus size: 18
227639 AATTTTTTAA
227649 ATTTTTTTAAAAA-ATTGTT
1 ATTTTTTTAAAAATA-T-TT
* *
227668 ATATTTTT-AAAATTTTT
1 ATTTTTTTAAAAATATTT
**
227685 AATTAATTTAAAAATATTT
1 -ATTTTTTTAAAAATATTT
227704 ATTTTTTTA
1 ATTTTTTTA
227713 TTATTAAAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 7
0.69 0.16 0.14
Matches are distributed among these distances:
17 2 0.06
18 17 0.50
19 15 0.44
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
ATTTTTTTAAAAATATTT
Found at i:233436 original size:9 final size:9
Alignment explanation
Indices: 233399--233452 Score: 56
Period size: 9 Copynumber: 6.0 Consensus size: 9
233389 TCGAAGGTGA
233399 AATTAATTT
1 AATTAATTT
233408 AATT-ATTT
1 AATTAATTT
*
233416 ATATTTATTT
1 A-ATTAATTT
233426 AATTAATTT
1 AATTAATTT
* *
233435 AATTGACTT
1 AATTAATTT
*
233444 ATTTAATTT
1 AATTAATTT
233453 GATTCTAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
8 5 0.14
9 27 0.73
10 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (9 bp):
AATTAATTT
Found at i:234400 original size:42 final size:43
Alignment explanation
Indices: 234322--234407 Score: 102
Period size: 42 Copynumber: 2.0 Consensus size: 43
234312 ATCAAGCTCC
* *
234322 TCAACTTCATAAGTACTCTTCTCTCCCATCTTCCTTCT-CTCT
1 TCAACTTCATAAGTACTCTTCTCTCCCACCTGCCTTCTCCTCT
** * **
234364 TCAACTTTGTAAGTATTCTTCTCTGTCACCTGCCTTCTCCTCT
1 TCAACTTCATAAGTACTCTTCTCTCCCACCTGCCTTCTCCTCT
234407 T
1 T
234408 TCCTTCCATG
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 31 0.86
43 5 0.14
ACGTcount: A:0.15, C:0.35, G:0.06, T:0.44
Consensus pattern (43 bp):
TCAACTTCATAAGTACTCTTCTCTCCCACCTGCCTTCTCCTCT
Found at i:236481 original size:11 final size:11
Alignment explanation
Indices: 236465--236505 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
236455 TAAGATAAAT
236465 TTATATTTATA
1 TTATATTTATA
236476 TTATATTTATA
1 TTATATTTATA
236487 -TAT-TTTATAA
1 TTATATTTAT-A
*
236497 TTAAATTTA
1 TTATATTTA
236506 AATAAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
11 13 0.50
12 4 0.15
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTATATTTATA
Found at i:236504 original size:21 final size:19
Alignment explanation
Indices: 236466--236505 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
236456 AAGATAAATT
*
236466 TATATTTATATTATATTTA
1 TATATTTATATTAAATTTA
236485 TATATTTTATAATTAAATTTA
1 TATA-TTTAT-ATTAAATTTA
236506 AATAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 5 0.28
21 9 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATATTTATATTAAATTTA
Found at i:237089 original size:32 final size:32
Alignment explanation
Indices: 237053--237117 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 32
237043 TCGTGTTGAG
*
237053 TTAAATTATAATTTAA-ATTTT-TTTATATTTTA
1 TTAAATT-TAATTCAATATTTTATTT-TATTTTA
237085 TTAAATTTAATTCAATATTTTATTTTATTTTA
1 TTAAATTTAATTCAATATTTTATTTTATTTTA
237117 T
1 T
237118 ATTAATATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 7 0.23
32 20 0.67
33 3 0.10
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (32 bp):
TTAAATTTAATTCAATATTTTATTTTATTTTA
Found at i:237114 original size:22 final size:23
Alignment explanation
Indices: 237065--237127 Score: 64
Period size: 22 Copynumber: 2.9 Consensus size: 23
237055 AAATTATAAT
237065 TTAAATTTT-T-TT-ATATTTTA
1 TTAAATTTTATATTAATATTTTA
237085 TTAAA-TTTA-ATTCAATATTTTA
1 TTAAATTTTATATT-AATATTTTA
**
237107 TTTTATTTTATATTAATATTT
1 TTAAATTTTATATTAATATTT
237128 ATATATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
19 3 0.09
20 7 0.20
22 11 0.31
23 11 0.31
24 3 0.09
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (23 bp):
TTAAATTTTATATTAATATTTTA
Found at i:237541 original size:23 final size:23
Alignment explanation
Indices: 237512--237561 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
237502 ATTTTTAATA
* *
237512 TTTAATTTATTTTTAAAAATATT
1 TTTAATTTATATTCAAAAATATT
*
237535 TTTAATTTATATTCAAATATATT
1 TTTAATTTATATTCAAAAATATT
237558 TTTA
1 TTTA
237562 CTATAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTAATTTATATTCAAAAATATT
Found at i:246444 original size:27 final size:26
Alignment explanation
Indices: 246414--246469 Score: 60
Period size: 27 Copynumber: 2.1 Consensus size: 26
246404 ATTTAAATAT
246414 AAATACAAATTT-TTTTTATATATTCAA
1 AAATACAAATTTATTTTTA-A-ATTCAA
**
246441 AAATTTAAATTTAATTTTTAAATTCAA
1 AAATACAAATTT-ATTTTTAAATTCAA
246468 AA
1 AA
246470 TATCTCTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
27 18 0.72
28 1 0.04
29 6 0.24
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.46
Consensus pattern (26 bp):
AAATACAAATTTATTTTTAAATTCAA
Found at i:246591 original size:22 final size:23
Alignment explanation
Indices: 246566--246619 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
246556 TTTACCTTTT
*
246566 ATTATTTTA-AATAT-TTTAATTA
1 ATTATTTTATAATATATTTAA-AA
246588 ATTAAATTTTATAATATATTTAAAA
1 ATT--ATTTTATAATATATTTAAAA
246613 ATTATTT
1 ATTATTT
246620 CATACAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
22 3 0.11
23 4 0.15
24 6 0.22
25 9 0.33
26 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTATTTTATAATATATTTAAAA
Found at i:246615 original size:25 final size:24
Alignment explanation
Indices: 246569--246616 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
246559 ACCTTTTATT
*
246569 ATTTTAAATATTTTAATTAATTAA
1 ATTTTAAATATTTTAATAAATTAA
246593 ATTTTATAATATATTTAA-AAATTA
1 ATTTTA-AATAT-TTTAATAAATTA
246617 TTTCATACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 10 0.48
26 5 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
ATTTTAAATATTTTAATAAATTAA
Found at i:246699 original size:15 final size:16
Alignment explanation
Indices: 246661--246702 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
246651 AAGTTTTATC
246661 AATAATAAATATAAAAT
1 AATAA-AAATATAAAAT
246678 AATAAAAAT-TAAAAT
1 AATAAAAATATAAAAT
*
246693 TA-AAAAATAT
1 AATAAAAATAT
246703 TTTAATTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 6 0.26
15 8 0.35
16 4 0.17
17 5 0.22
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AATAAAAATATAAAAT
Found at i:246907 original size:51 final size:50
Alignment explanation
Indices: 246805--246907 Score: 129
Period size: 50 Copynumber: 2.0 Consensus size: 50
246795 TAAAGAATTA
* * *
246805 AAAAATAATTTTTATTTAAATTTAATTATAAAATATATAAATATTATTAT
1 AAAAATAAATTTTATTTAAATTTAATTATAAAATATATAAATAGTAATAT
*
246855 AAAAATAAATTTTATTTTAATATTAATTAT-AAATA-ATAATATGAGTAATAT
1 AAAAATAAATTTTATTTAAAT-TTAATTATAAAATATATAA-AT-AGTAATAT
246906 AA
1 AA
246908 GCATATTTGA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
49 4 0.09
50 26 0.57
51 16 0.35
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (50 bp):
AAAAATAAATTTTATTTAAATTTAATTATAAAATATATAAATAGTAATAT
Found at i:247157 original size:2 final size:2
Alignment explanation
Indices: 247136--247179 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
247126 TATTTATCCC
* *
247136 TA TA -A TA TA TA CA TA CA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
247177 TA T
1 TA T
247180 GATGATGATG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:247594 original size:17 final size:19
Alignment explanation
Indices: 247566--247606 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
247556 ATCAATTATA
247566 ATTATAATTAATTA-AAAT
1 ATTATAATTAATTACAAAT
247584 ATTAT-ATTAATTACAAAT
1 ATTATAATTAATTACAAAT
*
247602 TTTAT
1 ATTAT
247607 TTTTATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTATAATTAATTACAAAT
Found at i:247802 original size:31 final size:29
Alignment explanation
Indices: 247750--247818 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
247740 TTTACAAATA
* *
247750 TATTAAAATTTTAATACAAAAAATTATTTTT
1 TATT-AAATTTAAAT-CAAAAAATAATTTTT
247781 ATAATTAAATTTAAAT-AAAAAATAATTTTT
1 -T-ATTAAATTTAAATCAAAAAATAATTTTT
247811 TATTAAAT
1 TATTAAAT
247819 AAATATTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 7 0.21
29 1 0.03
30 13 0.38
32 10 0.29
33 3 0.09
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (29 bp):
TATTAAATTTAAATCAAAAAATAATTTTT
Found at i:247822 original size:32 final size:31
Alignment explanation
Indices: 247767--247827 Score: 79
Period size: 30 Copynumber: 1.9 Consensus size: 31
247757 ATTTTAATAC
* *
247767 AAAAAATTATTTTTATAATTAAAT-TTAAAT
1 AAAAAATAATTTTTATAAATAAATATTAAAT
247797 AAAAAATAATTTTTTATTAAATAAATATTAA
1 AAAAAATAA-TTTTTA-TAAATAAATATTAA
247828 TTTAAATTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 8 0.31
31 6 0.23
32 8 0.31
33 4 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
AAAAAATAATTTTTATAAATAAATATTAAAT
Found at i:248674 original size:16 final size:16
Alignment explanation
Indices: 248653--248699 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
248643 AATAATAACG
248653 TATAAAATTTATATAA
1 TATAAAATTTATATAA
*
248669 TAT-AAA-TTATTATAT
1 TATAAAATTTA-TATAA
*
248684 TTTAAAATTTATATAA
1 TATAAAATTTATATAA
248700 AATATATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
14 3 0.12
15 9 0.36
16 10 0.40
17 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TATAAAATTTATATAA
Found at i:248683 original size:17 final size:17
Alignment explanation
Indices: 248661--248732 Score: 55
Period size: 17 Copynumber: 4.5 Consensus size: 17
248651 CGTATAAAAT
248661 TTATATAATATAAATTA
1 TTATATAATATAAATTA
**
248678 TTATATTTTA-AAATT-
1 TTATATAATATAAATTA
* *
248693 TATATAAAATATATATTA
1 T-TATATAATATAAATTA
248711 TTATA-AA-AT-AATTA
1 TTATATAATATAAATTA
*
248725 TAATATAA
1 TTATATAA
248733 AAAAAATTAC
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
14 8 0.19
15 5 0.12
16 13 0.30
17 16 0.37
18 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTATATAATATAAATTA
Found at i:248690 original size:31 final size:32
Alignment explanation
Indices: 248655--248715 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 32
248645 TAATAACGTA
248655 TAAAATTTATAT-AATATAAATTATTATATTT
1 TAAAATTTATATAAATATAAATTATTATATTT
*
248686 TAAAATTTATATAAAATATATATTATTATA
1 TAAAATTTATAT-AAATATAAATTATTATA
248716 AAATAATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 12 0.44
33 15 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (32 bp):
TAAAATTTATATAAATATAAATTATTATATTT
Found at i:249054 original size:24 final size:25
Alignment explanation
Indices: 248990--249076 Score: 95
Period size: 24 Copynumber: 3.4 Consensus size: 25
248980 ATTGATATTT
*
248990 ATAAAATTAAATGTTTAAAATATTTAA
1 ATAAAATT-AATTTTTAAAATA-TTAA
249017 ATTAAAATTAATTTTTAAAATATTAA
1 A-TAAAATTAATTTTTAAAATATTAA
* * *
249043 A-ATAATTTATTTTTAAAATATTATT
1 ATAAAATTAATTTTTAAAATATTA-A
249068 ATAAAATTA
1 ATAAAATTA
249077 TTTAAATTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
24 20 0.39
25 1 0.02
26 10 0.20
27 13 0.25
28 7 0.14
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (25 bp):
ATAAAATTAATTTTTAAAATATTAA
Found at i:249072 original size:13 final size:13
Alignment explanation
Indices: 249056--249110 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 13
249046 AATTTATTTT
249056 TAAAATATTATTA
1 TAAAATATTATTA
249069 T-AAA-ATTATT-
1 TAAAATATTATTA
249079 T-AAAT-TTATTA
1 TAAAATATTATTA
*
249090 TATAATTATTA-TA
1 TA-AAATATTATTA
249103 TAAAATAT
1 TAAAATAT
249111 ATTTTTAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
10 9 0.26
11 7 0.20
12 8 0.23
13 8 0.23
14 3 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TAAAATATTATTA
Found at i:249076 original size:11 final size:11
Alignment explanation
Indices: 249062--249102 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
249052 TTTTTAAAAT
249062 ATTATTATAAA
1 ATTATTATAAA
249073 ATTATT-TAAA
1 ATTATTATAAA
* *
249083 TTTATTATATA
1 ATTATTATAAA
249094 ATTATTATA
1 ATTATTATA
249103 TAAAATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
ATTATTATAAA
Found at i:249089 original size:21 final size:22
Alignment explanation
Indices: 249058--249099 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
249048 TTTATTTTTA
249058 AAATATTATTATAAAATTATTT
1 AAATATTATTATAAAATTATTT
*
249080 AAAT-TTATTATATAATTATT
1 AAATATTATTATAAAATTATT
249100 ATATAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AAATATTATTATAAAATTATTT
Found at i:249100 original size:24 final size:25
Alignment explanation
Indices: 249044--249106 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 25
249034 AAATATTAAA
249044 ATAATTTATT-TTTAAAATATTATTAT
1 ATAA-TTATTATTT-AAATATTATTAT
249070 A-AA--ATTATTTAAAT-TTATTAT
1 ATAATTATTATTTAAATATTATTAT
*
249091 ATAATTATTATATAAA
1 ATAATTATTATTTAAA
249107 ATATATTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
21 8 0.25
22 9 0.28
23 3 0.09
24 9 0.28
25 2 0.06
26 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
ATAATTATTATTTAAATATTATTAT
Found at i:249249 original size:17 final size:16
Alignment explanation
Indices: 249208--249268 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 16
249198 AATTTTTTAT
249208 ATATAATAAATAATAAA
1 ATATAA-AAATAATAAA
*
249225 TAAATAAAAATAATAAA
1 -ATATAAAAATAATAAA
*
249242 ATATTAAAATTTATATAAA
1 ATA-TAAAA-ATA-ATAAA
249261 ATATAAAA
1 ATATAAAA
249269 TATTTTAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
16 2 0.05
17 15 0.41
18 12 0.32
19 8 0.22
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
ATATAAAAATAATAAA
Found at i:249740 original size:11 final size:11
Alignment explanation
Indices: 249719--249822 Score: 88
Period size: 11 Copynumber: 9.3 Consensus size: 11
249709 CAATTATGAG
249719 TAATA-AAATA
1 TAATATAAATA
249729 TAATATAAATA
1 TAATATAAATA
*
249740 TATATTAAAAATATA
1 TA-A-T-ATAA-ATA
249755 TAATATAAAT-
1 TAATATAAATA
249765 TAATATAAATA
1 TAATATAAATA
* * *
249776 TAAAAT-ATTT
1 TAATATAAATA
*
249786 TAAATATAATTA
1 T-AATATAAATA
249798 TAATATAAATA
1 TAATATAAATA
*
249809 TTATATAAATA
1 TAATATAAATA
249820 TAA
1 TAA
249823 AAATAATTCT
Statistics
Matches: 76, Mismatches: 10, Indels: 15
0.75 0.10 0.15
Matches are distributed among these distances:
10 18 0.24
11 39 0.51
12 8 0.11
13 2 0.03
14 4 0.05
15 5 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TAATATAAATA
Found at i:249915 original size:13 final size:14
Alignment explanation
Indices: 249893--249931 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
249883 TATTATTAAA
249893 TATATAAATATT-T
1 TATATAAATATTAT
*
249906 TATATTAATATTAT
1 TATATAAATATTAT
*
249920 TAAATAAATATT
1 TATATAAATATT
249932 GACATAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TATATAAATATTAT
Found at i:250052 original size:14 final size:13
Alignment explanation
Indices: 250016--250073 Score: 66
Period size: 13 Copynumber: 4.5 Consensus size: 13
250006 GTTATCATAA
*
250016 TTATATTAAATA-
1 TTATATAAAATAT
250028 TTATAT-AAATAT
1 TTATATAAAATAT
*
250040 TTATTTAATAATAT
1 TTATATAA-AATAT
*
250054 TAATATAAAATAT
1 TTATATAAAATAT
250067 TTATATA
1 TTATATA
250074 TTTAATAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
11 5 0.13
12 11 0.28
13 12 0.31
14 11 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTATATAAAATAT
Found at i:250076 original size:31 final size:32
Alignment explanation
Indices: 250041--250108 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
250031 TATAAATATT
* *
250041 TATTTAATAATA-T-TAATATAAAATATTTATA
1 TATTTAATAAAATTATAATAT-AAATATCTATA
*
250072 TATTTAATAAAATTATAATATAAATATCTATT
1 TATTTAATAAAATTATAATATAAATATCTATA
250104 TATTT
1 TATTT
250109 TTAAAAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 11 0.34
32 15 0.47
33 6 0.19
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (32 bp):
TATTTAATAAAATTATAATATAAATATCTATA
Found at i:250103 original size:28 final size:28
Alignment explanation
Indices: 250029--250105 Score: 75
Period size: 31 Copynumber: 2.6 Consensus size: 28
250019 TATTAAATAT
* *
250029 TATATAAATATTTATTTAATAATATTAA
1 TATATAAATATATATTTAATAAAATTAA
*
250057 TATAAAATATTTATATATTTAATAAAATT-A
1 TATATAA-A--TATATATTTAATAAAATTAA
*
250087 TAATATAAATATCTATTTA
1 T-ATATAAATATATATTTA
250106 TTTTTAAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
28 15 0.38
29 1 0.03
30 3 0.08
31 21 0.52
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (28 bp):
TATATAAATATATATTTAATAAAATTAA
Found at i:250320 original size:6 final size:5
Alignment explanation
Indices: 250291--250458 Score: 62
Period size: 5 Copynumber: 33.6 Consensus size: 5
250281 AATAATTTAA
* * * *
250291 AATAT AATTT TATA- AATAT AATAT ATATAT AAAAT AATTAA AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT A-ATAT AATAT AA-TAT AATAT AATAT
* * * * ** * *
250342 AGTATT AATAT ATTTT AAAAT TTTAT AATAT AA-AT TAT-T AATAT ATTA-
1 AATA-T AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
* ** * *
250390 AATATT AATAT ACATATT AAAAT TTTAT -TTAT AATTAT AATAT AATAA
1 AATA-T AATAT A-ATA-T AATAT AATAT AATAT AA-TAT AATAT AATAT
*
250438 AATAT -ATA- AAAAT AATAT AAT
1 AATAT AATAT AATAT AATAT AAT
250459 TATATATATT
Statistics
Matches: 116, Mismatches: 33, Indels: 28
0.66 0.19 0.16
Matches are distributed among these distances:
4 21 0.18
5 67 0.58
6 26 0.22
7 2 0.02
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.44
Consensus pattern (5 bp):
AATAT
Found at i:250372 original size:36 final size:34
Alignment explanation
Indices: 250301--250389 Score: 94
Period size: 33 Copynumber: 2.6 Consensus size: 34
250291 AATATAATTT
250301 TATAAA-TA-TAATATATATATAAAATAATTAAAA
1 TATAAATTATTAATATAT-TATAAAATAATTAAAA
* * *
250334 TATAATATAGTATTAATATATTTTAAAAT-TTTATAA
1 TATAA-AT--TATTAATATATTATAAAATAATTAAAA
250370 TATAAATTATTAATATATTA
1 TATAAATTATTAATATATTA
250390 AATATTAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
33 17 0.36
34 1 0.02
35 2 0.04
36 10 0.21
37 9 0.19
38 8 0.17
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (34 bp):
TATAAATTATTAATATATTATAAAATAATTAAAA
Found at i:250415 original size:58 final size:64
Alignment explanation
Indices: 250296--250458 Score: 153
Period size: 55 Copynumber: 2.8 Consensus size: 64
250286 TTTAAAATAT
*
250296 AATTTTATAAATATAATATATATATAAAATAATTAAAATATAATATAGTATTAATATATTTTAA
1 AATTTTATAAATATAATATATATATAAAATAATTAAAATATAATATAATATTAATATATTTTAA
*
250360 AATTTTAT-AATATAA-AT-TAT-TAATAT-ATT-AAATATTAATATACATATTAA-A-ATTTT-
1 AATTTTATAAATATAATATATATATAAAATAATTAAAATA-TAATATA-ATATTAATATATTTTA
250416 -
64 A
*
250416 -A-TTTATAATTAT-A-ATATA-ATAAAAT-ATATAAAA-ATAATATAAT
1 AATTTTATAAATATAATATATATATAAAATAAT-TAAAATATAATATAAT
250459 TATATATATT
Statistics
Matches: 88, Mismatches: 4, Indels: 24
0.76 0.03 0.21
Matches are distributed among these distances:
54 10 0.11
55 21 0.24
56 2 0.02
57 3 0.03
58 10 0.11
59 11 0.12
60 11 0.12
61 3 0.03
62 2 0.02
63 7 0.08
64 8 0.09
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.44
Consensus pattern (64 bp):
AATTTTATAAATATAATATATATATAAAATAATTAAAATATAATATAATATTAATATATTTTAA
Found at i:250441 original size:48 final size:47
Alignment explanation
Indices: 250318--250442 Score: 137
Period size: 48 Copynumber: 2.6 Consensus size: 47
250308 ATAATATATA
* * * * *
250318 TATAAAATAATTAAAATATAATATAGTATTAATATATTTTAAAATTT
1 TATAATATAATTATAATATAATAAAATATTAATATATATTAAAATTT
*
250365 TATAATATAAATTATTAATAT-ATTAAATATTAATATACATATTAAAATTT
1 TATAATAT-AATTA-TAATATAATAAAATATTAATAT--ATATTAAAATTT
*
250415 TAT-TTATAATTATAATATAATAAAATAT
1 TATAATATAATTATAATATAATAAAATAT
250443 ATAAAAATAA
Statistics
Matches: 65, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
47 13 0.20
48 30 0.46
49 8 0.12
50 14 0.22
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.46
Consensus pattern (47 bp):
TATAATATAATTATAATATAATAAAATATTAATATATATTAAAATTT
Found at i:251001 original size:18 final size:18
Alignment explanation
Indices: 250978--251013 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
250968 CGCAGTCCAT
250978 ACTGAAATTCTAGCTCAA
1 ACTGAAATTCTAGCTCAA
250996 ACTGAAATTCTAGCTCAA
1 ACTGAAATTCTAGCTCAA
251014 GAAATGGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.22, G:0.11, T:0.28
Consensus pattern (18 bp):
ACTGAAATTCTAGCTCAA
Found at i:252423 original size:28 final size:29
Alignment explanation
Indices: 252392--252458 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 29
252382 TGATTATTCG
* *
252392 ATATAAAATAATATAAAAA-ATAATTATA
1 ATATAAAATAATAAAAAAATATAAATATA
* *
252420 ATATGATATATTATAAAAAAATATAAATATA
1 ATAT-A-AAATAATAAAAAAATATAAATATA
252451 ATATAAAA
1 ATATAAAA
252459 ATATTAATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
28 4 0.13
29 3 0.10
30 12 0.39
31 12 0.39
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (29 bp):
ATATAAAATAATAAAAAAATATAAATATA
Found at i:253081 original size:24 final size:26
Alignment explanation
Indices: 253051--253114 Score: 80
Period size: 24 Copynumber: 2.5 Consensus size: 26
253041 ATGAGTTATT
*
253051 ATTTAATAAATAAAA-ATTATTT-AA
1 ATTTAATATATAAAATATTATTTAAA
*
253075 ATTTAAT-TATAAAATATTTTTTAAA
1 ATTTAATATATAAAATATTATTTAAA
253100 ATTTTAATATATAAA
1 A-TTTAATATATAAA
253115 TTAAATAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 6 0.18
24 13 0.38
25 3 0.09
26 6 0.18
27 6 0.18
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
ATTTAATATATAAAATATTATTTAAA
Found at i:256054 original size:2 final size:2
Alignment explanation
Indices: 256049--256095 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
256039 GAGCCCCCCT
256049 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
256091 TC TC T
1 TC TC T
256096 AAATGACCTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:256246 original size:2 final size:2
Alignment explanation
Indices: 256239--256269 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
256229 AATATGAGAA
256239 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
256270 ATCTAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:257320 original size:5 final size:5
Alignment explanation
Indices: 257310--257337 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
257300 TACAGATATA
257310 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
257338 TTGAGGGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:257584 original size:2 final size:2
Alignment explanation
Indices: 257577--257614 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
257567 GTAATTTTTA
257577 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
257615 GCGTCCGTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:258846 original size:16 final size:15
Alignment explanation
Indices: 258819--258850 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
258809 GTTAATAATA
258819 AATATAACATTATAT
1 AATATAACATTATAT
258834 AATATAACTATTATAT
1 AATATAAC-ATTATAT
258850 A
1 A
258851 TTAAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (15 bp):
AATATAACATTATAT
Found at i:260558 original size:2 final size:2
Alignment explanation
Indices: 260551--260585 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
260541 ACACAAACAC
260551 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
260586 AAGAACAAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:264136 original size:21 final size:20
Alignment explanation
Indices: 264099--264137 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
264089 AAAGCGCCAT
* *
264099 ATAATATTTTAAGAGGCAAA
1 ATAATATTTCAAAAGGCAAA
264119 ATAATAATTTCAAAAGGCA
1 ATAAT-ATTTCAAAAGGCA
264138 GAGTAGGACA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.51, C:0.08, G:0.13, T:0.28
Consensus pattern (20 bp):
ATAATATTTCAAAAGGCAAA
Found at i:268459 original size:2 final size:2
Alignment explanation
Indices: 268452--268480 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
268442 CACAAAAACA
268452 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
268481 AACACCTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:268589 original size:17 final size:18
Alignment explanation
Indices: 268557--268612 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 18
268547 ACCAAAAAAG
268557 AAATAAAATCGGAAAAAT-A
1 AAATAAAATC--AAAAATGA
*
268576 ATATAAAATC-AAAATGA
1 AAATAAAATCAAAAATGA
*
268593 AAATAAAATTAAAAA-GA
1 AAATAAAATCAAAAATGA
268610 AAA
1 AAA
268613 GGAAAAAGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
16 5 0.16
17 14 0.44
18 4 0.12
19 9 0.28
ACGTcount: A:0.71, C:0.04, G:0.07, T:0.18
Consensus pattern (18 bp):
AAATAAAATCAAAAATGA
Found at i:268749 original size:3 final size:3
Alignment explanation
Indices: 268741--268767 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
268731 AGAGAGAGAG
268741 AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA
268768 GAGATGTGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:270853 original size:51 final size:51
Alignment explanation
Indices: 270766--270863 Score: 133
Period size: 51 Copynumber: 1.9 Consensus size: 51
270756 ATAGTCGAGC
* **
270766 TCTATGTTACTTGGATTAGGTGTGAGTGCCAAAAATAAGTAAATGTCTGAT
1 TCTATGTTACTTGGACTAGGTGTGAGCACCAAAAATAAGTAAATGTCTGAT
* * * *
270817 TCTATGTTACTTGGACTATGTGTGAGCACCAGAAATAGGTACATGTC
1 TCTATGTTACTTGGACTAGGTGTGAGCACCAAAAATAAGTAAATGTC
270864 CAATACATGT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (51 bp):
TCTATGTTACTTGGACTAGGTGTGAGCACCAAAAATAAGTAAATGTCTGAT
Found at i:272589 original size:215 final size:212
Alignment explanation
Indices: 272218--272648 Score: 544
Period size: 215 Copynumber: 2.0 Consensus size: 212
272208 AGTTTGGTAG
* ** ** * *
272218 GATAACCAGGAATGGAATTCAATGCAACCATTCCAGTGATGTCTTCACTGTTAAAGAATTTTAGC
1 GATAACCAGGAATGGAATCCAACCCAACCATTCCAGTGATGTCTTCACCATGAAAGAACTTTAGC
* * * * *
272283 AAGGAGCAAACTCCACAAGCGTTTTCTGAATATATGTTTAAAAACACGAACTCCCCTCTTGCACG
66 AAGGAGAAAACTCAACAAGCATTTTCTAAATATATGTTTAAAAACACGAACTCCCCTCTAGCACG
* * * *
272348 ACTTTTTAGATGCATGGAACAAACAACATTGATCTAAGTTTAATGGCTTCCA-TTTGTAGATTTT
131 ACTTTTTAGATGCATGGAACAAACAAC----ATCAAAGTGTAAGGGCTGCCATTTTGTAGATTTT
*
272412 GGTGGTGAAGACCCGAATGAT
192 GGTGGTGAAGACCCAAATGAT
* ** * *
272433 GATAACCAGGAATGGAATCCAACCCAACTATTGTAGTGATGTCTTCACCATGACATAACTTTAGC
1 GATAACCAGGAATGGAATCCAACCCAACCATTCCAGTGATGTCTTCACCATGAAAGAACTTTAGC
** *
272498 GTGGAGAAAACTGCAAC-AGCATTTTCTAAATATATGTTTAAAAACAGGAACTCCCCTCTAGCAA
66 AAGGAGAAAACT-CAACAAGCATTTTCTAAATATATGTTTAAAAACACGAACTCCCCTCTAGC-A
* *
272562 TG-CTTTTTAGATGCATGGAACAAACAACATCAAAGTGTAAGGGCTGCCATTTTGTATATTTTGG
129 CGACTTTTTAGATGCATGGAACAAACAACATCAAAGTGTAAGGGCTGCCATTTTGTAGATTTTGG
272626 TGGTGAAGACCCAAATGAT
194 TGGTGAAGACCCAAATGAT
272645 GATA
1 GATA
272649 TCAGCAGTAT
Statistics
Matches: 186, Mismatches: 27, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
211 17 0.09
212 35 0.19
215 129 0.69
216 5 0.03
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (212 bp):
GATAACCAGGAATGGAATCCAACCCAACCATTCCAGTGATGTCTTCACCATGAAAGAACTTTAGC
AAGGAGAAAACTCAACAAGCATTTTCTAAATATATGTTTAAAAACACGAACTCCCCTCTAGCACG
ACTTTTTAGATGCATGGAACAAACAACATCAAAGTGTAAGGGCTGCCATTTTGTAGATTTTGGTG
GTGAAGACCCAAATGAT
Found at i:289622 original size:31 final size:30
Alignment explanation
Indices: 289572--289667 Score: 97
Period size: 31 Copynumber: 3.1 Consensus size: 30
289562 TTTTTAAATT
*
289572 ATTTATTTTTATATATTTTTAATATATAATA
1 ATTTATATTTATAT-TTTTTAATATATAATA
** *
289603 ATTTATAATTTATATTTTTTAATATATTTTT
1 ATTTAT-ATTTATATTTTTTAATATATAATA
*
289634 A-TTATATTTTTA-TTTTTAATATTATATATA
1 ATTTATATTTATATTTTTTAATA-TATA-ATA
289664 ATTT
1 ATTT
289668 TTTTTATTTA
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
28 9 0.17
29 9 0.17
30 6 0.11
31 22 0.42
32 7 0.13
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (30 bp):
ATTTATATTTATATTTTTTAATATATAATA
Done.