Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold59
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: 3999109
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 268233 characters in sequence are not A, C, G, or T
File 17 of 25
Found at i:2487113 original size:11 final size:11
Alignment explanation
Indices: 2487097--2487174 Score: 50
Period size: 11 Copynumber: 7.1 Consensus size: 11
2487087 TATAATCATG
*
2487097 TATTTATGTTA
1 TATTTATATTA
2487108 TATTTATATTA
1 TATTTATATTA
* *
2487119 TTTTTTATATTG
1 -TATTTATATTA
*
2487131 TA-TTATATTT
1 TATTTATATTA
* * *
2487141 TAATTATTTTT
1 TATTTATATTA
**
2487152 TATAAATATTA
1 TATTTATATTA
*
2487163 TGTTTATATTA
1 TATTTATATTA
2487174 T
1 T
2487175 GTCTCAATTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
10 9 0.18
11 33 0.65
12 9 0.18
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (11 bp):
TATTTATATTA
Found at i:2487137 original size:28 final size:27
Alignment explanation
Indices: 2487105--2487174 Score: 88
Period size: 28 Copynumber: 2.6 Consensus size: 27
2487095 TGTATTTATG
**
2487105 TTATATTTATATTATTTTTTATATTGTA
1 TTATATTTATATTATTTTTTATA-AATA
2487133 TTATATTT-TAATTATTTTTTATAAATA
1 TTATATTTAT-ATTATTTTTTATAAATA
*
2487160 TTATGTTTATATTAT
1 TTATATTTATATTAT
2487175 GTCTCAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 15 0.41
28 22 0.59
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (27 bp):
TTATATTTATATTATTTTTTATAAATA
Found at i:2487565 original size:24 final size:24
Alignment explanation
Indices: 2487538--2487584 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
2487528 AGAAAATTTA
2487538 TATTTGGGTCATGTTCATTTCATG
1 TATTTGGGTCATGTTCATTTCATG
2487562 TATTTGGGTCATGTTCATTTCAT
1 TATTTGGGTCATGTTCATTTCAT
2487585 ATTTCAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.17, C:0.13, G:0.19, T:0.51
Consensus pattern (24 bp):
TATTTGGGTCATGTTCATTTCATG
Found at i:2487801 original size:16 final size:15
Alignment explanation
Indices: 2487770--2487810 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
2487760 ATTCGTATCA
2487770 TATTAATATTATTTTT
1 TATT-ATATTATTTTT
2487786 TATTATATTATATTTT
1 TATTATATTAT-TTTT
*
2487802 AATTATATT
1 TATTATATT
2487811 TTTATTTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TATTATATTATTTTT
Found at i:2490263 original size:9 final size:8
Alignment explanation
Indices: 2490238--2490271 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
2490228 ATATTAATAT
2490238 AAATATTA
1 AAATATTA
*
2490246 AGATATTA
1 AAATATTA
2490254 AAATTATTA
1 AAA-TATTA
2490263 AAATATTA
1 AAATATTA
2490271 A
1 A
2490272 TATTTCAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (8 bp):
AAATATTA
Found at i:2490354 original size:18 final size:19
Alignment explanation
Indices: 2490323--2490364 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
2490313 AATATTGTAT
* *
2490323 TAATAAATACTTAA-AATA
1 TAATAAAAAATTAATAATA
*
2490341 TAATAAAAAATTAATCATA
1 TAATAAAAAATTAATAATA
2490360 TAATA
1 TAATA
2490365 TTTAAATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (19 bp):
TAATAAAAAATTAATAATA
Found at i:2490476 original size:14 final size:14
Alignment explanation
Indices: 2490436--2490480 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
2490426 AATAAATTAT
**
2490436 TAAT-TTTTAATTT
1 TAATATTTTAATAA
2490449 TAATATTTTAAATAA
1 TAATATTTT-AATAA
2490464 TAATATTTTAATAA
1 TAATATTTTAATAA
2490478 TAA
1 TAA
2490481 AAGATTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 4 0.14
14 12 0.43
15 12 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TAATATTTTAATAA
Found at i:2491505 original size:21 final size:21
Alignment explanation
Indices: 2491481--2491533 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
2491471 AATGTTCGTT
* **
2491481 TAAAAATATTTAGTAATTGGA
1 TAAAAATATTTAATAATTACA
* *
2491502 TAAATATTTTTAATAATTACA
1 TAAAAATATTTAATAATTACA
*
2491523 TAAAATTATTT
1 TAAAAATATTT
2491534 TTTATTTAAT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (21 bp):
TAAAAATATTTAATAATTACA
Found at i:2493034 original size:20 final size:20
Alignment explanation
Indices: 2493005--2493053 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2492995 ATTAACAAAT
2493005 TTACAT-AATATTATTAT-AA
1 TTACATAAATA-TATTATAAA
*
2493024 TTATATAAATATATTATAAA
1 TTACATAAATATATTATAAA
2493044 TTACATAAAT
1 TTACATAAAT
2493054 GTTTATGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (20 bp):
TTACATAAATATATTATAAA
Found at i:2493059 original size:19 final size:18
Alignment explanation
Indices: 2493005--2493053 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
2492995 ATTAACAAAT
2493005 TTACATAATATTATTATAA
1 TTACATAA-ATTATTATAA
*
2493024 TTATATAAATATATTATAAA
1 TTACATAAAT-TATTAT-AA
2493044 TTACATAAAT
1 TTACATAAAT
2493054 GTTTATGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 2 0.08
19 13 0.50
20 11 0.42
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (18 bp):
TTACATAAATTATTATAA
Found at i:2496484 original size:27 final size:28
Alignment explanation
Indices: 2496447--2496522 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
2496437 ACAAAAATTA
* * *
2496447 TCTTTTGTGTTTGTCAAAAATGA-TAGT
1 TCTTTTATGTTTATAAAAAATGAGTAGT
2496474 TCTTTTATGTTTATAAAAAAT-AGTAGT
1 TCTTTTATGTTTATAAAAAATGAGTAGT
*
2496501 TCTTTTTTGTTTATAAAAAATG
1 TCTTTTATGTTTATAAAAAATG
2496523 GTGGCTTGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
26 1 0.02
27 42 0.98
ACGTcount: A:0.32, C:0.05, G:0.13, T:0.50
Consensus pattern (28 bp):
TCTTTTATGTTTATAAAAAATGAGTAGT
Found at i:2498298 original size:23 final size:22
Alignment explanation
Indices: 2498264--2498306 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
2498254 CAAATTAATT
*
2498264 TTTTATACATATTATTATAAAA
1 TTTTACACATATTATTATAAAA
2498286 TTTTACACAATATTATTATAA
1 TTTTACAC-ATATTATTATAA
2498307 TTATATTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTTACACATATTATTATAAAA
Found at i:2502004 original size:7 final size:7
Alignment explanation
Indices: 2501989--2502018 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
2501979 AAAATAAAAA
2501989 ATTTAAAT
1 ATTT-AAT
2501997 ATTTAAT
1 ATTTAAT
2502004 ATTTAAT
1 ATTTAAT
2502011 ATTTAAT
1 ATTTAAT
2502018 A
1 A
2502019 AAAATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.82
8 4 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
ATTTAAT
Found at i:2502131 original size:17 final size:19
Alignment explanation
Indices: 2502097--2502133 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2502087 AAAAACATAT
2502097 TATATAAATAATTATAAAA
1 TATATAAATAATTATAAAA
2502116 TATATAAAT-ATT-TAAAA
1 TATATAAATAATTATAAAA
2502133 T
1 T
2502134 TAATTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TATATAAATAATTATAAAA
Found at i:2502152 original size:10 final size:10
Alignment explanation
Indices: 2502137--2502183 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
2502127 TTAAAATTAA
2502137 TTTTTATAAT
1 TTTTTATAAT
*
2502147 TTTTTAAAAT
1 TTTTTATAAT
*
2502157 TTTTAATAAT
1 TTTTTATAAT
2502167 TTTTTATCAAAT
1 TTTTTAT--AAT
2502179 TTTTT
1 TTTTT
2502184 TCGATTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
10 23 0.74
12 8 0.26
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:2502160 original size:20 final size:21
Alignment explanation
Indices: 2502137--2502183 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 21
2502127 TTAAAATTAA
2502137 TTTTTATAATTTTTTA-AAAT
1 TTTTTATAATTTTTTACAAAT
*
2502157 TTTTAATAATTTTTTATCAAAT
1 TTTTTATAATTTTTTA-CAAAT
2502179 TTTTT
1 TTTTT
2502184 TCGATTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 15 0.65
22 8 0.35
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTTATAATTTTTTACAAAT
Found at i:2502205 original size:16 final size:16
Alignment explanation
Indices: 2502184--2502214 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2502174 CAAATTTTTT
2502184 TCGATTTAAAAATATC
1 TCGATTTAAAAATATC
*
2502200 TCGATTTAATAATAT
1 TCGATTTAAAAATAT
2502215 ATATCAAACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (16 bp):
TCGATTTAAAAATATC
Found at i:2504016 original size:23 final size:24
Alignment explanation
Indices: 2503983--2504053 Score: 65
Period size: 23 Copynumber: 3.0 Consensus size: 24
2503973 AATATTTTTA
*
2503983 TAAATAAAAAAATAAAAATTATTT
1 TAAATATAAAAATAAAAATTATTT
* *
2504007 TAAAT-TAAAAA-AATTAATTATTA
1 TAAATATAAAAATAA-AAATTATTT
* **
2504030 TAAATATTAACTTAAAAATTATTT
1 TAAATATAAAAATAAAAATTATTT
2504054 CATAAACTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
22 2 0.06
23 17 0.47
24 15 0.42
25 2 0.06
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (24 bp):
TAAATATAAAAATAAAAATTATTT
Found at i:2504029 original size:26 final size:25
Alignment explanation
Indices: 2503973--2504030 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
2503963 ATCTAATTAT
2503973 AATATT-TTTATAAATAAAAAAATA
1 AATATTATTTATAAATAAAAAAATA
*
2503997 AAAATTATTT-TAAATTAAAAAAATTA
1 AATATTATTTATAAA-TAAAAAAA-TA
*
2504023 ATTATTAT
1 AATATTAT
2504031 AAATATTAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 9 0.32
25 11 0.39
26 8 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATATTATTTATAAATAAAAAAATA
Found at i:2504368 original size:15 final size:17
Alignment explanation
Indices: 2504336--2504375 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
2504326 ATGAAATTAT
2504336 ATATTTTTACGATACTA
1 ATATTTTTACGATACTA
*
2504353 A-ATTTTTA-GATGCTA
1 ATATTTTTACGATACTA
2504368 ATATTTTT
1 ATATTTTT
2504376 TATTTCTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 7 0.33
16 13 0.62
17 1 0.05
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (17 bp):
ATATTTTTACGATACTA
Found at i:2504835 original size:31 final size:29
Alignment explanation
Indices: 2504798--2504868 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 29
2504788 ATATTTAAAT
* * *
2504798 TATAATTATAAATATTAAAAATATAATAAA
1 TATAATTATAAATA-AAAAAATAAAAAAAA
2504828 TATTAATTATAAATAAAAAAATAAAAAAAA
1 TA-TAATTATAAATAAAAAAATAAAAAAAA
*
2504858 TAAAATTATAA
1 TATAATTATAA
2504869 TATCACAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 8 0.22
30 16 0.44
31 12 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (29 bp):
TATAATTATAAATAAAAAAATAAAAAAAA
Found at i:2505456 original size:19 final size:18
Alignment explanation
Indices: 2505432--2505467 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2505422 TATTAAAATA
2505432 ATATTTAAATAAATTATTC
1 ATATTT-AATAAATTATTC
*
2505451 ATATTTGATAAATTATT
1 ATATTTAATAAATTATT
2505468 TTTTATTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (18 bp):
ATATTTAATAAATTATTC
Found at i:2505544 original size:23 final size:23
Alignment explanation
Indices: 2505505--2505569 Score: 60
Period size: 23 Copynumber: 2.7 Consensus size: 23
2505495 ATAAATAATT
*
2505505 TATTTATTAATAA-TAAAAATATA
1 TATTTAATAA-AATTAAAAATATA
* *
2505528 TATTTAATAAAATTAAAATTTTA
1 TATTTAATAAAATTAAAAATATA
2505551 TATTATAAATAAAAATTAA
1 TATT-T-AAT-AAAATTAA
2505570 TATTAAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 2 0.06
23 21 0.60
24 1 0.03
25 3 0.09
26 8 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TATTTAATAAAATTAAAAATATA
Found at i:2506098 original size:31 final size:32
Alignment explanation
Indices: 2506051--2506138 Score: 117
Period size: 31 Copynumber: 2.8 Consensus size: 32
2506041 TTATTTTAAA
*
2506051 AAAATAATATAATTAATTTAAAATTTAAAATT
1 AAAATAATTTAATTAATTTAAAATTTAAAATT
* *
2506083 -AATTAATTTAATTAATTTTAAATTTAAAATT
1 AAAATAATTTAATTAATTTAAAATTTAAAATT
*
2506114 AAAATAATTAAATT-ATATTAAAATT
1 AAAATAATTTAATTAAT-TTAAAATT
2506139 AATAATTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
31 30 0.62
32 18 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
AAAATAATTTAATTAATTTAAAATTTAAAATT
Found at i:2506152 original size:25 final size:24
Alignment explanation
Indices: 2506106--2506163 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
2506096 AATTTTAAAT
2506106 TTAAAATTAAAATAATTAAATTATA
1 TTAAAATTAAAATAATTAAATT-TA
* * *
2506131 TTAAAATTAATAAT-TTTTAATTTT
1 TTAAAATTAA-AATAATTAAATTTA
2506155 TTAAAATTA
1 TTAAAATTA
2506164 TTTTTATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 10 0.34
25 16 0.55
26 3 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TTAAAATTAAAATAATTAAATTTA
Found at i:2506303 original size:31 final size:29
Alignment explanation
Indices: 2506231--2506309 Score: 77
Period size: 31 Copynumber: 2.6 Consensus size: 29
2506221 ATGAGTTTTA
* * *
2506231 AATTTAAGTTTATAAATAAATTTATATTT
1 AATTTAATTTTATTAATAAATTTAAATTT
*
2506260 ATATTTATATTTTATTAATATATTTAAAATATT
1 A-ATTTA-ATTTTATTAATAAATTT-AAAT-TT
*
2506293 AATTTAATTTTTTTAAT
1 AATTTAATTTTATTAAT
2506310 TTTTTTAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
29 1 0.02
30 5 0.12
31 24 0.59
32 8 0.20
33 3 0.07
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (29 bp):
AATTTAATTTTATTAATAAATTTAAATTT
Found at i:2506312 original size:8 final size:9
Alignment explanation
Indices: 2506295--2506321 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
2506285 AAAATATTAA
2506295 TTTAATTTT
1 TTTAATTTT
2506304 TTTAATTTT
1 TTTAATTTT
2506313 TTTAATTTT
1 TTTAATTTT
2506322 ATAATTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTAATTTT
Found at i:2506379 original size:17 final size:17
Alignment explanation
Indices: 2506354--2506386 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2506344 AATCATTAAA
*
2506354 TTAATATTTTAAATTAC
1 TTAAAATTTTAAATTAC
2506371 TTAAAATTTTAAATTA
1 TTAAAATTTTAAATTA
2506387 AATTAATTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAAAATTTTAAATTAC
Found at i:2506596 original size:3 final size:3
Alignment explanation
Indices: 2506588--2506634 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
2506578 AGGTAAAATA
* *
2506588 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT GAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2506635 GATTAATTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2506773 original size:21 final size:21
Alignment explanation
Indices: 2506749--2506799 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
2506739 TATAAAATAT
2506749 TATATTAAATATATATTTATA
1 TATATTAAATATATATTTATA
* * *
2506770 TATACTCATTATATATTTATA
1 TATATTAAATATATATTTATA
*
2506791 TAAATTAAA
1 TATATTAAA
2506800 ATTTAAAATT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (21 bp):
TATATTAAATATATATTTATA
Found at i:2506983 original size:25 final size:27
Alignment explanation
Indices: 2506909--2506986 Score: 79
Period size: 27 Copynumber: 2.8 Consensus size: 27
2506899 ATATTTAATA
*
2506909 ATAATTTATTTATTTTATTTATATGATAT
1 ATAA-TTATATATTTTATTT-TATGATAT
* *
2506938 ATATTTACATATTATTAATTTT-T-ATAT
1 ATAATTATATATT-TT-ATTTTATGATAT
2506965 ATAATTATATATTTTATTTTAT
1 ATAATTATATATTTTATTTTAT
2506987 TTTATTATTA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
25 5 0.12
26 3 0.07
27 15 0.37
28 8 0.20
29 6 0.15
30 4 0.10
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (27 bp):
ATAATTATATATTTTATTTTATGATAT
Found at i:2507877 original size:22 final size:22
Alignment explanation
Indices: 2507831--2507878 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
2507821 TTAATTTAAA
*
2507831 ATAAA-AATTTTAATTATTATT
1 ATAAATAATATTAATTATTATT
2507852 -TAAATAATATTAATATATT-TT
1 ATAAATAATATTAAT-TATTATT
2507873 ATAAAT
1 ATAAAT
2507879 TAAATATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 4 0.17
21 10 0.43
22 9 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAAATAATATTAATTATTATT
Found at i:2508201 original size:14 final size:14
Alignment explanation
Indices: 2508182--2508245 Score: 51
Period size: 15 Copynumber: 4.4 Consensus size: 14
2508172 TGAGATAGAA
2508182 TAAAAAATAATAAT
1 TAAAAAATAATAAT
*
2508196 T-AAAAATATTTAAT
1 TAAAAAATA-ATAAT
* *
2508210 TAAAATAT-ATGTAT
1 TAAAAAATAAT-AAT
2508224 ATAAAAAATAAATAAT
1 -TAAAAAAT-AATAAT
2508240 TAAAAA
1 TAAAAA
2508246 TGATTAAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 11
0.69 0.11 0.20
Matches are distributed among these distances:
13 8 0.21
14 8 0.21
15 18 0.47
16 2 0.05
17 2 0.05
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (14 bp):
TAAAAAATAATAAT
Found at i:2508246 original size:14 final size:14
Alignment explanation
Indices: 2508184--2508246 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
2508174 AGATAGAATA
2508184 AAAAAT-AATAATT
1 AAAAATAAATAATT
**
2508197 AAAAATATTTAATT
1 AAAAATAAATAATT
** *
2508211 AAAATATATGTATATA
1 AAAA-ATAAATA-ATT
2508227 AAAAATAAATAATT
1 AAAAATAAATAATT
2508241 AAAAAT
1 AAAAAT
2508247 GATTAAAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
13 6 0.15
14 17 0.43
15 11 0.28
16 6 0.15
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (14 bp):
AAAAATAAATAATT
Found at i:2508271 original size:35 final size:35
Alignment explanation
Indices: 2508232--2508343 Score: 118
Period size: 35 Copynumber: 3.2 Consensus size: 35
2508222 ATATAAAAAA
* *
2508232 TAAATAATTAAAAATGATTAAAATTATATTTATAT
1 TAAATAATTAAAAATAATTAAAATAATATTTATAT
* * * *
2508267 TAAATGA-TAAAATATAAATAAAATAATATTCATGT
1 TAAATAATTAAAA-ATAATTAAAATAATATTTATAT
* * * *
2508302 TAAATAATTAAAAATTATAAAAATGATATTTATTT
1 TAAATAATTAAAAATAATTAAAATAATATTTATAT
2508337 TAAATAA
1 TAAATAA
2508344 GAATTTAATT
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
34 5 0.08
35 52 0.84
36 5 0.08
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (35 bp):
TAAATAATTAAAAATAATTAAAATAATATTTATAT
Found at i:2509069 original size:29 final size:28
Alignment explanation
Indices: 2509029--2509105 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 28
2509019 TTAGATCAAT
* * *
2509029 TTTTTATAATTAAAATTATAAAATTTTTA
1 TTTTTATTATTAAAATTATAAAA-TGTAA
2509058 TTTTTATTATTAAAATTA-AAAATGTAA
1 TTTTTATTATTAAAATTATAAAATGTAA
2509085 TATTTTATTATTAATAATTAT
1 T-TTTTATTATTAA-AATTAT
2509106 TTAAATTGAT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
27 4 0.10
28 16 0.38
29 22 0.52
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (28 bp):
TTTTTATTATTAAAATTATAAAATGTAA
Found at i:2509753 original size:20 final size:21
Alignment explanation
Indices: 2509728--2509768 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2509718 TTTATTTTTA
*
2509728 AATAATT-TATATAAATTAAT
1 AATAATTGAATATAAATTAAT
*
2509748 AATAATTGAATATAATTTAAT
1 AATAATTGAATATAAATTAAT
2509769 CGAGTTTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
AATAATTGAATATAAATTAAT
Found at i:2513995 original size:50 final size:50
Alignment explanation
Indices: 2513936--2514035 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
2513926 CATTTAACTG
*
2513936 ATAGATTATATTAATCTTTTATTTTATTTTACTTTGGAAACAATGGCATC
1 ATAGATTATATTAATCTTTTACTTTATTTTACTTTGGAAACAATGGCATC
2513986 ATAGATTATATTAATCTTTTACTTTATTTTACTTTGGAAACAATGGCATC
1 ATAGATTATATTAATCTTTTACTTTATTTTACTTTGGAAACAATGGCATC
2514036 TTGTTGCCGA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.32, C:0.11, G:0.10, T:0.47
Consensus pattern (50 bp):
ATAGATTATATTAATCTTTTACTTTATTTTACTTTGGAAACAATGGCATC
Found at i:2514974 original size:36 final size:35
Alignment explanation
Indices: 2514912--2514988 Score: 136
Period size: 36 Copynumber: 2.2 Consensus size: 35
2514902 AGGTGATTTT
*
2514912 GAACAACTTGCCTTTTCAGCTTGTTTGTTTTCCAA
1 GAACCACTTGCCTTTTCAGCTTGTTTGTTTTCCAA
2514947 GAACCACTTGCCTTTTGCAGCTTGTTTGTTTTCCAA
1 GAACCACTTGCCTTTT-CAGCTTGTTTGTTTTCCAA
2514983 GAACCA
1 GAACCA
2514989 AAAGTTGGCG
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
35 15 0.38
36 25 0.62
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.39
Consensus pattern (35 bp):
GAACCACTTGCCTTTTCAGCTTGTTTGTTTTCCAA
Found at i:2516894 original size:23 final size:23
Alignment explanation
Indices: 2516836--2516886 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
2516826 ATTTTTTTAT
*
2516836 TATTTTTAAA-CAATAAAATATA
1 TATTTTTAAATTAATAAAATATA
2516858 TATTTTTAAATTAATAAAA-ATA
1 TATTTTTAAATTAATAAAATATA
2516880 -ATTTTTA
1 TATTTTTA
2516887 TTATTTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 7 0.26
22 13 0.48
23 7 0.26
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TATTTTTAAATTAATAAAATATA
Found at i:2517192 original size:16 final size:16
Alignment explanation
Indices: 2517173--2517218 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
2517163 AAATTTTTTT
2517173 ATAATTAATATATAAA
1 ATAATTAATATATAAA
* *
2517189 ATAATTATTATTTAAA
1 ATAATTAATATATAAA
2517205 A-AA--AATATATAAA
1 ATAATTAATATATAAA
2517218 A
1 A
2517219 AAATATATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 9 0.35
15 2 0.08
16 15 0.58
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
ATAATTAATATATAAA
Found at i:2517467 original size:18 final size:17
Alignment explanation
Indices: 2517417--2517487 Score: 63
Period size: 17 Copynumber: 3.9 Consensus size: 17
2517407 GTTAATTAAA
* *
2517417 TTAATAATCATATATAT
1 TTAATAATTATATTTAT
*
2517434 TTAA-AATTAAATTTTAT
1 TTAATAATTATA-TTTAT
2517451 TTAATAATTATTATTTAT
1 TTAATAATTA-TATTTAT
2517469 TTAAATATATTTATATTTA
1 TT-AATA-A-TTATATTTA
2517488 AAATCTTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
16 5 0.11
17 12 0.27
18 12 0.27
19 5 0.11
20 7 0.16
21 3 0.07
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (17 bp):
TTAATAATTATATTTAT
Found at i:2517569 original size:18 final size:20
Alignment explanation
Indices: 2517546--2517593 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
2517536 ATTATGTAAA
2517546 ATATAATAT-A-AAATTGAG
1 ATATAATATAATAAATTGAG
2517564 ATATAATATGAATAAATTGAG
1 ATATAATAT-AATAAATTGAG
*
2517585 ATATGATAT
1 ATATAATAT
2517594 GAACAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 9 0.35
20 1 0.04
21 16 0.62
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.35
Consensus pattern (20 bp):
ATATAATATAATAAATTGAG
Found at i:2517582 original size:21 final size:21
Alignment explanation
Indices: 2517556--2517596 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2517546 ATATAATATA
2517556 AAATTGAGATATAATATGAAT
1 AAATTGAGATATAATATGAAT
*
2517577 AAATTGAGATATGATATGAA
1 AAATTGAGATATAATATGAA
2517597 CAAAATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.17, T:0.32
Consensus pattern (21 bp):
AAATTGAGATATAATATGAAT
Found at i:2518330 original size:21 final size:24
Alignment explanation
Indices: 2518295--2518354 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 24
2518285 TATTTTAAAT
* *
2518295 ATATAAAATATAATAAAA-AT-ATT
1 ATAT-AAATACAATAAAACATAATA
2518318 ATATAAA-ACAATAAAACATAATA
1 ATATAAATACAATAAAACATAATA
2518341 ATATAAATACAATA
1 ATATAAATACAATA
2518355 CATAAACGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 8 0.25
22 5 0.16
23 13 0.41
24 6 0.19
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (24 bp):
ATATAAATACAATAAAACATAATA
Found at i:2519424 original size:84 final size:83
Alignment explanation
Indices: 2519322--2519478 Score: 190
Period size: 84 Copynumber: 1.9 Consensus size: 83
2519312 AAATTTTTAC
* * * ** * * * *
2519322 TAAATTGAATCACTATGATAAATTA-AGTAAAATATATTATGAATTGAGATATGATATAAATATA
1 TAAATTAAATCACAATGATAAACTATA-TAAAATATAAAATAAATTGAGATATAATATAAACACA
2519386 ATATAATATACTATATTTTT
65 ATAT-ATATACTATATTTTT
* *
2519406 TAAATTAAATTACAATGATCAACTATATAAAATATAAAATAAATTGAGATATAATATAAACACAA
1 TAAATTAAATCACAATGATAAACTATATAAAATATAAAATAAATTGAGATATAATATAAACACAA
2519471 TATATATA
66 TATATATA
2519479 AAAATTAAAT
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
83 5 0.08
84 55 0.90
85 1 0.02
ACGTcount: A:0.52, C:0.05, G:0.06, T:0.36
Consensus pattern (83 bp):
TAAATTAAATCACAATGATAAACTATATAAAATATAAAATAAATTGAGATATAATATAAACACAA
TATATATACTATATTTTT
Found at i:2519513 original size:11 final size:11
Alignment explanation
Indices: 2519454--2519532 Score: 76
Period size: 11 Copynumber: 7.5 Consensus size: 11
2519444 ATAAATTGAG
2519454 ATATAATATAA
1 ATATAATATAA
* * *
2519465 ACACAATATAT
1 ATATAATATAA
*
2519476 ATA-AAAATTAA
1 ATATAATA-TAA
2519487 ATAT-A-ATAA
1 ATATAATATAA
2519496 A-ATAATATAA
1 ATATAATATAA
*
2519506 ATATAATATGA
1 ATATAATATAA
2519517 ATATAATATAA
1 ATATAATATAA
2519528 ATATA
1 ATATA
2519533 TAAATGTATT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
8 2 0.04
9 5 0.09
10 9 0.16
11 39 0.71
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (11 bp):
ATATAATATAA
Found at i:2519571 original size:28 final size:29
Alignment explanation
Indices: 2519434--2519572 Score: 92
Period size: 28 Copynumber: 4.7 Consensus size: 29
2519424 TCAACTATAT
* *
2519434 AAAATATA-AAATAAATTGAGATATAATATAA
1 AAAATATATAAATAAATTAAAATAT-A-AT-A
2519465 ACACAATATATATAA-AAATT-AAATATAAT-
1 A-A-AATATATA-AATAAATTAAAATATAATA
*
2519494 AAAATAATATAAATATAA-TATGAATATAATA
1 AAAAT-ATATAAATA-AATTA-AAATATAATA
* **
2519525 TAAATATATAAATGTATTAAAATAT-ATA
1 AAAATATATAAATAAATTAAAATATAATA
*
2519553 AAAATATATAATTAAATTAA
1 AAAATATATAAATAAATTAA
2519573 TATTAATTTT
Statistics
Matches: 87, Mismatches: 10, Indels: 25
0.71 0.08 0.20
Matches are distributed among these distances:
27 5 0.06
28 27 0.31
29 9 0.10
30 18 0.21
31 7 0.08
32 2 0.02
33 11 0.13
34 6 0.07
35 2 0.02
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (29 bp):
AAAATATATAAATAAATTAAAATATAATA
Found at i:2520071 original size:11 final size:11
Alignment explanation
Indices: 2520055--2520079 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2520045 TCTCACACAC
2520055 AAAAAATAAAT
1 AAAAAATAAAT
2520066 AAAAAATAAAT
1 AAAAAATAAAT
2520077 AAA
1 AAA
2520080 TAAACAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAAATAAAT
Found at i:2520078 original size:15 final size:16
Alignment explanation
Indices: 2520053--2520088 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
2520043 TTTCTCACAC
2520053 ACAAA-AAATAAATAA
1 ACAAATAAATAAATAA
2520068 A-AAATAAATAAATAA
1 ACAAATAAATAAATAA
2520083 ACAAAT
1 ACAAAT
2520089 TTATTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 3 0.16
15 12 0.63
16 4 0.21
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.17
Consensus pattern (16 bp):
ACAAATAAATAAATAA
Found at i:2523748 original size:35 final size:35
Alignment explanation
Indices: 2523702--2523772 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
2523692 TGGAGCAGGG
* *
2523702 AACTCTGCCTTAATCTTTTGTTACATCTTGAAACT
1 AACTCTCCCTTAATCTTTTGTTACATCCTGAAACT
2523737 AACTCTCCCTTAATCTTTTGTTACATCCTGAAACT
1 AACTCTCCCTTAATCTTTTGTTACATCCTGAAACT
2523772 A
1 A
2523773 TGCAAAATGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.27, C:0.25, G:0.07, T:0.41
Consensus pattern (35 bp):
AACTCTCCCTTAATCTTTTGTTACATCCTGAAACT
Found at i:2525224 original size:37 final size:36
Alignment explanation
Indices: 2525099--2525225 Score: 113
Period size: 37 Copynumber: 3.5 Consensus size: 36
2525089 TAATGATTGC
2525099 AAGGGTAAATTATAGAAAAATCTTAAAATT-ATTA-AA
1 AAGGGTAAATTATA-AAAAATCTT-AAATTAATTATAA
* *
2525135 AA-GG-AAATTATAAAAAAT-ATATAATTAATTAATAC
1 AAGGGTAAATTATAAAAAATCTTA-AATTAATT-ATAA
**
2525170 AACAGT-AATTATAAAAAAATCTTAAATTAATTACTAA
1 AAGGGTAAATTAT-AAAAAATCTTAAATTAATTA-TAA
*
2525207 AAGGGTAAATCATAAAAAA
1 AAGGGTAAATTATAAAAAA
2525226 GAAAAGACAT
Statistics
Matches: 73, Mismatches: 8, Indels: 19
0.73 0.08 0.19
Matches are distributed among these distances:
31 1 0.01
32 5 0.07
33 9 0.12
34 9 0.12
35 5 0.07
36 10 0.14
37 27 0.37
38 7 0.10
ACGTcount: A:0.58, C:0.05, G:0.08, T:0.29
Consensus pattern (36 bp):
AAGGGTAAATTATAAAAAATCTTAAATTAATTATAA
Found at i:2529250 original size:2 final size:2
Alignment explanation
Indices: 2529245--2529269 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2529235 TCTCTCTCTT
2529245 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 T
2529270 TTATTTATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2532495 original size:12 final size:12
Alignment explanation
Indices: 2532482--2532538 Score: 57
Period size: 12 Copynumber: 4.9 Consensus size: 12
2532472 ATTTATTATA
2532482 ATTATAAATA-T
1 ATTATAAATATT
2532493 A--ATAAATATT
1 ATTATAAATATT
*
2532503 ATTATAATTTATT
1 ATTATAA-ATATT
* *
2532516 ATGATAAATTTT
1 ATTATAAATATT
2532528 ATTATAAATAT
1 ATTATAAATAT
2532539 CAAAAATAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
9 7 0.19
10 2 0.06
11 1 0.03
12 16 0.44
13 10 0.28
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (12 bp):
ATTATAAATATT
Found at i:2532529 original size:25 final size:27
Alignment explanation
Indices: 2532473--2532534 Score: 83
Period size: 25 Copynumber: 2.4 Consensus size: 27
2532463 TCGTATCATA
2532473 TTTATTATAATTATAAATATAATAAAT
1 TTTATTATAATTATAAATATAATAAAT
* * *
2532500 ATTATTATAATT-T-ATTATGATAAAT
1 TTTATTATAATTATAAATATAATAAAT
2532525 TTTATTATAA
1 TTTATTATAA
2532535 ATATCAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 19 0.61
26 1 0.03
27 11 0.35
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (27 bp):
TTTATTATAATTATAAATATAATAAAT
Found at i:2538947 original size:19 final size:20
Alignment explanation
Indices: 2538910--2538947 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2538900 TTGGATAAGT
*
2538910 TTTAAATATGATATAATATA
1 TTTAAATATAATATAATATA
2538930 TTTAAATATAAT-TAATAT
1 TTTAAATATAATATAATAT
2538948 TATATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
TTTAAATATAATATAATATA
Found at i:2539327 original size:15 final size:16
Alignment explanation
Indices: 2539289--2539330 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
2539279 TATAAATGGT
2539289 ATATAAATTTA-TATA
1 ATATAAATTTATTATA
* *
2539304 TTATTAATTTATTA-A
1 ATATAAATTTATTATA
2539319 ATATAAATTTAT
1 ATATAAATTTAT
2539331 ATTTAAATAC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 20 0.91
16 2 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATAAATTTATTATA
Found at i:2539348 original size:30 final size:30
Alignment explanation
Indices: 2539289--2539349 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 30
2539279 TATAAATGGT
* *
2539289 ATATAAATTTATATATTATTAATTTATTAA
1 ATATAAATTTATATATTAATAATTGATTAA
2539319 ATATAAATTTATAT-TTAAATACA-TGATTAA
1 ATATAAATTTATATATT-AATA-ATTGATTAA
2539349 A
1 A
2539350 AAAAAGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 2 0.07
30 24 0.89
31 1 0.04
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (30 bp):
ATATAAATTTATATATTAATAATTGATTAA
Found at i:2539831 original size:20 final size:20
Alignment explanation
Indices: 2539784--2539831 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
2539774 ATTAAATTAG
*
2539784 TAATTTTTTAAATAAAATTT
1 TAATATTTTAAATAAAATTT
2539804 TAAATATTTTAAA-AATAATTT
1 T-AATATTTTAAATAA-AATTT
2539825 TAATATT
1 TAATATT
2539832 GAATAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TAATATTTTAAATAAAATTT
Found at i:2540519 original size:17 final size:18
Alignment explanation
Indices: 2540497--2540531 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2540487 TTACTTTTTA
*
2540497 ATTAAATA-AAAATAATT
1 ATTAAATATAAAAAAATT
2540514 ATTAAATATAAAAAAATT
1 ATTAAATATAAAAAAATT
2540532 TAATTATCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
ATTAAATATAAAAAAATT
Found at i:2541652 original size:34 final size:35
Alignment explanation
Indices: 2541614--2541688 Score: 91
Period size: 34 Copynumber: 2.2 Consensus size: 35
2541604 TTTATAAAAA
* * *
2541614 TAATTTTAAATTTTAA-ATTAATTTAAATAAA-ATT
1 TAATTTTAAA-TATAATATCAAATTAAATAAATATT
*
2541648 TAATTTTATATATAATATCAAATTAAATAAATATT
1 TAATTTTAAATATAATATCAAATTAAATAAATATT
2541683 TAATTT
1 TAATTT
2541689 CCAATAGAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
33 4 0.11
34 22 0.63
35 9 0.26
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (35 bp):
TAATTTTAAATATAATATCAAATTAAATAAATATT
Found at i:2543449 original size:22 final size:22
Alignment explanation
Indices: 2543405--2543454 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
2543395 TTATTTAAAG
* *
2543405 AAATTATTTTATATTATATTTT
1 AAATAATTTTATATTATAATTT
*
2543427 ATATAATTTTATAATTA-AATTT
1 AAATAATTTTAT-ATTATAATTT
2543449 AAATAA
1 AAATAA
2543455 AATATTATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
AAATAATTTTATATTATAATTT
Found at i:2546329 original size:21 final size:20
Alignment explanation
Indices: 2546303--2546403 Score: 66
Period size: 20 Copynumber: 5.0 Consensus size: 20
2546293 ATGTATATTT
2546303 ATATATTTTTATATATTATA
1 ATATATTTTTATATATTATA
* *
2546323 A-ATATATTTAAAATATT-TGA
1 ATATAT-TTTTATATATTAT-A
2546343 ATGA-ATTTTTATATATTACTA
1 AT-ATATTTTTATATATTA-TA
* *
2546364 TTA-ATATTTTATAAATTATA
1 ATATAT-TTTTATATATTATA
* *
2546384 ATTTATTTATATATTATTAT
1 ATATATTTTTATA-TATTAT
2546404 TTTATTTTTA
Statistics
Matches: 62, Mismatches: 10, Indels: 17
0.70 0.11 0.19
Matches are distributed among these distances:
19 5 0.08
20 33 0.53
21 22 0.35
22 2 0.03
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (20 bp):
ATATATTTTTATATATTATA
Found at i:2546394 original size:18 final size:19
Alignment explanation
Indices: 2546362--2546410 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
2546352 TATATATTAC
*
2546362 TATTAATAT-TTTATAAAT
1 TATTAATTTATTTATAAAT
*
2546380 TA-TAATTTATTTATATAT
1 TATTAATTTATTTATAAAT
*
2546398 TATTATTTTATTT
1 TATTAATTTATTT
2546411 TTATTATAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 5 0.19
18 12 0.46
19 9 0.35
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TATTAATTTATTTATAAAT
Found at i:2546413 original size:21 final size:19
Alignment explanation
Indices: 2546347--2546414 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 19
2546337 ATTTGAATGA
*
2546347 ATTTTTATATATTACTATTA
1 ATTTTTATATATTA-TATTT
*
2546367 ATATTTTATAAATTATAATTT
1 AT-TTTTATATATTAT-ATTT
*
2546388 ATTTATATATTATTAT-TTT
1 ATTTTTATA-TATTATATTT
2546407 ATTTTTAT
1 ATTTTTAT
2546415 TATAGTAGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
19 10 0.25
20 9 0.22
21 21 0.52
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTTTATATATTATATTT
Found at i:2547697 original size:16 final size:16
Alignment explanation
Indices: 2547664--2547709 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
2547654 TGGATTTGAA
* **
2547664 TTAATAAAAATTTTAT
1 TTAATATAAATTAAAT
2547680 TTAATATAAATTAAAT
1 TTAATATAAATTAAAT
2547696 TT--TATAAATTAAAT
1 TTAATATAAATTAAAT
2547710 GAGTAACTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 12 0.44
16 15 0.56
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTAATATAAATTAAAT
Found at i:2549254 original size:17 final size:16
Alignment explanation
Indices: 2549232--2549265 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2549222 GAGACAGTGT
*
2549232 ATATTCTGCTGTGAATG
1 ATATTCTG-TGTAAATG
2549249 ATATTCTGTGTAAATG
1 ATATTCTGTGTAAATG
2549265 A
1 A
2549266 CAATTCTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (16 bp):
ATATTCTGTGTAAATG
Found at i:2551388 original size:12 final size:12
Alignment explanation
Indices: 2551367--2551396 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2551357 TTAATTAAAG
2551367 ATTA-TTTATTT
1 ATTATTTTATTT
2551378 ATTATTTTATTT
1 ATTATTTTATTT
2551390 ATTATTT
1 ATTATTT
2551397 AATATTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
ATTATTTTATTT
Found at i:2551508 original size:29 final size:31
Alignment explanation
Indices: 2551455--2551517 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 31
2551445 AGTTATTATA
* *
2551455 TAAATTTATATTATATTTTTTATTTATTT-T
1 TAAATTTATATTAAATTATTTATTTATTTGT
*
2551485 TAAATTT-TTTTAAATTATTTATTTATTTGT
1 TAAATTTATATTAAATTATTTATTTATTTGT
2551515 TAA
1 TAA
2551518 TAGATGTCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 18 0.62
30 11 0.38
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (31 bp):
TAAATTTATATTAAATTATTTATTTATTTGT
Found at i:2552413 original size:2 final size:2
Alignment explanation
Indices: 2552406--2552439 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2552396 TATTTTCTGC
2552406 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
2552440 ATCTATAGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2554560 original size:105 final size:105
Alignment explanation
Indices: 2554449--2554665 Score: 398
Period size: 105 Copynumber: 2.1 Consensus size: 105
2554439 CTTAATAGTC
2554449 TTTTTTCACGTTCTTGATTTATTGGCAGCTAGGATTAGGATGACTCAACAAATTTAGCAGAATGA
1 TTTTTTCACGTTCTTGATTTATTGGCAGCTAGGATTAGGATGACTCAACAAATTTAGCAGAATGA
*
2554514 TTTTACACACAAATTTTCCCATTTTTGACATGTACAGAGT
66 TTTTACACACAAATTTTCCCATTTATGACATGTACAGAGT
*
2554554 TTTTTTCATGTTCTTGATTTATTGGCAGCTAGGATTAGGATGACTCAACAAATTTAGCAGAATGA
1 TTTTTTCACGTTCTTGATTTATTGGCAGCTAGGATTAGGATGACTCAACAAATTTAGCAGAATGA
*
2554619 TTTTACACTCAAATTTTCCCATTTATGACATGTACAGAGT
66 TTTTACACACAAATTTTCCCATTTATGACATGTACAGAGT
2554659 TTGTTTT
1 TT-TTTT
2554666 AGGTCAAGAT
Statistics
Matches: 108, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
105 104 0.96
106 4 0.04
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (105 bp):
TTTTTTCACGTTCTTGATTTATTGGCAGCTAGGATTAGGATGACTCAACAAATTTAGCAGAATGA
TTTTACACACAAATTTTCCCATTTATGACATGTACAGAGT
Found at i:2555412 original size:2 final size:2
Alignment explanation
Indices: 2555405--2555429 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2555395 GGTAACATAT
2555405 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
2555430 TCTTGGTGCT
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:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2556091 original size:9 final size:9
Alignment explanation
Indices: 2556077--2556101 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2556067 ATTTTCGTTG
2556077 AAAAAATTA
1 AAAAAATTA
2556086 AAAAAATTA
1 AAAAAATTA
2556095 AAAAAAT
1 AAAAAAT
2556102 GAAATTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAAAATTA
Found at i:2556723 original size:21 final size:20
Alignment explanation
Indices: 2556685--2556754 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
2556675 TAATAAATAA
*
2556685 ATTAAAATTTA-T-TTTTAT
1 ATTAATATTTATTATTTTAT
2556703 ATTAATATTTATATATTTTAT
1 ATTAATATTTAT-TATTTTAT
*
2556724 AATTAA-ATTTATTATTTAAATT
1 -ATTAATATTTATTATTT-TA-T
2556746 ATTAATATT
1 ATTAATATT
2556755 AATTCAACCG
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
18 10 0.23
20 6 0.14
21 18 0.42
22 9 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTAATATTTATTATTTTAT
Found at i:2558097 original size:24 final size:24
Alignment explanation
Indices: 2558052--2558099 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2558042 GTGATTTTCT
*
2558052 TTAAAATAAAGTAATTAAATAAAA
1 TTAAAATAAAGTAATGAAATAAAA
*
2558076 TTAAAATAAATTAA-GAATATAAAA
1 TTAAAATAAAGTAATGAA-ATAAAA
2558100 AAATCTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (24 bp):
TTAAAATAAAGTAATGAAATAAAA
Found at i:2558351 original size:11 final size:10
Alignment explanation
Indices: 2558331--2558378 Score: 51
Period size: 11 Copynumber: 4.5 Consensus size: 10
2558321 ATAATTCATT
*
2558331 TATTTGTATA
1 TATTTATATA
2558341 GTATTTATATA
1 -TATTTATATA
2558352 TATTTTATATTA
1 TA-TTTATA-TA
2558364 TATTTATATA
1 TATTTATATA
*
2558374 AATTT
1 TATTT
2558379 TGATAAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
10 8 0.24
11 21 0.64
12 4 0.12
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (10 bp):
TATTTATATA
Found at i:2558631 original size:26 final size:24
Alignment explanation
Indices: 2558575--2558632 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 24
2558565 GATCTAACTC
* *
2558575 AAATTATTTTTCATTTTAATAAAA
1 AAATTATTTTTAAATTTAATAAAA
*
2558599 AATATTATTATTTAAATTTAATTATAA
1 AA-ATTATT-TTTAAATTTAA-TAAAA
2558626 AAATTAT
1 AAATTAT
2558633 AAAATTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 2 0.07
25 6 0.21
26 14 0.50
27 6 0.21
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
AAATTATTTTTAAATTTAATAAAA
Found at i:2559352 original size:13 final size:13
Alignment explanation
Indices: 2559334--2559380 Score: 58
Period size: 13 Copynumber: 3.4 Consensus size: 13
2559324 GTTATTTTTT
2559334 AAATAAATTATTA
1 AAATAAATTATTA
2559347 AAATAATATTAATTTA
1 AAATAA-ATT-A-TTA
*
2559363 AAATAAATTATCA
1 AAATAAATTATTA
2559376 AAATA
1 AAATA
2559381 TTATTATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 13 0.43
14 4 0.13
15 4 0.13
16 9 0.30
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATAAATTATTA
Found at i:2559368 original size:29 final size:29
Alignment explanation
Indices: 2559334--2559392 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
2559324 GTTATTTTTT
*
2559334 AAATAAATTATTAAAATAATATTAATTTA
1 AAATAAATTATCAAAATAATATTAATTTA
* *
2559363 AAATAAATTATCAAAATATTATTATTTTA
1 AAATAAATTATCAAAATAATATTAATTTA
2559392 A
1 A
2559393 TTCGTAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (29 bp):
AAATAAATTATCAAAATAATATTAATTTA
Found at i:2560300 original size:20 final size:20
Alignment explanation
Indices: 2560275--2560315 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
2560265 CTACTTGCAG
*
2560275 ATTTATTTACTTCAATACTT
1 ATTTATATACTTCAATACTT
2560295 ATTTATATACTTCAATACTT
1 ATTTATATACTTCAATACTT
2560315 A
1 A
2560316 ATACTTGTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.15, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTATATACTTCAATACTT
Found at i:2563226 original size:24 final size:24
Alignment explanation
Indices: 2563174--2563230 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
2563164 CGAGTATGAT
*
2563174 AATATATATTAATTTTATATTTTA
1 AATATATATTAATTTTATATATTA
*
2563198 TATAT-TATGTAATTTT-TATAATTA
1 AATATATAT-TAATTTTATAT-ATTA
2563222 AATATATAT
1 AATATATAT
2563231 ATATATATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
23 6 0.22
24 18 0.67
25 3 0.11
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
AATATATATTAATTTTATATATTA
Found at i:2563321 original size:15 final size:15
Alignment explanation
Indices: 2563301--2563333 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2563291 CTTATTAAAA
2563301 AAATATTAAATTAAT
1 AAATATTAAATTAAT
*
2563316 AAATATTAAATTATT
1 AAATATTAAATTAAT
2563331 AAA
1 AAA
2563334 AAAATTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAATATTAAATTAAT
Found at i:2563340 original size:12 final size:12
Alignment explanation
Indices: 2563323--2563350 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2563313 AATAAATATT
2563323 AAATTATTAAAA
1 AAATTATTAAAA
2563335 AAATTATTAAAA
1 AAATTATTAAAA
2563347 AAAT
1 AAAT
2563351 ATAATATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAATTATTAAAA
Found at i:2563361 original size:35 final size:34
Alignment explanation
Indices: 2563286--2563361 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 34
2563276 ACTTGTATTT
**
2563286 TTAAACTTATTAAAAAAATATTAAATTAATAAATA
1 TTAAA-TTATTAAAAAAATATTAAAAAAATAAATA
2563321 TTAAATTATTAAAAAAATTATTAAAAAAATATAATA
1 TTAAATTATTAAAAAAA-TATTAAAAAAATA-AATA
2563357 -TAAAT
1 TTAAAT
2563362 GAATTTAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
34 12 0.32
35 21 0.57
36 4 0.11
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (34 bp):
TTAAATTATTAAAAAAATATTAAAAAAATAAATA
Found at i:2564564 original size:19 final size:18
Alignment explanation
Indices: 2564540--2564575 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2564530 AAGATTATTT
2564540 ATTTATTAATAATAATATA
1 ATTTATTAATAA-AATATA
*
2564559 ATTTATTGATAAAATAT
1 ATTTATTAATAAAATAT
2564576 TAAAATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
ATTTATTAATAAAATATA
Found at i:2566596 original size:24 final size:22
Alignment explanation
Indices: 2566539--2566596 Score: 53
Period size: 24 Copynumber: 2.5 Consensus size: 22
2566529 ATATAAACTT
* *
2566539 TTAAAATTATAAATATTTAATA
1 TTAAAATTTTAAATATTAAATA
*
2566561 TTCACAATTTTTAAATATTAAATAAA
1 TT-A-AAATTTTAAATATTAAAT--A
2566587 TTAAAATTTT
1 TTAAAATTTT
2566597 TTACAAACCG
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
22 2 0.07
23 1 0.04
24 21 0.75
25 1 0.04
26 3 0.11
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (22 bp):
TTAAAATTTTAAATATTAAATA
Found at i:2567038 original size:2 final size:2
Alignment explanation
Indices: 2567031--2567077 Score: 85
Period size: 2 Copynumber: 23.0 Consensus size: 2
2567021 AACTACTACC
2567031 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
2567074 AT AT
1 AT AT
2567078 CAATAGTGAC
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2570938 original size:7 final size:7
Alignment explanation
Indices: 2570920--2570961 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
2570910 TCAAATAAAT
2570920 ATATTT-
1 ATATTTA
2570926 ATATTTA
1 ATATTTA
2570933 ATATTTA
1 ATATTTA
*
2570940 GTATTTA
1 ATATTTA
2570947 ATATTTCA
1 ATATTT-A
2570955 ATATTTA
1 ATATTTA
2570962 TTTAATATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
6 6 0.19
7 19 0.59
8 7 0.22
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (7 bp):
ATATTTA
Found at i:2571372 original size:15 final size:15
Alignment explanation
Indices: 2571291--2571452 Score: 53
Period size: 15 Copynumber: 10.9 Consensus size: 15
2571281 AAGTTATAAG
2571291 AAATAATTATATTATGT
1 AAATAATTAT-TTAT-T
*
2571308 TAATATATT-TTTATT
1 AAATA-ATTATTTATT
*
2571323 -AA-AATTATAATATAT
1 AAATAATTAT-TTAT-T
*
2571338 AATTAAATTATTT-TT
1 AAAT-AATTATTTATT
2571353 AAAATAATTATTTATT
1 -AAATAATTATTTATT
2571369 AAAT-ATTA--TATGT
1 AAATAATTATTTAT-T
* *
2571382 -AATAATTATATAAT
1 AAATAATTATTTATT
*
2571396 AAATATTTA-TT-TT
1 AAATAATTATTTATT
2571409 -AATAATT-TTTATAAT
1 AAATAATTATTTAT--T
*
2571424 AATTAATTAATTT-TT
1 AAATAATT-ATTTATT
* *
2571439 AAAAAATTAATTAT
1 AAATAATTATTTAT
2571453 AATTTAAATG
Statistics
Matches: 109, Mismatches: 14, Indels: 46
0.64 0.08 0.27
Matches are distributed among these distances:
12 17 0.16
13 9 0.08
14 14 0.13
15 33 0.30
16 17 0.16
17 7 0.06
18 12 0.11
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (15 bp):
AAATAATTATTTATT
Found at i:2571385 original size:27 final size:27
Alignment explanation
Indices: 2571355--2571420 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
2571345 TTATTTTTAA
2571355 AATAATTATTTATTAAATA-TTATATGT
1 AATAATTATTTATTAAATATTTAT-TGT
* * *
2571382 AATAATTATATAATAAATATTTATTTT
1 AATAATTATTTATTAAATATTTATTGT
2571409 AATAATT-TTTAT
1 AATAATTATTTAT
2571421 AATAATTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
26 3 0.09
27 26 0.79
28 4 0.12
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (27 bp):
AATAATTATTTATTAAATATTTATTGT
Found at i:2571450 original size:19 final size:20
Alignment explanation
Indices: 2571407--2571451 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
2571397 AATATTTATT
*
2571407 TTAA-TAATTTTTATAATAA
1 TTAATTAATTTTTATAAAAA
2571426 TTAATTAATTTTTA-AAAAA
1 TTAATTAATTTTTATAAAAA
2571445 TTAATTA
1 TTAATTA
2571452 TAATTTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTAATTAATTTTTATAAAAA
Found at i:2572263 original size:24 final size:24
Alignment explanation
Indices: 2572227--2572272 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2572217 AGATGTAAAA
*
2572227 TTTAAATAACAAATTGTAAATTTT
1 TTTAAATAACAAATTGCAAATTTT
* *
2572251 TTTAAGTATCAAATTGCAAATT
1 TTTAAATAACAAATTGCAAATT
2572273 GAATTATAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (24 bp):
TTTAAATAACAAATTGCAAATTTT
Found at i:2574155 original size:2 final size:2
Alignment explanation
Indices: 2574150--2574178 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2574140 TAGGTGTGTG
2574150 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
2574179 GCTTCAGCAG
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:2577175 original size:14 final size:13
Alignment explanation
Indices: 2577140--2577173 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
2577130 AATTATATCT
2577140 TATATTTATAATA
1 TATATTTATAATA
*
2577153 GACTATTTATAATA
1 TA-TATTTATAATA
2577167 TATATTT
1 TATATTT
2577174 TAAAATTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (13 bp):
TATATTTATAATA
Found at i:2579053 original size:16 final size:17
Alignment explanation
Indices: 2579010--2579056 Score: 60
Period size: 16 Copynumber: 2.7 Consensus size: 17
2579000 TAAATATTTG
2579010 TATTTAATATATTTTTAT
1 TATTTAATA-ATTTTTAT
*
2579028 TTTATTAATAATTTTT-T
1 TAT-TTAATAATTTTTAT
2579045 TATTTAATAATT
1 TATTTAATAATT
2579057 AAAAATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 9 0.35
17 3 0.12
18 8 0.31
19 6 0.23
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTTAATAATTTTTAT
Found at i:2579584 original size:19 final size:18
Alignment explanation
Indices: 2579557--2579592 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2579547 TAAATTCAAA
2579557 TTTTAATATTTATGATATC
1 TTTTAATATTTAT-ATATC
*
2579576 TTTTTATATTTATATAT
1 TTTTAATATTTATATAT
2579593 TACGACGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTTAATATTTATATATC
Found at i:2579818 original size:19 final size:18
Alignment explanation
Indices: 2579785--2579824 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
2579775 AAACAATTAT
2579785 AATATAATAAAATATATA
1 AATATAATAAAATATATA
2579803 AATATAATATAAATATATA
1 AATATAATA-AAATATATA
2579822 AAT
1 AAT
2579825 TATCACGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AATATAATAAAATATATA
Found at i:2581288 original size:2 final size:2
Alignment explanation
Indices: 2581281--2581318 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2581271 ATGGAGCCTC
2581281 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
2581319 TCCATTAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2582321 original size:165 final size:162
Alignment explanation
Indices: 2582125--2582451 Score: 584
Period size: 165 Copynumber: 2.0 Consensus size: 162
2582115 AATATATTTA
2582125 ACATGATATACTTAATACATATATAATATTTTTATTTAAAATTTTGATAAATTTAATAATTTATA
1 ACATGATATACTTAATACATATATAATATTTTTATTTAAAATTTTGATAAATTTAATAATTTATA
2582190 TTATATTTATTATTTAAAAAAGTTTAAATATAATATTATATGATAAAAAATT-TCGATATCTATG
66 TTATATTTATTATTTAAAAAA-TTTAAATATAATATT-TATGATAAAAAATTCT-GATATCTATG
2582254 TTAAAAAAAACCTCTAATACACTATTATAAAAAAAG
128 TT-AAAAAAACCTCTAATACACTATTATAAAAAAAG
2582290 ACATGATATACTTAATACATATATAATATTTTTATTTAAAATTTTGATAAATTTAATAATTTATA
1 ACATGATATACTTAATACATATATAATATTTTTATTTAAAATTTTGATAAATTTAATAATTTATA
*
2582355 TTATATTTATTATTTAAAAAATTTAACTATAATATTTATGATAAAAAATTCTGATATCTATGTTA
66 TTATATTTATTATTTAAAAAATTTAAATATAATATTTATGATAAAAAATTCTGATATCTATGTTA
* *
2582420 AAAAAACCTCTAATACACTATTGTAAGAAAAG
131 AAAAAACCTCTAATACACTATTATAAAAAAAG
2582452 CAATTTTTGT
Statistics
Matches: 158, Mismatches: 3, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
162 31 0.20
163 26 0.16
164 15 0.09
165 86 0.54
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (162 bp):
ACATGATATACTTAATACATATATAATATTTTTATTTAAAATTTTGATAAATTTAATAATTTATA
TTATATTTATTATTTAAAAAATTTAAATATAATATTTATGATAAAAAATTCTGATATCTATGTTA
AAAAAACCTCTAATACACTATTATAAAAAAAG
Found at i:2583082 original size:199 final size:198
Alignment explanation
Indices: 2582703--2583104 Score: 571
Period size: 199 Copynumber: 2.0 Consensus size: 198
2582693 ATCATTGATG
*
2582703 TTAAAAAAGACGAGATACAATAAATATATACTCCGTAATAGATGTAAGGTTATAATTGGATAGCT
1 TTAAAAAAGACGAGATACAATAAATATATACTCCGTAATAGATGTAAGGATATAATTGGATAGCT
* * * * *
2582768 GTAAACTCAGATTCGAATTACCCATAAGTAATTTGGCACTGTGTTTTGAAACTTGCAACTATATG
66 GTAAACTCAGATTCGAATTACCCATAAGTAATCTGGCACTGTATTTTGAAAATTGCAAATATATA
* *
2582833 TACATGATTTAGTGTTCATACACTTTATAGGTATGCATATATAA-ATATATATATATAT-ATATA
131 TACATGATTTACTGTTCATACACTTTATAGATATGCA-ATATAATATATATATATATATGA-ATA
2582896 TTAATA
194 -TAATA
* * * *
2582902 TTAAAAAAGATGAGATACAATATATATGTACTCCTTAATAGATGTAAGGATATAATTGGATAGCT
1 TTAAAAAAGACGAGATACAATAAATATATACTCCGTAATAGATGTAAGGATATAATTGGATAGCT
*
2582967 GTAAACTCAGATTCGAATTACCCATAATTAATCTGGCACTGTATTTTGAAAATT-CTAAAAATAT
66 GTAAACTCAGATTCGAATTACCCATAAGTAATCTGGCACTGTATTTTGAAAATTGC----AA-AT
*
2583031 ATATATACCTGATTTACTGTTCATACACTTTATAGATATGC-ATAT-ATATATATATATATATGA
126 ATATATACATGATTTACTGTTCATACACTTTATAGATATGCAATATAATATATATATATATATGA
2583094 ATATAATA
191 ATATAATA
2583102 TTA
1 TTA
2583105 TGCCACTTCC
Statistics
Matches: 182, Mismatches: 14, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
198 1 0.01
199 110 0.60
200 9 0.05
201 21 0.12
202 3 0.02
203 38 0.21
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (198 bp):
TTAAAAAAGACGAGATACAATAAATATATACTCCGTAATAGATGTAAGGATATAATTGGATAGCT
GTAAACTCAGATTCGAATTACCCATAAGTAATCTGGCACTGTATTTTGAAAATTGCAAATATATA
TACATGATTTACTGTTCATACACTTTATAGATATGCAATATAATATATATATATATATGAATATA
ATA
Found at i:2583981 original size:34 final size:33
Alignment explanation
Indices: 2583933--2584152 Score: 237
Period size: 34 Copynumber: 6.5 Consensus size: 33
2583923 TGGTAAAAAC
* *
2583933 CACCATTTAATCAACAATGGCAACCTATCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
2583966 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
2584000 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
2584034 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * * *
2584068 CTCCCATTTAGTTAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
* *
2584102 CACCCATTTAATCAATAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
2584136 CACCATTTAATCAACAA
1 CACCATTTAATCAACAA
2584153 ATATATTACA
Statistics
Matches: 156, Mismatches: 22, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
33 21 0.13
34 129 0.83
35 6 0.04
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.26
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:2584049 original size:68 final size:67
Alignment explanation
Indices: 2583935--2584152 Score: 267
Period size: 68 Copynumber: 3.2 Consensus size: 67
2583925 GTAAAAACCA
* * * *
2583935 CCATTTAATCAACAATGGCAACCTATCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
2584000 CAC
65 CAC
* * * *
2584003 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
2584068 CTC
65 CAC
* * * * * *
2584071 CCATTTAGTTAACAATGGCAAACCACCAAATCACCCATTTAATCAATAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
2584136 CA-
65 CAC
2584138 CCATTTAATCAACAA
1 CCATTTAATCAACAA
2584153 ATATATTACA
Statistics
Matches: 127, Mismatches: 21, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
67 15 0.12
68 111 0.87
69 1 0.01
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.26
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:2584077 original size:102 final size:101
Alignment explanation
Indices: 2583933--2584152 Score: 341
Period size: 102 Copynumber: 2.2 Consensus size: 101
2583923 TGGTAAAAAC
* * *
2583933 CACCATTTAATCAACAATGGCAACCTATCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
*
2583998 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAATAATGGTAAACTACCAAAT
** * * * *
2584034 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTTAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
2584099 AATCACCCATTTAATCAATAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAATAATGGTAAACTACCAAAT
2584136 CACCATTTAATCAACAA
1 CACCATTTAATCAACAA
2584153 ATATATTACA
Statistics
Matches: 106, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 15 0.14
102 91 0.86
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.26
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAATAATGGTAAACTACCAAAT
Found at i:2584374 original size:19 final size:21
Alignment explanation
Indices: 2584345--2584386 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
2584335 GTTTTCAAGC
*
2584345 AAGAGAATAAAATCCC-AATT
1 AAGAGAATAAAAACCCTAATT
2584365 AAGA-AATAAAAACCCTAATT
1 AAGAGAATAAAAACCCTAATT
2584385 AA
1 AA
2584387 AGATTCAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.60, C:0.14, G:0.07, T:0.19
Consensus pattern (21 bp):
AAGAGAATAAAAACCCTAATT
Found at i:2585177 original size:14 final size:15
Alignment explanation
Indices: 2585152--2585181 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2585142 TTTAAATTTC
2585152 CATAAGATATTATAT
1 CATAAGATATTATAT
2585167 CATAA-ATATTATAT
1 CATAAGATATTATAT
2585181 C
1 C
2585182 TTGCAATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (15 bp):
CATAAGATATTATAT
Found at i:2598054 original size:5 final size:5
Alignment explanation
Indices: 2598014--2598095 Score: 56
Period size: 5 Copynumber: 15.0 Consensus size: 5
2598004 CCGAGACTGA
* * *
2598014 AATTT GATTT AAATTAT AATTA AATTAT AATGTTT AATTT AGTTTT AATTT
1 AATTT AATTT -AATT-T AATTT AATT-T AA--TTT AATTT A-ATTT AATTT
* *
2598065 GATTTT TATTT AATTT AATTT AATTT AATTT
1 -AATTT AATTT AATTT AATTT AATTT AATTT
2598096 CGATAATAAC
Statistics
Matches: 60, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
5 37 0.62
6 17 0.28
7 4 0.07
8 2 0.03
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (5 bp):
AATTT
Found at i:2598087 original size:10 final size:10
Alignment explanation
Indices: 2598014--2598095 Score: 56
Period size: 11 Copynumber: 7.5 Consensus size: 10
2598004 CCGAGACTGA
*
2598014 AATTTGATTT
1 AATTTAATTT
*
2598024 AAATTATAATTA
1 -AATT-TAATTT
2598036 AATTATAATGTTT
1 AATT-TAA--TTT
*
2598049 AATTTAGTTTT
1 AATTTA-ATTT
*
2598060 AATTTGATTTT
1 AATTT-AATTT
*
2598071 TATTTAATTT
1 AATTTAATTT
2598081 AATTTAATTT
1 AATTTAATTT
2598091 AATTT
1 AATTT
2598096 CGATAATAAC
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
10 18 0.31
11 28 0.47
12 7 0.12
13 6 0.10
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (10 bp):
AATTTAATTT
Found at i:2598254 original size:18 final size:21
Alignment explanation
Indices: 2598214--2598258 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
2598204 TTAAGTGTCG
2598214 AATAAAAAATATTATGACTTTA
1 AATAAAAAATATTATGAC-TTA
2598236 AATAAAAAA-ATTAT-A-TTA
1 AATAAAAAATATTATGACTTA
2598254 AATAA
1 AATAA
2598259 TATTATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 8 0.35
20 1 0.04
21 5 0.22
22 9 0.39
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
AATAAAAAATATTATGACTTA
Found at i:2600125 original size:32 final size:36
Alignment explanation
Indices: 2600043--2600190 Score: 106
Period size: 32 Copynumber: 4.4 Consensus size: 36
2600033 ATTATAAAAT
* *
2600043 TATAAAAAAAATT-TATAATATAAATATAATATAAA
1 TATATAAAAATTTATATAATATAAATATAATATAAA
* *
2600078 TACATCAAAATTTATATAATATAAAT-T-A-AT-AA
1 TATATAAAAATTTATATAATATAAATATAATATAAA
**
2600110 TATATAAAAATTTATAT-A-A-AAATATAATAT-TT
1 TATATAAAAATTTATATAATATAAATATAATATAAA
* * *
2600142 TAAATAAAATTTTA-ATAA-AAAAATAATAATAT-AA
1 TATATAAAAATTTATATAATATAAAT-ATAATATAAA
*
2600176 TA-ATAAAAATATATA
1 TATATAAAAATTTATA
2600191 AATTATTGAG
Statistics
Matches: 91, Mismatches: 14, Indels: 17
0.75 0.11 0.14
Matches are distributed among these distances:
29 4 0.04
30 2 0.02
31 4 0.04
32 33 0.36
33 15 0.16
34 11 0.12
35 10 0.11
36 12 0.13
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (36 bp):
TATATAAAAATTTATATAATATAAATATAATATAAA
Found at i:2600134 original size:20 final size:20
Alignment explanation
Indices: 2600111--2600150 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2600101 AATTAATAAT
*
2600111 ATATAAAAATTTATATAAAA
1 ATATAAAAATTTAAATAAAA
* *
2600131 ATATAATATTTTAAATAAAA
1 ATATAAAAATTTAAATAAAA
2600151 TTTTAATAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATATAAAAATTTAAATAAAA
Found at i:2602322 original size:22 final size:22
Alignment explanation
Indices: 2602297--2602343 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
2602287 CTTAAATATA
2602297 AGAATTAGAAAACAAAAATGAT
1 AGAATTAGAAAACAAAAATGAT
2602319 AGAATTAGAAAACAAAAATGAT
1 AGAATTAGAAAACAAAAATGAT
2602341 AGA
1 AGA
2602344 GATCGGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.64, C:0.04, G:0.15, T:0.17
Consensus pattern (22 bp):
AGAATTAGAAAACAAAAATGAT
Found at i:2602357 original size:22 final size:22
Alignment explanation
Indices: 2602297--2602357 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
2602287 CTTAAATATA
*
2602297 AGAATTAGAAAACAAAAATGAT
1 AGAATCAGAAAACAAAAATGAT
*
2602319 AGAATTAGAAAACAAAAATGAT
1 AGAATCAGAAAACAAAAATGAT
*
2602341 AGAGATCGGAAAA-AAAA
1 AGA-ATCAGAAAACAAAA
2602358 TTGAAATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 29 0.81
23 7 0.19
ACGTcount: A:0.64, C:0.05, G:0.16, T:0.15
Consensus pattern (22 bp):
AGAATCAGAAAACAAAAATGAT
Found at i:2607028 original size:39 final size:40
Alignment explanation
Indices: 2606972--2607076 Score: 99
Period size: 38 Copynumber: 2.7 Consensus size: 40
2606962 TTTGGAATGT
** * *
2606972 TCTAGAATACCGTGGAAGGTTTTGGAAGATTTTATAA-GA
1 TCTAGAATAATGTGGAAGGTTTTGGAAGATTCTAGAAGGA
** * *
2607011 TTCTAG-ATGTTGTGGAA-GCTTTGGAATATTCTAGAAGGA
1 -TCTAGAATAATGTGGAAGGTTTTGGAAGATTCTAGAAGGA
*
2607050 TCTAGAATAATGTAGAAGGTTTTGGAA
1 TCTAGAATAATGTGGAAGGTTTTGGAA
2607077 CATTGTGGAG
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
38 20 0.39
39 18 0.35
40 13 0.25
ACGTcount: A:0.32, C:0.07, G:0.27, T:0.34
Consensus pattern (40 bp):
TCTAGAATAATGTGGAAGGTTTTGGAAGATTCTAGAAGGA
Found at i:2607180 original size:20 final size:21
Alignment explanation
Indices: 2607157--2607202 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
2607147 TGTAGAAAGA
2607157 TCTAGAACGTGTA-AGATATT
1 TCTAGAACGTGTATAGATATT
* *
2607177 TCTAG-ACTTGTATAGATTTT
1 TCTAGAACGTGTATAGATATT
2607197 TCTAGA
1 TCTAGA
2607203 TGTAAATTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.41
Consensus pattern (21 bp):
TCTAGAACGTGTATAGATATT
Found at i:2607206 original size:18 final size:18
Alignment explanation
Indices: 2607166--2607207 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
2607156 ATCTAGAACG
2607166 TGTAAGATATTTCTAGAC
1 TGTAAGATATTTCTAGAC
*
2607184 TTGTATAGATTTTTCTAGA-
1 -TGTA-AGATATTTCTAGAC
2607203 TGTAA
1 TGTAA
2607208 ATTGTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 4 0.19
19 4 0.19
20 12 0.57
ACGTcount: A:0.31, C:0.07, G:0.17, T:0.45
Consensus pattern (18 bp):
TGTAAGATATTTCTAGAC
Found at i:2613201 original size:17 final size:18
Alignment explanation
Indices: 2613162--2613206 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
2613152 CATAAATCTA
2613162 TATTAAATATTATATTAT
1 TATTAAATATTATATTAT
2613180 T-TTAAATA-TATAATT-T
1 TATTAAATATTAT-ATTAT
*
2613196 TATTAACTATT
1 TATTAAATATT
2613207 TACTAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
16 5 0.22
17 16 0.70
18 2 0.09
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTAAATATTATATTAT
Found at i:2614620 original size:13 final size:13
Alignment explanation
Indices: 2614594--2614640 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
2614584 TATAGTATAA
*
2614594 ATAAAAA-ATGAT
1 ATAAAAATATTAT
2614606 ATAAAAATATTAT
1 ATAAAAATATTAT
*
2614619 ATTAAAAT-TTAT
1 ATAAAAATATTAT
2614631 ATATAAAATA
1 ATA-AAAATA
2614641 AAAAATTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 13 0.45
13 16 0.55
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (13 bp):
ATAAAAATATTAT
Found at i:2614774 original size:25 final size:27
Alignment explanation
Indices: 2614746--2614798 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
2614736 ATAATAATAT
*
2614746 TTTATTTTT-AGT-ATTTATATAATTA
1 TTTATTTTTAAGTAATTTATACAATTA
*
2614771 TTTATTTTTAATTAATTTATACAATTA
1 TTTATTTTTAAGTAATTTATACAATTA
2614798 T
1 T
2614799 ATAATAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 9 0.38
26 2 0.08
27 13 0.54
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (27 bp):
TTTATTTTTAAGTAATTTATACAATTA
Found at i:2615300 original size:45 final size:43
Alignment explanation
Indices: 2615219--2615305 Score: 102
Period size: 45 Copynumber: 2.0 Consensus size: 43
2615209 ATTATTTGTA
* * * **
2615219 TAAATTTTAAATTTGATATTTATATTAATGTAATAATATAATTT
1 TAAATTTTAAATTTAAAATTTAAATTAAAATAATAATA-AATTT
*
2615263 TAAATTATTAAATTTAAAATTTAAATTAAAATTATAATAAATT
1 TAAATT-TTAAATTTAAAATTTAAATTAAAATAATAATAAATT
2615306 ATATAAAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
44 10 0.28
45 26 0.72
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.48
Consensus pattern (43 bp):
TAAATTTTAAATTTAAAATTTAAATTAAAATAATAATAAATTT
Found at i:2615476 original size:14 final size:14
Alignment explanation
Indices: 2615454--2615493 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
2615444 ATATATAATG
*
2615454 ATTATATATTTTTA
1 ATTAAATATTTTTA
2615468 ATTAAATATTTTTA
1 ATTAAATATTTTTA
*
2615482 A-TAATTATTTTT
1 ATTAAATATTTTT
2615494 GTTATTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 10 0.42
14 14 0.58
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTAAATATTTTTA
Done.