Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold167
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: 4199719
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.33
Warning! 197959 characters in sequence are not A, C, G, or T
File 19 of 22
Found at i:3163583 original size:18 final size:16
Alignment explanation
Indices: 3163560--3163612 Score: 54
Period size: 15 Copynumber: 3.2 Consensus size: 16
3163550 TATTATATAA
3163560 TATATATTAATTTTATAT
1 TATATA-TAATTTT-TAT
*
3163578 TTTATATAATTTTTAT
1 TATATATAATTTTTAT
**
3163594 TATATA-AAAATTTAT
1 TATATATAATTTTTAT
3163609 TATA
1 TATA
3163613 ATATTATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
15 11 0.35
16 8 0.26
17 7 0.23
18 5 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATATATAATTTTTAT
Found at i:3163606 original size:27 final size:27
Alignment explanation
Indices: 3163576--3163632 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
3163566 TTAATTTTAT
* *
3163576 ATTTTA-TATAATTTTTATTATATAAAA
1 ATTTTATTATAA-TATTATAATATAAAA
3163603 A-TTTATTATAATATTATAATATAAAA
1 ATTTTATTATAATATTATAATATAAAA
3163629 ATTT
1 ATTT
3163633 AAAATTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 18 0.69
27 8 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
ATTTTATTATAATATTATAATATAAAA
Found at i:3163705 original size:14 final size:15
Alignment explanation
Indices: 3163670--3163729 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 15
3163660 AAAATTTAAC
*
3163670 AAAAATATTAAATTAAT
1 AAAAATA-TATATT-AT
3163687 AAAAATATATATT-T
1 AAAAATATATATTAT
3163701 AAAAATA-A-ATTAT
1 AAAAATATATATTAT
3163714 AAAAAATATAATATTA
1 -AAAAATAT-ATATTA
3163730 ACATATTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
12 3 0.08
13 2 0.05
14 15 0.41
16 6 0.16
17 11 0.30
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AAAAATATATATTAT
Found at i:3163768 original size:10 final size:10
Alignment explanation
Indices: 3163761--3163785 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3163751 TTATATATTT
3163761 ATAAATATAA
1 ATAAATATAA
3163771 ATAAATATAA
1 ATAAATATAA
3163781 ATAAA
1 ATAAA
3163786 ATTTATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
ATAAATATAA
Found at i:3163811 original size:35 final size:35
Alignment explanation
Indices: 3163748--3163815 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 35
3163738 AAATCAATTT
3163748 AAATTATATATTTATAAATATAAATAAATATAAATA
1 AAATTATATATTTATAAATATAAATAAAT-TAAATA
* *
3163784 AAATT-TATATTTAT-ATTTTAAATTAAATTAAA
1 AAATTATATATTTATAAATATAAA-TAAATTAAA
3163816 ATTTTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 10 0.34
35 14 0.48
36 5 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (35 bp):
AAATTATATATTTATAAATATAAATAAATTAAATA
Found at i:3163865 original size:17 final size:18
Alignment explanation
Indices: 3163835--3163872 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
3163825 ATATTTATTA
*
3163835 TTAATATCATATTTAAAT
1 TTAATATCAAATTTAAAT
*
3163853 TTAA-ATCAAATTTAATT
1 TTAATATCAAATTTAAAT
3163870 TTA
1 TTA
3163873 TTTAATTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (18 bp):
TTAATATCAAATTTAAAT
Found at i:3165178 original size:3 final size:3
Alignment explanation
Indices: 3165170--3165211 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
3165160 CTCCTTTGTT
* *
3165170 GGA GGA GGA GGA GGA AGA GGAA GTA -GA GGA GGA GGA GGA GGA
1 GGA GGA GGA GGA GGA GGA GG-A GGA GGA GGA GGA GGA GGA GGA
3165212 CGAAGAGTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 1 0.03
3 30 0.91
4 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.60, T:0.02
Consensus pattern (3 bp):
GGA
Found at i:3171377 original size:15 final size:15
Alignment explanation
Indices: 3171357--3171386 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3171347 GGGGGACACG
*
3171357 TGAAAGGAAAGGGAA
1 TGAAAGGAAAAGGAA
3171372 TGAAAGGAAAAGGAA
1 TGAAAGGAAAAGGAA
3171387 GGATTCTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.37, T:0.07
Consensus pattern (15 bp):
TGAAAGGAAAAGGAA
Found at i:3171933 original size:40 final size:40
Alignment explanation
Indices: 3171874--3171976 Score: 172
Period size: 40 Copynumber: 2.6 Consensus size: 40
3171864 TGACTGCCCG
* *
3171874 GTGAATACCAAGCGTTCCATGGAGGAAGT-TAATCGCCCCT
1 GTGAATACCAAGCGCTCCATGGAGGAACTGT-ATCGCCCCT
3171914 GTGAATACCAAGCGCTCCATGGAGGAACTGTATCGCCCCT
1 GTGAATACCAAGCGCTCCATGGAGGAACTGTATCGCCCCT
3171954 GTGAATACCAAGCGCTCCATGGA
1 GTGAATACCAAGCGCTCCATGGA
3171977 AGGAGTATGC
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
40 59 0.98
41 1 0.02
ACGTcount: A:0.27, C:0.27, G:0.25, T:0.20
Consensus pattern (40 bp):
GTGAATACCAAGCGCTCCATGGAGGAACTGTATCGCCCCT
Found at i:3173452 original size:30 final size:30
Alignment explanation
Indices: 3173416--3173533 Score: 200
Period size: 30 Copynumber: 3.9 Consensus size: 30
3173406 TCGAAGGATA
*
3173416 TGTCATCGAGATGTTGAGACTTTTGGAGTT
1 TGTCATCGAGATGTTGAGAATTTTGGAGTT
* *
3173446 TGTCATCGAGATGTTCAGACTTTTGGAGTT
1 TGTCATCGAGATGTTGAGAATTTTGGAGTT
*
3173476 TGTCATCGAGATGTTGAGAATTTTGGAGTA
1 TGTCATCGAGATGTTGAGAATTTTGGAGTT
3173506 TGTCATCGAGATGTTGAGAATTTTGGAG
1 TGTCATCGAGATGTTGAGAATTTTGGAG
3173534 AAATGGGGCG
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 84 1.00
ACGTcount: A:0.23, C:0.09, G:0.30, T:0.38
Consensus pattern (30 bp):
TGTCATCGAGATGTTGAGAATTTTGGAGTT
Found at i:3180139 original size:56 final size:55
Alignment explanation
Indices: 3180036--3180140 Score: 138
Period size: 56 Copynumber: 1.9 Consensus size: 55
3180026 GTTTTACGGC
* * *
3180036 TGAAACTGATTTGGGCTTTTGGTCCGGTTAGTTAATGACATAGCAATGACTTCAT
1 TGAAACTGATTTGGACTTTTGGTCCAGTTAGTTAATGACATAACAATGACTTCAT
* * **
3180091 TGAAATTGATTTGGATTTTTGGGTCCAGTTAGTTAATGGTATAACAATGA
1 TGAAACTGATTTGGACTTTT-GGTCCAGTTAGTTAATGACATAACAATGA
3180141 GCTCAGTTTC
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
55 17 0.40
56 25 0.60
ACGTcount: A:0.28, C:0.10, G:0.24, T:0.38
Consensus pattern (55 bp):
TGAAACTGATTTGGACTTTTGGTCCAGTTAGTTAATGACATAACAATGACTTCAT
Found at i:3180282 original size:13 final size:13
Alignment explanation
Indices: 3180266--3180290 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3180256 TAAACATATG
3180266 AAATAATTAAAAA
1 AAATAATTAAAAA
3180279 AAATAATTAAAA
1 AAATAATTAAAA
3180291 TTTTTAAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAATTAAAAA
Found at i:3186069 original size:17 final size:18
Alignment explanation
Indices: 3186033--3186070 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3186023 ACTTATCATG
* *
3186033 TCTTTTGCATCATCTTTC
1 TCTTTTGCAACATATTTC
3186051 TCTTTTGCAAC-TATTTC
1 TCTTTTGCAACATATTTC
3186068 TCT
1 TCT
3186071 CGCCATAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.13, C:0.26, G:0.05, T:0.55
Consensus pattern (18 bp):
TCTTTTGCAACATATTTC
Found at i:3187888 original size:12 final size:12
Alignment explanation
Indices: 3187858--3187906 Score: 71
Period size: 12 Copynumber: 4.1 Consensus size: 12
3187848 TTTGGCCTTC
*
3187858 TTTTCTTTTTCC
1 TTTTCTTTTTCT
* *
3187870 TTATCTTCTTCT
1 TTTTCTTTTTCT
3187882 TTTTCTTTTTCT
1 TTTTCTTTTTCT
3187894 TTTTCTTTTTCT
1 TTTTCTTTTTCT
3187906 T
1 T
3187907 CTCCTTCTCC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTCTTTTTCT
Found at i:3187905 original size:18 final size:18
Alignment explanation
Indices: 3187858--3187906 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
3187848 TTTGGCCTTC
*
3187858 TTTTCTTTTTCCTTATCT
1 TTTTCTTTTTCTTTATCT
* *
3187876 TCTTCTTTTTCTTTTTCT
1 TTTTCTTTTTCTTTATCT
3187894 TTTTCTTTTTCTT
1 TTTTCTTTTTCTT
3187907 CTCCTTCTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTCTTTTTCTTTATCT
Found at i:3192563 original size:19 final size:21
Alignment explanation
Indices: 3192514--3192564 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
3192504 TATTTTTATT
*
3192514 TAAATATAAATATAAAATATA
1 TAAATATTAATATAAAATATA
3192535 TAAATATTAATATAAAA-ATA
1 TAAATATTAATATAAAATATA
*
3192555 -AATTATTAAT
1 TAAATATTAAT
3192565 TTTATAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 9 0.32
20 3 0.11
21 16 0.57
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TAAATATTAATATAAAATATA
Found at i:3199226 original size:2 final size:2
Alignment explanation
Indices: 3199219--3199267 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
3199209 ATGGTGAATT
3199219 TA TA TA TA TA TA TA TA TA 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
3199261 TA TA TA T
1 TA TA TA T
3199268 TTTAAGATCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3199335 original size:45 final size:45
Alignment explanation
Indices: 3199286--3199371 Score: 102
Period size: 45 Copynumber: 1.9 Consensus size: 45
3199276 CTAAATCGGG
* *
3199286 TTTATATATAT-ATATATATTAAAAAATAATTTTTATATTAAAATT
1 TTTATATATATAAAATA-AATAAAAAATAATTTTTATATTAAAATT
* * * *
3199331 TTTATTTTTATAAAATAAATAAAATATTATTTTTATATTAA
1 TTTATATATATAAAATAAATAAAAAATAATTTTTATATTAA
3199372 TATTAATAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
45 30 0.88
46 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (45 bp):
TTTATATATATAAAATAAATAAAAAATAATTTTTATATTAAAATT
Found at i:3199452 original size:22 final size:24
Alignment explanation
Indices: 3199408--3199472 Score: 73
Period size: 23 Copynumber: 2.8 Consensus size: 24
3199398 TTTAGATTTA
* * *
3199408 TATT-TATATTTATATTATTTTAT
1 TATTATATATTTAAATAATATTAT
3199431 TATTATAT-TTTAAA-AATATTAT
1 TATTATATATTTAAATAATATTAT
*
3199453 TATTTTATATTTAAATAATA
1 TATTATATATTTAAATAATA
3199473 ATTTACGTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 13 0.37
23 15 0.43
24 7 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TATTATATATTTAAATAATATTAT
Found at i:3199460 original size:24 final size:24
Alignment explanation
Indices: 3199411--3199477 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
3199401 AGATTTATAT
*
3199411 TTATATTT--ATATTATTTTATTA
1 TTATATTTAAATAATATTTTATTA
3199433 TTATATTTTAAA-AATATTATTATT-
1 TTATA-TTTAAATAATATT-TTATTA
*
3199457 TTATATTTAAATAATAATTTA
1 TTATATTTAAATAATATTTTA
3199478 CGTTAAATAC
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
22 5 0.13
23 12 0.32
24 15 0.39
25 6 0.16
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TTATATTTAAATAATATTTTATTA
Found at i:3199828 original size:16 final size:15
Alignment explanation
Indices: 3199806--3199859 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 15
3199796 AATCTAAATT
3199806 TAAAAAAGTTTGAATCC
1 TAAAAAA-TTTGAAT-C
* *
3199823 AAAAAAATTTGAATT
1 TAAAAAATTTGAATC
3199838 TAAAATAATTTGAATC
1 TAAAA-AATTTGAATC
3199854 TAAAAA
1 TAAAAA
3199860 GACTTAAACT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 5 0.16
16 21 0.66
17 6 0.19
ACGTcount: A:0.56, C:0.06, G:0.07, T:0.31
Consensus pattern (15 bp):
TAAAAAATTTGAATC
Found at i:3200238 original size:13 final size:13
Alignment explanation
Indices: 3200220--3200263 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
3200210 ATCTAGAATT
*
3200220 TAAAATAATAAAA
1 TAAAATAAAAAAA
*
3200233 TAAAATAACAAAA
1 TAAAATAAAAAAA
*
3200246 TAAATTAAAAAAA
1 TAAAATAAAAAAA
3200259 TAAAA
1 TAAAA
3200264 GCTGTAACAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.20
Consensus pattern (13 bp):
TAAAATAAAAAAA
Found at i:3200245 original size:21 final size:21
Alignment explanation
Indices: 3200221--3200261 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3200211 TCTAGAATTT
3200221 AAAAT-AATAAAATAAAATAAC
1 AAAATAAATAAAA-AAAATAAC
*
3200242 AAAATAAATTAAAAAAATAA
1 AAAATAAATAAAAAAAATAA
3200262 AAGCTGTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (21 bp):
AAAATAAATAAAAAAAATAAC
Found at i:3200344 original size:10 final size:10
Alignment explanation
Indices: 3200331--3200355 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3200321 AGCAATATAG
3200331 TATAATAGAA
1 TATAATAGAA
3200341 TATAATAGAA
1 TATAATAGAA
3200351 TATAA
1 TATAA
3200356 AGTTAACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (10 bp):
TATAATAGAA
Found at i:3200352 original size:15 final size:16
Alignment explanation
Indices: 3200315--3200352 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
3200305 ATGCTATATT
*
3200315 TAGAATAGCAATATAG
1 TAGAATAGCAATATAA
*
3200331 TATAATAG-AATATAA
1 TAGAATAGCAATATAA
3200346 TAGAATA
1 TAGAATA
3200353 TAAAGTTAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.55, C:0.03, G:0.13, T:0.29
Consensus pattern (16 bp):
TAGAATAGCAATATAA
Found at i:3201144 original size:24 final size:23
Alignment explanation
Indices: 3201109--3201156 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
3201099 ATTAGTTAAA
3201109 ATTAAAAGTATTTTTAAATATTTT
1 ATTAAAAGTA-TTTTAAATATTTT
*
3201133 ATTAAATA-TATTTTAAATTTTTT
1 ATTAAA-AGTATTTTAAATATTTT
3201156 A
1 A
3201157 ATATTAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 13 0.59
24 8 0.36
25 1 0.05
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
ATTAAAAGTATTTTAAATATTTT
Found at i:3201327 original size:18 final size:17
Alignment explanation
Indices: 3201306--3201342 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
3201296 ATTTAAAAAT
*
3201306 TTAATTTTATATAATAAA
1 TTAATTATATAT-ATAAA
3201324 TTAATTATATATATAAA
1 TTAATTATATATATAAA
3201341 TT
1 TT
3201343 TCAATTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTAATTATATATATAAA
Found at i:3201668 original size:14 final size:14
Alignment explanation
Indices: 3201634--3201674 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3201624 AGAGTTAGTA
3201634 TTATATTATTAAATT
1 TTATATT-TTAAATT
* *
3201649 TAATATTTTAATTT
1 TTATATTTTAAATT
3201663 TTATATTTTAAA
1 TTATATTTTAAA
3201675 AATAATAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTATATTTTAAATT
Found at i:3201712 original size:18 final size:17
Alignment explanation
Indices: 3201671--3201718 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
3201661 TTTTATATTT
*
3201671 TAAAAATAATAAAATAAA
1 TAAAAATAAT-TAATAAA
3201689 TAAAAATAATTAATAATA
1 TAAAAATAATTAATAA-A
3201707 TTAAAAA-AATTA
1 -TAAAAATAATTA
3201719 TTTAAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 5 0.19
18 16 0.59
19 6 0.22
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAAATAATTAATAAA
Found at i:3201715 original size:22 final size:23
Alignment explanation
Indices: 3201677--3201766 Score: 64
Period size: 22 Copynumber: 4.0 Consensus size: 23
3201667 ATTTTAAAAA
*
3201677 TAATAA-AATAAATAAAAATAAT
1 TAATAATATTAAATAAAAATAAT
* *
3201699 TAATAATATTAAA-AAAATTATT
1 TAATAATATTAAATAAAAATAAT
3201721 TAA-AATATTAATATAATATAA-AAT
1 TAATAATATTAA-ATAA-A-AATAAT
* *
3201745 T-ATATATTTTATATAAAAATAA
1 TAATA-ATATTAAATAAAAATAA
3201767 GATTAAATTA
Statistics
Matches: 53, Mismatches: 7, Indels: 15
0.71 0.09 0.20
Matches are distributed among these distances:
21 8 0.15
22 19 0.36
23 11 0.21
24 9 0.17
25 6 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
TAATAATATTAAATAAAAATAAT
Found at i:3201716 original size:21 final size:21
Alignment explanation
Indices: 3201690--3201731 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3201680 TAAAATAAAT
3201690 AAAAA-TAATTAATAATATTAA
1 AAAAATTAATTAA-AATATTAA
*
3201711 AAAAATTATTTAAAATATTAA
1 AAAAATTAATTAAAATATTAA
3201732 TATAATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAAATTAATTAAAATATTAA
Found at i:3201841 original size:24 final size:23
Alignment explanation
Indices: 3201783--3201845 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 23
3201773 ATTATCAATC
3201783 AAATTTAAGATATTT-T-TTATATA
1 AAATTTAA-A-ATTTATATTATATA
3201806 AAATTTAAAATTTATATTATATA
1 AAATTTAAAATTTATATTATATA
*
3201829 ATATATTAAAATTTATA
1 AAAT-TTAAAATTTATA
3201846 AAAATTTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
21 4 0.11
22 2 0.06
23 18 0.50
24 12 0.33
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
AAATTTAAAATTTATATTATATA
Found at i:3201858 original size:24 final size:23
Alignment explanation
Indices: 3201801--3201859 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
3201791 GATATTTTTT
**
3201801 ATATAAA-ATTTAAAATTTATATT
1 ATATAAATA-TTAAAATTTATAAA
3201824 ATATAATATATTAAAATTTATAAAA
1 ATATAA-ATATTAAAATTTAT-AAA
*
3201849 ATTTAAATATT
1 ATATAAATATT
3201860 TTTTAATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 6 0.20
24 17 0.57
25 7 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
ATATAAATATTAAAATTTATAAA
Found at i:3202557 original size:2 final size:2
Alignment explanation
Indices: 3202552--3202601 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
3202542 TTATATACAT
3202552 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3202594 AG AG AG AG
1 AG AG AG AG
3202602 GGAAAAAAGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3203006 original size:22 final size:22
Alignment explanation
Indices: 3202980--3203022 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
3202970 TTATTTGATG
*
3202980 TTAAAATTTAAAGATAAAATTA
1 TTAAAATTTAAAAATAAAATTA
3203002 TTAAAATTTAAAAATAAAATT
1 TTAAAATTTAAAAATAAAATT
3203023 TTTATCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
TTAAAATTTAAAAATAAAATTA
Found at i:3203128 original size:16 final size:15
Alignment explanation
Indices: 3203078--3203129 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 15
3203068 ATTTTACACT
*
3203078 TAATAATAATAAATTA
1 TAATATTAATAAA-TA
*
3203094 TCATATTAATAATAATA
1 TAATATTAAT-A-AATA
3203111 TAATATTTAATAAATA
1 TAATA-TTAATAAATA
3203127 TAA
1 TAA
3203130 AATAATTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 15 0.50
17 8 0.27
18 7 0.23
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (15 bp):
TAATATTAATAAATA
Found at i:3203133 original size:18 final size:18
Alignment explanation
Indices: 3203077--3203133 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 18
3203067 TATTTTACAC
3203077 TTAATAATAATAAATTATCAT
1 TTAATAATAATAAA--AT-AT
*
3203098 ATTAATAATAATATAATAT
1 -TTAATAATAATAAAATAT
3203117 TTAATAA-ATATAAAATA
1 TTAATAATA-ATAAAATA
3203134 ATTATATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 1 0.03
18 14 0.44
19 2 0.06
20 2 0.06
22 13 0.41
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
TTAATAATAATAAAATAT
Found at i:3204755 original size:252 final size:249
Alignment explanation
Indices: 3204306--3204767 Score: 683
Period size: 252 Copynumber: 1.8 Consensus size: 249
3204296 CGACGACATG
* * * * *
3204306 GAGCAAGCTCCAACAAGTTCAGAAGTAGGTAACGGAGCTACGCCCGTCTCTGAAGGCAACACGTC
1 GAGCAAGCTCCAACAACTTCAGAAGTAGGTAACGGAACTACGCCCATCTCTGAAGACAACACATC
** *
3204371 AGCTATGGTGACTGACCCTGAAGGTTCGCAGAATTTACCAAGGTTTAGGCGAACTGACTCGATTG
66 AGCTATGGTGACTGACCCTGAAGGTTCGCAGAATTTACCAAGAATTAGGCGAACTGACTCGATGG
* * * ** *
3204436 GTGTTCAACTTCGACCAAGGAGATTACTATCTGGAAATTGGAGTGCCGGAGAACTTCTTCTTGAA
131 GTGCTCAACTTCGACCAAGGAGATTACCATCTAGAAATTGGAGTGCAAGAGAACTTCTTCCTGAA
*
3204501 GATGTTGATGAAGATGCCACTATTCCAAATGGAGCAAGCAACTTCCACCAAGGA
196 GATGTTGACGAAGATGCCACTATTCCAAATGGAGCAAGCAACTTCCACCAAGGA
* * * *
3204555 GAGCAAGCTCCAACTACTTCAGAAGTAGGTACCGGAATTGCGCCCATCTCTGAAGACAACACATC
1 GAGCAAGCTCCAACAACTTCAGAAGTAGGTAACGGAACTACGCCCATCTCTGAAGACAACACATC
* *
3204620 AGCTACT-GTGACTGACCCTGAAGAAGGTTCGCTGAATTTACCAAGAATTAGGCGAACTGATTCG
66 AGCTA-TGGTGACTGACCCT---GAAGGTTCGCAGAATTTACCAAGAATTAGGCGAACTGACTCG
*
3204684 ATGGGTGCTCAACTTCGACCAAGGAGATTACCATCTAGAAATTTGAGTGCAAGAGAACTTCTTCC
127 ATGGGTGCTCAACTTCGACCAAGGAGATTACCATCTAGAAATTGGAGTGCAAGAGAACTTCTTCC
3204749 TGAAGATGTTGACGAAGAT
192 TGAAGATGTTGACGAAGAT
3204768 CCAGATGCTT
Statistics
Matches: 187, Mismatches: 22, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
249 73 0.39
250 1 0.01
252 113 0.60
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.23
Consensus pattern (249 bp):
GAGCAAGCTCCAACAACTTCAGAAGTAGGTAACGGAACTACGCCCATCTCTGAAGACAACACATC
AGCTATGGTGACTGACCCTGAAGGTTCGCAGAATTTACCAAGAATTAGGCGAACTGACTCGATGG
GTGCTCAACTTCGACCAAGGAGATTACCATCTAGAAATTGGAGTGCAAGAGAACTTCTTCCTGAA
GATGTTGACGAAGATGCCACTATTCCAAATGGAGCAAGCAACTTCCACCAAGGA
Found at i:3209513 original size:13 final size:12
Alignment explanation
Indices: 3209468--3209511 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
3209458 TATATTTAAC
*
3209468 AATAATTATAAA
1 AATATTTATAAA
3209480 AATAAGTTTAT-AA
1 AAT-A-TTTATAAA
3209493 AATATTTATAAA
1 AATATTTATAAA
3209505 AATATTT
1 AATATTT
3209512 TAATAACAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
11 5 0.18
12 13 0.46
13 6 0.21
14 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (12 bp):
AATATTTATAAA
Found at i:3209605 original size:14 final size:14
Alignment explanation
Indices: 3209588--3209623 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 14
3209578 TATTATTTTG
3209588 TTTATATAACAGTA
1 TTTATATAACAGTA
3209602 TTTACATATAACAGTA
1 TTT--ATATAACAGTA
3209618 TTTATA
1 TTTATA
3209624 AAATAAGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 6 0.30
16 14 0.70
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (14 bp):
TTTATATAACAGTA
Found at i:3209612 original size:16 final size:16
Alignment explanation
Indices: 3209591--3209621 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3209581 TATTTTGTTT
3209591 ATATAACAGTATTTAC
1 ATATAACAGTATTTAC
3209607 ATATAACAGTATTTA
1 ATATAACAGTATTTA
3209622 TAAAATAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (16 bp):
ATATAACAGTATTTAC
Found at i:3209989 original size:2 final size:2
Alignment explanation
Indices: 3209977--3210015 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3209967 AAACTCACGT
*
3209977 TC TC CC TC 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 TC TC TC TC T
3210016 TGTTTTCTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:3210885 original size:20 final size:20
Alignment explanation
Indices: 3210860--3210899 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3210850 TCAAAGAAAG
3210860 GTCAAAGAAACATCATAATA
1 GTCAAAGAAACATCATAATA
3210880 GTCAAAGAAACATCATAATA
1 GTCAAAGAAACATCATAATA
3210900 AAGTAAGTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.15, G:0.10, T:0.20
Consensus pattern (20 bp):
GTCAAAGAAACATCATAATA
Found at i:3212040 original size:2 final size:2
Alignment explanation
Indices: 3212033--3212067 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3212023 ATTGAAAAGG
3212033 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
3212068 GCACACGTAT
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:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3213892 original size:5 final size:5
Alignment explanation
Indices: 3213882--3213910 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
3213872 TTTATATAGA
3213882 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
3213911 TTATTGCCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:3214353 original size:14 final size:14
Alignment explanation
Indices: 3214334--3214361 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3214324 GCCAATCAGG
3214334 GTCATTATTAGAGA
1 GTCATTATTAGAGA
3214348 GTCATTATTAGAGA
1 GTCATTATTAGAGA
3214362 ACCGAAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (14 bp):
GTCATTATTAGAGA
Found at i:3219970 original size:14 final size:13
Alignment explanation
Indices: 3219951--3219981 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
3219941 GTCATTTCCA
3219951 TTTTCTTTTTTTT
1 TTTTCTTTTTTTT
3219964 CTTTTCTTTTTTTT
1 -TTTTCTTTTTTTT
3219978 TTTT
1 TTTT
3219982 AATAATTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTCTTTTTTTT
Found at i:3220961 original size:19 final size:19
Alignment explanation
Indices: 3220926--3220972 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
3220916 AAATATATAA
*
3220926 ATTGCTTTTATTTTATATT
1 ATTGTTTTTATTTTATATT
*
3220945 TTTGTATTTTA-TTTATATT
1 ATTGT-TTTTATTTTATATT
3220964 ATTGTTTTT
1 ATTGTTTTT
3220973 GATAATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 4 0.17
19 15 0.62
20 5 0.21
ACGTcount: A:0.19, C:0.02, G:0.06, T:0.72
Consensus pattern (19 bp):
ATTGTTTTTATTTTATATT
Found at i:3221359 original size:2 final size:2
Alignment explanation
Indices: 3221352--3221377 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3221342 TGGAGTTGTT
3221352 TA 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
3221378 AGCATGAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3221604 original size:6 final size:6
Alignment explanation
Indices: 3221593--3221626 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
3221583 ATTAGTTACA
3221593 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAA
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAA
3221627 CATAGTGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
TAAAAT
Found at i:3221811 original size:23 final size:24
Alignment explanation
Indices: 3221765--3221811 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3221755 AATATTTGAT
** *
3221765 ATATTTTTTAATTAATGATTTAAA
1 ATATTTTAAAATTAATGATGTAAA
3221789 ATATTTTAAAATTAAT-ATGTAAA
1 ATATTTTAAAATTAATGATGTAAA
3221812 TTTAAATTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (24 bp):
ATATTTTAAAATTAATGATGTAAA
Found at i:3228634 original size:14 final size:14
Alignment explanation
Indices: 3228615--3228642 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3228605 TACACATTTC
3228615 CTTTTTCTTTTTTT
1 CTTTTTCTTTTTTT
3228629 CTTTTTCTTTTTTT
1 CTTTTTCTTTTTTT
3228643 GTATTTTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
CTTTTTCTTTTTTT
Found at i:3230623 original size:20 final size:20
Alignment explanation
Indices: 3230599--3230642 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
3230589 TTAAATTTTA
*
3230599 AAAAATAAATAAAAATTATAT
1 AAAATTAAATAAAAATTAT-T
* *
3230620 AAAATTAAATTAAATTTATT
1 AAAATTAAATAAAAATTATT
3230640 AAA
1 AAA
3230643 TTATATAGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAATTAAATAAAAATTATT
Found at i:3230634 original size:10 final size:10
Alignment explanation
Indices: 3230611--3230648 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
3230601 AAATAAATAA
*
3230611 AAATTATATA
1 AAATTATATT
*
3230621 AAATTAAATT
1 AAATTATATT
3230631 AAATT-TATT
1 AAATTATATT
3230640 AAATTATAT
1 AAATTATAT
3230649 AGATATAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
AAATTATATT
Found at i:3230838 original size:15 final size:15
Alignment explanation
Indices: 3230806--3230848 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
3230796 TATTATTAAT
*
3230806 ATTTAAAATTAATTAA
1 ATTT-AAATTAATAAA
*
3230822 ATTTAATTTAATAAA
1 ATTTAAATTAATAAA
3230837 ATTTAAATTAAT
1 ATTTAAATTAAT
3230849 TTAAATCGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 20 0.83
16 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTTAAATTAATAAA
Found at i:3232793 original size:14 final size:14
Alignment explanation
Indices: 3232760--3232829 Score: 58
Period size: 14 Copynumber: 5.0 Consensus size: 14
3232750 ATTATGTTAA
*
3232760 TAATAATTATA-TT
1 TAATTATTATATTT
3232773 TAATTATTATATTT
1 TAATTATTATATTT
*
3232787 TATTTATTATA--T
1 TAATTATTATATTT
3232799 TAATT-TTATACTTAT
1 TAATTATTATA-TT-T
3232814 TAAATATATTATATTT
1 T-AAT-TATTATATTT
3232830 AAAATTATCA
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
11 5 0.11
12 5 0.11
13 10 0.22
14 12 0.26
15 2 0.04
16 4 0.09
17 3 0.07
18 5 0.11
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (14 bp):
TAATTATTATATTT
Found at i:3232804 original size:13 final size:14
Alignment explanation
Indices: 3232765--3232831 Score: 59
Period size: 13 Copynumber: 4.8 Consensus size: 14
3232755 GTTAATAATA
3232765 ATTATATTTAA-TT
1 ATTATATTTAATTT
*
3232778 ATTATATTTTATTT
1 ATTATATTTAATTT
3232792 ATTATA-TTAATTT
1 ATTATATTTAATTT
* *
3232805 -TATACTTATTAAATAT
1 AT-TA--TATTTAATTT
3232821 ATTATATTTAA
1 ATTATATTTAA
3232832 AATTATCAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
12 1 0.02
13 18 0.42
14 14 0.33
15 2 0.05
16 7 0.16
17 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (14 bp):
ATTATATTTAATTT
Found at i:3232825 original size:18 final size:18
Alignment explanation
Indices: 3232725--3232830 Score: 76
Period size: 18 Copynumber: 5.9 Consensus size: 18
3232715 ATTTTAAATA
* *
3232725 TAAATATAATAGATTTAT
1 TAAATATATTATATTTAT
* *
3232743 TAAATATATTAT-GTTAA
1 TAAATATATTATATTTAT
3232760 T-AATA-ATTATATTTAAT
1 TAAATATATTATATTT-AT
* *
3232777 T-ATTATATTTTATTTAT
1 TAAATATATTATATTTAT
* * *
3232794 TATATTAATTTTATACTTAT
1 TA-AAT-ATATTATATTTAT
3232814 TAAATATATTATATTTA
1 TAAATATATTATATTTA
3232831 AAATTATCAA
Statistics
Matches: 68, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
15 5 0.07
16 6 0.09
17 12 0.18
18 28 0.41
19 5 0.07
20 12 0.18
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (18 bp):
TAAATATATTATATTTAT
Found at i:3233714 original size:19 final size:19
Alignment explanation
Indices: 3233670--3233714 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
3233660 AAATAATTAA
*
3233670 AAATAAATAAAAATATTTC
1 AAATCAATAAAAATATTTC
* * *
3233689 CATTCAATAAAAATATTTT
1 AAATCAATAAAAATATTTC
3233708 AAATCAA
1 AAATCAA
3233715 ATTAAATTCA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATCAATAAAAATATTTC
Found at i:3235178 original size:19 final size:20
Alignment explanation
Indices: 3235134--3235180 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
3235124 TTATTATTTT
* *
3235134 TTACAAAA-ATAAATATAAC
1 TTACAAAATAAAAAAATAAC
3235153 TTA-AAAATAAAAAAATAA-
1 TTACAAAATAAAAAAATAAC
3235171 TTACAAAATA
1 TTACAAAATA
3235181 TTAAAATTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (20 bp):
TTACAAAATAAAAAAATAAC
Found at i:3235186 original size:19 final size:19
Alignment explanation
Indices: 3235134--3235193 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
3235124 TTATTATTTT
3235134 TTACAAAA-ATAAATATAAC
1 TTACAAAATATAAA-ATAAC
*
3235153 TTA-AAAATAAAAAAATAA-
1 TTACAAAAT-ATAAAATAAC
*
3235171 TTACAAAATATTAAAATTAC
1 TTACAAAATA-TAAAATAAC
3235191 TTA
1 TTA
3235194 TCCTACATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
18 8 0.24
19 18 0.55
20 7 0.21
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (19 bp):
TTACAAAATATAAAATAAC
Found at i:3235882 original size:18 final size:18
Alignment explanation
Indices: 3235859--3235921 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
3235849 TTTTCTTTTC
3235859 TATTTTTAAAAATATATT
1 TATTTTTAAAAATATATT
* * *
3235877 TATTTTTATATAT-TTTT
1 TATTTTTAAAAATATATT
*
3235894 TA-TTTTAAAAATATCTT
1 TATTTTTAAAAATATATT
3235911 TATTTATTAAA
1 TATTT-TTAAA
3235922 TGTAAATTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
16 8 0.22
17 10 0.28
18 13 0.36
19 5 0.14
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTTTTAAAAATATATT
Found at i:3235912 original size:17 final size:17
Alignment explanation
Indices: 3235862--3235915 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
3235852 TCTTTTCTAT
3235862 TTTTAAAAATATATTTA
1 TTTTAAAAATATATTTA
* * *
3235879 TTTT-TATATATTTTTTA
1 TTTTAAAAATA-TATTTA
*
3235896 TTTTAAAAATATCTTTA
1 TTTTAAAAATATATTTA
3235913 TTT
1 TTT
3235916 ATTAAATGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
16 4 0.14
17 21 0.72
18 4 0.14
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTAAAAATATATTTA
Found at i:3245019 original size:2 final size:2
Alignment explanation
Indices: 3245012--3245041 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3245002 TAGTTATTAC
3245012 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
3245042 GGAAGCTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3245649 original size:2 final size:2
Alignment explanation
Indices: 3245642--3245671 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3245632 TTAATCACAA
3245642 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
3245672 GTAACACTCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3245824 original size:24 final size:24
Alignment explanation
Indices: 3245777--3245825 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
3245767 TCTTCTTTTC
**
3245777 TCTTATTCTTCTTATTTTTGTAAG
1 TCTTATTCTTCTTATTTTAATAAG
*
3245801 TCTTATTCTTCTTCTTTTAATAAG
1 TCTTATTCTTCTTATTTTAATAAG
3245825 T
1 T
3245826 TTTAAAGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.06, T:0.61
Consensus pattern (24 bp):
TCTTATTCTTCTTATTTTAATAAG
Found at i:3246392 original size:2 final size:2
Alignment explanation
Indices: 3246385--3246413 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3246375 TAAAGATAAA
3246385 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3246414 AAAGTGAAAG
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3253441 original size:11 final size:11
Alignment explanation
Indices: 3253425--3253450 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3253415 CTGAATATGA
3253425 TTAACATAGGG
1 TTAACATAGGG
3253436 TTAACATAGGG
1 TTAACATAGGG
3253447 TTAA
1 TTAA
3253451 AATGCTTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (11 bp):
TTAACATAGGG
Found at i:3266008 original size:6 final size:6
Alignment explanation
Indices: 3265994--3266033 Score: 71
Period size: 6 Copynumber: 6.5 Consensus size: 6
3265984 GGAAAAAAAA
3265994 GGGAGAG GGGAAG GGGAAG GGGAAG GGGAAG GGGAAG GGG
1 GGGA-AG GGGAAG GGGAAG GGGAAG GGGAAG GGGAAG GGG
3266034 GAGATCGGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 29 0.88
7 4 0.12
ACGTcount: A:0.30, C:0.00, G:0.70, T:0.00
Consensus pattern (6 bp):
GGGAAG
Found at i:3266372 original size:24 final size:22
Alignment explanation
Indices: 3266327--3266369 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
3266317 TGTGTTTCAA
*
3266327 TTTTTTTTATTTAATTATTTAT
1 TTTTTTTTATTTAATAATTTAT
*
3266349 TTTTTTCTTATTTTATAATTT
1 TTTTTT-TTATTTAATAATTT
3266370 TATCACATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTTTTTTATTTAATAATTTAT
Found at i:3273180 original size:2 final size:2
Alignment explanation
Indices: 3273173--3273208 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3273163 CTTCGATTGC
3273173 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3273209 ATATATATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3273509 original size:28 final size:28
Alignment explanation
Indices: 3273449--3273505 Score: 93
Period size: 25 Copynumber: 2.1 Consensus size: 28
3273439 TTATTAAATT
3273449 TTAAATTTCTTTTAATTTTATAATCAAA
1 TTAAATTTCTTTTAATTTTATAATCAAA
3273477 TTAAATTT-TTTT-A-TTTATAATCAAA
1 TTAAATTTCTTTTAATTTTATAATCAAA
3273502 TTAA
1 TTAA
3273506 TAAAAAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
25 16 0.55
26 1 0.03
27 4 0.14
28 8 0.28
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.54
Consensus pattern (28 bp):
TTAAATTTCTTTTAATTTTATAATCAAA
Found at i:3274952 original size:2 final size:2
Alignment explanation
Indices: 3274945--3274978 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
3274935 TTTGGATAAC
*
3274945 AT AT AT AT AT AT AT AT AT AT AT GT AT AT GAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
3274979 AATGAAACGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3278146 original size:2 final size:2
Alignment explanation
Indices: 3278134--3278174 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
3278124 GGCCATGCCG
*
3278134 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3278175 CAGGAAAAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3281354 original size:19 final size:18
Alignment explanation
Indices: 3281318--3281390 Score: 71
Period size: 19 Copynumber: 4.1 Consensus size: 18
3281308 ATTTGAGAGG
*
3281318 ATTTAAATAAA-AATATTA
1 ATTTAAA-AAATAAAATTA
3281336 TATTTAAAAAATAAAATTA
1 -ATTTAAAAAATAAAATTA
*
3281355 A-ATAAAATAATAAAATTA
1 ATTTAAAA-AATAAAATTA
*
3281373 CTTTAAAAAAT-AAATTA
1 ATTTAAAAAATAAAATTA
3281390 A
1 A
3281391 ACTTTAGATA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
17 11 0.24
18 17 0.37
19 18 0.39
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (18 bp):
ATTTAAAAAATAAAATTA
Found at i:3281384 original size:18 final size:17
Alignment explanation
Indices: 3281336--3281386 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 17
3281326 AAAAATATTA
3281336 TATTTAAAAAATAAAAT
1 TATTTAAAAAATAAAAT
**
3281353 TAAATAAAATAATAAAAT
1 TATTTAAAA-AATAAAAT
3281371 TACTTTAAAAAATAAA
1 TA-TTTAAAAAATAAA
3281387 TTAAACTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 7 0.25
18 16 0.57
19 5 0.18
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
TATTTAAAAAATAAAAT
Found at i:3281406 original size:36 final size:37
Alignment explanation
Indices: 3281318--3281407 Score: 105
Period size: 37 Copynumber: 2.4 Consensus size: 37
3281308 ATTTGAGAGG
3281318 ATTTAAATAAAAATATTATATTTAAAAAATAAAATTAA
1 ATTTAAATAAAAA-ATTATATTTAAAAAATAAAATTAA
* *
3281356 A-TAAAATAATAAAATTA-CTTTAAAAAAT-AAATTAA
1 ATTTAAATAA-AAAATTATATTTAAAAAATAAAATTAA
*
3281391 ACTTTAGATAAAAAATT
1 A-TTTAAATAAAAAATT
3281408 TTAAATTCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
35 8 0.18
36 16 0.36
37 17 0.38
38 4 0.09
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.34
Consensus pattern (37 bp):
ATTTAAATAAAAAATTATATTTAAAAAATAAAATTAA
Found at i:3281466 original size:21 final size:21
Alignment explanation
Indices: 3281441--3281494 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
3281431 CAAATAAAAA
3281441 TTTTAGTTATAAATTTTATAT
1 TTTTAGTTATAAATTTTATAT
*
3281462 TTTTA-TAATATAATTTTATAT
1 TTTTAGTTATA-AATTTTATAT
*
3281483 ATTT-GTTA-AAAT
1 TTTTAGTTATAAAT
3281495 ATATGTATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 3 0.11
20 5 0.18
21 20 0.71
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (21 bp):
TTTTAGTTATAAATTTTATAT
Found at i:3281474 original size:22 final size:24
Alignment explanation
Indices: 3281448--3281497 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
3281438 AAATTTTAGT
*
3281448 TATAAATTT-TATATTT-TTATAA
1 TATAAATTTATATATTTGTTAAAA
*
3281470 TATAATTTTATATATTTGTTAAAA
1 TATAAATTTATATATTTGTTAAAA
3281494 TATA
1 TATA
3281498 TGTATAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 8 0.33
23 7 0.29
24 9 0.38
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
TATAAATTTATATATTTGTTAAAA
Found at i:3284997 original size:2 final size:2
Alignment explanation
Indices: 3284990--3285021 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3284980 TGGGGGAGCT
3284990 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3285022 TTCAGATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3286868 original size:24 final size:23
Alignment explanation
Indices: 3286841--3286897 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
3286831 TATACTTATT
*
3286841 TATTTAATTTTTATAAATTTTAAA
1 TATTTAATTTTTAT-AACTTTAAA
* *
3286865 TATTAAATATTTATAACTTTAAA
1 TATTTAATTTTTATAACTTTAAA
3286888 T-TTTATATTT
1 TATTTA-ATTT
3286898 ACGCATATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
22 3 0.11
23 12 0.44
24 12 0.44
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
TATTTAATTTTTATAACTTTAAA
Found at i:3286892 original size:15 final size:15
Alignment explanation
Indices: 3286854--3286894 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
3286844 TTAATTTTTA
3286854 TAAATTTTA-AATAT
1 TAAATTTTATAATAT
3286868 TAAATATTTATAACT-T
1 TAAAT-TTTATAA-TAT
3286884 TAAATTTTATA
1 TAAATTTTATA
3286895 TTTACGCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 5 0.21
15 10 0.42
16 8 0.33
17 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (15 bp):
TAAATTTTATAATAT
Found at i:3287495 original size:16 final size:16
Alignment explanation
Indices: 3287447--3287497 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 16
3287437 TAAATCAAGT
*
3287447 AAATATT-ATTTTTTA
1 AAATATTAATATTTTA
*
3287462 AAAT-TTAA-ATATTAA
1 AAATATTAATAT-TTTA
3287477 AAATATTAATATTTTA
1 AAATATTAATATTTTA
3287493 AAATA
1 AAATA
3287498 AATTTTATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
14 3 0.10
15 12 0.41
16 12 0.41
17 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATATTAATATTTTA
Found at i:3292533 original size:15 final size:16
Alignment explanation
Indices: 3292508--3292537 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3292498 ATGGATAATA
3292508 AATAAATTTAAATATT
1 AATAAATTTAAATATT
3292524 AATAAA-TTAAATAT
1 AATAAATTTAAATAT
3292538 ATTTATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATAAATTTAAATATT
Found at i:3292541 original size:25 final size:22
Alignment explanation
Indices: 3292506--3292567 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
3292496 AAATGGATAA
3292506 TAAATAAATTTAAATATTAATAAAT
1 TAAATAAATTT--ATATTAA-AAAT
*
3292531 TAAATATATTTATATTAAAAAT
1 TAAATAAATTTATATTAAAAAT
* *
3292553 TAAAAAAAATTATAT
1 TAAATAAATTTATAT
3292568 ATATTCGATC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 16 0.48
23 7 0.21
25 10 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATAAATTTATATTAAAAAT
Found at i:3309620 original size:5 final size:5
Alignment explanation
Indices: 3309610--3309636 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
3309600 AAACATAGAT
3309610 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
3309637 ATAATTCACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:3310216 original size:33 final size:32
Alignment explanation
Indices: 3310130--3310222 Score: 82
Period size: 33 Copynumber: 2.8 Consensus size: 32
3310120 AGATAGAAGA
3310130 AAAATATAATTATTAAAATTTAAAATTAAAAAAATT
1 AAAATAT--TTATTAAAATTTAAAATT--AAAAATT
3310166 AAAATATTTA-TATAAATTGATAAAATT-AAAATT
1 AAAATATTTATTA-AAATT--TAAAATTAAAAATT
* * *
3310199 AAATTTTTTATTAAAATTTTAAAT
1 AAAATATTTATTAAAATTTAAAAT
3310223 AATTAAATTT
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
31 5 0.10
33 21 0.42
34 10 0.20
36 14 0.28
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (32 bp):
AAAATATTTATTAAAATTTAAAATTAAAAATT
Found at i:3310246 original size:27 final size:28
Alignment explanation
Indices: 3310195--3310251 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
3310185 ATAAAATTAA
*
3310195 AATTAAATTTTTTATTAAAATTTTAAAT
1 AATTAAATTTTTTATTAAAACTTTAAAT
*
3310223 AATTAAA-TTTTT-TTATAAACTTTATAT
1 AATTAAATTTTTTATTA-AAACTTTAAAT
3310250 AA
1 AA
3310252 ATTCATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 3 0.12
27 16 0.62
28 7 0.27
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (28 bp):
AATTAAATTTTTTATTAAAACTTTAAAT
Found at i:3310635 original size:16 final size:16
Alignment explanation
Indices: 3310611--3310653 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
3310601 TTAATAATAA
3310611 AAATATAAATTAATTAT
1 AAAT-TAAATTAATTAT
3310628 AAATTAAATTAA-TAT
1 AAATTAAATTAATTAT
3310643 AAA--AAATTAAT
1 AAATTAAATTAAT
3310654 ATTTTTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 7 0.28
15 6 0.24
16 8 0.32
17 4 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAATTAAATTAATTAT
Found at i:3310651 original size:13 final size:14
Alignment explanation
Indices: 3310615--3310655 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
3310605 TAATAAAAAT
3310615 ATAAATTAATTATAA
1 ATAAATTAA-TATAA
3310630 ATTAAATTAATATAA
1 A-TAAATTAATATAA
3310645 A-AAATTAATAT
1 ATAAATTAATAT
3310656 TTTTAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 10 0.40
15 7 0.28
16 8 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
ATAAATTAATATAA
Found at i:3312026 original size:20 final size:19
Alignment explanation
Indices: 3312003--3312041 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
3311993 ACGATTTTTT
*
3312003 ATATTAATATCATTAATTAA
1 ATATAAATATCA-TAATTAA
*
3312023 ATATAAATATGATAATTAA
1 ATATAAATATCATAATTAA
3312042 TAAGCTTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (19 bp):
ATATAAATATCATAATTAA
Found at i:3312188 original size:24 final size:23
Alignment explanation
Indices: 3312143--3312190 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
3312133 ATATTAATTT
*
3312143 AAAAAATTAATATATATATAATA
1 AAAAAATTAATATAAATATAATA
3312166 AAAAAATTATATATCAAAT-TAATA
1 AAAAAATTA-ATAT-AAATATAATA
3312190 A
1 A
3312191 TTTTTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 9 0.41
24 10 0.45
25 3 0.14
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAAAATTAATATAAATATAATA
Found at i:3313339 original size:24 final size:25
Alignment explanation
Indices: 3313290--3313344 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 25
3313280 ATTTAAAATG
*
3313290 ATTATATAAATATAATATGTATAAA
1 ATTATATAAATATAATATATATAAA
3313315 ATTATA-AAATATAATATA-ATAAA
1 ATTATATAAATATAATATATATAAA
*
3313338 AATATAT
1 ATTATAT
3313345 TTTTAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 10 0.37
24 11 0.41
25 6 0.22
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (25 bp):
ATTATATAAATATAATATATATAAA
Found at i:3313379 original size:21 final size:21
Alignment explanation
Indices: 3313349--3313396 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 21
3313339 ATATATTTTT
3313349 AAATT-TT-ATATAAATAT--
1 AAATTATTAATATAAATATAA
3313366 AAATTATTAATATAAATATAA
1 AAATTATTAATATAAATATAA
3313387 AAATTATTAA
1 AAATTATTAA
3313397 GATTAATTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.19
18 2 0.07
19 10 0.37
21 10 0.37
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATTATTAATATAAATATAA
Found at i:3313679 original size:20 final size:19
Alignment explanation
Indices: 3313655--3313694 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3313645 ATTAAAAAAA
3313655 TTAT-TTTTAT-ATTAATAT
1 TTATATTTTATAATTAA-AT
3313673 TTATATTTTATAATTAAAT
1 TTATATTTTATAATTAAAT
3313692 TTA
1 TTA
3313695 AATAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 11 0.55
20 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTATATTTTATAATTAAAT
Found at i:3313769 original size:11 final size:11
Alignment explanation
Indices: 3313755--3313779 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3313745 TTCAAATATT
3313755 TTTTCTTTATA
1 TTTTCTTTATA
3313766 TTTTCTTTATA
1 TTTTCTTTATA
3313777 TTT
1 TTT
3313780 GTTTTTTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTCTTTATA
Found at i:3315841 original size:24 final size:24
Alignment explanation
Indices: 3315813--3315862 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
3315803 TGTGTATTAA
*
3315813 TATAATTAATAATGTTA-ATTATAT
1 TATAATTAAT-ATATTATATTATAT
3315837 TATAATTAATATATTATATTATAT
1 TATAATTAATATATTATATTATAT
3315861 TA
1 TA
3315863 ATTAACTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TATAATTAATATATTATATTATAT
Found at i:3315866 original size:9 final size:9
Alignment explanation
Indices: 3315807--3315891 Score: 53
Period size: 9 Copynumber: 10.1 Consensus size: 9
3315797 ACTATTTGTG
3315807 TATTAA-TA
1 TATTAATTA
*
3315815 TAATTAATAA
1 T-ATTAATTA
*
3315825 TGTTAATTA
1 TATTAATTA
3315834 TATT-A-TA
1 TATTAATTA
3315841 -ATTAA-TA
1 TATTAATTA
3315848 TATTATATTA
1 TATTA-ATTA
3315858 TATTAATTA
1 TATTAATTA
*
3315867 -ACTT-TTTA
1 TA-TTAATTA
3315875 -ATTAATTA
1 TATTAATTA
3315883 TATT-ATTA
1 TATTAATTA
3315891 T
1 T
3315892 TTTTTTTATT
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
6 3 0.05
7 7 0.11
8 19 0.31
9 24 0.39
10 9 0.15
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (9 bp):
TATTAATTA
Found at i:3315866 original size:14 final size:15
Alignment explanation
Indices: 3315827--3315866 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
3315817 ATTAATAATG
3315827 TTAATTATATTATAA
1 TTAATTATATTATAA
3315842 TTAA-TATATTAT-A
1 TTAATTATATTATAA
3315855 TTATATTA-ATTA
1 TTA-ATTATATTA
3315867 ACTTTTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 4 0.17
14 13 0.57
15 6 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTAATTATATTATAA
Found at i:3318438 original size:2 final size:2
Alignment explanation
Indices: 3318431--3318457 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3318421 TTGGTAGAAC
3318431 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3318458 GTGCCAAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3325956 original size:20 final size:21
Alignment explanation
Indices: 3325909--3325957 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
3325899 ATAAATTTAA
3325909 ATTAATTTATATTAAATAATT
1 ATTAATTTATATTAAATAATT
*
3325930 ATT-ATTTAT-TTAAATATTT
1 ATTAATTTATATTAAATAATT
*
3325949 TTTAATTTA
1 ATTAATTTA
3325958 AAATTTTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 11 0.44
20 11 0.44
21 3 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTAATTTATATTAAATAATT
Found at i:3326878 original size:7 final size:7
Alignment explanation
Indices: 3326868--3326911 Score: 52
Period size: 7 Copynumber: 5.9 Consensus size: 7
3326858 ATTAATTAAA
3326868 ATAAAAT
1 ATAAAAT
*
3326875 ATAAAAA
1 ATAAAAT
3326882 ATAAATAT
1 ATAAA-AT
3326890 GATAAGAAT
1 -ATAA-AAT
3326899 ATAAAAT
1 ATAAAAT
3326906 ATAAAA
1 ATAAAA
3326912 AAATTATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
7 20 0.62
8 5 0.16
9 6 0.19
10 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (7 bp):
ATAAAAT
Found at i:3326968 original size:13 final size:13
Alignment explanation
Indices: 3326950--3326974 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3326940 TATTTTAAAT
3326950 AATAAAAAATATG
1 AATAAAAAATATG
3326963 AATAAAAAATAT
1 AATAAAAAATAT
3326975 ACACACGTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (13 bp):
AATAAAAAATATG
Found at i:3339294 original size:17 final size:17
Alignment explanation
Indices: 3339272--3339305 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3339262 AAAAAATTAT
3339272 TTTTAT-ATTAATATTTA
1 TTTTATAATTAA-ATTTA
3339289 TTTTATAATTAAATTTA
1 TTTTATAATTAAATTTA
3339306 AATAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTATAATTAAATTTA
Found at i:3340211 original size:21 final size:21
Alignment explanation
Indices: 3340185--3340226 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3340175 AAGGCCAAAA
3340185 AGGCTTTGAACCATTTTTGTG
1 AGGCTTTGAACCATTTTTGTG
3340206 AGGCTTTGAACCATTTTTGTG
1 AGGCTTTGAACCATTTTTGTG
3340227 GGATATGCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.14, G:0.24, T:0.43
Consensus pattern (21 bp):
AGGCTTTGAACCATTTTTGTG
Found at i:3344920 original size:20 final size:21
Alignment explanation
Indices: 3344881--3344920 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
3344871 AACAGTACTG
3344881 TCTGCCACGTGGCCAATAAAGT
1 TCTGCCACGT-GCCAATAAAGT
*
3344903 TCTGCCACGT-CGAATAAA
1 TCTGCCACGTGCCAATAAA
3344921 AAATAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
22 10 0.59
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.23
Consensus pattern (21 bp):
TCTGCCACGTGCCAATAAAGT
Found at i:3347655 original size:22 final size:22
Alignment explanation
Indices: 3347630--3347671 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3347620 CGCAATGTGC
*
3347630 AATGAAGCAAGATTTGTCAAGA
1 AATGAAGCAAGAATTGTCAAGA
*
3347652 AATGAATCAAGAATTGTCAA
1 AATGAAGCAAGAATTGTCAA
3347672 TTGAACAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.10, G:0.19, T:0.24
Consensus pattern (22 bp):
AATGAAGCAAGAATTGTCAAGA
Found at i:3349229 original size:2 final size:2
Alignment explanation
Indices: 3349224--3349257 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3349214 CTCTCTCTCA
3349224 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
3349258 GTGGCATGCA
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:3363597 original size:17 final size:18
Alignment explanation
Indices: 3363572--3363605 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3363562 AAATTTTTTT
*
3363572 AATTCTAAATA-TAAAAA
1 AATTATAAATATTAAAAA
3363589 AATTATAAATATTAAAA
1 AATTATAAATATTAAAA
3363606 TTTTAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
AATTATAAATATTAAAAA
Found at i:3365631 original size:16 final size:16
Alignment explanation
Indices: 3365610--3365662 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
3365600 ATTATACGAT
*
3365610 TATAATTAAAATATGA
1 TATAATTAAAATATAA
* *
3365626 TATAATAAAAAAATAA
1 TATAATTAAAATATAA
3365642 TATTAA-TAAAATATAAA
1 TA-TAATTAAAATAT-AA
3365659 TATA
1 TATA
3365663 TAAATATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
16 23 0.77
17 7 0.23
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
TATAATTAAAATATAA
Found at i:3365665 original size:8 final size:8
Alignment explanation
Indices: 3365647--3365767 Score: 65
Period size: 8 Copynumber: 15.1 Consensus size: 8
3365637 AATAATATTA
3365647 ATAAA-AT
1 ATAAATAT
3365654 ATAAATAT
1 ATAAATAT
3365662 ATAAATATTT
1 ATAAATA--T
* *
3365672 TTAAAATTT
1 AT-AAATAT
*
3365681 ATACA-AT
1 ATAAATAT
3365688 ATAAATA-
1 ATAAATAT
*
3365695 ATTAATAT
1 ATAAATAT
*
3365703 TTAAAATTTAT
1 AT-AAA--TAT
3365714 ATAAATAT
1 ATAAATAT
3365722 AT-AATAT
1 ATAAATAT
* *
3365729 TTTAA-AT
1 ATAAATAT
*
3365736 ATAATTAT
1 ATAAATAT
3365744 AT-AATAT
1 ATAAATAT
*
3365751 AAAAATAT
1 ATAAATAT
3365759 ATAAATAT
1 ATAAATAT
3365767 A
1 A
3365768 ATATGAATTT
Statistics
Matches: 85, Mismatches: 17, Indels: 23
0.68 0.14 0.18
Matches are distributed among these distances:
7 31 0.36
8 37 0.44
9 4 0.05
10 5 0.06
11 8 0.09
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (8 bp):
ATAAATAT
Found at i:3365703 original size:58 final size:57
Alignment explanation
Indices: 3365615--3365782 Score: 150
Period size: 56 Copynumber: 2.9 Consensus size: 57
3365605 ACGATTATAA
* * *
3365615 TTAAA-ATATGATATAATAAAAAAATAATATTAATAAAATATAAATATATAAATATTT
1 TTAAATATATTATACAATATAAAAATAATATTAATAAAATATAAATATATAAATA-TT
*
3365672 TTAAA-AT-TTATACAATATAAATAATTAATATTTAA-AATTTATATAAATATAT-AATATT
1 TTAAATATATTATACAATATAAA-AA-TAATA-TTAATAA--AATATAAATATATAAATATT
* * * * *
3365730 TTAAATATAATTATATAATATAAAAAT-ATATAAATATAATATGAATTTATAAA
1 TTAAATAT-ATTATACAATATAAAAATAATATTAATAAAATATAAATATATAAA
3365783 AATTGCTCAC
Statistics
Matches: 91, Mismatches: 10, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
56 21 0.23
57 14 0.15
58 18 0.20
59 11 0.12
60 14 0.15
61 13 0.14
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (57 bp):
TTAAATATATTATACAATATAAAAATAATATTAATAAAATATAAATATATAAATATT
Found at i:3365709 original size:31 final size:33
Alignment explanation
Indices: 3365651--3365766 Score: 104
Period size: 26 Copynumber: 3.6 Consensus size: 33
3365641 ATATTAATAA
3365651 AATATAAATATATAAATATTTTTAAAATTTATAC
1 AATATAAATATATAAATA-TTTTAAAATTTATAC
*
3365685 AATATAAATA-ATTAATA-TTTAAAA-TT-T--
1 AATATAAATATATAAATATTTTAAAATTTATAC
*
3365712 -ATATAAATATAT-AATATTTTAAATATAATTATAT
1 AATATAAATATATAAATATTTTAAA-AT--TTATAC
3365746 AATATAAAAATATATAAATAT
1 AATAT--AAATATATAAATAT
3365767 AATATGAATT
Statistics
Matches: 68, Mismatches: 1, Indels: 22
0.75 0.01 0.24
Matches are distributed among these distances:
26 13 0.19
27 8 0.12
28 1 0.01
29 1 0.01
30 2 0.03
31 9 0.13
32 1 0.01
33 6 0.09
34 10 0.15
35 4 0.06
37 8 0.12
38 5 0.07
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (33 bp):
AATATAAATATATAAATATTTTAAAATTTATAC
Found at i:3365715 original size:26 final size:26
Alignment explanation
Indices: 3365652--3365735 Score: 78
Period size: 31 Copynumber: 2.9 Consensus size: 26
3365642 TATTAATAAA
3365652 ATATAAATATATAAATATTTTTAAAATTT
1 ATATAAATATAT-AATA--TTTAAAATTT
*
3365681 ATACAATATAAATAATTAATATTTAAAATTT
1 ATATAA-AT--AT-A-TAATATTTAAAATTT
*
3365712 ATATAAATATATAATATTTTAAAT
1 ATATAAATATATAATATTTAAAAT
3365736 ATAATTATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 13
0.75 0.05 0.21
Matches are distributed among these distances:
26 12 0.26
27 1 0.02
28 2 0.04
29 5 0.11
30 4 0.09
31 15 0.32
32 2 0.04
33 5 0.11
34 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (26 bp):
ATATAAATATATAATATTTAAAATTT
Found at i:3365785 original size:21 final size:21
Alignment explanation
Indices: 3365712--3365785 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 21
3365702 TTTAAAATTT
* **
3365712 ATATAAATATATAATATTTTAA
1 ATATAAAAATATAATA-TAAAA
**
3365734 ATATAATTATATAATATAAAA
1 ATATAAAAATATAATATAAAA
* * *
3365755 ATATATAAATATAATATGAAT
1 ATATAAAAATATAATATAAAA
*
3365776 TTATAAAAAT
1 ATATAAAAAT
3365786 TGCTCACATT
Statistics
Matches: 42, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
21 27 0.64
22 15 0.36
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (21 bp):
ATATAAAAATATAATATAAAA
Found at i:3367631 original size:12 final size:12
Alignment explanation
Indices: 3367614--3367650 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3367604 GATAAAAATG
3367614 ATAATTATATAA
1 ATAATTATATAA
3367626 ATAATT-TATTAA
1 ATAATTATA-TAA
3367638 ATAATTATA-AA
1 ATAATTATATAA
3367649 AT
1 AT
3367651 TTATTTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 6 0.26
12 15 0.65
13 2 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
ATAATTATATAA
Found at i:3368544 original size:2 final size:2
Alignment explanation
Indices: 3368537--3368562 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3368527 AATATTAGTC
3368537 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
3368563 TGCTTTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3368843 original size:31 final size:31
Alignment explanation
Indices: 3368798--3368856 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
3368788 ATTCAAAAAA
*
3368798 ATTAATTTATTAATTATATA-TATTTTTAAT
1 ATTAATTTATTAATTAAATATTATTTTTAAT
*
3368828 ATTATTTTAATTAATTAAATATTATTTTT
1 ATTAATTT-ATTAATTAAATATTATTTTT
3368857 TAAAATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 7 0.28
31 11 0.44
32 7 0.28
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (31 bp):
ATTAATTTATTAATTAAATATTATTTTTAAT
Found at i:3369768 original size:17 final size:17
Alignment explanation
Indices: 3369746--3369780 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3369736 AATAAATATT
*
3369746 ATATATATATTTCAAAA
1 ATATATATATTACAAAA
*
3369763 ATATATTTATTACAAAA
1 ATATATATATTACAAAA
3369780 A
1 A
3369781 AATCCATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATATATATTACAAAA
Found at i:3372706 original size:20 final size:20
Alignment explanation
Indices: 3372683--3372751 Score: 57
Period size: 22 Copynumber: 3.2 Consensus size: 20
3372673 TAATTTATAT
3372683 TATATTTATATATTTTATTA
1 TATATTTATATATTTTATTA
* * * *
3372703 TATAATAATTGTATTTATGATTT
1 TATATTTA-TATATTT-T-ATTA
3372726 TATATTTATATAAATTTTATTA
1 TATATTTATAT--ATTTTATTA
3372748 TATA
1 TATA
3372752 AATTATTCAT
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
20 6 0.17
21 6 0.17
22 10 0.28
23 10 0.28
24 4 0.11
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TATATTTATATATTTTATTA
Done.