Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001836.1 Hibiscus syriacus cultivar Beakdansim tig00003715_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: 2428596
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 12
Found at i:1741625 original size:20 final size:20
Alignment explanation
Indices: 1741600--1741639 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1741590 TATATACTAA
1741600 GTTAATCTATTTATTTAGTT
1 GTTAATCTATTTATTTAGTT
1741620 GTTAATCTATTTATTTAGTT
1 GTTAATCTATTTATTTAGTT
1741640 CAATTTCACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.05, G:0.10, T:0.60
Consensus pattern (20 bp):
GTTAATCTATTTATTTAGTT
Found at i:1742449 original size:21 final size:21
Alignment explanation
Indices: 1742424--1742476 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
1742414 TTGGAGTGTG
*
1742424 GGGGAATCGGTACCCCCTCAT
1 GGGGAATCAGTACCCCCTCAT
*
1742445 GGGGAATCAGTACTCCCTCAT
1 GGGGAATCAGTACCCCCTCAT
*
1742466 GGGTAATCAGT
1 GGGGAATCAGT
1742477 TCCCTAATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.26, G:0.28, T:0.23
Consensus pattern (21 bp):
GGGGAATCAGTACCCCCTCAT
Found at i:1742769 original size:20 final size:20
Alignment explanation
Indices: 1742731--1742769 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1742721 CATTTGAAAG
*
1742731 ATTTGGAGTAATATTTTGAT
1 ATTTGGAGTAATATATTGAT
1742751 ATTT-GAGTAATTATATTGA
1 ATTTGGAGTAA-TATATTGA
1742770 ATATACTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (20 bp):
ATTTGGAGTAATATATTGAT
Found at i:1745241 original size:22 final size:23
Alignment explanation
Indices: 1745195--1745244 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
1745185 TTCCCCTGTG
1745195 GGGGGAATCAGTTCCCCTTCAAA
1 GGGGGAATCAGTTCCCCTTCAAA
1745218 GGGGGAATCAGTTCCCCTTC-AA
1 GGGGGAATCAGTTCCCCTTCAAA
1745240 GGGGG
1 GGGGG
1745245 TATCGATTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 7 0.26
23 20 0.74
ACGTcount: A:0.22, C:0.24, G:0.34, T:0.20
Consensus pattern (23 bp):
GGGGGAATCAGTTCCCCTTCAAA
Found at i:1747049 original size:13 final size:13
Alignment explanation
Indices: 1747031--1747057 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1747021 GTATATCTAT
1747031 TGGATATTGATAG
1 TGGATATTGATAG
1747044 TGGATATTGATAG
1 TGGATATTGATAG
1747057 T
1 T
1747058 ATAAATACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.30, T:0.41
Consensus pattern (13 bp):
TGGATATTGATAG
Found at i:1749391 original size:21 final size:21
Alignment explanation
Indices: 1749367--1749407 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1749357 ATCCAAGGTG
1749367 ATGTGAAAAGAT-TGTTTAATT
1 ATGT-AAAAGATATGTTTAATT
*
1749388 ATGTAAAAGGTATGTTTAAT
1 ATGTAAAAGATATGTTTAAT
1749408 CAAATTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.39, C:0.00, G:0.20, T:0.41
Consensus pattern (21 bp):
ATGTAAAAGATATGTTTAATT
Found at i:1749980 original size:14 final size:14
Alignment explanation
Indices: 1749961--1749990 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1749951 TATCTGGAAG
1749961 CTTTCTTTCTTCTT
1 CTTTCTTTCTTCTT
1749975 CTTTCTTTCTTCTT
1 CTTTCTTTCTTCTT
1749989 CT
1 CT
1749991 CGTGGGTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (14 bp):
CTTTCTTTCTTCTT
Found at i:1751889 original size:20 final size:20
Alignment explanation
Indices: 1751864--1751904 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1751854 AGCAAGACAT
1751864 GTCAGTTCTCCTTACCGAAG
1 GTCAGTTCTCCTTACCGAAG
1751884 GTCAGTTCTCCTTACCGAAG
1 GTCAGTTCTCCTTACCGAAG
1751904 G
1 G
1751905 CCAGATCAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (20 bp):
GTCAGTTCTCCTTACCGAAG
Found at i:1771608 original size:19 final size:19
Alignment explanation
Indices: 1771586--1771639 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
1771576 ATTGTTTCCA
1771586 ACAGTCTGTTTTCTACTAT
1 ACAGTCTGTTTTCTACTAT
*
1771605 ACAGTCTGTTTTCTTTCTAT
1 ACAGTCTGTTTTC-TACTAT
1771625 --AGTCTGATTTTCTAC
1 ACAGTCTG-TTTTCTAC
1771640 ATGGTATCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 8 0.26
19 18 0.58
20 5 0.16
ACGTcount: A:0.19, C:0.20, G:0.11, T:0.50
Consensus pattern (19 bp):
ACAGTCTGTTTTCTACTAT
Found at i:1773755 original size:36 final size:36
Alignment explanation
Indices: 1773708--1773779 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
1773698 CCTAGCATTC
* *
1773708 GCCAAGAACCAGATTCAGATCTTGTTGCCTCTGAAA
1 GCCAAGAACCAGATTCAGATCCTGTTGCATCTGAAA
*
1773744 GCCAAGAACCAGATTCGGATCCTGTTGCATCTGAAA
1 GCCAAGAACCAGATTCAGATCCTGTTGCATCTGAAA
1773780 CAGAAGGTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.24
Consensus pattern (36 bp):
GCCAAGAACCAGATTCAGATCCTGTTGCATCTGAAA
Found at i:1775717 original size:19 final size:19
Alignment explanation
Indices: 1775695--1775749 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
1775685 GACTGTTTCC
1775695 TACAGTCTGTTTTCTACTA
1 TACAGTCTGTTTTCTACTA
*
1775714 TACAGTCTGTTTTCTTTCTA
1 TACAGTCTGTTTTC-TACTA
1775734 T--AGTCTGATTTTCTAC
1 TACAGTCTG-TTTTCTAC
1775750 ATTTTCATGG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 8 0.25
19 19 0.59
20 5 0.16
ACGTcount: A:0.18, C:0.20, G:0.11, T:0.51
Consensus pattern (19 bp):
TACAGTCTGTTTTCTACTA
Found at i:1781530 original size:30 final size:29
Alignment explanation
Indices: 1781496--1781570 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
1781486 TTGCACCCAA
* *
1781496 AAAAAAGTTCGAGTACCAAATTGCTCTGTT
1 AAAAAAGTTAG-GTACCAAATTGCTCCGTT
* *
1781526 AAAAAGGTTAGGTACCTAATTGCTCCGTT
1 AAAAAAGTTAGGTACCAAATTGCTCCGTT
* *
1781555 AAAGAGGTTAGGTACC
1 AAAAAAGTTAGGTACC
1781571 TAAAGGCACC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 31 0.77
30 9 0.22
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (29 bp):
AAAAAAGTTAGGTACCAAATTGCTCCGTT
Found at i:1781571 original size:29 final size:29
Alignment explanation
Indices: 1781508--1781573 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 29
1781498 AAAAGTTCGA
* *
1781508 GTACCAAATTGCTCTGTTAAAAAGGTTAG
1 GTACCTAATTGCTCCGTTAAAAAGGTTAG
*
1781537 GTACCTAATTGCTCCGTTAAAGAGGTTAG
1 GTACCTAATTGCTCCGTTAAAAAGGTTAG
1781566 GTACCTAA
1 GTACCTAA
1781574 AGGCACCAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (29 bp):
GTACCTAATTGCTCCGTTAAAAAGGTTAG
Found at i:1796129 original size:23 final size:23
Alignment explanation
Indices: 1796050--1796131 Score: 82
Period size: 23 Copynumber: 3.7 Consensus size: 23
1796040 TTGTGCATAA
*
1796050 TGCATCGATGCA-TCCTTTGAATA
1 TGCATCGATGCACTCC-TTGAATG
* * *
1796073 TGCATCGAT--ACACCTTAAAGG
1 TGCATCGATGCACTCCTTGAATG
1796094 TGCA-CTGATGCACTCCTTGAATG
1 TGCATC-GATGCACTCCTTGAATG
1796117 TGCATCGATGCACTC
1 TGCATCGATGCACTC
1796132 TGCTGTGCAT
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
20 1 0.02
21 12 0.26
22 2 0.04
23 31 0.66
24 1 0.02
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.29
Consensus pattern (23 bp):
TGCATCGATGCACTCCTTGAATG
Found at i:1798429 original size:13 final size:13
Alignment explanation
Indices: 1798411--1798436 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1798401 GAGTAATTTT
1798411 AAAATTATTTTCA
1 AAAATTATTTTCA
1798424 AAAATTATTTTCA
1 AAAATTATTTTCA
1798437 TAGAAAATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
AAAATTATTTTCA
Found at i:1802210 original size:18 final size:19
Alignment explanation
Indices: 1802178--1802230 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 19
1802168 ATTCCAGTAT
*
1802178 TGAAATTTCTTGAATTTA-
1 TGAAATTTCTGGAATTTAC
* *
1802196 TGGAATTTTTGGAA-TTAC
1 TGAAATTTCTGGAATTTAC
1802214 TGAAATTTCTGGAATTT
1 TGAAATTTCTGGAATTT
1802231 CTGGTATTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 3 0.11
18 23 0.82
19 2 0.07
ACGTcount: A:0.30, C:0.06, G:0.17, T:0.47
Consensus pattern (19 bp):
TGAAATTTCTGGAATTTAC
Found at i:1802211 original size:27 final size:27
Alignment explanation
Indices: 1802181--1802239 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
1802171 CCAGTATTGA
*
1802181 AATTTCTTG-AATTTATGGAATTTTTGG
1 AATTTC-TGAAATTTATGGAATTTCTGG
* *
1802208 AATTACTGAAATTTCTGGAATTTCTGG
1 AATTTCTGAAATTTATGGAATTTCTGG
*
1802235 TATTT
1 AATTT
1802240 AAAATTTAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 2 0.08
27 24 0.92
ACGTcount: A:0.27, C:0.07, G:0.17, T:0.49
Consensus pattern (27 bp):
AATTTCTGAAATTTATGGAATTTCTGG
Found at i:1802239 original size:18 final size:18
Alignment explanation
Indices: 1802181--1802239 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
1802171 CCAGTATTGA
* *
1802181 AATTTCTTGAATTTATGG
1 AATTTCTGGAATTTCTGG
* * *
1802199 AATTTTTGGAATTACTGA
1 AATTTCTGGAATTTCTGG
1802217 AATTTCTGGAATTTCTGG
1 AATTTCTGGAATTTCTGG
*
1802235 TATTT
1 AATTT
1802240 AAAATTTAAG
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.27, C:0.07, G:0.17, T:0.49
Consensus pattern (18 bp):
AATTTCTGGAATTTCTGG
Found at i:1803161 original size:33 final size:31
Alignment explanation
Indices: 1803123--1803197 Score: 114
Period size: 33 Copynumber: 2.3 Consensus size: 31
1803113 GGGTTATATG
1803123 ACAATGATGTATGAGATCATACAAGAATGTTAT
1 ACAATGATGTATGAGATCATACAAGAATG--AT
*
1803156 ACAATGATATATGAGATCATACAAGAATGAT
1 ACAATGATGTATGAGATCATACAAGAATGAT
1803187 ACAAGTGATGT
1 ACAA-TGATGT
1803198 GAACTTTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
31 6 0.15
32 5 0.13
33 28 0.72
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (31 bp):
ACAATGATGTATGAGATCATACAAGAATGAT
Found at i:1804811 original size:14 final size:15
Alignment explanation
Indices: 1804792--1804824 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1804782 CCGACAGTCG
1804792 AAAA-TTTTTTAGTT
1 AAAATTTTTTTAGTT
1804806 AAAATTTTTTTAGTT
1 AAAATTTTTTTAGTT
1804821 AAAA
1 AAAA
1804825 AATTTCATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (15 bp):
AAAATTTTTTTAGTT
Found at i:1805575 original size:223 final size:222
Alignment explanation
Indices: 1805177--1806259 Score: 1467
Period size: 223 Copynumber: 4.9 Consensus size: 222
1805167 GGGGTATTAT
*
1805177 AAGACATGTACGTCCATATACAGATTTGTTACAGTAGGTGTGCTCCACTTGAGTGTTGGTGGGAC
1 AAGACATGTATGTCCATATACAGATTTGTTACAGTAGGTGTGCTCCACTTGAGTGTTGGTGGGA-
* *
1805242 TTGGGGATTGAGATTTTAGTGCAATTGAAGTTGAGGTC-TGTGGGACTTTCGATT-AGGTCATCA
65 TTGGGGATCGAGATTGTAGTGCAATTGAAGTTGAGG-CATGTGGGACTTTCGATTGA-GTCATCA
* * * *
1805305 TTAACACTCAGATTGATGTTCAAGATTTCTTGAGTGTGGACTGCTTTGCACGGTAGAGTACCAGG
128 TTGACACTCAGATTGATGTTCGAGATTTCTTGAGTGGGGACTGCTTTGCATGGTAGAGTACCAGG
*
1805370 GAATTCCTTTTATGTGCCAGTGGCAAGTGC
193 GAATTCCTTTTGTGTGCCAGTGGCAAGTGC
* * * *
1805400 AAGACATGTATGTTCATATACAAATATGTTACAGTAGTTGTGCTCCACTTGAGTGTTGGTGGGAT
1 AAGACATGTATGTCCATATACAGATTTGTTACAGTAGGTGTGCTCCACTTGAGTGTTGGTGGGAT
** * * * *
1805465 TGAGAAATCGAGATTGCAGTGCAATTGAAGTTGAGGCATGTGGGACTTTCCATTGGGTCATCATA
66 TG-GGGATCGAGATTGTAGTGCAATTGAAGTTGAGGCATGTGGGACTTTCGATTGAGTCATCATT
* * * * *
1805530 GACACTCAGATTGATGTTCGGGATTTCTTCAGTGGGGAATGCTTTGCATGGTAGAGTACTAGTGA
130 GACACTCAGATTGATGTTCGAGATTTCTTGAGTGGGGACTGCTTTGCATGGTAGAGTACCAGGGA
* * *
1805595 ATTCATTTTGTGT-ACATGTGGCAAGTGA
195 ATTCCTTTTGTGTGCCA-GTGGCAAGTGC
* * *
1805623 AAGACGTGTATGCCCATATACATATTTGTTACAGTAGGTGTGCTCCACTTGAGTGTTGGTGGGAC
1 AAGACATGTATGTCCATATACAGATTTGTTACAGTAGGTGTGCTCCACTTGAGTGTTGGTGGGA-
* * * *
1805688 TGGGGGATCAAGATTGTAGTGCAATTGAAGTTGAGGCCTGTGAGACTTTCGATTGAGTCATCATT
65 TTGGGGATCGAGATTGTAGTGCAATTGAAGTTGAGGCATGTGGGACTTTCGATTGAGTCATCATT
* *
1805753 GACACTCAAATTAATGTTCGAGATTTCTTGAGTGGGGACTGCTTTGCATGGTAGAGTACCAGGGA
130 GACACTCAGATTGATGTTCGAGATTTCTTGAGTGGGGACTGCTTTGCATGGTAGAGTACCAGGG-
*
1805818 AATT-CTTTTGTGTGCCTGTGGCAAGTGC
194 AATTCCTTTTGTGTGCCAGTGGCAAGTGC
* * * * *
1805846 AAGACATGTATGTCCATATACAGATTTGTTACAATGGGTGTGTTCCACTTGAGTATTTGTGGGAT
1 AAGACATGTATGTCCATATACAGATTTGTTACAGTAGGTGTGCTCCACTTGAGTGTTGGTGGGAT
* * * * * * *
1805911 TGGGGGATCGAAATTGTAGTGTAATTGAAGTGGAGGCCTGTGGAACTTTTGATTGAGTTATCATT
66 T-GGGGATCGAGATTGTAGTGCAATTGAAGTTGAGGCATGTGGGACTTTCGATTGAGTCATCATT
* * * *
1805976 GACGCCCAGATTGATGTTTGAGATTTCTTGAGTGGGGATTGCTTTGCATGGTAGAGTACCAGGGA
130 GACACTCAGATTGATGTTCGAGATTTCTTGAGTGGGGACTGCTTTGCATGGTAGAGTACCAGGGA
* * *
1806041 ATCCCTTTTGTGTGTCTA-TGACAAGTGC
195 ATTCCTTTTGTGTG-CCAGTGGCAAGTGC
*
1806069 AAGACATGTATGTCCATATACAGATTTGTTATAGTAGGTGTGCTCCACTTGAGTGTTGGTGGGAT
1 AAGACATGTATGTCCATATACAGATTTGTTACAGTAGGTGTGCTCCACTTGAGTGTTGGTGGGAT
* * * *
1806134 TGGATGATCGAGATTGCAGTGCAATTGAAGTTGAGGCATCTGGGACTTTCGATTGTGTCATCATT
66 TGG-GGATCGAGATTGTAGTGCAATTGAAGTTGAGGCATGTGGGACTTTCGATTGAGTCATCATT
* *
1806199 GACGCTCAGATTGATGTTC-AGAATTTCTTAAGTGGGGACTGCTTTGCATGGTAGAGTACCA
130 GACACTCAGATTGATGTTCGAG-ATTTCTTGAGTGGGGACTGCTTTGCATGGTAGAGTACCA
1806260 TGGGTACGGG
Statistics
Matches: 747, Mismatches: 101, Indels: 24
0.86 0.12 0.03
Matches are distributed among these distances:
222 14 0.02
223 725 0.97
224 8 0.01
ACGTcount: A:0.24, C:0.14, G:0.29, T:0.33
Consensus pattern (222 bp):
AAGACATGTATGTCCATATACAGATTTGTTACAGTAGGTGTGCTCCACTTGAGTGTTGGTGGGAT
TGGGGATCGAGATTGTAGTGCAATTGAAGTTGAGGCATGTGGGACTTTCGATTGAGTCATCATTG
ACACTCAGATTGATGTTCGAGATTTCTTGAGTGGGGACTGCTTTGCATGGTAGAGTACCAGGGAA
TTCCTTTTGTGTGCCAGTGGCAAGTGC
Found at i:1813213 original size:4 final size:4
Alignment explanation
Indices: 1813200--1813240 Score: 75
Period size: 4 Copynumber: 10.5 Consensus size: 4
1813190 TGAATGGATC
1813200 AGTT -GTT AGTT AGTT AGTT AGTT AGTT AGTT AGTT AGTT AG
1 AGTT AGTT AGTT AGTT AGTT AGTT AGTT AGTT AGTT AGTT AG
1813241 CAATCTGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 3 0.08
4 33 0.92
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (4 bp):
AGTT
Found at i:1818834 original size:16 final size:17
Alignment explanation
Indices: 1818815--1818853 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
1818805 TTTGAGAAAA
*
1818815 TATTTATTTGG-TATTT
1 TATTTATTTGGATAATT
*
1818831 TATTCATTTGGATAATT
1 TATTTATTTGGATAATT
1818848 TATTTA
1 TATTTA
1818854 GAATAGGCCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.26, C:0.03, G:0.10, T:0.62
Consensus pattern (17 bp):
TATTTATTTGGATAATT
Found at i:1822941 original size:11 final size:11
Alignment explanation
Indices: 1822922--1822955 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1822912 AAGAACACCA
1822922 AAAGAAAAACTT
1 AAAG-AAAACTT
1822934 AAAGAAAACTT
1 AAAGAAAACTT
*
1822945 AATGAAAACTT
1 AAAGAAAACTT
1822956 GATGTAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.62, C:0.09, G:0.09, T:0.21
Consensus pattern (11 bp):
AAAGAAAACTT
Found at i:1822966 original size:12 final size:11
Alignment explanation
Indices: 1822927--1822970 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
1822917 CACCAAAAGA
*
1822927 AAAACTTAAAG
1 AAAACTTAATG
1822938 AAAACTTAATG
1 AAAACTTAATG
*
1822949 AAAACTTGATG
1 AAAACTTAATG
1822960 TAAAAC-TAATG
1 -AAAACTTAATG
1822971 CCCTAGCTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 24 0.83
12 5 0.17
ACGTcount: A:0.55, C:0.09, G:0.11, T:0.25
Consensus pattern (11 bp):
AAAACTTAATG
Found at i:1824055 original size:27 final size:26
Alignment explanation
Indices: 1823990--1824055 Score: 62
Period size: 27 Copynumber: 2.5 Consensus size: 26
1823980 AGCCACATAA
1823990 CTTCTTTTTTTCATTGCACAATCTCT
1 CTTCTTTTTTTCATTGCACAATCTCT
** * *
1824016 CTTTCTTCATTTCGTTTGCACAAT-TTT
1 C-TTCTTTTTTTC-ATTGCACAATCTCT
1824043 GCTTCTTTTTTTC
1 -CTTCTTTTTTTC
1824056 TTTTATTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
26 1 0.03
27 20 0.65
28 10 0.32
ACGTcount: A:0.12, C:0.24, G:0.06, T:0.58
Consensus pattern (26 bp):
CTTCTTTTTTTCATTGCACAATCTCT
Found at i:1825255 original size:6 final size:6
Alignment explanation
Indices: 1825244--1825277 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
1825234 AAATCAAGAA
1825244 AAAAAT AAAAAT AAAAAT -AAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
1825278 GAACGAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:1825259 original size:11 final size:11
Alignment explanation
Indices: 1825244--1825276 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
1825234 AAATCAAGAA
1825244 AAAAATAAAAAT
1 AAAAAT-AAAAT
1825256 AAAAATAAAAT
1 AAAAATAAAAT
1825267 AAAAATAAAA
1 AAAAATAAAA
1825277 AGAACGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.71
12 6 0.29
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:1825265 original size:17 final size:16
Alignment explanation
Indices: 1825232--1825277 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 16
1825222 TTGTACTCCG
1825232 AAAAATCAAGAAAAAAAT
1 AAAAAT-AA-AAAAAAAT
1825250 AAAAATAAAAATAAAAT
1 AAAAATAAAAA-AAAAT
1825267 AAAAATAAAAA
1 AAAAATAAAAA
1825278 GAACGAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 3 0.11
17 18 0.67
18 6 0.22
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.13
Consensus pattern (16 bp):
AAAAATAAAAAAAAAT
Found at i:1831064 original size:2 final size:2
Alignment explanation
Indices: 1831057--1831081 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1831047 TTACAACCTA
1831057 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 A
1831082 ACTTTTAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1831773 original size:13 final size:13
Alignment explanation
Indices: 1831757--1831851 Score: 65
Period size: 13 Copynumber: 7.5 Consensus size: 13
1831747 ATGTATAAAT
*
1831757 TAAATGAATATAA
1 TAAATAAATATAA
1831770 TAAATAAATATAA
1 TAAATAAATATAA
* *
1831783 T-AATAAAAATCA
1 TAAATAAATATAA
*
1831795 TTAAT-AATATTAA
1 TAAATAAATA-TAA
*
1831808 -ATATTAAATATAA
1 TA-AATAAATATAA
* *
1831821 TAAATAATTAGAA
1 TAAATAAATATAA
1831834 TACAAT-AATAT-A
1 TA-AATAAATATAA
1831846 TAAATA
1 TAAATA
1831852 TAGTAATTAA
Statistics
Matches: 63, Mismatches: 12, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
11 3 0.05
12 16 0.25
13 36 0.57
14 8 0.13
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (13 bp):
TAAATAAATATAA
Found at i:1831787 original size:16 final size:16
Alignment explanation
Indices: 1831766--1831858 Score: 53
Period size: 16 Copynumber: 5.3 Consensus size: 16
1831756 TTAAATGAAT
1831766 ATAATAAATAAATATA
1 ATAATAAATAAATATA
1831782 ATAATAAA-AATCATTAATA
1 ATAATAAATAA--A-T-ATA
*
1831801 ATATTAAATATTAAATATA
1 ATAAT-AA-A-TAAATATA
* *
1831820 ATAAATAATTAGAATACA
1 AT-AATAAATA-AATATA
*
1831838 ATAATATATAAATATA
1 ATAATAAATAAATATA
*
1831854 GTAAT
1 ATAAT
1831859 TAAAGTAGAT
Statistics
Matches: 59, Mismatches: 8, Indels: 20
0.68 0.09 0.23
Matches are distributed among these distances:
15 2 0.03
16 17 0.29
17 9 0.15
18 8 0.14
19 14 0.24
20 5 0.08
21 2 0.03
23 2 0.03
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (16 bp):
ATAATAAATAAATATA
Found at i:1831985 original size:22 final size:22
Alignment explanation
Indices: 1831941--1831982 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
1831931 AAATATTAAA
1831941 TATAATTAATAATTAATAATAT
1 TATAATTAATAATTAATAATAT
1831963 TATAATT-ATAATT-ATAATAT
1 TATAATTAATAATTAATAATAT
1831983 ATTTTGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.35
21 6 0.30
22 7 0.35
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TATAATTAATAATTAATAATAT
Found at i:1834768 original size:6 final size:6
Alignment explanation
Indices: 1834757--1834791 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
1834747 CTGACTTCTT
*
1834757 CCTCTA CCTCTA CCTCTA CCTCTA CCTCTT CCTCT
1 CCTCTA CCTCTA CCTCTA CCTCTA CCTCTA CCTCT
1834792 CTGGGTAGCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.11, C:0.51, G:0.00, T:0.37
Consensus pattern (6 bp):
CCTCTA
Found at i:1836663 original size:18 final size:18
Alignment explanation
Indices: 1836636--1836706 Score: 90
Period size: 18 Copynumber: 3.8 Consensus size: 18
1836626 TGAATATTTA
1836636 TCCCGAAGGACCACTATG
1 TCCCGAAGGACCACTATG
1836654 TCCC-AGAGGACCACTGATTG
1 TCCCGA-AGGACCACT-A-TG
* *
1836674 TTCCGAAGAACCACTATG
1 TCCCGAAGGACCACTATG
1836692 TCCCGAAGGACCACT
1 TCCCGAAGGACCACT
1836707 GATAATCCCT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
17 1 0.02
18 28 0.62
19 2 0.04
20 13 0.29
21 1 0.02
ACGTcount: A:0.28, C:0.32, G:0.21, T:0.18
Consensus pattern (18 bp):
TCCCGAAGGACCACTATG
Found at i:1837367 original size:64 final size:65
Alignment explanation
Indices: 1837277--1837421 Score: 161
Period size: 64 Copynumber: 2.3 Consensus size: 65
1837267 ATTCCTTGAC
* * * *
1837277 GGGTGCATCGATGCAC-AATCTATGCATCGGTACA-TAAATCTCATTCGATGTTTGTGTTTTAAG
1 GGGTGCATCGATGCACTAATCTATGCATCGATACACT-AATCACATTCGATGTTTGTATTTTAAA
1837340 G
65 G
* * * *
1837341 GGGTGCATCGATGCACTACT-TGTGCATCGATACACTAATGACATTCGATGTTTTTATTTTAAAG
1 GGGTGCATCGATGCACTAATCTATGCATCGATACACTAATCACATTCGATGTTTGTATTTTAAAG
** *
1837405 AAGTGCATCGATACACT
1 GGGTGCATCGATGCACT
1837422 TCATGTGTAT
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
64 65 0.96
65 3 0.04
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (65 bp):
GGGTGCATCGATGCACTAATCTATGCATCGATACACTAATCACATTCGATGTTTGTATTTTAAAG
Found at i:1840101 original size:2 final size:2
Alignment explanation
Indices: 1840094--1840128 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1840084 ATGCATAAGT
1840094 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1840129 GTGTGTGTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1840133 original size:2 final size:2
Alignment explanation
Indices: 1840128--1840152 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1840118 TATATATATA
1840128 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
1840153 TCATATGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1841059 original size:21 final size:21
Alignment explanation
Indices: 1841033--1841072 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1841023 GAAGTTACTG
*
1841033 TAGCAGTGCATCGGTACACTA
1 TAGCAGTGCATCGATACACTA
1841054 TAGCAGTGCATCGATACAC
1 TAGCAGTGCATCGATACAC
1841073 AATTTATATT
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:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (21 bp):
TAGCAGTGCATCGATACACTA
Found at i:1841119 original size:21 final size:21
Alignment explanation
Indices: 1841093--1841134 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1841083 CGATGTTTTT
1841093 GTGCATCGGTACACTGTAGCA
1 GTGCATCGGTACACTGTAGCA
1841114 GTGCATCGGTACACTGTAGCA
1 GTGCATCGGTACACTGTAGCA
1841135 CTGTTTATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (21 bp):
GTGCATCGGTACACTGTAGCA
Found at i:1841151 original size:12 final size:12
Alignment explanation
Indices: 1841134--1841191 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
1841124 ACACTGTAGC
*
1841134 ACTGTTTATAGT
1 ACTGTTCATAGT
*
1841146 ACTGTTCATGGT
1 ACTGTTCATAGT
*
1841158 GCTGTTCATAGT
1 ACTGTTCATAGT
* * **
1841170 ATTGTTTACGGT
1 ACTGTTCATAGT
1841182 ACTGTTCATA
1 ACTGTTCATA
1841192 CTGTATAATA
Statistics
Matches: 33, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.45
Consensus pattern (12 bp):
ACTGTTCATAGT
Found at i:1841186 original size:24 final size:24
Alignment explanation
Indices: 1841134--1841191 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
1841124 ACACTGTAGC
* *
1841134 ACTGTTTATAGTACTGTTCATGGT
1 ACTGTTCATAGTACTGTTCACGGT
* * *
1841158 GCTGTTCATAGTATTGTTTACGGT
1 ACTGTTCATAGTACTGTTCACGGT
1841182 ACTGTTCATA
1 ACTGTTCATA
1841192 CTGTATAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.45
Consensus pattern (24 bp):
ACTGTTCATAGTACTGTTCACGGT
Found at i:1847000 original size:16 final size:16
Alignment explanation
Indices: 1846978--1847020 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
1846968 TTGGACCTAA
1846978 AAATTTCAAAATAATC
1 AAATTTCAAAATAATC
*
1846994 CAATTTCAAAATAATC
1 AAATTTCAAAATAATC
1847010 AAATTTCAAAA
1 AAATTTCAAAA
1847021 ATATTTTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.56, C:0.14, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATTTCAAAATAATC
Found at i:1847603 original size:20 final size:22
Alignment explanation
Indices: 1847581--1847622 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
1847571 TTATAAATAA
1847581 TTTTTA-AAAATAATATTTAAT
1 TTTTTATAAAATAATATTTAAT
1847602 TTTTTATTAAAATAATATTTA
1 TTTTTA-TAAAATAATATTTA
1847623 TATAATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.32
23 13 0.68
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTTTATAAAATAATATTTAAT
Found at i:1847631 original size:23 final size:22
Alignment explanation
Indices: 1847576--1847633 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
1847566 TTTTTTTATA
*
1847576 AATAATTTTTAAAAATAATATTT
1 AATAATTATT-AAAATAATATTT
**
1847599 AATTTTTTATTAAAATAATATTT
1 AA-TAATTATTAAAATAATATTT
1847622 ATATAATTATTA
1 A-ATAATTATTA
1847634 TTTATTTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
23 22 0.79
24 6 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
AATAATTATTAAAATAATATTT
Found at i:1847648 original size:25 final size:24
Alignment explanation
Indices: 1847618--1847664 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 24
1847608 TTAAAATAAT
1847618 ATTTATATAATT-ATTATTTATTTAA
1 ATTTAT-TAATTAATTA-TTATTTAA
1847643 ATTTATTAATTAATTATTATTT
1 ATTTATTAATTAATTATTATTT
1847665 GTGCTAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTTATTAATTAATTATTATTTAA
Found at i:1852489 original size:43 final size:43
Alignment explanation
Indices: 1852317--1852647 Score: 377
Period size: 43 Copynumber: 7.8 Consensus size: 43
1852307 TAATTAGCAA
* * * * *
1852317 CGTTTGTTCTAAAAACGCCGCTATAGATC-CGGCCATTTGTGA
1 CGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTTGCGG
* *
1852359 CGTTTGTT-CAAAAAAGCCGTTATAGATCT-GACCTTTTGCGG
1 CGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTTGCGG
* * ** * * * *
1852400 CATTAGTTTGAAAAATGCTGCTATGGTTCT-GACCTTTTGCGG
1 CGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTTGCGG
* * * *
1852442 CGTTTATTCCAAAAATGCCGCTATAGATCTCGACCTATTACGG
1 CGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTTGCGG
* *
1852485 CGTTTGTTCCAAAAACGCCGCTATAGATCTTGA-CTTGTTGCAG
1 CGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTT-TTGCGG
* * *
1852528 CGTTTGTTCCAAAAATGTCGCAATAGATC-CGACCTTTTGCGG
1 CGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTTGCGG
1852570 CGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTTGCGG
1 CGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTTGCGG
**
1852613 CGTTTGTTCCAAAAACGTTGCTATAGATCTCGACC
1 CGTTTGTTCCAAAAACGCCGCTATAGATCTCGACC
1852648 CTATTACGGC
Statistics
Matches: 242, Mismatches: 41, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
41 31 0.13
42 92 0.38
43 119 0.49
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (43 bp):
CGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTTGCGG
Found at i:1852508 original size:85 final size:85
Alignment explanation
Indices: 1852317--1852657 Score: 375
Period size: 85 Copynumber: 4.0 Consensus size: 85
1852307 TAATTAGCAA
* * * * * * * *
1852317 CGTTTGTTCTAAAAACGCCGCTATAGATCCGGCCATTTGTGACGTTTGTT-CAAAAAAGCCGTTA
1 CGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAATGCCGCTA
* *
1852381 TAGATCT-GACCTTTTGCGG
66 TAGATCTCGACCTATTACGG
* * ** * * * * *
1852400 CATTAGTTTGAAAAATGCTGCTATGGTTCTGACCTTTTGCGGCGTTTATTCCAAAAATGCCGCTA
1 CGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAATGCCGCTA
1852465 TAGATCTCGACCTATTACGG
66 TAGATCTCGACCTATTACGG
* *
1852485 CGTTTGTTCCAAAAACGCCGCTATAGATCTTGA-CTTGTTGCAGCGTTTGTTCCAAAAATGTCGC
1 CGTTTGTTCCAAAAACGCCGCTATAGATC-TGACCTT-TTGCGGCGTTTGTTCCAAAAATGCCGC
* * *
1852549 AATAGATC-CGACCTTTTGCGG
64 TATAGATCTCGACCTATTACGG
* **
1852570 CGTTTGTTCCAAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGTTGCT
1 CGTTTGTTCCAAAAACGCCGCTATAGATCT-GACCTTTTGCGGCGTTTGTTCCAAAAATGCCGCT
1852635 ATAGATCTCGACCCTATTACGG
65 ATAGATCTCGA-CCTATTACGG
1852657 C
1 C
1852658 ATTTTTTTTC
Statistics
Matches: 212, Mismatches: 38, Indels: 12
0.81 0.15 0.05
Matches are distributed among these distances:
83 36 0.17
84 20 0.09
85 107 0.50
86 40 0.19
87 9 0.04
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (85 bp):
CGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAATGCCGCTA
TAGATCTCGACCTATTACGG
Found at i:1855000 original size:26 final size:26
Alignment explanation
Indices: 1854971--1855084 Score: 69
Period size: 26 Copynumber: 4.5 Consensus size: 26
1854961 CCCTAAAGCA
1854971 CTTTAACCTACACAACCTTAATGAAT
1 CTTTAACCTACACAACCTTAATGAAT
* * * **
1854997 CTTTGACCTACAAAATCCTTCA-CCA-
1 CTTTAACCTACACAA-CCTTAATGAAT
* * *
1855022 CTTTAACCTTA-ACGAAACAT-AT-AACA
1 CTTTAACC-TACAC-AACCTTAATGAA-T
1855048 CTTTAACC-ACACAACCTTAATGAAT
1 CTTTAACCTACACAACCTTAATGAAT
*
1855073 CTTTGACCTACA
1 CTTTAACCTACA
1855085 AAATCCTTCA
Statistics
Matches: 64, Mismatches: 14, Indels: 20
0.65 0.14 0.20
Matches are distributed among these distances:
24 7 0.11
25 21 0.33
26 31 0.48
27 5 0.08
ACGTcount: A:0.38, C:0.29, G:0.04, T:0.29
Consensus pattern (26 bp):
CTTTAACCTACACAACCTTAATGAAT
Found at i:1855030 original size:25 final size:24
Alignment explanation
Indices: 1854969--1855106 Score: 64
Period size: 26 Copynumber: 5.5 Consensus size: 24
1854959 TACCCTAAAG
* * *
1854969 CACTTTAACCTACACAACCTTAATG
1 CACTTTAACCTACAAAACCTTCA-C
* *
1854994 AATCTTTGACCTACAAAATCCTTCAC
1 CA-CTTTAACCTACAAAA-CCTTCAC
* * *
1855020 CACTTTAACCTTAACGAAACATAT-AA
1 CACTTTAACC-T-ACAAAACCT-TCAC
* * *
1855046 CACTTTAACC-ACACAACCTTAATG
1 CACTTTAACCTACAAAACCTTCA-C
* *
1855070 AATCTTTGACCTACAAAATCCTTCAC
1 CA-CTTTAACCTACAAAA-CCTTCAC
1855096 CACTTTAACCT
1 CACTTTAACCT
1855107 TAACGAAACA
Statistics
Matches: 82, Mismatches: 21, Indels: 20
0.67 0.17 0.16
Matches are distributed among these distances:
22 1 0.01
23 7 0.09
24 1 0.01
25 23 0.28
26 34 0.41
27 16 0.20
ACGTcount: A:0.37, C:0.30, G:0.04, T:0.29
Consensus pattern (24 bp):
CACTTTAACCTACAAAACCTTCAC
Found at i:1855073 original size:76 final size:77
Alignment explanation
Indices: 1854969--1855133 Score: 323
Period size: 76 Copynumber: 2.2 Consensus size: 77
1854959 TACCCTAAAG
1854969 CACTTTAACCTACACAACCTTAATGAATCTTTGACCTACAAAATCCTTCACCACTTTAACCTTAA
1 CACTTTAACCTACACAACCTTAATGAATCTTTGACCTACAAAATCCTTCACCACTTTAACCTTAA
1855034 CGAAACATATAA
66 CGAAACATATAA
1855046 CACTTTAACC-ACACAACCTTAATGAATCTTTGACCTACAAAATCCTTCACCACTTTAACCTTAA
1 CACTTTAACCTACACAACCTTAATGAATCTTTGACCTACAAAATCCTTCACCACTTTAACCTTAA
1855110 CGAAACATATAA
66 CGAAACATATAA
1855122 CACTTTAACCTA
1 CACTTTAACCTA
1855134 AATTCACTCC
Statistics
Matches: 87, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
76 76 0.87
77 11 0.13
ACGTcount: A:0.39, C:0.29, G:0.04, T:0.28
Consensus pattern (77 bp):
CACTTTAACCTACACAACCTTAATGAATCTTTGACCTACAAAATCCTTCACCACTTTAACCTTAA
CGAAACATATAA
Found at i:1855414 original size:7 final size:7
Alignment explanation
Indices: 1855398--1855428 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1855388 TACAATATCT
1855398 GTGAACA
1 GTGAACA
*
1855405 GTGAATA
1 GTGAACA
1855412 GTGAACA
1 GTGAACA
1855419 GTGAACA
1 GTGAACA
1855426 GTG
1 GTG
1855429 TACCGATGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.39, C:0.10, G:0.32, T:0.19
Consensus pattern (7 bp):
GTGAACA
Found at i:1856038 original size:44 final size:44
Alignment explanation
Indices: 1855907--1856323 Score: 600
Period size: 44 Copynumber: 9.4 Consensus size: 44
1855897 AATTTCTTAT
* * *
1855907 CAATATACATACCATTTAATCCATAAGCTTGTAAGCTTATTTTAC
1 CAATATACTTACCA-TTATTCCATAAGCTCGTAAGCTTATTTTAC
* * *
1855952 CAATATACTTACCATTAAATCCCTAAGCTCGTAAGTTTATTTTAC
1 CAATATACTTACCATT-ATTCCATAAGCTCGTAAGCTTATTTTAC
*
1855997 CAATATACTTACCATTATTCCATAAGCTCGTAAGTTTATTTTAC
1 CAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTAC
* *
1856041 CAATGTACTTACCATTATTCAATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTAC
*
1856085 CAATATATTTACCATTATTCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTAC
* * * *
1856129 CAATATTCTTACTATAATTTCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTAC
* * * *
1856173 CAATATACTTACTATAATTTCATAAGCTTGTAAGCTTATTTTAC
1 CAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTAC
* *
1856217 CAATATACTTACTATTATTTCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTAC
* * *
1856261 CAATATACTTACTATAATTTCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTAC
*
1856305 CAATATACTTACTATTATT
1 CAATATACTTACCATTATT
1856324 TGCATCATTG
Statistics
Matches: 348, Mismatches: 23, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
44 294 0.84
45 54 0.16
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.41
Consensus pattern (44 bp):
CAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTAC
Found at i:1856553 original size:60 final size:60
Alignment explanation
Indices: 1856477--1856651 Score: 235
Period size: 60 Copynumber: 2.9 Consensus size: 60
1856467 TTCCTTCTCA
* *
1856477 TTTTAGCACAAGAAGTGCCCTATTCTAGAATCCATACCATTAGTATGATTCCTTTACCAT
1 TTTTAGCACATGAAGTGCCCTATTCGAGAATCCATACCATTAGTATGATTCCTTTACCAT
* * *
1856537 TTTTAGCACATGAAGTGCCCTATTCGAGAATTCAAACCATTAGTATGATCCCTTTACCAT
1 TTTTAGCACATGAAGTGCCCTATTCGAGAATCCATACCATTAGTATGATTCCTTTACCAT
* * * * *
1856597 TTTTAGCACGTGAAGTACCCTATAT-GAAAATCCATACTAGTAGTATGATTTCCTT
1 TTTTAGCACATGAAGTGCCCTAT-TCGAGAATCCATACCATTAGTATGA-TTCCTT
1856652 ATCCTCGTAG
Statistics
Matches: 100, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
60 94 0.94
61 6 0.06
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (60 bp):
TTTTAGCACATGAAGTGCCCTATTCGAGAATCCATACCATTAGTATGATTCCTTTACCAT
Found at i:1856722 original size:59 final size:59
Alignment explanation
Indices: 1856640--1856959 Score: 317
Period size: 59 Copynumber: 5.4 Consensus size: 59
1856630 ATACTAGTAG
* ** * * * *
1856640 TATGATTTCCTTATCCTCGTAGCACCCTTAGTGTTTTTTCTGGAAATCCATACACTCAG
1 TATGATTTCCTTATCATTTTAGCACCCTTAGTGCTCTATCTGGAAATCCATACACTCAA
* * * * * * *
1856699 TATGATTCCCTTACCATTTTAGCA-CATATAATG-TCCTATCTGAAAATCCATATATTCAA
1 TATGATTTCCTTATCATTTTAGCACCCT-TAGTGCT-CTATCTGGAAATCCATACACTCAA
* * *
1856758 TATGATTTCCTTATCATTTTAGCAAACCC--AGTGATCCATATGGAAATCCATACACTCAA
1 TATGATTTCCTTATCATTTTAGC--ACCCTTAGTGCTCTATCTGGAAATCCATACACTCAA
* * * * *
1856817 TATGATTTCCTTATCATTTTAGCA-CATATAATGCCCTATCTGGAAATCCATATATTCAA
1 TATGATTTCCTTATCATTTTAGCACCCT-TAGTGCTCTATCTGGAAATCCATACACTCAA
* * * *
1856876 TATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCAA
1 TATGATTTCCTTATCATTTTAGCACCCTTAGTGCTCTATCTGGAAATCCATACACTCAA
*
1856935 TATGATTTCTTTATCATTTTAGCAC
1 TATGATTTCCTTATCATTTTAGCAC
1856960 ATATAGTTCC
Statistics
Matches: 211, Mismatches: 40, Indels: 20
0.78 0.15 0.07
Matches are distributed among these distances:
56 1 0.00
57 1 0.00
58 3 0.01
59 202 0.96
60 2 0.01
61 1 0.00
62 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.38
Consensus pattern (59 bp):
TATGATTTCCTTATCATTTTAGCACCCTTAGTGCTCTATCTGGAAATCCATACACTCAA
Found at i:1856749 original size:118 final size:117
Alignment explanation
Indices: 1856614--1856964 Score: 472
Period size: 118 Copynumber: 3.0 Consensus size: 117
1856604 ACGTGAAGTA
* * * * ** * ***
1856614 CCCTATATGAAAATCCATACTAGT-AGTATGATTTCCTTATCCTCGTAGCACCCTTAGTGTTTTT
1 CCCTATCTGAAAATCCATA-TATTCAATATGATTTCCTTATCATTTTAGCACCC-TAGTGATCCA
* * * *
1856678 TCTGGAAATCCATACACTCAGTATGATTCCCTTACCATTTTAGCACATATAATG
64 TATGGAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACATATAATG
*
1856732 TCCTATCTGAAAATCCATATATTCAATATGATTTCCTTATCATTTTAGCAAACCC-AGTGATCCA
1 CCCTATCTGAAAATCCATATATTCAATATGATTTCCTTATCATTTTAGC--ACCCTAGTGATCCA
1856796 TATGGAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACATATAATG
64 TATGGAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACATATAATG
* * *
1856850 CCCTATCTGGAAATCCATATATTCAATATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCAT
1 CCCTATCTGAAAATCCATATATTCAATATGATTTCCTTATCATTTTAGCACCCT-AGTGATCCAT
*
1856915 ATGGAAATCCATACACTCAATATGATTTCTTTATCATTTTAGCACATATA
65 ATGGAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACATATA
1856965 GTTCCATTTG
Statistics
Matches: 208, Mismatches: 20, Indels: 10
0.87 0.08 0.04
Matches are distributed among these distances:
116 3 0.01
117 3 0.01
118 198 0.95
120 4 0.02
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.37
Consensus pattern (117 bp):
CCCTATCTGAAAATCCATATATTCAATATGATTTCCTTATCATTTTAGCACCCTAGTGATCCATA
TGGAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACATATAATG
Found at i:1856830 original size:177 final size:177
Alignment explanation
Indices: 1856618--1856958 Score: 402
Period size: 177 Copynumber: 1.9 Consensus size: 177
1856608 GAAGTACCCT
* * * * * *** *
1856618 ATATGAAAATCCATACTAGTAGTATGATTTCCTTATCCTCGTAGCACCCT-TAGTGTTTTTTCTG
1 ATATGAAAATCCATACTACTAATATGATTTCCTTATCATCGTAGCA-CATATAATGCCCTATCTG
* * *
1856682 GAAATCCATACACTCAGTATGATTCCCTTACCATTTTAGCACA-TATAATG-TCCTATCTGAAAA
65 GAAATCCATACACTCAATATGATTCCCTTACCATTTTAGCACACT-CAATGCTCC-ATATGAAAA
* *
1856745 TCCATATATTCAATATGATTTCCTTATCATTTTAGCAAACCCAGTGATCC
128 TCCATACACTCAATATGATTTCCTTATCATTTTAGCAAACCCAGTGATCC
* **
1856795 ATATGGAAATCCATAC-ACTCAATATGATTTCCTTATCATTTTAGCACATATAATGCCCTATCTG
1 ATATGAAAATCCATACTACT-AATATGATTTCCTTATCATCGTAGCACATATAATGCCCTATCTG
* * * * * *
1856859 GAAATCCATATATTCAATATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATC
65 GAAATCCATACACTCAATATGATTCCCTTACCATTTTAGCACACTCAATGCTCCATATGAAAATC
*
1856924 CATACACTCAATATGATTTCTTTATCATTTTAGCA
130 CATACACTCAATATGATTTCCTTATCATTTTAGCA
1856959 CATATAGTTC
Statistics
Matches: 136, Mismatches: 24, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
176 4 0.03
177 128 0.94
178 4 0.03
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (177 bp):
ATATGAAAATCCATACTACTAATATGATTTCCTTATCATCGTAGCACATATAATGCCCTATCTGG
AAATCCATACACTCAATATGATTCCCTTACCATTTTAGCACACTCAATGCTCCATATGAAAATCC
ATACACTCAATATGATTTCCTTATCATTTTAGCAAACCCAGTGATCC
Found at i:1856988 original size:59 final size:58
Alignment explanation
Indices: 1856680--1856980 Score: 354
Period size: 59 Copynumber: 5.1 Consensus size: 58
1856670 GTGTTTTTTC
* * * * *
1856680 TGGAAATCCATACACTCAGTATGATTCCCTTACCATTTTAGCACATATAATGTCCTATC
1 TGGAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACATATAGTGTCC-ATA
* * * * ***
1856739 TGAAAATCCATATATTCAATATGATTTCCTTATCATTTTAGCAAACCCAGTGATCCATA
1 TGGAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACATATAGTG-TCCATA
* * *
1856798 TGGAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACATATAATGCCCTATC
1 TGGAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACATATAGTGTCC-ATA
* * *
1856857 TGGAAATCCATATATTCAATATGATTTCCTTATCATTTTAGCACACT-CAGTGCTCCATA
1 TGGAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACA-TATAGTG-TCCATA
* *
1856916 TGGAAATCCATACACTCAATATGATTTCTTTATCATTTTAGCACATATAGT-TCCATT
1 TGGAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACATATAGTGTCCATA
*
1856973 TGGTAATC
1 TGGAAATC
1856981 ACTATACATA
Statistics
Matches: 203, Mismatches: 34, Indels: 12
0.82 0.14 0.05
Matches are distributed among these distances:
57 12 0.06
58 3 0.01
59 182 0.90
60 6 0.03
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.37
Consensus pattern (58 bp):
TGGAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACATATAGTGTCCATA
Found at i:1862520 original size:44 final size:44
Alignment explanation
Indices: 1862389--1862893 Score: 731
Period size: 44 Copynumber: 11.4 Consensus size: 44
1862379 AATTTCTTAT
* *
1862389 CAATATACATACCATTTAATCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCA-TTATTCCATAAGCTCGTAAGCTTATTTTAC
* *
1862434 CAATATACTTACCATTAAATCCCTAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATT-ATTCCATAAGCTCGTAAGCTTATTTTAC
* * *
1862479 CAATATACTTATCATTATTCCATAAGCTCGTAAGTTTATTTTTC
1 CAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTAC
*
1862523 CAATATACTTACCATTATTCCATAAGCTCATAAGCTTATTTTAC
1 CAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTAC
*
1862567 CAATATACTTACCATTATTCCATAAGCTCGTAAGTTTATTTTAC
1 CAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTAC
*
1862611 CAATATACTTACCATTATTCCATAAGCTCATAAGCTTATTTTAC
1 CAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTAC
*
1862655 CAATATACTTACCATTTTTCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTAC
* * * * *
1862699 CAATATTCTTACTATAATTTCATAAGCTCGTAAGTTTATTTTAC
1 CAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTAC
* * ** * *
1862743 CAATATACTTACTATAATTTTAAAAACTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTAC
* *
1862787 CAATATACTTACTATTATTTCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTAC
* * * *
1862831 CAATATACTTACTATAATTTCATAAGATCGTAAGCTTATTTTAC
1 CAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTAC
*
1862875 CAATATACTTACTATTATT
1 CAATATACTTACCATTATT
1862894 TGCATCACTG
Statistics
Matches: 424, Mismatches: 35, Indels: 3
0.92 0.08 0.01
Matches are distributed among these distances:
44 369 0.87
45 55 0.13
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.41
Consensus pattern (44 bp):
CAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTAC
Found at i:1863114 original size:60 final size:60
Alignment explanation
Indices: 1863047--1863212 Score: 228
Period size: 60 Copynumber: 2.8 Consensus size: 60
1863037 TTCCTTCTCA
* * *
1863047 TTTTAGCACAAGAAGTGCCCTATTCTAGAATCCATACCATTAGTATAAT-TCCTTTACGAT
1 TTTTAGCACATGAAGTGCCCTATTCAAGAATCCATACCATTAGTATAATCT-CTTTACCAT
*
1863107 TTTTAGCACATGAAGTGCCCTATTCAAGAATCCATACCATTAGTATGATCTCTTTACCAT
1 TTTTAGCACATGAAGTGCCCTATTCAAGAATCCATACCATTAGTATAATCTCTTTACCAT
* * **
1863167 TTTTAGCAGATGAAGTGCCCTATATGAA-AATCCATATTATTAGTAT
1 TTTTAGCACATGAAGTGCCCTAT-TCAAGAATCCATACCATTAGTAT
1863213 GATTTCCTTA
Statistics
Matches: 96, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
60 92 0.96
61 4 0.04
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.36
Consensus pattern (60 bp):
TTTTAGCACATGAAGTGCCCTATTCAAGAATCCATACCATTAGTATAATCTCTTTACCAT
Found at i:1863311 original size:59 final size:59
Alignment explanation
Indices: 1863248--1863534 Score: 346
Period size: 59 Copynumber: 4.9 Consensus size: 59
1863238 TAGTGTTTTT
* * *
1863248 TCTGGAAATCCATACACTCAGTATGATTCCCTTACCATTTTAGCACATATAATGC-CCTA
1 TCTGGAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACATATAATGCTCC-A
*** *** *
1863307 TCTGGAAATCCATATTTTCAATATGATTTCCTTATCATTTTAGCACACCCAGTGCTCCA
1 TCTGGAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACATATAATGCTCCA
*
1863366 TATGGAAATCCATACACTCAATAT-AGTTTCCTTATCATTTTAGCACATATAATGC-CCTA
1 TCTGGAAATCCATACACTCAATATGA-TTTCCTTATCATTTTAGCACATATAATGCTCC-A
* * * *** *
1863425 TCTGGAAATCCATATATTCAATATGATTTCCTTATCATTTTAGCTCACCCAGTGCTCCA
1 TCTGGAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACATATAATGCTCCA
* *
1863484 TATGGAAATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACATATA
1 TCTGGAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACATATA
1863535 GTGACATTTG
Statistics
Matches: 189, Mismatches: 34, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
58 3 0.02
59 181 0.96
60 5 0.03
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (59 bp):
TCTGGAAATCCATACACTCAATATGATTTCCTTATCATTTTAGCACATATAATGCTCCA
Found at i:1863372 original size:118 final size:118
Alignment explanation
Indices: 1863250--1863534 Score: 509
Period size: 118 Copynumber: 2.4 Consensus size: 118
1863240 GTGTTTTTTC
* *
1863250 TGGAAATCCATACACTCAGTATGATTCCCTTACCATTTTAGCACATATAATGCCCTATCTGGAAA
1 TGGAAATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACATATAATGCCCTATCTGGAAA
*
1863315 TCCATATTTTCAATATGATTTCCTTATCATTTTAGCACACCCAGTGCTCCATA
66 TCCATATATTCAATATGATTTCCTTATCATTTTAGCACACCCAGTGCTCCATA
*
1863368 TGGAAATCCATACACTCAATAT-AGTTTCCTTATCATTTTAGCACATATAATGCCCTATCTGGAA
1 TGGAAATCCATACACTCAGTATGA-TTTCCTTATCATTTTAGCACATATAATGCCCTATCTGGAA
*
1863432 ATCCATATATTCAATATGATTTCCTTATCATTTTAGCTCACCCAGTGCTCCATA
65 ATCCATATATTCAATATGATTTCCTTATCATTTTAGCACACCCAGTGCTCCATA
1863486 TGGAAATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACATATA
1 TGGAAATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACATATA
1863535 GTGACATTTG
Statistics
Matches: 159, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
117 1 0.01
118 157 0.99
119 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.36
Consensus pattern (118 bp):
TGGAAATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACATATAATGCCCTATCTGGAAA
TCCATATATTCAATATGATTTCCTTATCATTTTAGCACACCCAGTGCTCCATA
Found at i:1866169 original size:46 final size:46
Alignment explanation
Indices: 1866116--1866227 Score: 206
Period size: 46 Copynumber: 2.4 Consensus size: 46
1866106 CTTCCTATTC
*
1866116 ATTTAAGGTTCAAAGCTTTATTATTAAAGATAAAATGTTTATATAT
1 ATTTAAGGTTAAAAGCTTTATTATTAAAGATAAAATGTTTATATAT
*
1866162 ATTTAAGGTTAAAAGCTTTATTATTAAAGCTAAAATGTTTATATAT
1 ATTTAAGGTTAAAAGCTTTATTATTAAAGATAAAATGTTTATATAT
1866208 ATTTAAGGTTAAAAGCTTTA
1 ATTTAAGGTTAAAAGCTTTA
1866228 CTAGTTAATT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 64 1.00
ACGTcount: A:0.41, C:0.04, G:0.12, T:0.43
Consensus pattern (46 bp):
ATTTAAGGTTAAAAGCTTTATTATTAAAGATAAAATGTTTATATAT
Found at i:1866174 original size:25 final size:25
Alignment explanation
Indices: 1866146--1866221 Score: 97
Period size: 25 Copynumber: 3.2 Consensus size: 25
1866136 TTATTAAAGA
1866146 TAAAATGTTTATATATATTTAAGGT
1 TAAAATGTTTATATATATTTAAGGT
* * *
1866171 TAAAA-GCTT-TAT-TA-TTAAAGC
1 TAAAATGTTTATATATATTTAAGGT
1866192 TAAAATGTTTATATATATTTAAGGT
1 TAAAATGTTTATATATATTTAAGGT
1866217 TAAAA
1 TAAAA
1866222 GCTTTACTAG
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
21 10 0.24
22 5 0.12
23 6 0.15
24 5 0.12
25 15 0.37
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (25 bp):
TAAAATGTTTATATATATTTAAGGT
Found at i:1866227 original size:25 final size:24
Alignment explanation
Indices: 1866111--1866227 Score: 88
Period size: 25 Copynumber: 5.0 Consensus size: 24
1866101 TATTACTTCC
*
1866111 TATTCATTTAAGGTTCAAAGC-TT-
1 TATT-ATTTAAGGTTAAAAGCTTTA
* *
1866134 TATTA-TTAAAGATAAAATG-TTTA
1 TATTATTTAAGGTTAAAA-GCTTTA
1866157 TATATATTTAAGGTTAAAAGC-TT-
1 TAT-TATTTAAGGTTAAAAGCTTTA
* *
1866180 TATTA-TTAAAGCTAAAATG-TTTA
1 TATTATTTAAGGTTAAAA-GCTTTA
1866203 TATATATTTAAGGTTAAAAGCTTTA
1 TAT-TATTTAAGGTTAAAAGCTTTA
1866228 CTAGTTAATT
Statistics
Matches: 73, Mismatches: 9, Indels: 22
0.70 0.09 0.21
Matches are distributed among these distances:
21 19 0.26
22 9 0.12
23 13 0.18
24 8 0.11
25 24 0.33
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (24 bp):
TATTATTTAAGGTTAAAAGCTTTA
Found at i:1866296 original size:23 final size:23
Alignment explanation
Indices: 1866256--1866349 Score: 134
Period size: 23 Copynumber: 4.1 Consensus size: 23
1866246 TATGTTTTCT
* *
1866256 AACACTAGATTAGTATGTTCGTG
1 AACACTAAATGAGTATGTTCGTG
*** *
1866279 AATGTTAAATGAGCATGTTCGTG
1 AACACTAAATGAGTATGTTCGTG
1866302 AACACTAAATGAGTATGTTCGTG
1 AACACTAAATGAGTATGTTCGTG
1866325 AACACTAAATGAGTATGTTCGTG
1 AACACTAAATGAGTATGTTCGTG
1866348 AA
1 AA
1866350 TGTTCATTAA
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (23 bp):
AACACTAAATGAGTATGTTCGTG
Found at i:1877270 original size:36 final size:37
Alignment explanation
Indices: 1877219--1877304 Score: 104
Period size: 36 Copynumber: 2.4 Consensus size: 37
1877209 TTTGGTTCAC
* * *
1877219 GGAATATAAGATTACCAGTGATAATATGATTACCAGCG
1 GGAATAT-AGATTACCAGCGAGAATATGATTACCAGCA
*
1877257 GGAATAT-GATTACCAGCGGGAATATGATTACCAGCA
1 GGAATATAGATTACCAGCGAGAATATGATTACCAGCA
*
1877293 GGAACA-AGATTA
1 GGAATATAGATTA
1877305 TTGAGAATGT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
36 35 0.83
38 7 0.17
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.23
Consensus pattern (37 bp):
GGAATATAGATTACCAGCGAGAATATGATTACCAGCA
Found at i:1877304 original size:18 final size:18
Alignment explanation
Indices: 1877241--1877296 Score: 103
Period size: 18 Copynumber: 3.1 Consensus size: 18
1877231 TACCAGTGAT
1877241 AATATGATTACCAGCGGG
1 AATATGATTACCAGCGGG
1877259 AATATGATTACCAGCGGG
1 AATATGATTACCAGCGGG
*
1877277 AATATGATTACCAGCAGG
1 AATATGATTACCAGCGGG
1877295 AA
1 AA
1877297 CAAGATTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.21
Consensus pattern (18 bp):
AATATGATTACCAGCGGG
Found at i:1879007 original size:3 final size:3
Alignment explanation
Indices: 1878999--1879023 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1878989 CCCGTTAACC
1878999 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
1879024 AATAAGTCTG
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:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:1883149 original size:11 final size:11
Alignment explanation
Indices: 1883135--1883163 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1883125 TTTGGGATCG
1883135 TCAGATCATCT
1 TCAGATCATCT
1883146 TCAGATCATCT
1 TCAGATCATCT
1883157 TCAGATC
1 TCAGATC
1883164 TGACAACAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (11 bp):
TCAGATCATCT
Found at i:1883477 original size:2 final size:2
Alignment explanation
Indices: 1883466--1883501 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1883456 TGTATATTCG
1883466 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1883502 TATTTAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1892905 original size:19 final size:19
Alignment explanation
Indices: 1892881--1892971 Score: 164
Period size: 19 Copynumber: 4.8 Consensus size: 19
1892871 CGAATGCAAT
*
1892881 GAGTGCATCGATGCATAGG
1 GAGTGCATCGATGCATAAG
*
1892900 GAGTGCATCGATGCATAAT
1 GAGTGCATCGATGCATAAG
1892919 GAGTGCATCGATGCATAAG
1 GAGTGCATCGATGCATAAG
1892938 GAGTGCATCGATGCATAAG
1 GAGTGCATCGATGCATAAG
1892957 GAGTGCATCGATGCA
1 GAGTGCATCGATGCA
1892972 CCTGCTTAAA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 69 1.00
ACGTcount: A:0.30, C:0.16, G:0.32, T:0.22
Consensus pattern (19 bp):
GAGTGCATCGATGCATAAG
Found at i:1893669 original size:18 final size:18
Alignment explanation
Indices: 1893606--1893672 Score: 89
Period size: 18 Copynumber: 3.6 Consensus size: 18
1893596 AGGGATAATC
*
1893606 AGTGGTCTTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
1893624 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
1893643 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
1893662 AGTGGTCCTTC
1 AGTGGTCCTTC
1893673 TGGATAAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
18 24 0.57
19 4 0.10
20 14 0.33
ACGTcount: A:0.18, C:0.21, G:0.30, T:0.31
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:1897414 original size:17 final size:16
Alignment explanation
Indices: 1897392--1897425 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1897382 ATCGCCTACC
1897392 AAATTTCACTATTCACG
1 AAATTT-ACTATTCACG
*
1897409 AAATTTATTATTCACG
1 AAATTTACTATTCACG
1897425 A
1 A
1897426 GAATAGTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.38, C:0.18, G:0.06, T:0.38
Consensus pattern (16 bp):
AAATTTACTATTCACG
Found at i:1902164 original size:2 final size:2
Alignment explanation
Indices: 1902157--1902187 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1902147 TCACAAGTAG
*
1902157 TC TC TC TC TC TC TC TC TC TC TC AC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1902188 ATTACTCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.03, C:0.48, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:1904947 original size:14 final size:14
Alignment explanation
Indices: 1904930--1904978 Score: 71
Period size: 14 Copynumber: 3.5 Consensus size: 14
1904920 AACGAGTGAG
1904930 CATAAACAAACGAA
1 CATAAACAAACGAA
* **
1904944 CATAAACGAATAAA
1 CATAAACAAACGAA
1904958 CATAAACAAACGAA
1 CATAAACAAACGAA
1904972 CATAAAC
1 CATAAAC
1904979 GAATGGATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.63, C:0.20, G:0.06, T:0.10
Consensus pattern (14 bp):
CATAAACAAACGAA
Found at i:1904961 original size:28 final size:28
Alignment explanation
Indices: 1904914--1904982 Score: 111
Period size: 28 Copynumber: 2.5 Consensus size: 28
1904904 GGGTCTGGAA
* * *
1904914 AACATAAACGAGTGAGCATAAACAAACG
1 AACATAAACGAATAAACATAAACAAACG
1904942 AACATAAACGAATAAACATAAACAAACG
1 AACATAAACGAATAAACATAAACAAACG
1904970 AACATAAACGAAT
1 AACATAAACGAAT
1904983 GGATTATCGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.59, C:0.17, G:0.12, T:0.12
Consensus pattern (28 bp):
AACATAAACGAATAAACATAAACAAACG
Found at i:1905438 original size:20 final size:20
Alignment explanation
Indices: 1905413--1905505 Score: 78
Period size: 21 Copynumber: 4.5 Consensus size: 20
1905403 TTTTCCCAAT
1905413 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
1905433 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
**
1905453 TTCGCAATATGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
1905474 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
1905495 TCGCAATGCGA
1 TCGCAATGCGA
1905506 TACTGACTAT
Statistics
Matches: 54, Mismatches: 17, Indels: 3
0.73 0.23 0.04
Matches are distributed among these distances:
20 25 0.46
21 29 0.54
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:1905455 original size:41 final size:41
Alignment explanation
Indices: 1905410--1905505 Score: 165
Period size: 41 Copynumber: 2.3 Consensus size: 41
1905400 CGATTTTCCC
1905410 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
**
1905451 AATTCGCAATATGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
1905492 AAATCGCAATGCGA
1 AATTCGCAATGCGA
1905506 TACTGACTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.20
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:1905459 original size:21 final size:20
Alignment explanation
Indices: 1905413--1905505 Score: 78
Period size: 20 Copynumber: 4.5 Consensus size: 20
1905403 TTTTCCCAAT
*
1905413 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
1905433 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
** *
1905453 TTCGCAATATGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
1905474 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
1905495 TCGCAATGCGA
1 TCGCAATGCGA
1905506 TACTGACTAT
Statistics
Matches: 54, Mismatches: 17, Indels: 3
0.73 0.23 0.04
Matches are distributed among these distances:
20 27 0.50
21 27 0.50
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:1905518 original size:41 final size:41
Alignment explanation
Indices: 1905432--1905566 Score: 107
Period size: 41 Copynumber: 3.3 Consensus size: 41
1905422 GAATAAGTAA
* * *
1905432 ATCGCAACGCGAATTGGGAAATTCGCAAT-ATGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGA-G-ATACTG-ACT
*
1905473 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGAGATACTGACT
* * ** * *
1905514 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGAGATACTGACT
*
1905555 TTCGCAACGCGA
1 ATCGCAACGCGA
1905567 TACTGACTTT
Statistics
Matches: 77, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
40 4 0.05
41 71 0.92
42 2 0.03
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGAGATACTGACT
Found at i:1905519 original size:20 final size:20
Alignment explanation
Indices: 1905494--1905588 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
1905484 AATTGGGAAA
*
1905494 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
1905514 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
1905535 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
1905555 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1905575 TTCGCAACGCGATA
1 ATCGCAACGCGATA
1905589 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1905567 original size:41 final size:41
Alignment explanation
Indices: 1905491--1905568 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
1905481 GCGAATTGGG
* * *
1905491 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
* *
1905532 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
1905569 CTGACTTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
Found at i:1905804 original size:22 final size:22
Alignment explanation
Indices: 1905776--1905819 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1905766 CACTCTCTCA
1905776 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1905798 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1905820 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1906092 original size:20 final size:20
Alignment explanation
Indices: 1906063--1906106 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1906053 GCGATTTTAG
1906063 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
1906083 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
1906103 TTTC
1 TTTC
1906107 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.18, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:1907447 original size:18 final size:18
Alignment explanation
Indices: 1907426--1907470 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
1907416 TCCACTTCGG
1907426 GAGCCATCACCTCTACC-A
1 GAGCCATCACCTC-ACCTA
*
1907444 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCTA
1907462 GAGCCATCA
1 GAGCCATCA
1907471 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.29, C:0.40, G:0.13, T:0.18
Consensus pattern (18 bp):
GAGCCATCACCTCACCTA
Found at i:1907991 original size:19 final size:20
Alignment explanation
Indices: 1907937--1908003 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1907927 TAGTTTACTT
* *
1907937 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1907957 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1907977 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1907996 TCGCAACG
1 TCGCAACG
1908004 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1908011 original size:14 final size:14
Alignment explanation
Indices: 1907992--1908049 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1907982 ATGCGAAATG
1907992 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1908006 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
1908022 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1908038 AAAATCGCAACG
1 AAAATCGCAACG
1908050 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1908034 original size:32 final size:33
Alignment explanation
Indices: 1907976--1908066 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
1907966 GGAAATGGCT
1907976 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1908009 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1908041 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
1908067 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1908102 original size:14 final size:14
Alignment explanation
Indices: 1908083--1908140 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1908073 TTGTGTTTCG
1908083 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1908097 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1908113 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
1908129 CGTTGCGATTTT
1 CGTTGCGATTTT
1908141 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1908117 original size:32 final size:32
Alignment explanation
Indices: 1908078--1908198 Score: 143
Period size: 32 Copynumber: 3.5 Consensus size: 32
1908068 GCGATTTGTG
1908078 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1908110 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
* * *
1908143 TTTCGCATTGCGATAGCCATTTCTGCGTTGCGATAGTCA
1 TTTCGCGTTGCGAT-----TTTGT-CGTTGCGAT-TTCA
1908182 TTTCGCGTTGCGATTTT
1 TTTCGCGTTGCGATTTT
1908199 AAGTTTCGTG
Statistics
Matches: 77, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
32 27 0.35
33 18 0.23
34 3 0.04
38 5 0.06
39 24 0.31
ACGTcount: A:0.12, C:0.20, G:0.24, T:0.45
Consensus pattern (32 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
Found at i:1908155 original size:19 final size:19
Alignment explanation
Indices: 1908097--1908214 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
1908087 GCGATTTTGT
1908097 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1908115 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
1908129 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
1908148 CATTGCGATAGCCATTTCTG
1 CGTTGCGATTTTCATTTC-G
**
1908168 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1908187 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
1908207 TGTTGCGA
1 CGTTGCGA
1908215 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.19, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1910086 original size:14 final size:14
Alignment explanation
Indices: 1910067--1910102 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1910057 ATTGTTTAAT
1910067 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1910081 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1910095 TGATTTGT
1 TGATTTGT
1910103 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1910244 original size:18 final size:19
Alignment explanation
Indices: 1910219--1910285 Score: 83
Period size: 18 Copynumber: 3.8 Consensus size: 19
1910209 ATCGCAACGA
*
1910219 GAAAATCGCAATGTGAAAT
1 GAAAATCGCAATGCGAAAT
1910238 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1910256 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
1910270 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
1910286 TTTTCATTTC
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
14 11 0.26
15 1 0.02
16 2 0.05
17 2 0.05
18 17 0.40
19 10 0.23
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.15
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:1910361 original size:20 final size:20
Alignment explanation
Indices: 1910311--1910361 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1910301 GCGATATTCT
* *
1910311 CGTTGCGATAACCATTTTCG
1 CGTTGCGATAGCCATTTTCA
1910331 CGTTGCGATAGCCATTTTCA
1 CGTTGCGATAGCCATTTTCA
1910351 CGTTGCGATAG
1 CGTTGCGATAG
1910362 TCAAATGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCA
Found at i:1910745 original size:14 final size:14
Alignment explanation
Indices: 1910726--1910761 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1910716 ATTGTTTAAT
1910726 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1910740 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1910754 TGATTTGT
1 TGATTTGT
1910762 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1912056 original size:24 final size:24
Alignment explanation
Indices: 1912000--1912058 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
1911990 AGTCAGTATT
* *
1912000 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACA
* *
1912024 CGGACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTGGTCAATACA
*
1912048 CGAATTTTGAT
1 CGAAATTTGAT
1912059 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACA
Found at i:1912250 original size:12 final size:12
Alignment explanation
Indices: 1912233--1912257 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1912223 ATATAATCCT
1912233 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1912245 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1912257 G
1 G
1912258 TCCCCGAAGA
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:1914867 original size:20 final size:20
Alignment explanation
Indices: 1914782--1914875 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
1914772 CGCTAAGTAA
*
1914782 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* * *
1914802 ATCGTGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
1914822 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
1914843 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
1914863 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
1914876 TTTCCCAATT
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 45 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:1914894 original size:41 final size:41
Alignment explanation
Indices: 1914864--1914959 Score: 138
Period size: 41 Copynumber: 2.3 Consensus size: 41
1914854 ATAGTCAGTA
* * *
1914864 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
* * *
1914905 TCGCATTGCGAATTTCCCAATTCGCGTTACGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
1914946 TCGCATTGCGAATT
1 TCGCATTGCGAATT
1914960 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:1914908 original size:20 final size:20
Alignment explanation
Indices: 1914864--1914956 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
1914854 ATAGTCAGTA
* **
1914864 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
1914885 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
1914905 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
* *
1914926 TCGCGTTACGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
1914946 TCGCATTGCGA
1 TCGCATTGCGA
1914957 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:1915503 original size:20 final size:20
Alignment explanation
Indices: 1915480--1915592 Score: 217
Period size: 20 Copynumber: 5.7 Consensus size: 20
1915470 ATTTTTTAAT
1915480 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1915500 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1915520 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1915540 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1915560 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
1915580 TCGCAACGCGAAT
1 TCGCAATGCGAAT
1915593 CTGACTATCG
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
20 92 1.00
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1915842 original size:22 final size:22
Alignment explanation
Indices: 1915788--1915834 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
1915778 GGAGACATCC
1915788 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
1915810 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
1915832 GTC
1 GTC
1915835 TCTATCTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.23, C:0.40, G:0.15, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:1916234 original size:18 final size:19
Alignment explanation
Indices: 1916208--1916258 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
1916198 GATAGTTAAA
*
1916208 TTCGCGTTGCGA-GTCATT
1 TTCGTGTTGCGATGTCATT
*
1916226 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGA-TGTCATT
1916246 TTCGTGTTGCGAT
1 TTCGTGTTGCGAT
1916259 TTTAAGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 11 0.38
19 1 0.03
20 17 0.59
ACGTcount: A:0.10, C:0.18, G:0.25, T:0.47
Consensus pattern (19 bp):
TTCGTGTTGCGATGTCATT
Found at i:1916246 original size:20 final size:20
Alignment explanation
Indices: 1916221--1916261 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1916211 GCGTTGCGAG
1916221 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGTGTTGCGATTT
1916241 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGTGTTGCGATTT
1916261 T
1 T
1916262 AAGTTTCAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.10, C:0.15, G:0.20, T:0.56
Consensus pattern (20 bp):
TCATTTTCGTGTTGCGATTT
Found at i:1916268 original size:20 final size:20
Alignment explanation
Indices: 1916225--1916268 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1916215 TGCGAGTCAT
* *
1916225 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
1916245 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
1916265 TTTC
1 TTTC
1916269 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:1918156 original size:20 final size:20
Alignment explanation
Indices: 1918131--1918183 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1918121 GAAGAATAGT
**
1918131 TTACTATCGCAATGCAAAAA
1 TTACTATCGCAACACAAAAA
*
1918151 TTACTATCGCAACACGAAAA
1 TTACTATCGCAACACAAAAA
*
1918171 TGACTATCGCAAC
1 TTACTATCGCAAC
1918184 GAGAGAATCG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.42, C:0.25, G:0.11, T:0.23
Consensus pattern (20 bp):
TTACTATCGCAACACAAAAA
Found at i:1918224 original size:53 final size:53
Alignment explanation
Indices: 1918156--1918321 Score: 142
Period size: 53 Copynumber: 3.1 Consensus size: 53
1918146 AAAAATTACT
1918156 ATCGCAACACGAAAATGACTATCGCAACGAGAGAATCGTAATGCGAAATGAAA
1 ATCGCAACACGAAAATGACTATCGCAACGAGAGAATCGTAATGCGAAATGAAA
* * * * ** **
1918209 ATCGCAACAAC-AAAATCAC-AACGCGAA-AATG-GCTATCACAATGCGAAAATGACT
1 ATCGCAAC-ACGAAAATGACTATCGC-AACGA-GAG-AATCGTAATGCG-AAATGAAA
** ** *
1918263 ATCGCAATGCGAATTTGACTATCGCAACGAAAGAATCGTAATGCGAAATGAAA
1 ATCGCAACACGAAAATGACTATCGCAACGAGAGAATCGTAATGCGAAATGAAA
1918316 ATCGCA
1 ATCGCA
1918322 TTGCGATTCT
Statistics
Matches: 83, Mismatches: 21, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
52 6 0.07
53 40 0.48
54 31 0.37
55 6 0.07
ACGTcount: A:0.44, C:0.20, G:0.19, T:0.17
Consensus pattern (53 bp):
ATCGCAACACGAAAATGACTATCGCAACGAGAGAATCGTAATGCGAAATGAAA
Found at i:1918248 original size:20 final size:20
Alignment explanation
Indices: 1918223--1918285 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
1918213 CAACAACAAA
* *
1918223 ATCACAACGCGAAAATGGCT
1 ATCACAATGCGAAAATGACT
1918243 ATCACAATGCGAAAATGACT
1 ATCACAATGCGAAAATGACT
* **
1918263 ATCGCAATGCGAATTTGACT
1 ATCACAATGCGAAAATGACT
1918283 ATC
1 ATC
1918286 GCAACGAAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.22
Consensus pattern (20 bp):
ATCACAATGCGAAAATGACT
Found at i:1918286 original size:20 final size:20
Alignment explanation
Indices: 1918231--1918289 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
1918221 AAATCACAAC
* *
1918231 GCGAAAATGGCTATCACAAT
1 GCGAAAATGACTATCGCAAT
1918251 GCGAAAATGACTATCGCAAT
1 GCGAAAATGACTATCGCAAT
**
1918271 GCGAATTTGACTATCGCAA
1 GCGAAAATGACTATCGCAA
1918290 CGAAAGAATC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.22
Consensus pattern (20 bp):
GCGAAAATGACTATCGCAAT
Found at i:1918388 original size:20 final size:20
Alignment explanation
Indices: 1918334--1918402 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
1918324 GCGATTCTCT
**
1918334 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
1918354 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
1918374 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
1918394 TGTTGCGAT
1 CGTTGCGAT
1918403 TTTAAGTTTC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1918977 original size:21 final size:21
Alignment explanation
Indices: 1918886--1918990 Score: 86
Period size: 21 Copynumber: 5.0 Consensus size: 21
1918876 GACTCACCTT
*
1918886 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
* *
1918908 T-ATTGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
1918928 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
1918949 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
1918970 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
1918991 CCAACATTCT
Statistics
Matches: 61, Mismatches: 21, Indels: 3
0.72 0.25 0.04
Matches are distributed among these distances:
20 3 0.05
21 57 0.93
22 1 0.02
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:1918983 original size:42 final size:42
Alignment explanation
Indices: 1918912--1918993 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
1918902 CTCCCCTATT
*
1918912 GTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCACC
1 GTTCAAGAGGCCACTATCATCCCTCAAGAGGT-CCCTCCCACC
* ** *
1918954 GTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCA
1 GTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
1918994 ACATTCTAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 32 0.94
43 2 0.06
ACGTcount: A:0.22, C:0.38, G:0.20, T:0.21
Consensus pattern (42 bp):
GTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCACC
Found at i:1920381 original size:14 final size:14
Alignment explanation
Indices: 1920362--1920397 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1920352 ATTGTTTAAT
1920362 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1920376 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1920390 TGATTTGT
1 TGATTTGT
1920398 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1920598 original size:33 final size:33
Alignment explanation
Indices: 1920539--1920634 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
1920529 ACGAGATTCG
*
1920539 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCA-TTTCGCGTTGCGATTCTCT
*
1920573 TGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
** *
1920606 CGTTGCGATAGTCATTTCCACGTTGCGAT
1 CGTTGCGATTTTCATTT-CGCGTTGCGAT
1920635 AGTCAATTTC
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 32 0.58
34 23 0.42
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:1920631 original size:20 final size:19
Alignment explanation
Indices: 1920574--1920694 Score: 117
Period size: 20 Copynumber: 6.4 Consensus size: 19
1920564 CGATTCTCTT
**
1920574 GTTGCGATTTTCATTTCGC
1 GTTGCGATAGTCATTTCGC
*
1920593 GTTGCGAT--TC---TCTC
1 GTTGCGATAGTCATTTCGC
*
1920607 GTTGCGATAGTCATTTCCAC
1 GTTGCGATAGTCATTT-CGC
*
1920627 GTTGCGATAGTCAATTTCGT
1 GTTGCGATAGTC-ATTTCGC
*
1920647 GTTGCGATAGTCATTTCCGT
1 GTTGCGATAGTCATTT-CGC
1920667 GTTGCGATAGTCATATTCGC
1 GTTGCGATAGTCAT-TTCGC
1920687 GTTGCGAT
1 GTTGCGAT
1920695 TTCCGCGTTG
Statistics
Matches: 88, Mismatches: 5, Indels: 17
0.80 0.05 0.15
Matches are distributed among these distances:
14 11 0.12
16 2 0.02
17 2 0.02
19 13 0.15
20 54 0.61
21 6 0.07
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.40
Consensus pattern (19 bp):
GTTGCGATAGTCATTTCGC
Found at i:1920662 original size:40 final size:40
Alignment explanation
Indices: 1920606--1920694 Score: 135
Period size: 40 Copynumber: 2.2 Consensus size: 40
1920596 GCGATTCTCT
1920606 CGTTGCGATAGTCATTTCCACGTTGCGATAGTCA-ATTTCG
1 CGTTGCGATAGTCATTTCCACGTTGCGATAGTCATA-TTCG
* **
1920646 TGTTGCGATAGTCATTTCCGTGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCATTTCCACGTTGCGATAGTCATATTCG
1920686 CGTTGCGAT
1 CGTTGCGAT
1920695 TTCCGCGTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 43 0.98
41 1 0.02
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (40 bp):
CGTTGCGATAGTCATTTCCACGTTGCGATAGTCATATTCG
Found at i:1921320 original size:20 final size:20
Alignment explanation
Indices: 1921295--1921361 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
1921285 AAATTCAGTA
1921295 TTGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
*
1921315 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
1921335 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
1921355 TTGCGAT
1 TTGCGAT
1921362 TTACGTATTC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.30
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:1921371 original size:20 final size:20
Alignment explanation
Indices: 1921348--1921400 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1921338 CGATAGTCAG
*
1921348 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1921368 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
1921388 ATTCGTATTGCGA
1 ATTCGCATTGCGA
1921401 ATTAGGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1921654 original size:21 final size:21
Alignment explanation
Indices: 1921629--1921669 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1921619 GTGTTGTTTA
1921629 AAATTTAATTGTTAGGGATTG
1 AAATTTAATTGTTAGGGATTG
*
1921650 AAATTTAATTGTTTGGGATT
1 AAATTTAATTGTTAGGGATT
1921670 ATTGTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (21 bp):
AAATTTAATTGTTAGGGATTG
Done.