Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004693.1 Hibiscus syriacus cultivar Beakdansim tig00010533_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: 2620943
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 9 of 12
Found at i:1810410 original size:22 final size:22
Alignment explanation
Indices: 1810369--1810410 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1810359 TTAATACTTA
**
1810369 AATTATATTTAATTTTAATTTT
1 AATTATATTTAATTACAATTTT
*
1810391 AATTTTATTTAATTACAATT
1 AATTATATTTAATTACAATT
1810411 AAGTTAATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
AATTATATTTAATTACAATTTT
Found at i:1811647 original size:24 final size:23
Alignment explanation
Indices: 1811603--1811649 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
1811593 TTTATCATTT
*
1811603 GTTTAATGTTCATAAATGTGTTC
1 GTTTAATGTTCATAAACGTGTTC
1811626 GTTTATATGTTC-TCAAACGTGTTC
1 GTTTA-ATGTTCAT-AAACGTGTTC
1811650 ATGAGCATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (23 bp):
GTTTAATGTTCATAAACGTGTTC
Found at i:1811710 original size:22 final size:22
Alignment explanation
Indices: 1811659--1811710 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
1811649 CATGAGCATG
1811659 TTCATTTAGTGTTCGTTTAACA
1 TTCATTTAGTGTTCGTTTAACA
* ** * *
1811681 ATGTTTTAGTGTTTGTTTATCA
1 TTCATTTAGTGTTCGTTTAACA
1811703 TTCATTTA
1 TTCATTTA
1811711 TATATATTTG
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.21, C:0.10, G:0.13, T:0.56
Consensus pattern (22 bp):
TTCATTTAGTGTTCGTTTAACA
Found at i:1820024 original size:6 final size:6
Alignment explanation
Indices: 1820009--1820790 Score: 1464
Period size: 6 Copynumber: 132.5 Consensus size: 6
1819999 ATAAGTCATA
*
1820009 ATATAC ATATAA ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1820057 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1820105 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1820153 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1820201 ATATAC ATATAC ATATAC ATATAC ATAT-- ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1820247 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1820295 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1820343 ATATAC ATATAC ATATAC --ATAC ATATAC --ATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1820387 --ATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1820433 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1820481 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATAT--
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1820527 ATATAC A-ATAC --ATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1820572 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1820620 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1820668 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1820716 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1820764 ATATAC ATATAC ATATAC ATATAC ATA
1 ATATAC ATATAC ATATAC ATATAC ATA
1820791 CCTTAGAGTA
Statistics
Matches: 762, Mismatches: 2, Indels: 24
0.97 0.00 0.03
Matches are distributed among these distances:
4 24 0.03
5 4 0.01
6 734 0.96
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.33
Consensus pattern (6 bp):
ATATAC
Found at i:1826487 original size:44 final size:45
Alignment explanation
Indices: 1826374--1826487 Score: 106
Period size: 44 Copynumber: 2.6 Consensus size: 45
1826364 TTAGGTAAGA
* * * * *
1826374 TCTAGGTCATATACCATCAACATCTCACAAGTACCCTAGGTGAGG
1 TCTAGGTCACATAACATCAACACCTCACAAGTACCATAGCTGAGG
** * ** *
1826419 TCCGGGTCACATATCATCGGCACCTCAC-AGTATCATATGCT-AGG
1 TCTAGGTCACATAACATCAACACCTCACAAGTACCATA-GCTGAGG
1826463 TCTAGGTCACATAACATCAACACCT
1 TCTAGGTCACATAACATCAACACCT
1826488 TGCTACGATA
Statistics
Matches: 53, Mismatches: 15, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
44 30 0.57
45 23 0.43
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.25
Consensus pattern (45 bp):
TCTAGGTCACATAACATCAACACCTCACAAGTACCATAGCTGAGG
Found at i:1826675 original size:31 final size:27
Alignment explanation
Indices: 1826609--1826672 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
1826599 GGATATTTCT
*
1826609 CAAATAACTAGACGATCGTCACACACA
1 CAAATAACTAGACGATCATCACACACA
1826636 CAAATAACTAGACGATCATCACACACA
1 CAAATAACTAGACGATCATCACACACA
1826663 CAAATAACTA
1 CAAATAACTA
1826673 ACTCGAGTGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.48, C:0.28, G:0.08, T:0.16
Consensus pattern (27 bp):
CAAATAACTAGACGATCATCACACACA
Found at i:1832611 original size:20 final size:20
Alignment explanation
Indices: 1832588--1832636 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1832578 AAAGTCAAAT
*
1832588 TCACAACGCGAATAGGTAAA
1 TCACAACGCGAATAGATAAA
** *
1832608 TCACAACGATAATATATAAA
1 TCACAACGCGAATAGATAAA
1832628 TCACAACGC
1 TCACAACGC
1832637 AAATTCTCCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.47, C:0.22, G:0.12, T:0.18
Consensus pattern (20 bp):
TCACAACGCGAATAGATAAA
Found at i:1832857 original size:135 final size:135
Alignment explanation
Indices: 1832605--1832862 Score: 419
Period size: 135 Copynumber: 1.9 Consensus size: 135
1832595 GCGAATAGGT
*
1832605 AAATCACAACGATAATATATAAATCACAACGCAAATTCTCCAAATTTGCAACTCCAATTTCGCAA
1 AAATCACAACGATAATATATAAATCACAACGCAAATTCTCCAAATTCGCAACTCCAATTTCGCAA
*
1832670 TGCTAATTACCGATATAGGTAATTAGCGTTGCGAAAACGAAATTCGCATTGCGATTTTCCAAATT
66 TGCTAATTACCAATATAGGTAATTAGCGTTGCGAAAACGAAATTCGCATTGCGATTTTCCAAATT
1832735 CGCAA
131 CGCAA
* * * * * *
1832740 AAATTACAACGATAATATGTAAATCGA-TACTCAAATTCTCCAAATTCGCAACTCGAATTTTGCA
1 AAATCACAACGATAATATATAAATC-ACAACGCAAATTCTCCAAATTCGCAACTCCAATTTCGCA
*
1832804 ATGCTAATTACCAATATAGGTAATTAGCGTTGCGAAAACGAAATTCGCGTTGCGATTTT
65 ATGCTAATTACCAATATAGGTAATTAGCGTTGCGAAAACGAAATTCGCATTGCGATTTT
1832863 GGAGAATCGC
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
135 112 0.99
136 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.29
Consensus pattern (135 bp):
AAATCACAACGATAATATATAAATCACAACGCAAATTCTCCAAATTCGCAACTCCAATTTCGCAA
TGCTAATTACCAATATAGGTAATTAGCGTTGCGAAAACGAAATTCGCATTGCGATTTTCCAAATT
CGCAA
Found at i:1832935 original size:104 final size:103
Alignment explanation
Indices: 1832788--1833096 Score: 325
Period size: 104 Copynumber: 2.9 Consensus size: 103
1832778 TCCAAATTCG
* * * *
1832788 CAACTCGAATTTTGCAATGCTAATTACCAATATAGGTAATTAGCGTTGCGAAAACGAAATTCGCG
1 CAACTTGAATTTCGCAACGCTAATTACC-ATATAGGTAATTAGCGTTGCGAAAATGAAATTCGCG
* ** **
1832853 TTGCGATTTTGGAGAATCGCGTCGCGAATTTTGT-TTTCA
65 TTGCGATTTTGGAGAATCGCGTTGCGAA-TAGGTAAATCA
* *
1832892 CAACTTGAATTTCGCAACGCTAATTACC-TACTTCGGTAATTAGCGTTGCGAAAATGAAATTTGC
1 CAACTTGAATTTCGCAACGCTAATTACCATA--TAGGTAATTAGCGTTGCGAAAATGAAATTCGC
* * *
1832956 ATTGTGATTTTGGAGAATCGCGTTGCGAATAGGTAAATCG
64 GTTGCGATTTTGGAGAATCGCGTTGCGAATAGGTAAATCA
* * *
1832996 CAACGTGAATTCTCCAAATTCACAACGCCAATTACCGATATAGGTAATTAGCGTTGCGAAAATGA
1 CAACTTGAA---T-----TTCGCAACGCTAATTACC-ATATAGGTAATTAGCGTTGCGAAAATGA
*
1833061 AATTCGTGTTGCGATTTTGGAGAATCGCGTTGCGAA
57 AATTCGCGTTGCGATTTTGGAGAATCGCGTTGCGAA
1833097 AACAAAATTC
Statistics
Matches: 170, Mismatches: 22, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
102 2 0.01
103 3 0.02
104 90 0.53
107 1 0.01
112 72 0.42
114 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (103 bp):
CAACTTGAATTTCGCAACGCTAATTACCATATAGGTAATTAGCGTTGCGAAAATGAAATTCGCGT
TGCGATTTTGGAGAATCGCGTTGCGAATAGGTAAATCA
Found at i:1833147 original size:20 final size:21
Alignment explanation
Indices: 1833122--1833238 Score: 95
Period size: 20 Copynumber: 5.8 Consensus size: 21
1833112 GCGATTTTCC
1833122 AAATTCGCAACGCGAA-AGTT
1 AAATTCGCAACGCGAATAGTT
*
1833142 AAATTCGCAATGCGAATAGTT
1 AAATTCGCAACGCGAATAGTT
**
1833163 AAA-TCGCAACGATAATA-TGT
1 AAATTCGCAACGCGAATAGT-T
* * *
1833183 -AATTCACAATGCGAATAGGT
1 AAATTCGCAACGCGAATAGTT
**
1833203 AAA-TCGCAACGATAATA-TGT
1 AAATTCGCAACGCGAATAGT-T
1833223 AAA-TCGCAACGCGAAT
1 AAATTCGCAACGCGAAT
1833239 TCTCCAAATT
Statistics
Matches: 75, Mismatches: 16, Indels: 12
0.73 0.16 0.12
Matches are distributed among these distances:
19 3 0.04
20 63 0.84
21 9 0.12
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.23
Consensus pattern (21 bp):
AAATTCGCAACGCGAATAGTT
Found at i:1833187 original size:40 final size:40
Alignment explanation
Indices: 1833143--1833238 Score: 156
Period size: 40 Copynumber: 2.4 Consensus size: 40
1833133 GCGAAAGTTA
*
1833143 AATTCGCAATGCGAATAGTTAAATCGCAACGATAATATGT
1 AATTCGCAATGCGAATAGGTAAATCGCAACGATAATATGT
*
1833183 AATTCACAATGCGAATAGGTAAATCGCAACGATAATATGT
1 AATTCGCAATGCGAATAGGTAAATCGCAACGATAATATGT
* *
1833223 AAATCGCAACGCGAAT
1 AATTCGCAATGCGAAT
1833239 TCTCCAAATT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.24
Consensus pattern (40 bp):
AATTCGCAATGCGAATAGGTAAATCGCAACGATAATATGT
Found at i:1833478 original size:21 final size:20
Alignment explanation
Indices: 1833454--1833565 Score: 109
Period size: 21 Copynumber: 5.5 Consensus size: 20
1833444 TCTATTTGTA
1833454 TTGCGAATTTGGAAAATCGCG
1 TTGCGAATTTGG-AAATCGCG
1833475 TTGCGAATTTGGAAAATCGCG
1 TTGCGAATTTGG-AAATCGCG
* * ***
1833496 TTGCGATTTTGGAACTTATG
1 TTGCGAATTTGGAAATCGCG
* **
1833516 TTGCGAAATTGGAGTTCGCG
1 TTGCGAATTTGGAAATCGCG
* *
1833536 TTACGAATTT-GAGATCGCG
1 TTGCGAATTTGGAAATCGCG
1833555 TTGCGAATTTG
1 TTGCGAATTTG
1833566 TTGGTCATTT
Statistics
Matches: 74, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
19 17 0.23
20 25 0.34
21 32 0.43
ACGTcount: A:0.24, C:0.13, G:0.29, T:0.34
Consensus pattern (20 bp):
TTGCGAATTTGGAAATCGCG
Found at i:1833542 original size:20 final size:20
Alignment explanation
Indices: 1833519--1833561 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
1833509 ACTTATGTTG
*
1833519 CGAAATTGGAGTTCGCGTTA
1 CGAAATTGGAGATCGCGTTA
* *
1833539 CG-AATTTGAGATCGCGTTG
1 CGAAATTGGAGATCGCGTTA
1833558 CGAA
1 CGAA
1833562 TTTGTTGGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (20 bp):
CGAAATTGGAGATCGCGTTA
Found at i:1840229 original size:3 final size:3
Alignment explanation
Indices: 1840221--1840280 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
1840211 TTCGTCCCTG
1840221 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1840269 TTA TTA TTA TTA
1 TTA TTA TTA TTA
1840281 AATAATTAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1840386 original size:13 final size:13
Alignment explanation
Indices: 1840370--1840402 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
1840360 CCCAAGCTCG
1840370 AAGCCCATCAGCC
1 AAGCCCATCAGCC
1840383 AAGCCCATCAGCC
1 AAGCCCATCAGCC
1840396 AAGCCCA
1 AAGCCCA
1840403 CAAGTGAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.33, C:0.45, G:0.15, T:0.06
Consensus pattern (13 bp):
AAGCCCATCAGCC
Found at i:1840738 original size:10 final size:10
Alignment explanation
Indices: 1840723--1840752 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
1840713 AAGGGAAGAA
1840723 AACCAACAAC
1 AACCAACAAC
1840733 AACCAACAAC
1 AACCAACAAC
1840743 AACCAACAAC
1 AACCAACAAC
1840753 CAAGAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.60, C:0.40, G:0.00, T:0.00
Consensus pattern (10 bp):
AACCAACAAC
Found at i:1842126 original size:17 final size:16
Alignment explanation
Indices: 1842097--1842138 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
1842087 AACACAGATC
1842097 AATT-TTTTATCTTTTAA
1 AATTATTTTATC--TTAA
1842114 AATTATTTT-TCTTAA
1 AATTATTTTATCTTAA
1842129 AATTATTTTA
1 AATTATTTTA
1842139 AAATGTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 13 0.57
17 6 0.26
18 4 0.17
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (16 bp):
AATTATTTTATCTTAA
Found at i:1852933 original size:228 final size:228
Alignment explanation
Indices: 1852657--1853312 Score: 981
Period size: 228 Copynumber: 2.9 Consensus size: 228
1852647 GACCAAATGA
* *
1852657 AGGGTCGACTCCTTTTGGATGTTGTAGTCAGCCAAGGTACGGCCGTCCTCGAGCTGTTTTCCAGC
1 AGGGTCGACTCCTTCTGGATGTTGTAGTCAGCCAAGGTACGGCCGTCCTCGAGCTGTTTTCCGGC
*
1852722 GAAGATGAGACGTTGCTGGTCCGGTGGGATTCCTTCCTTGTCTTGGATCTTGGCCTTGACGTTGT
66 GAAGATGAGACGTTGCTGGTCCGGTGGGATCCCTTCCTTGTCTTGGATCTTGGCCTTGACGTTGT
1852787 CGATGGTGTCGGAGCTCTCGACTTCCAAGGTGATTGTTTTGCCGGTCAGGGTTTTCACGAAGATT
131 CGATGGTGTCGGAGCTCTCGACTTCCAAGGTGATTGTTTTGCCGGTCAGGGTTTTCACGAAGATT
1852852 TGCATGCCTCCACGAAGACGGAGGACAAGGTGG
196 TGCATGCCTCCACGAAGACGGAGGACAAGGTGG
* * * * * *
1852885 AGGGTCGACTCCTTCTGGATATTATAGTCCGCCAAGGTACGGCCGTCCTCGAGTTGCTTCCCGGC
1 AGGGTCGACTCCTTCTGGATGTTGTAGTCAGCCAAGGTACGGCCGTCCTCGAGCTGTTTTCCGGC
* * *
1852950 GAAGATTAG-CCTCTGCTGGTCTGGTGGGATCCCTTCCTTGTCTTGGATCTTGGCCTTGACGTTG
66 GAAGATGAGACGT-TGCTGGTCCGGTGGGATCCCTTCCTTGTCTTGGATCTTGGCCTTGACGTTG
* * *
1853014 TCGATGGTGTCGGAGCTCTCGACTTCCAAGGTGATGGTTTTACCGGTAAGGGTTTTCACGAAGAT
130 TCGATGGTGTCGGAGCTCTCGACTTCCAAGGTGATTGTTTTGCCGGTCAGGGTTTTCACGAAGAT
*
1853079 TTGCATGCCTCCACGAAGACGGAGGACGAGGTGG
195 TTGCATGCCTCCACGAAGACGGAGGACAAGGTGG
* * * *
1853113 AGGGTTGACTCCTTCTGGATGTTGTAATCGGCCAAGGTACGACCGTCCTCGAGCTGTTTTCCGGC
1 AGGGTCGACTCCTTCTGGATGTTGTAGTCAGCCAAGGTACGGCCGTCCTCGAGCTGTTTTCCGGC
* * * * * * *
1853178 GAAGATGAGACGCTGTTGGTCCGGAGGAATCCCTTCCTTGTCTTGGATCTTCGCCTTGACATTAT
66 GAAGATGAGACGTTGCTGGTCCGGTGGGATCCCTTCCTTGTCTTGGATCTTGGCCTTGACGTTGT
* * * * * * * *
1853243 CAATGGTGTCGGAGCTCTCGACCTCGAGGGTGATTGTCTTGCCGGTCAGGGTCTTAACGAAGATC
131 CGATGGTGTCGGAGCTCTCGACTTCCAAGGTGATTGTTTTGCCGGTCAGGGTTTTCACGAAGATT
1853308 TGCAT
196 TGCAT
1853313 CTTGTTTGGC
Statistics
Matches: 380, Mismatches: 46, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
227 2 0.01
228 377 0.99
229 1 0.00
ACGTcount: A:0.17, C:0.23, G:0.30, T:0.29
Consensus pattern (228 bp):
AGGGTCGACTCCTTCTGGATGTTGTAGTCAGCCAAGGTACGGCCGTCCTCGAGCTGTTTTCCGGC
GAAGATGAGACGTTGCTGGTCCGGTGGGATCCCTTCCTTGTCTTGGATCTTGGCCTTGACGTTGT
CGATGGTGTCGGAGCTCTCGACTTCCAAGGTGATTGTTTTGCCGGTCAGGGTTTTCACGAAGATT
TGCATGCCTCCACGAAGACGGAGGACAAGGTGG
Found at i:1854496 original size:2 final size:2
Alignment explanation
Indices: 1854489--1854520 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1854479 ATCTTTCATA
1854489 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1854521 TTTGCTAATG
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1854870 original size:27 final size:27
Alignment explanation
Indices: 1854795--1854871 Score: 79
Period size: 25 Copynumber: 2.9 Consensus size: 27
1854785 TGTTACCTTA
*
1854795 ATCAAGTTGCTCAAACCATACCCTGAT
1 ATCAAGTTGCTCGAACCATACCCTGAT
** *
1854822 A--AAGTTGCTCGAATTATGCCCT-ACT
1 ATCAAGTTGCTCGAACCATACCCTGA-T
*
1854847 ATCAAGTTTCTCGAACCATACCCTG
1 ATCAAGTTGCTCGAACCATACCCTG
1854872 TTACCAACTT
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
24 1 0.03
25 19 0.50
27 18 0.47
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.29
Consensus pattern (27 bp):
ATCAAGTTGCTCGAACCATACCCTGAT
Found at i:1859752 original size:8 final size:8
Alignment explanation
Indices: 1859741--1859773 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
1859731 AGCCGACAAG
1859741 GCTAGAAA
1 GCTAGAAA
*
1859749 GCTAGCAA
1 GCTAGAAA
1859757 GCTAGAAA
1 GCTAGAAA
1859765 GCTAGAAA
1 GCTAGAAA
1859773 G
1 G
1859774 AATGAACTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.45, C:0.15, G:0.27, T:0.12
Consensus pattern (8 bp):
GCTAGAAA
Found at i:1870812 original size:22 final size:21
Alignment explanation
Indices: 1870786--1870891 Score: 140
Period size: 22 Copynumber: 4.8 Consensus size: 21
1870776 ATGAAATTTT
* *
1870786 TCCCGATGACCTCATATATATG
1 TCCCGAGGACCT-ATGTATATG
1870808 TCCCGAAGGACCTATGTATATG
1 TCCCG-AGGACCTATGTATATG
1870830 TCCCGAAGGACCTATGTATATG
1 TCCCG-AGGACCTATGTATATG
*
1870852 TCCCAAAGGACCTATGTATATG
1 TCCC-GAGGACCTATGTATATG
1870874 TCCCGAAGGACCTATGTA
1 TCCCG-AGGACCTATGTA
1870892 ACCTTCGACT
Statistics
Matches: 77, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
22 71 0.92
23 6 0.08
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (21 bp):
TCCCGAGGACCTATGTATATG
Found at i:1870850 original size:44 final size:44
Alignment explanation
Indices: 1870793--1870891 Score: 171
Period size: 44 Copynumber: 2.2 Consensus size: 44
1870783 TTTTCCCGAT
* *
1870793 GACCTCATATATATGTCCCGAAGGACCTATGTATATGTCCCGAAG
1 GACCT-ATGTATATGTCCCAAAGGACCTATGTATATGTCCCGAAG
1870838 GACCTATGTATATGTCCCAAAGGACCTATGTATATGTCCCGAAG
1 GACCTATGTATATGTCCCAAAGGACCTATGTATATGTCCCGAAG
1870882 GACCTATGTA
1 GACCTATGTA
1870892 ACCTTCGACT
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
44 47 0.90
45 5 0.10
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.27
Consensus pattern (44 bp):
GACCTATGTATATGTCCCAAAGGACCTATGTATATGTCCCGAAG
Found at i:1873633 original size:23 final size:23
Alignment explanation
Indices: 1873599--1873659 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
1873589 CTTATATAAA
*
1873599 TGCACCAAAGTGCCACATAGAAT
1 TGCACCATAGTGCCACATAGAAT
* *
1873622 TGCACCATAGTGCCGCGTAGAAT
1 TGCACCATAGTGCCACATAGAAT
*
1873645 TGCACCGTAGTGCCA
1 TGCACCATAGTGCCA
1873660 TATAATAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.20
Consensus pattern (23 bp):
TGCACCATAGTGCCACATAGAAT
Found at i:1873846 original size:103 final size:103
Alignment explanation
Indices: 1873675--1873890 Score: 405
Period size: 103 Copynumber: 2.1 Consensus size: 103
1873665 TAATGTCCAT
1873675 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGCGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGCGTCTCACCA
1873740 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* * *
1873778 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCATCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGCGTCTCACCA
1873843 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1873881 AAGGACCACA
1 AAGGACCACA
1873891 ATGTCCCGAA
Statistics
Matches: 110, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGCGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1873896 original size:18 final size:18
Alignment explanation
Indices: 1873873--1873926 Score: 108
Period size: 18 Copynumber: 3.0 Consensus size: 18
1873863 GAATACATAT
1873873 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
1873891 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
1873909 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
1873927 TATCATTCCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.33, C:0.33, G:0.22, T:0.11
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACA
Found at i:1874020 original size:139 final size:139
Alignment explanation
Indices: 1873770--1874029 Score: 511
Period size: 139 Copynumber: 1.9 Consensus size: 139
1873760 GAATACATAT
1873770 ATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTG
1 ATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTG
*
1873835 TCTCATCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCACAATGTCCCGA
66 TCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCACAATGTCCCGA
1873900 AGGACCACA
131 AGGACCACA
1873909 ATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTG
1 ATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTG
1873974 TCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCACA
66 TCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCACA
1874030 TAGACCCTCG
Statistics
Matches: 120, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 120 1.00
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (139 bp):
ATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTG
TCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCACAATGTCCCGA
AGGACCACA
Found at i:1875340 original size:21 final size:21
Alignment explanation
Indices: 1875310--1875350 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1875300 TTTTATTCGC
* *
1875310 TTGAAGGGGTATCGGTTCCCT
1 TTGAAGGGGTACCGATTCCCT
*
1875331 TTGAATGGGTACCGATTCCC
1 TTGAAGGGGTACCGATTCCC
1875351 CTAGCCCAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.22, G:0.29, T:0.32
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCT
Found at i:1879702 original size:23 final size:22
Alignment explanation
Indices: 1879676--1879740 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
1879666 ATATGAAATT
*
1879676 TGTCCCGAATGACCTCATGTATA
1 TGTCCCGAAGGACCT-ATGTATA
* *
1879699 TGTCACGGAGGACCTATGTATA
1 TGTCCCGAAGGACCTATGTATA
* *
1879721 TGTTCCGAAGGATCTATGTA
1 TGTCCCGAAGGACCTATGTA
1879741 CCTCGACTCT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
22 23 0.66
23 12 0.34
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (22 bp):
TGTCCCGAAGGACCTATGTATA
Found at i:1882177 original size:20 final size:20
Alignment explanation
Indices: 1882154--1882196 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1882144 GATAATCAAA
1882154 TTCGCGTTGCGATTGTCATT
1 TTCGCGTTGCGATTGTCATT
* *
1882174 TTCGTGTTGCGATTTTCATT
1 TTCGCGTTGCGATTGTCATT
1882194 TTC
1 TTC
1882197 AGAAACTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.09, C:0.19, G:0.21, T:0.51
Consensus pattern (20 bp):
TTCGCGTTGCGATTGTCATT
Found at i:1882387 original size:25 final size:24
Alignment explanation
Indices: 1882333--1882387 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1882323 TGTTTATTAT
* *
1882333 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
1882357 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
1882383 TGTTT
1 TGTTT
1882388 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:1883537 original size:18 final size:18
Alignment explanation
Indices: 1883516--1883563 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
1883506 TCCACTTCGG
1883516 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
1883534 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1883552 GAGCCATCACCT
1 GAGCCATCACCT
1883564 AATCGACCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1884139 original size:19 final size:19
Alignment explanation
Indices: 1884098--1884195 Score: 82
Period size: 19 Copynumber: 5.4 Consensus size: 19
1884088 TAGTTTACTT
* **
1884098 TCGCAACACGAAAATGACTA
1 TCGCAATACG-AAATGAAAA
1884118 TCGCAATACGAAATGAAAA
1 TCGCAATACGAAATGAAAA
1884137 TCGC-A-ACGACAA-G---A
1 TCGCAATACGA-AATGAAAA
*
1884151 TCGCAATGCGAAATGAAAA
1 TCGCAATACGAAATGAAAA
**
1884170 TCGCAACGCGAAATGAAAA
1 TCGCAATACGAAATGAAAA
1884189 TCGCAAT
1 TCGCAAT
1884196 GCGATTTATG
Statistics
Matches: 65, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
14 5 0.08
15 3 0.05
16 4 0.06
17 5 0.08
18 3 0.05
19 36 0.55
20 9 0.14
ACGTcount: A:0.46, C:0.21, G:0.18, T:0.14
Consensus pattern (19 bp):
TCGCAATACGAAATGAAAA
Found at i:1884199 original size:19 final size:19
Alignment explanation
Indices: 1884117--1884199 Score: 97
Period size: 19 Copynumber: 4.6 Consensus size: 19
1884107 GAAAATGACT
*
1884117 ATCGCAATACGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1884136 ATCGCAA--CGACAA-G---
1 ATCGCAATGCGA-AATGAAA
1884150 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1884169 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1884188 ATCGCAATGCGA
1 ATCGCAATGCGA
1884200 TTTATGTTTC
Statistics
Matches: 55, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
14 7 0.13
15 2 0.04
16 4 0.07
17 4 0.07
18 2 0.04
19 36 0.65
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1884243 original size:33 final size:33
Alignment explanation
Indices: 1884206--1884285 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
1884196 GCGATTTATG
* * * *
1884206 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATCTTATCATTGCGATTTTCA
1884239 TTTCGCATTGCGATCTTATCATTGCGATTTTCA
1 TTTCGCATTGCGATCTTATCATTGCGATTTTCA
1884272 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
1884286 AGCCATTTCC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.46
Consensus pattern (33 bp):
TTTCGCATTGCGATCTTATCATTGCGATTTTCA
Found at i:1884251 original size:19 final size:19
Alignment explanation
Indices: 1884227--1884285 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
1884217 GATTTTGTCG
1884227 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1884246 TTGCGATCTT-A--T--CA
1 TTGCGATTTTCATTTCGCA
1884260 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1884279 TTGCGAT
1 TTGCGAT
1884286 AGCCATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 11 0.33
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 18 0.55
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1884304 original size:20 final size:20
Alignment explanation
Indices: 1884270--1884344 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
1884260 TTGCGATTTT
*
1884270 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
1884289 CATTTCCGCGTTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
1884309 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGC
*
1884329 CATTTTCGCGTTGCGA
1 CATTTCCGCGTTGCGA
1884345 AAGTATGTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
19 5 0.10
20 47 0.90
ACGTcount: A:0.16, C:0.27, G:0.24, T:0.33
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:1884764 original size:21 final size:20
Alignment explanation
Indices: 1884712--1884767 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
1884702 GACTCACCTG
*
1884712 TCATCCCTCAAGAGTCCCCT
1 TCATCCCTCAAGAGGCCCCT
* **
1884732 CCAATCGTTCAAGAGGCCCCT
1 TC-ATCCCTCAAGAGGCCCCT
1884753 ATCATCCCTCAAGAG
1 -TCATCCCTCAAGAG
1884768 TCTCCCCCAC
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
20 1 0.04
21 25 0.93
22 1 0.04
ACGTcount: A:0.25, C:0.39, G:0.14, T:0.21
Consensus pattern (20 bp):
TCATCCCTCAAGAGGCCCCT
Found at i:1886405 original size:19 final size:19
Alignment explanation
Indices: 1886381--1886445 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
1886371 ACAACGAGAG
1886381 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1886400 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1886419 AATCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
1886433 AATCGCAATGCGA
1 AATCGCAATGCGA
1886446 TTTTTATTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
14 11 0.26
15 1 0.02
16 2 0.05
17 2 0.05
19 27 0.63
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1886477 original size:20 final size:20
Alignment explanation
Indices: 1886452--1886525 Score: 130
Period size: 20 Copynumber: 3.7 Consensus size: 20
1886442 GCGATTTTTA
1886452 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
*
1886472 TTTCGCGTTGCGATAGCCAT
1 TTTCGCGTTGCGATAGTCAT
*
1886492 TTTCACGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
1886512 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
1886526 TTCCCCGTTG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.39
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:1886540 original size:34 final size:36
Alignment explanation
Indices: 1886457--1886544 Score: 108
Period size: 40 Copynumber: 2.4 Consensus size: 36
1886447 TTTTATTTCG
*
1886457 CGTTGCGATAGTCATTTTCGCGTTGCGATAGCCATTTTCA
1 CGTTGCGATAGTCATTTTCGCGTTGC---AG-CATTTCCA
*
1886497 CGTTGCGATAGTCATTTTCGCGTTGC-G-ATTTCCC
1 CGTTGCGATAGTCATTTTCGCGTTGCAGCATTTCCA
1886531 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
1886545 AATGAATGTC
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
34 19 0.41
36 1 0.02
40 26 0.57
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (36 bp):
CGTTGCGATAGTCATTTTCGCGTTGCAGCATTTCCA
Found at i:1886893 original size:20 final size:20
Alignment explanation
Indices: 1886868--1886950 Score: 132
Period size: 20 Copynumber: 4.2 Consensus size: 20
1886858 ATTCTGTATT
*
1886868 ATCTCGTTGCGATAGTCAGA
1 ATCTCGTTGCGAAAGTCAGA
1886888 ATCTCGTTGCGAAAGTCAGA
1 ATCTCGTTGCGAAAGTCAGA
1886908 ATCGT-GTTGCGAAAGTCAGA
1 ATC-TCGTTGCGAAAGTCAGA
*
1886928 ATCACGTTGCGAAAGTCAGA
1 ATCTCGTTGCGAAAGTCAGA
1886948 ATC
1 ATC
1886951 GTGATTTTTG
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
20 58 0.98
21 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.25
Consensus pattern (20 bp):
ATCTCGTTGCGAAAGTCAGA
Found at i:1887661 original size:24 final size:24
Alignment explanation
Indices: 1887634--1887687 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1887624 GTATTCGAAA
*
1887634 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
1887658 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
1887682 TTTGAT
1 TTTGAT
1887688 GATGTTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:1887879 original size:12 final size:12
Alignment explanation
Indices: 1887862--1887886 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1887852 ATATAATCAT
1887862 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1887874 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1887886 G
1 G
1887887 TCCCCGGAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1890201 original size:20 final size:20
Alignment explanation
Indices: 1890134--1890206 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
1890124 GACATTCATT
1890134 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACACGGAAA
**
1890154 TGACGT-TCGCAATCATC-TTAA
1 TGAC-TATCGCAA-CA-CGGAAA
* *
1890175 TGTCTATCGCAACGCGGAAA
1 TGACTATCGCAACACGGAAA
*
1890195 TGACTATTGCAA
1 TGACTATCGCAA
1890207 TGCAAAATAA
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 1 0.03
20 24 0.60
21 14 0.35
22 1 0.03
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (20 bp):
TGACTATCGCAACACGGAAA
Found at i:1890248 original size:33 final size:33
Alignment explanation
Indices: 1890211--1890293 Score: 132
Period size: 33 Copynumber: 2.5 Consensus size: 33
1890201 TTGCAATGCA
1890211 AAATAAAAATCGCAACGAGAGAATCGCAATA-CG
1 AAATAAAAATCGCAACGAGAGAATCGCAA-AGCG
*
1890244 AAATAAAAATCGCAACGAGGGAATCGCAAAGCG
1 AAATAAAAATCGCAACGAGAGAATCGCAAAGCG
*
1890277 AAATGAAAATCGCAACG
1 AAATAAAAATCGCAACG
1890294 CGATTTTAGT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
32 1 0.02
33 46 0.98
ACGTcount: A:0.51, C:0.18, G:0.20, T:0.11
Consensus pattern (33 bp):
AAATAAAAATCGCAACGAGAGAATCGCAAAGCG
Found at i:1890315 original size:19 final size:19
Alignment explanation
Indices: 1890293--1890352 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
1890283 AAATCGCAAC
1890293 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
1890312 GCGATTTT-G--T--CGTT
1 GCGATTTTAGTTTCGCGTT
1890326 GCGATTTTCA-TTTCGCGTT
1 GCGATTTT-AGTTTCGCGTT
1890345 GCGATTTT
1 GCGATTTT
1890353 CATTTCGCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
14 12 0.34
16 1 0.03
17 1 0.03
18 1 0.03
19 20 0.57
ACGTcount: A:0.10, C:0.17, G:0.25, T:0.48
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:1890353 original size:19 final size:19
Alignment explanation
Indices: 1890322--1890360 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1890312 GCGATTTTGT
1890322 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
1890341 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
1890360 C
1 C
1890361 ATTACGATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1890368 original size:19 final size:19
Alignment explanation
Indices: 1890327--1890368 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1890317 TTTGTCGTTG
* *
1890327 CGATTTTCATTTCGCGTTG
1 CGATTTTCATTTCGCATTA
1890346 CGATTTTCATTTCGCATTA
1 CGATTTTCATTTCGCATTA
1890365 CGAT
1 CGAT
1890369 AGTCATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.45
Consensus pattern (19 bp):
CGATTTTCATTTCGCATTA
Found at i:1890374 original size:19 final size:19
Alignment explanation
Indices: 1890333--1890376 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1890323 GTTGCGATTT
* * **
1890333 TCATTTCGCGTTGCGATTT
1 TCATTTCGCATTACGATAG
1890352 TCATTTCGCATTACGATAG
1 TCATTTCGCATTACGATAG
1890371 TCATTT
1 TCATTT
1890377 TTGCCTTCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.18, C:0.20, G:0.16, T:0.45
Consensus pattern (19 bp):
TCATTTCGCATTACGATAG
Found at i:1890494 original size:14 final size:14
Alignment explanation
Indices: 1890475--1890508 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1890465 CATCAATTAA
1890475 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1890489 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1890503 ACAAAT
1 ACAAAT
1890509 AAATTAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1891927 original size:21 final size:21
Alignment explanation
Indices: 1891861--1891927 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1891851 GTGAATCGGG
*
1891861 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1891881 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1891903 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1891924 CTCT
1 CTCT
1891928 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1891946 original size:42 final size:41
Alignment explanation
Indices: 1891861--1891983 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1891851 GTGAATCGGG
* * * *
1891861 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
1891903 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
1891945 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
1891984 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:1893191 original size:18 final size:18
Alignment explanation
Indices: 1893168--1893211 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
1893158 CTAATTCTGA
1893168 AAAATAAGATACTGCACG
1 AAAATAAGATACTGCACG
**
1893186 AAAATAAGATGTTGCACG
1 AAAATAAGATACTGCACG
1893204 AAAATAAG
1 AAAATAAG
1893212 CACAATACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.52, C:0.11, G:0.18, T:0.18
Consensus pattern (18 bp):
AAAATAAGATACTGCACG
Found at i:1895358 original size:21 final size:21
Alignment explanation
Indices: 1895334--1895381 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
1895324 TGACTGTGGC
*
1895334 GGAGGACTAGAAGCTGGGGGT
1 GGAGGACTAGAAGCTGAGGGT
*
1895355 GGAGGACTAGAAGGTGAGGGT
1 GGAGGACTAGAAGCTGAGGGT
1895376 GGAGGA
1 GGAGGA
1895382 GACAAAGTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.27, C:0.06, G:0.54, T:0.12
Consensus pattern (21 bp):
GGAGGACTAGAAGCTGAGGGT
Found at i:1896457 original size:36 final size:35
Alignment explanation
Indices: 1896400--1896468 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 35
1896390 GAAGCCAAAC
* *
1896400 TGAATGGAAACTTCAAGTCTTTCATTCATCGGTTT
1 TGAATGGAAACTTAAAGTCTTTCAGTCATCGGTTT
*
1896435 TGAATGGATACTTAAAAGTCTTTCAGTCATCGGT
1 TGAATGGAAACTT-AAAGTCTTTCAGTCATCGGT
1896469 CTTACCTGCG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 12 0.40
36 18 0.60
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.38
Consensus pattern (35 bp):
TGAATGGAAACTTAAAGTCTTTCAGTCATCGGTTT
Found at i:1897534 original size:32 final size:32
Alignment explanation
Indices: 1897449--1897537 Score: 99
Period size: 32 Copynumber: 2.8 Consensus size: 32
1897439 CTTTCAAAAC
*
1897449 TTACAAAATAATTATTAAA-TTTATCTAATAG
1 TTACAAAATAATTATTAAATTTTATCGAATAG
** * *
1897480 TTACAAAATGGTTATTATATTTTATCGAATTG
1 TTACAAAATAATTATTAAATTTTATCGAATAG
* * *
1897512 TTATAAAATTATCATTAAATTTTATC
1 TTACAAAATAATTATTAAATTTTATC
1897538 AAAATATTAA
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
31 16 0.34
32 31 0.66
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.46
Consensus pattern (32 bp):
TTACAAAATAATTATTAAATTTTATCGAATAG
Found at i:1899319 original size:17 final size:17
Alignment explanation
Indices: 1899297--1899341 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
1899287 TGGGACTGGG
*
1899297 TCTGGGCCTGGATCGGT
1 TCTGGGCCTGGATCAGT
1899314 TCTGGGCCTGGATCAGT
1 TCTGGGCCTGGATCAGT
1899331 TCTGGGCCTGG
1 TCTGGGCCTGG
1899342 TGCGGGTTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.07, C:0.24, G:0.40, T:0.29
Consensus pattern (17 bp):
TCTGGGCCTGGATCAGT
Found at i:1906117 original size:25 final size:23
Alignment explanation
Indices: 1906068--1906117 Score: 55
Period size: 25 Copynumber: 2.1 Consensus size: 23
1906058 AGTTATTTCG
* *
1906068 AATTAATAAATAAAATATTATTT
1 AATTAATAAATAAAATATAAATT
*
1906091 AATTAATTCAAATTAAATATAAATT
1 AATTAA-T-AAATAAAATATAAATT
1906116 AA
1 AA
1906118 AGGGTTATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 6 0.27
24 1 0.05
25 15 0.68
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
AATTAATAAATAAAATATAAATT
Found at i:1907905 original size:20 final size:21
Alignment explanation
Indices: 1907880--1907925 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
1907870 GACTGTGGCA
1907880 GAGGACTAGAAGCTG-GGGTG
1 GAGGACTAGAAGCTGAGGGTG
*
1907900 GAGGACTAGAAGGTGAGGGTG
1 GAGGACTAGAAGCTGAGGGTG
1907921 GAGGA
1 GAGGA
1907926 GACAAAGACA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.28, C:0.07, G:0.52, T:0.13
Consensus pattern (21 bp):
GAGGACTAGAAGCTGAGGGTG
Found at i:1913728 original size:21 final size:21
Alignment explanation
Indices: 1913702--1913749 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
1913692 TGAATTTGGC
* *
1913702 GGAGGACTAGCAGCTGGGGGT
1 GGAGGACTAGAAGCTGAGGGT
*
1913723 GGAGGACTAGAAGGTGAGGGT
1 GGAGGACTAGAAGCTGAGGGT
1913744 GGAGGA
1 GGAGGA
1913750 GACAAAGACG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.25, C:0.08, G:0.54, T:0.12
Consensus pattern (21 bp):
GGAGGACTAGAAGCTGAGGGT
Found at i:1914819 original size:36 final size:35
Alignment explanation
Indices: 1914762--1914833 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 35
1914752 GAAGCCAAAC
*
1914762 TGAATGGAAACTTCAAGTCTTTCATTCATCGGTCT
1 TGAATGGAAACTTAAAGTCTTTCATTCATCGGTCT
*
1914797 TGAATGGATACTTAAAAGTCTTTCATTCATCGGTCT
1 TGAATGGAAACTT-AAAGTCTTTCATTCATCGGTCT
1914833 T
1 T
1914834 ACCTGCGACT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 12 0.35
36 22 0.65
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (35 bp):
TGAATGGAAACTTAAAGTCTTTCATTCATCGGTCT
Found at i:1915922 original size:32 final size:32
Alignment explanation
Indices: 1915886--1915956 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
1915876 ATCTAATAGT
* * * *
1915886 TAAAATGGTTATTATATTTTATCAAATTGTTA
1 TAAAATGATCATTAAATTTTATCAAATTATTA
1915918 TAAAATGATCATTAAATTTTATCAAATTATTA
1 TAAAATGATCATTAAATTTTATCAAATTATTA
1915950 -AAAATGA
1 TAAAATGA
1915957 AAATTGAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
31 7 0.20
32 28 0.80
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (32 bp):
TAAAATGATCATTAAATTTTATCAAATTATTA
Found at i:1920356 original size:3 final size:3
Alignment explanation
Indices: 1920342--1920419 Score: 126
Period size: 3 Copynumber: 26.7 Consensus size: 3
1920332 TGTCGAGGAG
1920342 GAA G-A GAA -AA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1920388 GAA GAA GAA GAA GAA GAA GAGA GAA -AA GAA GA
1 GAA GAA GAA GAA GAA GAA GA-A GAA GAA GAA GA
1920420 GAGTTAATGG
Statistics
Matches: 71, Mismatches: 0, Indels: 8
0.90 0.00 0.10
Matches are distributed among these distances:
2 6 0.08
3 62 0.87
4 3 0.04
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1923929 original size:21 final size:21
Alignment explanation
Indices: 1923905--1923952 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1923895 TGACTGTGGC
* *
1923905 GGAGGACTAGCAGCTTG-GGGT
1 GGAGGACTAGAAG-GTGAGGGT
1923926 GGAGGACTAGAAGGTGAGGGT
1 GGAGGACTAGAAGGTGAGGGT
1923947 GGAGGA
1 GGAGGA
1923953 GACAAAGATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.25, C:0.08, G:0.52, T:0.15
Consensus pattern (21 bp):
GGAGGACTAGAAGGTGAGGGT
Found at i:1926545 original size:3 final size:3
Alignment explanation
Indices: 1926531--1926601 Score: 105
Period size: 3 Copynumber: 24.7 Consensus size: 3
1926521 TGTCGAGGAG
1926531 GAA G-A GAA -AA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1926577 GAA GAA GAA GAA -AGA GAA -AA GAA GA
1 GAA GAA GAA GAA GA-A GAA GAA GAA GA
1926602 GAGTTAATGG
Statistics
Matches: 63, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
2 7 0.11
3 55 0.87
4 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1932459 original size:21 final size:21
Alignment explanation
Indices: 1932435--1932482 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1932425 TGACTGTGGC
* *
1932435 GGAGGACTAGCAGCTTG-GGGT
1 GGAGGACTAGAAG-GTGAGGGT
1932456 GGAGGACTAGAAGGTGAGGGT
1 GGAGGACTAGAAGGTGAGGGT
1932477 GGAGGA
1 GGAGGA
1932483 GACAAAGATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.25, C:0.08, G:0.52, T:0.15
Consensus pattern (21 bp):
GGAGGACTAGAAGGTGAGGGT
Found at i:1940865 original size:20 final size:19
Alignment explanation
Indices: 1940831--1940880 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
1940821 AAATGATTTT
* *
1940831 ATTTTG-AAAATAAAATTA
1 ATTTTGAAAAACAAAATGA
1940849 GATTTTGAAAAACAAAATGA
1 -ATTTTGAAAAACAAAATGA
1940869 AGTTTTGAAAAA
1 A-TTTTGAAAAA
1940881 TGATTTTGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 7 0.26
20 20 0.74
ACGTcount: A:0.54, C:0.02, G:0.12, T:0.32
Consensus pattern (19 bp):
ATTTTGAAAAACAAAATGA
Found at i:1942430 original size:20 final size:19
Alignment explanation
Indices: 1942405--1942460 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
1942395 ATATTTCAGT
* *
1942405 CTGGTTTCGAAACCCCTTGC
1 CTGGTTTCAAAACCCC-TGA
1942425 CTGGTTTCAAAACACCCTGA
1 CTGGTTTCAAAAC-CCCTGA
* *
1942445 CTAGTTTCTAAACCCC
1 CTGGTTTCAAAACCCC
1942461 ATGTTCCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 3 0.10
20 25 0.81
21 3 0.10
ACGTcount: A:0.23, C:0.34, G:0.14, T:0.29
Consensus pattern (19 bp):
CTGGTTTCAAAACCCCTGA
Found at i:1946178 original size:30 final size:30
Alignment explanation
Indices: 1946142--1946207 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
1946132 AAAAAAAGAT
*
1946142 TAAATAAGAA-AAAATAATTTAAAG-TGAAAA
1 TAAATAA-AATAAAA-AATGTAAAGTTGAAAA
*
1946172 TAAATAAAATAGAAAATGTAAAGTTGAAAA
1 TAAATAAAATAAAAAATGTAAAGTTGAAAA
1946202 TAAATA
1 TAAATA
1946208 TGGTAAAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 10 0.31
30 22 0.69
ACGTcount: A:0.65, C:0.00, G:0.11, T:0.24
Consensus pattern (30 bp):
TAAATAAAATAAAAAATGTAAAGTTGAAAA
Found at i:1950491 original size:43 final size:44
Alignment explanation
Indices: 1950406--1950497 Score: 111
Period size: 44 Copynumber: 2.1 Consensus size: 44
1950396 GAGTGTTTTA
* *
1950406 ATTGGGGTGAAATTGGTTTCAAAATTAAAAATAAGGTAAATATG
1 ATTGGGGTAAAATTGGTTTCAAAATTAAAAATAAGATAAATATG
*
1950450 ATTGGGGTAAAATAT-GTTT-AAAATTTAAAATAGAGAT-AATATG
1 ATTGGGGTAAAAT-TGGTTTCAAAATTAAAAATA-AGATAAATATG
1950493 -TTGGG
1 ATTGGG
1950498 ATAGGAGTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
42 5 0.12
43 18 0.42
44 19 0.44
45 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.23, T:0.34
Consensus pattern (44 bp):
ATTGGGGTAAAATTGGTTTCAAAATTAAAAATAAGATAAATATG
Found at i:1953873 original size:21 final size:21
Alignment explanation
Indices: 1953848--1953889 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1953838 GTGAAAATAA
1953848 TGAAAATAGAAAAT-GTAAAAT
1 TGAAAATA-AAAATGGTAAAAT
*
1953869 TGAAAATAAATATGGTAAAAT
1 TGAAAATAAAAATGGTAAAAT
1953890 ATAGCCTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.60, C:0.00, G:0.14, T:0.26
Consensus pattern (21 bp):
TGAAAATAAAAATGGTAAAAT
Found at i:1957043 original size:21 final size:21
Alignment explanation
Indices: 1957019--1957066 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
1957009 TGACTGTGGC
* *
1957019 GGAGGACTAGCAGCTGGGGGT
1 GGAGGACTAGAAGCTGAGGGT
*
1957040 GGAGGACTAGAAGGTGAGGGT
1 GGAGGACTAGAAGCTGAGGGT
1957061 GGAGGA
1 GGAGGA
1957067 GACAAAGACG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.25, C:0.08, G:0.54, T:0.12
Consensus pattern (21 bp):
GGAGGACTAGAAGCTGAGGGT
Found at i:1959254 original size:425 final size:425
Alignment explanation
Indices: 1958460--1959301 Score: 1508
Period size: 425 Copynumber: 2.0 Consensus size: 425
1958450 TTAATTGATT
* *
1958460 TTTGTTTTAATTTATATTTTTTTATGGTTGGATTTGACATCGTCATGCTTGATCAAGATGATGTT
1 TTTGTTTTAATTTATACTTTTTTATGGTTGGATTTGACATCGTCATGATTGATCAAGATGATGTT
*
1958525 TATTTGTTGCCATGATGATCTTTCTTGTTTTGGACCATCGAATTGGATTTGGATACGCTATTTGC
66 TATTTGTTGCCATGATAATCTTTCTTGTTTTGGACCATCGAATTGGATTTGGATACGCTATTTGC
*
1958590 AGTCGTGGACGGTTTTTCATGTCACTCGACTTTGATTTGTGGATTGTCAATGGTCTTTTAGTAAT
131 AGTCGTGGACGGTTTTTCATGTCACTCGACTTTGATTTATGGATTGTCAATGGTCTTTTAGTAAT
1958655 TTGATTCATTTTGTGGTTCATTTATCGATGCAATTAAATATGTTCCTATCTATCTTTTGTTCGAA
196 TTGATTCATTTTGTGG-T--TTTATCGATGCAATTAAATATGTTCCTATCTATCTTTTGTTCGAA
* *
1958720 TTTTTTAGTTAGATTTTTAATCTTTTCCTTCTATGATCTTGTGTGATCTTAATGACTAATTTTTA
258 TTTTTTAGTTAGATTTTTAATATTTTCCTTCTATGATATTGTGTGATCTTAATGACTAATTTTTA
*
1958785 TATTAATGGTGATAAGAAAATATCTTAATTGCGTGTTTAGTTTACGTTTATGATTGTAAACTTTC
323 TATTAATGGTGATAAGAAAATATCTTAATTGCGTGTTTAGTTTACGTTTATGATTGTAAACATTC
1958850 TTTATAATTATGAATATTTCTTCTTTTTTTTAATAAAAC
388 TTTATAATTATGAATATTTCTT-TTTTTTTTAATAAAAC
1958889 TTTGTTTTAATTTAT-CTTTTTTATGGTTGGATTTGACATCGTCATGATTGATCAAGATGATGTT
1 TTTGTTTTAATTTATACTTTTTTATGGTTGGATTTGACATCGTCATGATTGATCAAGATGATGTT
* *
1958953 TATTTGTTGTCATGCTAATCTTTCTTGTTTTGGACCATCGAATTGGATTTGGATACGCTATTTGC
66 TATTTGTTGCCATGATAATCTTTCTTGTTTTGGACCATCGAATTGGATTTGGATACGCTATTTGC
* *
1959018 ATTCGTGGACGGTTTTTTCATGTCACTCGACTTTGATTTATGGATTGTCAGTGGTCTTTTAGTAA
131 AGTCGTGGACGG-TTTTTCATGTCACTCGACTTTGATTTATGGATTGTCAATGGTCTTTTAGTAA
*
1959083 TTTGATTTATTTTGTGG-TTTATCGATGCAATTAAATATGTTCCTATCTATCTTTTGTTCGAATT
195 TTTGATTCATTTTGTGGTTTTATCGATGCAATTAAATATGTTCCTATCTATCTTTTGTTCGAATT
1959147 TTTTAGTTAGATTTTTAATATTTTCCTTCTATGATATTGTGTGATCTTAATGACTAATTTTTATA
260 TTTTAGTTAGATTTTTAATATTTTCCTTCTATGATATTGTGTGATCTTAATGACTAATTTTTATA
*
1959212 TTAATGGTGATAAGAAAATATCTTAATTGTGTGTTTAGTTTACGTTTATGATTGTAAACATTCTT
325 TTAATGGTGATAAGAAAATATCTTAATTGCGTGTTTAGTTTACGTTTATGATTGTAAACATTCTT
1959277 TATAATTATGAATATTTCTTTTTTT
390 TATAATTATGAATATTTCTTTTTTT
1959302 AATAAAACTA
Statistics
Matches: 399, Mismatches: 13, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
424 5 0.01
425 193 0.48
428 120 0.30
429 81 0.20
ACGTcount: A:0.23, C:0.11, G:0.16, T:0.50
Consensus pattern (425 bp):
TTTGTTTTAATTTATACTTTTTTATGGTTGGATTTGACATCGTCATGATTGATCAAGATGATGTT
TATTTGTTGCCATGATAATCTTTCTTGTTTTGGACCATCGAATTGGATTTGGATACGCTATTTGC
AGTCGTGGACGGTTTTTCATGTCACTCGACTTTGATTTATGGATTGTCAATGGTCTTTTAGTAAT
TTGATTCATTTTGTGGTTTTATCGATGCAATTAAATATGTTCCTATCTATCTTTTGTTCGAATTT
TTTAGTTAGATTTTTAATATTTTCCTTCTATGATATTGTGTGATCTTAATGACTAATTTTTATAT
TAATGGTGATAAGAAAATATCTTAATTGCGTGTTTAGTTTACGTTTATGATTGTAAACATTCTTT
ATAATTATGAATATTTCTTTTTTTTTTAATAAAAC
Found at i:1959534 original size:32 final size:32
Alignment explanation
Indices: 1959463--1959556 Score: 109
Period size: 32 Copynumber: 3.0 Consensus size: 32
1959453 CTTTCAGAAC
* * * *
1959463 TTACAAAATAATTATTA-AATTTATCTAATAG
1 TTACAAAATGATTATTATATTTTATCAAATTG
* *
1959494 TTACAAAATGGTTATTATATTTTATCGAATTG
1 TTACAAAATGATTATTATATTTTATCAAATTG
* *
1959526 TTATAAAATGATCATTATATTTTATCAAATT
1 TTACAAAATGATTATTATATTTTATCAAATT
1959557 ATTAAAATTG
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 15 0.28
32 38 0.72
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.46
Consensus pattern (32 bp):
TTACAAAATGATTATTATATTTTATCAAATTG
Found at i:1959909 original size:23 final size:23
Alignment explanation
Indices: 1959865--1959910 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1959855 TATCTAAATT
*
1959865 TTTATAAATTCAATCATTAATAA
1 TTTATAAATTCAATCATAAATAA
* *
1959888 TTTATAAATTCACTCGTAAATAA
1 TTTATAAATTCAATCATAAATAA
1959911 AATTTTACGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.41
Consensus pattern (23 bp):
TTTATAAATTCAATCATAAATAA
Found at i:1962074 original size:3 final size:3
Alignment explanation
Indices: 1962068--1962093 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1962058 GAAGAGAAAA
1962068 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
1962094 AGAGAAAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1964188 original size:21 final size:21
Alignment explanation
Indices: 1964164--1964210 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
1964154 GACTGTGGCA
*
1964164 GAGGACTAGCAGCTG-GTGGTG
1 GAGGACTAGAAGCTGAG-GGTG
*
1964185 GAGGACTAGAAGGTGAGGGTG
1 GAGGACTAGAAGCTGAGGGTG
1964206 GAGGA
1 GAGGA
1964211 GACAAAGACG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.26, C:0.09, G:0.51, T:0.15
Consensus pattern (21 bp):
GAGGACTAGAAGCTGAGGGTG
Found at i:1966288 original size:16 final size:15
Alignment explanation
Indices: 1966254--1966296 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
1966244 TATGATAATT
1966254 AAATAAATAAAAATA
1 AAATAAATAAAAATA
**
1966269 AAATAAATAAATTCTA
1 AAATAAATAAA-AATA
1966285 AAATAAATAAAA
1 AAATAAATAAAA
1966297 CACAATGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (15 bp):
AAATAAATAAAAATA
Found at i:1968197 original size:19 final size:20
Alignment explanation
Indices: 1968153--1968197 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1968143 ATTTGTTTTT
*
1968153 AATAAATTTTTATCTATGAA
1 AATAAATTTTTATCTATCAA
* *
1968173 ATTAAATTTTTAT-TTTCAA
1 AATAAATTTTTATCTATCAA
1968192 AATAAA
1 AATAAA
1968198 ATATTAAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (20 bp):
AATAAATTTTTATCTATCAA
Found at i:1968337 original size:20 final size:20
Alignment explanation
Indices: 1968301--1968339 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1968291 AGATCACACT
*
1968301 CGCGACAGCCGTAACACGTC
1 CGCGACAGCCATAACACGTC
*
1968321 CGCGACAGCCATTACACGT
1 CGCGACAGCCATAACACGT
1968340 TATGTAACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.38, G:0.23, T:0.13
Consensus pattern (20 bp):
CGCGACAGCCATAACACGTC
Found at i:1971492 original size:64 final size:65
Alignment explanation
Indices: 1971424--1971544 Score: 172
Period size: 64 Copynumber: 1.9 Consensus size: 65
1971414 AACACTTGAT
* *
1971424 GCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCTGCGA
1 GCATCGATGCACCAAGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATAGCCTGCGA
*****
1971488 GCATCGATGCATGTCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATA
1 GCATCGATGCACCAAGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATA
1971545 TTCAGAGTGC
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
64 39 0.80
65 10 0.20
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (65 bp):
GCATCGATGCACCAAGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATAGCCTGCGA
Found at i:1971575 original size:65 final size:65
Alignment explanation
Indices: 1971442--1971601 Score: 196
Period size: 65 Copynumber: 2.5 Consensus size: 65
1971432 GCACCAAGTG
* * *****
1971442 TGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCTGCGAGCATCGATGCATGTCTTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGAGCATCGATGCATGGAGAA
* ** *
1971506 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGAGAA
1 TGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGAGCATCGATGCATGGAGAA
* *
1971571 TGCATCGGTGCATGGAATGCATTCGATGTTT
1 TGCATCGATGCATGAAATGCATTCGATGTTT
1971602 CAATTAATTC
Statistics
Matches: 81, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
64 27 0.33
65 54 0.67
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.31
Consensus pattern (65 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGAGCATCGATGCATGGAGAA
Found at i:1971590 original size:17 final size:19
Alignment explanation
Indices: 1971552--1971598 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
1971542 ATATTCAGAG
1971552 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
1971571 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
1971588 TGCATTCGATG
1 TGCA-TCGATG
1971599 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:1971857 original size:21 final size:20
Alignment explanation
Indices: 1971818--1971857 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1971808 GAATCGAATA
* *
1971818 TAAAATTTTAACATCATTTG
1 TAAAATCTTAAAATCATTTG
1971838 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAA-TCATTT
1971858 AACTTAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (20 bp):
TAAAATCTTAAAATCATTTG
Found at i:1974145 original size:15 final size:15
Alignment explanation
Indices: 1974122--1974156 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1974112 ATAACTTGGA
*
1974122 AAAGTAAAAGAAAAT
1 AAAGAAAAAGAAAAT
1974137 AAAGAAAAAGAAAAT
1 AAAGAAAAAGAAAAT
*
1974152 GAAGA
1 AAAGA
1974157 CTTTAATTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (15 bp):
AAAGAAAAAGAAAAT
Found at i:1975990 original size:19 final size:19
Alignment explanation
Indices: 1975962--1975998 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1975952 ACATTAGCAG
*
1975962 TGCATGTTCTAGAATGCAC
1 TGCATATTCTAGAATGCAC
1975981 TGCATATTCTAGAATGCA
1 TGCATATTCTAGAATGCA
1975999 TATTCCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (19 bp):
TGCATATTCTAGAATGCAC
Found at i:1976102 original size:36 final size:36
Alignment explanation
Indices: 1976055--1976316 Score: 389
Period size: 36 Copynumber: 7.3 Consensus size: 36
1976045 GAAAACGAAC
* *
1976055 ACTTGGATCGGAAGTGCTGATGCTTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
*
1976091 ACTTGAATCGGAAGTGCCGATGCTTCATTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
* *
1976127 ACTTGAATCGGAAGTGCCGATGTTTCCTTTCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
* * *
1976163 ATTTGAATCAGAAGCGCCGATGCTTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
* * * * *
1976199 ACTTGAATCAGAAATGCCGATGCTTCATTCTGTTTG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
1976235 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
*
1976271 ACTTGAATCGGAAGTGCCGATGCTTTCTTCCGTTCG
1 ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
*
1976307 ATTTGAATCG
1 ACTTGAATCG
1976317 TCGGTGCACC
Statistics
Matches: 202, Mismatches: 24, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 202 1.00
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (36 bp):
ACTTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCG
Found at i:1977674 original size:14 final size:14
Alignment explanation
Indices: 1977655--1977682 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1977645 TAGGGCAAAG
1977655 ATATAAGAGAATTT
1 ATATAAGAGAATTT
1977669 ATATAAGAGAATTT
1 ATATAAGAGAATTT
1977683 TCGTGATGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (14 bp):
ATATAAGAGAATTT
Found at i:1980890 original size:21 final size:21
Alignment explanation
Indices: 1980864--1980910 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1980854 CGTCTTTGTC
*
1980864 TCCTCCACCCTCACCTGCTAA
1 TCCTCCACCCCCACCTGCTAA
**
1980885 TCCTCCACCCCCAGTTGCTAA
1 TCCTCCACCCCCACCTGCTAA
1980906 TCCTC
1 TCCTC
1980911 TGCCACAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.17, C:0.51, G:0.06, T:0.26
Consensus pattern (21 bp):
TCCTCCACCCCCACCTGCTAA
Found at i:1985075 original size:21 final size:21
Alignment explanation
Indices: 1985051--1985096 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1985041 TGACTGTGGC
* *
1985051 GGAGAACTAGCAGCTGGGGGT
1 GGAGAACTAGAAGCTGAGGGT
* *
1985072 GGAGGACTAGAAGGTGAGGGT
1 GGAGAACTAGAAGCTGAGGGT
1985093 GGAG
1 GGAG
1985097 GAGACAAAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.09, G:0.52, T:0.13
Consensus pattern (21 bp):
GGAGAACTAGAAGCTGAGGGT
Found at i:1986481 original size:21 final size:21
Alignment explanation
Indices: 1986452--1986650 Score: 237
Period size: 21 Copynumber: 9.7 Consensus size: 21
1986442 ATTCTGACTA
* *
1986452 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTTCCTAAT
*
1986473 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCTAAT
* *
1986494 TCGCATTGCGATTTACGTAA-
1 TCGCATTGCGATTTTCCTAAT
1986514 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCTAAT
1986535 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCTAAT
* *
1986556 TCGCATTGCGATTTACGTAA-
1 TCGCATTGCGATTTTCCTAAT
* * *
1986576 TCACATTGCGATTTACGTAA-
1 TCGCATTGCGATTTTCCTAAT
1986596 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCTAAT
* * *
1986617 TCGCACTT-AGATTTACGTAA-
1 TCGCA-TTGCGATTTTCCTAAT
1986637 TCGCATTGCGATTT
1 TCGCATTGCGATTT
1986651 AGTAAATCGC
Statistics
Matches: 156, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
19 2 0.01
20 64 0.41
21 88 0.56
22 2 0.01
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCTAAT
Found at i:1986505 original size:62 final size:62
Alignment explanation
Indices: 1986451--1986651 Score: 316
Period size: 62 Copynumber: 3.3 Consensus size: 62
1986441 GATTCTGACT
* * *
1986451 ATCGCATTGCGATTTCCCAAATTCGCGTTGCGATTTTCCTAATTCGCATTGCGATTTACGTA
1 ATCGCATTGCGATTTACCTAATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTA
*
1986513 ATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTA
1 ATCGCATTGCGATTTACCTAATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTA
* * *
1986575 ATCACATTGCGATTTACGTAA-TCGCATTGCGATTTTCCTAATTCGCACTT-AGATTTACGTA
1 ATCGCATTGCGATTTACCTAATTCGCATTGCGATTTTCCTAATTCGCA-TTGCGATTTACGTA
1986636 ATCGCATTGCGATTTA
1 ATCGCATTGCGATTTA
1986652 GTAAATCGCA
Statistics
Matches: 130, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
61 51 0.39
62 79 0.61
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.38
Consensus pattern (62 bp):
ATCGCATTGCGATTTACCTAATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTA
Found at i:1986523 original size:41 final size:41
Alignment explanation
Indices: 1986452--1986650 Score: 267
Period size: 41 Copynumber: 4.8 Consensus size: 41
1986442 ATTCTGACTA
* ** *
1986452 TCGCATTGCGATTTCCCAAATTCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGTAA-TCGCATTGCGATTTTCCTAAT
1986494 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
* * * *
1986535 TCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGTAA-
1 TCGCATTGCGATTTACGTAA-TCGCATTGCGATTTTCCTAAT
*
1986576 TCACATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
*
1986617 TCGCACTT-AGATTTACGTAATCGCATTGCGATTT
1 TCGCA-TTGCGATTTACGTAATCGCATTGCGATTT
1986651 AGTAAATCGC
Statistics
Matches: 139, Mismatches: 15, Indels: 7
0.86 0.09 0.04
Matches are distributed among these distances:
40 18 0.13
41 84 0.60
42 37 0.27
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.39
Consensus pattern (41 bp):
TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAAT
Found at i:1987551 original size:24 final size:24
Alignment explanation
Indices: 1987524--1987577 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1987514 GTATTCGAAA
1987524 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1987548 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1987572 TTTGAT
1 TTTGAT
1987578 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1990115 original size:20 final size:19
Alignment explanation
Indices: 1990087--1990141 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
1990077 CAATCATCTT
*
1990087 AATGTCTATCGCAACGCAGA
1 AATGACTATCGCAACGC-GA
*
1990107 AATGACTATCGCAATGCGA
1 AATGACTATCGCAACGCGA
**
1990126 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
1990142 AGAGAATCGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.18
Consensus pattern (19 bp):
AATGACTATCGCAACGCGA
Found at i:1990129 original size:19 final size:17
Alignment explanation
Indices: 1990094--1990244 Score: 77
Period size: 19 Copynumber: 8.8 Consensus size: 17
1990084 CTTAATGTCT
*
1990094 ATCGCAACGCAGAAATGA
1 ATCGCAATGC-GAAATGA
1990112 CTATCGCAATGCGAAATGAAA
1 --ATCGCAATGCGAAATG--A
*
1990133 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
1990147 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
1990166 ATCGCAA--CGATA-GA
1 ATCGCAATGCGAAATGA
1990180 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
**
1990199 ATCGCAA--CG-AGGGA
1 ATCGCAATGCGAAATGA
*
1990213 ATCGCAAAGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
1990232 ATCGCAACGCGAA
1 ATCGCAATGCGAA
1990245 TTTAGTTTCG
Statistics
Matches: 104, Mismatches: 10, Indels: 35
0.70 0.07 0.23
Matches are distributed among these distances:
14 24 0.23
16 14 0.13
17 14 0.13
19 42 0.40
20 9 0.09
21 1 0.01
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (17 bp):
ATCGCAATGCGAAATGA
Found at i:1990151 original size:14 final size:14
Alignment explanation
Indices: 1990132--1990219 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
1990122 GCGAAATGAA
1990132 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1990146 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
1990165 AATCGCAACGATAG
1 AATCGCAACGAGAG
*
1990179 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
1990198 AATCGCAACGAGGG
1 AATCGCAACGAGAG
1990212 AATCGCAA
1 AATCGCAA
1990220 AGCGAAATGA
Statistics
Matches: 57, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
14 26 0.46
15 2 0.04
16 4 0.07
17 4 0.07
18 2 0.04
19 19 0.33
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.12
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1990156 original size:33 final size:33
Alignment explanation
Indices: 1990114--1990240 Score: 227
Period size: 33 Copynumber: 3.8 Consensus size: 33
1990104 AGAAATGACT
1990114 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1990147 ATCGCAATGCGAAATGAAAATCGCAACGATAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1990180 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1990213 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1990241 CGAATTTAGT
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 90 1.00
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1990262 original size:19 final size:18
Alignment explanation
Indices: 1990240--1990301 Score: 79
Period size: 19 Copynumber: 3.3 Consensus size: 18
1990230 AAATCGCAAC
*
1990240 GCGAATTTAGTTTCGCGTT
1 GCGATTTTA-TTTCGCGTT
1990259 GCGATTTTCATTTCGCGTT
1 GCGATTTT-ATTTCGCGTT
*
1990278 GCGATTTTTATTTCGCATT
1 GCGA-TTTTATTTCGCGTT
1990297 GCGAT
1 GCGAT
1990302 AGTCATTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
18 1 0.03
19 33 0.85
20 5 0.13
ACGTcount: A:0.15, C:0.18, G:0.23, T:0.45
Consensus pattern (18 bp):
GCGATTTTATTTCGCGTT
Found at i:1990309 original size:19 final size:19
Alignment explanation
Indices: 1990250--1990301 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
1990240 GCGAATTTAG
1990250 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
1990269 TTTCGCGTTGCGATTTTTA
1 TTTCGCGTTGCGATTTTCA
*
1990288 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
1990302 AGTCATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.48
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:1990427 original size:14 final size:14
Alignment explanation
Indices: 1990408--1990444 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1990398 CATCAATTAA
1990408 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1990422 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1990436 ACAAATCAA
1 ACAAATCAA
1990445 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1991830 original size:21 final size:21
Alignment explanation
Indices: 1991806--1991881 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
1991796 GTGGGAGAGA
*
1991806 CCTCTTCAACGATGACAGTGG
1 CCTCTTCAACGATGACAGGGG
* * *
1991827 CCTCTTGAACGGTGAGAGGGG
1 CCTCTTCAACGATGACAGGGG
* * * *
1991848 ACTC-TCGAGGAATGATAGGGG
1 CCTCTTCAACG-ATGACAGGGG
1991869 CCTCTTCAACGAT
1 CCTCTTCAACGAT
1991882 AGGAGTGGAC
Statistics
Matches: 40, Mismatches: 13, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
20 3 0.08
21 33 0.82
22 4 0.10
ACGTcount: A:0.24, C:0.24, G:0.30, T:0.22
Consensus pattern (21 bp):
CCTCTTCAACGATGACAGGGG
Found at i:1992345 original size:19 final size:19
Alignment explanation
Indices: 1992305--1992375 Score: 79
Period size: 19 Copynumber: 3.6 Consensus size: 19
1992295 TCTGGAACTT
*
1992305 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG--AAATG
** *
1992326 ACTATCGCAGCGCGAAATG
1 AAAATCGCAACGCGAAATG
1992345 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
1992364 AAAAGCGCAACG
1 AAAATCGCAACG
1992376 ACAAAATCGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 32 0.76
21 10 0.24
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:1992442 original size:20 final size:20
Alignment explanation
Indices: 1992417--1992455 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1992407 ACGCATTATA
1992417 GTTTCGCGTTGCGATTTTTG
1 GTTTCGCGTTGCGATTTTTG
1992437 GTTTCGCGTTGCGATTTTT
1 GTTTCGCGTTGCGATTTTT
1992456 TCATTGCGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.05, C:0.15, G:0.28, T:0.51
Consensus pattern (20 bp):
GTTTCGCGTTGCGATTTTTG
Found at i:1992480 original size:33 final size:33
Alignment explanation
Indices: 1992438--1992521 Score: 141
Period size: 33 Copynumber: 2.5 Consensus size: 33
1992428 CGATTTTTGG
1992438 TTTCGCGTTGCGATTTTTTCATTGCGATTTTCA
1 TTTCGCGTTGCGATTTTTTCATTGCGATTTTCA
* * *
1992471 TTTCGCGTTGCGATTTTCTCGTTGCGATTTTCG
1 TTTCGCGTTGCGATTTTTTCATTGCGATTTTCA
1992504 TTTCGCGTTGCGATTTTT
1 TTTCGCGTTGCGATTTTT
1992522 ATTCTCTCGT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.08, C:0.19, G:0.21, T:0.51
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTTTCATTGCGATTTTCA
Found at i:1992493 original size:14 final size:14
Alignment explanation
Indices: 1992438--1992502 Score: 58
Period size: 14 Copynumber: 4.3 Consensus size: 14
1992428 CGATTTTTGG
*
1992438 TTTCGCGTTGCGAT
1 TTTCTCGTTGCGAT
* *
1992452 TTTTTCATTGCGAT
1 TTTCTCGTTGCGAT
1992466 TTTCATTTCGCGTTGCGAT
1 TTTC---T--CGTTGCGAT
1992485 TTTCTCGTTGCGAT
1 TTTCTCGTTGCGAT
1992499 TTTC
1 TTTC
1992503 GTTTCGCGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
14 27 0.66
16 1 0.02
17 1 0.02
19 12 0.29
ACGTcount: A:0.09, C:0.20, G:0.20, T:0.51
Consensus pattern (14 bp):
TTTCTCGTTGCGAT
Found at i:1992532 original size:20 final size:19
Alignment explanation
Indices: 1992459--1992546 Score: 96
Period size: 19 Copynumber: 4.8 Consensus size: 19
1992449 GATTTTTTCA
*
1992459 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCTCG
1992478 TTGCGA---T--TTTCTCG
1 TTGCGATTTTCATTTCTCG
* *
1992492 TTGCGATTTTCGTTTCGCG
1 TTGCGATTTTCATTTCTCG
*
1992511 TTGCGATTTTTATTCTCTCG
1 TTGCGATTTTCATT-TCTCG
1992531 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1992547 AACCAAAAGA
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
14 12 0.21
16 1 0.02
17 1 0.02
19 26 0.46
20 17 0.30
ACGTcount: A:0.09, C:0.20, G:0.19, T:0.51
Consensus pattern (19 bp):
TTGCGATTTTCATTTCTCG
Found at i:1992747 original size:94 final size:92
Alignment explanation
Indices: 1992635--1992912 Score: 383
Period size: 94 Copynumber: 3.1 Consensus size: 92
1992625 ATGGATTGCA
* *
1992635 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGTT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACA-AGTT
1992700 TAGCAGAATTGGCAGCAAACGAACAAAT
65 TAGCAGAATTGGCAGCAAACGAACAAAT
*
1992728 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCATAGTGTTAAAGAATACATAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACA-AGT
*
1992793 TTAGCAGAATTGGCAGC-AAC---CGAAT
64 TTAGCAGAATTGGCAGCAAACGAACAAAT
*
1992818 ATACTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAATA-AAT---AGT
1 TTACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAA-AGAATACAAGT
* * *
1992879 TTAGCAGTATTGGCAGCAACCGAATAAAT
64 TTAGCAGAATTGGCAGCAAACGAACAAAT
1992908 TTACT
1 TTACT
1992913 AAGCAATCTA
Statistics
Matches: 167, Mismatches: 11, Indels: 17
0.86 0.06 0.09
Matches are distributed among these distances:
86 19 0.11
87 2 0.01
89 19 0.11
90 45 0.27
91 1 0.01
93 7 0.04
94 74 0.44
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (92 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACAAGTTT
AGCAGAATTGGCAGCAAACGAACAAAT
Found at i:1994632 original size:20 final size:20
Alignment explanation
Indices: 1994607--1994669 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
1994597 TTTTGGTTGA
1994607 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
1994627 AATGAAAATCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
**
1994646 AAATGACTATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
1994667 AAT
1 AAT
1994670 CGCAACACGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.03
20 35 0.95
21 1 0.03
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:1994673 original size:14 final size:14
Alignment explanation
Indices: 1994654--1994742 Score: 61
Period size: 14 Copynumber: 5.6 Consensus size: 14
1994644 GGAAATGACT
1994654 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
1994668 ATCGCAACACGAAATGAAA
1 ATCGC-A-ACG--A-GAGA
*
1994687 ATCACAACGAGAGA
1 ATCGCAACGAGAGA
*
1994701 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
1994720 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
1994734 ATCGCAACG
1 ATCGCAACG
1994743 CGAATTTGGG
Statistics
Matches: 59, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 26 0.44
15 3 0.05
16 5 0.08
17 5 0.08
18 3 0.05
19 17 0.29
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:1994695 original size:33 final size:33
Alignment explanation
Indices: 1994605--1994746 Score: 185
Period size: 33 Copynumber: 4.1 Consensus size: 33
1994595 TCTTTTGGTT
1994605 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAAC--GAG-A-G--AATCGCAACGC
** *
1994644 GGAAATGACTATCGCAACGAGAGAATCGCAACAC
1 -GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
1994678 GAAATGAAAATCACAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1994711 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1994744 GAA
1 GAA
1994747 TTTGGGAAAT
Statistics
Matches: 94, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
33 64 0.68
34 10 0.11
36 1 0.01
37 1 0.01
38 3 0.03
40 15 0.16
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:2007459 original size:2 final size:2
Alignment explanation
Indices: 2007452--2007504 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
2007442 CTTATACGTG
2007452 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
2007494 TA TA TA TA TA T
1 TA TA TA TA TA T
2007505 CTTTTTGCAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2007813 original size:13 final size:13
Alignment explanation
Indices: 2007795--2007824 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2007785 TTTCATTTTG
2007795 TTTTATCTTTTAT
1 TTTTATCTTTTAT
2007808 TTTTATCTTTTAT
1 TTTTATCTTTTAT
2007821 TTTT
1 TTTT
2007825 TTCATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTATCTTTTAT
Found at i:2013363 original size:34 final size:35
Alignment explanation
Indices: 2013268--2013722 Score: 269
Period size: 36 Copynumber: 13.0 Consensus size: 35
2013258 GGTTTATCTC
* *
2013268 AAAACAAGTTTTGTCTCTCTTGAGACAGTTTCTCTT
1 AAAACAAATTTTGTCTCTC-TGAGACATTTTCTCTT
2013304 AAAACAAATTTTGTCTCTCTTGAGACATTTTCTCTT
1 AAAACAAATTTTGTCTCTC-TGAGACATTTTCTCTT
****
2013340 AAAATTTTTTTTGTCTCTC-GAGACATTTTCTCTT
1 AAAACAAATTTTGTCTCTCTGAGACATTTTCTCTT
* *
2013374 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTT
1 AAAACAAATTTTGTCTCTC-TGAGACATTTTCTCTT
* * *
2013410 GAAACAAA----ATCT-T-TGA-ATATGTTT-TCCTT
1 AAAACAAATTTTGTCTCTCTGAGACAT-TTTCT-CTT
* * * *
2013439 TAAACAAATTTCGTCTCTCTCGAGACAGTTTCTTTT
1 AAAACAAATTTTGTCTCTCT-GAGACATTTTCTCTT
** * * *
2013475 GGAACTAAATTTTGTCTCTTTTGAGATAGTTTCTCTT
1 AAAAC-AAATTTTGTCTC-TCTGAGACATTTTCTCTT
* * *
2013512 GAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTT
1 AAAACAAATTTTGTCTCTC-TGAGACATTTTCTCTT
* * *
2013548 GAAACAAA----ATCT-T-TGA-ATCTGTTTTC-CTT
1 AAAACAAATTTTGTCTCTCTGAGA-C-ATTTTCTCTT
* * * *
2013577 TAAACAAATTTCGTCTCTCTCGAGACAATTTCTTTT
1 AAAACAAATTTTGTCTCTCT-GAGACATTTTCTCTT
* * *
2013613 AAAACTGAGTTTTGTCTCTCTTGAGACAGTTTCTCTT
1 AAAAC-AAATTTTGTCTCTC-TGAGACATTTTCTCTT
* * ** *
2013650 GAAACAAATTTTGTCTCTCTTGAAACAGATTCCCTT
1 AAAACAAATTTTGTCTCTC-TGAGACATTTTCTCTT
* * *
2013686 GAAACAAAGTTTTGTCTCTCTTGAGACAGTTCCTCTT
1 AAAACAAA-TTTTGTCTCTC-TGAGACATTTTCTCTT
2013723 GAAGCACCAA
Statistics
Matches: 333, Mismatches: 56, Indels: 59
0.74 0.12 0.13
Matches are distributed among these distances:
28 3 0.01
29 30 0.09
30 4 0.01
31 2 0.01
32 6 0.02
33 6 0.02
34 32 0.10
35 7 0.02
36 156 0.47
37 84 0.25
38 3 0.01
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (35 bp):
AAAACAAATTTTGTCTCTCTGAGACATTTTCTCTT
Found at i:2013470 original size:65 final size:66
Alignment explanation
Indices: 2013365--2013608 Score: 271
Period size: 65 Copynumber: 3.6 Consensus size: 66
2013355 TCTCGAGACA
* * *
2013365 TTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATAT
1 TTTTCTCTTTAAACAAATTTCGTCTCTCTCGAGACAGTTTCCCTTGAAACAAAATCTTTGAATAT
2013430 G
66 G
** * *
2013431 TTTTC-CTTTAAACAAATTTCGTCTCTCTCGAGACAGTTTCTTTTGGAACTAAATTTTGTCTCTT
1 TTTTCTCTTTAAACAAATTTCGTCTCTCTCGAGACAGTTTCCCTTGAAAC-AAA------ATC-T
2013495 TTGAGATA-G
58 TTGA-ATATG
* * * *
2013504 -TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCT
1 TTTTCTCTTTAAACAAATTTCGTCTCTCTCGAGACAGTTTCCCTTGAAACAAAATCTTTGAATAT
2013568 G
66 G
*
2013569 TTTTC-CTTTAAACAAATTTCGTCTCTCTCGAGACAATTTC
1 TTTTCTCTTTAAACAAATTTCGTCTCTCTCGAGACAGTTTC
2013609 TTTTAAAACT
Statistics
Matches: 147, Mismatches: 19, Indels: 25
0.77 0.10 0.13
Matches are distributed among these distances:
64 2 0.01
65 75 0.51
66 14 0.10
72 9 0.06
73 44 0.30
74 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.42
Consensus pattern (66 bp):
TTTTCTCTTTAAACAAATTTCGTCTCTCTCGAGACAGTTTCCCTTGAAACAAAATCTTTGAATAT
G
Found at i:2013506 original size:37 final size:36
Alignment explanation
Indices: 2013432--2013725 Score: 275
Period size: 36 Copynumber: 8.3 Consensus size: 36
2013422 TTGAATATGT
* * *
2013432 TTTC-CTTTAAACAAATTTCGTCTCTCTCGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * * *
2013467 TTTCTTTTGGAACTAAATTTTGTCTCTTTTGAGATAG
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
2013504 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * *
2013540 TTTCCCTTGAAACAAA------ATCT-TTGA-ATCTG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGA-CAG
* * * *
2013569 TTT-TCCTTTAAACAAATTTCGTCTCTCTCGAGACAA
1 TTTCT-CTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * * *
2013605 TTTCTTTTAAAACTGAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
*
2013642 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAAACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* *
2013678 ATTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGACAG
*
2013715 TTCCTCTTGAA
1 TTTCTCTTGAA
2013726 GCACCAATCT
Statistics
Matches: 206, Mismatches: 38, Indels: 28
0.76 0.14 0.10
Matches are distributed among these distances:
28 1 0.00
29 19 0.09
30 3 0.01
35 7 0.03
36 88 0.43
37 88 0.43
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:2013521 original size:73 final size:73
Alignment explanation
Indices: 2013432--2013725 Score: 279
Period size: 73 Copynumber: 4.2 Consensus size: 73
2013422 TTGAATATGT
* ** * *
2013432 TTTC-CTTTAAACAAATTTCGTCTCTCTCGAGACAGTTTCTTTTGGAACTAAATTTTGTCTCTTT
1 TTTCTCTTGAAACAAATTTCGTCTCTCTCGAGACAGTTTCCCTTGAAACTAAATTTTGTCTCTCT
*
2013496 TGAGATAG
66 TGAGACAG
* * *
2013504 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAA------ATCT-T
1 TTTCTCTTGAAACAAATTTCGTCTCTCTCGAGACAGTTTCCCTTGAAACTAAATTTTGTCTCTCT
*
2013561 TGA-ATCTG
66 TGAGA-CAG
* * ** * * *
2013569 TTT-TCCTTTAAACAAATTTCGTCTCTCTCGAGACAATTTCTTTTAAAACTGAGTTTTGTCTCTC
1 TTTCT-CTTGAAACAAATTTCGTCTCTCTCGAGACAGTTTCCCTTGAAACTAAATTTTGTCTCTC
2013633 TTGAGACAG
65 TTGAGACAG
* * * *
2013642 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAAACAGATTCCCTTGAAAC-AAAGTTTTGTCTCTC
1 TTTCTCTTGAAACAAATTTCGTCTCTCTCGAGACAGTTTCCCTTGAAACTAAA-TTTTGTCTCTC
2013706 TTGAGACAG
65 TTGAGACAG
*
2013715 TTCCTCTTGAA
1 TTTCTCTTGAA
2013726 GCACCAATCT
Statistics
Matches: 176, Mismatches: 32, Indels: 27
0.75 0.14 0.11
Matches are distributed among these distances:
64 2 0.01
65 45 0.26
66 4 0.02
72 11 0.06
73 112 0.64
74 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (73 bp):
TTTCTCTTGAAACAAATTTCGTCTCTCTCGAGACAGTTTCCCTTGAAACTAAATTTTGTCTCTCT
TGAGACAG
Found at i:2013533 original size:138 final size:138
Alignment explanation
Indices: 2013296--2013693 Score: 586
Period size: 138 Copynumber: 2.9 Consensus size: 138
2013286 CTTGAGACAG
* * * * * ***
2013296 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACATTTTCTCTTAAAA-TTTTTTTTGTCTCTC-
1 TTTC-CTTTAAACAAATTTCGTCTCTCTCGAGACAATTTCTTTTAAAACTAAATTTTGTCTCTCT
* *
2013359 -GAGACATTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTT
65 TGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTT
2013423 TGAATATGT
130 TGAATATGT
* ** *
2013432 TTTCCTTTAAACAAATTTCGTCTCTCTCGAGACAGTTTCTTTTGGAACTAAATTTTGTCTCTTTT
1 TTTCCTTTAAACAAATTTCGTCTCTCTCGAGACAATTTCTTTTAAAACTAAATTTTGTCTCTCTT
*
2013497 GAGATAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTT
66 GAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTT
*
2013562 GAATCTGT
131 GAATATGT
* *
2013570 TTTCCTTTAAACAAATTTCGTCTCTCTCGAGACAATTTCTTTTAAAACTGAGTTTTGTCTCTCTT
1 TTTCCTTTAAACAAATTTCGTCTCTCTCGAGACAATTTCTTTTAAAACTAAATTTTGTCTCTCTT
* *
2013635 GAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAAACAGATTCCCTTGAAACAAA
66 GAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
2013694 GTTTTGTCTC
Statistics
Matches: 235, Mismatches: 24, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
135 36 0.15
136 15 0.06
138 184 0.78
ACGTcount: A:0.27, C:0.19, G:0.11, T:0.42
Consensus pattern (138 bp):
TTTCCTTTAAACAAATTTCGTCTCTCTCGAGACAATTTCTTTTAAAACTAAATTTTGTCTCTCTT
GAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTT
GAATATGT
Found at i:2013669 original size:21 final size:21
Alignment explanation
Indices: 2013644--2013709 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
2013634 TGAGACAGTT
2013644 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
*
2013665 TCTCTTGAAACAGA---T-TC
1 TCTCTTGAAACAAATTTTGTC
2013682 -C-CTTGAAACAAAGTTTTGTC
1 TCTCTTGAAACAAA-TTTTGTC
2013702 TCTCTTGA
1 TCTCTTGA
2013710 GACAGTTCCT
Statistics
Matches: 36, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
15 10 0.28
16 1 0.03
17 2 0.06
18 1 0.03
19 1 0.03
20 2 0.06
21 14 0.39
22 5 0.14
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.39
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTGTC
Done.