Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008428.1 Hibiscus syriacus cultivar Beakdansim tig00111213_pilon, whole genome shotgun sequence
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: 6915314
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 24 of 30
Found at i:5466919 original size:267 final size:269
Alignment explanation
Indices: 5466512--5466998 Score: 775
Period size: 267 Copynumber: 1.8 Consensus size: 269
5466502 GAATCAGGGT
*
5466512 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAAACCTGTTCCGCTTAC
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTT-GAAAAGAGAAACCTGTTCCACTTAC
* * * *
5466577 TCTGAAGGGAATATCAGATCTGGGGAAGTTGATCCATTGAATCAGGGTAGACTTGTTCCACTTTC
65 TCTGAAGGGAATATCAGATCTGGAGAAGTTGATCCATTGAATCAGAGCAGACTTGTTCCACTTAC
* ***
5466642 TCTAAAGGGAATATCAAATCTTGGAAAAGAGAGACCTGTTCTGCTTACTCTGAAGGGAATATCAG
130 TCTAAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCAATTACTCTGAAGGGAATATCAG
*
5466707 ATCTGGGGAAGTTTATCCATTGAATCAGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAAT
195 ATCTGGGGAAGTTGATCCATTGAATCAGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAAT
5466772 CTTGGAGAAG
260 CTTGGAGAAG
* *
5466782 AGACTTGTTCCGCTTACTCTGAAGGGAATATCAAATCTT--AAAGAAGAGACCTGTTCCACTTAC
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAAAAG-AGAAACCTGTTCCACTTAC
5466845 TCTGAAGGGAATATCAGATCT-GAGAAGTTGATCCATTGAATC-GAAGCAGACTTGTTCCACTTA
65 TCTGAAGGGAATATCAGATCTGGAGAAGTTGATCCATTGAATCAG-AGCAGACTTGTTCCACTTA
* *
5466908 CTCTGAAGGGAATATCAAATCTTGGAGAAGAGAGACATGTTCCAATTACTCTGAAGGGAATATCA
129 CTCTAAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCAATTACTCTGAAGGGAATATCA
* *
5466973 GCTCTGGGGGAGTTGATCCATTGAAT
194 GATCTGGGGAAGTTGATCCATTGAAT
5466999 TGGGATCAAA
Statistics
Matches: 199, Mismatches: 16, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
266 1 0.01
267 122 0.61
268 38 0.19
270 38 0.19
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (269 bp):
AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAAAAGAGAAACCTGTTCCACTTACT
CTGAAGGGAATATCAGATCTGGAGAAGTTGATCCATTGAATCAGAGCAGACTTGTTCCACTTACT
CTAAAGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCAATTACTCTGAAGGGAATATCAGA
TCTGGGGAAGTTGATCCATTGAATCAGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATC
TTGGAGAAG
Found at i:5468130 original size:17 final size:16
Alignment explanation
Indices: 5468097--5468149 Score: 65
Period size: 17 Copynumber: 3.3 Consensus size: 16
5468087 CATCCTTTTA
5468097 TTTTTTTC-TTTTC-T
1 TTTTTTTCTTTTTCAT
5468111 TTTTTTTCATTTTTCAT
1 TTTTTTTC-TTTTTCAT
*
5468128 TTTTTAGTCTTTTTCAT
1 TTTTT-TTCTTTTTCAT
5468145 TTTTT
1 TTTTT
5468150 AGGCGAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
14 8 0.24
16 5 0.15
17 19 0.56
18 2 0.06
ACGTcount: A:0.08, C:0.11, G:0.02, T:0.79
Consensus pattern (16 bp):
TTTTTTTCTTTTTCAT
Found at i:5476456 original size:32 final size:33
Alignment explanation
Indices: 5476410--5476477 Score: 129
Period size: 32 Copynumber: 2.1 Consensus size: 33
5476400 AACTATCATT
5476410 ACCGCACCCTAAAAAGTATGTCCTCTTTAGGTA
1 ACCGCACCCTAAAAAGTATGTCCTCTTTAGGTA
5476443 ACCGCA-CCTAAAAAGTATGTCCTCTTTAGGTA
1 ACCGCACCCTAAAAAGTATGTCCTCTTTAGGTA
5476475 ACC
1 ACC
5476478 AATAAGCCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 29 0.83
33 6 0.17
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (33 bp):
ACCGCACCCTAAAAAGTATGTCCTCTTTAGGTA
Found at i:5480791 original size:32 final size:32
Alignment explanation
Indices: 5480709--5480807 Score: 110
Period size: 32 Copynumber: 3.1 Consensus size: 32
5480699 AACAGAAAGC
* * *
5480709 AACCAGAATCAAAATTAACCTGAACTGAAA-T
1 AACCTGAATCAAAATCAACCAGAACTGAAATT
* * *
5480740 AACCTGAACCAAAACCAACCCGAACTGAAATT
1 AACCTGAATCAAAATCAACCAGAACTGAAATT
* **
5480772 AACTTGAATCAAAATCAACCAGAACCAAAATT
1 AACCTGAATCAAAATCAACCAGAACTGAAATT
5480804 AACC
1 AACC
5480808 CGAACTAAAA
Statistics
Matches: 55, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
31 25 0.45
32 30 0.55
ACGTcount: A:0.51, C:0.25, G:0.08, T:0.16
Consensus pattern (32 bp):
AACCTGAATCAAAATCAACCAGAACTGAAATT
Found at i:5480800 original size:16 final size:16
Alignment explanation
Indices: 5480708--5480823 Score: 72
Period size: 16 Copynumber: 7.3 Consensus size: 16
5480698 AAACAGAAAG
* *
5480708 CAACCAGAATCAAAAT
1 CAACCTGAACCAAAAT
* **
5480724 TAACCTGAACTGAAAT
1 CAACCTGAACCAAAAT
*
5480740 -AACCTGAACCAAAAC
1 CAACCTGAACCAAAAT
* **
5480755 CAACCCGAACTGAAAT
1 CAACCTGAACCAAAAT
* * *
5480771 TAACTTGAATCAAAAT
1 CAACCTGAACCAAAAT
*
5480787 CAACCAGAACCAAAAT
1 CAACCTGAACCAAAAT
* * * *
5480803 TAACCCGAACTAAAAA
1 CAACCTGAACCAAAAT
5480819 CAACC
1 CAACC
5480824 CAAACCGATA
Statistics
Matches: 72, Mismatches: 27, Indels: 2
0.71 0.27 0.02
Matches are distributed among these distances:
15 12 0.17
16 60 0.83
ACGTcount: A:0.51, C:0.27, G:0.08, T:0.15
Consensus pattern (16 bp):
CAACCTGAACCAAAAT
Found at i:5482126 original size:32 final size:31
Alignment explanation
Indices: 5482090--5482184 Score: 91
Period size: 32 Copynumber: 2.9 Consensus size: 31
5482080 ATCCAAACCG
*
5482090 AAAATCAACTGATCTGATATTGACCCGACCCA
1 AAAATCAA-TGATCCGATATTGACCCGACCCA
* * * *
5482122 AAAATCAATTGATCCAATATTGATCCGAACCG
1 AAAATCAA-TGATCCGATATTGACCCGACCCA
* *
5482154 AAAACCAATCGATCCGAAAATTGACCCGACC
1 AAAATCAAT-GATCCG-ATATTGACCCGACC
5482185 AGATACCCGA
Statistics
Matches: 50, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
31 1 0.02
32 38 0.76
33 11 0.22
ACGTcount: A:0.40, C:0.27, G:0.13, T:0.20
Consensus pattern (31 bp):
AAAATCAATGATCCGATATTGACCCGACCCA
Found at i:5484518 original size:22 final size:22
Alignment explanation
Indices: 5484466--5484518 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
5484456 TTAGCACTCG
* *
5484466 TACTAAAGTGCCTTGACAGTGA
1 TACTAAAGTGCATTAACAGTGA
** * *
5484488 TACGGAAGTGTATTAACATTGA
1 TACTAAAGTGCATTAACAGTGA
5484510 TACTAAAGT
1 TACTAAAGT
5484519 TCCTAAGGCA
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (22 bp):
TACTAAAGTGCATTAACAGTGA
Found at i:5484566 original size:2 final size:2
Alignment explanation
Indices: 5484559--5484597 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
5484549 TACTTCTCGT
*
5484559 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AT AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
5484598 TACATTACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.46, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:5487824 original size:3 final size:3
Alignment explanation
Indices: 5487810--5487847 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
5487800 AAATATGTAA
*
5487810 AAT AAT ATT AAT AAT AAT AAT ACAT -AT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AA
5487848 GAACGAGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.87
4 2 0.06
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:5488151 original size:48 final size:48
Alignment explanation
Indices: 5488083--5488467 Score: 406
Period size: 48 Copynumber: 8.3 Consensus size: 48
5488073 CCGCTGTCAC
* * * * ** *
5488083 AGGGAATACCAAACCTTGGAAAAAAGAGATATGTTCCGCTT-CTTCTGA
1 AGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTAC-TCTGA
* *
5488131 AGGGAATATCAAATCATGGA-AAAAGAGACCTGTTCCACTTACTCTGA
1 AGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTGA
* * * *
5488178 AGGGAATGTCAGATC-T---G--G-TAGACTTGTTCCACTTACTCTGA
1 AGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTGA
*
5488219 AGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCGCTTACTCTGA
1 AGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTGA
* * * **
5488267 AGGAAATATCAGATCTTGGAGAAGATAGATTTGTTCCACTTACTCTGA
1 AGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTGA
* *
5488315 AGGGAATATCAAATCTTTGAGAAGAGAGACCTGTTCCGCTTACTCTGA
1 AGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTGA
* * * *
5488363 AGGGAATATCAGATC-T---G--G-CAGACTTGTTCCACTTACTCTAA
1 AGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTGA
*
5488404 AGAGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTGA
1 AGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTGA
*
5488452 AGGGAATATCAGATCT
1 AGGGAATATCAAATCT
5488468 GGGGGAGTTG
Statistics
Matches: 280, Mismatches: 41, Indels: 32
0.79 0.12 0.09
Matches are distributed among these distances:
41 66 0.24
42 3 0.01
44 1 0.00
45 2 0.01
46 1 0.00
47 38 0.14
48 169 0.60
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (48 bp):
AGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTGA
Found at i:5488269 original size:89 final size:89
Alignment explanation
Indices: 5488126--5488469 Score: 519
Period size: 89 Copynumber: 3.8 Consensus size: 89
5488116 TTCCGCTTCT
* * *
5488126 TCTGAAGGGAATATCAAATCATGGA-AAAAGAGACCTGTTCCACTTACTCTGAAGGGAATGTCAG
1 TCTGAAGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTGAAGGGAATATCAG
5488190 ATCTGGTAGACTTGTTCCACTTAC
66 ATCTGGTAGACTTGTTCCACTTAC
* *
5488214 TCTGAAGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCGCTTACTCTGAAGGAAATATCAG
1 TCTGAAGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTGAAGGGAATATCAG
*
5488279 ATCTTGGAGAAGATAGATTTGTTCCACTTAC
66 ATC-T---G--G-TAGACTTGTTCCACTTAC
* *
5488310 TCTGAAGGGAATATCAAATCTTTGAGAAGAGAGACCTGTTCCGCTTACTCTGAAGGGAATATCAG
1 TCTGAAGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTGAAGGGAATATCAG
*
5488375 ATCTGGCAGACTTGTTCCACTTAC
66 ATCTGGTAGACTTGTTCCACTTAC
* *
5488399 TCTAAAGAGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTGAAGGGAATATCAG
1 TCTGAAGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTGAAGGGAATATCAG
5488464 ATCTGG
66 ATCTGG
5488470 GGGAGTTGAT
Statistics
Matches: 234, Mismatches: 14, Indels: 15
0.89 0.05 0.06
Matches are distributed among these distances:
88 24 0.10
89 121 0.52
90 2 0.01
92 1 0.00
93 1 0.00
95 2 0.01
96 83 0.35
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.27
Consensus pattern (89 bp):
TCTGAAGGGAATATCAAATCTTGGAGAAGAGAGACCTGTTCCACTTACTCTGAAGGGAATATCAG
ATCTGGTAGACTTGTTCCACTTAC
Found at i:5488359 original size:185 final size:184
Alignment explanation
Indices: 5488109--5488467 Score: 585
Period size: 185 Copynumber: 1.9 Consensus size: 184
5488099 TGGAAAAAAG
*
5488109 AGATATGTTCCGCTTCTTCTGAAGGGAATATCAAATCATGGAAAAAGAGACCTGTTCCACTTACT
1 AGATATGTTCCACTTCTTCTGAAGGGAATATCAAATCATGGAAAAAGAGACCTGTTCCACTTACT
* * * *
5488174 CTGAAGGGAATGTCAGATCTGGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGA
66 CTGAAGGGAATATCAGATCTGGCAGACTTGTTCCACTTACTCTAAAGAGAATATCAAATCTTGGA
*
5488239 GAAGAGAGACCTGTTCCGCTTACTCTGAAGGAAATATCAGATCTTGGAGAAGAT
131 GAAGAGAGACCTGTTCCACTTACTCTGAAGGAAATATCAGATCTTGGAGAAGAT
* * * * *
5488293 AGATTTGTTCCACTTAC-TCTGAAGGGAATATCAAATCTTTGAGAAGAGAGACCTGTTCCGCTTA
1 AGATATGTTCCACTT-CTTCTGAAGGGAATATCAAATCATGGA-AAAAGAGACCTGTTCCACTTA
5488357 CTCTGAAGGGAATATCAGATCTGGCAGACTTGTTCCACTTACTCTAAAGAGAATATCAAATCTTG
64 CTCTGAAGGGAATATCAGATCTGGCAGACTTGTTCCACTTACTCTAAAGAGAATATCAAATCTTG
*
5488422 GAGAAGAGAGACCTGTTCCACTTACTCTGAAGGGAATATCAGATCT
129 GAGAAGAGAGACCTGTTCCACTTACTCTGAAGGAAATATCAGATCT
5488468 GGGGGAGTTG
Statistics
Matches: 161, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
184 36 0.22
185 125 0.78
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (184 bp):
AGATATGTTCCACTTCTTCTGAAGGGAATATCAAATCATGGAAAAAGAGACCTGTTCCACTTACT
CTGAAGGGAATATCAGATCTGGCAGACTTGTTCCACTTACTCTAAAGAGAATATCAAATCTTGGA
GAAGAGAGACCTGTTCCACTTACTCTGAAGGAAATATCAGATCTTGGAGAAGAT
Found at i:5489652 original size:26 final size:27
Alignment explanation
Indices: 5489604--5489664 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
5489594 CCTCCTTTTA
*
5489604 TTTTTTTC-TTTTCTTTCTCTTTC-TT
1 TTTTTTTCATTTTCTGTCTCTTTCATT
*
5489629 TTATTTTTCATTTT-TGTCTTTTTCATT
1 TT-TTTTTCATTTTCTGTCTCTTTCATT
5489656 TTTTTTTCA
1 TTTTTTTCA
5489665 AGCGAAATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 2 0.06
26 21 0.68
27 8 0.26
ACGTcount: A:0.07, C:0.15, G:0.02, T:0.77
Consensus pattern (27 bp):
TTTTTTTCATTTTCTGTCTCTTTCATT
Found at i:5502842 original size:3 final size:3
Alignment explanation
Indices: 5502828--5502868 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
5502818 CAAATATGTA
*
5502828 AAT AAT ATT AAT AAT AAT AAT AAT ACAT -AT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AA
5502869 GAACGAGATG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 30 0.88
4 2 0.06
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:5504591 original size:21 final size:21
Alignment explanation
Indices: 5504517--5504636 Score: 95
Period size: 21 Copynumber: 5.8 Consensus size: 21
5504507 TATCAAACTC
*
5504517 CTGGTATAGATACACAA-T-AT
1 CTGGTATGGATAC-CAACTCAT
* * *
5504537 TTGGCATGGATACCAACACAT
1 CTGGTATGGATACCAACTCAT
*
5504558 CTAGG-ATGAATACCAACTCAT
1 CT-GGTATGGATACCAACTCAT
** *
5504579 CTTTTATGGATACCAATTCAT
1 CTGGTATGGATACCAACTCAT
5504600 CTGGTATGGATACCAACTC-T
1 CTGGTATGGATACCAACTCAT
* **
5504620 CTGTTATCAATACCAAC
1 CTGGTATGGATACCAAC
5504637 GTTTTGGTAT
Statistics
Matches: 79, Mismatches: 17, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
19 3 0.04
20 25 0.32
21 49 0.62
22 2 0.03
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (21 bp):
CTGGTATGGATACCAACTCAT
Found at i:5504601 original size:42 final size:41
Alignment explanation
Indices: 5504542--5504636 Score: 111
Period size: 42 Copynumber: 2.3 Consensus size: 41
5504532 AATATTTGGC
*
5504542 ATGGATACCAACACATCTAGG-ATGAATACCAACTCATCTTTT
1 ATGGATACCAACACATCT-GGTATGAATACCAACTC-TCTGTT
** *
5504584 ATGGATACCAATTCATCTGGTATGGATACCAACTCTCTGTT
1 ATGGATACCAACACATCTGGTATGAATACCAACTCTCTGTT
**
5504625 ATCAATACCAAC
1 ATGGATACCAAC
5504637 GTTTTGGTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
41 16 0.36
42 29 0.64
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.29
Consensus pattern (41 bp):
ATGGATACCAACACATCTGGTATGAATACCAACTCTCTGTT
Found at i:5507611 original size:24 final size:24
Alignment explanation
Indices: 5507584--5507653 Score: 122
Period size: 24 Copynumber: 2.9 Consensus size: 24
5507574 TGCATGACAT
5507584 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
*
5507608 TGTACATAGATATTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
*
5507632 TGTATATAGATGTTTTATACAT
1 TGTACATAGATGTTTTATACAT
5507654 TATCAGGAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.44
Consensus pattern (24 bp):
TGTACATAGATGTTTTATACATCA
Found at i:5508404 original size:18 final size:18
Alignment explanation
Indices: 5508381--5508420 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
5508371 TATATACTTA
5508381 GCGTGTGATGATTTTCAC
1 GCGTGTGATGATTTTCAC
*
5508399 GCGTGTGTTGATTTTCAC
1 GCGTGTGATGATTTTCAC
5508417 GCGT
1 GCGT
5508421 AGGTAAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.12, C:0.17, G:0.30, T:0.40
Consensus pattern (18 bp):
GCGTGTGATGATTTTCAC
Found at i:5508683 original size:5 final size:5
Alignment explanation
Indices: 5508673--5508703 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
5508663 TGTGATAATT
5508673 TGATA TGATA TGATA TGATA TGATA TGATA T
1 TGATA TGATA TGATA TGATA TGATA TGATA T
5508704 TTTTATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.19, T:0.42
Consensus pattern (5 bp):
TGATA
Found at i:5509474 original size:170 final size:170
Alignment explanation
Indices: 5509192--5509534 Score: 686
Period size: 170 Copynumber: 2.0 Consensus size: 170
5509182 CATATATTCT
5509192 AATCTCATCCTTTTCTTTTAAATAATTGAAGATCGTCTGAGCTAAACGTTAACTTGCTGACTAGG
1 AATCTCATCCTTTTCTTTTAAATAATTGAAGATCGTCTGAGCTAAACGTTAACTTGCTGACTAGG
5509257 ATATTATAAAACCATATTCTGATGATGTCTACTGGAACCATCGTTGCTTTTAAACACTAGTTTGA
66 ATATTATAAAACCATATTCTGATGATGTCTACTGGAACCATCGTTGCTTTTAAACACTAGTTTGA
5509322 CGACATAATGTTTCAAGCACTGACTCAATAATATAATATA
131 CGACATAATGTTTCAAGCACTGACTCAATAATATAATATA
5509362 AATCTCATCCTTTTCTTTTAAATAATTGAAGATCGTCTGAGCTAAACGTTAACTTGCTGACTAGG
1 AATCTCATCCTTTTCTTTTAAATAATTGAAGATCGTCTGAGCTAAACGTTAACTTGCTGACTAGG
5509427 ATATTATAAAACCATATTCTGATGATGTCTACTGGAACCATCGTTGCTTTTAAACACTAGTTTGA
66 ATATTATAAAACCATATTCTGATGATGTCTACTGGAACCATCGTTGCTTTTAAACACTAGTTTGA
5509492 CGACATAATGTTTCAAGCACTGACTCAATAATATAATATA
131 CGACATAATGTTTCAAGCACTGACTCAATAATATAATATA
5509532 AAT
1 AAT
5509535 GGATCCATAA
Statistics
Matches: 173, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
170 173 1.00
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.35
Consensus pattern (170 bp):
AATCTCATCCTTTTCTTTTAAATAATTGAAGATCGTCTGAGCTAAACGTTAACTTGCTGACTAGG
ATATTATAAAACCATATTCTGATGATGTCTACTGGAACCATCGTTGCTTTTAAACACTAGTTTGA
CGACATAATGTTTCAAGCACTGACTCAATAATATAATATA
Found at i:5517780 original size:29 final size:29
Alignment explanation
Indices: 5517711--5517785 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 29
5517701 AAAATATTTC
*
5517711 AATTTCATCCCTAAACTATAAAAATATTCT
1 AATTTCAT-CCTAAACTATAAAAACATTCT
* **
5517741 AAATT-AGTCCTTAAACT-TTTAAACATTCT
1 AATTTCA-TCC-TAAACTATAAAAACATTCT
5517770 AATTTCATCCTAAACT
1 AATTTCATCCTAAACT
5517786 GTATGTATAC
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
28 6 0.16
29 19 0.51
30 12 0.32
ACGTcount: A:0.40, C:0.20, G:0.01, T:0.39
Consensus pattern (29 bp):
AATTTCATCCTAAACTATAAAAACATTCT
Found at i:5525056 original size:6 final size:6
Alignment explanation
Indices: 5525045--5525207 Score: 209
Period size: 6 Copynumber: 27.2 Consensus size: 6
5525035 TCGGGAATGC
* *
5525045 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGCG TATGCG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
* * * * * * * *
5525093 TATGCG TATGCG TATGCG TATGCG TATGCG TATGCG TATGCG TATGCG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
* * *
5525141 TATGCG TATGCG TATGTG TATGTG TATGTA TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
5525189 TATGTG TATGTG TATGTG T
1 TATGTG TATGTG TATGTG T
5525208 TTGGTTTAGT
Statistics
Matches: 153, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 153 1.00
ACGTcount: A:0.17, C:0.07, G:0.33, T:0.43
Consensus pattern (6 bp):
TATGTG
Found at i:5526962 original size:16 final size:17
Alignment explanation
Indices: 5526941--5526983 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
5526931 ATGTAAAAAT
5526941 AAATATTTAAATTTA-A
1 AAATATTTAAATTTATA
** *
5526957 AAATATAAAAATTTATT
1 AAATATTTAAATTTATA
5526974 AAATATTTAA
1 AAATATTTAA
5526984 TTAAATAAAG
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATATTTAAATTTATA
Found at i:5529708 original size:13 final size:13
Alignment explanation
Indices: 5529664--5529710 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
5529654 CTGTTCTTTG
*
5529664 ATATTGAAAACTAA
1 ATATTTAAAA-TAA
5529678 ATA-TTAAAATAA
1 ATATTTAAAATAA
*
5529690 TTTATTTAAAATAA
1 -ATATTTAAAATAA
5529704 ATATTTA
1 ATATTTA
5529711 TTTATTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 3 0.11
13 13 0.46
14 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (13 bp):
ATATTTAAAATAA
Found at i:5530967 original size:14 final size:15
Alignment explanation
Indices: 5530948--5530977 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
5530938 GGGCTTTGTA
5530948 ATTTAATAT-TATTT
1 ATTTAATATATATTT
5530962 ATTTAATATATATTT
1 ATTTAATATATATTT
5530977 A
1 A
5530978 ATAATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTAATATATATTT
Found at i:5530984 original size:3 final size:3
Alignment explanation
Indices: 5530976--5531038 Score: 99
Period size: 3 Copynumber: 20.7 Consensus size: 3
5530966 AATATATATT
*
5530976 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
5531024 TAA TAT TATA TAA TA
1 TAA TAA TA-A TAA TA
5531039 TGGGTAAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
3 53 0.96
4 2 0.04
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:5531691 original size:229 final size:229
Alignment explanation
Indices: 5531354--5532596 Score: 2162
Period size: 229 Copynumber: 5.4 Consensus size: 229
5531344 GATAGAATTA
*
5531354 TTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTAT
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTAT
* * * * * * *
5531419 GAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCT
63 GAACT-TTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAATTCT
*
5531483 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTT-TCTG
127 TCTCATTATGAACTTTTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAAC-CTTCTCTG
*** * * *
5531547 GCAATGTTGATCCATCAAATGATGAATTCAAACAAAAAG
191 GCAAAAATAATCCATCAAGTGATGAATTCAGACAAAAAG
*
5531586 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
5531651 CTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAATTCTTCTC
66 CTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAATTCTTCTC
*
5531716 ATTATGAACTTTTTCTTCCTTCTTCAGATGACGAGTTCTTCTCA-T-T--ACCTTCTTTGGC-AA
131 ATTATGAACTTTTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACCTTCTCTGGCAAA
5531776 AATAATCCATCAAGTGATGAATTCAGACAAAAAG
196 AATAATCCATCAAGTGATGAATTCAGACAAAAAG
5531810 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
5531875 CTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAATTCTTCTC
66 CTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAATTCTTCTC
*
5531940 ATTATGAACTTTTTATTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACCTTCTCTGGCAAA
131 ATTATGAACTTTTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACCTTCTCTGGCAAA
*
5532005 AATAATCCATCAAGTGATGAATTCATACAAAAAG
196 AATAATCCATCAAGTGATGAATTCAGACAAAAAG
5532039 TTGAACAAGTTCTTCTCA-TATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
5532103 CTTTCTCT-GAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAATTCTTCTC
66 CTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAATTCTTCTC
5532167 ATTATGAACTTTTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACCTTCTCTGGCAAA
131 ATTATGAACTTTTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACCTTCTCTGGCAAA
5532232 AATAATCCATCAAGTGATGAATTCAGACAAAAAG
196 AATAATCCATCAAGTGATGAATTCAGACAAAAAG
5532266 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
5532331 CTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAATTCTTCTC
66 CTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAATTCTTCTC
*
5532396 ATTATGAACTTTTTCTTCCTTCTTCAGATGACGAGTTCTTCTTATTATGAACCTTCTCTGGCAAA
131 ATTATGAACTTTTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACCTTCTCTGGCAAA
*
5532461 AATAATCCATCAAGTGATGAATTCAGACAAAAGG
196 AATAATCCATCAAGTGATGAATTCAGACAAAAAG
* *
5532495 TTGAACAAATTCTTCTCATTATGAACTTCTTGTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
*
5532560 CTTTCTCTGGAAATGATGATCCATCAAATGATAGATT
66 CTTTCTCTGGAAATGATGATCCATCAAATGATGGATT
5532597 TGAATCTTTG
Statistics
Matches: 974, Mismatches: 28, Indels: 21
0.95 0.03 0.02
Matches are distributed among these distances:
224 205 0.21
225 8 0.01
226 1 0.00
227 172 0.18
228 122 0.13
229 422 0.43
232 44 0.05
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (229 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
CTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAATTCTTCTC
ATTATGAACTTTTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACCTTCTCTGGCAAA
AATAATCCATCAAGTGATGAATTCAGACAAAAAG
Found at i:5531702 original size:113 final size:114
Alignment explanation
Indices: 5531354--5532591 Score: 1683
Period size: 116 Copynumber: 10.9 Consensus size: 114
5531344 GATAGAATTA
*
5531354 TTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTAT
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-A-GAGTTCTTCTCATTAT
* * * *
5531419 GAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGA
64 GAACT-TTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCAAAAGG
5531470 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTAT
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-A-GAGTTCTTCTCATTAT
* * * *
5531535 GAACTCTT-TCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAAG
64 GAACT-TTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCAAAAGG
*
5531586 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGAT-GAGTTCTTCTCATTATGA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGA
* *
5531650 ACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGG
66 ACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCAAAAGG
* *
5531699 TTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGACGAGTTCTTCTCA-T-T
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-A-GAGTTCTTCTCATTAT
* * * * *
5531762 --ACCTTCTTTGGCAAA--ATAATCCATCAAGTGATGAATTC-AGACAAAAAG
64 GAACTTTCTCTGG-AAATGATGATCCATCAAATGATGAATTCAAG-CAAAAGG
5531810 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-GAGTTCTTCTCATTATGA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGA
* *
5531874 ACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGG
66 ACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCAAAAGG
* * *
5531923 TTGAACAAATTCTTCTCATTATGAACTTTTTATTCCTTCTTCAGATGACGAGTTCTTCTCATTAT
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-A-GAGTTCTTCTCATTAT
* * * * *
5531988 GAACCTTCTCTGGCAAA-AATAATCCATCAAGTGATGAATTCATA-CAAAAAG
64 GAACTTTCTCTGG-AAATGATGATCCATCAAATGATGAATTCA-AGCAAAAGG
5532039 TTGAACAAGTTCTTCTCA-TATGAACTTCTTCTTCCTTCTTCAGAT-GAGTTCTTCTCATTATGA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGA
* *
5532102 ACTTTCTCT-GAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGG
66 ACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCAAAAGG
* *
5532150 TTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTAT
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-A-GAGTTCTTCTCATTAT
* * * * *
5532215 GAACCTTCTCTGGCAAA-AATAATCCATCAAGTGATGAATTC-AGACAAAAAG
64 GAACTTTCTCTGG-AAATGATGATCCATCAAATGATGAATTCAAG-CAAAAGG
5532266 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-GAGTTCTTCTCATTATGA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGA
* *
5532330 ACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGG
66 ACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCAAAAGG
* * *
5532379 TTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGACGAGTTCTTCTTATTAT
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-A-GAGTTCTTCTCATTAT
* * * *
5532444 GAACCTTCTCTGGCAAA-AATAATCCATCAAGTGATGAATTC-AGACAAAAGG
64 GAACTTTCTCTGG-AAATGATGATCCATCAAATGATGAATTCAAG-CAAAAGG
* *
5532495 TTGAACAAATTCTTCTCATTATGAACTTCTTGTTCCTTCTTCAGAT-GAGTTCTTCTCATTATGA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGA
5532559 ACTTTCTCTGGAAATGATGATCCATCAAATGAT
66 ACTTTCTCTGGAAATGATGATCCATCAAATGAT
5532592 AGATTTGAAT
Statistics
Matches: 1001, Mismatches: 85, Indels: 75
0.86 0.07 0.06
Matches are distributed among these distances:
108 12 0.01
109 1 0.00
110 7 0.01
111 116 0.12
112 78 0.08
113 311 0.31
114 5 0.00
115 56 0.06
116 405 0.40
117 10 0.01
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (114 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGA
ACTTTCTCTGGAAATGATGATCCATCAAATGATGAATTCAAGCAAAAGG
Found at i:5533547 original size:83 final size:83
Alignment explanation
Indices: 5533366--5533884 Score: 968
Period size: 83 Copynumber: 6.2 Consensus size: 83
5533356 CTTATTTCTA
* * * *
5533366 CTATGAGCAAATTCATCTTCCAAATTCAATAATTGGTTCTGTCCAACCAGATCAGAATAACTCAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAG-ATAACTCAA
5533431 AGAACACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
5533450 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
5533515 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
5533533 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
5533598 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
5533616 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
5533681 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
5533699 CTATGAGCACATTCATGTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
5533764 GAACACTTCCTA-AAGATG
66 GAACACTTCC-AGAAGATG
5533782 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
5533847 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
5533865 CTATGAGCACATTCATCTTC
1 CTATGAGCACATTCATCTTC
5533885 CACACTATAA
Statistics
Matches: 427, Mismatches: 6, Indels: 5
0.97 0.01 0.01
Matches are distributed among these distances:
82 1 0.00
83 374 0.88
84 52 0.12
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (83 bp):
CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:5543969 original size:13 final size:13
Alignment explanation
Indices: 5543925--5543971 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
5543915 CTGTTCTTTG
*
5543925 ATATTGAAAACTAA
1 ATATTTAAAA-TAA
5543939 ATA-TTAAAATAA
1 ATATTTAAAATAA
*
5543951 TTTATTTAAAATAA
1 -ATATTTAAAATAA
5543965 ATATTTA
1 ATATTTA
5543972 TTTATTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 3 0.11
13 13 0.46
14 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (13 bp):
ATATTTAAAATAA
Found at i:5545355 original size:14 final size:15
Alignment explanation
Indices: 5545336--5545365 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
5545326 GGGCTTTGTA
5545336 ATTTAATAT-TATTT
1 ATTTAATATATATTT
5545350 ATTTAATATATATTT
1 ATTTAATATATATTT
5545365 A
1 A
5545366 ATAATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTAATATATATTT
Found at i:5545372 original size:3 final size:3
Alignment explanation
Indices: 5545364--5545443 Score: 124
Period size: 3 Copynumber: 26.7 Consensus size: 3
5545354 AATATATATT
* *
5545364 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
5545412 TGA TAA TAA TAA TAA TAA TAA TAA TTA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5545444 TGGGTAAAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:5547304 original size:139 final size:139
Alignment explanation
Indices: 5547153--5547500 Score: 386
Period size: 138 Copynumber: 2.5 Consensus size: 139
5547143 CCCTAATTGA
* * * * * *
5547153 TTTAACCAATTATTGAACCAAATAAAT-GAAATGGACCCTCGGGCATTAAGGCGAGGGCCAAATC
1 TTTAACCAATTATTGAATCGAAT-AATCGAAATGGACACTCAGGCATTAAGGCGAAGGACAAATC
*
5547217 AAATATTCCCCTAAATTAAAGGACT-AAAGTGAAATTAAGCCTAAAAT-GAATGCTCTAATATTA
65 AAATATT-CCCTAAATTAAAGGACTAAAAGTGAAATTAAGCCTAAAATAG-AGGCTCTAATATTA
5547280 ATCATAATCAT-T
128 ATCATAAT-ATAT
* * * ** * *
5547292 TTTAGCCAATTATTGGATCGAATAATCGAAATGAACACTCAAAC-TTAAGGCGAAAGATAAAT-A
1 TTTAACCAATTATTGAATCGAATAATCGAAATGGACACTCAGGCATTAAGGCGAAGGACAAATCA
* *
5547355 GAATATTCCCTAAATTAAAGGACTAAAAGTGAAATTAAGCCTAAAATAGAGGCTTTAATGTTAAT
66 -AATATTCCCTAAATTAAAGGACTAAAAGTGAAATTAAGCCTAAAATAGAGGCTCTAATATTAAT
* *
5547420 CCTAATTTAT
130 CATAATATAT
* * * * *
5547430 TTTAACCAATTATTGAATTGGATAATCAAAATGGACACT-ATGGCATTAAGGCGATGGTCAAATC
1 TTTAACCAATTATTGAATCGAATAATCGAAATGGACACTCA-GGCATTAAGGCGAAGGACAAATC
5547494 AAATATT
65 AAATATT
5547501 TTTTAATTTT
Statistics
Matches: 171, Mismatches: 30, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
137 20 0.12
138 98 0.57
139 52 0.30
140 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (139 bp):
TTTAACCAATTATTGAATCGAATAATCGAAATGGACACTCAGGCATTAAGGCGAAGGACAAATCA
AATATTCCCTAAATTAAAGGACTAAAAGTGAAATTAAGCCTAAAATAGAGGCTCTAATATTAATC
ATAATATAT
Found at i:5559986 original size:20 final size:20
Alignment explanation
Indices: 5559961--5559999 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5559951 TTTATAAAAT
*
5559961 ATTTTATAGCTATTATTTAC
1 ATTTTATAACTATTATTTAC
5559981 ATTTTATAACTATTATTTA
1 ATTTTATAACTATTATTTA
5560000 TGTTTATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (20 bp):
ATTTTATAACTATTATTTAC
Found at i:5562640 original size:69 final size:70
Alignment explanation
Indices: 5562538--5562677 Score: 273
Period size: 69 Copynumber: 2.0 Consensus size: 70
5562528 GATTTATTGC
5562538 TCCTACTGTTTCCCTTAATTAATCAAATTTTAAAAAAATTATTATTTTTTTGGGTGTTGTATTTA
1 TCCTACTGTTTCCCTTAATTAATCAAATTTTAAAAAAATTATTATTTTTTTGGGTGTTGTATTTA
5562603 ACTAA
66 ACTAA
5562608 TCCTA-TGTTTCCCTTAATTAATCAAATTTTAAAAAAATTATTATTTTTTTGGGTGTTGTATTTA
1 TCCTACTGTTTCCCTTAATTAATCAAATTTTAAAAAAATTATTATTTTTTTGGGTGTTGTATTTA
5562672 ACTAA
66 ACTAA
5562677 T
1 T
5562678 TTTATTTTTC
Statistics
Matches: 70, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
69 65 0.93
70 5 0.07
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.49
Consensus pattern (70 bp):
TCCTACTGTTTCCCTTAATTAATCAAATTTTAAAAAAATTATTATTTTTTTGGGTGTTGTATTTA
ACTAA
Found at i:5563517 original size:26 final size:26
Alignment explanation
Indices: 5563481--5563547 Score: 116
Period size: 26 Copynumber: 2.6 Consensus size: 26
5563471 TTAGGGTTAT
* *
5563481 AGACCCTTAGCGGTGTACTCATGGCG
1 AGACCCTTAGCAGAGTACTCATGGCG
5563507 AGACCCTTAGCAGAGTACTCATGGCG
1 AGACCCTTAGCAGAGTACTCATGGCG
5563533 AGACCCTTAGCAGAG
1 AGACCCTTAGCAGAG
5563548 GATTAAGGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.25, C:0.27, G:0.28, T:0.19
Consensus pattern (26 bp):
AGACCCTTAGCAGAGTACTCATGGCG
Found at i:5569520 original size:105 final size:105
Alignment explanation
Indices: 5569329--5569557 Score: 314
Period size: 105 Copynumber: 2.2 Consensus size: 105
5569319 GTGAAAGAGT
*
5569329 TATTGATAATAGTGTTGAACATTTGGTCACTAAAAAACACCTAGTGTGACAACATTGGTGGTCAC
1 TATTGATAATAGTGTTGAACATTTGGTCACTAAAAAACACCTAGTGTGACAACATTGATGGTCAC
* * *
5569394 AAAATATACTTTAAGTATCAAAGAAATTTATCACAATTTC
66 AAAATATAATTTAAGTATCAAAGAAATTCATCACAATTTA
* * ** * * * *
5569434 TATTGATAATAGTATTGAACATTTGGTCATTAAAAATTACTTGGTGTGACAATATTGATTGTCAC
1 TATTGATAATAGTGTTGAACATTTGGTCACTAAAAAACACCTAGTGTGACAACATTGATGGTCAC
* * *
5569499 AAAATATAATTTTAGTGTCAAATAAATTCATCACAATTTA
66 AAAATATAATTTAAGTATCAAAGAAATTCATCACAATTTA
*
5569539 TATTGATAATTGTGTTGAA
1 TATTGATAATAGTGTTGAA
5569558 TAGATGACCA
Statistics
Matches: 107, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
105 107 1.00
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (105 bp):
TATTGATAATAGTGTTGAACATTTGGTCACTAAAAAACACCTAGTGTGACAACATTGATGGTCAC
AAAATATAATTTAAGTATCAAAGAAATTCATCACAATTTA
Found at i:5570426 original size:13 final size:13
Alignment explanation
Indices: 5570401--5570434 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
5570391 AGCATTATGG
5570401 AAAGAAAAAAATA
1 AAAGAAAAAAATA
* *
5570414 AAATAAAATAATA
1 AAAGAAAAAAATA
5570427 AAAGAAAA
1 AAAGAAAA
5570435 GTGGAGATGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (13 bp):
AAAGAAAAAAATA
Found at i:5573498 original size:17 final size:16
Alignment explanation
Indices: 5573476--5573509 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
5573466 TAAAAACAGT
5573476 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
5573493 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
5573509 A
1 A
5573510 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:5575011 original size:193 final size:193
Alignment explanation
Indices: 5574638--5575026 Score: 721
Period size: 192 Copynumber: 2.0 Consensus size: 193
5574628 GCGACATTAC
5574638 TTCCCAAAGAATCTTTTTCTTGCTATCCCTGCACACCATAGACAAAGTGCACCTTTCCCTCAAAA
1 TTCCCAAAGAATCTTTTTCTTGCTATCCCTG-ACACCATAGACAAAGTGCACCTTTCCCTCAAAA
5574703 AGCACCATTAAGAAATAAAATAGCACAGCCACCACAAATGTAACTATATGCAACTACATGATCCT
65 AGCACCATTAAGAAATAAAATAGCACAGCCACCACAAATGTAACTATATGCAACTACATGATCCT
5574768 AAAATAACAAAATGAGCTTTTAAACAAACAATAACTTAAGTGAAAAAGGCTTTAAAAGTAGCCT
130 AAAATAACAAAATGAGCTTTTAAACAAACAATAACTTAAGTGAAAAAGGCTTTAAAAGTAGCCT
5574832 TTCCC-AAGAATCTTTTT-TTGCTATGCCCCTG-CACCATAGACAAAGTGCACCTTTCCCTCAAA
1 TTCCCAAAGAATCTTTTTCTTGCTAT--CCCTGACACCATAGACAAAGTGCACCTTTCCCTCAAA
5574894 AAGCACCATTAAGAAATAAAATAGCACAGCCACCACAAATGTAACTATATGCAACTACATGATCC
64 AAGCACCATTAAGAAATAAAATAGCACAGCCACCACAAATGTAACTATATGCAACTACATGATCC
5574959 TAAAATAACTAAAATGAGCTTTTAAACAAACAATAACTTAAGTGAAAAAGGCTTTAAAAGTAGCC
129 TAAAATAAC-AAAATGAGCTTTTAAACAAACAATAACTTAAGTGAAAAAGGCTTTAAAAGTAGCC
5575024 T
193 T
5575025 TT
1 TT
5575027 TTAGGAAGTT
Statistics
Matches: 192, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
192 112 0.58
193 70 0.36
194 10 0.05
ACGTcount: A:0.41, C:0.23, G:0.11, T:0.25
Consensus pattern (193 bp):
TTCCCAAAGAATCTTTTTCTTGCTATCCCTGACACCATAGACAAAGTGCACCTTTCCCTCAAAAA
GCACCATTAAGAAATAAAATAGCACAGCCACCACAAATGTAACTATATGCAACTACATGATCCTA
AAATAACAAAATGAGCTTTTAAACAAACAATAACTTAAGTGAAAAAGGCTTTAAAAGTAGCCT
Found at i:5577312 original size:19 final size:20
Alignment explanation
Indices: 5577290--5577332 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
5577280 AGAGAAAGGT
5577290 AAAAGTTAA-AATGAAAGAG
1 AAAAGTTAATAATGAAAGAG
* *
5577309 AAAA-TTAATAATTAAAGAT
1 AAAAGTTAATAATGAAAGAG
5577328 AAAAG
1 AAAAG
5577333 AAAATCTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.65, C:0.00, G:0.14, T:0.21
Consensus pattern (20 bp):
AAAAGTTAATAATGAAAGAG
Found at i:5577323 original size:25 final size:26
Alignment explanation
Indices: 5577277--5577337 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 26
5577267 ATGAATGAAA
**
5577277 GAAAGAGAAAGGTAAAAGTTAAA-AT
1 GAAAGAGAAAATTAAAAGTTAAAGAT
5577302 GAAAGAGAAAATTAATAA-TTAAAGAT
1 GAAAGAGAAAATTAA-AAGTTAAAGAT
5577328 -AAA-AGAAAAT
1 GAAAGAGAAAAT
5577338 CTTAAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 7 0.22
25 21 0.66
26 4 0.12
ACGTcount: A:0.64, C:0.00, G:0.18, T:0.18
Consensus pattern (26 bp):
GAAAGAGAAAATTAAAAGTTAAAGAT
Found at i:5583251 original size:18 final size:17
Alignment explanation
Indices: 5583228--5583262 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5583218 TAAAAACAGT
5583228 AAATAAAAAGATAAATAA
1 AAATAAAAAGA-AAATAA
*
5583246 AAATAAGAAGAAAATAA
1 AAATAAAAAGAAAATAA
5583263 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (17 bp):
AAATAAAAAGAAAATAA
Found at i:5591583 original size:9 final size:9
Alignment explanation
Indices: 5591569--5591593 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5591559 CAGCCCGCAT
5591569 ATTCTCCAC
1 ATTCTCCAC
5591578 ATTCTCCAC
1 ATTCTCCAC
5591587 ATTCTCC
1 ATTCTCC
5591594 CTACCATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.44, G:0.00, T:0.36
Consensus pattern (9 bp):
ATTCTCCAC
Found at i:5607484 original size:15 final size:16
Alignment explanation
Indices: 5607448--5607485 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
5607438 TTTTTATCAA
5607448 TTTAAATATTTAATAT
1 TTTAAATATTTAATAT
* *
5607464 TATAAATA-TTATTAT
1 TTTAAATATTTAATAT
5607479 TTTAAAT
1 TTTAAAT
5607486 GTCTAAACTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTAAATATTTAATAT
Found at i:5609688 original size:12 final size:12
Alignment explanation
Indices: 5609671--5609700 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5609661 ACAAACATGT
5609671 GCACGCACACTC
1 GCACGCACACTC
5609683 GCACGCACACTC
1 GCACGCACACTC
*
5609695 ACACGC
1 GCACGC
5609701 GTGCGCACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.50, G:0.17, T:0.07
Consensus pattern (12 bp):
GCACGCACACTC
Found at i:5609726 original size:2 final size:2
Alignment explanation
Indices: 5609721--5609752 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5609711 GTGTGTGTAT
5609721 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5609753 ACCTGTGGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5626080 original size:9 final size:10
Alignment explanation
Indices: 5626061--5626098 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
5626051 GGACCGGCTG
*
5626061 AAAACCGGGA
1 AAAACCGGAA
5626071 AAAACCGGAA
1 AAAACCGGAA
5626081 AAAACCGGAA
1 AAAACCGGAA
5626091 AAAACCGG
1 AAAACCGG
5626099 GATTTTTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.55, C:0.21, G:0.24, T:0.00
Consensus pattern (10 bp):
AAAACCGGAA
Found at i:5629619 original size:14 final size:14
Alignment explanation
Indices: 5629590--5629630 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
5629580 AAGTTCTAAG
*
5629590 AATAATAATAAAATA
1 AATAA-AATAATATA
5629605 AATAAAATAATATA
1 AATAAAATAATATA
5629619 AATAAAATAATA
1 AATAAAATAATA
5629631 AATGTAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 20 0.80
15 5 0.20
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AATAAAATAATATA
Found at i:5632878 original size:53 final size:53
Alignment explanation
Indices: 5632816--5633234 Score: 606
Period size: 53 Copynumber: 7.9 Consensus size: 53
5632806 TTCAACCAGT
*
5632816 GGGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTGCTTAC
1 GGGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTGCCTAC
* * *
5632869 GGGTTCGCTCCCTCTTGCTTCAAGGAATAGAACTC-AAAATATCTTCTTCCTAC
1 GGGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAACA-ATCTTCTGCCTAC
* *
5632922 GGGTTCACTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTGTCTAC
1 GGGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTGCCTAC
* * * * *
5632975 GAGTTTGCTCCTTTTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTTCCTAC
1 GGGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTGCCTAC
* * ** * **
5633028 GGGTTCGCTCCCTCTTACTTCAGGGCTTAGAACTCGAATAATCTTCTTTCTAC
1 GGGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTGCCTAC
* *
5633081 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCGAC
1 GGGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTGCCTAC
* *
5633134 GAGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTTCCTAC
1 GGGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTGCCTAC
* *
5633187 AGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
1 GGGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTG
5633235 GTGTGATTCT
Statistics
Matches: 323, Mismatches: 41, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
52 3 0.01
53 317 0.98
54 3 0.01
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.31
Consensus pattern (53 bp):
GGGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTGCCTAC
Found at i:5633668 original size:42 final size:42
Alignment explanation
Indices: 5633622--5634007 Score: 249
Period size: 42 Copynumber: 9.1 Consensus size: 42
5633612 AGACTCACAA
* *
5633622 ATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTATTG
1 ATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTG
* * *
5633664 ATGACCTGAATGATTTCATCATCATGATCGAAAGACTTACTG
1 ATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTG
** * * * **
5633706 AT-A---GATTTG-CTTCA-CTACTCTTCGGT-G-AAGACTTACCA
1 ATGACCCGA-AGGATTTCATC-A-TCAT-GCTCGAAAGACTTACTG
* *
5633744 ATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTG
1 ATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTG
* *
5633786 ATGGA-CCAAATGATTTCATCATCATGCTCGAAAGACTTACTG
1 AT-GACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTG
* * * **
5633828 ATGACACTTACTGACA-GATTTGCTTCA-CTACT-CTTCGGTGAAGGCTTACAA
1 ATGAC-C---C-GA-AGGATTT-CATCATC-A-TGC-TC-G-AAAGACTTACTG
* * * *
5633879 ATTACCCGAATGATTTAATCATCATGCTCGAAAGACTTACTA
1 ATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTG
* * *
5633921 AT-AGCCCAAAGGACTTCATCATCATGCTCGAAAGACTTATTG
1 ATGA-CCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTG
* *
5633963 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
1 ATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTG
5634005 ATG
1 ATG
5634008 GTACTTATTG
Statistics
Matches: 269, Mismatches: 44, Indels: 62
0.72 0.12 0.17
Matches are distributed among these distances:
37 1 0.00
38 18 0.07
39 7 0.03
40 4 0.01
41 9 0.03
42 176 0.65
43 4 0.01
44 3 0.01
45 6 0.02
46 9 0.03
47 8 0.03
48 7 0.03
49 3 0.01
50 2 0.01
51 12 0.04
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (42 bp):
ATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTG
Found at i:5633765 original size:122 final size:122
Alignment explanation
Indices: 5633612--5633964 Score: 447
Period size: 135 Copynumber: 2.8 Consensus size: 122
5633602 AAGGCTCGAG
* * * *
5633612 AGACTCACAAATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTATTGATGACCTGAATGA
1 AGACTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGACC-AAATGA
*
5633677 TTTCATCATCATGATCGAAAGACTTACTGAT-AGATTTGCTTCACTACTCTTCGGTGA
65 TTTCATCATCATGCTCGAAAGACTTACTGATAAGATTTGCTTCACTACTCTTCGGTGA
*
5633734 AGACTTACCAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGACCAAATGA
1 AGACTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGAT-GACCAAATGA
5633799 TTTCATCATCATGCTCGAAAGACTTACTGATGACACTTACTGACAGATTTGCTTCACTACTCTTC
65 TTTCATCATCATGCTCGAAAGACTTAC---TG------A-T-A-AGATTTGCTTCACTACTCTTC
5633864 GGTGA
118 GGTGA
* * * * *
5633869 AGGCTTACAAATTACCCGAATGATTTAATCATCATGCTCGAAAGACTTACTAATAGCCCAAAGGA
1 AGACTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGAT-GACCAAATGA
* *
5633934 CTTCATCATCATGCTCGAAAGACTTATTGAT
65 TTTCATCATCATGCTCGAAAGACTTACTGAT
5633965 GGCCCGAAGG
Statistics
Matches: 202, Mismatches: 15, Indels: 25
0.83 0.06 0.10
Matches are distributed among these distances:
122 81 0.40
123 4 0.02
125 3 0.01
126 1 0.00
131 1 0.00
132 3 0.01
135 109 0.54
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (122 bp):
AGACTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGACCAAATGAT
TTCATCATCATGCTCGAAAGACTTACTGATAAGATTTGCTTCACTACTCTTCGGTGA
Found at i:5634029 original size:177 final size:177
Alignment explanation
Indices: 5633733--5634155 Score: 598
Period size: 177 Copynumber: 2.4 Consensus size: 177
5633723 CTCTTCGGTG
* * * * * *
5633733 AAGACTTACCAATTA-CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGACCAAAT
1 AAGACTTACTAA-TAGCCCAAAGGATTTAATCATCATGCTCGAAAGACTTATTGATGGCCCGAAG
*
5633797 GATTTCATCATCATGCTCGAAAGACTTACTGATGACACTTACTGACAGATTTGCTTCACTACTCT
65 GACTTCATCATCATGCTCGAAAGACTTACTGATGACACTTACTGACAGATTTGCTTCACTACTCT
* *
5633862 TCGGTGAAGGCTTACAAATTACCCGAATGATTTAATCATCATGCTCGA
130 TCGGTGAAGGATTACAAATTACCCGAAGGATTTAATCATCATGCTCGA
* *
5633910 AAGACTTACTAATAGCCCAAAGGACTTCATCATCATGCTCGAAAGACTTATTGATGGCCCGAAGG
1 AAGACTTACTAATAGCCCAAAGGATTTAATCATCATGCTCGAAAGACTTATTGATGGCCCGAAGG
** * ** *
5633975 ACTTCATCATCATGCTCGAAAGACTTACTGATGGTACTTATTGATGGGTTTGCTTCACTACTCTT
66 ACTTCATCATCATGCTCGAAAGACTTACTGATGACACTTACTGACAGATTTGCTTCACTACTCTT
* *
5634040 CTGTGAAGGATTACAAATTACCCTAAGGATTTAATCATCATGCTCGA
131 CGGTGAAGGATTACAAATTACCCGAAGGATTTAATCATCATGCTCGA
* * * * *
5634087 AACACTTACTGATGGCCCTAAA-GATTTAAGCATAATGCTCGAAAGACTTATTGATGGCCCGAAG
1 AAGACTTACTAATAGCCC-AAAGGATTTAATCATCATGCTCGAAAGACTTATTGATGGCCCGAAG
5634151 GACTT
65 GACTT
5634156 ACTAAGTGAG
Statistics
Matches: 218, Mismatches: 26, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
176 2 0.01
177 213 0.98
178 3 0.01
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.29
Consensus pattern (177 bp):
AAGACTTACTAATAGCCCAAAGGATTTAATCATCATGCTCGAAAGACTTATTGATGGCCCGAAGG
ACTTCATCATCATGCTCGAAAGACTTACTGATGACACTTACTGACAGATTTGCTTCACTACTCTT
CGGTGAAGGATTACAAATTACCCGAAGGATTTAATCATCATGCTCGA
Found at i:5634125 original size:42 final size:42
Alignment explanation
Indices: 5634060--5634146 Score: 129
Period size: 42 Copynumber: 2.1 Consensus size: 42
5634050 TTACAAATTA
* * *
5634060 CCCTAAGGATTTAATCATCATGCTCGAAACACTTACTGATGG
1 CCCTAAAGATTTAAGCATAATGCTCGAAACACTTACTGATGG
* *
5634102 CCCTAAAGATTTAAGCATAATGCTCGAAAGACTTATTGATGG
1 CCCTAAAGATTTAAGCATAATGCTCGAAACACTTACTGATGG
5634144 CCC
1 CCC
5634147 GAAGGACTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (42 bp):
CCCTAAAGATTTAAGCATAATGCTCGAAACACTTACTGATGG
Found at i:5634345 original size:42 final size:42
Alignment explanation
Indices: 5634298--5634377 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
5634288 CAAATGACTT
* *
5634298 ATCATCTTGCTCT-AAAGGCTTACAGATGACCCGAAGGATTTC
1 ATCATCATGCT-TGAAAGACTTACAGATGACCCGAAGGATTTC
* *
5634340 ATCATCATGCTTGAAAGACTTACTGATGGCCCGAAGGA
1 ATCATCATGCTTGAAAGACTTACAGATGACCCGAAGGA
5634378 CTTAAATTAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 1 0.03
42 32 0.97
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (42 bp):
ATCATCATGCTTGAAAGACTTACAGATGACCCGAAGGATTTC
Found at i:5638875 original size:151 final size:151
Alignment explanation
Indices: 5638657--5638960 Score: 608
Period size: 151 Copynumber: 2.0 Consensus size: 151
5638647 AGTGACCATC
5638657 TTAAAACAACTTTCATTGAACACAAAGGTCTCGGTACATCAAACAAACTTTATATATAATGGACA
1 TTAAAACAACTTTCATTGAACACAAAGGTCTCGGTACATCAAACAAACTTTATATATAATGGACA
5638722 GCTTTCGCTCCGAACTTTTCTATCTTCTTCAAAAACCAATTTAATTTCCACTCATGCTCGGGGGT
66 GCTTTCGCTCCGAACTTTTCTATCTTCTTCAAAAACCAATTTAATTTCCACTCATGCTCGGGGGT
5638787 CGAGTTGTCAATCTGTTTCAA
131 CGAGTTGTCAATCTGTTTCAA
5638808 TTAAAACAACTTTCATTGAACACAAAGGTCTCGGTACATCAAACAAACTTTATATATAATGGACA
1 TTAAAACAACTTTCATTGAACACAAAGGTCTCGGTACATCAAACAAACTTTATATATAATGGACA
5638873 GCTTTCGCTCCGAACTTTTCTATCTTCTTCAAAAACCAATTTAATTTCCACTCATGCTCGGGGGT
66 GCTTTCGCTCCGAACTTTTCTATCTTCTTCAAAAACCAATTTAATTTCCACTCATGCTCGGGGGT
5638938 CGAGTTGTCAATCTGTTTCAA
131 CGAGTTGTCAATCTGTTTCAA
5638959 TT
1 TT
5638961 CTCTTGCAAA
Statistics
Matches: 153, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
151 153 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (151 bp):
TTAAAACAACTTTCATTGAACACAAAGGTCTCGGTACATCAAACAAACTTTATATATAATGGACA
GCTTTCGCTCCGAACTTTTCTATCTTCTTCAAAAACCAATTTAATTTCCACTCATGCTCGGGGGT
CGAGTTGTCAATCTGTTTCAA
Found at i:5645837 original size:29 final size:30
Alignment explanation
Indices: 5645782--5645838 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
5645772 TTTTAATCCT
* *
5645782 TAAACTTTTACAACTTTACACTTTAGTCTC
1 TAAACTTTCACAAATTTACACTTTAGTCTC
5645812 TAAACTTTCA-AAATTTACA-TTCTAGTC
1 TAAACTTTCACAAATTTACACTT-TAGTC
5645839 ACCAATCCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 2 0.08
29 13 0.54
30 9 0.38
ACGTcount: A:0.33, C:0.21, G:0.04, T:0.42
Consensus pattern (30 bp):
TAAACTTTCACAAATTTACACTTTAGTCTC
Found at i:5646698 original size:234 final size:238
Alignment explanation
Indices: 5646280--5646742 Score: 898
Period size: 234 Copynumber: 2.0 Consensus size: 238
5646270 ATCAATATGA
5646280 GATAGAAAAGAACTTGCTAAAATGATGATTGTTTATGATTGTCATTTAGTTTTGTTGAACGTGAG
1 GATAGAAAAGAACTTGCTAAAATGATGATTGTTTATGATTGTCATTTAGTTTTGTTGAACGTGAG
5646345 GAACTTCGTCATATATGTAATATAGTCATTCCTAGTTTTACTCCTTCCCCACGTGCTACTATTTT
66 GAACTTCGTCATATATGTAATATAGTCATTCCTAGTTTTACTCCTTCCCCACGTGCTACTATTTT
5646410 ATTGAAAAAAGTAATAATTTGAATAATTATTTCATTAATTTATCTTCTAGAGTATGTGTTACCAC
131 ATTGAAAAAAGTAATAATTTGAATAATTATTTCATTAATTTATCTTCTAGAGTATGTGTTACCAC
5646475 ATATACATGGACATCAGGTC-AAATTTAT-ATATGTCTTATTG
196 ATATACATGGACATCAGGTCAAAATTTATCATATGTCTTATTG
5646516 GATAGAAAAGAACTTGCTAAAATGATGATTGTTTATGATTGTCATTTAGTTTTGTTGAACGTGAG
1 GATAGAAAAGAACTTGCTAAAATGATGATTGTTTATGATTGTCATTTAGTTTTGTTGAACGTGAG
5646581 GAACTTCGTCATATATGT-ATATAGTCATTCCTAG-TTTACTCCTTCCCCACGTGCTACTATTTT
66 GAACTTCGTCATATATGTAATATAGTCATTCCTAGTTTTACTCCTTCCCCACGTGCTACTATTTT
5646644 ATTGAAAAAAGTAATAATTTGAATAATTATTTCATTAATTTATCTTCTAGAGTATGTGTTACCAC
131 ATTGAAAAAAGTAATAATTTGAATAATTATTTCATTAATTTATCTTCTAGAGTATGTGTTACCAC
5646709 ATATACATGGACATCAGGTCAAAATTTATCATAT
196 ATATACATGGACATCAGGTCAAAATTTATCATAT
5646743 ATATGTCTTA
Statistics
Matches: 225, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
234 114 0.51
235 24 0.11
236 87 0.39
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (238 bp):
GATAGAAAAGAACTTGCTAAAATGATGATTGTTTATGATTGTCATTTAGTTTTGTTGAACGTGAG
GAACTTCGTCATATATGTAATATAGTCATTCCTAGTTTTACTCCTTCCCCACGTGCTACTATTTT
ATTGAAAAAAGTAATAATTTGAATAATTATTTCATTAATTTATCTTCTAGAGTATGTGTTACCAC
ATATACATGGACATCAGGTCAAAATTTATCATATGTCTTATTG
Found at i:5647596 original size:371 final size:371
Alignment explanation
Indices: 5646913--5647637 Score: 1225
Period size: 371 Copynumber: 2.0 Consensus size: 371
5646903 ACCATGCTAG
* *
5646913 TTCTAATAATATAGCGATCAAGTATTTGAAGAAAATTCTTAACTTGTGGGATGATAGTGTGTTGA
1 TTCTAATAATATAGCAATCAAGTATTTGAAGAAAATTCTTAACTTGTCGGATGATAGTGTGTTGA
5646978 ATGCTGAATTTTTGCATATGAGATGTGTTGCACATATTTTGAATTTGGTTGTTAAGGATGGATTG
66 ATGCTGAATTTTTGCATATGAGATGTGTTGCACATATTTTGAATTTGGTTGTTAAGGATGGATTG
*
5647043 AAAGATATTGATGCTTCTGTTATGAGAGTTCATTCTACTATAAAATATGTGAGGTTTTCCCATAC
131 AAAGATATTGATGCTTCTGTTATGAGAGTTCATTCTACTATAAAATATGTGAGGTATTCCCATAC
*
5647108 AAAACTTCAAACGTTTAAAGTTTATGTTGAAGAGGAGAATATAAATTCTAAATCTCTGGTTTGCT
196 AAAACTTCAAAAGTTTAAAGTTTATGTTGAAGAGGAGAATATAAATTCTAAATCTCTGGTTTGCT
* * **
5647173 TGGACTTTATACAAGGTTTAATTCCACCTATTACATGCTTAAAAGTGCTTTGGTGTTTAGGAAGA
261 TGGACTTGATAAAAGGTGGAATTCCACCTATTACATGCTTAAAAGTGCTTTGGTGTTTAGGAAGA
*
5647238 CATTCAAAAATATGAAAACTTAGTACCCTCCTTACACAAAGGAGCT
326 CATTCAAAAATATGAAAACTAAGTACCCTCCTTACACAAAGGAGCT
* * * * *
5647284 TTCTAATGATATAGTAATTAAGTATTTGAAGCAAATTTTTAACTTGTCGGATGATAGTGTGTTGA
1 TTCTAATAATATAGCAATCAAGTATTTGAAGAAAATTCTTAACTTGTCGGATGATAGTGTGTTGA
5647349 ATGCTGAATTTTTGCATATGAGATGTGTTGCACATATTTTGAATTTGGTTGTTAAGGATGGATTG
66 ATGCTGAATTTTTGCATATGAGATGTGTTGCACATATTTTGAATTTGGTTGTTAAGGATGGATTG
* *
5647414 AAAGATGTTGATGCTTCTGTTATGAGAGTTCATTCTACTGTAAAATATGTGAGGTATTCCCATAC
131 AAAGATATTGATGCTTCTGTTATGAGAGTTCATTCTACTATAAAATATGTGAGGTATTCCCATAC
* * * * *
5647479 GAAACTTCAAAAGTTTAAAGTTTGTGTTGAAGATGAGAATATAAATTCTAAATCTTTTGTTTGCT
196 AAAACTTCAAAAGTTTAAAGTTTATGTTGAAGAGGAGAATATAAATTCTAAATCTCTGGTTTGCT
* * *
5647544 TGGACTTGATAAAAGGTGGAATTCTATCTATTCCATGCTTAAAAGTGCTTTGGTGTTTAGGAAGA
261 TGGACTTGATAAAAGGTGGAATTCCACCTATTACATGCTTAAAAGTGCTTTGGTGTTTAGGAAGA
*
5647609 CATTCAAAGATATGAAAACTAAGTACCCT
326 CATTCAAAAATATGAAAACTAAGTACCCT
5647638 TTATGAAAGA
Statistics
Matches: 329, Mismatches: 25, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
371 329 1.00
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.37
Consensus pattern (371 bp):
TTCTAATAATATAGCAATCAAGTATTTGAAGAAAATTCTTAACTTGTCGGATGATAGTGTGTTGA
ATGCTGAATTTTTGCATATGAGATGTGTTGCACATATTTTGAATTTGGTTGTTAAGGATGGATTG
AAAGATATTGATGCTTCTGTTATGAGAGTTCATTCTACTATAAAATATGTGAGGTATTCCCATAC
AAAACTTCAAAAGTTTAAAGTTTATGTTGAAGAGGAGAATATAAATTCTAAATCTCTGGTTTGCT
TGGACTTGATAAAAGGTGGAATTCCACCTATTACATGCTTAAAAGTGCTTTGGTGTTTAGGAAGA
CATTCAAAAATATGAAAACTAAGTACCCTCCTTACACAAAGGAGCT
Found at i:5649456 original size:21 final size:19
Alignment explanation
Indices: 5649417--5649455 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
5649407 GGGCCTTTTT
*
5649417 GGGCATGGGCTAAGAGAGA
1 GGGCATGAGCTAAGAGAGA
5649436 GGGCATGAGCTAAGAGAGA
1 GGGCATGAGCTAAGAGAGA
5649455 G
1 G
5649456 AAAAAGGTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.46, T:0.10
Consensus pattern (19 bp):
GGGCATGAGCTAAGAGAGA
Found at i:5653118 original size:22 final size:23
Alignment explanation
Indices: 5653088--5653131 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
5653078 TTTATTTATT
5653088 TATTAATATTTATAATAATATAA
1 TATTAATATTTATAATAATATAA
* *
5653111 TATT-ATATTTTTAATATTATA
1 TATTAATATTTATAATAATATA
5653132 TAAAATAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTAATATTTATAATAATATAA
Found at i:5653147 original size:31 final size:32
Alignment explanation
Indices: 5653080--5653160 Score: 89
Period size: 31 Copynumber: 2.6 Consensus size: 32
5653070 AAATATTATT
5653080 TATT-TATTTATTAATATTTATAATAATATAA
1 TATTATATTTATTAATATTTATAATAATATAA
*
5653111 TATTATATTT-TTAATA-TTAT-ATAAAATAA
1 TATTATATTTATTAATATTTATAATAATATAA
*
5653140 TCAATTATATTATAATAATAT
1 T--ATTATATT-TATTAATAT
5653161 AAGATATTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
29 9 0.21
30 4 0.10
31 18 0.43
32 6 0.14
33 5 0.12
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (32 bp):
TATTATATTTATTAATATTTATAATAATATAA
Found at i:5653277 original size:23 final size:23
Alignment explanation
Indices: 5653251--5653295 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
5653241 AATAATATTT
5653251 TAATAAATATATTTAAAATATAC
1 TAATAAATATATTTAAAATATAC
* *
5653274 TAATTAATATTTTTAAAATATA
1 TAATAAATATATTTAAAATATA
5653296 ATATAACACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
TAATAAATATATTTAAAATATAC
Found at i:5653607 original size:20 final size:20
Alignment explanation
Indices: 5653570--5653608 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5653560 CCGGAAAACG
**
5653570 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATCAAATTCA
*
5653590 TTTTCCAGAATTCAAATTC
1 TTTTCCAGAAATCAAATTC
5653609 CAGTAATTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATCAAATTCA
Found at i:5653615 original size:29 final size:30
Alignment explanation
Indices: 5653582--5653654 Score: 130
Period size: 30 Copynumber: 2.5 Consensus size: 30
5653572 TTCCAGAAAT
5653582 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
5653611 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
*
5653641 GTAATTCTTTTTCC
1 GTAATTCATTTTCC
5653655 GGAAAACCAA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 16 0.38
30 26 0.62
ACGTcount: A:0.30, C:0.21, G:0.07, T:0.42
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:5653654 original size:15 final size:15
Alignment explanation
Indices: 5653582--5653654 Score: 94
Period size: 15 Copynumber: 4.9 Consensus size: 15
5653572 TTCCAGAAAT
5653582 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
5653597 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
5653611 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
5653626 GTAATTCAAATTCCA
1 GTAATTCATTTTCCA
*
5653641 GTAATTCTTTTTCC
1 GTAATTCATTTTCC
5653655 GGAAAACCAA
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
14 12 0.25
15 36 0.75
ACGTcount: A:0.30, C:0.21, G:0.07, T:0.42
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:5655494 original size:23 final size:23
Alignment explanation
Indices: 5655464--5655523 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
5655454 CATTTTATAT
* *
5655464 GGCACTTCGGTGCAATTCTACGC
1 GGCACTTCGGTACAATTCTACAC
*
5655487 GGCACTTCGGTACAATTCTACAT
1 GGCACTTCGGTACAATTCTACAC
5655510 GGCACTTCGGTACA
1 GGCACTTCGGTACA
5655524 TTTATACGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.27
Consensus pattern (23 bp):
GGCACTTCGGTACAATTCTACAC
Found at i:5660364 original size:23 final size:23
Alignment explanation
Indices: 5660305--5660364 Score: 104
Period size: 22 Copynumber: 2.7 Consensus size: 23
5660295 ACATTTTATA
5660305 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
5660328 TGGCAC-TCGGTGCAATTCTATG
1 TGGCACTTCGGTGCAATTCTACG
5660350 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
5660365 TTTATACGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
22 21 0.60
23 14 0.40
ACGTcount: A:0.17, C:0.25, G:0.28, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:5675344 original size:6 final size:6
Alignment explanation
Indices: 5675296--5675343 Score: 78
Period size: 6 Copynumber: 7.8 Consensus size: 6
5675286 ATCTTTAATC
*
5675296 CATATA CATATA CATATA CATATA CATATA CATATA CCATATG CATAT
1 CATATA CATATA CATATA CATATA CATATA CATATA -CATATA CATAT
5675344 GTATATGCAT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
6 35 0.88
7 5 0.12
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.33
Consensus pattern (6 bp):
CATATA
Found at i:5675349 original size:6 final size:6
Alignment explanation
Indices: 5675296--5675361 Score: 60
Period size: 6 Copynumber: 10.8 Consensus size: 6
5675286 ATCTTTAATC
* * * * * *
5675296 CATATA CATATA CATATA CATATA CATATA CATATAC CATATG CATATG
1 CATATG CATATG CATATG CATATG CATATG CATAT-G CATATG CATATG
*
5675345 TATATG CATATG CATAT
1 CATATG CATATG CATAT
5675362 TGGGGTAAGG
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
6 50 0.91
7 5 0.09
ACGTcount: A:0.42, C:0.17, G:0.06, T:0.35
Consensus pattern (6 bp):
CATATG
Found at i:5684894 original size:6 final size:6
Alignment explanation
Indices: 5684883--5684912 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
5684873 CGTATTCTTT
5684883 CTCCGG CTCCGG CTCCGG CTCCGG CCTCCG
1 CTCCGG CTCCGG CTCCGG CTCCGG -CTCCG
5684913 ACACCGGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.78
7 5 0.22
ACGTcount: A:0.00, C:0.53, G:0.30, T:0.17
Consensus pattern (6 bp):
CTCCGG
Found at i:5687988 original size:27 final size:27
Alignment explanation
Indices: 5687946--5688013 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
5687936 CTGTAGGAAT
5687946 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
5687971 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
5687998 TATAGAGATATGATTT
1 TATAGAGATATGATTT
5688014 TGTAAATAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 7 0.17
27 34 0.83
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:5690325 original size:368 final size:368
Alignment explanation
Indices: 5689648--5690383 Score: 1418
Period size: 368 Copynumber: 2.0 Consensus size: 368
5689638 CAGATTTGTC
* *
5689648 ACCTGTAACTACTCCCATTGATCCACCGGTAGTACCCATCACTACTTTACCCATACCTACTTTAA
1 ACCTGTAACTACTCCCATTGATCCACCGGTAGTACCCATCACTACTTCACACATACCTACTTTAA
*
5689713 ATACCCTTCCTGAAAATACACCTACTCCTATTCAAAATATTCCATAAACACCACCAATCAAACAG
66 ATACCCTTCCTGAAAATACACCTACTCCTATTCAAAATATTCCATAAACACCACCAATCAAACAA
5689778 CTCCGTTTCTATACAAGGAAAAGAAAACATATTCCTGAGGCTGTTTTGCAATCTGATGCTTGCCG
131 CTCCGTTTCTATACAAGGAAAAGAAAACATATTCCTGAGGCTGTTTTGCAATCTGATGCTTGCCG
5689843 AGAATTGAATTTGGGTCCAGCTGCCGAAATAGAAGAAGAAATCAGTAAGTCCACTTCCCCTACTC
196 AGAATTGAATTTGGGTCCAGCTGCCGAAATAGAAGAAGAAATCAGTAAGTCCACTTCCCCTACTC
5689908 TAGATGACTTCCCTATTGCTATTAGAAAAGGGGTTAGACAGTACACCAAGCATCTTATTGAAAAA
261 TAGATGACTTCCCTATTGCTATTAGAAAAGGGGTTAGACAGTACACCAAGCATCTTATTGAAAAA
5689973 TTTGCTGGTTATAATTCATTGATGCCATCTTTTCAAGCATTTA
326 TTTGCTGGTTATAATTCATTGATGCCATCTTTTCAAGCATTTA
5690016 ACCTGTAACTACTCCCATTGATCCACCGGTAGTACCCATCACTACTTCACACATACCTACTTTAA
1 ACCTGTAACTACTCCCATTGATCCACCGGTAGTACCCATCACTACTTCACACATACCTACTTTAA
*
5690081 ATACCCTTCCTGAAAATATACCTACTCCTATTCAAAATATTCCATAAACACCACCAATCAAACAA
66 ATACCCTTCCTGAAAATACACCTACTCCTATTCAAAATATTCCATAAACACCACCAATCAAACAA
5690146 CTCCGTTTCTATACAAGGAAAAGAAAACATATTCCTGAGGCTGTTTTGCAATCTGATGCTTGCCG
131 CTCCGTTTCTATACAAGGAAAAGAAAACATATTCCTGAGGCTGTTTTGCAATCTGATGCTTGCCG
*
5690211 AGAATTGGATTTGGGTCCAGCTGCCGAAATAGAAGAAGAAATCAGTAAGTCCACTTCCCCTACTC
196 AGAATTGAATTTGGGTCCAGCTGCCGAAATAGAAGAAGAAATCAGTAAGTCCACTTCCCCTACTC
*
5690276 TAGATGACTTCTCTATTGCTATTAGAAAAGGGGTTAGACAGTACACCAAGCATCTTATTGAAAAA
261 TAGATGACTTCCCTATTGCTATTAGAAAAGGGGTTAGACAGTACACCAAGCATCTTATTGAAAAA
5690341 TTTGCTGGTTATAATTCATTGATGCCATCTTTTCAAGCATTTA
326 TTTGCTGGTTATAATTCATTGATGCCATCTTTTCAAGCATTTA
5690384 CAGCAAACTT
Statistics
Matches: 362, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
368 362 1.00
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.29
Consensus pattern (368 bp):
ACCTGTAACTACTCCCATTGATCCACCGGTAGTACCCATCACTACTTCACACATACCTACTTTAA
ATACCCTTCCTGAAAATACACCTACTCCTATTCAAAATATTCCATAAACACCACCAATCAAACAA
CTCCGTTTCTATACAAGGAAAAGAAAACATATTCCTGAGGCTGTTTTGCAATCTGATGCTTGCCG
AGAATTGAATTTGGGTCCAGCTGCCGAAATAGAAGAAGAAATCAGTAAGTCCACTTCCCCTACTC
TAGATGACTTCCCTATTGCTATTAGAAAAGGGGTTAGACAGTACACCAAGCATCTTATTGAAAAA
TTTGCTGGTTATAATTCATTGATGCCATCTTTTCAAGCATTTA
Found at i:5699480 original size:761 final size:752
Alignment explanation
Indices: 5697940--5699352 Score: 1673
Period size: 761 Copynumber: 1.8 Consensus size: 752
5697930 ACCCGACCCG
*
5697940 AAATAATATATTTATTAAAATATTATTTTTATTCAATAAAAATAGGGATTTAATTGAAAAAAATA
1 AAATAATATATTTATTAAAATATTATTTTTATTCAATAAAAATAGGAATTTAATTGAAAAAAATA
* * *
5698005 ATATATAGAGGGTATTATTATAATTATCCCTAAACATATAAGGTAAAATTATAATTTTTTTGGTC
66 ATATATAGAGGGTATAATTATAATTATCCCTAAACATATAAGATAAAATTATAATTTTTTCGGTC
5698070 GGGTTGAATACTTTTCACCCTAAATCCGAACCCGACCAGACCTAAACATAACTTTAAAAAAATCT
131 GGGTTGAATACTTTTCACCCTAAATCCGAA-CC-ACCAGACCTAAACATAACTTTAAAAAAATCT
* *
5698135 GACCAAAACTCGATTTTTAAAAAAAAAATGACCTAGTAGGGTCAAATCGGGTCAAAACCTGTTGG
194 GACCAAAACTCCATTTTTAAAAAAAAAATGACC-AGTA--GTCAAA---GGTCAAAACCTGTTGA
*
5698200 GTTCGATTCTTATGCCTATACCTAATCTTGATACTTAAAAATAAACACATAATTATATTAGTGTA
253 GTTCGATTCTCATGCCTATACCTAATCTTGATACTTAAAAATAAACACATAATTATATTAGTGTA
*
5698265 AGTATGTTTATGTGTTTTTAAAGAAATAAAAAATTAAAAATAATAAAAATATATATTAAGTTATT
318 AGTATGTTTATGTGTTTTTAAAGAAATAAAAAATTAAAAATAATAAAAATATATATTAAGCTATT
* *
5698330 TGTATACTAATTTATTAAATATATATATATATATATTAAAAATACTAGAAAATTAGATTATATAT
383 TGTATAATAA-TTATT-AATATATATATATATATATTAAAAATAATAGAAAATTAGATTATATAT
5698395 AAACTTTCATGTAAATATTTTAACTTTAATATTGAGAATTCAACTTGTAAAAAATATATCTCAAT
446 AAACTTTCATGTAAATATTTTAACTTTAATATTGAGAATTCAACTTGTAAAAAATATATCTCAAT
* * * *
5698460 GATAATTTGGTAAAATATATACTTTTCTTATTTTATGTTTCTTCAACTGAACATTGTAATCTTAC
511 GACAATTCGGTAAAATATACACTTTTCTTATTTTATGTTTCTTCAACTAAACATTGTAATCTTAC
* * **
5698525 ATTCATGCCAAATAAACCAAACAAGATAATATAATATTCCCTTTAATGTGTTAAGTAATATAAAA
576 ATTCATGCAAAATAAACCAAACAACATAATATAATATTCCCGCTAATGTGTTAAGTAATATAAAA
* * *** * ****
5698590 ATGTGTAAATTACATCGATATAAGTATGCACATCTTTCAATATCTTGATTAGGGATGGGCATGGG
641 ATGTGTAAATTACATC-ATATAAGTAT-CACATCTTACAATATCGTGA-TACCAATGGACACCCC
** ** * ** * * * * ** *
5698655 TCGGGTCGGGTCGGGTCGAATTTTCAATCCACCCAATCTGACCCTACCCA
703 TCAAGTCAAGTAGAATCGAAGTTTCAACCCACACAAACTGACCAAAACCA
*
5698705 AAATAATATATTTATTAAAAAATATTATTTTTATTGAATAAAAA-AGGAATTTAATTGAAAGAAA
1 AAATAATATATTTATT--AAAATATTATTTTTATTCAATAAAAATAGGAATTTAATTGAAA-AAA
* * *
5698769 ATATTATATAG-GGGTATAATTGTAATTATCCCTAAATATATAAGATAAAATTATAATTTTTTCG
63 ATAATATATAGAGGGTATAATTATAATTATCCCTAAACATATAAGATAAAATTATAATTTTTTCG
* * * * *
5698833 AGTTGGGTTGGGTCAAATATTTTTCACCCTAAATCTGAA-C-CC-GACTTGAACATAACTTTAAA
128 -GTCGGGTT--G---AATACTTTTCACCCTAAATCCGAACCACCAGACCTAAACATAACTTT--A
* *
5698895 AAAAAAT-TGACCAAAAC-CCATTTTTTTAAAAAAAAAAATTGA-CACG-A-TC-AA-GTTAGAA
185 AAAAAATCTGACCAAAACTCCA--TTTTT-AAAAAAAAAA-TGACCA-GTAGTCAAAGGTCAAAA
* *
5698953 -CTCGTTGAGTTCAGGTTC-CATGCAC-ATACCTAATCTTGATACTTAAACATAAACACATAATT
245 CCT-GTTGAGTTC-GATTCTCATGC-CTATACCTAATCTTGATACTTAAAAATAAACACATAATT
*
5699015 ATATTGGTGTAAGTATGTTTATGTGTTTTTAAAGAAATAAAAATAATTAAAAATAATAAAAATAT
307 ATATTAGTGTAAGTATGTTTATGTGTTTTTAAAGAAAT-AAAA-AATTAAAAATAATAAAAATAT
5699080 ATATTAAGCTATTTG-AGTAATAA-T-TT-ATA-ATATATATATATATTAAAAATAATAGAAAAT
370 ATATTAAGCTATTTGTA-TAATAATTATTAATATATATATATATATATTAAAAATAATAGAAAAT
* * * *
5699140 TGGATTATCTATGAACTTTCATGTAAATATTTTAACTTTAATATTGATAATTCAACTTGTTAAAA
434 TAGATTATATATAAACTTTCATGTAAATATTTTAACTTTAATATTGAGAATTCAACTTG-TAAAA
* * *
5699205 AATATATCTCAATGACAATTCGGTAAAATTTACATTTTTCTTATTTTACAT-TTTTTTCAACTAA
498 AATATATCTCAATGACAATTCGGTAAAATATACACTTTTCTTATTTT--ATGTTTCTTCAACTAA
* **
5699269 ACATTGTAATCTTACATTCATGTCAAACAATATAA-TATAACATTACATAATATAATATTTTCGC
561 ACATTGTAATCTTACATTCATG-C-AA-AATA-AACCA-AACA--ACATAATATAATATTCCCGC
5699333 TAATGTGTTAAGTAATATAA
619 TAATGTGTTAAGTAATATAA
5699353 CATTTCGATA
Statistics
Matches: 574, Mismatches: 42, Indels: 64
0.84 0.06 0.09
Matches are distributed among these distances:
757 85 0.15
758 50 0.09
759 33 0.06
760 7 0.01
761 92 0.16
762 15 0.03
763 46 0.08
765 53 0.09
766 65 0.11
767 62 0.11
768 12 0.02
769 16 0.03
770 13 0.02
771 3 0.01
772 22 0.04
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (752 bp):
AAATAATATATTTATTAAAATATTATTTTTATTCAATAAAAATAGGAATTTAATTGAAAAAAATA
ATATATAGAGGGTATAATTATAATTATCCCTAAACATATAAGATAAAATTATAATTTTTTCGGTC
GGGTTGAATACTTTTCACCCTAAATCCGAACCACCAGACCTAAACATAACTTTAAAAAAATCTGA
CCAAAACTCCATTTTTAAAAAAAAAATGACCAGTAGTCAAAGGTCAAAACCTGTTGAGTTCGATT
CTCATGCCTATACCTAATCTTGATACTTAAAAATAAACACATAATTATATTAGTGTAAGTATGTT
TATGTGTTTTTAAAGAAATAAAAAATTAAAAATAATAAAAATATATATTAAGCTATTTGTATAAT
AATTATTAATATATATATATATATATTAAAAATAATAGAAAATTAGATTATATATAAACTTTCAT
GTAAATATTTTAACTTTAATATTGAGAATTCAACTTGTAAAAAATATATCTCAATGACAATTCGG
TAAAATATACACTTTTCTTATTTTATGTTTCTTCAACTAAACATTGTAATCTTACATTCATGCAA
AATAAACCAAACAACATAATATAATATTCCCGCTAATGTGTTAAGTAATATAAAAATGTGTAAAT
TACATCATATAAGTATCACATCTTACAATATCGTGATACCAATGGACACCCCTCAAGTCAAGTAG
AATCGAAGTTTCAACCCACACAAACTGACCAAAACCA
Found at i:5699588 original size:31 final size:31
Alignment explanation
Indices: 5699550--5699619 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
5699540 CTTTTAAAAC
* *
5699550 TTGTAATACAG-TCTCCCAACATTTAGT-TCGT
1 TTGTAATA-AGATCCCCCAACATTTAATCT-GT
*
5699581 TTGTAATATGATCCCCCAACATTTAATCTGT
1 TTGTAATAAGATCCCCCAACATTTAATCTGT
5699612 TTGTAATA
1 TTGTAATA
5699620 TGGTCCCCGA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 1 0.03
31 32 0.94
32 1 0.03
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (31 bp):
TTGTAATAAGATCCCCCAACATTTAATCTGT
Found at i:5699620 original size:31 final size:31
Alignment explanation
Indices: 5699564--5699627 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
5699554 AATACAGTCT
*
5699564 CCCAACATTTAGTTCGTTTGTAATATGATCC
1 CCCAACATTTAATTCGTTTGTAATATGATCC
*
5699595 CCCAACATTTAA-TCTGTTTGTAATATGGTCC
1 CCCAACATTTAATTC-GTTTGTAATATGATCC
5699626 CC
1 CC
5699628 GATGTAACCG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 2 0.07
31 28 0.93
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (31 bp):
CCCAACATTTAATTCGTTTGTAATATGATCC
Found at i:5701621 original size:31 final size:31
Alignment explanation
Indices: 5701586--5701680 Score: 147
Period size: 31 Copynumber: 3.1 Consensus size: 31
5701576 CGATTACGTT
**
5701586 GGGGACCATATTACAAACAAACTAAATGTTG
1 GGGGACCATATTGTAAACAAACTAAATGTTG
5701617 GGGGACCATATTGTAAACAAACTAAATGTTG
1 GGGGACCATATTGTAAACAAACTAAATGTTG
*
5701648 AGGGACCATATTGTAAA-AGAACTAAATGTTG
1 GGGGACCATATTGTAAACA-AACTAAATGTTG
5701679 GG
1 GG
5701681 AGGTTGTATT
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
30 1 0.02
31 58 0.98
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.24
Consensus pattern (31 bp):
GGGGACCATATTGTAAACAAACTAAATGTTG
Found at i:5702248 original size:29 final size:29
Alignment explanation
Indices: 5702206--5702351 Score: 265
Period size: 29 Copynumber: 5.0 Consensus size: 29
5702196 AATTTTATGA
5702206 TTCAATCTTAGCTCCGTCCTCGTTCATCC
1 TTCAATCTTAGCTCCGTCCTCGTTCATCC
5702235 TTCAATCTTAGCTCCGTCCTCGTTCATCC
1 TTCAATCTTAGCTCCGTCCTCGTTCATCC
5702264 TTCAATCTTAGCTCCGTCCTCGTTCATCC
1 TTCAATCTTAGCTCCGTCCTCGTTCATCC
* * *
5702293 TTCAATCTTAGCACTGTCTTCGTTCATCC
1 TTCAATCTTAGCTCCGTCCTCGTTCATCC
5702322 TTCAATCTTAGCTCCGTCCTCGTTCATCC
1 TTCAATCTTAGCTCCGTCCTCGTTCATCC
5702351 T
1 T
5702352 GCTTTTTTTC
Statistics
Matches: 111, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 111 1.00
ACGTcount: A:0.14, C:0.36, G:0.10, T:0.39
Consensus pattern (29 bp):
TTCAATCTTAGCTCCGTCCTCGTTCATCC
Found at i:5703744 original size:28 final size:29
Alignment explanation
Indices: 5703691--5703760 Score: 90
Period size: 28 Copynumber: 2.4 Consensus size: 29
5703681 ATATCACATG
* * *
5703691 ATCACTTTAGGTGACATAACACATATCAT
1 ATCACTTTGGGTGACATAACAAATATCAA
5703720 ATCACTTTGGGT-A-ATCAACAAATATCAA
1 ATCACTTTGGGTGACAT-AACAAATATCAA
5703748 ATCACTTTGGGTG
1 ATCACTTTGGGTG
5703761 GGTAATTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 2 0.06
28 23 0.64
29 11 0.31
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (29 bp):
ATCACTTTGGGTGACATAACAAATATCAA
Found at i:5704331 original size:18 final size:18
Alignment explanation
Indices: 5704308--5704343 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
5704298 ACTCCATGTG
5704308 TAAATTCATTAGATTACA
1 TAAATTCATTAGATTACA
5704326 TAAATTCATTAGATTACA
1 TAAATTCATTAGATTACA
5704344 CACCCAATGA
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:0.44, C:0.11, G:0.06, T:0.39
Consensus pattern (18 bp):
TAAATTCATTAGATTACA
Found at i:5723442 original size:22 final size:22
Alignment explanation
Indices: 5723417--5723470 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
5723407 GGTACCCTGG
*
5723417 GTATCGATACTATTCTTCCCAT
1 GTATCGATACTATTCTTCCCAA
* *
5723439 GTATTGATACTGTTCTTCCCAA
1 GTATCGATACTATTCTTCCCAA
5723461 GTATCGATAC
1 GTATCGATAC
5723471 CATTTAAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (22 bp):
GTATCGATACTATTCTTCCCAA
Found at i:5724030 original size:16 final size:14
Alignment explanation
Indices: 5723997--5724030 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
5723987 TCTCACATAT
5723997 GAAGAAGAAAGGAA
1 GAAGAAGAAAGGAA
5724011 -AAGAAGAAA-GAA
1 GAAGAAGAAAGGAA
5724023 GAAGAAGA
1 GAAGAAGA
5724031 GAACTCTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.16
13 16 0.84
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (14 bp):
GAAGAAGAAAGGAA
Found at i:5729386 original size:12 final size:11
Alignment explanation
Indices: 5729357--5729388 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
5729347 TTTAATTTTT
5729357 AAAATTGAACC
1 AAAATTGAACC
5729368 AAAATTGAACC
1 AAAATTGAACC
5729379 ACAAATTGAA
1 A-AAATTGAA
5729389 AAACTCAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.60
12 8 0.40
ACGTcount: A:0.56, C:0.16, G:0.09, T:0.19
Consensus pattern (11 bp):
AAAATTGAACC
Found at i:5734915 original size:19 final size:18
Alignment explanation
Indices: 5734887--5734931 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
5734877 TAAATTGTTA
* *
5734887 AATTAATATATTTGATAAT
1 AATTATTATATTT-AAAAT
5734906 AATTATTATATTTAAAAT
1 AATTATTATATTTAAAAT
5734924 AATATATT
1 AAT-TATT
5734932 GTAATAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
AATTATTATATTTAAAAT
Found at i:5735693 original size:2 final size:2
Alignment explanation
Indices: 5735686--5735712 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5735676 CAAAATCAGA
5735686 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5735713 AAGGGAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5738650 original size:14 final size:14
Alignment explanation
Indices: 5738631--5738660 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5738621 ATAAACAAGG
*
5738631 TTTTTTAATTATTA
1 TTTTTTAAGTATTA
5738645 TTTTTTAAGTATTA
1 TTTTTTAAGTATTA
5738659 TT
1 TT
5738661 ATTATTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (14 bp):
TTTTTTAAGTATTA
Found at i:5738681 original size:20 final size:19
Alignment explanation
Indices: 5738635--5738681 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
5738625 ACAAGGTTTT
*
5738635 TTAATTATTATTTTTTAAG
1 TTAATTATTATTTTCTAAG
*
5738654 TATTATTATTATTTTCTATAG
1 T-TAATTATTATTTTCTA-AG
5738675 TTAATTA
1 TTAATTA
5738682 CGTCATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 19 0.83
21 3 0.13
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (19 bp):
TTAATTATTATTTTCTAAG
Found at i:5741211 original size:36 final size:36
Alignment explanation
Indices: 5741171--5741309 Score: 260
Period size: 36 Copynumber: 3.9 Consensus size: 36
5741161 ATTTATCCAT
*
5741171 TATCAGCTTTGATACATTCGTGTATTAATGTTATCA
1 TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
5741207 TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
5741243 TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
1 TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
*
5741279 TATCAGCTTTGGTACATTCGTGTATCAATGT
1 TATCAGCTTTGATACATTCGTGTATCAATGT
5741310 CCAGCACCGT
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 101 1.00
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (36 bp):
TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
Found at i:5748832 original size:36 final size:36
Alignment explanation
Indices: 5748787--5748889 Score: 161
Period size: 36 Copynumber: 2.9 Consensus size: 36
5748777 ATTTATCCAT
* *
5748787 TATCTGCTTTGATACATTCTTGTATCAATGTTATCA
1 TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
*
5748823 TATCAGCTTTGATACATTCGTGTATCAGTGTTATCA
1 TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
* *
5748859 TATCAGCTTTGGTACATTCGTGTATCGATGT
1 TATCAGCTTTGATACATTCGTGTATCAATGT
5748890 CCAGCACCGT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 61 1.00
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.44
Consensus pattern (36 bp):
TATCAGCTTTGATACATTCGTGTATCAATGTTATCA
Found at i:5749514 original size:14 final size:14
Alignment explanation
Indices: 5749495--5749527 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5749485 TAGAACTATT
5749495 TTAGTTTA-TTTTA
1 TTAGTTTAGTTTTA
5749508 CTTAGTTTAGTTTTA
1 -TTAGTTTAGTTTTA
5749523 TTAGT
1 TTAGT
5749528 ATCTATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.21, C:0.03, G:0.12, T:0.64
Consensus pattern (14 bp):
TTAGTTTAGTTTTA
Found at i:5750238 original size:2 final size:2
Alignment explanation
Indices: 5750233--5750265 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5750223 TTAATAAAAA
5750233 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5750266 ATAATAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5750698 original size:60 final size:59
Alignment explanation
Indices: 5750634--5750748 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 59
5750624 AGCTAATACT
*
5750634 ATCATTCTAAATTAGTCCTCAAAC-TTTTAAACATTTCATTTTCACCCACAAACTATGATA
1 ATCATTCTAAATTAGTCC-CAAACTTTTTAAACATTTCAATTTCACCC-CAAACTATGATA
* * * *
5750694 ATCATTCTAAATTGGTCCCCAACTTTTTGAACATTTCAATTTCATCCCAAACTAT
1 ATCATTCTAAATTAGTCCCAAACTTTTTAAACATTTCAATTTCACCCCAAACTAT
5750749 ACGTATATAC
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 12 0.24
60 37 0.76
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.37
Consensus pattern (59 bp):
ATCATTCTAAATTAGTCCCAAACTTTTTAAACATTTCAATTTCACCCCAAACTATGATA
Found at i:5751159 original size:16 final size:16
Alignment explanation
Indices: 5751134--5751167 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5751124 GATTAAGCGT
*
5751134 TAAATTATTCAAATGC
1 TAAATAATTCAAATGC
*
5751150 TAAATAATTCATATGC
1 TAAATAATTCAAATGC
5751166 TA
1 TA
5751168 TGTATAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (16 bp):
TAAATAATTCAAATGC
Found at i:5751250 original size:27 final size:27
Alignment explanation
Indices: 5751212--5751277 Score: 132
Period size: 27 Copynumber: 2.4 Consensus size: 27
5751202 GATAATGGCT
5751212 CTGAATCATTCAGAATGTACTTCTGTA
1 CTGAATCATTCAGAATGTACTTCTGTA
5751239 CTGAATCATTCAGAATGTACTTCTGTA
1 CTGAATCATTCAGAATGTACTTCTGTA
5751266 CTGAATCATTCA
1 CTGAATCATTCA
5751278 ACATTGTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (27 bp):
CTGAATCATTCAGAATGTACTTCTGTA
Found at i:5751296 original size:23 final size:23
Alignment explanation
Indices: 5751266--5751342 Score: 145
Period size: 23 Copynumber: 3.3 Consensus size: 23
5751256 TACTTCTGTA
5751266 CTGAATCATTCAACATTGTTTTG
1 CTGAATCATTCAACATTGTTTTG
*
5751289 CTGAATCATTCAACACTGTTTTG
1 CTGAATCATTCAACATTGTTTTG
5751312 CTGAATCATTCAACATTGTTTTG
1 CTGAATCATTCAACATTGTTTTG
5751335 CTGAATCA
1 CTGAATCA
5751343 ATCAGCACTG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.40
Consensus pattern (23 bp):
CTGAATCATTCAACATTGTTTTG
Found at i:5751713 original size:30 final size:29
Alignment explanation
Indices: 5751664--5751740 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 29
5751654 TATTTTTAAT
5751664 TAAGTACTTAAAATATTTTTTAATCAAAA
1 TAAGTACTTAAAATATTTTTTAATCAAAA
*
5751693 TAAGTACTTAAAGTTATTTTTTAATCAAAA
1 TAAGTACTTAAA-ATATTTTTTAATCAAAA
5751723 T-AGATA-TCTAAAATATTT
1 TAAG-TACT-TAAAATATTT
5751741 AATTTTTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
29 20 0.47
30 23 0.53
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.43
Consensus pattern (29 bp):
TAAGTACTTAAAATATTTTTTAATCAAAA
Found at i:5761921 original size:41 final size:41
Alignment explanation
Indices: 5761864--5761957 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
5761854 TATAAGTTTA
5761864 GTGGGTAGTGGGCGAGTGTGGATATAAAAGTCATACCCGCC
1 GTGGGTAGTGGGCGAGTGTGGATATAAAAGTCATACCCGCC
*
5761905 GTGGGTAGTGGGCGAGTGTGGATATAAAAGTCATACTCGCC
1 GTGGGTAGTGGGCGAGTGTGGATATAAAAGTCATACCCGCC
5761946 GTGGGTAGTGGG
1 GTGGGTAGTGGG
5761958 TAGGTGATGG
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:0.22, C:0.14, G:0.40, T:0.23
Consensus pattern (41 bp):
GTGGGTAGTGGGCGAGTGTGGATATAAAAGTCATACCCGCC
Found at i:5763618 original size:8 final size:8
Alignment explanation
Indices: 5763582--5763654 Score: 101
Period size: 8 Copynumber: 8.9 Consensus size: 8
5763572 GCATGTATAA
*
5763582 ATAAATAT
1 ATAAATAC
5763590 ATAAATAC
1 ATAAATAC
**
5763598 ATAGTTGTAC
1 ATA--AATAC
5763608 ATAAATAC
1 ATAAATAC
5763616 ATAAATAC
1 ATAAATAC
5763624 ATAAATAC
1 ATAAATAC
5763632 ATAAATAC
1 ATAAATAC
5763640 ATAAATAC
1 ATAAATAC
5763648 ATAAATA
1 ATAAATA
5763655 GTAGAAGTAA
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
8 52 0.90
10 6 0.10
ACGTcount: A:0.59, C:0.10, G:0.03, T:0.29
Consensus pattern (8 bp):
ATAAATAC
Found at i:5765317 original size:20 final size:21
Alignment explanation
Indices: 5765292--5765361 Score: 79
Period size: 22 Copynumber: 3.3 Consensus size: 21
5765282 GAAATAATAA
*
5765292 AAAAACTA-TATTATATTTCC
1 AAAAACTATTATTATATTTTC
* *
5765312 AAAAACTATGTAATAGATTTTC
1 AAAAACTAT-TATTATATTTTC
*
5765334 AAAAAATATTATATATATTTTC
1 AAAAACTATTAT-TATATTTTC
5765356 AAAAAC
1 AAAAAC
5765362 CATTTTCAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
20 8 0.20
21 2 0.05
22 30 0.75
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.37
Consensus pattern (21 bp):
AAAAACTATTATTATATTTTC
Found at i:5765498 original size:35 final size:35
Alignment explanation
Indices: 5765328--5765707 Score: 368
Period size: 35 Copynumber: 10.9 Consensus size: 35
5765318 TATGTAATAG
* * **
5765328 ATTTTCAAAAAATAT-TA-TATATATTTTCAAAAACC
1 ATTTT-AAAAACTATATACTATATGTTTTC-AAAATT
* * *
5765363 ATTTTCAAAACCATAT--TATATGGTTTCAAAAATGT
1 ATTTTAAAAACTATATACTATATGTTTTC-AAAAT-T
* *
5765398 -TTTTCAAAACTATATACTATATG-TTCCAAAATT
1 ATTTTAAAAACTATATACTATATGTTTTCAAAATT
*
5765431 ATTTTAAAAACTATAT--TATACGTTTTCAAAATT
1 ATTTTAAAAACTATATACTATATGTTTTCAAAATT
5765464 ATTTTAAAAACTATATACTATATGTTTTCAAAATT
1 ATTTTAAAAACTATATACTATATGTTTTCAAAATT
5765499 ATTTTAGAAAA-TATATACTATATGTTTTCAAAATT
1 ATTTTA-AAAACTATATACTATATGTTTTCAAAATT
* *
5765534 AGTTTAAAAACTATATACTATATTTTTTCAAAATT
1 ATTTTAAAAACTATATACTATATGTTTTCAAAATT
**
5765569 AGTTTT-AAAACTATATACTATATGTTTTCAAAACC
1 A-TTTTAAAAACTATATACTATATGTTTTCAAAATT
* * **
5765604 GTTTT-AAAACTATATACTATATGTTTTAAAAACC
1 ATTTTAAAAACTATATACTATATGTTTTCAAAATT
* * * * *
5765638 GTTTTAAAAACTATATATTATACGTTTTTAAAAATA
1 ATTTTAAAAACTATATACTATATG-TTTTCAAAATT
** * *
5765674 AGTTTCCAAAACTATATATTATATATTTTCAAAA
1 A-TTTTAAAAACTATATACTATATGTTTTCAAAA
5765708 ATCATATTAT
Statistics
Matches: 300, Mismatches: 31, Indels: 27
0.84 0.09 0.08
Matches are distributed among these distances:
32 5 0.02
33 26 0.09
34 94 0.31
35 126 0.42
36 30 0.10
37 19 0.06
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.43
Consensus pattern (35 bp):
ATTTTAAAAACTATATACTATATGTTTTCAAAATT
Found at i:5767072 original size:29 final size:30
Alignment explanation
Indices: 5767030--5767101 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
5767020 CCTGAAGGAC
*
5767030 CTATCCAGAGGTCACACAGA-CCCCGGTAA
1 CTATCCAGAGGTCACAAAGATCCCCGGTAA
* *
5767059 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGATCCCCGGTAA
*
5767089 CTATCCATAGGTC
1 CTATCCAGAGGTC
5767102 CCGAAGAACC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
29 18 0.47
30 20 0.53
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGATCCCCGGTAA
Found at i:5767118 original size:30 final size:30
Alignment explanation
Indices: 5767030--5767128 Score: 83
Period size: 30 Copynumber: 3.3 Consensus size: 30
5767020 CCTGAAGGAC
* * **
5767030 CTATCCAGAGGTCACACAG-ACCCCGGTAA
1 CTATCCATAGGTCACAAAGAACCTAGGTAA
* * * *
5767059 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCATAGGTCACAAAGAACCTAGGTAA
* *
5767089 CTATCCATAGGTCCCGAAGAACCTAGGTAAA
1 CTATCCATAGGTCACAAAGAACCTAGGT-AA
*
5767120 CTGTCCATA
1 CTATCCATA
5767129 TGTTCCTTAG
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
29 17 0.30
30 30 0.53
31 10 0.18
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.20
Consensus pattern (30 bp):
CTATCCATAGGTCACAAAGAACCTAGGTAA
Found at i:5767175 original size:31 final size:31
Alignment explanation
Indices: 5767087--5767181 Score: 93
Period size: 31 Copynumber: 3.1 Consensus size: 31
5767077 GATCCTCGGT
* * * * *
5767087 AACTATCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCAAAGAACATAGGTA
**
5767118 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCAAAGAACATAGGTA
* *
5767149 TACTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATATGT-TCCAAAGAACATAGGTA
5767180 AA
1 AA
5767182 ACCCTCGACT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
31 48 0.92
32 4 0.08
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (31 bp):
AACTGTCCATATGTTCCAAAGAACATAGGTA
Found at i:5768113 original size:31 final size:31
Alignment explanation
Indices: 5768075--5768261 Score: 313
Period size: 31 Copynumber: 6.0 Consensus size: 31
5768065 CCCGAAGGAC
* *
5768075 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
5768106 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
5768137 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
5768168 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
5768199 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
5768230 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
5768261 C
1 C
5768262 CCTCGACCCT
Statistics
Matches: 148, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
31 147 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:5769098 original size:21 final size:21
Alignment explanation
Indices: 5769068--5769112 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5769058 ATTCTGTCGT
* *
5769068 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
5769089 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
5769110 TTG
1 TTG
5769113 CCCAGAACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:5770397 original size:64 final size:64
Alignment explanation
Indices: 5770284--5770448 Score: 201
Period size: 64 Copynumber: 2.6 Consensus size: 64
5770274 TCTTTCAATG
* * *
5770284 AATGTATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTTTT-TATTT-
1 AATGCATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCCATTCGATGTTTTCTATTTA
* * *
5770346 AATGGGGATGCATCGATGCACTCCTTATGCATCGATGCAT-AAATCCTATTCGATGTTTTCTATT
1 AAT--GCATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCC-ATTCGATGTTTTCTATT
5770410 TA
63 TA
* * *
5770412 AATTCATGCATCGATGCACTGCATGTGCATCGATGCA
1 AATGCATGCATCGATGCACTACTTGTGCATCGATGCA
5770449 CCTTAAACAA
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
62 3 0.03
63 5 0.06
64 72 0.82
65 5 0.06
66 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (64 bp):
AATGCATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCCATTCGATGTTTTCTATTTA
Found at i:5773903 original size:30 final size:30
Alignment explanation
Indices: 5773835--5773961 Score: 78
Period size: 31 Copynumber: 4.2 Consensus size: 30
5773825 GAAGGACCTA
* * * * *
5773835 TCCAGAGGTCACACAGACCCCA-GTAACTA
1 TCCATAGGTCACAAAGAACCTAGGTAACTG
* * * *
5773864 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAACTG
* *
5773894 TCCATAGGTCCCGAAGAACCTAGGTAAACTG
1 TCCATAGGTCACAAAGAACCTAGGT-AACTG
* ** *
5773925 TCCATATGTTC-CTTAGAACATAGGTATACTG
1 TCCATA-GGTCACAAAGAACCTAGGTA-ACTG
5773956 TCCATA
1 TCCATA
5773962 TGTCTCGAAA
Statistics
Matches: 78, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
29 17 0.22
30 26 0.33
31 32 0.41
32 3 0.04
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (30 bp):
TCCATAGGTCACAAAGAACCTAGGTAACTG
Found at i:5773927 original size:31 final size:31
Alignment explanation
Indices: 5773889--5773983 Score: 111
Period size: 31 Copynumber: 3.1 Consensus size: 31
5773879 GATCCTCGGT
* *
5773889 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* **
5773920 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* *
5773951 TACTGTCCATATGTCTCGAA-AGACATAGGTA
1 AACTGTCCATATGTCCCGAAGA-ACATAGGTA
5773982 AA
1 AA
5773984 ACCCTCGACT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
30 1 0.02
31 51 0.98
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGAAGAACATAGGTA
Found at i:5774731 original size:64 final size:64
Alignment explanation
Indices: 5774618--5774782 Score: 201
Period size: 64 Copynumber: 2.6 Consensus size: 64
5774608 TCTTTCAATG
* * *
5774618 AATGTATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTTTT-TATTT-
1 AATGCATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCCATTCGATGTTTTCTATTTA
* * *
5774680 AATGGGGATGCATCGATGCACTCCTTATGCATCGATGCAT-AAATCCTATTCGATGTTTTCTATT
1 AAT--GCATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCC-ATTCGATGTTTTCTATT
5774744 TA
63 TA
* * *
5774746 AATTCATGCATCGATGCACTGCATGTGCATCGATGCA
1 AATGCATGCATCGATGCACTACTTGTGCATCGATGCA
5774783 CCTTAAACAA
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
62 3 0.03
63 5 0.06
64 72 0.82
65 5 0.06
66 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (64 bp):
AATGCATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCCATTCGATGTTTTCTATTTA
Found at i:5776618 original size:31 final size:31
Alignment explanation
Indices: 5776575--5776670 Score: 104
Period size: 31 Copynumber: 3.1 Consensus size: 31
5776565 AATTAATTAG
* * *
5776575 TCACTAATGTTATCGATTTAG-AATAAATTTA
1 TCACTAACGTTATCGATTT-GTAACAAATTGA
*
5776606 TCACTAACGTTATCAATTTGTAACAAATTGA
1 TCACTAACGTTATCGATTTGTAACAAATTGA
* * * *
5776637 TTACTAACGTTATCGATATGTAATAAATCGA
1 TCACTAACGTTATCGATTTGTAACAAATTGA
5776668 TCA
1 TCA
5776671 TTTTTCGTTA
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
30 1 0.02
31 53 0.98
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.38
Consensus pattern (31 bp):
TCACTAACGTTATCGATTTGTAACAAATTGA
Found at i:5779163 original size:38 final size:38
Alignment explanation
Indices: 5779096--5779220 Score: 198
Period size: 38 Copynumber: 3.3 Consensus size: 38
5779086 TTTATTTTGT
* *
5779096 TCGGATCGGGACGGG-TTTTTTAAGTGTGATATTCGGG
1 TCGGGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGG
* *
5779133 TCGAGTCGGGTCGGGTTTTTTTAAGCGTGATATTCGGG
1 TCGGGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGG
5779171 TCGGGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGG
1 TCGGGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGG
5779209 TCGGGTTCGGGT
1 TCGGG-TCGGGT
5779221 TTAGGGTGAA
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
37 12 0.15
38 62 0.77
39 6 0.08
ACGTcount: A:0.12, C:0.12, G:0.39, T:0.37
Consensus pattern (38 bp):
TCGGGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGG
Found at i:5779814 original size:17 final size:17
Alignment explanation
Indices: 5779788--5779850 Score: 81
Period size: 17 Copynumber: 3.6 Consensus size: 17
5779778 TATGGAATTG
*
5779788 GATTCTAATTCTTGACA
1 GATTCCAATTCTTGACA
* *
5779805 AATTCCAATTCCTGACA
1 GATTCCAATTCTTGACA
*
5779822 GATTCCAATTCCTTCACA
1 GATTCCAATT-CTTGACA
5779840 GATTCCAATTC
1 GATTCCAATTC
5779851 CCTCAGAAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
17 24 0.62
18 15 0.38
ACGTcount: A:0.30, C:0.27, G:0.08, T:0.35
Consensus pattern (17 bp):
GATTCCAATTCTTGACA
Found at i:5780281 original size:2 final size:2
Alignment explanation
Indices: 5780274--5780299 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5780264 ACGTCGAATT
5780274 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
5780300 CATTGGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5783367 original size:36 final size:35
Alignment explanation
Indices: 5783219--5783393 Score: 206
Period size: 35 Copynumber: 4.9 Consensus size: 35
5783209 CCTTAGATCC
*
5783219 ATAAGGAATTATCAGCTGATCGGTGTTGAACCTAT
1 ATAAGGAATTACCAGCTGATCGGTGTTGAACCTAT
* *
5783254 ATAAGGAATTACCAACCGATCGGTGTTGAACCTAT
1 ATAAGGAATTACCAGCTGATCGGTGTTGAACCTAT
* * * *
5783289 ATAAGGAATTACCAACCGATCGGTGCTGAACCTGT
1 ATAAGGAATTACCAGCTGATCGGTGTTGAACCTAT
* * *
5783324 ATAAGGAATTACCAGCTTGATCAGAGCTGAACCTAT
1 ATAAGGAATTACCAGC-TGATCGGTGTTGAACCTAT
* * * *
5783360 ATGAGGAATTATCAGCTTGATCAGAGTTGAACCT
1 ATAAGGAATTACCAGC-TGATCGGTGTTGAACCT
5783394 GCAGAGTCTT
Statistics
Matches: 126, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 80 0.63
36 46 0.37
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (35 bp):
ATAAGGAATTACCAGCTGATCGGTGTTGAACCTAT
Found at i:5791026 original size:2 final size:2
Alignment explanation
Indices: 5791019--5791049 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5791009 CTTCCCTTCA
5791019 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5791050 ATTAAAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5794845 original size:14 final size:14
Alignment explanation
Indices: 5794802--5794837 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
5794792 AAGTCAATGG
5794802 GTTGACTCAGACGA
1 GTTGACTCAGACGA
5794816 GTTGACTCAGACGA
1 GTTGACTCAGACGA
5794830 GTTGACTC
1 GTTGACTC
5794838 GATCGAGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (14 bp):
GTTGACTCAGACGA
Found at i:5804229 original size:2 final size:2
Alignment explanation
Indices: 5804222--5804248 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5804212 CCTCCCTTCA
5804222 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5804249 ATTAGAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5804403 original size:19 final size:21
Alignment explanation
Indices: 5804361--5804403 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
5804351 TAAAACATTG
5804361 TATATGTTAATTCTTTCTTGC
1 TATATGTTAATTCTTTCTTGC
5804382 TATATGTT-ATTCTTTC-TGC
1 TATATGTTAATTCTTTCTTGC
5804401 TAT
1 TAT
5804404 TCAAAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.27
20 8 0.36
21 8 0.36
ACGTcount: A:0.19, C:0.14, G:0.09, T:0.58
Consensus pattern (21 bp):
TATATGTTAATTCTTTCTTGC
Found at i:5809880 original size:27 final size:26
Alignment explanation
Indices: 5809838--5809912 Score: 71
Period size: 25 Copynumber: 2.8 Consensus size: 26
5809828 TATAGCACCA
* **
5809838 TTTTCAAAATATTTACTAAAATGTCATTT
1 TTTTCAAAA-A-TTACAAAAATAACA-TT
**
5809867 TTTTCAAAAATTACGGAAATAACATT
1 TTTTCAAAAATTACAAAAATAACATT
5809893 TTTT-AAAAATTACAAAAATA
1 TTTTCAAAAATTACAAAAATA
5809913 GCACCCTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
25 14 0.35
26 6 0.15
27 10 0.25
28 1 0.03
29 9 0.22
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (26 bp):
TTTTCAAAAATTACAAAAATAACATT
Found at i:5809904 original size:110 final size:111
Alignment explanation
Indices: 5809772--5809973 Score: 291
Period size: 110 Copynumber: 1.8 Consensus size: 111
5809762 TGGTCAACGA
* * * *
5809772 AAATAGCATTTTTTTCAAAATTACGAAAATAGCTCCATTATAAAATTAATTACCAATATAG-CAC
1 AAATAACATTTTTTTAAAAATTACAAAAATAGCACCATTATAAAATTAATTACCAATAT-GTCAC
*
5809836 CATTTTCAAAATATTTACTAAAATGTCATTTTTTTCAAAAATTACGG
65 CATTTTCAAAATAATTACTAAAATGTCATTTTTTTCAAAAATTACGG
* * ** *
5809883 AAATAACA-TTTTTTAAAAATTACAAAAATAGCACCCTTTTTGAATTAATTCCCAATATGTCACC
1 AAATAACATTTTTTTAAAAATTACAAAAATAGCACCATTATAAAATTAATTACCAATATGTCACC
5809947 ATTTTCAAAATAATTACTAAAATGTCA
66 ATTTTCAAAATAATTACTAAAATGTCA
5809974 ATCGGTCAAC
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
109 1 0.01
110 72 0.90
111 7 0.09
ACGTcount: A:0.43, C:0.15, G:0.05, T:0.36
Consensus pattern (111 bp):
AAATAACATTTTTTTAAAAATTACAAAAATAGCACCATTATAAAATTAATTACCAATATGTCACC
ATTTTCAAAATAATTACTAAAATGTCATTTTTTTCAAAAATTACGG
Done.