Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold8
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: 6381039
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 22487 characters in sequence are not A, C, G, or T
File 11 of 33
Found at i:1467730 original size:24 final size:24
Alignment explanation
Indices: 1467689--1467752 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
1467679 TTTTTTAAAA
* * *
1467689 AATAAGTATATAATTTTATTT-TT
1 AATAAATATATTATTTAATTTATT
1467712 AATAAAGTAATATTATTTAATTTATT
1 AATAAA-T-ATATTATTTAATTTATT
*
1467738 TATAAATATATTATT
1 AATAAATATATTATT
1467753 ATTATATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
23 5 0.15
24 9 0.26
25 13 0.38
26 7 0.21
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (24 bp):
AATAAATATATTATTTAATTTATT
Found at i:1468374 original size:15 final size:15
Alignment explanation
Indices: 1468356--1468397 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
1468346 TTATATTTTT
1468356 ATAAAATTTTATTAA
1 ATAAAATTTTATTAA
*
1468371 ATAATAATTTATATTAT
1 ATAA-AATTT-TATTAA
1468388 AT-AAATTTTA
1 ATAAAATTTTA
1468398 ATATTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 2 0.08
15 9 0.38
16 6 0.25
17 7 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATAAAATTTTATTAA
Found at i:1468391 original size:17 final size:17
Alignment explanation
Indices: 1468340--1468391 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
1468330 TGGTTGTGTT
*
1468340 TAATAA-TTATATTTTTA
1 TAATAATTTATA-TTATA
*
1468357 TAA-AATTT-TATTAAA
1 TAATAATTTATATTATA
1468372 TAATAATTTATATTATA
1 TAATAATTTATATTATA
1468389 TAA
1 TAA
1468392 ATTTTAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 6 0.21
16 9 0.31
17 14 0.48
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TAATAATTTATATTATA
Found at i:1468418 original size:14 final size:13
Alignment explanation
Indices: 1468392--1468433 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
1468382 TATTATATAA
1468392 ATTTTAATATTTT
1 ATTTTAATATTTT
1468405 ATTTTAATTATTTT
1 ATTTTAA-TATTTT
*
1468419 A--TTAATATTAT
1 ATTTTAATATTTT
1468430 ATTT
1 ATTT
1468434 AGGTAATTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
11 6 0.24
12 4 0.16
13 8 0.32
14 7 0.28
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
ATTTTAATATTTT
Found at i:1471042 original size:22 final size:21
Alignment explanation
Indices: 1471017--1471073 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 21
1471007 AAAAAAATTA
*
1471017 TTAAATTACTTTTTAATATT-TT
1 TTAAATTA-TTTTTAAT-TTACT
1471039 TTAAATTTATTTTTAATTTACT
1 TTAAA-TTATTTTTAATTTACT
1471061 TTAAATTATTTTT
1 TTAAATTATTTTT
1471074 TTGATATCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
21 10 0.31
22 19 0.59
23 3 0.09
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.65
Consensus pattern (21 bp):
TTAAATTATTTTTAATTTACT
Found at i:1471164 original size:19 final size:18
Alignment explanation
Indices: 1471132--1471181 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
1471122 CTTAATAATT
1471132 TATTTTA-TATTATTAAAAA
1 TATTTTATTA-TATT-AAAA
* *
1471151 TATTTTATTATATTTATA
1 TATTTTATTATATTAAAA
1471169 TATTTTATT-TATT
1 TATTTTATTATATT
1471182 TATAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 4 0.14
18 11 0.39
19 11 0.39
20 2 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TATTTTATTATATTAAAA
Found at i:1471173 original size:18 final size:17
Alignment explanation
Indices: 1471150--1471185 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
1471140 ATTATTAAAA
1471150 ATATTTTATTATATTTAT
1 ATATTTTATT-TATTTAT
1471168 ATATTTTATTTATTTAT
1 ATATTTTATTTATTTAT
1471185 A
1 A
1471186 AAAAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATATTTTATTTATTTAT
Found at i:1471550 original size:14 final size:13
Alignment explanation
Indices: 1471518--1471560 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1471508 TATTTATATA
1471518 TTATTAATAAATT
1 TTATTAATAAATT
* *
1471531 TAATTAATATCATT
1 TTATTAATA-AATT
*
1471545 TTATTAAAAAATT
1 TTATTAATAAATT
1471558 TTA
1 TTA
1471561 AAATATTAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
13 14 0.58
14 10 0.42
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (13 bp):
TTATTAATAAATT
Found at i:1471591 original size:18 final size:18
Alignment explanation
Indices: 1471568--1471603 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1471558 TTAAAATATT
1471568 AATATTTAAAATAAAATA
1 AATATTTAAAATAAAATA
*
1471586 AATATTTAAAATCAAATA
1 AATATTTAAAATAAAATA
1471604 TAAACTTGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
AATATTTAAAATAAAATA
Found at i:1472077 original size:2 final size:2
Alignment explanation
Indices: 1472017--1472063 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
1472007 ATACTAATTT
*
1472017 TC TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1472059 TC TC T
1 TC TC T
1472064 TTCAAAAGTC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:1473355 original size:23 final size:23
Alignment explanation
Indices: 1473329--1473379 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1473319 TATACAGTAA
*
1473329 ATATTATTATTTATGTCATAATT
1 ATATTATTATTTATATCATAATT
* *
1473352 ATATTATTTTTTATATTATAATT
1 ATATTATTATTTATATCATAATT
*
1473375 GTATT
1 ATATT
1473380 TAAAATTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (23 bp):
ATATTATTATTTATATCATAATT
Found at i:1474134 original size:12 final size:12
Alignment explanation
Indices: 1474117--1474141 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1474107 ATTATTTAAA
1474117 ATAAATTTTTAT
1 ATAAATTTTTAT
1474129 ATAAATTTTTAT
1 ATAAATTTTTAT
1474141 A
1 A
1474142 ATTAAATAAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATAAATTTTTAT
Found at i:1474139 original size:25 final size:25
Alignment explanation
Indices: 1474094--1474148 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
1474084 ACTCATGATT
*
1474094 TAAATTTTTTATTATTATTTA-AAA
1 TAAATTTTTTATAATTATTTATAAA
*
1474118 TAAATTTTTATATAAATT-TTTATAAT
1 TAAATTTTT-TAT-AATTATTTATAAA
1474144 TAAAT
1 TAAAT
1474149 AAAATAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 9 0.35
25 7 0.27
26 10 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TAAATTTTTTATAATTATTTATAAA
Found at i:1477386 original size:27 final size:27
Alignment explanation
Indices: 1477372--1477445 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 27
1477362 TATAATTATA
1477372 TTTAAAATATTATATATTTATATAAAT
1 TTTAAAATATTATATATTTATATAAAT
1477399 TTTAAAATATTA-ATAATTTATAT---T
1 TTTAAAATATTATAT-ATTTATATAAAT
*
1477423 TTATAAATTATTAATATATTTAT
1 TT-TAAAATATT-ATATATTTAT
1477446 TATTTATATC
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
24 3 0.07
25 8 0.19
26 9 0.21
27 22 0.52
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TTTAAAATATTATATATTTATATAAAT
Found at i:1477387 original size:22 final size:23
Alignment explanation
Indices: 1477346--1477443 Score: 66
Period size: 20 Copynumber: 4.3 Consensus size: 23
1477336 TATTATAGTT
* *
1477346 TTATATTTTGATATA-T-TATAA
1 TTATATTTTAAAATATTATATAA
1477367 TTATA-TTTAAAATATTATATATTTA
1 TTATATTTTAAAATATTATATA---A
*
1477392 TATAAATTTTAAAATATTA-ATAA
1 T-TATATTTTAAAATATTATATAA
*
1477415 TTTATATTTTATAA-ATTAT-TAA
1 -TTATATTTTAAAATATTATATAA
1477437 -TATATTT
1 TTATATTT
1477444 ATTATTTATA
Statistics
Matches: 63, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
20 14 0.22
21 6 0.10
22 11 0.17
23 11 0.17
24 1 0.02
25 2 0.03
26 6 0.10
27 12 0.19
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (23 bp):
TTATATTTTAAAATATTATATAA
Found at i:1477421 original size:33 final size:33
Alignment explanation
Indices: 1477384--1477454 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
1477374 TAAAATATTA
1477384 TATATTTATATAAATT-TTAAAATATTAATAATT
1 TATATTT-TATAAATTATTAAAATATTAATAATT
* * *
1477417 TATATTTTATAAATTATTAATATATTTATTATT
1 TATATTTTATAAATTATTAAAATATTAATAATT
1477450 TATAT
1 TATAT
1477455 CATATTTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 8 0.24
33 26 0.76
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (33 bp):
TATATTTTATAAATTATTAAAATATTAATAATT
Found at i:1477447 original size:15 final size:15
Alignment explanation
Indices: 1477429--1477486 Score: 50
Period size: 15 Copynumber: 3.8 Consensus size: 15
1477419 TATTTTATAA
1477429 ATTATTAATATATTT
1 ATTATTAATATATTT
1477444 ATTATTTATATCATATTT
1 ATTA-TTA-AT-ATATTT
*
1477462 A-TATTAAT-TTTTT
1 ATTATTAATATATTT
1477475 ATGTATT-ATATA
1 AT-TATTAATATA
1477487 ATCATATATT
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
13 5 0.14
14 2 0.06
15 11 0.31
16 6 0.17
17 4 0.11
18 7 0.20
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (15 bp):
ATTATTAATATATTT
Found at i:1478312 original size:19 final size:19
Alignment explanation
Indices: 1478276--1478329 Score: 90
Period size: 19 Copynumber: 2.7 Consensus size: 19
1478266 TTTTTAATAG
1478276 ATAATATGATATAATTTATTA
1 ATAATAT-ATA-AATTTATTA
1478297 ATAATATATAAATTTATTA
1 ATAATATATAAATTTATTA
1478316 ATAATATATAAATT
1 ATAATATATAAATT
1478330 ATAAGTGAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 23 0.70
20 3 0.09
21 7 0.21
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
ATAATATATAAATTTATTA
Found at i:1478614 original size:41 final size:39
Alignment explanation
Indices: 1478527--1478616 Score: 92
Period size: 41 Copynumber: 2.2 Consensus size: 39
1478517 ATTGAATAAA
1478527 AATTATAAAAAATTTAAAATTAAAAAAATAAAATAATATC
1 AATT-TAAAAAATTTAAAATTAAAAAAATAAAATAATATC
** * * *
1478567 CTTTTAATAAATTTATAATTACAAAAAAATATAAATAA-ATT
1 AATTTAAAAAATTTAAAATT--AAAAAAATA-AAATAATATC
1478608 AATTTAAAA
1 AATTTAAAA
1478617 TAAAAAATCT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
39 14 0.36
40 2 0.05
41 17 0.44
42 6 0.15
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (39 bp):
AATTTAAAAAATTTAAAATTAAAAAAATAAAATAATATC
Found at i:1478629 original size:19 final size:19
Alignment explanation
Indices: 1478593--1478641 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 19
1478583 AATTACAAAA
1478593 AAATATAAATAAATTAATTT
1 AAATATAAA-AAATTAATTT
1478613 AAA-ATAAAAAATCTAATTT
1 AAATATAAAAAAT-TAATTT
1478632 AAATATAAAA
1 AAATATAAAA
1478642 CTAAAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.15
19 14 0.52
20 9 0.33
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATATAAAAAATTAATTT
Found at i:1479150 original size:33 final size:32
Alignment explanation
Indices: 1479112--1479186 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 32
1479102 AAAATATTTT
* * * *
1479112 TTATTTTAATTTTAATTATATTATAGATGAATA
1 TTATTTTAA-TTTAATAATATTAGAAATAAATA
1479145 TTATTTTTAATTTAATAATATTAGAAATAAATA
1 TTA-TTTTAATTTAATAATATTAGAAATAAATA
1479178 TTATTTTAA
1 TTATTTTAA
1479187 AATTTTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 6 0.16
33 25 0.68
34 6 0.16
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (32 bp):
TTATTTTAATTTAATAATATTAGAAATAAATA
Found at i:1479255 original size:22 final size:22
Alignment explanation
Indices: 1479229--1479290 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
1479219 AAGATATTTC
1479229 ATTTTTAAAATTTTTAAAAATA
1 ATTTTTAAAATTTTTAAAAATA
* *
1479251 ATTTTTTAATTTTTTAAAAATA
1 ATTTTTAAAATTTTTAAAAATA
* *
1479273 ATTATTAATTATTTTTAA
1 ATTTTTAA-AATTTTTAA
1479291 TTTTTTAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 26 0.79
23 7 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTTTTAAAATTTTTAAAAATA
Found at i:1479266 original size:31 final size:30
Alignment explanation
Indices: 1479230--1479304 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
1479220 AGATATTTCA
1479230 TTTTTAAAATTTTTAAAAATAATTTTTTAAT
1 TTTTTAAAATTTTTAAAAATAA-TTTTTAAT
** ** *
1479261 TTTTTAAAAATAATTATTAATTATTTTTAAT
1 TTTTT-AAAATTTTTAAAAATAATTTTTAAT
1479292 TTTTTAAAATTTT
1 TTTTTAAAATTTT
1479305 ATAATAAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
30 6 0.17
31 18 0.50
32 12 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (30 bp):
TTTTTAAAATTTTTAAAAATAATTTTTAAT
Found at i:1481111 original size:3 final size:3
Alignment explanation
Indices: 1481103--1481128 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1481093 TTGGAAAATC
1481103 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
1481129 ATCCAAAGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1481367 original size:14 final size:15
Alignment explanation
Indices: 1481330--1481367 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1481320 GAACAAAAAA
1481330 TAAAATTATATATGT
1 TAAAATTATATATGT
*
1481345 TAAAATTATA-ATTT
1 TAAAATTATATATGT
*
1481359 TAAATTTAT
1 TAAAATTAT
1481368 TGAATATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
TAAAATTATATATGT
Found at i:1483354 original size:19 final size:20
Alignment explanation
Indices: 1483326--1483366 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1483316 TTTCAATTAA
*
1483326 TTTTACAAAA-ATTAAATAT
1 TTTTACAAAATATAAAATAT
*
1483345 TTTTATAAAATATAAAATAT
1 TTTTACAAAATATAAAATAT
1483365 TT
1 TT
1483367 ATTAGCATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTTACAAAATATAAAATAT
Found at i:1483764 original size:15 final size:15
Alignment explanation
Indices: 1483725--1483764 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
1483715 AAAAGATCTA
1483725 ATTAATATAAAATTTT
1 ATTAATA-AAAATTTT
* *
1483741 ACTATTAAAAATTTT
1 ATTAATAAAAATTTT
1483756 ATTAATAAA
1 ATTAATAAA
1483765 TTTTAAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTAATAAAAATTTT
Found at i:1483787 original size:19 final size:20
Alignment explanation
Indices: 1483749--1483788 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1483739 TTACTATTAA
*
1483749 AAATTTTATTAATAAATTTT
1 AAATTTTATAAATAAATTTT
*
1483769 AAATTTTA-AAATGAATTTT
1 AAATTTTATAAATAAATTTT
1483788 A
1 A
1483789 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
AAATTTTATAAATAAATTTT
Found at i:1491593 original size:31 final size:32
Alignment explanation
Indices: 1491539--1491599 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
1491529 AAATTGATCA
* *
1491539 AAAATTATTTTTTGTTATTTTAAT-TTTTATT
1 AAAATTATATTTTGTAATTTTAATCTTTTATT
1491570 AAAATTATATTTTG-AATTGTTAATCTTTTA
1 AAAATTATATTTTGTAATT-TTAATCTTTTA
1491600 ATTATATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 3 0.12
31 18 0.69
32 5 0.19
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.61
Consensus pattern (32 bp):
AAAATTATATTTTGTAATTTTAATCTTTTATT
Found at i:1491667 original size:23 final size:20
Alignment explanation
Indices: 1491612--1491669 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 20
1491602 TATATAATGA
1491612 ATATTATAATATTTAATTAAAT
1 ATATT-TAATA-TTAATTAAAT
*
1491634 ATATTT-TTATTAATTAATTATT
1 ATATTTAATATTAATTAA--A-T
1491656 ATATTTAATATTAA
1 ATATTTAATATTAA
1491670 AATTAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
19 8 0.27
20 2 0.07
21 2 0.07
22 12 0.40
23 6 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATTTAATATTAATTAAAT
Found at i:1491675 original size:12 final size:12
Alignment explanation
Indices: 1491645--1491687 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
1491635 TATTTTTATT
*
1491645 AATTAATTATTAT
1 AATTAA-TATTAA
*
1491658 ATTTAATATTAA
1 AATTAATATTAA
*
1491670 AATTAAAATTAA
1 AATTAATATTAA
1491682 AATTAA
1 AATTAA
1491688 ATATATTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
12 21 0.81
13 5 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AATTAATATTAA
Found at i:1496639 original size:62 final size:62
Alignment explanation
Indices: 1496538--1496663 Score: 180
Period size: 62 Copynumber: 2.0 Consensus size: 62
1496528 ATTTTTATAT
* * * *
1496538 ATATTATAGATTATAAATAAATAAAATGAACTAAGAGTTTAGTTCATACAGTTATCATTAAA
1 ATATAATAGATTATAAATAAATAAAATGAACTAAAAGTTTAGTTCATACAATTACCATTAAA
* * * *
1496600 ATATAATATATTATAAGTAAATAAAATGGATTAAAAGTTTAGTTCATACAATTACCATTAAA
1 ATATAATAGATTATAAATAAATAAAATGAACTAAAAGTTTAGTTCATACAATTACCATTAAA
1496662 AT
1 AT
1496664 GGGATATATT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (62 bp):
ATATAATAGATTATAAATAAATAAAATGAACTAAAAGTTTAGTTCATACAATTACCATTAAA
Found at i:1496984 original size:3 final size:3
Alignment explanation
Indices: 1496976--1497002 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1496966 TGGATCAACC
1496976 CTG CTG CTG CTG CTG CTG CTG CTG CTG
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG
1497003 GCGGTGCTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.33, T:0.33
Consensus pattern (3 bp):
CTG
Found at i:1497512 original size:2 final size:2
Alignment explanation
Indices: 1497507--1497552 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1497497 ATATTAAAAG
1497507 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1497549 AT AT
1 AT AT
1497553 CACGTTGTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1500381 original size:2 final size:2
Alignment explanation
Indices: 1500374--1500406 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1500364 TCAAATACAA
1500374 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 A
1500407 ATTTTGGGCC
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1501545 original size:13 final size:13
Alignment explanation
Indices: 1501527--1501556 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1501517 AAGTATAATT
1501527 ATAAAATTTTAAA
1 ATAAAATTTTAAA
1501540 ATAAAATTTTAAA
1 ATAAAATTTTAAA
1501553 ATAA
1 ATAA
1501557 TAAAATAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATAAAATTTTAAA
Found at i:1501552 original size:21 final size:21
Alignment explanation
Indices: 1501523--1501565 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1501513 ATTTAAGTAT
**
1501523 AATTATAAAATTTTAAAATAA
1 AATTATAAAATAATAAAATAA
*
1501544 AATTTTAAAATAATAAAATAA
1 AATTATAAAATAATAAAATAA
1501565 A
1 A
1501566 CTTACAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AATTATAAAATAATAAAATAA
Found at i:1502751 original size:21 final size:21
Alignment explanation
Indices: 1502727--1502766 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1502717 TTTAAAAAAT
1502727 TATTATTA-AATTAATATTTTA
1 TATTATTATAATTAA-ATTTTA
*
1502748 TATTTTTATAATTAAATTT
1 TATTATTATAATTAAATTT
1502767 AATTCAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTATTATAATTAAATTTTA
Found at i:1503159 original size:21 final size:20
Alignment explanation
Indices: 1503121--1503160 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1503111 TTTAATATGT
**
1503121 ATAATTTTTTATTTAAAATA
1 ATAATTTTTTATGAAAAATA
1503141 ATAATTTTTATATGAAAAAT
1 ATAATTTTT-TATGAAAAAT
1503161 TATTAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
ATAATTTTTTATGAAAAATA
Found at i:1503190 original size:31 final size:30
Alignment explanation
Indices: 1503133--1503192 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1503123 AATTTTTTAT
*
1503133 TTAAAATAATAATTTTTATATGAAAAATTA
1 TTAAAATAATAATTTTAATATGAAAAATTA
*
1503163 TTAAAATAATTA-TTTAATATGTTAAAAATT
1 TTAAAATAATAATTTTAATATG--AAAAATT
1503193 TTTTTGGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 8 0.31
30 11 0.42
31 7 0.27
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (30 bp):
TTAAAATAATAATTTTAATATGAAAAATTA
Found at i:1503849 original size:18 final size:18
Alignment explanation
Indices: 1503828--1503876 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
1503818 ATATATATAT
1503828 ATATATATATAAATTTTG
1 ATATATATATAAATTTTG
* *
1503846 ATATTTCAT-TAAATTTTT
1 ATATAT-ATATAAATTTTG
1503864 AT-TATATA-AAATT
1 ATATATATATAAATT
1503877 ATAATTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
16 7 0.27
17 2 0.08
18 15 0.58
19 2 0.08
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (18 bp):
ATATATATATAAATTTTG
Found at i:1503913 original size:35 final size:37
Alignment explanation
Indices: 1503874--1503970 Score: 98
Period size: 35 Copynumber: 2.8 Consensus size: 37
1503864 ATTATATAAA
1503874 ATTATAATTTATTTA-TATA-CTTATATTACATTTAT
1 ATTATAATTTATTTATTATATCTTATATTACATTTAT
** * *
1503909 ATTATTTTTTATTTATTATATTTTATATTATATTT-T
1 ATTATAATTTATTTATTATATCTTATATTACATTTAT
*
1503945 AATTATTA-TT-TTTATTATAT-TTATAT
1 -ATTATAATTTATTTATTATATCTTATAT
1503971 CATGTTTAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
34 6 0.11
35 23 0.43
36 7 0.13
37 18 0.33
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (37 bp):
ATTATAATTTATTTATTATATCTTATATTACATTTAT
Found at i:1503938 original size:26 final size:25
Alignment explanation
Indices: 1503904--1503966 Score: 85
Period size: 26 Copynumber: 2.6 Consensus size: 25
1503894 TTATATTACA
* *
1503904 TTTATATTATTTTTTATTTATTATAT
1 TTTATATTATATTTTAATTATTAT-T
1503930 TTTATATTATATTTTAATTATTA-T
1 TTTATATTATATTTTAATTATTATT
1503954 TTT-TATTATATTT
1 TTTATATTATATTT
1503967 ATATCATGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
23 10 0.29
24 4 0.11
26 21 0.60
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (25 bp):
TTTATATTATATTTTAATTATTATT
Found at i:1503950 original size:23 final size:24
Alignment explanation
Indices: 1503874--1503970 Score: 87
Period size: 23 Copynumber: 4.1 Consensus size: 24
1503864 ATTATATAAA
* *
1503874 ATTATAATTTAT-TTATATACTTAT
1 ATTATATTTTATATTATAT-TTTAT
* *
1503898 ATTACA-TTTATATTATTTTTTATTT
1 ATTATATTTTATATTATATTTTA--T
1503923 ATTATATTTTATATTATATTTTA-
1 ATTATATTTTATATTATATTTTAT
1503946 ATTATTATTTT-TATTATA-TTTAT
1 ATTA-TATTTTATATTATATTTTAT
1503969 AT
1 AT
1503971 CATGTTTAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 13
0.77 0.06 0.16
Matches are distributed among these distances:
22 4 0.06
23 21 0.34
24 16 0.26
25 6 0.10
26 15 0.24
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (24 bp):
ATTATATTTTATATTATATTTTAT
Found at i:1505747 original size:20 final size:20
Alignment explanation
Indices: 1505722--1505781 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
1505712 CAATTATATT
1505722 TAAATTATTATATATTTATA
1 TAAATTATTATATATTTATA
* *
1505742 TAAATTTTTACATATTTATA
1 TAAATTATTATATATTTATA
**
1505762 TATTTATATTATAT-TTTATA
1 TAAAT-TATTATATATTTATA
1505782 AAAAAATTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 27 0.82
21 6 0.18
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
TAAATTATTATATATTTATA
Found at i:1505993 original size:17 final size:17
Alignment explanation
Indices: 1505960--1505996 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1505950 TTTTTTAATT
1505960 TAAATTTAATTATAAAA
1 TAAATTTAATTATAAAA
1505977 TAAATATTAATTA-AAAA
1 TAAAT-TTAATTATAAAA
1505994 TAA
1 TAA
1505997 TTTTTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAATTTAATTATAAAA
Found at i:1506122 original size:2 final size:2
Alignment explanation
Indices: 1506115--1506145 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1506105 GTTCATGTAA
1506115 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 A
1506146 CACGTATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1506942 original size:30 final size:31
Alignment explanation
Indices: 1506898--1506960 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 31
1506888 TTTAACATCT
1506898 AAAATTAACAAAA-TTAAAAATAA-AATAAA
1 AAAATTAACAAAATTTAAAAATAATAATAAA
*
1506927 AAAATTTAATAAAATTTTAAAAATAATAATAAA
1 AAAA-TTAACAAAA-TTTAAAAATAATAATAAA
1506960 A
1 A
1506961 TTTAACGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 4 0.14
30 8 0.28
32 10 0.34
33 7 0.24
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (31 bp):
AAAATTAACAAAATTTAAAAATAATAATAAA
Found at i:1511305 original size:22 final size:23
Alignment explanation
Indices: 1511280--1511341 Score: 56
Period size: 22 Copynumber: 2.8 Consensus size: 23
1511270 TATTATTCAA
1511280 TAATAAAAAAATTATTTTAAT-T
1 TAATAAAAAAATTATTTTAATAT
* * * *
1511302 TAATTATAAAA-TATATAAATAT
1 TAATAAAAAAATTATTTTAATAT
* *
1511324 TAATATAAAAATAATTTT
1 TAATAAAAAAATTATTTT
1511342 TTAAATTAAT
Statistics
Matches: 28, Mismatches: 10, Indels: 3
0.68 0.24 0.07
Matches are distributed among these distances:
21 7 0.25
22 18 0.64
23 3 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TAATAAAAAAATTATTTTAATAT
Found at i:1511371 original size:20 final size:18
Alignment explanation
Indices: 1511339--1511388 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 18
1511329 TAAAAATAAT
1511339 TTTTTAAATTAATATT-AA
1 TTTTTAAATTAAT-TTGAA
1511357 TTTTTAAATGATAATTTGAA
1 TTTTTAAAT--TAATTTGAA
1511377 TTTTTAAATTAA
1 TTTTTAAATTAA
1511389 GTTCAATTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 12 0.41
19 2 0.07
20 15 0.52
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (18 bp):
TTTTTAAATTAATTTGAA
Found at i:1517784 original size:12 final size:12
Alignment explanation
Indices: 1517756--1517799 Score: 54
Period size: 11 Copynumber: 3.7 Consensus size: 12
1517746 CTTGAGGTAA
*
1517756 AAATTTTCATATT
1 AAATTTT-ATTTT
1517769 AAATTTTATTTT
1 AAATTTTATTTT
*
1517781 AAA-TTAATTTT
1 AAATTTTATTTT
1517792 AAATTTTA
1 AAATTTTA
1517800 AAATTTAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.37
12 10 0.37
13 7 0.26
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (12 bp):
AAATTTTATTTT
Found at i:1518379 original size:2 final size:2
Alignment explanation
Indices: 1518372--1518410 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1518362 AAACTAGCAA
1518372 AT AT 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 AT AT A
1518411 AAGATTGTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1520000 original size:27 final size:25
Alignment explanation
Indices: 1519951--1520000 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
1519941 TTAAAGATGA
**
1519951 TTAAATAAAAATTGAAATTAATAAT
1 TTAAATAAAAATTGAAAAAAATAAT
1519976 TTAAATTAAAAGATTGAAAAAAATA
1 TTAAA-TAAAA-ATTGAAAAAAATA
1520001 TTGTTATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.24
26 5 0.24
27 11 0.52
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (25 bp):
TTAAATAAAAATTGAAAAAAATAAT
Found at i:1520084 original size:24 final size:23
Alignment explanation
Indices: 1520017--1520085 Score: 59
Period size: 24 Copynumber: 2.9 Consensus size: 23
1520007 TATAGATTGA
*
1520017 AATATATTTTATAAAATTAAATAT
1 AATATATTTAATAAAA-TAAATAT
** *
1520041 AATATA-AAAATATGATATAAATAT
1 AATATATTTAATA--AAATAAATAT
1520065 AATATATTTAATAAACATAAA
1 AATATATTTAATAAA-ATAAA
1520086 ATTAGTATAA
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
23 4 0.12
24 24 0.71
25 6 0.18
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (23 bp):
AATATATTTAATAAAATAAATAT
Found at i:1520295 original size:23 final size:23
Alignment explanation
Indices: 1520252--1520295 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1520242 TATCTTATTG
*
1520252 ATTTTACTCATTTATTGATTTTT
1 ATTTTACTCATTTATTAATTTTT
*
1520275 ATTTTA-TTATTTGATTAATTT
1 ATTTTACTCATTT-ATTAATTT
1520296 ATAAAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.66
Consensus pattern (23 bp):
ATTTTACTCATTTATTAATTTTT
Found at i:1520304 original size:13 final size:13
Alignment explanation
Indices: 1520288--1520330 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
1520278 TTATTATTTG
1520288 ATTA-ATTTATAAA
1 ATTATATTTA-AAA
1520301 ATTATATTTAAAA
1 ATTATATTTAAAA
*
1520314 ATAATATTTAATAA
1 ATTATATTTAA-AA
1520328 ATT
1 ATT
1520331 TAAAATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 17 0.65
14 9 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTATATTTAAAA
Found at i:1520599 original size:16 final size:16
Alignment explanation
Indices: 1520578--1520610 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1520568 TTATAAAACT
*
1520578 TATTTTTATATTTATA
1 TATTTTTATAATTATA
1520594 TATTTTTATAATTATA
1 TATTTTTATAATTATA
1520610 T
1 T
1520611 TTAAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTTTTATAATTATA
Found at i:1520664 original size:20 final size:20
Alignment explanation
Indices: 1520600--1520670 Score: 58
Period size: 19 Copynumber: 3.5 Consensus size: 20
1520590 TATATATTTT
*
1520600 TATAA-TTATATTTAAATAA
1 TATAATTTAAATTTAAATAA
* *
1520619 TAAATATTTTAATTATTAAAT-A
1 T--ATAATTTAAAT-TTAAATAA
1520641 -ATAATTTAAATTTAAATAA
1 TATAATTTAAATTTAAATAA
*
1520660 TATAAATTAAA
1 TATAATTTAAA
1520671 AATTTTTATA
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
18 6 0.15
19 11 0.28
20 9 0.22
21 3 0.08
22 5 0.12
23 6 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TATAATTTAAATTTAAATAA
Found at i:1521550 original size:20 final size:20
Alignment explanation
Indices: 1521511--1521550 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1521501 TATTATTTTT
*
1521511 ATATTATAATTATATTTAAA
1 ATATTATAATTATATATAAA
1521531 ATATTATATATT-TATATAAA
1 ATATTATA-ATTATATATAAA
1521551 TTTTGATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTATAATTATATATAAA
Found at i:1523410 original size:13 final size:14
Alignment explanation
Indices: 1523352--1523418 Score: 50
Period size: 13 Copynumber: 4.8 Consensus size: 14
1523342 TGATATTATC
*
1523352 AATAAATTTAATTA
1 AATAAAATTAATTA
*
1523366 ATTAAAAATTAA--A
1 AAT-AAAATTAATTA
**
1523379 AATATAATATTTTTTA
1 AATA-AA-ATTAATTA
1523395 AAT-AAATTAATTA
1 AATAAAATTAATTA
1523408 AATAAAATTAA
1 AATAAAATTAA
1523419 AAAATTATAA
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
12 1 0.03
13 14 0.35
14 14 0.35
15 7 0.17
16 4 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATAAAATTAATTA
Found at i:1523800 original size:15 final size:16
Alignment explanation
Indices: 1523780--1523820 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
1523770 ATTAAAATTT
1523780 TTAAAAAATA-TTTAA
1 TTAAAAAATATTTTAA
1523795 TT-AAAAATATTTTAA
1 TTAAAAAATATTTTAA
*
1523810 ATAAATAAATA
1 TTAAA-AAATA
1523821 AAAATATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 7 0.32
15 8 0.36
16 2 0.09
17 5 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TTAAAAAATATTTTAA
Found at i:1524289 original size:19 final size:20
Alignment explanation
Indices: 1524253--1524302 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
1524243 AAATAAAATT
1524253 AATAAAAAATAAACTTTTAA
1 AATAAAAAATAAACTTTTAA
* *
1524273 CAATAAAAAAT-GATTTTTAA
1 -AATAAAAAATAAACTTTTAA
1524293 AATAAAAAAT
1 AATAAAAAAT
1524303 TTGTTAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 10 0.37
20 7 0.26
21 10 0.37
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (20 bp):
AATAAAAAATAAACTTTTAA
Found at i:1524309 original size:17 final size:16
Alignment explanation
Indices: 1524285--1524329 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 16
1524275 ATAAAAAATG
1524285 ATTTTTAAAATAAAAA
1 ATTTTTAAAATAAAAA
1524301 ATTTGTTAAAA-AATTAAA
1 ATTT-TTAAAATAA--AAA
1524319 ATTTTTAAAAT
1 ATTTTTAAAAT
1524330 TATATATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 6 0.24
17 12 0.48
18 7 0.28
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (16 bp):
ATTTTTAAAATAAAAA
Found at i:1525433 original size:6 final size:6
Alignment explanation
Indices: 1525422--1525455 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
1525412 TATACTTTGT
1525422 AAAATA AAAATAA AAAATAA AAAATA AAAATA AA
1 AAAATA AAAAT-A AAAAT-A AAAATA AAAATA AA
1525456 TAAACATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 14 0.52
7 13 0.48
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:1525439 original size:7 final size:7
Alignment explanation
Indices: 1525422--1525455 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
1525412 TATACTTTGT
1525422 AAAAT-A
1 AAAATAA
1525428 AAAATAA
1 AAAATAA
1525435 AAAATAA
1 AAAATAA
1525442 AAAAT-A
1 AAAATAA
1525448 AAAATAA
1 AAAATAA
1525455 A
1 A
1525456 TAAACATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 11 0.42
7 15 0.58
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAATAA
Found at i:1525440 original size:13 final size:13
Alignment explanation
Indices: 1525422--1525455 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1525412 TATACTTTGT
1525422 AAAAT-AAAAATAA
1 AAAATAAAAAAT-A
1525435 AAAATAAAAAATA
1 AAAATAAAAAATA
1525448 AAAATAAA
1 AAAATAAA
1525456 TAAACATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 14 0.70
14 6 0.30
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAATAAAAAATA
Found at i:1527066 original size:86 final size:87
Alignment explanation
Indices: 1526852--1527286 Score: 239
Period size: 86 Copynumber: 5.0 Consensus size: 87
1526842 TAAAGTTTTA
* * * * * * *
1526852 AAGTTTATTTATGACATTCAGACTCAAAAGTCTATATTATTATTAAGAAAATATTAAAAATATTA
1 AAGTTTATCTATAATATCCAGACTCAAAA-TTTGTATTATTATTAAAAAAATATTAAAAATATTA
*
1526917 TATATTTAAGTCAAAAAATTTTG
65 TATATTTAAGTCAAAAAATCTTG
* ** * *
1526940 AAGTTTATTTATAATATTTAAACTTAAAAATTTGTATTATTATTAAAAAAATATTAAAAA-ATT-
1 AAGTTTATCTATAATATCCAGAC-TCAAAATTTGTATTATTATTAAAAAAATATTAAAAATATTA
* *
1527003 TATATTTATGTCGAAAAATCTTG
65 TATATTTAAGTCAAAAAATCTTG
* *
1527026 AAGTTCT-TCTATTATATCCGGACTCAAAATTATGTATTATTATTTAACAAAAAT-TTACATACA
1 AAGTT-TATCTATAATATCCAGACTCAAAATT-TGTATTATTA-TTAA-AAAAATATTA-A-A-A
* * *** * * *
1527089 A-GTT-GA-A--TAA-TCTTGAAGTTTTA
59 ATATTATATATTTAAGTCAAAAAATCTTG
* * * * * * * * * *
1527112 AAGTTCATTTATGACATCCAAACTCAAAAGTCTATATTATCATT-AAAAAATATTTAAAATATTT
1 AAGTTTATCTATAATATCCAGACTCAAAA-TTTGTATTATTATTAAAAAAATATTAAAAATATTA
* * * *
1527176 TATAATTAATTCTAAAAGTCTTG
65 TATATTTAAGTCAAAAAATCTTG
* * * * * * * *
1527199 AAGTTCATTTATAACATCCAAATTCAAAAGTTTGTATTATAATTAAAAAAAT-TAAAAAATATTT
1 AAGTTTATCTATAATATCCAGACTCAAAA-TTTGTATTATTATTAAAAAAATATTAAAAATATTA
* *
1527263 TATATTTAAAT-AAAAAAACTTG
65 TATATTTAAGTCAAAAAATCTTG
1527285 AA
1 AA
1527287 ATTGATTTAT
Statistics
Matches: 274, Mismatches: 55, Indels: 38
0.75 0.15 0.10
Matches are distributed among these distances:
81 2 0.01
82 3 0.01
83 8 0.03
84 4 0.01
85 9 0.03
86 95 0.35
87 81 0.30
88 60 0.22
89 7 0.03
90 5 0.02
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (87 bp):
AAGTTTATCTATAATATCCAGACTCAAAATTTGTATTATTATTAAAAAAATATTAAAAATATTAT
ATATTTAAGTCAAAAAATCTTG
Found at i:1527267 original size:260 final size:257
Alignment explanation
Indices: 1526792--1527270 Score: 642
Period size: 260 Copynumber: 1.9 Consensus size: 257
1526782 AGATTCAAAT
* * *
1526792 TCAAAAGTTTGTATTATTATTCAAAAATTTATATTCAAATCGAACAATTTTAAAGTTTTAAAGTT
1 TCAAAAGTTTGTATTATTATTCAAAAATTTACATACAAATCGAACAATCTTAAAGTTTTAAAGTT
* * * * *
1526857 TATTTATGACATTCAGACTCAAAAGTCTATATTATTATTAAGAAAATATTAAAAATATTATATAT
66 CATTTATGACATCCAAACTCAAAAGTCTATATTATCATTAAGAAAATATTAAAAATATTATATAA
* * * ** *
1526922 TTAAGTCAAAAAATTTTGAAGTTTATTTATAATATTTAAACTTAAAAATTTGTATTATTATTAAA
131 TTAAGTCAAAAAATCTTGAAGTTCATTTATAACATCCAAACTTAAAAATTTGTATTATAATTAAA
*
1526987 AAAATATTAAAAAATTTATATTTATGTCGAAAAATCTTGAAGTTCTTCTATTATATCCGGAC
196 AAAATATAAAAAAATTTATATTTATGTCGAAAAATCTTGAAGTTCTTCTATTATATCCGGAC
* * * *
1527049 TCAAAA-TTATGTATTATTATTTAACAAAAATTTACATACAAGTTGAATAATCTTGAAGTTTTAA
1 TCAAAAGTT-TGTATTATTA-TT--CAAAAATTTACATACAAATCGAACAATCTTAAAGTTTTAA
* *
1527113 AGTTCATTTATGACATCCAAACTCAAAAGTCTATATTATCATTAA-AAAATATTTAAAATATTTT
62 AGTTCATTTATGACATCCAAACTCAAAAGTCTATATTATCATTAAGAAAATATTAAAAATATTAT
* * * *
1527177 ATAATTAATTCTAAAAGTCTTGAAGTTCATTTATAACATCCAAA-TTCAAAAGTTTGTATTATAA
127 ATAATTAAGTCAAAAAATCTTGAAGTTCATTTATAACATCCAAACTT-AAAAATTTGTATTATAA
1527241 TTAAAAAAAT-TAAAAAATATTTTATATTTA
191 TTAAAAAAATATAAAAAA-A-TTTATATTTA
1527271 AATAAAAAAA
Statistics
Matches: 190, Mismatches: 25, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
256 2 0.01
257 16 0.08
258 10 0.05
259 78 0.41
260 84 0.44
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (257 bp):
TCAAAAGTTTGTATTATTATTCAAAAATTTACATACAAATCGAACAATCTTAAAGTTTTAAAGTT
CATTTATGACATCCAAACTCAAAAGTCTATATTATCATTAAGAAAATATTAAAAATATTATATAA
TTAAGTCAAAAAATCTTGAAGTTCATTTATAACATCCAAACTTAAAAATTTGTATTATAATTAAA
AAAATATAAAAAAATTTATATTTATGTCGAAAAATCTTGAAGTTCTTCTATTATATCCGGAC
Found at i:1529355 original size:16 final size:16
Alignment explanation
Indices: 1529330--1529366 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1529320 TCTGAGCATC
*
1529330 AAAAGTTTTAAACTCA
1 AAAAGATTTAAACTCA
*
1529346 AAAAGATTTAAATTCA
1 AAAAGATTTAAACTCA
1529362 AAAAG
1 AAAAG
1529367 TTCAAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.57, C:0.08, G:0.08, T:0.27
Consensus pattern (16 bp):
AAAAGATTTAAACTCA
Found at i:1531767 original size:6 final size:6
Alignment explanation
Indices: 1531756--1531800 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
1531746 TTGCAAGAGG
1531756 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TAT
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TAT
1531801 ATCATCTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (6 bp):
TATGTA
Found at i:1538956 original size:18 final size:17
Alignment explanation
Indices: 1538925--1538960 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1538915 ATTAAATTTA
*
1538925 TAAATTTATTCATAAAT
1 TAAATTTATACATAAAT
1538942 TAAATTTTATACATAAAT
1 TAAA-TTTATACATAAAT
1538960 T
1 T
1538961 TTTTAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAATTTATACATAAAT
Found at i:1539614 original size:9 final size:9
Alignment explanation
Indices: 1539600--1539625 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1539590 GATTCTACAA
1539600 AAAAAAAAG
1 AAAAAAAAG
1539609 AAAAAAAAG
1 AAAAAAAAG
1539618 AAAAAAAA
1 AAAAAAAA
1539626 ATATCTGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:1540624 original size:32 final size:32
Alignment explanation
Indices: 1540588--1540682 Score: 85
Period size: 32 Copynumber: 3.1 Consensus size: 32
1540578 TTTTAATTTT
*
1540588 ATATAGTTTTATTAATTTAATT-TTTAATATAA
1 ATATAATTTTATT-ATTTAATTATTTAATATAA
* *
1540620 ATATAATTTTATTTTTTAATTATTT-AT-TAT
1 ATATAATTTTATTATTTAATTATTTAATATAA
*
1540650 ATAT-ATTTTA--ATTTAATATTTTTAATAATAA
1 ATATAATTTTATTATTTAAT-TATTTAAT-ATAA
1540681 AT
1 AT
1540683 TTTTAATATA
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
27 6 0.12
28 4 0.08
29 8 0.15
30 6 0.12
31 13 0.25
32 15 0.29
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (32 bp):
ATATAATTTTATTATTTAATTATTTAATATAA
Found at i:1540661 original size:58 final size:61
Alignment explanation
Indices: 1540565--1540682 Score: 147
Period size: 58 Copynumber: 2.0 Consensus size: 61
1540555 CAACTTTTTG
* *
1540565 TAATTTCATTTTTTTTTAATTTTATATAGTTTTATTAATTT-A-ATTTTTAAT-ATAAATA
1 TAATTTCATTTTTTATTAATTTTATATAGTATTATTAATTTAATATTTTTAATAATAAATA
* *
1540623 TAATTTTATTTTTTAATTATTTATTATATA-TATT-TTAATTTAATATTTTTAATAATAAAT
1 TAATTTCATTTTTT-ATTAATT-TTATATAGTATTATTAATTTAATATTTTTAATAATAAAT
1540683 TTTTAATATA
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
58 20 0.39
59 9 0.18
60 16 0.31
61 6 0.12
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (61 bp):
TAATTTCATTTTTTATTAATTTTATATAGTATTATTAATTTAATATTTTTAATAATAAATA
Found at i:1540672 original size:14 final size:15
Alignment explanation
Indices: 1540650--1540690 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
1540640 TATTTATTAT
*
1540650 ATATATTTTAAT-TTA
1 ATAT-TTTTAATAATA
1540665 ATATTTTTAATAATA
1 ATATTTTTAATAATA
1540680 A-ATTTTTAATA
1 ATATTTTTAATA
1540691 TAACTCATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 17 0.71
15 7 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATATTTTTAATAATA
Found at i:1541058 original size:5 final size:5
Alignment explanation
Indices: 1541048--1541127 Score: 50
Period size: 5 Copynumber: 17.6 Consensus size: 5
1541038 AAACACTATA
* * *
1541048 ATAAT ATAAT ATAAA ATAAT ATAA- ATAA- ATTAT A-AAT AT-TT A-AAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
* * *
1541093 ATATT AAAAT A-AAT ATAAT ATAA- ATTAT -TAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
1541128 TTAGAATTTA
Statistics
Matches: 57, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
4 24 0.42
5 33 0.58
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:1541083 original size:11 final size:11
Alignment explanation
Indices: 1541067--1541130 Score: 57
Period size: 11 Copynumber: 6.2 Consensus size: 11
1541057 TATAAAATAA
1541067 TATAAATAAAT
1 TATAAATAAAT
1541078 TATAAAT--AT
1 TATAAATAAAT
*
1541087 T-TAAATATAT
1 TATAAATAAAT
1541097 TA-AAATAAA-
1 TATAAATAAAT
1541106 TATAATATAAAT
1 TATAA-ATAAAT
* *
1541118 TATTAATATAT
1 TATAAATAAAT
1541129 TA
1 TA
1541131 GAATTTATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
8 5 0.11
9 5 0.11
10 11 0.25
11 19 0.43
12 4 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TATAAATAAAT
Found at i:1541091 original size:19 final size:19
Alignment explanation
Indices: 1541061--1541128 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 19
1541051 ATATAATATA
1541061 AAATAATATAAATAAATTAT
1 AAAT-ATATAAATAAATTAT
* *
1541081 AAATATTTAAATATATTA-
1 AAATATATAAATAAATTAT
1541099 AAATAAATATAATATAAATTAT
1 AAAT--ATATAA-ATAAATTAT
*
1541121 TAATATAT
1 AAATATAT
1541129 TAGAATTTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
18 4 0.10
19 12 0.31
20 13 0.33
21 7 0.18
22 3 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAATATATAAATAAATTAT
Found at i:1541095 original size:40 final size:40
Alignment explanation
Indices: 1541050--1541126 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
1541040 ACACTATAAT
1541050 AATATAATATAAAAT-AATATAA-ATAAATTATAAATATTTA
1 AATAT-AT-TAAAATAAATATAATATAAATTATAAATATTTA
*
1541090 AATATATTAAAATAAATATAATATAAATTATTAATAT
1 AATATATTAAAATAAATATAATATAAATTATAAATAT
1541127 ATTAGAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
38 6 0.18
39 9 0.26
40 19 0.56
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (40 bp):
AATATATTAAAATAAATATAATATAAATTATAAATATTTA
Found at i:1541115 original size:33 final size:32
Alignment explanation
Indices: 1541068--1541181 Score: 92
Period size: 33 Copynumber: 3.4 Consensus size: 32
1541058 ATAAAATAAT
1541068 ATAAATA-AATTATAAATATTTAAATATATTAAA
1 ATAAATATAA-TATAAAT-TTTAAATATATTAAA
1541101 ATAAATATAATATAAATTATT-AATATATTAGAA
1 ATAAATATAATATAAATT-TTAAATATATTA-AA
* * **
1541134 TTTATAATAAAATATATTTTTTAAATATTATT-AA
1 -ATA-AATATAATATAAATTTTAAATA-TATTAAA
1541168 A-AAATATAAATATA
1 ATAAATAT-AATATA
1541182 CTATACATAC
Statistics
Matches: 67, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
31 4 0.06
32 17 0.25
33 18 0.27
34 8 0.12
35 16 0.24
36 4 0.06
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (32 bp):
ATAAATATAATATAAATTTTAAATATATTAAA
Found at i:1541145 original size:44 final size:39
Alignment explanation
Indices: 1541058--1541147 Score: 110
Period size: 40 Copynumber: 2.2 Consensus size: 39
1541048 ATAATATAAT
1541058 ATAAAAT-AATATAAATAAATTATAAATATTTAAATATA
1 ATAAAATAAATATAAATAAATTATAAATATTTAAATATA
* *
1541096 TTAAAATAAATATAATATAAATTATTAATATATTAGAATTTATA
1 ATAAAATAAATATAA-ATAAATTATAAATAT-TTA-AA--TATA
1541140 ATAAAATA
1 ATAAAATA
1541148 TATTTTTTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
38 6 0.14
39 7 0.16
40 14 0.33
41 3 0.07
42 2 0.05
44 11 0.26
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (39 bp):
ATAAAATAAATATAAATAAATTATAAATATTTAAATATA
Found at i:1541699 original size:2 final size:2
Alignment explanation
Indices: 1541694--1541728 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1541684 CAAAAAAAAT
* *
1541694 TA TA TA TA TA TA TA TA TA TA TA TA TT TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1541729 TTTGAATAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (2 bp):
TA
Found at i:1542086 original size:3 final size:3
Alignment explanation
Indices: 1542078--1542103 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1542068 AGATTGCTAA
1542078 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1542104 AATTGAAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1542228 original size:16 final size:17
Alignment explanation
Indices: 1542207--1542245 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
1542197 TTATTATATT
1542207 ATATAAAATTAT-TAAA
1 ATATAAAATTATATAAA
*
1542223 ATATAATATTATATAAA
1 ATATAAAATTATATAAA
*
1542240 AAATAA
1 ATATAA
1542246 TATAAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
ATATAAAATTATATAAA
Found at i:1542245 original size:17 final size:16
Alignment explanation
Indices: 1542209--1542248 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
1542199 ATTATATTAT
* *
1542209 ATAAAATTATTAAAAT
1 ATAATATTATTAAAAA
1542225 ATAATATTATATAAAAA
1 ATAATATTAT-TAAAAA
1542242 ATAATAT
1 ATAATAT
1542249 AAATATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATAATATTATTAAAAA
Found at i:1542252 original size:28 final size:26
Alignment explanation
Indices: 1542202--1542254 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1542192 TGATGTTATT
* *
1542202 ATATTATATAAAATTATTAAAATATA
1 ATATTATATAAAAATAATAAAATATA
1542228 ATATTATATAAAAAATAATATAAATAT
1 ATATTATAT-AAAAATAATA-AAATAT
1542255 TTTATAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 9 0.39
27 8 0.35
28 6 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
ATATTATATAAAAATAATAAAATATA
Found at i:1542269 original size:19 final size:20
Alignment explanation
Indices: 1542240--1542277 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1542230 ATTATATAAA
1542240 AAATAATATAAATATTTTAT
1 AAATAATATAAATATTTTAT
1542260 AAAT-ATATAAATATTTTA
1 AAATAATATAAATATTTTA
1542278 AATTTATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATAATATAAATATTTTAT
Found at i:1542304 original size:30 final size:29
Alignment explanation
Indices: 1542260--1542338 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
1542250 AATATTTTAT
1542260 AAATATATAAATATTTTAAATTTATATA-AA
1 AAATAT-TAAATA-TTTAAATTTATATATAA
* * *
1542290 AAATATTAATATATTAAAATTTATTTATAT
1 AAATATTAA-ATATTTAAATTTATATATAA
*
1542320 AAATATAAAATATTTAAAT
1 AAATATTAAATATTTAAAT
1542339 ATAATTAGGA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
29 24 0.57
30 18 0.43
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
AAATATTAAATATTTAAATTTATATATAA
Found at i:1542335 original size:19 final size:19
Alignment explanation
Indices: 1542244--1542335 Score: 66
Period size: 19 Copynumber: 4.8 Consensus size: 19
1542234 TATAAAAAAT
1542244 AATAT-AAATATTT-TATA
1 AATATAAAATATTTATATA
* *
1542261 AATATATAAATATTTTAAATT
1 AATATA-AAATA-TTTATATA
* *
1542282 TATATAAAAAATATTA-ATA
1 AATATAAAATAT-TTATATA
*
1542301 TAT-TAAAATTTATTTATATA
1 AATATAAAA--TATTTATATA
1542321 AATATAAAATATTTA
1 AATATAAAATATTTA
1542336 AATATAATTA
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
17 5 0.08
18 5 0.08
19 20 0.34
20 17 0.29
21 12 0.20
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AATATAAAATATTTATATA
Found at i:1542671 original size:2 final size:2
Alignment explanation
Indices: 1542664--1542695 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1542654 TATTTCCTAA
1542664 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1542696 ACACACACAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1549857 original size:33 final size:32
Alignment explanation
Indices: 1549817--1549952 Score: 107
Period size: 33 Copynumber: 4.1 Consensus size: 32
1549807 TTAAAAAATA
1549817 ATATTAAATATTATATAATATAAATATATAATT
1 ATATTAAATATTATATAATATAAATATATAA-T
* *
1549850 ATTTTAAA-ATTTATATAAAATAAAT-TATTAAT
1 ATATTAAATA-TTATATAATATAAATATA-TAAT
* * *
1549882 ATATTAAAAATTATGTAAATATAAAATAATTTAAT
1 ATATTAAATATTATAT-AATAT-AAAT-ATATAAT
* * *
1549917 ATGTTATAATATTATAAAATATATAA-ATAAAAT
1 ATATTA-AATATTATATAATATA-AATATATAAT
1549950 ATA
1 ATA
1549953 AATATATTAA
Statistics
Matches: 81, Mismatches: 13, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
32 16 0.20
33 36 0.44
34 5 0.06
35 16 0.20
36 8 0.10
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (32 bp):
ATATTAAATATTATATAATATAAATATATAAT
Found at i:1549883 original size:18 final size:20
Alignment explanation
Indices: 1549862--1549910 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 20
1549852 TTTAAAATTT
1549862 ATATAAAATAAATTAT-T-A
1 ATATAAAATAAATTATGTAA
*
1549880 ATATATTAA-AAATTATGTAA
1 ATATA-AAATAAATTATGTAA
1549900 ATATAAAATAA
1 ATATAAAATAA
1549911 TTTAATATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 12 0.48
19 5 0.20
20 8 0.32
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
ATATAAAATAAATTATGTAA
Found at i:1551584 original size:17 final size:18
Alignment explanation
Indices: 1551559--1551592 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1551549 ATATTTAATT
1551559 TTATATTAA-AAATATAA
1 TTATATTAATAAATATAA
*
1551576 TTATTTTAATAAATATA
1 TTATATTAATAAATATA
1551593 TAAATATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTATATTAATAAATATAA
Found at i:1551593 original size:20 final size:20
Alignment explanation
Indices: 1551547--1551609 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 20
1551537 ATATAATTTG
* * *
1551547 AAATATTTAATT-TTATATT
1 AAATATATAATTATTTTAAT
*
1551566 AAAAATATAATTATTTTAAT
1 AAATATATAATTATTTTAAT
* *
1551586 AAATATATAAATATTTAAAT
1 AAATATATAATTATTTTAAT
1551606 AAAT
1 AAAT
1551610 CATTACTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 10 0.28
20 26 0.72
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AAATATATAATTATTTTAAT
Found at i:1552295 original size:19 final size:19
Alignment explanation
Indices: 1552273--1552310 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
1552263 AATTTAATTA
1552273 TTAAT-ATAAAAATATTTTT
1 TTAATAATAAAAA-ATTTTT
1552292 TTAATAATAAAAAATTTTT
1 TTAATAATAAAAAATTTTT
1552311 AAAACAACCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTAATAATAAAAAATTTTT
Found at i:1552983 original size:38 final size:40
Alignment explanation
Indices: 1552941--1553028 Score: 103
Period size: 37 Copynumber: 2.3 Consensus size: 40
1552931 TATAATTTTT
*
1552941 ATTTAATTTAATTTAATTAATAAAA-TATTTT-TATTT-AA
1 ATTTAATTTAATTTAATTAA-AAAATTATTTTAAATTTAAA
**
1552979 ATTTAA-TTAATTTTTTTAAAAAATTATTTTAAATTTAAA
1 ATTTAATTTAATTTAATTAAAAAATTATTTTAAATTTAAA
*
1553018 ATTAAATTTAA
1 ATTTAATTTAA
1553029 ATAAAAATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
36 4 0.10
37 17 0.40
38 10 0.24
39 7 0.17
40 4 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (40 bp):
ATTTAATTTAATTTAATTAAAAAATTATTTTAAATTTAAA
Found at i:1554414 original size:10 final size:10
Alignment explanation
Indices: 1554401--1554526 Score: 55
Period size: 9 Copynumber: 13.7 Consensus size: 10
1554391 TATCATATTC
1554401 ATATATTATA
1 ATATATTATA
1554411 ATATATT-TA
1 ATATATTATA
* *
1554420 AAATTTTAT-
1 ATATATTATA
1554429 ATAT-TTAT-
1 ATATATTATA
* *
1554437 ATAAATTTTA
1 ATATATTATA
1554447 ATATATTAATA
1 ATATATT-ATA
1554458 ATTTATATTAT-
1 A--TATATTATA
* *
1554469 ATAAATTTTA
1 ATATATTATA
1554479 ATAT-TT-T-
1 ATATATTATA
1554486 -TATA-TATA
1 ATATATTATA
1554494 AT-TA-TATA
1 ATATATTATA
1554502 ATAT-TTATA
1 ATATATTATA
* *
1554511 TTATTTTA-A
1 ATATATTATA
1554520 ATATATT
1 ATATATT
1554527 TATATCATAT
Statistics
Matches: 89, Mismatches: 13, Indels: 29
0.68 0.10 0.22
Matches are distributed among these distances:
6 4 0.04
7 1 0.01
8 16 0.18
9 36 0.40
10 20 0.22
11 4 0.04
12 2 0.02
13 6 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
ATATATTATA
Found at i:1554416 original size:18 final size:18
Alignment explanation
Indices: 1554374--1554417 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
1554364 AGCTTAAATT
*
1554374 TAATA-ATTCGTATATTA
1 TAATATATTCATATATTA
1554391 T-ATCATATTCATATATTA
1 TAAT-ATATTCATATATTA
1554409 TAATATATT
1 TAATATATT
1554418 TAAAATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 2 0.09
17 2 0.09
18 17 0.74
19 2 0.09
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (18 bp):
TAATATATTCATATATTA
Found at i:1554450 original size:20 final size:20
Alignment explanation
Indices: 1554409--1554531 Score: 94
Period size: 20 Copynumber: 6.7 Consensus size: 20
1554399 TCATATATTA
1554409 TAATATA-TT-TA-AAATTT
1 TAATATATTTATATAAATTT
1554426 T-ATATATTTATATAAATTT
1 TAATATATTTATATAAATTT
1554445 TAATATA-TTA-AT-AA--T
1 TAATATATTTATATAAATTT
1554460 T--TATA-TTATATAAATTT
1 TAATATATTTATATAAATTT
* *
1554477 TAATATTTTTATATATAATTA
1 TAATATATTTATATA-AATTT
*
1554498 T-ATAATATTTATAT-TATTT
1 TAAT-ATATTTATATAAATTT
1554517 TAAATATATTTATAT
1 T-AATATATTTATAT
1554532 CATATTTAAT
Statistics
Matches: 86, Mismatches: 5, Indels: 27
0.73 0.04 0.23
Matches are distributed among these distances:
13 7 0.08
14 2 0.02
15 4 0.05
16 5 0.06
17 7 0.08
18 4 0.05
19 17 0.20
20 24 0.28
21 16 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TAATATATTTATATAAATTT
Found at i:1554469 original size:32 final size:32
Alignment explanation
Indices: 1554428--1554536 Score: 114
Period size: 32 Copynumber: 3.3 Consensus size: 32
1554418 TAAAATTTTA
*
1554428 TATATTTATATAAATTTTAATATATTAATAATT
1 TATA-TTATATAAATTTTAATATTTTAATAATT
* *
1554461 TATATTATATAAATTTTAATATTTTTAT-ATA
1 TATATTATATAAATTTTAATATTTTAATAATT
*
1554492 TA-ATTATATAATATTTATATTATTTTAAATATATT
1 TATATTATATAA-ATTT-TAATATTTT-AATA-ATT
*
1554527 TATATCATAT
1 TATATTATAT
1554537 TTAATTATCA
Statistics
Matches: 63, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
30 9 0.14
31 8 0.13
32 30 0.48
33 6 0.10
35 4 0.06
36 6 0.10
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (32 bp):
TATATTATATAAATTTTAATATTTTAATAATT
Found at i:1554511 original size:11 final size:11
Alignment explanation
Indices: 1554477--1554539 Score: 58
Period size: 11 Copynumber: 5.8 Consensus size: 11
1554467 ATATAAATTT
*
1554477 TAATATTTTTA
1 TAATATTTATA
*
1554488 TATATAATTATA
1 TA-ATATTTATA
1554500 TAATATTTATA
1 TAATATTTATA
* *
1554511 TTAT-TTTAAA
1 TAATATTTATA
1554521 T-ATATTTATA
1 TAATATTTATA
*
1554531 TCATATTTA
1 TAATATTTA
1554540 ATTATCAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
9 2 0.05
10 12 0.28
11 20 0.47
12 9 0.21
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (11 bp):
TAATATTTATA
Found at i:1554524 original size:31 final size:31
Alignment explanation
Indices: 1554464--1554544 Score: 96
Period size: 31 Copynumber: 2.7 Consensus size: 31
1554454 AATAATTTAT
* *
1554464 ATTATATAA-ATTT-TAATATTTTTATATATA
1 ATTATATAATATTTATATTA-TTTTAAATATA
1554494 ATTATATAATATTTATATTATTTTAAATATA
1 ATTATATAATATTTATATTATTTTAAATATA
* *
1554525 TTTATATCATATTTA-ATTAT
1 ATTATATAATATTTATATTAT
1554545 CAAATTGAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
30 14 0.31
31 27 0.60
32 4 0.09
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (31 bp):
ATTATATAATATTTATATTATTTTAAATATA
Found at i:1554528 original size:10 final size:10
Alignment explanation
Indices: 1554401--1554540 Score: 58
Period size: 10 Copynumber: 14.0 Consensus size: 10
1554391 TATCATATTC
1554401 ATATA-TTATA
1 ATATATTTA-A
1554411 ATATATTTAA
1 ATATATTTAA
1554421 A-AT-TTT--
1 ATATATTTAA
*
1554427 ATATATTTAT
1 ATATATTTAA
* *
1554437 ATAAATTTTA
1 ATATATTTAA
*
1554447 ATATATTAATA
1 ATATATTTA-A
* *
1554458 ATTTATATTAT
1 ATATAT-TTAA
* *
1554469 ATAAATTTTA
1 ATATATTTAA
* *
1554479 ATATTTTTAT
1 ATATATTTAA
* *
1554489 ATATAATTAT
1 ATATATTTAA
*
1554499 ATAATATTTAT
1 AT-ATATTTAA
1554510 AT-TATTTTAA
1 ATATA-TTTAA
*
1554520 ATATATTTAT
1 ATATATTTAA
1554530 ATCATATTTAA
1 AT-ATATTTAA
1554541 TTATCAAATT
Statistics
Matches: 96, Mismatches: 23, Indels: 21
0.69 0.16 0.15
Matches are distributed among these distances:
6 1 0.01
7 2 0.02
8 6 0.06
9 4 0.04
10 50 0.52
11 31 0.32
12 2 0.02
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (10 bp):
ATATATTTAA
Found at i:1555696 original size:18 final size:18
Alignment explanation
Indices: 1555636--1555696 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
1555626 ATATTTTAAA
1555636 AAATTTAAATAAA-AATATT
1 AAATTTAAA-AAATAA-ATT
* *
1555655 AGATATAAAAAATAAAATT
1 AAATTTAAAAAAT-AAATT
*
1555674 -TATTTAAAAAATAAATT
1 AAATTTAAAAAATAAATT
1555691 AAATTT
1 AAATTT
1555697 GAATTTAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
17 5 0.15
18 17 0.50
19 10 0.29
20 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
AAATTTAAAAAATAAATT
Found at i:1555769 original size:18 final size:18
Alignment explanation
Indices: 1555732--1555791 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 18
1555722 TTGATCGATT
1555732 TATTTTTA-ATTATATAATA
1 TATTTTTATATT-TAT-ATA
1555751 TATTTTTATATTTATATA
1 TATTTTTATATTTATATA
1555769 TATTATTT-TATTTATATAA
1 TATT-TTTATATTTATAT-A
1555788 TATT
1 TATT
1555792 ATGTAATAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
18 16 0.42
19 19 0.50
20 3 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TATTTTTATATTTATATA
Found at i:1555892 original size:24 final size:24
Alignment explanation
Indices: 1555848--1555903 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
1555838 AAAAATTATC
1555848 TATATTTTAAAATTAATAAAAAAT
1 TATATTTTAAAATTAATAAAAAAT
1555872 TATATTGTTAAAGA-TAA-AAAAAAT
1 TATATT-TTAAA-ATTAATAAAAAAT
*
1555896 AATATTTT
1 TATATTTT
1555904 TTATTTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 2 0.07
24 18 0.62
25 8 0.28
26 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (24 bp):
TATATTTTAAAATTAATAAAAAAT
Found at i:1556622 original size:12 final size:12
Alignment explanation
Indices: 1556615--1556639 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1556605 TTTAATTTTA
1556615 AAAATAATTATT
1 AAAATAATTATT
1556627 AAAATAATTATT
1 AAAATAATTATT
1556639 A
1 A
1556640 TTTCTAATAA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAATAATTATT
Found at i:1558604 original size:7 final size:7
Alignment explanation
Indices: 1558592--1558621 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
1558582 TTAAATTCAG
1558592 TTATATA
1 TTATATA
1558599 TTATATA
1 TTATATA
1558606 TTATATA
1 TTATATA
1558613 TATATATA
1 T-TATATA
1558621 T
1 T
1558622 ATTCTCAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TTATATA
Found at i:1559062 original size:5 final size:5
Alignment explanation
Indices: 1559052--1559077 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1559042 CGAAATTGAA
1559052 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
1559078 CGACGATCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:1560571 original size:2 final size:2
Alignment explanation
Indices: 1560566--1560630 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
1560556 TCTCTCTCGC
1560566 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1560608 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
1560631 GCACACATAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1566267 original size:24 final size:22
Alignment explanation
Indices: 1566229--1566274 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
1566219 AACTCTTGTT
1566229 AAATTATAAATTTTAATATATTAA
1 AAATTATAAATTTT-AT-TATTAA
1566253 AAATTATGAAA-TTTATTATTAA
1 AAATTAT-AAATTTTATTATTAA
1566275 TTATTATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 6 0.29
23 2 0.10
24 10 0.48
25 3 0.14
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
AAATTATAAATTTTATTATTAA
Found at i:1566962 original size:2 final size:2
Alignment explanation
Indices: 1566957--1566981 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1566947 GGTTTGCATA
1566957 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
1566982 GGTATTTGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1567926 original size:22 final size:21
Alignment explanation
Indices: 1567899--1567944 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
1567889 ATAAAATTAT
*
1567899 TTTAAAATGTAATATTTAATAA
1 TTTAAAATGTAACA-TTAATAA
* *
1567921 TTTAAACTTTAACATTAATAA
1 TTTAAAATGTAACATTAATAA
1567942 TTT
1 TTT
1567945 TTCTTCTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (21 bp):
TTTAAAATGTAACATTAATAA
Found at i:1568878 original size:24 final size:24
Alignment explanation
Indices: 1568849--1568896 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1568839 TGATTTTATC
**
1568849 CATAATATTTTTATTAAATTGATT
1 CATAATATTTCAATTAAATTGATT
*
1568873 CATAATATTTCAATTGAATTGATT
1 CATAATATTTCAATTAAATTGATT
1568897 ATTTGAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (24 bp):
CATAATATTTCAATTAAATTGATT
Found at i:1569312 original size:2 final size:2
Alignment explanation
Indices: 1569305--1569333 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1569295 GGGGAAAATG
1569305 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1569334 GAGAGAATGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1569683 original size:2 final size:2
Alignment explanation
Indices: 1569676--1569700 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1569666 GAAGAAGATC
1569676 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
1569701 ATTGAGCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1573736 original size:23 final size:23
Alignment explanation
Indices: 1573706--1573751 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1573696 TGGGTATAAG
1573706 TTGTTGTATGTCACACAAGTTCT
1 TTGTTGTATGTCACACAAGTTCT
1573729 TTGTTGTATGTCACACAAGTTCT
1 TTGTTGTATGTCACACAAGTTCT
1573752 ACTGCTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.43
Consensus pattern (23 bp):
TTGTTGTATGTCACACAAGTTCT
Found at i:1573762 original size:23 final size:23
Alignment explanation
Indices: 1573710--1573762 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
1573700 TATAAGTTGT
* *
1573710 TGTATGTCACACAAGTTCTTTGT
1 TGTATGTCACACAAGTTCTCTGC
1573733 TGTATGTCACACAAGTTCTACTGC
1 TGTATGTCACACAAGTTCT-CTGC
1573757 TG-ATGT
1 TGTATGT
1573763 AAATATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 23 0.85
24 4 0.15
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.40
Consensus pattern (23 bp):
TGTATGTCACACAAGTTCTCTGC
Found at i:1583991 original size:2 final size:2
Alignment explanation
Indices: 1583984--1584011 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1583974 ACATGCATAA
1583984 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
1584012 GTACATGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1584803 original size:2 final size:2
Alignment explanation
Indices: 1584796--1584824 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1584786 ATGAATAAAG
1584796 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1584825 GCACTCCGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.