Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000482.1 Hibiscus syriacus cultivar Beakdansim tig00000916_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: 2886609
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 16
Found at i:1370997 original size:73 final size:74
Alignment explanation
Indices: 1370919--1371062 Score: 245
Period size: 73 Copynumber: 2.0 Consensus size: 74
1370909 TGCACAACAG
*
1370919 GGTGCATCGATGCACTAATTGCATTCGAAATGGAGTGCATGGATGCACTGCA-TGGTGCATCGAT
1 GGTGCATCGATGCACTAATTGCATTCGAAATGGAGTGCATGGATGCACTGCAGGGGTGCATCGAT
1370983 GCACTGTAT
66 GCACTGTAT
* * *
1370992 GGTGCATCGATGCATTAATTGCATTCTAAATGGAGTGCATGGATGCACTGCAGGGGTGCATGGAT
1 GGTGCATCGATGCACTAATTGCATTCGAAATGGAGTGCATGGATGCACTGCAGGGGTGCATCGAT
1371057 GCACTG
66 GCACTG
1371063 CAGGGCTGTA
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
73 50 0.76
74 16 0.24
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (74 bp):
GGTGCATCGATGCACTAATTGCATTCGAAATGGAGTGCATGGATGCACTGCAGGGGTGCATCGAT
GCACTGTAT
Found at i:1371050 original size:21 final size:21
Alignment explanation
Indices: 1371026--1371103 Score: 120
Period size: 21 Copynumber: 3.7 Consensus size: 21
1371016 TCTAAATGGA
1371026 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
1371047 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
* * **
1371068 CTGTATGGATGCACTGCAATG
1 GTGCATGGATGCACTGCAGGG
1371089 GTGCATGGATGCACT
1 GTGCATGGATGCACT
1371104 TTGACACCCT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.21, C:0.19, G:0.37, T:0.23
Consensus pattern (21 bp):
GTGCATGGATGCACTGCAGGG
Found at i:1371349 original size:21 final size:21
Alignment explanation
Indices: 1371325--1371364 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1371315 ATGTTTAATG
1371325 AAAAAGATACCAATTGTTAAC
1 AAAAAGATACCAATTGTTAAC
* *
1371346 AAAATGATATCAATTGTTA
1 AAAAAGATACCAATTGTTA
1371365 CCAATCGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATACCAATTGTTAAC
Found at i:1374012 original size:21 final size:21
Alignment explanation
Indices: 1373941--1374043 Score: 120
Period size: 21 Copynumber: 4.9 Consensus size: 21
1373931 CATTCGAAAT
1373941 GGAGTGCATGGATGCACTGCA
1 GGAGTGCATGGATGCACTGCA
* * *
1373962 -TAGTGCATCGATGCACTAG-T
1 GGAGTGCATGGATGCACT-GCA
1373982 GGCAGGTGCATGGATGCACTGCA
1 GG-A-GTGCATGGATGCACTGCA
*
1374005 GGGGTGCATGGATGCACTGCA
1 GGAGTGCATGGATGCACTGCA
*
1374026 GGAGTGCATGGATTCACT
1 GGAGTGCATGGATGCACT
1374044 TTGACACCCT
Statistics
Matches: 68, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
20 15 0.22
21 35 0.51
22 2 0.03
23 16 0.24
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.22
Consensus pattern (21 bp):
GGAGTGCATGGATGCACTGCA
Found at i:1375346 original size:17 final size:17
Alignment explanation
Indices: 1375313--1375346 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1375303 TGACCACCAA
* *
1375313 CCAACTTGTCAACTTTG
1 CCAACTTGCCAAATTTG
1375330 CCAACTTGCCAAATTTG
1 CCAACTTGCCAAATTTG
1375347 ACAATTTGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.32
Consensus pattern (17 bp):
CCAACTTGCCAAATTTG
Found at i:1381043 original size:6 final size:6
Alignment explanation
Indices: 1381032--1381150 Score: 67
Period size: 6 Copynumber: 19.8 Consensus size: 6
1381022 ATGCATACAG
* * * * *
1381032 ACATAT ACATAT ACATAC ACATAC ACATAC GCATAC GCATAC GCATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
* * *** * * * * * *** *
1381080 GCATAT AGGCAC GCATAC GCATAC GCATAC GCATAT AGGCAC GCATAC
1 ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC ACATAC
1381128 ACATAC ACATAC ACATAC ACATA
1 ACATAC ACATAC ACATAC ACATA
1381151 TAGGCACGCA
Statistics
Matches: 90, Mismatches: 23, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 90 1.00
ACGTcount: A:0.41, C:0.29, G:0.11, T:0.18
Consensus pattern (6 bp):
ACATAC
Found at i:1381094 original size:30 final size:30
Alignment explanation
Indices: 1381060--1381144 Score: 143
Period size: 30 Copynumber: 2.8 Consensus size: 30
1381050 ACATACACAT
1381060 ACGCATACGCATACGCATACGCATATAGGC
1 ACGCATACGCATACGCATACGCATATAGGC
1381090 ACGCATACGCATACGCATACGCATATAGGC
1 ACGCATACGCATACGCATACGCATATAGGC
* * *
1381120 ACGCATACACATACACATACACATA
1 ACGCATACGCATACGCATACGCATA
1381145 CACATATAGG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.38, C:0.31, G:0.15, T:0.16
Consensus pattern (30 bp):
ACGCATACGCATACGCATACGCATATAGGC
Found at i:1381165 original size:18 final size:18
Alignment explanation
Indices: 1381102--1381168 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 18
1381092 GCATACGCAT
*
1381102 ACGCATACGCATATAGGC
1 ACGCATACACATATAGGC
* ***
1381120 ACGCATACACATACACAT
1 ACGCATACACATATAGGC
*
1381138 ACACATACACATATAGGC
1 ACGCATACACATATAGGC
*
1381156 ACGCACACACATA
1 ACGCATACACATA
1381169 GATTAAAGAT
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.42, C:0.31, G:0.12, T:0.15
Consensus pattern (18 bp):
ACGCATACACATATAGGC
Found at i:1381166 original size:30 final size:30
Alignment explanation
Indices: 1381060--1381168 Score: 110
Period size: 30 Copynumber: 3.4 Consensus size: 30
1381050 ACATACACAT
* *
1381060 ACGCATACGCATACGCATACGCATATAGGC
1 ACGCACACACATACGCATACGCATATAGGC
* *
1381090 ACGCATACGCATACGCATACGCATATAGGC
1 ACGCACACACATACGCATACGCATATAGGC
* *
1381120 ACGCATACACATACACATACACATACACATATAGGC
1 ACG----CAC--ACACATACGCATACGCATATAGGC
1381156 ACGCACACACATA
1 ACGCACACACATA
1381169 GATTAAAGAT
Statistics
Matches: 69, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
30 40 0.58
32 3 0.04
34 2 0.03
36 24 0.35
ACGTcount: A:0.39, C:0.31, G:0.15, T:0.16
Consensus pattern (30 bp):
ACGCACACACATACGCATACGCATATAGGC
Found at i:1381166 original size:36 final size:36
Alignment explanation
Indices: 1381093--1381168 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
1381083 TATAGGCACG
* * * *
1381093 CATACGCATACGCATACGCATATAGGCACGCATACA
1 CATACACATACACATACACATATAGGCACGCACACA
1381129 CATACACATACACATACACATATAGGCACGCACACA
1 CATACACATACACATACACATATAGGCACGCACACA
1381165 CATA
1 CATA
1381169 GATTAAAGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.41, C:0.32, G:0.12, T:0.16
Consensus pattern (36 bp):
CATACACATACACATACACATATAGGCACGCACACA
Found at i:1389107 original size:24 final size:24
Alignment explanation
Indices: 1389069--1389122 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
1389059 TTAACATTGA
1389069 ATATTATAAAGTGAGAAGCTCAAAT
1 ATATTATAAAGTGAGAAG-TCAAAT
*
1389094 ATATT-TAAATTGAGAAGTC--AT
1 ATATTATAAAGTGAGAAGTCAAAT
1389115 ATATTATA
1 ATATTATA
1389123 TTTATATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 7 0.26
22 2 0.07
23 2 0.07
24 11 0.41
25 5 0.19
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (24 bp):
ATATTATAAAGTGAGAAGTCAAAT
Found at i:1392234 original size:23 final size:23
Alignment explanation
Indices: 1392208--1392255 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1392198 ATAAAGTACA
*
1392208 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
1392231 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
1392254 AT
1 AT
1392256 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:1393008 original size:18 final size:18
Alignment explanation
Indices: 1392985--1393021 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1392975 CGAAATATAT
1392985 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1393003 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
1393021 A
1 A
1393022 CTCCAATTAC
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:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:1393251 original size:23 final size:23
Alignment explanation
Indices: 1393225--1393289 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
1393215 ATGCGAGATA
1393225 GATACCTATTACATTATATAAAC
1 GATACCTATTACATTATATAAAC
**
1393248 GATACCTATTACATTATATAAGG
1 GATACCTATTACATTATATAAAC
* *
1393271 GCTACCTATTACATCATAT
1 GATACCTATTACATTATAT
1393290 GTTTACCTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.35
Consensus pattern (23 bp):
GATACCTATTACATTATATAAAC
Found at i:1393475 original size:30 final size:29
Alignment explanation
Indices: 1393435--1393501 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
1393425 TCATTTGCAC
* * *
1393435 AAAAAATTATTT-GATTGTTTTATATTTTAT
1 AAAATATTATTTAGAAT-TTTTA-ATTTAAT
1393465 AAAATATTATTTAGAATTTTTAATTTAAT
1 AAAATATTATTTAGAATTTTTAATTTAAT
1393494 AATAATAT
1 AA-AATAT
1393502 ATACCGTAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 8 0.25
30 21 0.66
31 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (29 bp):
AAAATATTATTTAGAATTTTTAATTTAAT
Found at i:1393671 original size:21 final size:22
Alignment explanation
Indices: 1393646--1393697 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
1393636 ACACTTTACA
*
1393646 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
1393669 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
1393692 ATATAA
1 ATATAA
1393698 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:1393682 original size:23 final size:23
Alignment explanation
Indices: 1393656--1393718 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1393646 ATATAACCAC
1393656 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
1393679 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
1393702 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1393719 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1394113 original size:23 final size:23
Alignment explanation
Indices: 1394087--1394154 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
1394077 ATATAACCAC
1394087 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
1394110 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
1394133 TACCTATTACATTATATTAACG
1 TACCTATTACATTATATAAACG
1394155 GTGAGGGGCA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1394323 original size:431 final size:422
Alignment explanation
Indices: 1393227--1394153 Score: 1048
Period size: 429 Copynumber: 2.2 Consensus size: 422
1393217 GCGAGATAGA
*
1393227 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACAT-ATATAT
* **** ** * ** ** * *** **
1393292 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
65 TAACCTAGGGCATACAAACTGAACATACTCCTCATAAAAAGGA-CGATACTTTGAGTAAAACACA
** * * *** * ** *
1393357 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
129 TGTAATCAATG--T--ATTTTTTGAACAGTG--TAATGGAATCCACCAACAATATCCATATAATA
* ** *
1393422 ATTTCATTTGCACAAAAAATTATTTGATTGTTT-TATATTTTATAAAATATTATTTAGAATTTTT
188 ATATCATAAGCACAAAAAATTATTTGATTGTTTAAATATTTTATAAAATATTATTTAGAATTTTT
1393486 AATTTAATAATAATATATACCGTAACGTAAAAATAAATCATTAGACGCCTATAATTACTAAATTA
253 AATTTAATAATAATATATACCGTAACGTAAAAATAAATCATTAGACGCCTATAATTACTAAATTA
*
1393551 ATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACATTGAAAAAAGTATGAA
318 ATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGAA
1393616 CACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
383 CACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
*
1393656 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACAT-ATATAT
* **** ** * ** ** * *** **
1393721 TTACCTATTTTATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
65 TAACCTAGGGCATACAAACTGAACATACTCCTCATAAAAAGGA-CGATACTTTGAGTAAAACACA
** * * *** * ** *
1393786 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
129 TGTAATCAATG--T--ATTTTTTGAACAGTG--TAATGGAATCCACCAACAATATCCATATAATA
* ** **
1393851 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
188 ATATCATAAGCACAAAAAATTATTTGATTGTTTAAATATTTTATAAAATATTATTTAGAATTTTT
1393916 AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
253 AATTTAATAATAATATATACCGTAACGT-AAAAATAAATCATTAGACGCCTATAATTACTAAATT
*
1393981 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
317 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGA
1394046 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
382 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAC
1394087 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACAT-TATATT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATATATATT
1394151 AAC
66 AAC
1394154 GGTGAGGGGC
Statistics
Matches: 491, Mismatches: 5, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
429 234 0.48
430 59 0.12
431 198 0.40
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.40
Consensus pattern (422 bp):
TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATATATATT
AACCTAGGGCATACAAACTGAACATACTCCTCATAAAAAGGACGATACTTTGAGTAAAACACATG
TAATCAATGTATTTTTTGAACAGTGTAATGGAATCCACCAACAATATCCATATAATAATATCATA
AGCACAAAAAATTATTTGATTGTTTAAATATTTTATAAAATATTATTTAGAATTTTTAATTTAAT
AATAATATATACCGTAACGTAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTA
AAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGAACACTTTTA
TAAAAAGGATAGACACTTTACAATATAACCAC
Found at i:1394687 original size:184 final size:184
Alignment explanation
Indices: 1394378--1394716 Score: 624
Period size: 184 Copynumber: 1.8 Consensus size: 184
1394368 TTTTAAATGG
* *
1394378 TATGGACATAAAGTACCGACACAATATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1394443 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
* *
1394508 GATGTATAAAATGTCGACATTTTTTTAAATCGTATCGACATATTTTTCTTCCAA
131 AATGTATAAAATGTCGACACTTTTTTAAATCGTATCGACATATTTTTCTTCCAA
1394562 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
*
1394627 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
*
1394692 AATGTGTAAAATGTCGACACTTTTT
131 AATGTATAAAATGTCGACACTTTTT
1394717 ATTTTTCCTT
Statistics
Matches: 149, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
184 149 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (184 bp):
TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
AATGTATAAAATGTCGACACTTTTTTAAATCGTATCGACATATTTTTCTTCCAA
Found at i:1394991 original size:24 final size:24
Alignment explanation
Indices: 1394954--1395006 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1394944 CCGTTCTATC
1394954 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
1394978 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
1395002 TATTT
1 TATTT
1395007 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:1395197 original size:20 final size:19
Alignment explanation
Indices: 1395151--1395197 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1395141 TCCGGTATCA
*
1395151 TTTTACCGTTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
1395170 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
1395191 TTTTACC
1 TTTTACC
1395198 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:1395345 original size:20 final size:20
Alignment explanation
Indices: 1395319--1395364 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
1395309 CACTTTTAAA
1395319 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
1395338 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
1395359 TTTACC
1 TTTACC
1395365 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:1396721 original size:2 final size:2
Alignment explanation
Indices: 1396714--1396808 Score: 190
Period size: 2 Copynumber: 47.5 Consensus size: 2
1396704 GTTTGAGATA
1396714 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
1396756 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
1396798 AT AT AT AT AT A
1 AT AT AT AT AT A
1396809 GAGATAGGGT
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 93 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1397476 original size:20 final size:19
Alignment explanation
Indices: 1397453--1397512 Score: 50
Period size: 20 Copynumber: 2.9 Consensus size: 19
1397443 AAACATAATC
1397453 TATATAATCTATTAATAAAA
1 TATATAAT-TATTAATAAAA
* *
1397473 TATAAAATATATATAA-CAAA
1 TATATAAT-TAT-TAATAAAA
1397493 TATTATAATTGATTAATAAA
1 TA-TATAATT-ATTAATAAA
1397513 TAAATATGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
20 19 0.61
21 12 0.39
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (19 bp):
TATATAATTATTAATAAAA
Found at i:1398033 original size:2 final size:2
Alignment explanation
Indices: 1398028--1398084 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
1398018 TGTGTGTGTC
1398028 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
1398070 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
1398085 CGTATTATCG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1398916 original size:22 final size:21
Alignment explanation
Indices: 1398886--1398926 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
1398876 TTTTATAAAT
1398886 ATTTTA-TTTTAATTCAATTAC
1 ATTTTATTTTTAA-TCAATTAC
1398907 ATTTATATTTTTAATCAATT
1 ATTT-TATTTTTAATCAATT
1398927 TATAATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.22
22 8 0.44
23 6 0.33
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTTTATTTTTAATCAATTAC
Found at i:1398935 original size:23 final size:23
Alignment explanation
Indices: 1398892--1398955 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
1398882 AAATATTTTA
* *
1398892 TTTTAATTCAA-TTACATTTATAT
1 TTTTAA-TCAATTTATAATTATAT
1398915 TTTTAATCAATTTATAATTATAT
1 TTTTAATCAATTTATAATTATAT
* * *
1398938 GTTT-AGCACTTTATAATT
1 TTTTAATCAATTTATAATT
1398956 TAACGTTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
22 16 0.46
23 19 0.54
ACGTcount: A:0.34, C:0.08, G:0.03, T:0.55
Consensus pattern (23 bp):
TTTTAATCAATTTATAATTATAT
Found at i:1402083 original size:3 final size:3
Alignment explanation
Indices: 1402064--1402111 Score: 51
Period size: 3 Copynumber: 14.7 Consensus size: 3
1402054 GGTTTTTTAA
*
1402064 AAT AAT AAAT AAGT AAT AAT ATTT AAT AAT AAT AAT AAT AAT ACAT AA
1 AAT AAT -AAT AA-T AAT AAT A-AT AAT AAT AAT AAT AAT AAT A-AT AA
1402112 AAGTTGAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
3 28 0.72
4 11 0.28
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1404097 original size:3 final size:3
Alignment explanation
Indices: 1404089--1404121 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1404079 GAATTGGGTT
1404089 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1404122 GATACACGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:1405073 original size:15 final size:15
Alignment explanation
Indices: 1405053--1405083 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1405043 ATATTTATAT
1405053 TTTTTAAATTCTTAA
1 TTTTTAAATTCTTAA
*
1405068 TTTTTAAATTTTTAA
1 TTTTTAAATTCTTAA
1405083 T
1 T
1405084 AATATTATTA
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:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTTAAATTCTTAA
Found at i:1405314 original size:21 final size:20
Alignment explanation
Indices: 1405282--1405320 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1405272 ATTCATATAT
*
1405282 CCAAACTTAAATCTCTAAAC
1 CCAAACTCAAATCTCTAAAC
1405302 CCAATACTCAAATCTCTAA
1 CCAA-ACTCAAATCTCTAA
1405321 CCCTAATCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.26
Consensus pattern (20 bp):
CCAAACTCAAATCTCTAAAC
Found at i:1407077 original size:13 final size:13
Alignment explanation
Indices: 1407059--1407083 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1407049 TATTTAGAGA
1407059 AATAAATTTATTT
1 AATAAATTTATTT
1407072 AATAAATTTATT
1 AATAAATTTATT
1407084 AACGTTGATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATAAATTTATTT
Found at i:1413798 original size:13 final size:13
Alignment explanation
Indices: 1413780--1413808 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1413770 CGATCGAAAT
1413780 AAGCGAAATCAAG
1 AAGCGAAATCAAG
1413793 AAGCGAAATCAAG
1 AAGCGAAATCAAG
1413806 AAG
1 AAG
1413809 TTTGATGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.14, G:0.24, T:0.07
Consensus pattern (13 bp):
AAGCGAAATCAAG
Found at i:1422904 original size:2 final size:2
Alignment explanation
Indices: 1422897--1422936 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1422887 CATTGGTAAC
1422897 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
1422937 GAATACACAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1436412 original size:3 final size:3
Alignment explanation
Indices: 1436406--1436513 Score: 146
Period size: 3 Copynumber: 35.7 Consensus size: 3
1436396 TTTTTTTTTA
* *
1436406 TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TGT TATT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
* *
1436452 TAT TAT TAT TAT TAT TAT TAT TGT TAT TGT TATT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
*
1436498 TA- TAT TAT TAA TAT TA
1 TAT TAT TAT TAT TAT TA
1436514 CATTTTACAC
Statistics
Matches: 92, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
2 2 0.02
3 84 0.91
4 6 0.07
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1436461 original size:40 final size:40
Alignment explanation
Indices: 1436406--1436512 Score: 198
Period size: 40 Copynumber: 2.7 Consensus size: 40
1436396 TTTTTTTTTA
1436406 TATTATTATTATTATTATTATTATTATTGTTATTGTTATT
1 TATTATTATTATTATTATTATTATTATTGTTATTGTTATT
1436446 TATTATTATTATTATTATTATTATTATTGTTATTGTTATT
1 TATTATTATTATTATTATTATTATTATTGTTATTGTTATT
*
1436486 TATTATTATTATTA-TATTATTAATATT
1 TATTATTATTATTATTATTATTATTATT
1436513 ACATTTTACA
Statistics
Matches: 66, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
39 12 0.18
40 54 0.82
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (40 bp):
TATTATTATTATTATTATTATTATTATTGTTATTGTTATT
Found at i:1436626 original size:25 final size:25
Alignment explanation
Indices: 1436598--1436671 Score: 114
Period size: 25 Copynumber: 3.0 Consensus size: 25
1436588 CTGAACCACC
1436598 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
1436623 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
* * *
1436648 AACAAATTAGGGTTT-TAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
1436672 TCCCCTAATG
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
24 8 0.17
25 38 0.83
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:1438621 original size:63 final size:63
Alignment explanation
Indices: 1438553--1438682 Score: 154
Period size: 63 Copynumber: 2.1 Consensus size: 63
1438543 AATGTGTGTT
* * * * *
1438553 TTTTTAAATAGT-AATTTATTTTATTTTATGTAAATGTCAATTTGCATTTGTATTCAATTCACA
1 TTTTTAAATAATCAATTTATTTTATTGTATGCAAACGTCAATTT-CATTTATATTCAATTCACA
** * * *
1438616 TTTTTAGTTAATCAATTTATTTTGTTGTATGCAAACGTCAATTTTATTTATATTCGATTCACA
1 TTTTTAAATAATCAATTTATTTTATTGTATGCAAACGTCAATTTCATTTATATTCAATTCACA
1438679 TTTT
1 TTTT
1438683 ATCAAAAGGG
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
63 29 0.52
64 27 0.48
ACGTcount: A:0.29, C:0.09, G:0.08, T:0.53
Consensus pattern (63 bp):
TTTTTAAATAATCAATTTATTTTATTGTATGCAAACGTCAATTTCATTTATATTCAATTCACA
Found at i:1445692 original size:52 final size:51
Alignment explanation
Indices: 1445635--1445776 Score: 169
Period size: 51 Copynumber: 2.8 Consensus size: 51
1445625 GGTTATGCGA
* * *
1445635 TAGATAAGGATAATTAATTAGTATTTTAATATAACACTT-ACTCTTAGAAAGT
1 TAGATAAGGATAACTAATAAGTAGTTTAATATAA-A-TTAACTCTTAGAAAGT
* * * *
1445687 TAGATAAAGATAACTACTAAGTAGTTTAGTTTAAATTAACTCTTAGAAAGT
1 TAGATAAGGATAACTAATAAGTAGTTTAATATAAATTAACTCTTAGAAAGT
* * *
1445738 TAGATAAGGATAACTACTAAGTAGTTTAGTTTAAATTAA
1 TAGATAAGGATAACTAATAAGTAGTTTAATATAAATTAA
1445777 ATACTTGTTC
Statistics
Matches: 81, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
50 2 0.02
51 52 0.64
52 27 0.33
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (51 bp):
TAGATAAGGATAACTAATAAGTAGTTTAATATAAATTAACTCTTAGAAAGT
Found at i:1445712 original size:25 final size:25
Alignment explanation
Indices: 1445684--1445763 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
1445674 ACTCTTAGAA
1445684 AGTTAGATAAAGATAACTACTAAGT
1 AGTTAGATAAAGATAACTACTAAGT
* * * *
1445709 AGTTTAGTTTAAA-TTAACT-CTTAGAA
1 AG-TTAG-ATAAAGATAACTACTAAG-T
*
1445735 AGTTAGATAAGGATAACTACTAAGT
1 AGTTAGATAAAGATAACTACTAAGT
1445760 AGTT
1 AGTT
1445764 TAGTTTAAAT
Statistics
Matches: 41, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
24 3 0.07
25 19 0.46
26 15 0.37
27 4 0.10
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.34
Consensus pattern (25 bp):
AGTTAGATAAAGATAACTACTAAGT
Found at i:1445726 original size:26 final size:26
Alignment explanation
Indices: 1445697--1445781 Score: 79
Period size: 26 Copynumber: 3.3 Consensus size: 26
1445687 TAGATAAAGA
1445697 TAACTACTAAGTAGTTTAGTTTAAAT
1 TAACTACTAAGTAGTTTAGTTTAAAT
* * *
1445723 TAACT-CTTAGAAAG-TTAG-ATAAGGA-
1 TAACTACTAAG-TAGTTTAGTTTAA--AT
1445748 TAACTACTAAGTAGTTTAGTTTAAAT
1 TAACTACTAAGTAGTTTAGTTTAAAT
*
1445774 TAAATACT
1 TAACTACT
1445782 TGTTCTCACC
Statistics
Matches: 45, Mismatches: 7, Indels: 14
0.68 0.11 0.21
Matches are distributed among these distances:
24 3 0.07
25 16 0.36
26 23 0.51
27 3 0.07
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (26 bp):
TAACTACTAAGTAGTTTAGTTTAAAT
Found at i:1445736 original size:51 final size:51
Alignment explanation
Indices: 1445674--1445776 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
1445664 TATAACACTT
1445674 ACTCTTAGAAAGTTAGATAAAGATAACTACTAAGTAGTTTAGTTTAAATTA
1 ACTCTTAGAAAGTTAGATAAAGATAACTACTAAGTAGTTTAGTTTAAATTA
*
1445725 ACTCTTAGAAAGTTAGATAAGGATAACTACTAAGTAGTTTAGTTTAAATTA
1 ACTCTTAGAAAGTTAGATAAAGATAACTACTAAGTAGTTTAGTTTAAATTA
1445776 A
1 A
1445777 ATACTTGTTC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.35
Consensus pattern (51 bp):
ACTCTTAGAAAGTTAGATAAAGATAACTACTAAGTAGTTTAGTTTAAATTA
Found at i:1452530 original size:51 final size:51
Alignment explanation
Indices: 1452458--1452562 Score: 156
Period size: 51 Copynumber: 2.1 Consensus size: 51
1452448 AATATAACAC
* * *
1452458 TAACTCTTAAAAAGTTAGATAAAGATAACTACCAAGTAGTTTAGTTTAAAT
1 TAACACTTAAAAAGTTAGATAAAGATAACTAACAAGTAGTTTAGTCTAAAT
* * *
1452509 TAACACTTAGAAAGTTAGATAAGGATAACTAATAAGTAGTTTAGTCTAAAT
1 TAACACTTAAAAAGTTAGATAAAGATAACTAACAAGTAGTTTAGTCTAAAT
1452560 TAA
1 TAA
1452563 ATACTTGTTC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.32
Consensus pattern (51 bp):
TAACACTTAAAAAGTTAGATAAAGATAACTAACAAGTAGTTTAGTCTAAAT
Found at i:1458300 original size:39 final size:41
Alignment explanation
Indices: 1458248--1458341 Score: 111
Period size: 39 Copynumber: 2.3 Consensus size: 41
1458238 TTCGGTTTGC
*
1458248 AAAAAACCGGTTTTAAAAAAAAACCGGATTTTT-T-CGGAT
1 AAAAAACCAGTTTTAAAAAAAAACCGGATTTTTATCCGGAT
* ** * *
1458287 AAAAAATCAGTTTTTTAAAAAATCCGGTTTTTTATCCGGAT
1 AAAAAACCAGTTTTAAAAAAAAACCGGATTTTTATCCGGAT
*
1458328 AAAAAACCGGTTTT
1 AAAAAACCAGTTTT
1458342 TAATCCGGTA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
39 27 0.60
40 1 0.02
41 17 0.38
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (41 bp):
AAAAAACCAGTTTTAAAAAAAAACCGGATTTTTATCCGGAT
Found at i:1458307 original size:16 final size:17
Alignment explanation
Indices: 1458286--1458320 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1458276 TTTTTTCGGA
1458286 TAAAAAAT-CAGTTTTT
1 TAAAAAATCCAGTTTTT
*
1458302 TAAAAAATCCGGTTTTT
1 TAAAAAATCCAGTTTTT
1458319 TA
1 TA
1458321 TCCGGATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.43
Consensus pattern (17 bp):
TAAAAAATCCAGTTTTT
Found at i:1458337 original size:24 final size:24
Alignment explanation
Indices: 1458302--1458356 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
1458292 ATCAGTTTTT
*
1458302 TAAAAAATCCGGTTTTTTATCCGG
1 TAAAAAATCCGGTTTTTAATCCGG
1458326 ATAAAAAA-CCGGTTTTTAATCCGG
1 -TAAAAAATCCGGTTTTTAATCCGG
1458350 TAAAAAA
1 TAAAAAA
1458357 ACCGATCGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 7 0.24
24 15 0.52
25 7 0.24
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (24 bp):
TAAAAAATCCGGTTTTTAATCCGG
Found at i:1458341 original size:23 final size:25
Alignment explanation
Indices: 1458302--1458356 Score: 80
Period size: 23 Copynumber: 2.3 Consensus size: 25
1458292 ATCAGTTTTT
1458302 TAAAAAATCCGGTTTTTT-ATCCGG
1 TAAAAAATCCGGTTTTTTAATCCGG
1458326 ATAAAAAA-CCGG-TTTTTAATCCGG
1 -TAAAAAATCCGGTTTTTTAATCCGG
1458350 TAAAAAA
1 TAAAAAA
1458357 ACCGATCGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
23 12 0.41
24 10 0.34
25 7 0.24
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (25 bp):
TAAAAAATCCGGTTTTTTAATCCGG
Found at i:1463995 original size:11 final size:11
Alignment explanation
Indices: 1463965--1463996 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1463955 TGATGTAGTC
*
1463965 ATTTGTAGAAG
1 ATTTGTAGCAG
1463976 ATTTGTAGCAG
1 ATTTGTAGCAG
1463987 ATTTGTAGCA
1 ATTTGTAGCA
1463997 ATTAAAGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (11 bp):
ATTTGTAGCAG
Found at i:1471051 original size:20 final size:20
Alignment explanation
Indices: 1471025--1471072 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
1471015 TTATTATTCA
*
1471025 AATTTTATTTA-AAAATTTT
1 AATTTTATTTATAAAATTTG
1471044 AGATTTTATTTATAAAATTTG
1 A-ATTTTATTTATAAAATTTG
1471065 AATTTTAT
1 AATTTTAT
1471073 AAAATATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 1 0.04
20 17 0.65
21 8 0.31
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (20 bp):
AATTTTATTTATAAAATTTG
Found at i:1471073 original size:16 final size:16
Alignment explanation
Indices: 1471052--1471095 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1471042 TTAGATTTTA
1471052 TTTATAAAATTTGA-AT
1 TTTATAAAATTT-ATAT
*
1471068 TTTATAAAATATATAT
1 TTTATAAAATTTATAT
*
1471084 TTTTTAAAATTT
1 TTTATAAAATTT
1471096 TTTGTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 1 0.04
16 23 0.96
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
TTTATAAAATTTATAT
Found at i:1476553 original size:2 final size:2
Alignment explanation
Indices: 1476546--1476575 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1476536 AGTATGGTAA
1476546 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
1476576 TGCTCGGCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1487752 original size:21 final size:21
Alignment explanation
Indices: 1487728--1487770 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1487718 CAAGAGGTAG
1487728 TAATCAATTATTCATTTATCT
1 TAATCAATTATTCATTTATCT
1487749 TAATCAATTATTCATTTATCT
1 TAATCAATTATTCATTTATCT
1487770 T
1 T
1487771 GATCTGAGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.14, G:0.00, T:0.53
Consensus pattern (21 bp):
TAATCAATTATTCATTTATCT
Found at i:1490620 original size:20 final size:20
Alignment explanation
Indices: 1490595--1490633 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1490585 AGTGAATTGA
1490595 TTATAAAACTAAAAA-TAATT
1 TTATAAAA-TAAAAAGTAATT
*
1490615 TTATAATATAAAAAGTAAT
1 TTATAAAATAAAAAGTAAT
1490634 AAATAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (20 bp):
TTATAAAATAAAAAGTAATT
Found at i:1494975 original size:14 final size:16
Alignment explanation
Indices: 1494939--1494983 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
1494929 AAATGTTTGT
1494939 ACTTCTATATATTTATA
1 ACTT-TATATATTTATA
*
1494956 ACTTTATAAATTT-TA
1 ACTTTATATATTTATA
1494971 A-TTTATATATTTA
1 ACTTTATATATTTA
1494984 GATGATTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 10 0.40
15 3 0.12
16 8 0.32
17 4 0.16
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (16 bp):
ACTTTATATATTTATA
Found at i:1501566 original size:135 final size:136
Alignment explanation
Indices: 1501402--1501674 Score: 505
Period size: 136 Copynumber: 2.0 Consensus size: 136
1501392 AAATATAATA
*
1501402 TATTAAGATTTTATTTTTTTTAATAAATTATTAATAATATTAATATTTATGTATTGATTTTTTT-
1 TATTAAGATTTTATTTTTTTAAATAAATTATTAATAATATTAATATTTATGTATTGATTTTTTTA
1501466 AAAATACAA-TAAGATTTCATGCATTTAATTAAGATTTATGTTCGAGTTTGAGTTTGAGGCTTCA
66 AAAATA-AAGTAAGATTTCATGCATTTAATTAAGATTTATGTTCGAGTTTGAGTTTGAGGCTTCA
1501530 ATCGAGT
130 ATCGAGT
1501537 TATTAAGATTTTATTTTTTTAAATAAATTATTAATAATATTAATATTTATGTATTGATTTTTTTA
1 TATTAAGATTTTATTTTTTTAAATAAATTATTAATAATATTAATATTTATGTATTGATTTTTTTA
*
1501602 AAAATAAAGTAAGATTTCATGCATTTAATTAAGGTTTATGTTCGAGTTTGAGTTTGAGGCTTCAA
66 AAAATAAAGTAAGATTTCATGCATTTAATTAAGATTTATGTTCGAGTTTGAGTTTGAGGCTTCAA
1501667 TCGAGT
131 TCGAGT
1501673 TA
1 TA
1501675 AGTTTAATAA
Statistics
Matches: 134, Mismatches: 2, Indels: 3
0.96 0.01 0.02
Matches are distributed among these distances:
135 65 0.49
136 69 0.51
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.48
Consensus pattern (136 bp):
TATTAAGATTTTATTTTTTTAAATAAATTATTAATAATATTAATATTTATGTATTGATTTTTTTA
AAAATAAAGTAAGATTTCATGCATTTAATTAAGATTTATGTTCGAGTTTGAGTTTGAGGCTTCAA
TCGAGT
Found at i:1502033 original size:2 final size:2
Alignment explanation
Indices: 1502021--1502093 Score: 130
Period size: 2 Copynumber: 37.0 Consensus size: 2
1502011 TCATTACGTG
*
1502021 TA TA TA CA 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
1502063 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1502094 AAACTTTCAA
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
1 1 0.01
2 67 0.99
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1505159 original size:41 final size:41
Alignment explanation
Indices: 1505069--1505164 Score: 106
Period size: 41 Copynumber: 2.3 Consensus size: 41
1505059 ACCTAGTACT
* *
1505069 TTAGTGGCGTTTCTGAAACAAACGCCATAATAGTTCGGAACA
1 TTAGTGGCGTTTTTGAAACAAACGCCACAATAGTTC-GAACA
* * *
1505111 TTTGTGGCGTTTTTTAAA-AAACGCCGCAATATGTT-GAACAA
1 TTAGTGGCGTTTTTGAAACAAACGCCACAATA-GTTCGAAC-A
1505152 TTAGTGGCGTTTT
1 TTAGTGGCGTTTT
1505165 GTTTGAAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
40 4 0.09
41 24 0.52
42 18 0.39
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (41 bp):
TTAGTGGCGTTTTTGAAACAAACGCCACAATAGTTCGAACA
Found at i:1511208 original size:35 final size:35
Alignment explanation
Indices: 1511167--1511464 Score: 240
Period size: 35 Copynumber: 8.3 Consensus size: 35
1511157 AGTAATATAG
1511167 TATAGTTTTTAAAAATATTTTTGAAAA-ATATAATA
1 TATAGTTTTT-AAAATATTTTTGAAAATATATAATA
* * *
1511202 TATAGTTTTCAAAAAACTGTTTCCGAAAATATATATATTA
1 TATAGTTTTTAAAATA-T-TTT-TGAAAATATATA-A-TA
* *
1511242 TATAGTTTTTTAAACATTTTTGAAAACTTGTATATAATA
1 TATAGTTTTTAAAATATTTTTGAAAA----TATATAATA
* *
1511281 TATAGGTTTTAAAACA-TTTTGAAAATTATATAATA
1 TATAGTTTTTAAAATATTTTTGAAAA-TATATAATA
*
1511316 TATAG-TTTTGAAATCA-TTTTG-AAA-ATATAATA
1 TATAGTTTTTAAAAT-ATTTTTGAAAATATATAATA
*
1511348 TATAGTTTTTAAAAATATTTTTAAAAATTTATATAATA
1 TATAGTTTTT-AAAATATTTTTGAAAA--TATATAATA
* *
1511386 TATAGTTTTAAAAAAACATTTTTGAAAACT-TAT-ATA
1 TATAGTTTT--TAAAATATTTTTGAAAA-TATATAATA
*
1511422 -ATA-TTTTTAAAATCATTTTTAAAAAT-TATAATA
1 TATAGTTTTTAAAAT-ATTTTTGAAAATATATAATA
1511455 TATAGTTTTT
1 TATAGTTTTT
1511465 TTTGAAATAT
Statistics
Matches: 218, Mismatches: 21, Indels: 48
0.76 0.07 0.17
Matches are distributed among these distances:
32 21 0.10
33 18 0.08
34 30 0.14
35 41 0.19
36 6 0.03
37 13 0.06
38 35 0.16
39 32 0.15
40 16 0.07
41 6 0.03
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (35 bp):
TATAGTTTTTAAAATATTTTTGAAAATATATAATA
Found at i:1511296 original size:39 final size:36
Alignment explanation
Indices: 1511167--1511464 Score: 207
Period size: 39 Copynumber: 8.3 Consensus size: 36
1511157 AGTAATATAG
* *
1511167 TATAGTTTTTAAAAATATTTTTGAAAA--ATATAATA
1 TATAGGTTTT-AAAACATTTTTGAAAATTATATAATA
* * *
1511202 TATA-GTTTTCAAAAAACTGTTTCCGAAAATATATATATTA
1 TATAGGTTTT-AAAACA-T-TTT-TGAAAAT-TATATAATA
* *
1511242 TATAGTTTTTTAAACATTTTTGAAAACTTGTATATAATA
1 TATAGGTTTTAAAACATTTTTGAAAA--T-TATATAATA
1511281 TATAGGTTTTAAAACA-TTTTGAAAATTATATAATA
1 TATAGGTTTTAAAACATTTTTGAAAATTATATAATA
*
1511316 TATA-GTTTTGAAATCA-TTTTG-AAA--ATATAATA
1 TATAGGTTTT-AAAACATTTTTGAAAATTATATAATA
* * *
1511348 TATAGTTTTTAAAAATATTTTTAAAAATTTATATAATA
1 TATAGGTTTT-AAAACATTTTTGAAAA-TTATATAATA
1511386 TATA-GTTTTAAAAAAACATTTTTGAAAACTTATAT-A-A
1 TATAGGTTTT---AAAACATTTTTGAAAA-TTATATAATA
*
1511423 TAT---TTTTAAAATCATTTTT-AAAAAT-TATAATA
1 TATAGGTTTTAAAA-CATTTTTGAAAATTATATAATA
*
1511455 TATAGTTTTT
1 TATAGGTTTT
1511465 TTTGAAATAT
Statistics
Matches: 215, Mismatches: 24, Indels: 48
0.75 0.08 0.17
Matches are distributed among these distances:
30 3 0.01
31 2 0.01
32 24 0.11
33 15 0.07
34 21 0.10
35 39 0.18
36 4 0.02
37 18 0.08
38 25 0.12
39 45 0.21
40 15 0.07
41 4 0.02
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (36 bp):
TATAGGTTTTAAAACATTTTTGAAAATTATATAATA
Found at i:1511346 original size:146 final size:139
Alignment explanation
Indices: 1511185--1511463 Score: 341
Period size: 146 Copynumber: 1.9 Consensus size: 139
1511175 TTAAAAATAT
* *
1511185 TTTTGAAAAATATAATATATAGTTTTCAAAAA-ACTGTTTCCGAAAATATATATATTATATAGTT
1 TTTTGAAAAATATAATATATAGTTTTCAAAAATA-T-TTT-CAAAAATATATATAATATATAGTT
** *
1511249 TT-TTAAACATTTTTGAAAACTTGTATATAATATATAGGTTTTAAAA-CATTTTGAAAATTATAT
63 TTAAAAAACATTTTTGAAAAC-T-TATAT-A-ATAT---TTTTAAAATCATTTTGAAAAAT-TAT
1511312 AATATATAGTTTTGAAATCA
120 AATATATAGTTTTGAAATCA
* * *
1511332 TTTTG-AAAATATAATATATAGTTTTTAAAAATATTTTTAAAAATTTATATAATATATAGTTTTA
1 TTTTGAAAAATATAATATATAGTTTTCAAAAATATTTTCAAAAATATATATAATATATAGTTTT-
*
1511396 AAAAAACATTTTTGAAAACTTATATAATATTTTTAAAATCATTTTTAAAAATTATAATATATAGT
65 AAAAAACATTTTTGAAAACTTATATAATATTTTTAAAATCATTTTGAAAAATTATAATATATAGT
1511461 TTT
130 TTT
1511464 TTTTGAAATA
Statistics
Matches: 119, Mismatches: 9, Indels: 16
0.83 0.06 0.11
Matches are distributed among these distances:
139 24 0.20
140 11 0.09
142 4 0.03
143 1 0.01
144 27 0.23
145 4 0.03
146 42 0.35
147 6 0.05
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (139 bp):
TTTTGAAAAATATAATATATAGTTTTCAAAAATATTTTCAAAAATATATATAATATATAGTTTTA
AAAAACATTTTTGAAAACTTATATAATATTTTTAAAATCATTTTGAAAAATTATAATATATAGTT
TTGAAATCA
Found at i:1511405 original size:107 final size:104
Alignment explanation
Indices: 1511234--1511464 Score: 283
Period size: 105 Copynumber: 2.2 Consensus size: 104
1511224 CCGAAAATAT
* * *
1511234 ATATATTATATAGTTTTTTAAACATTTTTGAAAACTTGTATATAATATATAGGTTTTAAAACA-T
1 ATATAATATATAG-TTTTTAAAAATTTTTGAAAAATTGTATATAATATATAGGTTTTAAAACATT
* *
1511298 TTTGAAAA-TTATATAATATATAGTTTTGAAATCA-TTTTGAAA
65 TTTGAAAACTTATAT-A-ATAT--TTTTAAAATCATTTTTAAAA
*
1511340 ATATAATATATAGTTTTTAAAAATATTTTTAAAAATT-TATATAATATATA-GTTTTAAAAAAAC
1 ATATAATATATAGTTTTTAAAAAT-TTTTGAAAAATTGTATATAATATATAGGTTTT---AAAAC
1511403 ATTTTTGAAAACTTATATAATATTTTTAAAATCATTTTTAAAA
62 ATTTTTGAAAACTTATATAATATTTTTAAAATCATTTTTAAAA
1511446 ATTATAATATATAGTTTTT
1 A-TATAATATATAGTTTTT
1511465 TTTGAAATAT
Statistics
Matches: 111, Mismatches: 6, Indels: 15
0.84 0.05 0.11
Matches are distributed among these distances:
104 5 0.05
105 33 0.30
106 30 0.27
107 27 0.24
108 10 0.09
109 6 0.05
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (104 bp):
ATATAATATATAGTTTTTAAAAATTTTTGAAAAATTGTATATAATATATAGGTTTTAAAACATTT
TTGAAAACTTATATAATATTTTTAAAATCATTTTTAAAA
Found at i:1511433 original size:72 final size:69
Alignment explanation
Indices: 1511273--1511463 Score: 227
Period size: 72 Copynumber: 2.8 Consensus size: 69
1511263 GAAAACTTGT
* * * *
1511273 ATATAATATATAGGTTTTAAAA-CA-TTTTGAAAATTATATAATATATAGTTTTGAAATCATTTT
1 ATATAATATATAGTTTTTAAAATCATTTTTAAAAATTATATAATATATAGTTTTAAAAACATTTT
1511336 GAAA
66 GAAA
1511340 ATATAATATATAGTTTTTAAAAAT-ATTTTTAAAAATTTATATAATATATAGTTTTAAAAAAACA
1 ATATAATATATAGTTTTT-AAAATCATTTTTAAAAA-TTATATAATATATAGTTTT--AAAAACA
1511404 TTTTTGAAA
62 -TTTTGAAA
1511413 ACT-T-ATATAATA-TTTTTAAAATCATTTTTAAAAA-T-TATAATATATAGTTTT
1 A-TATAATAT-ATAGTTTTTAAAATCATTTTTAAAAATTATATAATATATAGTTTT
1511464 TTTTGAAATA
Statistics
Matches: 110, Mismatches: 4, Indels: 18
0.83 0.03 0.14
Matches are distributed among these distances:
67 17 0.15
68 5 0.05
69 24 0.22
70 20 0.18
71 5 0.05
72 25 0.23
73 13 0.12
74 1 0.01
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (69 bp):
ATATAATATATAGTTTTTAAAATCATTTTTAAAAATTATATAATATATAGTTTTAAAAACATTTT
GAAA
Found at i:1511500 original size:19 final size:19
Alignment explanation
Indices: 1511471--1511541 Score: 67
Period size: 19 Copynumber: 3.7 Consensus size: 19
1511461 TTTTTTTGAA
1511471 ATATA-TATATTATATAGT
1 ATATATTATATTATATAGT
*
1511489 CTATATTATATTATTATTAGT
1 ATATATTATATTA-TA-TAGT
* *
1511510 ATTTATTATTATTAT-TATT
1 ATATATTA-TATTATATAGT
1511529 ATATATTAT-TTAT
1 ATATATTATATTAT
1511542 TTACTTTCCA
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
17 4 0.09
18 5 0.11
19 17 0.39
20 2 0.05
21 11 0.25
22 5 0.11
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (19 bp):
ATATATTATATTATATAGT
Found at i:1511505 original size:3 final size:3
Alignment explanation
Indices: 1511492--1511538 Score: 60
Period size: 3 Copynumber: 15.3 Consensus size: 3
1511482 ATATAGTCTA
*
1511492 TAT TA- TAT TAT TAT TAG TATT TAT TAT TAT TAT TAT TAT ATAT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT -TAT TAT
1511538 T
1 T
1511539 TATTTACTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 32 0.82
4 5 0.13
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1511518 original size:16 final size:16
Alignment explanation
Indices: 1511492--1511538 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
1511482 ATATAGTCTA
1511492 TATTATATTATTATTAG
1 TATT-TATTATTATTAG
*
1511509 TATTTATTATTATTAT
1 TATTTATTATTATTAG
1511525 TA-TTATATATTATT
1 TATTTAT-TATTATT
1511539 TATTTACTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 4 0.14
16 20 0.71
17 4 0.14
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (16 bp):
TATTTATTATTATTAG
Found at i:1512636 original size:16 final size:16
Alignment explanation
Indices: 1512615--1512648 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1512605 TTAGTCCACA
1512615 TTATTTT-TCTATTATT
1 TTATTTTAT-TATTATT
1512631 TTATTTTATTATTATT
1 TTATTTTATTATTATT
1512647 TT
1 TT
1512649 TAAACTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 16 0.94
17 1 0.06
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTATTATTATT
Found at i:1512681 original size:17 final size:18
Alignment explanation
Indices: 1512655--1512696 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
1512645 TTTTTAAACT
*
1512655 TTTTTTTTTTATTTCT-G
1 TTTTTCTTTTATTTCTAG
*
1512672 TTTTTCTTTTTTTTCTAG
1 TTTTTCTTTTATTTCTAG
1512690 TTTTTCT
1 TTTTTCT
1512697 ATTTTAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.05, C:0.10, G:0.05, T:0.81
Consensus pattern (18 bp):
TTTTTCTTTTATTTCTAG
Found at i:1512681 original size:18 final size:19
Alignment explanation
Indices: 1512654--1512702 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
1512644 ATTTTTAAAC
*
1512654 TTTTTTTTTTTATTTCT-G
1 TTTTTCTTTTTATTTCTAG
1512672 TTTTTCTTTTT-TTTCTAG
1 TTTTTCTTTTTATTTCTAG
1512690 TTTTTCTATTTTA
1 TTTTTCT-TTTTA
1512703 ACATTTTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 5 0.19
18 18 0.67
19 4 0.15
ACGTcount: A:0.08, C:0.08, G:0.04, T:0.80
Consensus pattern (19 bp):
TTTTTCTTTTTATTTCTAG
Found at i:1512808 original size:10 final size:9
Alignment explanation
Indices: 1512737--1512824 Score: 62
Period size: 9 Copynumber: 9.9 Consensus size: 9
1512727 TTCATATTGT
*
1512737 TTTTTTTTA
1 TTTTATTTA
1512746 TTTTATTTCACA
1 TTTTATTT---A
1512758 TTTTATTTA
1 TTTTATTTA
1512767 -TTTA-TTA
1 TTTTATTTA
1512774 TTATTA-TTA
1 TT-TTATTTA
*
1512783 TTTT-CTT-
1 TTTTATTTA
1512790 TTTTATTTA
1 TTTTATTTA
1512799 TTTTACTTTA
1 TTTTA-TTTA
1512809 TTTT-TTTA
1 TTTTATTTA
*
1512817 TCTTATTT
1 TTTTATTT
1512825 CCCTTAAATA
Statistics
Matches: 66, Mismatches: 3, Indels: 20
0.74 0.03 0.22
Matches are distributed among these distances:
7 7 0.11
8 18 0.27
9 24 0.36
10 8 0.12
12 9 0.14
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTATTTA
Found at i:1512877 original size:29 final size:27
Alignment explanation
Indices: 1512838--1512918 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 27
1512828 TTAAATATAT
*
1512838 TTTATATTTTTTTACTTTTATTTATTTA
1 TTTATATTTTTTTACATTT-TTTATTTA
* *
1512866 TTTAATATTTTTTATTCATTTTTTCTTTGA
1 TTT-ATATTTTTT-TACATTTTTTATTT-A
*
1512896 TTTATATTTTTTTATTATTTTTT
1 TTTATATTTTTTTA-CATTTTTT
1512919 TTCTCCCTCC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
28 4 0.09
29 31 0.70
30 9 0.20
ACGTcount: A:0.20, C:0.04, G:0.01, T:0.75
Consensus pattern (27 bp):
TTTATATTTTTTTACATTTTTTATTTA
Found at i:1512879 original size:14 final size:13
Alignment explanation
Indices: 1512838--1512919 Score: 53
Period size: 14 Copynumber: 5.9 Consensus size: 13
1512828 TTAAATATAT
1512838 TTTATATTTTTTTA
1 TTTATA-TTTTTTA
1512852 CTTT-TATTTATTTA
1 -TTTATATTT-TTTA
1512866 TTTAATATTTTTTA
1 TTT-ATATTTTTTA
* *
1512880 TTCATTTTTTCTTTGA
1 TTTA-TATTT-TTT-A
1512896 TTTATATTTTTT-
1 TTTATATTTTTTA
1512908 TATTAT-TTTTTT
1 T-TTATATTTTTT
1512920 TCTCCCTCCT
Statistics
Matches: 56, Mismatches: 4, Indels: 17
0.73 0.05 0.22
Matches are distributed among these distances:
12 7 0.12
13 11 0.20
14 19 0.34
15 15 0.27
16 4 0.07
ACGTcount: A:0.20, C:0.04, G:0.01, T:0.76
Consensus pattern (13 bp):
TTTATATTTTTTA
Found at i:1512879 original size:18 final size:18
Alignment explanation
Indices: 1512834--1512886 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
1512824 TCCCTTAAAT
* *
1512834 ATATTTTATATTTTTTTA
1 ATATTTTTTATTTATTTA
*
1512852 CT-TTTATTTATTTATTTA
1 ATATTT-TTTATTTATTTA
*
1512870 ATATTTTTTATTCATTT
1 ATATTTTTTATTTATTT
1512887 TTTCTTTGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
17 3 0.11
18 22 0.79
19 3 0.11
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.72
Consensus pattern (18 bp):
ATATTTTTTATTTATTTA
Found at i:1512919 original size:30 final size:29
Alignment explanation
Indices: 1512838--1512919 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 29
1512828 TTAAATATAT
* *
1512838 TTTATATTTTTTTACT-TTTATTTATTTA
1 TTTATATTTTTTTATTATTTTTTTATTTA
*
1512866 TTTA-ATATTTTTTATTCATTTTTTCT-TTGA
1 TTTATAT-TTTTTTATT-ATTTTTT-TATTTA
1512896 TTTATATTTTTTTATTATTTTTTT
1 TTTATATTTTTTTATTATTTTTTT
1512920 TCTCCCTCCT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
27 2 0.04
28 13 0.28
29 7 0.15
30 21 0.46
31 3 0.07
ACGTcount: A:0.20, C:0.04, G:0.01, T:0.76
Consensus pattern (29 bp):
TTTATATTTTTTTATTATTTTTTTATTTA
Found at i:1514744 original size:14 final size:15
Alignment explanation
Indices: 1514718--1514746 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1514708 CATTTGAACA
1514718 TATTTTGCATTTTTT
1 TATTTTGCATTTTTT
1514733 TATTTT-CATTTTTT
1 TATTTTGCATTTTTT
1514747 ACATTCACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.14, C:0.07, G:0.03, T:0.76
Consensus pattern (15 bp):
TATTTTGCATTTTTT
Found at i:1515709 original size:94 final size:94
Alignment explanation
Indices: 1515538--1515799 Score: 355
Period size: 94 Copynumber: 2.7 Consensus size: 94
1515528 ATATTATAAT
* * *
1515538 ATTATATATATACAATAAAGCTTGAGCTGTCCCTCTAAAGCAATTGGTTAAACGTCCTGGCTTTA
1 ATTATA-ATATACAATAAAGCTTGAGCTATCCCTCT-AAGCAATTGGTTAAACGCCCCGGCTTTA
*
1515603 TGGCTAAGATTCAGCTAGCCTGATAAAGGTG
64 TGGATAAGATTCAGCTAGCCTGATAAAGGTG
* * *
1515634 ATTATAATATACAATAAAGCTTGAGTTTTCCCTCTAAGCAATTGGTTAAACGCCCCGGCATTATG
1 ATTATAATATACAATAAAGCTTGAGCTATCCCTCTAAGCAATTGGTTAAACGCCCCGGCTTTATG
*
1515699 GATAATATTCAGCTAGCCTGATAAAGGTG
66 GATAAGATTCAGCTAGCCTGATAAAGGTG
* * *
1515728 ATTATAATAT-CTATACAATGATATTAAGCTATCCCTCTAGAGCAATTGGTTAAACGCCCCGGCT
1 ATTATAATATACAATA-AA-G--CTTGAGCTATCCCTCTA-AGCAATTGGTTAAACGCCCCGGCT
1515792 TTATGGAT
61 TTATGGAT
1515800 TCAACTAGCT
Statistics
Matches: 148, Mismatches: 13, Indels: 8
0.88 0.08 0.05
Matches are distributed among these distances:
93 4 0.03
94 66 0.45
95 28 0.19
96 6 0.04
97 13 0.09
98 31 0.21
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (94 bp):
ATTATAATATACAATAAAGCTTGAGCTATCCCTCTAAGCAATTGGTTAAACGCCCCGGCTTTATG
GATAAGATTCAGCTAGCCTGATAAAGGTG
Found at i:1517262 original size:48 final size:45
Alignment explanation
Indices: 1517206--1517320 Score: 149
Period size: 48 Copynumber: 2.5 Consensus size: 45
1517196 ACCTTTTATC
1517206 CCATAAGCTCATAAGCTTATTTTTACCAAAATACTTACCATTTAAATT
1 CCATAAGCTCATAAGCTTATTTTTACCAAAATACTTACCA-TT-AA-T
* ** * *
1517254 CCATAAGCTCGTAAGCTTATTTTTTTCAATATACTTGCCATTAAT
1 CCATAAGCTCATAAGCTTATTTTTACCAAAATACTTACCATTAAT
*
1517299 CCGTAAGCTCATAAGCTTATTT
1 CCATAAGCTCATAAGCTTATTT
1517321 GCATGGTTAC
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
45 21 0.35
46 2 0.03
47 2 0.03
48 35 0.58
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.39
Consensus pattern (45 bp):
CCATAAGCTCATAAGCTTATTTTTACCAAAATACTTACCATTAAT
Found at i:1521182 original size:33 final size:31
Alignment explanation
Indices: 1521144--1521283 Score: 102
Period size: 34 Copynumber: 4.1 Consensus size: 31
1521134 ACAAGTGAAA
*
1521144 TATTTTTTTTCATCTCTCATTTTTTTCTCTTCT
1 TATTTTTTTTC-TCTTTCATTTTTTT-TCTTCT
*
1521177 TATTTTCTTTCTCGTTTTCATTTTTTTTCTTCT
1 TATTTTTTTTCTC--TTTCATTTTTTTTCTTCT
* *
1521210 TCGTTTTCATTTTCTTTTTCTATTTTTTTTTCTTCT
1 T-ATTTT--TTTTCTCTTTC-A-TTTTTTTTCTTCT
*
1521246 TATGTTTTTTTC-CTTCTTCTGTTTTTTATTCTTCT
1 TAT-TTTTTTTCTC-T-TTC-ATTTTTT-TTCTTCT
1521281 TAT
1 TAT
1521284 AATATATATT
Statistics
Matches: 88, Mismatches: 8, Indels: 20
0.76 0.07 0.17
Matches are distributed among these distances:
32 2 0.02
33 17 0.19
34 31 0.35
35 16 0.18
36 22 0.25
ACGTcount: A:0.07, C:0.18, G:0.03, T:0.72
Consensus pattern (31 bp):
TATTTTTTTTCTCTTTCATTTTTTTTCTTCT
Found at i:1521203 original size:34 final size:33
Alignment explanation
Indices: 1521160--1521283 Score: 110
Period size: 34 Copynumber: 3.6 Consensus size: 33
1521150 TTTTCATCTC
1521160 TCATTTTTTTCTCTTCTTATTTTCTTTCTCGTTT
1 TCATTTTTTT-TCTTCTTATTTTCTTTCTCGTTT
* *
1521194 TCATTTTTTTTCTTCTTCGTTTTCATTT-TCTTTT
1 TCATTTTTTTTCTTCTT-ATTTTC-TTTCTCGTTT
*
1521228 TCTATTTTTTTTTCTTCTTATGTTT-TTT-TCCTTCT
1 TC-A-TTTTTTTTCTTCTTAT-TTTCTTTCTCGTT-T
*
1521263 TCTGTTTTTTATTCTTCTTAT
1 TC-ATTTTTT-TTCTTCTTAT
1521284 AATATATATT
Statistics
Matches: 78, Mismatches: 5, Indels: 13
0.81 0.05 0.14
Matches are distributed among these distances:
33 7 0.09
34 35 0.45
35 19 0.24
36 17 0.22
ACGTcount: A:0.06, C:0.18, G:0.03, T:0.73
Consensus pattern (33 bp):
TCATTTTTTTTCTTCTTATTTTCTTTCTCGTTT
Found at i:1521205 original size:18 final size:17
Alignment explanation
Indices: 1521144--1521283 Score: 89
Period size: 17 Copynumber: 8.2 Consensus size: 17
1521134 ACAAGTGAAA
1521144 TATTTTTTTTCATC-TCT
1 TATTTTTTTTC-TCTTCT
*
1521161 CA-TTTTTTTCTCTTCT
1 TATTTTTTTTCTCTTCT
*
1521177 TATTTTCTTTCTCGTT-T
1 TATTTTTTTTCTC-TTCT
1521194 TCATTTTTTTTCTTCTTCGT
1 T-ATTTTTTTTC-TCTTC-T
** *
1521214 T-TTCATTTTCT-TTTT
1 TATTTTTTTTCTCTTCT
1521229 CTATTTTTTTT-TCTTCT
1 -TATTTTTTTTCTCTTCT
1521246 TATGTTTTTTTC-CTTCT
1 TAT-TTTTTTTCTCTTCT
*
1521263 TCTGTTTTTTAT-TCTTCT
1 TAT-TTTTTT-TCTCTTCT
1521281 TAT
1 TAT
1521284 AATATATATT
Statistics
Matches: 97, Mismatches: 12, Indels: 27
0.71 0.09 0.20
Matches are distributed among these distances:
15 3 0.03
16 19 0.20
17 43 0.44
18 28 0.29
19 2 0.02
20 2 0.02
ACGTcount: A:0.07, C:0.18, G:0.03, T:0.72
Consensus pattern (17 bp):
TATTTTTTTTCTCTTCT
Found at i:1521205 original size:22 final size:23
Alignment explanation
Indices: 1521179--1521227 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
1521169 TCTCTTCTTA
1521179 TTTTCTT-TCTCGTTTTCATTTT-
1 TTTTCTTCT-TCGTTTTCATTTTC
1521201 TTTTCTTCTTCGTTTTCATTTTC
1 TTTTCTTCTTCGTTTTCATTTTC
1521224 TTTT
1 TTTT
1521228 TCTATTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.04, C:0.18, G:0.04, T:0.73
Consensus pattern (23 bp):
TTTTCTTCTTCGTTTTCATTTTC
Found at i:1521280 original size:15 final size:16
Alignment explanation
Indices: 1521198--1521272 Score: 62
Period size: 18 Copynumber: 4.4 Consensus size: 16
1521188 TCGTTTTCAT
1521198 TTTTTTTCTTCTTC-G
1 TTTTTTTCTTCTTCTG
* *
1521213 TTTTCATTTTCTTTTTCTATT
1 -TTT--TTTTCTTCTTC--TG
*
1521234 TTTTTTTCTTCTTATG
1 TTTTTTTCTTCTTCTG
1521250 TTTTTTTCCTTCTTCTG
1 TTTTTTT-CTTCTTCTG
1521267 TTTTTT
1 TTTTTT
1521273 ATTCTTCTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
16 11 0.23
17 14 0.30
18 19 0.40
20 3 0.06
ACGTcount: A:0.04, C:0.16, G:0.04, T:0.76
Consensus pattern (16 bp):
TTTTTTTCTTCTTCTG
Found at i:1521282 original size:35 final size:35
Alignment explanation
Indices: 1521162--1521283 Score: 103
Period size: 35 Copynumber: 3.5 Consensus size: 35
1521152 TTCATCTCTC
*
1521162 ATTTTTTTCTCTTCTTAT-TTTCT-TTCTCGTT-TTC-
1 ATTTTTTT-TCTTCTTATGTTT-TATT-TCCTTCTTCT
* * *
1521196 ATTTTTTTTCTTCTT-CGTTTTCATTTTCTTTTTCT
1 ATTTTTTTTCTTCTTATGTTTT-ATTTCCTTCTTCT
1521231 ATTTTTTTTTCTTCTTATGTTTT-TTTCCTTCTTCT
1 A-TTTTTTTTCTTCTTATGTTTTATTTCCTTCTTCT
*
1521266 GTTTTTTATTCTTCTTAT
1 ATTTTTT-TTCTTCTTAT
1521284 AATATATATT
Statistics
Matches: 73, Mismatches: 7, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
32 1 0.01
33 13 0.18
34 19 0.26
35 21 0.29
36 14 0.19
37 5 0.07
ACGTcount: A:0.07, C:0.17, G:0.03, T:0.73
Consensus pattern (35 bp):
ATTTTTTTTCTTCTTATGTTTTATTTCCTTCTTCT
Found at i:1528040 original size:84 final size:84
Alignment explanation
Indices: 1527897--1528543 Score: 832
Period size: 84 Copynumber: 7.7 Consensus size: 84
1527887 AAATCATTCC
* *
1527897 ACTACGCTCAGCTCCAAGGCAC-GCTATTTGCAGCATAACTCAAGGCTAGAAGGGCTATCTGCCA
1 ACTACGCTCAGCTCCAAGGCACATC-ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCA
*
1527961 CCAAAAGACCTTCGAGTTCG
65 ACAAAAGACCTTCGAGTTCG
* * *
1527981 ACTACGCTCAGCTCAAAGGCACATCATTTGTAGCATAACTCAAGGCTAGAAGGGTTATCTACCAA
1 ACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAA
* * *
1528046 CCAAATACCTTTGAGTTCG
66 CAAAAGACCTTCGAGTTCG
* * * ** * *
1528065 ACTACGCTCATCTCTAAGGCACATTATTTGCAGCATAGGTCAAGGCTAGAAGGGCTATCTGCCAC
1 ACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAA
* *
1528130 CAAAAGACCTTCAAGTTTG
66 CAAAAGACCTTCGAGTTCG
** * * *
1528149 ACTACGCTCAGCTCTGAGGAATATCATTTGTAGCATAACTCAAGGCTAGAAGGGTTATCTGCCGA
1 ACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCC-A
1528214 AC-AAAGACCTTCGAGTTCG
65 ACAAAAGACCTTCGAGTTCG
* * * * *
1528233 ACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTCAAGGCAAGAAGGGATATTTTCCAA
1 ACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAA
*
1528298 CAAAAGACCTTCGAGTTTG
66 CAAAAGACCTTCGAGTTCG
* * * * * * *
1528317 ACTACGCTCAGCTCCGAGGCACATCATTTGCAACATAGCTCAAGGCTATAAGGGATATTTGCTAA
1 ACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAA
*
1528382 C-AAAGACCTTCGAATTCG
66 CAAAAGACCTTCGAGTTCG
* * *
1528400 ACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTCAATGCTAAAAGGGTTATCTGCCAA
1 ACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAA
* *
1528465 CAAAAGACCTTTGAGTTTG
66 CAAAAGACCTTCGAGTTCG
* * * * *
1528484 ATTCCACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCT
1 ACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCT
1528544 ATTGAGTTAA
Statistics
Matches: 485, Mismatches: 74, Indels: 8
0.86 0.13 0.01
Matches are distributed among these distances:
83 75 0.15
84 407 0.84
85 3 0.01
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (84 bp):
ACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAA
CAAAAGACCTTCGAGTTCG
Found at i:1529266 original size:19 final size:20
Alignment explanation
Indices: 1529231--1529277 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
1529221 CTTTAGACAT
1529231 GGGGAATCGGTACCCCCTGG
1 GGGGAATCGGTACCCCCTGG
1529251 GGGGAATCGGTACCCCCTGG
1 GGGGAATCGGTACCCCCTGG
1529271 GGGGAAT
1 GGGGAAT
1529278 TGGTTCCCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.17, C:0.26, G:0.43, T:0.15
Consensus pattern (20 bp):
GGGGAATCGGTACCCCCTGG
Found at i:1535797 original size:21 final size:22
Alignment explanation
Indices: 1535773--1535822 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
1535763 TTGGTGTAGA
*
1535773 GGGAATCGATACCCCC-TGAAG
1 GGGAACCGATACCCCCTTGAAG
*
1535794 GGGAACCGATCCCCCCTTTGAAG
1 GGGAACCGATACCCCC-TTGAAG
1535817 GGGAAC
1 GGGAAC
1535823 TGATTCTCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 14 0.56
23 11 0.44
ACGTcount: A:0.26, C:0.30, G:0.30, T:0.14
Consensus pattern (22 bp):
GGGAACCGATACCCCCTTGAAG
Found at i:1537034 original size:21 final size:22
Alignment explanation
Indices: 1537010--1537062 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
1537000 AGTGTTTTAG
*
1537010 ATCTTCATGA-CCATTTTTTTC
1 ATCTTAATGATCCATTTTTTTC
1537031 ATC-TAATGATCCATTTTTTTC
1 ATCTTAATGATCCATTTTTTTC
1537052 ATC-TAATGATC
1 ATCTTAATGATC
1537063 TCTTGGTGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 5 0.17
21 25 0.83
ACGTcount: A:0.25, C:0.21, G:0.06, T:0.49
Consensus pattern (22 bp):
ATCTTAATGATCCATTTTTTTC
Found at i:1537039 original size:20 final size:21
Alignment explanation
Indices: 1537016--1537062 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
1537006 TTAGATCTTC
1537016 ATGA-CCATTTTTTTCATCTA
1 ATGATCCATTTTTTTCATCTA
1537036 ATGATCCATTTTTTTCATCTA
1 ATGATCCATTTTTTTCATCTA
1537057 ATGATC
1 ATGATC
1537063 TCTTGGTGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.49
Consensus pattern (21 bp):
ATGATCCATTTTTTTCATCTA
Found at i:1545587 original size:117 final size:117
Alignment explanation
Indices: 1545367--1545588 Score: 297
Period size: 117 Copynumber: 1.9 Consensus size: 117
1545357 CTTTCAAATC
*
1545367 GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTACAAGATTT
1 GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTACAAAATTT
* *
1545432 CATTTTGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAGTTTGTTTAATTT
66 CATTTTGATTTTCAAAATCCAGTTTCGTTTCTAAAAGAAGTTTGTTTAATTT
* * * * *
1545484 GAAAATTTCTTTTTCAA-AGTTTTCAGATTTTATTTTTGAAAGCTCTAACTTCTTTCT-CAAAAT
1 GAAAATTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTCTAA-ATCCTTCTACAAAAT
* * *
1545547 TTCATTTTGATTTTCTAAATCTAGTTTGGCTTTC-AAAAGAAG
64 TTCATTTTGATTTTCAAAATCCAGTTTCG-TTTCTAAAAGAAG
1545589 ACCATTTTAG
Statistics
Matches: 91, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
116 1 0.01
117 80 0.88
118 10 0.11
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.47
Consensus pattern (117 bp):
GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTACAAAATTT
CATTTTGATTTTCAAAATCCAGTTTCGTTTCTAAAAGAAGTTTGTTTAATTT
Found at i:1547977 original size:40 final size:36
Alignment explanation
Indices: 1547933--1548165 Score: 163
Period size: 40 Copynumber: 6.2 Consensus size: 36
1547923 TTTTTGAAAA
*
1547933 ATATAATATATAGTTTTCAAAAAACGGTTTTCAAAAATAT
1 ATATAATATATAGTTTTC--AAAAC-ATTTT-AAAAATAT
* *
1547973 ATATATTATATAGTTTTTCAAAACATTTTTGAAAACTTAT
1 ATATAATATATAG-TTTTCAAAACA-TTTT-AAAA-ATAT
*
1548013 ATATAATATATAGGTTTT-AAAACATTTTGAAAAT-T
1 ATATAATATATA-GTTTTCAAAACATTTTAAAAATAT
* * *
1548048 ATATAATATATAGTTTTGAAATCATTTTGAAAATAT
1 ATATAATATATAGTTTTCAAAACATTTTAAAAATAT
* * * * * *
1548084 A-AT-ATATA-ATTTTTAAAAATATTTTGACAATTTT
1 ATATAATATATAGTTTTCAAAACATTTT-AAAAATAT
* *
1548118 ATATAATATATAGTTTTAAAAAAACATTTTTGAAAACT-T
1 ATATAATATATAGTTTT--CAAAACA-TTTT-AAAAATAT
1548157 ATATAATAT
1 ATATAATAT
1548166 TTTTAAAATC
Statistics
Matches: 160, Mismatches: 20, Indels: 27
0.77 0.10 0.13
Matches are distributed among these distances:
33 13 0.08
34 15 0.09
35 32 0.20
36 8 0.05
37 8 0.05
38 4 0.03
39 35 0.22
40 39 0.24
41 6 0.04
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (36 bp):
ATATAATATATAGTTTTCAAAACATTTTAAAAATAT
Found at i:1548108 original size:107 final size:104
Alignment explanation
Indices: 1547973--1548208 Score: 282
Period size: 107 Copynumber: 2.2 Consensus size: 104
1547963 TCAAAAATAT
* *
1547973 ATATATTATATAGTTTTTCAAAACATTTTTGAAAACTTATATATAATATATAGGTTTT-AAAACA
1 ATATAATATATAGTTTTTAAAAACA-TTTTGAAAA-TTATATATAATATATA-GTTTTAAAAACA
*
1548037 -TTTTGAAAA-TTATATAATATATAGTTTTGAAATCA-TTTTGAAA
63 TTTTTGAAAACTTATAT-A-ATAT--TTTTAAAATCATTTTTGAAA
* * * *
1548080 ATATAATATATAATTTTTAAAAATATTTTGACAATTTTATATAATATATAGTTTTAAAAAAACAT
1 ATATAATATATAGTTTTTAAAAACATTTTGAAAATTATATATAATATATAGTTTT--AAAAACAT
1548145 TTTTGAAAACTTATATAATATTTTTAAAATCATTTTTGAAA
64 TTTTGAAAACTTATATAATATTTTTAAAATCATTTTTGAAA
*
1548186 ACTATAATATATAGTTTTGAAAA
1 A-TATAATATATAGTTTTTAAAA
1548209 CTTTTTTAAA
Statistics
Matches: 113, Mismatches: 9, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
104 5 0.04
105 25 0.22
106 17 0.15
107 50 0.44
108 10 0.09
109 6 0.05
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (104 bp):
ATATAATATATAGTTTTTAAAAACATTTTGAAAATTATATATAATATATAGTTTTAAAAACATTT
TTGAAAACTTATATAATATTTTTAAAATCATTTTTGAAA
Found at i:1548180 original size:72 final size:68
Alignment explanation
Indices: 1547924--1548229 Score: 223
Period size: 73 Copynumber: 4.3 Consensus size: 68
1547914 TTGAAAATGT
* * * * * *
1547924 TTTTGAAAAATATAATATATAGTTTTCAAAAAACGGTTTTCAAAAATATATATATTATATAGTTT
1 TTTTG-AAAATATAATATATAATTTT-TAAAATC-ATTTT-GAAAAT-TATATAATATATAG-TT
*
1547989 TTCAAAACA
60 TTAAAAACA
*
1547998 TTTTTGAAAACTTATATATAATATATAGGTTTTAAAA-CATTTTGAAAATTATATAATATATAGT
1 -TTTTGAAAA--TATA-AT-ATATA-A-TTTTTAAAATCATTTTGAAAATTATATAATATATAGT
* *
1548062 TTTGAAATCA
59 TTTAAAAACA
*
1548072 TTTTGAAAATATAATATATAATTTTTAAAAAT-ATTTTGACAATTTTATATAATATATAGTTTTA
1 TTTTGAAAATATAATATATAATTTTT-AAAATCATTTTGA-AA-ATTATATAATATATAGTTTT-
1548136 AAAAAACA
62 -AAAAACA
*
1548144 TTTTTGAAAACT-T-ATATA-ATATTTTTAAAATCATTTTTGAAAA--CTATAATATATAGTTTT
1 -TTTTGAAAA-TATAATATATA-ATTTTTAAAATCA-TTTTGAAAATTATATAATATATAGTTTT
*
1548204 GAAAAC-
62 AAAAACA
**
1548210 TTTTTTAAATATAATATATA
1 TTTTGAAAATATAATATATA
1548230 GTTTAAATTT
Statistics
Matches: 194, Mismatches: 17, Indels: 48
0.75 0.07 0.19
Matches are distributed among these distances:
64 1 0.01
65 8 0.04
66 5 0.03
67 10 0.05
68 12 0.06
69 23 0.12
70 21 0.11
71 10 0.05
72 19 0.10
73 25 0.13
74 14 0.07
75 18 0.09
76 9 0.05
77 6 0.03
78 6 0.03
79 4 0.02
80 3 0.02
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (68 bp):
TTTTGAAAATATAATATATAATTTTTAAAATCATTTTGAAAATTATATAATATATAGTTTTAAAA
ACA
Found at i:1548196 original size:35 final size:35
Alignment explanation
Indices: 1547923--1548233 Score: 193
Period size: 35 Copynumber: 8.8 Consensus size: 35
1547913 TTTGAAAATG
* * *
1547923 TTTTTGAAAAATATAATAT-ATAGTTTTCAAAAAACG
1 TTTTTGAAAACTATAATATAATAGTTTT--TAAAACA
* * *
1547959 GTTTTCAAAAATATATATATTATATAGTTTTTCAAAACA
1 TTTTTGAAAACTATA-ATA-TA-ATAGTTTTT-AAAACA
*
1547998 TTTTTGAAAACTTATATATAATATATAGGTTTTAAAACA
1 TTTTTGAAAAC-TATA-AT-ATA-ATAGTTTTTAAAACA
* * *
1548037 -TTTTGAAAATTAT-ATAATATATAGTTTTGAAATCA
1 TTTTTGAAAACTATAAT-ATA-ATAGTTTTTAAAACA
*
1548072 -TTTTGAAAA-TATAATAT-ATAATTTTTAAAA-A
1 TTTTTGAAAACTATAATATAATAGTTTTTAAAACA
* * * *
1548103 TATTTTGACAATTTTATATAATATATAGTTTTAAAAAAACA
1 T-TTTTGAAAACTATA-AT-ATA-ATAGTTTT--TAAAACA
1548144 TTTTTGAAAACT-T-ATATAATA-TTTTTAAAATCA
1 TTTTTGAAAACTATAATATAATAGTTTTTAAAA-CA
*
1548177 TTTTTGAAAACTATAATAT-ATAGTTTTGAAAAC-
1 TTTTTGAAAACTATAATATAATAGTTTTTAAAACA
*
1548210 TTTTT-TAAA-TATAATAT-ATAGTTT
1 TTTTTGAAAACTATAATATAATAGTTT
1548234 AAATTTTTTT
Statistics
Matches: 229, Mismatches: 24, Indels: 49
0.76 0.08 0.16
Matches are distributed among these distances:
31 16 0.07
32 17 0.07
33 27 0.12
34 17 0.07
35 47 0.21
36 18 0.08
37 8 0.03
38 17 0.07
39 20 0.09
40 39 0.17
41 3 0.01
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (35 bp):
TTTTTGAAAACTATAATATAATAGTTTTTAAAACA
Found at i:1548227 original size:105 final size:104
Alignment explanation
Indices: 1548013--1548227 Score: 253
Period size: 105 Copynumber: 2.0 Consensus size: 104
1548003 GAAAACTTAT
*
1548013 ATATAATATATAGGTTTTAAAACATTTTGAAAATTATATAATATATAGTTTTGAAATCATTTTGA
1 ATATAATATATAGGTTTTAAAACATTTTGAAAATTATATAATATATA-TTTTAAAATCATTTTGA
* * *
1548078 AAATATAATATATAATTTTTAAAAATATTTTGACAATTTT
65 AAATATAATATATAATTTTGAAAAATATTTTGACAATATA
1548118 ATATAATATATA-GTTTTAAAAAAACATTTTTGAAAACTTATAT-A-ATAT-TTTTAAAATCATT
1 ATATAATATATAGGTTTT---AAAACA-TTTTGAAAA-TTATATAATATATATTTTAAAATCA-T
* * *
1548179 TTTGAAAACTATAATATATAGTTTTGAAAACT-TTTTTA-AATATA
60 TTTGAAAA-TATAATATATAATTTTGAAAAATATTTTGACAATATA
1548223 ATATA
1 ATATA
1548228 TAGTTTAAAT
Statistics
Matches: 96, Mismatches: 7, Indels: 14
0.82 0.06 0.12
Matches are distributed among these distances:
104 5 0.05
105 31 0.32
106 14 0.15
107 30 0.31
108 10 0.10
109 6 0.06
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.45
Consensus pattern (104 bp):
ATATAATATATAGGTTTTAAAACATTTTGAAAATTATATAATATATATTTTAAAATCATTTTGAA
AATATAATATATAATTTTGAAAAATATTTTGACAATATA
Found at i:1548242 original size:29 final size:32
Alignment explanation
Indices: 1548118--1548256 Score: 110
Period size: 34 Copynumber: 4.3 Consensus size: 32
1548108 TGACAATTTT
* *
1548118 ATATAATATATAGTTTTAAAAAAACATTTTTGAA
1 ATATAATATATAGTTTT--GAAAACTTTTTTGAA
* * *
1548152 A-ACTTATATAATA-TTTTTAAAATCATTTTTGAAA
1 ATA-TAATAT-ATAGTTTTGAAAA-CTTTTTTG-AA
1548186 ACTATAATATATAGTTTTGAAAACTTTTTT-AA
1 A-TATAATATATAGTTTTGAAAACTTTTTTGAA
**
1548218 ATATAATATATAG-TTT-AAATTTTTTTTGAA
1 ATATAATATATAGTTTTGAAAACTTTTTTGAA
1548248 ATAT-ATATA
1 ATATAATATA
1548257 CATTATATAG
Statistics
Matches: 90, Mismatches: 7, Indels: 21
0.76 0.06 0.18
Matches are distributed among these distances:
29 14 0.16
30 9 0.10
31 12 0.13
32 7 0.08
33 9 0.10
34 22 0.24
35 16 0.18
36 1 0.01
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.47
Consensus pattern (32 bp):
ATATAATATATAGTTTTGAAAACTTTTTTGAA
Found at i:1548315 original size:24 final size:24
Alignment explanation
Indices: 1548271--1548319 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1548261 ATATAGTCTA
1548271 TATTATATTATTATTAGTATTTAT
1 TATTATATTATTATTAGTATTTAT
* *
1548295 TATTATTATTTTTA-TATTATTTAT
1 TATTA-TATTATTATTAGTATTTAT
1548319 T
1 T
1548320 TACTTTCCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
TATTATATTATTATTAGTATTTAT
Found at i:1548321 original size:13 final size:13
Alignment explanation
Indices: 1548271--1548319 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
1548261 ATATAGTCTA
1548271 TATTATATTATTAT
1 TATTAT-TTATTAT
*
1548285 TAGTATTTATTAT
1 TATTATTTATTAT
1548298 TATTATTT-TTA-
1 TATTATTTATTAT
1548309 TATTATTTATT
1 TATTATTTATT
1548320 TACTTTCCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 8 0.25
12 5 0.16
13 14 0.44
14 5 0.16
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (13 bp):
TATTATTTATTAT
Found at i:1549499 original size:18 final size:19
Alignment explanation
Indices: 1549478--1549525 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
1549468 TATTTTAACA
1549478 ATTTTTTATTTTTCA-ATT
1 ATTTTTTATTTTTCATATT
* *
1549496 ATTTTTT-CTCTTCATATT
1 ATTTTTTATTTTTCATATT
*
1549514 GTTTTTTATTTT
1 ATTTTTTATTTT
1549526 ATTTCACGTT
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
17 5 0.22
18 16 0.70
19 2 0.09
ACGTcount: A:0.17, C:0.08, G:0.02, T:0.73
Consensus pattern (19 bp):
ATTTTTTATTTTTCATATT
Found at i:1549595 original size:17 final size:16
Alignment explanation
Indices: 1549494--1549597 Score: 50
Period size: 16 Copynumber: 6.1 Consensus size: 16
1549484 TATTTTTCAA
*
1549494 TTATTTTTTCTCTTCAT
1 TTATTTTTTATCTT-AT
* *
1549511 ATTGTTTTTTATTTTAT
1 -TTATTTTTTATCTTAT
**
1549528 TTCA-CGTTTAT-TTAT
1 TT-ATTTTTTATCTTAT
*
1549543 TTATTATTATTATTATTACT
1 TTATT-TT-TTA-TCTTA-T
* *
1549563 TTCTTTTTTATTTTAT
1 TTATTTTTTATCTTAT
1549579 TTATTTTTTAATCTTAT
1 TTATTTTTT-ATCTTAT
1549596 TT
1 TT
1549598 CCCTTAAATT
Statistics
Matches: 66, Mismatches: 12, Indels: 17
0.69 0.13 0.18
Matches are distributed among these distances:
14 1 0.02
15 6 0.09
16 17 0.26
17 17 0.26
18 15 0.23
19 5 0.08
20 5 0.08
ACGTcount: A:0.19, C:0.08, G:0.02, T:0.71
Consensus pattern (16 bp):
TTATTTTTTATCTTAT
Found at i:1549682 original size:11 final size:11
Alignment explanation
Indices: 1549668--1549698 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1549658 TTTATTCATT
1549668 TTTTTATTTGA
1 TTTTTATTTGA
1549679 TTTTTATTTGA
1 TTTTTATTTGA
*
1549690 TTATTATTT
1 TTTTTATTT
1549699 TTTCTCCCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.74
Consensus pattern (11 bp):
TTTTTATTTGA
Found at i:1549686 original size:29 final size:29
Alignment explanation
Indices: 1549640--1549701 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
1549630 TGTTTTTTTG
1549640 TTTTATTTATTTAATATTT-TTATTCATTT
1 TTTTATTTATTTAATATTTATTATT-ATTT
*
1549669 TTTTATTTGATTT-TTATTTGATTATTATTT
1 TTTTATTT-ATTTAATATTT-ATTATTATTT
1549699 TTT
1 TTT
1549702 CTCCCTCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 13 0.45
30 11 0.38
31 5 0.17
ACGTcount: A:0.21, C:0.02, G:0.03, T:0.74
Consensus pattern (29 bp):
TTTTATTTATTTAATATTTATTATTATTT
Found at i:1550102 original size:2 final size:2
Alignment explanation
Indices: 1550095--1550124 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1550085 CGATCGCGGC
1550095 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
1550125 TACTAATCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1550180 original size:24 final size:24
Alignment explanation
Indices: 1550148--1550195 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
1550138 AAGCTAGAAC
*
1550148 AAAAGATGATGTATTAGGATGGAT
1 AAAAGATGATGGATTAGGATGGAT
1550172 AAAAGATGATGGATTAGGATGGAT
1 AAAAGATGATGGATTAGGATGGAT
1550196 TTTTATCCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.31, T:0.27
Consensus pattern (24 bp):
AAAAGATGATGGATTAGGATGGAT
Found at i:1556285 original size:2 final size:2
Alignment explanation
Indices: 1556232--1556271 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
1556222 ACTTATATGC
* *
1556232 TA TA T- TA TG TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1556272 GTGTGTGTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1557738 original size:10 final size:9
Alignment explanation
Indices: 1557705--1557729 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1557695 TCCTTTACCA
1557705 TTTATTTTT
1 TTTATTTTT
1557714 TTTATTTTT
1 TTTATTTTT
1557723 TTTATTT
1 TTTATTT
1557730 ATTTCTATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTATTTTT
Found at i:1562903 original size:23 final size:23
Alignment explanation
Indices: 1562877--1562921 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1562867 CACCACAGCT
*
1562877 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
1562900 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
1562922 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:1563163 original size:151 final size:149
Alignment explanation
Indices: 1562889--1563205 Score: 539
Period size: 151 Copynumber: 2.1 Consensus size: 149
1562879 TATAATTGCA
1562889 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
**
1562953 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTT
*
1563018 CCACAGAATATATATATATATC
130 CCAAAG-A-ATATATATATATC
*
1563040 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
*
1563105 TCCTTAAGAATCATATACATATGCTAGGGATCATA-TATGTGTCTCACCAGACTTCACACATGTT
66 TCCTTAAGAATCATATACATATGCTAGGGATCA-AGTATGTGTCTCACAAGACTTCACACATGTT
1563169 CCAAAGAATATATATATATC
130 CCAAAGAATATATATATATC
1563189 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
1563206 CCCTCGACTC
Statistics
Matches: 159, Mismatches: 5, Indels: 6
0.94 0.03 0.04
Matches are distributed among these distances:
149 30 0.19
150 2 0.01
151 126 0.79
152 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.26
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTTC
CAAAGAATATATATATATC
Found at i:1564114 original size:18 final size:18
Alignment explanation
Indices: 1564093--1564127 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1564083 TCCCATCTAG
1564093 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
1564111 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
1564128 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:1564716 original size:64 final size:64
Alignment explanation
Indices: 1564619--1564779 Score: 182
Period size: 64 Copynumber: 2.5 Consensus size: 64
1564609 TAATGAAGGT
* * * * * *
1564619 ATGCATTGATGCACTACACCATGCATCGATGCATAAATCCTATTTGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACTCCA-TATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAAT--
*
1564682 GG
63 GC
* *
1564684 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCCATATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATGC
* *
1564748 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACTCCATATGCATCGATGCA
1564780 CCTTAAACAA
Statistics
Matches: 82, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 56 0.68
65 23 0.28
66 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCACTCCATATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATGC
Found at i:1568185 original size:149 final size:149
Alignment explanation
Indices: 1567945--1568246 Score: 543
Period size: 149 Copynumber: 2.0 Consensus size: 149
1567935 AAGTGCCACC
1567945 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAATCA
1 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAATCA
** *
1568010 TATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCACAGAATATATA
66 TATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTTCCAAAGAATATATA
1568075 TATATCCCGAAGGACCGCG
131 TATATCCCGAAGGACCGCG
*
1568094 TAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAATCA
1 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAATCA
*
1568159 TATACATATGCTAGGGATCATA-TATGTGTCTCACCAGACTTCACACATGTTCCAAAGAATATAT
66 TATACATATGCTAGGGATCA-AGTATGTGTCTCACAAGACTTCACACATGTTCCAAAGAATATAT
1568223 ATATATCCCGAAGGACCGCG
130 ATATATCCCGAAGGACCGCG
1568243 TAGA
1 TAGA
1568247 CCCTCGACTC
Statistics
Matches: 147, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
149 146 0.99
150 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCCTTAAGAATCA
TATACATATGCTAGGGATCAAGTATGTGTCTCACAAGACTTCACACATGTTCCAAAGAATATATA
TATATCCCGAAGGACCGCG
Found at i:1568798 original size:2 final size:2
Alignment explanation
Indices: 1568791--1568826 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1568781 TCTCTTAGAC
1568791 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
1568827 CACATGTTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1569178 original size:18 final size:18
Alignment explanation
Indices: 1569157--1569191 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1569147 TCCCATCTAG
1569157 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
1569175 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
1569192 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:1569781 original size:64 final size:63
Alignment explanation
Indices: 1569683--1569843 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
1569673 TAATGAAGGT
* * *
1569683 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAAT--
*
1569746 GG
62 GC
*
1569748 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATGC
* *
1569812 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
1569844 CCTTAAACAA
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
63 1 0.01
64 57 0.67
65 24 0.28
66 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATGC
Found at i:1575489 original size:66 final size:67
Alignment explanation
Indices: 1575413--1575544 Score: 178
Period size: 66 Copynumber: 2.0 Consensus size: 67
1575403 AATACTTCGC
* * * *
1575413 TTAGGATGAAAACCCGAGAGGGCGTCCTAAGTT-GAAAA-AAAAAGAAGAAGAAGAAGAAAAGAA
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTAGAAAAGAAAAAGAAAAAGAAGAA-AAAAGAA
1575476 CGT
65 CGT
* *
1575479 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTGAGAAAAGAAAAAGAAAAAGAGGAAAAAAGAA
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATT-AGAAAAGAAAAAGAAAAAGAAGAAAAAAGAA
1575544 C
65 C
1575545 AAAAGAAGAG
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
66 29 0.51
68 13 0.23
69 15 0.26
ACGTcount: A:0.52, C:0.11, G:0.27, T:0.11
Consensus pattern (67 bp):
TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTAGAAAAGAAAAAGAAAAAGAAGAAAAAAGAAC
GT
Found at i:1575553 original size:21 final size:21
Alignment explanation
Indices: 1575515--1575558 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
1575505 CTAAATTGAG
1575515 AAAAGAAAAAGAAAAAGAGGAA
1 AAAAGAAAAAGAAAAAGA-GAA
* *
1575537 AAAAGAACAA-AAGAAGAGAA
1 AAAAGAAAAAGAAAAAGAGAA
1575557 AA
1 AA
1575559 TAAGGTGGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 6 0.30
22 9 0.45
ACGTcount: A:0.77, C:0.02, G:0.20, T:0.00
Consensus pattern (21 bp):
AAAAGAAAAAGAAAAAGAGAA
Found at i:1576044 original size:1 final size:1
Alignment explanation
Indices: 1576038--1576094 Score: 51
Period size: 1 Copynumber: 57.0 Consensus size: 1
1576028 AGCATCTCCC
* * * * ** *
1576038 AAAAAAAACAAAAAAACAAACAAAAAACAAAAAAAAAAGTAAAAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1576095 GAATGTGCAC
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.88, C:0.09, G:0.02, T:0.02
Consensus pattern (1 bp):
A
Found at i:1576062 original size:11 final size:10
Alignment explanation
Indices: 1576038--1576094 Score: 66
Period size: 11 Copynumber: 5.7 Consensus size: 10
1576028 AGCATCTCCC
1576038 AAAAAAAAC-
1 AAAAAAAACA
1576047 -AAAAAAACA
1 AAAAAAAACA
1576056 AACAAAAAACA
1 AA-AAAAAACA
1576067 AAAAAAAA-A
1 AAAAAAAACA
1576076 GTAAAAAAAACA
1 --AAAAAAAACA
1576088 AAAAAAA
1 AAAAAAA
1576095 GAATGTGCAC
Statistics
Matches: 42, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
8 8 0.19
9 1 0.02
10 14 0.33
11 18 0.43
12 1 0.02
ACGTcount: A:0.88, C:0.09, G:0.02, T:0.02
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:1576063 original size:21 final size:21
Alignment explanation
Indices: 1576037--1576094 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
1576027 GAGCATCTCC
1576037 CAAAAAAAACAAAAAAACAAA-
1 CAAAAAAAACAAAAAAA-AAAG
1576058 C--AAAAAACAAAAAAAAAAG
1 CAAAAAAAACAAAAAAAAAAG
*
1576077 TAAAAAAAACAAAAAAAA
1 CAAAAAAAACAAAAAAAA
1576095 GAATGTGCAC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 3 0.09
19 14 0.42
21 16 0.48
ACGTcount: A:0.86, C:0.10, G:0.02, T:0.02
Consensus pattern (21 bp):
CAAAAAAAACAAAAAAAAAAG
Found at i:1576064 original size:19 final size:20
Alignment explanation
Indices: 1576038--1576094 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 20
1576028 AGCATCTCCC
*
1576038 AAAAAAAACAAAAAAACAA-
1 AAAAAAAACAAAAAAAAAAG
*
1576057 ACAAAAAACAAAAAAAAAAG
1 AAAAAAAACAAAAAAAAAAG
1576077 TAAAAAAAACAAAAAAAA
1 -AAAAAAAACAAAAAAAA
1576095 GAATGTGCAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.52
21 16 0.48
ACGTcount: A:0.88, C:0.09, G:0.02, T:0.02
Consensus pattern (20 bp):
AAAAAAAACAAAAAAAAAAG
Found at i:1576081 original size:28 final size:28
Alignment explanation
Indices: 1576037--1576092 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
1576027 GAGCATCTCC
*
1576037 CAAAAAAAACAAAAAAACAAACAAAAAA
1 CAAAAAAAACAAAAAAAAAAACAAAAAA
*
1576065 CAAAAAAAA-AAGTAAAAAAAACAAAAAA
1 CAAAAAAAACAA-AAAAAAAAACAAAAAA
1576093 AAGAATGTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.08
28 23 0.92
ACGTcount: A:0.86, C:0.11, G:0.02, T:0.02
Consensus pattern (28 bp):
CAAAAAAAACAAAAAAAAAAACAAAAAA
Done.