Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 176 of 182
Found at i:53536515 original size:35 final size:35
Alignment explanation
Indices: 53536476--53536546 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
53536466 GCATGAGAAT
53536476 TTTTTTAAAAAAAACACGAGAA-TTTTGAAACACGA
1 TTTTTTAAAAAAAACACGA-AAGTTTTGAAACACGA
* *
53536511 TTTTTTTAAAAAAACACGAAAGTTTTTGAATCACGA
1 TTTTTTAAAAAAAACACGAAAG-TTTTGAAACACGA
53536547 GAATTTTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
34 2 0.06
35 18 0.56
36 12 0.38
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.32
Consensus pattern (35 bp):
TTTTTTAAAAAAAACACGAAAGTTTTGAAACACGA
Found at i:53536560 original size:35 final size:33
Alignment explanation
Indices: 53536486--53536772 Score: 148
Period size: 35 Copynumber: 8.0 Consensus size: 33
53536476 TTTTTTAAAA
**
53536486 AAAACACGAGAA-TTTTGAAACACGA-TTTTTTT
1 AAAACACGA-AATTTTTGAAACACGAGAATTTTT
*
53536518 AAAAAAACACGAAAGTTTTTGAATCACGAGAATTTTT
1 ---AAAACACGAAA-TTTTTGAAACACGAGAATTTTT
*
53536555 GAAAACCCGAAAATTTTTGAAAACACGA-AGATTTTT
1 -AAAACACG-AAATTTTTG-AAACACGAGA-ATTTTT
*
53536591 AAAACACGATAATTTTTGAAACACAAGAATTTTTTTTT
1 AAAACACGA-AATTTTTGAAACACGAGAA----TTTTT
* * * * *
53536629 AAAACACAAAATTTTTTTAAAACACGAAAAATTGT
1 AAAACACGAAA--TTTTTGAAACACGAGAATTTTT
* * * *
53536664 GAAACAAGAGAATTGTTGAAAACACGAAAATTTTT
1 AAAACACGA-AATTTTTG-AAACACGAGAATTTTT
* * *
53536699 GAAAATATGAAAATTTTTGTAAACACGAAAATTTTTTT
1 -AAAACACG-AAATTTTTG-AAACACGAGAA--TTTTT
* *
53536737 GAAACACAGAAATTTTTAGAAAACACGAAAATTTTT
1 AAAACAC-GAAATTTTT-G-AAACACGAGAATTTTT
53536773 TGAATCACTG
Statistics
Matches: 200, Mismatches: 30, Indels: 43
0.73 0.11 0.16
Matches are distributed among these distances:
34 15 0.08
35 62 0.31
36 58 0.29
37 20 0.10
38 31 0.16
39 14 0.07
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.32
Consensus pattern (33 bp):
AAAACACGAAATTTTTGAAACACGAGAATTTTT
Found at i:53536590 original size:19 final size:18
Alignment explanation
Indices: 53536521--53536772 Score: 228
Period size: 18 Copynumber: 13.9 Consensus size: 18
53536511 TTTTTTTAAA
*
53536521 AAAACACGAAAGTTTTTG
1 AAAACACGAAAATTTTTG
* *
53536539 -AATCACGAGAATTTTTG
1 AAAACACGAAAATTTTTG
*
53536556 AAAACCCGAAAATTTTTG
1 AAAACACGAAAATTTTTG
*
53536574 AAAACACGAAGATTTTT-
1 AAAACACGAAAATTTTTG
*
53536591 AAAACACGATAATTTTTG
1 AAAACACGAAAATTTTTG
* ** *
53536609 AAACACAAGAATTTTTTTTT
1 AAA-ACACGAA-AATTTTTG
*
53536629 AAAACAC-AAAATTTTTTT
1 AAAACACGAAAA-TTTTTG
* *
53536647 AAAACACGAAAAATTGTG
1 AAAACACGAAAATTTTTG
* * *
53536665 -AAACAAGAGAATTGTTG
1 AAAACACGAAAATTTTTG
53536682 AAAACACGAAAATTTTTG
1 AAAACACGAAAATTTTTG
* *
53536700 AAAATATGAAAATTTTTG
1 AAAACACGAAAATTTTTG
*
53536718 TAAACACGAAAATTTTTTTG
1 AAAACACGAAAA--TTTTTG
53536738 -AAACAC-AGAAATTTTTAG
1 AAAACACGA-AAATTTTT-G
53536756 AAAACACGAAAATTTTT
1 AAAACACGAAAATTTTT
53536773 TGAATCACTG
Statistics
Matches: 187, Mismatches: 34, Indels: 25
0.76 0.14 0.10
Matches are distributed among these distances:
17 46 0.25
18 91 0.49
19 35 0.19
20 15 0.08
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (18 bp):
AAAACACGAAAATTTTTG
Found at i:53536788 original size:56 final size:55
Alignment explanation
Indices: 53536521--53536804 Score: 222
Period size: 53 Copynumber: 5.3 Consensus size: 55
53536511 TTTTTTTAAA
* * * *
53536521 AAAACACGAAAGTTTTTG-AATCACGAGAATTTTTGAAA-ACCCGA-AA-ATTTTTG
1 AAAACACGAAA-TTTTTGAAAACACGAAAATTTTTGAAACA-CAGAGAATTTTTTTG
* *
53536574 AAAACACGAAGATTTTT-AAAACACGATAATTTTTGAAACACA-AGAATTTTTTTTT
1 AAAACACGAA-ATTTTTGAAAACACGAAAATTTTTGAAACACAGAGAA-TTTTTTTG
* * * * *
53536629 AAAACACAAAATTTTTTTAAAACACGAAAAATTGTGAAACA-AGAGAA--TTGTTG
1 AAAACACGAAA-TTTTTGAAAACACGAAAATTTTTGAAACACAGAGAATTTTTTTG
* * *
53536682 AAAACACGAAAATTTTTGAAAATATGAAAATTTTTGTAAACAC-GAAAATTTTTTTG
1 AAAACACG-AAATTTTTGAAAACACGAAAATTTTTG-AAACACAGAGAATTTTTTTG
* *
53536738 -AAACACAGAAATTTTTAGAAAACACGAAAATTTTTTGAATCACTG-GAA---TTTTG
1 AAAACAC-GAAATTTTT-GAAAACACGAAAA-TTTTTGAAACACAGAGAATTTTTTTG
53536791 AAAACACG-AATTTT
1 AAAACACGAAATTTT
53536805 GCTGCACTGG
Statistics
Matches: 189, Mismatches: 23, Indels: 39
0.75 0.09 0.16
Matches are distributed among these distances:
52 7 0.04
53 72 0.38
54 21 0.11
55 34 0.18
56 48 0.25
57 7 0.04
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (55 bp):
AAAACACGAAATTTTTGAAAACACGAAAATTTTTGAAACACAGAGAATTTTTTTG
Found at i:53537083 original size:3 final size:3
Alignment explanation
Indices: 53537060--53537228 Score: 274
Period size: 3 Copynumber: 57.0 Consensus size: 3
53537050 TTTCTCTTTT
* *
53537060 TTC TTC TT- TT- TTC TT- TT- TTC TTC TTTC TCC TTC TTC TTTC TCC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC -TTC TTC
53537103 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
53537151 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
53537199 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
53537229 AAACCCTAGT
Statistics
Matches: 158, Mismatches: 4, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
2 8 0.05
3 144 0.91
4 6 0.04
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:53538053 original size:81 final size:80
Alignment explanation
Indices: 53537869--53538634 Score: 926
Period size: 81 Copynumber: 9.8 Consensus size: 80
53537859 TTGAAAGTAT
* * * * *
53537869 CTCGGCGTGTGGCCCGAGGCTCAACTCACCTCTAGCATTATGAGTTTATTTCTG-AAAAACAGAA
1 CTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAA
*
53537933 ATTT--AAAAGATAC
66 ATTTAAAAAAAATAC
** *
53537946 CTCGGTATGTGACCCGAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTGAAAAAAACAGA
1 CTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAAAACAGA
53538011 AATTTAAAAAAAATAC
65 AATTTAAAAAAAATAC
* *
53538027 CTCGGCGTGTGGCCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTG-AAAAACAGAA
1 CTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAA
*
53538091 ATTTAAAAGAAATAC
66 ATTTAAAAAAAATAC
* *
53538106 CTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTAAAAAAAACAGA
1 CTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-GAAAAAACAGA
*
53538171 AA-TT---GAAAATAC
65 AATTTAAAAAAAATAC
* * * * *
53538183 CTCAGC--ATGACCCGAGGCTCAACTCACTTCTCGTATTATGAGTTGATTTTTTTG-AAAAACAG
1 CTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAAACAG
*
53538245 AAA-TTAAAAAAAATAT
64 AAATTTAAAAAAAATAC
* * * *
53538261 CTCGGCGTGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTTATTTTTTAAAAAATAGAA
1 CTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAA
53538326 ATTT----AAAATAC
66 ATTTAAAAAAAATAC
* * * *
53538337 CTCAGC--GTGACCCGAGGCTCAACTCACATCTCGTATTATGAGTTGATTTTTTTG-AAAAACAG
1 CTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAAACAG
* *
53538399 AAATTTAAAAGAAATAT
64 AAATTTAAAAAAAATAC
* * *
53538416 CTCGGCATGTGACCCAAGGCTCAACTCACCTCTCGCAGTATGAGTTGATTTTTTGAAAAAACAGA
1 CTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAAACAGA
53538481 AATTTAAAAAAAATAC
65 AATTTAAAAAAAATAC
* * * *
53538497 CTCGGCGTGTGGCTCGAGGCTCAACTCACCTCTTGCAATATGAGTTAATTTTTG-AAAAACAGAA
1 CTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAA
*
53538561 ATTTAAAAGAAATAC
66 ATTTAAAAAAAATAC
* * * * *
53538576 ATCGGCGTGAG-TCCGAGGCTCAACTTACCTTTCGCAATATGAGTTGATTTTTGAAAAAA
1 CTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAA
53538635 AAAATAGAAA
Statistics
Matches: 591, Mismatches: 73, Indels: 48
0.83 0.10 0.07
Matches are distributed among these distances:
74 35 0.06
75 61 0.10
76 16 0.03
77 62 0.10
78 52 0.09
79 146 0.25
80 51 0.09
81 168 0.28
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.28
Consensus pattern (80 bp):
CTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAACAGAA
ATTTAAAAAAAATAC
Found at i:53538634 original size:79 final size:78
Alignment explanation
Indices: 53537844--53538633 Score: 880
Period size: 79 Copynumber: 10.1 Consensus size: 78
53537834 TTTCTTTTTA
* * * *
53537844 TTTGAAAAACAGAAA-TTGAAAG---TATCTCGGCGTGTGGCCCGAGGCTCAACTCACCTCTAGC
1 TTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCGTG-AGCCCGAGGCTCAACTCACCTCTCGC
* *
53537905 ATTATGAGTTTATT
65 AATATGAGTTGATT
* * *
53537919 TCTGAAAAACAGAAATTTAAAAG--ATACCTCGGTATGTGA-CCCGAGGCTCAACTCACCTTTCG
1 TTTGAAAAACAGAAATTTAAAAGAAATACCTCGG--CGTGAGCCCGAGGCTCAACTCACCTCTCG
53537981 CAATATGAGTTGATT
64 CAATATGAGTTGATT
* *
53537996 TTTGAAAAAAACAGAAATTTAAAAAAAATACCTCGGCGTGTGGCCCGAGGCTCAACTCACCTCTC
1 TTTG--AAAAACAGAAATTTAAAAGAAATACCTCGGCGTG-AGCCCGAGGCTCAACTCACCTCTC
*
53538061 GTAATATGAGTTGATT
63 GCAATATGAGTTGATT
*
53538077 TTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGC
1 TTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCGTGAG-CCCGAGGCTCAACTCACCTCTCGC
*
53538142 AATATGAGTTAATT
65 AATATGAGTTGATT
* * * * *
53538156 TTTAAAAAAAACAGAAA-TT--GA-AAATACCTCAGCATGA-CCCGAGGCTCAACTCACTTCTCG
1 TTT--GAAAAACAGAAATTTAAAAGAAATACCTCGGCGTGAGCCCGAGGCTCAACTCACCTCTCG
* *
53538216 TATTATGAGTTGATTTT
64 CAATATGAGTTGA--TT
* * *
53538233 TTTGAAAAACAGAAA-TTAAAAAAAATATCTCGGCGTGTGTCCCGAGGCTCAACTCACCTCTCGC
1 TTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCGTGAG-CCCGAGGCTCAACTCACCTCTCGC
*
53538297 AATATGAGTTTATTT
65 AATATGAGTTGA-TT
* * * * *
53538312 TTTAAAAAATAGAAATTT---A-AAATACCTCAGCGTGA-CCCGAGGCTCAACTCACATCTCGTA
1 TTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCGTGAGCCCGAGGCTCAACTCACCTCTCGCA
*
53538372 TTATGAGTTGATTTT
66 ATATGAGTTGA--TT
* *
53538387 TTTGAAAAACAGAAATTTAAAAGAAATATCTCGGCATGTGA-CCCAAGGCTCAACTCACCTCTCG
1 TTTGAAAAACAGAAATTTAAAAGAAATACCTCGGC--GTGAGCCCGAGGCTCAACTCACCTCTCG
*
53538451 CAGTATGAGTTGATTT
64 CAATATGAGTTGA-TT
* * * *
53538467 TTTGAAAAAACAGAAATTTAAAAAAAATACCTCGGCGTGTGGCTCGAGGCTCAACTCACCTCTTG
1 TTTG-AAAAACAGAAATTTAAAAGAAATACCTCGGCGTG-AGCCCGAGGCTCAACTCACCTCTCG
*
53538532 CAATATGAGTTAATT
64 CAATATGAGTTGATT
* * * *
53538547 TTTGAAAAACAGAAATTTAAAAGAAATACATCGGCGTGAGTCCGAGGCTCAACTTACCTTTCGCA
1 TTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCGTGAGCCCGAGGCTCAACTCACCTCTCGCA
53538612 ATATGAGTTGATT
66 ATATGAGTTGATT
53538625 TTTGAAAAA
1 TTTGAAAAA
53538634 AAAAATAGAA
Statistics
Matches: 612, Mismatches: 72, Indels: 59
0.82 0.10 0.08
Matches are distributed among these distances:
74 32 0.05
75 78 0.13
76 19 0.03
77 64 0.10
78 57 0.09
79 157 0.26
80 49 0.08
81 156 0.25
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.28
Consensus pattern (78 bp):
TTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCGTGAGCCCGAGGCTCAACTCACCTCTCGCA
ATATGAGTTGATT
Found at i:53539491 original size:19 final size:19
Alignment explanation
Indices: 53539469--53539505 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
53539459 TTCATCTTAA
*
53539469 TTTTTTCTTTTTTTTTGTT
1 TTTTTTCTTTTTTGTTGTT
*
53539488 TTTTTTGTTTTTTGTTGT
1 TTTTTTCTTTTTTGTTGT
53539506 GTGTGTTTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.00, C:0.03, G:0.11, T:0.86
Consensus pattern (19 bp):
TTTTTTCTTTTTTGTTGTT
Found at i:53545204 original size:4 final size:4
Alignment explanation
Indices: 53545195--53545219 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
53545185 ATGTACATGT
53545195 AATG AATG AATG AATG AATG AATG A
1 AATG AATG AATG AATG AATG AATG A
53545220 CCAATGGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (4 bp):
AATG
Found at i:53546964 original size:17 final size:17
Alignment explanation
Indices: 53546914--53547126 Score: 158
Period size: 18 Copynumber: 12.0 Consensus size: 17
53546904 ATTTAAAAAA
*
53546914 AAAACACGAAAGTTTTT
1 AAAACACGAAAATTTTT
* * *
53546931 GAATCACGAGAATTTTT
1 AAAACACGAAAATTTTT
*
53546948 CAAAACCCGAAAATTTTT
1 -AAAACACGAAAATTTTT
*
53546966 GAAAACACGAAGATTTTT
1 -AAAACACGAAAATTTTT
* * *
53546984 GAAACGCGACAATTTTT
1 AAAACACGAAAATTTTT
53547001 AAAACACAAGAAAATTTTTTT
1 AAAACAC--GAAAA--TTTTT
**
53547022 AAAACAC-AATTTTTTTT
1 AAAACACGAA-AATTTTT
*
53547039 AAAACACGAAAATTTGT
1 AAAACACGAAAATTTTT
* * *
53547056 GAAACACGAGAATTGTTG
1 AAAACACGAAAATT-TTT
53547074 AAAACACGAAAATTTTT
1 AAAACACGAAAATTTTT
* *
53547091 GAAAATATGAAAATTTTT
1 -AAAACACGAAAATTTTT
* *
53547109 GTAAACACAAAAATTTTT
1 -AAAACACGAAAATTTTT
53547127 TTGAAATGCA
Statistics
Matches: 151, Mismatches: 36, Indels: 17
0.74 0.18 0.08
Matches are distributed among these distances:
17 61 0.40
18 74 0.49
19 4 0.03
21 12 0.08
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.31
Consensus pattern (17 bp):
AAAACACGAAAATTTTT
Found at i:53546982 original size:36 final size:35
Alignment explanation
Indices: 53546914--53547226 Score: 183
Period size: 35 Copynumber: 8.8 Consensus size: 35
53546904 ATTTAAAAAA
* * *
53546914 AAAACACGAAAGTTTTTG-AATCACGAGAATTTTT
1 AAAACACGAAAATTTTTGAAAACACGAAAATTTTT
* *
53546948 CAAAACCCGAAAATTTTTGAAAACACGAAGATTTTT
1 -AAAACACGAAAATTTTTGAAAACACGAAAATTTTT
* * *
53546984 GAAACGCGACAATTTTT-AAAACACAAGAAAATTTTTTT
1 AAAACACGAAAATTTTTGAAAACAC--GAAAA--TTTTT
** * *
53547022 AAAACAC-AATTTTTTTTAAAACACGAAAATTTGT
1 AAAACACGAAAATTTTTGAAAACACGAAAATTTTT
* * *
53547056 GAAACACGAGAATTGTTGAAAACACGAAAATTTTT
1 AAAACACGAAAATTTTTGAAAACACGAAAATTTTT
* * * *
53547091 GAAAATATGAAAATTTTTGTAAACACAAAAATTTTTTT
1 -AAAACACGAAAATTTTTGAAAACACGAAAA--TTTTT
* *
53547129 GAAATGCA-G-AAATTTTTAGAAAACACGAAAAATGTTT
1 -AAA-ACACGAAAATTTTT-GAAAACACG-AAAATTTTT
* * * * *
53547166 GAATCACTG-GAA-TTCTAAAAACACGAAAATTTTT
1 AAAACAC-GAAAATTTTTGAAAACACGAAAATTTTT
* * *
53547200 GAAACACTG-GAATTTTTGAAAATACGA
1 AAAACAC-GAAAATTTTTGAAAACACGA
53547227 GGATTTTTTA
Statistics
Matches: 218, Mismatches: 44, Indels: 32
0.74 0.15 0.11
Matches are distributed among these distances:
34 36 0.17
35 72 0.33
36 50 0.23
37 21 0.10
38 34 0.16
39 5 0.02
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (35 bp):
AAAACACGAAAATTTTTGAAAACACGAAAATTTTT
Found at i:53547204 original size:17 final size:17
Alignment explanation
Indices: 53546915--53547220 Score: 172
Period size: 17 Copynumber: 17.2 Consensus size: 17
53546905 TTTAAAAAAA
*
53546915 AAACACGAAAGTTTTTG
1 AAACACGAAAATTTTTG
* * *
53546932 AATCACGAGAATTTTTCA
1 AAACACGAAAATTTTT-G
*
53546950 AAACCCGAAAATTTTTG
1 AAACACGAAAATTTTTG
*
53546967 AAAACACGAAGATTTTTG
1 -AAACACGAAAATTTTTG
* * *
53546985 AAACGCGACAATTTTTA
1 AAACACGAAAATTTTTG
*
53547002 AAACACAAGAAAATTTTTTTA
1 AAACAC--GAAAA--TTTTTG
** *
53547023 AAACAC-AATTTTTTTTA
1 AAACACGAA-AATTTTTG
*
53547040 AAACACGAAAATTTGTG
1 AAACACGAAAATTTTTG
* *
53547057 AAACACGAGAATTGTTG
1 AAACACGAAAATTTTTG
53547074 AAAACACGAAAATTTTTG
1 -AAACACGAAAATTTTTG
* *
53547092 AAAATATGAAAATTTTTG
1 -AAACACGAAAATTTTTG
*
53547110 TAAACACAAAAATTTTTTTG
1 -AAACACGAAAA--TTTTTG
53547130 AAATGCA-G-AAATTTTTAG
1 AAA--CACGAAAATTTTT-G
*
53547148 AAAACACGAAAAATGTTTG
1 -AAACACG-AAAATTTTTG
* * * **
53547167 AATCACTG-GAATTCTAA
1 AAACAC-GAAAATTTTTG
53547184 AAACACGAAAATTTTTG
1 AAACACGAAAATTTTTG
*
53547201 AAACACTG-GAATTTTTG
1 AAACAC-GAAAATTTTTG
53547218 AAA
1 AAA
53547221 ATACGAGGAT
Statistics
Matches: 221, Mismatches: 47, Indels: 42
0.71 0.15 0.14
Matches are distributed among these distances:
16 1 0.00
17 99 0.45
18 79 0.36
19 15 0.07
20 13 0.06
21 14 0.06
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.31
Consensus pattern (17 bp):
AAACACGAAAATTTTTG
Found at i:53547413 original size:20 final size:19
Alignment explanation
Indices: 53547390--53547456 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 19
53547380 TAAGGCACTA
*
53547390 GAAATTTTTTTTGAAGATAC
1 GAAATTTTTTTTGAA-ACAC
*
53547410 GAAA---ATTTTGAAACAC
1 GAAATTTTTTTTGAAACAC
*
53547426 AAGAATTTTTTTTGAAAACAC
1 GA-AATTTTTTTTG-AAACAC
53547447 GAAATTTTTT
1 GAAATTTTTT
53547457 GAATATTTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
16 4 0.11
17 9 0.24
20 17 0.46
21 7 0.19
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.40
Consensus pattern (19 bp):
GAAATTTTTTTTGAAACAC
Found at i:53547437 original size:19 final size:19
Alignment explanation
Indices: 53547415--53547459 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
53547405 GATACGAAAA
*
53547415 TTTTGAAACACAAGAATTTT
1 TTTTGAAA-ACAAGAATATT
*
53547435 TTTTGAAAACACGAA-ATT
1 TTTTGAAAACAAGAATATT
53547453 TTTTGAA
1 TTTTGAA
53547460 TATTTTCGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 9 0.39
19 6 0.26
20 8 0.35
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (19 bp):
TTTTGAAAACAAGAATATT
Found at i:53547827 original size:25 final size:24
Alignment explanation
Indices: 53547799--53547853 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
53547789 TTTTTTTCCC
*
53547799 TTTTTTTCCCTTCT-TTTTCCTTTT
1 TTTTTTTTCCTTCTCTTTT-CTTTT
*
53547823 TTTTTCTTTTCTTCTCTTTTCTTTT
1 TTTTT-TTTCCTTCTCTTTTCTTTT
53547848 TTTTTT
1 TTTTTT
53547854 CTTTTTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 6 0.22
25 17 0.63
26 4 0.15
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (24 bp):
TTTTTTTTCCTTCTCTTTTCTTTT
Found at i:53547832 original size:5 final size:5
Alignment explanation
Indices: 53547813--53547864 Score: 52
Period size: 5 Copynumber: 10.2 Consensus size: 5
53547803 TTTCCCTTCT
* * *
53547813 TTTTCC TTTTT TTTTC TTTTC TTCTC TTTTC TTTTTT TTTTC TTTT- TTTTC
1 TTTT-C TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC TTTTC TTTTC TTTTC
53547864 T
1 T
53547865 GGACTGGGCT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
4 4 0.11
5 26 0.68
6 8 0.21
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:53547832 original size:30 final size:27
Alignment explanation
Indices: 53547773--53547861 Score: 101
Period size: 26 Copynumber: 3.3 Consensus size: 27
53547763 TGGGCCCCCT
**
53547773 TTTTTTTCT-TTTTTCCTTTTTTTCCC
1 TTTTTTTCTCTTTTTCCTTTTTTTTTC
53547799 TTTTTTTCCCTTCTTTTTCCTTTTTTTTTC
1 TTTTTTT--C-TCTTTTTCCTTTTTTTTTC
* *
53547829 TTTTCTTCTC-TTTTCTTTTTTTTTTC
1 TTTTTTTCTCTTTTTCCTTTTTTTTTC
53547855 TTTTTTT
1 TTTTTTT
53547862 TCTGGACTGG
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
26 28 0.52
27 2 0.04
28 2 0.04
29 1 0.02
30 21 0.39
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (27 bp):
TTTTTTTCTCTTTTTCCTTTTTTTTTC
Found at i:53547840 original size:10 final size:10
Alignment explanation
Indices: 53547771--53547864 Score: 85
Period size: 10 Copynumber: 10.0 Consensus size: 10
53547761 CTTGGGCCCC
53547771 CTTTTTTT-T
1 CTTTTTTTCT
53547780 C-TTTTTTC-
1 CTTTTTTTCT
*
53547788 CTTTTTTTCC
1 CTTTTTTTCT
*
53547798 CTTTTTTTCC
1 CTTTTTTTCT
53547808 CTTCTTTTTC-
1 CTT-TTTTTCT
*
53547818 CTTTTTTTTT
1 CTTTTTTTCT
*
53547828 CTTTTCTTCT
1 CTTTTTTTCT
*
53547838 CTTTTCTT-T
1 CTTTTTTTCT
53547847 -TTTTTTTCT
1 CTTTTTTTCT
53547856 -TTTTTTTCT
1 CTTTTTTTCT
53547865 GGACTGGGCT
Statistics
Matches: 75, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
8 13 0.17
9 24 0.32
10 32 0.43
11 6 0.08
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (10 bp):
CTTTTTTTCT
Found at i:53548023 original size:20 final size:19
Alignment explanation
Indices: 53547998--53548048 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
53547988 TTGTTGTGGC
53547998 CTTTTTTTTTCTGCTT-TTT
1 CTTTTTTTTT-TGCTTATTT
53548017 GCTTTTTTTTTTGCTTAATTT
1 -CTTTTTTTTTTGCTT-ATTT
53548038 CTTTTTTTTTT
1 CTTTTTTTTTT
53548049 TGATTGGGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.17
20 21 0.72
21 3 0.10
ACGTcount: A:0.04, C:0.12, G:0.06, T:0.78
Consensus pattern (19 bp):
CTTTTTTTTTTGCTTATTT
Found at i:53548024 original size:19 final size:19
Alignment explanation
Indices: 53548000--53548046 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
53547990 GTTGTGGCCT
53548000 TTTTTTTTCTGCTT-TTTGC
1 TTTTTTTTCTGCTTATTT-C
*
53548019 TTTTTTTTTTGCTTAATTTC
1 TTTTTTTTCTGCTT-ATTTC
53548039 TTTTTTTT
1 TTTTTTTT
53548047 TTTGATTGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 13 0.52
20 9 0.36
21 3 0.12
ACGTcount: A:0.04, C:0.11, G:0.06, T:0.79
Consensus pattern (19 bp):
TTTTTTTTCTGCTTATTTC
Found at i:53548049 original size:21 final size:20
Alignment explanation
Indices: 53547998--53548050 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
53547988 TTGTTGTGGC
*
53547998 CTTTTTTTTTCTGCTTTTTG
1 CTTTTTTTTTTTGCTTTTTG
53548018 C-TTTTTTTTTTGCTTAATTT-
1 CTTTTTTTTTTTGCTT--TTTG
53548038 CTTTTTTTTTTTG
1 CTTTTTTTTTTTG
53548051 ATTGGGCTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 13 0.45
20 2 0.07
21 14 0.48
ACGTcount: A:0.04, C:0.11, G:0.08, T:0.77
Consensus pattern (20 bp):
CTTTTTTTTTTTGCTTTTTG
Found at i:53548141 original size:17 final size:17
Alignment explanation
Indices: 53548121--53548154 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
53548111 AATAATTTTA
*
53548121 TTTTTTCTCTTTTTTCT
1 TTTTTTCTCTTCTTTCT
*
53548138 TTTTTTTTCTTCTTTCT
1 TTTTTTCTCTTCTTTCT
53548155 CCTTCTTCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTCTCTTCTTTCT
Found at i:53548143 original size:10 final size:10
Alignment explanation
Indices: 53548121--53548182 Score: 56
Period size: 10 Copynumber: 6.2 Consensus size: 10
53548111 AATAATTTTA
53548121 TTTTTTC-TC
1 TTTTTTCTTC
*
53548130 TTTTTTCTTT
1 TTTTTTCTTC
53548140 TTTTTTCTTC
1 TTTTTTCTTC
* *
53548150 TTTCTCCTTC
1 TTTTTTCTTC
53548160 TTCTTCTTCTTC
1 TT-TT-TTCTTC
*
53548172 -TTCTTCTTC
1 TTTTTTCTTC
53548181 TT
1 TT
53548183 CAAACCCTAG
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
9 13 0.31
10 22 0.52
11 2 0.05
12 5 0.12
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTTTCTTC
Found at i:53548150 original size:3 final size:3
Alignment explanation
Indices: 53548144--53548183 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
53548134 TTCTTTTTTT
*
53548144 TTC TTC TTTC TCC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
53548184 AAACCCTAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:53548564 original size:30 final size:29
Alignment explanation
Indices: 53548530--53548654 Score: 126
Period size: 30 Copynumber: 4.2 Consensus size: 29
53548520 GGCCAAAACA
*
53548530 TAATTTCAAGAACATTTAGGGGTCAAAATG
1 TAATTTCAA-AAAATTTAGGGGTCAAAATG
*
53548560 TAATTTC-AAAAATTTGATGGGTCAAAATG
1 TAATTTCAAAAAATTT-AGGGGTCAAAATG
* * * *
53548589 TAATTTTAAAAAATTTTAGGGCTTAAAATA
1 TAATTTCAAAAAA-TTTAGGGGTCAAAATG
* *
53548619 TAATTTTAGGAAAATTTAGGGGTCAAAATG
1 TAATTTCA-AAAAATTTAGGGGTCAAAATG
*
53548649 CAATTT
1 TAATTT
53548655 TTTATTTTTA
Statistics
Matches: 79, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
28 6 0.08
29 19 0.24
30 47 0.59
31 7 0.09
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (29 bp):
TAATTTCAAAAAATTTAGGGGTCAAAATG
Found at i:53548655 original size:30 final size:28
Alignment explanation
Indices: 53548543--53548655 Score: 127
Period size: 30 Copynumber: 3.9 Consensus size: 28
53548533 TTTCAAGAAC
*
53548543 ATTTAGGGGTCAAAATGTAATTTCAAAA
1 ATTTAGGGGTCAAAATGTAATTTTAAAA
*
53548571 ATTTGATGGGTCAAAATGTAATTTTAAAAA
1 ATTT-AGGGGTCAAAATGTAATTTT-AAAA
* * *
53548601 ATTTTAGGGCTTAAAATATAATTTTAGGAAA
1 A-TTTAGGGGTCAAAATGTAATTTTA--AAA
*
53548632 ATTTAGGGGTCAAAATGCAATTTT
1 ATTTAGGGGTCAAAATGTAATTTT
53548656 TTATTTTTAT
Statistics
Matches: 70, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
28 4 0.06
29 19 0.27
30 40 0.57
31 7 0.10
ACGTcount: A:0.41, C:0.05, G:0.18, T:0.36
Consensus pattern (28 bp):
ATTTAGGGGTCAAAATGTAATTTTAAAA
Found at i:53561153 original size:22 final size:21
Alignment explanation
Indices: 53561123--53561164 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
53561113 AAAAAAACAT
*
53561123 TTTAATTTTCCTATTATTATTA
1 TTTAATTTTACTATT-TTATTA
*
53561145 TTTATTTTTACTATTTTATT
1 TTTAATTTTACTATTTTATT
53561165 TTTGCAGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTAATTTTACTATTTTATTA
Found at i:53564333 original size:18 final size:19
Alignment explanation
Indices: 53564312--53564351 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
53564302 TAAATCTACT
53564312 AAGGAAT-GTAAAAATAGA
1 AAGGAATGGTAAAAATAGA
* *
53564330 AAGGATTGGTCAAAATAGA
1 AAGGAATGGTAAAAATAGA
53564349 AAG
1 AAG
53564352 ATTCAATTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.55, C:0.03, G:0.25, T:0.17
Consensus pattern (19 bp):
AAGGAATGGTAAAAATAGA
Found at i:53566902 original size:13 final size:13
Alignment explanation
Indices: 53566884--53566909 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53566874 CCCGTAGGGC
53566884 CTGCTCCTGCGGT
1 CTGCTCCTGCGGT
53566897 CTGCTCCTGCGGT
1 CTGCTCCTGCGGT
53566910 GGCGATGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.38, G:0.31, T:0.31
Consensus pattern (13 bp):
CTGCTCCTGCGGT
Found at i:53569505 original size:21 final size:21
Alignment explanation
Indices: 53569479--53569519 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
53569469 ATCTGCTCAA
* *
53569479 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
53569500 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
53569520 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:53571254 original size:124 final size:124
Alignment explanation
Indices: 53571094--53571999 Score: 1803
Period size: 124 Copynumber: 7.3 Consensus size: 124
53571084 TAGTGTTTTC
53571094 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGA
1 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGA
53571159 GAGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCATT
66 GAGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCATT
53571218 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGA
1 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGA
53571283 GAGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCATT
66 GAGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCATT
53571342 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGA
1 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGA
53571407 GAGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCATT
66 GAGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCATT
53571466 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGA
1 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGA
53571531 GAGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCATT
66 GAGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCATT
53571590 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGA
1 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGA
53571655 GAGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCATT
66 GAGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCATT
53571714 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGA
1 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGA
53571779 GAGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCATT
66 GAGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCATT
53571838 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGA
1 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGA
53571903 GAGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCATT
66 GAGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCATT
*
53571962 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGA
1 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGA
53572000 AATTCTTTGG
Statistics
Matches: 781, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
124 781 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (124 bp):
GATCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGA
GAGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCATT
Found at i:53573337 original size:21 final size:21
Alignment explanation
Indices: 53573311--53573357 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
53573301 GGTATAGCAG
*
53573311 GATCACCACATGCCCCAATCT
1 GATCACCACATACCCCAATCT
** *
53573332 GATCACTTCATACCCCATTCT
1 GATCACCACATACCCCAATCT
53573353 GATCA
1 GATCA
53573358 ATATTTGAGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.38, G:0.09, T:0.26
Consensus pattern (21 bp):
GATCACCACATACCCCAATCT
Found at i:53574370 original size:9 final size:9
Alignment explanation
Indices: 53574358--53574386 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
53574348 CATATTTTTA
53574358 TTTTGATTT
1 TTTTGATTT
53574367 TTTTGA-TT
1 TTTTGATTT
53574375 TTTTGATTT
1 TTTTGATTT
53574384 TTT
1 TTT
53574387 GAATTCATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.79
Consensus pattern (9 bp):
TTTTGATTT
Found at i:53574376 original size:7 final size:8
Alignment explanation
Indices: 53574358--53574388 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
53574348 CATATTTTTA
53574358 TTTTGATTT
1 TTTTGA-TT
53574367 TTTTGATT
1 TTTTGATT
53574375 TTTTGATT
1 TTTTGATT
53574383 TTTTGA
1 TTTTGA
53574389 ATTCATGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 16 0.73
9 6 0.27
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.74
Consensus pattern (8 bp):
TTTTGATT
Found at i:53576996 original size:19 final size:20
Alignment explanation
Indices: 53576967--53577015 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
53576957 CACTTCGTGA
* *
53576967 AAATCTAATGCATATG-ATG
1 AAATGTAATGCAGATGCATG
*
53576986 CAATGTAATGCAGATGCATG
1 AAATGTAATGCAGATGCATG
53577006 AAATG-AATGC
1 AAATGTAATGC
53577016 CTAAAGAGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (20 bp):
AAATGTAATGCAGATGCATG
Found at i:53578553 original size:21 final size:21
Alignment explanation
Indices: 53578527--53578573 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
53578517 GGTATAGCAG
*
53578527 GATCACCACATGCCCCAATCT
1 GATCACCACATACCCCAATCT
** *
53578548 GATCACTTCATACCCCATTCT
1 GATCACCACATACCCCAATCT
53578569 GATCA
1 GATCA
53578574 ATATTTGAGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.38, G:0.09, T:0.26
Consensus pattern (21 bp):
GATCACCACATACCCCAATCT
Found at i:53579586 original size:9 final size:9
Alignment explanation
Indices: 53579574--53579602 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
53579564 CATATTTTTA
53579574 TTTTGATTT
1 TTTTGATTT
53579583 TTTTGA-TT
1 TTTTGATTT
53579591 TTTTGATTT
1 TTTTGATTT
53579600 TTT
1 TTT
53579603 GAATTCATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.79
Consensus pattern (9 bp):
TTTTGATTT
Found at i:53579592 original size:7 final size:8
Alignment explanation
Indices: 53579574--53579604 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
53579564 CATATTTTTA
53579574 TTTTGATTT
1 TTTTGA-TT
53579583 TTTTGATT
1 TTTTGATT
53579591 TTTTGATT
1 TTTTGATT
53579599 TTTTGA
1 TTTTGA
53579605 ATTCATGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 16 0.73
9 6 0.27
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.74
Consensus pattern (8 bp):
TTTTGATT
Found at i:53582212 original size:19 final size:20
Alignment explanation
Indices: 53582183--53582231 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
53582173 CACTTCGTGA
* *
53582183 AAATCTAATGCATATG-ATG
1 AAATGTAATGCAGATGCATG
*
53582202 CAATGTAATGCAGATGCATG
1 AAATGTAATGCAGATGCATG
53582222 AAATG-AATGC
1 AAATGTAATGC
53582232 CTAAAGAGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (20 bp):
AAATGTAATGCAGATGCATG
Found at i:53584750 original size:3 final size:3
Alignment explanation
Indices: 53584739--53584802 Score: 85
Period size: 3 Copynumber: 21.3 Consensus size: 3
53584729 CAATAATACC
* * *
53584739 AAT ACT AAT AAT AGT AA- AGAT GAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
53584784 AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
53584803 GCAAAAGTAC
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
2 1 0.02
3 52 0.98
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:53585257 original size:100 final size:100
Alignment explanation
Indices: 53585153--53585351 Score: 382
Period size: 100 Copynumber: 2.0 Consensus size: 100
53585143 ACGGCGTCGC
53585153 TTCACGTTTAGTATAAAAATAAAAAAAAAAACCAAAAAAACAATCAGTTC-TCATTTTACAAAAA
1 TTCACGTTTAGTATAAAAAT-AAAAAAAAAACCAAAAAAACAATCAGTTCTTCATTTTACAAAAA
53585217 AAACAGAGAAGGAGGGAGAGAGAGGGATGCTCTCTT
65 AAACAGAGAAGGAGGGAGAGAGAGGGATGCTCTCTT
53585253 TTCACGTTTAGTATAAAAATAAAAAAAAAACCAAAAAAACAATCAGTTCTTCATTTTACAAAAAA
1 TTCACGTTTAGTATAAAAATAAAAAAAAAACCAAAAAAACAATCAGTTCTTCATTTTACAAAAAA
53585318 AACAGAGAAGGAGGGAGAGAGAGGGATGCTCTCT
66 AACAGAGAAGGAGGGAGAGAGAGGGATGCTCTCT
53585352 CAGGCCACAA
Statistics
Matches: 98, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
99 29 0.30
100 69 0.70
ACGTcount: A:0.49, C:0.13, G:0.17, T:0.21
Consensus pattern (100 bp):
TTCACGTTTAGTATAAAAATAAAAAAAAAACCAAAAAAACAATCAGTTCTTCATTTTACAAAAAA
AACAGAGAAGGAGGGAGAGAGAGGGATGCTCTCTT
Found at i:53585468 original size:97 final size:97
Alignment explanation
Indices: 53585302--53585495 Score: 388
Period size: 97 Copynumber: 2.0 Consensus size: 97
53585292 CAATCAGTTC
53585302 TTCATTTTACAAAAAAAACAGAGAAGGAGGGAGAGAGAGGGATGCTCTCTCAGGCCACAAGTCTG
1 TTCATTTTACAAAAAAAACAGAGAAGGAGGGAGAGAGAGGGATGCTCTCTCAGGCCACAAGTCTG
53585367 GCCTGGGACTCCGGCGAGCCTCCGCCGTAGCG
66 GCCTGGGACTCCGGCGAGCCTCCGCCGTAGCG
53585399 TTCATTTTACAAAAAAAACAGAGAAGGAGGGAGAGAGAGGGATGCTCTCTCAGGCCACAAGTCTG
1 TTCATTTTACAAAAAAAACAGAGAAGGAGGGAGAGAGAGGGATGCTCTCTCAGGCCACAAGTCTG
53585464 GCCTGGGACTCCGGCGAGCCTCCGCCGTAGCG
66 GCCTGGGACTCCGGCGAGCCTCCGCCGTAGCG
53585496 CCACCGTGTG
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 97 1.00
ACGTcount: A:0.28, C:0.25, G:0.31, T:0.16
Consensus pattern (97 bp):
TTCATTTTACAAAAAAAACAGAGAAGGAGGGAGAGAGAGGGATGCTCTCTCAGGCCACAAGTCTG
GCCTGGGACTCCGGCGAGCCTCCGCCGTAGCG
Found at i:53586946 original size:44 final size:44
Alignment explanation
Indices: 53586880--53587319 Score: 219
Period size: 44 Copynumber: 10.3 Consensus size: 44
53586870 CCTTTAATCC
* * *
53586880 GCTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGACCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTGACCT
* * **
53586924 GCTCCGCTGTAATCTCAGGGAGATAAGATCTGA-AATTCTTTGGTCT
1 GCTCCACTGTAATCTCAGGGAGATAAGAT-T-ACTA-TCTTTGACCT
* * * * *
53586970 GTTCCACTATAATCTCAGGGAGATAAGA--CCTGA--TGTGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACT-ATCTTTGACCT
* * * *
53587011 TCTCTACTGTAA-CTTCAGAGAGATAAGA-T-C---CTTTAATCC-
1 GCTCCACTGTAATC-TCAGGGAGATAAGATTACTATCTTTGA-CCT
* * *
53587050 GCTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGACCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTGACCT
* * **
53587094 GCTCCGCTGTAATCTCAGGGAGATAAGATCTGA-AATTCTTTGGTCT
1 GCTCCACTGTAATCTCAGGGAGATAAGAT-T-ACTA-TCTTTGACCT
* * * * *
53587140 GTTCCACTATAATCTCAGGGAGATAAGA--CCTGA--TGTGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACT-ATCTTTGACCT
* * * *
53587181 TCTCTACTGTAA-CTTCAGAGAGATAAGA-T-C---CTTTAATCC-
1 GCTCCACTGTAATC-TCAGGGAGATAAGATTACTATCTTTGA-CCT
* * * * *
53587220 GCTCCATTGTAATCTCAAGGAGATAGGATTACTATCATTGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTGACCT
* * * *
53587264 GCTCCGCTGTAATCTCAGGGAGATAAGATCTGCT-TCTTTAACCA
1 GCTCCACTGTAATCTCAGGGAGATAAGAT-TACTATCTTTGACCT
53587308 GCTCCACTGTAA
1 GCTCCACTGTAA
53587320 CCAATGAAGG
Statistics
Matches: 293, Mismatches: 70, Indels: 66
0.68 0.16 0.15
Matches are distributed among these distances:
39 46 0.16
40 8 0.03
41 58 0.20
43 3 0.01
44 103 0.35
45 7 0.02
46 68 0.23
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (44 bp):
GCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTGACCT
Found at i:53587040 original size:87 final size:87
Alignment explanation
Indices: 53586930--53587210 Score: 294
Period size: 87 Copynumber: 3.3 Consensus size: 87
53586920 ACCTGCTCCG
*
53586930 CTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCACTATAATCTCAGGGAGATA
1 CTGTAATCTCAGAGAGATAAGATCTGAAATTCTTTGGTCTGTTCCACTATAATCTCAGGGAGATA
53586995 AGACCTGATGTGATCTTCTCTA
66 AGACCTGATGTGATCTTCTCTA
** * * * * *
53587017 CTGTAA-CTTCAGAGAGATAAGATC-------CTTTAATCCGCTCCATTGTAATCTCAAGGAGAT
1 CTGTAATC-TCAGAGAGATAAGATCTGAAATTCTTTGGTCTGTTCCACTATAATCTCAGGGAGAT
* * * * * **
53587074 AGGATTACT-ATCTTTGACCTGCTCCG
65 AAGA--CCTGA--TGTGATCTTCTCTA
*
53587100 CTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCACTATAATCTCAGGGAGATA
1 CTGTAATCTCAGAGAGATAAGATCTGAAATTCTTTGGTCTGTTCCACTATAATCTCAGGGAGATA
53587165 AGACCTGATGTGATCTTCTCTA
66 AGACCTGATGTGATCTTCTCTA
53587187 CTGTAA-CTTCAGAGAGATAAGATC
1 CTGTAATC-TCAGAGAGATAAGATC
53587211 CTTTAATCCG
Statistics
Matches: 148, Mismatches: 31, Indels: 30
0.71 0.15 0.14
Matches are distributed among these distances:
80 29 0.20
81 1 0.01
82 2 0.01
83 30 0.20
84 1 0.01
86 2 0.01
87 51 0.34
88 2 0.01
89 1 0.01
90 29 0.20
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (87 bp):
CTGTAATCTCAGAGAGATAAGATCTGAAATTCTTTGGTCTGTTCCACTATAATCTCAGGGAGATA
AGACCTGATGTGATCTTCTCTA
Found at i:53587091 original size:170 final size:170
Alignment explanation
Indices: 53586809--53587295 Score: 956
Period size: 170 Copynumber: 2.9 Consensus size: 170
53586799 TGCTCCGCTG
53586809 TAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCCTT
1 TAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCCTT
53586874 TAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGACCTGCTCCGCTGTAATCT
66 TAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGACCTGCTCCGCTGTAATCT
53586939 CAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCACTA
131 CAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCACTA
53586979 TAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCCTT
1 TAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCCTT
53587044 TAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGACCTGCTCCGCTGTAATCT
66 TAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGACCTGCTCCGCTGTAATCT
53587109 CAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCACTA
131 CAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCACTA
53587149 TAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCCTT
1 TAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCCTT
* *
53587214 TAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCATTGATCTGCTCCGCTGTAATCT
66 TAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGACCTGCTCCGCTGTAATCT
53587279 CAGGGAGATAAGATCTG
131 CAGGGAGATAAGATCTG
53587296 CTTCTTTAAC
Statistics
Matches: 315, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
170 315 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (170 bp):
TAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCCTT
TAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGACCTGCTCCGCTGTAATCT
CAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCACTA
Found at i:53588464 original size:21 final size:21
Alignment explanation
Indices: 53588438--53588484 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
53588428 GGTATAGCAG
*
53588438 GATCACCACATGCCCCAATCT
1 GATCACCACATACCCCAATCT
** *
53588459 GATCACTTCATACCCCATTCT
1 GATCACCACATACCCCAATCT
53588480 GATCA
1 GATCA
53588485 ATATTTGAGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.38, G:0.09, T:0.26
Consensus pattern (21 bp):
GATCACCACATACCCCAATCT
Found at i:53589497 original size:9 final size:9
Alignment explanation
Indices: 53589485--53589513 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
53589475 CATATTTTTA
53589485 TTTTGATTT
1 TTTTGATTT
53589494 TTTTGA-TT
1 TTTTGATTT
53589502 TTTTGATTT
1 TTTTGATTT
53589511 TTT
1 TTT
53589514 GAATTCATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.79
Consensus pattern (9 bp):
TTTTGATTT
Found at i:53589503 original size:7 final size:8
Alignment explanation
Indices: 53589485--53589515 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
53589475 CATATTTTTA
53589485 TTTTGATTT
1 TTTTGA-TT
53589494 TTTTGATT
1 TTTTGATT
53589502 TTTTGATT
1 TTTTGATT
53589510 TTTTGA
1 TTTTGA
53589516 ATTCATGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 16 0.73
9 6 0.27
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.74
Consensus pattern (8 bp):
TTTTGATT
Found at i:53592123 original size:19 final size:20
Alignment explanation
Indices: 53592094--53592142 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
53592084 CACTTCGTGA
* *
53592094 AAATCTAATGCATATG-ATG
1 AAATGTAATGCAGATGCATG
*
53592113 CAATGTAATGCAGATGCATG
1 AAATGTAATGCAGATGCATG
53592133 AAATG-AATGC
1 AAATGTAATGC
53592143 CTAAAGAGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (20 bp):
AAATGTAATGCAGATGCATG
Found at i:53594202 original size:18 final size:19
Alignment explanation
Indices: 53594179--53594217 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
53594169 TATAAAGAAA
53594179 AAAAATATG-CATATATAT
1 AAAAATATGACATATATAT
53594197 AAAAATATGTACATATATAT
1 AAAAATATG-ACATATATAT
53594217 A
1 A
53594218 TAGGTGTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
20 10 0.53
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.33
Consensus pattern (19 bp):
AAAAATATGACATATATAT
Found at i:53594664 original size:3 final size:3
Alignment explanation
Indices: 53594653--53594699 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
53594643 CAATAATACC
* * *
53594653 AAT ACT AAT AAT AGT AA- AGAT GAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
53594698 AA
1 AA
53594700 NNNNNNNNNN
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
2 1 0.03
3 35 0.97
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:53595591 original size:18 final size:19
Alignment explanation
Indices: 53595558--53595596 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
53595548 ATGTTTTAAT
53595558 AAATAAAAATTATTTTGAA
1 AAATAAAAATTATTTTGAA
* *
53595577 AAATATAAA-TATTTTTAA
1 AAATAAAAATTATTTTGAA
53595595 AA
1 AA
53595597 GTTTTAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
AAATAAAAATTATTTTGAA
Found at i:53602081 original size:22 final size:22
Alignment explanation
Indices: 53602056--53602123 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
53602046 CACTTAAAAG
53602056 TTTAATCTGGTTTAACTCTAAA
1 TTTAATCTGGTTTAACTCTAAA
53602078 TTT-A-C----TTAACT-TAAAA
1 TTTAATCTGGTTTAACTCT-AAA
53602094 GTTTAATCTGGTTTAACTCTAAA
1 -TTTAATCTGGTTTAACTCTAAA
53602117 TTTAATC
1 TTTAATC
53602124 AAGAATAGCC
Statistics
Matches: 37, Mismatches: 0, Indels: 18
0.67 0.00 0.33
Matches are distributed among these distances:
15 1 0.03
16 9 0.24
17 3 0.08
18 1 0.03
19 1 0.03
20 1 0.03
21 1 0.03
22 10 0.27
23 9 0.24
24 1 0.03
ACGTcount: A:0.34, C:0.13, G:0.07, T:0.46
Consensus pattern (22 bp):
TTTAATCTGGTTTAACTCTAAA
Found at i:53609888 original size:27 final size:27
Alignment explanation
Indices: 53609841--53609899 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
53609831 ATTAAATTAG
* * * *
53609841 TTTATAAATTCACATATTTTAATAA-T
1 TTTATAAATTAAAATAATTTAAAAACT
53609867 TTTATAAAATTAAAATAATTTAAAAACT
1 TTTAT-AAATTAAAATAATTTAAAAACT
53609895 TTTAT
1 TTTAT
53609900 TATATATCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 5 0.19
27 16 0.59
28 6 0.22
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (27 bp):
TTTATAAATTAAAATAATTTAAAAACT
Found at i:53611919 original size:20 final size:20
Alignment explanation
Indices: 53611877--53611921 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
53611867 AAATTTTGTT
*
53611877 ATAATTTTAATACTTTTTTAA
1 ATAATTTTAATAC-TTTTAAA
53611898 ATAATTTTAATGA-TTTTAAA
1 ATAATTTTAAT-ACTTTTAAA
53611918 ATAA
1 ATAA
53611922 AAAATTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 10 0.45
21 11 0.50
22 1 0.05
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
ATAATTTTAATACTTTTAAA
Found at i:53611966 original size:26 final size:25
Alignment explanation
Indices: 53611912--53611966 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
53611902 TTTTAATGAT
* * * *
53611912 TTTAAAATAAAAAATTATTTTATTT
1 TTTAAAATAAAAAATTAATTAAATG
53611937 TTTAAAATTAAAAAATTAATTAAATG
1 TTTAAAA-TAAAAAATTAATTAAATG
53611963 TTTA
1 TTTA
53611967 TGTGGAATTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
TTTAAAATAAAAAATTAATTAAATG
Found at i:53611997 original size:22 final size:22
Alignment explanation
Indices: 53611972--53612014 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
53611962 GTTTATGTGG
53611972 AATTCACGTGGCAATCCATGTA
1 AATTCACGTGGCAATCCATGTA
53611994 AATTCACGTGGCAATCCATGT
1 AATTCACGTGGCAATCCATGT
53612015 GAATGTCATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (22 bp):
AATTCACGTGGCAATCCATGTA
Found at i:53619770 original size:42 final size:40
Alignment explanation
Indices: 53619711--53619791 Score: 144
Period size: 42 Copynumber: 2.0 Consensus size: 40
53619701 CCCGCGATCA
53619711 TGTTAGAATAAACTACCCCTTTAGTACTCTGTCATTTATTGT
1 TGTTAGAATAAACTACCCCTTTAGTA--CTGTCATTTATTGT
53619753 TGTTAGAATAAACTACCCCTTTAGTACTGTCATTTATTG
1 TGTTAGAATAAACTACCCCTTTAGTACTGTCATTTATTG
53619792 GTGTAATCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
40 13 0.33
42 26 0.67
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (40 bp):
TGTTAGAATAAACTACCCCTTTAGTACTGTCATTTATTGT
Found at i:53625199 original size:144 final size:144
Alignment explanation
Indices: 53624936--53625221 Score: 448
Period size: 144 Copynumber: 2.0 Consensus size: 144
53624926 TGTTCTTTAT
* *
53624936 ACACACTCGGGTAACCATCTCTTTTATTATTTTCAAGTATTGTATTGTTATTGAGTGAGCTTTAT
1 ACACACTCGGGTAACCATCTCTTTTATTATTTTCAAGTATTGTATTGTCATTGAGCGAGCTTTAT
** *
53625001 CATTGTAATATCTTCCTTGAGAGGTGTCTTTAATCATTGTTATTATTTAACATATTTGTAAGGGG
66 CATTGTAATATCTTCCTTGAGAGACGTCTTCAATCATTGTTATTATTTAACATATTTGTAAGGGG
53625066 TTGCTTAAGGTTAC
131 TTGCTTAAGGTTAC
* * * *
53625080 ACACACTTGGGTAACCATCTCTTTTATTCTTTTCAATTGTTGTATT-TCCATTGAGCGAGCTTTA
1 ACACACTCGGGTAACCATCTCTTTTATTATTTTCAAGTATTGTATTGT-CATTGAGCGAGCTTTA
* *
53625144 TCATTGTAATATCTTCCTTGCGAGACGTCTTCAATCATTGTTATTATTTATCATATTTGTAAGGG
65 TCATTGTAATATCTTCCTTGAGAGACGTCTTCAATCATTGTTATTATTTAACATATTTGTAAGGG
*
53625209 TTTGCTTAAGGTT
130 GTTGCTTAAGGTT
53625222 TTTGAGTAGA
Statistics
Matches: 129, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
143 1 0.01
144 128 0.99
ACGTcount: A:0.24, C:0.15, G:0.16, T:0.45
Consensus pattern (144 bp):
ACACACTCGGGTAACCATCTCTTTTATTATTTTCAAGTATTGTATTGTCATTGAGCGAGCTTTAT
CATTGTAATATCTTCCTTGAGAGACGTCTTCAATCATTGTTATTATTTAACATATTTGTAAGGGG
TTGCTTAAGGTTAC
Found at i:53626391 original size:29 final size:29
Alignment explanation
Indices: 53626353--53626439 Score: 165
Period size: 29 Copynumber: 3.0 Consensus size: 29
53626343 CAATTTTATG
53626353 TTAATAATATATTTTAGCATTTTTAAATA
1 TTAATAATATATTTTAGCATTTTTAAATA
53626382 TTAATAATATATTTTAGCATTTTTAAATA
1 TTAATAATATATTTTAGCATTTTTAAATA
*
53626411 TTAATAATATATTTTAGCATCTTTAAATA
1 TTAATAATATATTTTAGCATTTTTAAATA
53626440 ATCTTCTTAA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 57 1.00
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (29 bp):
TTAATAATATATTTTAGCATTTTTAAATA
Found at i:53632184 original size:18 final size:19
Alignment explanation
Indices: 53632147--53632184 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
53632137 TAATTAAATA
* *
53632147 AAAAATTAAATTTATTTAT
1 AAAAATAAAATTTATATAT
53632166 AAAAATAAAATTT-TATAT
1 AAAAATAAAATTTATATAT
53632184 A
1 A
53632185 CATTTAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAAATAAAATTTATATAT
Found at i:53635344 original size:61 final size:61
Alignment explanation
Indices: 53635274--53635395 Score: 208
Period size: 61 Copynumber: 2.0 Consensus size: 61
53635264 CCAAAACAAG
* * * *
53635274 GGATGTCAGCTGTTTTCCAAGAAATTAGTAGTGGGAATGTTTCTGTAGGTAATCCTCTTTC
1 GGATGTCAGCTGTTTGCCAAGAAACTAGTAGTGGGAATGTCTCTGCAGGTAATCCTCTTTC
53635335 GGATGTCAGCTGTTTGCCAAGAAACTAGTAGTGGGAATGTCTCTGCAGGTAATCCTCTTTC
1 GGATGTCAGCTGTTTGCCAAGAAACTAGTAGTGGGAATGTCTCTGCAGGTAATCCTCTTTC
53635396 CCTCTCTCTC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.34
Consensus pattern (61 bp):
GGATGTCAGCTGTTTGCCAAGAAACTAGTAGTGGGAATGTCTCTGCAGGTAATCCTCTTTC
Found at i:53639267 original size:14 final size:14
Alignment explanation
Indices: 53639248--53639282 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
53639238 CCCATTCTGT
*
53639248 TGCGGTGTTCCACG
1 TGCGGTGTTCCACC
53639262 TGCGGTGTTCCACC
1 TGCGGTGTTCCACC
53639276 TGCGGTG
1 TGCGGTG
53639283 AAGTGCCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.06, C:0.29, G:0.37, T:0.29
Consensus pattern (14 bp):
TGCGGTGTTCCACC
Found at i:53651219 original size:15 final size:15
Alignment explanation
Indices: 53651199--53651241 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
53651189 TCACCACTCT
53651199 TAATTATAAAAAAAA
1 TAATTATAAAAAAAA
*
53651214 TAATTATAATAAAAA
1 TAATTATAAAAAAAA
*
53651229 TAATAATAAAAAA
1 TAATTATAAAAAA
53651242 TCTTAGGGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
TAATTATAAAAAAAA
Found at i:53661966 original size:60 final size:60
Alignment explanation
Indices: 53661874--53662000 Score: 166
Period size: 60 Copynumber: 2.1 Consensus size: 60
53661864 CTAAAACTAA
* * ** * *
53661874 AAAAAATCAATAAATTTAGCCATTAATGTTTACAAAATTTGTCATTTGAGTTTGAATTCT
1 AAAAATTCAATAAATTTAGCCATCAACATTTACAAAATTTATCATTTGAATTTGAATTCT
* *
53661934 AAAAATTCAATAAATTTAGCGC-TCAACATTTACAAAATTTATCATTTTAATTTTAATTCT
1 AAAAATTCAATAAATTTAGC-CATCAACATTTACAAAATTTATCATTTGAATTTGAATTCT
53661994 AAAAATT
1 AAAAATT
53662001 TTTAAAAAAT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 57 0.98
61 1 0.02
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (60 bp):
AAAAATTCAATAAATTTAGCCATCAACATTTACAAAATTTATCATTTGAATTTGAATTCT
Found at i:53662859 original size:60 final size:60
Alignment explanation
Indices: 53662727--53662843 Score: 155
Period size: 60 Copynumber: 2.0 Consensus size: 60
53662717 TTAGAAACAA
* * * * * *
53662727 AACTAAATTAACAAATTTTATAAATGTTGAGGGCTAAATCTATTGATTTTTTTGAATTAG
1 AACTAAATTGATAAATTTTATAAATATTGAAGGCTAAATCTATTGATATTTTTAAATTAG
* *
53662787 AACTAAATTGATAAATTTTATAAATATTGAAGGCTAAATTTTTTGA-ATTTTTAAATT
1 AACTAAATTGATAAATTTTATAAATATTGAAGGCTAAATCTATTGATATTTTTAAATT
53662844 TAGGATCAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
59 9 0.18
60 40 0.82
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (60 bp):
AACTAAATTGATAAATTTTATAAATATTGAAGGCTAAATCTATTGATATTTTTAAATTAG
Found at i:53666762 original size:12 final size:12
Alignment explanation
Indices: 53666745--53666773 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
53666735 GAGTTGACTC
53666745 TGGTGATGGTGG
1 TGGTGATGGTGG
53666757 TGGTGATGGTGG
1 TGGTGATGGTGG
53666769 TGGTG
1 TGGTG
53666774 GTGAAGAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.00, G:0.59, T:0.34
Consensus pattern (12 bp):
TGGTGATGGTGG
Found at i:53666766 original size:18 final size:18
Alignment explanation
Indices: 53666689--53666776 Score: 58
Period size: 18 Copynumber: 5.1 Consensus size: 18
53666679 CTTAGATGGG
* * *
53666689 GGTGGTGGTGACGGTGGC
1 GGTGATGGTGATGGTGGT
53666707 GGTGATGGTGATGGTGG-
1 GGTGATGGTGATGGTGGT
* * *
53666724 GG-G-TGGCGATGGAGTT
1 GGTGATGGTGATGGTGGT
* *
53666740 GACT-CTGGTGATGGTGGT
1 G-GTGATGGTGATGGTGGT
*
53666758 GGTGATGGTGGTGGTGGT
1 GGTGATGGTGATGGTGGT
53666776 G
1 G
53666777 AAGAAGAAGT
Statistics
Matches: 53, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
15 9 0.17
16 2 0.04
17 3 0.06
18 39 0.74
ACGTcount: A:0.09, C:0.06, G:0.57, T:0.28
Consensus pattern (18 bp):
GGTGATGGTGATGGTGGT
Found at i:53670347 original size:21 final size:21
Alignment explanation
Indices: 53670306--53670347 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
53670296 TGTTGAAGTC
* *
53670306 GTAATTAGTTATTAGTTGATT
1 GTAATTAGTTATCAGTCGATT
53670327 GTAATTA-TTATCAGTACGATT
1 GTAATTAGTTATCAGT-CGATT
53670348 TTTTTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.48
Consensus pattern (21 bp):
GTAATTAGTTATCAGTCGATT
Found at i:53684172 original size:20 final size:19
Alignment explanation
Indices: 53684129--53684179 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
53684119 CTTGAACCCA
* *
53684129 GAACCTTAAATTTAAACTT
1 GAACCTTAAACTCAAACTT
*
53684148 CAACCTTAAACTCATAACTT
1 GAACCTTAAACTCA-AACTT
*
53684168 GAACCTCAAACT
1 GAACCTTAAACT
53684180 TGAATTGATG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.41, C:0.25, G:0.04, T:0.29
Consensus pattern (19 bp):
GAACCTTAAACTCAAACTT
Found at i:53687172 original size:6 final size:7
Alignment explanation
Indices: 53687142--53687170 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
53687132 TAGAAACACA
53687142 GAGAAAG
1 GAGAAAG
53687149 GAGAAAG
1 GAGAAAG
53687156 GAGAAAG
1 GAGAAAG
53687163 GA-AAAG
1 GAGAAAG
53687169 GA
1 GA
53687171 AAGCGTGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (7 bp):
GAGAAAG
Found at i:53688770 original size:18 final size:18
Alignment explanation
Indices: 53688728--53688770 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
53688718 TTAGGATTCA
53688728 ATGATTTTTGAAGTTTAGG
1 ATGA-TTTTGAAGTTTAGG
53688747 ATTGATTTTG-AGTTTAGGG
1 A-TGATTTTGAAGTTTA-GG
53688766 ATGAT
1 ATGAT
53688771 AATGGAAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 10 0.45
19 9 0.41
20 3 0.14
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.47
Consensus pattern (18 bp):
ATGATTTTGAAGTTTAGG
Found at i:53701812 original size:17 final size:17
Alignment explanation
Indices: 53701779--53701812 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
53701769 AAAAATTATT
* *
53701779 TTAAAAATATTTTAAAA
1 TTAAAAAAATTTAAAAA
53701796 TTAAAAAAATTTAAAAA
1 TTAAAAAAATTTAAAAA
53701813 AAGTATTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAAAAAATTTAAAAA
Found at i:53701824 original size:41 final size:40
Alignment explanation
Indices: 53701736--53701854 Score: 141
Period size: 41 Copynumber: 2.8 Consensus size: 40
53701726 ATAAATATCA
* *
53701736 AAAAATTATTTTAAAAATTAAAACAAAAATAAAAAAAATTATTTT
1 AAAAA-TATTTT-AAAATT--AA-AAAAATTAAAAAAAGTATTTT
53701781 AAAAATATTTTAAAATTAAAAAAATTTAAAAAAAGTATTTT
1 AAAAATATTTTAAAATTAAAAAAA-TTAAAAAAAGTATTTT
*
53701822 AAAAGTATTTTAAAATTTAAAAAAA-TAAAAAAA
1 AAAAATATTTTAAAA-TTAAAAAAATTAAAAAAA
53701855 TAAAAAATTA
Statistics
Matches: 69, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
40 13 0.19
41 30 0.43
42 9 0.13
43 6 0.09
44 6 0.09
45 5 0.07
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.33
Consensus pattern (40 bp):
AAAAATATTTTAAAATTAAAAAAATTAAAAAAAGTATTTT
Found at i:53701825 original size:11 final size:11
Alignment explanation
Indices: 53701811--53701836 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
53701801 AAAATTTAAA
53701811 AAAAGTATTTT
1 AAAAGTATTTT
53701822 AAAAGTATTTT
1 AAAAGTATTTT
53701833 AAAA
1 AAAA
53701837 TTTAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:53702899 original size:22 final size:20
Alignment explanation
Indices: 53702870--53702909 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
53702860 TTAAGAGGTT
*
53702870 TAATAGAAATTTTTAAAAAAG
1 TAATAG-AATTTTCAAAAAAG
53702891 TAATGAGAATTTTCAAAAA
1 TAAT-AGAATTTTCAAAAA
53702910 TTTTGAAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.33
Consensus pattern (20 bp):
TAATAGAATTTTCAAAAAAG
Found at i:53712036 original size:266 final size:266
Alignment explanation
Indices: 53711562--53712089 Score: 1029
Period size: 266 Copynumber: 2.0 Consensus size: 266
53711552 CGTGATAAGA
53711562 GAAGGATGATAGTTTAATGGAGGACCACACAACCATTGCTCCGTGGCCCGAGAATTTAATGTGAC
1 GAAGGATGATAGTTTAATGGAGGACCACACAACCATTGCTCCGTGGCCCGAGAATTTAATGTGAC
*
53711627 AAGGATTATTTGAGAGCCGCTGAACTTTCTTAAAAGAGAAGCCAACGAGCACCATGAGGTTTAGT
66 AAGGATTATTCGAGAGCCGCTGAACTTTCTTAAAAGAGAAGCCAACGAGCACCATGAGGTTTAGT
*
53711692 GAGCAACGAGTCACGGCCCGGATTGAGTAAAAAGGAGATATAAGATACGTCCCTTTTGAAGAGTT
131 GAGCAACGAGTCACGGACCGGATTGAGTAAAAAGGAGATATAAGATACGTCCCTTTTGAAGAGTT
*
53711757 CGTGAGACTTATCTTAACGCTCGAATGAAGAAAATGATCGAATGTCTCCGCATATGAGGGCAAAG
196 CGTGAGACTTATCTTAACGCTCGAACGAAGAAAATGATCGAATGTCTCCGCATATGAGGGCAAAG
53711822 CCGTAT
261 CCGTAT
53711828 GAAGGATGATAGTTTAATGGAGGACCACACAACCATTGCTCCGTGGCCCGAGAATTTAATGTGAC
1 GAAGGATGATAGTTTAATGGAGGACCACACAACCATTGCTCCGTGGCCCGAGAATTTAATGTGAC
53711893 AAGGATTATTCGAGAGCCGCTGAACTTTCTTAAAAGAGAAGCCAACGAGCACCATGAGGTTTAGT
66 AAGGATTATTCGAGAGCCGCTGAACTTTCTTAAAAGAGAAGCCAACGAGCACCATGAGGTTTAGT
53711958 GAGCAACGAGTCACGGACCGGATTGAGTAAAAAGGAGATATAAGATACGTCCCTTTTGAAGAGTT
131 GAGCAACGAGTCACGGACCGGATTGAGTAAAAAGGAGATATAAGATACGTCCCTTTTGAAGAGTT
53712023 CGTGAGACTTATCTTAACGCTCGAACGAAGAAAATGATCGAATGTCTCCGCATATGAGGGCAAAG
196 CGTGAGACTTATCTTAACGCTCGAACGAAGAAAATGATCGAATGTCTCCGCATATGAGGGCAAAG
53712088 CC
261 CC
53712090 ATATATGTAT
Statistics
Matches: 259, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
266 259 1.00
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (266 bp):
GAAGGATGATAGTTTAATGGAGGACCACACAACCATTGCTCCGTGGCCCGAGAATTTAATGTGAC
AAGGATTATTCGAGAGCCGCTGAACTTTCTTAAAAGAGAAGCCAACGAGCACCATGAGGTTTAGT
GAGCAACGAGTCACGGACCGGATTGAGTAAAAAGGAGATATAAGATACGTCCCTTTTGAAGAGTT
CGTGAGACTTATCTTAACGCTCGAACGAAGAAAATGATCGAATGTCTCCGCATATGAGGGCAAAG
CCGTAT
Found at i:53712282 original size:62 final size:62
Alignment explanation
Indices: 53712216--53712399 Score: 314
Period size: 62 Copynumber: 3.0 Consensus size: 62
53712206 CACGTATCTC
*
53712216 TTCATTCATTAACATTACATTTCATTACATACAATAAATTTCCTAAAATCCAAAAATACGCG
1 TTCATGCATTAACATTACATTTCATTACATACAATAAATTTCCTAAAATCCAAAAATACGCG
* *
53712278 TTCATGCATTAACATTACATTTTATTACATACAATAAATTTCTTAAAATCCAAAAATACGCG
1 TTCATGCATTAACATTACATTTCATTACATACAATAAATTTCCTAAAATCCAAAAATACGCG
* * *
53712340 TTCATGCATCAACATTACATTTCATTGCATACAATAAATTTCCTAAAATCCAAAAGTACG
1 TTCATGCATTAACATTACATTTCATTACATACAATAAATTTCCTAAAATCCAAAAATACG
53712400 TCGAGTTTAG
Statistics
Matches: 114, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 114 1.00
ACGTcount: A:0.41, C:0.20, G:0.05, T:0.34
Consensus pattern (62 bp):
TTCATGCATTAACATTACATTTCATTACATACAATAAATTTCCTAAAATCCAAAAATACGCG
Found at i:53713657 original size:24 final size:23
Alignment explanation
Indices: 53713630--53713687 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
53713620 TCAGTGGAGG
* **
53713630 CCAAAAAAAAAAGAACAAATGAAA
1 CCAAAAAAAAAACAA-AAACAAAA
*
53713654 CCAAATAAAAAACAAAAACAAAA
1 CCAAAAAAAAAACAAAAACAAAA
*
53713677 ACAAAAAAAAA
1 CCAAAAAAAAA
53713688 CTCTACCGGG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 15 0.54
24 13 0.46
ACGTcount: A:0.79, C:0.14, G:0.03, T:0.03
Consensus pattern (23 bp):
CCAAAAAAAAAACAAAAACAAAA
Found at i:53713676 original size:12 final size:11
Alignment explanation
Indices: 53713631--53713687 Score: 51
Period size: 12 Copynumber: 4.9 Consensus size: 11
53713621 CAGTGGAGGC
53713631 CAAAAAAAAAA
1 CAAAAAAAAAA
* * *
53713642 GAACAAATGAAAC
1 CAA-AAA-AAAAA
*
53713655 CAAATAAAAAA
1 CAAAAAAAAAA
53713666 CAAAAACAAAAA
1 CAAAAA-AAAAA
53713678 CAAAAAAAAA
1 CAAAAAAAAA
53713688 CTCTACCGGG
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
11 14 0.40
12 16 0.46
13 5 0.14
ACGTcount: A:0.81, C:0.12, G:0.04, T:0.04
Consensus pattern (11 bp):
CAAAAAAAAAA
Found at i:53714121 original size:12 final size:13
Alignment explanation
Indices: 53714111--53714160 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
53714101 TAAAAAAATG
*
53714111 AAAAGAAAAATGAA
1 AAAAGAAAAAAG-A
53714125 AAAATGAAAAAAG-
1 AAAA-GAAAAAAGA
53714138 AAAAGAAAAAAGA
1 AAAAGAAAAAAGA
53714151 AAAAGAAAAA
1 AAAAGAAAAA
53714161 GGAGAGGCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
12 8 0.24
13 14 0.42
14 4 0.12
15 7 0.21
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (13 bp):
AAAAGAAAAAAGA
Found at i:53714125 original size:7 final size:6
Alignment explanation
Indices: 53714111--53714161 Score: 50
Period size: 6 Copynumber: 7.8 Consensus size: 6
53714101 TAAAAAAATG
53714111 AAAAGA AAAATGAA AAAATGA AAAA-A GAAAAGAA AAAAGA AAAAGA AAAAG
1 AAAAGA AAAA-G-A AAAA-GA AAAAGA -AAAAG-A AAAAGA AAAAGA AAAAG
53714162 GAGAGGCCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
5 1 0.03
6 20 0.50
7 11 0.28
8 8 0.20
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (6 bp):
AAAAGA
Found at i:53714128 original size:20 final size:20
Alignment explanation
Indices: 53714103--53714160 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 20
53714093 ACTTCACTTA
*
53714103 AAAAAATGAAAAGAAAAATG
1 AAAAAATGAAAAGAAAAAAG
53714123 AAAAAATGAAAA-AAGAAAAG
1 AAAAAATGAAAAGAA-AAAAG
53714143 AAAAAA-GAAAAAGAAAAA
1 AAAAAATG-AAAAGAAAAA
53714161 GGAGAGGCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
19 3 0.09
20 29 0.85
21 2 0.06
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (20 bp):
AAAAAATGAAAAGAAAAAAG
Found at i:53715230 original size:87 final size:87
Alignment explanation
Indices: 53715113--53715423 Score: 471
Period size: 87 Copynumber: 3.6 Consensus size: 87
53715103 AGAGAATAGA
* * *
53715113 TCAAAGA-AAGCAGATCTTGCCTTCCTGCATTAACAGTGAAGAAGATCGAAAACAAAGCTTTGCC
1 TCAAAGATAA-CAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCC
53715177 TCCATCGGTTGCAGTGGAGCTGG
65 TCCATCGGTTGCAGTGGAGCTGG
*
53715200 TCAAAGATAACAGATCTTGCCTTCCTGCATTAACACCGAAGCAGATCGAAAACAAAGCCTTGCCT
1 TCAAAGATAACAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCT
**
53715265 CCATCGGTTGCAGTCCAGCTGG
66 CCATCGGTTGCAGTGGAGCTGG
* * * * * * * *
53715287 TTAAAGATAACAAATCTTACCTTCCTGCGTTAACAGTGGAGCCGATCGAAAATAAAGCCTTGCCT
1 TCAAAGATAACAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCT
53715352 CCATCGGTTGCAGTGGAGCTGG
66 CCATCGGTTGCAGTGGAGCTGG
*
53715374 TCAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAA
1 TCAAAGATAACAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAA
53715424 NNNNNNNNNN
Statistics
Matches: 198, Mismatches: 25, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
87 196 0.99
88 2 0.01
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (87 bp):
TCAAAGATAACAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCT
CCATCGGTTGCAGTGGAGCTGG
Found at i:53722859 original size:34 final size:34
Alignment explanation
Indices: 53722784--53722861 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 34
53722774 ACAATAATAA
* *
53722784 ATATTTTATAAAATAAATTTATATTAATATTTAT
1 ATATTTTATAAAATAAATTTAAATAAATATTTAT
*
53722818 ATATTTTATAAATTAAATTTAAATAAA-ATATTAT
1 ATATTTTATAAAATAAATTTAAATAAATAT-TTAT
53722852 -TATTTT-TAAA
1 ATATTTTATAAA
53722862 CAATAACTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
32 4 0.10
33 8 0.20
34 28 0.70
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (34 bp):
ATATTTTATAAAATAAATTTAAATAAATATTTAT
Found at i:53733437 original size:15 final size:16
Alignment explanation
Indices: 53733406--53733439 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
53733396 TTCCAAAACA
53733406 TAAAATGTGAATCAAG
1 TAAAATGTGAATCAAG
*
53733422 TAAAATGT-ATTCAAG
1 TAAAATGTGAATCAAG
53733437 TAA
1 TAA
53733440 GCTCATAGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29
Consensus pattern (16 bp):
TAAAATGTGAATCAAG
Found at i:53736419 original size:67 final size:67
Alignment explanation
Indices: 53736311--53736447 Score: 220
Period size: 67 Copynumber: 2.0 Consensus size: 67
53736301 TCCAAGATTT
* * * *
53736311 TATTTGTTATACTTGATGAACCTACATAATGGGACATCTATTTAGAATAACTCATGTCAAACTTC
1 TATTTGTTAAACCTCATGAACCTACATAATGGGACATCTATTTAGAATAACTCACGTCAAACTTC
53736376 TC
66 TC
* *
53736378 TATTTGTTAAACCTCATGAACCTATATGATGGGACATCTATTTAGAATAACTCACGTCAAACTTC
1 TATTTGTTAAACCTCATGAACCTACATAATGGGACATCTATTTAGAATAACTCACGTCAAACTTC
53736443 TC
66 TC
53736445 TAT
1 TAT
53736448 AAAATTCGTT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (67 bp):
TATTTGTTAAACCTCATGAACCTACATAATGGGACATCTATTTAGAATAACTCACGTCAAACTTC
TC
Found at i:53739921 original size:40 final size:40
Alignment explanation
Indices: 53739850--53739925 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
53739840 GAATTTTTTG
* * *
53739850 GGAAATTTTATGGAATATGATATGTCAAATTTAGGGTCTA
1 GGAAATTTCATGGAATATGATAGGACAAATTTAGGGTCTA
* *
53739890 GGAAATTTCATGGAATATGATGGGACTAATTTAGGG
1 GGAAATTTCATGGAATATGATAGGACAAATTTAGGG
53739926 AAGGAAAACA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.34
Consensus pattern (40 bp):
GGAAATTTCATGGAATATGATAGGACAAATTTAGGGTCTA
Found at i:53741429 original size:13 final size:14
Alignment explanation
Indices: 53741411--53741444 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
53741401 TGGAATTCTT
*
53741411 AAAAATTGGGC-TG
1 AAAAATTGGGCAAG
53741424 AAAAATTGGGCAAG
1 AAAAATTGGGCAAG
53741438 AAAAATT
1 AAAAATT
53741445 TTAAAGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.50, C:0.06, G:0.24, T:0.21
Consensus pattern (14 bp):
AAAAATTGGGCAAG
Found at i:53749375 original size:21 final size:21
Alignment explanation
Indices: 53749349--53749389 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
53749339 AGACGAGCAA
* *
53749349 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
53749370 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
53749390 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:53783254 original size:4 final size:4
Alignment explanation
Indices: 53783245--53784030 Score: 1572
Period size: 4 Copynumber: 196.5 Consensus size: 4
53783235 AAATTTAGAG
53783245 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
53783293 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
53783341 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
53783389 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
53783437 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
53783485 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
53783533 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
53783581 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
53783629 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
53783677 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
53783725 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
53783773 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
53783821 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
53783869 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
53783917 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
53783965 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
53784013 CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CA
53784031 GGTAAGCAAC
Statistics
Matches: 782, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 782 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:53795125 original size:83 final size:83
Alignment explanation
Indices: 53794986--53795152 Score: 280
Period size: 83 Copynumber: 2.0 Consensus size: 83
53794976 CCGCCGTCGT
*
53794986 AGCTTCAATCTGTTCCACTACACCGCTAAGGAAGTAAGATCCACTGTTGTGGCTTCAATCTTTTT
1 AGCTTCAATCTGTTCCACTACACCGCTAAGGAAGTAAGATCCACCGTTGTGGCTTCAATCTTTTT
*
53795051 AATTGCAATATCAGGGAA
66 AATTACAATATCAGGGAA
* * * *
53795069 AGCTTCAATCTGTTCTACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTT
1 AGCTTCAATCTGTTCCACTACACCGCTAAGGAAGTAAGATCCACCGTTGTGGCTTCAATCTTTTT
53795134 AATTACAATATCAGGGAA
66 AATTACAATATCAGGGAA
53795152 A
1 A
53795153 CCAGATCCGC
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 78 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.32
Consensus pattern (83 bp):
AGCTTCAATCTGTTCCACTACACCGCTAAGGAAGTAAGATCCACCGTTGTGGCTTCAATCTTTTT
AATTACAATATCAGGGAA
Found at i:53795242 original size:100 final size:100
Alignment explanation
Indices: 53795069--53796401 Score: 1825
Period size: 100 Copynumber: 13.3 Consensus size: 100
53795059 TATCAGGGAA
*
53795069 AGCTTCAATCTGTTCTACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTT
1 AGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTT
*
53795134 AATTACAATATCAGGGAAACCAGATCCGCCGTCGT
66 AATTGCAATATCAGGGAAACCAGATCCGCCGTCGT
*
53795169 AGCTTCAATCTGTTTCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTT
1 AGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTT
*
53795234 AATTACAATATCAGGGAAACCAGATCCGCCGTCGT
66 AATTGCAATATCAGGGAAACCAGATCCGCCGTCGT
*
53795269 AGCTTCAATCTGTTTCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTT
1 AGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTT
* *
53795334 AATTGCAATATCAGGGAAACCAGATCCACCTTCGT
66 AATTGCAATATCAGGGAAACCAGATCCGCCGTCGT
53795369 AGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTT
1 AGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTT
* *
53795434 AATTGCAATATCAGGGAAACCAGATCCACCTTCGT
66 AATTGCAATATCAGGGAAACCAGATCCGCCGTCGT
*
53795469 AGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCATTGTGGCTTCAATCTTTTT
1 AGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTT
*** * * *
53795534 AATTGTGCTGTCGGGGAAACCAGATCCGCCGTTGT
66 AATTGCAATATCAGGGAAACCAGATCCGCCGTCGT
* * * * *
53795569 -GATTTCAATCTGCTCCACTGCACCGCCAAGGAAGTAAGATCCGCCGTTGTGGCTTTAATCTTTT
1 AG-CTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTT
** * * *
53795633 TAATTGCGCTGTCGGGGAAACCAGATCCGCCGTTGT
65 TAATTGCAATATCAGGGAAACCAGATCCGCCGTCGT
* * * * *
53795669 -GACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCCACCGTTGTGGCTTCAATCTTTT
1 AG-CTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTT
** * * * * *
53795733 TAATTGCGCTGTCGGGGAAACCAAATCCGCCATTGT
65 TAATTGCAATATCAGGGAAACCAGATCCGCCGTCGT
*
53795769 AGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTCTTT
1 AGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTT
* **
53795834 AATTACAATATCAGGGAAACCAGATCTACCGTCGT
66 AATTGCAATATCAGGGAAACCAGATCCGCCGTCGT
*
53795869 AGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTCTTT
1 AGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTT
* **
53795934 AATTACAATATCAGGGAAACCAGATCTACCGTCGT
66 AATTGCAATATCAGGGAAACCAGATCCGCCGTCGT
* * *
53795969 AGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATTCACCGTTGTGGCTTTAATCTTTTT
1 AGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTT
** * * *
53796034 AATTGCGCTGTCGGGGAAACCAAATCCGCCGT--T
66 AATTGCAATATCAGGGAAACCAGATCCGCCGTCGT
* * * * *
53796067 ATGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCTGCCGTTGTGGCTTCAATCTTT
1 A-G-CTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTT
* *
53796132 TTCATTGCAATATCAGGGAAACCAGATCTGCCGTCGT
64 TTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGT
* *
53796169 AGCTTCAATTTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCATTGTGGCTTCAATCTTTTT
1 AGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTT
** * * * *
53796234 AATTGCGCTGTCGGGGAAACCAGATCCGCCATTGT
66 AATTGCAATATCAGGGAAACCAGATCCGCCGTCGT
* ** * * *
53796269 -GACTTCAATCTGCTCCACTATACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTT
1 AG-CTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTT
** * *
53796333 TAATTGCGCTGTCAGGGAAACCAGATCCGCCGTTGT
65 TAATTGCAATATCAGGGAAACCAGATCCGCCGTCGT
* *
53796369 -GACTTCAATCTGCTCCACTACAAC-GCTAAGGAA
1 AG-CTTCAATCTGTTCCACTGC-ACTGCTAAGGAA
53796402 ATAAAAATAT
Statistics
Matches: 1126, Mismatches: 99, Indels: 16
0.91 0.08 0.01
Matches are distributed among these distances:
98 2 0.00
99 3 0.00
100 1115 0.99
101 4 0.00
102 2 0.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (100 bp):
AGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTT
AATTGCAATATCAGGGAAACCAGATCCGCCGTCGT
Found at i:53796402 original size:50 final size:50
Alignment explanation
Indices: 53796247--53796402 Score: 136
Period size: 50 Copynumber: 3.1 Consensus size: 50
53796237 TGCGCTGTCG
* * * *
53796247 GGGAAACCAGATCCGCCATTGTGACTTCAATCTGCTCCACTATACCGCCA
1 GGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCCACTACAACGCTA
*** * ** ** * * *
53796297 GGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGC-GCTG-TCA
1 GGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCCACTACAAC-GCT-A
53796347 GGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCCACTACAACGCTA
1 GGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCCACTACAACGCTA
*
53796397 AGGAAA
1 GGGAAA
53796403 TAAAAATATA
Statistics
Matches: 76, Mismatches: 26, Indels: 8
0.69 0.24 0.07
Matches are distributed among these distances:
49 1 0.01
50 73 0.96
51 2 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (50 bp):
GGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCCACTACAACGCTA
Found at i:53797720 original size:6 final size:7
Alignment explanation
Indices: 53797703--53797735 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
53797693 GCCTCTCTAT
53797703 TTTTTCA
1 TTTTTCA
53797710 TTTTTCA
1 TTTTTCA
53797717 -TTTTCA
1 TTTTTCA
53797723 TCTTTTCA
1 T-TTTTCA
53797731 TTTTT
1 TTTTT
53797736 ACACATCACT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.25
7 11 0.46
8 7 0.29
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTTCA
Found at i:53798798 original size:44 final size:45
Alignment explanation
Indices: 53798692--53798825 Score: 144
Period size: 44 Copynumber: 3.0 Consensus size: 45
53798682 ACAGGACAGA
* * *
53798692 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATAAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* * * *
53798738 ATAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATAAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
** * *
53798782 ACAGGAATAATTCATGTAAGTCCATGTTAAAGACATGGCATTGG
1 ACAGGAATAAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
53798826 CAGGATATTG
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 36 0.49
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (45 bp):
ACAGGAATAAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:53802903 original size:13 final size:13
Alignment explanation
Indices: 53802885--53802910 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53802875 TGTTCAATTT
53802885 TTTACTAGAAAAC
1 TTTACTAGAAAAC
53802898 TTTACTAGAAAAC
1 TTTACTAGAAAAC
53802911 AAATCTCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
TTTACTAGAAAAC
Found at i:53808605 original size:28 final size:29
Alignment explanation
Indices: 53808563--53808643 Score: 76
Period size: 29 Copynumber: 2.8 Consensus size: 29
53808553 AATTTTAATA
*
53808563 AAAAAATACATAAAATTTATTAAAAAT-CAG
1 AAAAAAT-TATAAAATTTA-TAAAAATGCAG
* * * *
53808593 -AAAAATTGTAAAATATATAGAAATGTAG
1 AAAAAATTATAAAATTTATAAAAATGCAG
53808621 AAAAAATTATAAAATTTTATAAA
1 AAAAAATTATAAAA-TTTATAAA
53808644 GTCGTAAGAA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
27 6 0.15
28 10 0.25
29 18 0.45
30 6 0.15
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (29 bp):
AAAAAATTATAAAATTTATAAAAATGCAG
Found at i:53808961 original size:24 final size:25
Alignment explanation
Indices: 53808928--53808976 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
53808918 ATTTTCATAT
*
53808928 TTTTTCTTATATTTAATAAATTTTA
1 TTTTTCTTATATTTAATAAAATTTA
* *
53808953 TTTTT-TTATTTTTATTAAAATTTA
1 TTTTTCTTATATTTAATAAAATTTA
53808977 ATAATTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (25 bp):
TTTTTCTTATATTTAATAAAATTTA
Found at i:53808963 original size:34 final size:33
Alignment explanation
Indices: 53808925--53809010 Score: 84
Period size: 34 Copynumber: 2.5 Consensus size: 33
53808915 ACAATTTTCA
*
53808925 TATTTTTTCTTATATTTAATAAATTTTATT-TTTT
1 TATTTTTT-TTA-ATTTAATAAATTTTATTAATTT
* *
53808959 TATTTTTATTAAAATTTAATAATTTTTATTGAATTT
1 TATTTTT-TT-TAATTTAATAAATTTTATT-AATTT
53808995 TATTTTTTGTTAATTT
1 TATTTTTT-TTAATTT
53809011 TTTTCCATGT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
34 24 0.56
35 8 0.19
36 11 0.26
ACGTcount: A:0.29, C:0.01, G:0.02, T:0.67
Consensus pattern (33 bp):
TATTTTTTTTAATTTAATAAATTTTATTAATTT
Found at i:53812826 original size:37 final size:37
Alignment explanation
Indices: 53812776--53812850 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
53812766 TATATTAGTA
53812776 AGTGTTATTTTTGGAAGATGTCATATGAACAATTAAG
1 AGTGTTATTTTTGGAAGATGTCATATGAACAATTAAG
53812813 AGTGTTATTTTTGGAAGATGTCATATGAACAATTAAG
1 AGTGTTATTTTTGGAAGATGTCATATGAACAATTAAG
53812850 A
1 A
53812851 TTGATAGTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.37
Consensus pattern (37 bp):
AGTGTTATTTTTGGAAGATGTCATATGAACAATTAAG
Found at i:53814082 original size:38 final size:37
Alignment explanation
Indices: 53814017--53814108 Score: 96
Period size: 38 Copynumber: 2.5 Consensus size: 37
53814007 ACCAGATTGG
* *
53814017 CACCTAGTGCCTCATCAGATAGTTCGAAGCAAAGTTGA
1 CACCTAGTGTCTCATCGGATAGTTCGAAGCAAAG-TGA
* *
53814055 CACCTAGTGTCTCATCGGCCTAG-TCGAAGTAAAGTGA
1 CACCTAGTGTCTCATCGG-ATAGTTCGAAGCAAAGTGA
* * *
53814092 TACCCAGTATCTCATCG
1 CACCTAGTGTCTCATCG
53814109 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
37 17 0.37
38 26 0.57
39 3 0.07
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (37 bp):
CACCTAGTGTCTCATCGGATAGTTCGAAGCAAAGTGA
Found at i:53814288 original size:18 final size:17
Alignment explanation
Indices: 53814242--53814295 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
53814232 TTTCCAATTC
53814242 TCAATTCAAATTCACTT
1 TCAATTCAAATTCACTT
*
53814259 TCATTTCAAAATGT-ACTT
1 TCAATTC-AAAT-TCACTT
53814277 TCAATATCAAATTCACTT
1 TCAAT-TCAAATTCACTT
53814295 T
1 T
53814296 TTTCTCACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
17 7 0.23
18 21 0.68
19 3 0.10
ACGTcount: A:0.35, C:0.20, G:0.02, T:0.43
Consensus pattern (17 bp):
TCAATTCAAATTCACTT
Found at i:53815561 original size:29 final size:29
Alignment explanation
Indices: 53815519--53815575 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
53815509 ATCTTTTCTT
* *
53815519 AATTTATTTTATAATATAATAATATAATC
1 AATTTAATTTATAATATAATAAAATAATC
53815548 AATTTAATTTATAATATAATAAAATAAT
1 AATTTAATTTATAATATAATAAAATAAT
53815576 AACAATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (29 bp):
AATTTAATTTATAATATAATAAAATAATC
Found at i:53834776 original size:44 final size:44
Alignment explanation
Indices: 53834659--53835109 Score: 233
Period size: 44 Copynumber: 10.5 Consensus size: 44
53834649 NNNNATCAGG
* * ** ***
53834659 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG--TCAGAGA
* * * *
53834705 TCTTATCTCCCTGAGGTTACATTGGAGCAAATTGAAGCCAGAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGTCAGAGA
* **
53834749 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAT-AGTA-A
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG-TCAG-AGA
* * * *
53834793 TCCTATCTCCTTGAGATTACAATGGAGCGGATT-AA---AG-GA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGTCAGAGA
* * * *
53834832 TCTTATCTCTCTGA-AGTTACAGTAGAGAAGA-TCACA-TCAG-G-
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGA-AGTCAGAGA
* *** ***
53834873 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG--TCAGAGA
* * * **
53834919 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACA-CTA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGTCAGAGA
* * * * *
53834962 TCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAAAATAAGAGA
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGTCAGAGA
* * * **
53835006 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACA-CTA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGTCAGAGA
* *
53835049 TCTTATCTCCCCGA-AGTTACAGTGGAGCGGATT-AA---AG-GA
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGTCAGAGA
* *
53835088 TCTTATCTCTCTGAGGTTACAG
1 TCTTATCTCCCTGAGATTACAG
53835110 CAGAGTAGAT
Statistics
Matches: 309, Mismatches: 75, Indels: 49
0.71 0.17 0.11
Matches are distributed among these distances:
38 2 0.01
39 44 0.14
40 3 0.01
41 26 0.08
42 9 0.03
43 61 0.20
44 96 0.31
45 3 0.01
46 65 0.21
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.27
Consensus pattern (44 bp):
TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGTCAGAGA
Found at i:53834983 original size:43 final size:43
Alignment explanation
Indices: 53834873--53835076 Score: 173
Period size: 43 Copynumber: 4.7 Consensus size: 43
53834863 TCACATCAGG
* * * * *
53834873 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGA-ATTTCAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACA---C-TA
53834919 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTA
* * * * * * **
53834962 TCCTATCTCCCTGA-AGTTACAGTGGAGCGGAT-TAAAATAAGAGA
1 TCTTATCTCCCTGAGA-TTACAGCGGAGCAGATCGAAGA-CA-CTA
53835006 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTA
* *
53835049 TCTTATCTCCCCGA-AGTTACAGTGGAGC
1 TCTTATCTCCCTGAGA-TTACAGCGGAGC
53835077 GGATTAAAGG
Statistics
Matches: 128, Mismatches: 23, Indels: 17
0.76 0.14 0.10
Matches are distributed among these distances:
42 5 0.04
43 54 0.42
44 30 0.23
45 4 0.03
46 34 0.27
47 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.25
Consensus pattern (43 bp):
TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTA
Found at i:53835096 original size:169 final size:164
Alignment explanation
Indices: 53834744--53835121 Score: 372
Period size: 169 Copynumber: 2.2 Consensus size: 164
53834734 AATTGAAGCC
* * * *
53834744 AGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGA
1 AGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTAATCCTATCTCCCTGAGA
* * * *
53834809 TTACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGT
66 TTACAATGGAGCGGATTAAAGGATCTTATCTCCCTGAAGTTACAGCAGAGAAGATCACAACAGAT
*
53834874 CTTATCTCCCTGAGATTACAGTGGAACAGACCAA
131 CTTATCTCCCCGAGATTACAGTGGAACAGACCAA
53834908 AGAATTTCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACT-ATCCTATCTCC
1 AG------AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTAATCCTATCTCC
* * *
53834972 CTGA-AGTTACAGTGGAGCGGATTAAAATAAGAGATCTTATCTCCCTG-AGATTACAGCGGAGCA
60 CTGAGA-TTACAATGGAGCGGATT---A-AAG-GATCTTATCTCCCTGAAG-TTACAGCAGAGAA
* * * **
53835035 GATCGA-AGACACTATCTTATCTCCCCGA-AGTTACAGTGGAGCGGATTAA
118 GATC-ACA-ACA-GATCTTATCTCCCCGAGA-TTACAGTGGAACAGACCAA
* * * *
53835084 AG-GATCTTATCTCTCTGAGGTTACAGCAGAGTAGATCG
1 AGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCG
53835122 CATCAAGTCT
Statistics
Matches: 176, Mismatches: 21, Indels: 29
0.78 0.09 0.13
Matches are distributed among these distances:
164 2 0.01
168 1 0.01
169 62 0.35
170 42 0.24
172 1 0.01
173 5 0.03
174 29 0.16
175 4 0.02
176 30 0.17
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (164 bp):
AGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTAATCCTATCTCCCTGAGA
TTACAATGGAGCGGATTAAAGGATCTTATCTCCCTGAAGTTACAGCAGAGAAGATCACAACAGAT
CTTATCTCCCCGAGATTACAGTGGAACAGACCAA
Found at i:53835120 original size:82 final size:85
Alignment explanation
Indices: 53834916--53835121 Score: 319
Period size: 87 Copynumber: 2.4 Consensus size: 85
53834906 AAAGAATTTC
*
53834916 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCCGAAGTTA
53834981 CAGTGGAGCGGATTAAAATAAG
66 CAGTGGAGCGGATT--AATAAG
*
53835003 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCTTATCTCCCCGAAGTTA
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCCGAAGTTA
53835068 CAGTGGAGCGGATT-A-AAG
66 CAGTGGAGCGGATTAATAAG
* * * *
53835086 -GATCTTATCTCTCTGAGGTTACAGCAGAGTAGATCG
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCG
53835122 CATCAAGTCT
Statistics
Matches: 113, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
82 32 0.28
83 3 0.03
84 1 0.01
87 77 0.68
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (85 bp):
AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCCGAAGTTA
CAGTGGAGCGGATTAATAAG
Found at i:53835928 original size:20 final size:20
Alignment explanation
Indices: 53835903--53835942 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
53835893 CATGACGGAA
53835903 GCAGC-AACAGAAACAGAAAC
1 GCAGCAAACAGAAACA-AAAC
*
53835923 GCAGCAAACAGTAACAAAAC
1 GCAGCAAACAGAAACAAAAC
53835943 AACAATAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.55, C:0.25, G:0.17, T:0.03
Consensus pattern (20 bp):
GCAGCAAACAGAAACAAAAC
Found at i:53836966 original size:9 final size:10
Alignment explanation
Indices: 53836950--53836996 Score: 51
Period size: 9 Copynumber: 4.5 Consensus size: 10
53836940 TATATAGGAG
53836950 TATATATTTT
1 TATATATTTT
53836960 T-TATATTTT
1 TATATATTTT
53836969 TATATATTTAT
1 TATATATTT-T
*
53836980 ATACATACTTTT
1 -TATATA-TTTT
53836992 TATAT
1 TATAT
53836997 TTTATGATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
9 9 0.29
10 8 0.26
11 5 0.16
12 6 0.19
13 3 0.10
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (10 bp):
TATATATTTT
Found at i:53836982 original size:10 final size:10
Alignment explanation
Indices: 53836950--53837064 Score: 51
Period size: 10 Copynumber: 11.4 Consensus size: 10
53836940 TATATAGGAG
53836950 TATATATTT-
1 TATATATTTA
* *
53836959 TTTATATTTT
1 TATATATTTA
53836969 TATATATTTA
1 TATATATTTA
53836979 TATACATACTTT-
1 TAT--ATA-TTTA
53836991 T-TATATTT-
1 TATATATTTA
*
53836999 TATGATAGTTA
1 TAT-ATATTTA
*
53837010 TATACGTATATA
1 TATA--TATTTA
** * *
53837022 CGTATATGTG
1 TATATATTTA
*
53837032 TACATATTTA
1 TATATATTTA
*
53837042 TATATATATA
1 TATATATTTA
53837052 TATATATTT-
1 TATATATTTA
53837061 TATA
1 TATA
53837065 ATGCATATAT
Statistics
Matches: 79, Mismatches: 18, Indels: 18
0.69 0.16 0.16
Matches are distributed among these distances:
8 4 0.05
9 16 0.20
10 42 0.53
11 4 0.05
12 10 0.13
13 3 0.04
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.56
Consensus pattern (10 bp):
TATATATTTA
Found at i:53837702 original size:109 final size:109
Alignment explanation
Indices: 53837505--53837712 Score: 355
Period size: 109 Copynumber: 1.9 Consensus size: 109
53837495 AAATGTTTCC
53837505 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
1 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
* *
53837570 CTCGTTCGACCAAATAGCTAAATATCCTTTTGAAAACTTTTCAA
66 CTCGTTCAACCAAATAGCTAAATATCCTATTGAAAACTTTTCAA
*
53837614 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
1 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
* *
53837679 CTCGTTTAACCAAATTG-TCAAATATCCTATTGAA
66 CTCGTTCAACCAAATAGCT-AAATATCCTATTGAA
53837713 TTTAAACTCA
Statistics
Matches: 93, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
108 1 0.01
109 92 0.99
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (109 bp):
AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
CTCGTTCAACCAAATAGCTAAATATCCTATTGAAAACTTTTCAA
Found at i:53838100 original size:11 final size:11
Alignment explanation
Indices: 53838081--53838126 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
53838071 TTTGTTGTTA
*
53838081 TGCTGCTATTT
1 TGCTACTATTT
53838092 TGCTACTATTT
1 TGCTACTATTT
* * *
53838103 CGCTATTATAT
1 TGCTACTATTT
53838114 TGCTACTATTT
1 TGCTACTATTT
53838125 TG
1 TG
53838127 TTGTTGTTGT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.17, C:0.17, G:0.13, T:0.52
Consensus pattern (11 bp):
TGCTACTATTT
Found at i:53838657 original size:12 final size:13
Alignment explanation
Indices: 53838642--53838671 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
53838632 TTTTATTTGT
53838642 TTTTTGTTTT-AA
1 TTTTTGTTTTAAA
53838654 TTTTTGTTTTAAA
1 TTTTTGTTTTAAA
53838667 TTTTT
1 TTTTT
53838672 TTATTTAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.77
Consensus pattern (13 bp):
TTTTTGTTTTAAA
Found at i:53851382 original size:18 final size:19
Alignment explanation
Indices: 53851350--53851387 Score: 60
Period size: 18 Copynumber: 2.0 Consensus size: 19
53851340 ATAATTATTT
53851350 AAAAAATTCTAAAGTTTATA
1 AAAAAATTC-AAAGTTTATA
53851370 AAAAAATTC-AAGTTTATA
1 AAAAAATTCAAAGTTTATA
53851388 TATATAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
20 9 0.50
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (19 bp):
AAAAAATTCAAAGTTTATA
Found at i:53854277 original size:74 final size:74
Alignment explanation
Indices: 53854156--53854303 Score: 235
Period size: 74 Copynumber: 2.0 Consensus size: 74
53854146 TATTACATCC
* * *
53854156 TTTCATTTATAATTATTTGAACACTGTAAATATTTGAAAATGTTCCAACAATAGTTT-AGGTTAA
1 TTTCATTTATAATTATTTGAACACTATAAATATTTGAAAATATTCCAACAATAATTTGA-GTTAA
*
53854220 ACTACTACAA
65 ACTACAACAA
*
53854230 TTTCATTTATAATTATTTGAATACTATAAATATTTGAAAATATTCCAACAATAATTTGAGTTAAA
1 TTTCATTTATAATTATTTGAACACTATAAATATTTGAAAATATTCCAACAATAATTTGAGTTAAA
53854295 CTACAACAA
66 CTACAACAA
53854304 CCGAGTGAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
74 67 0.99
75 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.39
Consensus pattern (74 bp):
TTTCATTTATAATTATTTGAACACTATAAATATTTGAAAATATTCCAACAATAATTTGAGTTAAA
CTACAACAA
Found at i:53856293 original size:39 final size:39
Alignment explanation
Indices: 53856198--53856297 Score: 114
Period size: 39 Copynumber: 2.5 Consensus size: 39
53856188 CCATGAAACC
**
53856198 ATCAGTAAAACACCATACCAGACTGAAATCAGCAGAGCAG
1 ATCA-TAAAACACCATACCAGACTGAAATCAGCAGAAAAG
* * *
53856238 ATGATCAAAC-CTCATACCAGACTGAAAGT-AGCATAAAAG
1 ATCATAAAACAC-CATACCAGACTGAAA-TCAGCAGAAAAG
53856277 ATCATAAAACACCATACCAGA
1 ATCATAAAACACCATACCAGA
53856298 ATCCACCGAT
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
38 1 0.02
39 44 0.88
40 5 0.10
ACGTcount: A:0.47, C:0.24, G:0.14, T:0.15
Consensus pattern (39 bp):
ATCATAAAACACCATACCAGACTGAAATCAGCAGAAAAG
Found at i:53859633 original size:65 final size:65
Alignment explanation
Indices: 53859517--53859656 Score: 165
Period size: 65 Copynumber: 2.2 Consensus size: 65
53859507 CACTATGATC
* * * * * ***
53859517 TATCATA-ATAAGACCCTTCTAGAATGGTTTCTAATATATCTGACAATACTCTTACATTGGTAAA
1 TATCATATATAAGACCCTTCTAGAACGATTTCTAATAGATCTAACAACACTCTTACATTAACAAA
* * * *
53859581 TATCATATATAAGATCCTTCTAGAACGATTTTTAATAGATCTAATAACACTCTTATATTAACAAA
1 TATCATATATAAGACCCTTCTAGAACGATTTCTAATAGATCTAACAACACTCTTACATTAACAAA
53859646 TATCATATATA
1 TATCATATATA
53859657 TATACACTAG
Statistics
Matches: 63, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
64 7 0.11
65 56 0.89
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (65 bp):
TATCATATATAAGACCCTTCTAGAACGATTTCTAATAGATCTAACAACACTCTTACATTAACAAA
Found at i:53861941 original size:156 final size:154
Alignment explanation
Indices: 53861672--53862450 Score: 1012
Period size: 156 Copynumber: 5.0 Consensus size: 154
53861662 CTACATGCAC
* *
53861672 CCTTTTCAGGAAATTGTATC---GAAGCCATCTGAGGAATTACTCTCCAAGGAGAAAATGGTATG
1 CCTTTTCAGGAAACTGTATCGAGGAAGCCATCTGAGAAATTACTC-CCAAGGAGAAAATGGTATG
* * * * *
53861734 TTCTTGTGTACATATTTATATCTTGAGTTGTGTGTTTGAGGATAGAGATAGGAATATAAATGTCA
65 TTCTTGTGCATATATTTATATTTTGAGTTGTGTGTTTGAGGATGGAGATAGGAATATAAAAGTCA
*
53861799 AATCAAGGATAACGAACTACGAACA
130 AATCAAGGATAATGAACTACGAACA
* *
53861824 CCTTTTTCAGGAAATTGAATCGAGGAAGCCATCTGAGAAATTACTCCACAAGGAGAAAATGGTAT
1 CC-TTTTCAGGAAACTGTATCGAGGAAGCCATCTGAGAAATTACTCC-CAAGGAGAAAATGGTAT
* * * * *
53861889 GTTCTTGTGCATTTATTTATACTTTGAGTTGTGCGTTAGAGGATGGAGATAGGAACATAAAAGTC
64 GTTCTTGTGCATATATTTATATTTTGAGTTGTGTGTTTGAGGATGGAGATAGGAATATAAAAGTC
*
53861954 AAATCAAGGATAATGAACTAGGAACA
129 AAATCAAGGATAATGAACTACGAACA
*
53861980 CCCTTTTCAGGAAACTGTATCGAGGAAGAAGCCATCTGGGAAATTACTCCACAAGGAGAAAATGG
1 -CCTTTTCAGGAAACTGTATCGA-G--GAAGCCATCTGAGAAATTACTCC-CAAGGAGAAAATGG
* * * * * * *
53862045 TATGTTCTTGTGCTTGTATTTATATTTTGAGTTGTGTGTTTTAGGATTGAGATATGAACAT-AAG
61 TATGTTCTTGTGCATATATTTATATTTTGAGTTGTGTGTTTGAGGATGGAGATAGGAATATAAAA
* * *
53862109 GTCAAATCAAGGGTGATGAACTA-GAAAAA
126 GTCAAATCAAGGATAATGAACTACG-AACA
* *
53862138 CCCTTTCAGGAAACTGTATCGAGGAAGAAGCCATATGAGAAATTACTCCCCAAGGAGAAAATGGT
1 CCTTTTCAGGAAACTGTATCGA-G--GAAGCCATCTGAGAAATTACT-CCCAAGGAGAAAATGGT
53862203 ATGTTCTTGTGCATATATTTATATTTTGAGTTGTGTGTTTGAGGATGGAGATAGGAATATAAAAG
62 ATGTTCTTGTGCATATATTTATATTTTGAGTTGTGTGTTTGAGGATGGAGATAGGAATATAAAAG
* *
53862268 TCAAATCAAGGATAATAAACTACGAGCA
127 TCAAATCAAGGATAATGAACTACGAACA
* * *
53862296 TCCTTTTCAGGAAACTATATCAAGGAAGCCATCTGAGAAATTACTCCCAAAGGAAAAAATGGTAT
1 -CCTTTTCAGGAAACTGTATCGAGGAAGCCATCTGAGAAATTACTCCC-AAGGAGAAAATGGTAT
* * * * *
53862361 TTTCTTGTGC-TCGTATTTATAGTTTGAGTCGTGTGTTTGAGGATGGAGATAGGGATATAAAAGT
64 GTTCTTGTGCAT-ATATTTATATTTTGAGTTGTGTGTTTGAGGATGGAGATAGGAATATAAAAGT
*
53862425 CAAATCAAGGATAATGAACTATGAAC
128 CAAATCAAGGATAATGAACTACGAAC
53862451 TTTTCTTTTG
Statistics
Matches: 554, Mismatches: 57, Indels: 28
0.87 0.09 0.04
Matches are distributed among these distances:
152 2 0.00
153 17 0.03
155 5 0.01
156 250 0.45
157 117 0.21
158 53 0.10
159 110 0.20
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.30
Consensus pattern (154 bp):
CCTTTTCAGGAAACTGTATCGAGGAAGCCATCTGAGAAATTACTCCCAAGGAGAAAATGGTATGT
TCTTGTGCATATATTTATATTTTGAGTTGTGTGTTTGAGGATGGAGATAGGAATATAAAAGTCAA
ATCAAGGATAATGAACTACGAACA
Found at i:53862236 original size:316 final size:311
Alignment explanation
Indices: 53861669--53862445 Score: 1048
Period size: 316 Copynumber: 2.5 Consensus size: 311
53861659 TAACTACATG
* *
53861669 CACCCTTTTCAGGAAATTGTATC---GAAGCCATCTGAGG-AATTACTCTCCAAGGAGAAAATGG
1 CACCCTTTTCAGGAAACTATATCAAAGAAGCCATCTG-GGAAATTACTC-CCAAGGAGAAAATGG
* *
53861730 TATGTTCTTGTG-TACATATTTATATCTTGAGTTGTGTGTTTGAGGATAGAGATAGGAATATAAA
64 TATGTTCTTGTGCT-CGTATTTATATTTTGAGTTGTGTGTTTGAGGATAGAGATAGGAATATAAA
* * * * * *
53861794 TGTCAAATCAAGGATAACGAACTACGAACACCTTTTTCAGGAAATTGAATCGAGGAAGCCATCTG
128 AGTCAAATCAAGGATAATGAACTACGAAAACCTCTTTCAGGAAACTGAATCGAGGAAGCCATATG
*
53861859 AGAAATTACTCCACAAGGAGAAAATGGTATGTTCTTGTGCATTTATTTATACTTTGAGTTGTGCG
193 AGAAATTACTCCACAAGGAGAAAATGGTATGTTCTTGTGCATATATTTATACTTTGAGTTGTGCG
* *
53861924 TTAGAGGATGGAGATAGGAACATAAAAGTCAAATCAAGGATAATGAACTAGGAA
258 TTAGAGGATGGAGATAGGAACATAAAAGTCAAATCAAGGATAATAAACTACGAA
*
53861978 CACCCTTTTCAGGAAACTGTATCGAGGAAGAAGCCATCTGGGAAATTACTCCACAAGGAGAAAAT
1 CACCCTTTTCAGGAAACTATATC-A--AAGAAGCCATCTGGGAAATTACTCC-CAAGGAGAAAAT
* * * * *
53862043 GGTATGTTCTTGTGCTTGTATTTATATTTTGAGTTGTGTGTTTTAGGATTGAGATATGAACAT-A
62 GGTATGTTCTTGTGCTCGTATTTATATTTTGAGTTGTGTGTTTGAGGATAGAGATAGGAATATAA
* * * *
53862107 AGGTCAAATCAAGGGTGATGAACTA-GAAAAACC-CTTTCAGGAAACTGTATCGAGGAAGAAGCC
127 AAGTCAAATCAAGGATAATGAACTACG-AAAACCTCTTTCAGGAAACTGAATCGA-G--GAAGCC
* *
53862170 ATATGAGAAATTACTCCCCAAGGAGAAAATGGTATGTTCTTGTGCATATATTTATATTTTGAGTT
188 ATATGAGAAATTACTCCACAAGGAGAAAATGGTATGTTCTTGTGCATATATTTATACTTTGAGTT
* * * *
53862235 GTGTGTTTGAGGATGGAGATAGGAATATAAAAGTCAAATCAAGGATAATAAACTACGAG
253 GTGCGTTAGAGGATGGAGATAGGAACATAAAAGTCAAATCAAGGATAATAAACTACGAA
* * * *
53862294 CATCCTTTTCAGGAAACTATATCAAGGAAGCCATCTGAGAAATTACTCCCAAAGGAAAAAATGGT
1 CACCCTTTTCAGGAAACTATATCAAAGAAGCCATCTGGGAAATTACTCCC-AAGGAGAAAATGGT
* * * * *
53862359 ATTTTCTTGTGCTCGTATTTATAGTTTGAGTCGTGTGTTTGAGGATGGAGATAGGGATATAAAAG
65 ATGTTCTTGTGCTCGTATTTATATTTTGAGTTGTGTGTTTGAGGATAGAGATAGGAATATAAAAG
53862424 TCAAATCAAGGATAATGAACTA
130 TCAAATCAAGGATAATGAACTA
53862446 TGAACTTTTC
Statistics
Matches: 410, Mismatches: 43, Indels: 25
0.86 0.09 0.05
Matches are distributed among these distances:
309 22 0.05
312 1 0.00
313 105 0.26
314 54 0.13
315 86 0.21
316 142 0.35
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.30
Consensus pattern (311 bp):
CACCCTTTTCAGGAAACTATATCAAAGAAGCCATCTGGGAAATTACTCCCAAGGAGAAAATGGTA
TGTTCTTGTGCTCGTATTTATATTTTGAGTTGTGTGTTTGAGGATAGAGATAGGAATATAAAAGT
CAAATCAAGGATAATGAACTACGAAAACCTCTTTCAGGAAACTGAATCGAGGAAGCCATATGAGA
AATTACTCCACAAGGAGAAAATGGTATGTTCTTGTGCATATATTTATACTTTGAGTTGTGCGTTA
GAGGATGGAGATAGGAACATAAAAGTCAAATCAAGGATAATAAACTACGAA
Done.