Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009175.1 Hibiscus syriacus cultivar Beakdansim tig00112738_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: 10629029
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 51
Found at i:1372012 original size:29 final size:30
Alignment explanation
Indices: 1371939--1372051 Score: 85
Period size: 30 Copynumber: 3.9 Consensus size: 30
1371929 AATAATAAAC
* *
1371939 ACTTAAAGGGTTAAAATAGTAAAAATAGAAA
1 ACTT-AAGGGCTAAAATAGTAAAAACAGAAA
* **
1371970 A-TTAGAGGACTAAAATAGTAATTACA-AAA
1 ACTTA-AGGGCTAAAATAGTAAAAACAGAAA
1371999 ACTTAAGGGCTAAAATA--ACAAAA-A-AAA
1 ACTTAAGGGCTAAAATAGTA-AAAACAGAAA
** *
1372026 ACTTAAGGAATAAATTAGTAAAAACA
1 ACTTAAGGGCTAAAATAGTAAAAACA
1372052 TAATCTTAAA
Statistics
Matches: 65, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
27 19 0.29
28 6 0.09
29 18 0.28
30 21 0.32
31 1 0.02
ACGTcount: A:0.58, C:0.07, G:0.13, T:0.21
Consensus pattern (30 bp):
ACTTAAGGGCTAAAATAGTAAAAACAGAAA
Found at i:1372023 original size:60 final size:61
Alignment explanation
Indices: 1371908--1372023 Score: 137
Period size: 60 Copynumber: 1.9 Consensus size: 61
1371898 ATAAATATTT
* * * * * **
1371908 AATTACGAGGACTAACATGGTAATAATAAACACTTAAAGGGTTAAAATAGTAAAAATAGAA
1 AATTACGAGGACTAAAATAGTAATAACAAAAACTTAAAGGGCTAAAATACAAAAAATAGAA
*
1371969 AATTA-GAGGACTAAAATAGTAATTACAAAAACTT-AAGGGCTAAAATAACAAAAAA
1 AATTACGAGGACTAAAATAGTAATAACAAAAACTTAAAGGGCTAAAAT-ACAAAAAA
1372024 AAACTTAAGG
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
59 11 0.24
60 30 0.65
61 5 0.11
ACGTcount: A:0.55, C:0.09, G:0.15, T:0.22
Consensus pattern (61 bp):
AATTACGAGGACTAAAATAGTAATAACAAAAACTTAAAGGGCTAAAATACAAAAAATAGAA
Found at i:1372048 original size:27 final size:27
Alignment explanation
Indices: 1371950--1372049 Score: 92
Period size: 27 Copynumber: 3.5 Consensus size: 27
1371940 CTTAAAGGGT
*
1371950 TAAAATAGTAAAAATAGAAAATTAGAGGAC
1 TAAAATAGTAAAAA-A-AAACTTA-AGGAC
* *
1371980 TAAAATAGTAATTACAAAAACTTAAGGGC
1 TAAAATAGTAA--AAAAAAACTTAAGGAC
** *
1372009 TAAAATAACAAAAAAAAACTTAAGGAA
1 TAAAATAGTAAAAAAAAACTTAAGGAC
*
1372036 TAAATTAGTAAAAA
1 TAAAATAGTAAAAA
1372050 CATAATCTTA
Statistics
Matches: 57, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
27 24 0.42
29 13 0.23
30 17 0.30
31 1 0.02
32 2 0.04
ACGTcount: A:0.61, C:0.06, G:0.12, T:0.21
Consensus pattern (27 bp):
TAAAATAGTAAAAAAAAACTTAAGGAC
Found at i:1373244 original size:3 final size:3
Alignment explanation
Indices: 1373236--1373280 Score: 56
Period size: 3 Copynumber: 14.7 Consensus size: 3
1373226 AAAATGTAAA
*
1373236 AAT AAT AAT AAAT AAT AAT AAT -AT AAT AAT AAAT AAA AAT AAT AA
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AA
1373281 AAAAGACCCG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 29 0.78
4 6 0.16
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1373250 original size:10 final size:10
Alignment explanation
Indices: 1373235--1373277 Score: 68
Period size: 10 Copynumber: 4.2 Consensus size: 10
1373225 CAAAATGTAA
1373235 AAATAATAAT
1 AAATAATAAT
1373245 AAATAATAAT
1 AAATAATAAT
1373255 AATATAATAAT
1 AA-ATAATAAT
*
1373266 AAATAAAAAT
1 AAATAATAAT
1373276 AA
1 AA
1373278 TAAAAAAGAC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
10 21 0.68
11 10 0.32
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AAATAATAAT
Found at i:1373263 original size:21 final size:21
Alignment explanation
Indices: 1373237--1373279 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1373227 AAATGTAAAA
*
1373237 ATAATAATAAATAATAATAAT
1 ATAATAATAAATAAAAATAAT
1373258 ATAATAATAAATAAAAATAAT
1 ATAATAATAAATAAAAATAAT
1373279 A
1 A
1373280 AAAAAGACCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
ATAATAATAAATAAAAATAAT
Found at i:1377425 original size:79 final size:79
Alignment explanation
Indices: 1377293--1377444 Score: 268
Period size: 79 Copynumber: 1.9 Consensus size: 79
1377283 ACGAATGAAC
* * *
1377293 AAAAGAATAATGCATATGGGTATATTATTGGCATGAAAGGATGTCATATTTGAAATGCATATGGG
1 AAAAGAATAATGCATATGGGTACATTATTGGCATGAAAGGATGCCATAGTTGAAATGCATATGGG
1377358 TGCATTATCAGAAT
66 TGCATTATCAGAAT
*
1377372 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGTTGAAATGCATATGGG
1 AAAAGAATAATGCATATGGGTACATTATTGGCATGAAAGGATGCCATAGTTGAAATGCATATGGG
1377437 TGCATTAT
66 TGCATTAT
1377445 TGGCATGAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
79 69 1.00
ACGTcount: A:0.37, C:0.09, G:0.24, T:0.30
Consensus pattern (79 bp):
AAAAGAATAATGCATATGGGTACATTATTGGCATGAAAGGATGCCATAGTTGAAATGCATATGGG
TGCATTATCAGAAT
Found at i:1377429 original size:45 final size:45
Alignment explanation
Indices: 1377380--1377641 Score: 235
Period size: 45 Copynumber: 6.1 Consensus size: 45
1377370 ATAAAAGAAT
*
1377380 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGTTGA
1 AATGCATATGGGTGCATTATCGGCATGAAAGGATGCCATAGTTGA
* *
1377425 AATGCATATGGGTGCATTATTGGCATGAAATGATGCCATAGTTGA
1 AATGCATATGGGTGCATTATCGGCATGAAAGGATGCCATAGTTGA
*
1377470 AATGCATATAGGTGCATTATCGGCAT-AAA--A-G--A-A--T--
1 AATGCATATGGGTGCATTATCGGCATGAAAGGATGCCATAGTTGA
* * * * * *
1377504 AATGGATATGGGCGTATTATCGCCATGAAAGGATGCCAAAAG--AA
1 AATGCATATGGGTGCATTATCGGCATGAAAGGATGCC-ATAGTTGA
* * * *
1377548 TAATGCATATGGGTGCATTATTGGCATGAAATGATGCTATAGCTGA
1 -AATGCATATGGGTGCATTATCGGCATGAAAGGATGCCATAGTTGA
** * * * *
1377594 AATGCATATGAATGCATTATCGGCATAAAAGTATGCTATACTTGA
1 AATGCATATGGGTGCATTATCGGCATGAAAGGATGCCATAGTTGA
1377639 AAT
1 AAT
1377642 ATATAATGGT
Statistics
Matches: 178, Mismatches: 25, Indels: 28
0.77 0.11 0.12
Matches are distributed among these distances:
34 21 0.12
35 3 0.02
36 1 0.01
37 1 0.01
38 2 0.01
39 1 0.01
41 2 0.01
42 2 0.01
44 6 0.03
45 138 0.78
46 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATCGGCATGAAAGGATGCCATAGTTGA
Found at i:1377471 original size:124 final size:124
Alignment explanation
Indices: 1377292--1377624 Score: 463
Period size: 124 Copynumber: 2.7 Consensus size: 124
1377282 AACGAATGAA
** * * *
1377292 CAAAAGAATAATGCATATGGGTATATTATTGGCATGAAAGGATGTCATATTTGAAATGCATATGG
1 CAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAATGATGCCATAGTTGAAATGCATATGG
* * * * *
1377357 GTGCATTATCAGAATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGC
66 GTGCATTATCGGCATAAAAGAATAATGCATATGGGCGCATTATCGCCATGAAAGGATGC
* *
1377416 C-ATAG-TTGAAATGCATATGGGTGCATTATTGGCATGAAATGATGCCATAGTTGAAATGCATAT
1 CAAAAGAAT--AATGCATATGGGTGCATTATTGGCATGAAATGATGCCATAGTTGAAATGCATAT
* * *
1377479 AGGTGCATTATCGGCATAAAAGAATAATGGATATGGGCGTATTATCGCCATGAAAGGATGC
64 GGGTGCATTATCGGCATAAAAGAATAATGCATATGGGCGCATTATCGCCATGAAAGGATGC
* * *
1377540 CAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAATGATGCTATAGCTGAAATGCATATGA
1 CAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAATGATGCCATAGTTGAAATGCATATGG
*
1377605 ATGCATTATCGGCATAAAAG
66 GTGCATTATCGGCATAAAAG
1377625 TATGCTATAC
Statistics
Matches: 183, Mismatches: 22, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
122 1 0.01
123 3 0.02
124 175 0.96
125 3 0.02
126 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28
Consensus pattern (124 bp):
CAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAATGATGCCATAGTTGAAATGCATATGG
GTGCATTATCGGCATAAAAGAATAATGCATATGGGCGCATTATCGCCATGAAAGGATGC
Found at i:1382536 original size:20 final size:20
Alignment explanation
Indices: 1382511--1382559 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1382501 TTCAATTGGC
*
1382511 ATCGATACCGAA-GGAGGAGT
1 ATCGATACCGAAGGGAAG-GT
1382531 ATCGATACCGAAGGGAAGGT
1 ATCGATACCGAAGGGAAGGT
1382551 ATCGATACC
1 ATCGATACC
1382560 ATTTTAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 23 0.85
21 4 0.15
ACGTcount: A:0.35, C:0.18, G:0.31, T:0.16
Consensus pattern (20 bp):
ATCGATACCGAAGGGAAGGT
Found at i:1383122 original size:45 final size:45
Alignment explanation
Indices: 1383071--1383349 Score: 192
Period size: 45 Copynumber: 6.7 Consensus size: 45
1383061 ATAAAAGAAT
* *
1383071 AATGCATATGGGTGAATTATTGGCATGAAAGGATACCATAGCTGA
1 AATGCATATGGGTGCATTATCGGCATGAAAGGATACCATAGCTGA
* *
1383116 AATGCATATAGGTGCATTATCGGCAT--AA--A-A-GA-A--T--
1 AATGCATATGGGTGCATTATCGGCATGAAAGGATACCATAGCTGA
*
1383150 AATGCATATGGGTGCATTATCGGCATGAAAGGATGCCATAGCTGA
1 AATGCATATGGGTGCATTATCGGCATGAAAGGATACCATAGCTGA
* *
1383195 AATGCATATGGGTGCATTATCGCCAT--AA--A-A-GA-A--T--
1 AATGCATATGGGTGCATTATCGGCATGAAAGGATACCATAGCTGA
* * * * *
1383229 AATGGATATGGGTGCATTATCGACATGAAAGGATGCCAAAAG--AA
1 AATGCATATGGGTGCATTATCGGCATGAAAGGATACC-ATAGCTGA
** * * *
1383273 TAATGCATATGGGCACATTATTGGCATGAAAGGATGCCATAGTTGA
1 -AATGCATATGGGTGCATTATCGGCATGAAAGGATACCATAGCTGA
* * *
1383319 AATGCATATAGGTGCATCATCGGCATAAAAG
1 AATGCATATGGGTGCATTATCGGCATGAAAG
1383350 TATGATATAC
Statistics
Matches: 182, Mismatches: 27, Indels: 50
0.70 0.10 0.19
Matches are distributed among these distances:
34 49 0.27
36 6 0.03
38 4 0.02
39 2 0.01
40 2 0.01
41 4 0.02
42 1 0.01
43 5 0.03
44 3 0.02
45 105 0.58
46 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.25
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATCGGCATGAAAGGATACCATAGCTGA
Found at i:1383164 original size:34 final size:34
Alignment explanation
Indices: 1383116--1383259 Score: 144
Period size: 34 Copynumber: 3.9 Consensus size: 34
1383106 CCATAGCTGA
*
1383116 AATGCATATAGGTGCATTATCGGCATAAAAGAAT
1 AATGCATATGGGTGCATTATCGGCATAAAAGAAT
1383150 AATGCATATGGGTGCATTATCGGCATGAAAGGATGCCATAGCT
1 AATGCATATGGGTGCATTATCGGCAT-AAA--A-G--A-A--T
*
1383193 GAAATGCATATGGGTGCATTATCGCCATAAAAGAAT
1 --AATGCATATGGGTGCATTATCGGCATAAAAGAAT
* * *
1383229 AATGGATATGGGTGCATTATCGACATGAAAG
1 AATGCATATGGGTGCATTATCGGCATAAAAG
1383260 GATGCCAAAA
Statistics
Matches: 94, Mismatches: 5, Indels: 22
0.78 0.04 0.18
Matches are distributed among these distances:
34 53 0.56
35 3 0.03
36 1 0.01
37 1 0.01
38 2 0.02
39 1 0.01
40 1 0.01
41 2 0.02
42 1 0.01
43 1 0.01
44 3 0.03
45 25 0.27
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (34 bp):
AATGCATATGGGTGCATTATCGGCATAAAAGAAT
Found at i:1383192 original size:79 final size:79
Alignment explanation
Indices: 1383061--1383266 Score: 349
Period size: 79 Copynumber: 2.6 Consensus size: 79
1383051 GAATGAATGA
* * *
1383061 ATAAAAGAATAATGCATATGGGTGAATTATTGGCATGAAAGGATACCATAGCTGAAATGCATATA
1 ATAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGCCATAGCTGAAATGCATATA
*
1383126 GGTGCATTATCGGC
66 GGTGCATTATCGCC
*
1383140 ATAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGCCATAGCTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGCCATAGCTGAAATGCATATA
1383205 GGTGCATTATCGCC
66 GGTGCATTATCGCC
* *
1383219 ATAAAAGAATAATGGATATGGGTGCATTATCGACATGAAAGGATGCCA
1 ATAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGCCA
1383267 AAAGAATAAT
Statistics
Matches: 120, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 120 1.00
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.25
Consensus pattern (79 bp):
ATAAAAGAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGCCATAGCTGAAATGCATATA
GGTGCATTATCGCC
Found at i:1390100 original size:36 final size:36
Alignment explanation
Indices: 1390029--1390107 Score: 104
Period size: 36 Copynumber: 2.2 Consensus size: 36
1390019 GACATTGGCA
* * * *
1390029 TTGGAAATGTTGTTTGTGGTTACTGTGTCATTGAGG
1 TTGGAGATGTTATTTATGGTTACTGTGGCATTGAGG
*
1390065 TTGGAGATGTTATTTATGGTTGCTGTGGCATTGAGG
1 TTGGAGATGTTATTTATGGTTACTGTGGCATTGAGG
*
1390101 CTGGAGA
1 TTGGAGA
1390108 AGTATCTTGC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.18, C:0.06, G:0.35, T:0.41
Consensus pattern (36 bp):
TTGGAGATGTTATTTATGGTTACTGTGGCATTGAGG
Found at i:1391604 original size:42 final size:41
Alignment explanation
Indices: 1391544--1391661 Score: 116
Period size: 42 Copynumber: 2.9 Consensus size: 41
1391534 ACCGACCCGA
* * *
1391544 ATATATTAATATT-TTAAAATAATATATTTATAATTATTTATT
1 ATATTTTAA-ATTATTAAAATAATATATTTATAATAAGTT-TT
*
1391586 ATATTTTAAATTATTAAAATAATATACTATATAATAAGTTTT
1 ATATTTTAAATTATTAAAATAATATA-TTTATAATAAGTTTT
* * * *
1391628 ATATTTTTAATAATT-ATAGAATATATTT-TAATAA
1 ATATTTTAAATTATTAAAATAATATATTTATAATAA
1391662 TATAAAAATA
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
39 6 0.09
40 2 0.03
41 11 0.17
42 36 0.55
43 10 0.15
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.51
Consensus pattern (41 bp):
ATATTTTAAATTATTAAAATAATATATTTATAATAAGTTTT
Found at i:1391671 original size:21 final size:22
Alignment explanation
Indices: 1391627--1391668 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1391617 TAATAAGTTT
*
1391627 TATATTTTTAATAATTATAGAA
1 TATATTTTTAATAATTATAAAA
1391649 TATA-TTTTAATAA-TATAAAA
1 TATATTTTTAATAATTATAAAA
1391669 ATAAAAATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 9 0.47
22 4 0.21
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TATATTTTTAATAATTATAAAA
Found at i:1392318 original size:19 final size:19
Alignment explanation
Indices: 1392294--1392348 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 19
1392284 TTATAATATT
*
1392294 ATATTTTTAATTGTTGTAA
1 ATATTTTTAATTGTTATAA
* *
1392313 ATATTTTTTCATGGTTATAA
1 ATA-TTTTTAATTGTTATAA
*
1392333 ATA-TTTTAATTTTTAT
1 ATATTTTTAATTGTTAT
1392349 TTATTATGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
18 10 0.34
19 3 0.10
20 16 0.55
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.60
Consensus pattern (19 bp):
ATATTTTTAATTGTTATAA
Found at i:1392633 original size:83 final size:83
Alignment explanation
Indices: 1392494--1392657 Score: 285
Period size: 83 Copynumber: 2.0 Consensus size: 83
1392484 TCGGCCCCTA
*
1392494 TTAAAATTTATATATTCAATATAATTTTAGTTTAATAGTATTTTGGTTTATGTAAAAATAAATAT
1 TTAAAATTTATATATTCAATATAATTTTAGTTTAATAGTATTTTGGTTCATGTAAAAATAAATAT
1392559 TTAAATTTAAAAAATAAG
66 TTAAATTTAAAAAATAAG
* *
1392577 TTAAAATTTATATATT-AGATATAATTTTGGTTTAATATTATTTTGGTTCATGTAAAAATAAATA
1 TTAAAATTTATATATTCA-ATATAATTTTAGTTTAATAGTATTTTGGTTCATGTAAAAATAAATA
1392641 TTTAAATTTAAAAAATA
65 TTTAAATTTAAAAAATA
1392658 TAAAAAATTA
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
82 1 0.01
83 76 0.99
ACGTcount: A:0.45, C:0.01, G:0.07, T:0.46
Consensus pattern (83 bp):
TTAAAATTTATATATTCAATATAATTTTAGTTTAATAGTATTTTGGTTCATGTAAAAATAAATAT
TTAAATTTAAAAAATAAG
Found at i:1393089 original size:17 final size:16
Alignment explanation
Indices: 1393069--1393113 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1393059 TATGTGATAC
1393069 AAAAATGTATTATTTTA
1 AAAAATG-ATTATTTTA
* *
1393086 AAAAATCATTTTTTTA
1 AAAAATGATTATTTTA
*
1393102 GAAAATGATTAT
1 AAAAATGATTAT
1393114 CCCACCTTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
16 17 0.74
17 6 0.26
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (16 bp):
AAAAATGATTATTTTA
Found at i:1401176 original size:21 final size:21
Alignment explanation
Indices: 1401150--1401194 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1401140 GATTTCTGAG
* *
1401150 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1401171 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1401192 CAA
1 CAA
1401195 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1401672 original size:2 final size:2
Alignment explanation
Indices: 1401665--1401695 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1401655 ATTACATGAG
1401665 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1401696 GGAATTGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1402573 original size:32 final size:32
Alignment explanation
Indices: 1402532--1402628 Score: 128
Period size: 32 Copynumber: 3.1 Consensus size: 32
1402522 GAGTCGAGGG
1402532 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
1402564 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
1402595 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
1402627 TT
1 TT
1402629 ACCGAGGATC
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
31 26 0.47
32 29 0.53
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:1402604 original size:31 final size:31
Alignment explanation
Indices: 1402531--1402631 Score: 125
Period size: 31 Copynumber: 3.2 Consensus size: 31
1402521 AGAGTCGAGG
1402531 GTTTACCTATGTTCT-ACGGAACATATGGACA
1 GTTTACCTATGTTCTAAC-GAACATATGGACA
**
1402562 GTTTTACCTATG-TCTTTCGAGACATATGGACA
1 G-TTTACCTATGTTCTAACGA-ACATATGGACA
* *
1402594 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTAACGAACATATGGACA
1402625 GTTTACC
1 GTTTACC
1402632 GAGGATCTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
31 32 0.53
32 28 0.47
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTAACGAACATATGGACA
Found at i:1402663 original size:30 final size:30
Alignment explanation
Indices: 1402619--1402712 Score: 136
Period size: 30 Copynumber: 3.1 Consensus size: 30
1402609 AAGGAACATA
1402619 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
1402650 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * * *
1402680 TGGATAGTTACCG-GGGTCTGTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1402709 TGGA
1 TGGA
1402713 TAGGTCCTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
29 17 0.29
30 35 0.59
31 7 0.12
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:1405368 original size:21 final size:21
Alignment explanation
Indices: 1405342--1405388 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
1405332 TTAATGACGT
*
1405342 TTTTTTAATTCTATAGCGGCA
1 TTTTTTAATTCTATAGCGGAA
*
1405363 TTTTTTAGTTCTATAGCGGAA
1 TTTTTTAATTCTATAGCGGAA
1405384 TTTTT
1 TTTTT
1405389 AAGCGCCACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.11, G:0.15, T:0.53
Consensus pattern (21 bp):
TTTTTTAATTCTATAGCGGAA
Found at i:1406357 original size:27 final size:27
Alignment explanation
Indices: 1406322--1406382 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
1406312 GCAAGATTCG
1406322 ATTC-ATTTAACTGCAAAGGACTACAA
1 ATTCAATTTAACTGCAAAGGACTACAA
* * *
1406348 ATTCAATTTACCTGCAAAGGAGTACAT
1 ATTCAATTTAACTGCAAAGGACTACAA
1406375 ATTCAATT
1 ATTCAATT
1406383 ATATAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
26 4 0.13
27 27 0.87
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.31
Consensus pattern (27 bp):
ATTCAATTTAACTGCAAAGGACTACAA
Found at i:1410434 original size:24 final size:24
Alignment explanation
Indices: 1410396--1410465 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
1410386 CAAAACAGAG
* *
1410396 TCCATGTCAAGTATCATATAAAAA
1 TCCAGGTCAAATATCATATAAAAA
* * *
1410420 TTCAGGTCAAATATCATATCAGAA
1 TCCAGGTCAAATATCATATAAAAA
* * *
1410444 TCCATGTCAAAAATCAGATAAA
1 TCCAGGTCAAATATCATATAAA
1410466 CTATTTATAT
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.46, C:0.17, G:0.10, T:0.27
Consensus pattern (24 bp):
TCCAGGTCAAATATCATATAAAAA
Found at i:1410465 original size:48 final size:47
Alignment explanation
Indices: 1410371--1410465 Score: 118
Period size: 48 Copynumber: 2.0 Consensus size: 47
1410361 ATTAAAACAT
* * ** *
1410371 AATTCAGGTCAAGTACAAAACAGAGTCCATGTCAAGTATCATATAAA
1 AATTCAGGTCAAATACAAAACAGAATCCATGTCAAAAATCAGATAAA
* *
1410418 AATTCAGGTCAAATATCATATCAGAATCCATGTCAAAAATCAGATAAA
1 AATTCAGGTCAAATA-CAAAACAGAATCCATGTCAAAAATCAGATAAA
1410466 CTATTTATAT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
47 14 0.35
48 26 0.65
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.24
Consensus pattern (47 bp):
AATTCAGGTCAAATACAAAACAGAATCCATGTCAAAAATCAGATAAA
Found at i:1411193 original size:29 final size:29
Alignment explanation
Indices: 1411153--1411244 Score: 87
Period size: 29 Copynumber: 3.2 Consensus size: 29
1411143 CATTTTACAC
* *
1411153 AAATAGCGCCCTTTTTAAAATAATTAC-CA
1 AAATAGCACCCTTTTCAAAATAATT-CTCA
* *
1411182 AAATAGCACCCTTTTCGAATTAATTCTCA
1 AAATAGCACCCTTTTCAAAATAATTCTCA
** * * *
1411211 AAATAGCACCAATTTCGAATTAATTCCCA
1 AAATAGCACCCTTTTCAAAATAATTCTCA
1411240 AAATA
1 AAATA
1411245 TCATTTTTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
28 1 0.02
29 54 0.98
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (29 bp):
AAATAGCACCCTTTTCAAAATAATTCTCA
Found at i:1411398 original size:9 final size:10
Alignment explanation
Indices: 1411384--1411419 Score: 56
Period size: 11 Copynumber: 3.6 Consensus size: 10
1411374 ACGGGTCATG
1411384 ACCGGTC-AA
1 ACCGGTCAAA
1411393 ACCGGTCAAA
1 ACCGGTCAAA
1411403 ACCGGTTCAAA
1 ACCGG-TCAAA
1411414 ACCGGT
1 ACCGGT
1411420 TTCTAGATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 7 0.28
10 8 0.32
11 10 0.40
ACGTcount: A:0.33, C:0.31, G:0.22, T:0.14
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:1417409 original size:243 final size:245
Alignment explanation
Indices: 1416974--1417469 Score: 852
Period size: 243 Copynumber: 2.0 Consensus size: 245
1416964 AGTTAGACCC
*
1416974 AAACCTAAGTGGTCACATATCCCTTTCAGAGTTTTTTTTTGTTTTTACAATTTATAGAATATTAC
1 AAACCTAAGTGGTCACATATCCCTTTCAGAG-----TTTTGTTTTTACAACTTATAGAATATTAC
* * *
1417039 ACAAAATATATTAATATTTCAGATATGTCCAAAATGATAGCAAATACATGTCACCAAATATAACT
61 ACAAAATATATTAATATTACAGATATGTCCAAAACGATAGCAAATACATGTCACCAAATACAACT
*
1417104 GAAAAATATATAGAAATATATGTTCGTACAAAATAAGTAGTTGATCTCCTCTAATGCCAAATCTG
126 GAAAAACATATAGAAATATATGTTCGTACAAAATAAGTAGTTGATCTCCTCTAATGCCAAATCTG
* * *
1417169 CTAGCTTATGGTCTGCTGTTATCTGAAAAAGGGTAAAAACTATATAATGAGCTAA
191 CTAGATTATGGTCTGCTATTATCTGAAAAAGGGTAAAAACTATAGAATGAGCTAA
*
1417224 AAACCTAAGTGGTCACATATCCCTTTCAGAG-TTT-TTTTTACAACTTATAGAATATTGCACAAA
1 AAACCTAAGTGGTCACATATCCCTTTCAGAGTTTTGTTTTTACAACTTATAGAATATTACACAAA
1417287 ATATATTAATATTACAGATATGTCCAAAACGATAGCAAATACATGTCACCAAATACAACTGAAAA
66 ATATATTAATATTACAGATATGTCCAAAACGATAGCAAATACATGTCACCAAATACAACTGAAAA
1417352 ACATATAGAAATATATGTTCGTACAAAATAAGTAGTTGATCTCCTCTAATGCCAAATCTGCTAGA
131 ACATATAGAAATATATGTTCGTACAAAATAAGTAGTTGATCTCCTCTAATGCCAAATCTGCTAGA
1417417 TTATGGTCTGCTATTATCTGAAAAAGGGTAAAAACTATAGAATGAGCTAA
196 TTATGGTCTGCTATTATCTGAAAAAGGGTAAAAACTATAGAATGAGCTAA
1417467 AAA
1 AAA
1417470 GCTCAGTGTG
Statistics
Matches: 237, Mismatches: 9, Indels: 7
0.94 0.04 0.03
Matches are distributed among these distances:
243 203 0.86
244 3 0.01
250 31 0.13
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (245 bp):
AAACCTAAGTGGTCACATATCCCTTTCAGAGTTTTGTTTTTACAACTTATAGAATATTACACAAA
ATATATTAATATTACAGATATGTCCAAAACGATAGCAAATACATGTCACCAAATACAACTGAAAA
ACATATAGAAATATATGTTCGTACAAAATAAGTAGTTGATCTCCTCTAATGCCAAATCTGCTAGA
TTATGGTCTGCTATTATCTGAAAAAGGGTAAAAACTATAGAATGAGCTAA
Found at i:1417869 original size:24 final size:24
Alignment explanation
Indices: 1417808--1417876 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 24
1417798 AAGTACAAAA
* *
1417808 CAGAGTCCATGTCAAGTATCATAT
1 CAGAATCCATGTCAAATATCATAT
* * ** *
1417832 AAAAATTTAGGTCAAATATCATAT
1 CAGAATCCATGTCAAATATCATAT
*
1417856 CAGAATCCATGTCAAAAATCA
1 CAGAATCCATGTCAAATATCA
1417877 GATAAACTAT
Statistics
Matches: 32, Mismatches: 13, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.28
Consensus pattern (24 bp):
CAGAATCCATGTCAAATATCATAT
Found at i:1418610 original size:29 final size:29
Alignment explanation
Indices: 1418570--1418637 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
1418560 CATTTTACAC
*
1418570 AAATAGCTCCCTCTTTAAAATAATTAC-CA
1 AAATAGCACCCTCTTTAAAATAATT-CTCA
* * *
1418599 AAATAGCACCCTTTTTGAATTAATTCTCA
1 AAATAGCACCCTCTTTAAAATAATTCTCA
*
1418628 AAACAGCACC
1 AAATAGCACC
1418638 AATTTCGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 1 0.03
29 32 0.97
ACGTcount: A:0.40, C:0.25, G:0.06, T:0.29
Consensus pattern (29 bp):
AAATAGCACCCTCTTTAAAATAATTCTCA
Found at i:1418690 original size:54 final size:55
Alignment explanation
Indices: 1418610--1418715 Score: 144
Period size: 54 Copynumber: 1.9 Consensus size: 55
1418600 AATAGCACCC
*
1418610 TTTTTGAATTAATTCTCAAAACAGCACCAATTTCGAATTAATTCCCAGAATATCA
1 TTTTTGAATAAATTCTCAAAACAGCACCAATTTCGAATTAATTCCCAGAATATCA
* * * *
1418665 TTTTTGAA-AAATTACT-AAAATAGCACCCATTTTGAATTAATTCCTAGAATA
1 TTTTTGAATAAATT-CTCAAAACAGCACCAATTTCGAATTAATTCCCAGAATA
1418716 GCACTGAAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
54 35 0.78
55 10 0.22
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.36
Consensus pattern (55 bp):
TTTTTGAATAAATTCTCAAAACAGCACCAATTTCGAATTAATTCCCAGAATATCA
Found at i:1418695 original size:29 final size:29
Alignment explanation
Indices: 1418591--1418719 Score: 79
Period size: 29 Copynumber: 4.6 Consensus size: 29
1418581 TCTTTAAAAT
* * *
1418591 AATTACCAAAATAGCACCCTTTTTGAATT
1 AATTACTAAAATAGCACCCATTTTGAATA
* * * *
1418620 AATT-CTCAAAACAGCACCAATTTCGAATT
1 AATTACT-AAAATAGCACCCATTTTGAATA
* * * * *
1418649 AATTCCCAGAATATCA---TTTTTGAA-A
1 AATTACTAAAATAGCACCCATTTTGAATA
*
1418674 AATTACTAAAATAGCACCCATTTTGAATT
1 AATTACTAAAATAGCACCCATTTTGAATA
* *
1418703 AATTCCTAGAATAGCAC
1 AATTACTAAAATAGCAC
1418720 TGAAACCGAA
Statistics
Matches: 74, Mismatches: 20, Indels: 12
0.70 0.19 0.11
Matches are distributed among these distances:
25 12 0.16
26 6 0.08
28 8 0.11
29 47 0.64
30 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (29 bp):
AATTACTAAAATAGCACCCATTTTGAATA
Found at i:1418730 original size:83 final size:83
Alignment explanation
Indices: 1418591--1418744 Score: 213
Period size: 83 Copynumber: 1.9 Consensus size: 83
1418581 TCTTTAAAAT
* **
1418591 AATTACCAAAATAGCACCCTTTTTGAATTAATTCTCAAAACAGCACCAATTTCGAATTAATTCCC
1 AATTACCAAAATAGCACCCATTTTGAATTAATTCTCAAAACAGCACCAATACCGAATTAATTCCC
1418656 AGAATATCATTTTTGAAA
66 AGAATATCATTTTTGAAA
* * * *
1418674 AATTACTAAAATAGCACCCATTTTGAATTAATTC-CTAGAATAGCACTGAA-ACCGAATTAATTC
1 AATTACCAAAATAGCACCCATTTTGAATTAATTCTC-AAAACAGCAC-CAATACCGAATTAATTC
1418737 CCAGAATA
64 CCAGAATA
1418745 GCACCGGTCA
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
82 1 0.02
83 59 0.95
84 2 0.03
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (83 bp):
AATTACCAAAATAGCACCCATTTTGAATTAATTCTCAAAACAGCACCAATACCGAATTAATTCCC
AGAATATCATTTTTGAAA
Found at i:1418779 original size:17 final size:17
Alignment explanation
Indices: 1418756--1418796 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
1418746 CACCGGTCAC
1418756 CGGTCAACGG-TCGGGT
1 CGGTCAACGGATCGGGT
1418772 CGGGTCAACGGATCGGGT
1 C-GGTCAACGGATCGGGT
1418790 CGGTCAA
1 CGGTCAA
1418797 ACCGGTTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.04
17 15 0.65
18 7 0.30
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.17
Consensus pattern (17 bp):
CGGTCAACGGATCGGGT
Found at i:1424100 original size:21 final size:21
Alignment explanation
Indices: 1424058--1424100 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1424048 TTTTCGGGCT
* * *
1424058 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
1424079 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
1424100 A
1 A
1424101 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:1424822 original size:149 final size:150
Alignment explanation
Indices: 1424635--1424950 Score: 537
Period size: 150 Copynumber: 2.1 Consensus size: 150
1424625 GGGTAGAGGG
* *
1424635 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTT-GAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
* * *
1424699 TGCTTGATCCTTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCTTTATAGACATCATT
66 TACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATAGACATCATT
*
1424764 ATATGGCACTACGGTGCAAT
131 ACATGGCACTACGGTGCAAT
*
1424784 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
*
1424849 TACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
66 TACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATAGACATCATT
1424914 ACATGGCACTACGGTGCAAT
131 ACATGGCACTACGGTGCAAT
1424934 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
1424951 TGTATTTATA
Statistics
Matches: 157, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
149 52 0.33
150 105 0.67
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.35
Consensus pattern (150 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
TACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATAGACATCATT
ACATGGCACTACGGTGCAAT
Found at i:1424962 original size:23 final size:23
Alignment explanation
Indices: 1424918--1424962 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1424908 ATCATTACAT
*
1424918 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* * *
1424941 GGCACTTCGGTGTATTTATACG
1 GGCACTACGGTGCAATTATACG
1424963 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1430624 original size:21 final size:21
Alignment explanation
Indices: 1430582--1430624 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1430572 TTTTCGGGCT
* * *
1430582 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
1430603 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
1430624 A
1 A
1430625 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:1431400 original size:152 final size:149
Alignment explanation
Indices: 1431165--1431482 Score: 530
Period size: 152 Copynumber: 2.1 Consensus size: 149
1431155 GGGTAGAGGG
* *
1431165 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
* *
1431230 GCTTGATCCTTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATTA
*
1431295 TATGGCACTACGGTGCAAT
131 CATGGCACTACGGTGCAAT
* *
1431314 TCTATGCGGTCCTTCGGGATATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACA
1 TCTACGCGGTCCTTCGGG--ACATATATATATTCTGTGGAACATGTGTGAAGTCTT-GAAAGACA
1431379 CATACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCA
63 CATACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCA
1431444 TTACATGGCACTACGGTGCAAT
128 TTACATGGCACTACGGTGCAAT
1431466 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
1431483 TGCATTTATA
Statistics
Matches: 157, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
149 17 0.11
151 34 0.22
152 106 0.68
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATTA
CATGGCACTACGGTGCAAT
Found at i:1431494 original size:23 final size:23
Alignment explanation
Indices: 1431450--1431494 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1431440 ATCATTACAT
*
1431450 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
1431473 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
1431495 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1454063 original size:19 final size:19
Alignment explanation
Indices: 1454033--1454077 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1454023 GGTGAGATAA
*
1454033 ATCTGCTCCTCTCGTTCTC
1 ATCTGTTCCTCTCGTTCTC
*
1454052 ATTTGTTCCTCTCGTTCTC
1 ATCTGTTCCTCTCGTTCTC
1454071 ATCTGTT
1 ATCTGTT
1454078 TCGTTGGCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.07, C:0.33, G:0.11, T:0.49
Consensus pattern (19 bp):
ATCTGTTCCTCTCGTTCTC
Found at i:1454648 original size:19 final size:20
Alignment explanation
Indices: 1454616--1454653 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
1454606 TTCTCTCATC
1454616 TCTTCTTCCTTCTT-TCTTA
1 TCTTCTTCCTTCTTCTCTTA
1454635 TCTTCTTCAC-TCTTCTCTT
1 TCTTCTTC-CTTCTTCTCTT
1454654 CTTCCAAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.05, C:0.34, G:0.00, T:0.61
Consensus pattern (20 bp):
TCTTCTTCCTTCTTCTCTTA
Found at i:1455156 original size:21 final size:21
Alignment explanation
Indices: 1455114--1455156 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1455104 TTTCTGGGCT
** *
1455114 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCAATACCCACTCA
*
1455135 AGGGGAATCAATACCCCCTCA
1 AGGGGAATCAATACCCACTCA
1455156 A
1 A
1455157 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCAATACCCACTCA
Found at i:1455885 original size:23 final size:23
Alignment explanation
Indices: 1455850--1455894 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1455840 ATTATTATAT
*
1455850 GGCACTACGGTGCAATTT-TACGC
1 GGCACTACAGTGC-ATTTATACGC
*
1455873 GGCACTTCAGTGCATTTATACG
1 GGCACTACAGTGCATTTATACG
1455895 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.29
Consensus pattern (23 bp):
GGCACTACAGTGCATTTATACGC
Found at i:1460034 original size:22 final size:21
Alignment explanation
Indices: 1459989--1460031 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1459979 CACTTGACAT
*
1459989 ATTTTTTAATATTAAAAAATA
1 ATTTTTTAATATAAAAAAATA
1460010 ATTTTTTCAA-ATAAAAAAATA
1 ATTTTTT-AATATAAAAAAATA
1460031 A
1 A
1460032 ATTAAAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTTTTTAATATAAAAAAATA
Found at i:1462746 original size:21 final size:20
Alignment explanation
Indices: 1462688--1462736 Score: 68
Period size: 17 Copynumber: 2.6 Consensus size: 20
1462678 CCATTATAAC
*
1462688 ATTTATTTTTTATTT---TA
1 ATTTATTTTTTATTTGAAAA
1462705 ATTTATTTTTTATTTGAAAA
1 ATTTATTTTTTATTTGAAAA
1462725 ATTTATTTTTTA
1 ATTTATTTTTTA
1462737 ATATTAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 15 0.54
20 13 0.46
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (20 bp):
ATTTATTTTTTATTTGAAAA
Found at i:1466571 original size:2 final size:2
Alignment explanation
Indices: 1466564--1466615 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1466554 TGTTTTCAGA
1466564 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
1466606 AT AT AT AT AT
1 AT AT AT AT AT
1466616 GTGTGTGTGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1467755 original size:21 final size:19
Alignment explanation
Indices: 1467725--1467771 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
1467715 ATAAATATTA
1467725 AAATAATTTATTTA--ATAT
1 AAAT-ATTTATTTATTATAT
1467743 AAATATTTATTTATTATAT
1 AAATATTTATTTATTATAT
*
1467762 ATATATTTAT
1 AAATATTTAT
1467772 GACTACATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 9 0.35
18 4 0.15
19 13 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
AAATATTTATTTATTATAT
Found at i:1468654 original size:15 final size:14
Alignment explanation
Indices: 1468630--1468671 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
1468620 CCTCGGTAAG
*
1468630 TTTCTCTTCTTTCTT
1 TTTCTTTTCTTTC-T
1468645 TTTCTTTTCTTTCT
1 TTTCTTTTCTTTCT
1468659 TTTCTGTTTCTTT
1 TTTCT-TTTCTTT
1468672 GCTGCTGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 6 0.24
15 19 0.76
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.76
Consensus pattern (14 bp):
TTTCTTTTCTTTCT
Found at i:1468662 original size:20 final size:20
Alignment explanation
Indices: 1468630--1468671 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1468620 CCTCGGTAAG
*
1468630 TTTCTCTTCTTTCTTTTTCT
1 TTTCTCTTCTTTCTGTTTCT
1468650 TTTCT-TTCTTTTCTGTTTCT
1 TTTCTCTTC-TTTCTGTTTCT
1468670 TT
1 TT
1468672 GCTGCTGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTCTCTTCTTTCTGTTTCT
Found at i:1469168 original size:3 final size:3
Alignment explanation
Indices: 1469160--1469233 Score: 80
Period size: 3 Copynumber: 25.0 Consensus size: 3
1469150 TTAATATATT
* * * *
1469160 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAT TAT TAT TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
*
1469206 T-A TAA TAA TTA T-A TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1469234 ATCAATATGG
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
2 4 0.06
3 57 0.90
4 2 0.03
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:1469207 original size:16 final size:16
Alignment explanation
Indices: 1469160--1469231 Score: 76
Period size: 16 Copynumber: 4.4 Consensus size: 16
1469150 TTAATATATT
*
1469160 TAATAATAATAATAATGA
1 TAATAATTAT-ATAAT-A
1469178 TAATAA-TA-ATAATA
1 TAATAATTATATAATA
* *
1469192 TTATTATTATATAATA
1 TAATAATTATATAATA
1469208 TAATAATTATATAATAA
1 TAATAATTATATAAT-A
1469225 TAATAAT
1 TAATAAT
1469232 AAATCAATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
14 5 0.11
15 7 0.15
16 19 0.41
17 9 0.20
18 6 0.13
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (16 bp):
TAATAATTATATAATA
Found at i:1469888 original size:229 final size:229
Alignment explanation
Indices: 1469549--1470334 Score: 1178
Period size: 229 Copynumber: 3.5 Consensus size: 229
1469539 GAATTATGCA
** *
1469549 AAAAG-TTGAACAAGCTCTTCTTATTATGAA---CTTCTTC-TTCTTCAGATGACGAGTTCTTCT
1 AAAAGATTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGACGAGTTCTTCT
* *
1469609 CATTATGAACTCTACCTGGCAATGTTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAA
66 CATTATGAACTCTTCTTGGCAATGTTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAA
1469674 ATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
131 ATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
1469739 GGAAAAGCTGATCCATCAAATGATGGATTTGAGC
196 GGAAAAGCTGATCCATCAAATGATGGATTTGAGC
*
1469773 AAAAGATTGAACAAATTCTCCTCATTATGAATTTCTTCTTCTTTCTTCAGATGACGAGTTCTTCT
1 AAAAGATTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGACGAGTTCTTCT
1469838 CATTATGAACTCTTCTTGGCAATGTTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAA
66 CATTATGAACTCTTCTTGGCAATGTTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAA
1469903 ATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
131 ATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
*
1469968 GGAAAAGCTGATCCATCAATTGATGGATTTGAGC
196 GGAAAAGCTGATCCATCAAATGATGGATTTGAGC
1470002 AAAAGATTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGACGAGTTCTTCT
1 AAAAGATTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGACGAGTTCTTCT
* *** * * * *
1470067 CATTATGAACTCTCCTTGGTGCTGTTGATCCATCAAATGATGAATTCAAGCAAAAGGGTTAAACA
66 CATTATGAACTCTTCTTGGCAATGTTAATCCATCAAATGATGAATTTAAACAAAA-GGTTGAACA
* * * ****
1470132 AGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAAC
130 AATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* * *
1470197 TGGAAAAGTTGATCCATCAAATGATGGA-TTCAGGT
195 TGGAAAAGCTGATCCATCAAATGATGGATTTGA-GC
* * * *
1470232 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCT
1 AAAAGATTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGACGAGTTCTTCT
* * * *
1470294 CATTATGAACTCTT-TCTGGAAAAGATAATCCATCAAGTGAT
66 CATTATGAACTCTTCT-TGGCAATGTTAATCCATCAAATGAT
1470335 AGATTTGAAT
Statistics
Matches: 515, Mismatches: 39, Indels: 13
0.91 0.07 0.02
Matches are distributed among these distances:
224 5 0.01
225 21 0.04
226 1 0.00
227 41 0.08
228 7 0.01
229 299 0.58
230 141 0.27
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (229 bp):
AAAAGATTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGACGAGTTCTTCT
CATTATGAACTCTTCTTGGCAATGTTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAA
ATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
GGAAAAGCTGATCCATCAAATGATGGATTTGAGC
Found at i:1469892 original size:116 final size:113
Alignment explanation
Indices: 1469546--1470334 Score: 960
Period size: 113 Copynumber: 6.9 Consensus size: 113
1469536 ATAGAATTAT
* ** * ** *
1469546 GCAAAAAGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTT-CTTC-AGATGACGAGTTCTTCT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA-GATGAGTTCTTCT
* * * * *
1469609 CATTATGAACTCTACCTGGCAATGTTAATCCATCAAATGATGAATTTAA
65 CATTATGAACTCTTCTTGGAAAAGTTGATCCATCAAATGATGAATTTAA
* *
1469658 ACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
1469723 ATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
66 ATTATGAACTCTTCT-TGGAAAAGTTGATCCATCAAATGATGAATTTAA
* * * *
1469771 GCAAAAGATTGAACAAATTCTCCTCATTATGAATTTCTTCTTCTTTCTTCAGATGACGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTT
* * *
1469836 CTCATTATGAACTCTTCTTGGCAATGTTAATCCATCAAATGATGAATTTAA
63 CTCATTATGAACTCTTCTTGGAAAAGTTGATCCATCAAATGATGAATTTAA
* *
1469887 ACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
1469952 ATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAATTGATGGATTTGA
66 ATTATGAACTCTTCT-TGGAAAAGTTGATCCATCAAATGATGAATTTAA
* * *
1470000 GCAAAAGATTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGACGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTT
* **** *
1470065 CTCATTATGAACTCTCCTTGGTGCTGTTGATCCATCAAATGATGAATTCAA
63 CTCATTATGAACTCTTCTTGGAAAAGTTGATCCATCAAATGATGAATTTAA
* * *
1470116 GCAAAAGGGTTAAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 GCAAAA-GGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
** * * *
1470181 CATTATGAACTCGAAC-TGGAAAAGTTGATCCATCAAATGATGGATTCAG
65 CATTATGAACTC-TTCTTGGAAAAGTTGATCCATCAAATGATGAATTTAA
* *
1470230 GTAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
1470295 ATTATGAACTCTT-TCTGGAAAAGATAATCCATCAAGTGAT
66 ATTATGAACTCTTCT-TGGAAAAGTTGATCCATCAAATGAT
1470335 AGATTTGAAT
Statistics
Matches: 582, Mismatches: 79, Indels: 31
0.84 0.11 0.04
Matches are distributed among these distances:
112 42 0.07
113 288 0.49
114 55 0.09
115 1 0.00
116 147 0.25
117 49 0.08
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTCTTCTTGGAAAAGTTGATCCATCAAATGATGAATTTAA
Found at i:1471275 original size:83 final size:83
Alignment explanation
Indices: 1471131--1471814 Score: 1161
Period size: 83 Copynumber: 8.2 Consensus size: 83
1471121 CTTATTTCTA
* * ** * * *
1471131 CTATGAGCAAAGTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTTTAGATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
1471196 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* * ** * * *
1471214 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTTTAGATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
1471279 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* *
1471297 CTATGAGCACATTCATTTTTCTTTCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACT
1 CTATGAGCACATTCA----TCTTTTAGATTCAATGATTGGTTTTACCAAACCAGATCAGATAACT
1471362 CAAAGAACACTTCCAGAAGATG
62 CAAAGAACACTTCCAGAAGATG
1471384 CTATGAGCACATTCATCTTTTAGATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTTTAGATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
*
1471449 GAACACTTCCAGAAGATA
66 GAACACTTCCAGAAGATG
1471467 CTATGAGCACATTCATCTTTTAGATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTTTAGATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
1471532 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
1471550 CTATGAGCACATTCATCTTTTAGATTCAATGATTGGTTTTACCAAACCAGACCAGATAACTCAAA
1 CTATGAGCACATTCATCTTTTAGATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
1471615 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
1471633 CTATGAGCACATTCATCTTTTAGATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTTTAGATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
1471698 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
1471716 CTATGAGCACATTCATCTTTTAGATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTTTAGATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
1471781 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
1471799 CTATGAGCAAATTCAT
1 CTATGAGCACATTCAT
1471815 TTATTCCAAT
Statistics
Matches: 583, Mismatches: 14, Indels: 8
0.96 0.02 0.01
Matches are distributed among these distances:
83 503 0.86
87 80 0.14
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (83 bp):
CTATGAGCACATTCATCTTTTAGATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:1472965 original size:7 final size:7
Alignment explanation
Indices: 1472953--1473025 Score: 62
Period size: 7 Copynumber: 10.3 Consensus size: 7
1472943 TGACCCCTCT
1472953 TTTTTTC
1 TTTTTTC
1472960 TTTTTTCCC
1 TTTTTT--C
1472969 TTTTTTTC
1 -TTTTTTC
1472977 TTTTTTC
1 TTTTTTC
* *
1472984 TCTCTTC
1 TTTTTTC
1472991 TTTTTT-
1 TTTTTTC
1472997 TTCTTTT-
1 TT-TTTTC
*
1473004 TCTTTT-
1 TTTTTTC
1473010 TTTTTTC
1 TTTTTTC
1473017 TTTTTTC
1 TTTTTTC
1473024 TT
1 TT
1473026 CAAGCATAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
6 11 0.20
7 36 0.65
8 1 0.02
9 1 0.02
10 6 0.11
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTTC
Found at i:1472991 original size:14 final size:13
Alignment explanation
Indices: 1472973--1473024 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 13
1472963 TTTCCCTTTT
1472973 TTTCTTTTTTCTC
1 TTTCTTTTTTCTC
*
1472986 TCTTCTTTTTTTTCTT
1 T-TTC--TTTTTTCTC
1473002 TTTCTTTTTT-T-
1 TTTCTTTTTTCTC
1473013 TTTCTTTTTTCT
1 TTTCTTTTTTCT
1473025 TCAAGCATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
11 10 0.29
12 2 0.06
13 7 0.21
14 3 0.09
15 3 0.09
16 9 0.26
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTCTTTTTTCTC
Found at i:1472995 original size:15 final size:15
Alignment explanation
Indices: 1472977--1473022 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
1472967 CCTTTTTTTC
1472977 TTTTTTCTCTCTTCTT
1 TTTTTTCT-TCTTCTT
*
1472993 TTTTTTCTTTTTCTT
1 TTTTTTCTTCTTCTT
1473008 TTTTTT-TTCTT-TT
1 TTTTTTCTTCTTCTT
1473021 TT
1 TT
1473023 CTTCAAGCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 4 0.14
14 4 0.14
15 12 0.43
16 8 0.29
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTTTCTTCTTCTT
Found at i:1473015 original size:17 final size:17
Alignment explanation
Indices: 1472952--1473021 Score: 70
Period size: 17 Copynumber: 3.8 Consensus size: 17
1472942 TTGACCCCTC
1472952 TTTTTTTCTTTTTTCCCTTT
1 TTTTTTTC-TTTTT--CTTT
1472972 TTTTCTTT-TTTCTCTCTTCT
1 TTTT-TTTCTTT-T-TCTT-T
1472992 TTTTTTTCTTTTTCTTT
1 TTTTTTTCTTTTTCTTT
1473009 TTTTTTTCTTTTT
1 TTTTTTTCTTTTT
1473022 TCTTCAAGCA
Statistics
Matches: 45, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
17 14 0.31
18 4 0.09
19 10 0.22
20 13 0.29
21 4 0.09
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTTTCTTTTTCTTT
Found at i:1484420 original size:21 final size:19
Alignment explanation
Indices: 1484390--1484436 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
1484380 ATAAATATTA
1484390 AAATAATTTATTTA--ATAT
1 AAAT-ATTTATTTATTATAT
1484408 AAATATTTATTTATTATAT
1 AAATATTTATTTATTATAT
*
1484427 ATATATTTAT
1 AAATATTTAT
1484437 GACTACATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 9 0.35
18 4 0.15
19 13 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
AAATATTTATTTATTATAT
Found at i:1485342 original size:15 final size:15
Alignment explanation
Indices: 1485304--1485335 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1485294 CCTTGGTAAG
*
1485304 TTTCTCTTCTTTCTT
1 TTTCTTTTCTTTCTT
1485319 TTTCTTTTCTTTCTT
1 TTTCTTTTCTTTCTT
1485334 TT
1 TT
1485336 CTGTTTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTCTTTTCTTTCTT
Found at i:1485842 original size:3 final size:3
Alignment explanation
Indices: 1485834--1485938 Score: 147
Period size: 3 Copynumber: 35.0 Consensus size: 3
1485824 TTAATATATT
* * * *
1485834 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TTA TTA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
1485882 TTA TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1485930 TAA TAA TAA
1 TAA TAA TAA
1485939 ATCAATATGG
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 96 1.00
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:1493179 original size:26 final size:25
Alignment explanation
Indices: 1493134--1493183 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1493124 GAGTTTTTTT
**
1493134 AAATAAAATTTTTATTTTTTAAGAA
1 AAATAAAATTTTTAAATTTTAAGAA
1493159 AAATAAAATTTTTAAAATTTTAAGA
1 AAATAAAATTTTT-AAATTTTAAGA
1493184 TTATGACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (25 bp):
AAATAAAATTTTTAAATTTTAAGAA
Found at i:1493711 original size:31 final size:31
Alignment explanation
Indices: 1493669--1493735 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
1493659 AATAGGGGAG
*
1493669 AAAA-TGATAAATTATGTCTACTACAGGTGT
1 AAAAGTGATAAATTATGTCTACTACAGGTGC
*
1493699 AAAAGTGATAAATTTTGTCTACTACAGGTGC
1 AAAAGTGATAAATTATGTCTACTACAGGTGC
1493730 AAAAGT
1 AAAAGT
1493736 TACCTTTTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 4 0.12
31 30 0.88
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.31
Consensus pattern (31 bp):
AAAAGTGATAAATTATGTCTACTACAGGTGC
Found at i:1505838 original size:21 final size:21
Alignment explanation
Indices: 1505812--1505896 Score: 73
Period size: 21 Copynumber: 3.9 Consensus size: 21
1505802 TTTTGGTGCA
*
1505812 GAGGGAATCGATCCCCCCTCT
1 GAGGGAACCGATCCCCCCTCT
* *
1505833 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATCCCCCCTCT
* *
1505854 GAATGGGAACCGATTCCCCCCACA
1 G-A-GGGAACCGA-TCCCCCCTCT
*
1505878 G-GGGAATCGATACCCCCCT
1 GAGGGAACCGAT-CCCCCCT
1505897 GGGGTTCTGT
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
20 1 0.02
21 33 0.65
22 1 0.02
23 9 0.18
24 7 0.14
ACGTcount: A:0.22, C:0.36, G:0.24, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATCCCCCCTCT
Found at i:1505861 original size:23 final size:21
Alignment explanation
Indices: 1505812--1505873 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
1505802 TTTTGGTGCA
* *
1505812 GAGGGAATCGATCCCCCCTCT
1 GAGGGAACCGATTCCCCCTCT
*
1505833 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCTCT
1505854 GAATGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
1505874 CACAGGGGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 19 0.53
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.24, T:0.19
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCTCT
Found at i:1506604 original size:12 final size:12
Alignment explanation
Indices: 1506587--1506612 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1506577 TAGTCGTCAA
1506587 CCAAATCCACCT
1 CCAAATCCACCT
1506599 CCAAATCCACCT
1 CCAAATCCACCT
1506611 CC
1 CC
1506613 TATCCCTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.54, G:0.00, T:0.15
Consensus pattern (12 bp):
CCAAATCCACCT
Found at i:1514165 original size:23 final size:23
Alignment explanation
Indices: 1514134--1514202 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
1514124 CACCACAGCT
* *
1514134 CGTATAATTGCACCAAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
1514157 CGTAGAATTGCACCGGAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
1514180 CGTAGAACTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
1514203 TATAATAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.29, C:0.28, G:0.25, T:0.19
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:1523283 original size:23 final size:23
Alignment explanation
Indices: 1523257--1523312 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
1523247 CAGCTCGTAT
1523257 AATTGCACCGAAGTGCAACATAG
1 AATTGCACCGAAGTGCAACATAG
* ** *
1523280 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCAACATAG
1523303 AATTGCACCG
1 AATTGCACCG
1523313 TAATGCCATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (23 bp):
AATTGCACCGAAGTGCAACATAG
Found at i:1525143 original size:24 final size:23
Alignment explanation
Indices: 1525107--1525152 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1525097 TCGAGGTAAG
*
1525107 AAAAATTTGCAAACGTAAATAAAT
1 AAAAATTTGCAAA-GCAAATAAAT
1525131 AAAAA-TTGTCAAAGCAAATAAA
1 AAAAATTTG-CAAAGCAAATAAA
1525153 AATGTTGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.61, C:0.09, G:0.09, T:0.22
Consensus pattern (23 bp):
AAAAATTTGCAAAGCAAATAAAT
Found at i:1535341 original size:22 final size:22
Alignment explanation
Indices: 1535309--1535351 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1535299 ACTGGTTATT
*
1535309 ATATATAATGTTTATCATGAAA
1 ATATATAATGTTTACCATGAAA
*
1535331 ATATATGATGTTTACCATGAA
1 ATATATAATGTTTACCATGAA
1535352 TGTTATTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.40
Consensus pattern (22 bp):
ATATATAATGTTTACCATGAAA
Found at i:1536545 original size:45 final size:45
Alignment explanation
Indices: 1536481--1536617 Score: 247
Period size: 45 Copynumber: 3.0 Consensus size: 45
1536471 TAAATAAATA
*
1536481 AATAAATAAAGGATGAGTAGTGAGTATTTTATGAGCTGTTAAGTT
1 AATAAATAAAGGATGAGTAGGGAGTATTTTATGAGCTGTTAAGTT
*
1536526 AATAAATAAAGGATGAGTAGGGAGTATTTTATGAGCTGTTAAATT
1 AATAAATAAAGGATGAGTAGGGAGTATTTTATGAGCTGTTAAGTT
*
1536571 AATAAATAAAGGATGAGTAGGGAATATTTTATGAGCTGTTAAGTT
1 AATAAATAAAGGATGAGTAGGGAGTATTTTATGAGCTGTTAAGTT
1536616 AA
1 AA
1536618 AACTGTATAT
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 88 1.00
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.34
Consensus pattern (45 bp):
AATAAATAAAGGATGAGTAGGGAGTATTTTATGAGCTGTTAAGTT
Found at i:1539170 original size:23 final size:23
Alignment explanation
Indices: 1539144--1539188 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1539134 CACCACAGCT
*
1539144 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
1539167 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
1539189 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:1539351 original size:157 final size:156
Alignment explanation
Indices: 1539156--1539457 Score: 480
Period size: 157 Copynumber: 1.9 Consensus size: 156
1539146 TATAATTGCA
1539156 CCGAAGTGCCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCAAAAGGACCACATATTAT
1 CCGAAGTGCCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCAAAAGGACCACATATTAT
* * * * * *
1539221 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAAGGACCAAGTATGTGCCTCA-AAGACCTCACAAATGTTC
* *
1539286 CACAGAATATATATATATATATATATC
130 CAAAGAATATACATATATATATATATC
**
1539313 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCCTAAGGACCACATATTA
1 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCAAAAGGACCACATATTA
*
1539377 TTCCTTAAGAATCATATACATATACTAAGGACCAAGTATGTGCCTCAAAGACCTCATAAATGTTC
65 TTCCTTAAGAATCATATACATATACTAAGGACCAAGTATGTGCCTCAAAGACCTCACAAATGTTC
1539442 CAAAGAATATACATAT
130 CAAAGAATATACATAT
1539458 GTCCCGAAGG
Statistics
Matches: 133, Mismatches: 11, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
156 30 0.23
157 103 0.77
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (156 bp):
CCGAAGTGCCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCAAAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAAGGACCAAGTATGTGCCTCAAAGACCTCACAAATGTTCC
AAAGAATATACATATATATATATATC
Found at i:1541032 original size:64 final size:62
Alignment explanation
Indices: 1540896--1541055 Score: 180
Period size: 64 Copynumber: 2.5 Consensus size: 62
1540886 TAATGAAGGT
* * * *
1540896 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCTTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGC
*
1540961 ATG-ATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAAT-TC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGC
* *
1541024 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
1541056 CCTTAAACAA
Statistics
Matches: 83, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
62 1 0.01
63 32 0.39
64 43 0.52
65 7 0.08
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (62 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGC
Found at i:1543226 original size:18 final size:18
Alignment explanation
Indices: 1543203--1543244 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
1543193 AATCAGGATC
1543203 TATTCTTAATCAGAAGAT
1 TATTCTTAATCAGAAGAT
*
1543221 TATTCTTAATCAGAGGAT
1 TATTCTTAATCAGAAGAT
1543239 TATTCT
1 TATTCT
1543245 AGAATCGGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (18 bp):
TATTCTTAATCAGAAGAT
Found at i:1554643 original size:52 final size:54
Alignment explanation
Indices: 1554560--1554665 Score: 162
Period size: 52 Copynumber: 2.0 Consensus size: 54
1554550 TATAATATCA
* *
1554560 TTGTGATTAGTTGTAATCCCCTAACTATAGGCTAGTCTCCTA-TT-TATGTGCC
1 TTGTAATTAGTTGTAATCCACTAACTATAGGCTAGTCTCCTATTTCTATGTGCC
* *
1554612 TTGTAATTAGTTGTAATCCACTAACTCTAGGCTAGTTTCCTATTTCTATGTGCC
1 TTGTAATTAGTTGTAATCCACTAACTATAGGCTAGTCTCCTATTTCTATGTGCC
1554666 CCATCTTGTG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
52 38 0.79
53 2 0.04
54 8 0.17
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.42
Consensus pattern (54 bp):
TTGTAATTAGTTGTAATCCACTAACTATAGGCTAGTCTCCTATTTCTATGTGCC
Found at i:1565655 original size:2 final size:2
Alignment explanation
Indices: 1565650--1565681 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1565640 TATATAACTT
1565650 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
1565682 ATTTTTGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1565884 original size:32 final size:31
Alignment explanation
Indices: 1565834--1565905 Score: 74
Period size: 32 Copynumber: 2.3 Consensus size: 31
1565824 AAATTCATTA
* * *
1565834 TATTTATAAAATATTTATAATTATTTCTTAT-T
1 TATTTATATAATAATTAT-ATT-TTTCGTATCT
*
1565866 TATTTATATATTAATTATATTTTTCGTATCT
1 TATTTATATAATAATTATATTTTTCGTATCT
*
1565897 TAATTATAT
1 TATTTATAT
1565906 TTTTCTATTC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 7 0.21
31 12 0.35
32 15 0.44
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (31 bp):
TATTTATATAATAATTATATTTTTCGTATCT
Found at i:1578387 original size:44 final size:44
Alignment explanation
Indices: 1578338--1578425 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
1578328 TGATTTTACT
1578338 AGACAACTCTAAATAACCCTTCCCAGACCATCTCATAACCACTC
1 AGACAACTCTAAATAACCCTTCCCAGACCATCTCATAACCACTC
1578382 AGACAACTCTAAATAACCCTTCCCAGACCATCTCATAACCACTC
1 AGACAACTCTAAATAACCCTTCCCAGACCATCTCATAACCACTC
1578426 CCTTCACCCG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.36, C:0.39, G:0.05, T:0.20
Consensus pattern (44 bp):
AGACAACTCTAAATAACCCTTCCCAGACCATCTCATAACCACTC
Found at i:1578427 original size:22 final size:22
Alignment explanation
Indices: 1578350--1578421 Score: 78
Period size: 22 Copynumber: 3.3 Consensus size: 22
1578340 ACAACTCTAA
1578350 ATAACCCTTCCCAGACCATCTC
1 ATAACCCTTCCCAGACCATCTC
* *
1578372 ATAACCAC-T--CAGACAACTCTAA
1 ATAACC-CTTCCCAGACCA-TCT-C
1578394 ATAACCCTTCCCAGACCATCTC
1 ATAACCCTTCCCAGACCATCTC
1578416 ATAACC
1 ATAACC
1578422 ACTCCCTTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
20 6 0.15
21 4 0.10
22 20 0.50
23 4 0.10
24 6 0.15
ACGTcount: A:0.35, C:0.40, G:0.04, T:0.21
Consensus pattern (22 bp):
ATAACCCTTCCCAGACCATCTC
Found at i:1589463 original size:30 final size:31
Alignment explanation
Indices: 1589416--1589473 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
1589406 ATAATTATAC
1589416 ATTTAGCCCTAAATTTTT-ATTCAATTTATTA
1 ATTTAGCCCTAAATTTTTAATT-AATTTATTA
*
1589447 ATTTAGTCCT-AATTTTTAATTAATTTA
1 ATTTAGCCCTAAATTTTTAATTAATTTA
1589474 ATAAAACCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 13 0.52
31 12 0.48
ACGTcount: A:0.33, C:0.10, G:0.03, T:0.53
Consensus pattern (31 bp):
ATTTAGCCCTAAATTTTTAATTAATTTATTA
Found at i:1593367 original size:22 final size:21
Alignment explanation
Indices: 1593342--1593401 Score: 57
Period size: 23 Copynumber: 2.8 Consensus size: 21
1593332 ATTCCCCTAC
*
1593342 AGGGGAATCGGTTCTCATTCAA
1 AGGGGAATCGGTTCCCATTC-A
* *
1593364 AGGGGGAATTGGTTCCCCTTCA
1 A-GGGGAATCGGTTCCCATTCA
* *
1593386 AGGGGTATCGATTCCC
1 AGGGGAATCGGTTCCC
1593402 TCTGCCCTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 12 0.39
22 3 0.10
23 16 0.52
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.27
Consensus pattern (21 bp):
AGGGGAATCGGTTCCCATTCA
Found at i:1593385 original size:23 final size:22
Alignment explanation
Indices: 1593343--1593390 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
1593333 TTCCCCTACA
*
1593343 GGGGAATCGGTTCTCATTCAAAG
1 GGGGAATCGGTTCCCATTC-AAG
* *
1593366 GGGGAATTGGTTCCCCTTCAAG
1 GGGGAATCGGTTCCCATTCAAG
1593388 GGG
1 GGG
1593391 TATCGATTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.21, C:0.19, G:0.35, T:0.25
Consensus pattern (22 bp):
GGGGAATCGGTTCCCATTCAAG
Found at i:1594833 original size:23 final size:23
Alignment explanation
Indices: 1594799--1594867 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
1594789 CACCACAGCT
*
1594799 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
1594822 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
1594845 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
1594868 TATAATAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:1596316 original size:21 final size:21
Alignment explanation
Indices: 1596286--1596370 Score: 116
Period size: 21 Copynumber: 4.0 Consensus size: 21
1596276 TTTTGTTCGT
* * * *
1596286 TTGAAGGGGTATCGGTTCCCT
1 TTGAATGGGTACCGATTCCCC
* *
1596307 TTAAATGGGTACCGGTTCCCC
1 TTGAATGGGTACCGATTCCCC
1596328 TTGAATGGGTACCGATTCCCC
1 TTGAATGGGTACCGATTCCCC
1596349 TTGAATGGGTACCGATTCCCC
1 TTGAATGGGTACCGATTCCCC
1596370 T
1 T
1596371 AGCCCAGAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.31
Consensus pattern (21 bp):
TTGAATGGGTACCGATTCCCC
Found at i:1598315 original size:13 final size:14
Alignment explanation
Indices: 1598286--1598316 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1598276 AACTATGCAA
1598286 GTGATATGAACTAT
1 GTGATATGAACTAT
1598300 GTGATATGAA-TAT
1 GTGATATGAACTAT
1598313 GTGA
1 GTGA
1598317 AATATGATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.35
Consensus pattern (14 bp):
GTGATATGAACTAT
Found at i:1599239 original size:19 final size:19
Alignment explanation
Indices: 1599215--1599256 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
1599205 TTGAATATGC
1599215 TTTGATCGATTTTGGTTAT
1 TTTGATCGATTTTGGTTAT
1599234 TTTGATCGATTTTGGTTAT
1 TTTGATCGATTTTGGTTAT
1599253 TTTG
1 TTTG
1599257 GTCAATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.14, C:0.05, G:0.21, T:0.60
Consensus pattern (19 bp):
TTTGATCGATTTTGGTTAT
Found at i:1599264 original size:19 final size:19
Alignment explanation
Indices: 1599215--1599264 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
1599205 TTGAATATGC
*
1599215 TTTGATCGATTTTGGTTAT
1 TTTGATCAATTTTGGTTAT
*
1599234 TTTGATCGATTTTGGTTAT
1 TTTGATCAATTTTGGTTAT
*
1599253 TTTGGTCAATTT
1 TTTGATCAATTT
1599265 ATGTAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.16, C:0.06, G:0.20, T:0.58
Consensus pattern (19 bp):
TTTGATCAATTTTGGTTAT
Found at i:1599764 original size:16 final size:16
Alignment explanation
Indices: 1599725--1599767 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
1599715 ATCATCAGTT
*
1599725 CTTATCACTCAAAATC
1 CTTATCAATCAAAATC
* *
1599741 ATTAATCAATCAAATTC
1 CTT-ATCAATCAAAATC
1599758 CTTATCAATC
1 CTTATCAATC
1599768 TTTAATTACC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.35
Consensus pattern (16 bp):
CTTATCAATCAAAATC
Found at i:1602427 original size:23 final size:23
Alignment explanation
Indices: 1602401--1602469 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
1602391 CACCACAGCT
*
1602401 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
1602424 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
1602447 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
1602470 TATAATAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:1603910 original size:21 final size:21
Alignment explanation
Indices: 1603886--1603949 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
1603876 TTTTGTTCGT
*
1603886 TTGAAGGGGTATCAGTTCCCC
1 TTGAATGGGTATCAGTTCCCC
*
1603907 TTGAATGGGTAT-TGATTCCCC
1 TTGAATGGGTATCAG-TTCCCC
* *
1603928 TTGAATGGGTACCAATTCCCC
1 TTGAATGGGTATCAGTTCCCC
1603949 T
1 T
1603950 AGCCCAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 1 0.03
21 35 0.97
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.33
Consensus pattern (21 bp):
TTGAATGGGTATCAGTTCCCC
Found at i:1610677 original size:3 final size:3
Alignment explanation
Indices: 1610669--1610715 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
1610659 GTTTTAAAAA
1610669 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1610716 CACATTTCAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1610779 original size:32 final size:32
Alignment explanation
Indices: 1610738--1610809 Score: 126
Period size: 32 Copynumber: 2.2 Consensus size: 32
1610728 GCCCAAATGG
* *
1610738 AGCCCAAAGATACTAACCCGAGAGGATCCATA
1 AGCCCAAAGATACAAACCCAAGAGGATCCATA
1610770 AGCCCAAAGATACAAACCCAAGAGGATCCATA
1 AGCCCAAAGATACAAACCCAAGAGGATCCATA
1610802 AGCCCAAA
1 AGCCCAAA
1610810 TTTAGATCCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.44, C:0.29, G:0.17, T:0.10
Consensus pattern (32 bp):
AGCCCAAAGATACAAACCCAAGAGGATCCATA
Found at i:1613093 original size:27 final size:27
Alignment explanation
Indices: 1613012--1613094 Score: 75
Period size: 27 Copynumber: 3.2 Consensus size: 27
1613002 TTTTATATTT
1613012 TAAATTGATATAATTCATATATAA-TAA
1 TAAATTGATATAATTCATATATAAGT-A
* ** * *
1613039 TAATTTTTTAAAATTTAT-TAT-AGT-
1 TAAATTGATATAATTCATATATAAGTA
*
1613063 TAAATTGATATTATTCATATATAAGTA
1 TAAATTGATATAATTCATATATAAGTA
1613090 TAAAT
1 TAAAT
1613095 ATAATTTAAC
Statistics
Matches: 41, Mismatches: 11, Indels: 8
0.68 0.18 0.13
Matches are distributed among these distances:
24 12 0.29
25 4 0.10
26 7 0.17
27 18 0.44
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (27 bp):
TAAATTGATATAATTCATATATAAGTA
Found at i:1620405 original size:23 final size:23
Alignment explanation
Indices: 1620356--1620418 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
1620346 GTGTTATATT
* **
1620356 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
* *
1620379 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAATATATTAATTAAA
1620402 ATATTATTTAAATATAT
1 ATA-T-TTTAAATATAT
1620419 AAATAATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 21 0.66
24 1 0.03
25 10 0.31
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:1620446 original size:19 final size:20
Alignment explanation
Indices: 1620394--1620446 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
1620384 TTAAATATCT
1620394 TTATTAAA-ATATTATTTAA
1 TTATTAAATATATTATTTAA
* *
1620413 ATATATAAATAATATTA-TTCA
1 TTAT-TAAAT-ATATTATTTAA
1620434 TTATTAAATATAT
1 TTATTAAATATAT
1620447 AAAGATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 7 0.25
20 9 0.32
21 6 0.21
22 6 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATTAAATATATTATTTAA
Found at i:1620458 original size:28 final size:27
Alignment explanation
Indices: 1620403--1620467 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 27
1620393 TTTATTAAAA
*
1620403 TATTATTTAAATATATAAATAATATTAT
1 TATTA-TTAAATATATAAAGAATATTAT
* *
1620431 TCATTATTAAATATATAAAGATTTTTAT
1 T-ATTATTAAATATATAAAGAATATTAT
1620459 TATATATTA
1 TAT-TATTA
1620468 TTAAAATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 2 0.06
28 26 0.81
29 4 0.12
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (27 bp):
TATTATTAAATATATAAAGAATATTAT
Found at i:1620503 original size:18 final size:18
Alignment explanation
Indices: 1620480--1620545 Score: 78
Period size: 18 Copynumber: 3.4 Consensus size: 18
1620470 AAAATAAAAA
1620480 TATAATATCTTATATTAT
1 TATAATATCTTATATTAT
* *
1620498 TATAATATAATTGATTATTTT
1 TATAATAT-CTT-A-TATTAT
1620519 ATATAATATCTTATATTAT
1 -TATAATATCTTATATTAT
1620538 TATAATAT
1 TATAATAT
1620546 AATTGATTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
18 16 0.40
19 7 0.17
20 2 0.05
21 7 0.17
22 8 0.20
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.55
Consensus pattern (18 bp):
TATAATATCTTATATTAT
Found at i:1620524 original size:17 final size:17
Alignment explanation
Indices: 1620502--1620565 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 17
1620492 TATTATTATA
1620502 ATATAATTGATTATTTT
1 ATATAATTGATTATTTT
* *
1620519 ATATAATATCTTATATTATTATA
1 ATAT-A-A--TT-GATTATT-TT
1620542 ATATAATTGATTATTTT
1 ATATAATTGATTATTTT
1620559 ATATAAT
1 ATATAAT
1620566 ATTAAAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
17 12 0.32
18 7 0.19
19 3 0.08
21 3 0.08
22 7 0.19
23 5 0.14
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.55
Consensus pattern (17 bp):
ATATAATTGATTATTTT
Found at i:1620526 original size:22 final size:22
Alignment explanation
Indices: 1620489--1620567 Score: 94
Period size: 22 Copynumber: 3.7 Consensus size: 22
1620479 ATATAATATC
*
1620489 TTATATTATTATAATATAATTGA
1 TTATTTTA-TATAATATAATTGA
*
1620512 TTATTTTATATAATAT-CTT-A
1 TTATTTTATATAATATAATTGA
*
1620532 -TATTAT-TATAATATAATTGA
1 TTATTTTATATAATATAATTGA
1620552 TTATTTTATATAATAT
1 TTATTTTATATAATAT
1620568 TAAAAATATA
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
18 8 0.17
19 7 0.15
20 2 0.04
21 7 0.15
22 16 0.34
23 7 0.15
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.56
Consensus pattern (22 bp):
TTATTTTATATAATATAATTGA
Found at i:1620526 original size:40 final size:40
Alignment explanation
Indices: 1620479--1620567 Score: 178
Period size: 40 Copynumber: 2.2 Consensus size: 40
1620469 TAAAATAAAA
1620479 ATATAATATCTTATATTATTATAATATAATTGATTATTTT
1 ATATAATATCTTATATTATTATAATATAATTGATTATTTT
1620519 ATATAATATCTTATATTATTATAATATAATTGATTATTTT
1 ATATAATATCTTATATTATTATAATATAATTGATTATTTT
1620559 ATATAATAT
1 ATATAATAT
1620568 TAAAAATATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (40 bp):
ATATAATATCTTATATTATTATAATATAATTGATTATTTT
Found at i:1620577 original size:31 final size:32
Alignment explanation
Indices: 1620531--1620611 Score: 89
Period size: 31 Copynumber: 2.6 Consensus size: 32
1620521 ATAATATCTT
* *
1620531 ATATTATTATAATATAATTGATTAT-TTTATAT-A
1 ATATTAATA-AATATAA-T-ATTATATTAATATAA
1620564 ATATTAA-AAATATAATATTATATTAATATAA
1 ATATTAATAAATATAATATTATATTAATATAA
1620595 ATATTAATAAATA-AATA
1 ATATTAATAAATATAATA
1620612 AATAATATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
29 5 0.12
30 7 0.16
31 19 0.44
32 6 0.14
33 6 0.14
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (32 bp):
ATATTAATAAATATAATATTATATTAATATAA
Found at i:1620578 original size:14 final size:15
Alignment explanation
Indices: 1620559--1620611 Score: 65
Period size: 14 Copynumber: 3.5 Consensus size: 15
1620549 TGATTATTTT
1620559 ATATAATATTAA-AA
1 ATATAATATTAATAA
*
1620573 ATATAATATTATATTA
1 ATATAATATTA-ATAA
1620589 ATATAAATATTAATAA
1 ATAT-AATATTAATAA
1620605 ATA-AATA
1 ATATAATA
1620612 AATAATATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
14 15 0.44
15 1 0.03
16 11 0.32
17 7 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATATAATATTAATAA
Found at i:1620585 original size:22 final size:23
Alignment explanation
Indices: 1620560--1620603 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
1620550 GATTATTTTA
*
1620560 TATAATATTAAAAATA-TAATAT
1 TATAATAATAAAAATATTAATAT
* *
1620582 TATATTAATATAAATATTAATA
1 TATAATAATAAAAATATTAATA
1620604 AATAAATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TATAATAATAAAAATATTAATAT
Found at i:1620607 original size:16 final size:16
Alignment explanation
Indices: 1620558--1620607 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
1620548 TTGATTATTT
1620558 TATATAATATTAA-AAA
1 TATA-AATATTAATAAA
*
1620574 TAT-AATATTATATTAA
1 TATAAATATTA-ATAAA
1620590 TATAAATATTAATAAA
1 TATAAATATTAATAAA
1620606 TA
1 TA
1620608 AATAAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 7 0.24
15 1 0.03
16 14 0.48
17 7 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TATAAATATTAATAAA
Found at i:1620858 original size:42 final size:42
Alignment explanation
Indices: 1620795--1620907 Score: 156
Period size: 42 Copynumber: 2.7 Consensus size: 42
1620785 AATTACATTC
*
1620795 CGGAAAATC-AATTACGAGAAACAAATACGGGAAAATATTTTT
1 CGGAAAA-CGAATTACGTGAAACAAATACGGGAAAATATTTTT
* **
1620837 CGGAAAACGAATTACGTGAAACAAACAAAGGAAAATATTTTT
1 CGGAAAACGAATTACGTGAAACAAATACGGGAAAATATTTTT
**
1620879 CAAAAAACGAATTACGTGAAACAAATACG
1 CGGAAAACGAATTACGTGAAACAAATACG
1620908 AAAATTCGGG
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
41 1 0.02
42 60 0.98
ACGTcount: A:0.50, C:0.13, G:0.16, T:0.20
Consensus pattern (42 bp):
CGGAAAACGAATTACGTGAAACAAATACGGGAAAATATTTTT
Found at i:1622018 original size:11 final size:11
Alignment explanation
Indices: 1622002--1622044 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
1621992 ATATTAATAG
1622002 TAATAAAAATT
1 TAATAAAAATT
*
1622013 TAATAAGAAATA
1 TAATAA-AAATT
*
1622025 AAATAAAAA-T
1 TAATAAAAATT
1622035 TAATAAAAAT
1 TAATAAAAAT
1622045 AAAGGTCGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
10 8 0.31
11 9 0.35
12 9 0.35
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (11 bp):
TAATAAAAATT
Found at i:1622037 original size:22 final size:22
Alignment explanation
Indices: 1622003--1622047 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 22
1621993 TATTAATAGT
1622003 AATAAAAATTTAATAAGAAATAA
1 AATAAAAATTTAATAA-AAATAA
1622026 AATAAAAA-TTAATAAAAATAA
1 AATAAAAATTTAATAAAAATAA
1622047 A
1 A
1622048 GGTCGAACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 7 0.32
22 7 0.32
23 8 0.36
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (22 bp):
AATAAAAATTTAATAAAAATAA
Found at i:1624566 original size:27 final size:27
Alignment explanation
Indices: 1624528--1624594 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
1624518 CCATTCAGTG
1624528 CTGAATGATTCAGCACAGAAGTACATT
1 CTGAATGATTCAGCACAGAAGTACATT
*
1624555 CTGAATGATTCAGCACAGAATTACATT
1 CTGAATGATTCAGCACAGAAGTACATT
1624582 CTGAATGATTCAG
1 CTGAATGATTCAG
1624595 AGTCATTATC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (27 bp):
CTGAATGATTCAGCACAGAAGTACATT
Found at i:1624797 original size:26 final size:26
Alignment explanation
Indices: 1624767--1624829 Score: 126
Period size: 26 Copynumber: 2.4 Consensus size: 26
1624757 CTTAAAATTT
1624767 ATTTAATTTTTTATATCTATTAAATC
1 ATTTAATTTTTTATATCTATTAAATC
1624793 ATTTAATTTTTTATATCTATTAAATC
1 ATTTAATTTTTTATATCTATTAAATC
1624819 ATTTAATTTTT
1 ATTTAATTTTT
1624830 AAAAAAACTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTTAATTTTTTATATCTATTAAATC
Found at i:1626784 original size:21 final size:21
Alignment explanation
Indices: 1626740--1626784 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1626730 ATACAACCGG
* **
1626740 GTTGCTGCAAATCTATAATCC
1 GTTGATGCAAATCTATAAGAC
*
1626761 GTTGATGCAAATCTCTAAGAC
1 GTTGATGCAAATCTATAAGAC
1626782 GTT
1 GTT
1626785 CCTCGTTGAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (21 bp):
GTTGATGCAAATCTATAAGAC
Found at i:1635708 original size:64 final size:63
Alignment explanation
Indices: 1635565--1635712 Score: 158
Period size: 64 Copynumber: 2.3 Consensus size: 63
1635555 AGGTGTATCA
* * ** *
1635565 ATGCACAGGTAGTGCATCAATGCACTCTTTTAAAATAAAAAATCGAATGCAATTAGTGCATCG
1 ATGCACAAGTAGTGCATCGATGCACTCCATTAAAATAAAAAATCGAATGCAATTAGTGCACCG
* * * *
1635628 ATGCATAAGGCA-TGCATCGATGCA-TCCCATTAATAATAAAACATCGAATGCATTTTA-TGCAC
1 ATGCACAA-GTAGTGCATCGATGCACT-CCATTAA-AATAAAAAATCGAATGCA-ATTAGTGCAC
1635690 CG
62 CG
1635692 ATGCACAAGTAGTGCATCGAT
1 ATGCACAAGTAGTGCATCGAT
1635713 ACATACCTTC
Statistics
Matches: 69, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
62 1 0.01
63 24 0.35
64 41 0.59
65 3 0.04
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (63 bp):
ATGCACAAGTAGTGCATCGATGCACTCCATTAAAATAAAAAATCGAATGCAATTAGTGCACCG
Found at i:1640959 original size:64 final size:65
Alignment explanation
Indices: 1640850--1641006 Score: 166
Period size: 64 Copynumber: 2.4 Consensus size: 65
1640840 TTAAAGGTGT
* ** *
1640850 ATCGATGCACAGGTAGTGCATCGATGCA-CTCTTTTAAAATAAAAACATTGAATGCA-ATTAGTG
1 ATCGATGCAAAGGTAGTGCATCGATGCATCTCCATTAAAATAAAAACATCGAATGCATATTA-TG
1640913 C
65 C
* *
1640914 ATCGATGCATAAGGTA-TGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGTATTTTAT
1 ATCGATGCA-AAGGTAGTGCATCGATGCATCTCCATTAA-AATAAAAACATCGAATGCATATTAT
1640976 GC
64 GC
1640978 A-CTGATGCACAA-GTAGTGCATCGATGCAT
1 ATC-GATGCA-AAGGTAGTGCATCGATGCAT
1641007 ACCTTCATTA
Statistics
Matches: 80, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
63 4 0.05
64 64 0.80
65 12 0.15
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (65 bp):
ATCGATGCAAAGGTAGTGCATCGATGCATCTCCATTAAAATAAAAACATCGAATGCATATTATGC
Found at i:1641557 original size:15 final size:15
Alignment explanation
Indices: 1641537--1641567 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1641527 GGTATAATAT
1641537 TCCTTCGGGATGTAG
1 TCCTTCGGGATGTAG
1641552 TCCTTCGGGATGTAG
1 TCCTTCGGGATGTAG
1641567 T
1 T
1641568 GGTCCTACGA
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:0.13, C:0.19, G:0.32, T:0.35
Consensus pattern (15 bp):
TCCTTCGGGATGTAG
Found at i:1644992 original size:20 final size:19
Alignment explanation
Indices: 1644953--1645004 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
1644943 TTTCTTTGAT
1644953 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
1644972 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
*
1644992 ATTTATAAAATAA
1 A-TTAAAAAATAA
1645005 GATATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:1645105 original size:120 final size:120
Alignment explanation
Indices: 1644862--1645096 Score: 291
Period size: 120 Copynumber: 2.0 Consensus size: 120
1644852 AATATATATT
* * * *
1644862 AATTTATATAT-ATTTAT-AAATAAAATATTTATTTATTTAGAAATATCAAAAAATGACTTCTAG
1 AATTAATATATAATTTATAAAATAAAATATTTATTTATTTAAAAATATCAAAAAATGACATCCAG
* * *
1644925 GTGCCTTAAGACAGCTCTTTTCTTTGATATTAAAAAATAAATAAATAATTAAAAC
66 GTACCTTAAGACAGCTCCTTTCTTTAATATTAAAAAATAAATAAATAATTAAAAC
* *
1644980 AATTAATATATAATTTATAAAATAAGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCA
1 AATTAATATATAATTTATAAAATAAAATATTTATTTATTTAAAAATATCAAAAAAT-GACATCCA
* ** * **
1645045 GTTATTTTAAGACTGC-CCTTTC-TTAATATTGGAAAATAAATAAAT-ATTAAAA
65 GGTACCTTAAGACAGCTCCTTTCTTTAATATTAAAAAATAAATAAATAATTAAAA
1645097 TAGGATTAAA
Statistics
Matches: 99, Mismatches: 15, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
118 17 0.17
119 26 0.26
120 39 0.39
121 17 0.17
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.38
Consensus pattern (120 bp):
AATTAATATATAATTTATAAAATAAAATATTTATTTATTTAAAAATATCAAAAAATGACATCCAG
GTACCTTAAGACAGCTCCTTTCTTTAATATTAAAAAATAAATAAATAATTAAAAC
Done.