Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 127 of 222
Found at i:41170091 original size:44 final size:44
Alignment explanation
Indices: 41170043--41170183 Score: 153
Period size: 44 Copynumber: 3.1 Consensus size: 44
41170033 AATATTAATT
41170043 ATTTTAAATTGTATAAATTCATATAAGAAAATTTATTATCAAGA
1 ATTTTAAATTGTATAAATTCATATAAGAAAATTTATTATCAAGA
* * * * * *
41170087 ATTTTATGAAAT-TATATA-TCATTAGTAA-ATTATATTTAATATTAATA
1 ATTTTA--AATTGTATAAATTCA-TA-TAAGA--AAATTTATTATCAAGA
41170134 ATTTTAAATTGTATAAATTCATATAAGAAAATTTATTATCAAGA
1 ATTTTAAATTGTATAAATTCATATAAGAAAATTTATTATCAAGA
41170178 ATTTTA
1 ATTTTA
41170184 TGAAATTATA
Statistics
Matches: 76, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
44 27 0.36
45 14 0.18
46 14 0.18
47 21 0.28
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.45
Consensus pattern (44 bp):
ATTTTAAATTGTATAAATTCATATAAGAAAATTTATTATCAAGA
Found at i:41170124 original size:47 final size:45
Alignment explanation
Indices: 41169972--41170201 Score: 170
Period size: 47 Copynumber: 5.0 Consensus size: 45
41169962 AGTAAATTCA
*
41169972 TATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCAT
1 TATAAGAA-AATTTATTATTAAGAATTTTATGAAATTATATATCAT
* * ** * *
41170018 TATTAA-ATTATATTTAATATTAATTATTTTA--AATTGTATAAATTCA-
1 TA-TAAGA--AAATTTATTATTAAGAATTTTATGAAAT-TATATA-TCAT
*
41170064 TATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCAT
1 TATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATCAT
* * * * *
41170109 TAGTAA-ATTATATTTAATATTAATAATTTTA--AATTGTATAAATTCA-
1 TA-TAAGA--AAATTTATTATTAAGAATTTTATGAAAT-TATATA-TCAT
* *
41170155 TATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTAT
1 TATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATCAT
41170200 TA
1 TA
41170202 AATTATATGT
Statistics
Matches: 139, Mismatches: 27, Indels: 37
0.68 0.13 0.18
Matches are distributed among these distances:
44 40 0.29
45 27 0.19
46 28 0.20
47 43 0.31
48 1 0.01
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (45 bp):
TATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATCAT
Found at i:41170205 original size:25 final size:24
Alignment explanation
Indices: 41170177--41170234 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
41170167 TATTATCAAG
* *
41170177 AATTTTATGAAATTATATATTATTA
1 AATTATATGAAATAATA-ATTATTA
*
41170202 AATTATATGTAATAATAATTATTTTA
1 AATTATATGAAATAATAATTA--TTA
41170228 AATTATA
1 AATTATA
41170235 CAAATTCATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 4 0.14
25 14 0.50
26 10 0.36
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (24 bp):
AATTATATGAAATAATAATTATTA
Found at i:41170274 original size:91 final size:91
Alignment explanation
Indices: 41169964--41170255 Score: 482
Period size: 91 Copynumber: 3.2 Consensus size: 91
41169954 TGGATTTTAG
* *
41169964 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
41170029 ATTTAATATTAATTATTTTAAATTGTA
65 ATTTAATATTAATTATTTTAAATTGTA
*
41170056 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTAGTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
*
41170121 TTTAATATTAATAATTTTAAATTGTA
66 TTTAATATTAATTATTTTAAATTGTA
41170147 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAA-T-TATAT-ATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
* * *
41170209 TGTAATAATAATTATTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTGTA
*
41170235 CAAATTCATATAAGAAAATTT
1 TAAATTCATATAAGAAAATTT
41170256 GTTAGTTATA
Statistics
Matches: 190, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
88 55 0.29
89 5 0.03
90 1 0.01
91 113 0.59
92 16 0.08
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TTTAATATTAATTATTTTAAATTGTA
Found at i:41170406 original size:130 final size:120
Alignment explanation
Indices: 41170275--41170687 Score: 781
Period size: 120 Copynumber: 3.4 Consensus size: 120
41170265 AATTATTTTA
*
41170275 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
41170340 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
41170395 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
41170460 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
41170515 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
*
41170580 ATAGTATCATATATTATGATTCGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
41170635 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
41170688 TAAATATAAT
Statistics
Matches: 288, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 288 1.00
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:41170424 original size:18 final size:17
Alignment explanation
Indices: 41170396--41170430 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41170386 ATTATTAAGA
*
41170396 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
41170413 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
41170431 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:41170544 original size:18 final size:17
Alignment explanation
Indices: 41170516--41170550 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41170506 ATTATTAAGA
*
41170516 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
41170533 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
41170551 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:41170670 original size:16 final size:16
Alignment explanation
Indices: 41170649--41170697 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
41170639 TTATTAAATT
41170649 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
41170665 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
41170680 AT-TATGTTTAAATATA
1 ATATAT-TTTAATTATA
41170696 AT
1 AT
41170698 TAAATTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 2 0.07
15 11 0.39
16 15 0.54
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:41170915 original size:45 final size:44
Alignment explanation
Indices: 41170835--41170925 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 44
41170825 ACCTCTATTT
41170835 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
* * *
41170879 CATTCAACCAAACA-ATTGATTTGCTATTACGCCTCTATTCTATTA
1 CATTCAACCAAACACA-AGA-TTACTATTACGCCTCTATTCCATTA
41170924 CA
1 CA
41170926 CATTTATTCT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 16 0.38
45 25 0.60
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.33
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
Found at i:41170923 original size:16 final size:16
Alignment explanation
Indices: 41170902--41170966 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
41170892 AATTGATTTG
41170902 CTATTACGCCTCTATT
1 CTATTACGCCTCTATT
* * *
41170918 CTATTACACATTTATT
1 CTATTACGCCTCTATT
41170934 CTATTACGCCTCTATT
1 CTATTACGCCTCTATT
41170950 CTATTACGCCTCTATT
1 CTATTACGCCTCTATT
41170966 C
1 C
41170967 CAATACAGCG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.22, C:0.29, G:0.05, T:0.45
Consensus pattern (16 bp):
CTATTACGCCTCTATT
Found at i:41174938 original size:6 final size:6
Alignment explanation
Indices: 41174927--41174954 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
41174917 AAATATTCAT
41174927 TGTTAA TGTTAA TGTTAA TGTTAA TGTT
1 TGTTAA TGTTAA TGTTAA TGTTAA TGTT
41174955 CTATTTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.54
Consensus pattern (6 bp):
TGTTAA
Found at i:41175147 original size:91 final size:91
Alignment explanation
Indices: 41174979--41175185 Score: 360
Period size: 91 Copynumber: 2.3 Consensus size: 91
41174969 GTTAAGATTC
*
41174979 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTACA
** *
41175044 TTTAATATTAATTATTTTAAATTATA
66 TGAAATAATAATTATTTTAAATTATA
*
41175070 TAAATTCATATAATAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTACA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTACA
41175135 TGAAATAATAATTATTTTAAATTATA
66 TGAAATAATAATTATTTTAAATTATA
*
41175161 CAAATTCATATAAGAAAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
41175186 GTTATAATTA
Statistics
Matches: 109, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
91 109 1.00
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.44
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTACA
TGAAATAATAATTATTTTAAATTATA
Found at i:41175152 original size:47 final size:46
Alignment explanation
Indices: 41175010--41175153 Score: 118
Period size: 47 Copynumber: 3.1 Consensus size: 46
41175000 ATTATCAAGA
* *
41175010 ATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATT
1 ATTTTATGAAATTATATATCATTATTAAATTA-AATTAATAATAATT
* * * * **
41175057 A-TTT-T-AAATTATATA-AATTCA-TATAATAAAATTTATTATCAAGA
1 ATTTTATGAAATTATATATCATT-ATTA-AATTAAATTAATAAT-AATT
* *
41175101 ATTTTATGAAATTATATATCATTATTAAATTACATGAAATAATAATT
1 ATTTTATGAAATTATATATCATTATTAAATTAAAT-TAATAATAATT
41175148 ATTTTA
1 ATTTTA
41175154 AATTATACAA
Statistics
Matches: 72, Mismatches: 16, Indels: 18
0.68 0.15 0.17
Matches are distributed among these distances:
43 11 0.15
44 18 0.25
45 4 0.06
46 4 0.06
47 26 0.36
48 9 0.12
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (46 bp):
ATTTTATGAAATTATATATCATTATTAAATTAAATTAATAATAATT
Found at i:41175162 original size:28 final size:28
Alignment explanation
Indices: 41175106--41175158 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
41175096 CAAGAATTTT
*
41175106 ATGAAATTATATATCATTATTAAATTAC
1 ATGAAATAATATATCATTATTAAATTAC
*
41175134 ATGAAATAATA-ATTATT-TTAAATTA
1 ATGAAATAATATATCATTATTAAATTA
41175159 TACAAATTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 8 0.35
27 5 0.22
28 10 0.43
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (28 bp):
ATGAAATAATATATCATTATTAAATTAC
Found at i:41175311 original size:117 final size:118
Alignment explanation
Indices: 41175190--41175495 Score: 431
Period size: 117 Copynumber: 2.6 Consensus size: 118
41175180 TTATTAGTTA
* * *
41175190 TAATTATTTTAAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTC
1 TAATTA-TTTAAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-
* * *
41175254 AAATTATATTTTATAG-ATCATATATTATGATTTTAGTAAATTC-ATAAGACTAT
64 AAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAATAAAAATAT
41175307 TAATTA-TTAAGGATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 TAATTATTTAA--ATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
41175371 AAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAAAATAT
64 AAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCA-ATAAAAATAT
* * * *
41175427 TGATTATTAAGAATTTTATTAAATTATATATTTCAATTATATTATATTTAATAATAATTATGTTT
1 TAATTATTTA-AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG-TT
41175492 AAAT
64 AAAT
41175496 ATGATTAAAT
Statistics
Matches: 170, Mismatches: 10, Indels: 14
0.88 0.05 0.07
Matches are distributed among these distances:
115 4 0.02
117 68 0.40
118 28 0.16
120 61 0.36
121 8 0.05
122 1 0.01
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (118 bp):
TAATTATTTAAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAA
ATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAATAAAAATAT
Found at i:41175353 original size:16 final size:16
Alignment explanation
Indices: 41175332--41175378 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
41175322 TTATTAAATT
41175332 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
41175348 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
41175363 AT-TATGTTAAATTATA
1 ATATAT-TTTAATTATA
41175379 TTTTATAGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.42
16 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:41175465 original size:120 final size:117
Alignment explanation
Indices: 41175201--41175495 Score: 448
Period size: 120 Copynumber: 2.5 Consensus size: 117
41175191 AATTATTTTA
* * *
41175201 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATATTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AAATTATATTT
* * *
41175265 TATAGATCATATATTATGATTTTAGTAAATTCATAAGACTATTAATTATTAAG
65 TATAGATCATATATTATGATTTGAGTAAATTCATAAAAATATTAATTATTAAG
*
41175318 GATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
*
41175383 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAAAATATTGATTATTAAG
66 ATAG-ATCATATATTATGATTTGAGTAAATTC--ATAAAAATATTAATTATTAAG
* *
41175438 AATTTTATTAAATTATATATTTCAATTATATTATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG-TTAAAT
41175496 ATGATTAAAT
Statistics
Matches: 162, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
117 62 0.38
118 28 0.17
120 66 0.41
121 6 0.04
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.50
Consensus pattern (117 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGATCATATATTATGATTTGAGTAAATTCATAAAAATATTAATTATTAAG
Found at i:41177507 original size:26 final size:26
Alignment explanation
Indices: 41177478--41177559 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
41177468 GGTGGTGGGC
41177478 AGAAGGAGAGGGAAAGAAAGAAAGAA
1 AGAAGGAGAGGGAAAGAAAGAAAGAA
* * * *
41177504 AGAACGA-AAGGAGAGGAAAGAAA-AG
1 AGAAGGAGAGGGA-AAGAAAGAAAGAA
* * *
41177529 GGAAGGAGAAGAGAAA-AAACAAAGAA
1 AGAAGGAG-AGGGAAAGAAAGAAAGAA
41177555 AGAAG
1 AGAAG
41177560 AAGAAAAGGA
Statistics
Matches: 40, Mismatches: 12, Indels: 8
0.67 0.20 0.13
Matches are distributed among these distances:
25 16 0.40
26 21 0.52
27 3 0.08
ACGTcount: A:0.62, C:0.02, G:0.35, T:0.00
Consensus pattern (26 bp):
AGAAGGAGAGGGAAAGAAAGAAAGAA
Found at i:41177547 original size:20 final size:21
Alignment explanation
Indices: 41177509--41177628 Score: 94
Period size: 20 Copynumber: 6.0 Consensus size: 21
41177499 AAGAAAGAAC
*
41177509 GAAAGGAGAGGA-AAGAAAAG
1 GAAAGGAGAAGAGAAGAAAAG
*
41177529 GGAAGGAGAAGAGAA-AAAA-
1 GAAAGGAGAAGAGAAGAAAAG
*
41177548 CAAA-GA-AAGAAGAAGAAAAG
1 GAAAGGAGAAG-AGAAGAAAAG
* *
41177568 GAAAGGGGAAGA-AAAAAGAAG
1 GAAAGGAGAAGAGAAGAA-AAG
*
41177589 GAAA-GAAAAG-GAAAGAAAAG
1 GAAAGGAGAAGAG-AAGAAAAG
*
41177609 GAAAGGAGAAGAGAAAAAAA
1 GAAAGGAGAAGAGAAGAAAA
41177629 AAAGAAGAAG
Statistics
Matches: 77, Mismatches: 12, Indels: 21
0.70 0.11 0.19
Matches are distributed among these distances:
17 3 0.04
18 6 0.08
19 6 0.08
20 32 0.42
21 26 0.34
22 4 0.05
ACGTcount: A:0.66, C:0.01, G:0.33, T:0.00
Consensus pattern (21 bp):
GAAAGGAGAAGAGAAGAAAAG
Found at i:41177571 original size:16 final size:16
Alignment explanation
Indices: 41177552--41177640 Score: 66
Period size: 15 Copynumber: 5.8 Consensus size: 16
41177542 AAAAAACAAA
41177552 GAAAGAAGAAGAAAAG
1 GAAAGAAGAAGAAAAG
**
41177568 GAAAGGGGAAG-AAA-
1 GAAAGAAGAAGAAAAG
41177582 -AAAGAAGGAAAGAAAAG
1 GAAAGAA-G-AAGAAAAG
*
41177599 GAAAGAA-AAGGAAAG
1 GAAAGAAGAAGAAAAG
41177614 GAGAAG-AGAA-AAAA-
1 GA-AAGAAGAAGAAAAG
*
41177628 AAAAGAAGAAGAA
1 GAAAGAAGAAGAA
41177641 GAGGGAAGGA
Statistics
Matches: 57, Mismatches: 7, Indels: 19
0.69 0.08 0.23
Matches are distributed among these distances:
13 7 0.12
14 6 0.11
15 21 0.37
16 17 0.30
18 6 0.11
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (16 bp):
GAAAGAAGAAGAAAAG
Found at i:41177579 original size:26 final size:26
Alignment explanation
Indices: 41177550--41177607 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
41177540 AGAAAAAACA
* *
41177550 AAGAAAGAAGAAGAAAAGGAAAGGGG
1 AAGAAAAAAGAAGAAAAGAAAAGGGG
* *
41177576 AAGAAAAAAGAAGGAAAGAAAA-GGA
1 AAGAAAAAAGAAGAAAAGAAAAGGGG
41177601 AAGAAAA
1 AAGAAAA
41177608 GGAAAGGAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 9 0.32
26 19 0.68
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (26 bp):
AAGAAAAAAGAAGAAAAGAAAAGGGG
Found at i:41177608 original size:80 final size:80
Alignment explanation
Indices: 41177495--41177642 Score: 235
Period size: 80 Copynumber: 1.9 Consensus size: 80
41177485 GAGGGAAAGA
* * * *
41177495 AAGAAAGAAAGAACGAAAGGAGAGGAAAGAAAAGGGAAGGAGAAGAGAAAAAACAAAGAAAGAAG
1 AAGAAAGAAAGAACGAAAGAAAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAAG-AAGAAG
41177560 AAGAAAAGGAAAGGGG
65 AAGAAAAGGAAAGGGG
*
41177576 AAGAAA-AAAGAAGGAAAGAAAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAAGAAGAAGA
1 AAGAAAGAAAGAACGAAAGAAAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAAGAAGAAGA
41177640 AGA
66 AGA
41177643 GGGAAGGAAG
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
79 10 0.16
80 46 0.74
81 6 0.10
ACGTcount: A:0.67, C:0.01, G:0.32, T:0.00
Consensus pattern (80 bp):
AAGAAAGAAAGAACGAAAGAAAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAAGAAGAAGA
AGAAAAGGAAAGGGG
Found at i:41177634 original size:29 final size:28
Alignment explanation
Indices: 41177585--41177665 Score: 76
Period size: 29 Copynumber: 2.8 Consensus size: 28
41177575 GAAGAAAAAA
*
41177585 GAAGGAAAGAAAAGGAAAGAAAAGGAA-AGG
1 GAAGG-AAGAAAA-AAAAGAAAA-GAAGAGG
41177615 AGAAGAGAA-AAAAAAAAGAAGAAGAAGAGG
1 -GAAG-GAAGAAAAAAAAGAA-AAGAAGAGG
*
41177645 GAAGGAAGGAAAAAAAGAAAA
1 GAAGGAAGAAAAAAAAGAAAA
41177666 AAAAAGGTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
28 5 0.11
29 23 0.52
30 9 0.20
31 6 0.14
32 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (28 bp):
GAAGGAAGAAAAAAAAGAAAAGAAGAGG
Found at i:41177668 original size:85 final size:82
Alignment explanation
Indices: 41177478--41177669 Score: 203
Period size: 80 Copynumber: 2.3 Consensus size: 82
41177468 GGTGGTGGGC
* * * * *
41177478 AGAAGGAGAGGGAAAGAAAG-AAAGAAAGAACGAAAGGAGAGGAAAGAAAAGGGAAGGAGAAGAG
1 AGAAGGA-A-GGAAAAAAAGAAAAAAAAGAACGAAAGAAAAGGAAAGAAAAGGAAAGGAGAAGAG
*
41177542 AAAAAACAAAGAAAGAAGA
64 AAAAAAAAAAGAAAGAAGA
*** *
41177561 AGAA--AAGG-AAAGGGGAAGAAAAAAGAAGGAAAGAAAAGGAAAGAAAAGGAAAGGAGAAGAGA
1 AGAAGGAAGGAAAAAAAGAA-AAAAAAGAACGAAAGAAAAGGAAAGAAAAGGAAAGGAGAAGAGA
41177623 AAAAAAAAAGAAGAAGAAGA
65 AAAAAAAAAG-A-AAGAAGA
*
41177643 GGGAAGGAAGGAAAAAAAGAAAAAAAA
1 -AGAAGGAAGGAAAAAAAGAAAAAAAA
41177670 AGGTAATTTT
Statistics
Matches: 87, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
78 3 0.03
79 3 0.03
80 49 0.56
81 2 0.02
82 7 0.08
83 7 0.08
85 10 0.11
86 6 0.07
ACGTcount: A:0.66, C:0.01, G:0.33, T:0.00
Consensus pattern (82 bp):
AGAAGGAAGGAAAAAAAGAAAAAAAAGAACGAAAGAAAAGGAAAGAAAAGGAAAGGAGAAGAGAA
AAAAAAAAGAAAGAAGA
Found at i:41183422 original size:18 final size:18
Alignment explanation
Indices: 41183401--41183437 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
41183391 ATCCCAATGA
*
41183401 TTGCCACCATCTTCTTCT
1 TTGCCACCACCTTCTTCT
41183419 TTGCCACCACCTTCTTCT
1 TTGCCACCACCTTCTTCT
41183437 T
1 T
41183438 CACCACCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.41, G:0.05, T:0.43
Consensus pattern (18 bp):
TTGCCACCACCTTCTTCT
Found at i:41183443 original size:18 final size:18
Alignment explanation
Indices: 41183404--41183445 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
41183394 CCAATGATTG
* **
41183404 CCACCATCTTCTTCTTTG
1 CCACCACCTTCTTCTTCA
41183422 CCACCACCTTCTTCTTCA
1 CCACCACCTTCTTCTTCA
41183440 CCACCA
1 CCACCA
41183446 ACCATATCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.17, C:0.48, G:0.02, T:0.33
Consensus pattern (18 bp):
CCACCACCTTCTTCTTCA
Found at i:41184461 original size:11 final size:11
Alignment explanation
Indices: 41184441--41184480 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
41184431 AAAAAAATAC
41184441 CTTCTTTTTCT
1 CTTCTTTTTCT
*
41184452 CTTCTCTTTCT
1 CTTCTTTTTCT
41184463 C-TCTTTTTCT
1 CTTCTTTTTCT
41184473 CTTCTTTT
1 CTTCTTTT
41184481 CCGCAACACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (11 bp):
CTTCTTTTTCT
Found at i:41184468 original size:21 final size:20
Alignment explanation
Indices: 41184443--41184481 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
41184433 AAAAATACCT
41184443 TCTTTTTCTCTTCTCTTTCTC
1 TCTTTTTCTCTTCT-TTTCTC
41184464 TCTTTTTCTCTTCTTTTC
1 TCTTTTTCTCTTCTTTTC
41184482 CGCAACACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (20 bp):
TCTTTTTCTCTTCTTTTCTC
Found at i:41184610 original size:27 final size:27
Alignment explanation
Indices: 41184570--41184629 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
41184560 GAGTAATGCT
*
41184570 GCCAATGCCTTTGGCACCATTGGTGCC
1 GCCAATGCCATTGGCACCATTGGTGCC
* *
41184597 GCCAATGGCATTGGCACCTTTGGTGCC
1 GCCAATGCCATTGGCACCATTGGTGCC
41184624 GCCAAT
1 GCCAAT
41184630 CGTTTTGGCG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.17, C:0.32, G:0.27, T:0.25
Consensus pattern (27 bp):
GCCAATGCCATTGGCACCATTGGTGCC
Found at i:41184637 original size:27 final size:27
Alignment explanation
Indices: 41184570--41184638 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
41184560 GAGTAATGCT
41184570 GCCAAT-GCCTTTGGCACCATTGGTGCC
1 GCCAATCG-CTTTGGCACCATTGGTGCC
* * *
41184597 GCCAATGGCATTGGCACCTTTGGTGCC
1 GCCAATCGCTTTGGCACCATTGGTGCC
*
41184624 GCCAATCGTTTTGGC
1 GCCAATCGCTTTGGC
41184639 GTAACCAAGG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
27 35 0.97
28 1 0.03
ACGTcount: A:0.14, C:0.30, G:0.28, T:0.28
Consensus pattern (27 bp):
GCCAATCGCTTTGGCACCATTGGTGCC
Found at i:41184822 original size:22 final size:22
Alignment explanation
Indices: 41184797--41184840 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
41184787 TATTTCTATG
*
41184797 ATTTTGTTTTTCTATTCTTTCA
1 ATTTTCTTTTTCTATTCTTTCA
* *
41184819 ATTTTCTTTTTTTTTTCTTTCA
1 ATTTTCTTTTTCTATTCTTTCA
41184841 TTTCATTAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.11, C:0.14, G:0.02, T:0.73
Consensus pattern (22 bp):
ATTTTCTTTTTCTATTCTTTCA
Found at i:41186963 original size:12 final size:12
Alignment explanation
Indices: 41186946--41186970 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41186936 GGTGTTCATT
41186946 CGGTTAACCGAC
1 CGGTTAACCGAC
41186958 CGGTTAACCGAC
1 CGGTTAACCGAC
41186970 C
1 C
41186971 CGAAATAACA
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:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:41187150 original size:9 final size:9
Alignment explanation
Indices: 41187132--41187189 Score: 80
Period size: 9 Copynumber: 6.4 Consensus size: 9
41187122 TTTGGTTAAA
41187132 AATTAACCG
1 AATTAACCG
*
41187141 AATTACCCG
1 AATTAACCG
41187150 AATTAACCG
1 AATTAACCG
*
41187159 AATTACCCG
1 AATTAACCG
*
41187168 AATTAACCA
1 AATTAACCG
*
41187177 AATTAACCA
1 AATTAACCG
41187186 AATT
1 AATT
41187190 GAATCACTAC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 44 1.00
ACGTcount: A:0.45, C:0.24, G:0.07, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:41187155 original size:18 final size:18
Alignment explanation
Indices: 41187132--41187181 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
41187122 TTTGGTTAAA
41187132 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
41187150 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
*
41187168 AATTAACCAAATTA
1 AATTAACCGAATTA
41187182 ACCAAATTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:41187319 original size:13 final size:13
Alignment explanation
Indices: 41187301--41187325 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41187291 TTATGATTGG
41187301 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
41187314 ATTGGGTTGGGT
1 ATTGGGTTGGGT
41187326 TGGGTTGAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:41187323 original size:18 final size:18
Alignment explanation
Indices: 41187296--41187330 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41187286 TAATTTTATG
41187296 ATTGGATTGGGTTGGGTA
1 ATTGGATTGGGTTGGGTA
*
41187314 ATTGGGTTGGGTTGGGT
1 ATTGGATTGGGTTGGGT
41187331 TGAATACTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.00, G:0.49, T:0.40
Consensus pattern (18 bp):
ATTGGATTGGGTTGGGTA
Found at i:41187341 original size:23 final size:23
Alignment explanation
Indices: 41187297--41187344 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
41187287 AATTTTATGA
**
41187297 TTGGATTGGGTTGGGTAATTGGG
1 TTGGATTGGGTTGAATAATTGGG
* *
41187320 TTGGGTTGGGTTGAATACTTGGG
1 TTGGATTGGGTTGAATAATTGGG
41187343 TT
1 TT
41187345 TAGATTGAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.12, C:0.02, G:0.44, T:0.42
Consensus pattern (23 bp):
TTGGATTGGGTTGAATAATTGGG
Found at i:41188692 original size:22 final size:22
Alignment explanation
Indices: 41188667--41188737 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
41188657 TATAATGTAA
41188667 TATTAAATTTTCTAACTGTATT
1 TATTAAATTTTCTAACTGTATT
* * * *
41188689 TATTATTATTATTATTA-TGTA-A
1 TATTA-AATT-TTCTAACTGTATT
41188711 TATTAAATTTTCTAACTGTATT
1 TATTAAATTTTCTAACTGTATT
41188733 TATTA
1 TATTA
41188738 TTATTATTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
20 4 0.11
21 7 0.19
22 15 0.41
23 7 0.19
24 4 0.11
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.56
Consensus pattern (22 bp):
TATTAAATTTTCTAACTGTATT
Found at i:41188696 original size:3 final size:3
Alignment explanation
Indices: 41188688--41188756 Score: 52
Period size: 3 Copynumber: 22.3 Consensus size: 3
41188678 CTAACTGTAT
* * * *
41188688 TTA TTA TTA TTA TTA TTA TGTA ATA TTA -AA TT- TTC TAA CTGTA TTTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA -T-TA -TTA
41188735 TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA T
41188757 AGAATCTAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
2 3 0.06
3 43 0.81
4 5 0.09
5 2 0.04
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:41188709 original size:44 final size:44
Alignment explanation
Indices: 41188661--41188750 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
41188651 TTATACTATA
41188661 ATGTAATATTAAATTTTCTAACTGTATTTATTATTATTATTATT
1 ATGTAATATTAAATTTTCTAACTGTATTTATTATTATTATTATT
41188705 ATGTAATATTAAATTTTCTAACTGTATTTATTATTATTATTATT
1 ATGTAATATTAAATTTTCTAACTGTATTTATTATTATTATTATT
41188749 AT
1 AT
41188751 TATTATAGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.57
Consensus pattern (44 bp):
ATGTAATATTAAATTTTCTAACTGTATTTATTATTATTATTATT
Found at i:41188740 original size:25 final size:25
Alignment explanation
Indices: 41188667--41188740 Score: 79
Period size: 25 Copynumber: 3.2 Consensus size: 25
41188657 TATAATGTAA
41188667 TATTAAATTTTCTAACTGTATTTAT
1 TATTAAATTTTCTAACTGTATTTAT
* * *
41188692 TATT--ATTAT-T-A-T-TATGTAA
1 TATTAAATTTTCTAACTGTATTTAT
41188711 TATTAAATTTTCTAACTGTATTTAT
1 TATTAAATTTTCTAACTGTATTTAT
41188736 TATTA
1 TATTA
41188741 TTATTATTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
19 9 0.24
20 1 0.03
21 5 0.14
22 2 0.05
23 5 0.14
24 1 0.03
25 14 0.38
ACGTcount: A:0.34, C:0.05, G:0.04, T:0.57
Consensus pattern (25 bp):
TATTAAATTTTCTAACTGTATTTAT
Found at i:41193532 original size:13 final size:13
Alignment explanation
Indices: 41193500--41193533 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
41193490 TCTTAATAAT
41193500 AATATTA-TATTA
1 AATATTATTATTA
41193512 AA-ATTATTATTA
1 AATATTATTATTA
41193524 AATATTATTA
1 AATATTATTA
41193534 ATAATTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 4 0.20
12 9 0.45
13 7 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AATATTATTATTA
Found at i:41193543 original size:34 final size:35
Alignment explanation
Indices: 41193499--41193569 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 35
41193489 TTCTTAATAA
41193499 TAATATTATATTAA-AATTATTATTAAA-TAT-TAT
1 TAATATTATATTAAGAA-TATTATTAAATTATATAT
*
41193532 TAATAATTATATTAAGAATGTTATTAAATTATATAT
1 TAAT-ATTATATTAAGAATATTATTAAATTATATAT
41193568 TA
1 TA
41193570 TTTTATTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
33 4 0.12
34 19 0.58
35 5 0.15
36 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (35 bp):
TAATATTATATTAAGAATATTATTAAATTATATAT
Found at i:41193650 original size:61 final size:57
Alignment explanation
Indices: 41193532--41193668 Score: 157
Period size: 61 Copynumber: 2.3 Consensus size: 57
41193522 TAAATATTAT
* * * *
41193532 TAATAATTATATTAAGAATGTTATTAAATTATATATTATTTTATTAAATTATTTTTAA
1 TAATAATTATATTAA-AATATGATTAAATTATATATTATTTTATTAAAATATATTTAA
* *
41193590 TAATAATTATGTTAAAATATGATTAAATTATTTATTTTTATTTTTATTAAAATATATTTAA
1 TAATAATTATATTAAAATATGATTAAATTA--TA-TATTA-TTTTATTAAAATATATTTAA
* *
41193651 CAATAATTTTATTAAAAT
1 TAATAATTATATTAAAAT
41193669 TTAATAACAA
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
57 13 0.20
58 14 0.21
59 2 0.03
60 4 0.06
61 33 0.50
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.53
Consensus pattern (57 bp):
TAATAATTATATTAAAATATGATTAAATTATATATTATTTTATTAAAATATATTTAA
Found at i:41193682 original size:25 final size:26
Alignment explanation
Indices: 41193631--41193682 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
41193621 TTATTTTTAT
*
41193631 TTTTATTAAAATATATTTAACAATAA
1 TTTTATTAAAATATATATAACAATAA
*
41193657 TTTTATTAAAATTTA-ATAACAATAA
1 TTTTATTAAAATATATATAACAATAA
41193682 T
1 T
41193683 CAACTACCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (26 bp):
TTTTATTAAAATATATATAACAATAA
Found at i:41194552 original size:27 final size:27
Alignment explanation
Indices: 41194513--41194590 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
41194503 TAGTATTGGC
*
41194513 GCCTATCTCAGAGGCGCCAATGGTGGT
1 GCCTATCTGAGAGGCGCCAATGGTGGT
* *
41194540 GCCTATCTGAGAGGCGCCATTAGTGGT
1 GCCTATCTGAGAGGCGCCAATGGTGGT
* *
41194567 GTC-ATGTTGAGAGGCGCCAATGGT
1 GCCTAT-CTGAGAGGCGCCAATGGT
41194591 TTGATTTTTC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 2 0.05
27 41 0.95
ACGTcount: A:0.19, C:0.22, G:0.35, T:0.24
Consensus pattern (27 bp):
GCCTATCTGAGAGGCGCCAATGGTGGT
Found at i:41199533 original size:16 final size:15
Alignment explanation
Indices: 41199502--41199545 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 15
41199492 GCAAAATCAA
41199502 ATAAAATTAAATTAT
1 ATAAAATTAAATTAT
*
41199517 ATAAAAGTTACATTAT
1 ATAAAA-TTAAATTAT
41199533 ATAAAAATTAAAT
1 AT-AAAATTAAAT
41199546 GAGTTAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.24
16 15 0.60
17 4 0.16
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (15 bp):
ATAAAATTAAATTAT
Found at i:41199719 original size:60 final size:60
Alignment explanation
Indices: 41199655--41199776 Score: 165
Period size: 60 Copynumber: 2.0 Consensus size: 60
41199645 ATACTAAACT
* * * * *
41199655 AAACACAACAACTTATAGCTTAATCCTAAATTACAAATAAATTAAATT-TTAAATAATTAC
1 AAACACAAAAACTTATAACATAATCCTAAATTACAAACAAATT-AATTATAAAATAATTAC
* *
41199715 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTAC
1 AAACACAAAAACTTATAACATAATCCTAAATTACAAACAAATTAATTATAAAATAATTAC
41199775 AA
1 AA
41199777 TATTCATACA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 4 0.07
60 50 0.93
ACGTcount: A:0.55, C:0.14, G:0.01, T:0.30
Consensus pattern (60 bp):
AAACACAAAAACTTATAACATAATCCTAAATTACAAACAAATTAATTATAAAATAATTAC
Found at i:41199795 original size:21 final size:21
Alignment explanation
Indices: 41199764--41200026 Score: 154
Period size: 21 Copynumber: 12.2 Consensus size: 21
41199754 AATTAATTAT
41199764 AAAATAATTACAATATTCATAC
1 AAAA-AATTACAATATTCATAC
41199786 AAAAAATTACAATATTACAATATATC
1 AAAAAATTACAATATT-C---ATA-C
***
41199812 CCGAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
*
41199833 --AAAATTACAAAATTACAATATTC
1 AAAAAATTACAATATT-C-ATA--C
41199856 ATACCAAAAAATTACAATATTCATAC
1 A-A--AAAA--TTACAATATTCATAC
41199882 AAAAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
* * *
41199903 --AAAA-TACTA-ATCCAAAAC
1 AAAAAATTACAATATTC-ATAC
* * * *
41199921 TATAAA-TACAA-ATTTAATTAT
1 AAAAAATTACAATA-TTCA-TAC
41199942 AAAATAATTACAATATTCATAC
1 AAAA-AATTACAATATTCATAC
41199964 --AAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
*
41199983 --AAAATTATAATATTCATAC
1 AAAAAATTACAATATTCATAC
*
41200002 AAAAAATTAGAATATTCATAC
1 AAAAAATTACAATATTCATAC
41200023 AAAA
1 AAAA
41200027 TACTAACCCA
Statistics
Matches: 194, Mismatches: 21, Indels: 53
0.72 0.08 0.20
Matches are distributed among these distances:
17 3 0.02
18 7 0.04
19 51 0.26
20 12 0.06
21 57 0.29
22 12 0.06
23 13 0.07
24 1 0.01
25 5 0.03
26 16 0.08
28 7 0.04
29 1 0.01
30 9 0.05
ACGTcount: A:0.55, C:0.14, G:0.01, T:0.30
Consensus pattern (21 bp):
AAAAAATTACAATATTCATAC
Found at i:41199839 original size:19 final size:19
Alignment explanation
Indices: 41199838--41200027 Score: 163
Period size: 19 Copynumber: 9.4 Consensus size: 19
41199828 CATACAAAAT
41199838 TACAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
41199857 TACCAAAAAATTACAATATTCA
1 TA-C--AAAATTACAATATTCA
41199879 TACAAAAAATTACAATATTCA
1 TAC--AAAATTACAATATTCA
* *
41199900 TACAAAA-TACTA-ATCCAA
1 TACAAAATTACAATATTC-A
*
41199918 AACTATAAA-TACAAATTTAATT-A
1 TAC-A-AAATTAC-AA--T-ATTCA
*
41199941 TAAAATAATTACAATATTCA
1 TACAA-AATTACAATATTCA
41199961 TACAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
*
41199980 TACAAAATTATAATATTCA
1 TACAAAATTACAATATTCA
*
41199999 TACAAAAAATTAGAATATTCA
1 TAC--AAAATTACAATATTCA
41200020 TACAAAAT
1 TACAAAAT
41200028 ACTAACCCAA
Statistics
Matches: 145, Mismatches: 10, Indels: 32
0.78 0.05 0.17
Matches are distributed among these distances:
17 3 0.02
18 7 0.05
19 50 0.34
20 13 0.09
21 42 0.29
22 23 0.16
23 5 0.03
25 2 0.01
ACGTcount: A:0.55, C:0.14, G:0.01, T:0.31
Consensus pattern (19 bp):
TACAAAATTACAATATTCA
Found at i:41200071 original size:120 final size:122
Alignment explanation
Indices: 41199838--41200062 Score: 348
Period size: 120 Copynumber: 1.8 Consensus size: 122
41199828 CATACAAAAT
41199838 TACAAAATTACAATATTCATACCAAAAAATTACAATATTCATACAAAAAATTACAATATTCATAC
1 TACAAAATTACAATATTCATACC-AAAAATTACAATATTCATACAAAAAATTACAATATTCATAC
* * *
41199903 AAAATACTAATCCAAAACTATAAATACAAATTTAATTATAAAATAATTACAATATTCA
65 AAAATACTAATCCAAAACTATAAACACAAATATAATAATAAAATAATTACAATATTCA
* *
41199961 TACAAAATTACAATATTCATA-C-AAAATTATAATATTCATACAAAAAATTAGAATATTCATACA
1 TACAAAATTACAATATTCATACCAAAAATTACAATATTCATACAAAAAATTACAATATTCATACA
*
41200024 AAATACTAA-CCCAAACTATAAACACTAAATATAGATAAT
66 AAATACTAATCCAAAACTATAAACAC-AAATATA-ATAAT
41200063 TTATAATTAA
Statistics
Matches: 94, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
119 14 0.15
120 54 0.57
121 4 0.04
122 1 0.01
123 21 0.22
ACGTcount: A:0.55, C:0.15, G:0.01, T:0.29
Consensus pattern (122 bp):
TACAAAATTACAATATTCATACCAAAAATTACAATATTCATACAAAAAATTACAATATTCATACA
AAATACTAATCCAAAACTATAAACACAAATATAATAATAAAATAATTACAATATTCA
Found at i:41200189 original size:17 final size:18
Alignment explanation
Indices: 41200163--41200204 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
41200153 ACCTTTTTTT
*
41200163 TTCT-TTCTTCTTC-TTC
1 TTCTCTTCTTCTCCTTTC
41200179 TTCTCTTCTTCTCCTTTC
1 TTCTCTTCTTCTCCTTTC
41200197 TCTCTCTT
1 T-TCTCTT
41200205 TTTTTTTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 4 0.18
17 8 0.36
18 4 0.18
19 6 0.27
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (18 bp):
TTCTCTTCTTCTCCTTTC
Found at i:41200342 original size:27 final size:27
Alignment explanation
Indices: 41200312--41200381 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
41200302 AGAAGGCCAC
41200312 CATTGGCACCTCCCTATGAGGCACATT
1 CATTGGCACCTCCCTATGAGGCACATT
*
41200339 CATTGGCACCTCTCTATGAGGCACATT
1 CATTGGCACCTCCCTATGAGGCACATT
* *
41200366 CATTGGCGCCTACCTA
1 CATTGGCACCTCCCTA
41200382 ATATGCGCCA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.21, C:0.33, G:0.19, T:0.27
Consensus pattern (27 bp):
CATTGGCACCTCCCTATGAGGCACATT
Found at i:41202281 original size:58 final size:60
Alignment explanation
Indices: 41202211--41202364 Score: 163
Period size: 58 Copynumber: 2.6 Consensus size: 60
41202201 GTTCAACTAT
* *
41202211 GATTAAACTTAATCACTTTAATAGTAAATTAATATAATACTTATC-C-AGATAAATATTA
1 GATTAAACTTAATCACTTTAATATTAAATTAATAGAATACTTATCACAAGATAAATATTA
* * *
41202269 GATTAAATTTAAT-A-TTAAATATATTAAATTAATAGAATATTTATCTACAAGATAAATATTA
1 GATTAAACTTAATCACTT-TA-ATATTAAATTAATAGAATACTTATC-ACAAGATAAATATTA
* * **
41202330 AATATTAAGATAATCACTTTAATATTAAATTAATA
1 GAT-TAAACTTAATCACTTTAATATTAAATTAATA
41202365 AAATGCTATC
Statistics
Matches: 78, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
56 2 0.03
57 2 0.03
58 34 0.44
60 1 0.01
61 14 0.18
62 21 0.27
63 2 0.03
64 2 0.03
ACGTcount: A:0.49, C:0.06, G:0.05, T:0.40
Consensus pattern (60 bp):
GATTAAACTTAATCACTTTAATATTAAATTAATAGAATACTTATCACAAGATAAATATTA
Found at i:41202404 original size:16 final size:16
Alignment explanation
Indices: 41202383--41202414 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
41202373 TCAGGATAAG
41202383 TATTAAATTAATTAAA
1 TATTAAATTAATTAAA
*
41202399 TATTAAATTTATTAAA
1 TATTAAATTAATTAAA
41202415 ATAATATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATTAAATTAATTAAA
Found at i:41205914 original size:43 final size:42
Alignment explanation
Indices: 41205848--41205975 Score: 138
Period size: 42 Copynumber: 3.0 Consensus size: 42
41205838 ATAGGATTTC
* *
41205848 TGATATGTG-TCATCGTGTAAGACCACGTCGGGGACGTTGGCA
1 TGATATGTGATTA-CGTGTAAGACCACGTCTGGGACGTTGGCA
*
41205890 TCGACT-TGTGTTTACGTGTAAGACC-CTGTCTGGGACAG-TGGCA
1 T-GA-TATGTGATTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCA
* *
41205933 TGATATGTGATTGCATGTAAGACCACGTCTGGGACGTTGGCA
1 TGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCA
41205975 T
1 T
41205976 TGTACGAGTT
Statistics
Matches: 73, Mismatches: 5, Indels: 16
0.78 0.05 0.17
Matches are distributed among these distances:
41 2 0.03
42 35 0.48
43 32 0.44
44 4 0.05
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (42 bp):
TGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCA
Found at i:41214084 original size:44 final size:46
Alignment explanation
Indices: 41214027--41214119 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 46
41214017 TACAACATCT
* *
41214027 ATTCTATTCAACCAAACAAAAGAA-CGTT-ATTACAACTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATCATTGATTACAACTCTATTCC
** *
41214071 ATTCCATTCAACCAAACAATTGAATTATTGATTACAACTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATCATTGATTACAACTCTATTCC
41214117 ATT
1 ATT
41214120 ACAGCTCTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 21 0.50
45 2 0.05
46 19 0.45
ACGTcount: A:0.39, C:0.24, G:0.04, T:0.33
Consensus pattern (46 bp):
ATTCCATTCAACCAAACAAAAGAATCATTGATTACAACTCTATTCC
Found at i:41214122 original size:16 final size:16
Alignment explanation
Indices: 41214101--41214171 Score: 115
Period size: 16 Copynumber: 4.4 Consensus size: 16
41214091 TGAATTATTG
*
41214101 ATTACAACTCTATTCC
1 ATTACAGCTCTATTCC
41214117 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
41214133 ATTATAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
41214149 ATTACAGCCCTATTCC
1 ATTACAGCTCTATTCC
41214165 ATTACAG
1 ATTACAG
41214172 TAAACCAAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.28, C:0.30, G:0.06, T:0.37
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:41220795 original size:25 final size:25
Alignment explanation
Indices: 41220767--41220845 Score: 65
Period size: 25 Copynumber: 3.3 Consensus size: 25
41220757 CTAATGGCCG
41220767 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
* *** ***
41220792 ATGTGAT-AAGGCCTAA-TGGCCA-
1 ATGTGATGAATGTGAAAGTGTATAT
41220814 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
*
41220839 GTGTGAT
1 ATGTGAT
41220846 AGGGCCTAAT
Statistics
Matches: 36, Mismatches: 15, Indels: 6
0.63 0.26 0.11
Matches are distributed among these distances:
22 7 0.19
23 8 0.22
24 8 0.22
25 13 0.36
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (25 bp):
ATGTGATGAATGTGAAAGTGTATAT
Found at i:41220818 original size:47 final size:47
Alignment explanation
Indices: 41220751--41221364 Score: 1032
Period size: 47 Copynumber: 13.1 Consensus size: 47
41220741 GAAATGATAG
41220751 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
41220798 TAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
41220845 TAGGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
41220892 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
41220939 TAGGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
41220986 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
41221033 TAGGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
41221080 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
41221127 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
41221174 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTAA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
41221221 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
41221268 TAAGGCCTAATGGCCGATGTG-TGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * * *
41221314 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
41221361 TAAG
1 TAAG
41221365 TCCCGAAGGG
Statistics
Matches: 531, Mismatches: 35, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
46 40 0.08
47 491 0.92
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:41221539 original size:37 final size:37
Alignment explanation
Indices: 41221483--41221561 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
41221473 CCGAGCTCTA
* * *
41221483 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
* *
41221520 AAGACCCGATAACTTCGTGTGGAGATTATGTCTGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
41221557 AAGAC
1 AAGAC
41221562 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.27
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:41241599 original size:167 final size:167
Alignment explanation
Indices: 41241316--41241759 Score: 746
Period size: 167 Copynumber: 2.7 Consensus size: 167
41241306 GCAACTGGTA
* *
41241316 GAATTCTAGTCACACCATATATTTAAGTCGATCCCAACAACGAACTTATTTCGGTGAATACAATG
1 GAATTCCAGTCACACCATATCTTTAAGTCGATCCCAACAACGAACTTATTTCGGTGAATACAATG
*
41241381 TTTTAGATTATCAAATAGTATCCCAAATGACTTTGATACTCAACATGAGAACTTCCAACTATAAT
66 TTTTAGATTATCAAATAGAATCCCAAATGACTTTGATACTCAACATGAGAACTTCCAACTATAAT
41241446 TTTCGGTGAAAACATGAGAACTTATTTCAGTATTGTT
131 TTTCGGTGAAAACATGAGAACTTATTTCAGTATTGTT
* *
41241483 GAATTCCAGTCACACCATATCTTTAAGTCGATCCCAACAACGAAATAATTTCGGTGAATACAATG
1 GAATTCCAGTCACACCATATCTTTAAGTCGATCCCAACAACGAACTTATTTCGGTGAATACAATG
* * *
41241548 TTTTAGATTATCAAATAGAATCCCAAATGACTTTGATACTTAACATGAGAACTTTCACCTATAAT
66 TTTTAGATTATCAAATAGAATCCCAAATGACTTTGATACTCAACATGAGAACTTCCAACTATAAT
* *
41241613 TTTCGGTGAAAACATGAGAACTTATTTCGGTGTTGTT
131 TTTCGGTGAAAACATGAGAACTTATTTCAGTATTGTT
* * * *
41241650 GAATTCCAGTCACACCATATCTTCAAGTTGATCCCAACAACGAACTTATTTCGTTGGATACAATG
1 GAATTCCAGTCACACCATATCTTTAAGTCGATCCCAACAACGAACTTATTTCGGTGAATACAATG
*
41241715 TTTTA-ATTATCAAATAGAATCCCAAATGAATTTGATACTCAACAT
66 TTTTAGATTATCAAATAGAATCCCAAATGACTTTGATACTCAACAT
41241760 AAGACTTACA
Statistics
Matches: 259, Mismatches: 18, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
166 38 0.15
167 221 0.85
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (167 bp):
GAATTCCAGTCACACCATATCTTTAAGTCGATCCCAACAACGAACTTATTTCGGTGAATACAATG
TTTTAGATTATCAAATAGAATCCCAAATGACTTTGATACTCAACATGAGAACTTCCAACTATAAT
TTTCGGTGAAAACATGAGAACTTATTTCAGTATTGTT
Found at i:41250162 original size:29 final size:29
Alignment explanation
Indices: 41250122--41250195 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
41250112 GTGTACTCTG
* **
41250122 TATATGTTGCCTTTGTGGCATACTTTATA
1 TATATGTAGCCTTTGTGGCATACACTATA
41250151 TATATGTAGCCTTTGTGGCATACACTATA
1 TATATGTAGCCTTTGTGGCATACACTATA
41250180 TATA--TAGCCTTTGTGG
1 TATATGTAGCCTTTGTGG
41250196 TGTACTCCAT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
27 12 0.29
29 30 0.71
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (29 bp):
TATATGTAGCCTTTGTGGCATACACTATA
Found at i:41253497 original size:48 final size:48
Alignment explanation
Indices: 41253423--41253661 Score: 307
Period size: 48 Copynumber: 5.0 Consensus size: 48
41253413 ATAAGTACTG
* * * *
41253423 ATATTCTATTGAGATACAAGGTTGGCACGGACTGTGTACAGGCCACCA
1 ATATTCTGTTAAGATACAAGGGTGGCACGGACTGTGTGCAGGCCACCA
* *
41253471 ATATTCTGTTAAGATACAAGGGTGGCACGGACTGTTTGCAGACCACCA
1 ATATTCTGTTAAGATACAAGGGTGGCACGGACTGTGTGCAGGCCACCA
* *
41253519 ATATTCTGTTAAGATACAAGGGTGGCACGTACTGTGTGTAGGCCACCA
1 ATATTCTGTTAAGATACAAGGGTGGCACGGACTGTGTGCAGGCCACCA
* * *
41253567 ATATTCTGTTAAGATACAGGGGTGGCACGGACTATGTGCAGGCCACCG
1 ATATTCTGTTAAGATACAAGGGTGGCACGGACTGTGTGCAGGCCACCA
* * ** * * * *
41253615 AGAGTCTGTTATTACACAAAGGTGGTACGGACTGTGTGTAGGCCACC
1 ATATTCTGTTAAGATACAAGGGTGGCACGGACTGTGTGCAGGCCACC
41253662 GAGAAATCTA
Statistics
Matches: 166, Mismatches: 25, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 166 1.00
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (48 bp):
ATATTCTGTTAAGATACAAGGGTGGCACGGACTGTGTGCAGGCCACCA
Found at i:41255494 original size:50 final size:50
Alignment explanation
Indices: 41255366--41255661 Score: 235
Period size: 50 Copynumber: 5.8 Consensus size: 50
41255356 GATAATAACA
* * * * **
41255366 TGCCAAAGCCATGTCCCGGACATGGTCTTACATGGGATG-TTTCAT-GTAC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GCTCTCATATTGG
* * * *
41255415 TGCCAATGCCATATCCTAGATATGGTCTTACATGGGAGTTCTCATATTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATATTGG
* * * *
41255465 TGCCCATGCCATGTCCCAGACATGGTCTT--ATGGGGGCCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAG-CTCTCATATTGG
* * * * *
41255514 TGTC-A-GCACTATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGC-C-ATGTCCCAGACATGGTCTTACATGGGAGCTCTCATATTGG
* * * *
41255564 TGCCAACGCCATTTCCGAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCAT-AT-T---GG
* *
41255619 ATGCCAATGCCATGTCCCAGACATGGTCTTACGTGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGCTCT
41255662 TTACCCAAAT
Statistics
Matches: 200, Mismatches: 32, Indels: 23
0.78 0.13 0.09
Matches are distributed among these distances:
47 2 0.01
48 9 0.05
49 68 0.34
50 72 0.36
51 8 0.04
52 2 0.01
55 2 0.01
56 37 0.19
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATATTGG
Found at i:41261741 original size:12 final size:12
Alignment explanation
Indices: 41261724--41261749 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41261714 AAGTATCTTG
41261724 TTATTAGAATCA
1 TTATTAGAATCA
41261736 TTATTAGAATCA
1 TTATTAGAATCA
41261748 TT
1 TT
41261750 TGGTTATGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (12 bp):
TTATTAGAATCA
Found at i:41263033 original size:16 final size:16
Alignment explanation
Indices: 41263009--41263044 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
41262999 ATTGCAAAAT
*
41263009 TTTTTTATACTATCTA
1 TTTTATATACTATCTA
*
41263025 TTTTATATACTATTTA
1 TTTTATATACTATCTA
41263041 TTTT
1 TTTT
41263045 TAAGATGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTATATACTATCTA
Found at i:41264318 original size:25 final size:25
Alignment explanation
Indices: 41264285--41264348 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
41264275 AATTCAAACC
* *
41264285 AAGCATTTGTGGCGAATTCTCTATA
1 AAGCCTTTGTGGCGAAGTCTCTATA
*
41264310 AAGCCTTTG-GGATGAAGTCTCTATA
1 AAGCCTTTGTGG-CGAAGTCTCTATA
*
41264335 AAGCCTTTATGGCG
1 AAGCCTTTGTGGCG
41264349 TATTATGCGA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
24 2 0.06
25 28 0.88
26 2 0.06
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (25 bp):
AAGCCTTTGTGGCGAAGTCTCTATA
Found at i:41277334 original size:19 final size:20
Alignment explanation
Indices: 41277296--41277345 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
41277286 GTGTCCCTTG
41277296 TTTTTGAAATTTCTCATATT
1 TTTTTGAAATTTCTCATATT
*
41277316 TTTTTGAAATTT-TCTTATT
1 TTTTTGAAATTTCTCATATT
* *
41277335 TATTTCAAATT
1 TTTTTGAAATT
41277346 AGTCCCTAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.26, C:0.08, G:0.04, T:0.62
Consensus pattern (20 bp):
TTTTTGAAATTTCTCATATT
Found at i:41288077 original size:21 final size:21
Alignment explanation
Indices: 41288048--41288103 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
41288038 CGAGGAAGCA
* *
41288048 AAGTTGCAACATTGGACTA-TG
1 AAGTCGCAACATT-CACTATTG
*
41288069 AAGTCGCAACATTCAGTATTG
1 AAGTCGCAACATTCACTATTG
41288090 AAGGTCGCAACATT
1 AA-GTCGCAACATT
41288104 TGAGCGAGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.10
21 16 0.53
22 11 0.37
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (21 bp):
AAGTCGCAACATTCACTATTG
Found at i:41302715 original size:15 final size:16
Alignment explanation
Indices: 41302684--41302723 Score: 64
Period size: 15 Copynumber: 2.5 Consensus size: 16
41302674 ATAGTAAAAA
41302684 TATAATTTTATTATTTT
1 TATAA-TTTATTATTTT
41302701 TATAATTTA-TATTTT
1 TATAATTTATTATTTT
41302716 TATAATTT
1 TATAATTT
41302724 TTAAAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 14 0.61
16 4 0.17
17 5 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATAATTTATTATTTT
Found at i:41303608 original size:4 final size:4
Alignment explanation
Indices: 41303599--41303633 Score: 61
Period size: 4 Copynumber: 8.5 Consensus size: 4
41303589 TATTATTTGT
41303599 TTAA TTAA TTAA TTAA TTAA TTTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA -TTAA TTAA TTAA TT
41303634 TCTTTAATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (4 bp):
TTAA
Found at i:41303641 original size:13 final size:13
Alignment explanation
Indices: 41303599--41303634 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
41303589 TATTATTTGT
41303599 TTAATTAA-TTAA
1 TTAATTAATTTAA
41303611 TTAATTAATTTAA
1 TTAATTAATTTAA
41303624 TTAATTAATTT
1 TTAATTAATTT
41303635 CTTTAATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 8 0.35
13 15 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAATTAATTTAA
Found at i:41303641 original size:17 final size:17
Alignment explanation
Indices: 41303599--41303633 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
41303589 TATTATTTGT
41303599 TTAA-TTAATTAATTAA
1 TTAATTTAATTAATTAA
41303615 TTAATTTAATTAATTAA
1 TTAATTTAATTAATTAA
41303632 TT
1 TT
41303634 TCTTTAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTAATTTAATTAATTAA
Found at i:41303651 original size:17 final size:18
Alignment explanation
Indices: 41303626--41303664 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
41303616 TAATTTAATT
41303626 AATTAATTTCTTT-AATCA
1 AATTAATTT-TTTCAATCA
41303644 AATT-ATTTTTTCAATCA
1 AATTAATTTTTTCAATCA
41303661 AATT
1 AATT
41303665 CTAATTCAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 3 0.15
17 13 0.65
18 4 0.20
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.51
Consensus pattern (18 bp):
AATTAATTTTTTCAATCA
Found at i:41304376 original size:19 final size:19
Alignment explanation
Indices: 41304347--41304389 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
41304337 GCATCAAAAG
*
41304347 AATAAGTCAAACTAGAT-A
1 AATAAGTCAAAATAGATCA
41304365 AATAATGTCAAAATAGATCA
1 AATAA-GTCAAAATAGATCA
41304385 AATAA
1 AATAA
41304390 CCACATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.23
19 11 0.50
20 6 0.27
ACGTcount: A:0.58, C:0.09, G:0.09, T:0.23
Consensus pattern (19 bp):
AATAAGTCAAAATAGATCA
Found at i:41306540 original size:11 final size:13
Alignment explanation
Indices: 41306516--41306547 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
41306506 TAGTTTATTA
41306516 ATATTTTAATATG
1 ATATTTTAATATG
41306529 AT-TTTTAA-ATG
1 ATATTTTAATATG
41306540 ATATTTTA
1 ATATTTTA
41306548 TTAATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (13 bp):
ATATTTTAATATG
Found at i:41308651 original size:26 final size:25
Alignment explanation
Indices: 41308598--41308658 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
41308588 CCATAATTAT
* **
41308598 ATATATTATATAATAAGACCTATGC
1 ATATATTATATAATAAGACCCACAC
*
41308623 ATATATGTATATAGTAAGACCCACAC
1 ATATAT-TATATAATAAGACCCACAC
41308649 ATAATATTAT
1 AT-ATATTAT
41308659 TTATGTATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 6 0.20
26 20 0.67
27 4 0.13
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.34
Consensus pattern (25 bp):
ATATATTATATAATAAGACCCACAC
Found at i:41315263 original size:35 final size:35
Alignment explanation
Indices: 41315153--41315504 Score: 169
Period size: 36 Copynumber: 9.9 Consensus size: 35
41315143 CAAATGAGTA
* * * *
41315153 TGCCTAGCACTTGCCAGTATAA-TCGAAAAATAAATA
1 TGCCTAGCACTGGTCGGTATAACT-G-AAAATAAATG
* * ** *
41315189 TGTCCTA-CACTGGTCAGTAAAACCAACAAATAAGTG
1 TG-CCTAGCACTGGTCGGTATAACTGA-AAATAAATG
* *
41315225 TGCCTAGCACTAGTCGGTATAACTGATAATAAATG
1 TGCCTAGCACTGGTCGGTATAACTGAAAATAAATG
* ** * * * *
41315260 TGCCCTA-CGCTGGTCTATAGAACCGAAAAATAAGTA
1 TG-CCTAGCACTGGTCGGTATAACTG-AAAATAAATG
* *
41315296 TGCCCAGCACTGGTCGGTATAACTGACAATAAATG
1 TGCCTAGCACTGGTCGGTATAACTGAAAATAAATG
* ** * *
41315331 CAT-CCTA-CGCTGGTCAATAGAACTGAAAAATAAGTG
1 --TGCCTAGCACTGGTCGGTATAACTG-AAAATAAATG
* * *
41315367 TGCCCATCACTGGTCGGTATAACCGAAAATAAATG
1 TGCCTAGCACTGGTCGGTATAACTGAAAATAAATG
* * * * * * * *
41315402 TGCGTTGCGCTAGTTGATAGAACTGAAGAATAAACG
1 TGCCTAGCACTGGTCGGTATAACTGAA-AATAAATG
* *
41315438 TGCCCAGCACTGGTCGGTATAA-TCGACAATAAATG
1 TGCCTAGCACTGGTCGGTATAACT-GAAAATAAATG
* * * *
41315473 TGTCCT-GCGCTGGTCAGTAGAACTGACAATAA
1 TG-CCTAGCACTGGTCGGTATAACTGAAAATAA
41315505 GTGGCCATTC
Statistics
Matches: 229, Mismatches: 71, Indels: 33
0.69 0.21 0.10
Matches are distributed among these distances:
34 1 0.00
35 110 0.48
36 113 0.49
37 5 0.02
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (35 bp):
TGCCTAGCACTGGTCGGTATAACTGAAAATAAATG
Found at i:41315291 original size:71 final size:70
Alignment explanation
Indices: 41315181--41315495 Score: 330
Period size: 71 Copynumber: 4.4 Consensus size: 70
41315171 ATAATCGAAA
* * * * *
41315181 AATAAATATGTCCTACACTGGTCAGTAAAACC-AACAAATAAGTGTGCCTAGCACTAGTCGGTAT
1 AATAAATGTGTCCTACGCTGGTCA-TAGAACCGAA-AAATAAGTGTGCCCAGCACTGGTCGGTAT
*
41315245 AACTGAT
64 AACTGAC
* *
41315252 AATAAATGTGCCCTACGCTGGTCTATAGAACCGAAAAATAAGTATGCCCAGCACTGGTCGGTATA
1 AATAAATGTGTCCTACGCTGGTC-ATAGAACCGAAAAATAAGTGTGCCCAGCACTGGTCGGTATA
41315317 ACTGAC
65 ACTGAC
** * *
41315323 AATAAATGCATCCTACGCTGGTCAATAGAACTGAAAAATAAGTGTGCCCATCACTGGTCGGTATA
1 AATAAATGTGTCCTACGCTGGTC-ATAGAACCGAAAAATAAGTGTGCCCAGCACTGGTCGGTATA
* *
41315388 ACCGAA
65 ACTGAC
* * * * * * **
41315394 AATAAATGTG-CGTTGCGCTAGTTGATAGAACTGAAGAATAAACGTGCCCAGCACTGGTCGGTAT
1 AATAAATGTGTC-CTACGCT-GGTCATAGAACCGAAAAATAAGTGTGCCCAGCACTGGTCGGTAT
41315458 AA-TCGAC
64 AACT-GAC
*
41315465 AATAAATGTGTCCTGCGCTGGTCAGTAGAAC
1 AATAAATGTGTCCTACGCTGGTCA-TAGAAC
41315496 TGACAATAAG
Statistics
Matches: 205, Mismatches: 32, Indels: 14
0.82 0.13 0.06
Matches are distributed among these distances:
70 4 0.02
71 195 0.95
72 6 0.03
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (70 bp):
AATAAATGTGTCCTACGCTGGTCATAGAACCGAAAAATAAGTGTGCCCAGCACTGGTCGGTATAA
CTGAC
Found at i:41315380 original size:36 final size:35
Alignment explanation
Indices: 41315216--41315507 Score: 135
Period size: 35 Copynumber: 8.3 Consensus size: 35
41315206 TAAAACCAAC
* * * *
41315216 AAATAAGTGTGCCTAGCACTAGTCGGTATAACTGA
1 AAATAAGTGTGCCCAGCACTGGTCGATAGAACTGA
* * * * *
41315251 TAATAAATGTGCCCTA-CGCTGGTCTATAGAACCGAA
1 AAATAAGTGTGCCC-AGCACTGGTCGATAGAACTG-A
* * *
41315287 AAATAAGTATGCCCAGCACTGGTCGGTATAACTGA
1 AAATAAGTGTGCCCAGCACTGGTCGATAGAACTGA
* * * * *
41315322 CAATAAATGCAT-CCTA-CGCTGGTCAATAGAACTGAA
1 AAATAAGTG--TGCCCAGCACTGGTCGATAGAACTG-A
* * * *
41315358 AAATAAGTGTGCCCATCACTGGTCGGTATAACCGA
1 AAATAAGTGTGCCCAGCACTGGTCGATAGAACTGA
* *** * * *
41315393 AAATAAATGTGCGTTGCGCTAGTTGATAGAACTGA
1 AAATAAGTGTGCCCAGCACTGGTCGATAGAACTGA
** * *
41315428 AGAATAAACGTGCCCAGCACTGGTCGGTATAA-TCGA
1 A-AATAAGTGTGCCCAGCACTGGTCGATAGAACT-GA
* * * * *
41315464 CAATAAATGTGTCCTGCGCTGGTC-AGTAGAACTGA
1 AAATAAGTGTGCCCAGCACTGGTCGA-TAGAACTGA
*
41315499 CAATAAGTG
1 AAATAAGTG
41315508 GCCATTCAAT
Statistics
Matches: 184, Mismatches: 61, Indels: 24
0.68 0.23 0.09
Matches are distributed among these distances:
34 1 0.01
35 108 0.59
36 74 0.40
37 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.24
Consensus pattern (35 bp):
AAATAAGTGTGCCCAGCACTGGTCGATAGAACTGA
Found at i:41315383 original size:142 final size:141
Alignment explanation
Indices: 41315216--41315507 Score: 372
Period size: 142 Copynumber: 2.1 Consensus size: 141
41315206 TAAAACCAAC
* * * *
41315216 AAATAAGTGTGCCTAGCACTAGTCGGTATAACTGATAATAAATGTGCCCTACGCTGGTCT-ATAG
1 AAATAAGTGTGCCCAGCACTAGTCGGTATAACCGAAAATAAATGTGCCCTACGCTAGT-TGATAG
**
41315280 AACCGAAAAATAAGTATGCCCAGCACTGGTCGGTATAA-CTGACAATAAATGCATCCTACGCTGG
65 AACCGAAAAATAAACATGCCCAGCACTGGTCGGTATAATC-GACAATAAATGCATCCTACGCTGG
41315344 TCAATAGAACTGAA
129 TCAATAGAACTG-A
* * ** *
41315358 AAATAAGTGTGCCCATCACTGGTCGGTATAACCGAAAATAAATGTGCGTTGCGCTAGTTGATAGA
1 AAATAAGTGTGCCCAGCACTAGTCGGTATAACCGAAAATAAATGTGCCCTACGCTAGTTGATAGA
* * * ** *
41315423 ACTGAAGAATAAACGTGCCCAGCACTGGTCGGTATAATCGACAATAAATGTGTCCTGCGCTGGTC
66 ACCGAAAAATAAACATGCCCAGCACTGGTCGGTATAATCGACAATAAATGCATCCTACGCTGGTC
*
41315488 AGTAGAACTGA
131 AATAGAACTGA
*
41315499 CAATAAGTG
1 AAATAAGTG
41315508 GCCATTCAAT
Statistics
Matches: 129, Mismatches: 19, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
141 10 0.08
142 118 0.91
143 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.24
Consensus pattern (141 bp):
AAATAAGTGTGCCCAGCACTAGTCGGTATAACCGAAAATAAATGTGCCCTACGCTAGTTGATAGA
ACCGAAAAATAAACATGCCCAGCACTGGTCGGTATAATCGACAATAAATGCATCCTACGCTGGTC
AATAGAACTGA
Found at i:41316156 original size:15 final size:15
Alignment explanation
Indices: 41316136--41316169 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
41316126 ACATTTCTAA
41316136 TATTTTATCTTT-TAT
1 TATTTTAT-TTTATAT
41316151 TATTTTATTTTATAT
1 TATTTTATTTTATAT
41316166 TATT
1 TATT
41316170 ATTAACATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.17
15 15 0.83
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (15 bp):
TATTTTATTTTATAT
Found at i:41316396 original size:48 final size:48
Alignment explanation
Indices: 41316325--41316417 Score: 186
Period size: 48 Copynumber: 1.9 Consensus size: 48
41316315 AGAGCACTTT
41316325 GTAAATGAAATAGCCCATCCAAGATTCAATTAACCTAAAAATTATAGA
1 GTAAATGAAATAGCCCATCCAAGATTCAATTAACCTAAAAATTATAGA
41316373 GTAAATGAAATAGCCCATCCAAGATTCAATTAACCTAAAAATTAT
1 GTAAATGAAATAGCCCATCCAAGATTCAATTAACCTAAAAATTAT
41316418 CTCTATAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.26
Consensus pattern (48 bp):
GTAAATGAAATAGCCCATCCAAGATTCAATTAACCTAAAAATTATAGA
Found at i:41324980 original size:16 final size:16
Alignment explanation
Indices: 41324959--41324989 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41324949 TTCATCACAA
41324959 CATAGATACATTTATG
1 CATAGATACATTTATG
*
41324975 CATAGATTCATTTAT
1 CATAGATACATTTAT
41324990 ATTAAAACAA
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:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (16 bp):
CATAGATACATTTATG
Found at i:41333831 original size:21 final size:21
Alignment explanation
Indices: 41333802--41333870 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 21
41333792 AAGCTCATAA
* *
41333802 AGCTTAACATAAGCTCGAAAG
1 AGCTGAACAGAAGCTCGAAAG
41333823 AGCTGAACAGAAGCTC-ATAAG
1 AGCTGAACAGAAGCTCGA-AAG
**
41333844 AGCTGAACAGAAGCTCGTGAG
1 AGCTGAACAGAAGCTCGAAAG
41333865 AGCTGA
1 AGCTGA
41333871 TCCACCCAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.02
21 41 0.98
ACGTcount: A:0.39, C:0.19, G:0.26, T:0.16
Consensus pattern (21 bp):
AGCTGAACAGAAGCTCGAAAG
Found at i:41333867 original size:42 final size:41
Alignment explanation
Indices: 41333787--41333870 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 41
41333777 CGAACACGCC
* *
41333787 AACAAAAGCTCATAAAGCTTAACATAAGCTCGAAAGAGCTG
1 AACAAAAGCTCATAAAGCTGAACAGAAGCTCGAAAGAGCTG
* **
41333828 AACAGAAGCTCATAAGAGCTGAACAGAAGCTCGTGAGAGCTG
1 AACAAAAGCTCATAA-AGCTGAACAGAAGCTCGAAAGAGCTG
41333870 A
1 A
41333871 TCCACCCAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 14 0.38
42 23 0.62
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15
Consensus pattern (41 bp):
AACAAAAGCTCATAAAGCTGAACAGAAGCTCGAAAGAGCTG
Found at i:41340778 original size:42 final size:42
Alignment explanation
Indices: 41340716--41340815 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 42
41340706 TTCCTCACCT
* *
41340716 GTGTAACTCACTGAGCTGCCACGCACG-CCTGTGTGCCAGGCC
1 GTGTAACTCACTGAACTGCCACACACGTCC-GTGTGCCAGGCC
* * * *
41340758 GTGTAACTCTCTGAATTGCCACACGCGTCCGTGTGCTAGGCC
1 GTGTAACTCACTGAACTGCCACACACGTCCGTGTGCCAGGCC
*
41340800 GTCTAACTCACT-AACT
1 GTGTAACTCACTGAACT
41340816 TGAAACACTA
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
41 3 0.06
42 43 0.90
43 2 0.04
ACGTcount: A:0.19, C:0.33, G:0.24, T:0.24
Consensus pattern (42 bp):
GTGTAACTCACTGAACTGCCACACACGTCCGTGTGCCAGGCC
Found at i:41341890 original size:9 final size:9
Alignment explanation
Indices: 41341874--41341915 Score: 66
Period size: 9 Copynumber: 4.7 Consensus size: 9
41341864 GAGTTAAACG
41341874 AATCGAGTT
1 AATCGAGTT
*
41341883 ATTCGAGTT
1 AATCGAGTT
41341892 AATCGAGTT
1 AATCGAGTT
41341901 AATCGAGTT
1 AATCGAGTT
*
41341910 ATTCGA
1 AATCGA
41341916 ATCAACTCGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (9 bp):
AATCGAGTT
Found at i:41342242 original size:30 final size:31
Alignment explanation
Indices: 41342208--41342267 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
41342198 AAACCTTTTA
*
41342208 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
41342238 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
41342268 TCTCACCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:41342916 original size:5 final size:5
Alignment explanation
Indices: 41342906--41342931 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
41342896 GAACAAATAT
41342906 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
41342932 ATTCCATCTC
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:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:41347358 original size:124 final size:124
Alignment explanation
Indices: 41346942--41347384 Score: 593
Period size: 127 Copynumber: 3.5 Consensus size: 124
41346932 GATAAAATCA
* * * * * * *
41346942 AAGCAGGATGCTTTATCAGAAGGATTTCTGAAGTCGCGCCCACGTGTACGCGCTTTTGCTATAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
* * *
41347007 AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTTTGAGCAAAGAGTATAAAAAATGCTCC
66 AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTA-AAAAAATGCTTC
* * * *
41347067 AAGTAGGATACTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGTGCTTTTGCTACAGC
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
* *
41347132 AGGTCCTGGAAGAAATAGTTTCGAGTTGACGTTTCTGTGCAAATAGTTTAAAAAAATGCTTC
66 AGGTCCTGGAA-AAATAATTTCGAGTTGACGTTTCTGAGCAAATAG--TAAAAAAATGCTTC
* *
41347194 AAGCAGGATGCTATT-TGAGAAGAATTTGTGAAATTGCGCCCTCGTGGACGCACTTTTGCTACAG
1 AAGCAGGATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
* * *
41347258 TAGGTCCTGGAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTACAAAAACGCTTC
65 TAGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTAAAAAAATGCTTC
* * * *
41347318 TAGCAGGATGCTATT-TGAGAAGAATTTGTGAAATCACGCCCTCGTAGACGTGCTTTTGCTACAG
1 AAGCAGGATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
41347382 TAG
65 TAG
41347385 CATGTTTGGG
Statistics
Matches: 281, Mismatches: 33, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
124 73 0.26
125 65 0.23
126 61 0.22
127 78 0.28
128 4 0.01
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (124 bp):
AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTAAAAAAATGCTTC
Found at i:41350594 original size:114 final size:114
Alignment explanation
Indices: 41350394--41350767 Score: 703
Period size: 114 Copynumber: 3.3 Consensus size: 114
41350384 TTTTTTCAAT
* *
41350394 TATTAATTGTTAGTAAAATTATCAAATTATATCAAATTATTAATTATTAGTACCAGTCAAAACAT
1 TATTAATGGTTAGTAAAATTATCAAATTATATCAAATTATTAATTGTTAGTACCAGTCAAAACAT
*
41350459 ATTTTCAAATCTAACATTATGTGAATGTAAAATTATTAATTGATAATTG
66 TTTTTCAAATCTAACATTATGTGAATGTAAAATTATTAATTGATAATTG
41350508 TATTAATGGTTAGTAAAATTATCAAATTATATCAAATTATTAATTGTTAGTACCAGTCAAAACAT
1 TATTAATGGTTAGTAAAATTATCAAATTATATCAAATTATTAATTGTTAGTACCAGTCAAAACAT
41350573 TTTTTCAAATCTAACATTATGTGAATGTAAAATTATTAATTGATAATTG
66 TTTTTCAAATCTAACATTATGTGAATGTAAAATTATTAATTGATAATTG
*
41350622 TATTAATGGTTAGTAAAATTATCAAATTATATCAAATTATTAATTGTTAGTGCCAGTCAAAACAT
1 TATTAATGGTTAGTAAAATTATCAAATTATATCAAATTATTAATTGTTAGTACCAGTCAAAACAT
*
41350687 TTTTTCAAATCTAACATTATGTGAATGTAAAATTATTAAGTGATAATTG
66 TTTTTCAAATCTAACATTATGTGAATGTAAAATTATTAATTGATAATTG
41350736 TATTAATGGTTAGTAAAATTATCAAATTATAT
1 TATTAATGGTTAGTAAAATTATCAAATTATAT
41350768 TTAAGTTAAG
Statistics
Matches: 255, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
114 255 1.00
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.41
Consensus pattern (114 bp):
TATTAATGGTTAGTAAAATTATCAAATTATATCAAATTATTAATTGTTAGTACCAGTCAAAACAT
TTTTTCAAATCTAACATTATGTGAATGTAAAATTATTAATTGATAATTG
Found at i:41350842 original size:43 final size:42
Alignment explanation
Indices: 41350770--41351045 Score: 313
Period size: 43 Copynumber: 6.5 Consensus size: 42
41350760 AATTATATTT
* *
41350770 AAGTTAAGGGTTAGAGTTTTTAAGTTAAGGGTTAGTGTTTTA
1 AAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTA
* * *
41350812 AAGTTAAGGGTTTAGGGTTTTTTATTTAAGGATTAGGG-TTTA
1 AAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTA
** *
41350854 GGGGTT-AGGGTTAGGGTTTTTAAGTTAAGGGTTTAGTGTTTTA
1 -AAGTTAAGGGTTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTA
* * * *
41350897 AAGTCAATGGTTATGGTTTTTAAGTTAAGGGTTTAGGGTTTTT
1 AAGTTAAGGGTTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTA
* * * *
41350940 AGGTTAAGGGTTTAGGGTTTTTAAGTTAAAAGTTTAGGGTTTTT
1 AAGTTAAGGG-TTAGGGTTTTTAAGTT-AAGGGTTAGGGTTTTA
* *
41350984 AAGTTAAGGGTTAGAGTTTTTAAGTTAAGGGTTAGGGTTTTT
1 AAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTA
41351026 AAGTTAAGGGTTTAGGGTTT
1 AAGTTAAGGG-TTAGGGTTT
41351046 GTCAATTAAA
Statistics
Matches: 197, Mismatches: 29, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
41 18 0.09
42 49 0.25
43 92 0.47
44 35 0.18
45 3 0.02
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (42 bp):
AAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTAGGGTTTTA
Found at i:41351054 original size:22 final size:22
Alignment explanation
Indices: 41350767--41351045 Score: 331
Period size: 21 Copynumber: 13.0 Consensus size: 22
41350757 TCAAATTATA
*
41350767 TTTAAGTTAAGGG-TTAGAGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
41350788 TTTAAGTTAAGGG-TTAGTGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
41350809 TTAAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
41350831 TTTTATTTAA-GGATTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
****
41350852 TAGGGGTT-AGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
41350872 TTTAAGTTAAGGGTTTAGTGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * * *
41350894 TTAAAGTCAATGG-TTATGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
41350915 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
41350937 TTTAGGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
**
41350959 TTTAAGTTAAAAGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
41350981 TTTAAGTTAAGGG-TTAGAGTT
1 TTTAAGTTAAGGGTTTAGGGTT
41351002 TTTAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
41351023 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
41351045 T
1 T
41351046 GTCAATTAAA
Statistics
Matches: 218, Mismatches: 34, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.06
21 107 0.49
22 98 0.45
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.45
Consensus pattern (22 bp):
TTTAAGTTAAGGGTTTAGGGTT
Found at i:41351612 original size:18 final size:18
Alignment explanation
Indices: 41351586--41351628 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
41351576 GACTCGAAAA
* *
41351586 AGGAAACATATAAGGGTT
1 AGGAAACATAAAAGGGCT
*
41351604 AGGATACATAAAAGGGCT
1 AGGAAACATAAAAGGGCT
41351622 AGGAAAC
1 AGGAAAC
41351629 GCACCTGGCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.47, C:0.09, G:0.28, T:0.16
Consensus pattern (18 bp):
AGGAAACATAAAAGGGCT
Found at i:41352286 original size:7 final size:7
Alignment explanation
Indices: 41352276--41352301 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
41352266 TTATATACAT
41352276 AATACTA
1 AATACTA
41352283 AATACTA
1 AATACTA
41352290 AATACTA
1 AATACTA
41352297 AATAC
1 AATAC
41352302 CAATCGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:41352507 original size:20 final size:20
Alignment explanation
Indices: 41352470--41352507 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41352460 TTTATTTTTA
*
41352470 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
41352490 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
41352508 TATCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:41353417 original size:12 final size:13
Alignment explanation
Indices: 41353400--41353428 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
41353390 AATTTTTACG
41353400 ATTT-AAAAAATA
1 ATTTAAAAAAATA
41353412 ATTTAAAAAAATA
1 ATTTAAAAAAATA
41353425 ATTT
1 ATTT
41353429 TTTTCAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.25
13 12 0.75
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATTTAAAAAAATA
Found at i:41353468 original size:11 final size:12
Alignment explanation
Indices: 41353454--41353490 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
41353444 AAAAATAGGG
41353454 ATTTAAGAG-AA
1 ATTTAAGAGCAA
41353465 ATTTAAGAGCAA
1 ATTTAAGAGCAA
*
41353477 A-TTGAGAGCAA
1 ATTTAAGAGCAA
41353488 ATT
1 ATT
41353491 GAGATTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 19 0.83
12 4 0.17
ACGTcount: A:0.49, C:0.05, G:0.19, T:0.27
Consensus pattern (12 bp):
ATTTAAGAGCAA
Found at i:41353500 original size:11 final size:11
Alignment explanation
Indices: 41353470--41353494 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41353460 GAGAAATTTA
41353470 AGAGCAAATTG
1 AGAGCAAATTG
41353481 AGAGCAAATTG
1 AGAGCAAATTG
41353492 AGA
1 AGA
41353495 TTAAATATGG
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:0.48, C:0.08, G:0.28, T:0.16
Consensus pattern (11 bp):
AGAGCAAATTG
Found at i:41353507 original size:51 final size:50
Alignment explanation
Indices: 41353446--41353545 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 50
41353436 AATTATTTAA
41353446 AAATAGGGATTTAAGAGAAATTT-AAGAGCAAATTGAGAGCAAATTGAGATT
1 AAATAGGGATTTAAGAGAAATTTGAAG-G-AAATTGAGAGCAAATTGAGATT
* * *
41353497 AAATATGGATTTCAGAGAAATTTGGAAGGAATTTGAGAGCAAATTGAGA
1 AAATAGGGATTTAAGAGAAATTT-GAAGGAAATTGAGAGCAAATTGAGA
41353546 GGAAATTTGA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
51 40 0.91
52 1 0.02
53 3 0.07
ACGTcount: A:0.45, C:0.04, G:0.25, T:0.26
Consensus pattern (50 bp):
AAATAGGGATTTAAGAGAAATTTGAAGGAAATTGAGAGCAAATTGAGATT
Found at i:41353555 original size:12 final size:12
Alignment explanation
Indices: 41353513--41353557 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
41353503 GGATTTCAGA
41353513 GAAATTTG-GAAG
1 GAAATTTGAG-AG
41353525 G-AATTTGAGAG
1 GAAATTTGAGAG
*
41353536 CAAA-TTGAGAG
1 GAAATTTGAGAG
41353547 GAAATTTGAGA
1 GAAATTTGAGA
41353558 AAAGATTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.42, C:0.02, G:0.31, T:0.24
Consensus pattern (12 bp):
GAAATTTGAGAG
Found at i:41354476 original size:31 final size:31
Alignment explanation
Indices: 41354441--41354516 Score: 125
Period size: 31 Copynumber: 2.5 Consensus size: 31
41354431 AAAATTTATT
*
41354441 ATTTTAGTCACTCTTGTTAGATAAATTGTCA
1 ATTTTAGTCACTCTTGTTAAATAAATTGTCA
* *
41354472 ATTTTAGTCACTCCTGTTAAATAAGTTGTCA
1 ATTTTAGTCACTCTTGTTAAATAAATTGTCA
41354503 ATTTTAGTCACTCT
1 ATTTTAGTCACTCT
41354517 ATGGTTTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.45
Consensus pattern (31 bp):
ATTTTAGTCACTCTTGTTAAATAAATTGTCA
Found at i:41355769 original size:31 final size:31
Alignment explanation
Indices: 41355718--41355797 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
41355708 TTTTAACGGT
** *
41355718 AGAGTGGCT-AAATTGTCAACTTACCTAACG
1 AGAGTGGCTAAAATTAACAACTTACCTAACA
* *
41355748 GGAGTGGCTAAAATTAACAACTTATCTAACA
1 AGAGTGGCTAAAATTAACAACTTACCTAACA
*
41355779 AGAGTGACTAAAA-TAACAA
1 AGAGTGGCTAAAATTAACAA
41355798 ATTTTGTAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
30 14 0.33
31 28 0.67
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.24
Consensus pattern (31 bp):
AGAGTGGCTAAAATTAACAACTTACCTAACA
Found at i:41355945 original size:38 final size:37
Alignment explanation
Indices: 41355886--41355962 Score: 84
Period size: 38 Copynumber: 2.1 Consensus size: 37
41355876 AATTTTTAAA
* * *
41355886 TATATATTTTAAAATTTTTTGAGTATCTTATCTATTTT
1 TATAAATTTTAAAATTGTTTGAAT-TCTTATCTATTTT
* *
41355924 TATAAATTTTAATAA-TGTTTGAATTTTTATGTATTTT
1 TATAAATTTTAA-AATTGTTTGAATTCTTATCTATTTT
41355961 TA
1 TA
41355963 ATTTTAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
37 13 0.39
38 18 0.55
39 2 0.06
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (37 bp):
TATAAATTTTAAAATTGTTTGAATTCTTATCTATTTT
Found at i:41356222 original size:31 final size:31
Alignment explanation
Indices: 41356154--41356230 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
41356144 AATGGTAAAA
* *
41356154 TGACTAAAATTGACTACTTATCTAATGGAAG
1 TGACTAAAATTAACAACTTATCTAATGGAAG
*
41356185 TAACTAAAATTAACAACTTATCTACCAT-G-AG
1 TGACTAAAATTAACAACTTATCTA--ATGGAAG
41356216 TGACTAAAA-TAACAA
1 TGACTAAAATTAACAA
41356231 TTTTTTAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
30 6 0.15
31 31 0.77
32 1 0.03
33 2 0.05
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.29
Consensus pattern (31 bp):
TGACTAAAATTAACAACTTATCTAATGGAAG
Found at i:41361141 original size:22 final size:22
Alignment explanation
Indices: 41361116--41361160 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
41361106 TTTTCTCAAC
41361116 CTTCAACTCCGGCACCGATCCA
1 CTTCAACTCCGGCACCGATCCA
* *
41361138 CTTCCAGTCCGGCACCGATCCA
1 CTTCAACTCCGGCACCGATCCA
41361160 C
1 C
41361161 CTTCGGTCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.47, G:0.16, T:0.18
Consensus pattern (22 bp):
CTTCAACTCCGGCACCGATCCA
Found at i:41362186 original size:15 final size:15
Alignment explanation
Indices: 41362163--41362194 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
41362153 GCTTATCCAA
41362163 TCATATTGGTAGAAC
1 TCATATTGGTAGAAC
*
41362178 TCATGTTGGTAGAAC
1 TCATATTGGTAGAAC
41362193 TC
1 TC
41362195 TAAAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (15 bp):
TCATATTGGTAGAAC
Found at i:41364895 original size:194 final size:193
Alignment explanation
Indices: 41364588--41364983 Score: 729
Period size: 194 Copynumber: 2.0 Consensus size: 193
41364578 AGACCTAAAA
* *
41364588 TTTTTTCTTTGTGTTTGCCAAAATATGGTACTGATATTTAAAAAAAAAAATGATTGCTATCTTCT
1 TTTTTTATTTGTGTTCGCCAAAATATGGTACTGATATTTAAAAAAAAAAATGATTGCTATCTTCT
41364653 TTACATTAAGATCTTTACTATTAAATTTGATCGCAAAACCATTTGTGCATTTTCATTTTTGCTGT
66 TTACATTAAGATCTTTACTATTAAATTTGATCGCAAAACCATTTGTGCATTTTCATTTTTGCTGT
*
41364718 GGTGAAGTGTTGGTCATTGGCTTCTTGCGCTTTTTCACATTGTTTTCTTGAATTTAGTTTGAC
131 GGTGAAGTGTTGGTCATTGGCTTCTTGCGCTTTTTCACATTGTTTTCTTGAATATAGTTTGAC
*
41364781 TTTTTTATTTGTGTTCGCCAAAATATGGTACTGATATTTAAAAAAAAAAATGATTGCTGTCTTCT
1 TTTTTTATTTGTGTTCGCCAAAATATGGTACTGATATTTAAAAAAAAAAATGATTGCTATCTTCT
*
41364846 GTTACATTAAGATCTTTACTATTAAATTTGATTGCAAAACCATTTGTGCATTTTCATTTTTGCTG
66 -TTACATTAAGATCTTTACTATTAAATTTGATCGCAAAACCATTTGTGCATTTTCATTTTTGCTG
*
41364911 TGGTGAAGTGTTGGTCATTGGCTTCTTGCGCTTTTTCACGTTGTTTTCTTGAATATAGTTTGAC
130 TGGTGAAGTGTTGGTCATTGGCTTCTTGCGCTTTTTCACATTGTTTTCTTGAATATAGTTTGAC
41364975 TTTTTTATT
1 TTTTTTATT
41364984 GCTATTGTGT
Statistics
Matches: 196, Mismatches: 6, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
193 62 0.32
194 134 0.68
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.47
Consensus pattern (193 bp):
TTTTTTATTTGTGTTCGCCAAAATATGGTACTGATATTTAAAAAAAAAAATGATTGCTATCTTCT
TTACATTAAGATCTTTACTATTAAATTTGATCGCAAAACCATTTGTGCATTTTCATTTTTGCTGT
GGTGAAGTGTTGGTCATTGGCTTCTTGCGCTTTTTCACATTGTTTTCTTGAATATAGTTTGAC
Found at i:41375536 original size:21 final size:21
Alignment explanation
Indices: 41375512--41375581 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
41375502 GAAAAATACT
41375512 AGGTGGGTTCGGGACTATTCC
1 AGGTGGGTTCGGGACTATTCC
* * ** *
41375533 AGGTGGG-CCTGGAAAATTACT
1 AGGTGGGTTCGGGACTATT-CC
41375554 AGGTGGGTTCGGGACTATTCC
1 AGGTGGGTTCGGGACTATTCC
*
41375575 GGGTGGG
1 AGGTGGG
41375582 CCTGGAAATA
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
20 7 0.19
21 22 0.61
22 7 0.19
ACGTcount: A:0.17, C:0.16, G:0.41, T:0.26
Consensus pattern (21 bp):
AGGTGGGTTCGGGACTATTCC
Found at i:41375559 original size:42 final size:42
Alignment explanation
Indices: 41375495--41375624 Score: 181
Period size: 42 Copynumber: 3.1 Consensus size: 42
41375485 TGCTTGTGGA
* * *
41375495 GGGCTTGGAAAAATACTAGGTGGGTTCGGGACTATTCCAGGT
1 GGGCCTGGAAAATTACTAGGTGGGTTCGGGACTATTCCGGGT
41375537 GGGCCTGGAAAATTACTAGGTGGGTTCGGGACTATTCCGGGT
1 GGGCCTGGAAAATTACTAGGTGGGTTCGGGACTATTCCGGGT
* * * *
41375579 GGGCCTGG-AAATATAATCGGCGGGTTCGGAACTATTCCGGGT
1 GGGCCTGGAAAAT-TACTAGGTGGGTTCGGGACTATTCCGGGT
41375621 GGGC
1 GGGC
41375625 TTGGTGGTGG
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
41 4 0.05
42 76 0.95
ACGTcount: A:0.21, C:0.17, G:0.38, T:0.25
Consensus pattern (42 bp):
GGGCCTGGAAAATTACTAGGTGGGTTCGGGACTATTCCGGGT
Found at i:41380860 original size:39 final size:38
Alignment explanation
Indices: 41380806--41380937 Score: 201
Period size: 39 Copynumber: 3.4 Consensus size: 38
41380796 GTTTGTGTCC
41380806 TTAATTATGTCTTAGTTTAAACATCATTAATATATGTAT
1 TTAATTATGTCTTAGTTTAAACATCATTAATATATGT-T
41380845 TTAATTATGTCTTAGTTTAAACATCATTAATATATGTCT
1 TTAATTATGTCTTAGTTTAAACATCATTAATATATGT-T
* * *
41380884 TTAATTATGTCTTATTTTGAACATCATTAATATGTGTT
1 TTAATTATGTCTTAGTTTAAACATCATTAATATATGTT
41380922 TTAATTAAGTGTCTTA
1 TTAATT-A-TGTCTTA
41380938 CATTCTGACA
Statistics
Matches: 87, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
38 7 0.08
39 73 0.84
40 7 0.08
ACGTcount: A:0.33, C:0.08, G:0.09, T:0.50
Consensus pattern (38 bp):
TTAATTATGTCTTAGTTTAAACATCATTAATATATGTT
Found at i:41381895 original size:29 final size:27
Alignment explanation
Indices: 41381862--41381916 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 27
41381852 GTGATTAAAT
41381862 AAAATTGACA-CAAGCAGAATTTAAAAGAA
1 AAAATTGACAGCAAG-A-AA-TTAAAAGAA
41381891 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATTGACAGCAAGAAATTAAAAGA
41381917 TAAGTCCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 8 0.32
28 2 0.08
29 11 0.44
30 4 0.16
ACGTcount: A:0.60, C:0.09, G:0.15, T:0.16
Consensus pattern (27 bp):
AAAATTGACAGCAAGAAATTAAAAGAA
Found at i:41388638 original size:29 final size:27
Alignment explanation
Indices: 41388605--41388659 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
41388595 GTGATTAAAT
41388605 AAAATCGACA-CAAGCAGAATTTAAAAGAA
1 AAAATCGACAGCAAG-A-AA-TTAAAAGAA
*
41388634 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATCGACAGCAAGAAATTAAAAGA
41388660 TAAGTCCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 8 0.33
28 2 0.08
29 10 0.42
30 4 0.17
ACGTcount: A:0.60, C:0.11, G:0.15, T:0.15
Consensus pattern (27 bp):
AAAATCGACAGCAAGAAATTAAAAGAA
Found at i:41396899 original size:41 final size:41
Alignment explanation
Indices: 41396849--41397075 Score: 202
Period size: 41 Copynumber: 5.5 Consensus size: 41
41396839 CTTAATTATT
* *
41396849 CCCTAAATTGCACATATGTGCCCCTATTTGTAGTTCGGTAC
1 CCCTAAATTGCACATACGTGCCCCTATTTGTACTTCGGTAC
* *
41396890 CCCTGAATTGCACATACGTGCCCCTATTTTTACTTCGGTAC
1 CCCTAAATTGCACATACGTGCCCCTATTTGTACTTCGGTAC
* * * ***
41396931 CCCTAAATTGCATATATGTGCCCCTTTTTGTACTTCAAAAC
1 CCCTAAATTGCACATACGTGCCCCTATTTGTACTTCGGTAC
* * ** *
41396972 CCTTAAATTGCATATACGTGCCTTTGTTTGTACTTCGGTAC
1 CCCTAAATTGCACATACGTGCCCCTATTTGTACTTCGGTAC
* * * ** * * * *
41397013 CCATGAGTAACACCTATGTGCCCCTTTTTATACTTCGGTAC
1 CCCTAAATTGCACATACGTGCCCCTATTTGTACTTCGGTAC
* * * *
41397054 CCTTGAATAGCACTTACGTGCC
1 CCCTAAATTGCACATACGTGCC
41397076 TTGTTACAAT
Statistics
Matches: 149, Mismatches: 37, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
41 149 1.00
ACGTcount: A:0.22, C:0.28, G:0.15, T:0.35
Consensus pattern (41 bp):
CCCTAAATTGCACATACGTGCCCCTATTTGTACTTCGGTAC
Found at i:41396942 original size:82 final size:82
Alignment explanation
Indices: 41396849--41397075 Score: 256
Period size: 82 Copynumber: 2.8 Consensus size: 82
41396839 CTTAATTATT
* * *
41396849 CCCTAAATTGCACATATGTGCCCCTATTTGTAGTTCGGTACCCCTGAATTGCACATACGTGCCCC
1 CCCTAAATTGCACATATGTGCCCCTTTTTGTACTTCGGTACCCTTGAATTGCACATACGTGCCCC
*
41396914 TATTTTTACTTCGGTAC
66 TATTTGTACTTCGGTAC
* *** * * **
41396931 CCCTAAATTGCATATATGTGCCCCTTTTTGTACTTCAAAACCCTTAAATTGCATATACGTGCCTT
1 CCCTAAATTGCACATATGTGCCCCTTTTTGTACTTCGGTACCCTTGAATTGCACATACGTGCCCC
*
41396996 TGTTTGTACTTCGGTAC
66 TATTTGTACTTCGGTAC
* * * ** * * * *
41397013 CCATGAGTAACACCTATGTGCCCCTTTTTATACTTCGGTACCCTTGAATAGCACTTACGTGCC
1 CCCTAAATTGCACATATGTGCCCCTTTTTGTACTTCGGTACCCTTGAATTGCACATACGTGCC
41397076 TTGTTACAAT
Statistics
Matches: 117, Mismatches: 28, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
82 117 1.00
ACGTcount: A:0.22, C:0.28, G:0.15, T:0.35
Consensus pattern (82 bp):
CCCTAAATTGCACATATGTGCCCCTTTTTGTACTTCGGTACCCTTGAATTGCACATACGTGCCCC
TATTTGTACTTCGGTAC
Found at i:41397075 original size:123 final size:123
Alignment explanation
Indices: 41396852--41397075 Score: 272
Period size: 123 Copynumber: 1.8 Consensus size: 123
41396842 AATTATTCCC
* * * **
41396852 TAAATTGCACATATGTGCCCCTATTTGTAGTTCGGTACCCCTGAATTGCACATACGTGCCCCTAT
1 TAAATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCATGAATAACACATACGTGCCCCTAT
* *
41396917 TTTTACTTCGGTACCCCTAAATTGCATATATGTGCCCCTTTTTGTACTTCAAAACCCT
66 TTTTACTTCGGTACCCCTAAATAGCATATACGTGCCCCTTTTTGTACTTCAAAACCCT
* ** * * * *
41396975 TAAATTGCATATACGTGCCTTTGTTTGTACTTCGGTACCCATGAGTAACACCTATGTGCCCCT-T
1 TAAATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCATGAATAACACATACGTGCCCCTAT
* *
41397039 TTTATACTTCGGTACCCTTGAATAGCACT-TACGTGCC
66 TTT-TACTTCGGTACCCCTAAATAGCA-TATACGTGCC
41397076 TTGTTACAAT
Statistics
Matches: 83, Mismatches: 16, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
122 4 0.05
123 78 0.94
124 1 0.01
ACGTcount: A:0.22, C:0.27, G:0.15, T:0.36
Consensus pattern (123 bp):
TAAATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCATGAATAACACATACGTGCCCCTAT
TTTTACTTCGGTACCCCTAAATAGCATATACGTGCCCCTTTTTGTACTTCAAAACCCT
Found at i:41404889 original size:5 final size:5
Alignment explanation
Indices: 41404879--41404903 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
41404869 AAAACAAAGT
41404879 AAATA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA
41404904 GAGTTCTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:41405883 original size:14 final size:14
Alignment explanation
Indices: 41405864--41405893 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
41405854 AGTGAGAGAG
*
41405864 GAGAGAAGAGTTGT
1 GAGAGAAGAGATGT
41405878 GAGAGAAGAGATGT
1 GAGAGAAGAGATGT
41405892 GA
1 GA
41405894 ATGAGGGATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.43, T:0.17
Consensus pattern (14 bp):
GAGAGAAGAGATGT
Done.