Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_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: 21326069
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 89
Found at i:1507991 original size:29 final size:27
Alignment explanation
Indices: 1507947--1508010 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 27
1507937 GTTTGCATTT
1507947 AAAAAAAAAAAAAAAACA-AAAAAAGCC
1 AAAAAAAAAAAAAAAA-ATAAAAAAGCC
*
1507974 AAAAAAAACAAAAGAAAAATCAAAAAGCC
1 AAAAAAAA-AAAA-AAAAATAAAAAAGCC
*
1508003 AAACAAAA
1 AAAAAAAA
1508011 GTCACAAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 8 0.25
28 5 0.16
29 19 0.59
ACGTcount: A:0.81, C:0.12, G:0.05, T:0.02
Consensus pattern (27 bp):
AAAAAAAAAAAAAAAAATAAAAAAGCC
Found at i:1514609 original size:18 final size:18
Alignment explanation
Indices: 1514582--1514618 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1514572 CCTATGCCAT
*
1514582 ATTGCTATCACATCTCAC
1 ATTGCCATCACATCTCAC
*
1514600 ATTGCCATCACATTTCAC
1 ATTGCCATCACATCTCAC
1514618 A
1 A
1514619 ATATCATCCA
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:0.30, C:0.32, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGCCATCACATCTCAC
Found at i:1515437 original size:21 final size:21
Alignment explanation
Indices: 1515411--1515458 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
1515401 ATTGATATAG
1515411 TTTATCCTTT-ATTTTAAATAA
1 TTTAT-CTTTAATTTTAAATAA
*
1515432 TTTATCTTTAAATTTTAACTAA
1 TTTATCTTT-AATTTTAAATAA
1515454 TTTAT
1 TTTAT
1515459 AATTATACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 4 0.17
21 5 0.21
22 15 0.62
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTATCTTTAATTTTAAATAA
Found at i:1515499 original size:15 final size:15
Alignment explanation
Indices: 1515475--1515505 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1515465 ACATTGAGTA
1515475 TTTTAGAAATTAAAT
1 TTTTAGAAATTAAAT
*
1515490 TTTTATAAATTAAAT
1 TTTTAGAAATTAAAT
1515505 T
1 T
1515506 AATGGTGTTC
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:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
TTTTAGAAATTAAAT
Found at i:1518253 original size:53 final size:53
Alignment explanation
Indices: 1518193--1518299 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
1518183 TAAACGCCAT
*
1518193 GCCCACATTGATCTTGATGATATCCAACAACGATTTAGTCCACTTGTGTTTTC
1 GCCCACATTGATCTTGATGATATCCAACAACGATTTAGTCCACTTGTGTATTC
1518246 GCCCACATTGATCTTGATGATATCCAACAACGATTTAGTCCACTTGTGTATTC
1 GCCCACATTGATCTTGATGATATCCAACAACGATTTAGTCCACTTGTGTATTC
1518299 G
1 G
1518300 ATTTGTATTA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (53 bp):
GCCCACATTGATCTTGATGATATCCAACAACGATTTAGTCCACTTGTGTATTC
Found at i:1519358 original size:18 final size:17
Alignment explanation
Indices: 1519335--1519381 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
1519325 TGTTTACAAG
1519335 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGT-AA
* *
1519353 GGAATTAGAATCTGTCA
1 GGAATTGGAATCTGTAA
1519370 GGAATTGGAATC
1 GGAATTGGAATC
1519382 CAATTCCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.34, C:0.09, G:0.30, T:0.28
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:1519709 original size:12 final size:12
Alignment explanation
Indices: 1519692--1519716 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1519682 GTTAATTAGT
1519692 TACCAAAAAATA
1 TACCAAAAAATA
1519704 TACCAAAAAATA
1 TACCAAAAAATA
1519716 T
1 T
1519717 TTTTATTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.16, G:0.00, T:0.20
Consensus pattern (12 bp):
TACCAAAAAATA
Found at i:1519985 original size:37 final size:38
Alignment explanation
Indices: 1519915--1519986 Score: 128
Period size: 38 Copynumber: 1.9 Consensus size: 38
1519905 AACCTGAACC
*
1519915 CGACCCGAATATCACGCTTAAAAAAACCCGACCCGGCT
1 CGACCCGAATATCACACTTAAAAAAACCCGACCCGGCT
1519953 CGACCCGAATATCACACTT-AAAAAACCCGACCCG
1 CGACCCGAATATCACACTTAAAAAAACCCGACCCG
1519987 AACAAAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 15 0.45
38 18 0.55
ACGTcount: A:0.36, C:0.38, G:0.14, T:0.12
Consensus pattern (38 bp):
CGACCCGAATATCACACTTAAAAAAACCCGACCCGGCT
Found at i:1520440 original size:14 final size:14
Alignment explanation
Indices: 1520421--1520449 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1520411 CATCCATTCT
1520421 TGGATGGAATTCAG
1 TGGATGGAATTCAG
1520435 TGGATGGAATTCAG
1 TGGATGGAATTCAG
1520449 T
1 T
1520450 TTCCCTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.34, T:0.31
Consensus pattern (14 bp):
TGGATGGAATTCAG
Found at i:1529519 original size:4 final size:4
Alignment explanation
Indices: 1529510--1529552 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
1529500 AACCAGTAAA
1529510 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAA
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAA
1529553 TGACAACCCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:1529869 original size:20 final size:21
Alignment explanation
Indices: 1529824--1529870 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
1529814 AGACAACGAT
1529824 GCTTGAAAGAACTCAAATATG
1 GCTTGAAAGAACTCAAATATG
* *
1529845 TCTTGAAAGAACT-AAATTTG
1 GCTTGAAAGAACTCAAATATG
1529865 GCTTGA
1 GCTTGA
1529871 TCATTCTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (21 bp):
GCTTGAAAGAACTCAAATATG
Found at i:1533237 original size:31 final size:29
Alignment explanation
Indices: 1533189--1533247 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
1533179 AAATACAAGA
* *
1533189 AATTTAAAATTAAAGGATCATATTAGAAGG
1 AATTTAAAAATAAAGGATCAAATT-GAAGG
*
1533219 AATTTAAAAATACGAGGATCAAATTGAAG
1 AATTTAAAAATA-AAGGATCAAATTGAAG
1533248 TTAATTAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.51, C:0.05, G:0.17, T:0.27
Consensus pattern (29 bp):
AATTTAAAAATAAAGGATCAAATTGAAGG
Found at i:1534531 original size:21 final size:21
Alignment explanation
Indices: 1534507--1534552 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1534497 AAACTATATA
*
1534507 ATATATTATATTTTCAAAATC
1 ATATAATATATTTTCAAAATC
* *
1534528 ATATAATATGTTTTCAAAATT
1 ATATAATATATTTTCAAAATC
1534549 ATAT
1 ATAT
1534553 TTTTTCAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (21 bp):
ATATAATATATTTTCAAAATC
Found at i:1534688 original size:24 final size:22
Alignment explanation
Indices: 1534645--1534692 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
1534635 CAAAATCGTG
1534645 TTTTAAAAAACTATATTATAAA
1 TTTTAAAAAACTATATTATAAA
* *
1534667 TTTTCAAAAACTATATTATATA
1 TTTTAAAAAACTATATTATAAA
1534689 TTTT
1 TTTT
1534693 TGAAATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTTAAAAAACTATATTATAAA
Found at i:1535249 original size:14 final size:14
Alignment explanation
Indices: 1535232--1535273 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
1535222 TTATACAAAC
*
1535232 ATTTTTAAACAATA
1 ATTTTTAAAAAATA
**
1535246 ATTTCAAAAAAATA
1 ATTTTTAAAAAATA
1535260 ATTTTTAAAAAATA
1 ATTTTTAAAAAATA
1535274 TACGAAAATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (14 bp):
ATTTTTAAAAAATA
Found at i:1545895 original size:42 final size:41
Alignment explanation
Indices: 1545848--1545944 Score: 104
Period size: 42 Copynumber: 2.3 Consensus size: 41
1545838 ATAATTTAAG
* * *
1545848 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATGAAA
1 TCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGAT-AAA
** * *
1545890 TCCTTCGGGTTATCTGTAAGCCTTTAGAGCAAGATGATAAG
1 TCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGATAAA
* *
1545931 TCATTTGGGCCATC
1 TCCTTCGGGCCATC
1545945 CATAAAACCT
Statistics
Matches: 44, Mismatches: 11, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
41 12 0.27
42 32 0.73
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.31
Consensus pattern (41 bp):
TCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGATAAA
Found at i:1546126 original size:42 final size:42
Alignment explanation
Indices: 1546064--1546153 Score: 153
Period size: 42 Copynumber: 2.1 Consensus size: 42
1546054 ACTTAGTAAG
* *
1546064 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAA
1 TCCTTCAGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
*
1546106 TCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTCAGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
1546148 TCCTTC
1 TCCTTC
1546154 GGGTAATTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (42 bp):
TCCTTCAGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
Found at i:1546242 original size:42 final size:41
Alignment explanation
Indices: 1546195--1546274 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 41
1546185 TGAAGCAAAT
*
1546195 CCATCAGTAAGTCTTTCGAGCATA-ATGATGAAATCCTTCAGG
1 CCATCAGTAAGTCGTTCGAGCA-AGATGAT-AAATCCTTCAGG
*
1546237 CCATCAGTAAGTCGTTCGGGCAAGATGATAAATCCTTC
1 CCATCAGTAAGTCGTTCGAGCAAGATGATAAATCCTTC
1546275 GTGTCATCCA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
41 10 0.29
42 25 0.71
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.28
Consensus pattern (41 bp):
CCATCAGTAAGTCGTTCGAGCAAGATGATAAATCCTTCAGG
Found at i:1546289 original size:41 final size:42
Alignment explanation
Indices: 1546195--1546297 Score: 115
Period size: 42 Copynumber: 2.5 Consensus size: 42
1546185 TGAAGCAAAT
* *
1546195 CCATCAGTAAGTCTTTCGAGCATAATGATGAAATCCTTCAGG
1 CCATCAGTAAGTCCTTCGGGCATAATGATGAAATCCTTCAGG
*
1546237 CCATCAGTAAGTCGTTCGGGCA-AGATGAT-AAATCCTTC-GTG
1 CCATCAGTAAGTCCTTCGGGCATA-ATGATGAAATCCTTCAG-G
*
1546278 TCATCCA-TAAGTCCTTCGGG
1 CCAT-CAGTAAGTCCTTCGGG
1546298 TAGGATGTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
40 1 0.02
41 26 0.48
42 27 0.50
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.28
Consensus pattern (42 bp):
CCATCAGTAAGTCCTTCGGGCATAATGATGAAATCCTTCAGG
Found at i:1546294 original size:122 final size:122
Alignment explanation
Indices: 1546073--1546294 Score: 320
Period size: 122 Copynumber: 1.8 Consensus size: 122
1546063 GTCCTTCGGG
* * * * *
1546073 CCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGCCATCAGTAAGTCTTTCGAGCAT
1 CCATCAATAAGTCTTTCGAGCATAATGATGAAATCCTTCAGGCCATCAGTAAGTCGTTCGAGCAA
***
1546138 GATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
66 GATGATTAAATCCTTCGGGTAATCCATAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
* *
1546195 CCATCAGTAAGTCTTTCGAGCATAATGATGAAATCCTTCAGGCCATCAGTAAGTCGTTCGGGCAA
1 CCATCAATAAGTCTTTCGAGCATAATGATGAAATCCTTCAGGCCATCAGTAAGTCGTTCGAGCAA
* *
1546260 GATGA-TAAATCCTTCGTGTCATCCATAAGTCCTTC
66 GATGATTAAATCCTTCGGGTAATCCATAAG-CCTTC
1546295 GGGTAGGATG
Statistics
Matches: 87, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
121 19 0.22
122 68 0.78
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (122 bp):
CCATCAATAAGTCTTTCGAGCATAATGATGAAATCCTTCAGGCCATCAGTAAGTCGTTCGAGCAA
GATGATTAAATCCTTCGGGTAATCCATAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
Found at i:1546805 original size:53 final size:53
Alignment explanation
Indices: 1546716--1546925 Score: 233
Period size: 53 Copynumber: 3.9 Consensus size: 53
1546706 AGAATTACAC
* * * *
1546716 CAGAAAATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGGACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAG
*
1546769 CAGACGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAG
* * * * ***
1546822 CAGAAGATTATTCAAGTTCTACTCCCTGAAGCAATAGGGAGCGAACCCGTTTT
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAG
* * * * * *
1546875 TAGAAGATTGTTTGAGTTCCTTAATCCCTG-AGAAATAGGGAGTGGACCCGT
1 CAGAAGATTGTTCGAGTT-C-TACTCCCTGAAGAAAGAGGGAGCGAACCCGT
1546926 CATTTGAAGA
Statistics
Matches: 134, Mismatches: 21, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
53 107 0.80
54 19 0.14
55 8 0.06
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGGGAGCGAACCCGTAAG
Found at i:1550200 original size:21 final size:21
Alignment explanation
Indices: 1550176--1550231 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
1550166 TCAAAGTTCT
*
1550176 GGGTATCGATTCCCCCCAAGG
1 GGGTACCGATTCCCCCCAAGG
1550197 GGGTACCGATTCCCCCCAAGG
1 GGGTACCGATTCCCCCCAAGG
1550218 GGGTACCGATTCCC
1 GGGTACCGATTCCC
1550232 TCACTGTTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.18, C:0.36, G:0.29, T:0.18
Consensus pattern (21 bp):
GGGTACCGATTCCCCCCAAGG
Found at i:1550297 original size:21 final size:21
Alignment explanation
Indices: 1550271--1550312 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1550261 ATTTGAATAT
*
1550271 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1550292 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1550313 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:1550379 original size:20 final size:22
Alignment explanation
Indices: 1550341--1550380 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1550331 TTTGAGTATA
1550341 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
1550363 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
1550381 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:1550634 original size:34 final size:32
Alignment explanation
Indices: 1550595--1550664 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
1550585 TTTTGTAAAG
*
1550595 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
1550629 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
1550661 GGGA
1 GGGA
1550665 GTTGTAAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:1552256 original size:12 final size:12
Alignment explanation
Indices: 1552239--1552283 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
1552229 ATTATTTATT
1552239 TAAATAATAATA
1 TAAATAATAATA
1552251 TAAATAATAATA
1 TAAATAATAATA
* *
1552263 TTAA-AACAA-A
1 TAAATAATAATA
1552273 -AAATAATAATA
1 TAAATAATAATA
1552284 AATAAAACAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
9 2 0.07
10 5 0.19
11 5 0.19
12 15 0.56
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (12 bp):
TAAATAATAATA
Found at i:1552276 original size:21 final size:22
Alignment explanation
Indices: 1552252--1552294 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
1552242 ATAATAATAT
*
1552252 AAATAATAAT-ATTAAAACAAA
1 AAATAATAATAAATAAAACAAA
1552273 AAATAATAATAAATAAAACAAA
1 AAATAATAATAAATAAAACAAA
1552295 TGAAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (22 bp):
AAATAATAATAAATAAAACAAA
Found at i:1552302 original size:21 final size:23
Alignment explanation
Indices: 1552252--1552294 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
1552242 ATAATAATAT
1552252 AAATAATAATATTAAAACAAAAA
1 AAATAATAATATTAAAACAAAAA
1552275 ATAATAATAA-A-TAAAACAAA
1 A-AATAATAATATTAAAACAAA
1552295 TGAAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 9 0.47
23 2 0.11
24 8 0.42
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (23 bp):
AAATAATAATATTAAAACAAAAA
Found at i:1552984 original size:113 final size:112
Alignment explanation
Indices: 1552735--1554046 Score: 1786
Period size: 113 Copynumber: 11.7 Consensus size: 112
1552725 GAATTCGAGC
* * * *
1552735 AACAAGTTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGAGTTCTTCTTATTATTAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
** * *
1552800 GCCCTGGCAATGCTG-TCCA-CGAATGATAAATTCAAGCGAAAAGTTG
66 TACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGC-AAAAGTTG
1552846 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* *
1552911 GACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAAGTTG
66 TACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGC-AAAAGTTG
*
1552959 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTTTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
** * **
1553024 TTTC-AGAAATATTGATCCATCGAATGATGAATTCAAGCGAAAAGTTG
66 TACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGC-AAAAGTTG
1553071 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* * * * *
1553136 GATCTGGTAGTGCTGATCCATCGAATGATGAATTCAAGCGAAAGGTTG
66 TACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGC-AAAAGTTG
1553184 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
** * *
1553249 TTTC-AGAAATGTTGATCCATCGAATGATGAATTC-AGCGAAAAGTTG
66 TACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGC-AAAAGTTG
*
1553295 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* * *
1553360 GACCTGGTAAA-GTTGATCCATC-AAGTGATGAATTCGAGCAAAAAGTTG
66 TACCTGG-AAATGCTGATCCATCGAA-TGATGAATTCAAGC-AAAAGTTG
*
1553408 AACAAGTT-TT-TCATTATG-ACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* * * *
1553470 TACCTGGTAATGATGATCCATTGAATGATGAATTCAAACAAAAGGTTG
66 TACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAA-GTTG
* * *
1553518 AACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTA
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* * * **
1553583 T-CTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGAGCAAAAGGTTG
66 TAC-CTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAA-GTTG
* *
1553631 AACAAGCTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* * ** *
1553696 TACCTGGAAATGCTGATCCATC-AAGTAATGGATTTGAGCAAAAGGTTA
66 TACCTGGAAATGCTGATCCATCGAA-TGATGAATTCAAGCAAAA-GTTG
* * * *
1553744 AACAAGCTCTTCTTAATATGAACTTCTTCTTCCTTATTCAGATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* * *
1553809 TACCTGGTAATGATGATCCATCGAATGATGAATTCAAACAAAAGGTTG
66 TACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAA-GTTG
* * *
1553857 AATAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTA
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
* * * ** *
1553922 T-CTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGAGCATAAGGTTG
66 TAC-CTGGAAATGCTGATCCATCGAATGATGAATTCAAGCA-AAAGTTG
* *
1553970 AACAAGCTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1554035 TACCTGGAAATG
66 TACCTGGAAATG
1554047 TTTTAAGAAA
Statistics
Matches: 1083, Mismatches: 98, Indels: 38
0.89 0.08 0.03
Matches are distributed among these distances:
109 6 0.01
110 80 0.07
111 164 0.15
112 170 0.16
113 657 0.61
114 6 0.01
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (112 bp):
AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
TACCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCAAAAGTTG
Found at i:1553289 original size:449 final size:446
Alignment explanation
Indices: 1552627--1554044 Score: 1898
Period size: 449 Copynumber: 3.2 Consensus size: 446
1552617 ATAGAATAAT
* *
1552627 GCAAAAGATTGAACAAG-T-TTCTCATTATGAACTTC-T-TT--TTCCTCAGATGAATTCTTCTC
1 GCAAAAG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
1552686 ATTATG-ACTCTCTCTGGAAAAGTTGATCCATCGAGTGATGAATT--CG--A-G--CAACAAGTT
65 ATTATGAACTCTCTCTGGAAAAGCTGATCCATCGAGTGATGAATTAGCGAAAGGTTGAACAAGTT
* * * * ** *
1552743 CTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGAGTTCTTCTTATTATTAACTCGCCCTGGC
130 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGA
*
1552808 AATGCTG-TCCA-CGAATGATAAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTT
195 AATGCTGATCCATCGAATGATGAATTC-AGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTT
*
1552871 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAA
259 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGATGATCCATCGAA
1552936 TGATGAATTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
324 TGATGAATTCAAGC-AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
* * *
1553001 TGAGTTTTTCTCATTATGAACTCTTTC-AGAAATATTGATCCATCGAATGATGAATTCAA
388 TGAGTTCTTCTCATTATGAACTCTATCTGGAAATA-TGATCCATCGAATGATGAATTCAA
1553060 GCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GC-AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
** * ** *
1553125 ATTATGAACTCGATCTGGTAGTGCTGATCCATCGAATGATGAATTCAAGCGAAAGGTTGAACAAG
65 ATTATGAACTCTCTCTGGAAAAGCTGATCCATCGAGTGATGAATT--AGCGAAAGGTTGAACAAG
** *
1553190 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTC-A
128 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
*
1553254 GAAATGTTGATCCATCGAATGATGAATTCAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACT
193 GAAATGCTGATCCATCGAATGATGAATTCAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACT
* * *
1553319 TCTTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTCGACCTGGTAAAGTTGATCCATC-A
258 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGATGATCCATCGA
* *
1553383 AGTGATGAATTCGAGCAAAAAGTTGAACAAGTT-TT-TCATTATG-ACTTATTCTTCCTTCTTCA
323 A-TGATGAATTCAAGC-AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
* * *
1553445 GATGAGTTCTTCTCATTATGAACTCTACCTGGTAATGATGATCCATTGAATGATGAATTCAA
386 GATGAGTTCTTCTCATTATGAACTCTATCTGGAAAT-ATGATCCATCGAATGATGAATTCAA
* * *
1553507 ACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
1553572 ATTATGAACTATCTCTGGAAAAGCTGATCCATCGAGTGATGGATTTGAGCAAAAGGTTGAACAAG
65 ATTATGAACTCTCTCTGGAAAAGCTGATCCATCGAGTGAT-GAATT-AGCGAAAGGTTGAACAAG
* *
1553637 CTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
128 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
* * * * * * *
1553702 GAAATGCTGATCCATC-AAGTAATGGATTTGAGC-AAAAGGTTAAACAAGCTCTTCTTAATATGA
193 GAAATGCTGATCCATCGAA-TGAT-GAATTCAGCGAAAA-GTTGAACAAGTTCTTCTCATTATGA
* *
1553765 ACTTCTTCTTCCTTATTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGTAATGATGATCCAT
255 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGATGATCCAT
* * *
1553830 CGAATGATGAATTCAAACAAAAGGTTGAATAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTT
320 CGAATGATGAATTCAAGCAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTT
* * * * **
1553895 CAGATGAGTTCTTCTCATTATGAACTATCTCTGGAAA-AGCTGATCCATCGAGTGATGGATTTGA
384 CAGATGAGTTCTTCTCATTATGAACTCTATCTGGAAATA--TGATCCATCGAATGATGAATTCAA
* * *
1553959 GCATAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTC
1 GCA-AAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1554024 ATTATGAACTCTAC-CTGGAAA
65 ATTATGAACTCT-CTCTGGAAA
1554045 TGTTTTAAGA
Statistics
Matches: 863, Mismatches: 85, Indels: 55
0.86 0.08 0.05
Matches are distributed among these distances:
433 11 0.01
434 6 0.01
435 17 0.02
436 1 0.00
437 2 0.00
439 25 0.03
440 31 0.04
444 2 0.00
446 49 0.06
447 204 0.24
448 42 0.05
449 302 0.35
450 18 0.02
451 8 0.01
452 142 0.16
453 3 0.00
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (446 bp):
GCAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCTCTCTGGAAAAGCTGATCCATCGAGTGATGAATTAGCGAAAGGTTGAACAAGTTC
TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAA
ATGCTGATCCATCGAATGATGAATTCAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCT
TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGATGATCCATCGAATG
ATGAATTCAAGCAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA
GTTCTTCTCATTATGAACTCTATCTGGAAATATGATCCATCGAATGATGAATTCAA
Found at i:1557561 original size:114 final size:114
Alignment explanation
Indices: 1557361--1557580 Score: 359
Period size: 114 Copynumber: 1.9 Consensus size: 114
1557351 GATCATGCAG
* * *
1557361 TTCATCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* *
1557426 ATACTTTCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAGCAAA
* * *
1557475 TTCATCTTTCAAATCTAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTTAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
1557540 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
66 ACACTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTA
1557581 CGAGAACATG
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 97 1.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAGCAAA
Found at i:1559735 original size:9 final size:8
Alignment explanation
Indices: 1559710--1559782 Score: 62
Period size: 8 Copynumber: 9.1 Consensus size: 8
1559700 ATTCAATTTC
*
1559710 TTCCCTTT
1 TTCCTTTT
1559718 TT-CTTTT
1 TTCCTTTT
*
1559725 TCCCTTTT
1 TTCCTTTT
1559733 TTCCTTTT
1 TTCCTTTT
*
1559741 TCTCATTTT
1 T-TCCTTTT
1559750 TT-C-TTT
1 TTCCTTTT
1559756 TTCATCTTTT
1 TTC--CTTTT
*
1559766 TTTCTTTT
1 TTCCTTTT
1559774 TTCCTTTT
1 TTCCTTTT
1559782 T
1 T
1559783 CCTCATTTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
6 5 0.10
7 5 0.10
8 29 0.56
9 8 0.15
10 5 0.10
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (8 bp):
TTCCTTTT
Found at i:1559750 original size:10 final size:9
Alignment explanation
Indices: 1559721--1559814 Score: 67
Period size: 8 Copynumber: 10.8 Consensus size: 9
1559711 TCCCTTTTTC
*
1559721 TTTTTCCCT
1 TTTTTCTCT
1559730 TTTTTC-C-
1 TTTTTCTCT
*
1559737 TTTTTCTCA
1 TTTTTCTCT
1559746 TTTTT-TC-
1 TTTTTCTCT
1559753 TTTTTCATCT
1 TTTTTC-TCT
1559763 TTTTT-TCT
1 TTTTTCTCT
1559771 TTTTTC-CT
1 TTTTTCTCT
*
1559779 TTTTCCTCAT
1 TTTTTCTC-T
*
1559789 TTTTTTTCAT
1 TTTTTCTC-T
1559799 CTTTTT-TCT
1 -TTTTTCTCT
1559808 TTTTTCT
1 TTTTTCT
1559815 TTCTTTGCTA
Statistics
Matches: 72, Mismatches: 3, Indels: 20
0.76 0.03 0.21
Matches are distributed among these distances:
7 11 0.15
8 24 0.33
9 16 0.22
10 16 0.22
11 5 0.07
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTTTCTCT
Found at i:1559792 original size:17 final size:17
Alignment explanation
Indices: 1559715--1559774 Score: 79
Period size: 16 Copynumber: 3.6 Consensus size: 17
1559705 ATTTCTTCCC
1559715 TTTTTCTTTTTCC-CTT
1 TTTTTCTTTTTCCTCTT
* *
1559731 TTTTCCTTTTT-CTCAT
1 TTTTTCTTTTTCCTCTT
*
1559747 TTTTTCTTTTTCATCTT
1 TTTTTCTTTTTCCTCTT
1559764 TTTTTCTTTTT
1 TTTTTCTTTTT
1559775 TCCTTTTTCC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
15 1 0.03
16 22 0.59
17 14 0.38
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTTCTTTTTCCTCTT
Found at i:1559810 original size:7 final size:7
Alignment explanation
Indices: 1559715--1559842 Score: 78
Period size: 7 Copynumber: 16.3 Consensus size: 7
1559705 ATTTCTTCCC
1559715 TTTTTCT
1 TTTTTCT
*
1559722 TTTTCCCT
1 TTTT-TCT
1559730 TTTTTCCT
1 TTTTT-CT
1559738 TTTTCTCAT
1 TTTT-TC-T
1559747 TTTTTCT
1 TTTTTCT
1559754 TTTTCATCTT
1 TTTT--TC-T
1559764 TTTTTCT
1 TTTTTCT
1559771 TTTTTCCT
1 TTTTT-CT
*
1559779 TTTTCCTCA
1 TTTT--TCT
1559788 TTTTT-T
1 TTTTTCT
**
1559794 TTCATCT
1 TTTTTCT
1559801 TTTTTCT
1 TTTTTCT
1559808 TTTTTCT
1 TTTTTCT
1559815 TTCTTTGCT
1 TT-TTT-CT
1559824 AGATTTTTCT
1 ---TTTTTCT
1559834 TTTTTCT
1 TTTTTCT
1559841 TT
1 TT
1559843 CTTTGTTGGA
Statistics
Matches: 97, Mismatches: 8, Indels: 32
0.71 0.06 0.23
Matches are distributed among these distances:
6 3 0.03
7 40 0.41
8 26 0.27
9 15 0.15
10 8 0.08
11 3 0.03
12 2 0.02
ACGTcount: A:0.05, C:0.20, G:0.02, T:0.74
Consensus pattern (7 bp):
TTTTTCT
Found at i:1559810 original size:16 final size:15
Alignment explanation
Indices: 1559715--1559783 Score: 77
Period size: 17 Copynumber: 4.4 Consensus size: 15
1559705 ATTTCTTCCC
*
1559715 TTTTTCTTTTTCCCT
1 TTTTTCTTTTTCTCT
1559730 TTTTTCCTTTTTCTCAT
1 TTTTT-CTTTTTCTC-T
1559747 TTTTTCTTTTTCATCTT
1 TTTTTCTTTTTC-TC-T
*
1559764 TTTTTCTTTTT-TCC
1 TTTTTCTTTTTCTCT
1559778 TTTTTC
1 TTTTTC
1559784 CTCATTTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
14 6 0.12
15 7 0.15
16 15 0.31
17 20 0.42
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTTCTTTTTCTCT
Found at i:1559831 original size:37 final size:38
Alignment explanation
Indices: 1559753--1559831 Score: 99
Period size: 37 Copynumber: 2.1 Consensus size: 38
1559743 TCATTTTTTC
**
1559753 TTTTTCATCTTTTTTTCTTTTTTCCTTTTTCCTCATTT
1 TTTTTCATCTTTTTTTCTTTTTTCCTTTTTCCTCAGAT
* *
1559791 TTTTTCATC-TTTTTTCTTTTTTCTTTCTTTGCT-AGAT
1 TTTTTCATCTTTTTTTCTTTTTTCCTT-TTTCCTCAGAT
1559828 TTTT
1 TTTT
1559832 CTTTTTTCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
37 22 0.61
38 14 0.39
ACGTcount: A:0.06, C:0.18, G:0.03, T:0.73
Consensus pattern (38 bp):
TTTTTCATCTTTTTTTCTTTTTTCCTTTTTCCTCAGAT
Found at i:1564119 original size:33 final size:33
Alignment explanation
Indices: 1564072--1564149 Score: 138
Period size: 33 Copynumber: 2.4 Consensus size: 33
1564062 CACAAGTATA
*
1564072 ATATATATATATATGATCAATGATATATGTTTT
1 ATATGTATATATATGATCAATGATATATGTTTT
*
1564105 ATATGTATATATATGATCAATGATGTATGTTTT
1 ATATGTATATATATGATCAATGATATATGTTTT
1564138 ATATGTATATAT
1 ATATGTATATAT
1564150 GTATATATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.37, C:0.03, G:0.12, T:0.49
Consensus pattern (33 bp):
ATATGTATATATATGATCAATGATATATGTTTT
Found at i:1564198 original size:22 final size:24
Alignment explanation
Indices: 1564148--1564198 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 24
1564138 ATATGTATAT
*
1564148 ATGTAT-ATATATGTACATATGCA
1 ATGTATAAAATATGTACATATGCA
*
1564171 AT-TATAAAATATGTATA-ATGC-
1 ATGTATAAAATATGTACATATGCA
1564192 ATGTATA
1 ATGTATA
1564199 TTTATATGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
21 2 0.08
22 11 0.46
23 11 0.46
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (24 bp):
ATGTATAAAATATGTACATATGCA
Found at i:1564888 original size:2 final size:2
Alignment explanation
Indices: 1564881--1564931 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
1564871 AGCTAACTTT
1564881 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
1564923 TA TA -A TA TA
1 TA TA TA TA TA
1564932 CACATATGTA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1565555 original size:18 final size:18
Alignment explanation
Indices: 1565529--1565568 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1565519 TTGTAAAAAA
*
1565529 ATATTTATATATACTTTT
1 ATATATATATATACTTTT
1565547 ATATATATATATACTTTT
1 ATATATATATATACTTTT
1565565 -TATA
1 ATATA
1565569 CTTATATAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (18 bp):
ATATATATATATACTTTT
Found at i:1565574 original size:19 final size:17
Alignment explanation
Indices: 1565533--1565576 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 17
1565523 AAAAAAATAT
1565533 TTATATATACTTTTATA
1 TTATATATACTTTTATA
1565550 TATATATATACTTTTTATA
1 T-TATATATAC-TTTTATA
1565569 CTTATATA
1 -TTATATA
1565577 GATAATTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.04
18 9 0.38
19 13 0.54
20 1 0.04
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (17 bp):
TTATATATACTTTTATA
Found at i:1565946 original size:14 final size:13
Alignment explanation
Indices: 1565929--1565971 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
1565919 TTAATAAAAT
1565929 TAATTTAATGATTA
1 TAATTTAA-GATTA
1565943 TAA-TTAAGAGTTA
1 TAATTTAAGA-TTA
1565956 TAATTTAAGGATTA
1 TAATTTAA-GATTA
1565970 TA
1 TA
1565972 GTTAATATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 2 0.08
13 10 0.38
14 12 0.46
15 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (13 bp):
TAATTTAAGATTA
Found at i:1566915 original size:15 final size:15
Alignment explanation
Indices: 1566895--1566927 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1566885 TTGCAGTAAG
1566895 GCGCGCCCCTGCAAC
1 GCGCGCCCCTGCAAC
1566910 GCGCGCCCCTGCAAC
1 GCGCGCCCCTGCAAC
1566925 GCG
1 GCG
1566928 TTATATGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.12, C:0.52, G:0.30, T:0.06
Consensus pattern (15 bp):
GCGCGCCCCTGCAAC
Found at i:1570755 original size:17 final size:17
Alignment explanation
Indices: 1570733--1570796 Score: 60
Period size: 17 Copynumber: 3.7 Consensus size: 17
1570723 TTCTACAAAA
1570733 ATATTTTATTATATTAT
1 ATATTTTATTATATTAT
*
1570750 ATATTTATTTATATATTAT
1 ATATTT-TAT-TATATTAT
*
1570769 -TATTATTAATATATT-T
1 ATATT-TTATTATATTAT
*
1570785 TTATTTTATTAT
1 ATATTTTATTAT
1570797 TTTTGCATGC
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
16 7 0.18
17 16 0.41
18 7 0.18
19 9 0.23
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATATTTTATTATATTAT
Found at i:1570783 original size:25 final size:27
Alignment explanation
Indices: 1570733--1570797 Score: 82
Period size: 25 Copynumber: 2.5 Consensus size: 27
1570723 TTCTACAAAA
1570733 ATATTTTATTA-TATTATATATTTATTT
1 ATATTTTATTATTATTATATA-TTATTT
*
1570760 ATATATTATTATTATTA-ATA-TATTT
1 ATATTTTATTATTATTATATATTATTT
*
1570785 TTATTTTATTATT
1 ATATTTTATTATT
1570798 TTTGCATGCC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 16 0.47
27 13 0.38
28 5 0.15
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (27 bp):
ATATTTTATTATTATTATATATTATTT
Found at i:1571323 original size:29 final size:30
Alignment explanation
Indices: 1571267--1571335 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
1571257 CCTAATTTTA
*
1571267 ATAT-TTTTATTTCTTTTTACATTGTTATAT
1 ATATATTTTATTTCATTTTACATTGTTAT-T
*
1571297 ATATATTTT-TTTCATTTT-CATTTTTATT
1 ATATATTTTATTTCATTTTACATTGTTATT
1571325 A-ATATTATTAT
1 ATATATT-TTAT
1571336 ATTAATATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
27 5 0.15
28 4 0.12
29 9 0.26
30 12 0.35
31 4 0.12
ACGTcount: A:0.26, C:0.06, G:0.01, T:0.67
Consensus pattern (30 bp):
ATATATTTTATTTCATTTTACATTGTTATT
Found at i:1573547 original size:21 final size:21
Alignment explanation
Indices: 1573495--1573547 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
1573485 TTCAGACGAA
1573495 GAGGACAAATCAAAGAAGATG
1 GAGGACAAATCAAAGAAGATG
*
1573516 GAGGAGAAAATC-AAGCAA-ATG
1 GAGGA-CAAATCAAAG-AAGATG
1573537 GAGGACCAAAT
1 GAGGA-CAAAT
1573548 GAATGTAGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 20 0.74
22 7 0.26
ACGTcount: A:0.51, C:0.11, G:0.28, T:0.09
Consensus pattern (21 bp):
GAGGACAAATCAAAGAAGATG
Found at i:1576246 original size:110 final size:110
Alignment explanation
Indices: 1576106--1576637 Score: 762
Period size: 110 Copynumber: 4.9 Consensus size: 110
1576096 TGATGGTAAT
* * *
1576106 AGCTCAACTTCACAGCGAATGGGCGACTGACTGTCAATAAATAACTTTTCAGTTTCATTCAGAGT
1 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
*
1576171 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGATACAACACA
66 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
* * *
1576216 AGCTCAACTTCATAGCGAAGGGGCGACTGACGGTCAACAAACAACTTTTCAGTTTTATTCAGAGT
1 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
* * * *
1576281 CAATTTCAATTTCACAACGAATGATATTGGACTCAAGAC-ACACA
66 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
* **
1576325 AGCTCAACTTCACAGCGAATGGGCGACTGGTTGTCAACAAACAACTTTTCAGTTTCATT----GT
1 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
* *
1576386 CAATTTCAACTTCACAACGAATGATATTGGACTCGAGACAACACA
66 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
*
1576431 AGCTCAAATTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
1 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
1576496 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
66 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
* * * *
1576541 AGCTCAACTTCACAGCGAAGGGGCTG-TTGGCTATCAACAAACAACTTTCCAG--T--TTCAGAG
1 AGCTCAACTTCACAGCGAAGGGGC-GACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAG
* *
1576601 TCAATTTCAACTTCAC-GATGAAGGATATTGGCCTCGA
65 TCAATTTCAACTTCACAG-CGAAGGATATTGGACTCGA
1576638 AACAGTAAAA
Statistics
Matches: 383, Mismatches: 32, Indels: 18
0.88 0.07 0.04
Matches are distributed among these distances:
105 40 0.10
106 100 0.26
108 1 0.00
109 58 0.15
110 183 0.48
111 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.25
Consensus pattern (110 bp):
AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
Found at i:1576481 original size:215 final size:216
Alignment explanation
Indices: 1576106--1576637 Score: 789
Period size: 215 Copynumber: 2.4 Consensus size: 216
1576096 TGATGGTAAT
* * *
1576106 AGCTCAACTTCACAGCGAATGGGCGACTGACTGTCAATAAATAACTTTTCAGTTTCATTCAGAGT
1 AGCTCAACTTCACAGCGAATGGGCGACTGGCTGTCAACAAACAACTTTTCAGTTTCATT----GT
* * * *
1576171 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGATACAACACAAGCTCAACTTCATAGCGAAG
62 CAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGCTCAAATTCACAGCGAAG
* *
1576236 GGGCGACTGACGGTCAACAAACAACTTTTCAGTTTTATTCAGAGTCAATTTCAATTTCACAACGA
127 GGGCGACTGACGGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGA
*
1576301 ATGATATTGGACTCAAGAC-ACACA
192 AGGATATTGGACTCAAGACAACACA
*
1576325 AGCTCAACTTCACAGCGAATGGGCGACTGGTTGTCAACAAACAACTTTTCAGTTTCATTGTCAAT
1 AGCTCAACTTCACAGCGAATGGGCGACTGGCTGTCAACAAACAACTTTTCAGTTTCATTGTCAAT
*
1576390 TTCAACTTCACAACGAATGATATTGGACTCGAGACAACACAAGCTCAAATTCACAGCGAAGGGGC
66 TTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGCTCAAATTCACAGCGAAGGGGC
* *
1576455 GACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGA
131 GACTGACGGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGA
*
1576520 TATTGGACTCGAGACAACACA
196 TATTGGACTCAAGACAACACA
* * * * **
1576541 AGCTCAACTTCACAGCGAAGGGGCTG-TTGGCTATCAACAAACAACTTTCCAGTTTCAGAGTCAA
1 AGCTCAACTTCACAGCGAATGGGC-GACTGGCTGTCAACAAACAACTTTTCAGTTTCATTGTCAA
* * *
1576605 TTTCAACTTCACGATGAAGGATATTGGCCTCGA
65 TTTCAACTTCACAACGAAGGATATTGGACTCGA
1576638 AACAGTAAAA
Statistics
Matches: 285, Mismatches: 26, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
215 140 0.49
216 89 0.31
217 1 0.00
219 55 0.19
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.25
Consensus pattern (216 bp):
AGCTCAACTTCACAGCGAATGGGCGACTGGCTGTCAACAAACAACTTTTCAGTTTCATTGTCAAT
TTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGCTCAAATTCACAGCGAAGGGGC
GACTGACGGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGA
TATTGGACTCAAGACAACACA
Found at i:1576852 original size:84 final size:84
Alignment explanation
Indices: 1576749--1577173 Score: 428
Period size: 84 Copynumber: 5.1 Consensus size: 84
1576739 AAGGGAATCG
* * *
1576749 TGCCCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGTATATCATTTGCAGCATAAC
1 TGCCAACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAAC
*
1576814 TTAAGTCGAGAAGGGTTATC
65 TTAAGTCAAGAAGGGTTATC
* * * *
1576834 TGCCAACCAAATACCTTCGAGTTCGGCTACGCTCAGCTTCAAGGCACATCATTTGCAGCATAGCT
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
*
1576899 TAAGTCAAGAAGGGATATC
66 TAAGTCAAGAAGGGTTATC
* * * * * * * *
1576918 TG----CCAAAGACCCTCGAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAAC
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAAC
* * * *
1576979 TCAAGGCAAAAAGGGTTATT
65 TTAAGTCAAGAAGGGTTATC
** * * * * *
1576999 TG-TGACCAAAAGACCTTCGAGTTCGACTACGCTAAGCTCCAAAGCATATTATTTGAAGCATAAC
1 TGCCAACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAAC
* *
1577063 TTAAGTCGAGAAGTGTTATC
65 TTAAGTCAAGAAGGGTTATC
** * * *
1577083 TGCCAACCAAAGACCTTCGAGTTTAACTACACTCAGCTCAAAGGCACCATCATTTGCAGCATAGC
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA-CATCATTTGCAGCATAAC
* * *
1577148 TCAAGGCAAGAAGGGATATC
65 TTAAGTCAAGAAGGGTTATC
*
1577168 TTCCAA
1 TGCCAA
1577174 AGACCTTCGA
Statistics
Matches: 270, Mismatches: 63, Indels: 14
0.78 0.18 0.04
Matches are distributed among these distances:
80 25 0.09
81 38 0.14
84 139 0.51
85 68 0.25
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (84 bp):
TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
TAAGTCAAGAAGGGTTATC
Found at i:1577031 original size:165 final size:162
Alignment explanation
Indices: 1576840--1577186 Score: 401
Period size: 165 Copynumber: 2.1 Consensus size: 162
1576830 TATCTGCCAA
* * * * * * *
1576840 CCAAATACCTTCGAGTTCGGCTACGCTCAGCTTCAAGGCACATCATTTGCAGCATAGCTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACGCTAAGCTCCAAAGCACATCATTTGAAGCATAACTTAAGTC
* * * *
1576905 AAGAAGGGATATCTG-CCAAAGACCCTCGAGTTTGATTACACTCAGCTTCGAGGGCA-CATCATT
66 AAGAAGGGATATCTGACCAAAGACCCTCGAGTTTAACTACACTCAGC-TCAAAGGCACCATCATT
* *
1576968 TACAACATAACTCAAGGCAAAAAGGGTTATTTGT
130 TACAACATAACTCAAGGCAAAAAGGGATATCT-T
* *
1577002 GACCAAAAGACCTTCGAGTTCGACTACGCTAAGCTCCAAAGCATATTATTTGAAGCATAACTTAA
1 --CC-AAAGACCTTCGAGTTCGACTACGCTAAGCTCCAAAGCACATCATTTGAAGCATAACTTAA
* * * *
1577067 GTCGAGAAGTGTTATCTGCCAACCAAAGACCTTCGAGTTTAACTACACTCAGCTCAAAGGCACCA
63 GTCAAGAAGGGATATCTG---ACCAAAGACCCTCGAGTTTAACTACACTCAGCTCAAAGGCACCA
* * * *
1577132 TCATTTGCAGCATAGCTCAAGGCAAGAAGGGATATCTT
125 TCATTTACAACATAACTCAAGGCAAAAAGGGATATCTT
1577170 CCAAAGACCTTCGAGTT
1 CCAAAGACCTTCGAGTT
1577187 TGATTCCATT
Statistics
Matches: 154, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
164 2 0.01
165 81 0.53
166 2 0.01
168 8 0.05
169 61 0.40
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.24
Consensus pattern (162 bp):
CCAAAGACCTTCGAGTTCGACTACGCTAAGCTCCAAAGCACATCATTTGAAGCATAACTTAAGTC
AAGAAGGGATATCTGACCAAAGACCCTCGAGTTTAACTACACTCAGCTCAAAGGCACCATCATTT
ACAACATAACTCAAGGCAAAAAGGGATATCTT
Found at i:1577782 original size:14 final size:13
Alignment explanation
Indices: 1577745--1577787 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
1577735 TAAACATGAG
*
1577745 AAAAGAATAATAA
1 AAAAGATTAATAA
1577758 AAAAGATTAATAA
1 AAAAGATTAATAA
*
1577771 AATAATATTAATAA
1 AA-AAGATTAATAA
1577785 AAA
1 AAA
1577788 TGAAAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 15 0.56
14 12 0.44
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (13 bp):
AAAAGATTAATAA
Found at i:1577876 original size:2 final size:2
Alignment explanation
Indices: 1577869--1577895 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1577859 AGAAAATGAA
1577869 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 A
1577896 AAGTAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1578314 original size:14 final size:14
Alignment explanation
Indices: 1578295--1578381 Score: 65
Period size: 14 Copynumber: 6.2 Consensus size: 14
1578285 TGCAGGGCCT
1578295 ATAAAAATAATAAA
1 ATAAAAATAATAAA
1578309 ATAAAAAT-ATAATA
1 ATAAAAATAATAA-A
*
1578323 ATAATAATAAT-AA
1 ATAAAAATAATAAA
* *
1578336 ATATATAT-ATAAA
1 ATAAAAATAATAAA
*
1578349 TATATAAATAA-ATAA
1 -ATAAAAATAATA-AA
*
1578364 ATATAATATAATAAA
1 ATA-AAAATAATAAA
1578379 ATA
1 ATA
1578382 TTTTTGTAGA
Statistics
Matches: 58, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
12 2 0.03
13 12 0.21
14 28 0.48
15 15 0.26
16 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
ATAAAAATAATAAA
Found at i:1578323 original size:3 final size:3
Alignment explanation
Indices: 1578295--1578335 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
1578285 TGCAGGGCCT
* *
1578295 ATA AAA ATA ATA A-A ATA AAA AT- ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1578336 ATATATATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:1578347 original size:12 final size:11
Alignment explanation
Indices: 1578303--1578382 Score: 62
Period size: 12 Copynumber: 7.5 Consensus size: 11
1578293 CTATAAAAAT
* *
1578303 AATAAAATAAA
1 AATATAATATA
1578314 AATATAATA-A
1 AATATAATATA
*
1578324 TA-ATAATAATA
1 AATATAAT-ATA
1578335 AATATATATATA
1 AATATA-ATATA
*
1578347 AATATATAAATA
1 AATATA-ATATA
1578359 AATA-AATAT-
1 AATATAATATA
1578368 AATATAATA-A
1 AATATAATATA
1578378 AATAT
1 AATAT
1578383 TTTTGTAGAC
Statistics
Matches: 58, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
9 9 0.16
10 15 0.26
11 11 0.19
12 21 0.36
13 2 0.03
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AATATAATATA
Found at i:1579264 original size:33 final size:33
Alignment explanation
Indices: 1579224--1579294 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1579214 AAAATGTTTC
* *
1579224 GGTTTTAGTGTTTTAATATGACTCAAATACGTT
1 GGTTTTAGTGTTTCAATAGGACTCAAATACGTT
1579257 GGTTTTAGTGTTTCAATAGGACTCAAATACGTT
1 GGTTTTAGTGTTTCAATAGGACTCAAATACGTT
1579290 GGTTT
1 GGTTT
1579295 ATTTTCTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.25, C:0.10, G:0.21, T:0.44
Consensus pattern (33 bp):
GGTTTTAGTGTTTCAATAGGACTCAAATACGTT
Found at i:1579377 original size:2 final size:2
Alignment explanation
Indices: 1579372--1579400 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1579362 ATTAATGATA
1579372 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 A
1579401 ATAAAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1580349 original size:14 final size:14
Alignment explanation
Indices: 1580330--1580370 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 14
1580320 ACGAATCGAA
1580330 CCGAACCGAAAAAC
1 CCGAACCGAAAAAC
1580344 CCGAACCGTTAAAAAAC
1 CCGAACCG---AAAAAC
1580361 CCGAACCGAA
1 CCGAACCGAA
1580371 TCGAAAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 10 0.42
17 14 0.58
ACGTcount: A:0.46, C:0.34, G:0.15, T:0.05
Consensus pattern (14 bp):
CCGAACCGAAAAAC
Found at i:1582554 original size:21 final size:20
Alignment explanation
Indices: 1582529--1582572 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
1582519 TAAATGTTTT
*
1582529 TTAATTCAAAAAAGTTTATAA
1 TTAATTCAAAAAA-TATATAA
* *
1582550 TTAATTTAAATAATATATAA
1 TTAATTCAAAAAATATATAA
1582570 TTA
1 TTA
1582573 TAAAATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
TTAATTCAAAAAATATATAA
Found at i:1582747 original size:184 final size:183
Alignment explanation
Indices: 1582508--1582894 Score: 614
Period size: 184 Copynumber: 2.1 Consensus size: 183
1582498 TTTTATAATT
* * * * *
1582508 TATATAA-AAATTAAATGTTTTTTAATTCAAAAAAGTTTATAATTAATTTAAATAATATATAATT
1 TATATAATATATTTAATATTTTTTAATTAAAAAAAGTTTACAATTAATTTAAATAATATATAATT
* *
1582572 ATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTA
66 ATAAAATAAAAATTTCAGATAAATTTTTTAATAAATTAATATTGATTTAGGTTTAAAAATTATTA
*
1582637 GATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGCTTAACCCATATGTTA
131 GATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGCTGAACCCATATGTTA
1582690 TATATAATATATTTAATATTTTTTAATTAAAAAATAGTTTACAATTAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTTAATTAAAAAA-AGTTTACAATTAATTTAAATAATATATAAT
* * *
1582755 TATAAAATAAAAATTTTATATAATTTTTTTAATAAATTAATATTGATTTAGGTTTAAAAATTATT
65 TATAAAATAAAAATTTCAGATAAATTTTTTAATAAATTAATATTGATTTAGGTTTAAAAATTATT
* * * *
1582820 GGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTGAGCCTATATGTTA
130 AGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGCTGAACCCATATGTTA
*
1582874 TATATAATATATTTAAAATTT
1 TATATAATATATTTAATATTT
1582895 AAAATTTAAT
Statistics
Matches: 187, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
182 7 0.04
183 22 0.12
184 158 0.84
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (183 bp):
TATATAATATATTTAATATTTTTTAATTAAAAAAAGTTTACAATTAATTTAAATAATATATAATT
ATAAAATAAAAATTTCAGATAAATTTTTTAATAAATTAATATTGATTTAGGTTTAAAAATTATTA
GATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGCTGAACCCATATGTTA
Found at i:1585604 original size:2 final size:2
Alignment explanation
Indices: 1585537--1585591 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1585527 GATGTGTAAG
1585537 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
1585579 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
1585592 CAAAAGTATA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1591479 original size:23 final size:23
Alignment explanation
Indices: 1591453--1591526 Score: 78
Period size: 23 Copynumber: 3.3 Consensus size: 23
1591443 AACATTTATA
1591453 TTCATGAAAAAAAGTTAAGTCTT
1 TTCATGAAAAAAAGTTAAGTCTT
* * * *
1591476 TTCAAGAAAAATAGTTAATTCAT
1 TTCATGAAAAAAAGTTAAGTCTT
* * *
1591499 TTCA-CACAAAAAGTCAAGTCTT
1 TTCATGAAAAAAAGTTAAGTCTT
1591521 TTCATG
1 TTCATG
1591527 TTAACCTTTT
Statistics
Matches: 39, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
22 16 0.41
23 23 0.59
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.34
Consensus pattern (23 bp):
TTCATGAAAAAAAGTTAAGTCTT
Found at i:1591912 original size:14 final size:17
Alignment explanation
Indices: 1591893--1591931 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1591883 AAAACTCTTC
1591893 TTCTATTT-ATT-CA-G
1 TTCTATTTGATTACAGG
1591907 TTCTATTTGATTACAGG
1 TTCTATTTGATTACAGG
1591924 TTCTATTT
1 TTCTATTT
1591932 TAATTTCACA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.36
15 3 0.14
16 2 0.09
17 9 0.41
ACGTcount: A:0.21, C:0.13, G:0.10, T:0.56
Consensus pattern (17 bp):
TTCTATTTGATTACAGG
Found at i:1596765 original size:23 final size:23
Alignment explanation
Indices: 1596739--1596788 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
1596729 AACATCTCTA
* *
1596739 TTCATGAAAAATAGTTAAGTCTT
1 TTCATGAAAAATAATTAAGTCAT
* *
1596762 TTCATGAATAATAATTAATTCAT
1 TTCATGAAAAATAATTAAGTCAT
1596785 TTCA
1 TTCA
1596789 CCCAAAAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (23 bp):
TTCATGAAAAATAATTAAGTCAT
Found at i:1598165 original size:31 final size:31
Alignment explanation
Indices: 1598129--1598188 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 31
1598119 AACTTAAAAG
1598129 AGTTTTACAATACT-GAGATTTAAATAATTTT
1 AGTTTTACAATACTAGA-ATTTAAATAATTTT
1598160 AGTTTTACAATACTAGAATTTAAATAATT
1 AGTTTTACAATACTAGAATTTAAATAATT
1598189 CATACAACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 26 0.93
32 2 0.07
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTAGAATTTAAATAATTTT
Found at i:1598808 original size:40 final size:36
Alignment explanation
Indices: 1598728--1598810 Score: 105
Period size: 40 Copynumber: 2.2 Consensus size: 36
1598718 ATCTATAATA
*
1598728 TAATATTAAAAATTAATATTTAATTTATTTAAAAAT
1 TAATATTAAAAATTAATATTTAATTTATTAAAAAAT
1598764 TAATATT-AAAATTAATATCTATAATATAATATTAAAAAAT
1 TAATATTAAAAATTAATAT-T-TAAT-T--TATTAAAAAAT
1598804 TAATATT
1 TAATATT
1598811 TAATTTATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
35 11 0.27
36 8 0.20
37 4 0.10
38 1 0.02
40 17 0.41
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (36 bp):
TAATATTAAAAATTAATATTTAATTTATTAAAAAAT
Found at i:1598809 original size:63 final size:64
Alignment explanation
Indices: 1598707--1598862 Score: 250
Period size: 63 Copynumber: 2.5 Consensus size: 64
1598697 TTATATGATA
1598707 TAAAATTAAATATCTATAATATAATATT-AAAAATTAATATTTAATTTATTT-AAAAATTAATAT
1 TAAAATT-AATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
1598770 TAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAAATTAATAT
1 TAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTT-AAAAAATTAATAT
*
1598835 TAAAATTAAAATC-A-AATATAATA-TAAAA
1 TAAAATTAATATCTATAATATAATATTAAAA
1598863 TTAAATATAA
Statistics
Matches: 89, Mismatches: 1, Indels: 7
0.92 0.01 0.07
Matches are distributed among these distances:
62 25 0.28
63 39 0.44
64 1 0.01
65 24 0.27
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (64 bp):
TAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
Found at i:1598814 original size:26 final size:26
Alignment explanation
Indices: 1598761--1598843 Score: 93
Period size: 25 Copynumber: 3.2 Consensus size: 26
1598751 TTTATTTAAA
1598761 AATTAATATT--AAAATTAATATCTAT
1 AATTAATATTAAAAAATTAATAT-TAT
1598786 AATATAATATTAAAAAATTAATATT-T
1 AAT-TAATATTAAAAAATTAATATTAT
* *
1598812 AATTTAT-TTAAAAAAATTAATATTAA
1 AATTAATATT-AAAAAATTAATATTAT
1598838 AATTAA
1 AATTAA
1598844 AATCAAATAT
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
24 2 0.04
25 20 0.40
26 16 0.32
27 1 0.02
28 11 0.22
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (26 bp):
AATTAATATTAAAAAATTAATATTAT
Found at i:1598869 original size:12 final size:12
Alignment explanation
Indices: 1598824--1598874 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
1598814 TTTATTTAAA
1598824 AAAATT-AATATT
1 AAAATTAAATA-T
1598836 AAAATTAAA-AT
1 AAAATTAAATAT
*
1598847 CAAA-TATAATAT
1 AAAATTA-AATAT
1598859 AAAATTAAATAT
1 AAAATTAAATAT
1598871 AAAA
1 AAAA
1598875 CCTATTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
10 2 0.06
11 6 0.18
12 21 0.64
13 4 0.12
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATTAAATAT
Found at i:1607600 original size:3 final size:3
Alignment explanation
Indices: 1607592--1607631 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
1607582 TTAAAAAGAA
*
1607592 AAT AAT AAT AAT AAT AAAT AAT GA- AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT A
1607632 GAATAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 1 0.03
3 29 0.88
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1607623 original size:24 final size:25
Alignment explanation
Indices: 1607591--1607637 Score: 87
Period size: 24 Copynumber: 1.9 Consensus size: 25
1607581 GTTAAAAAGA
1607591 AAATAATAATAATAATA-AATAATG
1 AAATAATAATAATAATAGAATAATG
1607615 AAATAATAATAATAATAGAATAA
1 AAATAATAATAATAATAGAATAA
1607638 AAAAAAGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (25 bp):
AAATAATAATAATAATAGAATAATG
Found at i:1609130 original size:28 final size:27
Alignment explanation
Indices: 1609099--1609181 Score: 69
Period size: 28 Copynumber: 3.0 Consensus size: 27
1609089 TAATATAATA
1609099 TAAATTATATATTATAATATATATTTTC
1 TAAA-TATATATTATAATATATATTTTC
* * *
1609127 TAAA-AAATATGATAAGTTATACATTTTC
1 TAAATATATATTATAA--TATATATTTTC
* * *
1609155 AAAACTATATAATATATTATATATTTT
1 TAAA-TATATATTATAATATATATTTT
1609182 TTTCAAAAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
26 9 0.21
28 26 0.62
30 7 0.17
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (27 bp):
TAAATATATATTATAATATATATTTTC
Found at i:1609136 original size:26 final size:24
Alignment explanation
Indices: 1609107--1609171 Score: 60
Period size: 26 Copynumber: 2.6 Consensus size: 24
1609097 TATAAATTAT
1609107 ATATTATAATATATATTTTCTAAAAA
1 ATATTATAATATATATTTTC--AAAA
* *
1609133 ATATGATAAGTTATACATTTTCAAAA
1 ATATTATAA--TATATATTTTCAAAA
*
1609159 CTA-TATAATATAT
1 ATATTATAATATAT
1609172 TATATATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
23 4 0.12
25 4 0.12
26 14 0.44
28 10 0.31
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (24 bp):
ATATTATAATATATATTTTCAAAA
Found at i:1610166 original size:74 final size:74
Alignment explanation
Indices: 1610047--1610227 Score: 195
Period size: 74 Copynumber: 2.4 Consensus size: 74
1610037 CCTCTAAGTG
* * * ** * *
1610047 AGTTTAAGCTAGTCTTGATTCTTTGGATGATTTCTTTTCATGGGTTTAA-TTCAAGAGAGACGA-
1 AGTTTAAGATAGTCTTGATTCTTTGGATGACTCCCCTTCACGGGTTTAAGTTAAAGA-AGACGAC
*
1610110 CTCTCATTCGC
65 CT-TCATTCAC
* * *
1610121 AGTTTAAGTTAGTCTTGAATCTTTGGATGACTCCCCTTCACGGGTTTAAGTTAAATAAGACGACC
1 AGTTTAAGATAGTCTTGATTCTTTGGATGACTCCCCTTCACGGGTTTAAGTTAAAGAAGACGACC
*
1610186 TTCTTTCAC
66 TTCATTCAC
* * *
1610195 AGTTTAAGACAATCTTGATTTTTTGGATGACTC
1 AGTTTAAGATAGTCTTGATTCTTTGGATGACTC
1610228 ATTTATGGGT
Statistics
Matches: 89, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
74 82 0.92
75 7 0.08
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (74 bp):
AGTTTAAGATAGTCTTGATTCTTTGGATGACTCCCCTTCACGGGTTTAAGTTAAAGAAGACGACC
TTCATTCAC
Found at i:1613721 original size:16 final size:17
Alignment explanation
Indices: 1613700--1613742 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
1613690 CTTATTCTGT
1613700 TTTCTAAATCC-TTTGC
1 TTTCTAAATCCTTTTGC
1613716 TTTCTAAATCCTTTTGC
1 TTTCTAAATCCTTTTGC
1613733 TTTCTAAATC
1 TTTCTAAATC
1613743 TTGCTGAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (17 bp):
TTTCTAAATCCTTTTGC
Found at i:1615709 original size:7 final size:7
Alignment explanation
Indices: 1615697--1615732 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
1615687 CTTGATCACG
1615697 AAAATAT
1 AAAATAT
1615704 AAAATAT
1 AAAATAT
1615711 AAAATAT
1 AAAATAT
1615718 -AAAT-T
1 AAAATAT
1615723 AAAAT-T
1 AAAATAT
1615729 AAAA
1 AAAA
1615733 ATCGATCCGA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 1 0.04
6 13 0.46
7 14 0.50
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AAAATAT
Found at i:1617355 original size:23 final size:21
Alignment explanation
Indices: 1617316--1617357 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
1617306 TGATAATTTT
*
1617316 TAAAAATTTTATTTTAAAATA
1 TAAAAATTTTATATTAAAATA
1617337 TAAAATATTATTATATTAAAA
1 TAAAA-ATT-TTATATTAAAA
1617358 AGCTTAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 3 0.17
23 10 0.56
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TAAAAATTTTATATTAAAATA
Found at i:1617546 original size:17 final size:16
Alignment explanation
Indices: 1617499--1617539 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
1617489 GCTTAGGTAA
* *
1617499 TTTTAAAAAACATTAT
1 TTTTAAAAAATATAAT
1617515 TTTTAAAAAATATAAT
1 TTTTAAAAAATATAAT
1617531 TTTTAAAAA
1 TTTTAAAAA
1617540 TTTATAAAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTTAAAAAATATAAT
Found at i:1618840 original size:13 final size:13
Alignment explanation
Indices: 1618810--1618839 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1618800 TTTTAAAAAA
1618810 TAAAATATTATTT
1 TAAAATATTATTT
1618823 TAAAATA-TATTT
1 TAAAATATTATTT
1618835 TAAAA
1 TAAAA
1618840 AAATAGACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TAAAATATTATTT
Found at i:1631186 original size:41 final size:42
Alignment explanation
Indices: 1631141--1631219 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
1631131 ATATTGACAA
*
1631141 AAAAATTA-GACACTTAT-ACAAATATTAAAAAAATTAATTAT
1 AAAAA-TAGGACACTAATAACAAATATTAAAAAAATTAATTAT
* * *
1631182 AAAAATAGGTCCCTAATAATAAATATTAAAAAAATTAA
1 AAAAATAGGACACTAATAACAAATATTAAAAAAATTAA
1631220 AATCATAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 2 0.06
41 11 0.34
42 19 0.59
ACGTcount: A:0.59, C:0.08, G:0.04, T:0.29
Consensus pattern (42 bp):
AAAAATAGGACACTAATAACAAATATTAAAAAAATTAATTAT
Found at i:1631806 original size:37 final size:40
Alignment explanation
Indices: 1631756--1631843 Score: 128
Period size: 41 Copynumber: 2.2 Consensus size: 40
1631746 AGGAGGATTA
1631756 AAAGCATGGGACC-T-TGTTGAGCAATGAT-CTGTCGGGC
1 AAAGCATGGGACCTTATGTTGAGCAATGATACTGTCGGGC
* *
1631793 AAAGCATGGGACCTTGATGTTGAGCAATGATATTGTCGTGC
1 AAAGCATGGGACCTT-ATGTTGAGCAATGATACTGTCGGGC
1631834 AAAGCATGGG
1 AAAGCATGGG
1631844 TTAAGTACTT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
37 13 0.29
38 1 0.02
40 14 0.31
41 17 0.38
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (40 bp):
AAAGCATGGGACCTTATGTTGAGCAATGATACTGTCGGGC
Found at i:1632673 original size:19 final size:18
Alignment explanation
Indices: 1632645--1632684 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
1632635 AAATACCCTT
**
1632645 AAAAAATAATTTTAAAAG
1 AAAAAATAATAATAAAAG
1632663 AAAATAATAATAATAAAAG
1 AAAA-AATAATAATAAAAG
1632682 AAA
1 AAA
1632685 GTAACAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (18 bp):
AAAAAATAATAATAAAAG
Found at i:1632786 original size:19 final size:19
Alignment explanation
Indices: 1632732--1632786 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
1632722 AACCAATAAT
1632732 AATAAACATAAAAT-AATTG
1 AATAAA-ATAAAATAAATTG
* *
1632751 GATGAAA-AAAATGAAATTG
1 AATAAAATAAAAT-AAATTG
1632770 AATAAAATAAAATAAAT
1 AATAAAATAAAATAAAT
1632787 GAAGATAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
17 5 0.17
18 1 0.03
19 18 0.62
20 5 0.17
ACGTcount: A:0.65, C:0.02, G:0.09, T:0.24
Consensus pattern (19 bp):
AATAAAATAAAATAAATTG
Found at i:1632889 original size:42 final size:37
Alignment explanation
Indices: 1632836--1632925 Score: 99
Period size: 37 Copynumber: 2.3 Consensus size: 37
1632826 TGTTTTTTTA
*
1632836 AAAAAGAAAATAATAATAAGAACAAAGAAATAAAAATATAAT
1 AAAAATAAAATAAT-ATAA-AA-AAA-AAATAAAAATAT-AT
* * *
1632878 GAAAATAAAATAATATAATAAAATAATAAAAATATAT
1 AAAAATAAAATAATATAAAAAAAAAATAAAAATATAT
1632915 AAAAATAAAAT
1 AAAAATAAAAT
1632926 GTATGTATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
37 12 0.28
38 11 0.26
39 3 0.07
40 1 0.02
41 4 0.09
42 12 0.28
ACGTcount: A:0.73, C:0.01, G:0.04, T:0.21
Consensus pattern (37 bp):
AAAAATAAAATAATATAAAAAAAAAATAAAAATATAT
Found at i:1632894 original size:19 final size:18
Alignment explanation
Indices: 1632870--1632999 Score: 84
Period size: 19 Copynumber: 6.5 Consensus size: 18
1632860 AAGAAATAAA
1632870 AATATAATGAAAATAAAAT
1 AATATAAT-AAAATAAAAT
*
1632889 AATATAATAAAATAATAAA
1 AATATAATAAAATAA-AAT
1632908 AATAT-ATAAAAATAAAATGT
1 AATATAAT-AAAATAAAA--T
* *
1632928 ATGTATAATATAATAAATACT
1 A-ATATAATAAAATAAA-A-T
1632949 AAATAGTAATAATAATAATAAT
1 -AATA-TAATAA-AATAA-AAT
1632971 AA-ATAATGAAAATAAATAT
1 AATATAAT-AAAATAAA-AT
1632990 ACATATAATA
1 A-ATATAATA
1633000 TTAATTAAAA
Statistics
Matches: 89, Mismatches: 7, Indels: 29
0.71 0.06 0.23
Matches are distributed among these distances:
18 12 0.13
19 34 0.38
20 6 0.07
21 20 0.22
22 10 0.11
23 6 0.07
24 1 0.01
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (18 bp):
AATATAATAAAATAAAAT
Found at i:1632898 original size:3 final size:3
Alignment explanation
Indices: 1632864--1632977 Score: 53
Period size: 3 Copynumber: 38.0 Consensus size: 3
1632854 AGAACAAAGA
*
1632864 AAT AAA AAT -AT AAT GAA- AAT AA- AAT AAT -AT AAT AA- AAT AAT
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
1632905 AAA AAT ATAT AAA AAT AA- AAT GTAT GTAT AAT -AT AAT AAAT ACT AAAT
1 AAT AAT A-AT AAT AAT AAT AAT -AAT -AAT AAT AAT AAT -AAT AAT -AAT
*
1632953 AGT AAT AAT AAT AAT AAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT
1632978 GAAAATAAAT
Statistics
Matches: 86, Mismatches: 12, Indels: 26
0.69 0.10 0.21
Matches are distributed among these distances:
2 14 0.16
3 53 0.62
4 19 0.22
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1632899 original size:13 final size:13
Alignment explanation
Indices: 1632881--1632990 Score: 52
Period size: 13 Copynumber: 8.1 Consensus size: 13
1632871 ATATAATGAA
1632881 AATAAAATAATAT
1 AATAAAATAATAT
1632894 AATAAAATAATA-
1 AATAAAATAATAT
1632906 AA-AATATATAA-A-
1 AATAA-A-ATAATAT
*
1632918 AATAAAATGTATGTAT
1 AATAAAA--TA-ATAT
*
1632934 AATATAATAA-AT
1 AATAAAATAATAT
*
1632946 ACTAAATAGTAATAAT
1 AATAAA-A-TAAT-AT
1632962 AATAATAATAA-AT
1 AATAA-AATAATAT
1632975 AATGAAAATAAATAT
1 AAT-AAAAT-AATAT
1632990 A
1 A
1632991 CATATAATAT
Statistics
Matches: 75, Mismatches: 6, Indels: 30
0.68 0.05 0.27
Matches are distributed among these distances:
11 3 0.04
12 13 0.17
13 29 0.39
14 9 0.12
15 7 0.09
16 13 0.17
17 1 0.01
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (13 bp):
AATAAAATAATAT
Found at i:1632905 original size:16 final size:16
Alignment explanation
Indices: 1632863--1633054 Score: 55
Period size: 16 Copynumber: 11.8 Consensus size: 16
1632853 AAGAACAAAG
*
1632863 AAATAAAAATATAATGA
1 AAATAATAATATAAT-A
1632880 AAATAAAATAATATAATA
1 AAAT--AATAATATAATA
*
1632898 AAATAATAAAAATATATAA
1 AAATAAT-AATATA-AT-A
* *
1632917 AAATAA-AATGTATGTA
1 AAATAATAATATA-ATA
*
1632933 TAAT-ATAATA-AATA
1 AAATAATAATATAATA
*
1632947 CTAAATAGT-A-ATAATA
1 --AAATAATAATATAATA
1632963 ATAATAATAA-ATAATGA
1 A-AATAATAATATAAT-A
1632980 AAAT-A-AATATACATA
1 AAATAATAATATA-ATA
* * *
1632995 TAATATTAAT-TAAAA
1 AAATAATAATATAATA
*
1633010 AAATAGTAATCATAGA-A
1 AAATAATAAT-ATA-ATA
* *
1633027 ATATAA-AATAAAATA
1 AAATAATAATATAATA
* *
1633042 AAGTAAGAATATA
1 AAATAATAATATA
1633055 TATATATAAC
Statistics
Matches: 131, Mismatches: 22, Indels: 45
0.66 0.11 0.23
Matches are distributed among these distances:
14 6 0.05
15 33 0.25
16 39 0.30
17 28 0.21
18 8 0.06
19 17 0.13
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.29
Consensus pattern (16 bp):
AAATAATAATATAATA
Found at i:1632941 original size:37 final size:38
Alignment explanation
Indices: 1632864--1632999 Score: 114
Period size: 40 Copynumber: 3.4 Consensus size: 38
1632854 AGAACAAAGA
*
1632864 AATAAAAATATAATGAAAATAAAATAATATAATAAAAT
1 AATAAAAATATAATAAAAATAAAATAATATAATAAAAT
* *
1632902 AATAAAAATAT-ATAAAAATAAAATGTATGTATAATATAAT
1 AATAAAAATATAATAAAAATAAAA--TA-ATATAATAAAAT
* *
1632942 AAATACTAAATAGTAATAATAATAATAATAA-ATAATGAAAAT
1 -AATA-AAAATA-TAATAAAAATAA-AATAATATAAT-AAAAT
* *
1632984 AAATATACATATAATA
1 -AATAAAAATATAATA
1633000 TTAATTAAAA
Statistics
Matches: 81, Mismatches: 8, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
37 11 0.14
38 11 0.14
39 2 0.02
40 15 0.19
41 14 0.17
42 14 0.17
43 3 0.04
44 9 0.11
45 2 0.02
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.29
Consensus pattern (38 bp):
AATAAAAATATAATAAAAATAAAATAATATAATAAAAT
Found at i:1632968 original size:22 final size:22
Alignment explanation
Indices: 1632870--1633019 Score: 67
Period size: 19 Copynumber: 7.1 Consensus size: 22
1632860 AAGAAATAAA
*
1632870 AATATAATGAA-AATAAA-A-T
1 AATATAATAAATAATAAATAGT
*
1632889 AATATAATAAAATAATAAA-AAT
1 AATATAAT-AAATAATAAATAGT
*
1632911 -ATATAA-AAATAA-AATGTATGTAT
1 AATATAATAAATAATAA-ATA-G--T
*
1632934 AATATAATAAATACTAAATAGT
1 AATATAATAAATAATAAATAGT
*
1632956 AATAATAAT-AATAATAAATAAT
1 AAT-ATAATAAATAATAAATAGT
* *
1632978 GA-A-AATAAAT-ATACATA-T
1 AATATAATAAATAATAAATAGT
*
1632996 AATATTAATTAA-AA-AAATAGT
1 AATA-TAATAAATAATAAATAGT
1633017 AAT
1 AAT
1633020 CATAGAAATA
Statistics
Matches: 101, Mismatches: 12, Indels: 34
0.69 0.08 0.23
Matches are distributed among these distances:
18 4 0.04
19 24 0.24
20 11 0.11
21 23 0.23
22 17 0.17
23 6 0.06
24 7 0.07
25 7 0.07
26 2 0.02
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (22 bp):
AATATAATAAATAATAAATAGT
Found at i:1633169 original size:10 final size:10
Alignment explanation
Indices: 1633118--1633169 Score: 52
Period size: 10 Copynumber: 4.9 Consensus size: 10
1633108 AGATAAAAAA
1633118 ATAATATAAT
1 ATAATATAAT
1633128 ATATATATATAT
1 ATA-ATATA-AT
1633140 ATATATATAAT
1 ATA-ATATAAT
*
1633151 AGGAA-ATAAT
1 A-TAATATAAT
1633161 ATAATATAA
1 ATAATATAA
1633170 CGCAAAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
9 2 0.06
10 13 0.36
11 9 0.25
12 12 0.33
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (10 bp):
ATAATATAAT
Found at i:1633734 original size:37 final size:37
Alignment explanation
Indices: 1633649--1633744 Score: 138
Period size: 37 Copynumber: 2.6 Consensus size: 37
1633639 GGATCCTATC
* ** * *
1633649 TTTAGGAGTTTAAATAATAGTAGAACTCTATCCTATT
1 TTTAGGAGTTTGAATCCTAGTAAAACTCTATCATATT
*
1633686 TTTAGGAGTTTGAATCCTAGTAAAATTCTATCATATT
1 TTTAGGAGTTTGAATCCTAGTAAAACTCTATCATATT
1633723 TTTAGGAGTTTGAATCCTAGTA
1 TTTAGGAGTTTGAATCCTAGTA
1633745 GGACGAAAAG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (37 bp):
TTTAGGAGTTTGAATCCTAGTAAAACTCTATCATATT
Found at i:1634678 original size:106 final size:106
Alignment explanation
Indices: 1634486--1635337 Score: 1285
Period size: 106 Copynumber: 8.0 Consensus size: 106
1634476 GCATTGTTCT
* * * * * *
1634486 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
1634551 CCAGTC-GTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1634592 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
1634657 CTAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1634698 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1634763 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1634804 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
1634869 CCAGTGGTCCCTTCGTCGCGAAGTTAAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1634910 GAGTCCAATATCCTTCGCTT-TGAAGTTAAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
1 GAGTCCAATATCCTTCG-TTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * *
1634974 ACTAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1635016 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1635081 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1635122 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1635187 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1635228 GATTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGAATTTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
1635293 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1635334 GAGT
1 GAGT
1635338 GGCACGATAT
Statistics
Matches: 682, Mismatches: 61, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
105 1 0.00
106 679 1.00
107 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.35
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1636974 original size:16 final size:16
Alignment explanation
Indices: 1636950--1636991 Score: 61
Period size: 14 Copynumber: 2.8 Consensus size: 16
1636940 GATTTTTGAT
*
1636950 TTTTCTTTTTTTCTTC
1 TTTTCTTTTTTGCTTC
1636966 --TTCTTTTTTGCTTC
1 TTTTCTTTTTTGCTTC
1636980 TTTTCTTTTTTG
1 TTTTCTTTTTTG
1636992 TTTTTGCCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 13 0.57
16 10 0.43
ACGTcount: A:0.00, C:0.17, G:0.05, T:0.79
Consensus pattern (16 bp):
TTTTCTTTTTTGCTTC
Found at i:1636995 original size:22 final size:22
Alignment explanation
Indices: 1636942--1636998 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
1636932 TTCTTTTTGA
*
1636942 TTTTTGATTTTT-CTTTTTTTCT
1 TTTTTG-TTTTTGCTTCTTTTCT
*
1636964 TCTTCT-TTTTTGCTTCTTTTCT
1 T-TTTTGTTTTTGCTTCTTTTCT
1636986 TTTTTGTTTTTGC
1 TTTTTGTTTTTGC
1636999 CCTTTTTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 8 0.28
22 18 0.62
23 3 0.10
ACGTcount: A:0.02, C:0.14, G:0.07, T:0.77
Consensus pattern (22 bp):
TTTTTGTTTTTGCTTCTTTTCT
Found at i:1638703 original size:22 final size:23
Alignment explanation
Indices: 1638651--1638705 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
1638641 CACCACAGCT
*
1638651 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
1638674 CGTAGAATTGCACCGGAGTGCGA
1 CGTAGAATTGCACCGAAGTGCCA
1638697 -GTAGAATTG
1 CGTAGAATTG
1638706 TACTGTAGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 9 0.31
23 20 0.69
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:1638903 original size:100 final size:98
Alignment explanation
Indices: 1638738--1638932 Score: 311
Period size: 100 Copynumber: 2.0 Consensus size: 98
1638728 GTCCATAAGG
* *
1638738 ACCACATATCATTCCTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACTT
1 ACCACATATCATTCCTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTT
1638803 CACACATGTTCCAAAGAATACATATACGTCCCGA
66 CACACATGTTCCAAAGAATAC-TATACGTCCCGA
* *
1638837 ACCACATATCATTCCTCAAGAATCATATACATATGCCCAAGGATCAAGTATGTGTCTCACTA-AC
1 ACCACATATCATTCCT-AAGAATCATATACATAT-ACCAAGGATCAAGTATGTGTCTCACCAGAC
*
1638901 TTCACACATGTTCCAAAGAATACTATATGTCC
64 TTCACACATGTTCCAAAGAATACTATACGTCC
1638933 GTTCCCTTGT
Statistics
Matches: 89, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
99 24 0.27
100 42 0.47
101 23 0.26
ACGTcount: A:0.36, C:0.26, G:0.11, T:0.27
Consensus pattern (98 bp):
ACCACATATCATTCCTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTT
CACACATGTTCCAAAGAATACTATACGTCCCGA
Found at i:1639280 original size:23 final size:23
Alignment explanation
Indices: 1639215--1639283 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
1639205 CACCACAGCT
* *
1639215 CGTATAATTGCACCGAAGTACCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
1639238 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
1639261 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
1639284 TATAATAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:1639481 original size:103 final size:103
Alignment explanation
Indices: 1639299--1639516 Score: 373
Period size: 103 Copynumber: 2.1 Consensus size: 103
1639289 TAATGTCCAT
* * *
1639299 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTCAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1639364 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
* * *
1639402 AATGACCACATATCATTCCTCAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACTA
1 AAGGACCACATATCATTCCTCAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
1639467 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATATCCCG
1639505 AAGGACCACATA
1 AAGGACCACATA
1639517 GACCCTCGAC
Statistics
Matches: 107, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTCAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATATCCCG
Found at i:1645123 original size:20 final size:19
Alignment explanation
Indices: 1645073--1645128 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
1645063 AAACCAATAT
1645073 AATAAACATAAAAT-AATTG
1 AATAAA-ATAAAATAAATTG
*
1645092 GATGAAAA-AAAATGAAATTG
1 AAT-AAAATAAAAT-AAATTG
1645112 AATAAAATAAAATAAAT
1 AATAAAATAAAATAAAT
1645129 GAGAAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 5 0.16
19 11 0.35
20 15 0.48
ACGTcount: A:0.66, C:0.02, G:0.09, T:0.23
Consensus pattern (19 bp):
AATAAAATAAAATAAATTG
Found at i:1645228 original size:17 final size:17
Alignment explanation
Indices: 1645206--1645246 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
1645196 AAGAAACTAA
1645206 AAATAATGA-AAATAAAT
1 AAATAAT-ATAAATAAAT
1645223 AAATAATATAAATAAAT
1 AAATAATATAAATAAAT
1645240 AATATAA
1 AA-ATAA
1645247 AAATATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.05
17 17 0.77
18 4 0.18
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (17 bp):
AAATAATATAAATAAAT
Found at i:1645239 original size:21 final size:21
Alignment explanation
Indices: 1645215--1645255 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1645205 AAAATAATGA
1645215 AAATAA-ATAAATAATATAAAT
1 AAATAATATAAA-AATATAAAT
1645236 AAATAATATAAAAATATAAA
1 AAATAATATAAAAATATAAA
1645256 AATGTATGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (21 bp):
AAATAATATAAAAATATAAAT
Found at i:1645412 original size:13 final size:13
Alignment explanation
Indices: 1645394--1645419 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1645384 AAACGTTAGG
1645394 AAAATATAGTAAA
1 AAAATATAGTAAA
1645407 AAAATATAGTAAA
1 AAAATATAGTAAA
1645420 TAAGTAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (13 bp):
AAAATATAGTAAA
Found at i:1645469 original size:22 final size:21
Alignment explanation
Indices: 1645437--1645489 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 21
1645427 ACATAGATAA
*
1645437 ATAATAATAATATA-ATATATAT
1 ATAAT-ATAATATAGA-AAATAT
1645459 ATATATATAATATAGAAAATAT
1 ATA-ATATAATATAGAAAATAT
1645481 ATAATATAA
1 ATAATATAA
1645490 CACAAAGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 6 0.21
22 19 0.68
23 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
ATAATATAATATAGAAAATAT
Found at i:1646053 original size:37 final size:37
Alignment explanation
Indices: 1645968--1646057 Score: 126
Period size: 37 Copynumber: 2.4 Consensus size: 37
1645958 GGATCCTATC
* * * * *
1645968 TTTAGGAGTTTAAATAATAGTAGAACTCTATCTTATT
1 TTTAGGAGTTTGAATCATAGCAAAACTATATCTTATT
*
1646005 TTTAGGAGTTTGAATCATAGCAAAATTATATCTTATT
1 TTTAGGAGTTTGAATCATAGCAAAACTATATCTTATT
1646042 TTTAGGAGTTTGAATC
1 TTTAGGAGTTTGAATC
1646058 CTAGTAGGAC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (37 bp):
TTTAGGAGTTTGAATCATAGCAAAACTATATCTTATT
Found at i:1649498 original size:2 final size:2
Alignment explanation
Indices: 1649493--1649527 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1649483 GTCTATACCA
1649493 AT AT 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 AT AT A
1649528 ACATAGATAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1650248 original size:42 final size:42
Alignment explanation
Indices: 1650166--1650256 Score: 119
Period size: 42 Copynumber: 2.2 Consensus size: 42
1650156 TCGAAATTAT
* *** *
1650166 GTGTTTGTTTCATGTAATTCGTTTTCCGGAAAATGTTTTCCC
1 GTGTTTGTTTCACGTAATTCGTTTTCCGGAAAAAAATTTCCA
* *
1650208 GTGTTTGTTTTACGTAATTCGTTTTTCGGAAAAAAATTTCCA
1 GTGTTTGTTTCACGTAATTCGTTTTCCGGAAAAAAATTTCCA
1650250 GTGTTTG
1 GTGTTTG
1650257 GTTAGAGGAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.47
Consensus pattern (42 bp):
GTGTTTGTTTCACGTAATTCGTTTTCCGGAAAAAAATTTCCA
Found at i:1650593 original size:25 final size:25
Alignment explanation
Indices: 1650565--1650638 Score: 64
Period size: 25 Copynumber: 3.0 Consensus size: 25
1650555 AGATATTATA
1650565 TTTTATTTATAAATATATAATAATT
1 TTTTATTTATAAATATATAATAATT
* **
1650590 TTTTATATATTTA-ATA-AAT-ATT
1 TTTTATTTATAAATATATAATAATT
*
1650612 ATTTATTTAATATTAATATATAATAAT
1 TTTTATTT-ATA--AATATATAATAAT
1650639 AATATTTAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 9
0.69 0.13 0.17
Matches are distributed among these distances:
22 9 0.25
23 5 0.14
24 3 0.08
25 11 0.31
26 3 0.08
27 3 0.08
28 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TTTTATTTATAAATATATAATAATT
Found at i:1650596 original size:50 final size:50
Alignment explanation
Indices: 1650497--1650638 Score: 120
Period size: 50 Copynumber: 2.9 Consensus size: 50
1650487 TATTAATATT
* *
1650497 TATA-ATAATATAATATTAT-T-TTTAATATAAA-A-AAAATCAATTATATTA
1 TATATATAATA-AATATTATATATTTAATATAAATATATAAT-AATT-TTTTA
*
1650545 TACTA-AT-ATAAGATATTATAT-TTTATTTATAAATATATAATAATTTTTTA
1 TA-TATATAATAA-ATATTATATATTTA-ATATAAATATATAATAATTTTTTA
* * *
1650595 TATATTTAATAAATATTATTTATTTAATATTAATATATAATAAT
1 TATATATAATAAATATTATATATTTAATATAAATATATAATAAT
1650639 AATATTTAAT
Statistics
Matches: 78, Mismatches: 7, Indels: 16
0.77 0.07 0.16
Matches are distributed among these distances:
47 1 0.01
48 12 0.15
49 11 0.14
50 37 0.47
51 13 0.17
52 4 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (50 bp):
TATATATAATAAATATTATATATTTAATATAAATATATAATAATTTTTTA
Found at i:1651052 original size:20 final size:20
Alignment explanation
Indices: 1651015--1651053 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1651005 CCGGAAAACG
**
1651015 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATCAAATTCA
*
1651035 TTTTCCAGAATTCAAATTC
1 TTTTCCAGAAATCAAATTC
1651054 CAGAAAACCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATCAAATTCA
Found at i:1660551 original size:15 final size:15
Alignment explanation
Indices: 1660533--1660571 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
1660523 GGGTCTGAAC
1660533 CTCTTCTTCATCTGA
1 CTCTTCTTCATCTGA
1660548 CTCTTCTTCATCTGA
1 CTCTTCTTCATCTGA
1660563 CTCTTCTTC
1 CTCTTCTTC
1660572 TACCATAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.10, C:0.36, G:0.05, T:0.49
Consensus pattern (15 bp):
CTCTTCTTCATCTGA
Found at i:1672390 original size:20 final size:20
Alignment explanation
Indices: 1672365--1672417 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1672355 TAATACAAAA
*
1672365 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATACTGACTT
*
1672385 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
1672405 TCGCAACGCGATA
1 TCGCAACGCGATA
1672418 ATACATAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:1672632 original size:22 final size:22
Alignment explanation
Indices: 1672604--1672647 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1672594 CACTCTCTCA
1672604 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1672626 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1672648 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1672952 original size:20 final size:20
Alignment explanation
Indices: 1672899--1672956 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
1672889 AGTTTCGATT
**
1672899 GTTGCGATAGTCAAATTCGC
1 GTTGCGATAGTCATTTTCGC
*
1672919 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGC
**
1672939 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
1672957 AGAAACTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.17, C:0.17, G:0.22, T:0.43
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGC
Found at i:1673147 original size:25 final size:24
Alignment explanation
Indices: 1673093--1673147 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1673083 TGTTTATTAT
* *
1673093 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
1673117 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
1673143 TGTTT
1 TGTTT
1673148 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:1674293 original size:18 final size:18
Alignment explanation
Indices: 1674272--1674316 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1674262 TCCACTTCGG
*
1674272 GAGCAATCACCTCGCCCA
1 GAGCAATCACCTCACCCA
*
1674290 GAGCTATCACCTCACCCA
1 GAGCAATCACCTCACCCA
*
1674308 GAGCCATCA
1 GAGCAATCA
1674317 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.29, C:0.42, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCAATCACCTCACCCA
Found at i:1674832 original size:20 final size:19
Alignment explanation
Indices: 1674809--1674864 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
1674799 AGCAACACGA
1674809 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGC-G
*
1674829 AAAT-AGCTATCGCAATGCG
1 AAATGA-CTATCGCAACGCG
**
1674848 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
1674865 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.16
Consensus pattern (19 bp):
AAATGACTATCGCAACGCG
Found at i:1674872 original size:14 final size:14
Alignment explanation
Indices: 1674853--1674910 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1674843 ATGCGAAATG
1674853 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1674867 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
1674883 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1674899 AAAATCGCAACG
1 AAAATCGCAACG
1674911 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Done.