Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold332
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: 2744988
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 17
Found at i:1184598 original size:13 final size:13
Alignment explanation
Indices: 1184580--1184605 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1184570 ACATTTTGGG
1184580 ATGTATCGATACA
1 ATGTATCGATACA
1184593 ATGTATCGATACA
1 ATGTATCGATACA
1184606 TATTGTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1184600 original size:33 final size:32
Alignment explanation
Indices: 1184558--1184625 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
1184548 CGTTACAAGC
*
1184558 CAATGTATCGATACATTTTGGGATGTATCGATA
1 CAATGTATCGATACATATTGGG-TGTATCGATA
*
1184591 CAATGTATCGATACATATTGTGTGTATCGATA
1 CAATGTATCGATACATATTGGGTGTATCGATA
1184623 CAA
1 CAA
1184626 ATTTGGCTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATATTGGGTGTATCGATA
Found at i:1185318 original size:22 final size:19
Alignment explanation
Indices: 1185277--1185313 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1185267 TTTTCTTTTC
1185277 TCTCCCCCTTAAAAAAATT
1 TCTCCCCCTTAAAAAAATT
*
1185296 TCTCCCCCTTAATAAAAT
1 TCTCCCCCTTAAAAAAAT
1185314 AATTTGACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (19 bp):
TCTCCCCCTTAAAAAAATT
Found at i:1187033 original size:20 final size:21
Alignment explanation
Indices: 1187004--1187044 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1186994 TGTTTTTGTT
1187004 GATGATTTTG-A-TGAAAAAC
1 GATGATTTTGAAGTGAAAAAC
1187023 GATGTATTTTGAAGTGAAAAAC
1 GATG-ATTTTGAAGTGAAAAAC
1187045 AAGAAATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 1 0.05
22 8 0.42
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (21 bp):
GATGATTTTGAAGTGAAAAAC
Found at i:1187194 original size:13 final size:13
Alignment explanation
Indices: 1187176--1187200 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1187166 ATAAACCCCT
1187176 TGTATCGATACAC
1 TGTATCGATACAC
1187189 TGTATCGATACA
1 TGTATCGATACA
1187201 TCTGAGTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:1192144 original size:13 final size:13
Alignment explanation
Indices: 1192126--1192150 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1192116 CATAAAATGT
1192126 TGTATCGATACAA
1 TGTATCGATACAA
1192139 TGTATCGATACA
1 TGTATCGATACA
1192151 TGTTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1192231 original size:13 final size:13
Alignment explanation
Indices: 1192213--1192237 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1192203 ATCACTTAAA
1192213 TGTATCGATACAT
1 TGTATCGATACAT
1192226 TGTATCGATACA
1 TGTATCGATACA
1192238 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1192302 original size:52 final size:52
Alignment explanation
Indices: 1192246--1192426 Score: 335
Period size: 52 Copynumber: 3.5 Consensus size: 52
1192236 CACTGATCTT
*
1192246 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1192298 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
1192350 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1192402 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1192427 TCATATTTCG
Statistics
Matches: 126, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 126 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1196957 original size:33 final size:32
Alignment explanation
Indices: 1196911--1196978 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
1196901 CATTACAAGC
* *
1196911 CAATGTATTGATACATTTTGGGATGTACCGATA
1 CAATGTATCGATACATATTGGG-TGTACCGATA
* *
1196944 CAATGTATCGATACATATTGTGTGTATCGATA
1 CAATGTATCGATACATATTGGGTGTACCGATA
1196976 CAA
1 CAA
1196979 ATTTGGCTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 12 0.39
33 19 0.61
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATATTGGGTGTACCGATA
Found at i:1197068 original size:13 final size:13
Alignment explanation
Indices: 1197050--1197074 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1197040 ACATATGGTC
1197050 ATGTATCGATACA
1 ATGTATCGATACA
1197063 ATGTATCGATAC
1 ATGTATCGATAC
1197075 TGTGCAATCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1199593 original size:11 final size:12
Alignment explanation
Indices: 1199567--1199618 Score: 54
Period size: 13 Copynumber: 4.3 Consensus size: 12
1199557 TAGTTTTCTA
*
1199567 TTTTCTTCTCTAT
1 TTTTC-TCTCTTT
1199580 TTTTC-CTC-TT
1 TTTTCTCTCTTT
*
1199590 TTTTCTTTCTTTT
1 TTTTCTCTC-TTT
1199603 TTTTCTCTCTTT
1 TTTTCTCTCTTT
1199615 TTTT
1 TTTT
1199619 GCTGAGTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
10 6 0.18
11 5 0.15
12 7 0.21
13 15 0.45
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTCTCTCTTT
Found at i:1199599 original size:24 final size:23
Alignment explanation
Indices: 1199567--1199617 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
1199557 TAGTTTTCTA
1199567 TTTTCTTCTCTATTTTTC-CTCTT
1 TTTTCTTCT-TATTTTTCTCTCTT
*
1199590 TTTTCTTTCTTTTTTTTCTCTCTT
1 TTTTC-TTCTTATTTTTCTCTCTT
1199614 TTTT
1 TTTT
1199618 TGCTGAGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTTCTTCTTATTTTTCTCTCTT
Found at i:1199755 original size:21 final size:20
Alignment explanation
Indices: 1199729--1199778 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
1199719 AAAAATCTCT
1199729 ATTTTTCATTTTTTTTATGCC
1 ATTTTTCATTTTTTTTAT-CC
1199750 ATTTTT--TTATTTTTTATCC
1 ATTTTTCATT-TTTTTTATCC
1199769 -TTTTTCATTT
1 ATTTTTCATTT
1199779 AATTTCTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
18 5 0.19
19 5 0.19
20 10 0.38
21 6 0.23
ACGTcount: A:0.14, C:0.12, G:0.02, T:0.72
Consensus pattern (20 bp):
ATTTTTCATTTTTTTTATCC
Found at i:1200384 original size:164 final size:164
Alignment explanation
Indices: 1200122--1200511 Score: 421
Period size: 165 Copynumber: 2.4 Consensus size: 164
1200112 TGAAATAATT
* * * * * * **
1200122 TAAATTTTTCAAAATTGATTTAAT-TTAATTTAATAACAAT-CTTAAATAAATTTTAAAAATTTT
1 TAAATTTTT-AAAAATGATTTAATATAAATTAAATAATAATATTTAAA-GAATTTTAAAAATTAA
* * * * *
1200185 AAACTAAAAAAAATGCCCCCGAAACCATGTACGGAGTAGAAAAC-TCGATTTTTCAAAAACAAAA
64 AAACCAAAAAAAATGCCCCCAAAAACATGTACGGAGCAAAAAACTTCG-TTTTTCAAAAACAAAA
* * **
1200249 AAATTTCA-AAGAAAATTTAAAACTCATGAAAATAAA
128 AAATTTAAGAAAAAAATGAAAAACTCATGAAAATAAA
1200285 TAAATTTTTAAAAATGGATTTAATATAAATTAAATAATAATATTTAAAGAATTTTAAAAATTAAA
1 TAAATTTTTAAAAAT-GATTTAATATAAATTAAATAATAATATTTAAAGAATTTTAAAAATTAAA
* * * ** * *
1200350 AACCAAGAAAAAT-CTCCCTAAAAACATTTACGGAGCAAAAAACTTCGTTTTTTGAAAATAAAGA
65 AACCAAAAAAAATGC-CCCCAAAAACATGTACGGAGCAAAAAACTTCGTTTTTCAAAAACAAAAA
* *
1200414 ATTTTAAGAAAAAAATGAAAAACTCATGAAAATGAA
129 AATTTAAGAAAAAAATGAAAAACTCATGAAAATAAA
* * * *
1200450 TCAATTTTTGAAAAATGATTTAATATGAATTAAATAATAATATTTGATGAATTTTAAAAATT
1 TAAATTTTT-AAAAATGATTTAATATAAATTAAATAATAATATTTAAAGAATTTTAAAAATT
1200512 TTAGATCAAC
Statistics
Matches: 190, Mismatches: 30, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
162 5 0.03
163 18 0.09
164 78 0.41
165 83 0.44
166 6 0.03
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (164 bp):
TAAATTTTTAAAAATGATTTAATATAAATTAAATAATAATATTTAAAGAATTTTAAAAATTAAAA
ACCAAAAAAAATGCCCCCAAAAACATGTACGGAGCAAAAAACTTCGTTTTTCAAAAACAAAAAAA
TTTAAGAAAAAAATGAAAAACTCATGAAAATAAA
Found at i:1200593 original size:165 final size:165
Alignment explanation
Indices: 1200267--1200628 Score: 394
Period size: 165 Copynumber: 2.2 Consensus size: 165
1200257 AAGAAAATTT
1200267 AAAACTCATGAAAATAAATAAATTTTTAAAAATGGATTTAATATAAATTAAATAATAATATTTAA
1 AAAACTCATGAAAATAAATAAATTTTTAAAAATGGATTTAATATAAATTAAATAATAATATTTAA
* * * *
1200332 AGAATTTTAAAAATTAAAAACCAAGAAAAATCTCCCTAAAAACATTTACGGAGCAAAAAACTTCG
66 AGAATTTTAAAAATTAAAAACCAAGAAAAATCTCCCTAAAAAAATTTACGAAACAAAAAACTTCA
* ** *
1200397 TTTTTTGAAAATAAAGAATTTTAAGAAAAAAATGA
131 TATTTCAAAAATAAAGAATTTCAAGAAAAAAATGA
* * * *
1200432 AAAACTCATGAAAATGAATCAATTTTTGAAAAAT-GATTTAATATGAATTAAATAATAATATTTG
1 AAAACTCATGAAAATAAATAAATTTTT-AAAAATGGATTTAATATAAATTAAATAATAATATTTA
* ** * * * * *
1200496 ATGAATTTTAAAAATTTTAGATCAACG-AAAATC-CTCTCAAAAAAATTTACGAAATAGAAAACT
65 AAGAATTTTAAAAATTAAAAACCAA-GAAAAATCTCCCT-AAAAAAATTTACGAAACAAAAAACT
* *
1200559 TCATATTTCAAAAATAGGAAGAATTCCAA-AAAAAATTG-
128 TCATATTTCAAAAATA--AAGAATTTCAAGAAAAAAATGA
* * * *
1200597 ACAAGTCAT-AAAATAAAAAGAATTTTTCAAAA
1 AAAACTCATGAAAATAAATA-AATTTTTAAAAA
1200629 CTGATTTTAT
Statistics
Matches: 163, Mismatches: 28, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
164 14 0.09
165 125 0.77
166 15 0.09
167 9 0.06
ACGTcount: A:0.53, C:0.09, G:0.08, T:0.30
Consensus pattern (165 bp):
AAAACTCATGAAAATAAATAAATTTTTAAAAATGGATTTAATATAAATTAAATAATAATATTTAA
AGAATTTTAAAAATTAAAAACCAAGAAAAATCTCCCTAAAAAAATTTACGAAACAAAAAACTTCA
TATTTCAAAAATAAAGAATTTCAAGAAAAAAATGA
Found at i:1203430 original size:160 final size:159
Alignment explanation
Indices: 1203262--1203709 Score: 505
Period size: 159 Copynumber: 2.8 Consensus size: 159
1203252 TAAAACATCA
* * **
1203262 AATTTTTCATTTCTTATGATACTCCAACCCCATAATCTTTGAAGGGATACTCCAACCTCATTTTT
1 AATTTTTCATATC-TAGGATACTCCAACCCCAT-ATCTCCGAAGGGATACTCCAACCTCATTTTT
1203327 ACTTACAAAACACTGAATTTTTCATCTTTGGGATTACTCTAACCCCACCAT-TTTGGAGAGGATA
64 ACTTACAAAACACTGAATTTTTCATCTTTGGGA-TACTCTAACCCCACCATCTTTGGAGAGGATA
*
1203391 CTCCAACCACATTTTTAATTTCAAAA-TACTG
128 CTCCAACCACATTTTTAATTCCAAAATTACTG
* * * * *
1203422 AATTTTTCATATCTAGGGGTACTCTAACCTCACTATCTCCGAAGAGATACTCCAACCCCATTTTT
1 AATTTTTCATATCTA-GGATACTCCAACCCCA-TATCTCCGAAGGGATACTCCAACCTCATTTTT
* * * * * * *
1203487 ACTTTCAAAACATTGAATTTTTCATATCTGGGGATACTC-AGCCCCATCATCTCT-GAGAGGATA
64 ACTTACAAAACACTGAATTTTTCATCT-TTGGGATACTCTAACCCCACCATCTTTGGAGAGGATA
* * * *
1203550 CTTCAACCCCATTTTTACTTCCAAAATTATTG
128 CTCCAACCACATTTTTAATTCCAAAATTACTG
* * * *
1203582 AATTTTTCATCTCTAGGATTCTCCAACCCCACCATCTCCGAGGGGATACTCCAACCTCATTTTTA
1 AATTTTTCATATCTAGGATACTCCAACCCCA-TATCTCCGAAGGGATACTCCAACCTCATTTTTA
* * * *
1203647 CTTCCAAAGCACTGAA-TTTTCATCTTTGGGGATACT-TCAACCCTACCATCTTTGAAG-GGATA
65 CTTACAAAACACTGAATTTTTCATCTTT-GGGATACTCT-AACCCCACCATCTTTGGAGAGGATA
1203709 C
128 C
1203710 GGCAACTCCT
Statistics
Matches: 239, Mismatches: 40, Indels: 19
0.80 0.13 0.06
Matches are distributed among these distances:
157 1 0.00
158 16 0.07
159 114 0.48
160 102 0.43
161 6 0.03
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (159 bp):
AATTTTTCATATCTAGGATACTCCAACCCCATATCTCCGAAGGGATACTCCAACCTCATTTTTAC
TTACAAAACACTGAATTTTTCATCTTTGGGATACTCTAACCCCACCATCTTTGGAGAGGATACTC
CAACCACATTTTTAATTCCAAAATTACTG
Found at i:1203697 original size:159 final size:158
Alignment explanation
Indices: 1203229--1203732 Score: 539
Period size: 160 Copynumber: 3.2 Consensus size: 158
1203219 TCAAAAGGGG
* * * * ** * *
1203229 TACTCTAACCTCATTTTTACTTCTAAAACATCAAATTTTTCATTTCTTATGATACTCCAACCCCA
1 TACTCCAACCCCATTTTTACTTCCAAAATATTGAATTTTTCATATC-TAGGATACTCCAACCCCA
* **
1203294 TAATCTTTGAAGGGATACTCCAACCTCATTTTTACTTACAAAACACTGAATTTTTCATCTTT-GG
65 CAATCTCCGAAGGGATACTCCAACCTCATTTTTACTTACAAAACACTGAATTTTTCATCTTTGGG
1203358 GATTACTCTAACCCCACCAT-TTTGGAGAGGA
130 GA-TACTC-AACCCCACCATCTTT-GAGAGGA
* * * * * * *
1203389 TACTCCAACCACATTTTTAATTTCAAAATACTGAATTTTTCATATCTAGGGGTACTCTAACCTCA
1 TACTCCAACCCCATTTTTACTTCCAAAATATTGAATTTTTCATATCTA-GGATACTCCAACCCCA
* * * * * * *
1203454 CTATCTCCGAAGAGATACTCCAACCCCATTTTTACTTTCAAAACATTGAATTTTTCATATCTGGG
65 CAATCTCCGAAGGGATACTCCAACCTCATTTTTACTTACAAAACACTGAATTTTTCATCTTTGGG
* * *
1203519 GATACTCAGCCCCATCATCTCTGAGAGGA
130 GATACTCAACCCCACCATCTTTGAGAGGA
* * *
1203548 TACTTCAACCCCATTTTTACTTCCAAAATTATTGAATTTTTCATCTCTAGGATTCTCCAACCCCA
1 TACTCCAACCCCATTTTTACTTCCAAAA-TATTGAATTTTTCATATCTAGGATACTCCAACCCCA
* * * *
1203613 CCATCTCCGAGGGGATACTCCAACCTCATTTTTACTTCCAAAGCACTGAA-TTTTCATCTTTGGG
65 CAATCTCCGAAGGGATACTCCAACCTCATTTTTACTTACAAAACACTGAATTTTTCATCTTTGGG
*
1203677 GATACTTCAACCCTACCATCTTTGA-AGGGA
130 GATAC-TCAACCCCACCATCTTTGAGA-GGA
** * *
1203707 TACGGCAACTCCTTTTTTCACTTCCA
1 TACTCCAACCCCATTTTT-ACTTCCA
1203733 CATTACCGAA
Statistics
Matches: 283, Mismatches: 54, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
158 18 0.06
159 129 0.46
160 132 0.47
161 4 0.01
ACGTcount: A:0.28, C:0.26, G:0.10, T:0.35
Consensus pattern (158 bp):
TACTCCAACCCCATTTTTACTTCCAAAATATTGAATTTTTCATATCTAGGATACTCCAACCCCAC
AATCTCCGAAGGGATACTCCAACCTCATTTTTACTTACAAAACACTGAATTTTTCATCTTTGGGG
ATACTCAACCCCACCATCTTTGAGAGGA
Found at i:1203724 original size:79 final size:79
Alignment explanation
Indices: 1203223--1203709 Score: 432
Period size: 80 Copynumber: 6.1 Consensus size: 79
1203213 AAAACATCAA
* * * * ***
1203223 AAGGGGTACTCTAACCTCATTTTTACTTCTAAAACA-TCAAATTTTTCAT-TTCTTATGATACTC
1 AAGGGATACTCCAACCTCATTTTTACTTCCAAAACACT-GAATTTTTCATCTT-TGGGGATACT-
**
1203286 CAACCCCATAATCTTTG
63 CAACCCCACCATCTTTG
*
1203303 AAGGGATACTCCAACCTCATTTTTACTTACAAAACACTGAATTTTTCATCTTT-GGGATTACTCT
1 AAGGGATACTCCAACCTCATTTTTACTTCCAAAACACTGAATTTTTCATCTTTGGGGA-TACTC-
1203367 AACCCCACCAT-TTTG
64 AACCCCACCATCTTTG
* * * * * * *
1203382 GAGAGGATACTCCAACCACATTTTTAATTTCAAAATACTGAATTTTTCATATCTAGGGG-TACTC
1 AAG-GGATACTCCAACCTCATTTTTACTTCCAAAACACTGAATTTTTCATCT-TTGGGGATACTC
* * **
1203446 TAACCTCACTATCTCCG
64 -AACCCCACCATCTTTG
* * * * * * *
1203463 AAGAGATACTCCAACCCCATTTTTACTTTCAAAACATTGAATTTTTCATATCTGGGGATACTCAG
1 AAGGGATACTCCAACCTCATTTTTACTTCCAAAACACTGAATTTTTCATCTTTGGGGATACTCAA
* *
1203528 CCCCATCATCTCTG
66 CCCCACCATCTTTG
* * * * * * *
1203542 -AGAGGATACTTCAACCCCATTTTTACTTCCAAAATTATTGAATTTTTCATCTCT-AGGATTCTC
1 AAG-GGATACTCCAACCTCATTTTTACTTCCAAAA-CACTGAATTTTTCATCTTTGGGGATACT-
**
1203605 CAACCCCACCATCTCCG
63 CAACCCCACCATCTTTG
* *
1203622 AGGGGATACTCCAACCTCATTTTTACTTCCAAAGCACTGAA-TTTTCATCTTTGGGGATACTTCA
1 AAGGGATACTCCAACCTCATTTTTACTTCCAAAACACTGAATTTTTCATCTTTGGGGATAC-TCA
*
1203686 ACCCTACCATCTTTG
65 ACCCCACCATCTTTG
1203701 AAGGGATAC
1 AAGGGATAC
1203710 GGCAACTCCT
Statistics
Matches: 336, Mismatches: 56, Indels: 31
0.79 0.13 0.07
Matches are distributed among these distances:
78 12 0.04
79 90 0.27
80 222 0.66
81 9 0.03
82 3 0.01
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (79 bp):
AAGGGATACTCCAACCTCATTTTTACTTCCAAAACACTGAATTTTTCATCTTTGGGGATACTCAA
CCCCACCATCTTTG
Found at i:1203803 original size:78 final size:77
Alignment explanation
Indices: 1203586--1203805 Score: 203
Period size: 78 Copynumber: 2.8 Consensus size: 77
1203576 TTATTGAATT
* * * * *
1203586 TTTCATCTCT-AGGATTCTCCAACCCCACCATCTCCGAGGGGATACTCCAACCTCATTTTT-ACT
1 TTTCATCTTTAAGGATACTTCAACCCTACCATCTTCGAGGGGATACTCCAACCT--TTTTTCACT
*
1203649 TCCAAAGCACTGAA
64 TCCAAAGCACCGAA
** * * **
1203663 TTTTCATCTTTGGGGATACTTCAACCCTACCATCTTTGAAGGGATACGGCAACTCCTTTTTTCAC
1 -TTTCATCTTTAAGGATACTTCAACCCTACCATCTTCGAGGGGATACTCCAA--CCTTTTTTCAC
* **
1203728 TTCCACATTACCGAA
63 TTCCAAAGCACCGAA
* *
1203743 -TTCATCTTTAAGGATACTTCAACCTTACTATCTTCGAGGGGATACTCCAACCTTGGTTTTCAC
1 TTTCATCTTTAAGGATACTTCAACCCTACCATCTTCGAGGGGATACTCCAACCTT--TTTTCAC
1203806 CCAAAAATTG
Statistics
Matches: 114, Mismatches: 22, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
76 4 0.04
78 58 0.51
79 36 0.32
80 13 0.11
81 3 0.03
ACGTcount: A:0.25, C:0.29, G:0.13, T:0.33
Consensus pattern (77 bp):
TTTCATCTTTAAGGATACTTCAACCCTACCATCTTCGAGGGGATACTCCAACCTTTTTTCACTTC
CAAAGCACCGAA
Found at i:1207358 original size:51 final size:51
Alignment explanation
Indices: 1207235--1207371 Score: 186
Period size: 51 Copynumber: 2.7 Consensus size: 51
1207225 TGCCTGCATG
* *
1207235 TATCGATACATTGAAGAATGTATCAATACATTTATGTCAAAAACCCAGAATG
1 TATCGATACAATGAAGAATGTATCAATACATTT-TGTCAAAAACCCAGAATA
* *
1207287 TATCGATACAATTAAGAATGTATCAATACATTTTGGTC-AAAACCCATAATA
1 TATCGATACAATGAAGAATGTATCAATACATTTT-GTCAAAAACCCAGAATA
* * *
1207338 TATCAATACAATGAAAAATGTATCGATACATTTT
1 TATCGATACAATGAAGAATGTATCAATACATTTT
1207372 CATTCTAGAA
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
51 42 0.55
52 34 0.45
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (51 bp):
TATCGATACAATGAAGAATGTATCAATACATTTTGTCAAAAACCCAGAATA
Found at i:1207456 original size:21 final size:22
Alignment explanation
Indices: 1207405--1207458 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
1207395 GACATGGTTC
1207405 TGTATTGATACATTTCAAAAAT
1 TGTATTGATACATTTCAAAAAT
* ***
1207427 T-TATCGATACA-TTCACTTAT
1 TGTATTGATACATTTCAAAAAT
1207447 TGTATTGATACA
1 TGTATTGATACA
1207459 AATTGTAGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 7 0.27
21 18 0.69
22 1 0.04
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (22 bp):
TGTATTGATACATTTCAAAAAT
Found at i:1208337 original size:20 final size:20
Alignment explanation
Indices: 1208314--1208387 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
1208304 ACAATTCAAA
1208314 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1208334 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1208355 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1208375 GTATCGATACATG
1 GTATCGATACATG
1208388 AAAAAGATGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1208358 original size:21 final size:21
Alignment explanation
Indices: 1208332--1208407 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1208322 ACATGTTGCA
1208332 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1208353 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
1208373 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
*
1208394 ATGTATCAATACAT
1 ATGTATCGATACAT
1208408 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1208365 original size:41 final size:41
Alignment explanation
Indices: 1208314--1208407 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1208304 ACAATTCAAA
1208314 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1208355 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
*
1208396 GTATCAATACAT
1 GTATCGATACAT
1208408 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
Found at i:1208464 original size:13 final size:13
Alignment explanation
Indices: 1208446--1208471 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1208436 TACAGCAAGT
1208446 ATGTATCGATACA
1 ATGTATCGATACA
1208459 ATGTATCGATACA
1 ATGTATCGATACA
1208472 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1212538 original size:15 final size:15
Alignment explanation
Indices: 1212518--1212548 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1212508 TAAAAATGTC
*
1212518 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1212533 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1212548 C
1 C
1212549 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1214643 original size:20 final size:21
Alignment explanation
Indices: 1214565--1214642 Score: 79
Period size: 20 Copynumber: 3.6 Consensus size: 21
1214555 ATGTCCAAAA
*
1214565 TGTATCGATACATGTTTT-TT
1 TGTATCGATACATCTTTTCTT
* *
1214585 TGTATCGATACATCTGGAAATTCTA
1 TGTATCGATACATCT----TTTCTT
1214610 TGTATCGATACAT-TTTTCTT
1 TGTATCGATACATCTTTTCTT
1214630 TGTATCGATACAT
1 TGTATCGATACAT
1214643 TGTATCGATA
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
20 31 0.65
24 3 0.06
25 14 0.29
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (21 bp):
TGTATCGATACATCTTTTCTT
Found at i:1214647 original size:13 final size:13
Alignment explanation
Indices: 1214629--1214667 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1214619 ACATTTTTCT
1214629 TTGTATCGATACA
1 TTGTATCGATACA
1214642 TTGTATCGATACA
1 TTGTATCGATACA
*
1214655 CTGTATCGATACA
1 TTGTATCGATACA
1214668 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1217134 original size:20 final size:20
Alignment explanation
Indices: 1217111--1217184 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
1217101 ACAATTCAAA
1217111 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1217131 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1217152 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1217172 GTATCGATACATG
1 GTATCGATACATG
1217185 AAAAAGATGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1217155 original size:21 final size:21
Alignment explanation
Indices: 1217129--1217204 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1217119 ACATGTTGCA
1217129 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1217150 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
1217170 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
*
1217191 ATGTATCAATACAT
1 ATGTATCGATACAT
1217205 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1217162 original size:41 final size:41
Alignment explanation
Indices: 1217111--1217204 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1217101 ACAATTCAAA
1217111 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1217152 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
*
1217193 GTATCAATACAT
1 GTATCGATACAT
1217205 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
Found at i:1217261 original size:13 final size:13
Alignment explanation
Indices: 1217243--1217268 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1217233 TACAGCAAGT
1217243 ATGTATCGATACA
1 ATGTATCGATACA
1217256 ATGTATCGATACA
1 ATGTATCGATACA
1217269 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1223750 original size:2 final size:2
Alignment explanation
Indices: 1223743--1223773 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1223733 GCCTCCCCCA
*
1223743 TC TC TC TC TC TC TC TC TC TC AC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1223774 TTGCATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.03, C:0.48, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:1228766 original size:26 final size:27
Alignment explanation
Indices: 1228737--1228791 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
1228727 CTATTTATAC
1228737 AGGGCTTTCTT-GATAAATACCTTCCT
1 AGGGCTTTCTTGGATAAATACCTTCCT
*
1228763 AGGGCTTTCTTGGATAAATACCTTTCT
1 AGGGCTTTCTTGGATAAATACCTTCCT
1228790 AG
1 AG
1228792 CGTCTTCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 11 0.41
27 16 0.59
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (27 bp):
AGGGCTTTCTTGGATAAATACCTTCCT
Found at i:1233366 original size:17 final size:19
Alignment explanation
Indices: 1233335--1233369 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1233325 TTTTTTTTTT
1233335 TGGAGAATGTAATTTTTCC
1 TGGAGAATGTAATTTTTCC
1233354 TGGAGAAT-T-ATTTTTC
1 TGGAGAATGTAATTTTTC
1233370 ACAATCATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 1 0.06
19 8 0.50
ACGTcount: A:0.26, C:0.09, G:0.20, T:0.46
Consensus pattern (19 bp):
TGGAGAATGTAATTTTTCC
Found at i:1236597 original size:3 final size:3
Alignment explanation
Indices: 1236589--1236631 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
1236579 TTAAGATGAC
1236589 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1236632 TGATTTTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1236958 original size:16 final size:16
Alignment explanation
Indices: 1236937--1236968 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1236927 ATTTAATTTT
*
1236937 ATTATGTATTTTGAAA
1 ATTATGAATTTTGAAA
1236953 ATTATGAATTTTGAAA
1 ATTATGAATTTTGAAA
1236969 TTTAGAAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (16 bp):
ATTATGAATTTTGAAA
Found at i:1245065 original size:42 final size:40
Alignment explanation
Indices: 1244963--1245616 Score: 392
Period size: 42 Copynumber: 15.6 Consensus size: 40
1244953 CCTCATCTAA
* * * *
1244963 AGTCTGTCTGTCAGCTTTGACCTTGGAGACTTTCCT-ATCTCAA
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGAC-TGCCTCA-CT--T
* ** *
1245006 AGTCTGCTTGTCGGCTTTGACCTTGGAGACCTTTCTACCCTT
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGA-CTGCCT-CACTT
* *
1245048 AGTCTGCCTGTCGGCTTTGACCTTGGAGAGTGCCTCATCTAA
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCA-CT-T
* * * * *
1245090 AGTTTGCCTGTCGACTTTGACCTAGGAGACTACCTCATTT
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACTT
* * * * * *
1245130 AGAGTTTGCATGTCGGTTTTGACCCTCGAGACTGCCTCATCTAA
1 --AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCA-CT-T
* * * * *
1245174 AGTCTGCCTATCGCCTTTGACCCTAGAGACTGCCTCATTT
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACTT
* * * ** *
1245214 AAAGTCTGCCTGTCAGCTTTGACCCTAGAGACCTTTCTACCCTT
1 --AGTCTGCCTGTCGGCTTTGACCTTGGAGA-CTGCCT-CACTT
* * ** *
1245258 AGTCTGCCTATCGACTTTGACCTTGGAGACTAACTCATTT
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACTT
* * ** *
1245298 AAAGTCTACCTGTCGGCTTTGACCTTAGAGACCACCTCATCTAA
1 --AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCA-CT-T
* * *
1245342 AGTTTGCCTGTCGGCTTTGACCCTGGAGACTGCCTCATTT
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACTT
* * * * *
1245382 AAAGTCTGCCCGTCGGCTTTAACCTTGCAGACTACCTCATCTAA
1 --AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCA-CT-T
* * *
1245426 AGTCTGCCTGTCGGCTTTGACCCTGGAGACTGACTCATTT
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACTT
* * * * ** *
1245466 AAAGTCTGTCTGTCAGCTTTGACCTTAGAGTCTTTTCTACCCTT
1 --AGTCTGCCTGTCGGCTTTGACCTTGGAGAC-TGCCT-CACTT
* * *
1245510 AGTCTGCCTATCGACTTTGACCTTGGAGACTGCCTCATTT
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACTT
* * * * *
1245550 AAAGTCTGCCTATCGGCTTTGACCCTGGAGACTACCTTATCTAA
1 --AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCA-CT-T
1245594 AGGTCTGCCTGTCGGCTTTGACC
1 A-GTCTGCCTGTCGGCTTTGACC
1245617 CGGGAGAATC
Statistics
Matches: 471, Mismatches: 110, Indels: 60
0.73 0.17 0.09
Matches are distributed among these distances:
40 7 0.01
41 16 0.03
42 378 0.80
43 61 0.13
44 9 0.02
ACGTcount: A:0.19, C:0.28, G:0.20, T:0.33
Consensus pattern (40 bp):
AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACTT
Found at i:1245144 original size:84 final size:83
Alignment explanation
Indices: 1244953--1245616 Score: 606
Period size: 84 Copynumber: 7.9 Consensus size: 83
1244943 CATATGAACG
* * * * *
1244953 CCTCATCTAAAGTCTGTCTGTCAGCTTTGACCTTGGAGACTTTCCT-ATCTCAAAGTCTGCTTGT
1 CCTCATTTAAAGTCTGCCTGTCGGCTTTGACCTTGGAGAC-TACCTCATCT-AAAGTCTGCCTGT
* *
1245017 CGGCTTTGACCTTGGAGACCTT
64 CGACTTTGACC-TGGAGA-CTA
* ** * * *
1245039 TCTACCCTT--AGTCTGCCTGTCGGCTTTGACCTTGGAGAGTGCCTCATCTAAAGTTTGCCTGTC
1 CCT-CATTTAAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTACCTCATCTAAAGTCTGCCTGTC
1245102 GACTTTGACCTAGGAGACTA
65 GACTTTGACCT-GGAGACTA
* * * * * * * *
1245122 CCTCATTTAGAGTTTGCATGTCGGTTTTGACCCTCGAGACTGCCTCATCTAAAGTCTGCCTATCG
1 CCTCATTTAAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTACCTCATCTAAAGTCTGCCTGTCG
* * *
1245187 CCTTTGACCCTAGAGACTG
66 ACTTTGA-CCTGGAGACTA
* * * ** * * *
1245206 CCTCATTTAAAGTCTGCCTGTCAGCTTTGACCCTAGAGACCTTTCT-ACCCT-TAGTCTGCCTAT
1 CCTCATTTAAAGTCTGCCTGTCGGCTTTGACCTTGGAGA-CTACCTCA-TCTAAAGTCTGCCTGT
1245269 CGACTTTGACCTTGGAGACTA
64 CGACTTTGACC-TGGAGACTA
* * * * *
1245290 ACTCATTTAAAGTCTACCTGTCGGCTTTGACCTTAGAGACCACCTCATCTAAAGTTTGCCTGTCG
1 CCTCATTTAAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTACCTCATCTAAAGTCTGCCTGTCG
* *
1245355 GCTTTGACCCTGGAGACTG
66 ACTTTGA-CCTGGAGACTA
* * *
1245374 CCTCATTTAAAGTCTGCCCGTCGGCTTTAACCTTGCAGACTACCTCATCTAAAGTCTGCCTGTCG
1 CCTCATTTAAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTACCTCATCTAAAGTCTGCCTGTCG
*
1245439 GCTTTGACCCTGGAGACTGA
66 ACTTTGA-CCTGGAGACT-A
* * * * ** * * *
1245459 -CTCATTTAAAGTCTGTCTGTCAGCTTTGACCTTAGAGTCT-TTTCTACCCT-TAGTCTGCCTAT
1 CCTCATTTAAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTACCTC-A-TCTAAAGTCTGCCTGT
*
1245521 CGACTTTGACCTTGGAGACTG
64 CGACTTTGACC-TGGAGACTA
* * *
1245542 CCTCATTTAAAGTCTGCCTATCGGCTTTGACCCTGGAGACTACCTTATCTAAAGGTCTGCCTGTC
1 CCTCATTTAAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTACCTCATCTAAA-GTCTGCCTGTC
*
1245607 GGCTTTGACC
65 GACTTTGACC
1245617 CGGGAGAATC
Statistics
Matches: 470, Mismatches: 88, Indels: 41
0.78 0.15 0.07
Matches are distributed among these distances:
82 3 0.01
83 18 0.04
84 381 0.81
85 64 0.14
86 2 0.00
87 2 0.00
ACGTcount: A:0.19, C:0.28, G:0.20, T:0.33
Consensus pattern (83 bp):
CCTCATTTAAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTACCTCATCTAAAGTCTGCCTGTCG
ACTTTGACCTGGAGACTA
Found at i:1245195 original size:126 final size:124
Alignment explanation
Indices: 1244952--1245616 Score: 543
Period size: 126 Copynumber: 5.3 Consensus size: 124
1244942 CCATATGAAC
* * * ** * *
1244952 GCCTCATCTAAAGTCTGTCTGTC-AGCTTTGACCTTGGAGACTTTCCTATCTCAAAGTCTGCTTG
1 GCCTCATCTAAAGTCTGCCTGTCGA-CTTTGACC-TAGAGAC-TTCCTA-CACTTAGTCTGCCTA
* * ** * * * *
1245016 TCGGCTTTGACCTTGGAGACCTTTCT-ACCCT-TAGTCTGCCTGTCGGCTTTGACCTTGGAGAGT
62 TCGACTTTGACCCTGGAGA-CTACCTCA-TCTAAAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
* * * * * *
1245079 GCCTCATCTAAAGTTTGCCTGTCGACTTTGACCTAGGAGACTACCT-CATTTAGAGTTTGCATGT
1 GCCTCATCTAAAGTCTGCCTGTCGACTTTGACCTA-GAGACTTCCTACACTT--AGTCTGCCTAT
** * * * * *
1245143 CGGTTTTGACCCTCGAGACTGCCTCATCTAAAGTCTGCCTATCGCCTTTGACCCTAGAGACT
63 CGACTTTGACCCTGGAGACTACCTCATCTAAAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
* * *
1245205 GCCTCATTTAAAGTCTGCCTGTC-AGCTTTGACCCTAGAGACCTTTCTACCCTTAGTCTGCCTAT
1 GCCTCATCTAAAGTCTGCCTGTCGA-CTTTGA-CCTAGAGA-CTTCCTACACTTAGTCTGCCTAT
* * * * * * *
1245269 CGACTTTGACCTTGGAGACTAACTCATTTAAAGTCTACCTGTCGGCTTTGACCTTAGAGACC
63 CGACTTTGACCCTGGAGACTACCTCATCTAAAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
* * * * * * **
1245331 ACCTCATCTAAAGTTTGCCTGTCGGCTTTGACCCTGGAGACTGCCT-CATTTAAAGTCTGCCCGT
1 GCCTCATCTAAAGTCTGCCTGTCGACTTTGA-CCTAGAGACTTCCTACACTT--AGTCTGCCTAT
* * * *
1245395 CGGCTTTAACCTTGCAGACTACCTCATCTAAAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
63 CGACTTTGACCCTGGAGACTACCTCATCTAAAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
* * * * * *
1245457 GACTCATTTAAAGTCTGTCTGTC-AGCTTTGACCTTAGAGTCTTTTCTACCCTTAGTCTGCCTAT
1 GCCTCATCTAAAGTCTGCCTGTCGA-CTTTGACC-TAGAGAC-TTCCTACACTTAGTCTGCCTAT
* * * *
1245521 CGACTTTGACCTTGGAGACTGCCTCATTTAAAGTCTGCCTATCGGCTTTGACCCTGGAGACT
63 CGACTTTGACCCTGGAGACTACCTCATCTAAAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
* * *
1245583 ACCTTATCTAAAGGTCTGCCTGTCGGCTTTGACC
1 GCCTCATCTAAA-GTCTGCCTGTCGACTTTGACC
1245617 CGGGAGAATC
Statistics
Matches: 430, Mismatches: 89, Indels: 38
0.77 0.16 0.07
Matches are distributed among these distances:
124 4 0.01
125 13 0.03
126 343 0.80
127 63 0.15
128 7 0.02
ACGTcount: A:0.19, C:0.28, G:0.20, T:0.33
Consensus pattern (124 bp):
GCCTCATCTAAAGTCTGCCTGTCGACTTTGACCTAGAGACTTCCTACACTTAGTCTGCCTATCGA
CTTTGACCCTGGAGACTACCTCATCTAAAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
Found at i:1246406 original size:36 final size:36
Alignment explanation
Indices: 1246361--1246430 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
1246351 GAACTCAAAG
* *
1246361 AAAAGAATAGCTTCCAGCAGCCTCCAATCCACGATC
1 AAAAAAATAGCTTCCAGCAACCTCCAATCCACGATC
* *
1246397 AAAAAAATAGCTTCCAGCAACCTCTAGTCCACGA
1 AAAAAAATAGCTTCCAGCAACCTCCAATCCACGA
1246431 CCAAGAAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.39, C:0.31, G:0.13, T:0.17
Consensus pattern (36 bp):
AAAAAAATAGCTTCCAGCAACCTCCAATCCACGATC
Found at i:1246511 original size:41 final size:41
Alignment explanation
Indices: 1246447--1246542 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
1246437 AACTCCAGCA
* * *
1246447 AGCAACAGCTTCCAGCAGCAGGAGTATCCGTAACCAACACT
1 AGCAACAGCTTCCAGCAACAGGAGCATCCGAAACCAACACT
* * * *
1246488 AGCAGCAGCTTCTAGCAATAGGAGCATTCGAAACCAACACT
1 AGCAACAGCTTCCAGCAACAGGAGCATCCGAAACCAACACT
1246529 -GACAACAGCTTCCA
1 AG-CAACAGCTTCCA
1246543 CGATAGCCTC
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
40 1 0.02
41 44 0.98
ACGTcount: A:0.35, C:0.30, G:0.19, T:0.16
Consensus pattern (41 bp):
AGCAACAGCTTCCAGCAACAGGAGCATCCGAAACCAACACT
Found at i:1246669 original size:61 final size:61
Alignment explanation
Indices: 1246604--1246834 Score: 223
Period size: 61 Copynumber: 3.8 Consensus size: 61
1246594 AACAGTAGCC
*
1246604 AAACAACAGCACGACAGCAACATTAGCAGCTCCAACAAGCAGGCAAGCTCGAACAGCAATG
1 AAACAACAGCACGACAGCAACAATAGCAGCTCCAACAAGCAGGCAAGCTCGAACAGCAATG
* ** * * *
1246665 AAACAATAGCACGGTAGCAACAACAGCAGCTTCAACAAGCAGGCAAGCAC-AACCAGCAATG
1 AAACAACAGCACGACAGCAACAATAGCAGCTCCAACAAGCAGGCAAGCTCGAA-CAGCAATG
* * * * * * *
1246726 AAATAATAGCACGACAACAACAATAGTAGCTCCAACAAGCAAGCAAACAT-GAACAGTAATG
1 AAACAACAGCACGACAGCAACAATAGCAGCTCCAACAAGCAGGCAAGC-TCGAACAGCAATG
* * * * * * * * *
1246787 AATCAACAACATGGCAGCAGCAACAGCAACTTCAACAAGTAGGCAAGC
1 AAACAACAGCACGACAGCAACAATAGCAGCTCCAACAAGCAGGCAAGC
1246835 AGGAAAAATG
Statistics
Matches: 134, Mismatches: 33, Indels: 6
0.77 0.19 0.03
Matches are distributed among these distances:
60 2 0.01
61 130 0.97
62 2 0.01
ACGTcount: A:0.45, C:0.26, G:0.18, T:0.10
Consensus pattern (61 bp):
AAACAACAGCACGACAGCAACAATAGCAGCTCCAACAAGCAGGCAAGCTCGAACAGCAATG
Found at i:1246831 original size:122 final size:122
Alignment explanation
Indices: 1246611--1246835 Score: 308
Period size: 122 Copynumber: 1.8 Consensus size: 122
1246601 GCCAAACAAC
* * * * * *
1246611 AGCACGACAGCAACATTAGCAGCTCCAACAAGCAGGCAAGCTCGAACAGCAATGAAACAATAGCA
1 AGCACGACAACAACAATAGCAGCTCCAACAAGCAAGCAAACTCGAACAGCAATGAAACAACAACA
* *
1246676 CGGTAGCAACAACAGCAGCTTCAACAAGCAGGCAAGCACAACCAGCAATGAAATAAT
66 CGGCAGCAACAACAGCAACTTCAACAAGCAGGCAAGCACAACCAGCAATGAAATAAT
* * *
1246733 AGCACGACAACAACAATAGTAGCTCCAACAAGCAAGCAAACAT-GAACAGTAATGAATCAACAAC
1 AGCACGACAACAACAATAGCAGCTCCAACAAGCAAGCAAAC-TCGAACAGCAATGAAACAACAAC
* * *
1246797 ATGGCAGCAGCAACAGCAACTTCAACAAGTAGGCAAGCA
65 ACGGCAGCAACAACAGCAACTTCAACAAGCAGGCAAGCA
1246836 GGAAAAATGA
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
122 87 0.99
123 1 0.01
ACGTcount: A:0.45, C:0.26, G:0.19, T:0.10
Consensus pattern (122 bp):
AGCACGACAACAACAATAGCAGCTCCAACAAGCAAGCAAACTCGAACAGCAATGAAACAACAACA
CGGCAGCAACAACAGCAACTTCAACAAGCAGGCAAGCACAACCAGCAATGAAATAAT
Found at i:1251078 original size:19 final size:19
Alignment explanation
Indices: 1251054--1251109 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
1251044 TGTATCGATA
* *
1251054 CATTGTATTGATACATGTT
1 CATTGTATCGATACATGCT
*
1251073 CATTGTATCGATACATACT
1 CATTGTATCGATACATGCT
1251092 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
1251110 AAATTAGTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (19 bp):
CATTGTATCGATACATGCT
Found at i:1251172 original size:13 final size:13
Alignment explanation
Indices: 1251154--1251184 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1251144 CAATACATGG
*
1251154 TACATTGTATCGA
1 TACATTGTATCCA
1251167 TACATTGTATCCA
1 TACATTGTATCCA
1251180 TACAT
1 TACAT
1251185 AATGAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (13 bp):
TACATTGTATCCA
Found at i:1253327 original size:3 final size:3
Alignment explanation
Indices: 1253319--1253373 Score: 51
Period size: 3 Copynumber: 18.7 Consensus size: 3
1253309 TTATCTATAC
* * * *
1253319 AAT AAT AAT AAT AAT AAT CAT AAT CAT AAT CAT AAT AAA AACT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT
1253365 -AT AA- AAT AA
1 AAT AAT AAT AA
1253374 AAAATTCATA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
2 4 0.10
3 35 0.85
4 2 0.05
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1256962 original size:21 final size:21
Alignment explanation
Indices: 1256938--1256983 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
1256928 ACAAACAACG
*
1256938 CCATCCACGATAAGCAGATGC
1 CCATCCACAATAAGCAGATGC
1256959 CCAT-CACAATAAGCAGATGC
1 CCATCCACAATAAGCAGATGC
1256979 CCATC
1 CCATC
1256984 ATCTCAAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.35, C:0.35, G:0.15, T:0.15
Consensus pattern (21 bp):
CCATCCACAATAAGCAGATGC
Found at i:1259677 original size:3 final size:3
Alignment explanation
Indices: 1259669--1259701 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1259659 ATTTTTTAAA
1259669 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1259702 CTAAAATCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1260870 original size:13 final size:13
Alignment explanation
Indices: 1260852--1260878 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1260842 ACATGACATC
1260852 GCCATTTTGTAAA
1 GCCATTTTGTAAA
1260865 GCCATTTTGTAAA
1 GCCATTTTGTAAA
1260878 G
1 G
1260879 GAGCCTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (13 bp):
GCCATTTTGTAAA
Found at i:1261304 original size:14 final size:13
Alignment explanation
Indices: 1261281--1261313 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 13
1261271 TTTTATTTTT
1261281 GGGGGGGGGGAGG
1 GGGGGGGGGGAGG
1261294 GGGGCGGGGGGAGG
1 GGGG-GGGGGGAGG
1261308 GGGGGG
1 GGGGGG
1261314 AGTGTGCAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.06, C:0.03, G:0.91, T:0.00
Consensus pattern (13 bp):
GGGGGGGGGGAGG
Found at i:1263665 original size:2 final size:2
Alignment explanation
Indices: 1263660--1263691 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1263650 AATATATGCA
*
1263660 AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1263692 TAAAAGACCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1280194 original size:4 final size:4
Alignment explanation
Indices: 1280185--1280216 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
1280175 CGTTGGCTAC
1280185 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
1280217 CATGTTATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTAT
Found at i:1280570 original size:25 final size:26
Alignment explanation
Indices: 1280506--1280576 Score: 65
Period size: 26 Copynumber: 2.7 Consensus size: 26
1280496 TATTTTTTAA
**
1280506 TTAATAAAAA-TATTTTTATTTAAAT
1 TTAATAAAAATTATTTTTAAATAAAT
* * *
1280531 TTATATGAAATTTATTTTTAAAT-ATT
1 TTA-ATAAAAATTATTTTTAAATAAAT
1280557 TTAATAAAAATTATTATTTA
1 TTAATAAAAATTATT-TTTA
1280577 TTAAAATTTA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
25 13 0.36
26 14 0.39
27 9 0.25
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (26 bp):
TTAATAAAAATTATTTTTAAATAAAT
Found at i:1280607 original size:47 final size:44
Alignment explanation
Indices: 1280548--1280651 Score: 124
Period size: 47 Copynumber: 2.3 Consensus size: 44
1280538 AAATTTATTT
*
1280548 TTAAATATTTTAATAAA-AATTATTAT-TTATTAAAATTTATATAAA
1 TTAAATATTTTAATAAATAATTATGATATTA-TAAAA--TATATAAA
1280593 TATAAAATATTTTAA-AAATAATTATGATATTATAAAATATATAAA
1 T-T-AAATATTTTAATAAATAATTATGATATTATAAAATATATAAA
*
1280638 TTTAATATTTTAAT
1 TTAAATATTTTAAT
1280652 TAAGTAATAT
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
43 10 0.19
44 1 0.02
45 10 0.19
46 4 0.08
47 24 0.46
48 3 0.06
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (44 bp):
TTAAATATTTTAATAAATAATTATGATATTATAAAATATATAAA
Found at i:1281134 original size:20 final size:21
Alignment explanation
Indices: 1281109--1281163 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
1281099 GTATCGATAC
**
1281109 AATGTATCGATACATGACCA-
1 AATGTATCGATACATGAAAAG
*
1281129 AATGTATCGATACTTGAAAAG
1 AATGTATCGATACATGAAAAG
1281150 AATGTATCGATACA
1 AATGTATCGATACA
1281164 GGTCATTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (21 bp):
AATGTATCGATACATGAAAAG
Found at i:1281233 original size:13 final size:13
Alignment explanation
Indices: 1281215--1281240 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1281205 ACACACAATA
1281215 TGTATCGATACAT
1 TGTATCGATACAT
1281228 TGTATCGATACAT
1 TGTATCGATACAT
1281241 CCCAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1281256 original size:33 final size:32
Alignment explanation
Indices: 1281195--1281262 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
1281185 GTAGCCAAAT
*
1281195 TTGTATCGATACACACAATATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
*
1281227 TTGTATCGATACATCCCAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
1281260 TTG
1 TTG
1281263 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:1287408 original size:13 final size:13
Alignment explanation
Indices: 1287390--1287423 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
1287380 CAGCATTCTC
*
1287390 TGTATCGATACAT
1 TGTATCGATACAG
1287403 TGTATCGATACAG
1 TGTATCGATACAG
1287416 TGTATCGA
1 TGTATCGA
1287424 CACAAGGGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1287593 original size:20 final size:20
Alignment explanation
Indices: 1287558--1287598 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
1287548 CAAATATCTT
1287558 GTTTTTCACTTCAAAATACATC
1 GTTTTTCAC-TCAAAAT-CATC
1287580 GTTTTTCA-TCAAAATCATC
1 GTTTTTCACTCAAAATCATC
1287599 AACAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
22 8 0.42
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (20 bp):
GTTTTTCACTCAAAATCATC
Found at i:1289306 original size:22 final size:22
Alignment explanation
Indices: 1289280--1289324 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1289270 CGAAAATGTT
1289280 AAATTATTTT-ACTAAGGGGGAG
1 AAATT-TTTTGACTAAGGGGGAG
*
1289302 AAATTTTTTGATTAAGGGGGAG
1 AAATTTTTTGACTAAGGGGGAG
1289324 A
1 A
1289325 GAAAAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.33
Consensus pattern (22 bp):
AAATTTTTTGACTAAGGGGGAG
Found at i:1289746 original size:22 final size:21
Alignment explanation
Indices: 1289716--1289761 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
1289706 CTAGATAAGT
1289716 ATAAATG-TTTTCAAGGCTTAAA
1 ATAAATGTTTTTCAA-G-TTAAA
*
1289738 ATAAGTGTTTTTCAAGTTAAA
1 ATAAATGTTTTTCAAGTTAAA
1289759 ATA
1 ATA
1289762 TATCAAAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 8 0.36
22 7 0.32
23 7 0.32
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (21 bp):
ATAAATGTTTTTCAAGTTAAA
Found at i:1289915 original size:20 final size:21
Alignment explanation
Indices: 1289890--1289944 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
1289880 GTATCAATAT
**
1289890 AATGTATCGATACATGACCA-
1 AATGTATCGATACATGAAAAG
*
1289910 AATGTATCGATACTTGAAAAG
1 AATGTATCGATACATGAAAAG
1289931 AATGTATCGATACA
1 AATGTATCGATACA
1289945 GGTCATTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (21 bp):
AATGTATCGATACATGAAAAG
Found at i:1290021 original size:20 final size:20
Alignment explanation
Indices: 1289977--1290028 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1289967 TAGCCAAATT
**
1289977 TGTATCGATACA-CACAATG
1 TGTATCGATACATCACAAAA
*
1289996 TGTATCGATACATCCCAAAA
1 TGTATCGATACATCACAAAA
1290016 TGTATCGATACAT
1 TGTATCGATACAT
1290029 TGGCTTGTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (20 bp):
TGTATCGATACATCACAAAA
Found at i:1291689 original size:414 final size:414
Alignment explanation
Indices: 1290917--1292078 Score: 1382
Period size: 414 Copynumber: 2.7 Consensus size: 414
1290907 AAGTAATATC
*
1290917 TATATGTAATAAATTACATATAAACATTATCATATTACATAAAATATTATTAAAACGGTAATGTA
1 TATATGTAATAAATTACATATAAACATTATCATATTACATAAAATATTATTAAAACTGTAATGTA
* *** *
1290982 TTTATGTAAAAAAAATTTTAAGAAAATTAAATATAATTTTTTTAAAATTATTTTTGATTTTTTAT
66 TTTATATAAAAATTCTTTTAAGAAAATTAAATATAATTTTTTCAAAATTATTTTTGA-TTTTTAT
*
1291047 TAAATAAATTATATATGTATGAAATTAATTTTTGAAG-TTAAAATATTTTTATAATTTTTATTTT
130 TAAATATA-TATATATGTATGAAATTAATTTTTGAAGTTTAAAA-ATTTTTAT-ATTTTTATTTT
* *
1291111 ATTAATATATTTTGTAATATTAGTAATAAATATATTATATTGATAAAAAATTAATTTTAT-GAAA
192 ATTAATATATTTT-TAATATTAGTAATAAATATATTATATTTATAAAAAATTAATTTTATGGTAA
* **
1291175 AATTTAGATTTTTTATTAGTTGGTATGAATTACAACTATAAATTAACAATTTTTATATAAATATT
256 AATTTAGATTTTTTATTA-TTTGTATGAATTACAACTATAAATTAACAATTTACATATAAATATT
* * * *
1291240 ATAGTTTACATAAATCATTAGAATGTATGTAATGTTTGTATGTAATATATGTTATTGGAAATGTA
320 ATAGTTTACATAAATCATTAGAATGTATATAATGTTTGTATATAACATATATTATTGGAAATGTA
* *
1291305 TTTCAGTAAAAAA-TATTGAAAGTAACGTT
385 TTTCAGCAAAAAATTATCGAAAGTAACGTT
* ** * *
1291334 TATATGTAACAAATTATTTATAAACATTATCATATTACATAAAATATTATTGAAACTGTAATGTG
1 TATATGTAATAAATTACATATAAACATTATCATATTACATAAAATATTATTAAAACTGTAATGTA
*
1291399 TTTATATACAAATTTCTTTTAAGAAAATTAAATATAA-TTTTTCAAAATTATTTTTGATTTTTAT
66 TTTATATA-AAAATTCTTTTAAGAAAATTAAATATAATTTTTTCAAAATTATTTTTGATTTTTAT
** * *
1291463 TAAATATAT-TATATGTATGACGTTAATTTTTGAAGTTTAAAGATTTTTATATTTTTATTTTGTT
130 TAAATATATATATATGTATGAAATTAATTTTTGAAGTTTAAAAATTTTTATATTTTTATTTTATT
1291527 AATATATTTTTAATATTAGTAATAAATATATTATATTTATAAAAAATTAATTTTATGGTAAAATT
195 AATATATTTTTAATATTAGTAATAAATATATTATATTTATAAAAAATTAATTTTATGGTAAAATT
* * ***
1291592 TAGATTTTTTATTATTTAGTATGAATTCCAACTACAAATTATTGATATTACATATAAATATTATA
260 TAGATTTTTTATTATTT-GTATGAATTACAACTATAAATTAACAAT-TTACATATAAATATTATA
*
1291657 GTTTACATAAATCATTAGAATGTATATAATGTTTGTATATAACATATATTATTGGTAATGTATTT
323 GTTTACATAAATCATTAGAATGTATATAATGTTTGTATATAACATATATTATTGGAAATGTATTT
** * *
1291722 TTGCAAAAAATTATCGAAGGTAATGTT
388 CAGCAAAAAATTATCGAAAGTAACGTT
* *
1291749 TATATGTAATAAATTACATATAAACATTATTGGATTAAATATAAATAAAGTTTTATATAAAACAT
1 TATATGTAATAAATTACATATAAACATTA-T-CA-T--AT-TACAT-AA-----A-AT-----AT
* * * *
1291814 TACTAAAATTATAATGTATTTATATAAAAAATTCTTTTAAGAAAATTAATTATAATTTTTTCAAA
48 TATTAAAACTGTAATGTATTTATAT-AAAAATTCTTTTAAGAAAATTAAATATAATTTTTTCAAA
*** *
1291879 ATTATTTTTGATTTTTGATTATATATTATATATAATTAAT-TATTTTAGTAATTTTTGAAG-TTA
112 ATTATTTTTGATTTTT-ATTA-A-A-TATATAT-A-T-ATGTATGAAATTAATTTTTGAAGTTTA
* * *
1291942 ATAAATTTATAT-TTTTTATTATATT-A-ATATTTTTAATATTAGAAATAAATAT-TT-TA--TA
170 A-AAATTTTTATATTTTTATTTTATTAATATATTTTTAATATTAGTAATAAATATATTATATTTA
*
1292000 -AAAAAATTAATTTTATGATAAAATTTAGATTTTTTTTATTAGTTTGTATGAATTACAACTATAA
234 TAAAAAATTAATTTTATGGTAAAATTTAGA--TTTTTTATTA-TTTGTATGAATTACAACTATAA
*
1292064 ATTACCAATATTACA
296 ATTAACAAT-TTACA
1292079 CACAATTTAC
Statistics
Matches: 641, Mismatches: 66, Indels: 58
0.84 0.09 0.08
Matches are distributed among these distances:
412 47 0.07
413 67 0.10
414 115 0.18
415 45 0.07
416 15 0.02
417 86 0.13
418 25 0.04
420 2 0.00
421 4 0.01
422 2 0.00
427 1 0.00
428 2 0.00
433 76 0.12
434 28 0.04
435 43 0.07
436 6 0.01
437 3 0.00
438 30 0.05
439 2 0.00
440 16 0.02
441 24 0.04
442 2 0.00
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (414 bp):
TATATGTAATAAATTACATATAAACATTATCATATTACATAAAATATTATTAAAACTGTAATGTA
TTTATATAAAAATTCTTTTAAGAAAATTAAATATAATTTTTTCAAAATTATTTTTGATTTTTATT
AAATATATATATATGTATGAAATTAATTTTTGAAGTTTAAAAATTTTTATATTTTTATTTTATTA
ATATATTTTTAATATTAGTAATAAATATATTATATTTATAAAAAATTAATTTTATGGTAAAATTT
AGATTTTTTATTATTTGTATGAATTACAACTATAAATTAACAATTTACATATAAATATTATAGTT
TACATAAATCATTAGAATGTATATAATGTTTGTATATAACATATATTATTGGAAATGTATTTCAG
CAAAAAATTATCGAAAGTAACGTT
Found at i:1293142 original size:87 final size:87
Alignment explanation
Indices: 1293035--1293205 Score: 288
Period size: 87 Copynumber: 2.0 Consensus size: 87
1293025 CAATCACTTA
* * *
1293035 AGAATTTGGGATATAATTCTCGAAGTGATTGTGAGGTTCTATCTTAACCTTTGAAAAAGATAGGT
1 AGAATTTGGGATATAATTCTCGAAATGATTATGAGGTTCTATCTTAACCTTTGAAAAAGATAGGG
*
1293100 AGAGAGATTCTTTCTTAGCTTG
66 AGAGAGATTCTATCTTAGCTTG
* *
1293122 AGAATTTGGGATATAATTCTCGAAATGATTATGAGGTTCTATTTTAGCCTTTGAAAAAGATAGGG
1 AGAATTTGGGATATAATTCTCGAAATGATTATGAGGTTCTATCTTAACCTTTGAAAAAGATAGGG
1293187 AGAGAGATTCTATCTTAGC
66 AGAGAGATTCTATCTTAGC
1293206 CTGTGAAAAG
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 78 1.00
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.36
Consensus pattern (87 bp):
AGAATTTGGGATATAATTCTCGAAATGATTATGAGGTTCTATCTTAACCTTTGAAAAAGATAGGG
AGAGAGATTCTATCTTAGCTTG
Found at i:1293205 original size:36 final size:34
Alignment explanation
Indices: 1293158--1293252 Score: 120
Period size: 34 Copynumber: 2.8 Consensus size: 34
1293148 GATTATGAGG
*
1293158 TTCTATTTTAGCCTTTGAAAAAGATAGGGAGAGAGA
1 TTCTATCTTAGCCTTTG-AAAAGATAGGGA-AGAGA
* * *
1293194 TTCTATCTTAGCCTGTGAAAAGATAGTGAAGAGG
1 TTCTATCTTAGCCTTTGAAAAGATAGGGAAGAGA
*
1293228 TTCTATCTTAGCC-TTCAAAAGATAG
1 TTCTATCTTAGCCTTTGAAAAGATAG
1293253 TGTTGTAAGG
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
33 10 0.19
34 17 0.32
35 11 0.21
36 15 0.28
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.32
Consensus pattern (34 bp):
TTCTATCTTAGCCTTTGAAAAGATAGGGAAGAGA
Found at i:1293237 original size:34 final size:34
Alignment explanation
Indices: 1293154--1293277 Score: 135
Period size: 35 Copynumber: 3.6 Consensus size: 34
1293144 AAATGATTAT
* *
1293154 GAGGTTCTATTTTAGCCTTTGAAAAAGATAGGGAGA
1 GAGGTTCTATCTTAGCC-TTG-AAAAGATAGTGAGA
*
1293190 GAGATTCTATCTTAGCCTGTGAAAAGATAGTGA-A
1 GAGGTTCTATCTTAGCCT-TGAAAAGATAGTGAGA
* *
1293224 GAGGTTCTATCTTAGCCTTCAAAAGATAGTGTTGTA
1 GAGGTTCTATCTTAGCCTTGAAAAGATAGTG-AG-A
*
1293260 -AGGTTATATCTTAGCCTT
1 GAGGTTCTATCTTAGCCTT
1293278 AAATGTAACA
Statistics
Matches: 77, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
33 12 0.16
34 18 0.23
35 29 0.38
36 18 0.23
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.34
Consensus pattern (34 bp):
GAGGTTCTATCTTAGCCTTGAAAAGATAGTGAGA
Found at i:1294627 original size:421 final size:421
Alignment explanation
Indices: 1293838--1294667 Score: 1561
Period size: 421 Copynumber: 2.0 Consensus size: 421
1293828 TGGCGTTTCT
1293838 GTGTCCAAAGGAGAAGAAGAGTGGAATGACCAAGACATAAAGTTGGCACAACTCAATGCAAAGGC
1 GTGTCCAAAGGAGAAGAAGAGTGGAATGACCAAGACATAAAGTTGGCACAACTCAATGCAAAGGC
1293903 AATGCTCACATTATTTTGTGCTTTCAGGCCAAGTAAATACAACCGAGTTTCACTTTGCAAAAGCA
66 AATGCTCACATTATTTTGTGCTTTCAGGCCAAGTAAATACAACCGAGTTTCACTTTGCAAAAGCA
1293968 CCAAGCAAGTGTAGGATAAACTCGAAACAACAAACGAGGGAATAAACCAAGTCAAAAAGTCAAAG
131 CCAAGCAAGTGTAGGATAAACTCGAAACAACAAACGAGGGAATAAACCAAGTCAAAAAGTCAAAG
*
1294033 ATAAGTATGCTCACTCTTAACTATGAGTTATTTAAGTTGAAACCCAATAAAACTATCAAGGAGAT
196 ATAAGTATGCTCACTCTTAACTATGAGTTATTTAAGATGAAACCCAATAAAACTATCAAGGAGAT
* *
1294098 ATCCGATAGGTTCATCGATATTATTGATGGGTTGGAAGCACTCGGTAAAGCCTATCCCAATAAGG
261 ATCCGATAGGTTCATCGATATTATTAATGGGTTGGAAGCACTCGGTAAAACCTATCCCAATAAGG
*
1294163 AGATGGTGAAGAAGCTTCTCAATAGCCTTCCAAAATTGTAGGAAGTGAAAGTCACAGCCATCGAA
326 AGATGGTGAAGAAGCTTCTCAATAGCCTTCCAAAATCGTAGGAAGTGAAAGTCACAGCCATCGAA
1294228 AAATCCAAAGATCTCAATATCGAGTGCTTCC
391 AAATCCAAAGATCTCAATATCGAGTGCTTCC
1294259 GTGTCCAAAGGAGAAGAAGAGTGGAATGACCAAGACATAAAGTTGGCACAACTCAATGCAAAGGC
1 GTGTCCAAAGGAGAAGAAGAGTGGAATGACCAAGACATAAAGTTGGCACAACTCAATGCAAAGGC
*
1294324 AATGCTCACATTATTTTGTGCTTTCGGGCCAAGTAAATACAACCGAGTTTCACTTTGCAAAAGCA
66 AATGCTCACATTATTTTGTGCTTTCAGGCCAAGTAAATACAACCGAGTTTCACTTTGCAAAAGCA
*
1294389 CCAAGCAAGTGTAGGATAAACTCGAAACAACAAACGAGGGAATAAACCAAGTTAAAAAGTCAAAG
131 CCAAGCAAGTGTAGGATAAACTCGAAACAACAAACGAGGGAATAAACCAAGTCAAAAAGTCAAAG
* * *
1294454 ATAAGTATGCTCACTCTTGACTATGAGTTATTTAAGATGAAGCCCATTAAAACTATCAAGGAGAT
196 ATAAGTATGCTCACTCTTAACTATGAGTTATTTAAGATGAAACCCAATAAAACTATCAAGGAGAT
*
1294519 ATCCGATAGGTTCATCGATATTATTAATGGGTTGGAAGCACTCGGTAAAACCTATCCCAATATGG
261 ATCCGATAGGTTCATCGATATTATTAATGGGTTGGAAGCACTCGGTAAAACCTATCCCAATAAGG
*
1294584 AGATGGTGAAGAAGCTTCTCAATAGCCTTCCAAAATCGTAGGAAGTGAAAGTCACAGCTATCGAA
326 AGATGGTGAAGAAGCTTCTCAATAGCCTTCCAAAATCGTAGGAAGTGAAAGTCACAGCCATCGAA
1294649 AAATCCAAAGATCTCAATA
391 AAATCCAAAGATCTCAATA
1294668 CACGCTCATT
Statistics
Matches: 398, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
421 398 1.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.23
Consensus pattern (421 bp):
GTGTCCAAAGGAGAAGAAGAGTGGAATGACCAAGACATAAAGTTGGCACAACTCAATGCAAAGGC
AATGCTCACATTATTTTGTGCTTTCAGGCCAAGTAAATACAACCGAGTTTCACTTTGCAAAAGCA
CCAAGCAAGTGTAGGATAAACTCGAAACAACAAACGAGGGAATAAACCAAGTCAAAAAGTCAAAG
ATAAGTATGCTCACTCTTAACTATGAGTTATTTAAGATGAAACCCAATAAAACTATCAAGGAGAT
ATCCGATAGGTTCATCGATATTATTAATGGGTTGGAAGCACTCGGTAAAACCTATCCCAATAAGG
AGATGGTGAAGAAGCTTCTCAATAGCCTTCCAAAATCGTAGGAAGTGAAAGTCACAGCCATCGAA
AAATCCAAAGATCTCAATATCGAGTGCTTCC
Found at i:1295288 original size:21 final size:22
Alignment explanation
Indices: 1295264--1295315 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
1295254 GAACTAGAGG
*
1295264 AGAAAATGAATGAGTTG-AAAA
1 AGAAAATGAATAAGTTGCAAAA
*
1295285 AGAAAA-GAAATAAGTTGCAAGA
1 AGAAAATG-AATAAGTTGCAAAA
1295307 AGAAAATGA
1 AGAAAATGA
1295316 TAAATTAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 1 0.04
21 14 0.54
22 10 0.38
23 1 0.04
ACGTcount: A:0.60, C:0.02, G:0.23, T:0.15
Consensus pattern (22 bp):
AGAAAATGAATAAGTTGCAAAA
Found at i:1296484 original size:18 final size:18
Alignment explanation
Indices: 1296457--1296508 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
1296447 TACATTATAT
*
1296457 ATTTAGATTTTTTAATAA
1 ATTTATATTTTTTAATAA
* *
1296475 ATTTATATTTTTTATTAT
1 ATTTATATTTTTTAATAA
*
1296493 ATTAATA-TTTTTAATA
1 ATTTATATTTTTTAATA
1296509 TTAGAAATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 8 0.28
18 21 0.72
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
ATTTATATTTTTTAATAA
Found at i:1301250 original size:13 final size:13
Alignment explanation
Indices: 1301231--1301269 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
1301221 ACTATTTATG
*
1301231 ATGTATCGATATA
1 ATGTATCGATACA
* *
1301244 CTGTATCAATACA
1 ATGTATCGATACA
1301257 ATGTATCGATACA
1 ATGTATCGATACA
1301270 TGAATAGTGA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1301466 original size:53 final size:53
Alignment explanation
Indices: 1301402--1301538 Score: 229
Period size: 53 Copynumber: 2.6 Consensus size: 53
1301392 CTACTACCAA
* *
1301402 TGTATCGATACATATTTTGTGTATCGATAGAAATTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTCCCAATGACC
* *
1301455 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTCCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTCCCAATGACC
1301508 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
1301539 TATGCAATCT
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 65 0.83
54 13 0.17
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTCCCAATGACC
Found at i:1301571 original size:20 final size:20
Alignment explanation
Indices: 1301508--1301578 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
1301498 CCCAATGTCC
**
1301508 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
1301528 TGTATCGATAC-TATGCAATC
1 TGTATCGATACATAT-TAATG
1301548 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
1301568 TGTATCGATAC
1 TGTATCGATAC
1301579 TTTTCAGGAT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:1301644 original size:21 final size:21
Alignment explanation
Indices: 1301618--1301658 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1301608 GTCAACCTTG
1301618 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
1301639 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
1301659 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:1304011 original size:33 final size:32
Alignment explanation
Indices: 1303950--1304012 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 32
1303940 ACAATTCGCT
*
1303950 GTGTATCGATACCAAGATCATGTATCGATATA
1 GTGTATCGATACAAAGATCATGTATCGATATA
1303982 GTGTATCGATACAAAGCAAT-ATGTATCGATA
1 GTGTATCGATACAAAG--ATCATGTATCGATA
1304013 CTTCTGAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 15 0.54
33 11 0.39
34 2 0.07
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (32 bp):
GTGTATCGATACAAAGATCATGTATCGATATA
Found at i:1308250 original size:28 final size:28
Alignment explanation
Indices: 1308216--1308287 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 28
1308206 TTCCTCTTCG
*
1308216 TTGATTTCTCTTCCTTTGATATTTCTTA
1 TTGATTTCTCTTCCTTTCATATTTCTTA
* * * *
1308244 TTTATTT-TGTTTCCCTTCATATTTCTTG
1 TTGATTTCT-CTTCCTTTCATATTTCTTA
*
1308272 TTGATTTCACTTCCTT
1 TTGATTTCTCTTCCTT
1308288 GATCTATAAA
Statistics
Matches: 33, Mismatches: 9, Indels: 4
0.72 0.20 0.09
Matches are distributed among these distances:
27 1 0.03
28 32 0.97
ACGTcount: A:0.12, C:0.19, G:0.07, T:0.61
Consensus pattern (28 bp):
TTGATTTCTCTTCCTTTCATATTTCTTA
Found at i:1308421 original size:181 final size:180
Alignment explanation
Indices: 1308109--1308473 Score: 534
Period size: 181 Copynumber: 2.0 Consensus size: 180
1308099 GTTATTCATC
* *
1308109 ATCTATAGAAAAAGTGTTCTATTATTATAACCCTTTTTCATCTTATAAAAAGATTGTTATTAGAG
1 ATCTATAAAAAAAGTGTTCTAGTATTATAACCCTTTTTCATCTTATAAAAAGATTGTTATTAGAG
* *
1308174 CTTCATATTCATATGTTACAAAAAATTCTTTATTCCTCTTCGTTGATTTCTCTTCCTTTGATATT
66 CTTCATATTCATATGTTACAAAAAATTCTTTATCCCTCTTCATTGATTTCTCTTCCTTTGATATT
* * * * *
1308239 TCTTATTTATTTTGTTTCCCTTCATATTTCTTGTTGATTTCACTTCCTTG
131 TCTTACTTATTTCGTTTCCATTAATATTTCTTATTGATTTCACTTCCTTG
* *
1308289 ATCTATAAAAAAAAGTGTTCTAGTGTTATAACCCTTTTTTATCTT-TAAAAAAGATTGTTATTAG
1 ATCTAT-AAAAAAAGTGTTCTAGTATTATAACCCTTTTTCATCTTAT-AAAAAGATTGTTATTAG
* * * * * * *
1308353 ATCTTTATATTCATATTTTACAAAGAATTCTTTGTCCCTCTTTATTGATTTTTCTTCCTTTGATA
64 AGCTTCATATTCATATGTTACAAAAAATTCTTTATCCCTCTTCATTGATTTCTCTTCCTTTGATA
*
1308418 TTTCTTGCTTATTTCGTTTCCATTAATATTTCTTATTGATTTCACTTCCTTG
129 TTTCTTACTTATTTCGTTTCCATTAATATTTCTTATTGATTTCACTTCCTTG
1308470 ATCT
1 ATCT
1308474 TTCTTATTTA
Statistics
Matches: 164, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
180 7 0.04
181 157 0.96
ACGTcount: A:0.25, C:0.16, G:0.08, T:0.50
Consensus pattern (180 bp):
ATCTATAAAAAAAGTGTTCTAGTATTATAACCCTTTTTCATCTTATAAAAAGATTGTTATTAGAG
CTTCATATTCATATGTTACAAAAAATTCTTTATCCCTCTTCATTGATTTCTCTTCCTTTGATATT
TCTTACTTATTTCGTTTCCATTAATATTTCTTATTGATTTCACTTCCTTG
Found at i:1308466 original size:28 final size:27
Alignment explanation
Indices: 1308394--1308481 Score: 79
Period size: 28 Copynumber: 3.2 Consensus size: 27
1308384 TTGTCCCTCT
**
1308394 TTATTGATTTTTCTTCCTTTGATATTTC
1 TTATTGATTTCACTTCC-TTGATATTTC
* ** *
1308422 TTGCTT-ATTTCGTTTCCATTAATATTTC
1 TT-ATTGATTTCACTTCC-TTGATATTTC
*
1308450 TTATTGATTTCACTTCCTTGATCTTTC
1 TTATTGATTTCACTTCCTTGATATTTC
1308477 TTATT
1 TTATT
1308482 TATTAACCAA
Statistics
Matches: 47, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
27 15 0.32
28 30 0.64
29 2 0.04
ACGTcount: A:0.16, C:0.17, G:0.07, T:0.60
Consensus pattern (27 bp):
TTATTGATTTCACTTCCTTGATATTTC
Found at i:1309631 original size:52 final size:51
Alignment explanation
Indices: 1309462--1309733 Score: 343
Period size: 52 Copynumber: 5.3 Consensus size: 51
1309452 TTTGGAAAGA
* * *
1309462 AAATGTATTGATACATTTTTTATTGTATCGATACATTC-GAGGTTTGATCC
1 AAATGTATCGATACATTTTTCATTGTATCGATACATTCTGAGTTTTGATCC
* * * *
1309512 AAATGTATTGATACATTTTTTATTATATCGATACATTCT-AGGTTTGATCC
1 AAATGTATCGATACATTTTTCATTGTATCGATACATTCTGAGTTTTGATCC
* * *
1309562 AAATGTATGGACACATTTTTCATTGTATCGATACATTTTGAGTTTTTGATCC
1 AAATGTATCGATACATTTTTCATTGTATCGATACATTCTGAG-TTTTGATCC
* *
1309614 AAAGGTATCGATACATTTTTCATTGTATCAATACATTCTGAGTTTTTGATCC
1 AAATGTATCGATACATTTTTCATTGTATCGATACATTCTGAG-TTTTGATCC
* * * *
1309666 AAATGTATAGTTACATTATTCATTGTATCGATACATTCTGGGTTTTGA-CC
1 AAATGTATCGATACATTTTTCATTGTATCGATACATTCTGAGTTTTGATCC
*
1309716 TAAATGTATCAATACATT
1 -AAATGTATCGATACATT
1309734 CTTTAATGTA
Statistics
Matches: 197, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
50 84 0.43
51 22 0.11
52 91 0.46
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.43
Consensus pattern (51 bp):
AAATGTATCGATACATTTTTCATTGTATCGATACATTCTGAGTTTTGATCC
Found at i:1310233 original size:14 final size:14
Alignment explanation
Indices: 1310200--1310234 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
1310190 CTAACTATAT
*
1310200 CTCAACCAAAAACA
1 CTCAACAAAAAACA
1310214 CT-AACAAAAAACA
1 CTCAACAAAAAACA
1310227 CTCAACAA
1 CTCAACAA
1310235 GATACCATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.60, C:0.31, G:0.00, T:0.09
Consensus pattern (14 bp):
CTCAACAAAAAACA
Found at i:1316786 original size:30 final size:31
Alignment explanation
Indices: 1316729--1316806 Score: 95
Period size: 30 Copynumber: 2.5 Consensus size: 31
1316719 ACATGTATGA
*
1316729 ATGTATCGATACATTCTATCTTTTTACCCAG
1 ATGTATCGATACATTTTATCTTTTTACCCAG
* * *
1316760 ATGTATCGATATATTTTGTC-TTTTACCTAG
1 ATGTATCGATACATTTTATCTTTTTACCCAG
* *
1316790 ATATATCAATACATTTT
1 ATGTATCGATACATTTT
1316807 TCAATGTATC
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 23 0.57
31 17 0.43
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.46
Consensus pattern (31 bp):
ATGTATCGATACATTTTATCTTTTTACCCAG
Found at i:1316821 original size:20 final size:20
Alignment explanation
Indices: 1316793--1316886 Score: 129
Period size: 20 Copynumber: 4.7 Consensus size: 20
1316783 TACCTAGATA
*
1316793 TATCAATACATT-TTTCAATG
1 TATCGATACATTCTTT-AATG
* *
1316813 TATCGATACATAT-ATGAATG
1 TATCGATACAT-TCTTTAATG
1316833 TATCGATACATTCTTTAATG
1 TATCGATACATTCTTTAATG
1316853 TATCGATACATTCTTTAATG
1 TATCGATACATTCTTTAATG
1316873 TATCGATACATTCT
1 TATCGATACATTCT
1316887 GTCTTTTTAC
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
19 1 0.01
20 64 0.96
21 2 0.03
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (20 bp):
TATCGATACATTCTTTAATG
Found at i:1317834 original size:20 final size:22
Alignment explanation
Indices: 1317794--1317841 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
1317784 TAGCCTTTGA
*
1317794 CCATGCATTTTTTTACTATGTT
1 CCATGCATTTTTTAACTATGTT
1317816 CCATGCA-TTTTTAAC-ATG-T
1 CCATGCATTTTTTAACTATGTT
1317835 CCA-GCAT
1 CCATGCAT
1317842 CTCATTGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 3 0.12
19 4 0.17
20 3 0.12
21 7 0.29
22 7 0.29
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.44
Consensus pattern (22 bp):
CCATGCATTTTTTAACTATGTT
Found at i:1328867 original size:11 final size:11
Alignment explanation
Indices: 1328853--1328877 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1328843 AATAGCAGAC
1328853 CTTGGTTCGCA
1 CTTGGTTCGCA
1328864 CTTGGTTCGCA
1 CTTGGTTCGCA
1328875 CTT
1 CTT
1328878 CCACGAGTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.28, G:0.24, T:0.40
Consensus pattern (11 bp):
CTTGGTTCGCA
Found at i:1331498 original size:13 final size:13
Alignment explanation
Indices: 1331480--1331505 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1331470 CATTTTGGGA
1331480 TGTATCGATACAT
1 TGTATCGATACAT
1331493 TGTATCGATACAT
1 TGTATCGATACAT
1331506 CTTGTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1331502 original size:33 final size:32
Alignment explanation
Indices: 1331460--1331523 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
1331450 TACAAGCCAA
*
1331460 TGTATCGATACATTTTGGGATGTATCGATACAT
1 TGTATCGATACATCTTGGG-TGTATCGATACAT
*
1331493 TGTATCGATACATCTTGTGTGTATCGATACA
1 TGTATCGATACATCTTGGGTGTATCGATACA
1331524 AACAGTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATCTTGGGTGTATCGATACAT
Found at i:1331538 original size:18 final size:18
Alignment explanation
Indices: 1331515--1331550 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1331505 TCTTGTGTGT
1331515 ATCGATACAAACAGTTAA
1 ATCGATACAAACAGTTAA
1331533 ATCGATACAAACAGTTAA
1 ATCGATACAAACAGTTAA
1331551 GGGTGGTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.17, G:0.11, T:0.22
Consensus pattern (18 bp):
ATCGATACAAACAGTTAA
Found at i:1331633 original size:20 final size:20
Alignment explanation
Indices: 1331583--1331678 Score: 77
Period size: 20 Copynumber: 4.8 Consensus size: 20
1331573 GCCAATCACC
* *
1331583 TGTATCGATACATTCTTAACA
1 TGTATCGATACATT-TGATCA
* * *
1331604 AGTATTGATACATTTGGTCA
1 TGTATCGATACATTTGATCA
* *
1331624 TGTATCGATAC-TGTGCATTA
1 TGTATCGATACATTTG-ATCA
***
1331644 TGTATCGATACATTTGAAGG
1 TGTATCGATACATTTGATCA
1331664 TGTATCGATACATTT
1 TGTATCGATACATTT
1331679 CAGGGTTTTG
Statistics
Matches: 59, Mismatches: 14, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
19 3 0.05
20 41 0.69
21 15 0.25
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATTTGATCA
Found at i:1332115 original size:29 final size:29
Alignment explanation
Indices: 1332080--1332138 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
1332070 AAGAAGTATG
1332080 CTCTCAATTCAAAATTCAACATCGTAACT
1 CTCTCAATTCAAAATTCAACATCGTAACT
*
1332109 CTCTCAATTCAATATTCAACATCGTAACT
1 CTCTCAATTCAAAATTCAACATCGTAACT
1332138 C
1 C
1332139 AGTGTTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.32
Consensus pattern (29 bp):
CTCTCAATTCAAAATTCAACATCGTAACT
Found at i:1332881 original size:21 final size:20
Alignment explanation
Indices: 1332851--1332889 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
1332841 CACATTTTTA
1332851 TCTAAATGTATCGATACATT
1 TCTAAATGTATCGATACATT
1332871 TCTAGAATGTATCGATACA
1 TCTA-AATGTATCGATACA
1332890 AGATCCCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (20 bp):
TCTAAATGTATCGATACATT
Found at i:1332985 original size:13 final size:13
Alignment explanation
Indices: 1332967--1332992 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1332957 ACATAAGTGT
1332967 TGTATCGATACAA
1 TGTATCGATACAA
1332980 TGTATCGATACAA
1 TGTATCGATACAA
1332993 AGTTGCCCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1333054 original size:13 final size:13
Alignment explanation
Indices: 1333036--1333061 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1333026 CATTATTCCA
1333036 TGTATCGATACAT
1 TGTATCGATACAT
1333049 TGTATCGATACAT
1 TGTATCGATACAT
1333062 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1334389 original size:13 final size:13
Alignment explanation
Indices: 1334371--1334397 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1334361 TACAGTGAGC
1334371 ATGTATCGATACA
1 ATGTATCGATACA
1334384 ATGTATCGATACA
1 ATGTATCGATACA
1334397 A
1 A
1334398 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1343143 original size:19 final size:20
Alignment explanation
Indices: 1343100--1343144 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1343090 TGCCAATCTT
* *
1343100 ATGTATCGATACAATTGTCC
1 ATGTATCGATACAAGTGACC
*
1343120 ATGTATCGATAC-AGTGAGC
1 ATGTATCGATACAAGTGACC
1343139 ATGTAT
1 ATGTAT
1343145 TAATACAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAAGTGACC
Found at i:1350068 original size:22 final size:23
Alignment explanation
Indices: 1350013--1350069 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
1350003 GATGAAAAGT
* *
1350013 CAAAAGTAAAAACACGAAAAAAA
1 CAAAAATAAAAACACAAAAAAAA
*
1350036 CAAAAACAAAAACA-AAAAAAAA
1 CAAAAATAAAAACACAAAAAAAA
* *
1350058 CACACATAAAAA
1 CAAAAATAAAAA
1350070 AGAGTGAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 16 0.57
23 12 0.43
ACGTcount: A:0.77, C:0.16, G:0.04, T:0.04
Consensus pattern (23 bp):
CAAAAATAAAAACACAAAAAAAA
Found at i:1350334 original size:5 final size:5
Alignment explanation
Indices: 1350310--1350356 Score: 60
Period size: 5 Copynumber: 9.2 Consensus size: 5
1350300 TGTTCTTTTC
*
1350310 CAAAA CACAAA -AAAA GAAAA CAAAAA CAAAA CAAAA CAAAA CAAAA C
1 CAAAA CA-AAA CAAAA CAAAA C-AAAA CAAAA CAAAA CAAAA CAAAA C
1350357 CCTTTCACTC
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
4 3 0.08
5 27 0.71
6 8 0.21
ACGTcount: A:0.79, C:0.19, G:0.02, T:0.00
Consensus pattern (5 bp):
CAAAA
Found at i:1350336 original size:21 final size:21
Alignment explanation
Indices: 1350311--1350355 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
1350301 GTTCTTTTCC
*
1350311 AAAACACAAA-AAAAGAAAACA
1 AAAACA-AAACAAAACAAAACA
1350332 AAAACAAAACAAAACAAAACA
1 AAAACAAAACAAAACAAAACA
1350353 AAA
1 AAA
1350356 CCCTTTCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.82, C:0.16, G:0.02, T:0.00
Consensus pattern (21 bp):
AAAACAAAACAAAACAAAACA
Found at i:1351322 original size:30 final size:30
Alignment explanation
Indices: 1351283--1351813 Score: 449
Period size: 30 Copynumber: 17.2 Consensus size: 30
1351273 AATTCTTCAA
*
1351283 ATCTCTTTTCAAAGTCCACAACTCAGTGGC
1 ATCTCTTTTCAAAGTCCACGACTCAGTGGC
* * * *
1351313 ATTTCTTTTCCCAAAGTCCACAACTTAGTGGT
1 ATCTCTTTT--CAAAGTCCACGACTCAGTGGC
** * * *
1351345 ATCTCTTCCCAAAGTCTATGACTTAGTGGC
1 ATCTCTTTTCAAAGTCCACGACTCAGTGGC
*
1351375 ATCTCTTCTT-AAAGTCCACAACTCAGTGGC
1 ATCTCTT-TTCAAAGTCCACGACTCAGTGGC
* * *
1351405 ATCGCTTTTCCCAAAGTCCATGACTCATTGGC
1 ATCTCTTTT--CAAAGTCCACGACTCAGTGGC
** *
1351437 ATCTCTTCCCAAAGTCCACAACTCAGTGGC
1 ATCTCTTTTCAAAGTCCACGACTCAGTGGC
* *
1351467 ATCTCTTCTCAAAGTCCACGACTTAGTGGC
1 ATCTCTTTTCAAAGTCCACGACTCAGTGGC
* * *
1351497 TTCTCTTTTCCTAAAGTCCGCGACTAAGTGGC
1 ATCTCTTTT-C-AAAGTCCACGACTCAGTGGC
* * *
1351529 ATTTCTTTTCAAAGTTCATGACTCAGTGGC
1 ATCTCTTTTCAAAGTCCACGACTCAGTGGC
* *
1351559 ATCTCTTCTCAAAGTCCACGACTTAGTGGC
1 ATCTCTTTTCAAAGTCCACGACTCAGTGGC
*
1351589 ATCTC--TTCCAAGTCCACGACTCAGTGGC
1 ATCTCTTTTCAAAGTCCACGACTCAGTGGC
* * ** *
1351617 ATCTTTTTTCTTCAAAGTTCATAACTTAGTGGC
1 ATC--TCTT-TTCAAAGTCCACGACTCAGTGGC
* *
1351650 ATCTCTTTTCTAAGTCCACAACTCAGTGGC
1 ATCTCTTTTCAAAGTCCACGACTCAGTGGC
* * *
1351680 ATCCTTTTCTTCCAAGTCCACGACTCAGTAGC
1 AT-CTCTT-TTCAAAGTCCACGACTCAGTGGC
* *
1351712 ATCTTTTTTCTTCAAAGTCCATGACTCAGTGGC
1 ATC--TCTT-TTCAAAGTCCACGACTCAGTGGC
** *
1351745 AATCTCTTCCCAAAGTCCATGACTCAGTGGC
1 -ATCTCTTTTCAAAGTCCACGACTCAGTGGC
* **
1351776 GTCT-TTTCGTCAAAGTCCATAACTCAGTGGC
1 ATCTCTTT--TCAAAGTCCACGACTCAGTGGC
*
1351807 ATTTCTT
1 ATCTCTT
1351814 CTTTAAGCCC
Statistics
Matches: 406, Mismatches: 74, Indels: 40
0.78 0.14 0.08
Matches are distributed among these distances:
28 23 0.06
29 4 0.01
30 177 0.44
31 53 0.13
32 100 0.25
33 46 0.11
34 3 0.01
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.33
Consensus pattern (30 bp):
ATCTCTTTTCAAAGTCCACGACTCAGTGGC
Found at i:1351416 original size:62 final size:60
Alignment explanation
Indices: 1351292--1351870 Score: 414
Period size: 62 Copynumber: 9.4 Consensus size: 60
1351282 AATCTCTTTT
** * * * *
1351292 CAAAGTCCACAACTCAGTGGCATTTCTT-TTCCCAAAGTCCACAACTTAGTGGTATCTCTTCC
1 CAAAGTCCATGACTCAGTGGCATCTCTTCTT---AAAGTCCACAACTCAGTGGCATCTTTTCC
* *
1351354 CAAAGTCTATGACTTAGTGGCATCTCTTCTTAAAGTCCACAACTCAGTGGCATCGCTTTTCC
1 CAAAGTCCATGACTCAGTGGCATCTCTTCTTAAAGTCCACAACTCAGTGGCAT--CTTTTCC
* ** * *
1351416 CAAAGTCCATGACTCATTGGCATCTCTTCCCAAAGTCCACAACTCAGTGGCATCTCTTCT
1 CAAAGTCCATGACTCAGTGGCATCTCTTCTTAAAGTCCACAACTCAGTGGCATCTTTTCC
* * * * * * *
1351476 CAAAGTCCACGACTTAGTGGCTTCTCTTTTCCTAAAGTCCGCGACTAAGTGGCATTTCTTTT--
1 CAAAGTCCATGACTCAGTGGCATCTC--TTCTTAAAGTCCACAACTCAGTGGCA--TCTTTTCC
* * * * *
1351538 CAAAGTTCATGACTCAGTGGCATCTCTTCTCAAAGTCCACGACTTAGTGGCATCTCTT-C
1 CAAAGTCCATGACTCAGTGGCATCTCTTCTTAAAGTCCACAACTCAGTGGCATCTTTTCC
* * * * * *
1351597 C-AAGTCCACGACTCAGTGGCATCTTTTTTCTTCAAAGTTCATAACTTAGTGGCATCTCTTT-T
1 CAAAGTCCATGACTCAGTGGCATC--TCTTCTT-AAAGTCCACAACTCAGTGGCATCT-TTTCC
* ** * * * * *
1351659 CTAAGTCCACAACTCAGTGGCATCCTTTTCTTCCAAGTCCACGACTCAGTAGCATCTTTTTTCTT
1 CAAAGTCCATGACTCAGTGGCAT-CTCTTCTT-AAAGTCCACAACTCAGTGGCATC--TTTTC-C
** ** * *
1351724 CAAAGTCCATGACTCAGTGGCAATCTCTTCCCAAAGTCCATGACTCAGTGGCGTCTTTTCGT
1 CAAAGTCCATGACTCAGTGGC-ATCTCTTCTTAAAGTCCACAACTCAGTGGCATCTTTTC-C
* * * * * * *
1351786 CAAAGTCCATAACTCAGTGGCATTTCTTCTTTAAGCCCATAACTCCGTGGCACTTTTTTCC
1 CAAAGTCCATGACTCAGTGGCATCTCTTCTTAAAGTCCACAACTCAGTGGCA-TCTTTTCC
* * *
1351847 TATTAAGTCCATAACTCCGTGGCA
1 CA--AAGTCCATGACTCAGTGGCA
1351871 CTTTTTTCCT
Statistics
Matches: 422, Mismatches: 73, Indels: 43
0.78 0.14 0.08
Matches are distributed among these distances:
58 25 0.06
59 1 0.00
60 74 0.18
61 45 0.11
62 181 0.43
63 44 0.10
64 26 0.06
65 24 0.06
66 2 0.00
ACGTcount: A:0.23, C:0.29, G:0.15, T:0.33
Consensus pattern (60 bp):
CAAAGTCCATGACTCAGTGGCATCTCTTCTTAAAGTCCACAACTCAGTGGCATCTTTTCC
Found at i:1351441 original size:92 final size:91
Alignment explanation
Indices: 1351283--1351815 Score: 513
Period size: 92 Copynumber: 5.8 Consensus size: 91
1351273 AATTCTTCAA
* * * * *
1351283 ATCTCTTTTCAAAGTCCACAACTCAGTGGCATTTCTTTTCCCAAAGTCCACAACTTAGTGGTATC
1 ATCTCTTCTCAAAGTCCACAACTCAGTGGCA-TCCTTTTCCCAAAGTCCACGACTCAGTGGCATC
* *
1351348 TCTTCCCAAAGTCTATGACTTAGTGGC
65 TCTTCTCAAAGTCTATGACTCAGTGGC
* * *
1351375 ATCTCTTCTTAAAGTCCACAACTCAGTGGCATCGCTTTTCCCAAAGTCCATGACTCATTGGCATC
1 ATCTCTTCTCAAAGTCCACAACTCAGTGGCATC-CTTTTCCCAAAGTCCACGACTCAGTGGCATC
* * **
1351440 TCTTCCCAAAGTCCACAACTCAGTGGC
65 TCTTCTCAAAGTCTATGACTCAGTGGC
* * * * * * *
1351467 ATCTCTTCTCAAAGTCCACGACTTAGTGGCTTCTCTTTTCCTAAAGTCCGCGACTAAGTGGCATT
1 ATCTCTTCTCAAAGTCCACAACTCAGTGGCATC-CTTTTCCCAAAGTCCACGACTCAGTGGCATC
*
1351532 TCTTTTCAAAGT-TCATGACTCAGTGGC
65 TCTTCTCAAAGTCT-ATGACTCAGTGGC
* * *
1351559 ATCTCTTCTCAAAGTCCACGACTTAGTGGCAT-CTCTT-CC-AAGTCCACGACTCAGTGGCATCT
1 ATCTCTTCTCAAAGTCCACAACTCAGTGGCATCCTTTTCCCAAAGTCCACGACTCAGTGGCATC-
* * *
1351621 TTTTTCTTCAAAGT-TCATAACTTAGTGGC
65 -TCTTC-TCAAAGTCT-ATGACTCAGTGGC
* * *
1351650 ATCTCTTTTCTAAGTCCACAACTCAGTGGCATCCTTTTCTTCC-AAGTCCACGACTCAGTAGCAT
1 ATCTCTTCTCAAAGTCCACAACTCAGTGGCATCCTTTTC--CCAAAGTCCACGACTCAGTGGCAT
* *
1351714 CTTTTTTCTTCAAAGTCCATGACTCAGTGGC
64 C--TCTTC-TCAAAGTCTATGACTCAGTGGC
* ** * * **
1351745 AATCTCTTCCCAAAGTCCATGACTCAGTGGCGT-CTTTTCGTCAAAGTCCATAACTCAGTGGCAT
1 -ATCTCTTCTCAAAGTCCACAACTCAGTGGCATCCTTTTC-CCAAAGTCCACGACTCAGTGGCAT
*
1351809 TTCTTCT
64 CTCTTCT
1351816 TTAAGCCCAT
Statistics
Matches: 369, Mismatches: 60, Indels: 24
0.81 0.13 0.05
Matches are distributed among these distances:
88 19 0.05
89 1 0.00
90 7 0.02
91 49 0.13
92 189 0.51
93 4 0.01
94 1 0.00
95 73 0.20
96 26 0.07
ACGTcount: A:0.23, C:0.29, G:0.15, T:0.33
Consensus pattern (91 bp):
ATCTCTTCTCAAAGTCCACAACTCAGTGGCATCCTTTTCCCAAAGTCCACGACTCAGTGGCATCT
CTTCTCAAAGTCTATGACTCAGTGGC
Found at i:1351859 original size:33 final size:32
Alignment explanation
Indices: 1351788--1351880 Score: 136
Period size: 33 Copynumber: 2.9 Consensus size: 32
1351778 CTTTTCGTCA
* *
1351788 AAGTCCATAACTCAGTGGCA-TTTCTT-CTTT
1 AAGTCCATAACTCCGTGGCACTTTTTTCCTTT
*
1351818 AAGCCCATAACTCCGTGGCACTTTTTTCCTATT
1 AAGTCCATAACTCCGTGGCACTTTTTTCCT-TT
1351851 AAGTCCATAACTCCGTGGCACTTTTTTCCT
1 AAGTCCATAACTCCGTGGCACTTTTTTCCT
1351881 GTGCATCTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
30 18 0.32
31 5 0.09
32 2 0.04
33 31 0.55
ACGTcount: A:0.22, C:0.28, G:0.13, T:0.38
Consensus pattern (32 bp):
AAGTCCATAACTCCGTGGCACTTTTTTCCTTT
Found at i:1351955 original size:32 final size:32
Alignment explanation
Indices: 1351919--1352018 Score: 137
Period size: 32 Copynumber: 3.1 Consensus size: 32
1351909 CCATGGCATC
* * *
1351919 CCTTTTTCTTGTAAGTTCACAACTCCGTGGCA
1 CCTTTTTCTTTTAAGTCCATAACTCCGTGGCA
*
1351951 CCTTTTTCTTTTTAAAGCCCATAACTCCGTGGCA
1 CCTTTTTC-TTTT-AAGTCCATAACTCCGTGGCA
*
1351985 CCTTTTCCTTTTAAGTCCATAACTCCGTGGCA
1 CCTTTTTCTTTTAAGTCCATAACTCCGTGGCA
1352017 CC
1 CC
1352019 CCCTTTTAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
32 29 0.48
33 7 0.12
34 24 0.40
ACGTcount: A:0.19, C:0.31, G:0.13, T:0.37
Consensus pattern (32 bp):
CCTTTTTCTTTTAAGTCCATAACTCCGTGGCA
Found at i:1352161 original size:43 final size:43
Alignment explanation
Indices: 1352107--1352196 Score: 126
Period size: 43 Copynumber: 2.1 Consensus size: 43
1352097 TTTCTCATCT
* * *
1352107 TTTAAGACCAATGTCGCTGGCCTTGATTCAACACATTGGCACC
1 TTTAAGACCAATATCGCTAGCCTTGAATCAACACATTGGCACC
* * *
1352150 TTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACC
1 TTTAAGACCAATATCGCTAGCCTTGAATCAACACATTGGCACC
1352193 TTTA
1 TTTA
1352197 CCCTCTTGGG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.31
Consensus pattern (43 bp):
TTTAAGACCAATATCGCTAGCCTTGAATCAACACATTGGCACC
Found at i:1352386 original size:21 final size:20
Alignment explanation
Indices: 1352362--1352429 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 20
1352352 ATGTCGCTGG
1352362 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCA-ATTGGCA
* *
1352383 CCTTTAAGTC--CAATATCGCTAA
1 CCTTGAA-TCAGCAAT-TGGC--A
1352405 CCTTGAATCAGCATATTGGCA
1 CCTTGAATCAGCA-ATTGGCA
1352426 CCTT
1 CCTT
1352430 TACCCTCTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 14
0.67 0.07 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.14
21 13 0.36
22 9 0.25
23 5 0.14
24 2 0.06
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (20 bp):
CCTTGAATCAGCAATTGGCA
Found at i:1352402 original size:43 final size:43
Alignment explanation
Indices: 1352349--1352847 Score: 276
Period size: 49 Copynumber: 10.9 Consensus size: 43
1352339 ATCTTTAAAA
1352349 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGT
* ** *
1352392 CCAATATCGCTAACCTTGAATCAGCATATTGGCACCTTTACCCTCTTGAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTA--------AGT
* * * * *
1352443 CCAATATTGCTGGCCCTGAATCAACACATTGGCA-C---AAGC
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGT
* * * *
1352482 CCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTCATCTTTAAGA
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGT
* *
1352531 CTAATGTCACTGGCCTTGAATCAGCACATTGGCACCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGT
* * *
1352574 CCAATATCGCTGGCCTTGAATCAGCATATTGGCGGCTTTACCTTTAAGA
1 CCAATGTCGCTGGCCTTGAATCAGCACATT---GGC---ACCTTTAAGT
*
1352623 CCAATGTCGCTGGCCTTGAATCAACACATTGGCACCTTCATCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGT
* * * * * *
1352672 TCAATATTGTTGGCCTTGAATCAGCATATTGGCATCTTTAACATTCCTAAGC
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-C-----C-TT--TAAGT
* ** * *
1352724 CCAATGTCGCTAGCCTTGTCTCAGCATATTGGCATTCTTCTTCAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCA--C--CTTTAAGT
* *
1352771 CCAATGTCGCTGGCCTTGAATCAGCACATCGGCA----TAAGA
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGT
* * *
1352810 CCAATGTTGCTGCCCTTGAATCAGCACATTAGCACCTT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT
1352848 CATCTTTAAG
Statistics
Matches: 355, Mismatches: 60, Indels: 82
0.71 0.12 0.16
Matches are distributed among these distances:
39 66 0.19
43 70 0.20
45 1 0.00
46 9 0.03
47 34 0.10
49 107 0.30
50 4 0.01
51 31 0.09
52 31 0.09
53 2 0.01
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.30
Consensus pattern (43 bp):
CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGT
Found at i:1352502 original size:182 final size:181
Alignment explanation
Indices: 1352206--1352657 Score: 631
Period size: 182 Copynumber: 2.5 Consensus size: 181
1352196 ACCCTCTTGG
* *
1352206 GTCCAATATTGCTAGCCTTGAATCAGCATATTGGCACCTTT-CTCATCTTTTAAGACCAATGTCC
1 GTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTAC-C--C-TTTAAGACCAATGTCG
* * * * * **
1352270 CTGGTCGTGAATCAGCACATCT-GCACAAGCCCAATATCGTTGGCCTTGAATTAGTATATTGGCA
62 CTGGCCCTGAATCAACACAT-TGGCACAAGCCCAATATCGCTGGCCTTGAATCAACATATTGGCA
* *
1352334 CTTTCATCTTTAAAACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAA
126 CCTTCATCTTTAAAACCAATGTCACTGGCCTTGAATCAGCACATTGGCACCTTTAA
* * * * *
1352390 GTCCAATATCGCTAACCTTGAATCAGCATATTGGCACCTTTACCCTCTTGAGTCCAATATTGCTG
1 GTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTACCCT-TTAAGACCAATGTCGCTG
1352455 GCCCTGAATCAACACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTT
65 GCCCTGAATCAACACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTT
* *
1352520 CATCTTTAAGACTAATGTCACTGGCCTTGAATCAGCACATTGGCACCTTTAA
130 CATCTTTAAAACCAATGTCACTGGCCTTGAATCAGCACATTGGCACCTTTAA
* **
1352572 GTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGGCTTTA-CCTTTAAGACCAATGTCGCTGG
1 GTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTACCCTTTAAGACCAATGTCGCTGG
*
1352636 CCTTGAATCAACACATTGGCAC
66 CCCTGAATCAACACATTGGCAC
1352658 CTTCATCTTT
Statistics
Matches: 238, Mismatches: 27, Indels: 10
0.87 0.10 0.04
Matches are distributed among these distances:
180 36 0.15
181 5 0.02
182 156 0.66
184 40 0.17
185 1 0.00
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (181 bp):
GTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTACCCTTTAAGACCAATGTCGCTGG
CCCTGAATCAACACATTGGCACAAGCCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTC
ATCTTTAAAACCAATGTCACTGGCCTTGAATCAGCACATTGGCACCTTTAA
Found at i:1352563 original size:49 final size:48
Alignment explanation
Indices: 1352482--1352987 Score: 351
Period size: 49 Copynumber: 10.6 Consensus size: 48
1352472 TGGCACAAGC
* * * *
1352482 CCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTCATCTTTAAGA
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTTTAAGT
* *
1352531 CTAATGTCACTGGCCTTGAATCAGCACATTGGCA---C--CTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTCATCTTTAAGT
* * * * * *
1352574 CCAATATCGCTGGCCTTGAATCAGCATATTGGCGGCTTTACCTTTAAGA
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGC-ACTTCATCTTTAAGT
*
1352623 CCAATGTCGCTGGCCTTGAATCAACACATTGGCACCTTCATCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTTTAAGT
* * * * * * * *
1352672 TCAATATTGTTGGCCTTGAATCAGCATATTGGCATCTTTAACATTCCTAAGC
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CTTCATC-TT--TAAGT
* ** * * *
1352724 CCAATGTCGCTAGCCTTGTCTCAGCATATTGGCA-TTCTTCTTCAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTCATCTTTAAGT
* *
1352771 CCAATGTCGCTGGCCTTGAATCAGCACATCGG-----CA----TAAGA
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTCATCTTTAAGT
* * *
1352810 CCAATGTTGCTGCCCTTGAATCAGCACATTAGCACCTTCATCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTTTAAGT
** * * * * * * *
1352859 CTGATATCGTTGGCCTTGAATTAGCATATTGGCATCTTTAACATTCCTAAGC
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CTTCATC-TT--TAAGT
* * ** * *
1352911 CCAATGTTGCTAGCCTTGTCTCAGCACATTGGCA-TTCTTCTTCAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTCATCTTTAAGT
* *
1352958 CTAATGTCGCTGGCCATGAATCAGCACATT
1 CCAATGTCGCTGGCCTTGAATCAGCACATT
1352988 ATCATTCTTC
Statistics
Matches: 345, Mismatches: 89, Indels: 48
0.72 0.18 0.10
Matches are distributed among these distances:
39 31 0.09
43 37 0.11
45 3 0.01
47 57 0.17
49 148 0.43
50 10 0.03
52 59 0.17
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (48 bp):
CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTCATCTTTAAGT
Found at i:1352660 original size:92 final size:93
Alignment explanation
Indices: 1352206--1352983 Score: 560
Period size: 92 Copynumber: 8.3 Consensus size: 93
1352196 ACCCTCTTGG
* * * *
1352206 GTCCAATATTGCTAGCCTTGAATCAGCATATTGGCACCTTTCTCATCTTTTAAGACCAATGTCCC
1 GTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TT-TCA-CCTTTAAGACCAATGTCGC
* *
1352271 TGGTCGTGAATCAGCACATCT-GCA-C---AA
63 TGGCCTTGAATCAGCACAT-TGGCACCTTTAA
* * * * * *
1352298 GCCCAATATCGTTGGCCTTGAATTAGTATATTGGCA-CTTTCATCTTTAAAACCAATGTCGCTGG
1 GTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTCACCTTTAAGACCAATGTCGCTGG
1352362 CCTTGAATCAGCACATTGGCACCTTTAA
66 CCTTGAATCAGCACATTGGCACCTTTAA
** * * * *
1352390 GTCCAATATCGCTAACCTTGAATCAGCATATTGGCACCTTT-ACCCTCTTGAGTCCAATATTGCT
1 GTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTCA-CCT-TTAAGACCAATGTCGCT
* *
1352454 GGCCCTGAATCAACACATTGGCA-C---AA
64 GGCCTTGAATCAGCACATTGGCACCTTTAA
* * * * *
1352480 GCCCAATATCGCTGGCCTTGAATCAACATATTGGCACC-TTCATCTTTAAGACTAATGTCACTGG
1 GTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTCACCTTTAAGACCAATGTCGCTGG
1352544 CCTTGAATCAGCACATTGGCACCTTTAA
66 CCTTGAATCAGCACATTGGCACCTTTAA
**
1352572 GTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGGCTTT-ACCTTTAAGACCAATGTCGCTGG
1 GTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTCACCTTTAAGACCAATGTCGCTGG
*
1352636 CCTTGAATCAACACATTGGCACCTTCATCTTTAA
66 CCTTGAATCAGCACATTGGCA----C--CTTTAA
* * * * * * *
1352670 GTTCAATATTGTTGGCCTTGAATCAGCATATTGGCATCTTTAACATTCCTAAGCCCAATGTCGCT
1 GTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTCACCTT--TAAGACCAATGTCGCT
* ** * *
1352735 AGCCTTGTCTCAGCATATTGGCATTCTTCTTCAA
64 GGCCTTGAATCAGCACATTGGCA--C--CTTTAA
* * * * *
1352769 GTCCAATGTCGCTGGCCTTGAATCAGCACATCGG-------CA----TAAGACCAATGTTGCTGC
1 GTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTCACCTTTAAGACCAATGTCGCTGG
*
1352823 CCTTGAATCAGCACATTAGCACCTTCATCTTTAA
66 CCTTGAATCAGCACATTGGCA----C--CTTTAA
** * * * * * * *
1352857 GTCTGATATCGTTGGCCTTGAATTAGCATATTGGCATCTTTAACATTCCTAAGCCCAATGTTGCT
1 GTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTCACCTT--TAAGACCAATGTCGCT
* ** *
1352922 AGCCTTGTCTCAGCACATTGGCATTCTTCTTCAA
64 GGCCTTGAATCAGCACATTGGCA--C--CTTTAA
* * *
1352956 GTCTAATGTCGCTGGCCATGAATCAGCA
1 GTCCAATATCGCTGGCCTTGAATCAGCA
1352984 CATTATCATT
Statistics
Matches: 549, Mismatches: 99, Indels: 69
0.77 0.14 0.10
Matches are distributed among these distances:
86 31 0.06
87 1 0.00
88 103 0.19
89 9 0.02
90 39 0.07
91 1 0.00
92 140 0.26
93 9 0.02
94 33 0.06
95 1 0.00
96 1 0.00
98 42 0.08
99 73 0.13
101 66 0.12
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.31
Consensus pattern (93 bp):
GTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTCACCTTTAAGACCAATGTCGCTGG
CCTTGAATCAGCACATTGGCACCTTTAA
Found at i:1352847 original size:187 final size:187
Alignment explanation
Indices: 1352618--1352986 Score: 623
Period size: 187 Copynumber: 2.0 Consensus size: 187
1352608 GCTTTACCTT
* * *
1352618 TAAGACCAATGTCGCTGGCCTTGAATCAACACATTGGCACCTTCATCTTTAAGT-TCAATATTGT
1 TAAGACCAATGTCGCTGCCCTTGAATCAACACATTAGCACCTTCATCTTTAAGTCT-AATATCGT
1352682 TGGCCTTGAATCAGCATATTGGCATCTTTAACATTCCTAAGCCCAATGTCGCTAGCCTTGTCTCA
65 TGGCCTTGAATCAGCATATTGGCATCTTTAACATTCCTAAGCCCAATGTCGCTAGCCTTGTCTCA
* *
1352747 GCATATTGGCATTCTTCTTCAAGTCCAATGTCGCTGGCCTTGAATCAGCACATCGGCA
130 GCACATTGGCATTCTTCTTCAAGTCCAATGTCGCTGGCCATGAATCAGCACATCGGCA
* * *
1352805 TAAGACCAATGTTGCTGCCCTTGAATCAGCACATTAGCACCTTCATCTTTAAGTCTGATATCGTT
1 TAAGACCAATGTCGCTGCCCTTGAATCAACACATTAGCACCTTCATCTTTAAGTCTAATATCGTT
* *
1352870 GGCCTTGAATTAGCATATTGGCATCTTTAACATTCCTAAGCCCAATGTTGCTAGCCTTGTCTCAG
66 GGCCTTGAATCAGCATATTGGCATCTTTAACATTCCTAAGCCCAATGTCGCTAGCCTTGTCTCAG
*
1352935 CACATTGGCATTCTTCTTCAAGTCTAATGTCGCTGGCCATGAATCAGCACAT
131 CACATTGGCATTCTTCTTCAAGTCCAATGTCGCTGGCCATGAATCAGCACAT
1352987 TATCATTCTT
Statistics
Matches: 170, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
187 169 0.99
188 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (187 bp):
TAAGACCAATGTCGCTGCCCTTGAATCAACACATTAGCACCTTCATCTTTAAGTCTAATATCGTT
GGCCTTGAATCAGCATATTGGCATCTTTAACATTCCTAAGCCCAATGTCGCTAGCCTTGTCTCAG
CACATTGGCATTCTTCTTCAAGTCCAATGTCGCTGGCCATGAATCAGCACATCGGCA
Found at i:1353872 original size:13 final size:13
Alignment explanation
Indices: 1353854--1353879 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1353844 CATTATTCCA
1353854 TGTATCGATACAT
1 TGTATCGATACAT
1353867 TGTATCGATACAT
1 TGTATCGATACAT
1353880 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1355423 original size:13 final size:13
Alignment explanation
Indices: 1355405--1355430 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1355395 ACATTTTAGG
1355405 ATGTATCGATACA
1 ATGTATCGATACA
1355418 ATGTATCGATACA
1 ATGTATCGATACA
1355431 TATTGTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1355425 original size:33 final size:32
Alignment explanation
Indices: 1355383--1355450 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 32
1355373 CGTTACAAGC
*
1355383 CAATGTATCGATACATTTTAG-GATGTATCGATA
1 CAATGTATCGATACATATT-GTG-TGTATCGATA
1355416 CAATGTATCGATACATATTGTGTGTATCGATA
1 CAATGTATCGATACATATTGTGTGTATCGATA
1355448 CAA
1 CAA
1355451 ATTTGGCTAC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 14 0.42
33 19 0.58
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATATTGTGTGTATCGATA
Found at i:1355509 original size:20 final size:20
Alignment explanation
Indices: 1355484--1355534 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
1355474 CCAATGACCT
**
1355484 GTATCGATACATTTTTTCAA
1 GTATCGATACATTTGGTCAA
*
1355504 GTATCGATACATTTGGTCAT
1 GTATCGATACATTTGGTCAA
1355524 GTATCGATACA
1 GTATCGATACA
1355535 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (20 bp):
GTATCGATACATTTGGTCAA
Found at i:1355540 original size:13 final size:13
Alignment explanation
Indices: 1355522--1355546 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1355512 ACATTTGGTC
1355522 ATGTATCGATACA
1 ATGTATCGATACA
1355535 ATGTATCGATAC
1 ATGTATCGATAC
1355547 TATGCAATCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1357862 original size:20 final size:21
Alignment explanation
Indices: 1357833--1357873 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1357823 TGTTTTTGTT
1357833 GATGATTTTG-A-TGAAAAAC
1 GATGATTTTGAAGTGAAAAAC
1357852 GATGTATTTTGAAGTGAAAAAC
1 GATG-ATTTTGAAGTGAAAAAC
1357874 AAGAAATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 1 0.05
22 8 0.42
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (21 bp):
GATGATTTTGAAGTGAAAAAC
Found at i:1358023 original size:13 final size:13
Alignment explanation
Indices: 1358005--1358029 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1357995 ATAAACCCCT
1358005 TGTATCGATACAC
1 TGTATCGATACAC
1358018 TGTATCGATACA
1 TGTATCGATACA
1358030 GAGAATGCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:1361925 original size:52 final size:52
Alignment explanation
Indices: 1361847--1361975 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
1361837 CGAAATATGA
* *
1361847 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
* *
1361899 AAATTTGGCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
1361951 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1361976 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
Found at i:1361988 original size:52 final size:51
Alignment explanation
Indices: 1361847--1361995 Score: 210
Period size: 52 Copynumber: 2.9 Consensus size: 51
1361837 CGAAATATGA
*
1361847 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
* * *
1361899 AAATTTGGCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
*
1361951 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1361996 ATGTATCGAT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 85 0.98
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
Found at i:1362002 original size:13 final size:13
Alignment explanation
Indices: 1361984--1362008 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1361974 CAAAGATCAG
1361984 TGTATCGATACAA
1 TGTATCGATACAA
1361997 TGTATCGATACA
1 TGTATCGATACA
1362009 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Done.