Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 18 of 295
Found at i:5655942 original size:191 final size:192
Alignment explanation
Indices: 5655445--5656057 Score: 1138
Period size: 192 Copynumber: 3.2 Consensus size: 192
5655435 CTTTCCAAGG
5655445 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
*
5655510 TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGAGGCACGCCGAGGTATTTTTAG
66 TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
5655575 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
131 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
5655637 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
*
5655702 TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCCGAGGTATTTTTAG
66 TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
5655767 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
131 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
*
5655829 -AAATCAACTCACATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
* *
5655893 TAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
66 TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
5655958 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
131 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
* **
5656020 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC
1 -AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC
5656058 GGCTCACATG
Statistics
Matches: 409, Mismatches: 10, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
191 187 0.46
192 190 0.46
193 32 0.08
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (192 bp):
AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
Found at i:5656097 original size:16 final size:17
Alignment explanation
Indices: 5656076--5656109 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5656066 TGCTGAGGTA
*
5656076 TTTTCAATTTATG-TTT
1 TTTTCAATCTATGCTTT
5656092 TTTTCAATCTATGCTTT
1 TTTTCAATCTATGCTTT
5656109 T
1 T
5656110 CAAAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.65
Consensus pattern (17 bp):
TTTTCAATCTATGCTTT
Found at i:5656273 original size:85 final size:88
Alignment explanation
Indices: 5656015--5656273 Score: 309
Period size: 91 Copynumber: 2.9 Consensus size: 88
5656005 TAATTTTTGT
5656015 TTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-GGCTCACATGCTGAGGTATTT
1 TTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGG-TCACATGCTGAGGTATTT
*
5656079 TCAATTTATGTTTTTTTCAA-TCTATGC
64 TCAATTTCTG-TTTTTT-AATTCTA-GC
* *
5656106 TTTTCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAAGG---CATGCTGAGGTATTT
1 TTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-AGGTCACATGCTGAGGTATTT
**
5656168 TCAATTTCTGCTTTACTAATTCTA-C
64 TCAATTTCTG-TTTTTTAATTCTAGC
* * *
5656193 TTTTC-AAATCAACTCATATTGCAAGAGGTGAGTTGAGTCTCAGGTCACACGCTGAGGTCTTTTC
1 TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGTCACATGCTGAGGTATTTTC
*
5656257 AAATTCTG-TTTTTAATT
66 AATTTCTGTTTTTTAATT
5656274 TCTGTTTTTT
Statistics
Matches: 148, Mismatches: 14, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
84 3 0.02
85 40 0.27
87 28 0.19
88 2 0.01
89 32 0.22
91 41 0.28
93 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (88 bp):
TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGTCACATGCTGAGGTATTTTC
AATTTCTGTTTTTTAATTCTAGC
Found at i:5656282 original size:13 final size:13
Alignment explanation
Indices: 5656260--5656293 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 13
5656250 TCTTTTCAAA
5656260 TTCTGTTTTTAAT
1 TTCTGTTTTTAAT
5656273 TTCTGTTTTTTTAAT
1 TTCTG--TTTTTAAT
5656288 TTCTGT
1 TTCTGT
5656294 GTTTCAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 6 0.32
15 13 0.68
ACGTcount: A:0.12, C:0.09, G:0.09, T:0.71
Consensus pattern (13 bp):
TTCTGTTTTTAAT
Found at i:5656285 original size:15 final size:15
Alignment explanation
Indices: 5656265--5656293 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5656255 TCAAATTCTG
5656265 TTTTTAATTTCTGTT
1 TTTTTAATTTCTGTT
5656280 TTTTTAATTTCTGT
1 TTTTTAATTTCTGT
5656294 GTTTCAAAAA
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:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (15 bp):
TTTTTAATTTCTGTT
Found at i:5656454 original size:54 final size:55
Alignment explanation
Indices: 5656370--5656587 Score: 306
Period size: 54 Copynumber: 4.1 Consensus size: 55
5656360 TCAATTTCTA
* *
5656370 CTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGC
1 CTTTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
*
5656425 CTTTT-AATTTCTATTTTTCAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
5656479 C--TT---TTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTCAATTTCTATTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* * * *
5656530 CTTTTGCAAATTCT-GTTTTCAAAAATCAACTCATATTGCGAGAAGTAAGTTGAGC
1 CTTTT-CAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
5656585 CTT
1 CTT
5656588 GGCTCACGTG
Statistics
Matches: 148, Mismatches: 8, Indels: 14
0.87 0.05 0.08
Matches are distributed among these distances:
50 12 0.08
51 35 0.24
52 2 0.01
53 2 0.01
54 47 0.32
55 41 0.28
56 5 0.03
57 4 0.03
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (55 bp):
CTTTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
Found at i:5656853 original size:13 final size:15
Alignment explanation
Indices: 5656829--5656862 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
5656819 TTTAATTTTC
5656829 AAAATTTCAAAAA-A
1 AAAATTTCAAAAATA
5656843 AAAATTT-AAAAATA
1 AAAATTTCAAAAATA
5656857 AAAATT
1 AAAATT
5656863 GCATTTTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAATTTCAAAAATA
Found at i:5656892 original size:30 final size:30
Alignment explanation
Indices: 5656858--5656959 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
5656848 TTAAAAATAA
* *
5656858 AAATTGCATTTTGACCCCTAAACTTTTC-TT
1 AAATTTCATTTTGACCCTTAAAC-TTTCATT
*
5656888 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCTTAAACTTTCATT
* * *
5656918 AAATTTCACTTAGACCCTTAAAATTTCATT
1 AAATTTCATTTTGACCCTTAAACTTTCATT
5656948 AAATTTCATTTT
1 AAATTTCATTTT
5656960 AATCCTAAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
29 4 0.06
30 59 0.94
ACGTcount: A:0.30, C:0.20, G:0.04, T:0.46
Consensus pattern (30 bp):
AAATTTCATTTTGACCCTTAAACTTTCATT
Found at i:5657356 original size:3 final size:3
Alignment explanation
Indices: 5657348--5657419 Score: 53
Period size: 3 Copynumber: 24.0 Consensus size: 3
5657338 GCTAGACTTT
* *
5657348 GAA GAA GAA GAA GGAA GAA GAA GGAT GAA GAA -AA GAG GAA GAA GAAA
1 GAA GAA GAA GAA -GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA G-AA
*
5657395 GAAA GAA -AA -AA GAA AAA GAA -AA GAA
1 G-AA GAA GAA GAA GAA GAA GAA GAA GAA
5657420 ATAATAAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
2 8 0.14
3 37 0.65
4 12 0.21
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (3 bp):
GAA
Found at i:5657366 original size:13 final size:12
Alignment explanation
Indices: 5657348--5657393 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 12
5657338 GCTAGACTTT
5657348 GAAGAAGAAGAAG
1 GAAGAAGAAG-AG
*
5657361 GAAGAAGAAGGAT
1 GAAGAAGAA-GAG
5657374 GAAGAA-AAGAG
1 GAAGAAGAAGAG
5657385 GAAGAAGAA
1 GAAGAAGAA
5657394 AGAAAGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 8 0.28
12 4 0.14
13 16 0.55
14 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.37, T:0.02
Consensus pattern (12 bp):
GAAGAAGAAGAG
Found at i:5657405 original size:24 final size:24
Alignment explanation
Indices: 5657348--5657420 Score: 69
Period size: 24 Copynumber: 3.0 Consensus size: 24
5657338 GCTAGACTTT
* *
5657348 GAAGAAGAAGAAGGAAGAAGAAGGAT
1 GAAGAA-AAG-AGGAAGAAGAAGAAA
5657374 GAAGAAAAGAGGAAGAAGAAAGAAA
1 GAAGAAAAGAGGAAGAAG-AAGAAA
**
5657399 GAA-AAAAGAAAAAGAA-AAGAAA
1 GAAGAAAAGAGGAAGAAGAAGAAA
5657421 TAATAAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
22 6 0.14
24 20 0.48
25 10 0.24
26 6 0.14
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.01
Consensus pattern (24 bp):
GAAGAAAAGAGGAAGAAGAAGAAA
Found at i:5657705 original size:11 final size:10
Alignment explanation
Indices: 5657683--5657746 Score: 74
Period size: 11 Copynumber: 6.1 Consensus size: 10
5657673 GGCCCAGCAG
5657683 AGAAAAAAAA
1 AGAAAAAAAA
5657693 AGAAAAGAAAA
1 AGAAAA-AAAA
* *
5657704 AGAAGAAAAG
1 AGAAAAAAAA
*
5657714 AGAAGGAAAAA
1 AGAA-AAAAAA
5657725 AGAAGAAAAAA
1 AGAA-AAAAAA
5657736 AGAAAAAAAA
1 AGAAAAAAAA
5657746 A
1 A
5657747 AAGAGGTTCA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
10 20 0.42
11 28 0.58
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:5657709 original size:14 final size:14
Alignment explanation
Indices: 5657686--5657748 Score: 60
Period size: 14 Copynumber: 4.5 Consensus size: 14
5657676 CCAGCAGAGA
5657686 AAAAAAAAGAAAAG
1 AAAAAAAAGAAAAG
*
5657700 AAAAAGAAGAAAAG
1 AAAAAAAAGAAAAG
*
5657714 AGAAGGAAAAA-AGAAG
1 A-AA--AAAAAGAAAAG
5657730 -AAAAAAAGAAAA-
1 AAAAAAAAGAAAAG
5657742 AAAAAAA
1 AAAAAAA
5657749 GAGGTTCAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
12 5 0.12
13 9 0.22
14 16 0.40
15 2 0.05
16 4 0.10
17 4 0.10
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGAAAAG
Found at i:5657712 original size:21 final size:21
Alignment explanation
Indices: 5657683--5657750 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
5657673 GGCCCAGCAG
*
5657683 AGAAAAAAAAAGAAAAGAAAA
1 AGAAGAAAAAAGAAAAGAAAA
* *
5657704 AGAAGAAAAGAG-AAGGAAAAA
1 AGAAGAAAAAAGAAAAG-AAAA
5657725 AGAAGAAAAAAAGAAAA-AAAA
1 AGAAG-AAAAAAGAAAAGAAAA
5657746 A-AAGA
1 AGAAGA
5657751 GGTTCAATTC
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
19 1 0.03
20 6 0.15
21 24 0.62
22 6 0.15
23 2 0.05
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (21 bp):
AGAAGAAAAAAGAAAAGAAAA
Found at i:5657747 original size:24 final size:24
Alignment explanation
Indices: 5657683--5657748 Score: 62
Period size: 29 Copynumber: 2.5 Consensus size: 24
5657673 GGCCCAGCAG
*
5657683 AGAAAAAAAAAGAAAAGAAAAAGA
1 AGAAAAAAAAAAAAAAGAAAAAGA
5657707 AGAAAAGAGAAGGAAAAAAGAAGAAAAA-A
1 AG-AAA-A-AA--AAAAAA-AAGAAAAAGA
5657736 AGAAAAAAAAAAA
1 AGAAAAAAAAAAA
5657749 GAGGTTCAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
24 7 0.20
25 3 0.09
26 3 0.09
27 3 0.09
28 3 0.09
29 8 0.23
30 8 0.23
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (24 bp):
AGAAAAAAAAAAAAAAGAAAAAGA
Found at i:5657916 original size:16 final size:17
Alignment explanation
Indices: 5657890--5657927 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
5657880 TTATATTTAT
5657890 ATTTTTAATTTAATTTG
1 ATTTTTAATTTAATTTG
* *
5657907 ATTTTT-ATTTTATTTT
1 ATTTTTAATTTAATTTG
5657923 ATTTT
1 ATTTT
5657928 AAATAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTTTAATTTAATTTG
Found at i:5658121 original size:18 final size:17
Alignment explanation
Indices: 5658077--5658600 Score: 202
Period size: 17 Copynumber: 29.9 Consensus size: 17
5658067 TCAATAATCC
5658077 TCGTGCTTTT-AAAAATT
1 TCGTG-TTTTCAAAAATT
*
5658094 CTCATG-TTTCAAAAATCT
1 -TCGTGTTTTCAAAAAT-T
5658112 TCGTGTTTTC-AAAATT
1 TCGTGTTTTCAAAAATT
*
5658128 CTAGTG-TTTCAAAAATTT
1 -TCGTGTTTTCAAAAA-TT
*
5658146 TCTTGTTTTCAGAAAAAAATT
1 TCGTGTTTTC----AAAAATT
*
5658167 TCGTGTTTT-ATAAATT
1 TCGTGTTTTCAAAAATT
* **
5658183 TCCGTATTTTCAAAAAAA
1 T-CGTGTTTTCAAAAATT
*
5658201 TCATGTCTTTCAAAAATTT
1 TCGTGT-TTTCAAAAA-TT
**
5658220 TCGTGTTTTCAAAAAAAA
1 TCGTGTTTTC-AAAAATT
5658238 T-GACTGTGTTTCAAAAATT
1 TCG--TGT-TTTCAAAAATT
***
5658257 TCCGTGTTAAAAAAAAATCT
1 T-CGTGTT-TTCAAAAAT-T
*
5658277 TCGTATTTTCAAAAAATTT
1 TCGTGTTTTC-AAAAA-TT
5658296 TCGTG-TTTCAAAAATCT
1 TCGTGTTTTCAAAAAT-T
5658313 TCGTGTTTTCAAAAATT
1 TCGTGTTTTCAAAAATT
*
5658330 TCG-GTGTTTCAAAGATTT
1 TCGTGT-TTTCAAA-AATT
*
5658348 TCGTGTTTTCAAAAACT
1 TCGTGTTTTCAAAAATT
* * **
5658365 CCGGTGATTTTTAAAAAAAAA
1 TC-GTG--TTTT-CAAAAATT
*
5658386 TCGT-TTTCTAAAAAATT
1 TCGTGTTT-TCAAAAATT
5658403 TCCGTG-TTTCAAAAATTT
1 T-CGTGTTTTCAAAAA-TT
5658421 TCGTGTTTT-AAAAATTT
1 TCGTGTTTTCAAAAA-TT
*
5658438 TCGTGTTTTTAAAAATT
1 TCGTGTTTTCAAAAATT
*
5658455 CTCGTATTTT----AATT
1 -TCGTGTTTTCAAAAATT
* *
5658469 T--T-TTTTAAGAAAAAAAT
1 TCGTGTTTT---CAAAAATT
*
5658486 T-GTG-TTTCAAAAAAATG
1 TCGTGTTTTC--AAAAATT
*
5658503 TCTTGTTTT-AAAAATT
1 TCGTGTTTTCAAAAATT
*
5658519 CTCGTG-TTTCAAAAAATG
1 -TCGTGTTTTC-AAAAATT
5658537 TCGTGTTTT-AAAAATTT
1 TCGTGTTTTCAAAAA-TT
**
5658554 TCGTG-TTTCTGAAATT
1 TCGTGTTTTCAAAAATT
5658570 TCCGTG-TTT-AAAAATT
1 T-CGTGTTTTCAAAAATT
5658586 CTCGTGTTTT-AAAAA
1 -TCGTGTTTTCAAAAA
5658601 AAAACTTTCA
Statistics
Matches: 390, Mismatches: 53, Indels: 127
0.68 0.09 0.22
Matches are distributed among these distances:
10 4 0.01
11 1 0.00
13 1 0.00
14 4 0.01
16 47 0.12
17 145 0.37
18 105 0.27
19 48 0.12
20 13 0.03
21 17 0.04
22 5 0.01
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (17 bp):
TCGTGTTTTCAAAAATT
Found at i:5658139 original size:16 final size:16
Alignment explanation
Indices: 5658088--5658141 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
5658078 CGTGCTTTTA
5658088 AAAATTCTCA-TGTTTC
1 AAAATTCT-AGTGTTTC
* *
5658104 AAAAATCTTCGTGTTTTC
1 AAAATTC-TAGTG-TTTC
5658122 AAAATTCTAGTGTTTC
1 AAAATTCTAGTGTTTC
5658138 AAAA
1 AAAA
5658142 ATTTTCTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 14 0.45
17 7 0.23
18 10 0.32
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (16 bp):
AAAATTCTAGTGTTTC
Found at i:5658227 original size:74 final size:75
Alignment explanation
Indices: 5658134--5658309 Score: 207
Period size: 74 Copynumber: 2.4 Consensus size: 75
5658124 AATTCTAGTG
* ** * * * **
5658134 TTTCAAAAATTTTCTTGTTTTCAGAAAAAAATTTC-GTGTTTTATAAATTTCCGTATTTTCAAAA
1 TTTCAAAAATTTTCGTGTTTTCA-AAAAAAATGACTGTGTTTCAAAAATTTCCGT-GTTAAAAAA
5658198 AAATCAT-GT-C
64 AAATCATCGTAC
5658208 TTTCAAAAATTTTCGTGTTTTCAAAAAAAATGACTGTGTTTCAAAAATTTCCGTGTTAAAAAAAA
1 TTTCAAAAATTTTCGTGTTTTCAAAAAAAATGACTGTGTTTCAAAAATTTCCGTGTTAAAAAAAA
* *
5658273 ATCTTCGTAT
66 ATCATCGTAC
5658283 TTTCAAAAAATTTTCGTG-TTTCAAAAA
1 TTTC-AAAAATTTTCGTGTTTTCAAAAA
5658310 TCTTCGTGTT
Statistics
Matches: 88, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
73 21 0.24
74 41 0.47
75 13 0.15
76 13 0.15
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (75 bp):
TTTCAAAAATTTTCGTGTTTTCAAAAAAAATGACTGTGTTTCAAAAATTTCCGTGTTAAAAAAAA
ATCATCGTAC
Found at i:5658250 original size:38 final size:37
Alignment explanation
Indices: 5658098--5658309 Score: 158
Period size: 38 Copynumber: 5.8 Consensus size: 37
5658088 AAAATTCTCA
* *
5658098 TGTTTCAAAAATCTTCGTGTTTTC----AAAATTCTAG
1 TGTTTCAAAAATTTTCGTGTTTTCAAAAAAAATACT-G
* *
5658132 TGTTTCAAAAATTTTCTTGTTTTCAGAAAAAAAT-TTCG
1 TGTTTCAAAAATTTTCGTGTTTTCA-AAAAAAATACT-G
* * * *
5658170 TGTTTTATAAATTTCCGTATTTTC-AAAAAAAT-CATG
1 TGTTTCAAAAATTTTCGTGTTTTCAAAAAAAATAC-TG
*
5658206 TCTTTCAAAAATTTTCGTGTTTTCAAAAAAAATGACTG
1 TGTTTCAAAAATTTTCGTGTTTTCAAAAAAAAT-ACTG
* *
5658244 TGTTTCAAAAATTTCCGTG--TTAAAAAAAAAT-CTTCG
1 TGTTTCAAAAATTTTCGTGTTTTCAAAAAAAATAC-T-G
*
5658280 TATTTTCAAAAAATTTTCGTG-TTTCAAAAA
1 T-GTTTC-AAAAATTTTCGTGTTTTCAAAAA
5658310 TCTTCGTGTT
Statistics
Matches: 143, Mismatches: 21, Indels: 23
0.76 0.11 0.12
Matches are distributed among these distances:
34 23 0.16
35 1 0.01
36 41 0.29
37 13 0.09
38 52 0.36
39 13 0.09
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (37 bp):
TGTTTCAAAAATTTTCGTGTTTTCAAAAAAAATACTG
Found at i:5658604 original size:21 final size:20
Alignment explanation
Indices: 5658579--5658632 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
5658569 TTCCGTGTTT
5658579 AAAAATTCTCGTGTTTTAAAA
1 AAAAATT-TCGTGTTTTAAAA
* * *
5658600 AAAAACTTTCATTTTTTTAAA
1 AAAAA-TTTCGTGTTTTAAAA
5658621 AAAAATTTCGTG
1 AAAAATTTCGTG
5658633 CTTCAAAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 5 0.19
21 20 0.74
22 2 0.07
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (20 bp):
AAAAATTTCGTGTTTTAAAA
Found at i:5662751 original size:17 final size:17
Alignment explanation
Indices: 5662725--5662768 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
5662715 AACACAGTTA
*
5662725 GAAGATGAAAAGCTAAT
1 GAAGAAGAAAAGCTAAT
5662742 GAAGAAGAAAAGCTAAT
1 GAAGAAGAAAAGCTAAT
5662759 GAAGAAGAAA
1 GAAGAAGAAA
5662769 GAGATGGTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.59, C:0.05, G:0.25, T:0.11
Consensus pattern (17 bp):
GAAGAAGAAAAGCTAAT
Found at i:5664522 original size:8 final size:8
Alignment explanation
Indices: 5664504--5664541 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
5664494 TTTAAGAAAT
5664504 TAATAATTA
1 TAATAA-TA
5664513 TAATAATA
1 TAATAATA
*
5664521 TAATAGT-
1 TAATAATA
5664528 TAATAATA
1 TAATAATA
5664536 TAATAA
1 TAATAA
5664542 AAGAAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
7 6 0.23
8 14 0.54
9 6 0.23
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (8 bp):
TAATAATA
Found at i:5664549 original size:24 final size:24
Alignment explanation
Indices: 5664503--5664549 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5664493 ATTTAAGAAA
* *
5664503 TTAATAATTATAATAATATAATAG
1 TTAATAATTATAATAAAAAAATAG
5664527 TTAATAA-TATAATAAAAGAAATA
1 TTAATAATTATAATAAAA-AAATA
5664550 ATAAAAGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (24 bp):
TTAATAATTATAATAAAAAAATAG
Found at i:5665270 original size:15 final size:15
Alignment explanation
Indices: 5665250--5665281 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
5665240 TTAATAGTTA
5665250 GAATGTATAATGAAT
1 GAATGTATAATGAAT
5665265 GAATGTATAATGAAT
1 GAATGTATAATGAAT
5665280 GA
1 GA
5665282 TATGATGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.22, T:0.31
Consensus pattern (15 bp):
GAATGTATAATGAAT
Found at i:5666256 original size:30 final size:29
Alignment explanation
Indices: 5666218--5666275 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
5666208 GTAAAAACTC
* *
5666218 AAAATTTAAAGGATTAA-AGTGTAAATATG
1 AAAATTT-AAGGACTAATAGTGCAAATATG
5666247 AAAAGTTTAAGGACTAATAGTGCAAATAT
1 AAAA-TTTAAGGACTAATAGTGCAAATAT
5666276 TTAAGGGTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.50, C:0.03, G:0.17, T:0.29
Consensus pattern (29 bp):
AAAATTTAAGGACTAATAGTGCAAATATG
Found at i:5668763 original size:46 final size:46
Alignment explanation
Indices: 5668696--5669111 Score: 579
Period size: 46 Copynumber: 9.0 Consensus size: 46
5668686 GTGTGCTCTT
** *
5668696 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
**
5668742 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAATC-
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAA-CA
** *
5668788 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
5668834 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
* * *
5668880 TGACA-GAAAATGAATAAAACCATGGTTGAAAGATACCATGGCAACG
1 TGATATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
*
5668926 TGATATGAAATGACTAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
* *
5668972 TGACA-GAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
5669018 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
* * * * * * *
5669064 TGACA-GAAAATGAGTAAGACCATAGTTGACAGACACTATGGCATCA
1 TGATATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
5669110 TG
1 TG
5669112 TCAAAGATAA
Statistics
Matches: 341, Mismatches: 22, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
45 4 0.01
46 334 0.98
47 3 0.01
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (46 bp):
TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
Found at i:5668853 original size:92 final size:92
Alignment explanation
Indices: 5668703--5669106 Score: 650
Period size: 92 Copynumber: 4.4 Consensus size: 92
5668693 CTTTGATATG
* * **
5668703 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGT
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAATAAGACCATGGT
*
5668768 TGAAAGATACCATGGCAATC-TGATATG-
66 TGAAAGATACCATGGCAA-CATGACA-GA
*
5668795 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAATAAGACCATGGT
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAATAAGACCATGGT
5668860 TGAAAGATACCATGGCAACATGACAGA
66 TGAAAGATACCATGGCAACATGACAGA
* * *
5668887 AAATGAATAAAACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGACTAAGACCATGGT
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAATAAGACCATGGT
5668952 TGAAAGATACCATGGCAACATGACAGA
66 TGAAAGATACCATGGCAACATGACAGA
*
5668979 AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAATAAGACCATGGT
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAATAAGACCATGGT
5669044 TGAAAGATACCATGGCAACATGACAGA
66 TGAAAGATACCATGGCAACATGACAGA
* * * *
5669071 AAATGAGTAAGACCATAGTTGACAGACACTATGGCA
1 AAATGAGTAAGACCATGGTTGAAAGATACCATGGCA
5669107 TCATGTCAAA
Statistics
Matches: 295, Mismatches: 15, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
91 2 0.01
92 293 0.99
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (92 bp):
AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAATAAGACCATGGT
TGAAAGATACCATGGCAACATGACAGA
Found at i:5670300 original size:13 final size:13
Alignment explanation
Indices: 5670282--5670333 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 13
5670272 GTCAGATCTG
5670282 CCCACGGCCTGGC
1 CCCACGGCCTGGC
5670295 CCCACGGCCATGGGAAC
1 CCCACGGCC-T-GG--C
*
5670312 CCCACGGGCTGGC
1 CCCACGGCCTGGC
*
5670325 CACACGGCC
1 CCCACGGCC
5670334 ATGTCCCAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
13 17 0.53
14 1 0.03
15 4 0.12
16 1 0.03
17 9 0.28
ACGTcount: A:0.15, C:0.48, G:0.31, T:0.06
Consensus pattern (13 bp):
CCCACGGCCTGGC
Found at i:5674530 original size:24 final size:24
Alignment explanation
Indices: 5674501--5674549 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
5674491 TTTAGTTTTA
*
5674501 ATCAATCATTTGAATTAATTAGTT
1 ATCAATCATTCGAATTAATTAGTT
*
5674525 ATCAATCATTCGAATTATTTAGTT
1 ATCAATCATTCGAATTAATTAGTT
5674549 A
1 A
5674550 AATATTAGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (24 bp):
ATCAATCATTCGAATTAATTAGTT
Found at i:5675074 original size:40 final size:40
Alignment explanation
Indices: 5675030--5675110 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
5675020 CAAACATTCT
5675030 CTCAACTCAAATAAACAACCATCCTTGGTTGCCCTTTATA
1 CTCAACTCAAATAAACAACCATCCTTGGTTGCCCTTTATA
5675070 CTCAACTCAAATAAACAACCATCCTTGGTTGCCCTTTATA
1 CTCAACTCAAATAAACAACCATCCTTGGTTGCCCTTTATA
5675110 C
1 C
5675111 CCTTAAGGTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.32, C:0.31, G:0.07, T:0.30
Consensus pattern (40 bp):
CTCAACTCAAATAAACAACCATCCTTGGTTGCCCTTTATA
Found at i:5677710 original size:11 final size:11
Alignment explanation
Indices: 5677690--5677719 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
5677680 ATTGAATTTT
5677690 AATTTAATTAAA
1 AATTT-ATTAAA
5677702 AATTTATTAAA
1 AATTTATTAAA
5677713 AATTTAT
1 AATTTAT
5677720 GTTTTTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
AATTTATTAAA
Found at i:5686896 original size:99 final size:99
Alignment explanation
Indices: 5686711--5686904 Score: 253
Period size: 99 Copynumber: 2.0 Consensus size: 99
5686701 ATAATTATCG
* * * * * **
5686711 TTAAAATTAAAAATTTTAAGTGTGAACTTGAGATAGATATCATTATTATACGTTATTTTTGGACC
1 TTAAAACTAAAAATTTTAAGTGTGAACTTGAGATAAATATCATAACTATACATTAACTTTGGACC
* *
5686776 AATGTGCGCTACATAAATTTTAATCTTGTGCGAT
66 AATGTCCACTACATAAATTTTAATCTTGTGCGAT
**
5686810 TTAAAACTAAAAATTTTAAGTGTGAACTTGAGATAAATATCATAACTATTTATTAACTTTGGACC
1 TTAAAACTAAAAATTTTAAGTGTGAACTTGAGATAAATATCATAACTATACATTAACTTTGGACC
* * * *
5686875 AATTTCCACTGCATGAGTTTTAATCTTGTG
66 AATGTCCACTACATAAATTTTAATCTTGTG
5686905 GAATTAAGTT
Statistics
Matches: 80, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
99 80 1.00
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (99 bp):
TTAAAACTAAAAATTTTAAGTGTGAACTTGAGATAAATATCATAACTATACATTAACTTTGGACC
AATGTCCACTACATAAATTTTAATCTTGTGCGAT
Found at i:5687056 original size:74 final size:74
Alignment explanation
Indices: 5686935--5687080 Score: 283
Period size: 74 Copynumber: 2.0 Consensus size: 74
5686925 ATGGGGCGTG
*
5686935 TTGGACCGTAACAAAATTTTAAGCCCGTTTGATAGGCCTTAGGCTTGGTCTAAAAATGGGTATAA
1 TTGGACCGTAACAAAATTTTAAGCCCGTTTGATAAGCCTTAGGCTTGGTCTAAAAATGGGTATAA
5687000 AATTTTACC
66 AATTTTACC
5687009 TTGGACCGTAACAAAATTTTAAGCCCGTTTGATAAGCCTTAGGCTTGGTCTAAAAATGGGTATAA
1 TTGGACCGTAACAAAATTTTAAGCCCGTTTGATAAGCCTTAGGCTTGGTCTAAAAATGGGTATAA
5687074 AATTTTA
66 AATTTTA
5687081 TCTTTAAGTC
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 71 1.00
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (74 bp):
TTGGACCGTAACAAAATTTTAAGCCCGTTTGATAAGCCTTAGGCTTGGTCTAAAAATGGGTATAA
AATTTTACC
Found at i:5687693 original size:30 final size:30
Alignment explanation
Indices: 5687626--5687694 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 30
5687616 TAGCACCATT
5687626 TTATATTTA--CATATTTCATAAAAAAATTA
1 TTATATTTATTCA-ATTTCATAAAAAAATTA
* *
5687655 TTATATTTATTCAATTTGATAAATAAATGTA
1 TTATATTTATTCAATTTCATAAAAAAAT-TA
5687686 TTA-ATTTAT
1 TTATATTTAT
5687695 GAGATGTGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 9 0.26
30 19 0.54
31 7 0.20
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.49
Consensus pattern (30 bp):
TTATATTTATTCAATTTCATAAAAAAATTA
Found at i:5687781 original size:30 final size:29
Alignment explanation
Indices: 5687716--5687781 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 29
5687706 AATAGAATCA
* *
5687716 AAATCAAAGTTTCATAATACAGTTAAATC
1 AAATCAAAGTTTCATAATACAATTAAACC
* * *
5687745 ATAATCAAAGTTTCATATCTATAATTACACC
1 A-AATCAAAGTTTCATA-ATACAATTAAACC
5687776 AAATCA
1 AAATCA
5687782 TAGATCATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 1 0.03
30 20 0.67
31 9 0.30
ACGTcount: A:0.47, C:0.17, G:0.05, T:0.32
Consensus pattern (29 bp):
AAATCAAAGTTTCATAATACAATTAAACC
Found at i:5705572 original size:14 final size:15
Alignment explanation
Indices: 5705547--5705579 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
5705537 GGTTTAATGG
5705547 TTATTATTGTTAAAA
1 TTATTATTGTTAAAA
*
5705562 TTATT-TTGTTAAAT
1 TTATTATTGTTAAAA
5705576 TTAT
1 TTAT
5705580 ATTTATTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (15 bp):
TTATTATTGTTAAAA
Found at i:5711378 original size:91 final size:91
Alignment explanation
Indices: 5711223--5711724 Score: 670
Period size: 91 Copynumber: 5.5 Consensus size: 91
5711213 TCGCTGTAGG
* * * *
5711223 ACCTCAACGAGGCAGCTAAGTGTTCATTTCTGTGAGCTGAAAATTGAAACAAATATGAGTTGGCT
1 ACCTCAATGAGGCAGCTAAATGTTCATTTCTTTGAGCTGAAAATCGAAACAAATATGAGTTGGCT
*
5711288 ACTTCTAACCTACTGATACGAAATGC
66 ACTTCTAACCTACCGATACGAAATGC
* *
5711314 ACCTCAATGAGACAGCTAAATGTTCATTTCTATGAGCTGAAAATCGAAACAAATATGAGTTGGCT
1 ACCTCAATGAGGCAGCTAAATGTTCATTTCTTTGAGCTGAAAATCGAAACAAATATGAGTTGGCT
* * * *
5711379 ACTTCTATCCTACCGCTACAAAATGT
66 ACTTCTAACCTACCGATACGAAATGC
* *
5711405 ATCTCAATGAGGCAGCTAAATGTTCATTTCTTTGAGCTGAAAGA-C-AAAGCAAATATGAGTCGG
1 ACCTCAATGAGGCAGCTAAATGTTCATTTCTTTGAGCTGAAA-ATCGAAA-CAAATATGAGTTGG
* *
5711468 CTACTTCTAAGCTACCAATACGAAATGC
64 CTACTTCTAACCTACCGATACGAAATGC
* * * *
5711496 ATCTCAACGAAGCAGCTAAATGTTCATTTCTTTGAGCTGAAAATC-AAAGCAAATATGAGTCGGC
1 ACCTCAATGAGGCAGCTAAATGTTCATTTCTTTGAGCTGAAAATCGAAA-CAAATATGAGTTGGC
* * *
5711560 TACTTCTAAGCTACCAATACGAAATGG
65 TACTTCTAACCTACCGATACGAAATGC
* * * *
5711587 ACCTCAATGAGGCAACTAAATGTTCATTTCTGTGAGCTGAAAATCAAAACAAATATGAGTTGACT
1 ACCTCAATGAGGCAGCTAAATGTTCATTTCTTTGAGCTGAAAATCGAAACAAATATGAGTTGGCT
* * *
5711652 ACTTTTAACCTACTGCTACGAAACTG-
66 ACTTCTAACCTACCGATACGAAA-TGC
*
5711678 ACCTCGATGAGGCAGCTAAATGTTCATTTCTTTGAGCTGAAAATCGA
1 ACCTCAATGAGGCAGCTAAATGTTCATTTCTTTGAGCTGAAAATCGA
5711725 GAGTGAATAG
Statistics
Matches: 367, Mismatches: 39, Indels: 10
0.88 0.09 0.02
Matches are distributed among these distances:
90 4 0.01
91 357 0.97
92 6 0.02
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.28
Consensus pattern (91 bp):
ACCTCAATGAGGCAGCTAAATGTTCATTTCTTTGAGCTGAAAATCGAAACAAATATGAGTTGGCT
ACTTCTAACCTACCGATACGAAATGC
Found at i:5711712 original size:273 final size:273
Alignment explanation
Indices: 5711225--5711719 Score: 778
Period size: 273 Copynumber: 1.8 Consensus size: 273
5711215 GCTGTAGGAC
* * * *
5711225 CTCAACGAGGCAGCTAAGTGTTCATTTCTGTGAGCTGAAAATTGAAACAAATATGAGTTGGCTAC
1 CTCAACGAAGCAGCTAAATGTTCATTTCTGTGAGCTGAAAATTCAAACAAATATGAGTCGGCTAC
** *
5711290 TTCTAACCTACTGATACGAAATGCACCTCAATGAGACAGCTAAATGTTCATTTCTATGAGCTGAA
66 TTCTAACCTACCAATACGAAATGCACCTCAATGAGACAACTAAATGTTCATTTCTATGAGCTGAA
* * * *
5711355 AATCGAAACAAATATGAGTTGGCTACTTCTATCCTACCGCTACAAAATGTATCTCAATGAGGCAG
131 AATCAAAACAAATATGAGTTGACTACTTCTAACCTACCGCTACAAAATGTACCTCAATGAGGCAG
5711420 CTAAATGTTCATTTCTTTGAGCTGAAAGACAAAGCAAATATGAGTCGGCTACTTCTAAGCTACCA
196 CTAAATGTTCATTTCTTTGAGCTGAAAGACAAAGCAAATATGAGTCGGCTACTTCTAAGCTACCA
5711485 ATACGAAATGCAT
261 ATACGAAATGCAT
*
5711498 CTCAACGAAGCAGCTAAATGTTCATTTCTTTGAGCTGAAAA-TCAAAGCAAATATGAGTCGGCTA
1 CTCAACGAAGCAGCTAAATGTTCATTTCTGTGAGCTGAAAATTCAAA-CAAATATGAGTCGGCTA
* * * *
5711562 CTTCTAAGCTACCAATACGAAATGGACCTCAATGAGGCAACTAAATGTTCATTTCTGTGAGCTGA
65 CTTCTAACCTACCAATACGAAATGCACCTCAATGAGACAACTAAATGTTCATTTCTATGAGCTGA
* * * *
5711627 AAATCAAAACAAATATGAGTTGACTACTTTTAACCTACTGCTACGAAACTG-ACCTCGATGAGGC
130 AAATCAAAACAAATATGAGTTGACTACTTCTAACCTACCGCTAC-AAAATGTACCTCAATGAGGC
5711691 AGCTAAATGTTCATTTCTTTGAGCTGAAA
194 AGCTAAATGTTCATTTCTTTGAGCTGAAA
5711720 ATCGAGAGTG
Statistics
Matches: 200, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
272 4 0.02
273 191 0.95
274 5 0.03
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.28
Consensus pattern (273 bp):
CTCAACGAAGCAGCTAAATGTTCATTTCTGTGAGCTGAAAATTCAAACAAATATGAGTCGGCTAC
TTCTAACCTACCAATACGAAATGCACCTCAATGAGACAACTAAATGTTCATTTCTATGAGCTGAA
AATCAAAACAAATATGAGTTGACTACTTCTAACCTACCGCTACAAAATGTACCTCAATGAGGCAG
CTAAATGTTCATTTCTTTGAGCTGAAAGACAAAGCAAATATGAGTCGGCTACTTCTAAGCTACCA
ATACGAAATGCAT
Found at i:5711922 original size:122 final size:122
Alignment explanation
Indices: 5711634--5713016 Score: 1722
Period size: 122 Copynumber: 11.3 Consensus size: 122
5711624 TGAAAATCAA
* * * * * * *
5711634 AACAAATATGAGTTGACTACTTTTAACCTACTGCTACGAAACT-GACCTCGATGAGGCAGCTAAA
1 AACAAATATGAATTGGCTACTTCTAACCTACCGATAC-AAAATGGACCTCAATGAGGCAGCTAAA
* * *
5711698 TGTTCATTTCTTTGAGCTGAAAATCGAGAGTGAATAGGTTTTTATGTTTCTCTAGCTCTG
65 TGTTCATTTCTGTGAGCTGAAAATC-AAAGTGAATAGG-TTTTATGTTTCTGTAGCTCTG
* * * **
5711758 AACAAATATGAATTGGCTAGTTCTAACCTACCAATACGAAATGGACCTCAAAAAGGCAGCTAAAT
1 AACAAATATGAATTGGCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAAT
* * *
5711823 GTTCGTTTCTGTGAACTGAAAACCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTG
66 GTTCATTTCTGTGAGCTGAAAATCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTG
*
5711880 AACAAATATGAATTGCCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAAT
1 AACAAATATGAATTGGCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAAT
* ** * * * *
5711945 GTTCACTTCCATGAGCTGAAAATCAAAGTGAATAGATTTTATGTTTCCGTAACACTG
66 GTTCATTTCTGTGAGCTGAAAATCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTG
* * * * *
5712002 AACAAATATGAATTGGCGACTTCTGACCTAGCGATACGAAATGTACCTCAATGAGGCAGCTAAAT
1 AACAAATATGAATTGGCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAAT
5712067 GTTCATTTCTGTGAGCTGAAAATCAAAGTGAATAGGTTTTTATGTTTCTGTAGCTCTG
66 GTTCATTTCTGTGAGCTGAAAATCAAAGTGAATAGG-TTTTATGTTTCTGTAGCTCTG
* *
5712125 AACAAATATGAATTGCCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCGGCTAAAT
1 AACAAATATGAATTGGCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAAT
** * * * * * *
5712190 GTTCATTTCCATAAGCTGAAAA-CCAA---AATAGATTTTATGTTTCAGTAACCCTG
66 GTTCATTTCTGTGAGCTGAAAATCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTG
* * * * * **
5712243 AACAAATATGAATTGGCTACTTCTGACCTACCGATACGAAATGTACCTAAATGAAGTGGCTAAAT
1 AACAAATATGAATTGGCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAAT
5712308 GTTCATTTCTGTGAGCTGAAAATCAAAAGTGAATAGGTCTTTATGTTTTCTGTAGCTCTG
66 GTTCATTTCTGTGAGCTGAAAATC-AAAGTGAATAGGT-TTTATG-TTTCTGTAGCTCTG
* * ** * * *
5712368 AACTAATAATGAATTGGCTACTTCTAACCAACCGATATGAAATAGACCTAAATGAGGCAGCAAAA
1 AACAAAT-ATGAATTGGCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAA
* * * *
5712433 TGTTCATTTCTCTGAGCTGAAAATCGAAGTGAATAGGTTTTATGTTTTTGTAGCTCTC
65 TGTTCATTTCTGTGAGCTGAAAATCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTG
** * * * *
5712491 AACAAATATGAATTTCCTACTTCTAACCTACCAATACAAAACGGCCCTCAATGAGCCAGCTAAAT
1 AACAAATATGAATTGGCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAAT
* * * * *
5712556 GTTCATTCCTGTGAGCTGAAAATTGAAA-TGAATAGATTTCATGTTTCTGTAGCTGTG
66 GTTCATTTCTGTGAGCTGAAAA-TCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTG
* *
5712613 AACAAATATGAATTGGCTACTTCTAACCTACTGATACGAAATGGACCTCAATGAGGCAGCTAAAT
1 AACAAATATGAATTGGCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAAT
* * * *
5712678 GTTTATTTCTATGAGCTAAAAATCAAAGTGAATAGGTTTTTATGTTTCTGCAGCTCTG
66 GTTCATTTCTGTGAGCTGAAAATCAAAGTGAATAGG-TTTTATGTTTCTGTAGCTCTG
* * * *
5712736 GACAAATATGAATTGGCTACTTCTAAGCTACTGATACGAAATGGACCTCAATGAGGCAGCTAAAT
1 AACAAATATGAATTGGCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAAT
5712801 GTTCATTTCTGTGAGCTGAAAATCAAAGTGAATAGGTTTTTATGTTTCTGTAGCTCTG
66 GTTCATTTCTGTGAGCTGAAAATCAAAGTGAATAGG-TTTTATGTTTCTGTAGCTCTG
* * * * *
5712859 AACTAATATGAATTGGCTACCTCTAACCTACCCATACAAAATGGAACTCAATGAGGCAGATAAAT
1 AACAAATATGAATTGGCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAAT
* * * * * * * **
5712924 GTTAATTTCTATGAGCTG-AAATCGAAGTAAATAGGTCTTATGTTTCTATA-ATCCA
66 GTTCATTTCTGTGAGCTGAAAATCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTG
* * *
5712979 AACGAATATGAATCT-GTTACTTCTAACCTATCGATACA
1 AACAAATATGAAT-TGGCTACTTCTAACCTACCGATACA
5713017 GAATAGGCAT
Statistics
Matches: 1086, Mismatches: 159, Indels: 32
0.85 0.12 0.03
Matches are distributed among these distances:
118 95 0.09
119 6 0.01
120 35 0.03
121 18 0.02
122 407 0.37
123 343 0.32
124 81 0.07
125 29 0.03
126 72 0.07
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (122 bp):
AACAAATATGAATTGGCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAAT
GTTCATTTCTGTGAGCTGAAAATCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTG
Found at i:5712497 original size:611 final size:611
Alignment explanation
Indices: 5711634--5712968 Score: 1835
Period size: 611 Copynumber: 2.2 Consensus size: 611
5711624 TGAAAATCAA
* * * * * *
5711634 AACAAATATGAGTTGACTACTTTTAACCTACTGCTACGAAACTGACCTCGATGAGGCAGCTAAAT
1 AACAAATATGAATTGGCTACTTCTAACCTACCGATACGAAA-TGACCTCAATGAGGCAGCTAAAT
* * *
5711699 GTTCATTTCTTTGAGCTGAAAATCGAGAGTGAATAGGTTTTTATG-TTTCTCTAGCTCTGAACAA
65 GTTCATTTCTATGAGCTGAAAATC-AAAGTGAATAGGTCTTTATGTTTTCTCTAGCTCTGAACAA
* * * * *
5711763 ATATGAATTGGCTAGTTCTAACCTACCAATACGAAATGGACCTCAAAAAGGCAGCTAAATGTTCG
129 ATATGAATTGGCTACTTCTAACCAACCAATACGAAATAGACCTCAAAAAGGCAGCAAAATGTTCA
* *
5711828 TTTCTGTGAACTGAAAACCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTGAACAAATATGAAT
194 TTTCTCTGAACTGAAAACCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTCAACAAATATGAAT
* * *
5711893 TGCCTACTTCTAACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAATGTTCACTTCC-AT
259 TGCCTACTTCTAACCTACCAATACAAAACGGACCTCAATGAGCCAGCTAAATGTTCA-TTCCTAT
*
5711957 GAGCTGAAAA-TCAAAGTGAATAGATTTTATGTTTCCGTAACACTGAACAAATATGAATTGGCGA
323 GAGCTGAAAATTCAAA-TGAATAGATTTCATGTTTCCGTAACACTGAACAAATATGAATTGGCGA
* * * *
5712021 CTTCTGACCTAGC-GATACGAAATGTACCTCAATGAGGCAGCTAAATGTTCATTTCTGTGAGCTG
387 CTTCTAACCTA-CTGATACGAAATGGACCTCAATGAGGCAGCTAAATGTTCATTTCTATGAGCTA
*
5712085 AAAATCAAAGTGAATAGGTTTTTATGTTTCTGTAGCTCTGAACAAATATGAATTGCCTACTTCTA
451 AAAATCAAAGTGAATAGGTTTTTATGTTTCTGCAGCTCTGAACAAATATGAATTGCCTACTTCTA
* *
5712150 ACCTACCGATACAAAATGGACCTCAATGAGGCGGCTAAATGTTCATTTCCATAAGCTGAAAA-CC
516 ACCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAATGTTCATTTCCATAAGCTGAAAATCA
5712214 AA-AATA-GATTTTATGTTTCAGTAACCCTG
581 AAGAATAGGATTTTATGTTTCAGTAACCCTG
* * * **
5712243 AACAAATATGAATTGGCTACTTCTGACCTACCGATACGAAATGTACCTAAATGAAGTGGCTAAAT
1 AACAAATATGAATTGGCTACTTCTAACCTACCGATACGAAATG-ACCTCAATGAGGCAGCTAAAT
* * *
5712308 GTTCATTTCTGTGAGCTGAAAATCAAAAGTGAATAGGTCTTTATGTTTTCTGTAGCTCTGAACTA
65 GTTCATTTCTATGAGCTGAAAATC-AAAGTGAATAGGTCTTTATGTTTTCTCTAGCTCTGAACAA
* * *
5712373 ATAATGAATTGGCTACTTCTAACCAACCGATATGAAATAGACCT-AAATGAGGCAGCAAAATGTT
129 AT-ATGAATTGGCTACTTCTAACCAACCAATACGAAATAGACCTCAAA-AAGGCAGCAAAATGTT
* * * *
5712437 CATTTCTCTGAGCTGAAAATCGAAGTGAATAGGTTTTATGTTTTTGTAGCTCTCAACAAATATGA
192 CATTTCTCTGAACTGAAAACCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTCAACAAATATGA
* * *
5712502 ATTTCCTACTTCTAACCTACCAATACAAAACGGCCCTCAATGAGCCAGCTAAATGTTCATTCCTG
257 ATTGCCTACTTCTAACCTACCAATACAAAACGGACCTCAATGAGCCAGCTAAATGTTCATTCCTA
* * * ** *
5712567 TGAGCTGAAAATTGAAATGAATAGATTTCATGTTTCTGTAGCTGTGAACAAATATGAATTGGCTA
322 TGAGCTGAAAATTCAAATGAATAGATTTCATGTTTCCGTAACACTGAACAAATATGAATTGGCGA
*
5712632 CTTCTAACCTACTGATACGAAATGGACCTCAATGAGGCAGCTAAATGTTTATTTCTATGAGCTAA
387 CTTCTAACCTACTGATACGAAATGGACCTCAATGAGGCAGCTAAATGTTCATTTCTATGAGCTAA
* *
5712697 AAATCAAAGTGAATAGGTTTTTATGTTTCTGCAGCTCTGGACAAATATGAATTGGCTACTTCTAA
452 AAATCAAAGTGAATAGGTTTTTATGTTTCTGCAGCTCTGAACAAATATGAATTGCCTACTTCTAA
* * * ** *
5712762 GCTACTGATACGAAATGGACCTCAATGAGGCAGCTAAATGTTCATTTCTGTGAGCTGAAAATCAA
517 CCTACCGATACAAAATGGACCTCAATGAGGCAGCTAAATGTTCATTTCCATAAGCTGAAAATCAA
* * * *
5712827 AGTGAATAGGTTTTTATGTTTCTGTAGCTCTG
582 A--GAATAGGATTTTATGTTTCAGTAACCCTG
* * * * * *
5712859 AACTAATATGAATTGGCTACCTCTAACCTACCCATACAAAATGGAACTCAATGAGGCAGATAAAT
1 AACAAATATGAATTGGCTACTTCTAACCTACCGATACGAAAT-GACCTCAATGAGGCAGCTAAAT
* * *
5712924 GTTAATTTCTATGAGCTG-AAATCGAAGTAAATAGGTC-TTATGTTT
65 GTTCATTTCTATGAGCTGAAAATCAAAGTGAATAGGTCTTTATGTTT
5712969 CTATAATCCA
Statistics
Matches: 634, Mismatches: 79, Indels: 22
0.86 0.11 0.03
Matches are distributed among these distances:
608 2 0.00
609 92 0.15
610 27 0.04
611 389 0.61
612 7 0.01
613 8 0.01
614 12 0.02
615 9 0.01
616 87 0.14
617 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (611 bp):
AACAAATATGAATTGGCTACTTCTAACCTACCGATACGAAATGACCTCAATGAGGCAGCTAAATG
TTCATTTCTATGAGCTGAAAATCAAAGTGAATAGGTCTTTATGTTTTCTCTAGCTCTGAACAAAT
ATGAATTGGCTACTTCTAACCAACCAATACGAAATAGACCTCAAAAAGGCAGCAAAATGTTCATT
TCTCTGAACTGAAAACCAAAGTGAATAGGTTTTATGTTTCTGTAGCTCTCAACAAATATGAATTG
CCTACTTCTAACCTACCAATACAAAACGGACCTCAATGAGCCAGCTAAATGTTCATTCCTATGAG
CTGAAAATTCAAATGAATAGATTTCATGTTTCCGTAACACTGAACAAATATGAATTGGCGACTTC
TAACCTACTGATACGAAATGGACCTCAATGAGGCAGCTAAATGTTCATTTCTATGAGCTAAAAAT
CAAAGTGAATAGGTTTTTATGTTTCTGCAGCTCTGAACAAATATGAATTGCCTACTTCTAACCTA
CCGATACAAAATGGACCTCAATGAGGCAGCTAAATGTTCATTTCCATAAGCTGAAAATCAAAGAA
TAGGATTTTATGTTTCAGTAACCCTG
Found at i:5717399 original size:128 final size:124
Alignment explanation
Indices: 5717172--5717425 Score: 375
Period size: 128 Copynumber: 2.0 Consensus size: 124
5717162 CTTCTAATTC
* * * * *
5717172 CCAATCAACAAAGCACAGTTCATTGCAATTGAATCTGAGAAATGGATAAAATTTTAATCATTTGT
1 CCAATCAACAAAGCACAGTTCATTACAATTGAATCTAAGAAATGAAAAAAATTTCAATCATTTGT
* *
5717237 TGAAATAAACATTTAAATTGGATCATTCAATAAGCATTCATTACTTAAGA-TTCAATTAT
66 TGAAATAAACACTTAAATCGGATCATTCAATAAGCATTCATTACTTAA-ACTTCAATTAT
*
5717296 CCAATCAACAAAGCACAGTTCATTACAATTGAATCTAAGAAATGTAAAAAAAAAATTTCATTCAT
1 CCAATCAACAAAGCACAGTTCATTACAATTGAATCTAAGAAATG----AAAAAAATTTCAATCAT
*
5717361 TTGTTGAAATAAACACTTAAATCGGATCATTCACTAAGCATTCATTACTTAAACTTCAATTAT
62 TTGTTGAAATAAACACTTAAATCGGATCATTCAATAAGCATTCATTACTTAAACTTCAATTAT
5717424 CC
1 CC
5717426 CAACAATAAT
Statistics
Matches: 116, Mismatches: 9, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
124 42 0.36
127 1 0.01
128 73 0.63
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.32
Consensus pattern (124 bp):
CCAATCAACAAAGCACAGTTCATTACAATTGAATCTAAGAAATGAAAAAAATTTCAATCATTTGT
TGAAATAAACACTTAAATCGGATCATTCAATAAGCATTCATTACTTAAACTTCAATTAT
Found at i:5722653 original size:48 final size:52
Alignment explanation
Indices: 5722583--5722681 Score: 118
Period size: 52 Copynumber: 2.0 Consensus size: 52
5722573 AATAATTATT
5722583 ATTTTAAATTATACAAATTCATA-AACT-A-T-AATCATATTAGTTATAATA
1 ATTTTAAATTATACAAATTCATATAACTAATTAAATCATATTAGTTATAATA
* * **
5722631 ATTTTAAATTTTATTAAA-TCATATATTTAATTAAATCATATTAGTTATAAT
1 ATTTTAAATTATA-CAAATTCATATAACTAATTAAATCATATTAGTTATAAT
5722682 CATATATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
48 17 0.40
49 5 0.12
50 1 0.02
51 1 0.02
52 18 0.43
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.46
Consensus pattern (52 bp):
ATTTTAAATTATACAAATTCATATAACTAATTAAATCATATTAGTTATAATA
Found at i:5722663 original size:17 final size:17
Alignment explanation
Indices: 5722638--5722671 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5722628 ATAATTTTAA
*
5722638 ATTTTATTAAATCATAT
1 ATTTAATTAAATCATAT
5722655 ATTTAATTAAATCATAT
1 ATTTAATTAAATCATAT
5722672 TAGTTATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAATCATAT
Found at i:5722688 original size:17 final size:16
Alignment explanation
Indices: 5722643--5722690 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
5722633 TTTAAATTTT
5722643 ATTAAATCATATATTTA
1 ATTAAATCATATA-TTA
5722660 ATTAAATC--ATATTA
1 ATTAAATCATATATTA
*
5722674 GTTATAATCATATATTA
1 ATTA-AATCATATATTA
5722691 TGATTTGAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 6 0.22
15 7 0.26
17 14 0.52
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (16 bp):
ATTAAATCATATATTA
Found at i:5722745 original size:54 final size:54
Alignment explanation
Indices: 5722687--5722865 Score: 137
Period size: 54 Copynumber: 3.1 Consensus size: 54
5722677 ATAATCATAT
5722687 ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
1 ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
* * * * * * * *
5722741 ATTATATATTTTAATTATATT-ATATTTAATAATAATTATGTTATTTTA-TATTTTACAGTATCA
1 ATTAT-GA-TTTGAGTAAATTCATA--TAAGAAT-ATTA-ATTA-TTAAGAATTTT--A-T-T-A
5722804 TA
54 -A
*
5722806 TATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
1 -ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
5722861 ATTAT
1 ATTAT
5722866 ATATTTTAAT
Statistics
Matches: 92, Mismatches: 17, Indels: 32
0.65 0.12 0.23
Matches are distributed among these distances:
54 10 0.11
55 5 0.05
56 10 0.11
57 7 0.08
58 5 0.05
59 9 0.10
60 6 0.07
61 9 0.10
62 5 0.05
63 7 0.08
64 10 0.11
65 4 0.04
66 5 0.05
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (54 bp):
ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
Found at i:5722748 original size:61 final size:61
Alignment explanation
Indices: 5722683--5722870 Score: 190
Period size: 61 Copynumber: 3.1 Consensus size: 61
5722673 AGTTATAATC
5722683 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * * * * * *
5722744 ATATATTTTAATTAT-ATTATATTTA-ATAATAATTATGTTATT-TT-A-TATTTTA-CAGTATC
1 ATATATTATGATT-TGAGTAAATTCATATAAGAA-TAT-TAATTATTAAGAATTTTATTA-AATT
*
5722803 ATATATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
5722864 ATATATT
1 ATATATT
5722871 TTAATTAAAA
Statistics
Matches: 94, Mismatches: 23, Indels: 20
0.69 0.17 0.15
Matches are distributed among these distances:
58 6 0.06
59 30 0.32
60 14 0.15
61 38 0.40
62 6 0.06
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:5722762 original size:18 final size:17
Alignment explanation
Indices: 5722731--5722765 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5722721 ATTATTAAGA
5722731 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
*
5722748 ATTTTAATTATATTATAT
1 ATTTT-ATTAAATTATAT
5722766 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:5722804 original size:120 final size:120
Alignment explanation
Indices: 5722680--5722902 Score: 419
Period size: 120 Copynumber: 1.9 Consensus size: 120
5722670 ATTAGTTATA
5722680 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
1 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
* *
5722745 TATATTTTAATTATATTATATTTAATAATAATTATGTTATTTTATATTTTACAGT
66 TATATTTTAATTAAAATATATTTAATAATAATTATGTTATTTTATATTTTACAGT
*
5722800 ATCATATATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
1 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
5722865 TATATTTTAATTAAAATATATTTAATAATAATTATGTT
66 TATATTTTAATTAAAATATATTTAATAATAATTATGTT
5722903 TAATATGATT
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 100 1.00
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.49
Consensus pattern (120 bp):
ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTA
TATATTTTAATTAAAATATATTTAATAATAATTATGTTATTTTATATTTTACAGT
Found at i:5722879 original size:18 final size:17
Alignment explanation
Indices: 5722851--5722885 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5722841 ATTATTAAGA
*
5722851 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
5722868 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
5722886 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:5722897 original size:54 final size:54
Alignment explanation
Indices: 5722714--5722899 Score: 142
Period size: 54 Copynumber: 3.2 Consensus size: 54
5722704 TTCATATAAG
* *
5722714 AATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATATTATATTT
1 AATAATAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAATTATATTT
* * * *
5722768 AATAATAATTATGT--TATTTTATATTTTACAGTATCATATATTATGGTTTGAGTAAATTCATAT
1 AATAATAATTAT-TAAGAATTT-TA--TTA-A--AT--TATA-TAT--TTTAATTAAATT-ATAT
**
5722831 AAG
53 -TT
* *
5722834 AATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTT
1 AATAATAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAATTATATTT
5722888 AATAATAATTAT
1 AATAATAATTAT
5722900 GTTTAATATG
Statistics
Matches: 99, Mismatches: 17, Indels: 32
0.67 0.11 0.22
Matches are distributed among these distances:
53 4 0.04
54 24 0.24
55 5 0.05
56 12 0.12
57 1 0.01
58 3 0.03
59 6 0.06
61 6 0.06
62 3 0.03
63 1 0.01
64 12 0.12
65 5 0.05
66 13 0.13
67 4 0.04
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.51
Consensus pattern (54 bp):
AATAATAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAATTATATTT
Found at i:5723001 original size:143 final size:147
Alignment explanation
Indices: 5722839--5723109 Score: 478
Period size: 143 Copynumber: 1.9 Consensus size: 147
5722829 ATAAGAATAT
*
5722839 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
5722904 -AATATGATTAAATTATTTATTATTGAT-AT-TAATCTTATTAAAATTTAAATAA-AATAATTTA
66 AAATATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAATTTA
5722965 CCAAAACAAATTTCTGC
131 CCAAAACAAATTTCTGC
5722982 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
5723047 AAATATGATTAAATTATTTATTTTTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
66 AAATATGATTAAATTATTTATTATTGATAAT--ATAATCTTATTAAAATTTAAATAACAATAA
5723110 CAATAATCAT
Statistics
Matches: 120, Mismatches: 2, Indels: 6
0.94 0.02 0.05
Matches are distributed among these distances:
143 64 0.53
144 26 0.22
145 2 0.02
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAATTTA
CCAAAACAAATTTCTGC
Found at i:5723022 original size:18 final size:17
Alignment explanation
Indices: 5722994--5723028 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5722984 ATTATTAAGA
*
5722994 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
5723011 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
5723029 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:5723239 original size:44 final size:45
Alignment explanation
Indices: 5723190--5723284 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
5723180 TTACACCTCT
* *
5723190 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
** *
5723234 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
5723279 ATTACA
1 ATTACA
5723285 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
Found at i:5723284 original size:16 final size:16
Alignment explanation
Indices: 5723263--5723295 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5723253 TTGATTTGCT
*
5723263 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
5723279 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
5723295 A
1 A
5723296 ATCCAATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.36, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:5723305 original size:21 final size:21
Alignment explanation
Indices: 5723276--5723318 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
5723266 ACACCTCTAT
*
5723276 TCCATTACACCTCTAATCCAA
1 TCCAATACACCTCTAATCCAA
5723297 TCCAATACACCTCTAATCCAA
1 TCCAATACACCTCTAATCCAA
5723318 T
1 T
5723319 ACAGCGAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.28
Consensus pattern (21 bp):
TCCAATACACCTCTAATCCAA
Found at i:5733136 original size:13 final size:13
Alignment explanation
Indices: 5733114--5733150 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
5733104 ATCACCCCCA
*
5733114 CACCCTACTAAAT
1 CACCCCACTAAAT
5733127 CACCCCACTAAAT
1 CACCCCACTAAAT
5733140 CACCCCACTAA
1 CACCCCACTAA
5733151 CTCCATCATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.38, C:0.46, G:0.00, T:0.16
Consensus pattern (13 bp):
CACCCCACTAAAT
Found at i:5733183 original size:29 final size:30
Alignment explanation
Indices: 5733125--5733194 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 30
5733115 ACCCTACTAA
*
5733125 ATCACCCCACTAAATCACCCCACTAACTCC
1 ATCACCCCACTAAACCACCCCACTAACTCC
* * *
5733155 ATCATCCCACTAAACCA-TCCACTATCTCC
1 ATCACCCCACTAAACCACCCCACTAACTCC
5733184 ATCACCCCACT
1 ATCACCCCACT
5733195 TGCCTATAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 20 0.57
30 15 0.43
ACGTcount: A:0.31, C:0.49, G:0.00, T:0.20
Consensus pattern (30 bp):
ATCACCCCACTAAACCACCCCACTAACTCC
Found at i:5733563 original size:3 final size:3
Alignment explanation
Indices: 5733541--5733708 Score: 77
Period size: 3 Copynumber: 57.7 Consensus size: 3
5733531 GGGGAGAGTG
* *
5733541 TTA TTT TTA -TA TTG TTA TTA TTA TTA TTTA TTA TTA -TA CTTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA -TTA TTA
* * * * * *
5733585 TTA TTA CTG TTA CTA TTA TTT TGTA TTA TTT TTA TCA TTA TTGA TTTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TT-A -TTA
* ** * * * *
5733633 TTA TTA TTA TTA -GA ACA TT- TT- TTT TTT TTA TT- TTT TTA TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
5733677 -TA TTA TTA TT- TTA TTA ATA -TA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5733709 GTCTTCTATT
Statistics
Matches: 126, Mismatches: 25, Indels: 28
0.70 0.14 0.16
Matches are distributed among these distances:
2 19 0.15
3 96 0.76
4 9 0.07
5 2 0.02
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5733669 original size:14 final size:14
Alignment explanation
Indices: 5733649--5733688 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
5733639 TTATTAGAAC
5733649 ATTTTTTT-TTTTT
1 ATTTTTTTATTTTT
5733662 ATTTTTTTATTTTT
1 ATTTTTTTATTTTT
* *
5733676 ATATTATTATTTT
1 ATTTTTTTATTTT
5733689 ATTAATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.82
Consensus pattern (14 bp):
ATTTTTTTATTTTT
Found at i:5733682 original size:11 final size:11
Alignment explanation
Indices: 5733660--5733708 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
5733650 TTTTTTTTTT
*
5733660 TTATTTTTTTA
1 TTATTTTATTA
5733671 TT-TTTATATTA
1 TTATTT-TATTA
5733682 TTATTTTATTA
1 TTATTTTATTA
* *
5733693 ATATATTATTA
1 TTATTTTATTA
5733704 TTATT
1 TTATT
5733709 GTCTTCTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
10 3 0.10
11 25 0.81
12 3 0.10
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:5733703 original size:19 final size:19
Alignment explanation
Indices: 5733660--5733705 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
5733650 TTTTTTTTTT
* **
5733660 TTATTTTTTTATTTTTATA
1 TTATTATTTTATTAATATA
5733679 TTATTATTTTATTAATATA
1 TTATTATTTTATTAATATA
5733698 TTATTATT
1 TTATTATT
5733706 ATTGTCTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTATTATTTTATTAATATA
Found at i:5733766 original size:18 final size:18
Alignment explanation
Indices: 5733725--5733768 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
5733715 TATTTTGTTG
*
5733725 TTGTTATTATTATTTTAA
1 TTGTTATTACTATTTTAA
*
5733743 TCGTTATTACTATGTTT-A
1 TTGTTATTACTAT-TTTAA
5733761 TTGTTATT
1 TTGTTATT
5733769 GTAGCATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.23, C:0.05, G:0.09, T:0.64
Consensus pattern (18 bp):
TTGTTATTACTATTTTAA
Found at i:5734526 original size:126 final size:126
Alignment explanation
Indices: 5734296--5734529 Score: 387
Period size: 126 Copynumber: 1.9 Consensus size: 126
5734286 TTCTCAATTG
* * * * * *
5734296 TTTTTAAAATAATGGCAATGTTCGGTATTTAAAGACTTTGAAGAATCGTGCCCTAACGTATTGGG
1 TTTTCAAAATAAAGGCAATGGTCGGTATTTAAAGAATTCGAAGAATCGTGCCCTAACGTACTGGG
* *
5734361 TTTTGCTTTCTTTGTTTGTCTTGAATATTCGGATATCCTCTTACCAGTTCACTCTAAAAAA
66 TTTCGCTTTCTTTGTTTGTCTTGAATATTCGAATATCCTCTTACCAGTTCACTCTAAAAAA
5734422 TTTTCAAAATAAAGGCAATGGTCGGTATTTAAAGAATTCGAAGAATCGTGCCCTAACGTACTGGG
1 TTTTCAAAATAAAGGCAATGGTCGGTATTTAAAGAATTCGAAGAATCGTGCCCTAACGTACTGGG
*
5734487 TTTCGCTTTCTTTGTTTGTTTTGAATATTCGAATATCCTCTTA
66 TTTCGCTTTCTTTGTTTGTCTTGAATATTCGAATATCCTCTTA
5734530 AGGCTAAAGC
Statistics
Matches: 99, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
126 99 1.00
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.40
Consensus pattern (126 bp):
TTTTCAAAATAAAGGCAATGGTCGGTATTTAAAGAATTCGAAGAATCGTGCCCTAACGTACTGGG
TTTCGCTTTCTTTGTTTGTCTTGAATATTCGAATATCCTCTTACCAGTTCACTCTAAAAAA
Found at i:5735854 original size:17 final size:19
Alignment explanation
Indices: 5735832--5735867 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
5735822 ATTTAATTGA
5735832 ATTTTTAAT-ATTT-TAAT
1 ATTTTTAATGATTTCTAAT
5735849 ATTTTTAATGATTTCTAAT
1 ATTTTTAATGATTTCTAAT
5735868 TTAAAAAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (19 bp):
ATTTTTAATGATTTCTAAT
Found at i:5739227 original size:129 final size:125
Alignment explanation
Indices: 5738919--5739244 Score: 354
Period size: 129 Copynumber: 2.6 Consensus size: 125
5738909 TGAGAAAAAA
* * *
5738919 AAAACACCTTCAACATAATATAGTTTATTTTGT-AAAT--GATATTTTTGTTATTACTTAACTAA
1 AAAA-ACC-TCAACATAATATAGTTTACTTTGTAAAATAAAATATTTTTGTTATTACTTAGCTAA
* *
5738981 ATTAGTGCATAGTTGACTCGTAGAAACAAATTCACTAAAGATTTAATATTAGTGGAGATGAC
64 ATTAGTGCATAATTGACTCGTAGAAACAAATTCACTAAAGATGTAATATTAGTGGAGATGAC
* * * * * *
5739043 AAAAATCTCAAGATTATATAATCTACTTTGTAAAATAAATATATTTTTGTTATTACTTAGCTGAA
1 AAAAACCTCAACATAATATAGTTTACTTTGTAAAATAAA-ATATTTTTGTTATTACTTAGCTAAA
* * * * * *
5739108 TTGGTGCATAATTGACTCGT-GACACCAAATTTAGTAAAAGGTGTAATATTAGTTGAGATGAC
65 TTAGTGCATAATTGACTCGTAGA-AACAAATTCACT-AAAGATGTAATATTAGTGGAGATGAC
* * * *
5739170 AAAATACCCTGAACATAATAGAGTTTACTTTGTAAAATAAAAGTATTTTTGTCATTACTTGGCTA
1 AAAA-A-CCTCAACATAATATAGTTTACTTTGTAAAATAAAA-TATTTTTGTTATTACTTAGCTA
*
5739235 AATTAATGCA
63 AATTAGTGCA
5739245 CAGTTGGCTT
Statistics
Matches: 164, Mismatches: 29, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
122 19 0.12
123 6 0.04
124 4 0.02
125 2 0.01
126 50 0.30
127 27 0.16
128 2 0.01
129 54 0.33
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (125 bp):
AAAAACCTCAACATAATATAGTTTACTTTGTAAAATAAAATATTTTTGTTATTACTTAGCTAAAT
TAGTGCATAATTGACTCGTAGAAACAAATTCACTAAAGATGTAATATTAGTGGAGATGAC
Found at i:5739523 original size:18 final size:17
Alignment explanation
Indices: 5739492--5739528 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
5739482 TATTAAAAAA
*
5739492 TATATTTTTTATAATTT
1 TATATTTTTAATAATTT
5739509 TATACTTTTTAATAATTT
1 TATA-TTTTTAATAATTT
5739527 TA
1 TA
5739529 AAAATTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
TATATTTTTAATAATTT
Found at i:5741736 original size:19 final size:20
Alignment explanation
Indices: 5741699--5741739 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
5741689 TATTTTATTC
5741699 AAAAGTAAAAAAAGAAAAAG
1 AAAAGTAAAAAAAGAAAAAG
* *
5741719 AAAAG-AAAGAAAGTAAAAG
1 AAAAGTAAAAAAAGAAAAAG
5741738 AA
1 AA
5741740 TCTATCCCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (20 bp):
AAAAGTAAAAAAAGAAAAAG
Found at i:5742504 original size:19 final size:20
Alignment explanation
Indices: 5742464--5742504 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
5742454 AAATTATAAA
* *
5742464 AAATTACCTTTAAAATATAT
1 AAATTACATATAAAATATAT
5742484 AAATTACATATAAAA-ATAT
1 AAATTACATATAAAATATAT
5742503 AA
1 AA
5742505 TTGCTCCACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATTACATATAAAATATAT
Found at i:5743877 original size:32 final size:29
Alignment explanation
Indices: 5743841--5743902 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 29
5743831 ATTAGTGAAA
*
5743841 TGTAAGAATCAAACCAAAATTAAAGTTAGATG
1 TGTAAAAAT-AAACC-AAATTAAAGTT-GATG
*
5743873 TGTAAAAATATACCAAATTAAAGTTGATG
1 TGTAAAAATAAACCAAATTAAAGTTGATG
5743902 T
1 T
5743903 ATAACATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 5 0.18
30 11 0.39
31 4 0.14
32 8 0.29
ACGTcount: A:0.48, C:0.08, G:0.15, T:0.29
Consensus pattern (29 bp):
TGTAAAAATAAACCAAATTAAAGTTGATG
Found at i:5749128 original size:28 final size:27
Alignment explanation
Indices: 5749091--5749173 Score: 121
Period size: 28 Copynumber: 3.0 Consensus size: 27
5749081 CACTTTGTGC
5749091 TATTCTGGTGTGTTTGGATGGATTATAT
1 TATTCTGGTGTGTTTGGA-GGATTATAT
5749119 TATTCTGGTGTGTTTGGGAGGATTATAT
1 TATTCTGGTGTGTTT-GGAGGATTATAT
* *
5749147 GATACTGGTGTGTTTTGGAGGATTATA
1 TATTCTGGTGTG-TTTGGAGGATTATA
5749174 CTGGTGTGTT
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
28 45 0.88
29 6 0.12
ACGTcount: A:0.19, C:0.04, G:0.31, T:0.46
Consensus pattern (27 bp):
TATTCTGGTGTGTTTGGAGGATTATAT
Found at i:5749143 original size:23 final size:23
Alignment explanation
Indices: 5749117--5749184 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 23
5749107 GATGGATTAT
5749117 ATTATTCTGGTGTGTTTGGGAGG
1 ATTATTCTGGTGTGTTTGGGAGG
*
5749140 ATTATATGATACTGGTGTGTTTTGGAGG
1 A-T-TAT--T-CTGGTGTGTTTGGGAGG
*
5749168 ATTATACTGGTGTGTTT
1 ATTATTCTGGTGTGTTT
5749185 TGGTTGGACA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
23 12 0.32
24 1 0.03
25 3 0.08
26 3 0.08
27 2 0.05
28 17 0.45
ACGTcount: A:0.18, C:0.04, G:0.32, T:0.46
Consensus pattern (23 bp):
ATTATTCTGGTGTGTTTGGGAGG
Found at i:5749447 original size:21 final size:21
Alignment explanation
Indices: 5749399--5749449 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
5749389 ATGTGTCATA
*
5749399 TTTCAGGCACCTTGTGTGTCG
1 TTTCAGGCACCTCGTGTGTCG
** *
5749420 TAACAGGCACCTCGTTTGTCG
1 TTTCAGGCACCTCGTGTGTCG
5749441 TTTCAGGCA
1 TTTCAGGCA
5749450 TTTATGTGTC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.16, C:0.25, G:0.25, T:0.33
Consensus pattern (21 bp):
TTTCAGGCACCTCGTGTGTCG
Found at i:5752590 original size:16 final size:17
Alignment explanation
Indices: 5752569--5752603 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
5752559 TAATATCTAG
5752569 GAAAATTA-TTAATTGA
1 GAAAATTAGTTAATTGA
5752585 GAAAATTAGTTTAATTGA
1 GAAAATTAG-TTAATTGA
5752603 G
1 G
5752604 GGGTTAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
18 9 0.53
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (17 bp):
GAAAATTAGTTAATTGA
Found at i:5757086 original size:7 final size:8
Alignment explanation
Indices: 5757061--5757088 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
5757051 GTATTCCCTT
5757061 AAATTGAA
1 AAATTGAA
5757069 AAATTGAA
1 AAATTGAA
5757077 AAATTGAA
1 AAATTGAA
5757085 AAAT
1 AAAT
5757089 AAAAGGGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.25
Consensus pattern (8 bp):
AAATTGAA
Found at i:5761208 original size:17 final size:17
Alignment explanation
Indices: 5761188--5761244 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
5761178 CTTTAAAAGA
5761188 ATAATGAGTTTAATAAT
1 ATAATGAGTTTAATAAT
* *
5761205 ATAA-GATATTTAAGTTAT
1 ATAATGA-GTTTAA-TAAT
*
5761223 CTTAATGAGTTTAATAAT
1 -ATAATGAGTTTAATAAT
5761241 ATAA
1 ATAA
5761245 GATATTTAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
16 2 0.07
17 12 0.40
18 6 0.20
19 8 0.27
20 2 0.07
ACGTcount: A:0.46, C:0.02, G:0.11, T:0.42
Consensus pattern (17 bp):
ATAATGAGTTTAATAAT
Found at i:5761229 original size:36 final size:36
Alignment explanation
Indices: 5761189--5761262 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
5761179 TTTAAAAGAA
5761189 TAATGAGTTTAATAATATAAGATATTTAAGTTATCT
1 TAATGAGTTTAATAATATAAGATATTTAAGTTATCT
5761225 TAATGAGTTTAATAATATAAGATATTTAAGTTATCT
1 TAATGAGTTTAATAATATAAGATATTTAAGTTATCT
5761261 TA
1 TA
5761263 GGAATTTGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.45
Consensus pattern (36 bp):
TAATGAGTTTAATAATATAAGATATTTAAGTTATCT
Found at i:5765906 original size:29 final size:30
Alignment explanation
Indices: 5765872--5765941 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 30
5765862 GAAATTCTTA
5765872 AAATATTTTAAAGAAT-TTTTTATATGTGT
1 AAATATTTTAAAGAATATTTTTATATGTGT
**
5765901 AAATATTTTTTGAGAATATTTTTATATGTGT
1 AAATA-TTTTAAAGAATATTTTTATATGTGT
*
5765932 AAATCTTTTA
1 AAATATTTTA
5765942 TTGGTTGCCA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 5 0.14
30 13 0.37
31 17 0.49
ACGTcount: A:0.36, C:0.01, G:0.10, T:0.53
Consensus pattern (30 bp):
AAATATTTTAAAGAATATTTTTATATGTGT
Found at i:5765926 original size:31 final size:30
Alignment explanation
Indices: 5765883--5765940 Score: 98
Period size: 31 Copynumber: 1.9 Consensus size: 30
5765873 AATATTTTAA
5765883 AGAATTTTTTATATGTGTAAATATTTTTTG
1 AGAATTTTTTATATGTGTAAATATTTTTTG
*
5765913 AGAATATTTTTATATGTGTAAATCTTTT
1 AGAAT-TTTTTATATGTGTAAATATTTT
5765941 ATTGGTTGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.55
Consensus pattern (30 bp):
AGAATTTTTTATATGTGTAAATATTTTTTG
Found at i:5766247 original size:73 final size:72
Alignment explanation
Indices: 5766146--5766304 Score: 275
Period size: 73 Copynumber: 2.2 Consensus size: 72
5766136 AGTCATTTAA
* *
5766146 AATT-TTTAAAATTTTAAATTAGTAATGATAAAATTATATTTTGACCTCTTAAAAATATAACATT
1 AATTCTTTAAAAATTTAAATTAGTAATGATAAAATTATATTTTGACATCTTAAAAATATAACATT
5766210 TTAATTT
66 TTAATTT
*
5766217 AATTCTTTAAAAATTTAAATATAGTGATGATAAAATTATATTTTGACATCTTAAAAATATAACAT
1 AATTCTTTAAAAATTTAAAT-TAGTAATGATAAAATTATATTTTGACATCTTAAAAATATAACAT
5766282 TTTAATTT
65 TTTAATTT
5766290 AATTCTTTAAAAATT
1 AATTCTTTAAAAATT
5766305 ACATTTAAAT
Statistics
Matches: 83, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
71 4 0.05
72 14 0.17
73 65 0.78
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (72 bp):
AATTCTTTAAAAATTTAAATTAGTAATGATAAAATTATATTTTGACATCTTAAAAATATAACATT
TTAATTT
Found at i:5773544 original size:33 final size:33
Alignment explanation
Indices: 5773497--5773561 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
5773487 AATATTAATA
*
5773497 ATTTATAAAATTTAATTAGAATATA-TAAATTAT
1 ATTTATAAAATTTAAATAGAAT-TAGTAAATTAT
*
5773530 ATTT-TAAATATTTAAATATAATTAGTAAATTA
1 ATTTATAAA-ATTTAAATAGAATTAGTAAATTA
5773562 AAGTACTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 6 0.21
33 22 0.79
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (33 bp):
ATTTATAAAATTTAAATAGAATTAGTAAATTAT
Found at i:5773749 original size:22 final size:22
Alignment explanation
Indices: 5773723--5773771 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
5773713 AAATTAGACT
5773723 AAAATTAACATTTATTGTTTAA
1 AAAATTAACATTTATTGTTTAA
* *
5773745 AAAA-TAGCATTTATTGTTTAG
1 AAAATTAACATTTATTGTTTAA
5773766 AAAATT
1 AAAATT
5773772 CAGTAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (22 bp):
AAAATTAACATTTATTGTTTAA
Found at i:5776384 original size:40 final size:40
Alignment explanation
Indices: 5776340--5776439 Score: 137
Period size: 40 Copynumber: 2.5 Consensus size: 40
5776330 ACATTGATTG
* *
5776340 TTAGCGGCGTTTTTCAAAAAGCACCATTATAGATCGAGCA
1 TTAGCGGCATTTTTCAAAAAGCACCACTATAGATCGAGCA
* *
5776380 TTAGCGGCATTTTTCAAAAAGCGCCGCTATAGATCGAGCA
1 TTAGCGGCATTTTTCAAAAAGCACCACTATAGATCGAGCA
* **
5776420 TTAACGGCACCTTTCAAAAA
1 TTAGCGGCATTTTTCAAAAA
5776440 ACGCCGCAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (40 bp):
TTAGCGGCATTTTTCAAAAAGCACCACTATAGATCGAGCA
Found at i:5776565 original size:40 final size:40
Alignment explanation
Indices: 5776511--5776635 Score: 153
Period size: 40 Copynumber: 3.1 Consensus size: 40
5776501 GTGCTTTTTG
* * *
5776511 AAAAACGCCGCTATAGATTAAGCATTAACGGCGCTTTTCA
1 AAAAACGCCGCTATAGATTGAGCATTAGCGACGCTTTTCA
* * * *
5776551 AAAAATGCCACTATAGATCGAGCATTAGCAACG-TATTTCA
1 AAAAACGCCGCTATAGATTGAGCATTAGCGACGCT-TTTCA
* *
5776591 AGAAACGTCGCTATAGATTGAGCATTAGCGACGCTTTTCA
1 AAAAACGCCGCTATAGATTGAGCATTAGCGACGCTTTTCA
5776631 AAAAA
1 AAAAA
5776636 TGCCTCAAAA
Statistics
Matches: 69, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
39 1 0.01
40 67 0.97
41 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.25
Consensus pattern (40 bp):
AAAAACGCCGCTATAGATTGAGCATTAGCGACGCTTTTCA
Found at i:5776731 original size:194 final size:195
Alignment explanation
Indices: 5776344--5776731 Score: 485
Period size: 195 Copynumber: 2.0 Consensus size: 195
5776334 TGATTGTTAG
* * * ** *
5776344 CGGCGTTTTTCAAAAAGCACCATTATAGATCGAGCATTAGCGGCATTTTTCAAAAAGCGCCGCTA
1 CGGCGCTTTTCAAAAAACACCACTATAGATCGAGCATTAGCAACATATTTCAAAAAGCGCCGCTA
*
5776409 TAGATCGAGCATTAACGGCACCTTTCAAAAAACGCCGCAAAAGAATTAAGCACAACGATGTCGTT
66 TAGATCGAGCATTAACGACACCTTTCAAAAAACGCCGCAAAAGAATTAAGCACAACGATGTCGTT
* * * *
5776474 TTATGTTGAGCTTTAGTGGAATTAGCGGTGCTTTTTGAAAAACGCCGCTATAGATTAAGCATTAA
131 TTATGTGGAGCTTTAGTGGAATTAACGGCGCTTTTTGAAAAACGCCGCTATAGATCAAGCATTAA
** * *
5776539 CGGCGCTTTTCAAAAAATGCCACTATAGATCGAGCATTAGCAACGTATTTCAAGAAA-CGTCGCT
1 CGGCGCTTTTCAAAAAACACCACTATAGATCGAGCATTAGCAACATATTTCAA-AAAGCGCCGCT
* * * * * * * * *
5776603 ATAGATTGAGCATTAGCGACGCTTTTCAAAAAATGCCTCAAAA-AGTTAAGCATAACGCCT-TCG
65 ATAGATCGAGCATTAACGACACCTTTCAAAAAACGCCGCAAAAGAATTAAGCACAACG-ATGTCG
* * * *
5776666 TTTTATGTGGAGCTTTAGTGGCATTAACGGCGCTTTTTGAAAAATGCCGCTATAGGTCGAGCATT
129 TTTTATGTGGAGCTTTAGTGGAATTAACGGCGCTTTTTGAAAAACGCCGCTATAGATCAAGCATT
5776731 A
194 A
5776732 GCAGCGTTTT
Statistics
Matches: 163, Mismatches: 28, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
194 73 0.45
195 87 0.53
196 3 0.02
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.28
Consensus pattern (195 bp):
CGGCGCTTTTCAAAAAACACCACTATAGATCGAGCATTAGCAACATATTTCAAAAAGCGCCGCTA
TAGATCGAGCATTAACGACACCTTTCAAAAAACGCCGCAAAAGAATTAAGCACAACGATGTCGTT
TTATGTGGAGCTTTAGTGGAATTAACGGCGCTTTTTGAAAAACGCCGCTATAGATCAAGCATTAA
Found at i:5777086 original size:18 final size:18
Alignment explanation
Indices: 5777063--5777100 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
5777053 ATTTCCTCAT
5777063 CAAGACAGAACAAGGTCA
1 CAAGACAGAACAAGGTCA
5777081 CAAGACAGAACAAGGTCA
1 CAAGACAGAACAAGGTCA
5777099 CA
1 CA
5777101 GAAGTTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.24, G:0.21, T:0.05
Consensus pattern (18 bp):
CAAGACAGAACAAGGTCA
Found at i:5777816 original size:21 final size:21
Alignment explanation
Indices: 5777777--5777835 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
5777767 TTGAAATTTT
* * *
5777777 GGGTTTATAATTTAAGGGTAA
1 GGGTTTAGAGTTTAGGGGTAA
* *
5777798 GGTTTTTAG-GTTTAGGGGTTA
1 GG-GTTTAGAGTTTAGGGGTAA
5777819 GGGTTTAGAGTTTAGGG
1 GGGTTTAGAGTTTAGGG
5777836 TTTATGGCTT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
20 5 0.17
21 21 0.70
22 4 0.13
ACGTcount: A:0.22, C:0.00, G:0.37, T:0.41
Consensus pattern (21 bp):
GGGTTTAGAGTTTAGGGGTAA
Found at i:5777821 original size:7 final size:7
Alignment explanation
Indices: 5777802--5777867 Score: 64
Period size: 7 Copynumber: 9.7 Consensus size: 7
5777792 GGGTAAGGTT
5777802 TTTA-GG
1 TTTAGGG
5777808 TTTAGGG
1 TTTAGGG
*
5777815 GTTAGGG
1 TTTAGGG
*
5777822 TTTAGAG
1 TTTAGGG
5777829 TTTAGGG
1 TTTAGGG
*
5777836 TTTATGG
1 TTTAGGG
*
5777843 CTT-GGG
1 TTTAGGG
5777849 TTTAGGG
1 TTTAGGG
* *
5777856 GTTAAGG
1 TTTAGGG
5777863 TTTAG
1 TTTAG
5777868 ATTTTCATAT
Statistics
Matches: 46, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
6 8 0.17
7 38 0.83
ACGTcount: A:0.17, C:0.02, G:0.39, T:0.42
Consensus pattern (7 bp):
TTTAGGG
Found at i:5777825 original size:14 final size:14
Alignment explanation
Indices: 5777806--5777867 Score: 72
Period size: 14 Copynumber: 4.5 Consensus size: 14
5777796 AAGGTTTTTA
5777806 GGTTTAGGGGTTAG
1 GGTTTAGGGGTTAG
* *
5777820 GGTTTAGAGTTTAG
1 GGTTTAGGGGTTAG
* *
5777834 GGTTTATGGCTT-G
1 GGTTTAGGGGTTAG
*
5777847 GGTTTAGGGGTTAA
1 GGTTTAGGGGTTAG
5777861 GGTTTAG
1 GGTTTAG
5777868 ATTTTCATAT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
13 11 0.28
14 28 0.72
ACGTcount: A:0.16, C:0.02, G:0.42, T:0.40
Consensus pattern (14 bp):
GGTTTAGGGGTTAG
Found at i:5777832 original size:27 final size:27
Alignment explanation
Indices: 5777802--5777867 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
5777792 GGGTAAGGTT
*
5777802 TTTAGGTTTAGGGGTTAGGGTTTA-GAG
1 TTTAGGTTTAGGGCTT-GGGTTTAGGAG
* *
5777829 TTTAGGGTTTATGGCTTGGGTTTAGGGG
1 TTTA-GGTTTAGGGCTTGGGTTTAGGAG
*
5777857 TTAAGGTTTAG
1 TTTAGGTTTAG
5777868 ATTTTCATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
27 17 0.53
28 15 0.47
ACGTcount: A:0.17, C:0.02, G:0.39, T:0.42
Consensus pattern (27 bp):
TTTAGGTTTAGGGCTTGGGTTTAGGAG
Found at i:5780204 original size:13 final size:14
Alignment explanation
Indices: 5780188--5780216 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5780178 TTTTAAATAT
5780188 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
5780201 TTATAATGGTTTAA
1 TTATAATGGTTTAA
5780215 TT
1 TT
5780217 CATCGTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:5780609 original size:21 final size:22
Alignment explanation
Indices: 5780580--5780622 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
5780570 AGCAAATTGC
*
5780580 TCAACTTAAAGTGGAGGCAGCA
1 TCAACTTAAAGAGGAGGCAGCA
5780602 TCAA-TTAAAGAGGAGGCAGCA
1 TCAACTTAAAGAGGAGGCAGCA
5780623 GCAAGGGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.40, C:0.16, G:0.28, T:0.16
Consensus pattern (22 bp):
TCAACTTAAAGAGGAGGCAGCA
Found at i:5780900 original size:47 final size:47
Alignment explanation
Indices: 5780828--5780918 Score: 155
Period size: 47 Copynumber: 1.9 Consensus size: 47
5780818 TGAATTTTTA
*
5780828 AAGTATCATTTAGATTTGCTATTATTGGTTGGATTTGATATTGCTTG
1 AAGTATCATTTAGATTTGCTATTATTGGTTGAATTTGATATTGCTTG
* *
5780875 AAGTATCATTTAGATTTGCTGTTATTGGTTGAATTTGATGTTGC
1 AAGTATCATTTAGATTTGCTATTATTGGTTGAATTTGATATTGC
5780919 AGGAAGGATT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.23, C:0.07, G:0.22, T:0.48
Consensus pattern (47 bp):
AAGTATCATTTAGATTTGCTATTATTGGTTGAATTTGATATTGCTTG
Found at i:5782898 original size:51 final size:51
Alignment explanation
Indices: 5782812--5782981 Score: 214
Period size: 51 Copynumber: 3.2 Consensus size: 51
5782802 TGAGTACTTC
* * *
5782812 TGATCAGTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAG
1 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
5782863 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAG
1 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTG---A-T--C-AG
* * *
5782921 TGATAAGTGATAAGTGGTAAGTGGTAGCTTTAGCTACACTTATCTGATTAG
1 TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
*
5782972 TGACAAGTGA
1 TGATAAGTGA
5782982 TAAATGTGAT
Statistics
Matches: 105, Mismatches: 7, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
51 54 0.51
54 2 0.02
55 2 0.02
57 1 0.01
58 46 0.44
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (51 bp):
TGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAG
Found at i:5782926 original size:58 final size:58
Alignment explanation
Indices: 5782861--5782984 Score: 221
Period size: 58 Copynumber: 2.1 Consensus size: 58
5782851 TTATCTGATC
5782861 AGTGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
* * *
5782919 AGTGATAAGTGATAAGTGGTAAGTGGTAGCTTTAGCTACACTTATCTGATTAGTGACA
1 AGTGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
5782977 AGTGATAA
1 AGTGATAA
5782985 ATGTGATCAG
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 63 1.00
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (58 bp):
AGTGATAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
Found at i:5785032 original size:30 final size:29
Alignment explanation
Indices: 5784998--5785069 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
5784988 ATAATTGGAC
* *
5784998 TTAAATTTTAAAATCTGAAAAAT-AGAAAGA
1 TTAAATTTTAAAA-AT-AAAAATAAAAAAGA
5785028 TTAAATTCTTAAAAATAAAAATAAAAAAGA
1 TTAAATT-TTAAAAATAAAAATAAAAAAGA
*
5785058 CTAAATTTTAAA
1 TTAAATTTTAAA
5785070 TTTATAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 11 0.30
30 20 0.54
31 6 0.16
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.31
Consensus pattern (29 bp):
TTAAATTTTAAAAATAAAAATAAAAAAGA
Found at i:5800692 original size:19 final size:18
Alignment explanation
Indices: 5800670--5800717 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
5800660 AAAAATTCTG
5800670 AAAAAAATAAAAAATAGGA
1 AAAAAAATAAAAAA-AGGA
* *
5800689 AAAAAATTATAAAAAAGGC
1 AAAAAAATA-AAAAAAGGA
*
5800708 AAATAAATAA
1 AAAAAAATAA
5800718 TAATGAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 1 0.04
19 18 0.75
20 5 0.21
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (18 bp):
AAAAAAATAAAAAAAGGA
Found at i:5800715 original size:20 final size:20
Alignment explanation
Indices: 5800669--5800720 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
5800659 AAAAAATTCT
5800669 GAAAAAAAT-A-AAAAATAG
1 GAAAAAAATAATAAAAATAG
*
5800687 GAAAAAAATTATAAAAA-AG
1 GAAAAAAATAATAAAAATAG
*
5800706 GCAAATAAATAATAA
1 G-AAAAAAATAATAA
5800721 TGAAATAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 9 0.31
19 4 0.14
20 16 0.55
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.15
Consensus pattern (20 bp):
GAAAAAAATAATAAAAATAG
Found at i:5803086 original size:11 final size:11
Alignment explanation
Indices: 5803060--5803092 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
5803050 TTAATTTAAT
5803060 ATATATTT-TA
1 ATATATTTATA
5803070 AT-TATTTATA
1 ATATATTTATA
5803080 ATATATTTATA
1 ATATATTTATA
5803091 AT
1 AT
5803093 TTATAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.24
10 6 0.29
11 10 0.48
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
ATATATTTATA
Found at i:5803094 original size:18 final size:19
Alignment explanation
Indices: 5803051--5803103 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
5803041 AAAACAGACT
5803051 TAATTTA-ATATATATTTTAA
1 TAATTTATA-ATATA-TTTAA
*
5803071 TTATTTATAATATATTT-A
1 TAATTTATAATATATTTAA
5803089 TAATTTATAATATAT
1 TAATTTATAATATAT
5803104 AAAATAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 15 0.50
19 3 0.10
20 11 0.37
21 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TAATTTATAATATATTTAA
Found at i:5803104 original size:20 final size:19
Alignment explanation
Indices: 5803055--5803104 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
5803045 CAGACTTAAT
5803055 TTAATATATATTTTAATTA
1 TTAATATATATTTTAATTA
*
5803074 TTTATAATATATTTATAATT-
1 TTAAT-ATATATTT-TAATTA
5803094 TATAATATATA
1 T-TAATATATA
5803105 AAATAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 4 0.15
20 14 0.54
21 8 0.31
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTAATATATATTTTAATTA
Found at i:5815969 original size:68 final size:68
Alignment explanation
Indices: 5815870--5816000 Score: 226
Period size: 68 Copynumber: 1.9 Consensus size: 68
5815860 GAAGTCCGTC
*
5815870 AGGACAATAAACATGAGATTATACTGTGTAAGACCATAACTAGGCTATGACAATAAATGAAGTTC
1 AGGACAATAAACATGAGATTATACTGTGTAAGACCATAACTAGGCTATGACAACAAATGAAGTTC
5815935 GGT
66 GGT
* * *
5815938 AGGACAATAAACATGAGATTATATTGTGTAAGACCATAGCTAGGCTATGATAACAAATGAAGT
1 AGGACAATAAACATGAGATTATACTGTGTAAGACCATAACTAGGCTATGACAACAAATGAAGT
5816001 CCACCAATAC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 59 1.00
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (68 bp):
AGGACAATAAACATGAGATTATACTGTGTAAGACCATAACTAGGCTATGACAACAAATGAAGTTC
GGT
Found at i:5816013 original size:68 final size:68
Alignment explanation
Indices: 5815872--5816037 Score: 208
Period size: 68 Copynumber: 2.4 Consensus size: 68
5815862 AGTCCGTCAG
* * **
5815872 GACAATAAACATGAGATTATACTGTGTAAGACCATAACTAGGCTATGACAATAAATGAAGTTCGG
1 GACAATAAACATGAGATTATACTGTGTAAGACCATAACTAGGCTATGACAACAAATGAAGTCCAC
* *
5815937 TAG
66 CAA
* * *
5815940 GACAATAAACATGAGATTATATTGTGTAAGACCATAGCTAGGCTATGATAACAAATGAAGTCCAC
1 GACAATAAACATGAGATTATACTGTGTAAGACCATAACTAGGCTATGACAACAAATGAAGTCCAC
5816005 CAA
66 CAA
* * *
5816008 TACAATAAATATGACATTATAC-GATGTAAG
1 GACAATAAACATGAGATTATACTG-TGTAAG
5816038 TGTTGGAAAA
Statistics
Matches: 84, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
67 1 0.01
68 83 0.99
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (68 bp):
GACAATAAACATGAGATTATACTGTGTAAGACCATAACTAGGCTATGACAACAAATGAAGTCCAC
CAA
Found at i:5822409 original size:21 final size:20
Alignment explanation
Indices: 5822356--5822414 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 20
5822346 TAATATATAT
*
5822356 TATTAGTAATATATGATATTA
1 TATTA-TAATATATTATATTA
*
5822377 -ATT-TAATTTATTATAATTA
1 TATTATAATATATTAT-ATTA
5822396 TATTATAATATATTTATAT
1 TATTATAATATA-TTATAT
5822415 GATAAATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
18 9 0.29
19 4 0.13
20 6 0.19
21 8 0.26
22 4 0.13
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.54
Consensus pattern (20 bp):
TATTATAATATATTATATTA
Found at i:5826175 original size:20 final size:20
Alignment explanation
Indices: 5826146--5826186 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
5826136 TCATTTAGAA
5826146 TTTTTATT-AATTTGACCAT
1 TTTTTATTAAATTTGACCAT
*
5826165 TTTTTAGTTAAATTTGATCAT
1 TTTTTA-TTAAATTTGACCAT
5826186 T
1 T
5826187 AATATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 2 0.11
21 11 0.58
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.59
Consensus pattern (20 bp):
TTTTTATTAAATTTGACCAT
Found at i:5828967 original size:25 final size:25
Alignment explanation
Indices: 5828929--5828985 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
5828919 AGCTCTCTCT
*
5828929 TGAGCCATAGAACGGGAAGCTCATG
1 TGAGCCATAGAACGGGAAGCTCATA
*
5828954 TGAGCCAT-GTAACGGGAATCTCATA
1 TGAGCCATAG-AACGGGAAGCTCATA
5828979 TGAGCCA
1 TGAGCCA
5828986 ATATCCGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 1 0.03
25 28 0.97
ACGTcount: A:0.32, C:0.21, G:0.28, T:0.19
Consensus pattern (25 bp):
TGAGCCATAGAACGGGAAGCTCATA
Found at i:5833897 original size:24 final size:24
Alignment explanation
Indices: 5833841--5833897 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
5833831 AAAGAATTAA
*
5833841 ATTATATCAAATTAAAATATTGAG
1 ATTATATCTAATTAAAATATTGAG
5833865 ATTATATCTAATTAAAATATTGAG
1 ATTATATCTAATTAAAATATTGAG
5833889 ATTATATCT
1 ATTATATCT
5833898 TAAATTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (24 bp):
ATTATATCTAATTAAAATATTGAG
Found at i:5836998 original size:11 final size:9
Alignment explanation
Indices: 5836968--5836992 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5836958 TAAATTTTTA
5836968 TTTTTAATT
1 TTTTTAATT
5836977 TTTTTAATT
1 TTTTTAATT
5836986 TTTTTAA
1 TTTTTAA
5836993 AATTTTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTTAATT
Found at i:5837291 original size:24 final size:25
Alignment explanation
Indices: 5837245--5837291 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
5837235 ATTAAACACC
5837245 TATTTAGTATGAATTTAAATTATTG
1 TATTTAGTATGAATTTAAATTATTG
*
5837270 TATTT-GT-TGAATATTATATTAT
1 TATTTAGTATGAAT-TTAAATTAT
5837292 ATAAAAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
24 10 0.50
25 5 0.25
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (25 bp):
TATTTAGTATGAATTTAAATTATTG
Found at i:5838099 original size:14 final size:14
Alignment explanation
Indices: 5838062--5838095 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
5838052 GTTTGCCAGT
5838062 AAAATATTTTCTGG
1 AAAATATTTTCTGG
5838076 AAAATGATTTT-TGG
1 AAAAT-ATTTTCTGG
5838090 AAAATA
1 AAAATA
5838096 ATTTACTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.05
14 13 0.68
15 5 0.26
ACGTcount: A:0.44, C:0.03, G:0.15, T:0.38
Consensus pattern (14 bp):
AAAATATTTTCTGG
Found at i:5838237 original size:22 final size:22
Alignment explanation
Indices: 5838210--5838251 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
5838200 CTGTTTTTAC
*
5838210 ATATATTAATAAATTTATATAT
1 ATATATTAATAAAATTATATAT
5838232 ATATATTAATAAAATTATAT
1 ATATATTAATAAAATTATAT
5838252 TTTAAATTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATATATTAATAAAATTATATAT
Found at i:5842368 original size:77 final size:78
Alignment explanation
Indices: 5842249--5842415 Score: 196
Period size: 77 Copynumber: 2.2 Consensus size: 78
5842239 TGAAATATGT
* ** * * * *
5842249 GATAAGTTGGTTTTATGTTGTGTATGCACATATAAATGTAAGGTTAAGAAAGGAACATCGA-CAT
1 GATAAGTTGCTTTTATGCAGTGGATGCACATATAAATATAAGGTGAAGAAAGGAAAATC-ACCAT
*
5842313 TACTG-AAATGTAC
65 TACTGAAAATATAC
*
5842326 GATAAGTTGCTTTTATGCAGTGGATGCATC-TCTAAATATAAGGTGAAGAAAGGAAAATCACCAT
1 GATAAGTTGCTTTTATGCAGTGGATGCA-CATATAAATATAAGGTGAAGAAAGGAAAATCACCAT
* *
5842390 TATTGAAAATATAT
65 TACTGAAAATATAC
5842404 GATAAGTTGCTT
1 GATAAGTTGCTT
5842416 CTATATAGTA
Statistics
Matches: 76, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
76 1 0.01
77 56 0.74
78 19 0.25
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.32
Consensus pattern (78 bp):
GATAAGTTGCTTTTATGCAGTGGATGCACATATAAATATAAGGTGAAGAAAGGAAAATCACCATT
ACTGAAAATATAC
Found at i:5848730 original size:22 final size:23
Alignment explanation
Indices: 5848703--5848747 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5848693 GGGTATCTAC
*
5848703 AAATCAAATC-TCTCAGATTACA
1 AAATCAAATCTTCTAAGATTACA
*
5848725 AAATCATATCTTCTAAGATTACA
1 AAATCAAATCTTCTAAGATTACA
5848748 TATCATATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.44, C:0.20, G:0.04, T:0.31
Consensus pattern (23 bp):
AAATCAAATCTTCTAAGATTACA
Found at i:5848752 original size:22 final size:22
Alignment explanation
Indices: 5848700--5848757 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
5848690 AAAGGGTATC
* *
5848700 TACAAATCAAATC-TCTCAGAT
1 TACAAATCATATCTTCTAAGAT
5848721 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
5848744 TACATATCATATCT
1 TACAAATCATATCT
5848758 AAGATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 19 0.59
23 10 0.31
ACGTcount: A:0.41, C:0.21, G:0.03, T:0.34
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:5852644 original size:53 final size:53
Alignment explanation
Indices: 5852464--5852718 Score: 234
Period size: 55 Copynumber: 4.8 Consensus size: 53
5852454 ATTAGGGTTT
* *
5852464 AAGGATACCGTGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGC-ATTGGTAA-G-TTCATAAGGC
* * ** * *
5852519 AAGGAAATCATGTAAGACCATATCAAGACACGGCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT-C-ATAAGGC
* * *
5852574 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCATAAGGC
* * * * *
5852627 AAGGCTACCATGTAAGACCATGTCAAGACATGGCAATGGTAAGTT--T--CGA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCATAAGGC
* * * *
5852676 AAGGATACCACGTAAGACCATGACAAGTCATGGCAATGGTAAG
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAG
5852719 GTACCCGTGT
Statistics
Matches: 167, Mismatches: 28, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
49 40 0.24
51 1 0.01
52 6 0.04
53 44 0.26
54 8 0.05
55 64 0.38
56 4 0.02
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.21
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTCATAAGGC
Found at i:5852670 original size:108 final size:110
Alignment explanation
Indices: 5852474--5852671 Score: 294
Period size: 108 Copynumber: 1.8 Consensus size: 110
5852464 AAGGATACCG
*
5852474 TGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGACCA
1 TGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGACCA
*
5852539 TATCAAGACACGGCATTGATAAGTTACTATAAGGCAAAGGTCCCA
66 TATCAAGACACGGCAATGATAAGTTACTATAAGGCAAAGGTCCCA
* **
5852584 TGTAAGACCATGCCAAGGCATGGC-ATTGGTGA-G-TTCATAAGGCAAGGCTACCATGTAAGACC
1 TGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAGACC
* * *
5852646 ATGTCAAGACATGGCAATGGTAAGTT
65 ATATCAAGACACGGCAATGATAAGTT
5852672 TCGAAAGGAT
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
107 3 0.04
108 45 0.57
109 7 0.09
110 24 0.30
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.22
Consensus pattern (110 bp):
TGTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGACCA
TATCAAGACACGGCAATGATAAGTTACTATAAGGCAAAGGTCCCA
Found at i:5856659 original size:22 final size:23
Alignment explanation
Indices: 5856632--5856676 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
5856622 GGGTATCTAC
5856632 AAATCAAATC-TCTAAGATTACA
1 AAATCAAATCTTCTAAGATTACA
*
5856654 AAATCATATCTTCTAAGATTACA
1 AAATCAAATCTTCTAAGATTACA
5856677 TATCATATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.47, C:0.18, G:0.04, T:0.31
Consensus pattern (23 bp):
AAATCAAATCTTCTAAGATTACA
Found at i:5856680 original size:17 final size:17
Alignment explanation
Indices: 5856658--5856708 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 17
5856648 ATTACAAAAT
5856658 CATATCTTCTAAGATTA
1 CATATCTTCTAAGATTA
*
5856675 CATATCATATCTAAGATTG
1 CATATC-T-TCTAAGATTA
*
5856694 CATATCTTCGAAGAT
1 CATATCTTCTAAGAT
5856709 CATGTTTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 13 0.43
18 2 0.07
19 15 0.50
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (17 bp):
CATATCTTCTAAGATTA
Found at i:5856681 original size:22 final size:22
Alignment explanation
Indices: 5856629--5856686 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
5856619 AAAGGGTATC
*
5856629 TACAAATCAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
5856650 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
5856673 TACATATCATATCT
1 TACAAATCATATCT
5856687 AAGATTGCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 3 0.09
22 19 0.58
23 11 0.33
ACGTcount: A:0.43, C:0.19, G:0.03, T:0.34
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:5856689 original size:19 final size:20
Alignment explanation
Indices: 5856642--5856699 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 20
5856632 AAATCAAATC
*
5856642 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTAC-ATATCATA--T
5856665 TCTAAGATTACATATCATA-
1 TCTAAGATTACATATCATAT
*
5856684 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
5856700 TTCGAAGATC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.45
22 7 0.21
23 11 0.33
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.36
Consensus pattern (20 bp):
TCTAAGATTACATATCATAT
Done.