Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 1 of 310
Found at i:124 original size:22 final size:22
Alignment explanation
Indices: 96--149 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 22
86 ATAATAAAAG
96 AAATATATAACAAATAACATAA
1 AAATATATAACAAATAACATAA
**
118 AAATATATGTATGAAATAACATAA
1 AAATATA--TAACAAATAACATAA
142 AAATATAT
1 AAATATAT
150 GAATAGCGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 8 0.29
24 20 0.71
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.28
Consensus pattern (22 bp):
AAATATATAACAAATAACATAA
Found at i:2797 original size:54 final size:53
Alignment explanation
Indices: 2718--2845 Score: 215
Period size: 54 Copynumber: 2.4 Consensus size: 53
2708 GAAAAGTAGA
2718 TTTTGAAAAACAGACATTAAAAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 TTTTGAAAAACAGACATTAAAAGGCTCAACTCACCTCTCGCAATATGA-TTGAT
*
2772 TTTTGAAAAACAGAAATTAAAAGGCTCAACTCACCTCTCGCAATATGATTGAT
1 TTTTGAAAAACAGACATTAAAAGGCTCAACTCACCTCTCGCAATATGATTGAT
2825 TCTTTG--AAACAGACATTAAAA
1 T-TTTGAAAAACAGACATTAAAA
2846 ACAGAAATTG
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
52 14 0.20
53 6 0.08
54 51 0.72
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (53 bp):
TTTTGAAAAACAGACATTAAAAGGCTCAACTCACCTCTCGCAATATGATTGAT
Found at i:3072 original size:88 final size:87
Alignment explanation
Indices: 2793--3198 Score: 512
Period size: 88 Copynumber: 4.7 Consensus size: 87
2783 AGAAATTAAA
* *
2793 AGGCTCAACTCACCTCTCGCAATATGA-TTGA-TTCTTTG-AAACAGACATTAAAAAC-AGAAAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTAAAAACAAG-AAT
* * *
2854 TGAAAATAGC-TCAGTGCATGAGCC-A
65 TGAAAATA-CTTCA--GCGTG-TCCTG
* * *
2879 AGACGCAACTCACCTCTCGCAATATGAGTTG--GTTTTTGAAAACATG-AATT-AAAAC-AGAAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACA-GAAATTAAAAACAAGAA-
* * * * *
2939 TTAAAAATACCTCGGCATGTGACCCG
64 TTGAAAATACTTCAGC--GTGTCCTG
2965 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTAAAAACAAGAAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG-AAAACAGAAATTAAAAACAAGAAT
3030 TGAAAATACTTCAGCGTGTCCTG
65 TGAAAATACTTCAGCGTGTCCTG
3053 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTAAAAACAAGAAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG-AAAACAGAAATTAAAAACAAGAAT
3118 TGAAAATACTTCAGCGTGTCCTG
65 TGAAAATACTTCAGCGTGTCCTG
3141 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAA-TAAAAACA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTAAAAACA
3199 TCAAAATACC
Statistics
Matches: 288, Mismatches: 18, Indels: 28
0.86 0.05 0.08
Matches are distributed among these distances:
84 2 0.01
85 5 0.02
86 86 0.30
87 21 0.07
88 142 0.49
89 10 0.03
90 18 0.06
91 4 0.01
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (87 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTAAAAACAAGAATT
GAAAATACTTCAGCGTGTCCTG
Found at i:14850 original size:20 final size:22
Alignment explanation
Indices: 14825--14869 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
14815 ATCTAACACC
14825 ATAATTAAATTTAT-TT-AAAA
1 ATAATTAAATTTATATTGAAAA
*
14845 ATAATTAATTTTATATTGAAAA
1 ATAATTAAATTTATATTGAAAA
14867 ATA
1 ATA
14870 TTTTACCAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.59
21 2 0.09
22 7 0.32
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
ATAATTAAATTTATATTGAAAA
Found at i:15596 original size:12 final size:12
Alignment explanation
Indices: 15579--15614 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
15569 AACATTTTGA
15579 CATTCATGCATT
1 CATTCATGCATT
15591 CATTCATGCATT
1 CATTCATGCATT
*
15603 CATTCATACATT
1 CATTCATGCATT
15615 GCATATCCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.28, C:0.25, G:0.06, T:0.42
Consensus pattern (12 bp):
CATTCATGCATT
Found at i:23960 original size:71 final size:70
Alignment explanation
Indices: 23861--24036 Score: 221
Period size: 71 Copynumber: 2.5 Consensus size: 70
23851 CTTTTCAAGG
* * * *
23861 AAAATCAACTCATATTGCAAG-AGATGAGTTGGGCCTCAAGACACGTTGAGGTATTTTTAATTTT
1 AAAATCAACTCATATTGCGAGAAG-TGAGTTGAGCCTCAAGACACGCTGAGGTATTTTTAATTTA
23925 TGTTTT
65 TGTTTT
** *
23931 CAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTAATTTA
1 -AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTTAATTTA
23996 TGTTTT
65 TGTTTT
** * *
24002 -AAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
24037 TTTAATTTCT
Statistics
Matches: 93, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
69 31 0.33
71 60 0.65
72 2 0.02
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (70 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTTAATTTAT
GTTTT
Found at i:24302 original size:76 final size:76
Alignment explanation
Indices: 24193--25160 Score: 363
Period size: 76 Copynumber: 12.5 Consensus size: 76
24183 TCTACTTTTT
* * *
24193 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACACGCTGAGGTAATTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCATCAGGCACACGCCGAGGT-ATTTCAATTT
* *
24257 CTGTCTTTCAAA
65 CCGTATTTCAAA
* *
24269 AAAAATCAACTCGTATTGCGAGCGGCGAGTTGAGCATCAGGTCACACGCCGAGGTATTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCATCAGG-CACACGCCGAGGTATTTCAATTT
*
24334 CCGTATTTCAATTTCTGCCTTTC
65 CCGTATTTCAA-----------A
* * * * * * * *
24357 AAAAA--AATTGACTCATAT-TGCGAGAGGTGAGTTGAGCCTCAGG-ACACACTGAGGTAATTTC
1 AAAAATCAACTCA-T-AT-TGCGAGA--GGCGAGTTGAGCATCAGGCACACGCCGAGGT-ATTTC
* *
24418 AATTTCTGT-TGTC-AA
60 AATTTCCGTATTTCAAA
* * * * * *
24433 AAAAATCAACTCGTATTGCGAGCGGCGAGTTGAGCCTTAGTCACACTCCGAGGTATTTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCATCAGGCACACGCCGAGGTA-TTTCAATTT
* * *
24498 CTGTTTTTCAATTTCTGCCTTTC
65 CCGTATTTCAA-----------A
* * * * * *
24521 AAAAA--AA-TCAACTCATAT-TGCGAGAGGTGAGTGGAGCCTCAGG-ACACGCTGAGGTAATTT
1 AAAAATCAACTC-A-T-AT-TGCGAGA--GGCGAGTTGAGCATCAGGCACACGCCGAGGT-ATTT
* * *
24581 CAATTTCTGT-TGTAAAA
59 CAATTTCCGTATTTCAAA
*** * * * *
24598 AAAAATCAACTCATATTGCG-GAAATGAGTTGAGCCTCAAG-A-AGTGCTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCATCAGGCACA-CGCCGAGGTA-TTTCAATT
** *
24660 TTTGTCTTTC-AA
64 TCCGTATTTCAAA
* * * * *
24672 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGACACGCTGAGGTAATTTCGATTT
1 AAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCATCAGGCACACGCCGAGGT-ATTTCAATTT
* *
24736 CTGT-TTT---T
65 CCGTATTTCAAA
* * * * *
24744 AAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ATACGCTGAGGTAATTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCATCAGGCACACGCCGAGGT-ATTTCAATTT
24808 -C-TATTGTCAAAAAA
65 CCGTATT-TC---AAA
*** * * * *
24822 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG-ACATGCTGAGGTATTTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCATCAGGCACACGCCGAGGTA-TTTCAATTT
** *
24886 TTGTCTTTCAAA
65 CCGTATTTCAAA
* * * ** *
24898 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGACATACTGAGGTAATTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCATCAGGCACACGCCGAGGT-ATTTCAATTT
24962 -C-TATTTTC---
65 CCGTA-TTTCAAA
* *** * * **
24970 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG-ACACGTTGAGGTATTTTCAATTT
1 AAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCATCAGGCACACGCCGAGGTA-TTTCAATTT
*
25034 CTGT-TTTC-AA
65 CCGTATTTCAAA
* * * * * *
25044 AAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCT-TGGTTCACATGCTGAGGTATTTTCAAT
1 AAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCATCAGG--CACACGCCGAGGTA-TTTCAAT
* *
25108 TTCTGTCTTTC-AA
63 TTCCGTATTTCAAA
* *
25121 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 AAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCATCAG
25161 ATCACACACT
Statistics
Matches: 710, Mismatches: 101, Indels: 160
0.73 0.10 0.16
Matches are distributed among these distances:
70 1 0.00
71 3 0.00
72 116 0.16
73 6 0.01
74 112 0.16
75 66 0.09
76 138 0.19
77 72 0.10
78 72 0.10
79 5 0.01
80 5 0.01
85 2 0.00
86 5 0.01
87 3 0.00
88 35 0.05
89 38 0.05
90 31 0.04
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (76 bp):
AAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCATCAGGCACACGCCGAGGTATTTCAATTTC
CGTATTTCAAA
Found at i:24341 original size:14 final size:14
Alignment explanation
Indices: 24322--24348 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
24312 ACACGCCGAG
24322 GTATTTCAATTTCC
1 GTATTTCAATTTCC
24336 GTATTTCAATTTC
1 GTATTTCAATTTC
24349 TGCCTTTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.19, G:0.07, T:0.52
Consensus pattern (14 bp):
GTATTTCAATTTCC
Found at i:24405 original size:90 final size:90
Alignment explanation
Indices: 24247--24423 Score: 241
Period size: 90 Copynumber: 2.0 Consensus size: 90
24237 CGCTGAGGTA
* * *
24247 ATTTCAATTTCTGTCTTTCAAAAAAAATCAACTCGTATTGCGAGCGGCGAGTTGAGCATCAGGTC
1 ATTTCAATTTCTGCCTTTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCATCAGG--
*
24312 ACACGCCGAGGT-ATTTCAATTTCCGT
64 ACACACCGAGGTAATTTCAATTTCCGT
** * *
24338 ATTTCAATTTCTGCCTTTC-AAAAAAATTGACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC
1 ATTTCAATTTCTGCCTTTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCATCAGGAC
*
24402 ACACTGAGGTAATTTCAATTTC
66 ACACCGAGGTAATTTCAATTTC
24424 TGTTGTCAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
88 10 0.13
89 11 0.14
90 37 0.49
91 18 0.24
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (90 bp):
ATTTCAATTTCTGCCTTTCAAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCATCAGGAC
ACACCGAGGTAATTTCAATTTCCGT
Found at i:24467 original size:164 final size:160
Alignment explanation
Indices: 24193--25160 Score: 879
Period size: 164 Copynumber: 6.2 Consensus size: 160
24183 TCTACTTTTT
24193 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
* * * * *
24258 TGTCTTTCAAAAAAAATCAACTCGTATTGCGAGCGGCGAGTTGAGCATCAGGTCACACGCCGAGG
66 TGT-TGTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACACGCCGAGG
24323 TATTTCAATTTCCGTATTTCAATTTCTGCCTTTCAA
127 TATTTCAATTT-C-TATTTCAATTTCTGCCTTTCAA
** *
24359 AAAAATTGACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
* * * * * *
24424 TGTTGTCAAAAAAATCAACTCGTATTGCGAGCGGCGAGTTGAGCCTTAGTCACACTCCGAGGTAT
66 TGTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG-GACACGCCGAGGTA-
*
24489 TTTCAATTTCTGTTTTTCAATTTCTGCCTTTCAA
129 TTTCAATTTC--TATTTCAATTTCTGCCTTTCAA
*
24523 AAAAATCAACTCATATTGCGAGAGGTGAGTGGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
* ** * * *
24588 TGTTGTAAAAAAAAATCAACTCATATTGCG-GAAATGAGTTGAGCCTCAAGA-AGTGCTGAGG--
66 TGTTGT-CAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA-CGCCGAGGTA
* *
24649 --T--A----T-TTTCAATTTTTGTCTTTCAA
129 TTTCAATTTCTATTTCAATTTCTGCCTTTCAA
* *
24672 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCGATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
** * * *
24737 TGTT-T-TTAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGATACGCTGAGGTAAT
66 TGTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCCGAGGT-AT
**
24800 TTCAATTTCTATTGTCAA----------AAAA
130 TTCAATTTCTATT-TCAATTTCTGCCTTTCAA
** * * * *
24822 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
* * ** *
24887 TGTCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACATACTGAGGTA
66 TGT-TGTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCCGAGGT-
24952 ATTTCAATTTC----T--A----T---TTTC--
128 ATTTCAATTTCTATTTCAATTTCTGCCTTTCAA
* ** * * *
24970 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
* * * * *
25035 TGTTTTCAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCT-TGGTTCACATGCTGAGG-
66 TGTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCCGAGGT
*
25098 ---T--A----T-TTTCAATTTCTGTCTTTCAA
128 ATTTCAATTTCTATTTCAATTTCTGCCTTTCAA
*
25121 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
25161 ATCACACACT
Statistics
Matches: 690, Mismatches: 68, Indels: 103
0.80 0.08 0.12
Matches are distributed among these distances:
140 1 0.00
141 1 0.00
142 1 0.00
143 1 0.00
145 2 0.00
146 58 0.08
147 30 0.04
148 76 0.11
149 89 0.13
150 63 0.09
151 36 0.05
152 2 0.00
154 61 0.09
156 1 0.00
158 2 0.00
159 2 0.00
160 4 0.01
162 1 0.00
163 19 0.03
164 151 0.22
165 24 0.03
166 65 0.09
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (160 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
TGTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCCGAGGTATT
TCAATTTCTATTTCAATTTCTGCCTTTCAA
Found at i:24493 original size:75 final size:73
Alignment explanation
Indices: 24338--25160 Score: 622
Period size: 74 Copynumber: 10.8 Consensus size: 73
24328 CAATTTCCGT
** *
24338 ATTTCAATTTCTGCCTTTCAAAAAAATTGACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
1 ATTTCAATTTCTG--TTTCAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGACA
24403 CACTGAGGTA
64 CACTGAGGTA
* * * *
24413 ATTTCAATTTCTGTTGTCAAAAAAATCAACTCGTATTGCGAGCGGCGAGTTGAGCCTTA-GTCAC
1 ATTTCAATTTCTGTT-TCAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGACAC
24477 ACTCCGAGGTA
65 ACT--GAGGTA
* *** * *
24488 TTTTCAATTTCTGTTTTTCAATTTCTGCCTTTCAAAAA--AA-TCAACTCATATTGCGAGAGGTG
1 ATTTCAATTTCTG--TTTCAA------------AAAAATCAACTC-A-T-ATTGCGAGAG--GCG
* *
24550 AGTGGAGCCTCAGGACACGCTGAGGTA
47 AGTTGAGCCTCAGGACACACTGAGGTA
* *** *
24577 ATTTCAATTTCTGTTGTAAAAAAAAATCAACTCATATTGCG-GAAATGAGTTGAGCCTCAAGA-A
1 ATTTCAATTTCTGTT-T-CAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGACA
**
24640 GTGCTGAGGTA
64 -CACTGAGGTA
* * * *
24651 TTTTCAATTTTTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACA
1 ATTTCAATTTCTG--TTTCAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGACA
*
24716 CGCTGAGGTA
64 CACTGAGGTA
* ** * * * *
24726 ATTTCGATTTCTGTTT-TTAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGATACG
1 ATTTCAATTTCTGTTTCAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGACACA
24790 CTGAGGTA
66 CTGAGGTA
* *** *
24798 ATTTCAATTTCTATTGTCAAAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG
1 ATTTCAATTTCTGTT-TC----AAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGG
**
24863 ACATGCTGAGGTA
61 ACACACTGAGGTA
* * * *
24876 TTTTCAATTTTTGTCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGAC
1 ATTTCAATTTCTG--TTTC-AAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGAC
*
24941 ATACTGAGGTA
63 ACACTGAGGTA
* * *** *
24952 ATTTCAATTTCTATTTTC--AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAC
1 ATTTCAATTTCT-GTTTCAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGACAC
**
25015 GTTGAGGTA
65 ACTGAGGTA
* * * * *
25024 TTTTCAATTTCTGTTTTCAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCT-TGGTTCA
1 ATTTCAATTTCTG-TTTCAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGG-ACA
25088 CATGCTGAGGTA
64 CA--CTGAGGTA
* * *
25100 TTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 ATTTCAATTTCTG--TTTCAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAG
25161 ATCACACACT
Statistics
Matches: 609, Mismatches: 89, Indels: 97
0.77 0.11 0.12
Matches are distributed among these distances:
72 125 0.21
73 15 0.02
74 130 0.21
75 72 0.12
76 91 0.15
77 51 0.08
78 60 0.10
79 5 0.01
80 4 0.01
85 2 0.00
86 2 0.00
87 3 0.00
88 11 0.02
89 20 0.03
90 12 0.02
91 6 0.01
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (73 bp):
ATTTCAATTTCTGTTTCAAAAAAATCAACTCATATTGCGAGAGGCGAGTTGAGCCTCAGGACACA
CTGAGGTA
Found at i:24507 original size:14 final size:14
Alignment explanation
Indices: 24488--24514 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
24478 CTCCGAGGTA
24488 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
24502 TTTTCAATTTCTG
1 TTTTCAATTTCTG
24515 CCTTTCAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:24520 original size:14 final size:14
Alignment explanation
Indices: 24489--24522 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
24479 TCCGAGGTAT
**
24489 TTTCAATTTCTGTT
1 TTTCAATTTCTGCC
24503 TTTCAATTTCTGCC
1 TTTCAATTTCTGCC
24517 TTTCAA
1 TTTCAA
24523 AAAAATCAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.06, T:0.56
Consensus pattern (14 bp):
TTTCAATTTCTGCC
Found at i:24584 original size:89 final size:89
Alignment explanation
Indices: 24414--24591 Score: 243
Period size: 90 Copynumber: 2.0 Consensus size: 89
24404 ACTGAGGTAA
* * * *
24414 TTTCAATTTCTGTTGTCAAAAAAATCAACTCGTATTGCGAGCGGCGAGTTGAGCCTTAGTCACAC
1 TTTCAATTTCTGTTGTCAAAAAAATCAACTCATATTGCGAGAGGCGAGTGGAGCCTCAGTCACAC
* *
24479 TCCGAGGTATTTTCAATTTCTGTT
66 GCCGAGGTAATTTCAATTTCTGTT
* *
24503 TTTCAATTTCTGCCTT-TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTGGAGCCTCAG-GAC
1 TTTCAATTTCTG--TTGTCAAAAAAATCAACTCATATTGCGAGAGGCGAGTGGAGCCTCAGTCAC
*
24566 ACGCTGAGGTAATTTCAATTTCTGTT
64 ACGCCGAGGTAATTTCAATTTCTGTT
24592 GTAAAAAAAA
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
89 37 0.47
90 39 0.50
91 2 0.03
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (89 bp):
TTTCAATTTCTGTTGTCAAAAAAATCAACTCATATTGCGAGAGGCGAGTGGAGCCTCAGTCACAC
GCCGAGGTAATTTCAATTTCTGTT
Found at i:24794 original size:72 final size:73
Alignment explanation
Indices: 24503--25160 Score: 750
Period size: 72 Copynumber: 8.8 Consensus size: 73
24493 AATTTCTGTT
* *
24503 TTTCAATTTCTGCCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTGGAGCCTCAGGACAC
1 TTTCAATTTCTG--TTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
24568 GCTGAGGTAA
64 GCTGAGGTAA
* ** *
24578 TTTCAATTTCTGTTGTAAAAAAAAATCAACTCATATTGCG-GAAATGAGTTGAGCCTCAAGA-AG
1 TTTCAATTTCTGTT-T-TAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA-
* *
24641 TGCTGAGGTAT
63 CGCTGAGGTAA
* *
24652 TTTCAATTTTTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACAC
1 TTTCAATTTCTGT-TTT-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
24717 GCTGAGGTAA
64 GCTGAGGTAA
* * * *
24727 TTTCGATTTCTGTTTT-TAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGATACGC
1 TTTCAATTTCTGTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
24791 TGAGGTAA
66 TGAGGTAA
* * ** *
24799 TTTCAATTTCTATTGTCAAAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGA
1 TTTCAATTTCTGTT-T----TAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGA
* *
24864 CATGCTGAGGTAT
61 CACGCTGAGGTAA
* *
24877 TTTCAATTTTTGTCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACA
1 TTTCAATTTCTGT-TTT--AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
**
24942 TACTGAGGTAA
63 CGCTGAGGTAA
* * * ** * *
24953 TTTCAATTTCTATTTT-CAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGT
1 TTTCAATTTCTGTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
*
25017 TGAGGTAT
66 TGAGGTAA
* *
25025 TTTCAATTTCTGTTTTCAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCT-TGGTTCAC
1 TTTCAATTTCTGTTTT-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---AC
* *
25089 ATGCTGAGGTAT
62 ACGCTGAGGTAA
*
25101 TTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 TTTCAATTTCTGT-TTT-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
25161 ATCACACACT
Statistics
Matches: 494, Mismatches: 66, Indels: 43
0.82 0.11 0.07
Matches are distributed among these distances:
72 125 0.25
73 5 0.01
74 98 0.20
75 75 0.15
76 88 0.18
77 41 0.08
78 61 0.12
79 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.32
Consensus pattern (73 bp):
TTTCAATTTCTGTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
TGAGGTAA
Found at i:24976 original size:226 final size:223
Alignment explanation
Indices: 24523--25155 Score: 972
Period size: 226 Copynumber: 2.8 Consensus size: 223
24513 TGCCTTTCAA
* *
24523 AAAAATCAACTCATATTGCGAGAGGTGAGTGGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
24588 TGTTGT-AAAAAAAAATCAACTCATATTGCG-GAAATGAGTTGAGCCTCAAGA-AGTGCTGAGGT
66 TGTTGTCAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACA-TGCTGAGGT
24650 ATTTTCAATTTTTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGAC
130 ATTTTCAATTTTTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGAC
* * * *
24715 ACGCTGAGGTAATTTCGATTTCTGTTTTT
195 ACACTGAGGTAATTTCAATTTCTATTTTC
*
24744 AAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGATACGCTGAGGTAATTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
*
24809 TATTGTCAAAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGG
66 TGTTGTC--AAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGG
24874 TATTTTCAATTTTTGTCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
129 TATTTTCAATTTTTGTCTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
*
24939 ACATACTGAGGTAATTTCAATTTCTATTTTC
193 ACACACTGAGGTAATTTCAATTTCTATTTTC
** * * *
24970 AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
* * ** **
25035 TGTTTTC--AAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCT-TGGTTCACATGCTGAG
66 TGTTGTCAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG---ACATGCTGAG
*
25097 GTATTTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
128 GTATTTTCAATTTTTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
25156 TTCAGATCAC
Statistics
Matches: 380, Mismatches: 23, Indels: 16
0.91 0.05 0.04
Matches are distributed among these distances:
221 68 0.18
222 36 0.09
223 37 0.10
224 55 0.14
225 50 0.13
226 134 0.35
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (223 bp):
AAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTC
TGTTGTCAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTA
TTTTCAATTTTTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACA
CACTGAGGTAATTTCAATTTCTATTTTC
Found at i:25033 original size:148 final size:148
Alignment explanation
Indices: 24503--25155 Score: 791
Period size: 148 Copynumber: 4.4 Consensus size: 148
24493 AATTTCTGTT
** * *
24503 TTTCAATTTCTGCCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTGGAGCCTCAGGACAC
1 TTTCAATTTCTATCTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACAC
** **
24568 GCTGAGGTAATTTCAATTTCTGTTGTAAAAAAAAATCAACTCATATTGCG-GAAATGAGTTGAGC
65 GCTGAGGTAATTTCAATTTCTGTT-TTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* *
24632 CTCAAGA-AGTGCTGAGGTAT
129 CTCAGGACA-TGCTGAGGTAA
* * **
24652 TTTCAATTTTTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACAC
1 TTTCAATTTCTATCTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACAC
* * *
24717 GCTGAGGTAATTTCGATTTCTGTTTT--TAAAATTCAACTCATATTGCGAGAGGTGAGTTGAGCC
65 GCTGAGGTAATTTCAATTTCTGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
* *
24780 TCAGGATACGCTGAGGTAA
130 TCAGGACATGCTGAGGTAA
* **
24799 TTTCAATTTCTAT-TGTCAAAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG
1 TTTCAATTTCTATCTTTC-----AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG
* * *
24863 ACATGCTGAGGTATTTTCAATTTTTGTCTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGT
61 ACACGCTGAGGTAATTTCAATTTCTGT-TTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGT
* *
24928 TGAGCCTCGGGACATACTGAGGTAA
124 TGAGCCTCAGGACATGCTGAGGTAA
* **
24953 TTTCAATTTCTAT-TTTC-AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACG
1 TTTCAATTTCTATCTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACG
* * *
25016 TTGAGGTATTTTCAATTTCTGTTTTCAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCT
66 CTGAGGTAATTTCAATTTCTGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
* *
25081 -TGGTTCACATGCTGAGGTAT
131 CAGG---ACATGCTGAGGTAA
*
25101 TTTCAATTTCTGTCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 TTTCAATTTCTATCTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
25156 TTCAGATCAC
Statistics
Matches: 445, Mismatches: 43, Indels: 30
0.86 0.08 0.06
Matches are distributed among these distances:
145 2 0.00
146 60 0.13
147 42 0.09
148 90 0.20
149 88 0.20
150 62 0.14
151 35 0.08
154 66 0.15
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.32
Consensus pattern (148 bp):
TTTCAATTTCTATCTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACG
CTGAGGTAATTTCAATTTCTGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
CAGGACATGCTGAGGTAA
Found at i:26057 original size:27 final size:25
Alignment explanation
Indices: 26028--26119 Score: 141
Period size: 25 Copynumber: 3.6 Consensus size: 25
26018 CCCTCCCAAA
26028 AAAAAACCTAACCCAAAAAAAAAGAG
1 AAAAAACCTAACCCAAAAAAAAA-AG
26054 AAAAAAACCTAACCCCAAAAAAAAAAG
1 -AAAAAACCTAA-CCCAAAAAAAAAAG
26081 AAAAAACCTAACCCAAAAAGAAAAAG
1 AAAAAACCTAACCCAAAAA-AAAAAG
26107 -AAAAACCTAACCC
1 AAAAAACCTAACCC
26120 CCNNNNNNNN
Statistics
Matches: 63, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
25 21 0.33
26 17 0.27
27 13 0.21
28 12 0.19
ACGTcount: A:0.67, C:0.23, G:0.05, T:0.04
Consensus pattern (25 bp):
AAAAAACCTAACCCAAAAAAAAAAG
Found at i:39184 original size:29 final size:28
Alignment explanation
Indices: 39146--39221 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 28
39136 ATTTAAATAA
*
39146 ATTTTTAAAATTTAAAAATAATAAAAACT
1 ATTTTAAAAATTTAAAAATAATAAAAA-T
* * *
39175 ATTTTCAAAAA-TTAAATATCATTAAAAT
1 ATTTT-AAAAATTTAAAAATAATAAAAAT
*
39203 TTTTTAAAAATTATAAAAA
1 ATTTTAAAAATT-TAAAAA
39222 ATTACAAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
27 5 0.13
28 6 0.16
29 23 0.61
30 4 0.11
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (28 bp):
ATTTTAAAAATTTAAAAATAATAAAAAT
Found at i:42446 original size:21 final size:21
Alignment explanation
Indices: 42420--42502 Score: 76
Period size: 21 Copynumber: 3.9 Consensus size: 21
42410 TGATCAGTAT
*
42420 ACGACACATAAAGTGCCTAAA
1 ACGACACACAAAGTGCCTAAA
* * * *
42441 ACGACACACGAGGTGCCTGAT
1 ACGACACACAAAGTGCCTAAA
* *
42462 ACGACACACGAGGTGCCTAAAA
1 ACGACACACAAAGTGCCT-AAA
*
42484 TACGACACATAAAGTGCCT
1 -ACGACACACAAAGTGCCT
42503 GATCGATAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
21 34 0.68
22 1 0.02
23 15 0.30
ACGTcount: A:0.39, C:0.27, G:0.20, T:0.14
Consensus pattern (21 bp):
ACGACACACAAAGTGCCTAAA
Found at i:42486 original size:23 final size:22
Alignment explanation
Indices: 42418--42492 Score: 91
Period size: 21 Copynumber: 3.5 Consensus size: 22
42408 CCTGATCAGT
** *
42418 ATACGACACATAAAGTGCCTAA
1 ATACGACACACGAGGTGCCTAA
*
42440 A-ACGACACACGAGGTGCCT-G
1 ATACGACACACGAGGTGCCTAA
42460 ATACGACACACGAGGTGCCTAAA
1 ATACGACACACGAGGTGCCT-AA
42483 ATACGACACA
1 ATACGACACA
42493 TAAAGTGCCT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.02
21 33 0.73
22 1 0.02
23 10 0.22
ACGTcount: A:0.40, C:0.27, G:0.20, T:0.13
Consensus pattern (22 bp):
ATACGACACACGAGGTGCCTAA
Found at i:42903 original size:15 final size:15
Alignment explanation
Indices: 42877--42933 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
42867 CATATATATT
42877 ATATAA-TTCAATCA
1 ATATAATTTCAATCA
42891 ATATAATTTCAATCA
1 ATATAATTTCAATCA
*
42906 AAATAATTTCAATCA
1 ATATAATTTCAATCA
*
42921 ATATAAATTCAAT
1 ATATAATTTCAAT
42934 AAATTCATCG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
14 6 0.15
15 33 0.85
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (15 bp):
ATATAATTTCAATCA
Found at i:43956 original size:5 final size:5
Alignment explanation
Indices: 43948--43989 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
43938 TCTTTAGTTT
43948 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT
43990 TAAAACATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:44025 original size:8 final size:8
Alignment explanation
Indices: 44012--44048 Score: 74
Period size: 8 Copynumber: 4.6 Consensus size: 8
44002 TATCTTTATT
44012 ATATAATA
1 ATATAATA
44020 ATATAATA
1 ATATAATA
44028 ATATAATA
1 ATATAATA
44036 ATATAATA
1 ATATAATA
44044 ATATA
1 ATATA
44049 CTAAACATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATAATA
Found at i:53047 original size:33 final size:33
Alignment explanation
Indices: 53010--53082 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
53000 TTTTGGGCCA
* **
53010 CACGCCCATATCCCATGCCCGTGTGAGTTCTGC
1 CACGCCCATATCCCACGCCCGTGTGAGTTCCAC
* * * *
53043 CACGCCCGTGTCCTACGCCTGTGTGAGTTCCAC
1 CACGCCCATATCCCACGCCCGTGTGAGTTCCAC
53076 CACGCCC
1 CACGCCC
53083 GTGTCTTAGT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.14, C:0.42, G:0.22, T:0.22
Consensus pattern (33 bp):
CACGCCCATATCCCACGCCCGTGTGAGTTCCAC
Found at i:59023 original size:14 final size:14
Alignment explanation
Indices: 59004--59030 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
58994 AGTCGTACAC
59004 AGTACGAGGAGTAT
1 AGTACGAGGAGTAT
59018 AGTACGAGGAGTA
1 AGTACGAGGAGTA
59031 GGATTCTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.37, T:0.19
Consensus pattern (14 bp):
AGTACGAGGAGTAT
Found at i:61395 original size:19 final size:19
Alignment explanation
Indices: 61371--61410 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
61361 ACCACATGAT
61371 ACCGCTTAGTATTAGTTAA
1 ACCGCTTAGTATTAGTTAA
61390 ACCGCTTAGTATTAGTTAA
1 ACCGCTTAGTATTAGTTAA
61409 AC
1 AC
61411 ATTAGACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (19 bp):
ACCGCTTAGTATTAGTTAA
Found at i:61691 original size:14 final size:14
Alignment explanation
Indices: 61669--61699 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
61659 CACTCTATAA
61669 TCTTCTCTCCTTTC
1 TCTTCTCTCCTTTC
*
61683 TCTTTTCTCCTTTC
1 TCTTCTCTCCTTTC
61697 TCT
1 TCT
61700 CATTTTCTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (14 bp):
TCTTCTCTCCTTTC
Found at i:63975 original size:55 final size:55
Alignment explanation
Indices: 63909--64018 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
63899 AAGCTAGATA
*
63909 CCGGTGCGGGTAATGGAGAAGATGGTGAACGAGTGTATGGAGTTACTTCGGCTGG
1 CCGGTGCGGGTAATGGAGAAGATGGTGAAAGAGTGTATGGAGTTACTTCGGCTGG
*
63964 CCGGTGCGGGTAATGGAGAAGATGGTTAAAGAGTGTATGGAGTTACTTCGGCTGG
1 CCGGTGCGGGTAATGGAGAAGATGGTGAAAGAGTGTATGGAGTTACTTCGGCTGG
64019 TAAAGCTTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.23, C:0.12, G:0.41, T:0.25
Consensus pattern (55 bp):
CCGGTGCGGGTAATGGAGAAGATGGTGAAAGAGTGTATGGAGTTACTTCGGCTGG
Found at i:64244 original size:70 final size:70
Alignment explanation
Indices: 64165--64305 Score: 273
Period size: 70 Copynumber: 2.0 Consensus size: 70
64155 ATATCTAAAA
*
64165 TATTTTAGATATAATTATAATATAAAATTTTAACTATAATCAAATTCAGTTTATATATTTTAAAT
1 TATTTTAGATATAATTATAATATAAAATTTTAACTATAATCAAATTCAATTTATATATTTTAAAT
64230 CGATT
66 CGATT
64235 TATTTTAGATATAATTATAATATAAAATTTTAACTATAATCAAATTCAATTTATATATTTTAAAT
1 TATTTTAGATATAATTATAATATAAAATTTTAACTATAATCAAATTCAATTTATATATTTTAAAT
64300 CGATT
66 CGATT
64305 T
1 T
64306 GAGAATTTAA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.48
Consensus pattern (70 bp):
TATTTTAGATATAATTATAATATAAAATTTTAACTATAATCAAATTCAATTTATATATTTTAAAT
CGATT
Found at i:65844 original size:23 final size:23
Alignment explanation
Indices: 65817--65860 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
65807 TTTAGAAATA
*
65817 TAAAAAATTAAAAATATAATTTT
1 TAAAAAATTAAAAAAATAATTTT
**
65840 TAAAATTTTAAAAAAATAATT
1 TAAAAAATTAAAAAAATAATT
65861 AATACTAACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
TAAAAAATTAAAAAAATAATTTT
Found at i:74406 original size:28 final size:27
Alignment explanation
Indices: 74363--74479 Score: 155
Period size: 28 Copynumber: 4.3 Consensus size: 27
74353 AGCATGGCTG
* * *
74363 CCAGAATAGAT-TTTGTGACAGAGTCA
1 CCAGAACAGATATTTGTGGCAGAGCCA
*
74389 CCAGATACAGATATTTGTGGCAGTGCCA
1 CCAGA-ACAGATATTTGTGGCAGAGCCA
74417 CCAGAATCAGATATTTGTGGCAGAGCCA
1 CCAGAA-CAGATATTTGTGGCAGAGCCA
*
74445 CCAGAAACAGATATTTGTGGCATAGCCA
1 CCAG-AACAGATATTTGTGGCAGAGCCA
74473 CCAGAAC
1 CCAGAAC
74480 GCTTCCTCCA
Statistics
Matches: 81, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
26 5 0.06
27 9 0.11
28 65 0.80
29 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.22
Consensus pattern (27 bp):
CCAGAACAGATATTTGTGGCAGAGCCA
Found at i:74447 original size:56 final size:54
Alignment explanation
Indices: 74363--74478 Score: 171
Period size: 56 Copynumber: 2.1 Consensus size: 54
74353 AGCATGGCTG
* *
74363 CCAGAATAGATTTTGTGACAGAGTCACCAGATACAGATATTTGTGGCAGT-GCCA
1 CCAGAATAGATTTTGTGACAGAGCCACCAGAAACAGATATTTGTGGCA-TAGCCA
*
74417 CCAGAATCAGATATTTGTGGCAGAGCCACCAGAAACAGATATTTGTGGCATAGCCA
1 CCAGAAT-AGAT-TTTGTGACAGAGCCACCAGAAACAGATATTTGTGGCATAGCCA
74473 CCAGAA
1 CCAGAA
74479 CGCTTCCTCC
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
54 7 0.12
55 5 0.09
56 44 0.79
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.22
Consensus pattern (54 bp):
CCAGAATAGATTTTGTGACAGAGCCACCAGAAACAGATATTTGTGGCATAGCCA
Found at i:81097 original size:6 final size:6
Alignment explanation
Indices: 81088--81115 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
81078 ATCTAAATAT
81088 AAATCC AAATCC AAATCC AAATCC AAAT
1 AAATCC AAATCC AAATCC AAATCC AAAT
81116 TTTCAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.29, G:0.00, T:0.18
Consensus pattern (6 bp):
AAATCC
Found at i:81103 original size:18 final size:18
Alignment explanation
Indices: 81076--81115 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
81066 AAAAATTTTA
* *
81076 AAATCTAAATATAAATCC
1 AAATCCAAATACAAATCC
*
81094 AAATCCAAATCCAAATCC
1 AAATCCAAATACAAATCC
81112 AAAT
1 AAAT
81116 TTTCAATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.55, C:0.23, G:0.00, T:0.23
Consensus pattern (18 bp):
AAATCCAAATACAAATCC
Found at i:82540 original size:33 final size:33
Alignment explanation
Indices: 82498--82736 Score: 210
Period size: 33 Copynumber: 7.2 Consensus size: 33
82488 ATGACTGCTA
* * *
82498 GGGAGAGTGATGTTGAAGGAGTAGAAACTGATG
1 GGGAGGGTGATGTTGAAGGAGTACAAGCTGATG
* * * *
82531 GGGAGAGTGATGTTGTAGGGGTACAAGCTAATG
1 GGGAGGGTGATGTTGAAGGAGTACAAGCTGATG
* * *
82564 GGGAGGGTAATGTTGAAGGGGTACAAGTTGATG
1 GGGAGGGTGATGTTGAAGGAGTACAAGCTGATG
* * * **
82597 GGAAGGGTGATGTTAAAGGAGTAGAAATTGATG
1 GGGAGGGTGATGTTGAAGGAGTACAAGCTGATG
** * * **
82630 ATGAGGGTGATGTAGAA-GAGGTACAAGCTAACA
1 GGGAGGGTGATGTTGAAGGA-GTACAAGCTGATG
*
82663 GGGAGGGTGATGTTGAAGGAGTAGAAGCTGATG
1 GGGAGGGTGATGTTGAAGGAGTACAAGCTGATG
* * * * *
82696 TGGAGGGTGATATAGAAGGGGTACAAGCTGATC
1 GGGAGGGTGATGTTGAAGGAGTACAAGCTGATG
*
82729 GGAAGGGT
1 GGGAGGGT
82737 AGAAGCTGAT
Statistics
Matches: 162, Mismatches: 42, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
32 2 0.01
33 158 0.98
34 2 0.01
ACGTcount: A:0.31, C:0.05, G:0.42, T:0.22
Consensus pattern (33 bp):
GGGAGGGTGATGTTGAAGGAGTACAAGCTGATG
Found at i:82676 original size:99 final size:99
Alignment explanation
Indices: 82499--82706 Score: 265
Period size: 99 Copynumber: 2.1 Consensus size: 99
82489 TGACTGCTAG
* * * * * * **
82499 GGAGAGTGATGTTGAAGGAGTAGAAACTGATGGGGAGAGTGATGTTGTAGGGGTACAAGCTAATG
1 GGAGGGTGATGTTAAAGGAGTAGAAACTGATGAGGAGAGTGATGTAGAAGAGGTACAAGCTAACA
* *
82564 GGGAGGGTAATGTTGAAGGGGTACAAGTTGATG-
66 GGGAGGGTAATGTTGAAGGAGTACAAGCTGATGT
* * *
82597 GGAAGGGTGATGTTAAAGGAGTAGAAATTGATGATGAGGGTGATGTAGAAGAGGTACAAGCTAAC
1 GG-AGGGTGATGTTAAAGGAGTAGAAACTGATGAGGAGAGTGATGTAGAAGAGGTACAAGCTAAC
* *
82662 AGGGAGGGTGATGTTGAAGGAGTAGAAGCTGATGT
65 AGGGAGGGTAATGTTGAAGGAGTACAAGCTGATGT
82697 GGAGGGTGAT
1 GGAGGGTGAT
82707 ATAGAAGGGG
Statistics
Matches: 93, Mismatches: 15, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
98 2 0.02
99 89 0.96
100 2 0.02
ACGTcount: A:0.31, C:0.04, G:0.42, T:0.23
Consensus pattern (99 bp):
GGAGGGTGATGTTAAAGGAGTAGAAACTGATGAGGAGAGTGATGTAGAAGAGGTACAAGCTAACA
GGGAGGGTAATGTTGAAGGAGTACAAGCTGATGT
Found at i:82821 original size:33 final size:31
Alignment explanation
Indices: 82733--82822 Score: 81
Period size: 33 Copynumber: 2.7 Consensus size: 31
82723 CTGATCGGAA
*
82733 GGGTAGAAGCTGATGGGGAGGGTGATGTAGATG
1 GGGTAGAAGC-GAT-GGGAGGGTGATGTAGAAG
* ** *
82766 GGGTACAAGTTATTGGGAAGGGTGATGTTGAAG
1 GGGTAGAAGCGA-TGGG-AGGGTGATGTAGAAG
82799 GGGTAGAAGGCGATGAGGAGGGTG
1 GGGTAGAA-GCGATG-GGAGGGTG
82823 TGACTGCTAC
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
32 4 0.09
33 37 0.82
34 4 0.09
ACGTcount: A:0.26, C:0.03, G:0.50, T:0.21
Consensus pattern (31 bp):
GGGTAGAAGCGATGGGAGGGTGATGTAGAAG
Found at i:86426 original size:30 final size:30
Alignment explanation
Indices: 86392--86448 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
86382 TCCTTAACTC
86392 AAACTTTGGAAAAATTACAATTTTGCCACT
1 AAACTTTGGAAAAATTACAATTTTGCCACT
* * * *
86422 AAACTTTTGCATATTTACAATTTTGCC
1 AAACTTTGGAAAAATTACAATTTTGCC
86449 CCTAGGCTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.39
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCACT
Found at i:88826 original size:27 final size:27
Alignment explanation
Indices: 88774--88827 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
88764 TTTAAGAATG
*
88774 TATACATAATATAGTATAAAATATATA
1 TATACATAATATAGAATAAAATATATA
*
88801 TATACGTAATATAGAATTTAAAATATA
1 TATACATAATATAGAA--TAAAATATA
88828 CCTAATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 14 0.61
29 9 0.39
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.37
Consensus pattern (27 bp):
TATACATAATATAGAATAAAATATATA
Found at i:88972 original size:22 final size:22
Alignment explanation
Indices: 88953--89028 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 22
88943 ATACTAATGC
88953 TAATAAATAAT-AAATATAATAA
1 TAAT-AATAATAAAATATAATAA
*
88975 TAATAGTAATAAAATATAATAGTA
1 TAATAATAATAAAATATAATA--A
*
88999 TATATAATATTAAAAT-TAA-AA
1 TA-ATAATAATAAAATATAATAA
89020 TAA-AATAAT
1 TAATAATAAT
89029 GAGAAAAAGT
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
19 5 0.11
20 1 0.02
21 8 0.17
22 14 0.30
23 1 0.02
24 6 0.13
25 11 0.24
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (22 bp):
TAATAATAATAAAATATAATAA
Found at i:88993 original size:28 final size:30
Alignment explanation
Indices: 88940--89007 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 30
88930 TTAAATGAAA
*
88940 ATAATACTAATGCTAATAAATAATAA-A-T
1 ATAATAATAATGCTAATAAATAATAATAGT
88968 ATAATAATAATAG-TAATAAA-ATATAATAGT
1 ATAATAATAAT-GCTAATAAATA-ATAATAGT
88998 ATATATAATA
1 ATA-ATAATA
89008 TTAAAATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
27 1 0.03
28 21 0.62
29 2 0.06
30 4 0.12
31 6 0.18
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.34
Consensus pattern (30 bp):
ATAATAATAATGCTAATAAATAATAATAGT
Found at i:90130 original size:3 final size:3
Alignment explanation
Indices: 90124--90392 Score: 89
Period size: 3 Copynumber: 90.0 Consensus size: 3
90114 TTGTTATCAC
* * * *
90124 TAT TAT T-T T-T TAT TCT TTT TAT TAT TACT TAT TAT CAA TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
* * * * *
90167 TAT TAT TAT TAT TAT TGT TAT CAT TAT TGT TAT TAT TAT TAT GAT TCT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
90215 T-T T-T TGT TAA TA- TAGC TAT TAT AAT TA- TAC T-T TAT TTT TAT
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
90256 GT-T TATT TATT TAT TCAT T-T TAT TAT TAGT CCAT TAA T-T TAT TAT
1 -TAT TA-T TA-T TAT T-AT TAT TAT TAT TA-T -TAT TAT TAT TAT TAT
* * * * * * *
90301 TAC TAA CA- TAT TCT TAT TAT TTT TAT TAACG TAT TAT TAT TATT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-A-T TAT TAT TAT TA-T TAT
* *
90348 TGCT CTAT T-T T-T TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 T-AT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
90393 CAATATTTAC
Statistics
Matches: 201, Mismatches: 42, Indels: 46
0.70 0.15 0.16
Matches are distributed among these distances:
2 24 0.12
3 150 0.75
4 24 0.12
5 3 0.01
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:90330 original size:23 final size:23
Alignment explanation
Indices: 90294--90345 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
90284 GTCCATTAAT
* *
90294 TTATTATTACTAACATATTCTTA
1 TTATTTTTACTAACATATTATTA
* *
90317 TTATTTTTATTAACGTATTATTA
1 TTATTTTTACTAACATATTATTA
90340 TTATTT
1 TTATTT
90346 GTTGCTCTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.60
Consensus pattern (23 bp):
TTATTTTTACTAACATATTATTA
Found at i:90526 original size:19 final size:19
Alignment explanation
Indices: 90499--90535 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
90489 TATTTCACTA
90499 TTATCATTTTTTATTACTG
1 TTATCATTTTTTATTACTG
*
90518 TTATTATTTTTTATTACT
1 TTATCATTTTTTATTACT
90536 TACTATCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.08, G:0.03, T:0.68
Consensus pattern (19 bp):
TTATCATTTTTTATTACTG
Found at i:90589 original size:37 final size:36
Alignment explanation
Indices: 90511--90591 Score: 87
Period size: 35 Copynumber: 2.2 Consensus size: 36
90501 ATCATTTTTT
* *
90511 ATTACTGTTATTATTTTTTATTACTTACTATCTAAC
1 ATTATTGTTATTATTTTTTATTACTTACCATCTAAC
*
90547 A-TATTGTTATTCTTTTTT-TTA-TTACCATCTTATTAC
1 ATTATTGTTATTATTTTTTATTACTTACCATC-TA--AC
90583 ATTATTGTT
1 ATTATTGTT
90592 TTTCAAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
33 7 0.18
34 5 0.13
35 15 0.39
36 4 0.11
37 7 0.18
ACGTcount: A:0.25, C:0.12, G:0.04, T:0.59
Consensus pattern (36 bp):
ATTATTGTTATTATTTTTTATTACTTACCATCTAAC
Found at i:90638 original size:34 final size:34
Alignment explanation
Indices: 90600--90697 Score: 81
Period size: 34 Copynumber: 2.9 Consensus size: 34
90590 TTTTTCAAAA
*
90600 TTATTGTTACAAATATTATTATTATTATTAATTT
1 TTATTATTACAAATATTATTATTATTATTAATTT
** * * * *
90634 TTATTATTTGACATATTATTCTTATCACTAATTT
1 TTATTATTACAAATATTATTATTATTATTAATTT
* * *
90668 TTCTTTCTTAC-TATCATTATTATTATTATT
1 TT-ATTATTACAAAT-ATTATTATTATTATT
90698 TTTCTATTTT
Statistics
Matches: 47, Mismatches: 15, Indels: 3
0.72 0.23 0.05
Matches are distributed among these distances:
34 31 0.66
35 16 0.34
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.59
Consensus pattern (34 bp):
TTATTATTACAAATATTATTATTATTATTAATTT
Found at i:95325 original size:60 final size:59
Alignment explanation
Indices: 95192--95326 Score: 148
Period size: 60 Copynumber: 2.2 Consensus size: 59
95182 GTGTTAACTA
* *
95192 GGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCTCTTACAGTAACAGAGTATACTG
1 GGCCTT-GCCCATATCAATATCAATCTGGGCCATAGCCTATTACAGT-ACAGAGTATACTG
* * * *
95253 GGCCTAGCCCATATCAGTATCAATCTGGGCCGTAGCCCTATTACAAGT-C-GAGATATATTG
1 GGCCTTGCCCATATCAATATCAATCTGGGCCATAG-CCTATTAC-AGTACAGAG-TATACTG
*
95313 GGCCTTGTCCATAT
1 GGCCTTGCCCATAT
95327 TGACACAGTT
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
59 3 0.05
60 45 0.71
61 12 0.19
62 3 0.05
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (59 bp):
GGCCTTGCCCATATCAATATCAATCTGGGCCATAGCCTATTACAGTACAGAGTATACTG
Found at i:95373 original size:19 final size:20
Alignment explanation
Indices: 95331--95374 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
95321 CCATATTGAC
** *
95331 ACAGTTGGGCCCATTTTAAT
1 ACAGTTGGGCCCATAATAAA
95351 ACAGTT-GGCCCATAATAAA
1 ACAGTTGGGCCCATAATAAA
95370 ACAGT
1 ACAGT
95375 CTCATATGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (20 bp):
ACAGTTGGGCCCATAATAAA
Found at i:96649 original size:17 final size:19
Alignment explanation
Indices: 96627--96664 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
96617 TGAGAGAAGG
*
96627 ATAGAA-AA-GAATAAAAA
1 ATAGAAGAAGGAAAAAAAA
96644 ATAGAAGAAGGAAAAAAAA
1 ATAGAAGAAGGAAAAAAAA
96663 AT
1 AT
96665 CCTAAAGGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 2 0.11
19 10 0.56
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.11
Consensus pattern (19 bp):
ATAGAAGAAGGAAAAAAAA
Found at i:98834 original size:30 final size:30
Alignment explanation
Indices: 98800--98886 Score: 165
Period size: 30 Copynumber: 2.9 Consensus size: 30
98790 CAAAACCCTA
98800 ACCACCTTGCCTCCCACTTGCACCTACTCC
1 ACCACCTTGCCTCCCACTTGCACCTACTCC
98830 ACCACCTTGCCTCCCACTTGCACCTACTCC
1 ACCACCTTGCCTCCCACTTGCACCTACTCC
*
98860 ACCACCTTGTCTCCCACTTGCACCTAC
1 ACCACCTTGCCTCCCACTTGCACCTAC
98887 ACCATCAAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.17, C:0.52, G:0.07, T:0.24
Consensus pattern (30 bp):
ACCACCTTGCCTCCCACTTGCACCTACTCC
Found at i:101412 original size:19 final size:19
Alignment explanation
Indices: 101388--101433 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
101378 CTTCCTTTCT
*
101388 TTTGCATT-CATTTCATGCA
1 TTTGCATTGCATTGCAT-CA
*
101407 TTTGCATTGCATTGCATTA
1 TTTGCATTGCATTGCATCA
101426 TTTGCATT
1 TTTGCATT
101434 AGGCTTTTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.50
Consensus pattern (19 bp):
TTTGCATTGCATTGCATCA
Found at i:109663 original size:87 final size:87
Alignment explanation
Indices: 109560--111127 Score: 2413
Period size: 87 Copynumber: 18.1 Consensus size: 87
109550 GTGGAGCAGA
*
109560 CTGAATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAATAGATCGAATGCGATGGACCTTAACC
1 CTGAATTTCCAGATCTTAACCCCCTAAGCAGTAGGGAAATAGATCGAATGCGATGGACCTTAACC
109625 CCCTAAGCAGTAGGGTAACAGG
66 CCCTAAGCAGTAGGGTAACAGG
*
109647 CTGAATTTCCAGATCTTAACCCCCTAAGCAGTAGAGAAATAGATCGAATGCGATGGACCTTAACC
1 CTGAATTTCCAGATCTTAACCCCCTAAGCAGTAGGGAAATAGATCGAATGCGATGGACCTTAACC
109712 CCCTAAGCAGTAGGGTAACAGG
66 CCCTAAGCAGTAGGGTAACAGG
109734 CTGAATTTCCAGATCTTAACCCCCTAAGCAGTAGGGAAATAGATCGAATGCGATGGACCTTAACC
1 CTGAATTTCCAGATCTTAACCCCCTAAGCAGTAGGGAAATAGATCGAATGCGATGGACCTTAACC
109799 CCCTAAGCAGTAGGGTAACAGG
66 CCCTAAGCAGTAGGGTAACAGG
109821 CTGAATTTCCAGATCTTAACCCCCTAAGCAGTAGGGAAATAGATCGAATGCGATGGACCTTAACC
1 CTGAATTTCCAGATCTTAACCCCCTAAGCAGTAGGGAAATAGATCGAATGCGATGGACCTTAACC
109886 CCCTAAGCAGTAGGGTAACAGG
66 CCCTAAGCAGTAGGGTAACAGG
109908 CTGAATTTCCAGATCTTAACCCCCTAAGCAGTAGGGAAATAGATCGAATGCGATGGACCTTAACC
1 CTGAATTTCCAGATCTTAACCCCCTAAGCAGTAGGGAAATAGATCGAATGCGATGGACCTTAACC
109973 CCCTAAGCAGTAGGGTAACAGG
66 CCCTAAGCAGTAGGGTAACAGG
109995 CTGAATTTCCAGATCTTAACCCCCTAAGCAGTAGGGAAATAGATCGAATGCGATGGACCTTAACC
1 CTGAATTTCCAGATCTTAACCCCCTAAGCAGTAGGGAAATAGATCGAATGCGATGGACCTTAACC
110060 CCCTAAGCAGTAGGGTAACAGG
66 CCCTAAGCAGTAGGGTAACAGG
110082 CTGAATTTCCAGATCTTAACCCCCTAAGCAGTAGGGAAATAGATCGAATGCGATGGACCTTAACC
1 CTGAATTTCCAGATCTTAACCCCCTAAGCAGTAGGGAAATAGATCGAATGCGATGGACCTTAACC
110147 CCCTAAGCAGTAGGGTAACAGG
66 CCCTAAGCAGTAGGGTAACAGG
110169 CTGAATTTCCAGATCTTAACCCCCTAAGCAGTAGGGAAATAGATCGAATGCGATGGACCTTAACC
1 CTGAATTTCCAGATCTTAACCCCCTAAGCAGTAGGGAAATAGATCGAATGCGATGGACCTTAACC
110234 CCCTAAGCAGTAGGGTAACAGG
66 CCCTAAGCAGTAGGGTAACAGG
110256 CTGAATTTCCAGATCTTAACCCCCTAAGCAGTAGGGAAATAGATCGAATGCGATGGACCTTAACC
1 CTGAATTTCCAGATCTTAACCCCCTAAGCAGTAGGGAAATAGATCGAATGCGATGGACCTTAACC
110321 CCCTAAGCAGTAGGGTAACAGG
66 CCCTAAGCAGTAGGGTAACAGG
110343 CTGAATTTCCAGATCTTAACCCCCTAAGCAGTAGGGAAATAGATCGAATGCGATGGACCTTAACC
1 CTGAATTTCCAGATCTTAACCCCCTAAGCAGTAGGGAAATAGATCGAATGCGATGGACCTTAACC
110408 CCCTAAGCAGTAGGGTAACAGG
66 CCCTAAGCAGTAGGGTAACAGG
* * * ** *
110430 CTGAATTTCCAGATCTTAACCCCCTAAGCAGTAGAGAAACAGATCGAA-GACGAAGGGTCTTAAA
1 CTGAATTTCCAGATCTTAACCCCCTAAGCAGTAGGGAAATAGATCGAATG-CGATGGACCTTAAC
110494 CCCCTAAGCAGTAGGGTAACAGG
65 CCCCTAAGCAGTAGGGTAACAGG
* * ** *
110517 TTGAATTTGCAGATCTTAACCCCCTAAGCAGTAGTGG-AGCAGATCGAAGGCGATGG-CCTTAAC
1 CTGAATTTCCAGATCTTAACCCCCTAAGCAGTAG-GGAAATAGATCGAATGCGATGGACCTTAAC
*
110580 CCCCTAAGCAGTAGGGTAGCAGG
65 CCCCTAAGCAGTAGGGTAACAGG
* * * * *
110603 CTAAATTTACAGATCTTAACCCCCTAAGTAGTAGGGAAACT-GATCGAA-GATGATGGGCCTTAA
1 CTGAATTTCCAGATCTTAACCCCCTAAGCAGTAGGGAAA-TAGATCGAATG-CGATGGACCTTAA
*
110666 ACCCCTAAGCAGTAGGGTAACAGG
64 CCCCCTAAGCAGTAGGGTAACAGG
* * * ** *
110690 CTGAATTTACAGATCTTATCCCCCTAAGTAGTAGTGG-AGCAGATCGAAGGCGATGG-CCTTAAC
1 CTGAATTTCCAGATCTTAACCCCCTAAGCAGTAG-GGAAATAGATCGAATGCGATGGACCTTAAC
* * *
110753 CCCCTAAGCAATAGAGTAGCAGG
65 CCCCTAAGCAGTAGGGTAACAGG
* * * * * * *
110776 CTAAATTTACAGATATTAACCCCCTAAGCAGTAGGGAAACAGATCGAA-GATGATGGGCCTTAAA
1 CTGAATTTCCAGATCTTAACCCCCTAAGCAGTAGGGAAATAGATCGAATG-CGATGGACCTTAAC
*
110840 CCCCTAAGCAGTAGGGTAACAAG
65 CCCCTAAGCAGTAGGGTAACAGG
* * * * * * **
110863 TTCAATTTACAGATCTTAACCCCCTAACCAGTAGGGAAATAGATCGAAGGTGA-CAAGCCTTAA-
1 CTGAATTTCCAGATCTTAACCCCCTAAGCAGTAGGGAAATAGATCGAATGCGATGGA-CCTTAAC
*
110926 CCCCTAAACAGTAGGGTAACAGG
65 CCCCTAAGCAGTAGGGTAACAGG
* * * * * *
110949 CTAAATTTACAGATCTTAACACCCTAAGCAGTAGGGAAACAGATCGAA-GACGATGGGCCTTAAA
1 CTGAATTTCCAGATCTTAACCCCCTAAGCAGTAGGGAAATAGATCGAATG-CGATGGACCTTAAC
*
111013 CCCCTAAGCAGTAGGGTAACAAG
65 CCCCTAAGCAGTAGGGTAACAGG
* * * * * *
111036 TTCAATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAA-GACGATGGGCCTTAAA
1 CTGAATTTCCAGATCTTAACCCCCTAAGCAGTAGGGAAATAGATCGAATG-CGATGGACCTTAAC
* * *
111100 CCCCTAAGCAATAGGGTACCAAG
65 CCCCTAAGCAGTAGGGTAACAGG
111123 CTGAA
1 CTGAA
111128 AATTACAACT
Statistics
Matches: 1389, Mismatches: 74, Indels: 36
0.93 0.05 0.02
Matches are distributed among these distances:
85 7 0.01
86 214 0.15
87 1162 0.84
88 6 0.00
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.20
Consensus pattern (87 bp):
CTGAATTTCCAGATCTTAACCCCCTAAGCAGTAGGGAAATAGATCGAATGCGATGGACCTTAACC
CCCTAAGCAGTAGGGTAACAGG
Found at i:111672 original size:30 final size:30
Alignment explanation
Indices: 111638--111723 Score: 163
Period size: 30 Copynumber: 2.9 Consensus size: 30
111628 AAAACCCTAG
111638 CCACCTTGCCTCCCACTTGCACCTACTCCA
1 CCACCTTGCCTCCCACTTGCACCTACTCCA
111668 CCACCTTGCCTCCCACTTGCACCTACTCCA
1 CCACCTTGCCTCCCACTTGCACCTACTCCA
*
111698 CCACCTTGTCTCCCACTTGCACCTAC
1 CCACCTTGCCTCCCACTTGCACCTAC
111724 ACCATCAAAT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 55 1.00
ACGTcount: A:0.16, C:0.52, G:0.07, T:0.24
Consensus pattern (30 bp):
CCACCTTGCCTCCCACTTGCACCTACTCCA
Found at i:112239 original size:3 final size:3
Alignment explanation
Indices: 112228--112319 Score: 77
Period size: 3 Copynumber: 30.3 Consensus size: 3
112218 TTTATTTTTT
* *
112228 TTA TT- TTA TTA TTT TTA CTA TTA TT- TATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
112272 TTA TTA TT- TCTCA TGTA TATA TTA TTA TT- TATA TTA TTA TTA -TA
1 TTA TTA TTA T-T-A T-TA T-TA TTA TTA TTA T-TA TTA TTA TTA TTA
112316 TTA T
1 TTA T
112320 ATATACCCTC
Statistics
Matches: 74, Mismatches: 6, Indels: 18
0.76 0.06 0.18
Matches are distributed among these distances:
2 7 0.09
3 58 0.78
4 7 0.09
5 2 0.03
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:112321 original size:30 final size:30
Alignment explanation
Indices: 112233--112323 Score: 91
Period size: 30 Copynumber: 3.0 Consensus size: 30
112223 TTTTTTTATT
* *
112233 TTATTATTTTTACTATTATTTATATTAT-TA
1 TTATTATTTATATTATTA-TTATATTATATA
*
112263 TTATTA-TTATTATTATT-TCTCAT-GTATATA
1 TTATTATTTA-TATTATTAT-T-ATATTATATA
112293 TTATTATTTATATTATTATTATATTATATA
1 TTATTATTTATATTATTATTATATTATATA
112323 T
1 T
112324 ACCCTCTCCA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
28 1 0.02
29 8 0.16
30 37 0.74
31 4 0.08
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (30 bp):
TTATTATTTATATTATTATTATATTATATA
Found at i:114750 original size:17 final size:17
Alignment explanation
Indices: 114717--114750 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
114707 ATTACAAAAT
* *
114717 CAAATCTTATCATATTA
1 CAAATCTTATAAGATTA
114734 CAAATCTTATAAGATTA
1 CAAATCTTATAAGATTA
114751 ATTTTCATAT
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:0.44, C:0.15, G:0.03, T:0.38
Consensus pattern (17 bp):
CAAATCTTATAAGATTA
Found at i:115046 original size:64 final size:66
Alignment explanation
Indices: 114967--115093 Score: 186
Period size: 64 Copynumber: 2.0 Consensus size: 66
114957 TTTTTAAAAA
* *
114967 ATATATAATTTATTAAGAAACTAAAAATTA-AATTAAATATACAAGT-AAAAAAATATTTAAATG
1 ATATATAATTGATTAAGAAACTAAAAATTAGAATTAAATATACAAGTGAAAAAAAAATTTAAATG
115030 T
66 T
* * * *
115031 ATATATAATTGATTAATAAACTAAAAATTAGACTTAAATATATATGTGAAAAAAAAATTTAAA
1 ATATATAATTGATTAAGAAACTAAAAATTAGAATTAAATATACAAGTGAAAAAAAAATTTAAA
115094 AATATTGATA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
64 28 0.51
65 13 0.24
66 14 0.25
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (66 bp):
ATATATAATTGATTAAGAAACTAAAAATTAGAATTAAATATACAAGTGAAAAAAAAATTTAAATG
T
Found at i:115348 original size:27 final size:26
Alignment explanation
Indices: 115317--115370 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
115307 ACTAATTAAA
115317 TAGACTAATTTATATTAGTAATTT-TTT
1 TAGACTAATTTA-ATT-GTAATTTATTT
**
115344 TAGACTTTTTTAATTGTAATTTATTT
1 TAGACTAATTTAATTGTAATTTATTT
115370 T
1 T
115371 TGGGCTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 7 0.29
26 7 0.29
27 10 0.42
ACGTcount: A:0.30, C:0.04, G:0.07, T:0.59
Consensus pattern (26 bp):
TAGACTAATTTAATTGTAATTTATTT
Found at i:117830 original size:22 final size:22
Alignment explanation
Indices: 117805--117846 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
117795 TATTATTTTT
*
117805 ATTTTTATATTTAATATTTTAG
1 ATTTTTATATTAAATATTTTAG
* *
117827 ATTTTTTTATTAAATTTTTT
1 ATTTTTATATTAAATATTTT
117847 TGAACAATCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (22 bp):
ATTTTTATATTAAATATTTTAG
Found at i:118580 original size:17 final size:19
Alignment explanation
Indices: 118552--118598 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
118542 TTAAAATCTA
118552 ATTAATTATATT-TATATTT
1 ATTAA-TATATTGTATATTT
*
118571 -TTAATATATTGTATCTTT
1 ATTAATATATTGTATATTT
118589 ATTAATATAT
1 ATTAATATAT
118599 AAATATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 6 0.24
18 10 0.40
19 9 0.36
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTAATATATTGTATATTT
Found at i:120190 original size:118 final size:120
Alignment explanation
Indices: 119999--120236 Score: 363
Period size: 118 Copynumber: 2.0 Consensus size: 120
119989 CTAGTGTTGG
*
119999 CATTGTGAATGCCGACATCTACTAAAATATTTTTTACTTTTTTATTTAAAATCCTAAAATACTAG
1 CATTGTGAATGCCGACACCTACTAAAATA---TTTACTTTTTTATTTAAAATCCTAAAATACTAG
*
120064 TATTTTTAAAGTGTATTTG-AAAAAAATACATATTAGTGCTGACAAACACAGTGTCGA
63 TATTTTTAAAGTGTATTTGAAAAAAAATACATATTAGTGCCGACAAACACAGTGTCGA
* * *
120121 CATTGTGAATGTCGACACCTATTAAAATA-TTATTTTTTTATTTAAAATCCTAAAATACTAGTAT
1 CATTGTGAATGCCGACACCTACTAAAATATTTACTTTTTTATTTAAAATCCTAAAATACTAGTAT
* *
120185 TTTTAAAGTGTATTTGAAAAAAAAATACATATTGGTGCCGACGAACACAGTG
66 TTTTAAAGTGTATTTG-AAAAAAAATACATATTAGTGCCGACAAACACAGTG
120237 CCTACACAAA
Statistics
Matches: 107, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
118 50 0.47
120 31 0.29
122 26 0.24
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (120 bp):
CATTGTGAATGCCGACACCTACTAAAATATTTACTTTTTTATTTAAAATCCTAAAATACTAGTAT
TTTTAAAGTGTATTTGAAAAAAAATACATATTAGTGCCGACAAACACAGTGTCGA
Found at i:124499 original size:26 final size:26
Alignment explanation
Indices: 124470--124551 Score: 146
Period size: 26 Copynumber: 3.2 Consensus size: 26
124460 TGATACAAAT
124470 TGATAATGGATTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
*
124496 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
*
124522 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
124548 TGAT
1 TGAT
124552 GGGAATTTCA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGATTAGGTAAATGTTCCA
Found at i:129172 original size:10 final size:12
Alignment explanation
Indices: 129146--129175 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
129136 TATTCATATG
129146 TATATTTAGGCA
1 TATATTTAGGCA
*
129158 TATATTTAGGAA
1 TATATTTAGGCA
129170 TATATT
1 TATATT
129176 AATATCTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47
Consensus pattern (12 bp):
TATATTTAGGCA
Found at i:130220 original size:7 final size:7
Alignment explanation
Indices: 130212--130262 Score: 77
Period size: 7 Copynumber: 7.4 Consensus size: 7
130202 AACCCCAAAC
*
130212 CCTTGAC
1 CCTTGAA
130219 CCTTGAA
1 CCTTGAA
*
130226 -CATGAA
1 CCTTGAA
130232 CCTTGAA
1 CCTTGAA
130239 CCTTGAA
1 CCTTGAA
130246 CCTTGAA
1 CCTTGAA
130253 CCTTGAA
1 CCTTGAA
130260 CCT
1 CCT
130263 CAAATCCATA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
6 5 0.12
7 35 0.88
ACGTcount: A:0.27, C:0.31, G:0.14, T:0.27
Consensus pattern (7 bp):
CCTTGAA
Found at i:132252 original size:26 final size:26
Alignment explanation
Indices: 132223--132276 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
132213 CTGTCAATAT
132223 TACATCATCATATTTTAATCACATTA
1 TACATCATCATATTTTAATCACATTA
132249 TACATCATCATATTTTAATCACATTA
1 TACATCATCATATTTTAATCACATTA
132275 TA
1 TA
132277 AAATAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.39, C:0.19, G:0.00, T:0.43
Consensus pattern (26 bp):
TACATCATCATATTTTAATCACATTA
Found at i:134130 original size:20 final size:19
Alignment explanation
Indices: 134085--134134 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
134075 GATGAACATC
*
134085 ATAAAAAGAATTTTAATATGA
1 ATAAAAA-AA-TTTAATATCA
134106 A-AAAAAAATTTAATATACA
1 ATAAAAAAATTTAATAT-CA
134125 ATAAAAAAAT
1 ATAAAAAAAT
134135 AATTTTTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 8 0.31
19 4 0.15
20 13 0.50
21 1 0.04
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (19 bp):
ATAAAAAAATTTAATATCA
Found at i:136815 original size:3 final size:3
Alignment explanation
Indices: 136809--136861 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
136799 TAAATGATGA
136809 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
136857 ATT AT
1 ATT AT
136862 GGTTTAGGTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:139444 original size:15 final size:14
Alignment explanation
Indices: 139424--139465 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
139414 TTTATTACAT
139424 TATTATTATTTCTTC
1 TATTATTATTT-TTC
*
139439 TATTATTATTTTTT
1 TATTATTATTTTTC
*
139453 TACTATTATTTTT
1 TATTATTATTTTT
139466 TAGACATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (14 bp):
TATTATTATTTTTC
Found at i:139507 original size:3 final size:3
Alignment explanation
Indices: 139499--139750 Score: 113
Period size: 3 Copynumber: 83.7 Consensus size: 3
139489 ACTAATGTCC
* * * * * * *
139499 TTA TTA TTA CTA TTA TTT TTA TTC TTT TTA TTA TTTA TCA TCA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
* * * * * * *
139545 -TA TTA TTA TTA TTA TTA TTG TTA CTA CTA GTA TTA TTA TAA CTA TTG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * **
139592 TT- TTA TTA CTA TTA CTA CTA CTA TTA TT- TT- TTA CCA TTA TTA TTAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
* * * *
139638 CCTA TTA TTA TTC TTA TTA GTA -TA TTA TTA TTTC TTA TT- TT- TTA
1 -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
* ** * *
139682 TTA TCA TTA TTA TTA ACA TTTA TTA TTA TTA TTA TTAA TGTA CTG TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TT-A T-TA TTA TTA
*
139730 TTC TCTA TTA TTA TTA TTA TT
1 TTA T-TA TTA TTA TTA TTA TT
139751 GTTGTTGTTG
Statistics
Matches: 189, Mismatches: 47, Indels: 26
0.72 0.18 0.10
Matches are distributed among these distances:
2 14 0.07
3 160 0.85
4 13 0.07
5 2 0.01
ACGTcount: A:0.29, C:0.09, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:139646 original size:14 final size:14
Alignment explanation
Indices: 139612--139649 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
139602 ATTACTACTA
* *
139612 CTATTATTTTTTAC
1 CTATTATTATTAAC
139626 C-ATTATTATTAAC
1 CTATTATTATTAAC
139639 CTATTATTATT
1 CTATTATTATT
139650 CTTATTAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (14 bp):
CTATTATTATTAAC
Found at i:139706 original size:22 final size:22
Alignment explanation
Indices: 139678--139719 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
139668 TTTCTTATTT
139678 TTTATTATCATTATTATTAACA
1 TTTATTATCATTATTATTAACA
*
139700 TTTATTATTATTATTATTAA
1 TTTATTATCATTATTATTAA
139720 TGTACTGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTATTATCATTATTATTAACA
Found at i:139755 original size:3 final size:3
Alignment explanation
Indices: 139749--139791 Score: 77
Period size: 3 Copynumber: 14.0 Consensus size: 3
139739 ATTATTATTA
139749 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTCG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT-G TTG
139792 ATAATTATCG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.00, C:0.02, G:0.33, T:0.65
Consensus pattern (3 bp):
TTG
Found at i:144591 original size:14 final size:14
Alignment explanation
Indices: 144572--144623 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
144562 CCAGAAGCAA
144572 AAAAATAAAAATAT
1 AAAAATAAAAATAT
*
144586 AAAAAT-TAAATA-
1 AAAAATAAAAATAT
*
144598 AAAAATATTAAA-AT
1 AAAAATA-AAAATAT
144612 AAAAATAAAAAT
1 AAAAATAAAAAT
144624 GGCTAAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
12 6 0.19
13 9 0.28
14 17 0.53
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAAATAAAAATAT
Found at i:144603 original size:12 final size:13
Alignment explanation
Indices: 144580--144617 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
144570 AAAAAAATAA
144580 AAATATAAAAATT
1 AAATATAAAAATT
*
144593 AAATAAAAAATATT
1 AAATATAAAA-ATT
144607 AAA-ATAAAAAT
1 AAATATAAAAAT
144618 AAAAATGGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 2 0.09
13 14 0.64
14 6 0.27
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
AAATATAAAAATT
Found at i:144623 original size:20 final size:20
Alignment explanation
Indices: 144572--144623 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
144562 CCAGAAGCAA
144572 AAAAATAAAAATATAAAAAT
1 AAAAATAAAAATATAAAAAT
* *
144592 -TAAATAAAAAATATTAAAAT
1 AAAAAT-AAAAATATAAAAAT
144612 AAAAATAAAAAT
1 AAAAATAAAAAT
144624 GGCTAAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 4 0.15
20 19 0.70
21 4 0.15
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (20 bp):
AAAAATAAAAATATAAAAAT
Found at i:152837 original size:30 final size:30
Alignment explanation
Indices: 152803--152863 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
152793 TCCTTAACTC
152803 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
152833 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
152863 A
1 A
152864 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:157511 original size:43 final size:44
Alignment explanation
Indices: 157445--157533 Score: 153
Period size: 43 Copynumber: 2.0 Consensus size: 44
157435 GATGGTGAAA
157445 GAGTGTATGGACTTACTTGGGCTGGTAAAGCTTTTGTTAATGAC
1 GAGTGTATGGACTTACTTGGGCTGGTAAAGCTTTTGTTAATGAC
* *
157489 GAGTGTATGG-GTTACTTTGGCTGGTAAAGCTTTTGTTAATGAC
1 GAGTGTATGGACTTACTTGGGCTGGTAAAGCTTTTGTTAATGAC
157532 GA
1 GA
157534 AAATAATGGA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
43 33 0.77
44 10 0.23
ACGTcount: A:0.22, C:0.10, G:0.30, T:0.37
Consensus pattern (44 bp):
GAGTGTATGGACTTACTTGGGCTGGTAAAGCTTTTGTTAATGAC
Found at i:157722 original size:32 final size:32
Alignment explanation
Indices: 157679--157755 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
157669 CAAAATAAAT
** *
157679 TATGAAAAGTTACGAATGTGAAGAGGCTTGAA
1 TATGAAAAGTTACGAATGCAAAGAGACTTGAA
* **
157711 TATGAAGAGTTAATAATGCAAAGAGACTTGAA
1 TATGAAAAGTTACGAATGCAAAGAGACTTGAA
*
157743 GATGAAAAGTTAC
1 TATGAAAAGTTAC
157756 ACACATGCAT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.44, C:0.06, G:0.25, T:0.25
Consensus pattern (32 bp):
TATGAAAAGTTACGAATGCAAAGAGACTTGAA
Found at i:161849 original size:28 final size:28
Alignment explanation
Indices: 161786--161883 Score: 128
Period size: 27 Copynumber: 3.5 Consensus size: 28
161776 ATATTAAGTC
*
161786 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
161813 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * *
161841 CGCACACTTAGTGCTGA-ACAATTTAAACC
1 CGCACACTTAGTGCT-ATATAA-TCAAACT
161870 CGCACACTTAGTGC
1 CGCACACTTAGTGC
161884 CAATCTCATG
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
27 22 0.34
28 22 0.34
29 20 0.31
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:165174 original size:459 final size:459
Alignment explanation
Indices: 164316--165232 Score: 1613
Period size: 459 Copynumber: 2.0 Consensus size: 459
164306 CAAAGCCTCA
*
164316 TAAGGTGCCATCTTAATACTTGATTGAAAACTATTGTTGTAAGCGAATTCAATCAAAGGTAAATA
1 TAAGGTGCCATCTTAATACTTGACTGAAAACTATTGTTGTAAGCGAATTCAATCAAAGGTAAATA
* *
164381 CCGTTCCCATGAACTACTGAACTCGAGGATGCAACATCTCAACATATCCTCAAGTATCTGAATTA
66 CCGTTCCCATGAACTACTAAACTCAAGGATGCAACATCTCAACATATCCTCAAGTATCTGAATTA
164446 TCCGCTCGGATTGACCATCGGTTTGGGGATGAAAAGCAGTGCTAAAATGCAGCTTGGTACCCAAG
131 TCCGCTCGGATTGACCATCGGTTTGGGGATGAAAAGCAGTGCTAAAATGCAGCTTGGTACCCAAG
164511 GCTTCTTACAATTTCTTCCAAAATCGTGAGGTGAATCTCGGATCTCAATCTGACACGATAGAAAT
196 GCTTCTTACAATTTCTTCCAAAATCGTGAGGTGAATCTCGGATCTCAATCTGACACGATAGAAAT
* * * *
164576 AGGTACCCCGTGTAATCTCACAATTTGATAAACGTACAATTCAGCTAGTTTATCCAATGAAAAAT
261 AGGTACCCCGTGTAATCTCACAATCTGAGAAACATACAATTCAGCTAATTTATCCAATGAAAAAT
* * *
164641 CCGTACGTACGGGGATGAAATGAGCCGACTTAGTCAGTCTATCAACAATAACCCATATCGCATCC
326 CCGTACGCACGGGGATGAAATGAGCCGACTTAGTCAGTCTATCAACAACAACCCAAATCGCATCC
164706 TTCTTACTTGCTGACAAAGGCAGTCCGGACACAAAGTCCATTGTGACTCGATCCCATTTCCACTC
391 TTCTTACTTGCTGACAAAGGCAGTCCGGACACAAAGTCCATTGTGACTCGATCCCATTTCCACTC
164771 GGGG
456 GGGG
164775 TAAGGTGCCATCTTAATACTTGACTGAAAACTATTGTTGTAAGCGAATTCAATCAAAGGTAAATA
1 TAAGGTGCCATCTTAATACTTGACTGAAAACTATTGTTGTAAGCGAATTCAATCAAAGGTAAATA
* * *
164840 CCGTTCCCATGAACCT-CTAAACTCAAGGATGCAGCATCTCAGCATATCCTCGAGTATCTGAATT
66 CCGTTCCCATGAA-CTACTAAACTCAAGGATGCAACATCTCAACATATCCTCAAGTATCTGAATT
*
164904 ATCCGCTCGGATTGACCATCGGTTTGGGGATGAAAAGCGGTGCTAAAATGCAGCTTGGTACCCAA
130 ATCCGCTCGGATTGACCATCGGTTTGGGGATGAAAAGCAGTGCTAAAATGCAGCTTGGTACCCAA
*
164969 GGCTTCTTACAATTTCTTCCAAAATCGTGAGGTGAATCTCGGATCTCTATCTGACACGATAGAAA
195 GGCTTCTTACAATTTCTTCCAAAATCGTGAGGTGAATCTCGGATCTCAATCTGACACGATAGAAA
* * *
165034 TAGGTACCCCGTTTAATCTCACAATCTGAGAAACATACAATTCGGGTAATTTATCCAATGAAAAA
260 TAGGTACCCCGTGTAATCTCACAATCTGAGAAACATACAATTCAGCTAATTTATCCAATGAAAAA
*
165099 TCCGTACGCACGGGGAT-AAAGTGAGCCGACTTAGTCAGTCTATCAACAACAACCCAAATCGTAT
325 TCCGTACGCACGGGGATGAAA-TGAGCCGACTTAGTCAGTCTATCAACAACAACCCAAATCGCAT
**
165163 CCTTCTTACTTGCTGACAGTGGCAGTCCGGACACAAAGTCCATTGTGACTCGATCCCATTTCCAC
389 CCTTCTTACTTGCTGACAAAGGCAGTCCGGACACAAAGTCCATTGTGACTCGATCCCATTTCCAC
165228 TCGGG
454 TCGGG
165233 TATCATGATC
Statistics
Matches: 435, Mismatches: 21, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
458 3 0.01
459 430 0.99
460 2 0.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (459 bp):
TAAGGTGCCATCTTAATACTTGACTGAAAACTATTGTTGTAAGCGAATTCAATCAAAGGTAAATA
CCGTTCCCATGAACTACTAAACTCAAGGATGCAACATCTCAACATATCCTCAAGTATCTGAATTA
TCCGCTCGGATTGACCATCGGTTTGGGGATGAAAAGCAGTGCTAAAATGCAGCTTGGTACCCAAG
GCTTCTTACAATTTCTTCCAAAATCGTGAGGTGAATCTCGGATCTCAATCTGACACGATAGAAAT
AGGTACCCCGTGTAATCTCACAATCTGAGAAACATACAATTCAGCTAATTTATCCAATGAAAAAT
CCGTACGCACGGGGATGAAATGAGCCGACTTAGTCAGTCTATCAACAACAACCCAAATCGCATCC
TTCTTACTTGCTGACAAAGGCAGTCCGGACACAAAGTCCATTGTGACTCGATCCCATTTCCACTC
GGGG
Found at i:171782 original size:32 final size:32
Alignment explanation
Indices: 171739--171815 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
171729 CAAAATAAAT
** *
171739 TATGAAAAGTTACGAATGTGAAGAGGCTTGAA
1 TATGAAAAGTTACGAATGCAAAGAGACTTGAA
* **
171771 TATGAAGAGTTAATAATGCAAAGAGACTTGAA
1 TATGAAAAGTTACGAATGCAAAGAGACTTGAA
*
171803 GATGAAAAGTTAC
1 TATGAAAAGTTAC
171816 ACACATGCAT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.44, C:0.06, G:0.25, T:0.25
Consensus pattern (32 bp):
TATGAAAAGTTACGAATGCAAAGAGACTTGAA
Found at i:175748 original size:15 final size:14
Alignment explanation
Indices: 175728--175769 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
175718 CGATGAATTT
175728 ATTGAATTTATATTG
1 ATTGAA-TTATATTG
*
175743 ATTGAAATTATTTTG
1 ATTG-AATTATATTG
175758 ATTGAATTATAT
1 ATTGAATTATAT
175770 AATATATGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 7 0.29
15 15 0.62
16 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (14 bp):
ATTGAATTATATTG
Found at i:176184 original size:23 final size:23
Alignment explanation
Indices: 176153--176226 Score: 75
Period size: 21 Copynumber: 3.4 Consensus size: 23
176143 ATCACTTTAC
176153 GTGTCGTATTTTAGGCACCTCAT
1 GTGTCGTATTTTAGGCACCTCAT
* *
176176 GTGTTGTA--TTAGGCACCTCGT
1 GTGTCGTATTTTAGGCACCTCAT
* *
176197 GTGTCG--TTTTAGGCACTTTAT
1 GTGTCGTATTTTAGGCACCTCAT
*
176218 GTGTTGTAT
1 GTGTCGTAT
176227 ACTGATTAGG
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
21 32 0.80
23 8 0.20
ACGTcount: A:0.15, C:0.16, G:0.26, T:0.43
Consensus pattern (23 bp):
GTGTCGTATTTTAGGCACCTCAT
Found at i:176189 original size:21 final size:21
Alignment explanation
Indices: 176163--176226 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
176153 GTGTCGTATT
176163 TTAGGCACCTCATGTGTTGTA
1 TTAGGCACCTCATGTGTTGTA
* * *
176184 TTAGGCACCTCGTGTGTCGTT
1 TTAGGCACCTCATGTGTTGTA
* *
176205 TTAGGCACTTTATGTGTTGTA
1 TTAGGCACCTCATGTGTTGTA
176226 T
1 T
176227 ACTGATTAGG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.16, C:0.17, G:0.25, T:0.42
Consensus pattern (21 bp):
TTAGGCACCTCATGTGTTGTA
Found at i:184748 original size:28 final size:29
Alignment explanation
Indices: 184682--184750 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 29
184672 ATTGGGGTCG
* * *
184682 ATGGGTCATATGTATGTGATTTGGGCCTA
1 ATGGGTCATATGAATGAGATTTAGGCCTA
**
184711 ATGGCCCATATGAATGAGA-TTAGGCCTA
1 ATGGGTCATATGAATGAGATTTAGGCCTA
*
184739 GTGGGTCATATG
1 ATGGGTCATATG
184751 CATGTATGTG
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
28 17 0.53
29 15 0.47
ACGTcount: A:0.25, C:0.13, G:0.30, T:0.32
Consensus pattern (29 bp):
ATGGGTCATATGAATGAGATTTAGGCCTA
Found at i:201320 original size:18 final size:18
Alignment explanation
Indices: 201297--201335 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
201287 TTTCGAAAAG
201297 ACTTAATTTGGTTTCCAA
1 ACTTAATTTGGTTTCCAA
201315 ACTTAATTTGGTTTCCAA
1 ACTTAATTTGGTTTCCAA
201333 ACT
1 ACT
201336 CATGAAAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.18, G:0.10, T:0.44
Consensus pattern (18 bp):
ACTTAATTTGGTTTCCAA
Found at i:205393 original size:24 final size:24
Alignment explanation
Indices: 205366--205413 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
205356 CATATCATAA
205366 TCCATTCATTCACATGCACTTTGT
1 TCCATTCATTCACATGCACTTTGT
205390 TCCATTCATTCACATGCACTTTGT
1 TCCATTCATTCACATGCACTTTGT
205414 CCCTAAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.29, G:0.08, T:0.42
Consensus pattern (24 bp):
TCCATTCATTCACATGCACTTTGT
Found at i:215180 original size:26 final size:26
Alignment explanation
Indices: 215144--215275 Score: 85
Period size: 26 Copynumber: 5.0 Consensus size: 26
215134 TACTTTTAAA
215144 TAAAT-AGTTAATAGAATCAATTGGT
1 TAAATCAGTTAATAGAATCAATTGGT
* *
215169 TAAATCAGTTAATAGAATCAGTT-GC
1 TAAATCAGTTAATAGAATCAATTGGT
*** *
215194 T--ATCAGTTAAGTTTTATCAAATACT-TT
1 TAAATCAGTTAA-TAGAATC-AAT--TGGT
*
215221 TAAATAAATAGTTAATAGAATCAATTGGT
1 TAAAT---CAGTTAATAGAATCAATTGGT
* *
215250 TAAATTAGTTAATAGAATCAGTTGGT
1 TAAATCAGTTAATAGAATCAATTGGT
215276 CAAACTAGCC
Statistics
Matches: 82, Mismatches: 14, Indels: 21
0.70 0.12 0.18
Matches are distributed among these distances:
23 9 0.11
24 4 0.05
25 9 0.11
26 36 0.44
27 2 0.02
28 1 0.01
29 8 0.10
30 3 0.04
31 4 0.05
32 6 0.07
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (26 bp):
TAAATCAGTTAATAGAATCAATTGGT
Found at i:215196 original size:81 final size:81
Alignment explanation
Indices: 215111--215273 Score: 317
Period size: 81 Copynumber: 2.0 Consensus size: 81
215101 TCAGCTTTCA
215111 GCTATCAGTTAAGTTTTATCAAATACTTTTAAATAAATAGTTAATAGAATCAATTGGTTAAATCA
1 GCTATCAGTTAAGTTTTATCAAATACTTTTAAATAAATAGTTAATAGAATCAATTGGTTAAATCA
215176 GTTAATAGAATCAGTT
66 GTTAATAGAATCAGTT
*
215192 GCTATCAGTTAAGTTTTATCAAATACTTTTAAATAAATAGTTAATAGAATCAATTGGTTAAATTA
1 GCTATCAGTTAAGTTTTATCAAATACTTTTAAATAAATAGTTAATAGAATCAATTGGTTAAATCA
215257 GTTAATAGAATCAGTT
66 GTTAATAGAATCAGTT
215273 G
1 G
215274 GTCAAACTAG
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (81 bp):
GCTATCAGTTAAGTTTTATCAAATACTTTTAAATAAATAGTTAATAGAATCAATTGGTTAAATCA
GTTAATAGAATCAGTT
Found at i:216012 original size:20 final size:18
Alignment explanation
Indices: 215987--216031 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 18
215977 AGAATTTAAA
*
215987 AAAAATCAAAATAACTTTTT
1 AAAAATCAAAA-AA-TTTAT
216007 AAAAATTCAAAAAATTTAT
1 AAAAA-TCAAAAAATTTAT
216026 AAAAAT
1 AAAAAT
216032 ATTTAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 1 0.04
19 9 0.39
20 7 0.30
21 6 0.26
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAAATCAAAAAATTTAT
Found at i:216906 original size:15 final size:15
Alignment explanation
Indices: 216886--216916 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
216876 TATACTTATT
216886 TTTTTAAATATTTTA
1 TTTTTAAATATTTTA
216901 TTTTTAAATATTTTA
1 TTTTTAAATATTTTA
216916 T
1 T
216917 AAATTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTTTAAATATTTTA
Found at i:219805 original size:24 final size:25
Alignment explanation
Indices: 219769--219819 Score: 95
Period size: 24 Copynumber: 2.1 Consensus size: 25
219759 ATTATAAAAA
219769 AAACACTTAGAGTTATTGAGATGCT
1 AAACACTTAGAGTTATTGAGATGCT
219794 AAACACTT-GAGTTATTGAGATGCT
1 AAACACTTAGAGTTATTGAGATGCT
219818 AA
1 AA
219820 GGCATCTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 18 0.69
25 8 0.31
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (25 bp):
AAACACTTAGAGTTATTGAGATGCT
Found at i:220813 original size:15 final size:15
Alignment explanation
Indices: 220793--220842 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
220783 TGTAGTTGAA
220793 GATGACGACGACAAC
1 GATGACGACGACAAC
* *
220808 GATGACGACGACGAT
1 GATGACGACGACAAC
* *
220823 GATGACGATGACAAG
1 GATGACGACGACAAC
220838 GATGA
1 GATGA
220843 AGATGATGCC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.38, C:0.18, G:0.32, T:0.12
Consensus pattern (15 bp):
GATGACGACGACAAC
Found at i:223184 original size:13 final size:13
Alignment explanation
Indices: 223163--223195 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
223153 AAATGAACTT
*
223163 AAAATTCTTTAAA
1 AAAAATCTTTAAA
223176 AAAAATC-TTAAA
1 AAAAATCTTTAAA
223188 AAAAATCT
1 AAAAATCT
223196 CAATATCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAAATCTTTAAA
Found at i:223453 original size:20 final size:21
Alignment explanation
Indices: 223411--223460 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
223401 TAGTTATATA
* *
223411 ATGTAATATAATATTATAGTAT
1 ATGT-ATATAATATAATACTAT
*
223433 A-GTATATAATGTAATACTAT
1 ATGTATATAATATAATACTAT
223453 ATGTATAT
1 ATGTATAT
223461 GTATTAATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 15 0.62
21 8 0.33
22 1 0.04
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (21 bp):
ATGTATATAATATAATACTAT
Found at i:224842 original size:20 final size:21
Alignment explanation
Indices: 224804--224844 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
224794 AAATTAATAC
224804 TAAATTTTAAAATATATTAAT
1 TAAATTTTAAAATATATTAAT
*
224825 TAAATTTTCAAA-ATATTAAT
1 TAAATTTTAAAATATATTAAT
224845 ATTATATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
TAAATTTTAAAATATATTAAT
Found at i:224848 original size:22 final size:21
Alignment explanation
Indices: 224796--224853 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
224786 TTAATTTAAA
*
224796 ATTAATACTAAATTTTAAAAT
1 ATTAATATTAAATTTTAAAAT
*
224817 A-TATTAATTAAATTTTCAAAAT
1 ATTAAT-ATTAAATTTT-AAAAT
*
224839 ATTAATATTATATTT
1 ATTAATATTAAATTT
224854 ATTTAACTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
20 3 0.10
21 10 0.33
22 14 0.47
23 3 0.10
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTAATATTAAATTTTAAAAT
Found at i:225870 original size:20 final size:19
Alignment explanation
Indices: 225826--225875 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
225816 AAATGGTAAT
*
225826 TAAATCAATTTGATTAAAA
1 TAAATCAAATTGATTAAAA
*
225845 TCAAATCAAATTGATTAGCAA
1 T-AAATCAAATTGATTA-AAA
*
225866 TAAATAAAAT
1 TAAATCAAAT
225876 AATGGTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 1 0.04
20 22 0.85
21 3 0.12
ACGTcount: A:0.54, C:0.08, G:0.06, T:0.32
Consensus pattern (19 bp):
TAAATCAAATTGATTAAAA
Found at i:227704 original size:24 final size:24
Alignment explanation
Indices: 227677--227728 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
227667 TTAGTAAGTC
*
227677 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
227701 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
227725 AAAT
1 AAAT
227729 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:229673 original size:24 final size:24
Alignment explanation
Indices: 229646--229697 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
229636 TTAGTAAGTC
*
229646 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
229670 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
229694 AAAT
1 AAAT
229698 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:232579 original size:70 final size:70
Alignment explanation
Indices: 232498--232635 Score: 258
Period size: 70 Copynumber: 2.0 Consensus size: 70
232488 AACTCTTCCT
*
232498 CCCTTTAGGGATTTTCGTCCTCGAAAATCTTACCAGAAAAGAGGTTAAGGTTTCAGCATAAATCC
1 CCCTTTAGGGATTTTCGTCCCCGAAAATCTTACCAGAAAAGAGGTTAAGGTTTCAGCATAAATCC
232563 TCCCC
66 TCCCC
*
232568 CCCTTTAGGGATTTTCGTCCCCGAAAATCTTATCAGAAAAGAGGTTAAGGTTTCAGCATAAATCC
1 CCCTTTAGGGATTTTCGTCCCCGAAAATCTTACCAGAAAAGAGGTTAAGGTTTCAGCATAAATCC
232633 TCC
66 TCC
232636 ATCCTGTAAT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 66 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (70 bp):
CCCTTTAGGGATTTTCGTCCCCGAAAATCTTACCAGAAAAGAGGTTAAGGTTTCAGCATAAATCC
TCCCC
Found at i:233881 original size:559 final size:559
Alignment explanation
Indices: 232812--233940 Score: 2091
Period size: 559 Copynumber: 2.0 Consensus size: 559
232802 TTACTCACAA
*
232812 TCTTTCAA-TAGCTCAAATAATCATTACTGTCTTAAATTCAAATTTTTCTGTCACATTCGACACT
1 TCTTT-AACTAGCTCAAATAATCATTACTGTCTTAAATTCAAATTTTTCTGTAACATTCGACACT
* * *********
232876 TTAAACTCTTGGAATCATGGAGTATGTAGCAATTTTTTTTTTTTTTCCAGACTATCCGTCTATTT
65 TCAAACTCTTGGAATCAGGGAGTATGTAGCAA-TAAAAAAAAATTTCCAGACTATCCGTCTATTT
232941 ACCCATGAATACATAAAATTCATTTCCAAACTCGAGGATCGATTTACATGCATATATCTCAATTT
129 ACCCATGAATACATAAAATTCATTTCCAAACTCGAGGATCGATTTACATGCATATATCTCAATTT
233006 ACCTTCCAACTGAATAACTTGTTCTGATTAAAACATTTTATTCCATCTTAACTGTCAAACAATAA
194 ACCTTCCAACTGAATAACTTGTTCTGATTAAAACATTTTATTCCATCTTAACTGTCAAACAATAA
233071 TAACCTTTCAAACAATTTCCTCTTCAAGTTGTTAGAACAACTCAATCACATAATCTTTCACAATT
259 TAACCTTTCAAACAATTTCCTCTTCAAGTTGTTAGAACAACTCAATCACATAATCTTTCACAATT
233136 CCGTAACATGCTAGTCAAAAAGCTTTACTAACGGCATTAGTTCAAACAAAACACCACATCTCGAT
324 CCGTAACATGCTAGTCAAAAAGCTTTACTAACGGCATTAGTTCAAACAAAACACCACATCTCGAT
233201 TTATGTCATTGACCTTAATCAATATTACCTAATAAAAGAAAATCAATATAAAAATTTAGCTTGAA
389 TTATGTCATTGACCTTAATCAATATTACCTAATAAAAGAAAATCAATATAAAAATTTAGCTTGAA
233266 CAGTCACAATCTACAATTTGTCGATGCCAATCTTCTTAAGAAAACTAGAAGAATTCCTGATAACA
454 CAGTCACAATCTACAATTTGTCGATGCCAATCTTCTTAAGAAAACTAGAAGAATTCCTGATAACA
233331 CATTCTTTAGATATCATACATGGATAAGTTGATTGTCCTCT
519 CATTCTTTAGATATCATACATGGATAAGTTGATTGTCCTCT
* *
233372 TCTTTAACTANGCTCAAATCATCATTACTGTCTTAAATTCAAATTTTTCTGTAATATTCGACACT
1 TCTTTAACTA-GCTCAAATAATCATTACTGTCTTAAATTCAAATTTTTCTGTAACATTCGACACT
233437 TCAAACTCTTGGAATCAGGGAGTATGTAGCAA-AAAAAAAAATTTCCAGACTATCCGTCTATTTA
65 TCAAACTCTTGGAATCAGGGAGTATGTAGCAATAAAAAAAAATTTCCAGACTATCCGTCTATTTA
233501 CCCATGAATACATAAAATTCATTTCCAAACTCGAGGATCGATTTACATGCATATATCTCAATTTA
130 CCCATGAATACATAAAATTCATTTCCAAACTCGAGGATCGATTTACATGCATATATCTCAATTTA
233566 CCTTCCAACTGAATAACTTGTTCTGATTAAAACATTTTATTCCATCTTAACTGTCAAACAATAAT
195 CCTTCCAACTGAATAACTTGTTCTGATTAAAACATTTTATTCCATCTTAACTGTCAAACAATAAT
233631 AACCTTTCAAACAATTTCCTCTTCAAGTTGTTAGAACAACTCAATCACATAATCTTTCACAATTC
260 AACCTTTCAAACAATTTCCTCTTCAAGTTGTTAGAACAACTCAATCACATAATCTTTCACAATTC
233696 CGTAACATGCTAGTCAAAAAGCTTTACTAACGGCATTAGTTCAAACAAAACACCACATCTCGATT
325 CGTAACATGCTAGTCAAAAAGCTTTACTAACGGCATTAGTTCAAACAAAACACCACATCTCGATT
233761 TATGTCATTGACCTTAATCAATATTACCTAATAAAAGAAAATCAATATAAAAATTTAGCTTGAAC
390 TATGTCATTGACCTTAATCAATATTACCTAATAAAAGAAAATCAATATAAAAATTTAGCTTGAAC
233826 AGTCACAATCTACAATTTGTCGATGCCAATCTTCTTAAGAAAACTAGAAGAATTCCTGATAACAC
455 AGTCACAATCTACAATTTGTCGATGCCAATCTTCTTAAGAAAACTAGAAGAATTCCTGATAACAC
233891 ATTCTTTAGATATCATACATGGATAAGTTGATTGTCCTCT
520 ATTCTTTAGATATCATACATGGATAAGTTGATTGTCCTCT
233931 TCTTTAACTA
1 TCTTTAACTA
233941 TGGCATCACT
Statistics
Matches: 553, Mismatches: 14, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
559 465 0.84
560 7 0.01
561 81 0.15
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.34
Consensus pattern (559 bp):
TCTTTAACTAGCTCAAATAATCATTACTGTCTTAAATTCAAATTTTTCTGTAACATTCGACACTT
CAAACTCTTGGAATCAGGGAGTATGTAGCAATAAAAAAAAATTTCCAGACTATCCGTCTATTTAC
CCATGAATACATAAAATTCATTTCCAAACTCGAGGATCGATTTACATGCATATATCTCAATTTAC
CTTCCAACTGAATAACTTGTTCTGATTAAAACATTTTATTCCATCTTAACTGTCAAACAATAATA
ACCTTTCAAACAATTTCCTCTTCAAGTTGTTAGAACAACTCAATCACATAATCTTTCACAATTCC
GTAACATGCTAGTCAAAAAGCTTTACTAACGGCATTAGTTCAAACAAAACACCACATCTCGATTT
ATGTCATTGACCTTAATCAATATTACCTAATAAAAGAAAATCAATATAAAAATTTAGCTTGAACA
GTCACAATCTACAATTTGTCGATGCCAATCTTCTTAAGAAAACTAGAAGAATTCCTGATAACACA
TTCTTTAGATATCATACATGGATAAGTTGATTGTCCTCT
Found at i:235631 original size:25 final size:24
Alignment explanation
Indices: 235556--235755 Score: 223
Period size: 25 Copynumber: 8.4 Consensus size: 24
235546 CACTAATGAA
*
235556 CAGAGAGCACTGAAGTGCT-ATA-
1 CAGAGAGCACTGACGTGCTAATAT
** *
235578 CAGAGAGCACAAATGTGCT-A-AT
1 CAGAGAGCACTGACGTGCTAATAT
235600 CAGAGAGCACTGACGTGCTAAATAT
1 CAGAGAGCACTGACGTGCT-AATAT
** *
235625 CAGAGAGCACAAATGTGCT-A-AT
1 CAGAGAGCACTGACGTGCTAATAT
235647 CAGAGAGCACTGACGTGCTAAATAT
1 CAGAGAGCACTGACGTGCT-AATAT
*
235672 CAGAGAGCACTGACGTACTAAATAT
1 CAGAGAGCACTGACGTGCT-AATAT
*
235697 CAGAGAGCACTGGCGTGCTAATAAT
1 CAGAGAGCACTGACGTGCTAAT-AT
*
235722 CAGAGAGCACTGGCGTGCTAATATT
1 CAGAGAGCACTGACGTGCTAATA-T
235747 CAGAGAGCA
1 CAGAGAGCA
235756 TGCTGAGGTC
Statistics
Matches: 154, Mismatches: 15, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.01
22 51 0.33
23 1 0.01
24 6 0.04
25 95 0.62
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.19
Consensus pattern (24 bp):
CAGAGAGCACTGACGTGCTAATAT
Found at i:235632 original size:47 final size:46
Alignment explanation
Indices: 235556--235731 Score: 230
Period size: 47 Copynumber: 3.7 Consensus size: 46
235546 CACTAATGAA
*
235556 CAGAGAGCACTGAAGTGCT-ATA-CAGAGAGCACAAATGTGCTAAT
1 CAGAGAGCACTGACGTGCTAATATCAGAGAGCACAAATGTGCTAAT
235600 CAGAGAGCACTGACGTGCTAAATATCAGAGAGCACAAATGTGCTAAT
1 CAGAGAGCACTGACGTGCT-AATATCAGAGAGCACAAATGTGCTAAT
** * *
235647 CAGAGAGCACTGACGTGCTAAATATCAGAGAGCACTGACGTACTAAATAT
1 CAGAGAGCACTGACGTGCT-AATATCAGAGAGCACAAATGTGCT--A-AT
*
235697 CAGAGAGCACTGGCGTGCTAATAATCAGAGAGCAC
1 CAGAGAGCACTGACGTGCTAAT-ATCAGAGAGCAC
235732 TGGCGTGCTA
Statistics
Matches: 119, Mismatches: 6, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
44 18 0.15
46 3 0.03
47 62 0.52
49 4 0.03
50 32 0.27
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.18
Consensus pattern (46 bp):
CAGAGAGCACTGACGTGCTAATATCAGAGAGCACAAATGTGCTAAT
Found at i:235703 original size:72 final size:72
Alignment explanation
Indices: 235598--235755 Score: 219
Period size: 72 Copynumber: 2.2 Consensus size: 72
235588 AAATGTGCTA
* *
235598 ATCAGAGAGCACTGACGTGCTAAATATCAGAGAGCACAAATGTGC-TAATCAGAGAGCACTGACG
1 ATCAGAGAGCACTGACGTACTAAATATCAGAGAGCACAAACGTGCATAATCAGAGAGCACTGACG
235662 TGCTAAAT
66 TGCT-AAT
*** *
235670 ATCAGAGAGCACTGACGTACTAAATATCAGAGAGCACTGGCGTGCTAATAATCAGAGAGCACTGG
1 ATCAGAGAGCACTGACGTACTAAATATCAGAGAGCACAAACGTGC--ATAATCAGAGAGCACTGA
235735 CGTGCTAAT
64 CGTGCTAAT
235744 ATTCAGAGAGCA
1 A-TCAGAGAGCA
235756 TGCTGAGGTC
Statistics
Matches: 76, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
72 40 0.53
74 4 0.05
75 32 0.42
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.20
Consensus pattern (72 bp):
ATCAGAGAGCACTGACGTACTAAATATCAGAGAGCACAAACGTGCATAATCAGAGAGCACTGACG
TGCTAAT
Found at i:235724 original size:50 final size:49
Alignment explanation
Indices: 235556--235755 Score: 227
Period size: 47 Copynumber: 4.2 Consensus size: 49
235546 CACTAATGAA
* ** *
235556 CAGAGAGCACTGAAGTGCT--ATA-CAGAGAGCACAAATGTGCT-A-AT
1 CAGAGAGCACTGACGTGCTAAATATCAGAGAGCACTGACGTGCTAATAT
** *
235600 CAGAGAGCACTGACGTGCTAAATATCAGAGAGCACAAATGTGCT-A-AT
1 CAGAGAGCACTGACGTGCTAAATATCAGAGAGCACTGACGTGCTAATAT
*
235647 CAGAGAGCACTGACGTGCTAAATATCAGAGAGCACTGACGTACTAAATAT
1 CAGAGAGCACTGACGTGCTAAATATCAGAGAGCACTGACGTGCT-AATAT
* *
235697 CAGAGAGCACTGGCGTGCT-AATAATCAGAGAGCACTGGCGTGCTAATATT
1 CAGAGAGCACTGACGTGCTAAAT-ATCAGAGAGCACTGACGTGCTAATA-T
235747 CAGAGAGCA
1 CAGAGAGCA
235756 TGCTGAGGTC
Statistics
Matches: 140, Mismatches: 8, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
44 18 0.13
46 3 0.02
47 62 0.44
49 8 0.06
50 49 0.35
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.19
Consensus pattern (49 bp):
CAGAGAGCACTGACGTGCTAAATATCAGAGAGCACTGACGTGCTAATAT
Found at i:244537 original size:227 final size:227
Alignment explanation
Indices: 244142--244600 Score: 909
Period size: 227 Copynumber: 2.0 Consensus size: 227
244132 GAACAAGCTA
244142 AACAAAGAGGGTATTTCCTTAAAGTAATAAAAATTTCCTCTTTACTCCATCCTAGGCTCATAAAT
1 AACAAAGAGGGTATTTCCTTAAAGTAATAAAAATTTCCTCTTTACTCCATCCTAGGCTCATAAAT
244207 GCTTCAACTTTTTTCTTCCAATTAGCGTTGCTAACTGAACAAATAACCCTAAGAGCATGTATAAA
66 GCTTCAACTTTTTTCTTCCAATTAGCGTTGCTAACTGAACAAATAACCCTAAGAGCATGTATAAA
*
244272 CCTAGATTCTGCCGGCTCTAGACCGATTTCTTTAATGGTTTTAATGGCGTAAACCATTCGAGCAT
131 CCTAGACTCTGCCGGCTCTAGACCGATTTCTTTAATGGTTTTAATGGCGTAAACCATTCGAGCAT
244337 GGCTTTGCAAAATGACCCTAGGTTGTAATACT
196 GGCTTTGCAAAATGACCCTAGGTTGTAATACT
244369 AACAAAGAGGGTATTTCCTTAAAGTAATAAAAATTTCCTCTTTACTCCATCCTAGGCTCATAAAT
1 AACAAAGAGGGTATTTCCTTAAAGTAATAAAAATTTCCTCTTTACTCCATCCTAGGCTCATAAAT
244434 GCTTCAACTTTTTTCTTCCAATTAGCGTTGCTAACTGAACAAATAACCCTAAGAGCATGTATAAA
66 GCTTCAACTTTTTTCTTCCAATTAGCGTTGCTAACTGAACAAATAACCCTAAGAGCATGTATAAA
244499 CCTAGACTCTGCCGGCTCTAGACCGATTTCTTTAATGGTTTTAATGGCGTAAACCATTCGAGCAT
131 CCTAGACTCTGCCGGCTCTAGACCGATTTCTTTAATGGTTTTAATGGCGTAAACCATTCGAGCAT
244564 GGCTTTGCAAAATGACCCTAGGTTGTAATACT
196 GGCTTTGCAAAATGACCCTAGGTTGTAATACT
244596 AACAA
1 AACAA
244601 TTTCCATATC
Statistics
Matches: 231, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
227 231 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.32
Consensus pattern (227 bp):
AACAAAGAGGGTATTTCCTTAAAGTAATAAAAATTTCCTCTTTACTCCATCCTAGGCTCATAAAT
GCTTCAACTTTTTTCTTCCAATTAGCGTTGCTAACTGAACAAATAACCCTAAGAGCATGTATAAA
CCTAGACTCTGCCGGCTCTAGACCGATTTCTTTAATGGTTTTAATGGCGTAAACCATTCGAGCAT
GGCTTTGCAAAATGACCCTAGGTTGTAATACT
Found at i:245416 original size:8 final size:8
Alignment explanation
Indices: 245405--245434 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
245395 CATTTTTAGT
*
245405 TTTTATAA
1 TTTTAAAA
245413 TTTTAAAA
1 TTTTAAAA
245421 TTTTAAAA
1 TTTTAAAA
245429 TTTTAA
1 TTTTAA
245435 TCTTGATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
TTTTAAAA
Found at i:248478 original size:12 final size:12
Alignment explanation
Indices: 248461--248486 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
248451 AACCATGCTA
248461 CATGGTTATTTC
1 CATGGTTATTTC
248473 CATGGTTATTTC
1 CATGGTTATTTC
248485 CA
1 CA
248487 CTCAATTCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.46
Consensus pattern (12 bp):
CATGGTTATTTC
Found at i:255606 original size:15 final size:15
Alignment explanation
Indices: 255586--255614 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
255576 TATAAGATAA
255586 TTTTCAATATTATTT
1 TTTTCAATATTATTT
255601 TTTTCAATATTATT
1 TTTTCAATATTATT
255615 AATTAACACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTCAATATTATTT
Found at i:257027 original size:16 final size:16
Alignment explanation
Indices: 256994--257027 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
256984 CCCATTTGTT
* *
256994 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
257010 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
257026 AA
1 AA
257028 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:259977 original size:38 final size:38
Alignment explanation
Indices: 259924--260001 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
259914 TGCCAGTGTA
259924 AGACCATATTAGGAACATGACATCGAAAATGTTATGAG
1 AGACCATATTAGGAACATGACATCGAAAATGTTATGAG
* *
259962 AGACCATGTTTGGAACATGACATCGAAAATGTTATGAG
1 AGACCATATTAGGAACATGACATCGAAAATGTTATGAG
260000 AG
1 AG
260002 CCAGTATAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.24
Consensus pattern (38 bp):
AGACCATATTAGGAACATGACATCGAAAATGTTATGAG
Found at i:260271 original size:48 final size:48
Alignment explanation
Indices: 260050--260274 Score: 204
Period size: 48 Copynumber: 4.7 Consensus size: 48
260040 ATTGTGTGCT
* * * * * * * *
260050 AGTGTAAGACCATGCCTGGGACAT-GACGTAGGCCACAATATGAGAGCA
1 AGTGTAAGACCATGTCTGGGACATAG-CATCGGCCTCGACATGTGAGCC
* * * *
260098 AGTGTAAAAACATGTCTGGGACATGGCATCGGCCTCAACATGTGAGCC
1 AGTGTAAGACCATGTCTGGGACATAGCATCGGCCTCGACATGTGAGCC
* * * *** * *
260146 AATGTAATACCATGTCTGGGACATAGCATCGGCAAT-GAGGCGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATAGCATCGGC-CTCGACATGTGAGCC
*
260194 AGTGTAAGACTC-TGTCTGGGACATGGCATCGGCCTCGACATGTGAGCC
1 AGTGTAAGAC-CATGTCTGGGACATAGCATCGGCCTCGACATGTGAGCC
*
260242 AGTGTAAGACCATGTCTAGGACATAGCATCGGC
1 AGTGTAAGACCATGTCTGGGACATAGCATCGGC
260275 AATTTACCCT
Statistics
Matches: 141, Mismatches: 31, Indels: 10
0.77 0.17 0.05
Matches are distributed among these distances:
47 2 0.01
48 136 0.96
49 3 0.02
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATAGCATCGGCCTCGACATGTGAGCC
Found at i:268503 original size:28 final size:28
Alignment explanation
Indices: 268463--268521 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
268453 ATACTAATTA
268463 TTTTACATTATTAATCCATTGATGGTAG
1 TTTTACATTATTAATCCATTGATGGTAG
*
268491 TTTTACATTATTAATCTATTGATGGTAG
1 TTTTACATTATTAATCCATTGATGGTAG
268519 TTT
1 TTT
268522 ATCTGGTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.27, C:0.08, G:0.14, T:0.51
Consensus pattern (28 bp):
TTTTACATTATTAATCCATTGATGGTAG
Found at i:280140 original size:12 final size:12
Alignment explanation
Indices: 280118--280147 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
280108 AAGGTGACTC
280118 TTTTA-TTTTTA
1 TTTTATTTTTTA
280129 TTTTATTTTTTA
1 TTTTATTTTTTA
280141 TTTTATT
1 TTTTATT
280148 ATTCTGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.28
12 13 0.72
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTATTTTTTA
Found at i:281326 original size:12 final size:14
Alignment explanation
Indices: 281279--281320 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
281269 TTTCATTCAA
281279 ATTATTTAC-TTTAT
1 ATTATTT-CTTTTAT
* *
281293 AATATTTATTTTAT
1 ATTATTTCTTTTAT
281307 ATTATTTCTTTTAT
1 ATTATTTCTTTTAT
281321 TTTTTCCCCT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTATTTCTTTTAT
Found at i:283944 original size:17 final size:16
Alignment explanation
Indices: 283912--283945 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
283902 TTTTTTTAAA
283912 ATGTTATAATAAGATG
1 ATGTTATAATAAGATG
*
283928 ATGTTATTAATATGATG
1 ATGTTA-TAATAAGATG
283945 A
1 A
283946 ATATTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (16 bp):
ATGTTATAATAAGATG
Found at i:285730 original size:3 final size:3
Alignment explanation
Indices: 285719--285757 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
285709 TTTTTTCTAA
* *
285719 TAT TGT TAT TAT TAT TAC TAT TAT TAT TAT TAT ATAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA
285758 GAGTATACTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:286081 original size:20 final size:20
Alignment explanation
Indices: 286026--286102 Score: 68
Period size: 20 Copynumber: 3.8 Consensus size: 20
286016 ATTTTCTTAT
286026 TATATTATTATGTATATTATTC
1 TATA-TATTATGTATATT-TTC
* *
286048 T-TTTAAATAT-TATATTTTC
1 TATAT-ATTATGTATATTTTC
* *
286067 TATATATTATGTATATATTA
1 TATATATTATGTATATTTTC
*
286087 TATATATTACGTATAT
1 TATATATTATGTATAT
286103 ATCTAGTAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
19 8 0.18
20 31 0.69
21 5 0.11
22 1 0.02
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (20 bp):
TATATATTATGTATATTTTC
Done.