Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009579.1 Hibiscus syriacus cultivar Beakdansim tig00116951_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: 6215474
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 29
Found at i:1800537 original size:26 final size:26
Alignment explanation
Indices: 1800508--1800575 Score: 93
Period size: 26 Copynumber: 2.7 Consensus size: 26
1800498 TTTCGTATCC
* *
1800508 TAAAATTTTATAAATTTACCTTATTT
1 TAAAATTTTATAAATTTACCTCATCT
* *
1800534 TAAAATTTTATAAGTTTATCTCATCT
1 TAAAATTTTATAAATTTACCTCATCT
1800560 TAAAATTTTA-AAATTT
1 TAAAATTTTATAAATTT
1800576 CATCCTTCTC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
25 5 0.14
26 32 0.86
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.51
Consensus pattern (26 bp):
TAAAATTTTATAAATTTACCTCATCT
Found at i:1800857 original size:29 final size:28
Alignment explanation
Indices: 1800797--1800851 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
1800787 GGTAGGACAA
1800797 TTTTAAAATAATTATTAATAATTATAGG
1 TTTTAAAATAATTATTAATAATTATAGG
*
1800825 TTTTAAAAAGTAATTATTTA-AATTATA
1 TTTT-AAAA-TAATTATTAATAATTATA
1800852 TTTTTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 4 0.17
29 11 0.46
30 9 0.38
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (28 bp):
TTTTAAAATAATTATTAATAATTATAGG
Found at i:1801923 original size:21 final size:21
Alignment explanation
Indices: 1801897--1801937 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1801887 CCGCGTAGAA
1801897 ATGTCCCGAAAGACCACATAG
1 ATGTCCCGAAAGACCACATAG
*
1801918 ATGTCCCGAATGACCACATA
1 ATGTCCCGAAAGACCACATA
1801938 TAACACATAT
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:0.37, C:0.29, G:0.17, T:0.17
Consensus pattern (21 bp):
ATGTCCCGAAAGACCACATAG
Found at i:1804800 original size:23 final size:23
Alignment explanation
Indices: 1804749--1804801 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
1804739 ACAACCTTAT
* *
1804749 ATGGCACTTCGGTGCATTTCTAC
1 ATGGCACTACGGTGCAATTCTAC
*
1804772 ACGGCACTACGGTGCAATTCTAC
1 ATGGCACTACGGTGCAATTCTAC
*
1804795 GTGGCAC
1 ATGGCAC
1804802 CTCGGAGCAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.21, C:0.28, G:0.25, T:0.26
Consensus pattern (23 bp):
ATGGCACTACGGTGCAATTCTAC
Found at i:1807791 original size:30 final size:30
Alignment explanation
Indices: 1807755--1807818 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
1807745 GAAGGACCTG
* *
1807755 TCCAGAGGTTACAAAGAACCCCGGTAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
* * *
1807785 TCCAGAGGTCATAAAGATCCTCGGCAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
1807815 TCCA
1 TCCA
1807819 TATGTTCCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGAACCCCGGCAACTA
Found at i:1811469 original size:23 final size:23
Alignment explanation
Indices: 1811436--1811503 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
1811426 AACCTTATAT
1811436 GGCACTTCGGTGAATTTCTACGC
1 GGCACTTCGGTGAATTTCTACGC
* *
1811459 GGCACTACGGTGCAA-TTCTACGT
1 GGCACTTCGGTG-AATTTCTACGC
* *
1811482 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGAATTTCTACG
1811504 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
22 1 0.03
23 35 0.92
24 2 0.05
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGAATTTCTACGC
Found at i:1812583 original size:18 final size:18
Alignment explanation
Indices: 1812560--1812597 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1812550 GCTTATATAA
1812560 CACCCAAAGAATAAAACC
1 CACCCAAAGAATAAAACC
1812578 CACCCAAAGAATAAAACC
1 CACCCAAAGAATAAAACC
1812596 CA
1 CA
1812598 ACTAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.55, C:0.34, G:0.05, T:0.05
Consensus pattern (18 bp):
CACCCAAAGAATAAAACC
Found at i:1826996 original size:12 final size:12
Alignment explanation
Indices: 1826979--1827019 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
1826969 AAACAATAGT
1826979 ATAAATTATAAA
1 ATAAATTATAAA
1826991 ATAAATT-TAAA
1 ATAAATTATAAA
*
1827002 ATATATTA-AAA
1 ATAAATTATAAA
1827013 CATAAAT
1 -ATAAAT
1827020 AAAACTTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 13 0.52
12 12 0.48
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (12 bp):
ATAAATTATAAA
Found at i:1832118 original size:23 final size:23
Alignment explanation
Indices: 1832092--1832144 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
1832082 TCAAAAACAG
*
1832092 ATTAGAAAATGAA-TTTATAAAAT
1 ATTAAAAAAT-AATTTTATAAAAT
1832115 ATTAAAAAATAATTTTATAAAAT
1 ATTAAAAAATAATTTTATAAAAT
*
1832138 TTTAAAA
1 ATTAAAA
1832145 GAAGTAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 2 0.07
23 25 0.93
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (23 bp):
ATTAAAAAATAATTTTATAAAAT
Found at i:1835462 original size:18 final size:18
Alignment explanation
Indices: 1835439--1835473 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1835429 ACTGAATATT
*
1835439 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
1835457 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
1835474 GATTATCCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.34, G:0.20, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1835608 original size:22 final size:23
Alignment explanation
Indices: 1835582--1835629 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
1835572 TTTATCACTG
*
1835582 TTCATGTAAACACATAAG-TCAC
1 TTCATATAAACACATAAGATCAC
* *
1835604 TTCATATACACACATATGATCAC
1 TTCATATAAACACATAAGATCAC
1835627 TTC
1 TTC
1835630 CATTATTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (23 bp):
TTCATATAAACACATAAGATCAC
Found at i:1836169 original size:18 final size:19
Alignment explanation
Indices: 1836126--1836169 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1836116 TAAGGGTTGT
1836126 ATCGATGCACTACATGTGC
1 ATCGATGCACTACATGTGC
1836145 ATCGATGCACT-CAT-TGC
1 ATCGATGCACTACATGTGC
1836162 ATTCGATG
1 A-TCGATG
1836170 TTTATTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.17
18 9 0.38
19 11 0.46
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (19 bp):
ATCGATGCACTACATGTGC
Found at i:1836220 original size:21 final size:22
Alignment explanation
Indices: 1836177--1836220 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
1836167 ATGTTTATTT
*
1836177 ATTTAAGAGTGCATCGGTACAC
1 ATTTAAGAGTGCATCGATACAC
* *
1836199 ATTTAAGA-TGTATCGATGCAC
1 ATTTAAGAGTGCATCGATACAC
1836220 A
1 A
1836221 CAACCCAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (22 bp):
ATTTAAGAGTGCATCGATACAC
Found at i:1839584 original size:21 final size:21
Alignment explanation
Indices: 1839558--1839612 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
1839548 TTTGTTCAAC
1839558 AATTCTTGTAATTGAATCTTT
1 AATTCTTGTAATTGAATCTTT
1839579 AATTCTTGTAATTGAATCTTT
1 AATTCTTGTAATTGAATCTTT
1839600 AATTCTTGTAATT
1 AATTCTTGTAATT
1839613 CTTTTGGGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (21 bp):
AATTCTTGTAATTGAATCTTT
Found at i:1842214 original size:18 final size:18
Alignment explanation
Indices: 1842191--1842225 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1842181 ACTGAATATT
1842191 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1842209 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
1842226 GATTATCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.23, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1842360 original size:22 final size:23
Alignment explanation
Indices: 1842334--1842381 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
1842324 TTTATCACTG
*
1842334 TTCATGTAAACACATAAG-TCAC
1 TTCATATAAACACATAAGATCAC
* *
1842356 TTCATATACACACATATGATCAC
1 TTCATATAAACACATAAGATCAC
1842379 TTC
1 TTC
1842382 CATTATTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (23 bp):
TTCATATAAACACATAAGATCAC
Found at i:1844826 original size:24 final size:24
Alignment explanation
Indices: 1844756--1844826 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
1844746 CAATATTATA
*
1844756 TGGCACTACGGTGC-ATTTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
* *
1844779 CGGCACTTCGGTGCAAATTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
* *
1844803 TGGCACTTTGGTGCAATTTATACG
1 TGGCACTTCGGTGCAATTTCTACG
1844827 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 12 0.30
24 28 0.70
ACGTcount: A:0.20, C:0.24, G:0.25, T:0.31
Consensus pattern (24 bp):
TGGCACTTCGGTGCAATTTCTACG
Found at i:1851163 original size:24 final size:24
Alignment explanation
Indices: 1851093--1851155 Score: 117
Period size: 24 Copynumber: 2.6 Consensus size: 24
1851083 ATTTCTATGC
1851093 GGCACTTTGGTGCAAATTCTACGT
1 GGCACTTTGGTGCAAATTCTACGT
1851117 GGCACTTTGGTGCAAATTCTACGT
1 GGCACTTTGGTGCAAATTCTACGT
*
1851141 GGCACTTCGGTGCAA
1 GGCACTTTGGTGCAA
1851156 TTTATACGAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.21, C:0.22, G:0.27, T:0.30
Consensus pattern (24 bp):
GGCACTTTGGTGCAAATTCTACGT
Found at i:1851894 original size:21 final size:21
Alignment explanation
Indices: 1851868--1851926 Score: 118
Period size: 21 Copynumber: 2.8 Consensus size: 21
1851858 GATATTTTGG
1851868 TGCATCGATGCACTGTAGCAA
1 TGCATCGATGCACTGTAGCAA
1851889 TGCATCGATGCACTGTAGCAA
1 TGCATCGATGCACTGTAGCAA
1851910 TGCATCGATGCACTGTA
1 TGCATCGATGCACTGTA
1851927 ACACTGTTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (21 bp):
TGCATCGATGCACTGTAGCAA
Found at i:1852224 original size:5 final size:5
Alignment explanation
Indices: 1852214--1852248 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
1852204 ACAACTATTA
*
1852214 ATATC ATATC ATA-C ATATC ATATC AAATC ATATC A
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC A
1852249 CTCATATACT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (5 bp):
ATATC
Found at i:1852487 original size:2 final size:2
Alignment explanation
Indices: 1852480--1852513 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1852470 CCTATTACAC
1852480 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
1852514 TGTATTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1852638 original size:23 final size:23
Alignment explanation
Indices: 1852612--1852680 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
1852602 CACCACAACT
*
1852612 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
1852635 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
1852658 TGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
1852681 TATAAGATGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:1853535 original size:2 final size:2
Alignment explanation
Indices: 1853464--1853517 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1853454 ACACACACAC
1853464 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
1853506 AT AT AT AT AT AT
1 AT AT AT AT AT AT
1853518 TACTTCTATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1853928 original size:19 final size:20
Alignment explanation
Indices: 1853891--1853928 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1853881 TCTTTTATAT
1853891 TCATATGATTTATTATCATA
1 TCATATGATTTATTATCATA
*
1853911 TCATATGGTTTA-TATCAT
1 TCATATGATTTATTATCAT
1853929 CATAACATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.50
Consensus pattern (20 bp):
TCATATGATTTATTATCATA
Found at i:1853937 original size:22 final size:20
Alignment explanation
Indices: 1853892--1853937 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1853882 CTTTTATATT
*
1853892 CATATGATTTATTATCATAT
1 CATATGATTTATTATCATAA
*
1853912 CATATGGTTTATATCATCATAA
1 CATATGATTTAT-T-ATCATAA
1853934 CATA
1 CATA
1853938 GCATATATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
21 1 0.05
22 10 0.45
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (20 bp):
CATATGATTTATTATCATAA
Found at i:1854337 original size:20 final size:20
Alignment explanation
Indices: 1854302--1854339 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1854292 TTCCCATTGA
*
1854302 AGTGCATCGGTACATTCTAC
1 AGTGCATCGATACATTCTAC
*
1854322 AGTGCATCGATGCATTCT
1 AGTGCATCGATACATTCT
1854340 TTAACATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAC
Found at i:1859983 original size:44 final size:44
Alignment explanation
Indices: 1859926--1860022 Score: 119
Period size: 44 Copynumber: 2.2 Consensus size: 44
1859916 GGCCTTGTGC
* * *
1859926 ATCGATGTACATTC-AA-GGAGTGCATCGATGCA-TCTTCATGATGT
1 ATCGATGCACATTCAAAGGGA-TACATCGATGCACTATTCA-G-TGT
1859970 ATCGATGCACATTCAAAGGGATACATCGATGCACTATTCAGTGT
1 ATCGATGCACATTCAAAGGGATACATCGATGCACTATTCAGTGT
1860014 ATCGATGCA
1 ATCGATGCA
1860023 TTATGGACAA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
44 25 0.53
45 14 0.30
46 8 0.17
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.29
Consensus pattern (44 bp):
ATCGATGCACATTCAAAGGGATACATCGATGCACTATTCAGTGT
Found at i:1859984 original size:21 final size:22
Alignment explanation
Indices: 1859922--1860010 Score: 67
Period size: 23 Copynumber: 3.9 Consensus size: 22
1859912 GCATGGCCTT
*
1859922 GTGCATCGATGTACATTCAAGGA
1 GTGCATCGATGCACATTC-AGGA
*
1859945 GTGCATCGATGCATC-TTCATGA
1 GTGCATCGATGCA-CATTCAGGA
*
1859967 -TGTATCGATGCACATTCAAAGG-
1 GTGCATCGATGCACATTC--AGGA
*
1859989 GATACATCGATGCACTATTCAG
1 G-TGCATCGATGCAC-ATTCAG
1860011 TGTATCGATG
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
20 1 0.02
21 14 0.26
22 3 0.06
23 19 0.36
24 12 0.23
25 4 0.08
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.28
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAGGA
Found at i:1865597 original size:64 final size:63
Alignment explanation
Indices: 1865464--1865626 Score: 161
Period size: 64 Copynumber: 2.5 Consensus size: 63
1865454 AAAAAGCCTC
* * * * *
1865464 GGTGCATCGATGCATGGCTTGTGTATCGGTGCATAAAATCAATTCGATGTTTTAATATATATG
1 GGTGCATCGATGCATGGCTTGTGCATCGGTACACAAAATCAATTCGATGTTTTAATATACAAG
*
1865527 GAGTGCATCGATGCATGG-TATGTGCATCGGTACACAAAATCCATTCGATGTTCAATTAA-A-AC
1 G-GTGCATCGATGCATGGCT-TGTGCATCGGTACACAAAATCAATTCGATGTT---TTAATATAC
1865589 AAG
61 AAG
* * * *
1865592 GGTGCATCGATGTATTGATTCATGCATCGGTACAC
1 GGTGCATCGATGCATGGCTT-GTGCATCGGTACAC
1865627 TTACCTGAAA
Statistics
Matches: 84, Mismatches: 9, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
63 2 0.02
64 59 0.70
65 18 0.21
66 1 0.01
67 4 0.05
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (63 bp):
GGTGCATCGATGCATGGCTTGTGCATCGGTACACAAAATCAATTCGATGTTTTAATATACAAG
Found at i:1865954 original size:21 final size:22
Alignment explanation
Indices: 1865930--1865971 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1865920 AGGTTTTTTG
*
1865930 GGACA-ACTCATAGGTCCTTCA
1 GGACATACTCACAGGTCCTTCA
*
1865951 GGACATATTCACAGGTCCTTC
1 GGACATACTCACAGGTCCTTC
1865972 GAGACAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (22 bp):
GGACATACTCACAGGTCCTTCA
Found at i:1867558 original size:19 final size:18
Alignment explanation
Indices: 1867532--1867728 Score: 72
Period size: 18 Copynumber: 10.7 Consensus size: 18
1867522 ATAGAAAAAT
1867532 AAAT-AAATAAAAATAAA
1 AAATAAAATAAAAATAAA
*
1867549 AACATAAAATAAAAGTAAA
1 AA-ATAAAATAAAAATAAA
* *
1867568 AAATATAATAGTAAAT-AA
1 AAATAAAATA-AAAATAAA
** *
1867586 AAAT-GTA-AAAAACAAA
1 AAATAAAATAAAAATAAA
* * *
1867602 GAATCAAAGAAAAA-AAA
1 AAATAAAATAAAAATAAA
1867619 GAAATAAAGACTACAAAAAGGTAAA
1 -AAATAAA-A-T--AAAAA--TAAA
* *
1867644 TAAATAAAA-ATAAATCGAAG
1 -AAATAAAATAAAAAT--AAA
*
1867664 AAATAAAATGAAAATAAA
1 AAATAAAATAAAAATAAA
1867682 AAAT-AAAT-AAAATAAA
1 AAATAAAATAAAAATAAA
* *
1867698 TAAAT-GAAGAAAAATAAA
1 -AAATAAAATAAAAATAAA
1867716 TAAAT-AAATAAAA
1 -AAATAAAATAAAA
1867729 TATTATTTTA
Statistics
Matches: 137, Mismatches: 24, Indels: 37
0.69 0.12 0.19
Matches are distributed among these distances:
15 3 0.02
16 14 0.10
17 17 0.12
18 51 0.37
19 26 0.19
20 10 0.07
22 5 0.04
24 1 0.01
25 10 0.07
ACGTcount: A:0.73, C:0.03, G:0.07, T:0.17
Consensus pattern (18 bp):
AAATAAAATAAAAATAAA
Found at i:1867649 original size:4 final size:4
Alignment explanation
Indices: 1867640--1867727 Score: 65
Period size: 4 Copynumber: 21.0 Consensus size: 4
1867630 TACAAAAAGG
* *
1867640 TAAA TAAA T-AA -AAA TAAA TCGAA GAAA TAAAA TGAAAA TAAA -AAA
1 TAAA TAAA TAAA TAAA TAAA T-AAA TAAA T-AAA T--AAA TAAA TAAA
*
1867685 TAAA TAAAA TAAA TAAA TGAAGA AAAA TAAA TAAA TAAA TAAA
1 TAAA T-AAA TAAA TAAA T-AA-A TAAA TAAA TAAA TAAA TAAA
1867728 ATATTATTTT
Statistics
Matches: 69, Mismatches: 6, Indels: 18
0.74 0.06 0.19
Matches are distributed among these distances:
3 7 0.10
4 42 0.61
5 14 0.20
6 6 0.09
ACGTcount: A:0.74, C:0.01, G:0.06, T:0.19
Consensus pattern (4 bp):
TAAA
Found at i:1867730 original size:31 final size:30
Alignment explanation
Indices: 1867645--1867727 Score: 91
Period size: 31 Copynumber: 2.8 Consensus size: 30
1867635 AAAGGTAAAT
** *
1867645 AAAT-AAAAATAAATCGAAGAAATAAAATGA
1 AAATAAAAAATAAATAAAATAAAT-AAATGA
1867675 AAATAAAAAATAAATAAAATAAATAAATGA
1 AAATAAAAAATAAATAAAATAAATAAATGA
1867705 AGAA-AAATAAATAAAT-AAATAAA
1 A-AATAAA-AAATAAATAAAATAAA
1867728 ATATTATTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
30 21 0.45
31 26 0.55
ACGTcount: A:0.75, C:0.01, G:0.06, T:0.18
Consensus pattern (30 bp):
AAATAAAAAATAAATAAAATAAATAAATGA
Found at i:1868229 original size:20 final size:20
Alignment explanation
Indices: 1868180--1868219 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1868170 AGCAAACCCA
1868180 AAACACCCGAAACCTTCGTC
1 AAACACCCGAAACCTTCGTC
1868200 AAACACCCGAAACCTTCGTC
1 AAACACCCGAAACCTTCGTC
1868220 TCACCCCCGA
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:0.35, C:0.40, G:0.10, T:0.15
Consensus pattern (20 bp):
AAACACCCGAAACCTTCGTC
Found at i:1868906 original size:19 final size:22
Alignment explanation
Indices: 1868857--1868900 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1868847 GAAAAAAAAG
1868857 TAATGATAATAATAATAAATAA
1 TAATGATAATAATAATAAATAA
*
1868879 TAATGATAATAATAGTAAATAA
1 TAATGATAATAATAATAAATAA
1868901 ATATAAAAAA
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:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (22 bp):
TAATGATAATAATAATAAATAA
Found at i:1869014 original size:33 final size:32
Alignment explanation
Indices: 1868969--1869065 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 32
1868959 CTATATATTA
1868969 TATATAAATTTTCAAAAATGTTTTTATAAAAAAC
1 TATAT-AATTTTCAAAAATGTTTTT-TAAAAAAC
*
1869003 TATATAATTTTCAAAAATTGGTTTTTT-TAAAAC
1 TATATAATTTTCAAAAA-T-GTTTTTTAAAAAAC
*
1869036 TATATAATTTTCTAAAATGTTTTTTAAAAA
1 TATATAATTTTCAAAAATGTTTTTTAAAAA
1869066 TTATATATTA
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
31 7 0.12
32 4 0.07
33 33 0.58
34 7 0.12
35 6 0.11
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.46
Consensus pattern (32 bp):
TATATAATTTTCAAAAATGTTTTTTAAAAAAC
Found at i:1869073 original size:33 final size:33
Alignment explanation
Indices: 1868914--1869073 Score: 121
Period size: 33 Copynumber: 4.6 Consensus size: 33
1868904 TAAAAAAACA
* * *
1868914 TTTTATAAAAACTATATAATATAAATTTCTAAAAACG
1 TTTTTTAAAAA-T-TAT-ATATAATTTTC-AAAAATG
1868951 TTTTTTAACTATATATTATATATAAATTTTCAAAAATG
1 TTTTTTAA--A-A-ATTATATAT-AATTTTCAAAAATG
1868989 TTTTTATAAAAA--ACTATATAATTTTCAAAAATTGG
1 TTTTT-TAAAAATTA-TATATAATTTTCAAAAA-T-G
* * *
1869024 TTTTTTTAAAA--CTATATAATTTTCTAAAATG
1 TTTTTTAAAAATTATATATAATTTTCAAAAATG
1869055 TTTTTTAAAAATTATATAT
1 TTTTTTAAAAATTATATAT
1869074 TATATAAGTT
Statistics
Matches: 104, Mismatches: 8, Indels: 26
0.75 0.06 0.19
Matches are distributed among these distances:
31 11 0.11
32 1 0.01
33 34 0.33
34 11 0.11
35 7 0.07
36 1 0.01
37 8 0.08
38 15 0.14
39 13 0.12
40 2 0.02
41 1 0.01
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (33 bp):
TTTTTTAAAAATTATATATAATTTTCAAAAATG
Found at i:1869096 original size:31 final size:31
Alignment explanation
Indices: 1869056--1869117 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
1869046 TCTAAAATGT
* * *
1869056 TTTTTAAAAATTATATATTATATAAGTTTTA
1 TTTTCAAAAAATAAATATTATATAAGTTTTA
1869087 TTTTCAAAAAATAAATATTATATAAGTTTTA
1 TTTTCAAAAAATAAATATTATATAAGTTTTA
1869118 AAAAAATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (31 bp):
TTTTCAAAAAATAAATATTATATAAGTTTTA
Found at i:1869199 original size:37 final size:36
Alignment explanation
Indices: 1869036--1869309 Score: 226
Period size: 37 Copynumber: 7.5 Consensus size: 36
1869026 TTTTTAAAAC
*
1869036 TATATA-ATTTTCTAAAATGTTTTTTAAAAATTATATAT
1 TATATATATTTTC-AAAATG--TTTTAAAAACTATATAT
* * *
1869074 TATATA-AGTTTT----AT-TTTCAAAAAATAAATAT
1 TATATATA-TTTTCAAAATGTTTTAAAAACTATATAT
* * *
1869105 TATATA-AGTTTTAAAAAAATATTTTTAAAAATTATATAT
1 TATATATA-TTTT--CAAAAT-GTTTTAAAAACTATATAT
*
1869144 TATATAAGATTTTCAAAATGATTTTAAAAA-TATATAT
1 TATAT-ATATTTTCAAAATG-TTTTAAAAACTATATAT
* *
1869181 TACATATATTTTCTAAAATGTTTTAAAAACAATATAT
1 TATATATATTTTC-AAAATGTTTTAAAAACTATATAT
*
1869218 TATATA-GTTTTCAAAAGTGTTTTAAAAACTATATAT
1 TATATATATTTTCAAAA-TGTTTTAAAAACTATATAT
* *
1869254 TATATACATTTTCAAAATGTTTTTATAAACTATATAT
1 TATATATATTTTCAAAATG-TTTTAAAAACTATATAT
1869291 TATATACGTATTTTCAAAA
1 TATATA--TATTTTCAAAA
1869310 AAAAACCATT
Statistics
Matches: 200, Mismatches: 17, Indels: 37
0.79 0.07 0.15
Matches are distributed among these distances:
31 26 0.13
34 2 0.01
35 4 0.02
36 47 0.23
37 61 0.31
38 21 0.10
39 33 0.17
40 5 0.03
41 1 0.00
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (36 bp):
TATATATATTTTCAAAATGTTTTAAAAACTATATAT
Found at i:1869292 original size:73 final size:74
Alignment explanation
Indices: 1869120--1869309 Score: 253
Period size: 73 Copynumber: 2.6 Consensus size: 74
1869110 AAGTTTTAAA
* *
1869120 AAAATATTTTTAAAAATTATATATTATATAAGATTTTCAAAATGATTTTAAAAATATATATTACA
1 AAAATGTTTTTAAAAACTATATATTATAT-AGATTTTCAAAATGATTTTAAAAATATATATTACA
*
1869185 TATATTTTCT
65 TACATTTTCT
* *
1869195 AAAATG-TTTTAAAAACAATATATTATATAG-TTTTCAAAAGTG-TTTTAAAAACTATATATTAT
1 AAAATGTTTTTAAAAACTATATATTATATAGATTTTCAAAA-TGATTTTAAAAA-TATATATTAC
1869257 ATACATTTTC-
64 ATACATTTTCT
*
1869267 AAAATGTTTTTATAAACTATATATTATATACGTATTTTCAAAA
1 AAAATGTTTTTAAAAACTATATATTATATA-G-ATTTTCAAAA
1869310 AAAAACCATT
Statistics
Matches: 102, Mismatches: 7, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
72 24 0.24
73 43 0.42
74 21 0.21
75 5 0.05
76 9 0.09
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (74 bp):
AAAATGTTTTTAAAAACTATATATTATATAGATTTTCAAAATGATTTTAAAAATATATATTACAT
ACATTTTCT
Found at i:1870202 original size:49 final size:49
Alignment explanation
Indices: 1870111--1870205 Score: 145
Period size: 49 Copynumber: 1.9 Consensus size: 49
1870101 ACTAGAGAAA
** *
1870111 CAGGGGCGGACCTCCATGGAGCCCGGGGTATCCCGGGTAACCCCTCATC
1 CAGGGGCGGACCTCCATGGAGCCCGGGGTATCCCAAGCAACCCCTCATC
* *
1870160 CAGGGGTGGACCTCCATGGTGCCCGGGGTATCCCAAGCAACCCCTC
1 CAGGGGCGGACCTCCATGGAGCCCGGGGTATCCCAAGCAACCCCTC
1870206 CACAAGTGCC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.17, C:0.37, G:0.32, T:0.15
Consensus pattern (49 bp):
CAGGGGCGGACCTCCATGGAGCCCGGGGTATCCCAAGCAACCCCTCATC
Found at i:1871430 original size:21 final size:21
Alignment explanation
Indices: 1871404--1871443 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1871394 TAAAAATTAT
*
1871404 TTAAAATATTATTATTTTTAC
1 TTAAAATATTAATATTTTTAC
1871425 TTAAAATATTAATATTTTT
1 TTAAAATATTAATATTTTT
1871444 TTAATATTTT
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:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (21 bp):
TTAAAATATTAATATTTTTAC
Found at i:1872197 original size:2 final size:2
Alignment explanation
Indices: 1872192--1872217 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1872182 TGATAAATAA
1872192 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
1872218 GTACATAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1873842 original size:21 final size:20
Alignment explanation
Indices: 1873817--1873868 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
1873807 TATGATCTTA
*
1873817 AAATTTAAAATAATAAACTTT
1 AAATTTAAAAT-ATAAACTCT
1873838 AAATTTTAAAATATAAACTCT
1 AAA-TTTAAAATATAAACTCT
1873859 AAATCTTAAA
1 AAAT-TTAAA
1873869 CCGTAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 1 0.04
21 19 0.68
22 8 0.29
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATTTAAAATATAAACTCT
Found at i:1878190 original size:26 final size:25
Alignment explanation
Indices: 1878142--1878192 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
1878132 AGAAAAATAG
* *
1878142 CACAAATTGTCTGTATATATATACA
1 CACAAATTGACTATATATATATACA
1878167 CACAAATTGACATATATATATATACA
1 CACAAATTGAC-TATATATATATACA
1878193 TAAGAAAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.33
Consensus pattern (25 bp):
CACAAATTGACTATATATATATACA
Found at i:1879810 original size:21 final size:20
Alignment explanation
Indices: 1879785--1879836 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
1879775 TATGATCTTA
*
1879785 AAATTTAAAATAATAAACTTT
1 AAATTTAAAAT-ATAAACTCT
1879806 AAATTTTAAAATATAAACTCT
1 AAA-TTTAAAATATAAACTCT
1879827 AAATCTTAAA
1 AAAT-TTAAA
1879837 CCGTAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 1 0.04
21 19 0.68
22 8 0.29
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATTTAAAATATAAACTCT
Found at i:1884900 original size:28 final size:28
Alignment explanation
Indices: 1884866--1884950 Score: 125
Period size: 28 Copynumber: 3.0 Consensus size: 28
1884856 GTCTTTGTTT
* * *
1884866 ACATTATATCGTCAATCCAATGCTTGAA
1 ACATTATATCGTCGAGCCAGTGCTTGAA
* *
1884894 ATATTATATTGTCGAGCCAGTGCTTGAA
1 ACATTATATCGTCGAGCCAGTGCTTGAA
1884922 ACATTATATCGTCGAGCCAGTGCTTGAA
1 ACATTATATCGTCGAGCCAGTGCTTGAA
1884950 A
1 A
1884951 GTAACAATGG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 50 1.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (28 bp):
ACATTATATCGTCGAGCCAGTGCTTGAA
Found at i:1889653 original size:18 final size:18
Alignment explanation
Indices: 1889630--1889669 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
1889620 TTTGGACATT
1889630 TGGGTTTTAAAATTTAAA
1 TGGGTTTTAAAATTTAAA
1889648 TGGGTTTTAAAATTTAAA
1 TGGGTTTTAAAATTTAAA
1889666 TGGG
1 TGGG
1889670 CAGTGGGTTG
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:0.00, G:0.23, T:0.42
Consensus pattern (18 bp):
TGGGTTTTAAAATTTAAA
Found at i:1889711 original size:2 final size:2
Alignment explanation
Indices: 1889704--1889752 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1889694 GTGGTTGAGT
1889704 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
1889746 TA TA TA T
1 TA TA TA T
1889753 TTAATTTGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1891748 original size:13 final size:13
Alignment explanation
Indices: 1891726--1891760 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
1891716 TTTATTATAT
1891726 ATATTT-ATAAAA
1 ATATTTAATAAAA
1891738 ATATTTAAT-AAA
1 ATATTTAATAAAA
1891750 ATATTTAATAA
1 ATATTTAATAA
1891761 TATAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 18 0.86
13 3 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTTAATAAAA
Found at i:1891828 original size:19 final size:18
Alignment explanation
Indices: 1891800--1891848 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
1891790 AATATATTTA
*
1891800 AAAACAATAAAATAAATG
1 AAAACAATAAAATAAACG
1891818 AAAACATATAAAATAAACG
1 AAAACA-ATAAAATAAACG
1891837 AAAA-AATAAAAT
1 AAAACAATAAAAT
1891849 TAAAAATCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 7 0.24
18 7 0.24
19 15 0.52
ACGTcount: A:0.73, C:0.06, G:0.04, T:0.16
Consensus pattern (18 bp):
AAAACAATAAAATAAACG
Found at i:1892677 original size:24 final size:24
Alignment explanation
Indices: 1892641--1892691 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1892631 GTTTGTATTT
* *
1892641 TCTCTGTTTTTTTTTCTATGTCTC
1 TCTCTATTCTTTTTTCTATGTCTC
* *
1892665 TCTCTATTCTTTTTTTTTTGTCTC
1 TCTCTATTCTTTTTTCTATGTCTC
1892689 TCT
1 TCT
1892692 GTCTCGTTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.04, C:0.22, G:0.06, T:0.69
Consensus pattern (24 bp):
TCTCTATTCTTTTTTCTATGTCTC
Found at i:1893142 original size:3 final size:3
Alignment explanation
Indices: 1893134--1893230 Score: 178
Period size: 3 Copynumber: 32.7 Consensus size: 3
1893124 AATATATATT
*
1893134 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1893182 TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1893229 TA
1 TA
1893231 TGGATAAAAA
Statistics
Matches: 91, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
2 2 0.02
3 89 0.98
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1893682 original size:113 final size:113
Alignment explanation
Indices: 1893544--1894322 Score: 1341
Period size: 113 Copynumber: 6.9 Consensus size: 113
1893534 TGATAGTATC
* *
1893544 AAAC-AAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
*** * * *
1893608 TCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGATGAATTC
66 TCATTATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
* *
1893656 AAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
*
1893721 TCATTCATGAACTTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
66 TCATT-ATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
1893770 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTT-TTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1893834 TCATTATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
66 TCATTATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
1893882 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
*
1893947 TCATTATGAACTTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
66 TCATTATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
1893995 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * *
1894060 TCATTATGAA-CTTATCTGGCAATGAATGATCCATCAAGTGATGAATTT
66 TCATTATGAACCTTCTCTGGCAATG-TTGATCCATCAAATGATGAATTT
1894108 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
*
1894173 TCATTATGAACTTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
66 TCATTATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
1894221 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* *
1894286 TCATTATGAA-CTTATCTGGCAATGAATGATCCATCAA
66 TCATTATGAACCTTCTCTGGCAATG-TTGATCCATCAA
1894323 GTGGATTTGA
Statistics
Matches: 635, Mismatches: 26, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
112 118 0.19
113 423 0.67
114 94 0.15
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (113 bp):
AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
TCATTATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
Found at i:1895224 original size:83 final size:84
Alignment explanation
Indices: 1895032--1895714 Score: 1277
Period size: 84 Copynumber: 8.2 Consensus size: 84
1895022 TTCATCTTTT
* * *
1895032 AATTCCAACGATTGGTTCTGTCC-AACCAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCT
1 AATT-CAATGATTGGTTCTG-CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1895096 ATTGAGCAAATTCATCTTCCA
64 ATTGAGCAAATTCATCTTCCA
1895117 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1895182 TG-GCAAATTCATCTTCCA
66 TGAGCAAATTCATCTTCCA
1895200 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1895265 TGAGCAAATTCATCTTCCA
66 TGAGCAAATTCATCTTCCA
1895284 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1895349 TG-GCAAATTCATCTTCCA
66 TGAGCAAATTCATCTTCCA
1895367 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1895432 TG-GCAAATTCATCTTCCA
66 TGAGCAAATTCATCTTCCA
*
1895450 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACTCTTCCAGAAGATGCTAT
1 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1895515 TGAGCAAATTCATCTTCCA
66 TGAGCAAATTCATCTTCCA
1895534 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1895599 TGAGCAAATTCATCTTCCA
66 TGAGCAAATTCATCTTCCA
1895618 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1895683 TG-GCAAATTCATCTTCCA
66 TGAGCAAATTCATCTTCCA
1895701 AATTCAATGATTGG
1 AATTCAATGATTGG
1895715 ACTAAGATAT
Statistics
Matches: 590, Mismatches: 5, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
83 280 0.47
84 306 0.52
85 4 0.01
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (84 bp):
AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
TGAGCAAATTCATCTTCCA
Found at i:1895298 original size:167 final size:167
Alignment explanation
Indices: 1895032--1895714 Score: 1289
Period size: 167 Copynumber: 4.1 Consensus size: 167
1895022 TTCATCTTTT
* * *
1895032 AATTCCAACGATTGGTTCTGTCC-AACCAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCT
1 AATT-CAATGATTGGTTCTG-CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1895096 ATTGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAG
64 ATTGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAG
1895161 AACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCA
129 AACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCA
1895200 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1895265 TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAA
66 TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAA
1895330 CACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCA
131 CACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCA
1895367 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1895432 TG-GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAA
66 TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAA
*
1895496 CTCTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCA
131 CACTTCCAGAAGATGCTATTG-GCAAATTCATCTTCCA
1895534 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1895599 TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAA
66 TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAA
1895664 CACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCA
131 CACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCA
1895701 AATTCAATGATTGG
1 AATTCAATGATTGG
1895715 ACTAAGATAT
Statistics
Matches: 507, Mismatches: 5, Indels: 7
0.98 0.01 0.01
Matches are distributed among these distances:
166 84 0.17
167 337 0.66
168 86 0.17
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (167 bp):
AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
TGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAA
CACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCA
Found at i:1901494 original size:15 final size:15
Alignment explanation
Indices: 1901474--1901504 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1901464 GGGGCATCAA
1901474 GAGAGCGGATCCATT
1 GAGAGCGGATCCATT
1901489 GAGAGCGGATCCATT
1 GAGAGCGGATCCATT
1901504 G
1 G
1901505 TCAATCAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.19, G:0.35, T:0.19
Consensus pattern (15 bp):
GAGAGCGGATCCATT
Found at i:1908034 original size:13 final size:13
Alignment explanation
Indices: 1908010--1908044 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
1908000 CTATTTATTT
1908010 ATATTT-ATAAAA
1 ATATTTAATAAAA
1908022 ATATTTAAT-AAA
1 ATATTTAATAAAA
1908034 ATATTTAATAA
1 ATATTTAATAA
1908045 TATAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 18 0.86
13 3 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTTAATAAAA
Found at i:1908111 original size:19 final size:18
Alignment explanation
Indices: 1908083--1908131 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
1908073 CAAATATTTA
*
1908083 AAAACAATAAAATAAATG
1 AAAACAATAAAATAAACG
1908101 AAAACATATAAAATAAACG
1 AAAACA-ATAAAATAAACG
1908120 AAAA-AATAAAAT
1 AAAACAATAAAAT
1908132 TAAAAATCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 7 0.24
18 7 0.24
19 15 0.52
ACGTcount: A:0.73, C:0.06, G:0.04, T:0.16
Consensus pattern (18 bp):
AAAACAATAAAATAAACG
Found at i:1909418 original size:3 final size:3
Alignment explanation
Indices: 1909410--1909489 Score: 142
Period size: 3 Copynumber: 26.7 Consensus size: 3
1909400 AATATATATT
* *
1909410 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAC
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1909458 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1909490 TGGATAAAAA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1913395 original size:20 final size:20
Alignment explanation
Indices: 1913372--1913500 Score: 152
Period size: 20 Copynumber: 6.3 Consensus size: 20
1913362 AATATGTAAA
1913372 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
1913392 TCGCAACGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
1913412 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
* * *
1913432 TCGCAACGCGGAATTTCAAAT
1 TCGCAACACAGAA-GTCAAAT
*
1913453 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
* * *
1913473 TCGCAACGCGGAATTTCAAAT
1 TCGCAACACAGAA-GTCAAAT
1913494 TCGCAAC
1 TCGCAAC
1913501 TGAATTTCAA
Statistics
Matches: 92, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.02
20 59 0.64
21 31 0.34
ACGTcount: A:0.40, C:0.26, G:0.16, T:0.19
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:1913468 original size:41 final size:40
Alignment explanation
Indices: 1913308--1913538 Score: 233
Period size: 40 Copynumber: 5.8 Consensus size: 40
1913298 AAATGACCAA
* * ***
1913308 CAAATTCGCAACGCG-ATCTCAAATTCGCAAC-CCAGTTT
1 CAAATTCGCAACGCGAATTTCAAATTCGCAACACAAAAGT
* *
1913346 CCAATTTCGCAACGCGAATATGT-AAA-TCGCAACACAGAAGT
1 -CAAATTCGCAACGCGAAT-T-TCAAATTCGCAACACAAAAGT
* *
1913387 CAAATTCGCAACGCG-ATAGTCAAATTCGCAACACAGAAGT
1 CAAATTCGCAACGCGAAT-TTCAAATTCGCAACACAAAAGT
1913427 CAAATTCGCAACGCGGAATTTCAAATTCGCAACACAAAAGT
1 CAAATTCGCAACGC-GAATTTCAAATTCGCAACACAAAAGT
** **
1913468 CAAATTCGCAACGCGGAATTTCAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGC-GAATTTCAAATTCGCAACACAAAAGT
*
1913508 CAAATTCGCAAC-TGAATTTCAAATTCGCAAC
1 CAAATTCGCAACGCGAATTTCAAATTCGCAAC
1913539 TAGATTTTCG
Statistics
Matches: 168, Mismatches: 16, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
38 19 0.11
39 20 0.12
40 67 0.40
41 59 0.35
42 3 0.02
ACGTcount: A:0.38, C:0.26, G:0.15, T:0.22
Consensus pattern (40 bp):
CAAATTCGCAACGCGAATTTCAAATTCGCAACACAAAAGT
Found at i:1913469 original size:61 final size:60
Alignment explanation
Indices: 1913386--1913519 Score: 180
Period size: 61 Copynumber: 2.2 Consensus size: 60
1913376 AACACAGAAG
* * *
1913386 TCAAATTCGCAACGCGATAGTCAAATTCGCAACACAGAA-GTCAAATTCGCAACGCGGAATT
1 TCAAATTCGCAACACAAAAGTCAAATTCGCAACACAGAATGTCAAATTCGCAA--CGGAATT
* * * *
1913447 TCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGGAATTTCAAATTCGCAACTGAATT
1 TCAAATTCGCAACACAAAAGTCAAATTCGCAACACAGAATGTCAAATTCGCAACGGAATT
1913507 TCAAATTCGCAAC
1 TCAAATTCGCAAC
1913520 TGAATTTCAA
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
60 19 0.29
61 34 0.52
62 12 0.18
ACGTcount: A:0.39, C:0.25, G:0.15, T:0.22
Consensus pattern (60 bp):
TCAAATTCGCAACACAAAAGTCAAATTCGCAACACAGAATGTCAAATTCGCAACGGAATT
Found at i:1913552 original size:20 final size:19
Alignment explanation
Indices: 1913426--1913577 Score: 144
Period size: 19 Copynumber: 7.7 Consensus size: 19
1913416 AACACAGAAG
*
1913426 TCAAATTCGCAACGCGGAATT
1 TCAAATTCGCAA--CTGAATT
** **
1913447 TCAAATTCGCAACACAAAAG
1 TCAAATTCGCAAC-TGAATT
*
1913467 TCAAATTCGCAACGCGGAATT
1 TCAAATTCGCAA--CTGAATT
1913488 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
1913507 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
1913526 TCAAATTCGCAACTAGATTT
1 TCAAATTCGCAACT-GAATT
* *
1913546 TCGAATTCGCAACACGAATT
1 TCAAATTCGCAAC-TGAATT
*
1913566 T-AATTTCGCAAC
1 TCAAATTCGCAAC
1913578 AAGTTTTAGT
Statistics
Matches: 111, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
19 49 0.44
20 35 0.32
21 26 0.23
22 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:1913574 original size:39 final size:38
Alignment explanation
Indices: 1913308--1913577 Score: 167
Period size: 40 Copynumber: 6.8 Consensus size: 38
1913298 AAATGACCAA
* ** *
1913308 CAAATTCGCAACGCG-ATCTCAAATTCGCAACCCAGTTT
1 CAAATTCGCAAC-CGAATTTCAAATTCGCAACTGAATTT
* * *
1913346 CCAATTTCGCAACGCGAATATGT-AAA-TCGCAACACAGAA-GT
1 -CAAATTCGCAAC-CGAAT-T-TCAAATTCGC-A-ACTGAATTT
* * *
1913387 CAAATTCGCAACGCG-ATAGTCAAATTCGCAACACAGAA-GT
1 CAAATTCGCAAC-CGAAT-TTCAAATTCGC-A-ACTGAATTT
** **
1913427 CAAATTCGCAACGCGGAATTTCAAATTCGCAACACAAAAGT
1 CAAATTCGCAAC-C-GAATTTCAAATTCGCAAC-TGAATTT
1913468 CAAATTCGCAACGCGGAATTTCAAATTCGCAACTGAATTT
1 CAAATTCGCAAC-C-GAATTTCAAATTCGCAACTGAATTT
* *
1913508 CAAATTCGCAACTGAATTTCAAATTCGCAACTAGATTTT
1 CAAATTCGCAACCGAATTTCAAATTCGCAACT-GAATTT
* *
1913547 CGAATTCGCAACACGAATTT-AATTTCGCAAC
1 CAAATTCGCAAC-CGAATTTCAAATTCGCAAC
1913578 AAGTTTTAGT
Statistics
Matches: 198, Mismatches: 20, Indels: 26
0.81 0.08 0.11
Matches are distributed among these distances:
38 20 0.10
39 48 0.24
40 73 0.37
41 51 0.26
42 6 0.03
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.24
Consensus pattern (38 bp):
CAAATTCGCAACCGAATTTCAAATTCGCAACTGAATTT
Found at i:1914526 original size:24 final size:24
Alignment explanation
Indices: 1914499--1914552 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1914489 GTATTCGAAA
1914499 TTTGATCTTGGTCAACACCCGGAC
1 TTTGATCTTGGTCAACACCCGGAC
* * *
1914523 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAACACCCGGAC
1914547 TTTGAT
1 TTTGAT
1914553 GATGTGATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATCTTGGTCAACACCCGGAC
Found at i:1916831 original size:19 final size:18
Alignment explanation
Indices: 1916798--1916833 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1916788 AAGCAAAAGG
1916798 AAATCAAATCGCAATCAA
1 AAATCAAATCGCAATCAA
*
1916816 AAATCAAAATCTCAATCA
1 AAATC-AAATCGCAATCA
1916834 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAATCGCAATCAA
Found at i:1917154 original size:13 final size:14
Alignment explanation
Indices: 1917132--1917174 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
1917122 CGCGAAAGTC
1917132 AAATTCGCAACGCG
1 AAATTCGCAACGCG
1917146 AAA-TCGCAAAC-CG
1 AAATTCGC-AACGCG
*
1917159 AAATTCGCAATGCG
1 AAATTCGCAACGCG
1917173 AA
1 AA
1917175 TTTGACTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.42, C:0.26, G:0.19, T:0.14
Consensus pattern (14 bp):
AAATTCGCAACGCG
Found at i:1917192 original size:20 final size:20
Alignment explanation
Indices: 1917169--1917221 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
1917159 AAATTCGCAA
*
1917169 TGCGAATTTGACTTTCGTGT
1 TGCGAATTTGACTTTCGGGT
1917189 TGCGAATTTGACTTTCGGGT
1 TGCGAATTTGACTTTCGGGT
1917209 TGCGAATTTGACT
1 TGCGAATTTGACT
1917222 ATCGCAACGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.17, C:0.15, G:0.26, T:0.42
Consensus pattern (20 bp):
TGCGAATTTGACTTTCGGGT
Found at i:1917339 original size:14 final size:13
Alignment explanation
Indices: 1917320--1917369 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
1917310 AATCAATTAA
1917320 ACATTATTGTGGGT
1 ACATTATT-TGGGT
*
1917334 ACATTATTT--GA
1 ACATTATTTGGGT
*
1917345 ACATTGTTATGGGT
1 ACATTATT-TGGGT
1917359 ACATTATTTGG
1 ACATTATTTGG
1917370 AAAATAATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
11 8 0.28
12 1 0.03
13 4 0.14
14 16 0.55
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (13 bp):
ACATTATTTGGGT
Found at i:1917347 original size:25 final size:25
Alignment explanation
Indices: 1917319--1917368 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
1917309 AAATCAATTA
*
1917319 AACATTATTGTGGGTACATTATTTG
1 AACATTATTATGGGTACATTATTTG
*
1917344 AACATTGTTATGGGTACATTATTTG
1 AACATTATTATGGGTACATTATTTG
1917369 GAAAATAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.28, C:0.08, G:0.20, T:0.44
Consensus pattern (25 bp):
AACATTATTATGGGTACATTATTTG
Found at i:1917774 original size:18 final size:18
Alignment explanation
Indices: 1917753--1917789 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1917743 GTAATTCGAG
1917753 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
1917771 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
1917789 T
1 T
1917790 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:1917796 original size:24 final size:24
Alignment explanation
Indices: 1917745--1917797 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1917735 TTTCATATGT
* * *
1917745 AATTCGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
1917769 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
1917793 AATTT
1 AATTT
1917798 CGGCTTCACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:1918293 original size:153 final size:153
Alignment explanation
Indices: 1918003--1918308 Score: 596
Period size: 153 Copynumber: 2.0 Consensus size: 153
1917993 AATGCCTTTC
1918003 AGATATTATCCATTTCAATCAGCTCACTGAGGTAGTTTAACCCTAAACCAAAACTGTCTTAGCTA
1 AGATATTATCCATTTCAATCAGCTCACTGAGGTAGTTTAACCCTAAACCAAAACTGTCTTAGCTA
1918068 AACATACTTGATGTAGAAGCACCTGCAGATTTAAAATCTCAATGGTGATGTATTGGTTCTCAAAC
66 AACATACTTGATGTAGAAGCACCTGCAGATTTAAAATCTCAATGGTGATGTATTGGTTCTCAAAC
1918133 AGTTTAAAGCGTCAGAAACGTTT
131 AGTTTAAAGCGTCAGAAACGTTT
1918156 AGATATTATCCATTTCAATCAGCTCACTGAGGTAGTTTAACCCTAAACCAAAACTGTCTTAGCTA
1 AGATATTATCCATTTCAATCAGCTCACTGAGGTAGTTTAACCCTAAACCAAAACTGTCTTAGCTA
1918221 AACATACTTGATGTAGAAGCACCTGCAGATTTAAAATCTCAATGGTGATGTATTTGGTTCTCAAA
66 AACATACTTGATGTAGAAGCACCTGCAGATTTAAAATCTCAATGGTGATGTA-TTGGTTCTCAAA
1918286 CAG-TTAAAGCGTCAGAAACGTTT
130 CAGTTTAAAGCGTCAGAAACGTTT
1918309 CGGGCGTATG
Statistics
Matches: 152, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
153 137 0.90
154 15 0.10
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (153 bp):
AGATATTATCCATTTCAATCAGCTCACTGAGGTAGTTTAACCCTAAACCAAAACTGTCTTAGCTA
AACATACTTGATGTAGAAGCACCTGCAGATTTAAAATCTCAATGGTGATGTATTGGTTCTCAAAC
AGTTTAAAGCGTCAGAAACGTTT
Found at i:1918915 original size:12 final size:12
Alignment explanation
Indices: 1918898--1918938 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
1918888 AGCAAAAGGA
*
1918898 AATCAAAATCGC
1 AATCAAAATCAC
*
1918910 AATCAAAATCAA
1 AATCAAAATCAC
*
1918922 AATCAAAATCCC
1 AATCAAAATCAC
1918934 AATCA
1 AATCA
1918939 CAACCGGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.56, C:0.24, G:0.02, T:0.17
Consensus pattern (12 bp):
AATCAAAATCAC
Found at i:1918919 original size:6 final size:6
Alignment explanation
Indices: 1918897--1918931 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1918887 AAGCAAAAGG
* *
1918897 AAATCA AAATCG CAATCA AAATCA AAATCA AAATC
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATC
1918932 CCAATCACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.60, C:0.20, G:0.03, T:0.17
Consensus pattern (6 bp):
AAATCA
Found at i:1919300 original size:20 final size:20
Alignment explanation
Indices: 1919275--1919312 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1919265 AAATCGTAAC
*
1919275 GCGAATTTGACTTTCGCATT
1 GCGAATTTGACTATCGCATT
1919295 GCGAATTTGACTATCGCA
1 GCGAATTTGACTATCGCA
1919313 ACGCTTATTT
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:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (20 bp):
GCGAATTTGACTATCGCATT
Found at i:1919463 original size:66 final size:64
Alignment explanation
Indices: 1919391--1919565 Score: 244
Period size: 66 Copynumber: 2.6 Consensus size: 64
1919381 AATTTAAAAC
1919391 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAA-AATTCTTATTTACACATC-AATT
1919456 A
64 A
* *
1919457 AACAAATCAACTTTTACAAATCAATTAAACAAGC-AAAAAAAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAAAATTCTTATTTACACATCAATTA
* *
1919520 AACAAATCAACTTTCAATGTATAATTCAATTAAACAAGCAAAAAAA
1 AACAAATCAAC-TT---T-TACAAATCAATTAAACAAGCAAAAAAA
1919566 GTGTACACCA
Statistics
Matches: 99, Mismatches: 4, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
63 16 0.16
64 18 0.18
65 6 0.06
66 34 0.34
67 1 0.01
68 18 0.18
69 6 0.06
ACGTcount: A:0.53, C:0.17, G:0.02, T:0.28
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAAAATTCTTATTTACACATCAATTA
Found at i:1920957 original size:42 final size:42
Alignment explanation
Indices: 1920911--1921013 Score: 145
Period size: 42 Copynumber: 2.5 Consensus size: 42
1920901 GCCGACGGGA
* *
1920911 CCTCTTGAATGATGATAGGGGCCTATTGAACGGTGGGAGGGG
1 CCTCTTGAATGATGATAGGGGCCTATTGAACGATAGGAGGGG
* * *
1920953 CCTCTTCG-ATGATGAGAGGGGCCTCTTGAACGATAGGAGGTG
1 CCTCTT-GAATGATGATAGGGGCCTATTGAACGATAGGAGGGG
1920995 CCTCTTGAATGATGATAGG
1 CCTCTTGAATGATGATAGG
1921014 TGCATCGGGC
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
41 1 0.02
42 51 0.96
43 1 0.02
ACGTcount: A:0.22, C:0.17, G:0.36, T:0.25
Consensus pattern (42 bp):
CCTCTTGAATGATGATAGGGGCCTATTGAACGATAGGAGGGG
Found at i:1921016 original size:21 final size:21
Alignment explanation
Indices: 1920911--1921009 Score: 103
Period size: 21 Copynumber: 4.7 Consensus size: 21
1920901 GCCGACGGGA
*
1920911 CCTCTTGAATGATGATAGGGG
1 CCTCTTGAATGATGAGAGGGG
* * * *
1920932 CCTATTGAACGGTGGGAGGGG
1 CCTCTTGAATGATGAGAGGGG
1920953 CCTCTTCG-ATGATGAGAGGGG
1 CCTCTT-GAATGATGAGAGGGG
* *
1920974 CCTCTTGAACGAT-AGGAGGTG
1 CCTCTTGAATGATGA-GAGGGG
1920995 CCTCTTGAATGATGA
1 CCTCTTGAATGATGA
1921010 TAGGTGCATC
Statistics
Matches: 62, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
20 2 0.03
21 58 0.94
22 2 0.03
ACGTcount: A:0.22, C:0.17, G:0.35, T:0.25
Consensus pattern (21 bp):
CCTCTTGAATGATGAGAGGGG
Found at i:1923185 original size:14 final size:14
Alignment explanation
Indices: 1923135--1923167 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1923125 TCGCAACACC
1923135 AAAATCGCAACGAG
1 AAAATCGCAACGAG
*
1923149 AAAATCGCAACGTG
1 AAAATCGCAACGAG
1923163 AAAAT
1 AAAAT
1923168 GAAAATCGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.52, C:0.18, G:0.18, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAG
Found at i:1923193 original size:19 final size:20
Alignment explanation
Indices: 1923148--1923195 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1923138 ATCGCAACGA
*
1923148 GAAAATCGCAACGTGAAAAT
1 GAAAATCGCAACGCGAAAAT
*
1923168 GAAAATCGCAACGCGAAACT
1 GAAAATCGCAACGCGAAAAT
1923188 -AAAATCGC
1 GAAAATCGC
1923196 GTTGCGATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.48, C:0.21, G:0.19, T:0.12
Consensus pattern (20 bp):
GAAAATCGCAACGCGAAAAT
Found at i:1923598 original size:22 final size:22
Alignment explanation
Indices: 1923567--1923618 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
1923557 AGATGGATAT
*
1923567 AGACGTATTTCGCCGGAGATGG
1 AGACGGATTTCGCCGGAGATGG
*
1923589 AGACGGATTTCGTCGGAGATGG
1 AGACGGATTTCGCCGGAGATGG
*
1923611 GGACGGAT
1 AGACGGAT
1923619 GTCACCGTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.23, C:0.15, G:0.40, T:0.21
Consensus pattern (22 bp):
AGACGGATTTCGCCGGAGATGG
Found at i:1923762 original size:20 final size:20
Alignment explanation
Indices: 1923734--1923821 Score: 97
Period size: 20 Copynumber: 4.3 Consensus size: 20
1923724 TGTATTTCGC
*
1923734 GTTGTGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
* **
1923754 GTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTG-ACTTTTGT
* *
1923775 GTTGCGAATTTGA-TTATCGC
1 GTTGCGAATTTGACTT-TTGT
1923795 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
1923815 GTTGCGA
1 GTTGCGA
1923822 TTTACATATT
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 2 0.04
20 35 0.62
21 19 0.34
ACGTcount: A:0.19, C:0.10, G:0.26, T:0.44
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTTGT
Found at i:1945979 original size:44 final size:45
Alignment explanation
Indices: 1945886--1945979 Score: 181
Period size: 45 Copynumber: 2.1 Consensus size: 45
1945876 CGAACCAAAC
1945886 GATTTTAGTGGTTAAGAGTATTGTTCTCATTTTTTTGAGATCTCG
1 GATTTTAGTGGTTAAGAGTATTGTTCTCATTTTTTTGAGATCTCG
1945931 GATTTTAGTGGTTAAGAGTATTGTTCTCA-TTTTTTGAGATCTCG
1 GATTTTAGTGGTTAAGAGTATTGTTCTCATTTTTTTGAGATCTCG
1945975 GATTT
1 GATTT
1945980 AAGCACCACA
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 20 0.41
45 29 0.59
ACGTcount: A:0.20, C:0.09, G:0.22, T:0.49
Consensus pattern (45 bp):
GATTTTAGTGGTTAAGAGTATTGTTCTCATTTTTTTGAGATCTCG
Found at i:1950617 original size:14 final size:14
Alignment explanation
Indices: 1950598--1950629 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1950588 CGTTCGTGAA
*
1950598 CGTTCGGTTATGTT
1 CGTTCGATTATGTT
1950612 CGTTCGATTATGTT
1 CGTTCGATTATGTT
1950626 CGTT
1 CGTT
1950630 TATGTTCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.16, G:0.25, T:0.50
Consensus pattern (14 bp):
CGTTCGATTATGTT
Found at i:1950626 original size:24 final size:24
Alignment explanation
Indices: 1950599--1950649 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
1950589 GTTCGTGAAC
*
1950599 GTTCGGTTATGTTCGTTCGA-TTAT
1 GTTCGGTTATGTTCATTC-ATTTAT
*
1950623 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGGTTATGTTCATTCATTTAT
1950647 GTT
1 GTT
1950650 TAACACAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.14, C:0.12, G:0.20, T:0.55
Consensus pattern (24 bp):
GTTCGGTTATGTTCATTCATTTAT
Found at i:1951844 original size:16 final size:16
Alignment explanation
Indices: 1951823--1951853 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1951813 AAAAAAAAAT
1951823 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1951839 TGTTCGTTTATGTTC
1 TGTTCGTTTATGTTC
1951854 TTTTATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1952203 original size:35 final size:35
Alignment explanation
Indices: 1952155--1952231 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
1952145 TCTAAATCCT
*
1952155 AAATTGAAGTATTTTAGAATTTTGGGTTTAAAATG
1 AAATTGAAGTATTTTAGAATTTGGGGTTTAAAATG
* * * *
1952190 TAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
1 AAATTGAAGTATTTTAGAATTTGGGGTTTAAAATG
1952225 AAATTGA
1 AAATTGA
1952232 GGACTATGTT
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:0.35, C:0.00, G:0.22, T:0.43
Consensus pattern (35 bp):
AAATTGAAGTATTTTAGAATTTGGGGTTTAAAATG
Found at i:1959521 original size:35 final size:35
Alignment explanation
Indices: 1959463--1959601 Score: 206
Period size: 35 Copynumber: 3.9 Consensus size: 35
1959453 TGAATAAGAA
* *
1959463 GAACGAAAGTAAGCATCGGCACTTTCGATTCAAGT
1 GAACGAAAGGAAGCATCGACACTTTCGATTCAAGT
* *
1959498 GAACAAAAGGAAGCATCGACACTTTCGATTCAAGAA
1 GAACGAAAGGAAGCATCGACACTTTCGATTCAAG-T
*
1959534 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAGT
1 GAACGAAAGGAAGCATCGACACTTTCGATTCAAGT
* *
1959569 GAACGGAAGGAAGCATCAACACTTTCGATTCAA
1 GAACGAAAGGAAGCATCGACACTTTCGATTCAA
1959602 TTGTTCATTT
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
35 61 0.66
36 32 0.34
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.19
Consensus pattern (35 bp):
GAACGAAAGGAAGCATCGACACTTTCGATTCAAGT
Found at i:1959579 original size:71 final size:71
Alignment explanation
Indices: 1959458--1959601 Score: 252
Period size: 71 Copynumber: 2.0 Consensus size: 71
1959448 GAAGGTGAAT
* *
1959458 AAGAAGAACGAAAGTAAGCATCGGCACTTTCGATTCAAGTGAACAAAAGGAAGCATCGACACTTT
1 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACAAAAGGAAGCATCAACACTTT
1959523 CGATTC
66 CGATTC
**
1959529 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACGGAAGGAAGCATCAACACTTT
1 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACAAAAGGAAGCATCAACACTTT
1959594 CGATTC
66 CGATTC
1959600 AA
1 AA
1959602 TTGTTCATTT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.19
Consensus pattern (71 bp):
AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACAAAAGGAAGCATCAACACTTT
CGATTC
Found at i:1961879 original size:216 final size:216
Alignment explanation
Indices: 1961500--1962104 Score: 938
Period size: 216 Copynumber: 2.8 Consensus size: 216
1961490 ATTTAAGAAT
* *
1961500 TAAAGTGAACAAATATGAAATTATAAATAAAAATTTAAATAAATTAAA-AAGCACACATTGATGA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAA-CACACATTGATGA
*
1961564 GGGATCAAATCGAAATAATTTTAAATTATGAGGATGAAATTAATACAAAAAAGTACTAAATTATA
65 GGGATCAAATCGAAATAATTTTAAATTATGAGGTTGAAATTAATACAAAAAAGTACTAAATTATA
* * * *
1961629 CACATTTAAAAAGTTTTGGGCCAATTAAAAAATAGAATTAAGTAATAAGTATGGATCAATATCAT
130 CACATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGATCAATATCAG
1961694 ATGCAAATAAAATTTGGAGGAC
195 ATGCAAATAAAATTTGGAGGAC
1961716 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
* * *
1961781 GGATCAAATCGAACTAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATAC
66 GGATCAAATCGAAATAATTTTAAATTATGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
* * * * *
1961846 CCATTTAAAAAGTTATAGGTCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGA
131 ACATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGATCAATATCAGA
1961911 TGCAAATAAAATTTGGAGGAC
196 TGCAAATAAAATTTGGAGGAC
* *
1961932 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATATATTAAACAACACA-A---A--AA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
* * *
1961991 GGATCAAATCAAAATAATTTAAAATTTTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
66 GGATCAAATCGAAATAATTTTAAATTATGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
* *
1962056 TCATTTAAAAAGTTATGGGCCAA-TTAATAAATATAAATAAGTAATAAGT
131 ACATTTAAAAAGTTATGGGCCAATTTAA-AAATAGAAATAAGTAATAAGT
1962105 TGAGAAAAAA
Statistics
Matches: 361, Mismatches: 26, Indels: 10
0.91 0.07 0.03
Matches are distributed among these distances:
209 4 0.01
210 101 0.28
212 1 0.00
215 1 0.00
216 252 0.70
217 2 0.01
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.29
Consensus pattern (216 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
GGATCAAATCGAAATAATTTTAAATTATGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
ACATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGATCAATATCAGA
TGCAAATAAAATTTGGAGGAC
Found at i:1962134 original size:2 final size:2
Alignment explanation
Indices: 1962129--1962219 Score: 78
Period size: 2 Copynumber: 44.0 Consensus size: 2
1962119 AAAACAACTA
* *
1962129 AT AT AT AT AT AT AT AT AT AT A- AT AT AA ACT AT AT AGT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT
* * *
1962172 AT AA AGT AT AT AT AT -T AT AT AT AT AA ACT AT AT AGT TT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT
1962214 AT AT AT
1 AT AT AT
1962220 TATGTATAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
1 2 0.03
2 65 0.90
3 5 0.07
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1962185 original size:42 final size:42
Alignment explanation
Indices: 1962134--1962216 Score: 148
Period size: 42 Copynumber: 1.9 Consensus size: 42
1962124 AACTAATATA
1962134 TATATATATATATATAATATAAACTATATAGTTTATATATAAAG
1 TATATATAT-TATAT-ATATAAACTATATAGTTTATATATAAAG
1962178 TATATATATTATATATATAAACTATATAGTTTATATATA
1 TATATATATTATATATATAAACTATATAGTTTATATATA
1962217 TATTATGTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
42 25 0.64
43 5 0.13
44 9 0.23
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (42 bp):
TATATATATTATATATATAAACTATATAGTTTATATATAAAG
Found at i:1962190 original size:9 final size:9
Alignment explanation
Indices: 1962130--1962195 Score: 53
Period size: 9 Copynumber: 7.0 Consensus size: 9
1962120 AAACAACTAA
1962130 TATATATAT
1 TATATATAT
1962139 ATATATATAT
1 -TATATATAT
* * *
1962149 AATATAAAC
1 TATATATAT
1962158 TATATAGT-T
1 TATATA-TAT
*
1962167 TATATATAAAG
1 TATATAT--AT
1962178 TATATATAT
1 TATATATAT
1962187 TATATATAT
1 TATATATAT
1962196 AAACTATATA
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
8 1 0.02
9 27 0.61
10 9 0.20
11 7 0.16
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (9 bp):
TATATATAT
Found at i:1962217 original size:22 final size:21
Alignment explanation
Indices: 1962136--1962218 Score: 105
Period size: 22 Copynumber: 3.9 Consensus size: 21
1962126 CTAATATATA
*
1962136 TATATATATATATAATATAAAC
1 TATATATTTATAT-ATATAAAC
* *
1962158 TATATAGTT-TATATATAAAG
1 TATATATTTATATATATAAAC
1962178 TATATATATTATATATATAAAC
1 TATATAT-TTATATATATAAAC
1962200 TATATAGTTTATATATATA
1 TATATA-TTTATATATATA
1962219 TTATGTATAA
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
20 13 0.25
21 5 0.09
22 34 0.64
23 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (21 bp):
TATATATTTATATATATAAAC
Found at i:1962227 original size:22 final size:21
Alignment explanation
Indices: 1962129--1962219 Score: 91
Period size: 20 Copynumber: 4.4 Consensus size: 21
1962119 AAAACAACTA
*
1962129 ATATATATATATATA-TATAT
1 ATATATATATATATAGTTTAT
*
1962149 A-ATATAAACTATATAGTTTAT
1 ATATATATA-TATATAGTTTAT
*
1962170 ATATAAAGTATATATA--TTAT
1 ATATATA-TATATATAGTTTAT
*
1962190 ATATATAAACTATATAGTTTAT
1 ATATATATA-TATATAGTTTAT
1962212 ATATATAT
1 ATATATAT
1962220 TATGTATAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
19 7 0.12
20 23 0.40
21 5 0.09
22 21 0.37
23 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.46
Consensus pattern (21 bp):
ATATATATATATATAGTTTAT
Found at i:1962327 original size:11 final size:11
Alignment explanation
Indices: 1962313--1962350 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1962303 ACTACATAGT
1962313 TTATATATAAA
1 TTATATATAAA
1962324 TTATATA-AGAA
1 TTATATATA-AA
1962335 TTATATATAAA
1 TTATATATAAA
*
1962346 CTATA
1 TTATA
1962351 CAATTTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
10 1 0.04
11 22 0.92
12 1 0.04
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (11 bp):
TTATATATAAA
Found at i:1962430 original size:22 final size:22
Alignment explanation
Indices: 1962314--1962430 Score: 87
Period size: 22 Copynumber: 5.3 Consensus size: 22
1962304 CTACATAGTT
**
1962314 TATATATAAATTATATAAGAAT-
1 TATATATAAATTATAT-AGTTTA
* * *
1962336 TATATATAAACTATACAATTTA
1 TATATATAAATTATATAGTTTA
* * * * *
1962358 TATTTAT-ATTTAAATAATATA
1 TATATATAAATTATATAGTTTA
*
1962379 TATTGTATAAATTATATAGTTTA
1 TA-TATATAAATTATATAGTTTA
1962402 T-TAATATAAATTATATAGTTTA
1 TAT-ATATAAATTATATAGTTTA
1962424 TATATAT
1 TATATAT
1962431 GTGTGTGGCT
Statistics
Matches: 73, Mismatches: 17, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
21 14 0.19
22 47 0.64
23 12 0.16
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (22 bp):
TATATATAAATTATATAGTTTA
Found at i:1962534 original size:33 final size:32
Alignment explanation
Indices: 1962497--1962691 Score: 103
Period size: 33 Copynumber: 5.6 Consensus size: 32
1962487 ATTTATATAC
1962497 TATATATATGAACTATAGTTTACATATGAATTA
1 TATATATAT-AACTATAGTTTACATATGAATTA
* *
1962530 TATATATA-AA-TATA-TATATATACT-AAGGTTAA
1 TATATATATAACTATAGTTTACATA-TGAA--TT-A
*
1962562 TATTTATATATGAACTATAGTTTACATATAAACTATCGTTAA
1 TA--TATATAT-AACTATAGTTTACATAT-GA--A---TT-A
* *
1962604 TATTTACATATGAACTATAGTTTACATATGAACTA
1 TA--TATATAT-AACTATAGTTTACATATGAATTA
**
1962639 TATATATA-AACTATATAGTTTACATATGACCTA
1 TATATATATAAC--TATAGTTTACATATGAATTA
1962672 TATATATATATACTATAGTT
1 TATATATATA-ACTATAGTT
1962692 GATATTTATA
Statistics
Matches: 133, Mismatches: 10, Indels: 38
0.73 0.06 0.21
Matches are distributed among these distances:
29 8 0.06
30 5 0.04
31 7 0.05
32 3 0.02
33 47 0.35
34 7 0.05
35 5 0.04
36 3 0.02
37 5 0.04
38 6 0.05
39 2 0.02
41 2 0.02
42 33 0.25
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (32 bp):
TATATATATAACTATAGTTTACATATGAATTA
Found at i:1962585 original size:18 final size:18
Alignment explanation
Indices: 1962564--1962716 Score: 72
Period size: 18 Copynumber: 8.4 Consensus size: 18
1962554 AAGGTTAATA
1962564 TTTATATATGAACTATAG
1 TTTATATATGAACTATAG
* * *
1962582 TTTACATATAAACTATCG
1 TTTATATATGAACTATAG
1962600 TTAATATTTACATATGAACTATAG
1 TT--TA--T--ATATGAACTATAG
*
1962624 TTTACATATGAACTATA-
1 TTTATATATGAACTATAG
1962641 --TATATA--AACTATATAG
1 TTTATATATGAAC--TATAG
* *
1962657 TTTACATATGACCTATA-
1 TTTATATATGAACTATAG
*
1962674 TATATATAT--ACTATAG
1 TTTATATATGAACTATAG
*
1962690 TTGATATTTAT-ATACTATAG
1 TT--TATATATGA-ACTATAG
1962710 TTTATAT
1 TTTATAT
1962717 TTATATACTA
Statistics
Matches: 101, Mismatches: 16, Indels: 36
0.66 0.10 0.24
Matches are distributed among these distances:
13 3 0.03
15 14 0.14
16 1 0.01
17 7 0.07
18 48 0.48
20 13 0.13
22 2 0.02
24 13 0.13
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (18 bp):
TTTATATATGAACTATAG
Found at i:1962603 original size:42 final size:42
Alignment explanation
Indices: 1962557--1962639 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
1962547 ATATACTAAG
*
1962557 GTTAATATTTATATATGAACTATAGTTTACATATAAACTATC
1 GTTAATATTTACATATGAACTATAGTTTACATATAAACTATC
*
1962599 GTTAATATTTACATATGAACTATAGTTTACATATGAACTAT
1 GTTAATATTTACATATGAACTATAGTTTACATATAAACTAT
1962640 ATATATAAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (42 bp):
GTTAATATTTACATATGAACTATAGTTTACATATAAACTATC
Found at i:1962677 original size:2 final size:2
Alignment explanation
Indices: 1962670--1962764 Score: 59
Period size: 2 Copynumber: 44.0 Consensus size: 2
1962660 ACATATGACC
* *
1962670 TA TA TA TA TA TA TA CTA TA GT- TGA TA TT TA TA TA CTA TA GTT TA
1 TA TA TA TA TA TA TA -TA TA -TA T-A TA TA TA TA TA -TA TA -TA TA
* *
1962714 TA TT TA TA TA CTA TA TA T- TA TA TA TA TA AA CTA TA TA TA CTA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA
1962756 TA TA GTA TA
1 TA TA -TA TA
1962765 GAGAAAATCG
Statistics
Matches: 74, Mismatches: 8, Indels: 22
0.71 0.08 0.21
Matches are distributed among these distances:
1 2 0.03
2 58 0.78
3 14 0.19
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1962734 original size:20 final size:20
Alignment explanation
Indices: 1962672--1962748 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
1962662 ATATGACCTA
1962672 TATATATATATACTATAGTT
1 TATATATATATACTATAGTT
* *
1962692 GATATTTATATACTATAGTT
1 TATATATATATACTATAGTT
*
1962712 TATATTTATATACTATA-TAT
1 TATATATATATACTATAGT-T
*
1962732 TATATATATAAACTATA
1 TATATATATATACTATA
1962749 TATACTATAT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
19 1 0.02
20 50 0.98
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (20 bp):
TATATATATATACTATAGTT
Found at i:1962759 original size:20 final size:20
Alignment explanation
Indices: 1962637--1962751 Score: 75
Period size: 20 Copynumber: 6.0 Consensus size: 20
1962627 ACATATGAAC
1962637 TATATATATAAACTATATAGT
1 TATATATATAAACTATATA-T
* * *
1962658 T-TACATAT-GAC-CTATA-
1 TATATATATAAACTATATAT
1962674 TATATATAT--ACTATAGT-T
1 TATATATATAAACTATA-TAT
* * *
1962692 GATATTTATATACTATAGT-T
1 TATATATATAAACTATA-TAT
* *
1962712 TATATTTATATACTATATAT
1 TATATATATAAACTATATAT
1962732 TATATATATAAACTATATAT
1 TATATATATAAACTATATAT
1962752 ACTATATAGT
Statistics
Matches: 77, Mismatches: 10, Indels: 15
0.75 0.10 0.15
Matches are distributed among these distances:
16 3 0.04
17 8 0.10
18 12 0.16
19 3 0.04
20 50 0.65
21 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (20 bp):
TATATATATAAACTATATAT
Found at i:1962983 original size:21 final size:21
Alignment explanation
Indices: 1962866--1963000 Score: 71
Period size: 21 Copynumber: 6.6 Consensus size: 21
1962856 ACACGAAATA
**
1962866 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
1962886 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
*
1962906 AAAATCGCAACGCGATTCTT-G
1 AAAATCGCAACGCGATT-TTCC
* ** *
1962927 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGATTTTCC
* **
1962948 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTTCC
* * * *
1962969 AGAATCGCAACGCGAATAT-G
1 AAAATCGCAACGCGATTTTCC
1962989 AAAATCGCAACG
1 AAAATCGCAACG
1963001 TGAACACATA
Statistics
Matches: 84, Mismatches: 27, Indels: 8
0.71 0.23 0.07
Matches are distributed among these distances:
19 1 0.01
20 35 0.42
21 46 0.55
22 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (21 bp):
AAAATCGCAACGCGATTTTCC
Found at i:1963018 original size:40 final size:40
Alignment explanation
Indices: 1962971--1963160 Score: 112
Period size: 40 Copynumber: 4.8 Consensus size: 40
1962961 GATTTTCCAG
* *
1962971 AATCGCAACGCGAATATGAAAATCGCAACGTG-AACACATA
1 AATCGCAACGCGAATACGAAAACCGCAACGTGTAAC-CATA
* * * * * *
1963011 AATCGCAATGCGTATCCGTAAACCGCAACGTGTATCCGTA
1 AATCGCAACGCGAATACGAAAACCGCAACGTGTAACCATA
* * * * * * * *
1963051 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAAAACCGCAACGTGTAACCATA
* * * * * * * *
1963091 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAAAACCGCAACGTGTAACCATA
* * * *
1963131 AATCGCAACGCGTATCCGTAAATCGCAACG
1 AATCGCAACGCGAATACGAAAACCGCAACG
1963161 ACAATACGTA
Statistics
Matches: 136, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 134 0.99
41 2 0.01
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (40 bp):
AATCGCAACGCGAATACGAAAACCGCAACGTGTAACCATA
Found at i:1963032 original size:20 final size:20
Alignment explanation
Indices: 1963009--1963203 Score: 293
Period size: 20 Copynumber: 9.7 Consensus size: 20
1962999 CGTGAACACA
*
1963009 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCGTATCCG
* *
1963029 TAAACCGCAACGTGTATCCG
1 TAAATCGCAACGCGTATCCG
1963049 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
1963069 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCGTATCCG
1963089 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
1963109 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCGTATCCG
1963129 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
* *
1963149 TAAATCGCAACGAC-AATACG
1 TAAATCGCAACG-CGTATCCG
*
1963169 TAAAATCGAAACGCGTATCCG
1 T-AAATCGCAACGCGTATCCG
1963190 TAAATCGCAACGCG
1 TAAATCGCAACGCG
1963204 ATTTTTAAAG
Statistics
Matches: 157, Mismatches: 15, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
20 141 0.90
21 16 0.10
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (20 bp):
TAAATCGCAACGCGTATCCG
Found at i:1963054 original size:60 final size:59
Alignment explanation
Indices: 1962971--1963199 Score: 255
Period size: 60 Copynumber: 3.8 Consensus size: 59
1962961 GATTTTCCAG
* ** * * *
1962971 AATCGCAACGCGAATATGAAAATCGCAACGTGAACACATAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGTGATC-CGTAAATCGCAATGCGTATCCGTA
* * *
1963031 AACCGCAACGTGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGTG-ATCCGTAAATCGCAATGCGTATCCGTA
*
1963091 AATCGCAACGCGTATCCGTAAATCGCAATGCGT-ATCCGTAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAA--CGTGATCCGTAAATCGCAATGCGTATCCGTA
* * * *
1963151 AATCGCAACGAC-AATACGTAAAATCGAAACGCGTATCCGTAAATCGCAA
1 AATCGCAACG-CGTATCCGT-AAATCGCAACGTG-ATCCGTAAATCGCAA
1963200 CGCGATTTTT
Statistics
Matches: 145, Mismatches: 17, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
59 2 0.01
60 115 0.79
61 26 0.18
62 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (59 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGTGATCCGTAAATCGCAATGCGTATCCGTA
Found at i:1963611 original size:33 final size:33
Alignment explanation
Indices: 1963572--1963642 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1963562 TTCACTTAGA
*
1963572 TTTCATTTCGTGTTGCGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTGCGATTCTCTCGTTGCGAT
*
1963605 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTGCGATTCTCTCGTTGCGAT
1963638 TTTCA
1 TTTCA
1963643 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.10, C:0.23, G:0.18, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTGCGATTCTCTCGTTGCGAT
Found at i:1963748 original size:21 final size:21
Alignment explanation
Indices: 1963722--1963811 Score: 114
Period size: 21 Copynumber: 4.4 Consensus size: 21
1963712 TGCAGAAGAG
1963722 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
* **
1963743 TCGCAACGCGA-AAATGACTA
1 TCGCAACGAGAGAAATGAAAA
1963763 TCTGCAACGAGAGAAATGAAAA
1 TC-GCAACGAGAGAAATGAAAA
*
1963785 TCGCAAC--GCGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
1963804 TCGCAACG
1 TCGCAACG
1963812 CGAAACCAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
19 18 0.31
20 9 0.15
21 23 0.39
22 9 0.15
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:1963799 original size:19 final size:19
Alignment explanation
Indices: 1963733--1963827 Score: 109
Period size: 19 Copynumber: 4.8 Consensus size: 19
1963723 CGCAACGAGA
1963733 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
1963752 GAAAATGACTATCTGCAACGAGA
1 G-AAATGAAAATC-GCAAC--GC
1963775 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1963794 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
**
1963813 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
1963828 TTGCGATTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
19 34 0.53
20 9 0.14
21 10 0.16
22 9 0.14
23 2 0.03
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1963845 original size:19 final size:19
Alignment explanation
Indices: 1963823--1963950 Score: 87
Period size: 19 Copynumber: 7.1 Consensus size: 19
1963813 GAAACCAAAA
*
1963823 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1963842 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1963856 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1963875 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1963889 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* **
1963909 CTCTCGTTGCGATAGTCATT
1 -TCGCGTTGCGATTTTCATT
* *
1963929 CTCTCGTTACGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1963949 TC
1 TC
1963951 AACCAAAAGA
Statistics
Matches: 88, Mismatches: 9, Indels: 24
0.73 0.07 0.20
Matches are distributed among these distances:
14 20 0.23
16 6 0.07
17 6 0.07
19 22 0.25
20 19 0.22
21 15 0.17
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1963864 original size:14 final size:14
Alignment explanation
Indices: 1963845--1963901 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1963835 TTTCATTTCG
1963845 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1963859 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1963878 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1963892 CGTTGCGATT
1 CGTTGCGATT
1963902 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1963870 original size:33 final size:33
Alignment explanation
Indices: 1963828--1963909 Score: 164
Period size: 33 Copynumber: 2.5 Consensus size: 33
1963818 CAAAATCGCA
1963828 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1963861 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1963894 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1963910 TCTCGTTGCG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.10, C:0.23, G:0.20, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1963912 original size:21 final size:21
Alignment explanation
Indices: 1963886--1963950 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
1963876 CGCGTTGCGA
1963886 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
**
1963907 TTCTCTCGTTGCGATAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
*
1963927 TTCTCTCGTTACGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
1963948 TTC
1 TTC
1963951 AACCAAAAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
20 17 0.45
21 21 0.55
ACGTcount: A:0.12, C:0.25, G:0.14, T:0.49
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1963947 original size:20 final size:20
Alignment explanation
Indices: 1963852--1963948 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
1963842 TCGCGTTGCG
1963852 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1963872 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
1963885 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
**
1963905 ATTTCTCTCGTTGCGATAGTC
1 A-TTCTCTCGTTGCGATTTTC
*
1963926 ATTCTCTCGTTACGATTTTC
1 ATTCTCTCGTTGCGATTTTC
1963946 ATT
1 ATT
1963949 TCAACCAAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
13 3 0.05
14 9 0.15
19 9 0.15
20 23 0.37
21 18 0.29
ACGTcount: A:0.12, C:0.24, G:0.16, T:0.47
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:1965916 original size:19 final size:19
Alignment explanation
Indices: 1965876--1966004 Score: 134
Period size: 19 Copynumber: 7.3 Consensus size: 19
1965866 TAGTTTACTT
* *
1965876 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1965896 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1965915 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1965934 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1965948 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1965967 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAACCAAAA
1965981 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1966000 TCGCA
1 TCGCA
1966005 TTGCGGTTTT
Statistics
Matches: 92, Mismatches: 7, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.22
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 47 0.51
20 13 0.14
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1965951 original size:14 final size:14
Alignment explanation
Indices: 1965930--1965988 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
1965920 ACGCGAAATG
1965930 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1965944 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
1965963 AAAATCGCAACGAC
1 AAAATCGCAACGAC
1965977 AAAATCGCAACG
1 AAAATCGCAACG
1965989 CGAAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.47, C:0.29, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1965955 original size:33 final size:33
Alignment explanation
Indices: 1965910--1966004 Score: 163
Period size: 33 Copynumber: 2.9 Consensus size: 33
1965900 AACGCGAAAC
**
1965910 CAAAATCGCAACGCGAAATGAAAATCGCAACGA
1 CAAAATCGCAACGCGAAACCAAAATCGCAACGA
*
1965943 CAGAATCGCAACGCGAAACCAAAATCGCAACGA
1 CAAAATCGCAACGCGAAACCAAAATCGCAACGA
1965976 CAAAATCGCAACGCGAAACCAAAATCGCA
1 CAAAATCGCAACGCGAAACCAAAATCGCA
1966005 TTGCGGTTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.07
Consensus pattern (33 bp):
CAAAATCGCAACGCGAAACCAAAATCGCAACGA
Done.