Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008480.1 Hibiscus syriacus cultivar Beakdansim tig00111311_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: 2515485
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 13
Found at i:1873903 original size:13 final size:14
Alignment explanation
Indices: 1873887--1873944 Score: 50
Period size: 13 Copynumber: 4.3 Consensus size: 14
1873877 ACATTTGCAT
1873887 ATTTGCAT-TTTAC
1 ATTTGCATCTTTAC
*
1873900 ATTTGCATCTTTTC
1 ATTTGCATCTTTAC
1873914 ATTTTGCA-C-TTAC
1 A-TTTGCATCTTTAC
* * *
1873927 ATTCGTATCTTTGC
1 ATTTGCATCTTTAC
1873941 ATTT
1 ATTT
1873945 AACATTCGCA
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
12 4 0.11
13 13 0.37
14 12 0.34
15 6 0.17
ACGTcount: A:0.19, C:0.19, G:0.09, T:0.53
Consensus pattern (14 bp):
ATTTGCATCTTTAC
Found at i:1873917 original size:21 final size:21
Alignment explanation
Indices: 1873869--1873918 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1873859 ATTCGCATTC
*
1873869 TGCATTCTACATTTGCATATT
1 TGCATTTTACATTTGCATATT
*
1873890 TGCATTTTACATTTGCATCTT
1 TGCATTTTACATTTGCATATT
*
1873911 TTCATTTT
1 TGCATTTT
1873919 GCACTTACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.20, C:0.18, G:0.08, T:0.54
Consensus pattern (21 bp):
TGCATTTTACATTTGCATATT
Found at i:1875180 original size:180 final size:181
Alignment explanation
Indices: 1874853--1875196 Score: 471
Period size: 180 Copynumber: 1.9 Consensus size: 181
1874843 AAAGGTTGAG
* *
1874853 GTAAAATGAGTGTAATGAAACGGGACCACTCCGCTGAAAATAGTAAGCTAATAAATTAAAGGTAA
1 GTAAAATGAGTGTAATAAAACGGGACCACTCCGCTGAAAACAGTAAGCTAATAAATTAAAGGTAA
* * * * * *
1874918 TTTCAAACAGTTATTGAGGTAAGTCTAAGCTTCATGAAGTGGTTATATTTAAACTGTGGCATTAA
66 TTTCAAACAGTTATTAAGGTAAATATAAGCTTCATGAAGTGGTTATATTCAAACTATGACATTAA
*
1874983 TTGTGACACGATGAATTTCCCGAGGTAAGAGAAATAAGCGAGAATAATGCA
131 TTGTAACACGATGAATTTCCCGAGGTAAGAGAAATAAGCGAGAATAATGCA
* * * *
1875034 GTAAAATGAGTGTAATAAAATGGG-CCACTCCGCT-AAAAGCATTAAGCTGATAAATTGAAGGTA
1 GTAAAATGAGTGTAATAAAACGGGACCACTCCGCTGAAAA-CAGTAAGCTAATAAATTAAAGGTA
* *
1875097 ATTTCAAACA-TCTATTAAGGTAAATATATGTTTCATGAAGTGGTTATATTCAAA-TCATGACAT
65 ATTTCAAACAGT-TATTAAGGTAAATATAAGCTTCATGAAGTGGTTATATTCAAACT-ATGACAT
** *
1875160 TAATTGTAACGTGATGAATTTCCCGAGGTAAGGGAAA
128 TAATTGTAACACGATGAATTTCCCGAGGTAAGAGAAA
1875197 AAAACAAAAG
Statistics
Matches: 142, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
179 6 0.04
180 114 0.80
181 22 0.15
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (181 bp):
GTAAAATGAGTGTAATAAAACGGGACCACTCCGCTGAAAACAGTAAGCTAATAAATTAAAGGTAA
TTTCAAACAGTTATTAAGGTAAATATAAGCTTCATGAAGTGGTTATATTCAAACTATGACATTAA
TTGTAACACGATGAATTTCCCGAGGTAAGAGAAATAAGCGAGAATAATGCA
Found at i:1876590 original size:74 final size:74
Alignment explanation
Indices: 1876469--1876683 Score: 324
Period size: 74 Copynumber: 2.9 Consensus size: 74
1876459 CCCAAACAAT
* *
1876469 ATGATATTTTTAAATGATTTTTTAAAGAAGCTAAGTCTGATTTTCAGAGGTTTCTTGATGATTAC
1 ATGATATTTTCAAATGAATTTTTAAAGAAGCTAAGTCTGATTTTCAGAGGTTTCTTGATGATTAC
1876534 TTGATTAAC
66 TTGATTAAC
*
1876543 ATGATATTTTCAAATGAATTTTTAAAGAAGCTAAGTTTGATTTTCAGAGGTTTCTTGATGATTAC
1 ATGATATTTTCAAATGAATTTTTAAAGAAGCTAAGTCTGATTTTCAGAGGTTTCTTGATGATTAC
1876608 TTGATTAAC
66 TTGATTAAC
* * * ** * *
1876617 GTGATGTTTTCAAATGAATTTTTAAAAAAGCTAAACCTGATTTTCA-AGGGTTTATTGATAATTA
1 ATGATATTTTCAAATGAATTTTTAAAGAAGCTAAGTCTGATTTTCAGA-GGTTTCTTGATGATTA
1876681 CTT
65 CTT
1876684 CAAATGAATT
Statistics
Matches: 129, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
73 1 0.01
74 128 0.99
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (74 bp):
ATGATATTTTCAAATGAATTTTTAAAGAAGCTAAGTCTGATTTTCAGAGGTTTCTTGATGATTAC
TTGATTAAC
Found at i:1876999 original size:17 final size:18
Alignment explanation
Indices: 1876948--1876989 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
1876938 AAAATGAAGA
1876948 GAAAAAAAACGAAA-AAAT
1 GAAAAAAAA-GAAATAAAT
1876966 GAAAAAAAAGAAATAAAT
1 GAAAAAAAAGAAATAAAT
1876984 GAAAAA
1 GAAAAA
1876990 TAATAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.07
Consensus pattern (18 bp):
GAAAAAAAAGAAATAAAT
Found at i:1877303 original size:16 final size:16
Alignment explanation
Indices: 1877282--1877326 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
1877272 TAATAAATAA
1877282 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1877298 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
*
1877314 ACAAACATAAACG
1 ACGAACATAAACG
1877327 TTGGAGACCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.58, C:0.22, G:0.11, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1878380 original size:14 final size:14
Alignment explanation
Indices: 1878363--1878416 Score: 80
Period size: 14 Copynumber: 4.1 Consensus size: 14
1878353 TGAACATAAG
1878363 CGAACATAACCGAA
1 CGAACATAACCGAA
1878377 CGAACAT-A---AA
1 CGAACATAACCGAA
1878387 CGAACATAACCGAA
1 CGAACATAACCGAA
1878401 CGAACATAACCGAA
1 CGAACATAACCGAA
1878415 CG
1 CG
1878417 TTCACGAACG
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
10 9 0.25
11 1 0.03
13 1 0.03
14 25 0.69
ACGTcount: A:0.50, C:0.28, G:0.15, T:0.07
Consensus pattern (14 bp):
CGAACATAACCGAA
Found at i:1878426 original size:24 final size:24
Alignment explanation
Indices: 1878354--1878415 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
1878344 ATAAATGAAT
*
1878354 GAACATAAGCGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
1878378 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
*
1878402 GAACATAACCGAAC
1 GAACATAAACGAAC
1878416 GTTCACGAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.52, C:0.26, G:0.15, T:0.08
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:1886679 original size:43 final size:40
Alignment explanation
Indices: 1886589--1886696 Score: 103
Period size: 43 Copynumber: 2.6 Consensus size: 40
1886579 AAAATAAATC
* *
1886589 TAAA-TAATAATAATAATTTATTAATAAATTATAAAAAACAA
1 TAAATTAATAAT-ATTATTT-TTAATAAATAATAAAAAACAA
* **
1886630 TAAATTAACTAATCCATTATTTTTAATAAATAATAAAATATTA
1 TAAATTAA-TAAT--ATTATTTTTAATAAATAATAAAAAACAA
*
1886673 TTAATTAATAATATTA-TTTTAATA
1 TAAATTAATAATATTATTTTTAATA
1886697 CAAAAAACAC
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
39 8 0.14
40 4 0.07
41 4 0.07
42 7 0.12
43 28 0.49
44 6 0.11
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (40 bp):
TAAATTAATAATATTATTTTTAATAAATAATAAAAAACAA
Found at i:1886694 original size:18 final size:19
Alignment explanation
Indices: 1886645--1886696 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
1886635 TAACTAATCC
1886645 ATTATTTTTAATAAATAATAA
1 ATTA-TTTTAATAAATAAT-A
* *
1886666 AATATTATTAATTAATAAT-
1 ATTATT-TTAATAAATAATA
1886685 ATTATTTTAATA
1 ATTATTTTAATA
1886697 CAAAAAACAC
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
18 5 0.19
19 5 0.19
20 2 0.08
21 14 0.54
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTATTTTAATAAATAATA
Found at i:1889289 original size:21 final size:21
Alignment explanation
Indices: 1889222--1889292 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
1889212 CTTAAGGATC
* * *
1889222 ACATATATATTCCAAAAGACA
1 ACATATATGTTCCAAAGGACT
* * *
1889243 AAATATATGTCCCAAAGAACT
1 ACATATATGTTCCAAAGGACT
* *
1889264 GCATATATGTTCCAAAGGATT
1 ACATATATGTTCCAAAGGACT
1889285 ACATATAT
1 ACATATAT
1889293 ATCCCGAAGG
Statistics
Matches: 38, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.45, C:0.17, G:0.10, T:0.28
Consensus pattern (21 bp):
ACATATATGTTCCAAAGGACT
Found at i:1890106 original size:21 final size:21
Alignment explanation
Indices: 1890062--1890106 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1890052 CTTCCCATAA
* *
1890062 CATGGTGCATCGGTGCCCTAT
1 CATGGTGCATCGATCCCCTAT
1890083 CATGGTGCATCGATACCCCT-T
1 CATGGTGCATCGAT-CCCCTAT
1890104 CAT
1 CAT
1890107 TAAATTCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.18, C:0.31, G:0.22, T:0.29
Consensus pattern (21 bp):
CATGGTGCATCGATCCCCTAT
Found at i:1890179 original size:20 final size:20
Alignment explanation
Indices: 1890150--1890202 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1890140 GCAGCCTTCG
*
1890150 TGCATGGATGCACAACAGGA
1 TGCATCGATGCACAACAGGA
*
1890170 TGCATCGATGCACATCAGGA
1 TGCATCGATGCACAACAGGA
1890190 TGCATCGATGCAC
1 TGCATCGATGCAC
1890203 TAAGTGCATT
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:0.30, C:0.25, G:0.26, T:0.19
Consensus pattern (20 bp):
TGCATCGATGCACAACAGGA
Found at i:1890289 original size:21 final size:21
Alignment explanation
Indices: 1890222--1890320 Score: 114
Period size: 21 Copynumber: 4.7 Consensus size: 21
1890212 TCGAAATGGA
*
1890222 GTGCATGGATGCACTGCA-TG
1 GTGCATGGATGCACTGCAGGG
*
1890242 GTGCATCGATGCACT--AGTGCAG
1 GTGCATGGATGCACTGCAG-G--G
* *
1890264 GTGCATGGATGCATTGTAGGG
1 GTGCATGGATGCACTGCAGGG
1890285 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
1890306 GTGCATGGATGCACT
1 GTGCATGGATGCACT
1890321 TTGACACCCT
Statistics
Matches: 67, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
18 1 0.01
20 14 0.21
21 35 0.52
22 14 0.21
23 1 0.01
24 2 0.03
ACGTcount: A:0.20, C:0.18, G:0.37, T:0.24
Consensus pattern (21 bp):
GTGCATGGATGCACTGCAGGG
Found at i:1890572 original size:21 final size:21
Alignment explanation
Indices: 1890543--1890582 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1890533 ATGTTTAATG
1890543 AAAAAGATA-CAAATTGTTAAC
1 AAAAAGATATC-AATTGTTAAC
*
1890564 AAAATGATATCAATTGTTA
1 AAAAAGATATCAATTGTTA
1890583 CCAATTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATATCAATTGTTAAC
Found at i:1891739 original size:19 final size:20
Alignment explanation
Indices: 1891696--1891743 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1891686 TCTAAATCCT
*
1891696 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
1891716 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
1891735 TTTTCAAAA
1 TTTTCAAAA
1891744 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:1892686 original size:31 final size:32
Alignment explanation
Indices: 1892622--1892686 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 32
1892612 CCGGGCTAAA
*
1892622 CTAGAACCTTTCCCTAGCTTTTACACAGGATAAG
1 CTAGAACCTTTCCC-A-CTTTTACAAAGGATAAG
1892656 CTAGAACCTTTCCC-C-TTTACAAAAGGATAAG
1 CTAGAACCTTTCCCACTTTTAC-AAAGGATAAG
1892687 AGATGTAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 5 0.17
31 10 0.34
34 14 0.48
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.28
Consensus pattern (32 bp):
CTAGAACCTTTCCCACTTTTACAAAGGATAAG
Found at i:1893056 original size:20 final size:20
Alignment explanation
Indices: 1893026--1893138 Score: 172
Period size: 20 Copynumber: 5.7 Consensus size: 20
1893016 GCAGCCTTCG
* * *
1893026 TGCATAGATGCATAGCAGGA
1 TGCATCGATGCACATCAGGA
* *
1893046 TGCATCAATGCACAGCAGGA
1 TGCATCGATGCACATCAGGA
*
1893066 TGTATCGATGCACATCAGGA
1 TGCATCGATGCACATCAGGA
1893086 TGCATCGATGCACATCAGGA
1 TGCATCGATGCACATCAGGA
1893106 TGCATCGATGCACATCAGGA
1 TGCATCGATGCACATCAGGA
1893126 TGCATCGATGCAC
1 TGCATCGATGCAC
1893139 TAAGTGCATT
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 86 1.00
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.20
Consensus pattern (20 bp):
TGCATCGATGCACATCAGGA
Found at i:1893089 original size:12 final size:12
Alignment explanation
Indices: 1893072--1893129 Score: 60
Period size: 10 Copynumber: 5.5 Consensus size: 12
1893062 AGGATGTATC
1893072 GATGCACATCAG
1 GATGCACATCAG
1893084 GATG--CATC--
1 GATGCACATCAG
1893092 GATGCACATCAG
1 GATGCACATCAG
1893104 GATG--CATC--
1 GATGCACATCAG
1893112 GATGCACATCAG
1 GATGCACATCAG
1893124 GATGCA
1 GATGCA
1893130 TCGATGCACT
Statistics
Matches: 38, Mismatches: 0, Indels: 16
0.70 0.00 0.30
Matches are distributed among these distances:
8 8 0.21
10 16 0.42
12 14 0.37
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (12 bp):
GATGCACATCAG
Found at i:1893900 original size:14 final size:14
Alignment explanation
Indices: 1893881--1893907 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1893871 ACTGTCCTAA
1893881 TGGTATCGATACCT
1 TGGTATCGATACCT
1893895 TGGTATCGATACC
1 TGGTATCGATACC
1893908 CCTTGAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (14 bp):
TGGTATCGATACCT
Found at i:1904311 original size:37 final size:34
Alignment explanation
Indices: 1904262--1904519 Score: 149
Period size: 34 Copynumber: 7.5 Consensus size: 34
1904252 TATAAATATC
* **
1904262 TATATATTATATAGTTTGCAAATGATTTTTTGAAATA
1 TATATAATATATAGTTTGCAAA--ACATTTTGAAA-A
**
1904299 TATATAATATATAGTTTTTAAAACATTTTGAAAA
1 TATATAATATATAGTTTGCAAAACATTTTGAAAA
** * *
1904333 TATATAATATATAGTTTTTAAAACGTTTCGAAAACA
1 TATATAATATATAGTTTGCAAAACATTTTG-AAA-A
* **
1904369 TATATATTATATAGTTTTTTAAAACATTTT-AAAA
1 TATATAATATATAG-TTTGCAAAACATTTTGAAAA
**
1904403 -ATATACATAATATAGTTTTTAAAACATTTTTGAAAA
1 TATATA-AT-ATATAGTTTGCAAAACA-TTTTGAAAA
* *
1904439 -CTAT-ATA-AT--TTTG-AAAACATTTTTAAAAAA
1 TATATAATATATAGTTTGCAAAACA-TTTT-GAAAA
* * *
1904469 TATATAATATATAATTT-TAAATA-TTTTTGAAAA
1 TATATAATATATAGTTTGCAAA-ACATTTTGAAAA
*
1904502 TATATATTATATAAGTTT
1 TATATAATATAT-AGTTT
1904520 TTGGAAAATG
Statistics
Matches: 186, Mismatches: 19, Indels: 35
0.77 0.08 0.15
Matches are distributed among these distances:
29 11 0.06
30 7 0.04
31 3 0.02
32 5 0.03
33 23 0.12
34 52 0.28
35 31 0.17
36 22 0.12
37 32 0.17
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (34 bp):
TATATAATATATAGTTTGCAAAACATTTTGAAAA
Found at i:1904341 original size:34 final size:34
Alignment explanation
Indices: 1904289--1904521 Score: 216
Period size: 34 Copynumber: 6.8 Consensus size: 34
1904279 GCAAATGATT
1904289 TTTTGAAATATATATAATATATAGTTTTTAAAACA
1 TTTTGAAA-ATATATAATATATAGTTTTTAAAACA
*
1904324 TTTTGAAAATATATAATATATAGTTTTTAAAACG
1 TTTTGAAAATATATAATATATAGTTTTTAAAACA
* *
1904358 TTTCGAAAACATATATATTATATAGTTTTTTAAAACA
1 TTTTG-AAA-ATATATAATATATAG-TTTTTAAAACA
1904395 TTTT-AAAA-ATATACATAATATAGTTTTTAAAACA
1 TTTTGAAAATATATA-AT-ATATAGTTTTTAAAACA
* *
1904429 TTTTTG-AAA-A-CT-ATATA-A-TTTTGAAAACA
1 -TTTTGAAAATATATAATATATAGTTTTTAAAACA
* * *
1904458 TTTTTAAAAAATATATAATATATA-ATTTTAAATA-T
1 -TTTT-GAAAATATATAATATATAGTTTTTAAA-ACA
*
1904493 TTTTGAAAATATATATTATATAAGTTTTT
1 TTTTGAAAATATATAATATAT-AGTTTTT
1904522 GGAAAATGTT
Statistics
Matches: 166, Mismatches: 16, Indels: 32
0.78 0.07 0.15
Matches are distributed among these distances:
29 15 0.09
30 1 0.01
31 6 0.04
32 3 0.02
33 21 0.13
34 53 0.32
35 39 0.23
36 15 0.09
37 13 0.08
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.45
Consensus pattern (34 bp):
TTTTGAAAATATATAATATATAGTTTTTAAAACA
Found at i:1904346 original size:71 final size:67
Alignment explanation
Indices: 1904262--1904521 Score: 223
Period size: 71 Copynumber: 3.8 Consensus size: 67
1904252 TATAAATATC
* **
1904262 TATATATTATATAGTTTGCAAATGATTTTTTGAAATATATATAATATATAGTTTTTAAAACATTT
1 TATATAATATATAGTTTTTAAAT-A-TTTTTGAAA-ATATATAATATATAGTTTTTAAAACATTT
1904327 TGAAAA
63 T-AAAA
* * *
1904333 TATATAATATATAGTTTTTAAA-ACGTTTCGAAAACATATATATTATATAGTTTTTTAAAACATT
1 TATATAATATATAGTTTTTAAATA-TTTTTG-AAA-ATATATAATATATAG-TTTTTAAAACATT
1904397 TTAAAA
62 TTAAAA
* * *
1904403 -ATATACATAATATAGTTTTTAAAACATTTTTG-AAA-A-CT-ATATA-A-TTTTGAAAACATTT
1 TATATA-AT-ATATAGTTTTT-AAATATTTTTGAAAATATATAATATATAGTTTTTAAAACA-TT
1904461 TTAAAAAA
62 TT--AAAA
* *
1904469 TATATAATATATA-ATTTTAAATATTTTTGAAAATATATATTATATAAGTTTTT
1 TATATAATATATAGTTTTTAAATATTTTTGAAAATATATAATATAT-AGTTTTT
1904522 GGAAAATGTT
Statistics
Matches: 154, Mismatches: 18, Indels: 35
0.74 0.09 0.17
Matches are distributed among these distances:
63 20 0.13
64 11 0.07
65 7 0.05
66 11 0.07
67 10 0.06
68 1 0.01
69 12 0.08
70 29 0.19
71 45 0.29
72 7 0.05
73 1 0.01
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.46
Consensus pattern (67 bp):
TATATAATATATAGTTTTTAAATATTTTTGAAAATATATAATATATAGTTTTTAAAACATTTTAA
AA
Found at i:1904455 original size:29 final size:29
Alignment explanation
Indices: 1904412--1904476 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
1904402 AATATACATA
* * * *
1904412 ATATAGTTTTTAAAACATTTTTGAAAACT
1 ATATAATTTTGAAAACATTTTTAAAAAAT
1904441 ATATAATTTTGAAAACATTTTTAAAAAAT
1 ATATAATTTTGAAAACATTTTTAAAAAAT
1904470 ATATAAT
1 ATATAAT
1904477 ATATAATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (29 bp):
ATATAATTTTGAAAACATTTTTAAAAAAT
Found at i:1904476 original size:63 final size:61
Alignment explanation
Indices: 1904384--1904507 Score: 162
Period size: 63 Copynumber: 2.0 Consensus size: 61
1904374 ATTATATAGT
*
1904384 TTTTTAAAACATTTTAAAAATATACATAATATAGT-TTTTAAAACATTTTTGAAAACTATATAA
1 TTTTGAAAACATTTTAAAAATATACATAATATA-TATTTT-AAACATTTTTGAAAA-TATATAA
* *
1904447 TTTTGAAAACATTTTTAAAAA-ATATATAATATATAATTTTAAATATTTTTGAAAATATATA
1 TTTTGAAAACA-TTTTAAAAATATACATAATATAT-ATTTTAAACATTTTTGAAAATATATA
1904508 TTATATAAGT
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
62 7 0.13
63 35 0.64
64 13 0.24
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.44
Consensus pattern (61 bp):
TTTTGAAAACATTTTAAAAATATACATAATATATATTTTAAACATTTTTGAAAATATATAA
Found at i:1904573 original size:22 final size:22
Alignment explanation
Indices: 1904543--1904592 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
1904533 TTTATATATA
*
1904543 TATTATTATTATTATGGTTATT
1 TATTTTTATTATTATGGTTATT
* **
1904565 TATTTTTATTTTTATTTTTATT
1 TATTTTTATTATTATGGTTATT
1904587 TATTTT
1 TATTTT
1904593 CATTTTCTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (22 bp):
TATTTTTATTATTATGGTTATT
Found at i:1904579 original size:16 final size:15
Alignment explanation
Indices: 1904560--1904603 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
1904550 ATTATTATGG
1904560 TTATTTATTTTTATTT
1 TTATTT-TTTTTATTT
1904576 TTATTTTTATTTATTT
1 TTATTTTT-TTTATTT
*
1904592 TCATTTTCTTTT
1 TTATTTT-TTTT
1904604 CCAGGTCCAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 2 0.08
16 22 0.88
17 1 0.04
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.80
Consensus pattern (15 bp):
TTATTTTTTTTATTT
Found at i:1904587 original size:6 final size:6
Alignment explanation
Indices: 1904563--1904587 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1904553 ATTATGGTTA
1904563 TTTATT TTTATT TTTATT TTTATT T
1 TTTATT TTTATT TTTATT TTTATT T
1904588 ATTTTCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTATT
Found at i:1905320 original size:24 final size:23
Alignment explanation
Indices: 1905277--1905321 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
1905267 CGCCGGTTTT
*
1905277 AAAGGTAATAATCTCCATCGATC
1 AAAGGTAATAATCTCAATCGATC
1905300 AAAGGTAAGTAAT-TCGAATCGA
1 AAAGGTAA-TAATCTC-AATCGA
1905322 ATGTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (23 bp):
AAAGGTAATAATCTCAATCGATC
Found at i:1906364 original size:21 final size:20
Alignment explanation
Indices: 1906325--1906362 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1906315 AGATTACGCA
1906325 GGGGGTACAGATTCCCCCTG
1 GGGGGTACAGATTCCCCCTG
1906345 GGGGGTATC-GATTCCCCC
1 GGGGGTA-CAGATTCCCCC
1906363 CTAATGGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.13, C:0.32, G:0.34, T:0.21
Consensus pattern (20 bp):
GGGGGTACAGATTCCCCCTG
Found at i:1909882 original size:34 final size:36
Alignment explanation
Indices: 1909824--1909892 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 36
1909814 TCCTGTTTGG
*
1909824 ACTTGTTTTATGAACTTTCTCATA-TTCTTTTTTAA
1 ACTTGTTTTATGAACTTTCACATATTTCTTTTTTAA
*
1909859 ACTTGTTTT-TGAACTTTGACATATTTCTTTTTTA
1 ACTTGTTTTATGAACTTTCACATATTTCTTTTTTA
1909893 TGAGGATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 12 0.39
35 19 0.61
ACGTcount: A:0.22, C:0.13, G:0.07, T:0.58
Consensus pattern (36 bp):
ACTTGTTTTATGAACTTTCACATATTTCTTTTTTAA
Found at i:1910400 original size:6 final size:7
Alignment explanation
Indices: 1910390--1910439 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 7
1910380 GTATACCCAA
1910390 ATTATA-
1 ATTATAT
1910396 ATTATAT
1 ATTATAT
1910403 ATATATAT
1 AT-TATAT
1910411 ATATATAT
1 AT-TATAT
1910419 ATTATAT
1 ATTATAT
1910426 A-TATAT
1 ATTATAT
1910432 A-TATAT
1 ATTATAT
1910438 AT
1 AT
1910440 ACACAATAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
6 18 0.44
7 8 0.20
8 15 0.37
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
ATTATAT
Found at i:1910405 original size:2 final size:2
Alignment explanation
Indices: 1910398--1910440 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1910388 AAATTATAAT
1910398 TA TA TA TA TA TA TA TA TA TA TA T- 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
1910439 TA
1 TA
1910441 CACAATAAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1910615 original size:95 final size:95
Alignment explanation
Indices: 1910433--1910689 Score: 293
Period size: 95 Copynumber: 2.7 Consensus size: 95
1910423 TATATATATA
* * * *
1910433 TATATATACACAATAAAGCTTGAGTTATCCCTCTAGAGCGATTGGTTAAACGCCCC-GACTTCAA
1 TATA-ATATACAATAAAGCTTGAGTTATCCCTCTAGAGCAATTGGTTAAACGCCCCAG-CTTTAT
*
1910497 GGATAAGATTCAGCTAGCCTGATAAAGGCGAT
64 GGATAAGATTCAACTAGCCTGATAAAGGCGAT
1910529 TATAATATACAATAAAGCTTGAGTTATCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTATGG
1 TATAATATACAATAAAGCTTGAGTTATCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTATGG
* ** *
1910594 ATAATATTCAACTAGTTTGATAAAGGTGAT
66 ATAAGATTCAACTAGCCTGATAAAGGCGAT
* * * ** * * *
1910624 TATAATAT-CTATACAATGATATTAAACTGTCCCTCTAGAGCAATTGGTTAAACGCACCAGATTT
1 TATAATATACAATA-AA-G--CTTGAGTTATCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTT
1910688 AT
62 AT
1910690 AGATTCAGCT
Statistics
Matches: 139, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
94 4 0.03
95 90 0.65
96 6 0.04
98 39 0.28
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (95 bp):
TATAATATACAATAAAGCTTGAGTTATCCCTCTAGAGCAATTGGTTAAACGCCCCAGCTTTATGG
ATAAGATTCAACTAGCCTGATAAAGGCGAT
Found at i:1912463 original size:372 final size:373
Alignment explanation
Indices: 1912031--1912728 Score: 1150
Period size: 372 Copynumber: 1.9 Consensus size: 373
1912021 CAATACAAGC
*
1912031 TTGGATTTCAACTTCACAACGAAGGATATTCAAGTCAATGATCAACTTCACAACGAAGGGGCCAT
1 TTGGATTTCAACTTCACAACGAAGGATATTCAAGTCAAGGATCAACTTCACAACGAAGGGGCCAT
* * *
1912096 CCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGTAACATTCATCTTTAAGATTGGA
66 CCACGGTTTCAACTTCACAACGAAGGGAATCGTGCTCACCAGCAACATTCATATTTAAGATTGGA
*
1912161 TTTCAACTTCACGATGAATGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATACACG
131 TTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATACACG
* *
1912226 GTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAATGACATTCATCTTTAGATTGGATTTAAA
196 ATTTCAACTTCACGACAAAGGGAATCGTGCTCACCAATGACATTCATCTTTAGATTGGATTTAAA
*
1912291 CTTCACGATGAACG-ATATCCAATTCAAGGC-TAACTTCACAACGAATGGGCTATCCACAGTTTC
261 CTTCACGATGAA-GAATATCCAATTCAAGGCTTAACTTCACAACGAATGGGCCATCCACAGTTTC
1912354 AACTTCATGACGAAGGGAATCGTGCTCACCAGCAACATTCCTCTTTAGA
325 AACTTCATGACGAAGGGAATCGTGCTCACCAGCAACATTCCTCTTTAGA
* * * * *
1912403 TTGGATTTCAACTTCACGATGAAGGATATAT-AATTCAAGGCTCAACTTCACAACGAAGGGGCTA
1 TTGGATTTCAACTTCACAACGAAGGATAT-TCAAGTCAAGGATCAACTTCACAACGAAGGGGCCA
*
1912467 TCCACTGTTTCAACTTCACAACGAAGGGAATCGTGCTCACCAGCAACATTCATATTTAAGATTGG
65 TCCACGGTTTCAACTTCACAACGAAGGGAATCGTGCTCACCAGCAACATTCATATTTAAGATTGG
* * * *
1912532 ATTTTAACTTCACGATGAAGGATATCCAATTTAAGGCTCAACTTCACAACGAATGGGCCATCCAC
130 ATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATACAC
* *
1912597 GATTTCAACTTCACGACAAAGGGAATCGTGCTCACCAGTGACATTCATCTTTAGATTGGATTTCA
195 GATTTCAACTTCACGACAAAGGGAATCGTGCTCACCAATGACATTCATCTTTAGATTGGATTTAA
* **
1912662 ACTTCACGATGAAGAATATCCAATTCAAGGCTTAACTTCATAACGAATGGGCCATCCATGGTTTC
260 ACTTCACGATGAAGAATATCCAATTCAAGGCTTAACTTCACAACGAATGGGCCATCCACAGTTTC
1912727 AA
325 AA
1912729 ATCCTGAATA
Statistics
Matches: 300, Mismatches: 23, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
371 1 0.00
372 267 0.89
373 32 0.11
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (373 bp):
TTGGATTTCAACTTCACAACGAAGGATATTCAAGTCAAGGATCAACTTCACAACGAAGGGGCCAT
CCACGGTTTCAACTTCACAACGAAGGGAATCGTGCTCACCAGCAACATTCATATTTAAGATTGGA
TTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATACACG
ATTTCAACTTCACGACAAAGGGAATCGTGCTCACCAATGACATTCATCTTTAGATTGGATTTAAA
CTTCACGATGAAGAATATCCAATTCAAGGCTTAACTTCACAACGAATGGGCCATCCACAGTTTCA
ACTTCATGACGAAGGGAATCGTGCTCACCAGCAACATTCCTCTTTAGA
Found at i:1912507 original size:124 final size:124
Alignment explanation
Indices: 1912031--1912728 Score: 1047
Period size: 125 Copynumber: 5.6 Consensus size: 124
1912021 CAATACAAGC
* * * * * *
1912031 TTGGATTTCAACTTCACAACGAAGGATATTCAAGTCAATGATCAACTTCACAACGAAGGGGCCAT
1 TTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
1912096 CCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGTAACATTCATCTTTAAGA
66 CCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGTAACATTCATCTTT-AGA
*
1912156 TTGGATTTCAACTTCACGATGAATGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
1 TTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
* * *
1912221 ACACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAATGACATTCATCTTTAGA
66 CCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGTAACATTCATCTTTAGA
* * * *
1912280 TTGGATTTAAACTTCACGATGAACGATATCCAATTCAAGGCT-AACTTCACAACGAATGGGCTAT
1 TTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
* * * *
1912344 CCACAGTTTCAACTTCATGACGAAGGGAATCGTGCTCACCAGCAACATTCCTCTTTAGA
66 CCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGTAACATTCATCTTTAGA
** *
1912403 TTGGATTTCAACTTCACGATGAAGGATATATAATTCAAGGCTCAACTTCACAACGAAGGGGCTAT
1 TTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
* * * *
1912468 CCACTGTTTCAACTTCACAACGAAGGGAATCGTGCTCACCAGCAACATTCATATTTAAGA
66 CCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGTAACATTCATCTTT-AGA
* * *
1912528 TTGGATTTTAACTTCACGATGAAGGATATCCAATTTAAGGCTCAACTTCACAACGAATGGGCCAT
1 TTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
* * *
1912593 CCACGATTTCAACTTCACGACAAAGGGAATCGTGCTCACCAGTGACATTCATCTTTAGA
66 CCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGTAACATTCATCTTTAGA
* * * *
1912652 TTGGATTTCAACTTCACGATGAAGAATATCCAATTCAAGGCTTAACTTCATAACGAATGGGCCAT
1 TTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
*
1912717 CCATGGTTTCAA
66 CCACGGTTTCAA
1912729 ATCCTGAATA
Statistics
Matches: 520, Mismatches: 51, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
123 110 0.21
124 188 0.36
125 222 0.43
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (124 bp):
TTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
CCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGTAACATTCATCTTTAGA
Found at i:1912893 original size:84 final size:84
Alignment explanation
Indices: 1912776--1913216 Score: 533
Period size: 84 Copynumber: 5.2 Consensus size: 84
1912766 TCACGACAAA
* * **
1912776 AAGGGTTATTTTCCAACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGTGCATCATTTG
1 AAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTG
*
1912841 CAGTATAACTCAAGGCTAG
66 CAGCATAACTCAAGGCTAG
* * * * * *
1912860 AAGGGTTATTTGCCAACAAAAGACCTTCAAGTTCGACTACACTCAACTCAAAGACATATTATTTG
1 AAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTG
*
1912925 CAGCATAACTCAAGGCTTG
66 CAGCATAACTCAAGGCTAG
* * * *
1912944 AAGGGTTATCTGCCAACCAAATACATTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTG
1 AAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTG
* * **
1913009 CAGCATAGCTCAAAGAAAG
66 CAGCATAACTCAAGGCTAG
* * *
1913028 AAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATTATGTG
1 AAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTG
1913093 CAGCATAACTCAAGGCTAG
66 CAGCATAACTCAAGGCTAG
* * ** * ** * *
1913112 AAGGGTTATCTGCCAATAAAAGACCTTCGAGTTCGGTTACACTCAGCTCAAAGAAATATCATTTA
1 AAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTG
* *
1913177 CAGCTTAGCTCAAGG-TAAG
66 CAGCATAACTCAAGGCT-AG
* * *
1913196 AAGGGCTATCTGTCAACAAAA
1 AAGGGTTATTTGCCAACAAAA
1913217 TTTTCAATTT
Statistics
Matches: 301, Mismatches: 55, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
83 1 0.00
84 300 1.00
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.24
Consensus pattern (84 bp):
AAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTG
CAGCATAACTCAAGGCTAG
Found at i:1913854 original size:37 final size:34
Alignment explanation
Indices: 1913816--1914050 Score: 225
Period size: 36 Copynumber: 6.8 Consensus size: 34
1913806 GCAAATGATT
1913816 TTTTGAAATATATATAATATATAGTTTTTAAAACA
1 TTTTGAAA-ATATATAATATATAGTTTTTAAAACA
* * *
1913851 TTTTGAAAACATAAATATTATATAGTTTTTTAAACA
1 TTTTG-AAA-ATATATAATATATAGTTTTTAAAACA
*
1913887 TTTTGAAAACATATATATATTATAGTTTTTTAAAACA
1 TTTTGAAAATATATA-ATA-TATAG-TTTTTAAAACA
1913924 TTTTGAAAATATATAATATATAGTTTTTAAAACA
1 TTTTGAAAATATATAATATATAGTTTTTAAAACA
* *
1913958 TTTTCG-AAA-A-CT-ATATA-A-TTTTGAAAACA
1 TTTT-GAAAATATATAATATATAGTTTTTAAAACA
* * *
1913987 TATTTAAAAAATATATAATATATA-ATTTTAAATA-T
1 T-TTT-GAAAATATATAATATATAGTTTTTAAA-ACA
*
1914022 TTTTGAAAATATATATTATATAAGTTTTT
1 TTTTGAAAATATATAATATAT-AGTTTTT
1914051 GGAAAATGTT
Statistics
Matches: 166, Mismatches: 20, Indels: 28
0.78 0.09 0.13
Matches are distributed among these distances:
29 11 0.07
30 4 0.02
31 8 0.05
32 2 0.01
33 17 0.10
34 32 0.19
35 28 0.17
36 40 0.24
37 24 0.14
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (34 bp):
TTTTGAAAATATATAATATATAGTTTTTAAAACA
Found at i:1913873 original size:73 final size:70
Alignment explanation
Indices: 1913792--1913974 Score: 185
Period size: 71 Copynumber: 2.5 Consensus size: 70
1913782 ATATATATAT
* *
1913792 ATATTATATAGTTTGCAAATGATTTTTTG-AAATATATATA-ATATATAG-TTTTTAAAACATTT
1 ATATTATATAGTTTGCAAA-CA--TTTTGAAAACATATATATAT-TATAGTTTTTTAAAACATTT
1913854 TGAAAACATAA
62 TG-AAA-ATAA
**
1913865 ATATTATATAGTTTTTTAAACATTTTGAAAACATATATATATTATAGTTTTTTAAAACATTTTGA
1 ATATTATATAG-TTTGCAAACATTTTGAAAACATATATATATTATAGTTTTTTAAAACATTTTGA
*
1913930 AAATAT
65 AAATAA
* **
1913936 ATAATATATAGTTTTTAAAACATTTTCGAAAAC-TATATA
1 ATATTATATAG-TTTGCAAACATTTT-GAAAACATATATA
1913975 ATTTTGAAAA
Statistics
Matches: 98, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
71 38 0.39
72 24 0.24
73 30 0.31
74 6 0.06
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.45
Consensus pattern (70 bp):
ATATTATATAGTTTGCAAACATTTTGAAAACATATATATATTATAGTTTTTTAAAACATTTTGAA
AATAA
Found at i:1913984 original size:29 final size:29
Alignment explanation
Indices: 1913938--1914005 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
1913928 GAAAATATAT
* * *
1913938 AATATATAGTTTTTAAAACAT-TTTCGAAA
1 AATATATAATTTTGAAAACATATTT-AAAA
*
1913967 ACTATATAATTTTGAAAACATATTTAAAA
1 AATATATAATTTTGAAAACATATTTAAAA
1913996 AATATATAAT
1 AATATATAAT
1914006 ATATAATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 30 0.91
30 3 0.09
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (29 bp):
AATATATAATTTTGAAAACATATTTAAAA
Found at i:1913985 original size:17 final size:17
Alignment explanation
Indices: 1913957--1913989 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1913947 TTTTTAAAAC
1913957 ATTTTCGAAAACTATATA
1 ATTTTCGAAAAC-ATATA
1913975 ATTTT-GAAAACATAT
1 ATTTTCGAAAACATAT
1913990 TTAAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.39
Consensus pattern (17 bp):
ATTTTCGAAAACATATA
Found at i:1914005 original size:65 final size:60
Alignment explanation
Indices: 1913913--1914036 Score: 158
Period size: 63 Copynumber: 2.0 Consensus size: 60
1913903 ATATTATAGT
* * *
1913913 TTTTTAAAACATTTTGAAAATATATAATATATAGTTTTTAAAACATTTTCGAAAACTATATAA
1 TTTTGAAAACATTTTAAAAATATATAATATATA-ATTTT-AAACATTTTCGAAAA-TATATAA
* *
1913976 TTTTGAAAACATATTTAAAAAATATATAATATATAATTTTAAATATTTTTGAAAATATATA
1 TTTTGAAAACAT-TTT-AAAAATATATAATATATAATTTTAAACATTTTCGAAAATATATA
1914037 TTATATAAGT
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
62 6 0.11
63 24 0.44
64 7 0.13
65 17 0.31
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (60 bp):
TTTTGAAAACATTTTAAAAATATATAATATATAATTTTAAACATTTTCGAAAATATATAA
Found at i:1914073 original size:2 final size:2
Alignment explanation
Indices: 1914061--1914095 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1914051 GGAAAATGTT
*
1914061 TA TA CA 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
1914096 CATGGTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1914881 original size:24 final size:23
Alignment explanation
Indices: 1914837--1914881 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
1914827 CGCCGGTTTT
*
1914837 AAAGGTAATAATCTCAGTCGATC
1 AAAGGTAATAATCTCAATCGATC
1914860 AAAGGTAAGTAAT-TCGAATCGA
1 AAAGGTAA-TAATCTC-AATCGA
1914882 ATGTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.24
Consensus pattern (23 bp):
AAAGGTAATAATCTCAATCGATC
Found at i:1925769 original size:21 final size:21
Alignment explanation
Indices: 1925743--1925790 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
1925733 GTTTCCAGAT
1925743 TCGCAACGCGAACATCGACAA
1 TCGCAACGCGAACATCGACAA
* *
1925764 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACATCGACAA
1925785 TCGCAA
1 TCGCAA
1925791 TGCAATTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.33, G:0.19, T:0.15
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACAA
Found at i:1925852 original size:21 final size:21
Alignment explanation
Indices: 1925828--1925897 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
1925818 TCCAAGCTCG
1925828 CGTTGCGATTTATTTCAAGTT
1 CGTTGCGATTTATTTCAAGTT
*
1925849 CGTTGCGA--TA-GTCGAAGTT
1 CGTTGCGATTTATTTC-AAGTT
* *
1925868 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGATTTATTTCAAGTT
1925891 CGTTGCG
1 CGTTGCG
1925898 GTAGTCCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
18 2 0.05
19 7 0.18
21 23 0.59
23 6 0.15
24 1 0.03
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.39
Consensus pattern (21 bp):
CGTTGCGATTTATTTCAAGTT
Found at i:1925871 original size:42 final size:42
Alignment explanation
Indices: 1925798--1925906 Score: 173
Period size: 42 Copynumber: 2.6 Consensus size: 42
1925788 CAATGCAATT
1925798 TTCCAAATTCGTTGCGGTAGTCCAAGCTCGCGTTGCGATTTA
1 TTCCAAATTCGTTGCGGTAGTCCAAGCTCGCGTTGCGATTTA
* * * * *
1925840 TTTCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTA
1 TTCCAAATTCGTTGCGGTAGTCCAAGCTCGCGTTGCGATTTA
1925882 TTCCAAATTCGTTGCGGTAGTCCAA
1 TTCCAAATTCGTTGCGGTAGTCCAA
1925907 AATTGCAACG
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.35
Consensus pattern (42 bp):
TTCCAAATTCGTTGCGGTAGTCCAAGCTCGCGTTGCGATTTA
Found at i:1926007 original size:6 final size:6
Alignment explanation
Indices: 1925996--1926038 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
1925986 TACACGTATT
1925996 ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1926039 CTACCCGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.27
6 27 0.73
ACGTcount: A:0.30, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1926831 original size:21 final size:21
Alignment explanation
Indices: 1926793--1927032 Score: 170
Period size: 21 Copynumber: 11.4 Consensus size: 21
1926783 ACTATCACAA
1926793 CGAATTTGGAATAAATCGCAACG
1 CGAATTTGGAAT--ATCGCAACG
* *
1926816 CGAACTTGGACTATCGCAA--
1 CGAATTTGGAATATCGCAACG
*
1926835 CGAATTTGTAATAAATCGCAACG
1 CGAATTTGGAAT--ATCGCAACG
* *
1926858 CGAATTTCGACTATCGCAA--
1 CGAATTTGGAATATCGCAACG
*
1926877 CGAATTTGTAATAAATCGCAACG
1 CGAATTTGGAAT--ATCGCAACG
* * *
1926900 CGAACTTGGACTTTCGCAA--
1 CGAATTTGGAATATCGCAACG
*
1926919 CAAATTTGGAATAAATCGCAACG
1 CGAATTTGGAAT--ATCGCAACG
*
1926942 CGAATTTGGAAAATCGCAACG
1 CGAATTTGGAATATCGCAACG
* *
1926963 CGGATTTGGAAAATCGCAACG
1 CGAATTTGGAATATCGCAACG
* ** * *
1926984 CGAACTACGACTATCGCAATG
1 CGAATTTGGAATATCGCAACG
* * *
1927005 CGAATATGTAA-ATCGCAATG
1 CGAATTTGGAATATCGCAACG
1927025 CGAATTTG
1 CGAATTTG
1927033 CAATGCGATA
Statistics
Matches: 169, Mismatches: 36, Indels: 27
0.73 0.16 0.12
Matches are distributed among these distances:
19 27 0.16
20 16 0.09
21 88 0.52
23 38 0.22
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.23
Consensus pattern (21 bp):
CGAATTTGGAATATCGCAACG
Found at i:1926838 original size:42 final size:42
Alignment explanation
Indices: 1926779--1927002 Score: 299
Period size: 42 Copynumber: 5.3 Consensus size: 42
1926769 ACTTGCGATT
*
1926779 TTGGACTATCACAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* *
1926821 TTGGACTATCGCAACGAATTTGTAATAAATCGCAACGCGAAT
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* *
1926863 TTCGACTATCGCAACGAATTTGTAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* * *
1926905 TTGGACTTTCGCAACAAATTTGGAATAAATCGCAACGCGAAT
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
** *
1926947 TTGGAAAATCGCAACGCGGATTTGG-A-AAATCGCAACGCGAAC
1 TTGGACTATCGCAA--CGAATTTGGAATAAATCGCAACGCGAAC
**
1926989 TACGACTATCGCAA
1 TTGGACTATCGCAA
1927003 TGCGAATATG
Statistics
Matches: 160, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
42 152 0.95
43 1 0.01
44 7 0.04
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (42 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
Found at i:1930066 original size:42 final size:45
Alignment explanation
Indices: 1929992--1930082 Score: 111
Period size: 42 Copynumber: 2.1 Consensus size: 45
1929982 ATTTTATACG
1929992 TTTATATATATATATATTCTTAATATTCTATTTT-TGTTTTTATTTA
1 TTTATATATATATATATTCTT-ATATTCTATTTTATGTTTTTA-TTA
*
1930038 TTTATATATAT-TATATT-TT-TACTT-TATTTTATTTTTTTATTA
1 TTTATATATATATATATTCTTATA-TTCTATTTTATGTTTTTATTA
1930080 TTT
1 TTT
1930083 TTTTCTTAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
42 14 0.33
43 9 0.21
44 2 0.05
45 6 0.14
46 11 0.26
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.69
Consensus pattern (45 bp):
TTTATATATATATATATTCTTATATTCTATTTTATGTTTTTATTA
Found at i:1932172 original size:7 final size:7
Alignment explanation
Indices: 1932155--1932188 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
1932145 GAACATTTCA
1932155 TGCATTTT
1 TGCA-TTT
1932163 TGCATTT
1 TGCATTT
1932170 TGCATTT
1 TGCATTT
1932177 TGCATTT
1 TGCATTT
1932184 TGCAT
1 TGCAT
1932189 ATACATTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 22 0.85
8 4 0.15
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.56
Consensus pattern (7 bp):
TGCATTT
Found at i:1933442 original size:13 final size:13
Alignment explanation
Indices: 1933424--1933478 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
1933414 GAACAAAAAG
1933424 AAAAAAAAGAGAAA
1 AAAAAAAAGAG-AA
1933438 AAAAACAAAGAGAA
1 AAAAA-AAAGAGAA
* *
1933452 AAAACAACGAGAA
1 AAAAAAAAGAGAA
*
1933465 AAAACAAAG-GAA
1 AAAAAAAAGAGAA
1933477 AA
1 AA
1933479 TTGAAGAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
12 5 0.14
13 15 0.41
14 11 0.30
15 6 0.16
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAGAA
Found at i:1933444 original size:26 final size:28
Alignment explanation
Indices: 1933415--1933468 Score: 85
Period size: 26 Copynumber: 2.0 Consensus size: 28
1933405 ATTCAATCAG
1933415 AACAAAAAGAAAAAA-AA-GAGAAAAAA
1 AACAAAAAGAAAAAACAACGAGAAAAAA
*
1933441 AACAAAGAGAAAAAACAACGAGAAAAAA
1 AACAAAAAGAAAAAACAACGAGAAAAAA
1933469 CAAAGGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 14 0.56
27 2 0.08
28 9 0.36
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (28 bp):
AACAAAAAGAAAAAACAACGAGAAAAAA
Found at i:1933447 original size:15 final size:15
Alignment explanation
Indices: 1933424--1933468 Score: 60
Period size: 13 Copynumber: 3.2 Consensus size: 15
1933414 GAACAAAAAG
1933424 AAAAA-AAAGAGAAA
1 AAAAACAAAGAGAAA
1933438 AAAAACAAAGAG--A
1 AAAAACAAAGAGAAA
*
1933451 AAAAACAACGAGAAA
1 AAAAACAAAGAGAAA
1933466 AAA
1 AAA
1933469 CAAAGGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 12 0.44
14 5 0.19
15 10 0.37
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAAACAAAGAGAAA
Found at i:1933469 original size:26 final size:25
Alignment explanation
Indices: 1933415--1933478 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 25
1933405 ATTCAATCAG
*
1933415 AACAAAAAGAAAAAAAAGAGAAAAAA
1 AACAAAGAGAAAAAAAAGAG-AAAAA
1933441 AACAAAGAGAAAAAACAACGAG-AAAA
1 AACAAAGAGAAAAAA-AA-GAGAAAAA
1933467 AACAAAG-GAAAA
1 AACAAAGAGAAAA
1933479 TTGAAGAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
25 5 0.14
26 25 0.71
27 2 0.06
28 3 0.09
ACGTcount: A:0.78, C:0.08, G:0.14, T:0.00
Consensus pattern (25 bp):
AACAAAGAGAAAAAAAAGAGAAAAA
Found at i:1935245 original size:36 final size:36
Alignment explanation
Indices: 1935200--1935292 Score: 143
Period size: 36 Copynumber: 2.6 Consensus size: 36
1935190 TAAACATTGA
*
1935200 AAACA-TTTCCCTTGAAATAAATTTCGTCTCTCTTG
1 AAACAGTTTCCCTTGAAACAAATTTCGTCTCTCTTG
*
1935235 AAACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTG
1 AAACAGTTTCCCTTGAAACAAATTTCGTCTCTCTTG
* *
1935271 AGATAGTTTCCCTTGAAACAAA
1 AAACAGTTTCCCTTGAAACAAA
1935293 ATATTTGAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 5 0.09
36 48 0.91
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.37
Consensus pattern (36 bp):
AAACAGTTTCCCTTGAAACAAATTTCGTCTCTCTTG
Found at i:1935301 original size:65 final size:66
Alignment explanation
Indices: 1935239--1935545 Score: 201
Period size: 65 Copynumber: 4.5 Consensus size: 66
1935229 CTCTTGAAAC
* * * * *
1935239 AGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATATTTGAATA
1 AGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCCCTTGAAACAAAATCTTTGAATA
1935304 T
66 T
*** * * * * **
1935305 -GTTTTATTTGAAACAAATTTCGTCTCCCTTAAGACAGTTT-CTTTTAGAACTAAGTTTTGTCTC
1 AGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCCCTTGA-AAC-AA------AATC
*
1935368 TCTTG-AGAT
58 T-TTGAATAT
* * *
1935377 AGTTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAATTTCCCTTGAAACAAAATCTTTGAATT
1 AGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCCCTTGAAACAAAATCTTTGAATA
1935442 T
66 T
* * ** * ***
1935443 A-TTTCCCCTAAAACAAATTTTATCTCCCTTGAGACAATTTCTCTTGAAACACAAAATCTCCAAA
1 AGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCCCTTG-AA-ACAAAATCTTTGAA
*
1935507 TTT
64 TAT
* * *
1935510 A-TTTCCCTTAAAACAAAATTTTGTTTCCCTTGAGAC
1 AGTTTCCCTTGAAAC-AAATTTCGTCTCCCTTGAGAC
1935546 CGTTTTCATG
Statistics
Matches: 188, Mismatches: 38, Indels: 28
0.74 0.15 0.11
Matches are distributed among these distances:
64 4 0.02
65 77 0.41
66 10 0.05
67 27 0.14
68 19 0.10
72 7 0.04
73 40 0.21
74 4 0.02
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (66 bp):
AGTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCCCTTGAAACAAAATCTTTGAATA
T
Found at i:1935316 original size:101 final size:100
Alignment explanation
Indices: 1935137--1935394 Score: 295
Period size: 101 Copynumber: 2.5 Consensus size: 100
1935127 CGCTTGAGAT
* * * *
1935137 AGTTTCCCTTGAAAAAAATTTTTGCCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAA
1 AGTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACA-AAACATTGAAA
* * *
1935202 ACATTTCCCTTGAAATAAATTTCGTCTCTCTTGAA-AC
64 ACATTTCACTTGAAACAAATTTCGTCTCCCTT-AAGAC
* * *
1935239 AGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATATTTGAATA
1 AGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAACA-TTGAAAA
** * *
1935304 TGTTTTATTTGAAACAAATTTCGTCTCCCTTAAGAC
65 CATTTCACTTGAAACAAATTTCGTCTCCCTTAAGAC
* * *
1935340 AGTTT-CTTTTAGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAA
1 AGTTTCCCTTGA-AAC-AAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAA
1935395 TTTCGTCTCT
Statistics
Matches: 134, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
100 10 0.07
101 70 0.52
102 54 0.40
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.39
Consensus pattern (100 bp):
AGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAACATTGAAAAC
ATTTCACTTGAAACAAATTTCGTCTCCCTTAAGAC
Found at i:1935405 original size:36 final size:36
Alignment explanation
Indices: 1935312--1935430 Score: 141
Period size: 36 Copynumber: 3.3 Consensus size: 36
1935302 TATGTTTTAT
* *
1935312 TTGAAACAAATTTCGTCTCCCTTAAGACAGTTTCT-
1 TTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCTC
* * * *
1935347 TTTAGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTC
1 TTGA-AAC-AAATTTCGTCTCTCTTGAGACAGTTTCTC
* *
1935385 TTGAAACAAATTTCGTCTCTCTTGAGACAATTTCCC
1 TTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCTC
1935421 TTGAAACAAA
1 TTGAAACAAA
1935431 ATCTTTGAAT
Statistics
Matches: 69, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
35 3 0.04
36 37 0.54
37 26 0.38
38 3 0.04
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.39
Consensus pattern (36 bp):
TTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCTC
Found at i:1935478 original size:138 final size:138
Alignment explanation
Indices: 1935225--1935484 Score: 358
Period size: 138 Copynumber: 1.9 Consensus size: 138
1935215 AATAAATTTC
* * *
1935225 GTCTCTCTTGAAACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC
1 GTCTCTCTTGAAACAGTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAATTTCCCTTGAAAC
* * ** * * *
1935290 AAAATATTTGAATATGTTTTATTTGAAACAAATTTCGTCTCCCTTAAGACAGTTTCTTTTAGAAC
66 AAAATATTTGAATATATTTCACCTAAAACAAATTTCATCTCCCTTAAGACAATTTCTTTTAGAAC
1935355 TAAGTTTT
131 TAAGTTTT
* * *
1935363 GTCTCTCTTGAGATAGTTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAATTTCCCTTGAAAC
1 GTCTCTCTTGAAACAGTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAATTTCCCTTGAAAC
* * * * *
1935428 AAAATCTTTGAATTTATTTCCCCTAAAACAAATTTTATCTCCCTTGAGACAATTTCT
66 AAAATATTTGAATATATTTCACCTAAAACAAATTTCATCTCCCTTAAGACAATTTCT
1935485 CTTGAAACAC
Statistics
Matches: 104, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
138 104 1.00
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (138 bp):
GTCTCTCTTGAAACAGTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAATTTCCCTTGAAAC
AAAATATTTGAATATATTTCACCTAAAACAAATTTCATCTCCCTTAAGACAATTTCTTTTAGAAC
TAAGTTTT
Found at i:1936439 original size:110 final size:110
Alignment explanation
Indices: 1936241--1936492 Score: 332
Period size: 110 Copynumber: 2.3 Consensus size: 110
1936231 GCTTCCCAAT
* * *
1936241 TTCAGAGCCAATTTCAACTTCACAACGAGGGATATTGGACTCAAGACAACACAAGCTCAAATTCA
1 TTCAGAGCCAATTTCAACTTAACAACGAAGGATATTGAACTCAAGACAACACAAGCTCAAATTCA
* *
1936306 TAACGAAGGGACGACTGATTGTCAACAAACAATTTTTTAGTTTCA
66 CAACGAAGGGACGACTGACTGTCAACAAACAATTTTTTAGTTTCA
* * * *
1936351 TTCAGAGTCAATTTCAACTTAACAGCGAAGGATATTGAACTCGAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTAACAACGAAGGATATTGAACTCAAGACAACACAAGCTCAAATTCA
* * * *
1936416 CAACGAAGGGGCGGCTGACTGTCAACAAACAATTTCTCAG-TTC-
66 CAACGAAGGGACGACTGACTGTCAACAAACAATTTTTTAGTTTCA
* * *
1936459 --CAAAGCCAATTTCAACTTCACAACGGAGGATATT
1 TTCAGAGCCAATTTCAACTTAACAACGAAGGATATT
1936493 AGACTCGAAA
Statistics
Matches: 124, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
106 29 0.23
109 3 0.02
110 92 0.74
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.24
Consensus pattern (110 bp):
TTCAGAGCCAATTTCAACTTAACAACGAAGGATATTGAACTCAAGACAACACAAGCTCAAATTCA
CAACGAAGGGACGACTGACTGTCAACAAACAATTTTTTAGTTTCA
Found at i:1937969 original size:20 final size:20
Alignment explanation
Indices: 1937892--1937962 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 20
1937882 ATATATATAT
*
1937892 TTTAAATTATATT-TTTTTA
1 TTTATATTATATTATTTTTA
* *
1937911 TTTATTTACTATATTCCTTTTTTA
1 TTTA--TATTATATT--ATTTTTA
1937935 TTTATATTATATTATTTTTA
1 TTTATATTATATTATTTTTA
1937955 TTGTATAT
1 TT-TATAT
1937963 ATCTTATATC
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
19 4 0.10
20 8 0.19
21 12 0.29
22 8 0.19
24 10 0.24
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (20 bp):
TTTATATTATATTATTTTTA
Found at i:1937980 original size:2 final size:2
Alignment explanation
Indices: 1937958--1938006 Score: 57
Period size: 2 Copynumber: 25.0 Consensus size: 2
1937948 ATTTTTATTG
*
1937958 TA TA TA TC T- TA TA TCA T- TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1937999 TA TG TA TA
1 TA TA TA TA
1938007 GATGTATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
1 2 0.05
2 37 0.90
3 2 0.05
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1938154 original size:18 final size:18
Alignment explanation
Indices: 1938109--1938169 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 18
1938099 CTATTTTTGT
* *
1938109 TTTTATTTATTTA-TATA
1 TTTTATTTTTTTACTTTA
* *
1938126 TATTATATTTTTACTTTA
1 TTTTATTTTTTTACTTTA
1938144 TTTTATTTTTTT-CTATTA
1 TTTTATTTTTTTACT-TTA
1938162 TTTT-TTTT
1 TTTTATTTT
1938170 CTTAATATCA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 16 0.44
18 20 0.56
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTATTTTTTTACTTTA
Found at i:1938303 original size:18 final size:18
Alignment explanation
Indices: 1938280--1938314 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1938270 TATTTTTATT
1938280 CCTTTTTAATTTATTTTA
1 CCTTTTTAATTTATTTTA
*
1938298 CCTTTTTTATTTATTTT
1 CCTTTTTAATTTATTTT
1938315 TACTCCATTA
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:0.17, C:0.11, G:0.00, T:0.71
Consensus pattern (18 bp):
CCTTTTTAATTTATTTTA
Found at i:1948178 original size:45 final size:45
Alignment explanation
Indices: 1948114--1948201 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
1948104 GATTATAGAG
* *
1948114 TTGCTTTGTGATATTATCTTAGTTTCATATGTTTATTTTTTTAAT
1 TTGCTTTGTGATATTATCTTAGTGTCATATGTTTAATTTTTTAAT
*
1948159 TTGCTTTGTGATATTATCTTAGTGTCGTATGTTTAATTTTTTA
1 TTGCTTTGTGATATTATCTTAGTGTCATATGTTTAATTTTTTA
1948202 TTTTATAAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.19, C:0.07, G:0.14, T:0.60
Consensus pattern (45 bp):
TTGCTTTGTGATATTATCTTAGTGTCATATGTTTAATTTTTTAAT
Found at i:1955467 original size:16 final size:16
Alignment explanation
Indices: 1955448--1955492 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
1955438 TATCTGAGTT
1955448 GTTTTCAACCTGACAA
1 GTTTTCAACCTGACAA
**
1955464 GTTTTCAACCTGACCT
1 GTTTTCAACCTGACAA
*
1955480 GTTTTTAACCTGA
1 GTTTTCAACCTGA
1955493 TCTGATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.38
Consensus pattern (16 bp):
GTTTTCAACCTGACAA
Found at i:1955676 original size:13 final size:13
Alignment explanation
Indices: 1955660--1955686 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1955650 GACATATTAT
1955660 ATAAAATTATTTA
1 ATAAAATTATTTA
1955673 ATAAAATTATTTA
1 ATAAAATTATTTA
1955686 A
1 A
1955687 ATGTATAATA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAAATTATTTA
Found at i:1955748 original size:14 final size:14
Alignment explanation
Indices: 1955726--1955772 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
1955716 TGCAAAGGAA
*
1955726 AATTAATATAGTTT
1 AATTTATATAGTTT
1955740 AATTTATATA----
1 AATTTATATAGTTT
1955750 AA-TTATATAGTTT
1 AATTTATATAGTTT
1955763 AATTTATATA
1 AATTTATATA
1955773 AAGAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:1955759 original size:23 final size:24
Alignment explanation
Indices: 1955725--1955774 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
1955715 ATGCAAAGGA
1955725 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
1955749 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
1955772 AAA
1 AAA
1955775 GAAAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:1957582 original size:32 final size:34
Alignment explanation
Indices: 1957499--1957586 Score: 114
Period size: 32 Copynumber: 2.7 Consensus size: 34
1957489 GTTCTATGGA
* *
1957499 ACATAAGGACAGAATTACCTA--TATTTTTCGGG
1 ACATATGGACAGAATTACCTATGTATTTTTCGAG
1957531 ACATATGGACAGAATTACCTATGTATTTTT-GAG
1 ACATATGGACAGAATTACCTATGTATTTTTCGAG
1957564 ACATATGGAC--AATATACCTATGT
1 ACATATGGACAGAAT-TACCTATGT
1957587 TCTCAGAAAC
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
31 3 0.06
32 29 0.57
33 12 0.24
34 7 0.14
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (34 bp):
ACATATGGACAGAATTACCTATGTATTTTTCGAG
Found at i:1957602 original size:31 final size:31
Alignment explanation
Indices: 1957531--1957651 Score: 107
Period size: 31 Copynumber: 3.8 Consensus size: 31
1957521 ATTTTTCGGG
* * ** *
1957531 ACATATGGACAGAATTACCTATGTATTTTTGAG
1 ACATATGGACAGTA-TACCTATGT-TCTAAGAA
* *
1957564 ACATATGGACAATATACCTATGTTCTCAGAA
1 ACATATGGACAGTATACCTATGTTCTAAGAA
** *
1957595 ACATATGGACAGTATAGTTATGTTCTAAGGA
1 ACATATGGACAGTATACCTATGTTCTAAGAA
* * *
1957626 ACATATAGACAGTTTACCTAGGTTCT
1 ACATATGGACAGTATACCTATGTTCT
1957652 TCGGGACCTA
Statistics
Matches: 72, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
31 51 0.71
32 9 0.12
33 12 0.17
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (31 bp):
ACATATGGACAGTATACCTATGTTCTAAGAA
Found at i:1958444 original size:19 final size:20
Alignment explanation
Indices: 1958397--1958448 Score: 79
Period size: 21 Copynumber: 2.6 Consensus size: 20
1958387 TCGAAATTCA
*
1958397 TTACTGTTCATATGGTATTG
1 TTACTGTTCATATCGTATTG
1958417 TTCACTGTTCATATCGTATT-
1 TT-ACTGTTCATATCGTATTG
1958437 TTACTGTTCATA
1 TTACTGTTCATA
1958449 AAACGTATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 10 0.33
20 4 0.13
21 16 0.53
ACGTcount: A:0.21, C:0.15, G:0.13, T:0.50
Consensus pattern (20 bp):
TTACTGTTCATATCGTATTG
Found at i:1959653 original size:21 final size:20
Alignment explanation
Indices: 1959595--1959654 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
1959585 TTATATTAGG
* *
1959595 GTTTATGGTTTAGGATTTAAT
1 GTTTA-GGTTTAGGGTTTAAA
* *
1959616 GTTTAGTGTATATGGTTTAAA
1 GTTTAG-GTTTAGGGTTTAAA
1959637 GTTTAGGATTTAGGGTTT
1 GTTTAGG-TTTAGGGTTT
1959655 TTTAATAAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
20 2 0.06
21 29 0.94
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (20 bp):
GTTTAGGTTTAGGGTTTAAA
Found at i:1959713 original size:2 final size:2
Alignment explanation
Indices: 1959706--1959859 Score: 94
Period size: 2 Copynumber: 79.0 Consensus size: 2
1959696 ATAGTATTTC
*
1959706 TA TA TA TA TA TA TA TA TA TA TA TA TC 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
* *
1959748 TA TA TCA TA TA T- TA CT- TA TA CT- TA TA CA TA CA TA TA TA CTA
1 TA TA T-A TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA -TA
* * *
1959789 TA T- TA -A TA TA AA T- TA TA -A TT TA TA -A CTA TA TA T- TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * * *
1959826 TA TA GTT TA TA CA TA TA TA -A TT TA TA CA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1959860 GTTTATACAT
Statistics
Matches: 117, Mismatches: 19, Indels: 32
0.70 0.11 0.19
Matches are distributed among these distances:
1 10 0.09
2 99 0.85
3 8 0.07
ACGTcount: A:0.45, C:0.06, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1959842 original size:15 final size:15
Alignment explanation
Indices: 1959824--1959870 Score: 85
Period size: 15 Copynumber: 3.1 Consensus size: 15
1959814 CTATATATTT
1959824 TATATAGTTTATACA
1 TATATAGTTTATACA
*
1959839 TATATAATTTATACA
1 TATATAGTTTATACA
1959854 TATATAGTTTATACA
1 TATATAGTTTATACA
1959869 TA
1 TA
1959871 CATACATACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (15 bp):
TATATAGTTTATACA
Found at i:1959873 original size:4 final size:4
Alignment explanation
Indices: 1959864--1961309 Score: 2303
Period size: 4 Copynumber: 368.8 Consensus size: 4
1959854 TATATAGTTT
1959864 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1959912 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1959960 AT-C ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC --AC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1960005 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1960053 ATAC ATAC ATAC ATAC A-AC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1960100 ATAC ATAC ATAC ATAC ATAC ATAC -TAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1960147 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT-C ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
1960194 -TAC ATA- ATAC ATAC ATAC ATAC ACATC AT-C ACTAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA-C ATAC A-TAC ATAC ATAC ATAC
1960241 ATAC ATAC ATAC AT-C ATAC ATAC ATGCAC ATAC ATA- ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC AT--AC ATAC ATAC ATAC ATAC ATAC
* * *
1960289 ATAC --AC ATGC ATGC ATAC ATGC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1960335 ATA- ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * *
1960382 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATGC ATGC ATGC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * *
1960430 ATAC ATAC ATAC ATGC ATAC ATAC ATAC ATAC ATGC ATGC ATAC ATGC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * *
1960478 ATGC ATCC ATAC ATGC ATGC ATGC ATGC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1960526 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1960574 ATAC ATAC ATAC ATAC ATAC ATAC ATAC A-AC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1960621 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A-AC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * *
1960668 ATAC ATAC ATAC ATAC ATGC ATGC ATGC ATGC ATGC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * *
1960716 -TGC ATAC ATAC ATAC ATAC ATGC ATGC ATAC ATAC --AC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1960761 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1960809 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1960857 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1960905 ATAC ATAC ATAC ATAC ATAC -TAC ATAC ATAC AT-- ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
1960950 ATAC ATAC ATAC ATAC AT-- ATAC ATAC ATAC ATAC ATAC ATAC ATAT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * *
1960996 ATAC ATAC ATAT ATAC ATAC ATAC ATAC ATAC ACAC ATAC ATAC ATGC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * *
1961044 -TAC ATAC ATGC ATAC ATAC ATGC ATAC ATGC ATAC AT-C ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1961090 ATAC --AC ATAC ATAC ATAC ATAC --AC ATAC ATAC ATATC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA-C ATAC ATAC
*
1961135 ATAC ATAC A-AC ATAC ATAC ATAC ATAT ATAC ATAC ATAC AT-- ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1961180 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC -TAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
1961227 ATAC ATAC ATAC ATAT ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1961275 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1961310 TTAATTAGGT
Statistics
Matches: 1362, Mismatches: 41, Indels: 78
0.92 0.03 0.05
Matches are distributed among these distances:
2 16 0.01
3 51 0.04
4 1283 0.94
5 8 0.01
6 4 0.00
ACGTcount: A:0.48, C:0.25, G:0.02, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:1961649 original size:21 final size:20
Alignment explanation
Indices: 1961591--1961650 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
1961581 TTATATTAGG
* *
1961591 GTTTATGGTTTAGGATTTAAT
1 GTTTA-GGTTTAGGGTTTAAA
* *
1961612 GTTTAGTGTATATGGTTTAAA
1 GTTTAG-GTTTAGGGTTTAAA
1961633 GTTTAGGATTTAGGGTTT
1 GTTTAGG-TTTAGGGTTT
1961651 TTTAATAAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
20 2 0.06
21 29 0.94
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (20 bp):
GTTTAGGTTTAGGGTTTAAA
Found at i:1961820 original size:14 final size:15
Alignment explanation
Indices: 1961801--1961842 Score: 68
Period size: 14 Copynumber: 2.9 Consensus size: 15
1961791 CTATATATTT
1961801 TATATAGTTTATAC-
1 TATATAGTTTATACA
*
1961815 TATATAATTTATACA
1 TATATAGTTTATACA
1961830 TATATAGTTTATA
1 TATATAGTTTATA
1961843 TAGGATTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (15 bp):
TATATAGTTTATACA
Found at i:1961913 original size:13 final size:14
Alignment explanation
Indices: 1961897--1961982 Score: 93
Period size: 14 Copynumber: 6.0 Consensus size: 14
1961887 TAGTTGATGC
*
1961897 ATATATTTCTATA-
1 ATATATTTATATAT
1961910 ATATATATTATATAT
1 ATATAT-TTATATAT
1961925 ATATATTATATATAT
1 ATATATT-TATATAT
* *
1961940 AGATATATATATAT
1 ATATATTTATATAT
*
1961954 ATATATATATATAT
1 ATATATTTATATAT
*
1961968 ATATAATCTATATAT
1 ATAT-ATTTATATAT
1961983 TACTTATACA
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
13 6 0.09
14 31 0.48
15 27 0.42
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (14 bp):
ATATATTTATATAT
Found at i:1961915 original size:2 final size:2
Alignment explanation
Indices: 1961906--1961982 Score: 108
Period size: 2 Copynumber: 40.5 Consensus size: 2
1961896 CATATATTTC
*
1961906 TA TA -A TA TA TA T- TA TA TA TA TA TA T- TA TA TA TA TA GA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1961945 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TC TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1961983 TACTTATACA
Statistics
Matches: 67, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
1 4 0.06
2 63 0.94
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1962571 original size:41 final size:42
Alignment explanation
Indices: 1962495--1962576 Score: 100
Period size: 41 Copynumber: 2.0 Consensus size: 42
1962485 ATTAAAATAA
*
1962495 TAATTAAGATTTAATTTTTAGTATAATAAAATAATA-ATTAT
1 TAATTAAAATTTAATTTTTAGTATAATAAAATAATAGATTAT
1962536 TAATTAATAATTTAATATTTTA-T-T-ATAAAATTAATAGATTA
1 TAATTAA-AATTTAAT-TTTTAGTATAATAAAA-TAATAGATTA
1962577 GTCATTTATC
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
40 6 0.17
41 13 0.36
42 12 0.33
43 5 0.14
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.48
Consensus pattern (42 bp):
TAATTAAAATTTAATTTTTAGTATAATAAAATAATAGATTAT
Found at i:1963191 original size:19 final size:20
Alignment explanation
Indices: 1963160--1963198 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
1963150 CCAGAAAACA
1963160 CTACAGTTTGTCACTGTGCT
1 CTACAGTTTGTCACTGTGCT
1963180 CTACAG-TTGTCACTGTGCT
1 CTACAGTTTGTCACTGTGCT
1963199 TGGTTGGACC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.15, C:0.26, G:0.21, T:0.38
Consensus pattern (20 bp):
CTACAGTTTGTCACTGTGCT
Found at i:1964191 original size:19 final size:19
Alignment explanation
Indices: 1964167--1964204 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1964157 CCAGAAAACA
1964167 CTACAGTTGTCACTGTGCT
1 CTACAGTTGTCACTGTGCT
1964186 CTACAGTTGTCACTGTGCT
1 CTACAGTTGTCACTGTGCT
1964205 TTGGTTGGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.21, T:0.37
Consensus pattern (19 bp):
CTACAGTTGTCACTGTGCT
Found at i:1965258 original size:55 final size:55
Alignment explanation
Indices: 1965161--1965268 Score: 144
Period size: 55 Copynumber: 2.0 Consensus size: 55
1965151 TAAGTTCATA
* * * * * * *
1965161 TTCGAGTTTCAATTGAGCTAAGTCTGAGAATGTTTTGGGTTCAAGCTTTTTCGAG
1 TTCGAGCTTCAATCGAGCTAAGTCTAAAAATATTTCGAGTTCAAGCTTTTTCGAG
*
1965216 TTCGAGCTTCAATCGAGCTAAGTCTAAAAATATTTCGAGTTCAAGTTTTTTCG
1 TTCGAGCTTCAATCGAGCTAAGTCTAAAAATATTTCGAGTTCAAGCTTTTTCG
1965269 TGCTCAAGTT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 45 1.00
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.39
Consensus pattern (55 bp):
TTCGAGCTTCAATCGAGCTAAGTCTAAAAATATTTCGAGTTCAAGCTTTTTCGAG
Found at i:1975573 original size:21 final size:21
Alignment explanation
Indices: 1975533--1975583 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
1975523 GTAAAATAAA
1975533 TAATTTTCAGATTAAAAGTGTTT
1 TAATTTT-AGATTAAAAGTG-TT
*
1975556 TAATTTTATATT-AAAGTGTT
1 TAATTTTAGATTAAAAGTGTT
*
1975576 GAATTTTA
1 TAATTTTA
1975584 AAAATTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 9 0.35
21 6 0.23
22 4 0.15
23 7 0.27
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (21 bp):
TAATTTTAGATTAAAAGTGTT
Found at i:1977536 original size:19 final size:19
Alignment explanation
Indices: 1977512--1977554 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
1977502 CAAACTAATA
*
1977512 AAAAATATTTTATCATCCT
1 AAAAATATTATATCATCCT
1977531 AAAAATATTATATCATCCT
1 AAAAATATTATATCATCCT
1977550 AAAAA
1 AAAAA
1977555 GTAGAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAATATTATATCATCCT
Found at i:1985655 original size:32 final size:31
Alignment explanation
Indices: 1985606--1985684 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 31
1985596 ATGGAATATT
* *
1985606 ATGCGACA-CACCTAAGTCACA-TGATCTGCC
1 ATGCGACACCACCTAAGTCACACTAATC-ACC
*
1985636 ATGCGACACCTACCTAAGTCGCACTAATCACC
1 ATGCGACACC-ACCTAAGTCACACTAATCACC
1985668 ATGCGACACCCACCTAA
1 ATGCGACA-CCACCTAA
1985685 CATGCAGTGG
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 8 0.19
31 1 0.02
32 27 0.64
33 6 0.14
ACGTcount: A:0.32, C:0.37, G:0.14, T:0.18
Consensus pattern (31 bp):
ATGCGACACCACCTAAGTCACACTAATCACC
Found at i:1987028 original size:13 final size:15
Alignment explanation
Indices: 1987001--1987031 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1986991 GACATATTTT
1987001 TATAATATTTATATA
1 TATAATATTTATATA
1987016 TATAATATTTATATA
1 TATAATATTTATATA
1987031 T
1 T
1987032 TCATTTGTAC
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATAATATTTATATA
Found at i:1990375 original size:30 final size:30
Alignment explanation
Indices: 1990335--1990395 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1990325 TTTCCAACGA
*
1990335 AAAGATGCCTTGCAGTTCCGATAACTTCAT
1 AAAGACGCCTTGCAGTTCCGATAACTTCAT
*
1990365 AAAGACGCCTTGCAGTTCTGATAACTTCAT
1 AAAGACGCCTTGCAGTTCCGATAACTTCAT
1990395 A
1 A
1990396 TGTCATGCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (30 bp):
AAAGACGCCTTGCAGTTCCGATAACTTCAT
Found at i:1994955 original size:15 final size:15
Alignment explanation
Indices: 1994935--1994965 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1994925 GTATCTTGTT
1994935 AAAGAAGAGGAGAAA
1 AAAGAAGAGGAGAAA
*
1994950 AAAGAAGTGGAGAAA
1 AAAGAAGAGGAGAAA
1994965 A
1 A
1994966 TGTTGAGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (15 bp):
AAAGAAGAGGAGAAA
Found at i:1997568 original size:24 final size:24
Alignment explanation
Indices: 1997541--1997605 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
1997531 TAGATGGACC
* **
1997541 AGGCTCAGGTGCGAAAGGACTCTA
1 AGGCTCGGGTGCGAAAGGACTAGA
1997565 AGGCTCGGGTGC-AAGAGGACTAGA
1 AGGCTCGGGTGCGAA-AGGACTAGA
1997589 AGGCTCGGGTGCTGAAA
1 AGGCTCGGGTGC-GAAA
1997606 AAGGAGCGGC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 2 0.06
24 30 0.86
25 1 0.03
26 2 0.06
ACGTcount: A:0.28, C:0.18, G:0.38, T:0.15
Consensus pattern (24 bp):
AGGCTCGGGTGCGAAAGGACTAGA
Found at i:2012505 original size:21 final size:21
Alignment explanation
Indices: 2012481--2012571 Score: 116
Period size: 21 Copynumber: 4.4 Consensus size: 21
2012471 TGAAAATCGT
2012481 GTTGCGATAGTCTACAGTGTC
1 GTTGCGATAGTCTACAGTGTC
2012502 GTTGCGATAGTCTACAGTGTC
1 GTTGCGATAGTCTACAGTGTC
* * *
2012523 GTTGCGAT--TTTCCA-TTTCGC
1 GTTGCGATAGTCTACAGTGT--C
2012543 GTTGCGATAGTCTACAGTGTC
1 GTTGCGATAGTCTACAGTGTC
2012564 GTTGCGAT
1 GTTGCGAT
2012572 TTTCCATTTC
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
18 2 0.03
19 4 0.07
20 9 0.15
21 38 0.64
22 4 0.07
23 2 0.03
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.36
Consensus pattern (21 bp):
GTTGCGATAGTCTACAGTGTC
Found at i:2012547 original size:20 final size:20
Alignment explanation
Indices: 2012522--2012591 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
2012512 TCTACAGTGT
2012522 CGTTGCGATTTTCCATTTCG
1 CGTTGCGATTTTCCATTTCG
* * *
2012542 CGTTGCGATAGTCTACA-GT-G
1 CGTTGCGAT--TTTCCATTTCG
2012562 TCGTTGCGATTTTCCATTTCG
1 -CGTTGCGATTTTCCATTTCG
2012583 CGTTGCGAT
1 CGTTGCGAT
2012592 AGTGTACAGT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
19 4 0.10
20 20 0.51
21 11 0.28
22 4 0.10
ACGTcount: A:0.13, C:0.23, G:0.24, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTTCCATTTCG
Found at i:2012554 original size:41 final size:41
Alignment explanation
Indices: 2012501--2012751 Score: 322
Period size: 41 Copynumber: 5.9 Consensus size: 41
2012491 TCTACAGTGT
2012501 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
1 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
2012542 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
1 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
* * * *
2012583 CGTTGCGATAGTGTACAGTGTCATTGCGATCGTTGCGATAGTTGAAAATCG
1 CGTTGCGATAGTCTACAGTGTCGTTGCGAT--TTTC--CA-TT-----TCG
* * *
2012634 CGTTGCGATAGTGTACAGTGTCATTGCGATTTTCCATCTCG
1 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
* *
2012675 CATTGCGATAGTGTACAGTGTCGTTGCGATTTTCCATTTCG
1 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
*
2012716 CGTTACGATAGTCTACAGTGTCGTTGCGATTTTCCA
1 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCA
2012752 AATTCGTCGC
Statistics
Matches: 187, Mismatches: 13, Indels: 20
0.85 0.06 0.09
Matches are distributed among these distances:
41 143 0.76
43 3 0.02
45 1 0.01
46 3 0.02
47 1 0.01
49 3 0.02
51 33 0.18
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
Found at i:2012660 original size:21 final size:21
Alignment explanation
Indices: 2012636--2012704 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
2012626 GAAAATCGCG
2012636 TTGCGATAGTGTACAGTGTCA
1 TTGCGATAGTGTACAGTGTCA
* * *
2012657 TTGCGAT--TTTCCA-TCTCGCA
1 TTGCGATAGTGTACAGTGT--CA
*
2012677 TTGCGATAGTGTACAGTGTCG
1 TTGCGATAGTGTACAGTGTCA
2012698 TTGCGAT
1 TTGCGAT
2012705 TTTCCATTTC
Statistics
Matches: 36, Mismatches: 7, Indels: 10
0.68 0.13 0.19
Matches are distributed among these distances:
18 2 0.06
19 4 0.11
20 9 0.25
21 15 0.42
22 4 0.11
23 2 0.06
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (21 bp):
TTGCGATAGTGTACAGTGTCA
Found at i:2012719 original size:133 final size:133
Alignment explanation
Indices: 2012501--2012745 Score: 418
Period size: 133 Copynumber: 1.8 Consensus size: 133
2012491 TCTACAGTGT
* * *
2012501 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGTCGT
1 CGTTGCGATAGTCTACAGTGTCATTGCGATTTTCCATCTCGCATTGCGATAGTCTACAGTGTCGT
* *
2012566 TGCGATTTTCCATTTCGCGTTGCGATAGTGTACAGTGTCATTGCGATCGTTGCGATAGTTGAAAA
66 TGCGATTTTCCATTTCGCGTTACGATAGTCTACAGTGTCATTGCGATCGTTGCGATAGTTGAAAA
2012631 TCG
131 TCG
* *
2012634 CGTTGCGATAGTGTACAGTGTCATTGCGATTTTCCATCTCGCATTGCGATAGTGTACAGTGTCGT
1 CGTTGCGATAGTCTACAGTGTCATTGCGATTTTCCATCTCGCATTGCGATAGTCTACAGTGTCGT
*
2012699 TGCGATTTTCCATTTCGCGTTACGATAGTCTACAGTGTCGTTGCGAT
66 TGCGATTTTCCATTTCGCGTTACGATAGTCTACAGTGTCATTGCGAT
2012746 TTTCCAAATT
Statistics
Matches: 104, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
133 104 1.00
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.36
Consensus pattern (133 bp):
CGTTGCGATAGTCTACAGTGTCATTGCGATTTTCCATCTCGCATTGCGATAGTCTACAGTGTCGT
TGCGATTTTCCATTTCGCGTTACGATAGTCTACAGTGTCATTGCGATCGTTGCGATAGTTGAAAA
TCG
Found at i:2013404 original size:6 final size:6
Alignment explanation
Indices: 2013393--2013424 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
2013383 CTCGTCTCGA
2013393 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GT
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GT
2013425 AATACGTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.16, G:0.50, T:0.34
Consensus pattern (6 bp):
GTCGTG
Found at i:2013522 original size:41 final size:41
Alignment explanation
Indices: 2013476--2013687 Score: 320
Period size: 41 Copynumber: 5.2 Consensus size: 41
2013466 AGAGAAAATT
2013476 ATCGCAACGACACTGTAGACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGACACTGTAGACTATCGCAACGCGAAATGGAAA
*
2013517 ATCGCAACAACACTGTAGACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGACACTGTAGACTATCGCAACGCGAAATGGAAA
*
2013558 ATCGCAACAACACTGTAGACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGACACTGTAGACTATCGCAACGCGAAATGGAAA
* *
2013599 ATCGTAACGACACTGTAGACTATCGCAACGCGAAAAGGAAA
1 ATCGCAACGACACTGTAGACTATCGCAACGCGAAATGGAAA
* * * *
2013640 ATCGCAACG-CGATTTTCA-ACTATCCCAACGCGAAATAGAAA
1 ATCGCAACGAC-ACTGT-AGACTATCGCAACGCGAAATGGAAA
2013681 ATCGCAA
1 ATCGCAA
2013688 TGCGATTTTC
Statistics
Matches: 159, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
40 1 0.01
41 157 0.99
42 1 0.01
ACGTcount: A:0.41, C:0.25, G:0.19, T:0.16
Consensus pattern (41 bp):
ATCGCAACGACACTGTAGACTATCGCAACGCGAAATGGAAA
Found at i:2013693 original size:41 final size:42
Alignment explanation
Indices: 2013494--2013716 Score: 207
Period size: 41 Copynumber: 5.4 Consensus size: 42
2013484 GACACTGTAG
* * *
2013494 ACTATCGCAACGCGAAAT-GGAAAATCGCAACAAC-ACTGT-A
1 ACTATCGCAACGCGAAATAGGAAAATCGCAAC-GCGATTTTCA
* * *
2013534 GACTATCGCAACGCGAAAT-GGAAAATCGCAACAAC-ACTGT-A
1 -ACTATCGCAACGCGAAATAGGAAAATCGCAAC-GCGATTTTCA
* * *
2013575 GACTATCGCAACGCGAAAT-GGAAAATCGTAACGAC-ACTGT-A
1 -ACTATCGCAACGCGAAATAGGAAAATCGCAACG-CGATTTTCA
2013616 GACTATCGCAACGCGAAA-AGGAAAATCGCAACGCGATTTTCA
1 -ACTATCGCAACGCGAAATAGGAAAATCGCAACGCGATTTTCA
* *
2013658 ACTATCCCAACGCGAAATA-GAAAATCGCAATGCGATTTTCA
1 ACTATCGCAACGCGAAATAGGAAAATCGCAACGCGATTTTCA
*
2013699 ACTATCGCAACGTGAAAT
1 ACTATCGCAACGCGAAAT
2013717 GCAGCGCGAA
Statistics
Matches: 168, Mismatches: 9, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
40 1 0.01
41 165 0.98
42 2 0.01
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.17
Consensus pattern (42 bp):
ACTATCGCAACGCGAAATAGGAAAATCGCAACGCGATTTTCA
Found at i:2013705 original size:21 final size:21
Alignment explanation
Indices: 2013640--2013710 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
2013630 GAAAAGGAAA
2013640 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
* ** ** *
2013661 ATCCCAACGCGAAATAGAA-A
1 ATCGCAACGCGATTTTCAACT
*
2013681 ATCGCAATGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
2013702 ATCGCAACG
1 ATCGCAACG
2013711 TGAAATGCAG
Statistics
Matches: 35, Mismatches: 14, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
20 13 0.37
21 22 0.63
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:2014879 original size:14 final size:14
Alignment explanation
Indices: 2014860--2014887 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2014850 CTTTTGCAAC
2014860 AATTGCAACGCGAA
1 AATTGCAACGCGAA
2014874 AATTGCAACGCGAA
1 AATTGCAACGCGAA
2014888 TTTGACTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.21, T:0.14
Consensus pattern (14 bp):
AATTGCAACGCGAA
Found at i:2017497 original size:93 final size:93
Alignment explanation
Indices: 2017341--2017532 Score: 357
Period size: 93 Copynumber: 2.1 Consensus size: 93
2017331 TATTATCAAC
*
2017341 AACATCTTCCTCGGCAGTGGCTGTTTCATCATCAAAATTCGGATATTGACCAAAATCAAAATCAT
1 AACATCTTCCTCGGCAGCGGCTGTTTCATCATCAAAATTCGGATATTGACCAAAATCAAAATCAT
*
2017406 TACACGCATGGTCTGTTTCTTCTTGTGA
66 TACACGCAGGGTCTGTTTCTTCTTGTGA
*
2017434 AACATCTTCCTCGGCAGCGGCTGTTTTATCATCAAAATTCGGATATTGACCAAAATCAAAATCAT
1 AACATCTTCCTCGGCAGCGGCTGTTTCATCATCAAAATTCGGATATTGACCAAAATCAAAATCAT
2017499 TACACGCAGGGTCTGTTTCTTCTTGTGA
66 TACACGCAGGGTCTGTTTCTTCTTGTGA
2017527 AACATC
1 AACATC
2017533 ATCAAAATCT
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 96 1.00
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (93 bp):
AACATCTTCCTCGGCAGCGGCTGTTTCATCATCAAAATTCGGATATTGACCAAAATCAAAATCAT
TACACGCAGGGTCTGTTTCTTCTTGTGA
Found at i:2017560 original size:24 final size:24
Alignment explanation
Indices: 2017533--2017586 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
2017523 GTGAAACATC
* *
2017533 ATCAAAATCTGATTATTGAACAAG
1 ATCAAAATCAGAGTATTGAACAAG
* * *
2017557 ATCAAAGTCAGGGTATTGACCAAG
1 ATCAAAATCAGAGTATTGAACAAG
2017581 ATCAAA
1 ATCAAA
2017587 TTTTGAATAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCAGAGTATTGAACAAG
Found at i:2018503 original size:20 final size:20
Alignment explanation
Indices: 2018478--2018587 Score: 64
Period size: 20 Copynumber: 5.5 Consensus size: 20
2018468 AACTAAAACC
2018478 TGTTGCGAAATTAAAATTCG
1 TGTTGCGAAATTAAAATTCG
*
2018498 TGTTGCGAATTTGAAAA-TCG
1 TGTTGCGAAATT-AAAATTCG
* * **
2018518 AGTTGCAAAAACAAAATTCG
1 TGTTGCGAAATTAAAATTCG
* *
2018538 CGTCGCG-AATTCAGAAA-TCG
1 TGTTGCGAAATT-A-AAATTCG
* * * *
2018558 AGTTGCGAATTTGAAATTCAA
1 TGTTGCGAAATTAAAATTC-G
2018579 TGTTGCGAA
1 TGTTGCGAA
2018588 TTTGGAAACT
Statistics
Matches: 66, Mismatches: 17, Indels: 13
0.69 0.18 0.14
Matches are distributed among these distances:
19 9 0.14
20 39 0.59
21 18 0.27
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (20 bp):
TGTTGCGAAATTAAAATTCG
Found at i:2018605 original size:20 final size:21
Alignment explanation
Indices: 2018542--2018631 Score: 71
Period size: 20 Copynumber: 4.4 Consensus size: 21
2018532 AATTCGCGTC
**
2018542 GCGAATTCAGAAA-TCGAGTT
1 GCGAATTTGGAAACTCGAGTT
* *
2018562 GCGAATTT-GAAATTCAATGTT
1 GCGAATTTGGAAACTCGA-GTT
2018583 GCGAATTTGGAAACT-GAGTT
1 GCGAATTTGGAAACTCGAGTT
* * *
2018603 GCGAAATTGG-AATTCGCGTT
1 GCGAATTTGGAAACTCGAGTT
*
2018623 GCAAATTTG
1 GCGAATTTG
2018632 TTGGTCATTT
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
19 7 0.12
20 33 0.58
21 12 0.21
22 5 0.09
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (21 bp):
GCGAATTTGGAAACTCGAGTT
Found at i:2020396 original size:21 final size:21
Alignment explanation
Indices: 2020370--2020411 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2020360 CTCTGACATT
*
2020370 ATAAATCGTTACATCAATACC
1 ATAAATCATTACATCAATACC
* *
2020391 ATAAATTATTATATCAATACC
1 ATAAATCATTACATCAATACC
2020412 GAAACAATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.19, G:0.02, T:0.33
Consensus pattern (21 bp):
ATAAATCATTACATCAATACC
Found at i:2025095 original size:29 final size:29
Alignment explanation
Indices: 2025044--2025099 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
2025034 AAATTTTGTC
*
2025044 TAGTGACTAAAATGTAACTTTTGAAAATT
1 TAGTGACTAAAATATAACTTTTGAAAATT
*
2025073 TAGTGACTAAAGTATAAAC-TTTGAAAA
1 TAGTGACTAAAATAT-AACTTTTGAAAA
2025100 GTTAAGGAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 21 0.88
30 3 0.12
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (29 bp):
TAGTGACTAAAATATAACTTTTGAAAATT
Found at i:2027502 original size:18 final size:18
Alignment explanation
Indices: 2027477--2027536 Score: 84
Period size: 18 Copynumber: 3.3 Consensus size: 18
2027467 ATGTTTACTA
2027477 TTATCATATGATTTTCAG
1 TTATCATATGATTTTCAG
* *
2027495 TGATCATATGATTTTTAG
1 TTATCATATGATTTTCAG
* *
2027513 TTATCAGATGATTTACAG
1 TTATCATATGATTTTCAG
2027531 TTATCA
1 TTATCA
2027537 AATAATTATA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.47
Consensus pattern (18 bp):
TTATCATATGATTTTCAG
Found at i:2032241 original size:44 final size:45
Alignment explanation
Indices: 2032191--2032282 Score: 134
Period size: 44 Copynumber: 2.1 Consensus size: 45
2032181 TTTGTAGTAA
*
2032191 TGAATTGCTATATAGAATAAAC-CTGTCCC-TTTGTGAAATTCTAG
1 TGAATTGCTATATAAAATAAACAC-GTCCCTTTTGTGAAATTCTAG
* *
2032235 TGAATTGCTCTATAAAATAAACACGTCCCTTTTGTGAAATTTTAG
1 TGAATTGCTATATAAAATAAACACGTCCCTTTTGTGAAATTCTAG
2032280 TGA
1 TGA
2032283 TATGTGACGA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
44 25 0.58
45 18 0.42
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (45 bp):
TGAATTGCTATATAAAATAAACACGTCCCTTTTGTGAAATTCTAG
Found at i:2032962 original size:21 final size:20
Alignment explanation
Indices: 2032921--2032964 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 20
2032911 ATATATATAT
*
2032921 ATTAACAAAAAAAATTTGAA
1 ATTAACAAAAAAAATTGGAA
2032941 ATTAA-AAAAAAAATCTAGGAA
1 ATTAACAAAAAAAAT-T-GGAA
2032962 ATT
1 ATT
2032965 TCAATACCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 9 0.43
20 6 0.29
21 6 0.29
ACGTcount: A:0.64, C:0.05, G:0.07, T:0.25
Consensus pattern (20 bp):
ATTAACAAAAAAAATTGGAA
Found at i:2041969 original size:226 final size:228
Alignment explanation
Indices: 2041575--2042029 Score: 887
Period size: 226 Copynumber: 2.0 Consensus size: 228
2041565 TACATATTTT
2041575 ATCCTAAGTTCACAAAACAATTGCAGAAAATATATATAAACAATAAACAATTAGACAATCCAGAA
1 ATCCTAAGTTCACAAAACAATTGCAGAAAATATATATAAACAATAAACAATTAGACAATCCAGAA
*
2041640 ACACACACGAATGCAAAGTGTAAAAGAAAAAAACTTACATGTTTGGATCCTCAACAAGGACGGCG
66 ACACACACGAATGCAAAGTGTAAAAGAAAAAAACTTACATGTTTGGATCCTCAACAAGGAAGGCG
2041705 GTTTCTTGAGCGAAGGTGTCCTGAAGCACGAGCTCTTCCTTTTCTCCATCTGCATCGGCC-TTTC
131 GTTTCTTGAGCGAAGGTGTCCTGAAGCACGAGCTCTTCCTTTTCTCCATCTGCATCGGCCTTTTC
2041769 GGTAACTTTAACGACGGCGCCT-CGGTTTGCAC
196 GGTAACTTTAACGACGGCGCCTCCGGTTTGCAC
2041801 ATCCTAAGTTCACAAAACAATTGCAGAAAATATATATAAACAATAAACAATTAGACAATCCAGAA
1 ATCCTAAGTTCACAAAACAATTGCAGAAAATATATATAAACAATAAACAATTAGACAATCCAGAA
2041866 ACACACACGAATGCAAAGTGTAAAAGAAAAAAACTTACATGTTTGGATCCTCAACAAGGAAGGCG
66 ACACACACGAATGCAAAGTGTAAAAGAAAAAAACTTACATGTTTGGATCCTCAACAAGGAAGGCG
2041931 GTTTCTTGAGCGAAGGTGTCCTGAAGCACGAGCTCTTCCTTTTCTCCATCTGCATCGGCCTTTTC
131 GTTTCTTGAGCGAAGGTGTCCTGAAGCACGAGCTCTTCCTTTTCTCCATCTGCATCGGCCTTTTC
2041996 GGTAACTTTAACGACGGCGCCTCCGGTTTGCAC
196 GGTAACTTTAACGACGGCGCCTCCGGTTTGCAC
2042029 A
1 A
2042030 GCAGGTATTG
Statistics
Matches: 226, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
226 189 0.84
227 26 0.12
228 11 0.05
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (228 bp):
ATCCTAAGTTCACAAAACAATTGCAGAAAATATATATAAACAATAAACAATTAGACAATCCAGAA
ACACACACGAATGCAAAGTGTAAAAGAAAAAAACTTACATGTTTGGATCCTCAACAAGGAAGGCG
GTTTCTTGAGCGAAGGTGTCCTGAAGCACGAGCTCTTCCTTTTCTCCATCTGCATCGGCCTTTTC
GGTAACTTTAACGACGGCGCCTCCGGTTTGCAC
Found at i:2042395 original size:6 final size:6
Alignment explanation
Indices: 2042384--2042414 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
2042374 CCAAATAACG
2042384 CCAGCC CCAGCC CCAGCC CCAGCC CCAGCC C
1 CCAGCC CCAGCC CCAGCC CCAGCC CCAGCC C
2042415 AGGCAGGCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.68, G:0.16, T:0.00
Consensus pattern (6 bp):
CCAGCC
Found at i:2043053 original size:3 final size:3
Alignment explanation
Indices: 2043039--2043092 Score: 65
Period size: 3 Copynumber: 18.0 Consensus size: 3
2043029 GAGGATGAGG
* * *
2043039 AGA AGA ATA AGA AGA AGA AGG AGA ATG- AGA AGA AGA AGA AGG AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA A-GA AGA AGA AGA AGA AGA AGA
2043084 AGA AGA AGA
1 AGA AGA AGA
2043093 TTAAAGAGTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
2 1 0.02
3 41 0.95
4 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.35, T:0.04
Consensus pattern (3 bp):
AGA
Found at i:2043060 original size:21 final size:21
Alignment explanation
Indices: 2043036--2043092 Score: 89
Period size: 21 Copynumber: 2.7 Consensus size: 21
2043026 ATGGAGGATG
*
2043036 AGGAGAAGAATAAGAAGAAGA
1 AGGAGAAGAAGAAGAAGAAGA
2043057 AGGAGAATG-AGAAGAAGAAGA
1 AGGAGAA-GAAGAAGAAGAAGA
2043078 AGGAGAAGAAGAAGA
1 AGGAGAAGAAGAAGA
2043093 TTAAAGAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 1 0.03
21 31 0.94
22 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.37, T:0.04
Consensus pattern (21 bp):
AGGAGAAGAAGAAGAAGAAGA
Found at i:2043069 original size:15 final size:15
Alignment explanation
Indices: 2043039--2043092 Score: 72
Period size: 15 Copynumber: 3.6 Consensus size: 15
2043029 GAGGATGAGG
* *
2043039 AGAAGAATAAGAAGA
1 AGAAGAAGAAGGAGA
* *
2043054 AGAAGGAGAATGAGA
1 AGAAGAAGAAGGAGA
2043069 AGAAGAAGAAGGAGA
1 AGAAGAAGAAGGAGA
2043084 AGAAGAAGA
1 AGAAGAAGA
2043093 TTAAAGAGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.61, C:0.00, G:0.35, T:0.04
Consensus pattern (15 bp):
AGAAGAAGAAGGAGA
Found at i:2049219 original size:2 final size:2
Alignment explanation
Indices: 2049212--2049263 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
2049202 AGTATACTTT
2049212 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
2049254 TA TA TA TA TA
1 TA TA TA TA TA
2049264 ATAATGGAAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2056922 original size:3 final size:3
Alignment explanation
Indices: 2056914--2056984 Score: 117
Period size: 3 Copynumber: 23.7 Consensus size: 3
2056904 TTAATATATT
2056914 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -ATA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
*
2056959 TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
2056985 TGGATAAAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
2 1 0.02
3 62 0.97
4 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2056923 original size:15 final size:16
Alignment explanation
Indices: 2056905--2056985 Score: 109
Period size: 15 Copynumber: 5.4 Consensus size: 16
2056895 TATATATGTT
*
2056905 TAATATAT-TTAATAA
1 TAATATATAATAATAA
2056920 TAATA-ATAATAATAA
1 TAATATATAATAATAA
2056935 TAATA-ATAATAATAA
1 TAATATATAATAATAA
*
2056950 TAATAAAT-ATAATAA
1 TAATATATAATAATAA
2056965 TAATAT-TAATAATAA
1 TAATATATAATAATAA
2056980 TAATAT
1 TAATAT
2056986 GGATAAAAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
14 3 0.05
15 56 0.92
16 2 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATATATAATAATAA
Done.