Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold79
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: 4189514
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 5041 characters in sequence are not A, C, G, or T
File 10 of 26
Found at i:1376394 original size:16 final size:18
Alignment explanation
Indices: 1376363--1376399 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
1376353 ACTCAACTTT
1376363 TAAAATGAAGTATAAATA
1 TAAAATGAAGTATAAATA
1376381 TAAAAT-AA-TATAAATA
1 TAAAATGAAGTATAAATA
1376397 TAA
1 TAA
1376400 CACAAATCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 11 0.58
17 2 0.11
18 6 0.32
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (18 bp):
TAAAATGAAGTATAAATA
Found at i:1377350 original size:5 final size:5
Alignment explanation
Indices: 1377340--1377381 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
1377330 TAATAATTTA
*
1377340 TATAT TATAT TATAT T-TA- TATAT TTTAT TATAT TATAAT TAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT-AT TAT
1377382 GTTTAAAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
3 1 0.03
4 4 0.12
5 22 0.69
6 5 0.16
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TATAT
Found at i:1377358 original size:18 final size:18
Alignment explanation
Indices: 1377335--1377381 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
1377325 AGTTTTAATA
1377335 ATTTATATATTATATTAT
1 ATTTATATATTATATTAT
*
1377353 ATTTATATATTTTATTAT
1 ATTTATATATTATATTAT
1377371 A-TTATA-ATTAT
1 ATTTATATATTAT
1377382 GTTTAAAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 4 0.15
17 5 0.19
18 18 0.67
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTATATATTATATTAT
Found at i:1377371 original size:30 final size:31
Alignment explanation
Indices: 1377340--1377397 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 31
1377330 TAATAATTTA
*
1377340 TATATTAT-ATTATATTTATA-TATTTTA-T
1 TATATTATAATTATATTTAAAGTATTTTATT
*
1377368 TATATTATAATTATGTTTAAAGTATTTTAT
1 TATATTATAATTATATTTAAAGTATTTTAT
1377398 ATTTATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 8 0.32
29 10 0.40
30 7 0.28
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.60
Consensus pattern (31 bp):
TATATTATAATTATATTTAAAGTATTTTATT
Found at i:1377407 original size:30 final size:29
Alignment explanation
Indices: 1377331--1377407 Score: 79
Period size: 30 Copynumber: 2.7 Consensus size: 29
1377321 ATTCAGTTTT
*
1377331 AATAATTTATATAT-TAT-ATTATATTTA
1 AATATTTTATATATATATAATTATATTTA
* *
1377358 TATATTTTAT-TATATTATAATTATGTTTA
1 AATATTTTATATATA-TATAATTATATTTA
*
1377387 AAGTATTTTATATTTATATAA
1 AA-TATTTTATATATATATAA
1377408 ATTTTTAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
26 3 0.08
27 8 0.20
28 3 0.08
29 10 0.25
30 13 0.32
31 3 0.08
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (29 bp):
AATATTTTATATATATATAATTATATTTA
Found at i:1380152 original size:21 final size:20
Alignment explanation
Indices: 1380127--1380190 Score: 89
Period size: 21 Copynumber: 3.2 Consensus size: 20
1380117 CTCATACAAG
1380127 TTAATTTTAAATATGATTAAT
1 TTAATTTTAAAT-TGATTAAT
1380148 TTAATTTTAAATTGATTTAAT
1 TTAATTTTAAATTGA-TTAAT
1380169 TTAA-TTTAAATT-ATT-AT
1 TTAATTTTAAATTGATTAAT
1380186 TTAAT
1 TTAAT
1380191 AATAAATATA
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.15
18 2 0.05
19 1 0.02
20 11 0.27
21 21 0.51
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
TTAATTTTAAATTGATTAAT
Found at i:1380222 original size:22 final size:21
Alignment explanation
Indices: 1380143--1380224 Score: 76
Period size: 22 Copynumber: 3.8 Consensus size: 21
1380133 TTAAATATGA
* *
1380143 TTAATTTAATTTTAAATTGAT
1 TTAATTTAATTATAAATTTAT
1380164 TTAATTTAATT-TAAATTATTAT
1 TTAATTTAATTATAAA-T-TTAT
* * *
1380186 TTAATAATAAATATATATTTAT
1 TTAAT-TTAATTATAAATTTAT
1380208 TTAAATTTAATTATAAA
1 TT-AATTTAATTATAAA
1380225 ATATATAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
20 4 0.08
21 12 0.24
22 22 0.45
23 8 0.16
24 3 0.06
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (21 bp):
TTAATTTAATTATAAATTTAT
Found at i:1380260 original size:19 final size:21
Alignment explanation
Indices: 1380209--1380261 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
1380199 TATATTTATT
1380209 TAAA-TTTAATTATAAAATATA
1 TAAATTTTAA-TATAAAATATA
*
1380230 TAAATATTAATATAAAA-ATA
1 TAAATTTTAATATAAAATATA
*
1380250 -AATTTTTAATAT
1 TAAATTTTAATAT
1380262 TTATTTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 10 0.36
20 3 0.11
21 11 0.39
22 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAATTTTAATATAAAATATA
Found at i:1380374 original size:21 final size:21
Alignment explanation
Indices: 1380350--1380390 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1380340 AAATTTAAAT
*
1380350 TATAAATCTATCCATAGACAA
1 TATAAATCAATCCATAGACAA
*
1380371 TATAAATCAATTCATAGACA
1 TATAAATCAATCCATAGACA
1380391 TCTTTAATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.17, G:0.05, T:0.29
Consensus pattern (21 bp):
TATAAATCAATCCATAGACAA
Found at i:1381006 original size:20 final size:18
Alignment explanation
Indices: 1380959--1381009 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
1380949 CGGTTTTAAT
*
1380959 TTTTTAATTTTTAAAATA
1 TTTTTAATATTTAAAATA
*
1380977 TTTTAAAATATTTATAAATA
1 TTTT-TAATATTTA-AAATA
1380997 TTTATTAATATTT
1 TTT-TTAATATTT
1381010 TATTACAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 4 0.15
19 7 0.26
20 15 0.56
21 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTTAATATTTAAAATA
Found at i:1381014 original size:11 final size:11
Alignment explanation
Indices: 1380967--1381012 Score: 55
Period size: 10 Copynumber: 4.5 Consensus size: 11
1380957 ATTTTTTAAT
1380967 TTTTA-AAATA
1 TTTTATAAATA
1380977 TTTTA-AAATA
1 TTTTATAAATA
1380987 -TTTATAAATA
1 TTTTATAAATA
*
1380997 -TTTATTAATA
1 TTTTATAAATA
1381007 TTTTAT
1 TTTTAT
1381013 TACAATATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
9 4 0.12
10 24 0.73
11 5 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTATAAATA
Found at i:1389862 original size:24 final size:24
Alignment explanation
Indices: 1389826--1389876 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
1389816 TTTTACTTAT
* *
1389826 TTTTTAAAATTTAGATAATAT-TA
1 TTTTTAAAATTTACATAAAATATA
1389849 TTTTTAAAATTTTACATAAAATATA
1 TTTTTAAAA-TTTACATAAAATATA
1389874 TTT
1 TTT
1389877 ATCTTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 9 0.38
24 10 0.42
25 5 0.21
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
TTTTTAAAATTTACATAAAATATA
Found at i:1389877 original size:23 final size:23
Alignment explanation
Indices: 1389828--1389877 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1389818 TTACTTATTT
* * *
1389828 TTTAAAATTTAGATAATATTATT
1 TTTAAAATTTACATAATAATATA
1389851 TTTAAAATTTTACATAA-AATATA
1 TTTAAAA-TTTACATAATAATATA
1389874 TTTA
1 TTTA
1389878 TCTTTAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
TTTAAAATTTACATAATAATATA
Found at i:1389954 original size:13 final size:13
Alignment explanation
Indices: 1389936--1389961 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1389926 TTATTTATCA
1389936 ATTATTTATTTTT
1 ATTATTTATTTTT
1389949 ATTATTTATTTTT
1 ATTATTTATTTTT
1389962 TATTTAAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
ATTATTTATTTTT
Found at i:1391497 original size:18 final size:18
Alignment explanation
Indices: 1391447--1391502 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
1391437 TAATAATTTT
*
1391447 TAAATTATTATATATTATA
1 TAAATAATT-TATATTATA
*
1391466 T--A-AATTTA-AATATA
1 TAAATAATTTATATTATA
1391480 TAAATAATTTATATTATA
1 TAAATAATTTATATTATA
1391498 TAAAT
1 TAAAT
1391503 TTTAATATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
14 6 0.20
15 2 0.07
16 4 0.13
17 7 0.23
18 10 0.33
19 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TAAATAATTTATATTATA
Found at i:1391498 original size:5 final size:5
Alignment explanation
Indices: 1391488--1391587 Score: 66
Period size: 5 Copynumber: 20.2 Consensus size: 5
1391478 TATAAATAAT
* * *
1391488 TTATA TTATA -TAAA TTTTA ATATA TTTTATA TCTATA TTATA TT-TA
1 TTATA TTATA TTATA TTATA TTATA -T-TATA T-TATA TTATA TTATA
* * * *
1391534 TAATA TT-TA -TATA TTATA TTATA TTATA TTTTA AT-TA TTATC TTCATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TT-ATA
1391582 TTATA T
1 TTATA T
1391588 GTTCATACAG
Statistics
Matches: 73, Mismatches: 14, Indels: 16
0.71 0.14 0.16
Matches are distributed among these distances:
3 1 0.01
4 13 0.18
5 45 0.62
6 10 0.14
7 4 0.05
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (5 bp):
TTATA
Found at i:1391525 original size:32 final size:31
Alignment explanation
Indices: 1391450--1391587 Score: 114
Period size: 32 Copynumber: 4.6 Consensus size: 31
1391440 TAATTTTTAA
*
1391450 ATTAT-TA-TATATTATATAAATTTAAATAT
1 ATTATATATTATATTATATAAATTTTAATAT
*
1391479 A-TAAATAATTTATATTATATAAATTTTAATAT
1 ATTATAT-A-TTATATTATATAAATTTTAATAT
* *
1391511 ATTTTATATCTATATTATAT---TTATAATAT
1 ATTATATAT-TATATTATATAAATTTTAATAT
*
1391540 -TTATATATTATATTATATTATATTTTAAT-T
1 ATTATATATTATATTATA-TAAATTTTAATAT
* *
1391570 ATTATCT-TCATATTATAT
1 ATTATATATTATATTATAT
1391588 GTTCATACAG
Statistics
Matches: 89, Mismatches: 9, Indels: 22
0.74 0.08 0.18
Matches are distributed among these distances:
27 9 0.10
28 10 0.11
29 11 0.12
30 11 0.12
31 12 0.13
32 33 0.37
33 3 0.03
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (31 bp):
ATTATATATTATATTATATAAATTTTAATAT
Found at i:1391525 original size:59 final size:58
Alignment explanation
Indices: 1391434--1391574 Score: 146
Period size: 59 Copynumber: 2.4 Consensus size: 58
1391424 TTAATATACT
*
1391434 TTATAATAATTTTTAA-ATTATTATATATTATA-TAAATTTA-AATATATAAATAATTTATA
1 TTAT-ATAAATTTTAATA-TATTATATATTATATTAAATTTATAATATATAAAT-A-TTATA
* * * *
1391493 TTATATAAATTTTAATATATTTTATATCTATATTATATTTATAATATTTATATATTATA
1 TTATATAAATTTTAATATATTATATAT-TATATTAAATTTATAATATATAAATATTATA
*
1391552 TTATATTATATTTTAAT-TATTAT
1 TTATA-TAAATTTTAATATATTAT
1391575 CTTCATATTA
Statistics
Matches: 70, Mismatches: 7, Indels: 10
0.80 0.08 0.11
Matches are distributed among these distances:
58 19 0.27
59 24 0.34
60 18 0.26
61 9 0.13
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (58 bp):
TTATATAAATTTTAATATATTATATATTATATTAAATTTATAATATATAAATATTATA
Found at i:1391533 original size:27 final size:26
Alignment explanation
Indices: 1391482--1391558 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 26
1391472 TAAATATATA
* *
1391482 AATAATTTATATTATA-TAAATTT-T
1 AATATTTTATATTATATTATATTTAT
1391506 AATATATTTTATATCTATATTATATTTAT
1 -A-ATATTTTATAT-TATATTATATTTAT
1391535 AATATTTATATATTATATTATATT
1 AATATTT-TATATTATATTATATT
1391559 ATATTTTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
25 1 0.02
26 10 0.22
27 21 0.47
28 12 0.27
29 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (26 bp):
AATATTTTATATTATATTATATTTAT
Found at i:1391539 original size:20 final size:18
Alignment explanation
Indices: 1391508--1391566 Score: 72
Period size: 17 Copynumber: 3.5 Consensus size: 18
1391498 TAAATTTTAA
1391508 TATATTTTATATCTATAT
1 TATATTTTATATCTATAT
*
1391526 TATA-TTTATA-ATAT-T
1 TATATTTTATATCTATAT
*
1391541 TATATATTATAT-TATAT
1 TATATTTTATATCTATAT
1391558 TATATTTTA
1 TATATTTTA
1391567 ATTATTATCT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
15 5 0.14
16 11 0.31
17 15 0.43
18 4 0.11
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
TATATTTTATATCTATAT
Found at i:1391753 original size:17 final size:17
Alignment explanation
Indices: 1391731--1391764 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1391721 ATAAATAATT
1391731 TTTTTAACTTAAATAAA
1 TTTTTAACTTAAATAAA
*
1391748 TTTTTAATTTAAATAAA
1 TTTTTAACTTAAATAAA
1391765 ATCTTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTTTAACTTAAATAAA
Found at i:1391771 original size:17 final size:17
Alignment explanation
Indices: 1391734--1391775 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1391724 AATAATTTTT
* * *
1391734 TTAACTTAAATAAATTT
1 TTAATTTAAATAAAATC
1391751 TTAATTTAAATAAAATC
1 TTAATTTAAATAAAATC
1391768 TTAATTTA
1 TTAATTTA
1391776 TGTTAAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (17 bp):
TTAATTTAAATAAAATC
Found at i:1391804 original size:23 final size:23
Alignment explanation
Indices: 1391778--1391828 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
1391768 TTAATTTATG
*
1391778 TTAAAAAGTTATTTAAATATAAA
1 TTAAAAAGTTATTTAAAAATAAA
**
1391801 TTAAAATTTTATTTAAAAATAAA
1 TTAAAAAGTTATTTAAAAATAAA
1391824 TTAAA
1 TTAAA
1391829 TATTAAATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
TTAAAAAGTTATTTAAAAATAAA
Found at i:1392169 original size:26 final size:26
Alignment explanation
Indices: 1392137--1392189 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
1392127 TAAAAAAAAA
*
1392137 TTATTATTACAGCATTTAATATAAAT
1 TTATTATTACAACATTTAATATAAAT
* *
1392163 TTATTATTACAATATTTATTATAAAT
1 TTATTATTACAACATTTAATATAAAT
1392189 T
1 T
1392190 CATCTTGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.51
Consensus pattern (26 bp):
TTATTATTACAACATTTAATATAAAT
Found at i:1392552 original size:18 final size:18
Alignment explanation
Indices: 1392531--1392565 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1392521 TACGATAAAA
* *
1392531 TATTTATTAAAATTTAAT
1 TATTTATCAAAACTTAAT
1392549 TATTTATCAAAACTTAA
1 TATTTATCAAAACTTAA
1392566 AAAATATGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (18 bp):
TATTTATCAAAACTTAAT
Found at i:1396750 original size:21 final size:21
Alignment explanation
Indices: 1396726--1396767 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1396716 GCCCTCAATT
*
1396726 TCTGCAAGTAAGCCTGTAACA
1 TCTGCAAGTAAGCCTGCAACA
*
1396747 TCTGCAATTAAGCCTGCAACA
1 TCTGCAAGTAAGCCTGCAACA
1396768 AAACCTGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (21 bp):
TCTGCAAGTAAGCCTGCAACA
Found at i:1396880 original size:30 final size:30
Alignment explanation
Indices: 1396844--1396907 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
1396834 CCTGCAGTTT
1396844 CTGCCAGATCCTCCACACCAACAAGGTCCA
1 CTGCCAGATCCTCCACACCAACAAGGTCCA
1396874 CTGCCAGATCCTCCACACCAACAAGGTCCA
1 CTGCCAGATCCTCCACACCAACAAGGTCCA
1396904 CTGC
1 CTGC
1396908 TAGGTCTTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.28, C:0.44, G:0.14, T:0.14
Consensus pattern (30 bp):
CTGCCAGATCCTCCACACCAACAAGGTCCA
Found at i:1396925 original size:30 final size:30
Alignment explanation
Indices: 1396844--1396925 Score: 110
Period size: 30 Copynumber: 2.7 Consensus size: 30
1396834 CCTGCAGTTT
*
1396844 CTGCCAGATCCTCCACACCAACAAGGTCCA
1 CTGCCAGATCCTCAACACCAACAAGGTCCA
*
1396874 CTGCCAGATCCTCCACACCAACAAGGTCCA
1 CTGCCAGATCCTCAACACCAACAAGGTCCA
* * * *
1396904 CTGCTAGGTCTTCAACTCCAAC
1 CTGCCAGATCCTCAACACCAAC
1396926 TGAAAGAGCT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.28, C:0.41, G:0.13, T:0.17
Consensus pattern (30 bp):
CTGCCAGATCCTCAACACCAACAAGGTCCA
Found at i:1401386 original size:14 final size:14
Alignment explanation
Indices: 1401350--1401391 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1401340 TAATTTTTTA
*
1401350 ATTTTTT-AAATAG
1 ATTTTTTAAAATAT
*
1401363 A-TTTTGAAAATAT
1 ATTTTTTAAAATAT
1401376 ATTTTTTAAAATAT
1 ATTTTTTAAAATAT
1401390 AT
1 AT
1401392 ATATTTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
12 4 0.17
13 7 0.29
14 13 0.54
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (14 bp):
ATTTTTTAAAATAT
Found at i:1401492 original size:13 final size:13
Alignment explanation
Indices: 1401474--1401507 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1401464 AATAATAGTT
1401474 AATTAAATTAAAA
1 AATTAAATTAAAA
* *
1401487 AATTAACTTAACA
1 AATTAAATTAAAA
1401500 AATTAAAT
1 AATTAAAT
1401508 ATTAATTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (13 bp):
AATTAAATTAAAA
Found at i:1401573 original size:114 final size:116
Alignment explanation
Indices: 1401428--1401925 Score: 445
Period size: 113 Copynumber: 4.3 Consensus size: 116
1401418 ATTATTTTTC
* * * * *
1401428 AAATTTAAAAAA-TATTAATTATTATTGTT-TTAAAAAAATAATAGTTAATTAA-ATTAAAAAAT
1 AAATTAAAAAAATTATT-ATAATTATTATTATTAAAAAAATAATATTTAATTAAGTTTAAAAAAT
1401490 TA-ACTTAACAAATT-AAATATTAATTATTATATTTTTAAAAATAAAAAATTT
65 TATA-TTAACAAATTAAAATATTAATTATTATATTTTTAAAAATAAAAAATTT
* * *
1401541 AAATTAAAAAAAGTTTTTTATAATTATTTTTTAATAAATAAAAATAATATTTAATTAAGTTTAAA
1 AAATTAAAAAAA--TTATTATAATTA-TTATT-ATTAA-AAAAATAATATTTAATTAAGTTT-AA
* *
1401606 AAAATTATATTATCAAATTAAAATATTAATTATTATATTTTTTTGAAAATAAAAAATTT
60 AAAATTATATTAACAAATTAAAATATTAATTATTATA--TTTTTAAAAATAAAAAATTT
* * * ** * * *
1401665 AAATTAAAAAAA-TATAAAAAGT-TTATTATT--ATTAAT--TTTTTAATAAAATTTTAAAAAAT
1 AAATTAAAAAAATTATTATAATTATTATTATTAAAAAAATAATATTTAAT-TAAGTTTAAAAAA-
*
1401724 TTACATTAACAAATTAAAATATTAATTATTATATTTTTAAAAATAAAAAATTTT
64 TTATATTAACAAATTAAAATATTAATTATTATATTTTTAAAAATAAAAAA-TTT
* * ** * *
1401778 AAATT--AAAAATTATTATAATTTTTAATAAAATAAAAAATAATATTTAATTAATTTTAAAAGAT
1 AAATTAAAAAAATTATTATAATTATTATTATTA-AAAAAATAATATTTAATTAAGTTTAAAA-AA
* *
1401841 TTATATGAACAAATTAAAATATT-A--ATTAT-TTTTTAAAAATAAAAAATTAA
64 TTATATTAACAAATTAAAATATTAATTATTATATTTTTAAAAATAAAAAATT-T
** * *
1401891 AAATTAAAAAAAACATAATAATTAATATTAATTAA
1 AAATTAAAAAAATTATTATAATTATTATT-ATTAA
1401926 TATTTGATTT
Statistics
Matches: 312, Mismatches: 45, Indels: 54
0.76 0.11 0.13
Matches are distributed among these distances:
111 5 0.02
112 25 0.08
113 59 0.19
114 41 0.13
115 27 0.09
116 14 0.04
117 31 0.10
118 13 0.04
119 22 0.07
120 2 0.01
121 24 0.08
122 18 0.06
124 31 0.10
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (116 bp):
AAATTAAAAAAATTATTATAATTATTATTATTAAAAAAATAATATTTAATTAAGTTTAAAAAATT
ATATTAACAAATTAAAATATTAATTATTATATTTTTAAAAATAAAAAATTT
Found at i:1401659 original size:53 final size:52
Alignment explanation
Indices: 1401602--1401790 Score: 186
Period size: 59 Copynumber: 3.5 Consensus size: 52
1401592 TAATTAAGTT
* * *
1401602 TAAAAAAATTATATTATCAAATTAAAATATTAATTATTATATTTTTTTGAAAA
1 TAAAAAATTTAAATTAACAAATTAAAATATTAATTATTATATTTTTTT-AAAA
* *
1401655 TAAAAAATTTAAATTAAAAAAATATAAAA-AGTTTATTATTATTAATTTTTTAATAAAA
1 TAAAAAATTTAAATT-AACAAAT-TAAAATA-TTAATTATTA-T-ATTTTTT--TAAAA
* *
1401713 TTTTAAAAAATTTACATTAACAAATTAAAATATTAATTATTATA-TTTTTAAAAA
1 ---TAAAAAATTTAAATTAACAAATTAAAATATTAATTATTATATTTTTTTAAAA
1401767 TAAAAAATTTTAAATTAA-AAATTA
1 TAAAAAA-TTTAAATTAACAAATTA
1401791 TTATAATTTT
Statistics
Matches: 114, Mismatches: 10, Indels: 26
0.76 0.07 0.17
Matches are distributed among these distances:
51 13 0.11
52 9 0.08
53 13 0.11
54 10 0.09
55 14 0.12
56 6 0.05
57 8 0.07
58 5 0.04
59 15 0.13
60 7 0.06
61 14 0.12
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (52 bp):
TAAAAAATTTAAATTAACAAATTAAAATATTAATTATTATATTTTTTTAAAA
Found at i:1401892 original size:14 final size:15
Alignment explanation
Indices: 1401873--1401901 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1401863 TAATTATTTT
1401873 TTAAAAA-TAAAAAA
1 TTAAAAATTAAAAAA
1401887 TTAAAAATTAAAAAA
1 TTAAAAATTAAAAAA
1401902 AACATAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
TTAAAAATTAAAAAA
Found at i:1402144 original size:13 final size:13
Alignment explanation
Indices: 1402126--1402151 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1402116 ATTTCTTCAA
1402126 AATATAAAAAAAT
1 AATATAAAAAAAT
1402139 AATATAAAAAAAT
1 AATATAAAAAAAT
1402152 TTTATTAAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AATATAAAAAAAT
Found at i:1402406 original size:16 final size:17
Alignment explanation
Indices: 1402387--1402419 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1402377 TAATCACCAC
1402387 AAATTTT-ATGACTTTT
1 AAATTTTAATGACTTTT
1402403 AAATTTTAATGACTTTT
1 AAATTTTAATGACTTTT
1402420 TCTGAACATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (17 bp):
AAATTTTAATGACTTTT
Found at i:1404428 original size:128 final size:129
Alignment explanation
Indices: 1404200--1404588 Score: 524
Period size: 128 Copynumber: 3.0 Consensus size: 129
1404190 AAATTAAAAA
** **
1404200 ATTTTATT-AAAATAATAA-AAAAACCC-TTTTTATTTTTTAATTT-ATTTTTTTTATTTTTTTA
1 ATTTTATTAAAAATAATAATAAAAACCCTTTTTTATTTTTTAATTTAAAATTTTTTATTTTTAAA
* *
1404261 AA-AATAATTAATATTTTAATTTGTTGATGTAAA-TTTTTTAAATTTAATTAAATATTATTTTT
66 AATAATAATTAATATTTTAATTTGTTAATATAAATTTTTTTAAATTTAATTAAATATTATTTTT
* **
1404323 ATTTTATTAAAAATTATAATAAAAACCCTTTTTTA-TTTTTAATTTAAAATTTTTTATTTAAAAA
1 ATTTTATTAAAAATAATAATAAAAACCCTTTTTTATTTTTTAATTTAAAATTTTTTATTTTTAAA
* * *
1404387 ATATAATAATTAATATTTTAATTTATTAAT-TAAATTTTTTTAAACTTAATTAAATATTGTTTTT
66 A-ATAATAATTAATATTTTAATTTGTTAATATAAATTTTTTTAAATTTAATTAAATATT-ATTTT
1404451 T
129 T
* *
1404452 ATTTTATTAAAAAATAATAATAATAACTCTTTTTTACTTTTTTAATTTAAAATTTTTTATTTTTT
1 ATTTTATT-AAAAATAATAATAAAAACCCTTTTTTA-TTTTTTAATTTAAAATTTTTTA--TTTT
*
1404517 TAAAAATAATAATTAATATTTTAATTTGTTAATATAATTTTTTTTAAAATTTAATTAAATATTAT
62 TAAAAATAATAATTAATATTTTAATTTGTTAATATAAATTTTTTT-AAATTTAATTAAATATTAT
1404582 TTTT
126 TTTT
1404586 ATT
1 ATT
1404589 AAAAATAATA
Statistics
Matches: 231, Mismatches: 20, Indels: 19
0.86 0.07 0.07
Matches are distributed among these distances:
123 8 0.03
124 9 0.04
125 18 0.08
126 19 0.08
127 5 0.02
128 46 0.20
129 13 0.06
130 24 0.10
132 21 0.09
133 27 0.12
134 25 0.11
135 16 0.07
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (129 bp):
ATTTTATTAAAAATAATAATAAAAACCCTTTTTTATTTTTTAATTTAAAATTTTTTATTTTTAAA
AATAATAATTAATATTTTAATTTGTTAATATAAATTTTTTTAAATTTAATTAAATATTATTTTT
Found at i:1404567 original size:25 final size:27
Alignment explanation
Indices: 1404547--1404614 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
1404537 TTAATTTGTT
*
1404547 AATATAATTTTTTTTAAAATTTAATTA
1 AATATAATTTTTATTAAAATTTAATTA
* *
1404574 AATATTATTTTTATTAAAAATAATAATT-
1 AATATAATTTTTATT-AAAAT-TTAATTA
*
1404602 AATATATTTTTTA
1 AATATAATTTTTA
1404615 AATTAAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
27 13 0.38
28 16 0.47
29 5 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
AATATAATTTTTATTAAAATTTAATTA
Found at i:1404594 original size:28 final size:29
Alignment explanation
Indices: 1404547--1404630 Score: 84
Period size: 27 Copynumber: 2.9 Consensus size: 29
1404537 TTAATTTGTT
* * *
1404547 AATATAATTTTT-TTTAAAAT-TTAATTA
1 AATATTATTTTTATTAAAAATAATAATTA
1404574 AATATTATTTTTATTAAAAATAATAATTA
1 AATATTATTTTTATTAAAAATAATAATTA
*
1404603 ATATATT-TTTTAAATTAAAAAATAATAA
1 A-ATATTATTTT-TATT-AAAAATAATAA
1404631 AATTTAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
27 11 0.23
28 7 0.15
29 11 0.23
30 8 0.17
31 11 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
AATATTATTTTTATTAAAAATAATAATTA
Found at i:1404620 original size:30 final size:30
Alignment explanation
Indices: 1404568--1404630 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
1404558 TTTTAAAATT
*
1404568 TAATTAAATATTATTTTTATT-AAAAATAA
1 TAATTAAATATTATTTTAATTAAAAAATAA
1404597 TAATTAATATATT-TTTTAAATTAAAAAATAA
1 TAATTAA-ATATTATTTT-AATTAAAAAATAA
1404628 TAA
1 TAA
1404631 AATTTAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 11 0.37
30 8 0.27
31 11 0.37
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
TAATTAAATATTATTTTAATTAAAAAATAA
Found at i:1404746 original size:15 final size:15
Alignment explanation
Indices: 1404726--1404758 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1404716 ACAATATTTT
1404726 AAAAA-TTATTTTAAA
1 AAAAATTTA-TTTAAA
1404741 AAAAATTTATTTAAA
1 AAAAATTTATTTAAA
1404756 AAA
1 AAA
1404759 TTTTAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AAAAATTTATTTAAA
Found at i:1404748 original size:12 final size:12
Alignment explanation
Indices: 1404721--1404768 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
1404711 TCAAAACAAT
**
1404721 ATTTTAAAAATT
1 ATTTTAAAAAAA
1404733 ATTTTAAAAAAA
1 ATTTTAAAAAAA
**
1404745 ATTTATTTAAAAA
1 ATTT-TAAAAAAA
1404758 ATTTTAAAAAA
1 ATTTTAAAAAA
1404769 TTATTATTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
12 19 0.66
13 10 0.34
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
ATTTTAAAAAAA
Found at i:1405110 original size:27 final size:27
Alignment explanation
Indices: 1405080--1405134 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
1405070 TAATATTTGA
1405080 TATATTTTAAATTTAAA-TATTAATATT
1 TATATTTTAAATTTAAATTA-TAATATT
**
1405107 TATATTTTATTTTTAAATTATAATATT
1 TATATTTTAAATTTAAATTATAATATT
1405134 T
1 T
1405135 TTTATTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 23 0.92
28 2 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (27 bp):
TATATTTTAAATTTAAATTATAATATT
Found at i:1409257 original size:31 final size:31
Alignment explanation
Indices: 1409219--1409283 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
1409209 TATTAGATCT
1409219 ATACTCTAACACTCATATCCGAATCAAAGTA
1 ATACTCTAACACTCATATCCGAATCAAAGTA
1409250 ATACTCTAACACTCATATCCGAATCAAAGTA
1 ATACTCTAACACTCATATCCGAATCAAAGTA
1409281 ATA
1 ATA
1409284 AAAATTCATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.43, C:0.25, G:0.06, T:0.26
Consensus pattern (31 bp):
ATACTCTAACACTCATATCCGAATCAAAGTA
Found at i:1411737 original size:20 final size:20
Alignment explanation
Indices: 1411699--1411755 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
1411689 ATATTAAATG
*
1411699 TAAATATATTTTA-AAATTTA
1 TAAAT-TATTTTATATATTTA
1411719 TAAATTATTTTATATATTTA
1 TAAATTATTTTATATATTTA
*
1411739 AAAATTATATTTATATA
1 TAAATTAT-TTTATATA
1411756 ATATATGATC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 7 0.21
20 18 0.55
21 8 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TAAATTATTTTATATATTTA
Found at i:1412196 original size:29 final size:29
Alignment explanation
Indices: 1412163--1412226 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
1412153 TTTTTTATTC
*
1412163 ATATAATAAATATATTAAAATTTTAATAT
1 ATATAATAAATATATTAAAATTTAAATAT
* * * *
1412192 TTATAATATATATATTTACATTTAAATAT
1 ATATAATAAATATATTAAAATTTAAATAT
1412221 ATATAA
1 ATATAA
1412227 ACATGAATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (29 bp):
ATATAATAAATATATTAAAATTTAAATAT
Found at i:1413889 original size:21 final size:21
Alignment explanation
Indices: 1413824--1413889 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
1413814 CGAGATATCT
* * *
1413824 ATTTAATTTAAATTAAATTAA
1 ATTTAAATTAATTTAATTTAA
* *
1413845 ATTTAAGATAAATTT--TTAATA
1 ATTTAA-ATTAATTTAATTTA-A
1413866 ATTTAAATTAATTTAATTTAA
1 ATTTAAATTAATTTAATTTAA
1413887 ATT
1 ATT
1413890 ATTATCTAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
20 9 0.26
21 17 0.50
22 8 0.24
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
ATTTAAATTAATTTAATTTAA
Found at i:1413942 original size:35 final size:35
Alignment explanation
Indices: 1413869--1413942 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
1413859 TTTAATAATT
* **
1413869 TAAATTAATTTAATTTAAATTATTATCTAAAATAA
1 TAAAATAATTTAATTTAAATTATTATAAAAAATAA
1413904 TAAAATAATTT-ATTTAAATTTAATTATAAAAAAT-A
1 TAAAATAATTTAATTTAAA-TT-ATTATAAAAAATAA
1413939 TAAA
1 TAAA
1413943 TATTAATATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
34 7 0.21
35 17 0.50
36 10 0.29
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (35 bp):
TAAAATAATTTAATTTAAATTATTATAAAAAATAA
Found at i:1414795 original size:20 final size:19
Alignment explanation
Indices: 1414744--1414799 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 19
1414734 GACTATGATT
**
1414744 TAATTTAATTTAATTTAAGAA
1 TAATTTAA-TTAAAATAA-AA
1414765 TAATTTAATTATAAATAAAA
1 TAATTTAATTA-AAATAAAA
1414785 TAA-TTATATTAAAAT
1 TAATTTA-ATTAAAAT
1414800 TTATTAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 7 0.23
20 12 0.39
21 12 0.39
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
TAATTTAATTAAAATAAAA
Found at i:1414825 original size:20 final size:23
Alignment explanation
Indices: 1414782--1414833 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 23
1414772 ATTATAAATA
*
1414782 AAATAATTATATTAAAATTTATT
1 AAATAATTATATTAAAATTAATT
1414805 AAAT-ATTAT-TTAAAA-TAATT
1 AAATAATTATATTAAAATTAATT
1414825 --ATAATTATA
1 AAATAATTATA
1414834 ACTAGATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 2 0.08
19 5 0.19
20 4 0.15
21 6 0.23
22 5 0.19
23 4 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
AAATAATTATATTAAAATTAATT
Found at i:1415186 original size:20 final size:20
Alignment explanation
Indices: 1415120--1415187 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
1415110 GTATTATATT
1415120 AAATATTTATATAAATTTTA
1 AAATATTTATATAAATTTTA
* *
1415140 ATATATTAATAATAAA--TT-
1 AAATATTTAT-ATAAATTTTA
1415158 -AA-A-TTATATAAATTTTA
1 AAATATTTATATAAATTTTA
1415175 AAATATTTATATA
1 AAATATTTATATA
1415188 TTTATATTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 14
0.67 0.07 0.25
Matches are distributed among these distances:
14 5 0.14
15 3 0.08
16 3 0.08
17 1 0.03
18 2 0.05
19 3 0.08
20 15 0.41
21 5 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATATTTATATAAATTTTA
Found at i:1415200 original size:11 final size:11
Alignment explanation
Indices: 1415184--1415218 Score: 52
Period size: 11 Copynumber: 3.0 Consensus size: 11
1415174 AAAATATTTA
1415184 TATATTTATAT
1 TATATTTATAT
1415195 TATATTTATAT
1 TATATTTATAT
1415206 TAATTATTTATAT
1 T-A-TATTTATAT
1415219 AAAATTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 12 0.55
12 1 0.05
13 9 0.41
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1415201 original size:19 final size:19
Alignment explanation
Indices: 1415177--1415218 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1415167 AAATTTTAAA
*
1415177 ATATTTATA-TATTTATATT
1 ATATTTATATTAATTAT-TT
1415196 ATATTTATATTAATTATTT
1 ATATTTATATTAATTATTT
1415215 ATAT
1 ATAT
1415219 AAAATTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATATTTATATTAATTATTT
Found at i:1416941 original size:16 final size:17
Alignment explanation
Indices: 1416920--1416957 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1416910 TAAGGTTAAT
1416920 AAAATAACAA-AATAAA
1 AAAATAACAATAATAAA
* *
1416936 AAAATAATAATAATTAA
1 AAAATAACAATAATAAA
1416953 AAAAT
1 AAAAT
1416958 CAAATAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAATAACAATAATAAA
Found at i:1417613 original size:17 final size:17
Alignment explanation
Indices: 1417568--1417616 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
1417558 TTAACGATCT
1417568 AAAATTA-TTAT-TTAA
1 AAAATTATTTATATTAA
* *
1417583 AATA-TATTAAATATTAA
1 AAAATTATT-TATATTAA
1417600 AAAATTATTTATATTAA
1 AAAATTATTTATATTAA
1417617 TAATTATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
14 2 0.08
15 4 0.15
16 2 0.08
17 14 0.54
18 4 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAAATTATTTATATTAA
Found at i:1419298 original size:2 final size:2
Alignment explanation
Indices: 1419291--1419316 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1419281 TCAAGCAAAT
1419291 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
1419317 ACAAGGTCAA
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:1422165 original size:17 final size:17
Alignment explanation
Indices: 1422130--1422195 Score: 70
Period size: 17 Copynumber: 4.1 Consensus size: 17
1422120 TTTATTATAA
1422130 TTATATTTAA-AATATT
1 TTATATTTAATAATATT
1422146 TTATATTTATATAA-ATT
1 TTATATTTA-ATAATATT
*
1422163 TTATA--TAATAATAAT
1 TTATATTTAATAATATT
*
1422178 TTATATTTTATAA-ATT
1 TTATATTTAATAATATT
1422194 TT
1 TT
1422196 TAAATATATA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
14 4 0.10
15 9 0.21
16 13 0.31
17 14 0.33
18 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTATATTTAATAATATT
Found at i:1422193 original size:31 final size:30
Alignment explanation
Indices: 1422116--1422195 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 30
1422106 TGTTGTATAT
* * *
1422116 TTTAT-TTATTAT-AATTATATTTAAAATAT
1 TTTATATT-TTATAAATTTTATATAAAATAA
1422145 TTTATATTTATATAAATTTTATATAATAATAA
1 TTTATATTT-TATAAATTTTATATAA-AATAA
1422177 TTTATATTTTATAAATTTT
1 TTTATATTTTATAAATTTT
1422196 TAAATATATA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
29 6 0.14
30 5 0.11
31 20 0.45
32 13 0.30
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
TTTATATTTTATAAATTTTATATAAAATAA
Found at i:1423642 original size:15 final size:15
Alignment explanation
Indices: 1423600--1423652 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
1423590 TTTTAATTTT
*
1423600 TAAAATTTTTAAATA
1 TAAAATATTTAAATA
* **
1423615 TCAAATAAATAAATA
1 TAAAATATTTAAATA
1423630 TAAAATATTTAAAATA
1 TAAAATATTT-AAATA
*
1423646 TATAATA
1 TAAAATA
1423653 AATTATTACT
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
15 18 0.62
16 11 0.38
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAAATATTTAAATA
Found at i:1425227 original size:2 final size:2
Alignment explanation
Indices: 1425220--1425249 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1425210 CTTCTTTTAC
1425220 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
1425250 TGGGTTTTTA
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:1425609 original size:11 final size:11
Alignment explanation
Indices: 1425593--1425617 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1425583 AGTTGAAGTT
1425593 ATTGTTATTTA
1 ATTGTTATTTA
1425604 ATTGTTATTTA
1 ATTGTTATTTA
1425615 ATT
1 ATT
1425618 TAATAATTTA
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:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (11 bp):
ATTGTTATTTA
Found at i:1429292 original size:22 final size:22
Alignment explanation
Indices: 1429253--1429296 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1429243 TTTATAAATC
*
1429253 TAAATTTAAGTTTCATTAATTT
1 TAAATTTAAGTTTAATTAATTT
1429275 TAAAGTTTAA-TTTAATTAATTT
1 TAAA-TTTAAGTTTAATTAATTT
1429297 ATATAATTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (22 bp):
TAAATTTAAGTTTAATTAATTT
Found at i:1429562 original size:14 final size:14
Alignment explanation
Indices: 1429512--1429562 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
1429502 ATAAATTTGA
1429512 TATATTA-ATAAAT
1 TATATTATATAAAT
*
1429525 TAAATTATATAAAT
1 TATATTATATAAAT
* ** *
1429539 TTTAAAATATATAT
1 TATATTATATAAAT
1429553 TATATTATAT
1 TATATTATAT
1429563 TTTTTATTTT
Statistics
Matches: 28, Mismatches: 9, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
13 6 0.21
14 22 0.79
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TATATTATATAAAT
Found at i:1429875 original size:18 final size:18
Alignment explanation
Indices: 1429852--1429898 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
1429842 TCAGCTTAAG
1429852 TACATATATATGTGTGTA
1 TACATATATATGTGTGTA
*
1429870 TACATATATGTGTGTGTA
1 TACATATATATGTGTGTA
*
1429888 TATATATATAT
1 TACATATATAT
1429899 ATATATATAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (18 bp):
TACATATATATGTGTGTA
Found at i:1429878 original size:16 final size:16
Alignment explanation
Indices: 1429857--1429894 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1429847 TTAAGTACAT
1429857 ATATATGTGTGTATAC
1 ATATATGTGTGTATAC
* *
1429873 ATATATGTGTGTGTAT
1 ATATATGTGTGTATAC
1429889 ATATAT
1 ATATAT
1429895 ATATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.03, G:0.18, T:0.47
Consensus pattern (16 bp):
ATATATGTGTGTATAC
Found at i:1430763 original size:2 final size:2
Alignment explanation
Indices: 1430756--1430786 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1430746 GGATAAATGC
*
1430756 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1430787 GCCTCAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1431279 original size:21 final size:21
Alignment explanation
Indices: 1431254--1431314 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
1431244 TTTAACATAT
1431254 ATTTTTATATTTATATTTAAA
1 ATTTTTATATTTATATTTAAA
* * * *
1431275 ATTTTAATATATATA-ATAAT
1 ATTTTTATATTTATATTTAAA
*
1431295 TTTTATTATATTTATATTTA
1 ATTT-TTATATTTATATTTA
1431315 TATAATGAAT
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
20 6 0.20
21 22 0.73
22 2 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTTTTATATTTATATTTAAA
Found at i:1433271 original size:18 final size:18
Alignment explanation
Indices: 1433231--1433269 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1433221 AAAGAAAAAC
* *
1433231 AAATCTCTTACATATTCT
1 AAATGTCTTACATATTAT
1433249 AAATGTCTTAACATATTAT
1 AAATGTCTT-ACATATTAT
1433268 AA
1 AA
1433270 TGCCATAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.41
Consensus pattern (18 bp):
AAATGTCTTACATATTAT
Found at i:1433896 original size:16 final size:15
Alignment explanation
Indices: 1433868--1433909 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 15
1433858 GTTAATTTGT
1433868 AAAATATTAATTATAA
1 AAAATA-TAATTATAA
1433884 ATAAATATAATTATAA
1 A-AAATATAATTATAA
1433900 AAATATATAA
1 AAA-ATATAA
1433910 AACTAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 2 0.08
16 17 0.71
17 5 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AAAATATAATTATAA
Found at i:1434065 original size:42 final size:40
Alignment explanation
Indices: 1434012--1434095 Score: 100
Period size: 41 Copynumber: 2.0 Consensus size: 40
1434002 AAATATTTAA
**
1434012 TTATCAATTTAAGAAACTATTTTATAT-TTAA-TATATTATTT
1 TTATCAATTTAA-AAA-TAAATTATATATTAATTATATT-TTT
1434053 TTATCAAATTTAAAAATAAATTATATATTAATTATATTTTT
1 TTATC-AATTTAAAAATAAATTATATATTAATTATATTTTT
1434094 TT
1 TT
1434096 CTATAAATAC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
40 8 0.21
41 17 0.45
42 13 0.34
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.54
Consensus pattern (40 bp):
TTATCAATTTAAAAATAAATTATATATTAATTATATTTTT
Found at i:1436205 original size:28 final size:28
Alignment explanation
Indices: 1436174--1436229 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
1436164 GGTGGATACG
1436174 TGAGAAAATTATAGGGACGGTGCTTCGC
1 TGAGAAAATTATAGGGACGGTGCTTCGC
1436202 TGAGAAAATTATAGGGACGGTGCTTCGC
1 TGAGAAAATTATAGGGACGGTGCTTCGC
1436230 AGCACACATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.14, G:0.32, T:0.25
Consensus pattern (28 bp):
TGAGAAAATTATAGGGACGGTGCTTCGC
Found at i:1436615 original size:27 final size:23
Alignment explanation
Indices: 1436584--1436646 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 23
1436574 TAATTTTATT
*
1436584 TATTATTTTTAATAGATTAAATAAAAA
1 TATTATTTTT-ATA-A-AAAAT-AAAA
1436611 TATTA-TTTTATAAAAAATAAAA
1 TATTATTTTTATAAAAAATAAAA
1436633 TATTA-TTTTATAAA
1 TATTATTTTTATAAA
1436647 GTAAGGTTAG
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
22 18 0.51
23 4 0.11
24 1 0.03
25 3 0.09
26 4 0.11
27 5 0.14
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
TATTATTTTTATAAAAAATAAAA
Found at i:1436635 original size:22 final size:23
Alignment explanation
Indices: 1436602--1436646 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
1436592 TTAATAGATT
1436602 AAATAAAAATATTATTTTATAAA
1 AAATAAAAATATTATTTTATAAA
1436625 AAAT-AAAATATTATTTTATAAA
1 AAATAAAAATATTATTTTATAAA
1436647 GTAAGGTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
AAATAAAAATATTATTTTATAAA
Found at i:1437551 original size:18 final size:19
Alignment explanation
Indices: 1437528--1437569 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1437518 AATATGACGT
**
1437528 ATGAA-TTTAAATTTTTGA
1 ATGAATTTTAAAGCTTTGA
1437546 ATGAATTTTAAAGCTTTGA
1 ATGAATTTTAAAGCTTTGA
1437565 ATGAA
1 ATGAA
1437570 AATTAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.40, C:0.02, G:0.14, T:0.43
Consensus pattern (19 bp):
ATGAATTTTAAAGCTTTGA
Found at i:1438199 original size:20 final size:20
Alignment explanation
Indices: 1438164--1438220 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
1438154 TAGAGTTAAG
*
1438164 TTTTTACAAATATAAATAAAT
1 TTTTTAAAAAT-TAAATAAAT
1438185 TTTTTAAAAATTAAATAAAT
1 TTTTTAAAAATTAAATAAAT
*
1438205 TATTTAAAAATTAAAT
1 TTTTTAAAAATTAAAT
1438221 TTCAATTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 24 0.71
21 10 0.29
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
TTTTTAAAAATTAAATAAAT
Found at i:1439838 original size:22 final size:23
Alignment explanation
Indices: 1439782--1439838 Score: 55
Period size: 22 Copynumber: 2.5 Consensus size: 23
1439772 TTGATTTATA
* *
1439782 TAATTATTTTTAAAATATAATATT
1 TAATAATTTTT-AAATATAAAATT
* *
1439806 TAATAA-ATTTAAATTTAAAATT
1 TAATAATTTTTAAATATAAAATT
1439828 TAA-AATTTTTA
1 TAATAATTTTTA
1439839 TTTTATTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
21 2 0.07
22 17 0.63
23 3 0.11
24 5 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TAATAATTTTTAAATATAAAATT
Found at i:1439960 original size:21 final size:20
Alignment explanation
Indices: 1439914--1439961 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 20
1439904 TGGCTATTTA
*
1439914 AATATTTATATTGTATCTAT
1 AATATTTATATTATATCTAT
1439934 -ATATTT-TATTATATCATAAT
1 AATATTTATATTATATC-T-AT
1439954 AATATTTA
1 AATATTTA
1439962 AAATATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
18 8 0.35
19 7 0.30
20 2 0.09
21 6 0.26
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (20 bp):
AATATTTATATTATATCTAT
Found at i:1440010 original size:18 final size:19
Alignment explanation
Indices: 1439969--1440011 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
1439959 TTAAAATATT
**
1439969 TTATATTATATAATTTTTA
1 TTATATTATATAATTCATA
*
1439988 ATATATTA-ATAATTCATA
1 TTATATTATATAATTCATA
1440006 TTATAT
1 TTATAT
1440012 AAATTTTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATATTATATAATTCATA
Found at i:1440047 original size:21 final size:20
Alignment explanation
Indices: 1439931--1440049 Score: 61
Period size: 21 Copynumber: 6.0 Consensus size: 20
1439921 ATATTGTATC
* *
1439931 TATATATTTT-ATTATATCA
1 TATATATTTTAATTATTTTA
* *
1439950 TAATAATATTTAAAATATTTTA
1 T-AT-ATATTTTAATTATTTTA
*
1439972 TAT-TA-TATAA-T-TTTTA
1 TATATATTTTAATTATTTTA
* *
1439988 -ATATATTAATAATTCATATTA
1 TATATATT-TTAATT-ATTTTA
* *
1440009 TATAAATTTTAAAATATTTTA
1 TATATATTTT-AATTATTTTA
1440030 TGATATATTTTAATTATTTT
1 T-ATATATTTTAATTATTTT
1440050 TTGTTTTATA
Statistics
Matches: 75, Mismatches: 13, Indels: 22
0.68 0.12 0.20
Matches are distributed among these distances:
15 2 0.03
16 7 0.09
17 2 0.03
18 7 0.09
19 4 0.05
20 2 0.03
21 27 0.36
22 24 0.32
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (20 bp):
TATATATTTTAATTATTTTA
Found at i:1440920 original size:22 final size:22
Alignment explanation
Indices: 1440893--1440936 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1440883 TTTAAATTTT
* *
1440893 TATTAAATTGATCAATTTAATA
1 TATTAAACTAATCAATTTAATA
*
1440915 TATTAAACTAATTAATTTAATA
1 TATTAAACTAATCAATTTAATA
1440937 ACAAAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (22 bp):
TATTAAACTAATCAATTTAATA
Found at i:1441876 original size:32 final size:30
Alignment explanation
Indices: 1441840--1441901 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 30
1441830 TGAATATATA
1441840 TAATTT-TATAAATATTTAAATTTAAATTTATT
1 TAATTTATATAAA-ATTTAAA-TT-AATTTATT
*
1441872 TAATTTATTTAAAATTTAAATTAATTTATT
1 TAATTTATATAAAATTTAAATTAATTTATT
1441902 AGTTATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 8 0.29
31 2 0.07
32 13 0.46
33 5 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
TAATTTATATAAAATTTAAATTAATTTATT
Found at i:1441900 original size:21 final size:19
Alignment explanation
Indices: 1441859--1441901 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
1441849 AAATATTTAA
*
1441859 ATTTAAATTTATTTAATTT
1 ATTTAAATTTAATTAATTT
1441878 ATTTAAAATTTAAATTAATTT
1 ATTT-AAATTT-AATTAATTT
1441899 ATT
1 ATT
1441902 AGTTATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 6 0.29
21 11 0.52
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTTAAATTTAATTAATTT
Found at i:1442699 original size:27 final size:27
Alignment explanation
Indices: 1442640--1442729 Score: 71
Period size: 29 Copynumber: 3.3 Consensus size: 27
1442630 TGATTCACCT
**
1442640 AAATATAA-TTTAAAT-TTTTATTAAA
1 AAATATAATTTTAAATATAATATTAAA
*
1442665 GTAA-ATAATTTTAAATATAATATTAAA
1 -AAATATAATTTTAAATATAATATTAAA
* *
1442692 AAATATAATAATTTTAATA-AATATAAAA
1 AAATATAAT--TTTAAATATAATATTAAA
1442720 ATAATATAAT
1 A-AATATAAT
1442730 AAATATGTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
25 4 0.08
26 11 0.21
27 13 0.25
28 9 0.17
29 15 0.29
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (27 bp):
AAATATAATTTTAAATATAATATTAAA
Found at i:1442708 original size:18 final size:18
Alignment explanation
Indices: 1442681--1442722 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1442671 AATTTTAAAT
1442681 ATAATATTAAAAAATATA
1 ATAATATTAAAAAATATA
* *
1442699 ATAATTTTAATAAATATA
1 ATAATATTAAAAAATATA
*
1442717 AAAATA
1 ATAATA
1442723 ATATAATAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
ATAATATTAAAAAATATA
Found at i:1442717 original size:15 final size:16
Alignment explanation
Indices: 1442676--1442717 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
1442666 TAAATAATTT
1442676 TAAATATAATATTAAA
1 TAAATATAATATTAAA
*
1442692 -AAATATAATAATTTTAA
1 TAAATATAAT-A-TTAAA
1442709 TAAATATAA
1 TAAATATAA
1442718 AAATAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 9 0.41
16 1 0.05
17 4 0.18
18 8 0.36
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAATATAATATTAAA
Found at i:1443030 original size:15 final size:16
Alignment explanation
Indices: 1442998--1443033 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1442988 AATAAAAAAA
1442998 TTAAAAATTTGAATTT
1 TTAAAAATTTGAATTT
*
1443014 TTAATAATTTG-ATTT
1 TTAAAAATTTGAATTT
1443029 TTAAA
1 TTAAA
1443034 TTATTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (16 bp):
TTAAAAATTTGAATTT
Found at i:1444439 original size:19 final size:19
Alignment explanation
Indices: 1444415--1444497 Score: 64
Period size: 19 Copynumber: 4.3 Consensus size: 19
1444405 TTAGAGATAA
1444415 TAGTTTAATATTATATATG
1 TAGTTTAATATTATATATG
*
1444434 TAGTTTAATTATTAAATA-G
1 TAGTTTAA-TATTATATATG
* * *
1444453 TAATTTAAGATCT-TGATAATT
1 TAGTTTAATAT-TAT-AT-ATG
1444474 TA-TCTTAATATTATATATG
1 TAGT-TTAATATTATATATG
1444493 TAGTT
1 TAGTT
1444498 AGAGATAATA
Statistics
Matches: 49, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
18 2 0.04
19 24 0.49
20 14 0.29
21 9 0.18
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.51
Consensus pattern (19 bp):
TAGTTTAATATTATATATG
Found at i:1446425 original size:3 final size:3
Alignment explanation
Indices: 1446417--1446452 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1446407 GTTGTCGTTG
1446417 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1446453 ACTATTTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1448125 original size:21 final size:20
Alignment explanation
Indices: 1448079--1448125 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
1448069 AAAAATAATA
* *
1448079 TTAATAAATTAAAAAATATT
1 TTAATTAATTAAAAAAGATT
1448099 TT--TTAATTATAAAAAGATT
1 TTAATTAATTA-AAAAAGATT
1448118 TTAATTAA
1 TTAATTAA
1448126 AAATAAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
18 6 0.27
19 10 0.45
20 2 0.09
21 4 0.18
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
TTAATTAATTAAAAAAGATT
Found at i:1449017 original size:8 final size:8
Alignment explanation
Indices: 1449004--1449028 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1448994 GATGAGTGTG
1449004 ATTATATT
1 ATTATATT
1449012 ATTATATT
1 ATTATATT
1449020 ATTATATT
1 ATTATATT
1449028 A
1 A
1449029 AATAGTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
ATTATATT
Found at i:1449126 original size:2 final size:2
Alignment explanation
Indices: 1449119--1449149 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1449109 ACTTGATACT
*
1449119 TC TC TC TC TC TC TC TC TC TT TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1449150 TTTTATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:1451693 original size:23 final size:23
Alignment explanation
Indices: 1451646--1451707 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 23
1451636 AAAATATAAA
*
1451646 ATAATTATAAATTTTGTTAACAATA-
1 ATAATTATAAA--TT-TTAAAAATAT
*
1451671 ATATTTAATAAATTTTAAAAATAT
1 ATAATT-ATAAATTTTAAAAATAT
1451695 ATAATTATAAATT
1 ATAATTATAAATT
1451708 AATAATTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
23 15 0.47
24 7 0.22
25 5 0.16
26 5 0.16
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATAATTATAAATTTTAAAAATAT
Found at i:1452533 original size:15 final size:14
Alignment explanation
Indices: 1452508--1452547 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
1452498 AATTAAATTG
1452508 ATATAATATTTTAT
1 ATATAATATTTTAT
1452522 ATATATATATTTTAT
1 ATATA-ATATTTTAT
*
1452537 CAAATAATATT
1 -ATATAATATT
1452548 ACTATTTACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 5 0.22
15 14 0.61
16 4 0.17
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (14 bp):
ATATAATATTTTAT
Found at i:1458681 original size:29 final size:31
Alignment explanation
Indices: 1458649--1458709 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
1458639 TTAATAAATA
* *
1458649 AATTAAT-ATTTTCT-CTACAATTATATATG
1 AATTAATAATTTTCTAATACAAATATATATG
**
1458678 AATTTTTAATTTTCTAATACAAATATATATG
1 AATTAATAATTTTCTAATACAAATATATATG
1458709 A
1 A
1458710 TATAGCATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 5 0.19
30 7 0.27
31 14 0.54
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.48
Consensus pattern (31 bp):
AATTAATAATTTTCTAATACAAATATATATG
Found at i:1463827 original size:13 final size:13
Alignment explanation
Indices: 1463800--1463836 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
1463790 ATGCGATTAT
*
1463800 AATTTAATTAA-A
1 AATTTTATTAATA
1463812 AATTTTATTAATA
1 AATTTTATTAATA
1463825 AATTTT-TTAATA
1 AATTTTATTAATA
1463837 TTAAAACTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 16 0.70
13 7 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
AATTTTATTAATA
Found at i:1464048 original size:34 final size:34
Alignment explanation
Indices: 1463990--1464077 Score: 96
Period size: 34 Copynumber: 2.6 Consensus size: 34
1463980 TTTTGAAAAA
1463990 TATAATAATTAAAATTAATAAATAAAAATAATAACAT
1 TATAATAATTAAAA-TAATAAATAAAAAT-ATAA-AT
*
1464027 TATAATAATT-AAA-AATTAATAAAAATATAAAT
1 TATAATAATTAAAATAATAAATAAAAATATAAAT
*
1464059 T-TAAT-ATTATAAT-ATAAAT
1 TATAATAATTAAAATAATAAAT
1464078 TTAATTTATA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
30 3 0.07
31 11 0.24
32 3 0.07
33 4 0.09
34 12 0.26
36 3 0.07
37 10 0.22
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (34 bp):
TATAATAATTAAAATAATAAATAAAAATATAAAT
Found at i:1464074 original size:19 final size:18
Alignment explanation
Indices: 1464050--1464087 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
1464040 AATTAATAAA
1464050 AATATAAATTTAATATTAT
1 AATATAAATTTAAT-TTAT
1464069 AATATAAATTTAATTTAT
1 AATATAAATTTAATTTAT
1464087 A
1 A
1464088 CTAACATTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AATATAAATTTAATTTAT
Found at i:1465569 original size:17 final size:17
Alignment explanation
Indices: 1465547--1465603 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
1465537 CGTTAAAACT
1465547 TTAAGCTCTCATCTAAC
1 TTAAGCTCTCATCTAAC
** * *
1465564 TTAAGCATCGGAGCATGAC
1 TTAAGC-TCTCATC-TAAC
1465583 TTAAGCTCTCATCTAAC
1 TTAAGCTCTCATCTAAC
1465600 TTAA
1 TTAA
1465604 CCATCTAAGC
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
17 13 0.43
18 8 0.27
19 9 0.30
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.32
Consensus pattern (17 bp):
TTAAGCTCTCATCTAAC
Found at i:1474588 original size:10 final size:10
Alignment explanation
Indices: 1474575--1474601 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1474565 AACTTTAAAC
1474575 CTCTTTGAGT
1 CTCTTTGAGT
1474585 CTCTTTGAGT
1 CTCTTTGAGT
1474595 CTCTTTG
1 CTCTTTG
1474602 GCCTCTTTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.07, C:0.22, G:0.19, T:0.52
Consensus pattern (10 bp):
CTCTTTGAGT
Found at i:1475054 original size:29 final size:30
Alignment explanation
Indices: 1475005--1475080 Score: 93
Period size: 29 Copynumber: 2.5 Consensus size: 30
1474995 TTTTTATTAC
*
1475005 TAATTTAATATATTAATATATTAA-ATTGATA
1 TAATTTAAT-TAATAATATATTAATATT-ATA
1475036 -AATTTAATTAATAATATATTAATATTATA
1 TAATTTAATTAATAATATATTAATATTATA
1475065 TTAATATTAATTAATA
1 -TAAT-TTAATTAATA
1475081 TTATTATAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
29 16 0.40
30 11 0.28
31 3 0.08
32 10 0.25
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (30 bp):
TAATTTAATTAATAATATATTAATATTATA
Found at i:1475058 original size:11 final size:11
Alignment explanation
Indices: 1475010--1475080 Score: 54
Period size: 11 Copynumber: 6.2 Consensus size: 11
1475000 ATTACTAATT
1475010 TAATATATTAA
1 TAATATATTAA
* *
1475021 TATATTAAATTGA
1 TA-A-TATATTAA
*
1475034 TAAATTTAATTAA
1 T-AATAT-ATTAA
1475047 TAATATATTAA
1 TAATATATTAA
*
1475058 TATTATATTAA
1 TAATATATTAA
*
1475069 TATTA-ATTAA
1 TAATATATTAA
1475079 TA
1 TA
1475081 TTATTATAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
10 7 0.14
11 22 0.45
12 6 0.12
13 13 0.27
14 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (11 bp):
TAATATATTAA
Found at i:1475079 original size:21 final size:21
Alignment explanation
Indices: 1475021--1475084 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
1475011 AATATATTAA
* *
1475021 TATATTAA-ATTGATAAAT-T
1 TATATTAATATTAATTAATAT
*
1475040 TA-ATTAATAATATATTAATAT
1 TATATTAATATTA-ATTAATAT
1475061 TATATTAATATTAATTAATAT
1 TATATTAATATTAATTAATAT
1475082 TAT
1 TAT
1475085 TATAAAGTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
18 5 0.14
19 4 0.11
20 5 0.14
21 14 0.38
22 9 0.24
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
TATATTAATATTAATTAATAT
Found at i:1475357 original size:16 final size:17
Alignment explanation
Indices: 1475337--1475377 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
1475327 AGAAAAAGGT
1475337 AAAAAATTAAAAAGAAGA
1 AAAAAATTAAAAAGAA-A
*
1475355 AAAAAGGTTAAAAAGAAA
1 AAAAA-ATTAAAAAGAAA
1475373 AAAAA
1 AAAAA
1475378 TGCAAGAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (17 bp):
AAAAAATTAAAAAGAAA
Found at i:1475374 original size:26 final size:25
Alignment explanation
Indices: 1475321--1475375 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
1475311 AATTAGAGAG
* **
1475321 AAAATAAGAAAAAGGTAAAAAATTA
1 AAAAGAAGAAAAAGGTAAAAAAGAA
*
1475346 AAAAGAAGAAAAAAGGTTAAAAAGAA
1 AAAAGAAG-AAAAAGGTAAAAAAGAA
1475372 AAAA
1 AAAA
1475376 AATGCAAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.11
Consensus pattern (25 bp):
AAAAGAAGAAAAAGGTAAAAAAGAA
Found at i:1475600 original size:23 final size:23
Alignment explanation
Indices: 1475568--1475621 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
1475558 AAATGAAATT
*
1475568 AAAAAT-AAAAGGAAAAAAACAA
1 AAAAATAAAAAAGAAAAAAACAA
* * *
1475590 AAAGATAAAAAAGATAAAAATAA
1 AAAAATAAAAAAGAAAAAAACAA
1475613 AAAAATAAA
1 AAAAATAAA
1475622 TATCAATAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 5 0.19
23 21 0.81
ACGTcount: A:0.81, C:0.02, G:0.07, T:0.09
Consensus pattern (23 bp):
AAAAATAAAAAAGAAAAAAACAA
Found at i:1475688 original size:18 final size:18
Alignment explanation
Indices: 1475665--1475700 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1475655 AAAAATATAC
*
1475665 AAAAAAATTTAAAAAAGA
1 AAAAAAATATAAAAAAGA
*
1475683 AAAAAAATATAATAAAGA
1 AAAAAAATATAAAAAAGA
1475701 GAGAAAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.17
Consensus pattern (18 bp):
AAAAAAATATAAAAAAGA
Found at i:1476120 original size:40 final size:38
Alignment explanation
Indices: 1476070--1476157 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 38
1476060 ATATATAGAA
*
1476070 AAAAATAAAAGAAAAAACAAAGTGAATAAAT-CAAAAAATT
1 AAAAA-AAAAGAAAAAACAAA--GAAAAAATACAAAAAATT
**
1476110 GAAAAAAAAAGTTAAAACAAAGAAAAAATAACAAAAAATT
1 -AAAAAAAAAGAAAAAACAAAGAAAAAAT-ACAAAAAATT
1476150 AAAAAAAA
1 AAAAAAAA
1476158 CAAAGGGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
38 7 0.17
39 8 0.19
40 22 0.52
41 5 0.12
ACGTcount: A:0.76, C:0.05, G:0.07, T:0.12
Consensus pattern (38 bp):
AAAAAAAAAGAAAAAACAAAGAAAAAATACAAAAAATT
Found at i:1476315 original size:21 final size:23
Alignment explanation
Indices: 1476269--1476326 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
1476259 AAACTAAGAG
*
1476269 AAAAAATAAAGTAAATAAATCAA
1 AAAAAATAAAGTAAATAAAACAA
*
1476292 AAAAAAT-AA-TAAAAAAACACAA
1 AAAAAATAAAGTAAATAAA-ACAA
*
1476314 AACAAAAAAAAGT
1 AA-AAAATAAAGT
1476327 TAGTAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 7 0.25
22 7 0.25
23 11 0.39
24 2 0.07
25 1 0.04
ACGTcount: A:0.78, C:0.07, G:0.03, T:0.12
Consensus pattern (23 bp):
AAAAAATAAAGTAAATAAAACAA
Found at i:1476610 original size:22 final size:21
Alignment explanation
Indices: 1476585--1476638 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
1476575 AATTAAAATG
*
1476585 AAAAATAAAAACAACAAAAGGA
1 AAAAATAAAAACAA-AAAAAGA
* ***
1476607 AAAATTAAAGGGAAAAAAAGA
1 AAAAATAAAAACAAAAAAAGA
1476628 AAAAATAAAAA
1 AAAAATAAAAA
1476639 TAAATATCAG
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.78, C:0.04, G:0.11, T:0.07
Consensus pattern (21 bp):
AAAAATAAAAACAAAAAAAGA
Found at i:1476775 original size:26 final size:26
Alignment explanation
Indices: 1476746--1476830 Score: 68
Period size: 26 Copynumber: 3.3 Consensus size: 26
1476736 AAATATATAA
1476746 GAAAAACATGAAAGTAAAAAGAAAAT
1 GAAAAACATGAAAGTAAAAAGAAAAT
* * *
1476772 GAAAAA-AAGAGA-TAAAATAAAAAAAT
1 GAAAAACATGAAAGT-AAA-AAGAAAAT
* * *
1476798 GAAAAAAATGATAGAAAAAAGAAAA-
1 GAAAAACATGAAAGTAAAAAGAAAAT
*
1476823 GATAAACA
1 GAAAAACA
1476831 ATAAAAAGTG
Statistics
Matches: 46, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
24 1 0.02
25 13 0.28
26 25 0.54
27 7 0.15
ACGTcount: A:0.73, C:0.02, G:0.14, T:0.11
Consensus pattern (26 bp):
GAAAAACATGAAAGTAAAAAGAAAAT
Found at i:1476888 original size:11 final size:10
Alignment explanation
Indices: 1476872--1476917 Score: 56
Period size: 10 Copynumber: 4.3 Consensus size: 10
1476862 ATGTTAAACG
*
1476872 AAAAAAATAT
1 AAAAAAATAA
1476882 AAAAAAATAA
1 AAAAAAATAA
1476892 AGCAAAAAATAA
1 A--AAAAAATAA
1476904 AAGAAAAATAA
1 AA-AAAAATAA
1476915 AAA
1 AAA
1476918 GTAAAAAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
10 12 0.38
11 10 0.31
12 10 0.31
ACGTcount: A:0.83, C:0.02, G:0.04, T:0.11
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:1476892 original size:23 final size:22
Alignment explanation
Indices: 1476866--1476957 Score: 69
Period size: 23 Copynumber: 3.9 Consensus size: 22
1476856 TAAAAAATGT
1476866 TAAACGAAAAAAATATAAAAAAA
1 TAAA-GAAAAAAATATAAAAAAA
* *
1476889 TAAAGCAAAAAATAAAAGAAAAA
1 TAAAGAAAAAAATATAA-AAAAA
*
1476912 TAAAAAGTAAAAAAACATAAAAGTAAA
1 T--AAAG-AAAAAAATATAAAA--AAA
* *
1476939 -AAAGTAAAAAAGATAAAAA
1 TAAAGAAAAAAATATAAAAA
1476958 TTAGAAAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
21 1 0.02
22 11 0.20
23 22 0.39
24 4 0.07
25 6 0.11
26 9 0.16
27 3 0.05
ACGTcount: A:0.77, C:0.03, G:0.08, T:0.12
Consensus pattern (22 bp):
TAAAGAAAAAAATATAAAAAAA
Found at i:1476916 original size:17 final size:16
Alignment explanation
Indices: 1476896--1476941 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
1476886 AAATAAAGCA
1476896 AAAAATAAAAGAAAAAT
1 AAAAATAAAA-AAAAAT
*
1476913 AAAAAGTAAAAAAACAT
1 AAAAA-TAAAAAAAAAT
*
1476930 AAAAGTAAAAAA
1 AAAAATAAAAAA
1476942 GTAAAAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 7 0.27
17 14 0.54
18 5 0.19
ACGTcount: A:0.80, C:0.02, G:0.07, T:0.11
Consensus pattern (16 bp):
AAAAATAAAAAAAAAT
Found at i:1476949 original size:16 final size:16
Alignment explanation
Indices: 1476894--1476957 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 16
1476884 AAAAATAAAG
1476894 CAAAAAA-TAAAAGAAA
1 CAAAAAAGTAAAA-AAA
*
1476910 AATAAAAAGTAAAAAAA
1 CA-AAAAAGTAAAAAAA
* *
1476927 CATAAAAGTAAAAAAG
1 CAAAAAAGTAAAAAAA
*
1476943 TAAAAAAGATAAAAA
1 CAAAAAAG-TAAAAA
1476958 TTAGAAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
16 19 0.49
17 15 0.38
18 5 0.13
ACGTcount: A:0.78, C:0.03, G:0.08, T:0.11
Consensus pattern (16 bp):
CAAAAAAGTAAAAAAA
Found at i:1476956 original size:7 final size:8
Alignment explanation
Indices: 1476913--1476957 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
1476903 AAAGAAAAAT
1476913 AAAAAGTA
1 AAAAAGTA
**
1476921 AAAAAACA
1 AAAAAGTA
*
1476929 TAAAAGTA
1 AAAAAGTA
1476937 AAAAAGTA
1 AAAAAGTA
1476945 AAAAAGATA
1 AAAAAG-TA
1476954 AAAA
1 AAAA
1476958 TTAGAAAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
8 24 0.80
9 6 0.20
ACGTcount: A:0.78, C:0.02, G:0.09, T:0.11
Consensus pattern (8 bp):
AAAAAGTA
Found at i:1476957 original size:24 final size:25
Alignment explanation
Indices: 1476913--1476966 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
1476903 AAAGAAAAAT
1476913 AAAAAGTAAAAAAACATAAAAGTA-
1 AAAAAGTAAAAAAACATAAAAGTAG
* *
1476937 AAAAAGT-AAAAAAGATAAAAATTAG
1 AAAAAGTAAAAAAACAT-AAAAGTAG
1476962 AAAAA
1 AAAAA
1476967 AGAGAAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 8 0.31
24 13 0.50
25 5 0.19
ACGTcount: A:0.76, C:0.02, G:0.09, T:0.13
Consensus pattern (25 bp):
AAAAAGTAAAAAAACATAAAAGTAG
Found at i:1477081 original size:17 final size:17
Alignment explanation
Indices: 1477061--1477103 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1477051 AACAAAGTAT
1477061 AAAAAAATTAGATAATA-
1 AAAAAAATTAGAT-ATAG
*
1477078 AAAAACAATTATATATAG
1 AAAAA-AATTAGATATAG
1477096 AAAAAAAT
1 AAAAAAAT
1477104 AAAAGGAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (17 bp):
AAAAAAATTAGATATAG
Found at i:1478296 original size:14 final size:14
Alignment explanation
Indices: 1478277--1478304 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1478267 GAAACACATA
1478277 ATCTAAAAGATGCT
1 ATCTAAAAGATGCT
1478291 ATCTAAAAGATGCT
1 ATCTAAAAGATGCT
1478305 GAAATATTAA
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:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (14 bp):
ATCTAAAAGATGCT
Found at i:1478707 original size:14 final size:14
Alignment explanation
Indices: 1478688--1478715 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1478678 AGAACACATA
1478688 ATCTAAAAGATGCT
1 ATCTAAAAGATGCT
1478702 ATCTAAAAGATGCT
1 ATCTAAAAGATGCT
1478716 GAAATATTAA
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:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (14 bp):
ATCTAAAAGATGCT
Found at i:1479534 original size:2 final size:2
Alignment explanation
Indices: 1479529--1479561 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1479519 ATATATATAT
1479529 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 A
1479562 ATTTTTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1480165 original size:2 final size:2
Alignment explanation
Indices: 1480158--1480187 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1480148 TCTACACATC
1480158 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1480188 TATATATATA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Done.