Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold92
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: 2337674
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 499 characters in sequence are not A, C, G, or T
File 14 of 19
Found at i:1671341 original size:19 final size:18
Alignment explanation
Indices: 1671314--1671361 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
1671304 TATAAAATTT
*
1671314 TAAATATAATTATAATATA
1 TAAAAATAATTATAA-ATA
1671333 TAAAAATAA-TATAAATA
1 TAAAAATAATTATAAATA
* *
1671350 CAAAAATTATTA
1 TAAAAATAATTA
1671362 AACTCATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 10 0.40
18 7 0.28
19 8 0.32
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAAAATAATTATAAATA
Found at i:1672399 original size:15 final size:15
Alignment explanation
Indices: 1672379--1672440 Score: 58
Period size: 15 Copynumber: 4.3 Consensus size: 15
1672369 ATTTCTTAAT
1672379 TATATAATATATATA
1 TATATAATATATATA
* *
1672394 TATATAATTTATATG
1 TATATAATATATATA
* * *
1672409 TGTATATTATATAAA
1 TATATAATATATATA
1672424 TA-ATAA-ATATATA
1 TATATAATATATATA
1672437 -ATAT
1 TATAT
1672441 TATAGTGTAA
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
12 1 0.03
13 8 0.22
14 3 0.08
15 24 0.67
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
TATATAATATATATA
Found at i:1672456 original size:39 final size:37
Alignment explanation
Indices: 1672377--1672449 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
1672367 TAATTTCTTA
*
1672377 ATTATATAATATATATATATATAATTTATATGTGTAT
1 ATTATATAATATATAAATATATAATTTATATGTGTAT
1672414 ATTATATAA-ATAATAAATATATAATATTATA-GTGTA
1 ATTATATAATAT-ATAAATATATAAT-TTATATGTGTA
1672450 AATATTAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
36 2 0.06
37 26 0.79
38 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (37 bp):
ATTATATAATATATAAATATATAATTTATATGTGTAT
Found at i:1672464 original size:39 final size:38
Alignment explanation
Indices: 1672384--1672467 Score: 100
Period size: 37 Copynumber: 2.2 Consensus size: 38
1672374 TTAATTATAT
* * *
1672384 AATATATATATATATAATTTATATGTGTATATTATATA
1 AATATATAAATATATAATTTATATGTGTATATTAAAAA
1672422 AATA-ATAAATATATAATATTATA-GTGTAAATATTAAAAA
1 AATATATAAATATATAAT-TTATATGTGT--ATATTAAAAA
1672461 AATATAT
1 AATATAT
1672468 TTTTATTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
37 16 0.41
38 9 0.23
39 12 0.31
40 2 0.05
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (38 bp):
AATATATAAATATATAATTTATATGTGTATATTAAAAA
Found at i:1674866 original size:25 final size:24
Alignment explanation
Indices: 1674838--1674893 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 24
1674828 TCGTATTAAT
1674838 ATTTAATAATTAAAAAATTATATAA
1 ATTTAATAATTAAAAAA-TATATAA
*
1674863 A-TT--TAATTATAAAATATATAA
1 ATTTAATAATTAAAAAATATATAA
1674884 ATATTAATAA
1 AT-TTAATAA
1674894 AAATATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
21 8 0.31
22 10 0.38
23 2 0.08
24 2 0.08
25 4 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
ATTTAATAATTAAAAAATATATAA
Found at i:1674869 original size:22 final size:22
Alignment explanation
Indices: 1674844--1674903 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 22
1674834 TAATATTTAA
1674844 TAATTAAAAAATTATATAAAT-T
1 TAATTAAAAAA-TATATAAATAT
*
1674866 TAATTATAAAATATATAAATAT
1 TAATTAAAAAATATATAAATAT
1674888 TAA-TAAAAATATATAT
1 TAATTAAAAA-ATATAT
1674904 TTTTTAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.41
22 20 0.59
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAATTAAAAAATATATAAATAT
Found at i:1674910 original size:20 final size:20
Alignment explanation
Indices: 1674846--1674902 Score: 73
Period size: 21 Copynumber: 2.9 Consensus size: 20
1674836 ATATTTAATA
*
1674846 ATTAA-AAAATTATATAAAT
1 ATTAATAAAAATATATAAAT
1674865 -TTAATTATAAAATATATAAAT
1 ATTAA-TA-AAAATATATAAAT
1674886 ATTAATAAAAATATATA
1 ATTAATAAAAATATATA
1674903 TTTTTTAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
18 4 0.12
20 11 0.33
21 14 0.42
22 4 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTAATAAAAATATATAAAT
Found at i:1675261 original size:21 final size:20
Alignment explanation
Indices: 1675224--1675266 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
1675214 TGGAATCGTA
*
1675224 ATTTAATATATTTATATTTT
1 ATTTAATATATTTATATATT
1675244 ATTT-ATATATTTTAATATATT
1 ATTTAATATA-TTT-ATATATT
1675265 AT
1 AT
1675267 AATAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 5 0.25
20 7 0.35
21 8 0.40
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTTAATATATTTATATATT
Found at i:1675567 original size:13 final size:13
Alignment explanation
Indices: 1675515--1675584 Score: 58
Period size: 13 Copynumber: 5.3 Consensus size: 13
1675505 ATTTTAAAAT
1675515 TTATATTTATATCA
1 TTATATTTATAT-A
1675529 TATAGTATTT-TA-A
1 T-TA-TATTTATATA
1675542 TTAT-TTTATTATA
1 TTATATTTA-TATA
1675555 TTATATTTATATA
1 TTATATTTATATA
*
1675568 TCATAATTTA-ATA
1 TTAT-ATTTATATA
1675581 TTAT
1 TTAT
1675585 TAAATTAATA
Statistics
Matches: 47, Mismatches: 2, Indels: 15
0.73 0.03 0.23
Matches are distributed among these distances:
10 3 0.06
11 1 0.02
12 4 0.09
13 20 0.43
14 10 0.21
15 4 0.09
16 5 0.11
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (13 bp):
TTATATTTATATA
Found at i:1676259 original size:65 final size:64
Alignment explanation
Indices: 1676190--1676328 Score: 149
Period size: 65 Copynumber: 2.1 Consensus size: 64
1676180 ATTATACTTA
* * * * * *
1676190 ATTAAATTTA-ATAATTTTAAA-TATTATTATATGTATATAATATATATAATATAAGT-TATTAA
1 ATTAAATTTATATAAATATAAATTATT-TTAAATATA-ATAATA-ATATAATATAAATATATAAA
1676252 TAT
63 T-T
*
1676255 ATTAAAATTTATATAAATATAAATTATTTTAAATATAATTATAATATAATATAAATATATAAATT
1 ATT-AAATTTATATAAATATAAATTATTTTAAATATAATAATAATATAATATAAATATATAAATT
1676320 ATTAAATTT
1 ATTAAATTT
1676329 TTATCACGGA
Statistics
Matches: 63, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
64 6 0.10
65 19 0.30
66 18 0.29
67 16 0.25
68 4 0.06
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (64 bp):
ATTAAATTTATATAAATATAAATTATTTTAAATATAATAATAATATAATATAAATATATAAATT
Found at i:1676275 original size:38 final size:39
Alignment explanation
Indices: 1676224--1676324 Score: 101
Period size: 38 Copynumber: 2.7 Consensus size: 39
1676214 TATTATATGT
1676224 ATATAATAT--ATATAATATAAGTTATTAATAT-ATTAAA
1 ATATAATATAAATATAATATAA-TTATTAATATAATTAAA
* * *
1676261 AT-TTATATAAATATAA-ATTATT-TTAAATATAATTATA
1 ATATAATATAAATATAATATAATTATT-AATATAATTAAA
1676298 ATATAATATAAATAT-ATA-AATTATTAA
1 ATATAATATAAATATAATATAATTATTAA
1676325 ATTTTTATCA
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
35 2 0.04
36 12 0.23
37 18 0.35
38 20 0.38
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (39 bp):
ATATAATATAAATATAATATAATTATTAATATAATTAAA
Found at i:1676287 original size:16 final size:16
Alignment explanation
Indices: 1676237--1676316 Score: 58
Period size: 16 Copynumber: 4.9 Consensus size: 16
1676227 TAATATATAT
*
1676237 AATATAAGTTATTAATA
1 AATATAAATTA-TAATA
*
1676254 TAT-TAAAATT-TATATA
1 AATAT-AAATTATA-ATA
**
1676270 AATATAAATTATTTTA
1 AATATAAATTATAATA
1676286 AATAT-AATTATAATA
1 AATATAAATTATAATA
1676301 TAATATAAATATATAA
1 -AATATAAAT-TATAA
1676317 ATTATTAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
15 10 0.20
16 23 0.47
17 11 0.22
18 5 0.10
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (16 bp):
AATATAAATTATAATA
Found at i:1676653 original size:20 final size:20
Alignment explanation
Indices: 1676630--1676667 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1676620 ATATTTTATA
1676630 ATTAATTTAAATAAAAATTT
1 ATTAATTTAAATAAAAATTT
* *
1676650 ATTATTTTAATTAAAAAT
1 ATTAATTTAAATAAAAAT
1676668 AATGTTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTAATTTAAATAAAAATTT
Found at i:1677228 original size:16 final size:17
Alignment explanation
Indices: 1677207--1677238 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1677197 GACGTTAAAA
1677207 TTAAATTTTAA-ATTTG
1 TTAAATTTTAATATTTG
1677223 TTAAATTTTAATATTT
1 TTAAATTTTAATATTT
1677239 TGTAAATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TTAAATTTTAATATTTG
Found at i:1677286 original size:78 final size:79
Alignment explanation
Indices: 1677169--1677316 Score: 235
Period size: 78 Copynumber: 1.9 Consensus size: 79
1677159 TTTTTAGTTA
*
1677169 TTATTTAAAAATAAAAATAAAAATTATAGACGTTAAAATTAAATTTTAAATTTGTTAAATTTTAA
1 TTATTTAAAAATAAAAATAAAAATGATAGACGTTAAAATTAAATTTTAAATTTGTTAAATTTTAA
1677234 TATTTTGTAAATTG
66 TATTTTGTAAATTG
* * * * *
1677248 TTATTTGAAAAT-GAAATAGAAATGATAGACGTTGAAATTAAATTTTAAATTTGTTAATTTTTAA
1 TTATTTAAAAATAAAAATAAAAATGATAGACGTTAAAATTAAATTTTAAATTTGTTAAATTTTAA
1677312 TATTT
66 TATTT
1677317 AAAAATTGAT
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
78 52 0.83
79 11 0.17
ACGTcount: A:0.45, C:0.01, G:0.09, T:0.45
Consensus pattern (79 bp):
TTATTTAAAAATAAAAATAAAAATGATAGACGTTAAAATTAAATTTTAAATTTGTTAAATTTTAA
TATTTTGTAAATTG
Found at i:1677989 original size:15 final size:16
Alignment explanation
Indices: 1677953--1677999 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
1677943 TTTTAATACC
*
1677953 TTAAAAAAT-TTTAAA
1 TTAAAATATATTTAAA
*
1677968 TATTAAATATATTTAAA
1 T-TAAAATATATTTAAA
1677985 TTAAAAATATATTTA
1 TT-AAAATATATTTA
1678000 TATCGTACGT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 1 0.04
16 7 0.27
17 18 0.69
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTTAAA
Found at i:1683456 original size:2 final size:2
Alignment explanation
Indices: 1683449--1683478 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1683439 TGTATATGTG
1683449 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
1683479 ATGTGTTGTG
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):
TA
Found at i:1683734 original size:17 final size:16
Alignment explanation
Indices: 1683712--1683747 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1683702 TCAATTCATT
1683712 TAAATTTCATTTAAATC
1 TAAATTTCA-TTAAATC
*
1683729 TAAATTTGATTAAATC
1 TAAATTTCATTAAATC
1683745 TAA
1 TAA
1683748 TTTGATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (16 bp):
TAAATTTCATTAAATC
Found at i:1683751 original size:15 final size:16
Alignment explanation
Indices: 1683712--1683753 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
1683702 TCAATTCATT
*
1683712 TAAATTTCATTTAAATC
1 TAAATTTGA-TTAAATC
1683729 TAAATTTGATTAAATC
1 TAAATTTGATTAAATC
1683745 T-AATTTGAT
1 TAAATTTGAT
1683754 AAAAAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 8 0.33
16 8 0.33
17 8 0.33
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (16 bp):
TAAATTTGATTAAATC
Found at i:1684114 original size:23 final size:24
Alignment explanation
Indices: 1684088--1684143 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 24
1684078 AAAAGATAAT
**
1684088 TTATATTA-AATAAATATTAAATA
1 TTATATTATAATAAATAAAAAATA
*
1684111 TTAT-TTATAATTAATAAAAAATA
1 TTATATTATAATAAATAAAAAATA
1684134 -TATATT-TAAT
1 TTATATTATAAT
1684144 TTAACAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TTATATTATAATAAATAAAAAATA
Found at i:1684138 original size:27 final size:27
Alignment explanation
Indices: 1684086--1684139 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
1684076 TTAAAAGATA
* *
1684086 ATTTATATTAAATAAATATTAAATATT
1 ATTTATATTAAATAAAAAATAAATATT
*
1684113 ATTTATAATT-AATAAAAAATATATATT
1 ATTTAT-ATTAAATAAAAAATAAATATT
1684140 TAATTTAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 20 0.87
28 3 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
ATTTATATTAAATAAAAAATAAATATT
Found at i:1684163 original size:20 final size:20
Alignment explanation
Indices: 1684121--1684177 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1684111 TTATTTATAA
* *
1684121 TTAATA-AAAAATAT-ATAT
1 TTAATATAACAATATAATTT
*
1684139 TTAATTTAACAATATAATTT
1 TTAATATAACAATATAATTT
1684159 TTAATATAACAATATAATT
1 TTAATATAACAATATAATT
1684178 ACTAGATCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
18 5 0.15
19 7 0.21
20 21 0.64
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAATATAACAATATAATTT
Found at i:1689684 original size:29 final size:30
Alignment explanation
Indices: 1689660--1689722 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
1689650 GTTAAAACGT
1689660 AATCTAAAATTTTAAAAAAAATAAAATCAG
1 AATCTAAAATTTTAAAAAAAATAAAATCAG
* * *
1689690 AATCTTAAATTTT-AAAAAAATCAAATTAG
1 AATCTAAAATTTTAAAAAAAATAAAATCAG
1689719 AATC
1 AATC
1689723 AATTTTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 18 0.60
30 12 0.40
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.30
Consensus pattern (30 bp):
AATCTAAAATTTTAAAAAAAATAAAATCAG
Found at i:1691113 original size:22 final size:22
Alignment explanation
Indices: 1691074--1691116 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1691064 CAAACACATA
* *
1691074 AATATTTTGAGATTTAATATTC
1 AATATTATGAGATATAATATTC
*
1691096 AATATTATGATATATAATATT
1 AATATTATGAGATATAATATT
1691117 TTTAAATAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (22 bp):
AATATTATGAGATATAATATTC
Found at i:1691606 original size:25 final size:25
Alignment explanation
Indices: 1691550--1691608 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
1691540 TAAAAATATT
*
1691550 TAAAT-TTTTTTATATATTTAAAAA
1 TAAATATTTTTAATATATTTAAAAA
**
1691574 -ATTTTATTTTTAATATATTTAAAAA
1 TA-AATATTTTTAATATATTTAAAAA
1691599 TAAATATTTT
1 TAAATATTTT
1691609 AAAAAATAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
23 1 0.04
24 1 0.04
25 24 0.89
26 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TAAATATTTTTAATATATTTAAAAA
Found at i:1691609 original size:15 final size:17
Alignment explanation
Indices: 1691585--1691623 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
1691575 TTTTATTTTT
1691585 AATATATTT-AAAAATA
1 AATATATTTAAAAAATA
1691601 AATAT-TTTAAAAAATA
1 AATATATTTAAAAAATA
*
1691617 AAAATAT
1 AATATAT
1691624 AAATATCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 3 0.15
16 16 0.80
17 1 0.05
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AATATATTTAAAAAATA
Found at i:1691696 original size:17 final size:17
Alignment explanation
Indices: 1691676--1691711 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1691666 ATATATCGGA
1691676 TAATATCTTAAATTTTT
1 TAATATCTTAAATTTTT
* *
1691693 TAATTTTTTAAATTTTT
1 TAATATCTTAAATTTTT
1691710 TA
1 TA
1691712 TCCAAACTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
TAATATCTTAAATTTTT
Found at i:1691711 original size:9 final size:9
Alignment explanation
Indices: 1691683--1691711 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1691673 GGATAATATC
1691683 TTAAATTTT
1 TTAAATTTT
1691692 TT-AATTTT
1 TTAAATTTT
1691700 TTAAATTTT
1 TTAAATTTT
1691709 TTA
1 TTA
1691712 TCCAAACTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTAAATTTT
Found at i:1691847 original size:19 final size:19
Alignment explanation
Indices: 1691801--1691848 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1691791 TTATAATTTT
*
1691801 ATAATTAAATTTAATAAAA
1 ATAATTTAATTTAATAAAA
*
1691820 ATATTTTTAATTT-ATAAATA
1 ATA-ATTTAATTTAATAAA-A
1691840 ATAATTTAA
1 ATAATTTAA
1691849 ATCGATGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATAATTTAATTTAATAAAA
Found at i:1692386 original size:12 final size:12
Alignment explanation
Indices: 1692369--1692393 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1692359 TACAGGTATA
1692369 TATATATATAAT
1 TATATATATAAT
1692381 TATATATATAAT
1 TATATATATAAT
1692393 T
1 T
1692394 GTCGGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TATATATATAAT
Found at i:1698734 original size:27 final size:27
Alignment explanation
Indices: 1698691--1698748 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
1698681 TTCGTTGTCT
*
1698691 TCATCATCATCGTCACCACCATCATCA
1 TCATCATCATCGTCACCACCACCATCA
* *
1698718 TCATCATCATC-TCCACCGCCGCCATCA
1 TCATCATCATCGT-CACCACCACCATCA
1698745 TCAT
1 TCAT
1698749 TGCCATTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.26, C:0.43, G:0.05, T:0.26
Consensus pattern (27 bp):
TCATCATCATCGTCACCACCACCATCA
Found at i:1698932 original size:9 final size:9
Alignment explanation
Indices: 1698889--1698937 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
1698879 AGGGTCTTCT
1698889 TCATCACCA
1 TCATCACCA
*
1698898 TAATCACCA
1 TCATCACCA
* *
1698907 CCACCACCA
1 TCATCACCA
* *
1698916 CCACCACCA
1 TCATCACCA
1698925 TCATCACCA
1 TCATCACCA
1698934 TCAT
1 TCAT
1698938 TATCATTGTC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.35, C:0.49, G:0.00, T:0.16
Consensus pattern (9 bp):
TCATCACCA
Found at i:1698932 original size:12 final size:12
Alignment explanation
Indices: 1698900--1698933 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1698890 CATCACCATA
1698900 ATCACCACCACC
1 ATCACCACCACC
*
1698912 ACCACCACCACC
1 ATCACCACCACC
*
1698924 ATCATCACCA
1 ATCACCACCA
1698934 TCATTATCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.35, C:0.56, G:0.00, T:0.09
Consensus pattern (12 bp):
ATCACCACCACC
Found at i:1699451 original size:23 final size:23
Alignment explanation
Indices: 1699425--1699505 Score: 92
Period size: 23 Copynumber: 3.3 Consensus size: 23
1699415 ATACATACAT
1699425 ATATTTATTATAGAAAAATTATA
1 ATATTTATTATAGAAAAATTATA
*
1699448 ATATTTATTGTATGTACAAACA-TATA
1 ATATTTATTATA-G-A-AAA-ATTATA
*
1699474 TACATTTATTATAGAAAAATTATA
1 -ATATTTATTATAGAAAAATTATA
1699498 ATATTTAT
1 ATATTTAT
1699506 CGTCTGTGTA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
23 19 0.40
24 8 0.17
25 2 0.04
26 8 0.17
27 11 0.23
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (23 bp):
ATATTTATTATAGAAAAATTATA
Found at i:1700314 original size:20 final size:20
Alignment explanation
Indices: 1700271--1700314 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1700261 ACGTTTAGTT
* * *
1700271 AAAAAGAAAGAAAGATAAAA
1 AAAAAAAAAAAAAGACAAAA
1700291 AAAAAAAAAAAAAGACAAAGA
1 AAAAAAAAAAAAAGACAAA-A
1700312 AAA
1 AAA
1700315 GTATACCTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.84, C:0.02, G:0.11, T:0.02
Consensus pattern (20 bp):
AAAAAAAAAAAAAGACAAAA
Found at i:1700701 original size:20 final size:18
Alignment explanation
Indices: 1700686--1700725 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1700676 ATAAATTATA
1700686 TTATATATTTTAAAATAT
1 TTATATATTTTAAAATAT
*
1700704 TTATATATTTATAATATAT
1 TTATATATTT-TAAAATAT
1700723 TTA
1 TTA
1700726 AATTATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTATATATTTTAAAATAT
Found at i:1700709 original size:18 final size:19
Alignment explanation
Indices: 1700676--1700725 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
1700666 TAATATGTTA
*
1700676 ATAAATTATATTATATATTT
1 ATAAAATAT-TTATATATTT
1700696 -TAAAATATTTATATATTT
1 ATAAAATATTTATATATTT
*
1700714 ATAATATATTTA
1 ATAAAATATTTA
1700726 AATTATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 10 0.37
19 17 0.63
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATAAAATATTTATATATTT
Found at i:1701470 original size:16 final size:16
Alignment explanation
Indices: 1701436--1701482 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
1701426 AATCAAACAA
*
1701436 AAATATAAAA-TAAAAT
1 AAATA-AAAATTAAATT
1701452 AAA-ACAAAATTAAATT
1 AAATA-AAAATTAAATT
1701468 AAATAAAAATTAAAT
1 AAATAAAAATTAAAT
1701483 ATTATTATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 5 0.19
16 21 0.78
17 1 0.04
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATAAAAATTAAATT
Found at i:1702019 original size:20 final size:19
Alignment explanation
Indices: 1701982--1702029 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1701972 TAAAGTGAAA
1701982 ATAATTTTTACATAATTTT
1 ATAATTTTTACATAATTTT
* *
1702001 ATAATATTTTATATTA-TTT
1 ATAAT-TTTTACATAATTTT
*
1702020 ATATTTTTTA
1 ATAATTTTTA
1702030 ATTCGATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 5 0.20
19 12 0.48
20 8 0.32
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
ATAATTTTTACATAATTTT
Found at i:1702595 original size:3 final size:3
Alignment explanation
Indices: 1702587--1702625 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
1702577 GTGAGACGAT
* *
1702587 ATA ATA ATA ATTA ATA ATA ATA ATA ATG ATA ATG ATA AT
1 ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA AT
1702626 GGTAGGATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:1708432 original size:29 final size:26
Alignment explanation
Indices: 1708381--1708476 Score: 88
Period size: 29 Copynumber: 3.5 Consensus size: 26
1708371 TTTTTATTAT
**
1708381 TTATATTTTAATATTATTAAATATGCATA
1 TTATATTTTAATAAAATT-AATAT--ATA
1708410 TTATATTTTAATAAAATATAATATAATA
1 TTATATTTTAATAAAAT-TAATAT-ATA
1708438 TTATTTATTTTAATAATAATTAATA-A-A
1 TTA--TATTTTAATAA-AATTAATATATA
1708465 TTATATTTTAAT
1 TTATATTTTAAT
1708477 GATAAATTGT
Statistics
Matches: 60, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
25 9 0.15
27 4 0.07
28 7 0.12
29 20 0.33
30 17 0.28
31 3 0.05
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (26 bp):
TTATATTTTAATAAAATTAATATATA
Found at i:1708452 original size:25 final size:25
Alignment explanation
Indices: 1708409--1708481 Score: 76
Period size: 25 Copynumber: 2.7 Consensus size: 25
1708399 AAATATGCAT
1708409 ATTATATTTTAATAA-AATATAATATAA
1 ATTATATTTTAATAATAAT-T-A-ATAA
1708436 TATTATTTATTTTAATAATAATTAATAA
1 -ATTA--TATTTTAATAATAATTAATAA
*
1708464 ATTATATTTTAATGATAA
1 ATTATATTTTAATAATAA
1708482 ATTGTAACAT
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
25 13 0.32
27 4 0.10
28 8 0.20
29 1 0.02
30 12 0.29
31 3 0.07
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (25 bp):
ATTATATTTTAATAATAATTAATAA
Found at i:1710169 original size:2 final size:2
Alignment explanation
Indices: 1710162--1710196 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1710152 TTTTACTTAC
1710162 AT AT AT 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 AT AT AT A
1710197 CATAGAGAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1712091 original size:16 final size:16
Alignment explanation
Indices: 1712059--1712092 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1712049 TCATTACTTG
*
1712059 AATCAAATTCAATAAA
1 AATCAAATTCAAAAAA
*
1712075 AATCAAATTGAAAAAA
1 AATCAAATTCAAAAAA
1712091 AA
1 AA
1712093 AACATTTGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.68, C:0.09, G:0.03, T:0.21
Consensus pattern (16 bp):
AATCAAATTCAAAAAA
Found at i:1713815 original size:18 final size:17
Alignment explanation
Indices: 1713783--1713821 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1713773 AAAATTATCA
**
1713783 ATTATTATATTTAATATT
1 ATTATTATAAATAATA-T
1713801 ATTATTATAAATAATAT
1 ATTATTATAAATAATAT
1713818 ATTA
1 ATTA
1713822 ATTAATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTATTATAAATAATAT
Found at i:1713825 original size:21 final size:20
Alignment explanation
Indices: 1713796--1713845 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
1713786 ATTATATTTA
1713796 ATATTATT-ATTATAAATAAT
1 ATATTATTAATTATAAA-AAT
*
1713816 ATATTAATTAATTTTAAAAAT
1 ATATT-ATTAATTATAAAAAT
1713837 ATATT-TTAA
1 ATATTATTAA
1713846 AAATACTCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 4 0.15
20 5 0.19
21 11 0.41
22 7 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTATTAATTATAAAAAT
Found at i:1713844 original size:13 final size:13
Alignment explanation
Indices: 1713826--1713850 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1713816 ATATTAATTA
1713826 ATTTTAAAAATAT
1 ATTTTAAAAATAT
1713839 ATTTTAAAAATA
1 ATTTTAAAAATA
1713851 CTCATCAATA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTTTAAAAATAT
Found at i:1714136 original size:2 final size:2
Alignment explanation
Indices: 1714129--1714157 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1714119 TTAGACAAAT
1714129 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1714158 AATTAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1715049 original size:109 final size:103
Alignment explanation
Indices: 1714845--1715056 Score: 266
Period size: 109 Copynumber: 2.0 Consensus size: 103
1714835 TCACTTTTTA
* *
1714845 AAAATAATTACTTGAATCAACTTAATTTAAATTTTAAATATGAGAAGTTTTATGTACTCATATAT
1 AAAATAATTACTTGAATCAACTTAATTTAAATTATAAATATGAGAAGTTTTATATACTCATATAT
*
1714910 TGGACTTTGAATAAGATTTCAAATCAATCTATTTTCAT
66 TGGACTTTGAATAAGATTTCAAATCAATCTATCTTCAT
* * * *
1714948 AAAATGATTACTTGAATCAA-TTAATTTAAGTTATAGATATGATAAGTTTTATATACTCATAAGT
1 AAAATAATTACTTGAATCAACTTAATTTAAATTATAAATATGAGAAGTTTTATATACTC------
*
1715012 ATTATATTGGACTTT-AAGTAAGATTTCGAATCAATCTATCTTCAT
60 A-TATATTGGACTTTGAA-TAAGATTTCAAATCAATCTATCTTCAT
1715057 TAATTGGTTC
Statistics
Matches: 93, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
102 33 0.35
103 19 0.20
108 3 0.03
109 38 0.41
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.42
Consensus pattern (103 bp):
AAAATAATTACTTGAATCAACTTAATTTAAATTATAAATATGAGAAGTTTTATATACTCATATAT
TGGACTTTGAATAAGATTTCAAATCAATCTATCTTCAT
Found at i:1715479 original size:126 final size:124
Alignment explanation
Indices: 1715242--1715487 Score: 359
Period size: 126 Copynumber: 2.0 Consensus size: 124
1715232 GAGTTGAATA
* *
1715242 TATTTGAGAATTGTTTTGATTCCATCCATAAGAGTCAATAGAAAAAGTAAATCCCTTATGATACA
1 TATTTAAGAATTGTTTTGATTCCATCCATAAGAGTCAATAGAAAAAGTAAATCCCTTATGATAAA
* *
1715307 CTATATCTAGCTCGATTATTACTAATATGAATAAATTTATCATTTCTTGAAATCTATCT
66 CCATATCTAGCTCGATTATTACTAATATGAATAAATTTATCATTTCTTAAAATCTATCT
* * *
1715366 TATTTAAGAATTGTTTTGATTCGATCCATGATAGTCAAATA-AAAAAGGTAAATCCCTTATGATA
1 TATTTAAGAATTGTTTTGATTCCATCCATAAGAGTC-AATAGAAAAA-GTAAATCCCTTATGAT-
* * * *
1715430 AAACCATATCTAGCTTGATTATTACTGATGTGAATAAATTTATTATTTCTTAAAATCT
63 AAACCATATCTAGCTCGATTATTACTAATATGAATAAATTTATCATTTCTTAAAATCT
1715488 TTGTTTGAAT
Statistics
Matches: 108, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
124 37 0.34
125 20 0.19
126 51 0.47
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (124 bp):
TATTTAAGAATTGTTTTGATTCCATCCATAAGAGTCAATAGAAAAAGTAAATCCCTTATGATAAA
CCATATCTAGCTCGATTATTACTAATATGAATAAATTTATCATTTCTTAAAATCTATCT
Found at i:1717344 original size:20 final size:20
Alignment explanation
Indices: 1717294--1717332 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1717284 ATAAATTATT
*
1717294 ATATATTAA-ATTTTATATAA
1 ATATA-TAATATTTTAAATAA
1717314 ATATATAATATTTTAAATA
1 ATATATAATATTTTAAATA
1717333 TAATTATGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATATAATATTTTAAATAA
Found at i:1717866 original size:16 final size:16
Alignment explanation
Indices: 1717847--1717904 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
1717837 GATCAGAATC
1717847 ATTTTAAATTTAAATT
1 ATTTTAAATTTAAATT
* * ** *
1717863 ATTTTAACTTCATGTC
1 ATTTTAAATTTAAATT
* *
1717879 ATTTTATATTTGAATT
1 ATTTTAAATTTAAATT
1717895 ATTTTAAATT
1 ATTTTAAATT
1717905 CAAGTCATTT
Statistics
Matches: 29, Mismatches: 13, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.57
Consensus pattern (16 bp):
ATTTTAAATTTAAATT
Found at i:1717881 original size:32 final size:32
Alignment explanation
Indices: 1717845--1717914 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
1717835 TAGATCAGAA
* *
1717845 TCATTTTAAATTTAAATTATTTTAACTTCATG
1 TCATTTTAAATTTAAATTATTTTAAATTCAAG
* *
1717877 TCATTTTATATTTGAATTATTTTAAATTCAAG
1 TCATTTTAAATTTAAATTATTTTAAATTCAAG
1717909 TCATTT
1 TCATTT
1717915 AAAGTTATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.33, C:0.09, G:0.04, T:0.54
Consensus pattern (32 bp):
TCATTTTAAATTTAAATTATTTTAAATTCAAG
Found at i:1717914 original size:16 final size:16
Alignment explanation
Indices: 1717845--1717914 Score: 52
Period size: 16 Copynumber: 4.4 Consensus size: 16
1717835 TAGATCAGAA
* *
1717845 TCATTTTAAATTTAAA
1 TCATTTTAAATTCAAG
* * *
1717861 TTATTTTAACTTCATG
1 TCATTTTAAATTCAAG
* *
1717877 TCATTTTATATTTGAA-
1 TCATTTTA-AATTCAAG
*
1717893 TTATTTTAAATTCAAG
1 TCATTTTAAATTCAAG
1717909 TCATTT
1 TCATTT
1717915 AAAGTTATTT
Statistics
Matches: 39, Mismatches: 13, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
15 5 0.13
16 30 0.77
17 4 0.10
ACGTcount: A:0.33, C:0.09, G:0.04, T:0.54
Consensus pattern (16 bp):
TCATTTTAAATTCAAG
Found at i:1718182 original size:21 final size:20
Alignment explanation
Indices: 1718158--1718205 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
1718148 AATTTTTTTA
1718158 TTAAATTA-AATTATATTAGAT
1 TTAAATTAGAATTA-ATTA-AT
1718179 TTAAATTAGAATTAATTAAT
1 TTAAATTAGAATTAATTAAT
*
1718199 TAAAATT
1 TTAAATT
1718206 TTCAAATTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 8 0.32
21 12 0.48
22 5 0.20
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (20 bp):
TTAAATTAGAATTAATTAAT
Found at i:1718803 original size:22 final size:22
Alignment explanation
Indices: 1718778--1718819 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1718768 ATTTTTATTT
1718778 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
1718800 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
1718820 ATATTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:1720217 original size:73 final size:72
Alignment explanation
Indices: 1720041--1720310 Score: 262
Period size: 73 Copynumber: 3.7 Consensus size: 72
1720031 CCAAATTTCC
* * * * * * * *
1720041 CCTACCTCCTTT-ATTTGTACAATGGCCTGCACCTTCAATATTTTGTTGATCATGATCATTATGA
1 CCTACCTCCTTTGA-ATGTACAA-GGCCTGCACTTTCAATATCTTGATGATGATAATGATCATGA
**
1720105 TCATGATGAT
64 T-GGGATGAT
* * **
1720115 CCGACCACCTTTGAATGTAGGAGCGCCTGCACTTTCAATATCTTGATGATGATAATGATCATGAT
1 CCTACCTCCTTTGAATGTACAAG-GCCTGCACTTTCAATATCTTGATGATGATAATGATCATGAT
1720180 GGGATGAT
65 GGGATGAT
* * *
1720188 CCTACCTCCTTTGAATTTACAAGGACCTGCACTTTCAATATCTTAATGATGTTAATGA-C--GAT
1 CCTACCTCCTTTGAATGTACAAGG-CCTGCACTTTCAATATCTTGATGATGATAATGATCATGAT
* *
1720250 GGGCTAAT
65 GGGATGAT
*
1720258 CCTACCTCCTTTGAATGTACTATGGCCTGCACCTTT-AATATCTTGATGATGAT
1 CCTACCTCCTTTGAATGTAC-AAGGCCTGCA-CTTTCAATATCTTGATGATGAT
1720311 GATGGGATGA
Statistics
Matches: 164, Mismatches: 27, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
70 49 0.30
71 7 0.04
72 2 0.01
73 56 0.34
74 49 0.30
75 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (72 bp):
CCTACCTCCTTTGAATGTACAAGGCCTGCACTTTCAATATCTTGATGATGATAATGATCATGATG
GGATGAT
Found at i:1720334 original size:36 final size:36
Alignment explanation
Indices: 1720287--1720359 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
1720277 CTATGGCCTG
1720287 CACCTTTAATATCTTGATGATGATGATGGGATGATC
1 CACCTTTAATATCTTGATGATGATGATGGGATGATC
1720323 CACCTTTAATATCTTGATGATGATGATGGGATGATC
1 CACCTTTAATATCTTGATGATGATGATGGGATGATC
1720359 C
1 C
1720360 TCAGAATTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (36 bp):
CACCTTTAATATCTTGATGATGATGATGGGATGATC
Found at i:1724752 original size:5 final size:5
Alignment explanation
Indices: 1724742--1724779 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
1724732 TCTGGAAACG
* *
1724742 TTTCT TTTCT TTTCT TTTCT TTTCT TATCT TATCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1724780 GTTCGGAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTCT
Found at i:1725370 original size:3 final size:3
Alignment explanation
Indices: 1725355--1725392 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
1725345 AATTGTAATG
* *
1725355 TAA TAA TGA -AA TAA TAA TAA TAA TAA TAA TAA TCA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1725393 AACTTTTCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
2 1 0.03
3 29 0.97
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1725888 original size:30 final size:30
Alignment explanation
Indices: 1725850--1725945 Score: 119
Period size: 30 Copynumber: 3.2 Consensus size: 30
1725840 TTTTAAAATT
1725850 TATTTAATTAATTAAATTATTAAAATATTA
1 TATTTAATTAATTAAATTATTAAAATATTA
* *
1725880 TTTTTAATTAAATTTAAATTA--AAAATAATA
1 TATTTAATT-AA-TTAAATTATTAAAATATTA
1725910 -ATTTAATTAATATAAATTATT-AAATATTA
1 TATTTAATTAAT-TAAATTATTAAAATATTA
1725939 TATTTAA
1 TATTTAA
1725946 ATTTATTTAA
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
27 1 0.02
28 9 0.16
29 14 0.25
30 22 0.39
31 2 0.04
32 8 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
TATTTAATTAATTAAATTATTAAAATATTA
Found at i:1726277 original size:23 final size:23
Alignment explanation
Indices: 1726234--1726297 Score: 56
Period size: 23 Copynumber: 2.6 Consensus size: 23
1726224 ATTTTTTTAT
*
1726234 TTAATTAAAAATAATTTAAATAA
1 TTAATTAAAAATAATTAAAATAA
* *
1726257 TTAATTAATTAATAATAAAATATATA
1 TTAATTAA-AAATAATTAAA-ATA-A
1726283 TTTAATTTAAAAATA
1 -TTAA-TTAAAAATA
1726298 TAATTTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
23 8 0.25
24 8 0.25
25 3 0.09
26 1 0.03
27 8 0.25
28 4 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TTAATTAAAAATAATTAAAATAA
Found at i:1726287 original size:27 final size:27
Alignment explanation
Indices: 1726229--1726289 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
1726219 TTTTTATTTT
* **
1726229 TTTATTTAATTAAAAATAATTTAAATA
1 TTTAATTAATTAAAAATAAAATAAATA
* * *
1726256 ATTAATTAATTAATAATAAAATATATA
1 TTTAATTAATTAAAAATAAAATAAATA
1726283 TTTAATT
1 TTTAATT
1726290 TAAAAATATA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
TTTAATTAATTAAAAATAAAATAAATA
Found at i:1726297 original size:27 final size:25
Alignment explanation
Indices: 1726231--1726297 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 25
1726221 TTTATTTTTT
**
1726231 TATTTAATTAAAAATAATTTAAATA
1 TATTTAATTAAAAATAATAAAAATA
*
1726256 -A-TTAATTAATTAATAATAAAATATA
1 TATTTAATTAA-AAATAATAAAA-ATA
1726281 TATTTAATTTAAAAATA
1 TATTTAA-TTAAAAATA
1726298 TAATTTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
23 8 0.24
24 9 0.27
25 3 0.09
26 1 0.03
27 8 0.24
28 4 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
TATTTAATTAAAAATAATAAAAATA
Found at i:1726302 original size:40 final size:37
Alignment explanation
Indices: 1726245--1726319 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 37
1726235 TAATTAAAAA
1726245 TAATTTAAATAATTAATTAATTAATAATAAAATATATATT
1 TAATTTAAATAATTAATT-ATTAA-AATAAAAT-TATATT
*
1726285 TAATTTAAA-AATATAATTTTTAAAATAAAATTATA
1 TAATTTAAATAAT-TAATTATTAAAATAAAATTATA
1726320 AAACTATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
37 4 0.12
38 8 0.24
39 7 0.21
40 14 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (37 bp):
TAATTTAAATAATTAATTATTAAAATAAAATTATATT
Found at i:1726303 original size:13 final size:13
Alignment explanation
Indices: 1726285--1726341 Score: 51
Period size: 14 Copynumber: 4.2 Consensus size: 13
1726275 AATATATATT
1726285 TAATTTAAAAATA
1 TAATTTAAAAATA
*
1726298 TAATTTTTAAAATA
1 TAA-TTTAAAAATA
* *
1726312 AAATTATAAAACTA
1 TAATT-TAAAAATA
* *
1726326 TAATTGAAATATA
1 TAATTTAAAAATA
1726339 TAA
1 TAA
1726342 AAATTATTTT
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
13 13 0.38
14 21 0.62
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (13 bp):
TAATTTAAAAATA
Found at i:1726311 original size:14 final size:14
Alignment explanation
Indices: 1726285--1726330 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
1726275 AATATATATT
1726285 TAATTTA-AAAATA
1 TAATTTATAAAATA
*
1726298 TAATTTTTAAAATA
1 TAATTTATAAAATA
*
1726312 -AAATTATAAAACTA
1 TAATTTATAAAA-TA
1726326 TAATT
1 TAATT
1726331 GAAATATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 15 0.58
14 8 0.31
15 3 0.12
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
TAATTTATAAAATA
Found at i:1726314 original size:19 final size:19
Alignment explanation
Indices: 1726265--1726320 Score: 51
Period size: 19 Copynumber: 2.8 Consensus size: 19
1726255 AATTAATTAA
1726265 TTAATAATAAAATAT-ATAT
1 TTAA-AATAAAATATAATAT
** *
1726284 TTAATTTAAAAATATAATTT
1 TTAAAAT-AAAATATAATAT
1726304 TTAAAATAAAATTATAA
1 TTAAAATAAAA-TATAA
1726321 AACTATAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 1 0.03
19 15 0.52
20 13 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TTAAAATAAAATATAATAT
Found at i:1727217 original size:6 final size:6
Alignment explanation
Indices: 1727208--1727256 Score: 64
Period size: 6 Copynumber: 8.3 Consensus size: 6
1727198 ATTTTAGTTT
* **
1727208 TTTAAA TTTAAA TTTAAA TTT-AT TTTAAA TTTTTA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
1727255 TT
1 TT
1727257 ATTTTAATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
5 4 0.11
6 32 0.89
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (6 bp):
TTTAAA
Found at i:1727233 original size:36 final size:35
Alignment explanation
Indices: 1727182--1727256 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 35
1727172 TTTACATTAG
* *
1727182 AATTTAAATTAATTTT-ATTTTAGTTTTTTAAATTTA
1 AATTTAAATTAATTTTAAATTT--TTATTTAAATTTA
*
1727218 AATTTAAATTTATTTTAAATTTTTATTTAAATTTA
1 AATTTAAATTAATTTTAAATTTTTATTTAAATTTA
1727253 AATT
1 AATT
1727257 ATTTTAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 16 0.46
36 15 0.43
37 4 0.11
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (35 bp):
AATTTAAATTAATTTTAAATTTTTATTTAAATTTA
Found at i:1727237 original size:23 final size:23
Alignment explanation
Indices: 1727207--1727252 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1727197 TATTTTAGTT
1727207 TTTTAAATTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTAAATTTA
**
1727230 TTTTAAATTTTTATTTAAATTTA
1 TTTTAAATTTAAATTTAAATTTA
1727253 AATTATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTTAAATTTAAATTTAAATTTA
Found at i:1729290 original size:15 final size:14
Alignment explanation
Indices: 1729270--1729319 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
1729260 AATATTTATT
1729270 TTATTAGTAATAATA
1 TTATTA-TAATAATA
1729285 TTATTA-AA-AATTA
1 TTATTATAATAA-TA
*
1729298 TTTTTATAATAATA
1 TTATTATAATAATA
*
1729312 TTAATATA
1 TTATTATA
1729320 TTTTTATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
12 2 0.07
13 9 0.31
14 10 0.34
15 8 0.28
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (14 bp):
TTATTATAATAATA
Found at i:1729306 original size:24 final size:22
Alignment explanation
Indices: 1729279--1729348 Score: 70
Period size: 24 Copynumber: 3.0 Consensus size: 22
1729269 TTTATTAGTA
*
1729279 ATAATATTATTAAAAATTATTTTT
1 ATAATAATATT-AAAA-TATTTTT
*
1729303 ATAATAATATTAATATATTTTT
1 ATAATAATATTAAAATATTTTT
1729325 ATAATTAA-ATTTAAAATAATTTTT
1 ATAA-TAATA-TTAAAAT-ATTTTT
1729349 TATTATTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
22 12 0.30
23 12 0.30
24 16 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATAATAATATTAAAATATTTTT
Found at i:1729384 original size:31 final size:32
Alignment explanation
Indices: 1729316--1729384 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
1729306 ATAATATTAA
*
1729316 TATATTTTTATAATTAAATTTAAAATAATTTT
1 TATATTATTATAATTAAATTTAAAATAATTTT
* *
1729348 T-TATTATT-TAATTATAATTT-TAATATTTTT
1 TATATTATTATAATTA-AATTTAAAATAATTTT
1729378 TATATTA
1 TATATTA
1729385 ATATTTATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
30 15 0.47
31 16 0.50
32 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (32 bp):
TATATTATTATAATTAAATTTAAAATAATTTT
Found at i:1729391 original size:22 final size:24
Alignment explanation
Indices: 1729362--1729414 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 24
1729352 TATTTAATTA
1729362 TAAT-TTTAATAT-TTTTTAT-AT
1 TAATATTTAATATATTTTTATAAT
1729383 TAATATTT-ATATATTTTTATAAT
1 TAATATTTAATATATTTTTATAAT
1729406 TAA-ATTTAA
1 TAATATTTAA
1729415 ATTGATGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 8 0.29
22 14 0.50
23 6 0.21
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TAATATTTAATATATTTTTATAAT
Found at i:1730706 original size:13 final size:13
Alignment explanation
Indices: 1730690--1730715 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1730680 TTTATTTTTT
1730690 AAATATATAATAA
1 AAATATATAATAA
1730703 AAATATATAATAA
1 AAATATATAATAA
1730716 TTTTTATATT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATATATAATAA
Found at i:1731942 original size:19 final size:19
Alignment explanation
Indices: 1731865--1731955 Score: 78
Period size: 19 Copynumber: 4.7 Consensus size: 19
1731855 AACAAAACAG
*
1731865 TATAATTTTTTTTATTTTTT
1 TATAA-TTTTTTTATATTTT
** *
1731885 ATATAAATTTTAATATATTTC
1 -TAT-AATTTTTTTATATTTT
*
1731906 TAT-ATTTATATTAT-TTTT
1 TATAATTT-TTTTATATTTT
1731924 TATAATTTTTTTATATTTT
1 TATAATTTTTTTATATTTT
*
1731943 AATAATTTTTTTA
1 TATAATTTTTTTA
1731956 CATTATAAAT
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
18 15 0.26
19 25 0.43
20 3 0.05
21 13 0.22
22 2 0.03
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (19 bp):
TATAATTTTTTTATATTTT
Found at i:1731950 original size:29 final size:30
Alignment explanation
Indices: 1731865--1731953 Score: 94
Period size: 29 Copynumber: 3.0 Consensus size: 30
1731855 AACAAAACAG
* *
1731865 TATAATTTTTTTTATTTTTTATATAAATTTT
1 TATAA-TTTTTTTATATTTTATATAATTTTT
* * * *
1731896 AAT-ATATTTCTATA-TTTATATTATTTTT
1 TATAATTTTTTTATATTTTATATAATTTTT
1731924 TATAATTTTTTTATATTTTA-ATAATTTTT
1 TATAATTTTTTTATATTTTATATAATTTTT
1731953 T
1 T
1731954 TACATTATAA
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
28 14 0.30
29 25 0.54
30 5 0.11
31 2 0.04
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (30 bp):
TATAATTTTTTTATATTTTATATAATTTTT
Found at i:1731963 original size:16 final size:17
Alignment explanation
Indices: 1731922--1731963 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
1731912 TATATTATTT
*
1731922 TTTATAATTTTTTTATA
1 TTTATAATTTTTTTACA
1731939 TTTTAATAATTTTTTTACA
1 -TTT-ATAATTTTTTTACA
1731958 -TTATAA
1 TTTATAA
1731964 ATTATATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 4 0.18
17 2 0.09
18 3 0.14
19 13 0.59
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTATAATTTTTTTACA
Found at i:1732117 original size:20 final size:19
Alignment explanation
Indices: 1732094--1732167 Score: 57
Period size: 20 Copynumber: 3.8 Consensus size: 19
1732084 CATAGATTAA
1732094 ATAATTTAAAATATAATTAT
1 ATAATTTAAAATATAA-TAT
*
1732114 ATAAATATAATACATATAA-A-
1 AT-AATTTAA-A-ATATAATAT
1732134 ATAA-TTAAAATATAATAT
1 ATAATTTAAAATATAATAT
1732152 A-ATATTTATAAATATA
1 ATA-ATTTA-AAATATA
1732168 TTTTTAAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 16
0.71 0.03 0.26
Matches are distributed among these distances:
16 6 0.14
17 3 0.07
18 5 0.11
19 5 0.11
20 11 0.25
21 7 0.16
22 1 0.02
23 6 0.14
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (19 bp):
ATAATTTAAAATATAATAT
Found at i:1732121 original size:14 final size:14
Alignment explanation
Indices: 1732094--1732167 Score: 64
Period size: 14 Copynumber: 5.2 Consensus size: 14
1732084 CATAGATTAA
1732094 ATAATT-TA-AAAT
1 ATAATTATATAAAT
1732106 ATAATTATATAAAT
1 ATAATTATATAAAT
*
1732120 ATAATACATATAAA-
1 ATAAT-TATATAAAT
*
1732134 ATAATTAAAATATAAT
1 ATAATT-ATATA-AAT
*
1732150 ATAATATTTATAAAT
1 ATAAT-TATATAAAT
1732165 ATA
1 ATA
1732168 TTTTTAAAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
12 6 0.12
13 2 0.04
14 18 0.36
15 15 0.30
16 8 0.16
17 1 0.02
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (14 bp):
ATAATTATATAAAT
Found at i:1735122 original size:2 final size:2
Alignment explanation
Indices: 1735117--1735142 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1735107 ATATATATAT
1735117 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
1735143 TTAAATGCTG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1736970 original size:19 final size:20
Alignment explanation
Indices: 1736946--1737003 Score: 68
Period size: 19 Copynumber: 3.0 Consensus size: 20
1736936 ATTATTAAAT
1736946 AAATTTATTTGATAT-TTT-A
1 AAATTTATTT-ATATATTTAA
1736965 AAATTT-TTTATATATTTAA
1 AAATTTATTTATATATTTAA
*
1736984 AAATTTATATTTTATATTTA
1 AAATTTAT-TTATATATTTA
1737004 TATTTAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
17 4 0.12
18 6 0.18
19 13 0.38
20 1 0.03
21 10 0.29
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
AAATTTATTTATATATTTAA
Found at i:1745334 original size:28 final size:29
Alignment explanation
Indices: 1745277--1745342 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 29
1745267 ATAATATCTG
* * * *
1745277 TATTTTTATTATATTTAAATATTTTTATA
1 TATTATTATTAAATTTAAATAATCTTATA
1745306 TATTATTATTAAATTT-AATAATCTTATA
1 TATTATTATTAAATTTAAATAATCTTATA
*
1745334 TATAATTAT
1 TATTATTAT
1745343 AAAAATATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 18 0.56
29 14 0.44
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (29 bp):
TATTATTATTAAATTTAAATAATCTTATA
Found at i:1745352 original size:14 final size:15
Alignment explanation
Indices: 1745333--1745364 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1745323 ATAATCTTAT
1745333 ATATAAT-TATAAAA
1 ATATAATATATAAAA
1745347 ATATAATATATAAAA
1 ATATAATATATAAAA
1745362 ATA
1 ATA
1745365 ATTAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
ATATAATATATAAAA
Found at i:1747417 original size:17 final size:17
Alignment explanation
Indices: 1747395--1747446 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
1747385 GCCCACTCCT
* *
1747395 TTTTTTGTATCTTTCTG
1 TTTTTTGTATATTTCTC
* *
1747412 TTTTTTTTTTATTTCTC
1 TTTTTTGTATATTTCTC
*
1747429 TTTTTTGCTATTTTTCTC
1 TTTTTTG-TATATTTCTC
1747447 AATTTTTTAT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
17 19 0.70
18 8 0.30
ACGTcount: A:0.06, C:0.13, G:0.06, T:0.75
Consensus pattern (17 bp):
TTTTTTGTATATTTCTC
Found at i:1748071 original size:3 final size:3
Alignment explanation
Indices: 1748065--1748094 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1748055 ATTTTTTTAA
1748065 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1748095 TTAGGAGAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1748998 original size:18 final size:19
Alignment explanation
Indices: 1748965--1749003 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
1748955 GAAATAAAAA
1748965 ATTCATATATTTTTATTAT
1 ATTCATATATTTTTATTAT
*
1748984 ATTCATGTA-TTTTATTAT
1 ATTCATATATTTTTATTAT
1749002 AT
1 AT
1749004 CTTAATCGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (19 bp):
ATTCATATATTTTTATTAT
Found at i:1749904 original size:16 final size:16
Alignment explanation
Indices: 1749883--1749937 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
1749873 ATTTATATAA
1749883 AATTTAATATATTAAT
1 AATTTAATATATTAAT
1749899 AATTT-ATATCATATAA-
1 AATTTAATAT-AT-TAAT
* *
1749915 AATTTAAAATATTTAT
1 AATTTAATATATTAAT
1749931 ATATTTA
1 A-ATTTA
1749938 TAATATATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
15 6 0.19
16 15 0.47
17 11 0.34
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTTAATATATTAAT
Found at i:1749915 original size:32 final size:33
Alignment explanation
Indices: 1749863--1749939 Score: 102
Period size: 32 Copynumber: 2.3 Consensus size: 33
1749853 TCATATTTAA
* * *
1749863 AATATTTTATATTTATATAAAATTTAATATATT
1 AATAATTTATATTCATATAAAATTTAAAATATT
1749896 AATAATTTATA-TCATATAAAATTTAAAATATT
1 AATAATTTATATTCATATAAAATTTAAAATATT
*
1749928 TATATATTTATA
1 AATA-ATTTATA
1749940 ATATATTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 22 0.56
33 17 0.44
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (33 bp):
AATAATTTATATTCATATAAAATTTAAAATATT
Found at i:1749945 original size:19 final size:19
Alignment explanation
Indices: 1749808--1749954 Score: 76
Period size: 19 Copynumber: 7.6 Consensus size: 19
1749798 AGATTTGATA
1749808 ATTTATATATTTAT-ATCAT
1 ATTTATATATTTATAAT-AT
* *
1749827 ATTTATATATTTTTTAA-AA
1 ATTTATATA-TTTATAATAT
1749846 ATTATAATCATATTTA-AA-AT
1 ATT-T-AT-ATATTTATAATAT
*
1749866 ATTT-TATATTTAT-ATAAA
1 ATTTATATATTTATAAT-AT
*
1749884 ATTTAATATATTAATAATTTAT
1 ATTT-ATATATTTATAA--TAT
* *
1749906 ATCATATAAAATTTA-AA-AT
1 AT-TTAT-ATATTTATAATAT
1749925 ATTTATATATTTATAATAT
1 ATTTATATATTTATAATAT
*
1749944 ATTTTTATATT
1 ATTTATATATT
1749955 ACATTAACAT
Statistics
Matches: 98, Mismatches: 13, Indels: 34
0.68 0.09 0.23
Matches are distributed among these distances:
16 8 0.08
17 7 0.07
18 10 0.10
19 30 0.31
20 19 0.19
21 7 0.07
22 10 0.10
23 7 0.07
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTATATATTTATAATAT
Found at i:1750308 original size:22 final size:21
Alignment explanation
Indices: 1750285--1750325 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1750275 TATTTAAATT
1750285 ATTA-TTTAA-TAATTATAAA
1 ATTATTTTAATTAATTATAAA
1750304 ATTATTTTAATTTAATTATAAA
1 ATTATTTTAA-TTAATTATAAA
1750326 TATATATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 5 0.26
22 10 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTATTTTAATTAATTATAAA
Found at i:1752383 original size:16 final size:16
Alignment explanation
Indices: 1752354--1752400 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1752344 TTTAACCTCT
*
1752354 TATTTATTCAAAAAAT-
1 TATTTATT-TAAAAATC
*
1752370 TTTTTATCTTAAAAATC
1 TATTTAT-TTAAAAATC
1752387 TATTTATTTAAAAA
1 TATTTATTTAAAAA
1752401 ATAATAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 19 0.73
17 7 0.27
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (16 bp):
TATTTATTTAAAAATC
Found at i:1752578 original size:18 final size:17
Alignment explanation
Indices: 1752555--1752604 Score: 68
Period size: 16 Copynumber: 3.0 Consensus size: 17
1752545 TAAAAAAAAA
1752555 ATAAAATAATTTAAACTT
1 ATAAAATAATTTAAA-TT
1752573 ATAAAAT-ATTTAAATT
1 ATAAAATAATTTAAATT
*
1752589 -CAAAATAATTTAAATT
1 ATAAAATAATTTAAATT
1752605 TGATGTAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 5 0.17
16 11 0.37
17 7 0.23
18 7 0.23
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (17 bp):
ATAAAATAATTTAAATT
Found at i:1754689 original size:16 final size:16
Alignment explanation
Indices: 1754670--1754716 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
1754660 AATATTTTAT
1754670 ATTTATATAAATTTTG
1 ATTTATATAAATTTTG
*
1754686 ATTTAT-TAATAATTTTT
1 ATTTATAT-A-AATTTTG
1754703 A-TTATATAAATTTT
1 ATTTATATAAATTTT
1754717 AAAATATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
15 7 0.26
16 12 0.44
17 8 0.30
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
ATTTATATAAATTTTG
Found at i:1754690 original size:32 final size:32
Alignment explanation
Indices: 1754654--1754716 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
1754644 TCACAATTAA
1754654 ATTTA-AAAT-ATTTTATATTTATATAAATTTTG
1 ATTTATAAATAATTTT-TA-TTATATAAATTTTG
*
1754686 ATTTATTAATAATTTTTATTATATAAATTTT
1 ATTTATAAATAATTTTTATTATATAAATTTT
1754717 AAAATATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 18 0.64
33 5 0.18
34 5 0.18
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (32 bp):
ATTTATAAATAATTTTTATTATATAAATTTTG
Found at i:1754716 original size:14 final size:15
Alignment explanation
Indices: 1754669--1754717 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 15
1754659 AAATATTTTA
1754669 TATTTATATAAATTT
1 TATTTATATAAATTT
*
1754684 TGATTTATTAATAATTTT
1 T-ATTTA-T-ATAAATTT
1754702 TA-TTATATAAATTT
1 TATTTATATAAATTT
1754716 TA
1 TA
1754718 AAATATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 9 0.31
15 2 0.07
16 8 0.28
17 2 0.07
18 8 0.28
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (15 bp):
TATTTATATAAATTT
Found at i:1756177 original size:28 final size:28
Alignment explanation
Indices: 1756146--1756317 Score: 86
Period size: 29 Copynumber: 6.0 Consensus size: 28
1756136 TTAACTTATA
1756146 AAATTATTTTTAAAATATAATATTTAAT
1 AAATTATTTTTAAAATATAATATTTAAT
** *
1756174 AAATTTAAATTT-AAATTTAAATATTT-AT
1 AAA-TTATTTTTAAAATAT-AATATTTAAT
* * * * *
1756202 AATTTATTTTTATTTAATTTTATTTATTAATT
1 AAATTATTTTTA--AAATATAATAT-TTAA-T
* * *
1756234 AATTTATTTTTAAAAAATAATATTAAAT
1 AAATTATTTTTAAAATATAATATTTAAT
** *
1756262 -AATT-TTTTATTTAATTTAATTAATTT-AT
1 AAATTATTTT-TAAAATATAA-T-ATTTAAT
1756290 ATAATTATTTTT-AAATATAATATTTAAT
1 A-AATTATTTTTAAAATATAATATTTAAT
1756318 GCTTTTAAAT
Statistics
Matches: 106, Mismatches: 23, Indels: 30
0.67 0.14 0.19
Matches are distributed among these distances:
26 4 0.04
27 19 0.18
28 19 0.18
29 28 0.26
30 18 0.17
31 5 0.05
32 13 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
AAATTATTTTTAAAATATAATATTTAAT
Found at i:1756193 original size:21 final size:21
Alignment explanation
Indices: 1756158--1756207 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
1756148 ATTATTTTTA
*
1756158 AAATATAATATTTAATAAATTT
1 AAATTTAATATTTAA-AAATTT
*
1756180 AAATTTAA-ATTTAAATATTT
1 AAATTTAATATTTAAAAATTT
1756200 ATAATTTA
1 A-AATTTA
1756208 TTTTTATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.24
21 12 0.48
22 7 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
AAATTTAATATTTAAAAATTT
Found at i:1756217 original size:17 final size:17
Alignment explanation
Indices: 1756195--1756245 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
1756185 TAAATTTAAA
1756195 TATTTATAATTTATTTT
1 TATTTATAATTTATTTT
*
1756212 TA-TT-TAATTT-TATT
1 TATTTATAATTTATTTT
*
1756226 TATTAATTAATTTATTTT
1 TATTTA-TAATTTATTTT
1756244 TA
1 TA
1756246 AAAAATAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
14 5 0.19
15 7 0.26
16 2 0.07
17 8 0.30
18 5 0.19
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TATTTATAATTTATTTT
Found at i:1756220 original size:88 final size:89
Alignment explanation
Indices: 1756123--1756302 Score: 222
Period size: 88 Copynumber: 2.0 Consensus size: 89
1756113 TGTTTTGCTA
* *
1756123 TTATTTAATTTAATTAACTT-ATAAAATTATTTTTAAAATATAATATTTAATAAATTTAAATTTA
1 TTATTTAATTTAATTAA-TTAATAAAATTATTTTTAAAAAATAATATTAAATAAATTTAAATTT-
*
1756187 AATTTAAAT-ATTTATA-ATTTATTT
64 AATTTAAATAATTTATATAATTATTT
* * * * * **
1756211 TTATTTAATTTTATTTATTAATTAATTTATTTTTAAAAAATAATATTAAATAATTTTTTATTTAA
1 TTATTTAATTTAATTAATTAATAAAATTATTTTTAAAAAATAATATTAAATAAATTTAAATTTAA
*
1756276 TTTAATTAATTTATATAATTATTT
66 TTTAAATAATTTATATAATTATTT
1756300 TTA
1 TTA
1756303 AATATAATAT
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
87 10 0.13
88 58 0.74
89 10 0.13
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.57
Consensus pattern (89 bp):
TTATTTAATTTAATTAATTAATAAAATTATTTTTAAAAAATAATATTAAATAAATTTAAATTTAA
TTTAAATAATTTATATAATTATTT
Found at i:1756252 original size:56 final size:56
Alignment explanation
Indices: 1756191--1756316 Score: 141
Period size: 57 Copynumber: 2.2 Consensus size: 56
1756181 AATTTAAATT
* * *
1756191 TAAATATTTATAAT-TTATTTTTATTTAATTTTATTTATTAAT-TAATTTATTTTTAAA
1 TAAATATTTA-AATAAT-TTTTTATTTAATTTAATTAATTAATATAA-TTATTTTTAAA
*
1756248 -AAATAATATTAAATAATTTTTTATTTAATTTAATTAATTTATATAATTATTTTTAAA
1 TAAAT-AT-TTAAATAATTTTTTATTTAATTTAATTAATTAATATAATTATTTTTAAA
1756305 TATAATATTTAA
1 TA-AATATTTAA
1756317 TGCTTTTAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
56 4 0.07
57 42 0.71
58 10 0.17
59 3 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (56 bp):
TAAATATTTAAATAATTTTTTATTTAATTTAATTAATTAATATAATTATTTTTAAA
Found at i:1757175 original size:16 final size:15
Alignment explanation
Indices: 1757127--1757178 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 15
1757117 AATATATTTA
1757127 AAAATTTTTAATATATT
1 AAAATTTTTAA-ATA-T
1757144 AAAATTTATATAAATAT
1 AAAATTT-T-TAAATAT
1757161 AAAATATTTTAAATAT
1 AAAAT-TTTTAAATAT
1757177 AA
1 AA
1757179 TTATATTAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
16 9 0.28
17 14 0.44
18 6 0.19
19 3 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AAAATTTTTAAATAT
Found at i:1757247 original size:12 final size:13
Alignment explanation
Indices: 1757223--1757252 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1757213 TTTGAATAAT
1757223 TTTAAATTTTATA
1 TTTAAATTTTATA
1757236 TTTAAA-TTTATA
1 TTTAAATTTTATA
1757248 TTTAA
1 TTTAA
1757253 CACGATCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTAAATTTTATA
Found at i:1757338 original size:19 final size:19
Alignment explanation
Indices: 1757310--1757353 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1757300 TATTAAAAAA
1757310 TTAT-TTTTATAA-TAATAT
1 TTATATTTTATAATTAA-AT
1757328 TTATATTTTATAATTAAAT
1 TTATATTTTATAATTAAAT
1757347 TTA-ATTT
1 TTATATTT
1757354 AAAATATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.33
19 13 0.54
20 3 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATATTTTATAATTAAAT
Found at i:1757816 original size:20 final size:20
Alignment explanation
Indices: 1757792--1757830 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1757782 TTTATTAACG
1757792 ATTTTT-TTTAAATATATTT
1 ATTTTTGTTTAAATATATTT
*
1757811 ATTTTTGTTTAAATTTATTT
1 ATTTTTGTTTAAATATATTT
1757831 TTTGAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (20 bp):
ATTTTTGTTTAAATATATTT
Found at i:1758297 original size:27 final size:26
Alignment explanation
Indices: 1758266--1758335 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 26
1758256 TTTAAAATTT
*
1758266 ATATAAATATAAAATATCTTAAATATA
1 ATATAAATATAAAATAT-ATAAATATA
* *
1758293 TTATAAAATACAAAATATATAAATATA
1 ATAT-AAATATAAAATATATAAATATA
1758320 ATATAAATATATAAAT
1 ATATAAATATA-AAAT
1758336 TAATATTAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
26 6 0.17
27 18 0.50
28 12 0.33
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (26 bp):
ATATAAATATAAAATATATAAATATA
Found at i:1758327 original size:19 final size:19
Alignment explanation
Indices: 1758266--1758341 Score: 72
Period size: 19 Copynumber: 4.2 Consensus size: 19
1758256 TTTAAAATTT
1758266 ATATAAATATA-AAATAT-
1 ATATAAATATATAAATATA
* * *
1758283 CT-TAAATATAT-TATAAA
1 ATATAAATATATAAATATA
*
1758300 ATACAAAATATATAAATATA
1 ATA-TAAATATATAAATATA
1758320 ATATAAATATATAAAT-TA
1 ATATAAATATATAAATATA
1758338 ATAT
1 ATAT
1758342 TAAGCCTTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
16 11 0.24
17 2 0.04
18 6 0.13
19 20 0.43
20 7 0.15
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (19 bp):
ATATAAATATATAAATATA
Found at i:1758958 original size:3 final size:3
Alignment explanation
Indices: 1758950--1758988 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1758940 AAAAATTCAT
1758950 TTA 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 TTA
1758989 GCATGGTGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1760071 original size:23 final size:23
Alignment explanation
Indices: 1760028--1760072 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1760018 TCATTACTTT
**
1760028 AAAATAATAAATTTATTTTATAA
1 AAAATAATAAATTTAAATTATAA
1760051 AAAATAA-AAATTTCAAATTATA
1 AAAATAATAAATTT-AAATTATA
1760073 TTAACTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
AAAATAATAAATTTAAATTATAA
Found at i:1760969 original size:30 final size:29
Alignment explanation
Indices: 1760918--1761003 Score: 77
Period size: 30 Copynumber: 2.8 Consensus size: 29
1760908 ATATTTTACG
*
1760918 AATATAAATATAATA-AGTAAAATTTAATTT
1 AATAT-AATATAATATA-TAAAATTTAATGT
*
1760948 AAATATAATATAATATATAAAA-ATAATGT
1 -AATATAATATAATATATAAAATTTAATGT
*
1760977 AATCGTAATATAAATATATAAATATTT
1 AAT-ATAATAT-AATATATAAA-ATTT
1761004 TAAATTTTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
28 3 0.07
29 11 0.24
30 24 0.52
31 7 0.15
32 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.38
Consensus pattern (29 bp):
AATATAATATAATATATAAAATTTAATGT
Found at i:1764662 original size:20 final size:19
Alignment explanation
Indices: 1764637--1764675 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
1764627 TTAATTTAAT
1764637 TTTATAT-TAATATAAATAAA
1 TTTATATAT-ATAT-AATAAA
1764657 TTTATATATATATAATAAA
1 TTTATATATATATAATAAA
1764676 ATTAGAACGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 11 0.61
21 1 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTATATATATATAATAAA
Found at i:1764678 original size:20 final size:20
Alignment explanation
Indices: 1764637--1764675 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1764627 TTAATTTAAT
1764637 TTTATATTAATATAAATAAA
1 TTTATATTAATATAAATAAA
1764657 TTTATA-T-ATATATAATAAA
1 TTTATATTAATATA-AATAAA
1764676 ATTAGAACGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 7 0.39
20 6 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTATATTAATATAAATAAA
Found at i:1766142 original size:24 final size:25
Alignment explanation
Indices: 1766115--1766166 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
1766105 TCAATTTAGT
*
1766115 TTAAAAACAT-ATAATAAAATAAAC
1 TTAAAAACATAATAATAAAATAAAA
*
1766139 TT-AAAATATAATAATAAAATAAAA
1 TTAAAAACATAATAATAAAATAAAA
1766163 TTAA
1 TTAA
1766167 GTATATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.25
24 17 0.71
25 1 0.04
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (25 bp):
TTAAAAACATAATAATAAAATAAAA
Found at i:1766276 original size:20 final size:21
Alignment explanation
Indices: 1766231--1766277 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
1766221 CATTTTTATG
1766231 TATATTAATTTTTTAAAAAAT
1 TATATTAATTTTTTAAAAAAT
* **
1766252 AATATTAA-TTTTTAAAATTT
1 TATATTAATTTTTTAAAAAAT
1766272 TATATT
1 TATATT
1766278 TTTATTTTAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TATATTAATTTTTTAAAAAAT
Found at i:1770216 original size:2 final size:2
Alignment explanation
Indices: 1770204--1770236 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1770194 AAAACACATG
*
1770204 AT AT TT 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 AT AT A
1770237 CACACACACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1770849 original size:20 final size:21
Alignment explanation
Indices: 1770816--1770869 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 21
1770806 TATTTGTACT
*
1770816 ATATT-TATATTAT-TTT-TA
1 ATATTATATATTATATTTAAA
1770834 ATATTATA-ATTATATTTAAA
1 ATATTATATATTATATTTAAA
1770854 ATATTATATATTATAT
1 ATATTATATATTATAT
1770870 AAAATTTGAC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
18 10 0.32
19 5 0.16
20 9 0.29
21 7 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATTATATATTATATTTAAA
Found at i:1770870 original size:23 final size:23
Alignment explanation
Indices: 1770815--1770870 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 23
1770805 ATATTTGTAC
**
1770815 TATAT-TTATATTATTTTTAATAT
1 TATATATTATA-TATTTAAAATAT
1770838 TATA-A-T-TATATTTAAAATAT
1 TATATATTATATATTTAAAATAT
1770858 TATATATTATATA
1 TATATATTATATA
1770871 AAATTTGACA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
20 14 0.52
21 3 0.11
22 2 0.07
23 8 0.30
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TATATATTATATATTTAAAATAT
Found at i:1772012 original size:8 final size:8
Alignment explanation
Indices: 1771989--1772040 Score: 59
Period size: 8 Copynumber: 6.1 Consensus size: 8
1771979 ATATAAATTA
*
1771989 TATAAATT
1 TATATATT
1771997 TAATATATT
1 T-ATATATT
1772006 TATATATT
1 TATATATT
1772014 TATATTATAT
1 TATA-TAT-T
*
1772024 TATATATA
1 TATATATT
1772032 TATATATT
1 TATATATT
1772040 T
1 T
1772041 TTTCGTATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
8 20 0.53
9 13 0.34
10 5 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (8 bp):
TATATATT
Found at i:1772390 original size:27 final size:27
Alignment explanation
Indices: 1772360--1772451 Score: 80
Period size: 27 Copynumber: 3.2 Consensus size: 27
1772350 TATGATAATA
1772360 TTAAATTTAATTTAAAATATAAATATT
1 TTAAATTTAATTTAAAATATAAATATT
*
1772387 TTAAATTTAATATAATATAAATTATTAATATAT
1 TTAAATTTAAT-T--TA-AAA-TATAAATAT-T
* *
1772420 TAAAATTT-ATATAAATATATAAA-ATT
1 TTAAATTTAATTTAAA-ATATAAATATT
1772446 TTAAAT
1 TTAAAT
1772452 AAAATTATAG
Statistics
Matches: 53, Mismatches: 5, Indels: 15
0.73 0.07 0.21
Matches are distributed among these distances:
26 6 0.11
27 13 0.25
28 8 0.15
29 3 0.06
30 2 0.04
31 3 0.06
32 10 0.19
33 8 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
TTAAATTTAATTTAAAATATAAATATT
Done.