Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009614.1 Hibiscus syriacus cultivar Beakdansim tig00117000_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: 2129691
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 10
Found at i:1777284 original size:253 final size:261
Alignment explanation
Indices: 1776820--1777327 Score: 780
Period size: 253 Copynumber: 2.0 Consensus size: 261
1776810 AATCGGAAAT
* * ***
1776820 ATTATCAAGTACAATAACATATTAGGTACCGTTTATATAATGTAATAAGTAGCACTTATATAATA
1 ATTATCAAGCAAAATAACATATTAGGTACAACTTATATAATGTAATAAGTAGCACTTATATAATA
* *
1776885 AAATAGGTTAATTACTAGAAACATTATTAAGCACAATAATATATTAGGTACCGCTTATATAATGT
66 AAATAGGTTAATTACTAGAAACATTATTAAGCACAACAATATATTAGGTACCACTTATATAATGT
*
1776950 AATAGGTAGCACTTATATAATAAAATAAGTTAATTACTGGAAACATTATCAAACACAATAACATA
131 AATAGGTAACACTTATATAATAAAATAAGTTAATTACTGGAAACATTATCAAACACAATAACATA
*
1777015 TTAGGTAACACTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTGAAAA
196 TTAGGTAACACTTATATAACGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTGAAAA
1777080 C
261 C
* *
1777081 ATTATCAAGCAAAATAACATATTAGGTACAACTTATATAATGTAATAGGTAGCGCTTATATAATA
1 ATTATCAAGCAAAATAACATATTAGGTACAACTTATATAATGTAATAAGTAGCACTTATATAATA
* * *
1777146 TAATAGGTTAATTACT-GAAA-A-TATT-ATCA-AGCAA-A-A-TAGGTACCACTTATATAATGT
66 AAATAGGTTAATTACTAGAAACATTATTAAGCACAACAATATATTAGGTACCACTTATATAATGT
* * *
1777203 AATAGGTAACACTTATATAATAAAATAGGTTAATTACTGGAAATATTATCAAGCACAATAACATA
131 AATAGGTAACACTTATATAATAAAATAAGTTAATTACTGGAAACATTATCAAACACAATAACATA
* * *
1777268 TTAGGTATCGCTTATATAACGTAATAGGTAGCTCTTATATAATAAAATAGGTTAATTACT
196 TTAGGTAACACTTATATAACGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACT
1777328 TAATTTGTTA
Statistics
Matches: 227, Mismatches: 20, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
253 137 0.60
254 1 0.00
255 1 0.00
256 3 0.01
257 3 0.01
258 4 0.02
259 1 0.00
260 4 0.02
261 73 0.32
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (261 bp):
ATTATCAAGCAAAATAACATATTAGGTACAACTTATATAATGTAATAAGTAGCACTTATATAATA
AAATAGGTTAATTACTAGAAACATTATTAAGCACAACAATATATTAGGTACCACTTATATAATGT
AATAGGTAACACTTATATAATAAAATAAGTTAATTACTGGAAACATTATCAAACACAATAACATA
TTAGGTAACACTTATATAACGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTGAAAA
C
Found at i:1777295 original size:23 final size:23
Alignment explanation
Indices: 1777260--1777319 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
1777250 ATCAAGCACA
* *
1777260 ATAACATATTAGGTATCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
* *
1777283 ATAACGTAATAGGTAGCTCTTAT
1 ATAACATAATAGGTAGCGCTTAT
* *
1777306 ATAATAAAATAGGT
1 ATAACATAATAGGT
1777320 TAATTACTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:1777874 original size:24 final size:23
Alignment explanation
Indices: 1777847--1777902 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
1777837 TTATCAATGA
1777847 TAACAATAAAACAATATTATTTAT
1 TAACAATAAAACAATATTATTT-T
*
1777871 TAACAA-AATAATAATATTATTTT
1 TAACAATAA-AACAATATTATTTT
1777894 TAA-AATAAA
1 TAACAATAAA
1777903 TATTGCAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
22 3 0.10
23 8 0.28
24 18 0.62
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (23 bp):
TAACAATAAAACAATATTATTTT
Found at i:1778293 original size:200 final size:198
Alignment explanation
Indices: 1777904--1778344 Score: 645
Period size: 200 Copynumber: 2.2 Consensus size: 198
1777894 TAAAATAAAT
* *
1777904 ATTGCAAATTTACCTATTACATTATAATTATTGGTTTCGATGTTTTTGGGATCGATACAATTTTA
1 ATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACAATTTTA
*
1777969 AATGTATCGACACTTTATGCGTGAACCTCGTTGGGCATTCATTCTGGAAAAAAGTATCGACACAA
66 AATGTATCGACACTTTATGCGTGAACCTCGTTGGACATTCATTCTGGAAAAAAGTATCGACACAA
* *
1778034 ACTTAAAATGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGGTATATTTATACCGAG
131 ACTTAAAATGTGTCGATACATTATGTAGACATATTCTCTCATAAAACCGGTATATTTATACC-AG
1778099 -TAC
195 TTAC
* *
1778102 ATTGTAAATTTACCTATTACATTGTAATTATCGGTTTCGATGTTTTTGGGATCGATAC-TTTTAA
1 ATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACAATTT--
* * * * *
1778166 TAAATGTATCGACACTTTATGTGTGCACTTCGTTTGACATTCATTCTGGACAAAATGTATCGACA
64 TAAATGTATCGACACTTTATGCGTGAACCTCGTTGGACATTCATTCTGGA-AAAAAGTATCGACA
*** * * *
1778231 C-TTTTTAAATTTGTGTCGATACATTATGTTGACATATTCTCTCATAAAATCGGTATATTTATAC
128 CAAACTTAAA-ATGTGTCGATACATTATGTAGACATATTCTCTCATAAAACCGGTATATTTATAC
1778295 CAGTTAC
192 CAGTTAC
*
1778302 ATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGATGT
1 ATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGT
1778345 AATATAGTGT
Statistics
Matches: 218, Mismatches: 20, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
197 3 0.01
198 55 0.25
199 52 0.24
200 108 0.50
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (198 bp):
ATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACAATTTTA
AATGTATCGACACTTTATGCGTGAACCTCGTTGGACATTCATTCTGGAAAAAAGTATCGACACAA
ACTTAAAATGTGTCGATACATTATGTAGACATATTCTCTCATAAAACCGGTATATTTATACCAGT
TAC
Found at i:1778482 original size:31 final size:31
Alignment explanation
Indices: 1778441--1778519 Score: 83
Period size: 30 Copynumber: 2.5 Consensus size: 31
1778431 TTATAATAAA
1778441 TAAT-AAATATAATTTATAATAATTTTATT-T
1 TAATAAAATATAATTTATAATAATTTT-TTAT
* *
1778471 TAATAAAATATAA-TAATCATAATTTTTTAT
1 TAATAAAATATAATTTATAATAATTTTTTAT
*
1778501 TTATAAAATTATAGATTTA
1 TAATAAAA-TATA-ATTTA
1778520 ATATTTTTGT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
29 2 0.05
30 23 0.57
31 12 0.30
32 1 0.03
33 2 0.05
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (31 bp):
TAATAAAATATAATTTATAATAATTTTTTAT
Found at i:1779879 original size:23 final size:22
Alignment explanation
Indices: 1779833--1779896 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
1779823 TGATTCCCTC
1779833 AAGGAGGGAATCGGTTTCCATTCA
1 AAGG-GGGAATCGG-TTCCATTCA
*
1779857 AAGGGGGAATCGGTTCCTCTTCA
1 AAGGGGGAATCGGTTCC-ATTCA
* * *
1779880 AGGGGGGTATCGATTCC
1 AAGGGGGAATCGGTTCC
1779897 CTCTGTACAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 4 0.11
23 27 0.77
24 4 0.11
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (22 bp):
AAGGGGGAATCGGTTCCATTCA
Found at i:1779882 original size:22 final size:22
Alignment explanation
Indices: 1779831--1779885 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 22
1779821 ATTGATTCCC
1779831 TCAAGGAGGGAATCGGTTTCCAT
1 TCAAGG-GGGAATCGGTTTCCAT
*
1779854 TCAAAGGGGGAATCGG-TTCCTCT
1 TC-AAGGGGGAATCGGTTTCC-AT
1779877 TCAAGGGGG
1 TCAAGGGGG
1779886 GTATCGATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 11 0.38
23 14 0.48
24 4 0.14
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.24
Consensus pattern (22 bp):
TCAAGGGGGAATCGGTTTCCAT
Found at i:1782400 original size:29 final size:29
Alignment explanation
Indices: 1782358--1782438 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
1782348 TTCCATATGT
*
1782358 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTGGTGA
1782386 TCATGTAGCTCATGTCATTTCTCTGGTGA
1 TCATGTAGCTCATGTCATTTCTCTGGTGA
1782415 TCATGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
1782439 ATATCACATA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 7 0.14
29 38 0.76
30 5 0.10
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.43
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTGGTGA
Found at i:1787219 original size:24 final size:24
Alignment explanation
Indices: 1787187--1787240 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
1787177 TTGTACACTC
1787187 GAGCAGTGGAGTGTATCTCCTATT
1 GAGCAGTGGAGTGTATCTCCTATT
*
1787211 GAGCAGTGGAGTGTATCTCCTGTT
1 GAGCAGTGGAGTGTATCTCCTATT
1787235 GAGCAG
1 GAGCAG
1787241 AGGATTCCGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (24 bp):
GAGCAGTGGAGTGTATCTCCTATT
Found at i:1789216 original size:15 final size:15
Alignment explanation
Indices: 1789192--1789225 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1789182 CCGTAGGACC
1789192 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
*
1789207 ACTACGTCCCGAAGG
1 ACTACATCCCGAAGG
1789222 ACTA
1 ACTA
1789226 TTATACCCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.15
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:1789352 original size:29 final size:29
Alignment explanation
Indices: 1789310--1789390 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
1789300 TTCCATATGT
*
1789310 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTGGTGA
1789338 TCATGTAGCTCATGTCATTTCTCTGGTGA
1 TCATGTAGCTCATGTCATTTCTCTGGTGA
1789367 TCATGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
1789391 ATATCACATA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 7 0.14
29 38 0.76
30 5 0.10
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.43
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTGGTGA
Found at i:1789838 original size:64 final size:64
Alignment explanation
Indices: 1789769--1789925 Score: 158
Period size: 64 Copynumber: 2.5 Consensus size: 64
1789759 TAATGAAGGT
* **
1789769 ATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATGCATTCGAT-GTTTTATTATTAATGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCATTCGATCGTTTTATT-TTAAAAG
1789832 A
64 A
* * * * * *
1789833 ATGCATCGATGCA-TGCCTTATGTATTGATGCACTAATTGCATTCGATCTTTTTATTTTAAAAGA
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAGA
* * *
1789897 GTGTATCGATGCACTACCTGTGCATCGAT
1 ATGCATCGATGCACTACTTGTGCATCGAT
1789926 ACACCTTCAA
Statistics
Matches: 73, Mismatches: 16, Indels: 8
0.75 0.16 0.08
Matches are distributed among these distances:
63 1 0.01
64 63 0.86
65 9 0.12
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAGA
Found at i:1793052 original size:117 final size:117
Alignment explanation
Indices: 1792832--1793052 Score: 277
Period size: 117 Copynumber: 1.9 Consensus size: 117
1792822 CTTTCAAATC
* *
1792832 GAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCATTCTTCAATATTT
1 GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCATTCTTCAACATTT
* *
1792897 CATTTTGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAGTTTGTTTAATTT
66 CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTT
* * * * *
1792949 GAAAATTTCTTTTTCAA-AGTTTTCAGATTTTATTTTTGAAAGCTCTAACTCCTT-TCTCAACAT
1 GAAAATTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTCTAAATCATTCT-TCAACAT
* * **
1793012 TTCATTTTGATTTTCCAAGTCTGTTTTAGATTTC-AAAAGAA
64 TTCATTTTGATTTTCAAAATCCATTTTAG-TTTCTAAAAGAA
1793053 AATCATTTTT
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
116 2 0.02
117 82 0.93
118 4 0.05
ACGTcount: A:0.29, C:0.14, G:0.09, T:0.48
Consensus pattern (117 bp):
GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCATTCTTCAACATTT
CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTT
Found at i:1794777 original size:24 final size:25
Alignment explanation
Indices: 1794709--1794777 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 25
1794699 TAAATAATAT
*
1794709 TAAATAA-ATTATTCTAATATT-TTAA
1 TAAATAATATTA-T-TATTATTGTTAA
1794734 -AAATAATATTATTATT-TTGTTAA
1 TAAATAATATTATTATTATTGTTAA
1794757 TAAATAATATTATT-TTATTGT
1 TAAATAATATTATTATTATTGT
1794778 ATTTGATGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
22 2 0.05
23 9 0.23
24 24 0.62
25 4 0.10
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (25 bp):
TAAATAATATTATTATTATTGTTAA
Found at i:1799486 original size:29 final size:29
Alignment explanation
Indices: 1799454--1799567 Score: 153
Period size: 29 Copynumber: 4.0 Consensus size: 29
1799444 TATAATTTTT
1799454 TTAAAAATAT-TTTTATTTTTATATTTAAC
1 TTAAAAATATATTTTATTTTTAT-TTTAAC
*
1799483 TTAAAAATATATATTATTTTTATTTTAAC
1 TTAAAAATATATTTTATTTTTATTTTAAC
*
1799512 TTAAAAATATATTTTATTTTTATCTTAAC
1 TTAAAAATATATTTTATTTTTATTTTAAC
* *
1799541 TATTAAAA-ATATTTT-TCTTTATTTTAA
1 T-TAAAAATATATTTTATTTTTATTTTAA
1799568 TAGAGCTCAA
Statistics
Matches: 77, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
28 10 0.13
29 51 0.66
30 16 0.21
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (29 bp):
TTAAAAATATATTTTATTTTTATTTTAAC
Found at i:1799621 original size:13 final size:13
Alignment explanation
Indices: 1799603--1799629 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1799593 TATTTTTATC
1799603 TTAAATTATTAAA
1 TTAAATTATTAAA
1799616 TTAAATTATTAAA
1 TTAAATTATTAAA
1799629 T
1 T
1799630 ATATATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTAAATTATTAAA
Found at i:1808346 original size:23 final size:22
Alignment explanation
Indices: 1808288--1808347 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 22
1808278 GGTAATTTTC
1808288 TATA-TAAATCATTAATAATTAT
1 TATATTAAAT-ATTAATAATTAT
* *
1808310 TAAATTAATTTATTAATAATTACT
1 TATATTAA-ATATTAATAATTA-T
1808334 TATATTAAATATTA
1 TATATTAAATATTA
1808348 TAAAATAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
22 3 0.10
23 19 0.61
24 9 0.29
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (22 bp):
TATATTAAATATTAATAATTAT
Found at i:1808521 original size:20 final size:21
Alignment explanation
Indices: 1808483--1808522 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1808473 ATGATGGATG
1808483 AACTAAAATTCTAAGGGGGTC
1 AACTAAAATTCTAAGGGGGTC
*
1808504 AACTAAAATTCTAGGGGGG
1 AACTAAAATTCTAAGGGGG
1808523 CAAAACAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.28, T:0.23
Consensus pattern (21 bp):
AACTAAAATTCTAAGGGGGTC
Found at i:1811557 original size:23 final size:23
Alignment explanation
Indices: 1811509--1811566 Score: 68
Period size: 25 Copynumber: 2.6 Consensus size: 23
1811499 GATTGATAAA
*
1811509 AAAT-TATAATTATATAAATTTT
1 AAATATATAATTATATAAATTTG
1811531 AAATAATATTAATTATA-AAA-TTG
1 AAAT-ATA-TAATTATATAAATTTG
1811554 AAATATATAATTA
1 AAATATATAATTA
1811567 CATCGATTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
21 6 0.19
22 7 0.22
23 6 0.19
24 5 0.16
25 8 0.25
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
AAATATATAATTATATAAATTTG
Found at i:1811566 original size:25 final size:24
Alignment explanation
Indices: 1811509--1811566 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 24
1811499 GATTGATAAA
* *
1811509 AAAT-TATAATT-ATATAAATTTT
1 AAATATATAATTAATATAAAATTG
1811531 AAATA-AT-ATTAATTATAAAATTG
1 AAATATATAATTAA-TATAAAATTG
1811554 AAATATATAATTA
1 AAATATATAATTA
1811567 CATCGATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
21 3 0.10
22 7 0.24
23 13 0.45
24 2 0.07
25 4 0.14
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
AAATATATAATTAATATAAAATTG
Found at i:1816087 original size:20 final size:20
Alignment explanation
Indices: 1816062--1816140 Score: 79
Period size: 20 Copynumber: 4.0 Consensus size: 20
1816052 TTGTTAGAGC
*
1816062 GAAAGTATCGAAACT-TTAGG
1 GAAAGTTTCGAAACTCTT-GG
*
1816082 GAAAGTTTTGAAACTCTTGG
1 GAAAGTTTCGAAACTCTTGG
* *
1816102 GATAGTTTCGAAACTCTTGA
1 GAAAGTTTCGAAACTCTTGG
* * *
1816122 GATAGTTTCAAAATTCTTG
1 GAAAGTTTCGAAACTCTTG
1816141 AAAAATATCG
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 49 0.96
21 2 0.04
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.34
Consensus pattern (20 bp):
GAAAGTTTCGAAACTCTTGG
Found at i:1820487 original size:15 final size:15
Alignment explanation
Indices: 1820467--1820500 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1820457 GTATTCTTAC
1820467 ATTTTTATTTTATTT
1 ATTTTTATTTTATTT
* *
1820482 ATTTTTGTTTTGTTT
1 ATTTTTATTTTATTT
1820497 ATTT
1 ATTT
1820501 AATGTTGCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (15 bp):
ATTTTTATTTTATTT
Found at i:1821748 original size:38 final size:37
Alignment explanation
Indices: 1821673--1821746 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 37
1821663 TTGGAAAATG
* *
1821673 TTTATATATTTTCTTTAAAAAATTTAAATTCATAAAA
1 TTTATATATTTTCTTTAAAAAATTGAAAATCATAAAA
*
1821710 TTTATATAATTGTT-TTTACAAAATTGAAAAT-ATAAAA
1 TTTATAT-ATT-TTCTTTAAAAAATTGAAAATCATAAAA
1821747 ATGTTTAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 13 0.41
38 17 0.53
39 2 0.06
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (37 bp):
TTTATATATTTTCTTTAAAAAATTGAAAATCATAAAA
Found at i:1827889 original size:35 final size:35
Alignment explanation
Indices: 1827850--1827920 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
1827840 TACTGCATAT
* *
1827850 GTGAACAGAGAAATTGCAGAATGTTTAAGGAGTTA
1 GTGAACAAAGAAATTGCAGAATGTTTAAGAAGTTA
*
1827885 GTGAAGAAAGAAATTGCAGAATGTTTAAGAAGTTA
1 GTGAACAAAGAAATTGCAGAATGTTTAAGAAGTTA
1827920 G
1 G
1827921 AAGCGAGGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.42, C:0.04, G:0.28, T:0.25
Consensus pattern (35 bp):
GTGAACAAAGAAATTGCAGAATGTTTAAGAAGTTA
Found at i:1828334 original size:3 final size:3
Alignment explanation
Indices: 1828326--1828350 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1828316 TAACAGGTCT
1828326 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
1828351 AGAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1830356 original size:24 final size:23
Alignment explanation
Indices: 1830305--1830356 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
1830295 TTACACATAG
1830305 GAAAAATGCGAAGATTTACCTTA
1 GAAAAATGCGAAGATTTACCTTA
1830328 GAAAAATGCGAAGATTTACCTTA
1 GAAAAATGCGAAGATTTACCTTA
1830351 GAAAAA
1 GAAAAA
1830357 ATGAAATGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.48, C:0.12, G:0.17, T:0.23
Consensus pattern (23 bp):
GAAAAATGCGAAGATTTACCTTA
Found at i:1832194 original size:22 final size:20
Alignment explanation
Indices: 1832156--1832224 Score: 74
Period size: 17 Copynumber: 3.5 Consensus size: 20
1832146 AGAACCTATC
1832156 ATCCCGAAGGATGTCATCGT
1 ATCCCGAAGGATGTCATCGT
1832176 ATCCCGAAGGA---CAT-GT
1 ATCCCGAAGGATGTCATCGT
*
1832192 CATCCCGAAGGATGTAATCTGT
1 -ATCCCGAAGGATGTCATC-GT
*
1832214 ATCCCGTAGGA
1 ATCCCGAAGGA
1832225 CCTATCATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
16 2 0.05
17 14 0.34
20 13 0.32
21 10 0.24
22 2 0.05
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.23
Consensus pattern (20 bp):
ATCCCGAAGGATGTCATCGT
Found at i:1832195 original size:37 final size:38
Alignment explanation
Indices: 1832138--1832232 Score: 129
Period size: 37 Copynumber: 2.5 Consensus size: 38
1832128 CTCGTATAAA
* * *
1832138 TATCCCGAAGAACCTATCATCCCGAAGGATGTCATC-G
1 TATCCCGAAGGACATATCATCCCGAAGGATGTAATCTG
*
1832175 TATCCCGAAGGACATGTCATCCCGAAGGATGTAATCTG
1 TATCCCGAAGGACATATCATCCCGAAGGATGTAATCTG
* *
1832213 TATCCCGTAGGACCTATCAT
1 TATCCCGAAGGACATATCAT
1832233 ATGTCTTATA
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
37 32 0.64
38 18 0.36
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.24
Consensus pattern (38 bp):
TATCCCGAAGGACATATCATCCCGAAGGATGTAATCTG
Found at i:1832198 original size:17 final size:17
Alignment explanation
Indices: 1832139--1832203 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 17
1832129 TCGTATAAAT
* * *
1832139 ATCCCGAAGAACCTATC
1 ATCCCGAAGGACATGTC
1832156 ATCCCGAAGGATGTCATCGT-
1 ATCCCGAAGGA---CAT-GTC
1832176 ATCCCGAAGGACATGTC
1 ATCCCGAAGGACATGTC
1832193 ATCCCGAAGGA
1 ATCCCGAAGGA
1832204 TGTAATCTGT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
16 2 0.05
17 24 0.60
20 13 0.32
21 1 0.03
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.18
Consensus pattern (17 bp):
ATCCCGAAGGACATGTC
Found at i:1832452 original size:46 final size:45
Alignment explanation
Indices: 1832381--1832468 Score: 140
Period size: 46 Copynumber: 1.9 Consensus size: 45
1832371 ATGTGTAACC
* *
1832381 ATGTATTTCATATCATATTACATGTATCACGTATTACATATTTAT
1 ATGTATTTCATATCATATCACATGTATCACATATTACATATTTAT
*
1832426 ATGTCATTTCATATCATATCACATGTATCACATATTGCATATT
1 ATGT-ATTTCATATCATATCACATGTATCACATATTACATATT
1832469 ATGTAACATA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 4 0.10
46 35 0.90
ACGTcount: A:0.33, C:0.16, G:0.07, T:0.44
Consensus pattern (45 bp):
ATGTATTTCATATCATATCACATGTATCACATATTACATATTTAT
Found at i:1832838 original size:20 final size:20
Alignment explanation
Indices: 1832815--1832852 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1832805 TTTCCTTTAG
*
1832815 GGGGGAATCGATTCCCCCCA
1 GGGGGAATCGATACCCCCCA
1832835 GGGGGAATCGATACCCCC
1 GGGGGAATCGATACCCCC
1832853 TGAACATACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.34, G:0.32, T:0.13
Consensus pattern (20 bp):
GGGGGAATCGATACCCCCCA
Found at i:1842995 original size:59 final size:59
Alignment explanation
Indices: 1842865--1842995 Score: 135
Period size: 62 Copynumber: 2.2 Consensus size: 59
1842855 ATTAGACTTG
* * *
1842865 TAAGTAAAT-ATTAAATATATATATATAATAATAATAATAATAATAAAATAGTAAAAAA
1 TAAGTGAATAATTAAATATATATATATAATAATAATAATAATAACAAAATAATAAAAAA
* *
1842923 TCAAATGAAAATAATT-AATATATATATATATATACAT-ATAATAATAACATGAATAAT-AAAAA
1 T-AAGTG--AATAATTAAATATATATATATA-ATA-ATAATAATAATAACA-AAATAATAAAAAA
1842985 TAAGTGAATAA
1 TAAGTGAATAA
1842996 ATATCCATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
58 1 0.02
59 8 0.13
61 21 0.35
62 23 0.38
63 7 0.12
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (59 bp):
TAAGTGAATAATTAAATATATATATATAATAATAATAATAATAACAAAATAATAAAAAA
Found at i:1844421 original size:211 final size:206
Alignment explanation
Indices: 1843995--1844507 Score: 742
Period size: 211 Copynumber: 2.5 Consensus size: 206
1843985 CATTATTCCA
* * ** * *
1843995 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACGGGGAAATTGTTTGGTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTGTTTGTTGACAA
* * **
1844059 CCAGCCGTCCCTTCGTTGTGAAGTTGAATTTGTGTTCTCTCGAGTCCAATATCCTTCGTTGTGAA
65 CCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCATTCTCTCGAGTCCAATATCCTTCGTTGTGAA
*
1844124 GTTGAAATTGAATCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCATCGTGAAGTTGAACT
130 GTTGAAATTGAATCTGAATGAAATTTTATTGACAAGCAGCGGTCCCTTCATCGTGAAGTTGAACT
*
1844189 TGCGTTGTCTGG
195 TGCGTTGTCTAG
*
1844201 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTTGTTGACAAC
* * *
1844265 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
66 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCATTCTCTCGAGTCCAATATCCTTCGTTGTGAAG
** * **
1844330 TTGAAATTGGCTCTGAGATTGGGAAATTGTTTATTGACAATCAGCGGTCCCTTTGTCGTGAAGTT
131 TTGAAATTGAATCTGA-A-T--GAAA-T-TTTATTGACAAGCAGCGGTCCCTTCATCGTGAAGTT
1844395 GAACTTGCGTTGTCTAG
190 GAACTTGCGTTGTCTAG
*
1844412 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTTGTTGACAAC
*
1844477 CAACCGTCCCTTCGTCGTGAAGTTGAACTTG
66 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTG
1844508 TGTTGTCTCG
Statistics
Matches: 274, Mismatches: 25, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
205 81 0.30
206 47 0.17
207 2 0.01
209 4 0.01
210 1 0.00
211 100 0.36
212 39 0.14
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (206 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTTGTTGACAAC
CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCATTCTCTCGAGTCCAATATCCTTCGTTGTGAAG
TTGAAATTGAATCTGAATGAAATTTTATTGACAAGCAGCGGTCCCTTCATCGTGAAGTTGAACTT
GCGTTGTCTAG
Found at i:1844428 original size:106 final size:106
Alignment explanation
Indices: 1843995--1844520 Score: 735
Period size: 106 Copynumber: 5.0 Consensus size: 106
1843985 CATTATTCCA
* * ** *
1843995 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACGGGGAAATTGTTTGGTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAATTGTTTGTTGACAA
* * * * *
1844059 CCAGCCGTCCCTTCGTTGTGAAGTTGAATTTGTGTTCTCTCG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
** *
1844101 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGA-A-T--GAAA-T-TTTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTTGTTGACAAC
* *
1844160 CAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
* *
1844201 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTTGTTGACAAC
* *
1844265 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
* *
1844306 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTTATTGACAAT
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTTGTTGACAAC
* *
1844371 CAGCGGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
* *
1844412 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTTGTTGACAAC
* * *
1844477 CAACCGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTCG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
1844518 AGT
1 AGT
1844521 GGCACGATAT
Statistics
Matches: 378, Mismatches: 34, Indels: 16
0.88 0.08 0.04
Matches are distributed among these distances:
100 82 0.22
101 2 0.01
102 5 0.01
104 3 0.01
105 104 0.28
106 182 0.48
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (106 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG
Found at i:1845495 original size:38 final size:38
Alignment explanation
Indices: 1845422--1845498 Score: 122
Period size: 36 Copynumber: 2.1 Consensus size: 38
1845412 GAAATGATTT
*
1845422 CAAAGGTTTTTTTCTAACGGAAACTGTCTCAAGAGAGA
1 CAAAGGTTTGTTTCTAACGGAAACTGTCTCAAGAGAGA
*
1845460 CAAA-GTTTGTTTC-AAGGGAAACTGTCTCAAGAGAGA
1 CAAAGGTTTGTTTCTAACGGAAACTGTCTCAAGAGAGA
1845496 CAA
1 CAA
1845499 TAGTAAGCAC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 25 0.68
37 8 0.22
38 4 0.11
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (38 bp):
CAAAGGTTTGTTTCTAACGGAAACTGTCTCAAGAGAGA
Found at i:1846427 original size:21 final size:21
Alignment explanation
Indices: 1846401--1846440 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1846391 CATTTTTGTT
1846401 CATTTGATGCT-AAATGGTTGA
1 CATTTGATGCTCAAA-GGTTGA
1846422 CATTTGATGCTCAAAGGTT
1 CATTTGATGCTCAAAGGTT
1846441 TGATGGGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.38
Consensus pattern (21 bp):
CATTTGATGCTCAAAGGTTGA
Found at i:1848441 original size:22 final size:22
Alignment explanation
Indices: 1848416--1848459 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1848406 CATTTTTGTT
1848416 CATTTGATGCT-AAATGGTTTGA
1 CATTTGATGCTCAAA-GGTTTGA
1848438 CATTTGATGCTCAAAGGTTTGA
1 CATTTGATGCTCAAAGGTTTGA
1848460 TGGGGTAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (22 bp):
CATTTGATGCTCAAAGGTTTGA
Found at i:1849069 original size:22 final size:22
Alignment explanation
Indices: 1849040--1849088 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1849030 CTTGCATGTA
1849040 TTTTTTGTCCCTTTTT-CTTTT
1 TTTTTTGTCCCTTTTTGCTTTT
* *
1849061 TCTTTTTGTTCTTTTTTGCTTTT
1 T-TTTTTGTCCCTTTTTGCTTTT
1849084 TTTTT
1 TTTTT
1849089 GCTTTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 17 0.71
23 6 0.25
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (22 bp):
TTTTTTGTCCCTTTTTGCTTTT
Found at i:1849078 original size:10 final size:9
Alignment explanation
Indices: 1849057--1849104 Score: 53
Period size: 9 Copynumber: 5.2 Consensus size: 9
1849047 TCCCTTTTTC
1849057 TTTTTCTTT
1 TTTTTCTTT
*
1849066 TTGTTCTTT
1 TTTTTCTTT
1849075 TTTGCTT-TTT
1 TTT--TTCTTT
*
1849085 TTTTGCTTT
1 TTTTTCTTT
1849094 TTTTTCTTT
1 TTTTTCTTT
1849103 TT
1 TT
1849105 GCCCTTTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
8 1 0.03
9 23 0.72
10 6 0.19
11 2 0.06
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.83
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:1849093 original size:28 final size:29
Alignment explanation
Indices: 1849050--1849104 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
1849040 TTTTTTGTCC
*
1849050 CTTTTTCTTTTTCTTTTTGTTCTTTTTTG
1 CTTTTTCTTTTGCTTTTTGTTCTTTTTTG
*
1849079 CTTTTT-TTTTGCTTTTTTTTCTTTTT
1 CTTTTTCTTTTGCTTTTTGTTCTTTTT
1849105 GCCCTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.00, C:0.13, G:0.05, T:0.82
Consensus pattern (29 bp):
CTTTTTCTTTTGCTTTTTGTTCTTTTTTG
Found at i:1849112 original size:28 final size:28
Alignment explanation
Indices: 1849041--1849113 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 28
1849031 TTGCATGTAT
*
1849041 TTTTTGTCCCTTTTTCTTTTTCTTTTTGTTC
1 TTTTTG-CCC-TTTT-TTTTGCTTTTTGTTC
* *
1849072 TTTTTTG-CTTTTTTTTTGCTTTTTTTTC
1 -TTTTTGCCCTTTTTTTTGCTTTTTGTTC
1849100 TTTTTGCCCTTTTT
1 TTTTTGCCCTTTTT
1849114 ATTCTGATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
27 6 0.17
28 19 0.53
29 4 0.11
30 1 0.03
32 6 0.17
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.77
Consensus pattern (28 bp):
TTTTTGCCCTTTTTTTTGCTTTTTGTTC
Found at i:1850301 original size:8 final size:8
Alignment explanation
Indices: 1850285--1850323 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
1850275 ATTGTAGATG
1850285 AAAATGCA
1 AAAATGCA
*
1850293 AAAAGGCA
1 AAAATGCA
1850301 AAAATGC-
1 AAAATGCA
1850308 AAAATGCA
1 AAAATGCA
*
1850316 AGAATGCA
1 AAAATGCA
1850324 TGAAATGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (8 bp):
AAAATGCA
Found at i:1850311 original size:15 final size:15
Alignment explanation
Indices: 1850285--1850323 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1850275 ATTGTAGATG
1850285 AAAATGCAAAAAGGCA
1 AAAATGC-AAAAGGCA
*
1850301 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
1850316 AGAATGCA
1 AAAATGCA
1850324 TGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:1850862 original size:18 final size:18
Alignment explanation
Indices: 1850839--1850878 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
1850829 ATTAGTCTTT
1850839 CAGAAGTGGATGTGAATC
1 CAGAAGTGGATGTGAATC
1850857 CAGAAGTGGATGTGAATC
1 CAGAAGTGGATGTGAATC
1850875 CAGA
1 CAGA
1850879 CTTGAAGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.33, T:0.20
Consensus pattern (18 bp):
CAGAAGTGGATGTGAATC
Found at i:1864802 original size:31 final size:32
Alignment explanation
Indices: 1864751--1864823 Score: 105
Period size: 31 Copynumber: 2.3 Consensus size: 32
1864741 ATCGGGCCAG
1864751 ATATATATATTTAAACTAAA-TATATAAATATT
1 ATATATATATTTAAACTAAATTA-ATAAATATT
* *
1864783 ATATATA-ATTTAAATTAAATTAATTAATATT
1 ATATATATATTTAAACTAAATTAATAAATATT
1864814 ATATATATAT
1 ATATATATAT
1864824 AATAATTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
31 26 0.70
32 11 0.30
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (32 bp):
ATATATATATTTAAACTAAATTAATAAATATT
Found at i:1872226 original size:14 final size:16
Alignment explanation
Indices: 1872194--1872224 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1872184 ATTTAATGAA
1872194 ATTTTAA-ATAATTAT
1 ATTTTAATATAATTAT
1872209 ATTTTAATATAATTAT
1 ATTTTAATATAATTAT
1872225 TTAATAACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTTAATATAATTAT
Found at i:1872768 original size:21 final size:22
Alignment explanation
Indices: 1872716--1872769 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
1872706 AGTCGTACTT
*
1872716 TTTTTAATTTTATTTTTCTGAA
1 TTTTTAATTTTATTCTTCTGAA
1872738 TTTTTAAATTTTA-TCTT-TGAA
1 TTTTT-AATTTTATTCTTCTGAA
1872759 TTATTTAATTT
1 TT-TTTAATTT
1872770 GTTTCTTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 11 0.38
22 11 0.38
23 7 0.24
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.67
Consensus pattern (22 bp):
TTTTTAATTTTATTCTTCTGAA
Found at i:1872777 original size:22 final size:21
Alignment explanation
Indices: 1872715--1872766 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 21
1872705 TAGTCGTACT
* *
1872715 TTTTTTAATTTTATTTTTCTGAA
1 TTTTTAAATTTTA-TCTT-TGAA
1872738 TTTTTAAATTTTATCTTTGAA
1 TTTTTAAATTTTATCTTTGAA
1872759 TTATTTAA
1 TT-TTTAA
1872767 TTTGTTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 6 0.23
22 8 0.31
23 12 0.46
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (21 bp):
TTTTTAAATTTTATCTTTGAA
Found at i:1872840 original size:23 final size:23
Alignment explanation
Indices: 1872812--1872862 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
1872802 AGACTATTAA
1872812 TTTAAAAAAT-ATATATATATAAT
1 TTTAAAAAATCATATAT-TATAAT
* *
1872835 TTTAAAATATCATATATTTTAAT
1 TTTAAAAAATCATATATTATAAT
1872858 TTTAA
1 TTTAA
1872863 TTTATTTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTAAAAAATCATATATTATAAT
Found at i:1872841 original size:22 final size:24
Alignment explanation
Indices: 1872809--1872862 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 24
1872799 TTTAGACTAT
*
1872809 TAATTTAAAAAATAT-ATATA-TA
1 TAATTTTAAAAATATCATATATTA
*
1872831 TAATTTT-AAAATATCATATATTT
1 TAATTTTAAAAATATCATATATTA
1872854 TAATTTTAA
1 TAATTTTAA
1872863 TTTATTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 7 0.26
22 11 0.41
23 8 0.30
24 1 0.04
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
TAATTTTAAAAATATCATATATTA
Found at i:1872853 original size:17 final size:17
Alignment explanation
Indices: 1872824--1872856 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1872814 TAAAAAATAT
1872824 ATATATATAATTTTAAA
1 ATATATATAATTTTAAA
1872841 ATATCATAT-ATTTTAA
1 ATAT-ATATAATTTTAA
1872857 TTTTAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATATATAATTTTAAA
Found at i:1875677 original size:23 final size:23
Alignment explanation
Indices: 1875650--1875693 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1875640 TTCCCTAAAG
1875650 GGGGAATCAGTTCCCATTCAAAT
1 GGGGAATCAGTTCCCATTCAAAT
* *
1875673 GGGGAATCGGTTCCCCTTCAA
1 GGGGAATCAGTTCCCATTCAA
1875694 GGGGGTATCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (23 bp):
GGGGAATCAGTTCCCATTCAAAT
Found at i:1877656 original size:15 final size:15
Alignment explanation
Indices: 1877638--1877672 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1877628 AAGATCTTGA
1877638 GTTTCCTCATCTTTC
1 GTTTCCTCATCTTTC
*
1877653 GTTTCCTCATCTTTT
1 GTTTCCTCATCTTTC
1877668 GTTTC
1 GTTTC
1877673 TTCCTTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.06, C:0.29, G:0.09, T:0.57
Consensus pattern (15 bp):
GTTTCCTCATCTTTC
Found at i:1879485 original size:22 final size:21
Alignment explanation
Indices: 1879443--1879482 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1879433 AAGACTGTTT
1879443 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
1879464 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
1879483 ATAGAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:1881975 original size:13 final size:13
Alignment explanation
Indices: 1881954--1881983 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1881944 CCCTCCTTTG
*
1881954 CCCTCCCTCCCTC
1 CCCTACCTCCCTC
1881967 CCCTACCTCCCTC
1 CCCTACCTCCCTC
1881980 CCCT
1 CCCT
1881984 CTCATTTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.03, C:0.73, G:0.00, T:0.23
Consensus pattern (13 bp):
CCCTACCTCCCTC
Found at i:1882836 original size:2 final size:2
Alignment explanation
Indices: 1882829--1882887 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1882819 GATTACGCAT
1882829 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
1882871 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
1882888 GTATGATGTG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1883161 original size:16 final size:15
Alignment explanation
Indices: 1883136--1883176 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
1883126 AATCTTTCAT
*
1883136 TTTTATTTTTCAAACA
1 TTTTAATTTTCAAA-A
*
1883152 TTTTAATTTTTAAAA
1 TTTTAATTTTCAAAA
1883167 TTTTAATTTT
1 TTTTAATTTT
1883177 GATCAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTAATTTTCAAAA
Found at i:1883171 original size:15 final size:17
Alignment explanation
Indices: 1883133--1883176 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
1883123 AACAATCTTT
*
1883133 CATTTTTATTTTTCAAA
1 CATTTTAATTTTTCAAA
1883150 CATTTTAATTTTT-AAA
1 CATTTTAATTTTTCAAA
1883166 -ATTTTAATTTT
1 CATTTTAATTTT
1883177 GATCAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 11 0.42
16 3 0.12
17 12 0.46
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (17 bp):
CATTTTAATTTTTCAAA
Found at i:1884040 original size:60 final size:60
Alignment explanation
Indices: 1883869--1884041 Score: 213
Period size: 60 Copynumber: 2.9 Consensus size: 60
1883859 TGTATCATGC
* * * * * * **
1883869 TTATAGGGTATTGTTTTATTGAATTCCTTGATTATTAAAAATTATAAAATAATTCTTTTG
1 TTATAGGGTATTGTTTTGTTGAGTTCCATGATTATTAAAACTTAAAAAATAGTTCTTTAA
* *
1883929 TTATAGAGTATTGTTTTGTTGAGTCCCATGATTATTAAAACTTAAAAAATAGTTCTTTAA
1 TTATAGGGTATTGTTTTGTTGAGTTCCATGATTATTAAAACTTAAAAAATAGTTCTTTAA
** *
1883989 TTATAGGGTATTACTTTGTTGAGTTTCC-TGATTATTAAAACTTACAAAATAGT
1 TTATAGGGTATTGTTTTGTTGAG-TTCCATGATTATTAAAACTTAAAAAATAGT
1884042 CACTTGATTA
Statistics
Matches: 97, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
60 94 0.97
61 3 0.03
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.46
Consensus pattern (60 bp):
TTATAGGGTATTGTTTTGTTGAGTTCCATGATTATTAAAACTTAAAAAATAGTTCTTTAA
Found at i:1884999 original size:15 final size:16
Alignment explanation
Indices: 1884961--1885011 Score: 59
Period size: 15 Copynumber: 3.1 Consensus size: 16
1884951 AAATATATTA
1884961 ATTTTATAAAAAAAATT
1 ATTTTAT-AAAAAAATT
* *
1884978 ATATTATAAAAATA-T
1 ATTTTATAAAAAAATT
1884993 ATTTTATAAAATAAATT
1 ATTTTATAAAA-AAATT
1885010 AT
1 AT
1885012 ACAGAAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 11 0.39
16 8 0.29
17 9 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATTTTATAAAAAAATT
Found at i:1885251 original size:23 final size:23
Alignment explanation
Indices: 1885225--1885290 Score: 105
Period size: 23 Copynumber: 2.9 Consensus size: 23
1885215 TGTACTTCTG
* *
1885225 TGCTGAATCATTCAGCACTGTTT
1 TGCTGAATCAGTCAACACTGTTT
*
1885248 TGCTGAATCAGTCAATACTGTTT
1 TGCTGAATCAGTCAACACTGTTT
1885271 TGCTGAATCAGTCAACACTG
1 TGCTGAATCAGTCAACACTG
1885291 AATCATTCAG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (23 bp):
TGCTGAATCAGTCAACACTGTTT
Found at i:1885384 original size:41 final size:41
Alignment explanation
Indices: 1885333--1885414 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
1885323 ATGTTGAATG
* * *
1885333 GTTCAACATTCAGCGCTGAATGATTCCATTAAGAGGCAAAC
1 GTTCAACATTCAACGCTAAATGATTCCATTAAGAGACAAAC
* *
1885374 GTTCAGCATTCAACGCTAAATGATTCTATTAAGAGACAAAC
1 GTTCAACATTCAACGCTAAATGATTCCATTAAGAGACAAAC
1885415 ATACGGTCCC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.26
Consensus pattern (41 bp):
GTTCAACATTCAACGCTAAATGATTCCATTAAGAGACAAAC
Found at i:1901097 original size:28 final size:28
Alignment explanation
Indices: 1901052--1901106 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
1901042 AATGAAATGC
* *
1901052 TACATGCCGTAATATAGGTTTCAAATTA
1 TACATGACGCAATATAGGTTTCAAATTA
*
1901080 TACATGACGCAATTTAGGTTTCAAATT
1 TACATGACGCAATATAGGTTTCAAATT
1901107 GATATTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (28 bp):
TACATGACGCAATATAGGTTTCAAATTA
Found at i:1903185 original size:17 final size:17
Alignment explanation
Indices: 1903157--1903199 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1903147 TTACTCGCCT
* *
1903157 CGCATCCGCCCGTCCCC
1 CGCATCCACCCGCCCCC
*
1903174 CGTATCCACCCGCCCCC
1 CGCATCCACCCGCCCCC
1903191 CGCATCCAC
1 CGCATCCAC
1903200 TCGACCCACC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.12, C:0.63, G:0.14, T:0.12
Consensus pattern (17 bp):
CGCATCCACCCGCCCCC
Found at i:1904184 original size:2 final size:2
Alignment explanation
Indices: 1904179--1904215 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1904169 ATTATATAAA
1904179 AT AT 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 AT AT A
1904216 AGCTCAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1906218 original size:24 final size:23
Alignment explanation
Indices: 1906140--1906227 Score: 90
Period size: 23 Copynumber: 3.8 Consensus size: 23
1906130 CAATCTTATA
* *
1906140 TGGCACTACGGTGTAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
1906163 TGGCACTTCGGTGCATTTCTACA
1 TGGCACTTCGGTGCAATTCTACG
*
1906186 CGGTC-CTTCGG-GACAAATTCTACG
1 TGG-CACTTCGGTG-C-AATTCTACG
1906210 TGGCACTTCGGTGCAATT
1 TGGCACTTCGGTGCAATT
1906228 TATATGAGCT
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
22 1 0.02
23 33 0.63
24 17 0.33
25 1 0.02
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.31
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:1912726 original size:24 final size:23
Alignment explanation
Indices: 1912648--1912735 Score: 106
Period size: 23 Copynumber: 3.8 Consensus size: 23
1912638 CAATCTTATA
*
1912648 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
1912671 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* **
1912694 CGGTTCTTCGG-GACAAATTCTACG
1 TGGCACTTCGGTG-C-AATTCTACG
1912718 TGGCACTTCGGTGCAATT
1 TGGCACTTCGGTGCAATT
1912736 TATATGAGCT
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
22 1 0.02
23 34 0.64
24 17 0.32
25 1 0.02
ACGTcount: A:0.18, C:0.25, G:0.26, T:0.31
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:1917213 original size:27 final size:27
Alignment explanation
Indices: 1917157--1917215 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
1917147 CTAAAAATAT
* *
1917157 TATTATTTTATATATATGATATTAATA
1 TATTATTTTATATATATGATAATAAAA
**
1917184 TATTATTTTA-ATATCATTTTAATAAAA
1 TATTATTTTATATAT-ATGATAATAAAA
1917211 TATTA
1 TATTA
1917216 ATTATTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 4 0.15
27 23 0.85
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (27 bp):
TATTATTTTATATATATGATAATAAAA
Found at i:1917286 original size:17 final size:19
Alignment explanation
Indices: 1917264--1917304 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1917254 ATGTAATATT
*
1917264 TTATTTTT-ATA-ATTATA
1 TTATTTTTAATATATAATA
1917281 TTATTTTTAATATATAATA
1 TTATTTTTAATATATAATA
1917300 TTATT
1 TTATT
1917305 CTTTTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.38
18 3 0.14
19 10 0.48
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TTATTTTTAATATATAATA
Found at i:1917287 original size:22 final size:22
Alignment explanation
Indices: 1917260--1917326 Score: 57
Period size: 22 Copynumber: 3.0 Consensus size: 22
1917250 TATAATGTAA
1917260 TATTTTATTTTTATAATTATAT
1 TATTTTATTTTTATAATTATAT
* *
1917282 TATTTT-TAATATATAA-TATTAT
1 TATTTTAT-TTTTATAATTA-TAT
*
1917304 TCTTTTATTTTTAATAATATATA
1 TATTTTATTTTT-ATAAT-TATA
1917327 ATAAATTGCA
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
21 3 0.09
22 22 0.65
23 5 0.15
24 2 0.06
25 2 0.06
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (22 bp):
TATTTTATTTTTATAATTATAT
Found at i:1917289 original size:44 final size:46
Alignment explanation
Indices: 1917241--1917326 Score: 115
Period size: 44 Copynumber: 1.9 Consensus size: 46
1917231 TTATTGACAA
1917241 TTTTAATAATATAAT-GTAATATTTTATTTTT-ATAAT-TATATTAT
1 TTTTAAT-ATATAATAGTAATATTTTATTTTTAATAATATATATTAT
* * *
1917285 TTTTAATATATAATATTATTCTTTTATTTTTAATAATATATA
1 TTTTAATATATAATAGTAATATTTTATTTTTAATAATATATA
1917327 ATAAATTGCA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 7 0.19
44 20 0.56
45 5 0.14
46 4 0.11
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (46 bp):
TTTTAATATATAATAGTAATATTTTATTTTTAATAATATATATTAT
Found at i:1917294 original size:14 final size:16
Alignment explanation
Indices: 1917257--1917304 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
1917247 TAATATAATG
*
1917257 TAATATTTTATTTTTA
1 TAATATATTATTTTTA
1917273 TAATTATATTATTTTTAA
1 TAA-TATATTATTTTT-A
1917291 TATATAATATTATT
1 TA-AT-ATATTATT
1917305 CTTTTATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 3 0.11
17 11 0.41
18 4 0.15
19 9 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TAATATATTATTTTTA
Found at i:1917610 original size:17 final size:17
Alignment explanation
Indices: 1917588--1917642 Score: 74
Period size: 17 Copynumber: 3.1 Consensus size: 17
1917578 ATTATTATTT
1917588 TTAATATTTTAATAATA
1 TTAATATTTTAATAATA
1917605 TTAATATTTTAATAAATAA
1 TTAATATTTTAAT-AAT-A
*
1917624 TTAATATAATTAATAATA
1 TTAATAT-TTTAATAATA
1917642 T
1 T
1917643 ATTATTCTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
17 13 0.38
18 5 0.15
19 11 0.32
20 5 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTAATATTTTAATAATA
Found at i:1917628 original size:25 final size:26
Alignment explanation
Indices: 1917558--1917630 Score: 78
Period size: 25 Copynumber: 2.8 Consensus size: 26
1917548 TAATATATGT
* *
1917558 TTTTTCATATATAATATAATATTATTA
1 TTTTTAATATATAAT-TAATATTAATA
*
1917585 TTTTTAATATTTTAA-TAATATTAATA
1 TTTTTAATA-TATAATTAATATTAATA
*
1917611 -TTTTAATAAATAATTAATAT
1 TTTTTAATATATAATTAATAT
1917631 AATTAATAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
24 3 0.08
25 14 0.36
26 10 0.26
27 8 0.21
28 4 0.10
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (26 bp):
TTTTTAATATATAATTAATATTAATA
Found at i:1918458 original size:35 final size:35
Alignment explanation
Indices: 1918411--1918487 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 35
1918401 AAAACAGTCA
* *
1918411 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* * * *
1918446 TCAATTTTATTCTAAACCCTAAATTCTAAAATACT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
1918481 TCAATTT
1 TCAATTT
1918488 AAGGTAATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.01, T:0.39
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:1918634 original size:17 final size:17
Alignment explanation
Indices: 1918606--1918638 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1918596 ATATAATGTA
1918606 TGAATCATTTATATTTTT
1 TGAATCATTTAT-TTTTT
1918624 TGAAT-ATTTATTTTT
1 TGAATCATTTATTTTT
1918639 AATAAGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.64
Consensus pattern (17 bp):
TGAATCATTTATTTTTT
Found at i:1919305 original size:129 final size:129
Alignment explanation
Indices: 1919107--1919349 Score: 407
Period size: 129 Copynumber: 1.9 Consensus size: 129
1919097 TTTCTTCTAA
* * *
1919107 TTAGGAGGTGACATGTGTCACCATAACACATATCATGATCATGTGTTAACACATGTCAGATCCTG
1 TTAGGAGGTAACATGTGTCACCATAACACATATCATGATCATGTGCTAACACATGTCAGATCCTA
1919172 ATTAAATGATTAA-TTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAATAT
66 ATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAATAT
* * * *
1919235 TTAGGTGGTAACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGATCCT
1 TTAGGAGGTAACATGTGTCACC-ATAACACATATCATGATCATGTGCTAACACATGTCAGATCCT
1919300 AATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
65 AATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
1919350 TATATAAATA
Statistics
Matches: 106, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
128 20 0.19
129 51 0.48
130 35 0.33
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (129 bp):
TTAGGAGGTAACATGTGTCACCATAACACATATCATGATCATGTGCTAACACATGTCAGATCCTA
ATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAATAT
Found at i:1920563 original size:20 final size:19
Alignment explanation
Indices: 1920540--1920610 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 19
1920530 TTTTTAATAT
*
1920540 TATATTAATATATACTCAGA
1 TATATTAATATATAAT-AGA
1920560 TATATT-ATA-ATAATAGA
1 TATATTAATATATAATAGA
*
1920577 TGATATTAATCATATATAATAAA
1 T-ATATT-A--ATATATAATAGA
1920600 T-TATTAATATA
1 TATATTAATATA
1920611 ATTCATATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
17 4 0.09
18 14 0.33
19 3 0.07
20 7 0.16
21 4 0.09
22 3 0.07
23 8 0.19
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (19 bp):
TATATTAATATATAATAGA
Found at i:1920680 original size:24 final size:22
Alignment explanation
Indices: 1920630--1920690 Score: 59
Period size: 24 Copynumber: 2.7 Consensus size: 22
1920620 ATGTATTATT
*
1920630 TTTATAAATATAATATTATTAA
1 TTTATAAATATAATAATATTAA
* *
1920652 ATTATTAATAATAAGTAATATTAA
1 TTTATAAAT-ATAA-TAATATTAA
* *
1920676 TTTATATATTTAATA
1 TTTATAAATATAATA
1920691 TTAATATAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
22 9 0.30
23 7 0.23
24 14 0.47
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TTTATAAATATAATAATATTAA
Found at i:1920705 original size:19 final size:19
Alignment explanation
Indices: 1920636--1920706 Score: 58
Period size: 19 Copynumber: 3.7 Consensus size: 19
1920626 TATTTTTATA
*
1920636 AATATAATATTATTAA-ATT
1 AATATAATAAT-TTAATATT
* *
1920655 ATTAATAATAA-GTAATATT
1 AAT-ATAATAATTTAATATT
*
1920674 AAT-TTATATATTTAATATT
1 AATATAATA-ATTTAATATT
1920693 AATATAATAATTTA
1 AATATAATAATTTA
1920707 GTAGTATGTT
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
17 4 0.10
18 4 0.10
19 22 0.55
20 10 0.25
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (19 bp):
AATATAATAATTTAATATT
Found at i:1921328 original size:20 final size:20
Alignment explanation
Indices: 1921288--1921329 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1921278 AAGAGTGATA
**
1921288 AACTAAAATTCTAGGGGGCG
1 AACTAAAATTCTAGGAAGCG
*
1921308 AACTAAAATTTTAGGAAGCG
1 AACTAAAATTCTAGGAAGCG
1921328 AA
1 AA
1921330 ACAGATTTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.43, C:0.12, G:0.24, T:0.21
Consensus pattern (20 bp):
AACTAAAATTCTAGGAAGCG
Found at i:1927130 original size:19 final size:19
Alignment explanation
Indices: 1927106--1927147 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
1927096 CTAATTACAT
1927106 GTTTGAATGAAATTGAAAA
1 GTTTGAATGAAATTGAAAA
1927125 GTTTGAATGAAATTGAAAA
1 GTTTGAATGAAATTGAAAA
1927144 GTTT
1 GTTT
1927148 AAAAATTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (19 bp):
GTTTGAATGAAATTGAAAA
Found at i:1927419 original size:2 final size:2
Alignment explanation
Indices: 1927412--1927464 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
1927402 TGCGAACTTT
* *
1927412 TA TA TA TA TA TA TA GA TA TA TA TA TA TA TA TC 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
1927454 TA TA TA TA TA T
1 TA TA TA TA TA T
1927465 GACAAAATGC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1928243 original size:85 final size:85
Alignment explanation
Indices: 1928154--1928462 Score: 376
Period size: 85 Copynumber: 3.6 Consensus size: 85
1928144 TGACGCGCAA
* * * * *
1928154 TTGTGTGTCATAAATCTATGACGCGCAT-TAATGACGTT-CTTTGAGTGTCATTGAAGCCCCCAC
1 TTGTGCGTCATAAATTTATGACACGCATGT-ATGAC-TTACATTGAGTGTCATTGAAGCCCCCAT
1928217 CATAAATTAAGATGACACACAT
64 CATAAATTAAGATGACACACAT
* * * *
1928239 TTGTGCGTCATAAATTTATGACACGCATGTATGTCTTATA-T-ATTTCGTCATTGAAGCCCCCGT
1 TTGTGCGTCATAAATTTATGACACGCATGTATGACTTACATTGA-GT-GTCATTGAAGCCCCCAT
1928302 CATAAATTAAGATGACACACAT
64 CATAAATTAAGATGACACACAT
* **
1928324 TTGTGCGTCATAAATTTATGACACGCATGTATGACTTACATTGCGCATCATTGAAGCCCCCATCA
1 TTGTGCGTCATAAATTTATGACACGCATGTATGACTTACATTGAGTGTCATTGAAGCCCCCATCA
* * *
1928389 TAAA-TATGCTTGACATACAT
66 TAAATTAAG-ATGACACACAT
* * *
1928409 TTGTGTGTCATAAATTTATGACACGCATATATGACTTACATTGCGTGTCATTGA
1 TTGTGCGTCATAAATTTATGACACGCATGTATGACTTACATTGAGTGTCATTGA
1928463 TGCACACGCC
Statistics
Matches: 194, Mismatches: 23, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
83 1 0.01
84 7 0.04
85 184 0.95
86 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (85 bp):
TTGTGCGTCATAAATTTATGACACGCATGTATGACTTACATTGAGTGTCATTGAAGCCCCCATCA
TAAATTAAGATGACACACAT
Found at i:1928531 original size:4 final size:4
Alignment explanation
Indices: 1928522--1928586 Score: 62
Period size: 4 Copynumber: 16.8 Consensus size: 4
1928512 TTTCAAAAAT
* * * *
1928522 TATA TATA TATA TATA TATA AATA TATA TAAA TATA AAT- TA-A TAAA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* *
1928568 TAAA TAAA TATA TATA TAT
1 TATA TATA TATA TATA TAT
1928587 TGTAGATTGA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
3 3 0.06
4 49 0.94
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (4 bp):
TATA
Found at i:1928537 original size:10 final size:10
Alignment explanation
Indices: 1928522--1928586 Score: 62
Period size: 10 Copynumber: 6.7 Consensus size: 10
1928512 TTTCAAAAAT
1928522 TATATATATA
1 TATATATATA
1928532 TATATATATA
1 TATATATATA
*
1928542 AATATATATA
1 TATATATATA
* *
1928552 AATATAAAT-
1 TATATATATA
*
1928561 TA-ATAAATA
1 TATATATATA
* *
1928570 AATAAATATA
1 TATATATATA
1928580 TATATAT
1 TATATAT
1928587 TGTAGATTGA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
8 6 0.13
9 2 0.04
10 37 0.82
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
TATATATATA
Found at i:1929787 original size:107 final size:108
Alignment explanation
Indices: 1929601--1929815 Score: 423
Period size: 107 Copynumber: 2.0 Consensus size: 108
1929591 GAATGATCGT
1929601 TCGAAGTCCTCACCAAAACATTTATCCAATTGAGGCTAACCCTTTTGTTAGATCCACTTTGAGTT
1 TCGAAGTCCTCACCAAAACATTTATCCAATTGAGGCTAACCCTTTTGTTAGATCCACTTTGAGTT
1929666 GTACAATTTCATTGCCCTAT-AAAATTGATGAAATATATCAAA
66 GTACAATTTCATTGCCCTATAAAAATTGATGAAATATATCAAA
1929708 TCGAAGTCCTCACCAAAACATTTATCCAATTGAGGCTAACCCTTTTGTTAGATCCACTTTGAGTT
1 TCGAAGTCCTCACCAAAACATTTATCCAATTGAGGCTAACCCTTTTGTTAGATCCACTTTGAGTT
1929773 GTACAATTTCATTGCCCTATAAAAATTGATGAAATATATCAAA
66 GTACAATTTCATTGCCCTATAAAAATTGATGAAATATATCAAA
1929816 GAATATACTA
Statistics
Matches: 107, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
107 85 0.79
108 22 0.21
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.33
Consensus pattern (108 bp):
TCGAAGTCCTCACCAAAACATTTATCCAATTGAGGCTAACCCTTTTGTTAGATCCACTTTGAGTT
GTACAATTTCATTGCCCTATAAAAATTGATGAAATATATCAAA
Found at i:1930606 original size:40 final size:41
Alignment explanation
Indices: 1930562--1930638 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 41
1930552 TTCCCTCTTC
*
1930562 GGTGTCCATTCTTCTTT-CTCCTCTTCCTTTT-TTTCTTTGT
1 GGTGTCCATTCTCCTTTAC-CCTCTTCCTTTTGTTTCTTTGT
*
1930602 GGTGTCCCTTCTCCTTTACCCTCTTCCTTTTGTTTCT
1 GGTGTCCATTCTCCTTTACCCTCTTCCTTTTGTTTCT
1930639 CTTTTTCCGT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
40 27 0.82
41 6 0.18
ACGTcount: A:0.03, C:0.31, G:0.10, T:0.56
Consensus pattern (41 bp):
GGTGTCCATTCTCCTTTACCCTCTTCCTTTTGTTTCTTTGT
Found at i:1934527 original size:15 final size:15
Alignment explanation
Indices: 1934507--1934546 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
1934497 ATGCTTTCTT
1934507 TTTCCTTCTTTGACG
1 TTTCCTTCTTTGACG
1934522 TTTCCTTCTTTGACG
1 TTTCCTTCTTTGACG
*
1934537 TTTTCTTCTT
1 TTTCCTTCTT
1934547 AAACGTTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.05, C:0.25, G:0.10, T:0.60
Consensus pattern (15 bp):
TTTCCTTCTTTGACG
Found at i:1939034 original size:56 final size:53
Alignment explanation
Indices: 1938966--1939080 Score: 185
Period size: 56 Copynumber: 2.1 Consensus size: 53
1938956 AAATCAATAT
1938966 AAAAAATCAAGAACACACACAAGCACTATAAGCATAACAATTAACAAACAAAGAAC
1 AAAAAATCAAGAACACACACAAGCACTATAAGCATAACAATT---AAACAAAGAAC
* *
1939022 AAAAACTCAAGAACACACACAAGTACTATAAGCATAACAATTAAACAAAGAAC
1 AAAAAATCAAGAACACACACAAGCACTATAAGCATAACAATTAAACAAAGAAC
1939075 AAAAAA
1 AAAAAA
1939081 CTCGCTACAT
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
53 16 0.29
56 40 0.71
ACGTcount: A:0.62, C:0.20, G:0.07, T:0.11
Consensus pattern (53 bp):
AAAAAATCAAGAACACACACAAGCACTATAAGCATAACAATTAAACAAAGAAC
Found at i:1939246 original size:26 final size:26
Alignment explanation
Indices: 1939217--1939356 Score: 91
Period size: 32 Copynumber: 4.9 Consensus size: 26
1939207 TCGACAATGA
*
1939217 TTCGTGTGGAGGAGTCGCGACGCTAG
1 TTCGTGTGGAGGAGCCGCGACGCTAG
* * *
1939243 TTCGGGTGGATGAGCCGCGATGCTGGTTTAGG
1 TTCGTGTGGAGGAGCCGCGA--C--G-CTA-G
* *
1939275 TTCGTGTCGAGGAGCCGCGACGCTGG
1 TTCGTGTGGAGGAGCCGCGACGCTAG
* *
1939301 TTCGTGTGGAGGAACCGTGACGCTGGTTTAGG
1 TTCGTGTGGAGGAGCCGCGACGC-----TA-G
*
1939333 TTCGTCTGGAGGAGCCGCGACGCT
1 TTCGTGTGGAGGAGCCGCGACGCT
1939357 GGATTAGATT
Statistics
Matches: 86, Mismatches: 16, Indels: 23
0.69 0.13 0.18
Matches are distributed among these distances:
26 38 0.44
27 2 0.02
28 2 0.02
30 2 0.02
31 3 0.03
32 39 0.45
ACGTcount: A:0.14, C:0.21, G:0.41, T:0.24
Consensus pattern (26 bp):
TTCGTGTGGAGGAGCCGCGACGCTAG
Found at i:1939290 original size:32 final size:32
Alignment explanation
Indices: 1939254--1939378 Score: 127
Period size: 32 Copynumber: 4.1 Consensus size: 32
1939244 TCGGGTGGAT
*
1939254 GAGCCGCGATGCTGGTTTAGGTTCGTGTCGAG
1 GAGCCGCGACGCTGGTTTAGGTTCGTGTCGAG
*
1939286 GAGCCGCGACGC-----T-GGTTCGTGTGGAG
1 GAGCCGCGACGCTGGTTTAGGTTCGTGTCGAG
* * * *
1939312 GAACCGTGACGCTGGTTTAGGTTCGTCTGGAG
1 GAGCCGCGACGCTGGTTTAGGTTCGTGTCGAG
* * *
1939344 GAGCCGCGACGCTGGATTAGATTCGTGGCGAG
1 GAGCCGCGACGCTGGTTTAGGTTCGTGTCGAG
1939376 GAG
1 GAG
1939379 ATCGAGCGCT
Statistics
Matches: 75, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
26 22 0.29
27 1 0.01
31 1 0.01
32 51 0.68
ACGTcount: A:0.15, C:0.20, G:0.42, T:0.23
Consensus pattern (32 bp):
GAGCCGCGACGCTGGTTTAGGTTCGTGTCGAG
Found at i:1939357 original size:58 final size:58
Alignment explanation
Indices: 1939217--1939358 Score: 203
Period size: 58 Copynumber: 2.4 Consensus size: 58
1939207 TCGACAATGA
* * * * *
1939217 TTCGTGTGGAGGAGTCGCGACGCTAGTTCGGGTGGATGAGCCGCGATGCTGGTTTAGG
1 TTCGTGTGGAGGAGCCGCGACGCTGGTTCGGGTGGAGGAACCGCGACGCTGGTTTAGG
* * *
1939275 TTCGTGTCGAGGAGCCGCGACGCTGGTTCGTGTGGAGGAACCGTGACGCTGGTTTAGG
1 TTCGTGTGGAGGAGCCGCGACGCTGGTTCGGGTGGAGGAACCGCGACGCTGGTTTAGG
*
1939333 TTCGTCTGGAGGAGCCGCGACGCTGG
1 TTCGTGTGGAGGAGCCGCGACGCTGG
1939359 ATTAGATTCG
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 74 1.00
ACGTcount: A:0.13, C:0.20, G:0.42, T:0.24
Consensus pattern (58 bp):
TTCGTGTGGAGGAGCCGCGACGCTGGTTCGGGTGGAGGAACCGCGACGCTGGTTTAGG
Found at i:1939766 original size:85 final size:84
Alignment explanation
Indices: 1939614--1939778 Score: 203
Period size: 85 Copynumber: 1.9 Consensus size: 84
1939604 TATGACGCAC
**
1939614 ATTTATGACACGCATTTATGATGCTCATTGCGCGTCATTAAAGCCACCGTCACAAATGAAGACGA
1 ATTTATGACACGCATTTATGAT-CTCATTGCGCGTCATTAAAGCCACCGTCACAAAAAAAGACGA
*
1939679 CACACATTTGTGTGTTATAA
65 CACACATTCGTGTGTTATAA
*
1939699 ATTTATGACACGCATTTATGA-CTTACATTGCGTGTCATTGAAA--CACACGTCA-ATAAAAAAG
1 ATTTATGACACGCATTTATGATC-T-CATTGCGCGTCATT-AAAGCCAC-CGTCACA-AAAAAAG
*
1939760 ATGACACACATTCGTGTGT
61 ACGACACACATTCGTGTGT
1939779 CGTGATTGTA
Statistics
Matches: 70, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
83 1 0.01
84 5 0.07
85 61 0.87
86 3 0.04
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (84 bp):
ATTTATGACACGCATTTATGATCTCATTGCGCGTCATTAAAGCCACCGTCACAAAAAAAGACGAC
ACACATTCGTGTGTTATAA
Found at i:1957785 original size:18 final size:18
Alignment explanation
Indices: 1957762--1957799 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
1957752 GAGAGTCCCC
1957762 AGCCTGCTGAAC-CTGAAG
1 AGCCTGCT-AACGCTGAAG
1957780 AGCCTGCTAACGCTGAAG
1 AGCCTGCTAACGCTGAAG
1957798 AG
1 AG
1957800 ACCGATGACC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.29, C:0.26, G:0.29, T:0.16
Consensus pattern (18 bp):
AGCCTGCTAACGCTGAAG
Found at i:1964591 original size:17 final size:17
Alignment explanation
Indices: 1964550--1964591 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1964540 AATTGCTTCA
* * *
1964550 GCATCTAATTTGGTTTT
1 GCATCTATTTTGATTGT
1964567 GCATCTATTTTGATTGT
1 GCATCTATTTTGATTGT
1964584 GCATCTAT
1 GCATCTAT
1964592 ATGCTCTACG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.19, C:0.14, G:0.17, T:0.50
Consensus pattern (17 bp):
GCATCTATTTTGATTGT
Found at i:1984943 original size:25 final size:26
Alignment explanation
Indices: 1984906--1984956 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
1984896 CATTGTAATT
*
1984906 TTAAATATATTCTCT-TTTAAATAAAA
1 TTAAATATATTCTATATTTAAA-AAAA
*
1984932 TTAATTAT-TTCTATATTTAAAAAAA
1 TTAAATATATTCTATATTTAAAAAAA
1984957 CTTACCTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (26 bp):
TTAAATATATTCTATATTTAAAAAAA
Found at i:1994263 original size:3 final size:3
Alignment explanation
Indices: 1994255--1994281 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1994245 GTAGTTTACC
1994255 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1994282 GATGTTATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1995812 original size:39 final size:39
Alignment explanation
Indices: 1995743--1995846 Score: 138
Period size: 39 Copynumber: 2.7 Consensus size: 39
1995733 TAGATTTTTT
* *
1995743 ATTCTTAA-TTCTCAAATTAATTCACCACAACATTCTAA
1 ATTCTTAATTTCTTAAATTATTTCACCACAACATTCTAA
* *
1995781 ATTCTTAATTTCTTAAATTATTTTACTACAACATTCTAA
1 ATTCTTAATTTCTTAAATTATTTCACCACAACATTCTAA
* * *
1995820 AATATTAATTTCTTGAATTATTTCACC
1 ATTCTTAATTTCTTAAATTATTTCACC
1995847 CTGAAAATCT
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
38 8 0.14
39 48 0.86
ACGTcount: A:0.37, C:0.18, G:0.01, T:0.44
Consensus pattern (39 bp):
ATTCTTAATTTCTTAAATTATTTCACCACAACATTCTAA
Found at i:1998008 original size:20 final size:20
Alignment explanation
Indices: 1997983--1998020 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1997973 AATATTGTAT
1997983 ATTTAAATATTT-AATTTATC
1 ATTTAAA-ATTTGAATTTATC
1998003 ATTTAAAATTTGAATTTA
1 ATTTAAAATTTGAATTTA
1998021 AGTATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (20 bp):
ATTTAAAATTTGAATTTATC
Found at i:1998509 original size:9 final size:9
Alignment explanation
Indices: 1998489--1998518 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1998479 GAATAAAACT
1998489 ATTATA-AA
1 ATTATATAA
1998497 ATTATATAA
1 ATTATATAA
1998506 ATTATATAA
1 ATTATATAA
1998515 ATTA
1 ATTA
1998519 GAGTAGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.29
9 15 0.71
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
ATTATATAA
Found at i:1998665 original size:19 final size:21
Alignment explanation
Indices: 1998627--1998676 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
1998617 ACTTAATTAA
*
1998627 ACAACTAAAAAAATTATATAT
1 ACAAATAAAAAAATTATATAT
1998648 ACAAATAAAAAAATTATATAT
1 ACAAATAAAAAAATTATATAT
*
1998669 TCAAATAA
1 ACAAATAA
1998677 TTATTATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (21 bp):
ACAAATAAAAAAATTATATAT
Found at i:1998737 original size:3 final size:3
Alignment explanation
Indices: 1998724--1998775 Score: 95
Period size: 3 Copynumber: 17.0 Consensus size: 3
1998714 TACTGACATA
1998724 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1998770 AAT AAT
1 AAT AAT
1998776 GGCATATTGT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:2005354 original size:230 final size:230
Alignment explanation
Indices: 2004951--2005410 Score: 920
Period size: 230 Copynumber: 2.0 Consensus size: 230
2004941 TTCCAAGAAA
2004951 CCAATCTTCTTTCAGGCATTTTAACAAACACTTTTTCAGCCAAGTCCAAACACCCACAACTTGCA
1 CCAATCTTCTTTCAGGCATTTTAACAAACACTTTTTCAGCCAAGTCCAAACACCCACAACTTGCA
2005016 TAGAAATGAATCAAACTGTTGTTTACATAAACATCGGGACCGAACCTTTAATACCCCAAATCTCG
66 TAGAAATGAATCAAACTGTTGTTTACATAAACATCGGGACCGAACCTTTAATACCCCAAATCTCG
2005081 GGTCAATAGTTTGATTCAACTCGAGATTCATAAGTTGAACTCATTATGTAACATCCCAAACTATA
131 GGTCAATAGTTTGATTCAACTCGAGATTCATAAGTTGAACTCATTATGTAACATCCCAAACTATA
2005146 GGTTAGTGACCAAATTGTAAAGTTTCAGAATTTGG
196 GGTTAGTGACCAAATTGTAAAGTTTCAGAATTTGG
2005181 CCAATCTTCTTTCAGGCATTTTAACAAACACTTTTTCAGCCAAGTCCAAACACCCACAACTTGCA
1 CCAATCTTCTTTCAGGCATTTTAACAAACACTTTTTCAGCCAAGTCCAAACACCCACAACTTGCA
2005246 TAGAAATGAATCAAACTGTTGTTTACATAAACATCGGGACCGAACCTTTAATACCCCAAATCTCG
66 TAGAAATGAATCAAACTGTTGTTTACATAAACATCGGGACCGAACCTTTAATACCCCAAATCTCG
2005311 GGTCAATAGTTTGATTCAACTCGAGATTCATAAGTTGAACTCATTATGTAACATCCCAAACTATA
131 GGTCAATAGTTTGATTCAACTCGAGATTCATAAGTTGAACTCATTATGTAACATCCCAAACTATA
2005376 GGTTAGTGACCAAATTGTAAAGTTTCAGAATTTGG
196 GGTTAGTGACCAAATTGTAAAGTTTCAGAATTTGG
2005411 TGACTAAAGT
Statistics
Matches: 230, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
230 230 1.00
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (230 bp):
CCAATCTTCTTTCAGGCATTTTAACAAACACTTTTTCAGCCAAGTCCAAACACCCACAACTTGCA
TAGAAATGAATCAAACTGTTGTTTACATAAACATCGGGACCGAACCTTTAATACCCCAAATCTCG
GGTCAATAGTTTGATTCAACTCGAGATTCATAAGTTGAACTCATTATGTAACATCCCAAACTATA
GGTTAGTGACCAAATTGTAAAGTTTCAGAATTTGG
Found at i:2007238 original size:102 final size:102
Alignment explanation
Indices: 2007015--2007230 Score: 389
Period size: 102 Copynumber: 2.1 Consensus size: 102
2007005 TTCGAGGGTC
2007015 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
2007080 TTGATCCTTGGCATATGTATAGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATAGATTCTTAAGGAATGA
2007117 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGT-AAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
2007181 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATA-GATTCTTAAGGAATGA
2007219 TATGTGGTCCTT
1 TATGTGGTCCTT
2007231 ATGGACATTA
Statistics
Matches: 110, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
101 38 0.35
102 72 0.65
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.37
Consensus pattern (102 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATAGATTCTTAAGGAATGA
Found at i:2007291 original size:47 final size:47
Alignment explanation
Indices: 2007237--2007356 Score: 188
Period size: 47 Copynumber: 2.6 Consensus size: 47
2007227 CCTTATGGAC
**
2007237 ATTATTATATGGCACTACGGTGCAATTCTACGTGGCACTCCGATGCA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCAGCACTCCGATGCA
*
2007284 ATTATTATATGGCACTACGGTGCAATTCTACGCAGCACTCCGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCAGCACTCCGATGCA
* *
2007331 ATTA-TATGTGGCACTTCGGTGCAATT
1 ATTATTATATGGCACTACGGTGCAATT
2007357 ATATGAGCTG
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
46 20 0.29
47 48 0.71
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.31
Consensus pattern (47 bp):
ATTATTATATGGCACTACGGTGCAATTCTACGCAGCACTCCGATGCA
Found at i:2007357 original size:23 final size:23
Alignment explanation
Indices: 2007237--2007361 Score: 124
Period size: 23 Copynumber: 5.3 Consensus size: 23
2007227 CCTTATGGAC
*
2007237 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
2007261 ATTCTACGTGGCACTCCGATGCA
1 ATTATATGTGGCACTACGGTGCA
*
2007284 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * ** *
2007308 ATTCTACGCAGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
2007331 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
2007354 ATTATATG
1 ATTATATG
2007362 AGCTGTGGTG
Statistics
Matches: 79, Mismatches: 21, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
23 58 0.73
24 21 0.27
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.31
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:2013148 original size:24 final size:24
Alignment explanation
Indices: 2013079--2013224 Score: 154
Period size: 23 Copynumber: 6.2 Consensus size: 24
2013069 CCTTATGGAC
2013079 ATTATTATATGGCACTACGGTGCA
1 ATTATTATATGGCACTACGGTGCA
* ** *
2013103 ATT-CTATGCGGCACTCCGGTGCA
1 ATTATTATATGGCACTACGGTGCA
*
2013126 ATTATTATATGGCACTACAGTGCA
1 ATTATTATATGGCACTACGGTGCA
2013150 ATTATTATATGGCACTACGGTGCA
1 ATTATTATATGGCACTACGGTGCA
* *** * *
2013174 ATT-CTACGCGACACTCCGGTGCA
1 ATTATTATATGGCACTACGGTGCA
* *
2013197 ATTA-TATGTGGCACTTCGGTGCA
1 ATTATTATATGGCACTACGGTGCA
2013220 ATTAT
1 ATTAT
2013225 ATGAGCTGTG
Statistics
Matches: 99, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
23 55 0.56
24 44 0.44
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (24 bp):
ATTATTATATGGCACTACGGTGCA
Found at i:2013195 original size:71 final size:70
Alignment explanation
Indices: 2013079--2013224 Score: 238
Period size: 71 Copynumber: 2.1 Consensus size: 70
2013069 CCTTATGGAC
* *
2013079 ATTATTATATGGCACTACGGTGCAATTCTATGCGGCACTCCGGTGCAATTATTATATGGCACTAC
1 ATTATTATATGGCACTACGGTGCAATTCTACGCGACACTCCGGTGCAATTA-TATATGGCACTAC
2013144 AGTGCA
65 AGTGCA
* * *
2013150 ATTATTATATGGCACTACGGTGCAATTCTACGCGACACTCCGGTGCAATTATATGTGGCACTTCG
1 ATTATTATATGGCACTACGGTGCAATTCTACGCGACACTCCGGTGCAATTATATATGGCACTACA
2013215 GTGCA
66 GTGCA
2013220 ATTAT
1 ATTAT
2013225 ATGAGCTGTG
Statistics
Matches: 70, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
70 21 0.30
71 49 0.70
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (70 bp):
ATTATTATATGGCACTACGGTGCAATTCTACGCGACACTCCGGTGCAATTATATATGGCACTACA
GTGCA
Found at i:2013584 original size:23 final size:23
Alignment explanation
Indices: 2013558--2013612 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
2013548 TGATATGGAC
2013558 ATAAGAGATCATATGAACATGAG
1 ATAAGAGATCATATGAACATGAG
2013581 ATAAGAGATCATATGAACATGAG
1 ATAAGAGATCATATGAACATGAG
2013604 ATAAGAGAT
1 ATAAGAGAT
2013613 ATGAATGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.49, C:0.07, G:0.22, T:0.22
Consensus pattern (23 bp):
ATAAGAGATCATATGAACATGAG
Found at i:2016842 original size:110 final size:110
Alignment explanation
Indices: 2016649--2016870 Score: 444
Period size: 110 Copynumber: 2.0 Consensus size: 110
2016639 CTCGTTATTA
2016649 TCACTACAGCCTGCATCGACGGATTCGAGCCTTTTGACATCAAAAAGTTGTCTCTATGTTTCAAC
1 TCACTACAGCCTGCATCGACGGATTCGAGCCTTTTGACATCAAAAAGTTGTCTCTATGTTTCAAC
2016714 TTACCGGTTGTGAATATTGGGTTTCTAAATTTTATATGTTTTTGT
66 TTACCGGTTGTGAATATTGGGTTTCTAAATTTTATATGTTTTTGT
2016759 TCACTACAGCCTGCATCGACGGATTCGAGCCTTTTGACATCAAAAAGTTGTCTCTATGTTTCAAC
1 TCACTACAGCCTGCATCGACGGATTCGAGCCTTTTGACATCAAAAAGTTGTCTCTATGTTTCAAC
2016824 TTACCGGTTGTGAATATTGGGTTTCTAAATTTTATATGTTTTTGT
66 TTACCGGTTGTGAATATTGGGTTTCTAAATTTTATATGTTTTTGT
2016869 TC
1 TC
2016871 TTATGATTGA
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
110 112 1.00
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.40
Consensus pattern (110 bp):
TCACTACAGCCTGCATCGACGGATTCGAGCCTTTTGACATCAAAAAGTTGTCTCTATGTTTCAAC
TTACCGGTTGTGAATATTGGGTTTCTAAATTTTATATGTTTTTGT
Found at i:2021203 original size:24 final size:24
Alignment explanation
Indices: 2021176--2021259 Score: 159
Period size: 24 Copynumber: 3.5 Consensus size: 24
2021166 CTGGCCGAGT
2021176 ATTTAACGAGCCTTCCACGTAAGC
1 ATTTAACGAGCCTTCCACGTAAGC
2021200 ATTTAACGAGCCTTCCACGTAAGC
1 ATTTAACGAGCCTTCCACGTAAGC
*
2021224 ATTTAACCAGCCTTCCACGTAAGC
1 ATTTAACGAGCCTTCCACGTAAGC
2021248 ATTTAACGAGCC
1 ATTTAACGAGCC
2021260 AACTGTGTTT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25
Consensus pattern (24 bp):
ATTTAACGAGCCTTCCACGTAAGC
Found at i:2025011 original size:20 final size:21
Alignment explanation
Indices: 2024957--2025022 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
2024947 AGCGCAGCGT
2024957 GAATAGTAAAAATC-ACAACGC
1 GAATAGTAAAAATCGA-AACGC
*
2024978 GAATAGTAAAAATCGAAACAC
1 GAATAGTAAAAATCGAAACGC
*
2024999 GAATAGT-AAAATCGCAACGC
1 GAATAGTAAAAATCGAAACGC
2025019 GAAT
1 GAAT
2025023 TTAGAAAATC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
20 15 0.37
21 25 0.61
22 1 0.02
ACGTcount: A:0.52, C:0.17, G:0.17, T:0.15
Consensus pattern (21 bp):
GAATAGTAAAAATCGAAACGC
Found at i:2025032 original size:21 final size:20
Alignment explanation
Indices: 2024965--2025036 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 20
2024955 GTGAATAGTA
*
2024965 AAAATCACAACGCGAA-TAG
1 AAAATCGCAACGCGAATTAG
* *
2024984 TAAAAATCGAAACACGAA-TAG
1 --AAAATCGCAACGCGAATTAG
2025005 TAAAATCGCAACGCGAATTTAG
1 -AAAATCGCAACGCGAA-TTAG
2025027 AAAATCGCAA
1 AAAATCGCAA
2025037 AATTGCGTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
20 14 0.33
21 26 0.60
22 3 0.07
ACGTcount: A:0.51, C:0.18, G:0.15, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACGCGAATTAG
Found at i:2025452 original size:20 final size:20
Alignment explanation
Indices: 2025427--2025502 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
2025417 TTACTATTCA
2025427 CGTTGCGAATTTGACTATCG
1 CGTTGCGAATTTGACTATCG
* *
2025447 CGTTGCGAATTTGACTTTTG
1 CGTTGCGAATTTGACTATCG
* *
2025467 TGTTACGAATTTGACTATCG
1 CGTTGCGAATTTGACTATCG
2025487 CGTTGCGAATTTGACT
1 CGTTGCGAATTTGACT
2025503 TCTGTGTTAC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (20 bp):
CGTTGCGAATTTGACTATCG
Found at i:2025476 original size:40 final size:40
Alignment explanation
Indices: 2025432--2025540 Score: 159
Period size: 40 Copynumber: 2.7 Consensus size: 40
2025422 ATTCACGTTG
*
2025432 CGAATTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTA
1 CGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTA
2025472 CGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTA
1 CGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTA
* *
2025512 CG-ATTT-ATATATTCGCGTTGCGAAATTGA
1 CGAATTTGA-CTA-TCGCGTTGCGAATTTGA
2025541 AAACTGAGTT
Statistics
Matches: 64, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
38 1 0.02
39 6 0.09
40 57 0.89
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (40 bp):
CGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTA
Found at i:2028438 original size:21 final size:21
Alignment explanation
Indices: 2028409--2028448 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2028399 TTTTTATTAT
* *
2028409 TTTATTAAAAGAATTGGTATG
1 TTTAGTAAAACAATTGGTATG
*
2028430 TTTAGTAAAACACTTGGTA
1 TTTAGTAAAACAATTGGTA
2028449 CATTTAGACT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (21 bp):
TTTAGTAAAACAATTGGTATG
Found at i:2030124 original size:22 final size:22
Alignment explanation
Indices: 2030106--2030165 Score: 111
Period size: 22 Copynumber: 2.7 Consensus size: 22
2030096 GAATTAATAT
2030106 TCAATACTAGTGGATTTAACAC
1 TCAATACTAGTGGATTTAACAC
*
2030128 TCAATACTAATGGATTTAACAC
1 TCAATACTAGTGGATTTAACAC
2030150 TCAATACTAGTGGATT
1 TCAATACTAGTGGATT
2030166 GAGCATTATG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (22 bp):
TCAATACTAGTGGATTTAACAC
Found at i:2034593 original size:2 final size:2
Alignment explanation
Indices: 2034586--2034637 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
2034576 ATTGCATAAG
2034586 AT AT AT AT AT 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 AT AT AT AT AT
2034628 AT AT AT AT AT
1 AT AT AT AT AT
2034638 TCATATGATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2035055 original size:23 final size:23
Alignment explanation
Indices: 2034991--2035055 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
2034981 ATTATACGGT
* *
2034991 ACTTTGGTGCATCTCTACGCGGC
1 ACTTCGGTGCATTTCTACGCGGC
* * *
2035014 ACTACGGTGCAATTCTACGTGGC
1 ACTTCGGTGCATTTCTACGCGGC
*
2035037 ACTTCGGTGCATTTATACG
1 ACTTCGGTGCATTTCTACG
2035056 AGCTGTGGTG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.31
Consensus pattern (23 bp):
ACTTCGGTGCATTTCTACGCGGC
Done.