Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 197 of 198
Found at i:61530248 original size:155 final size:154
Alignment explanation
Indices: 61529965--61530305 Score: 562
Period size: 155 Copynumber: 2.2 Consensus size: 154
61529955 CGTATTTTTC
*
61529965 TTTTTTCTCGGATTTTATTACTTTCAATAAAAATATACTATTTTCGTATTTTATTATTTTACATT
1 TTTTTTCCCGGATTTTATTACTTTCAATAAAAATATACTATTTTCGTATTTTATTATTTTACATT
61530030 ATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTGTTTTTTAAATAAATTTAAAAAAAAC
66 ATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTGTTTTTTAAATAAATTTAAAAAAAA-
61530095 CCTTATTTCGACCATTTGTTCGTAT
130 CCTTATTTCGACCATTTGTTCGTAT
61530120 TTTTTTCCCTGGATTTTATTACTTT-AA-AAAATATATACTATTTTC-TAATTTTATTATTTTAC
1 TTTTTTCCC-GGATTTTATTACTTTCAATAAAA-ATATACTATTTTCGT-ATTTTATTATTTTAC
* * *
61530182 ATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTAAATAAATTTAAGAAA
63 ATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTGTTTTTTAAATAAATTTAAAAAA
* *
61530247 AACCTTATTTCGTCCCTTTGTTCGTAT
128 AACCTTATTTCGACCATTTGTTCGTAT
*
61530274 TTTTTTTCCGGATTTTATTACTTTCAATAAAA
1 TTTTTTCCCGGATTTTATTACTTTCAATAAAA
61530306 CTCACACTAA
Statistics
Matches: 174, Mismatches: 7, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
153 15 0.09
154 38 0.22
155 106 0.61
156 15 0.09
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.52
Consensus pattern (154 bp):
TTTTTTCCCGGATTTTATTACTTTCAATAAAAATATACTATTTTCGTATTTTATTATTTTACATT
ATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTGTTTTTTAAATAAATTTAAAAAAAAC
CTTATTTCGACCATTTGTTCGTAT
Found at i:61530481 original size:27 final size:27
Alignment explanation
Indices: 61530440--61530505 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
61530430 TACGAACATG
* * *
61530440 TTGGTGCCTCATCTGTCACAGGCACCA
1 TTGGTGCCGCCTCTGCCACAGGCACCA
*
61530467 TTGGTGCTGCCTCTGCCACAGGCACCA
1 TTGGTGCCGCCTCTGCCACAGGCACCA
61530494 TTGGTGCCGCCT
1 TTGGTGCCGCCT
61530506 GTGGCAGGCC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.14, C:0.35, G:0.26, T:0.26
Consensus pattern (27 bp):
TTGGTGCCGCCTCTGCCACAGGCACCA
Found at i:61530613 original size:22 final size:23
Alignment explanation
Indices: 61530566--61530615 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
61530556 TAGTAAATAA
*
61530566 ATTTTTTTGTATATTATTTTAGT
1 ATTTTTTTGTATATTATTTTAAT
*
61530589 ATTTTTTT-TAT-TTTTTTGTAAT
1 ATTTTTTTGTATATTATTT-TAAT
61530611 ATTTT
1 ATTTT
61530616 GGTAAAAGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 5 0.21
22 11 0.46
23 8 0.33
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.74
Consensus pattern (23 bp):
ATTTTTTTGTATATTATTTTAAT
Found at i:61536039 original size:15 final size:15
Alignment explanation
Indices: 61536019--61536072 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
61536009 ATACTACAAA
61536019 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
61536034 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
61536051 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
61536068 ATATT
1 ATATT
61536073 AATATTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.44
16 1 0.03
17 7 0.22
18 1 0.03
19 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:61536374 original size:11 final size:11
Alignment explanation
Indices: 61536343--61536424 Score: 58
Period size: 11 Copynumber: 7.5 Consensus size: 11
61536333 TGTTTTACTA
*
61536343 TTGTTTTTTTG
1 TTGTTGTTTTG
61536354 TTG-TGTTTTG
1 TTGTTGTTTTG
61536364 TTGTTGTTTTG
1 TTGTTGTTTTG
* ** *
61536375 CTGTCATTTCG
1 TTGTTGTTTTG
* *
61536386 CTGTTGTATTG
1 TTGTTGTTTTG
** *
61536397 TTACTATTTTG
1 TTGTTGTTTTG
61536408 TTGTTGTTATTG
1 TTGTTGTT-TTG
61536420 TTGTT
1 TTGTT
61536425 TAGATATTGT
Statistics
Matches: 52, Mismatches: 17, Indels: 3
0.72 0.24 0.04
Matches are distributed among these distances:
10 9 0.17
11 35 0.67
12 8 0.15
ACGTcount: A:0.06, C:0.06, G:0.22, T:0.66
Consensus pattern (11 bp):
TTGTTGTTTTG
Found at i:61537988 original size:270 final size:270
Alignment explanation
Indices: 61537507--61538052 Score: 1092
Period size: 270 Copynumber: 2.0 Consensus size: 270
61537497 TTGTCAGCCT
61537507 GATTAATTTATTTTTCTATATGCAGATCTGAATTTGAAGGCTGAACTTCTTCGAAAATATCACAC
1 GATTAATTTATTTTTCTATATGCAGATCTGAATTTGAAGGCTGAACTTCTTCGAAAATATCACAC
61537572 ATGCTGCTAAATGATGCGAGAAGAGAGCTGAATTTGTTTAGTATTAGTGAGTGCAGGGAACGATA
66 ATGCTGCTAAATGATGCGAGAAGAGAGCTGAATTTGTTTAGTATTAGTGAGTGCAGGGAACGATA
61537637 CTCAAACTTTAAATTTTACTTAAAAGTTATGCAACAACATTTTATTTTTATTTTTTTTCAAAATT
131 CTCAAACTTTAAATTTTACTTAAAAGTTATGCAACAACATTTTATTTTTATTTTTTTTCAAAATT
61537702 TTCATTTTAAATCATGCCACATAAGGGAAGAGAGTCCTCTATTTATAGACAAAGCCTTAAAACAT
196 TTCATTTTAAATCATGCCACATAAGGGAAGAGAGTCCTCTATTTATAGACAAAGCCTTAAAACAT
61537767 CAACGGTTAA
261 CAACGGTTAA
61537777 GATTAATTTATTTTTCTATATGCAGATCTGAATTTGAAGGCTGAACTTCTTCGAAAATATCACAC
1 GATTAATTTATTTTTCTATATGCAGATCTGAATTTGAAGGCTGAACTTCTTCGAAAATATCACAC
61537842 ATGCTGCTAAATGATGCGAGAAGAGAGCTGAATTTGTTTAGTATTAGTGAGTGCAGGGAACGATA
66 ATGCTGCTAAATGATGCGAGAAGAGAGCTGAATTTGTTTAGTATTAGTGAGTGCAGGGAACGATA
61537907 CTCAAACTTTAAATTTTACTTAAAAGTTATGCAACAACATTTTATTTTTATTTTTTTTCAAAATT
131 CTCAAACTTTAAATTTTACTTAAAAGTTATGCAACAACATTTTATTTTTATTTTTTTTCAAAATT
61537972 TTCATTTTAAATCATGCCACATAAGGGAAGAGAGTCCTCTATTTATAGACAAAGCCTTAAAACAT
196 TTCATTTTAAATCATGCCACATAAGGGAAGAGAGTCCTCTATTTATAGACAAAGCCTTAAAACAT
61538037 CAACGGTTAA
261 CAACGGTTAA
61538047 GATTAA
1 GATTAA
61538053 GTTACATGGT
Statistics
Matches: 276, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
270 276 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.36
Consensus pattern (270 bp):
GATTAATTTATTTTTCTATATGCAGATCTGAATTTGAAGGCTGAACTTCTTCGAAAATATCACAC
ATGCTGCTAAATGATGCGAGAAGAGAGCTGAATTTGTTTAGTATTAGTGAGTGCAGGGAACGATA
CTCAAACTTTAAATTTTACTTAAAAGTTATGCAACAACATTTTATTTTTATTTTTTTTCAAAATT
TTCATTTTAAATCATGCCACATAAGGGAAGAGAGTCCTCTATTTATAGACAAAGCCTTAAAACAT
CAACGGTTAA
Found at i:61542655 original size:96 final size:96
Alignment explanation
Indices: 61542530--61542720 Score: 373
Period size: 96 Copynumber: 2.0 Consensus size: 96
61542520 ATACTGAATT
*
61542530 GGAAGCTGAGATTGGGATTTTGAAGAAAAATCAGAGTGAATTGAAGATGGAAATTGTGAAATTGA
1 GGAAGCTGAGATTGGGATTTTGAAGAAAAATCAGAGTGAACTGAAGATGGAAATTGTGAAATTGA
61542595 AGCAAAAAAATGATGAATCTAATGATAAACA
66 AGCAAAAAAATGATGAATCTAATGATAAACA
61542626 GGAAGCTGAGATTGGGATTTTGAAGAAAAATCAGAGTGAACTGAAGATGGAAATTGTGAAATTGA
1 GGAAGCTGAGATTGGGATTTTGAAGAAAAATCAGAGTGAACTGAAGATGGAAATTGTGAAATTGA
61542691 AGCAAAAAAATGATGAATCTAATGATAAAC
66 AGCAAAAAAATGATGAATCTAATGATAAAC
61542721 TGAGTGTTTT
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 94 1.00
ACGTcount: A:0.46, C:0.06, G:0.25, T:0.24
Consensus pattern (96 bp):
GGAAGCTGAGATTGGGATTTTGAAGAAAAATCAGAGTGAACTGAAGATGGAAATTGTGAAATTGA
AGCAAAAAAATGATGAATCTAATGATAAACA
Found at i:61542975 original size:42 final size:43
Alignment explanation
Indices: 61542923--61543130 Score: 144
Period size: 42 Copynumber: 5.0 Consensus size: 43
61542913 AGAGTTTGCT
* * *
61542923 TGAGCTTAT-GGGAACTGATCAAACG-GTGACAAAGAGCTTGAA
1 TGAGCCTATAGGGAACTGACCAAA-GTGTCACAAAGAGCTTGAA
* * **
61542965 TGAGCCTATGGGGAA-TGGCCAAAGTGTCACAAAGAGCTTGCC
1 TGAGCCTATAGGGAACTGACCAAAGTGTCACAAAGAGCTTGAA
* * * * **
61543007 TGAGCCTATAGGG-ACTGACCAGAGGGTCACCAAGAACTTGCC
1 TGAGCCTATAGGGAACTGACCAAAGTGTCACAAAGAGCTTGAA
* * **
61543049 TGAGCCTAT--GGAGACTGACCAGAGGGTCACCAAAGA-CTTGCC
1 TGAGCCTATAGGGA-ACTGACCAAAGTGTCA-CAAAGAGCTTGAA
* * * *
61543091 TGAGCCTA-CGGGGACTGACCAAAGTGTCCCAAAGACCTTG
1 TGAGCCTATAGGGAACTGACCAAAGTGTCACAAAGAGCTTG
61543131 CCTAAGCCAA
Statistics
Matches: 140, Mismatches: 17, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
40 2 0.01
41 8 0.06
42 118 0.84
43 12 0.09
ACGTcount: A:0.30, C:0.23, G:0.29, T:0.18
Consensus pattern (43 bp):
TGAGCCTATAGGGAACTGACCAAAGTGTCACAAAGAGCTTGAA
Found at i:61543131 original size:42 final size:42
Alignment explanation
Indices: 61542951--61543287 Score: 318
Period size: 42 Copynumber: 8.0 Consensus size: 42
61542941 TCAAACGGTG
* ** * * *
61542951 ACAAAGAGCTTGAATGAGCCTATGGGGAATGGCCAAAGTGTC
1 ACAAAGACCTTGCCTGAGCCTATGGAGACTGACCAAAGTGTC
* * *
61542993 ACAAAGAGCTTGCCTGAGCCTATAGG-GACTGACCAGAGGGTC
1 ACAAAGACCTTGCCTGAGCCTAT-GGAGACTGACCAAAGTGTC
* * * *
61543035 ACCAAGAACTTGCCTGAGCCTATGGAGACTGACCAGAGGGTC
1 ACAAAGACCTTGCCTGAGCCTATGGAGACTGACCAAAGTGTC
* *
61543077 ACCAAAGA-CTTGCCTGAGCCTACGGGGACTGACCAAAGTGTC
1 A-CAAAGACCTTGCCTGAGCCTATGGAGACTGACCAAAGTGTC
* * * * * * *
61543119 CCAAAGACCTTGCCTAAGCCAATTGAGACCGACCAACGTATC
1 ACAAAGACCTTGCCTGAGCCTATGGAGACTGACCAAAGTGTC
* * * * *
61543161 ACAAAGACCTTGCCTAAGCCAATGGAGACCGACCAACGTATC
1 ACAAAGACCTTGCCTGAGCCTATGGAGACTGACCAAAGTGTC
* * ** * *
61543203 ACAAAGACCTTGCCTAAGCCAATGGAGACCAACCAATGTATC
1 ACAAAGACCTTGCCTGAGCCTATGGAGACTGACCAAAGTGTC
* * *
61543245 ACAAAGACCTTGCCTGAGCCTATGGAGATTGGCGAAAGTGTC
1 ACAAAGACCTTGCCTGAGCCTATGGAGACTGACCAAAGTGTC
61543287 A
1 A
61543288 GCAACTCTAA
Statistics
Matches: 256, Mismatches: 35, Indels: 8
0.86 0.12 0.03
Matches are distributed among these distances:
41 8 0.03
42 241 0.94
43 7 0.03
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.17
Consensus pattern (42 bp):
ACAAAGACCTTGCCTGAGCCTATGGAGACTGACCAAAGTGTC
Found at i:61548390 original size:20 final size:20
Alignment explanation
Indices: 61548367--61548406 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
61548357 AATAAACATC
61548367 AAAAATTTATTTTAAAAATA
1 AAAAATTTATTTTAAAAATA
61548387 AAAAATTTATTTTAAAAATA
1 AAAAATTTATTTTAAAAATA
61548407 TTTTAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAAATTTATTTTAAAAATA
Found at i:61548404 original size:21 final size:22
Alignment explanation
Indices: 61548349--61548404 Score: 73
Period size: 20 Copynumber: 2.6 Consensus size: 22
61548339 AGCCCGGCCC
*
61548349 ATTT-TTTTAATAAACATCAAAA
1 ATTTATTTTAA-AAACATAAAAA
61548371 ATTTATTTT-AAAA-ATAAAAA
1 ATTTATTTTAAAAACATAAAAA
61548391 ATTTATTTTAAAAA
1 ATTTATTTTAAAAA
61548405 TATTTTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 15 0.48
21 7 0.23
22 5 0.16
23 4 0.13
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTTATTTTAAAAACATAAAAA
Found at i:61551890 original size:16 final size:18
Alignment explanation
Indices: 61551852--61551887 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
61551842 TTTTAAATGT
*
61551852 TAAAAATTACATAATATA
1 TAAAAATAACATAATATA
61551870 TAAAAATAACATAATATA
1 TAAAAATAACATAATATA
61551888 AAATATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAAATAACATAATATA
Found at i:61553271 original size:11 final size:12
Alignment explanation
Indices: 61553255--61553293 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
61553245 AGTGTTTTGG
61553255 TGCTGTTATTTT
1 TGCTGTTATTTT
*
61553267 T-CTGTTGTTTT
1 TGCTGTTATTTT
*
61553278 TGTTGTTATTTT
1 TGCTGTTATTTT
61553290 TGCT
1 TGCT
61553294 ACTGTTTTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.05, C:0.08, G:0.18, T:0.69
Consensus pattern (12 bp):
TGCTGTTATTTT
Found at i:61553286 original size:23 final size:24
Alignment explanation
Indices: 61553258--61553305 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
61553248 GTTTTGGTGC
**
61553258 TGTTATTTTT-CTGTTGTTTTTGT
1 TGTTATTTTTGCTACTGTTTTTGT
61553281 TGTTATTTTTGCTACTGTTTTTGT
1 TGTTATTTTTGCTACTGTTTTTGT
61553305 T
1 T
61553306 ATTTGCACTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.06, C:0.06, G:0.17, T:0.71
Consensus pattern (24 bp):
TGTTATTTTTGCTACTGTTTTTGT
Found at i:61559629 original size:29 final size:31
Alignment explanation
Indices: 61559559--61559631 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 31
61559549 AAGTTTTAAA
* * *
61559559 TATACATTTGAACCATAATTAGAGTTCAACG
1 TATACAATTGCACCATAATTAAAGTTCAACG
* * *
61559590 TGTATAATTGCACCA-AATTAAAGTT-AATG
1 TATACAATTGCACCATAATTAAAGTTCAACG
61559619 TATACAATTGCAC
1 TATACAATTGCAC
61559632 ATTAAATCAA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
29 14 0.41
30 9 0.26
31 11 0.32
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (31 bp):
TATACAATTGCACCATAATTAAAGTTCAACG
Found at i:61559656 original size:29 final size:27
Alignment explanation
Indices: 61559590--61559656 Score: 62
Period size: 31 Copynumber: 2.3 Consensus size: 27
61559580 GAGTTCAACG
* *
61559590 TGTATAATTGCACCAAATTAAAGTTAA
1 TGTATAATTGCACCAAATCAAAATTAA
* *
61559617 TGTATACAATTGCACATTAAATCAAAATTCA
1 TGTAT--AATTGCAC--CAAATCAAAATTAA
61559648 TGTATAATT
1 TGTATAATT
61559657 TTGAGATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
27 5 0.16
29 12 0.38
31 15 0.47
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (27 bp):
TGTATAATTGCACCAAATCAAAATTAA
Found at i:61564825 original size:21 final size:22
Alignment explanation
Indices: 61564801--61564841 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
61564791 ATAATTAAAA
*
61564801 TATTTCAT-TACAATAAACTTT
1 TATTTAATATACAATAAACTTT
61564822 TATTTAATATACAATAAACT
1 TATTTAATATACAATAAACT
61564842 AATAATTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (22 bp):
TATTTAATATACAATAAACTTT
Found at i:61566829 original size:12 final size:12
Alignment explanation
Indices: 61566812--61566837 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
61566802 TCCTTCAACA
61566812 CCGCCACCTCCG
1 CCGCCACCTCCG
61566824 CCGCCACCTCCG
1 CCGCCACCTCCG
61566836 CC
1 CC
61566838 TCTTGCAGCT
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:0.08, C:0.69, G:0.15, T:0.08
Consensus pattern (12 bp):
CCGCCACCTCCG
Found at i:61567079 original size:141 final size:141
Alignment explanation
Indices: 61566825--61567119 Score: 536
Period size: 141 Copynumber: 2.1 Consensus size: 141
61566815 CCACCTCCGC
* *
61566825 CGCCACCTCCGCCTCTTGCAGCTGCATATCGTAAACCAAGGCGAAGTTATCAAGCTGTTGGCCTG
1 CGCCACCTCCGCCTCCTGCAGCTGCATATCGTAAACCAAGGCGAAGTTATCAAGCTGTTGGCCGG
61566890 AAAGAGAATGTGAATAATACTCAAAAGTTTCATGTTGAGTACGATGGAAGTGAGTCTCCGGCTCC
66 AAAGAGAATGTGAATAATACTCAAAAGTTTCATGTTGAGTACGATGGAAGTGAGTCTCCGGCTCC
61566955 GCAGCCAGTAA
131 GCAGCCAGTAA
* *
61566966 CGCCACCGCCGCCTCCTGCAGCTGGATATCGTAAACCAAGGCGAAGTTATCAAGCTGTTGGCCGG
1 CGCCACCTCCGCCTCCTGCAGCTGCATATCGTAAACCAAGGCGAAGTTATCAAGCTGTTGGCCGG
*
61567031 AAAGAGAATGTGAATAATGCTCAAAAGTTTCATGTTGAGTACGATGGAAGTGAGTCTCCGGCTCC
66 AAAGAGAATGTGAATAATACTCAAAAGTTTCATGTTGAGTACGATGGAAGTGAGTCTCCGGCTCC
*
61567096 TCAGCCAGTAA
131 GCAGCCAGTAA
61567107 CGCCACCTCCGCC
1 CGCCACCTCCGCC
61567120 GCCTCCTCCT
Statistics
Matches: 147, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
141 147 1.00
ACGTcount: A:0.27, C:0.26, G:0.25, T:0.22
Consensus pattern (141 bp):
CGCCACCTCCGCCTCCTGCAGCTGCATATCGTAAACCAAGGCGAAGTTATCAAGCTGTTGGCCGG
AAAGAGAATGTGAATAATACTCAAAAGTTTCATGTTGAGTACGATGGAAGTGAGTCTCCGGCTCC
GCAGCCAGTAA
Found at i:61576025 original size:15 final size:14
Alignment explanation
Indices: 61575998--61576025 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
61575988 AATTAGTGTT
61575998 GAAAACTAAAAAAA
1 GAAAACTAAAAAAA
61576012 GAAAACTAAAAAAA
1 GAAAACTAAAAAAA
61576026 CGGGGGAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.79, C:0.07, G:0.07, T:0.07
Consensus pattern (14 bp):
GAAAACTAAAAAAA
Found at i:61593401 original size:12 final size:11
Alignment explanation
Indices: 61593379--61593410 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
61593369 ATATCTAGAA
61593379 TTTAATTTTTT
1 TTTAATTTTTT
61593390 TTTAATTTTTT
1 TTTAATTTTTT
*
61593401 TTTACTTTTT
1 TTTAATTTTT
61593411 AGATTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTAATTTTTT
Found at i:61598757 original size:14 final size:13
Alignment explanation
Indices: 61598740--61598775 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 13
61598730 ATATTGCATC
61598740 ATTATTATTGTATT
1 ATTATTATT-TATT
61598754 ATTATTTATTTATT
1 ATTA-TTATTTATT
61598768 ATTATTAT
1 ATTATTAT
61598776 AACCATGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.19
14 12 0.57
15 5 0.24
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (13 bp):
ATTATTATTTATT
Found at i:61615404 original size:7 final size:7
Alignment explanation
Indices: 61615392--61615437 Score: 92
Period size: 7 Copynumber: 6.6 Consensus size: 7
61615382 TATAAAATAC
61615392 TTTCTAT
1 TTTCTAT
61615399 TTTCTAT
1 TTTCTAT
61615406 TTTCTAT
1 TTTCTAT
61615413 TTTCTAT
1 TTTCTAT
61615420 TTTCTAT
1 TTTCTAT
61615427 TTTCTAT
1 TTTCTAT
61615434 TTTC
1 TTTC
61615438 ATATATATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.13, C:0.15, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTCTAT
Found at i:61615448 original size:21 final size:21
Alignment explanation
Indices: 61615392--61615448 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
61615382 TATAAAATAC
* *
61615392 TTTCTATTTTCTATTTTCTAT
1 TTTCTATTATATATTTTCTAT
* *
61615413 TTTCTATTTTCTATTTTCTAT
1 TTTCTATTATATATTTTCTAT
61615434 TTTC-ATATATATATT
1 TTTCTAT-TATATATT
61615449 AATCATCACG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 2 0.06
21 31 0.94
ACGTcount: A:0.19, C:0.12, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTCTATTATATATTTTCTAT
Found at i:61616068 original size:4 final size:4
Alignment explanation
Indices: 61616061--61616105 Score: 90
Period size: 4 Copynumber: 11.2 Consensus size: 4
61616051 AATGAATGAA
61616061 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
61616106 TGATTGAAGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:61616184 original size:71 final size:70
Alignment explanation
Indices: 61616037--61616186 Score: 198
Period size: 71 Copynumber: 2.1 Consensus size: 70
61616027 TATTTAAATG
* *
61616037 ATTGAAGGATTTAAAATGAATGAAACATACATACATACATACATACATACATACATACATACATA
1 ATTGAAGGATTTAAAATGAATGAAACATACATACATACATACATACATACATACATAAAAACATA
*
61616102 CATAT
66 AATAT
*
61616107 GATTGAAGGATTTAAAATGAATGAAACATACATACATACATACATATATGA-A-ACATAGAAAAC
1 -ATTGAAGGATTTAAAATGAATGAAACATACATACATACATACATACAT-ACATACATA-AAAAC
61616170 TATAAAT-T
63 -ATAAATAT
61616178 ATTTGAAGG
1 A-TTGAAGG
61616187 CATTCCTTCG
Statistics
Matches: 71, Mismatches: 4, Indels: 8
0.86 0.05 0.10
Matches are distributed among these distances:
70 6 0.08
71 59 0.83
72 6 0.08
ACGTcount: A:0.50, C:0.12, G:0.11, T:0.27
Consensus pattern (70 bp):
ATTGAAGGATTTAAAATGAATGAAACATACATACATACATACATACATACATACATAAAAACATA
AATAT
Found at i:61616918 original size:23 final size:22
Alignment explanation
Indices: 61616892--61616939 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
61616882 TTATGAATAT
61616892 ATTAAAATA-ATATAAACTTAAAA
1 ATTAAAATACATATAAA--TAAAA
* *
61616915 ATTAGAATACTTATAAATAAAA
1 ATTAAAATACATATAAATAAAA
61616937 ATT
1 ATT
61616940 CTAATGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 8 0.36
23 8 0.36
24 6 0.27
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (22 bp):
ATTAAAATACATATAAATAAAA
Found at i:61622225 original size:19 final size:19
Alignment explanation
Indices: 61622193--61622232 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
61622183 TACATCCCAC
*
61622193 AATTTATTTATTTTTTATA
1 AATTTATTTATTTTCTATA
61622212 AATTATATTT-TTTTCTATA
1 AATT-TATTTATTTTCTATA
61622231 AA
1 AA
61622233 CGTAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
AATTTATTTATTTTCTATA
Found at i:61624162 original size:27 final size:25
Alignment explanation
Indices: 61624122--61624171 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 25
61624112 TATGAAGAGG
61624122 GCAAAATGCAAAAAATACATTTCAACA
1 GCAAAATGCAAAAAAT-C-TTTCAACA
61624149 GCAAAAT-CATAAAAATCTTTCAA
1 GCAAAATGCA-AAAAATCTTTCAA
61624172 AATATAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 6 0.27
26 3 0.14
27 13 0.59
ACGTcount: A:0.54, C:0.18, G:0.06, T:0.22
Consensus pattern (25 bp):
GCAAAATGCAAAAAATCTTTCAACA
Found at i:61628025 original size:17 final size:17
Alignment explanation
Indices: 61628003--61628036 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
61627993 AAAATTTGTG
61628003 TTTATTTAGAATAAAAT
1 TTTATTTAGAATAAAAT
**
61628020 TTTATTTTTAATAAAAT
1 TTTATTTAGAATAAAAT
61628037 ATAATGAGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTATTTAGAATAAAAT
Found at i:61638385 original size:23 final size:23
Alignment explanation
Indices: 61638358--61638402 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
61638348 TTTATGAAAC
61638358 TTTAAGA-AATAAATTTTTTAATT
1 TTTAAGATAAT-AATTTTTTAATT
* *
61638381 TTTAATATAATTATTTTTTAAT
1 TTTAAGATAATAATTTTTTAAT
61638403 ACAATATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
TTTAAGATAATAATTTTTTAATT
Found at i:61640489 original size:9 final size:9
Alignment explanation
Indices: 61640475--61640504 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
61640465 ATTGATACAC
61640475 CATACCAAT
1 CATACCAAT
61640484 CATACCAAT
1 CATACCAAT
*
61640493 CATACAAAT
1 CATACCAAT
61640502 CAT
1 CAT
61640505 TGAATCATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (9 bp):
CATACCAAT
Found at i:61643121 original size:192 final size:192
Alignment explanation
Indices: 61642783--61643181 Score: 584
Period size: 192 Copynumber: 2.1 Consensus size: 192
61642773 CCACCTTGCT
* *
61642783 CAACACTGAGCATGCTACTTGCTAGTTCATTAATCAATGATCCGATCTGTTCACTGGAATCGTGA
1 CAACACTGAGCATGCTACTTGCTAGTTCAATAATCAATGATCCGATCTGTTCACTAGAATCGTGA
* * * *
61642848 TTGTAAACCGATGTGTGAATGATGTTATTCATTATGATTTGAAGCGTCGGAAACTCTTTAGTTTG
66 TTGTAAACCGATGCGTGAATGATGTTATTCATTATGATTTGAAGAGTCCGAAACTCTTTACTTTG
* * * *
61642913 ATGCTTAGTCTGTTTCGGTATGAGAGGAATTGTTGAAAAACTGAATCAGTGACTGCATCGAC
131 ATGCATAGTCTGTTTCGGTACGAGAAGAATTGTTGAAAAACTGAATCAGTAACTGCATCGAC
* *
61642975 CAACACTGAGCATGCTACTTGTTAGTTCAATAATCAATGATCCGATCTGTTCACTAGAGTCGTGA
1 CAACACTGAGCATGCTACTTGCTAGTTCAATAATCAATGATCCGATCTGTTCACTAGAATCGTGA
* * * *
61643040 TTGTAAATCGATGCGTGAATGATGTTACTT-TTTATGATTTGAAGAGTCCGAAGCTTTTTACTTT
66 TTGTAAACCGATGCGTGAATGATGTTA-TTCATTATGATTTGAAGAGTCCGAAACTCTTTACTTT
* * * * *
61643104 GATGCATATTTTGTTTCGGTACGGGAAGAATTGTTGAAAAATTGAATCAGTAACTGCATCGAT
130 GATGCATAGTCTGTTTCGGTACGAGAAGAATTGTTGAAAAACTGAATCAGTAACTGCATCGAC
*
61643167 CAACACAGAGCATGC
1 CAACACTGAGCATGC
61643182 AAATGCGTAA
Statistics
Matches: 184, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
192 182 0.99
193 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.34
Consensus pattern (192 bp):
CAACACTGAGCATGCTACTTGCTAGTTCAATAATCAATGATCCGATCTGTTCACTAGAATCGTGA
TTGTAAACCGATGCGTGAATGATGTTATTCATTATGATTTGAAGAGTCCGAAACTCTTTACTTTG
ATGCATAGTCTGTTTCGGTACGAGAAGAATTGTTGAAAAACTGAATCAGTAACTGCATCGAC
Found at i:61643862 original size:42 final size:42
Alignment explanation
Indices: 61643798--61643885 Score: 167
Period size: 42 Copynumber: 2.1 Consensus size: 42
61643788 CATGAGGTTT
61643798 ACGTGACATGCTACGTGCCACTACCTAGTTATTCAGCCAGCC
1 ACGTGACATGCTACGTGCCACTACCTAGTTATTCAGCCAGCC
*
61643840 ACGTGACATGCTACGTGGCACTACCTAGTTATTCAGCCAGCC
1 ACGTGACATGCTACGTGCCACTACCTAGTTATTCAGCCAGCC
61643882 ACGT
1 ACGT
61643886 TAGTATTTAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (42 bp):
ACGTGACATGCTACGTGCCACTACCTAGTTATTCAGCCAGCC
Found at i:61646131 original size:31 final size:29
Alignment explanation
Indices: 61646067--61646132 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 29
61646057 ATCATTTAGG
61646067 TATTATATAATTAATATTATATGTTTATTT
1 TATT-TATAATTAATATTATATGTTTATTT
61646097 TATTTATAATATAATTATTGATAT-TTT-TTAT
1 TATTTATAAT-TAA-TATT-ATATGTTTATT-T
61646128 TATTT
1 TATTT
61646133 TATATCTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
29 6 0.19
30 9 0.28
31 13 0.41
32 4 0.12
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (29 bp):
TATTTATAATTAATATTATATGTTTATTT
Found at i:61661484 original size:20 final size:20
Alignment explanation
Indices: 61661461--61661499 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
61661451 AGCTTTTGAG
* *
61661461 TGCTTTGCAAATCTTTGAAA
1 TGCTTTGAAAATATTTGAAA
61661481 TGCTTTGAAAATATTTGAA
1 TGCTTTGAAAATATTTGAA
61661500 CACTAAACGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.41
Consensus pattern (20 bp):
TGCTTTGAAAATATTTGAAA
Found at i:61664045 original size:21 final size:21
Alignment explanation
Indices: 61664021--61664062 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
61664011 TTTCATGTTG
*
61664021 TTTTAATT-TTTTTTGTTAATT
1 TTTTAATTATTGTTT-TTAATT
61664042 TTTTAATTATTGTTTTTAATT
1 TTTTAATTATTGTTTTTAATT
61664063 AATAAACATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (21 bp):
TTTTAATTATTGTTTTTAATT
Found at i:61666912 original size:7 final size:7
Alignment explanation
Indices: 61666900--61666931 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
61666890 TTATCTGATT
61666900 AGTGACA
1 AGTGACA
61666907 AGTGACA
1 AGTGACA
61666914 AGTGACA
1 AGTGACA
*
61666921 AGTGATA
1 AGTGACA
61666928 AGTG
1 AGTG
61666932 GTAGCTTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.41, C:0.09, G:0.31, T:0.19
Consensus pattern (7 bp):
AGTGACA
Found at i:61666946 original size:58 final size:58
Alignment explanation
Indices: 61666856--61666972 Score: 216
Period size: 58 Copynumber: 2.0 Consensus size: 58
61666846 ACTTCTGATC
* *
61666856 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACATTTATCTGATTAGTGACAAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACA
61666914 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACA
61666972 A
1 A
61666973 ATGTGATCCG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (58 bp):
AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACA
Found at i:61669817 original size:7 final size:7
Alignment explanation
Indices: 61669805--61669838 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
61669795 CGTATACCCT
61669805 TGGCTGG
1 TGGCTGG
61669812 TGGCTGG
1 TGGCTGG
61669819 TGGCTGG
1 TGGCTGG
61669826 TGGCTGG
1 TGGCTGG
61669833 TGGCTG
1 TGGCTG
61669839 CTAGTGGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.00, C:0.15, G:0.56, T:0.29
Consensus pattern (7 bp):
TGGCTGG
Found at i:61671022 original size:84 final size:84
Alignment explanation
Indices: 61670900--61671055 Score: 242
Period size: 84 Copynumber: 1.9 Consensus size: 84
61670890 GTGTTGATCT
* * *
61670900 TTTTTAAGTATGGGTTGTCATATTAGTACAATGATAAATGCTGTATACGGATAACAAACATCCTC
1 TTTTTAAGTATGGATTGTCATATTAGTACAACGATAAATGCTGTATACGGATAACAAACATCCAC
61670965 TAACTCACATAAGGTTATC
66 TAACTCACATAAGGTTATC
* * *
61670984 TTTTTAAGTATGGATTGTCATATTAAG-ACAACGGTAAATGCTGTATACGGATGACAGACATCCA
1 TTTTTAAGTATGGATTGTCATATT-AGTACAACGATAAATGCTGTATACGGATAACAAACATCCA
61671048 CTAACTCA
65 CTAACTCA
61671056 TAGAGGATTG
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
84 63 0.97
85 2 0.03
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Consensus pattern (84 bp):
TTTTTAAGTATGGATTGTCATATTAGTACAACGATAAATGCTGTATACGGATAACAAACATCCAC
TAACTCACATAAGGTTATC
Found at i:61681150 original size:14 final size:15
Alignment explanation
Indices: 61681117--61681154 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
61681107 TAAGCAACAA
*
61681117 GTAAACCTTAAAATC
1 GTAAATCTTAAAATC
*
61681132 TTAAATCTT-AAATC
1 GTAAATCTTAAAATC
61681146 GTAAATCTT
1 GTAAATCTT
61681155 GACTTCAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.37
Consensus pattern (15 bp):
GTAAATCTTAAAATC
Found at i:61694464 original size:11 final size:11
Alignment explanation
Indices: 61694448--61694474 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
61694438 TTTAAATGTG
61694448 TTTTTTTAAAT
1 TTTTTTTAAAT
61694459 TTTTTTTAAAT
1 TTTTTTTAAAT
61694470 TTTTT
1 TTTTT
61694475 AATAATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTTTAAAT
Found at i:61701154 original size:10 final size:10
Alignment explanation
Indices: 61701139--61701170 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
61701129 AAAACTCAGA
61701139 TTTTCTTTTT
1 TTTTCTTTTT
61701149 TTTTCTTTTT
1 TTTTCTTTTT
61701159 TTTTCTTTTT
1 TTTTCTTTTT
61701169 TT
1 TT
61701171 AGCATTGAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:61714144 original size:2 final size:2
Alignment explanation
Indices: 61714137--61714161 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
61714127 TCAGCTCCCA
61714137 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 A
61714162 AGTATACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:61718087 original size:3 final size:3
Alignment explanation
Indices: 61718079--61718104 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
61718069 ATTAAGTATA
61718079 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
61718105 CAACCAAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:61727061 original size:12 final size:13
Alignment explanation
Indices: 61727038--61727066 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
61727028 TGATTACTTG
61727038 AATTTAGTTAATT
1 AATTTAGTTAATT
61727051 AATTT-GTTAATT
1 AATTTAGTTAATT
61727063 AATT
1 AATT
61727067 GAACTTGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (13 bp):
AATTTAGTTAATT
Found at i:61737380 original size:83 final size:81
Alignment explanation
Indices: 61737238--61737413 Score: 241
Period size: 83 Copynumber: 2.1 Consensus size: 81
61737228 TTTTTCCCTC
*
61737238 TTTG-TTGAATATGAATTACATGGACTTAAAGATCTTGTTTTTATTTAATGTGTTGTGATATTTT
1 TTTGATTGAATATGAATTACATGGACTTAAAGATCTTGTTTTTATTTAATGTGTTGTGATA-TCT
61737302 TTTATGGGTTTTGCTTG
65 TTTATGGGTTTTGCTTG
* * *
61737319 TTTTGATTGAATATGCATTACTTGGACTTAAAGATCTTGTTTTTATTT-GT-TGTATGATGATAT
1 -TTTGATTGAATATGAATTACATGGACTTAAAGATCTTGTTTTTATTTAATGTGT-TG-TGATAT
*
61737382 CTTTTCTGGGTTTTGCTTG
63 CTTTTATGGGTTTTGCTTG
61737401 TTTGAATTGAATA
1 TTTG-ATTGAATA
61737414 CTGTTAGGTA
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
81 7 0.08
82 33 0.39
83 45 0.53
ACGTcount: A:0.22, C:0.06, G:0.19, T:0.52
Consensus pattern (81 bp):
TTTGATTGAATATGAATTACATGGACTTAAAGATCTTGTTTTTATTTAATGTGTTGTGATATCTT
TTATGGGTTTTGCTTG
Found at i:61739671 original size:27 final size:28
Alignment explanation
Indices: 61739640--61739695 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
61739630 ATATGAAAAT
*
61739640 TTAATATATTAAT-ATTT-AAAAATTATA
1 TTAATAAATT-ATGATTTAAAAAATTATA
*
61739667 TTAATAAATTATGTTTTAAAAAATTATA
1 TTAATAAATTATGATTTAAAAAATTATA
61739695 T
1 T
61739696 CAAATTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 2 0.08
27 12 0.48
28 11 0.44
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (28 bp):
TTAATAAATTATGATTTAAAAAATTATA
Found at i:61741180 original size:3 final size:3
Alignment explanation
Indices: 61741172--61741204 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
61741162 GAAGTGAGCA
61741172 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
61741205 GAAATCACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:61744835 original size:22 final size:22
Alignment explanation
Indices: 61744793--61744835 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
61744783 TAAGAAAATA
*
61744793 ATATATTTTTAATTGATATTTT
1 ATATATTTTTAATTGAAATTTT
*
61744815 ATATCTTTTATAATT-AAATTT
1 ATATATTTT-TAATTGAAATTT
61744836 AAAATAGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
ATATATTTTTAATTGAAATTTT
Found at i:61745746 original size:18 final size:18
Alignment explanation
Indices: 61745723--61745758 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
61745713 ATTTATAATA
*
61745723 TTTTATATTATGTTATTT
1 TTTTATATTATGTAATTT
61745741 TTTTATATTATGTAATTT
1 TTTTATATTATGTAATTT
61745759 ATAACACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
TTTTATATTATGTAATTT
Found at i:61745861 original size:24 final size:25
Alignment explanation
Indices: 61745832--61745880 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
61745822 TAAAAAAATT
*
61745832 ATATATAAAATTATAAT-AAATAAAAA
1 ATAT-TAAAA-TAAAATAAAATAAAAA
61745858 ATATTAAAATAAAATAAAATAAA
1 ATATTAAAATAAAATAAAATAAA
61745881 TATACATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 12 0.57
26 4 0.19
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (25 bp):
ATATTAAAATAAAATAAAATAAAAA
Found at i:61745878 original size:29 final size:30
Alignment explanation
Indices: 61745822--61745882 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
61745812 TTAAAAATAT
* *
61745822 TAAAAAAATTATATATAAAATTATAATAAA
1 TAAAAAAATTATAAATAAAATTAAAATAAA
61745852 TAAAAAATATTA-AAATAAAA-TAAAATAAA
1 TAAAAAA-ATTATAAATAAAATTAAAATAAA
61745881 TA
1 TA
61745883 TACATTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 10 0.36
30 14 0.50
31 4 0.14
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (30 bp):
TAAAAAAATTATAAATAAAATTAAAATAAA
Found at i:61750020 original size:125 final size:127
Alignment explanation
Indices: 61749787--61750114 Score: 375
Period size: 126 Copynumber: 2.6 Consensus size: 127
61749777 AACAAAAAGA
** ** * *
61749787 ATCCAACTGAAACAAATTTTTGAAGCTATAAATACACTAATGAAATGCAAACAATGAAAGCTTTA
1 ATCCAACCAAAACAAATTCATGAAGCTATAAATAAACTAATGAAATGCAAACAATCAAAGCTTTA
* * **
61749852 CCGTAAAGCACAAATCATAACATGGTCCACTTCG-GGGGGAAAA-AACATCAAGCTAAGAGC
66 CCATAAAGCACAAATCATAACACGGTCCACTTCGAGGGAAAAAACAACATCAAGCTAAGAGC
* *
61749912 ATCCAACCAAAACAAATTCATGTAGCTATAAGTAAACTAATGAAATGCAAACAA-CATAAGCTTT
1 ATCCAACCAAAACAAATTCATGAAGCTATAAATAAACTAATGAAATGCAAACAATCA-AAGC-TT
61749976 TACCATAAAGCACAAATCATAACACGGTCCACTTC-AGGGAAAAAACAACATCAAGCTAAGAGC
64 TACCATAAAGCACAAATCATAACACGGTCCACTTCGAGGGAAAAAACAACATCAAGCTAAGAGC
* * * * *
61750039 ATCCACATC-TAAGAAATTCTTCAAGCTATGAAATACAA-TAAT-AAATGCAAACAA-CAAAAGC
1 ATCCA-ACCAAAACAAATTCATGAAGCTAT-AAATA-AACTAATGAAATGCAAACAATC-AAAGC
* *
61750100 TTTACCTTTAAGCAC
62 TTTACCATAAAGCAC
61750115 GAACCAAAAA
Statistics
Matches: 174, Mismatches: 21, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
124 1 0.01
125 51 0.29
126 55 0.32
127 54 0.31
128 11 0.06
129 2 0.01
ACGTcount: A:0.46, C:0.21, G:0.12, T:0.21
Consensus pattern (127 bp):
ATCCAACCAAAACAAATTCATGAAGCTATAAATAAACTAATGAAATGCAAACAATCAAAGCTTTA
CCATAAAGCACAAATCATAACACGGTCCACTTCGAGGGAAAAAACAACATCAAGCTAAGAGC
Found at i:61750085 original size:127 final size:125
Alignment explanation
Indices: 61749787--61750102 Score: 388
Period size: 127 Copynumber: 2.5 Consensus size: 125
61749777 AACAAAAAGA
** * * *
61749787 ATCCAACTGAAACAAATTTTTGAAGCTATAAATACACTAATGAAATGCAAACAATGAAAGC-TTT
1 ATCCAACCAAAACAAATTCTTGAAGCTATAAATACAATAATGAAATGCAAACAA-CAAAGCTTTT
* * * **
61749851 ACCGTAAAGCACAAATCATAACATGGTCCACTTCGGGGGGAAAAAACATCAAGCTAAGAGC
65 ACCATAAAGCACAAATCATAACACGGTCCACTTCAGGGAAAAAAAACATCAAGCTAAGAGC
* * *
61749912 ATCCAACCAAAACAAATTCATGTAGCTATAAGTA-AACTAATGAAATGCAAACAACATAAGCTTT
1 ATCCAACCAAAACAAATTCTTGAAGCTATAAATACAA-TAATGAAATGCAAACAACA-AAGCTTT
61749976 TACCATAAAGCACAAATCATAACACGGTCCACTTCAGGGAAAAAACAACATCAAGCTAAGAGC
64 TACCATAAAGCACAAATCATAACACGGTCCACTTCAGGGAAAAAA-AACATCAAGCTAAGAGC
* * * *
61750039 ATCCACATC-TAAGAAATTCTTCAAGCTATGAAATACAATAAT-AAATGCAAACAACAAAAGCTT
1 ATCCA-ACCAAAACAAATTCTTGAAGCTAT-AAATACAATAATGAAATGCAAACAAC-AAAGCTT
61750102 T
63 T
61750103 ACCTTTAAGC
Statistics
Matches: 163, Mismatches: 20, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
124 2 0.01
125 49 0.30
126 42 0.26
127 57 0.35
128 11 0.07
129 2 0.01
ACGTcount: A:0.46, C:0.20, G:0.13, T:0.21
Consensus pattern (125 bp):
ATCCAACCAAAACAAATTCTTGAAGCTATAAATACAATAATGAAATGCAAACAACAAAGCTTTTA
CCATAAAGCACAAATCATAACACGGTCCACTTCAGGGAAAAAAAACATCAAGCTAAGAGC
Found at i:61763179 original size:6 final size:5
Alignment explanation
Indices: 61763145--61763178 Score: 50
Period size: 5 Copynumber: 6.4 Consensus size: 5
61763135 AAATTATCTC
61763145 TTCTT CTTCTT CTTCTT TTCTT TTCTT TTCTT TT
1 TTCTT -TTCTT -TTCTT TTCTT TTCTT TTCTT TT
61763179 TTATGAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 17 0.61
6 11 0.39
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (5 bp):
TTCTT
Found at i:61763765 original size:29 final size:29
Alignment explanation
Indices: 61763733--61763806 Score: 78
Period size: 31 Copynumber: 2.5 Consensus size: 29
61763723 CAATTCAAGT
*
61763733 TTCATGTATATAATT-ACATCAAATCAAAA
1 TTCATGTATA-AATTAACATCAAACCAAAA
* * *
61763762 TTCATATATCAAATTACACATTAAACCAAAT
1 TTCATGTAT-AAATTA-ACATCAAACCAAAA
61763793 TTCATGTATAAATT
1 TTCATGTATAAATT
61763807 TAATATTTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
29 12 0.32
30 6 0.16
31 19 0.51
ACGTcount: A:0.46, C:0.15, G:0.03, T:0.36
Consensus pattern (29 bp):
TTCATGTATAAATTAACATCAAACCAAAA
Found at i:61764844 original size:22 final size:21
Alignment explanation
Indices: 61764816--61764874 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 21
61764806 TTTTTTTTTG
61764816 TATTTTTTAAATTTAAGTCACT
1 TATTTTTTAAATTTAAGTCA-T
* *
61764838 TATTTTTATGAGTTT-AGTCAT
1 TATTTTT-TAAATTTAAGTCAT
* *
61764859 TAATTTTTAAAATTAA
1 TATTTTTTAAATTTAA
61764875 AATTTTAAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
20 4 0.14
21 8 0.28
22 12 0.41
23 5 0.17
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.54
Consensus pattern (21 bp):
TATTTTTTAAATTTAAGTCAT
Found at i:61767877 original size:58 final size:59
Alignment explanation
Indices: 61767753--61767877 Score: 137
Period size: 58 Copynumber: 2.1 Consensus size: 59
61767743 ACTAACTTGG
* * * * **
61767753 AAAAAAAAGTTTAGACCCCAATGTGAGAAAAATTGTCAAGTTCAAGGACTAACTTTTAC
1 AAAAAAAAATTTAGACCCCAATATAAGAAAAATTGTCAAGTTCAAGGACGAACTTAGAC
* * * *
61767812 AAGAAAAAATTTAG-GCCCAATATAAGAATAATTGTCAAGTTC-AGGATCGATCTTAGAC
1 AAAAAAAAATTTAGACCCCAATATAAGAAAAATTGTCAAGTTCAAGGA-CGAACTTAGAC
61767870 AAAAAAAA
1 AAAAAAAA
61767878 TAAAGTTTAA
Statistics
Matches: 54, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
57 4 0.07
58 38 0.70
59 12 0.22
ACGTcount: A:0.47, C:0.14, G:0.15, T:0.24
Consensus pattern (59 bp):
AAAAAAAAATTTAGACCCCAATATAAGAAAAATTGTCAAGTTCAAGGACGAACTTAGAC
Found at i:61782579 original size:31 final size:31
Alignment explanation
Indices: 61782492--61782579 Score: 72
Period size: 31 Copynumber: 2.9 Consensus size: 31
61782482 TGTATTCATG
* * *
61782492 AACTTTAA-TTTGATGCAATCATACACGTGA
1 AACTTTAATTTTGATTCAATCATATATGTGA
* * * * * *
61782522 AACTCTAATTGTGGTTGAAAT-GTATATTTGA
1 AACTTTAATTTTGATT-CAATCATATATGTGA
61782553 AACTTTAATTTTGATTCAATCATATAT
1 AACTTTAATTTTGATTCAATCATATAT
61782580 ATTTAAATAA
Statistics
Matches: 41, Mismatches: 14, Indels: 5
0.68 0.23 0.08
Matches are distributed among these distances:
30 10 0.24
31 28 0.68
32 3 0.07
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.41
Consensus pattern (31 bp):
AACTTTAATTTTGATTCAATCATATATGTGA
Found at i:61785614 original size:25 final size:26
Alignment explanation
Indices: 61785580--61785635 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
61785570 TGTGAGTGTG
*
61785580 TTGAAACATGTT-ATAGTAATAGATC
1 TTGAAACATGTTAATAGTAATAGAGC
61785605 TTGAAACATGTTAATAGTAATAGAGC
1 TTGAAACATGTTAATAGTAATAGAGC
61785631 TTGAA
1 TTGAA
61785636 CTTCCATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 12 0.41
26 17 0.59
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.34
Consensus pattern (26 bp):
TTGAAACATGTTAATAGTAATAGAGC
Found at i:61790756 original size:23 final size:22
Alignment explanation
Indices: 61790726--61790768 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
61790716 CGCTTTATTA
61790726 TTTTTATTTAATAAAAAATATAT
1 TTTTTATTT-ATAAAAAATATAT
*
61790749 TTTTTATTTTTAAAAAATAT
1 TTTTTATTTATAAAAAATAT
61790769 TTTATCATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTTATTTATAAAAAATATAT
Found at i:61790952 original size:3 final size:3
Alignment explanation
Indices: 61790944--61790983 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
61790934 TATCTCAATG
61790944 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
61790984 TAACTACAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:61791584 original size:21 final size:22
Alignment explanation
Indices: 61791560--61791600 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
61791550 TATTTTTTAG
*
61791560 AATATTTAAATA-TCAATATAA
1 AATATTAAAATATTCAATATAA
61791581 AATATTAAAATATTCAATAT
1 AATATTAAAATATTCAATAT
61791601 TATTATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (22 bp):
AATATTAAAATATTCAATATAA
Found at i:61793949 original size:21 final size:19
Alignment explanation
Indices: 61793927--61793992 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 19
61793917 AATTTAATTA
61793927 AAATATATAAACTATATTTT
1 AAATATATAAA-TATATTTT
*
61793947 AAATATTTAAATATAATTATT
1 AAATATATAAATAT-ATT-TT
*
61793968 AAATATTTATAATTAGTATTTT
1 AAATA--TATAAATA-TATTTT
61793990 AAA
1 AAA
61793993 AAATATTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
19 3 0.08
20 13 0.34
21 7 0.18
22 5 0.13
23 9 0.24
24 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (19 bp):
AAATATATAAATATATTTT
Found at i:61803397 original size:32 final size:33
Alignment explanation
Indices: 61803361--61803429 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 33
61803351 GAATCGAAAT
*
61803361 TAAAA-TTTATATATATACAATT-AAAATTATAA
1 TAAAAGTTT-TATATATACAATTAAAAATAATAA
* * *
61803393 TAAAAGTTTTATTTGTATAATTAAAAATAATAA
1 TAAAAGTTTTATATATACAATTAAAAATAATAA
61803426 TAAA
1 TAAA
61803430 CTCGCATAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
32 15 0.48
33 16 0.52
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (33 bp):
TAAAAGTTTTATATATACAATTAAAAATAATAA
Found at i:61813260 original size:28 final size:28
Alignment explanation
Indices: 61813220--61813276 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
61813210 TGAGGGTTAA
61813220 AGTTGTTATTATGCCAATTTTAAAAGCT
1 AGTTGTTATTATGCCAATTTTAAAAGCT
*
61813248 AGTTGTTATTATGTCAATTTTAAAAGCT
1 AGTTGTTATTATGCCAATTTTAAAAGCT
61813276 A
1 A
61813277 CCACGATTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (28 bp):
AGTTGTTATTATGCCAATTTTAAAAGCT
Found at i:61813389 original size:59 final size:60
Alignment explanation
Indices: 61813316--61813447 Score: 185
Period size: 59 Copynumber: 2.2 Consensus size: 60
61813306 GACGACATTG
* * *
61813316 AATAATTGGGTGATCATTCTATAACTTTTCATAGTTGGGTGACCAAAAAAAAAA-ATACT
1 AATAGTTGGGTGATCATTCTATAACTTTTCATAATTGAGTGACCAAAAAAAAAATATACT
* * * * *
61813375 AATAGTTGGGTGATCGTTTTGTAACTTTTCATAATTGATTGACCAAAAAAAAAATTTACT
1 AATAGTTGGGTGATCATTCTATAACTTTTCATAATTGAGTGACCAAAAAAAAAATATACT
61813435 AATAGTTGGGTGA
1 AATAGTTGGGTGA
61813448 CTACTAGTGT
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
59 47 0.73
60 17 0.27
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (60 bp):
AATAGTTGGGTGATCATTCTATAACTTTTCATAATTGAGTGACCAAAAAAAAAATATACT
Found at i:61827866 original size:29 final size:29
Alignment explanation
Indices: 61827782--61827866 Score: 71
Period size: 31 Copynumber: 2.8 Consensus size: 29
61827772 GACTAAATCA
* * *
61827782 AAATTAAAGTTTCAAGTATACATTTGAACC
1 AAATTAAAATTT-ATGTATACAATTGAACC
** * * *
61827812 ACAATTAGAGTTTTATGTGTATAATTGCACC
1 A-AATTA-AAATTTATGTATACAATTGAACC
61827843 AAATTAAAATTTATGTATACAATT
1 AAATTAAAATTTATGTATACAATT
61827867 ACACATCAAA
Statistics
Matches: 42, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
29 14 0.33
30 6 0.14
31 18 0.43
32 4 0.10
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (29 bp):
AAATTAAAATTTATGTATACAATTGAACC
Found at i:61828257 original size:18 final size:20
Alignment explanation
Indices: 61828234--61828274 Score: 68
Period size: 18 Copynumber: 2.1 Consensus size: 20
61828224 CTTATAAATA
61828234 TTTTTATAAT-TT-TGTATT
1 TTTTTATAATCTTATGTATT
61828252 TTTTTATAATCTTATGTATT
1 TTTTTATAATCTTATGTATT
61828272 TTT
1 TTT
61828275 ATCAAGAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 10 0.48
19 2 0.10
20 9 0.43
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (20 bp):
TTTTTATAATCTTATGTATT
Found at i:61831028 original size:15 final size:16
Alignment explanation
Indices: 61831001--61831040 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
61830991 AAATTTGTTT
*
61831001 TTTTAATAAATTT-AAG
1 TTTTAA-AAATTTCAAA
61831017 TTTTAAAAATTTCAAA
1 TTTTAAAAATTTCAAA
61831033 TTTTAAAA
1 TTTTAAAA
61831041 TCCACAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (16 bp):
TTTTAAAAATTTCAAA
Found at i:61834883 original size:682 final size:654
Alignment explanation
Indices: 61833586--61834927 Score: 1910
Period size: 682 Copynumber: 2.0 Consensus size: 654
61833576 AATTTTAAAT
61833586 TTTTTTAGGAATTATTGTTAAATTGAAACCAGTAAGCATCTATTTTTATTGTTTTCAGAAGATAA
1 TTTTTTAGGAATTATTGTTAAATTGAAACCAGTAAGCATCTATTTTTATTGTTTTCAGAAGATAA
* *
61833651 GAATAAATGTGTGTCTTTATATTTGGTTTATTGGCTATAGGTATTCACTCTTCACTCTCGTAAGT
66 GAATAAATGTGTGTCTTTATATTTGGTTTATTGGCTATAGGTACTCACTATTCACTCTCGTAAGT
61833716 TTGAGTCGCAAGCGATTTATGTCATAAGTTCCAACAAAAGATATAAAATAAATGAAAAAGTATCA
131 TTGAGTCGCAAGCGATTTATGTCATAAGTTCCAACAAAAGATATAAAATAAATGAAAAAGTATCA
* * *
61833781 AACAAATCATATAAAAACATGTTTGTAATTCATATATATTTTTCATGATTAATTATGTATGTGTT
196 AACAAATCA-AT----A-A----T-TAATTCATATATATTTTTCACGATTAATTATGCAAGTGTT
*
61833846 TTTAATTTAAATTTTATTAAGCCTTATTCATATTTATTTCGATTATTACTTTATTCTAATTATAA
250 TTTAATTTAAATTTTATTAACCCTTATTCATATTTATTTCGATTATTACTTTATTCTAATTATAA
* *
61833911 GCGGATGAAAGTGTAACCCTCTTATACTTCTAAACCCCTAAGCATGTTTTCATTTAAGAAACCAC
315 GCGGATGAAAGTGTAACCCTCTTATACTTCTAAACCCCTAACCATGTTTTCAATT-AGAAA-CAC
* *
61833976 CTTCCATAAATAAAAAGAAGAGAAGAAGATGAAGATTGATTGGTTATTGAGCCACTAAAAGAGGC
378 CTTCCATAAAGAAAAAGAACAGAAGAAGATGAAGATTGATTGGTTATTGAGCCACTAAAAGAGGC
*
61834041 GGCGGAGGAGGGGTCGCCTAAAATTGGAAATTTGTATTTTTTTTATAATAAAATGATTCTCCTTT
443 GGCGGAGGAGGGGTCGCCTAAAATTGGAAATTTGTATTTTTCTTATAATAAAATGATTCTCCTTT
*
61834106 GAATATTCCAAGCTGTCCATTAGTTTGAATGGTAAAGTCTATATGAAGTATGGATAGTAATGTCT
508 GAATATTCCAAGCTGTCCATTAGTTTGAATAGTAAAGTCTATATGAAGTATGGATAGTAATGTCT
*
61834171 ATGGATATTATTCCAAATCATCAGCTTTATCCACCAACATAGTTGAGCTATTGACACGTGTCTAT
573 ATGGATATTATTCCAAATCATCAACTTTATCCACCAACATAGTTGAGCTATTGACACGTGTCTAT
61834236 TTATTTGCTTTTTTAGG
638 TTATTTGCTTTTTTAGG
61834253 TTTTTTAGGAATTATTGTTAAATTGAAACCAGTAAGCATCTATTTTTATTGTTTTCAGAAGATGA
1 TTTTTTAGGAATTATTGTTAAATTGAAACCAGTAAGCATCTATTTTTATTGTTTTCAGAAGAT-A
*
61834318 A-AATAAATGTGTGTCTTTATATTTGGTTTATTGGCTATGGGTACTCACTATTCACTCTCGTAAG
65 AGAATAAATGTGTGTCTTTATATTTGGTTTATTGGCTATAGGTACTCACTATTCACTCTCGTAAG
61834382 TTTGAGTCGCAAGCTTTGTACTTGATTTATGTCATAAGTTCCAACAAAAGATATAAAATAAATGA
130 TTTGAGTCGCAA-----G--C--GATTTATGTCATAAGTTCCAACAAAAGATATAAAATAAATGA
* *
61834447 AAAAGTATGAAACAAATC-AT-A-TAATTCATATATATTTTTCACGATTCATTATGCAAGTGTTT
186 AAAAGTATCAAACAAATCAATAATTAATTCATATATATTTTTCACGATTAATTATGCAAGTGTTT
61834509 TTAATTTAAATTTTATTAACCCTTATTCATATTTATTCTAATATAGAGTTGAATATATTTCGATT
251 TTAATTTAAATTTTATTAA-CC-----C----TTATTC----AT--A--T---T-TATTTCGATT
*
61834574 ATTACTTTATTTTAATTATAAGCGGATGAAAGTGTAACCCTCTTATACTTCTAAACCCCTAACCA
294 ATTACTTTATTCTAATTATAAGCGGATGAAAGTGTAACCCTCTTATACTTCTAAACCCCTAACCA
* *** * * **** *
61834639 TG-TTT-AATT-GATA-TGGTTTCATTTAAGAAACCACCTTCCATAA-ATAGATGAAGATTGATT
359 TGTTTTCAATTAGAAACACCTTCCA-TAAAGAAA--A-AGAACAGAAGA-AGATGAAGATTGATT
61834699 GGTTATTGAGCCACTAAAAGAGGCGGCGGAGGAGGGGTCGCCTAAAATTGGAAATTTGTATTTTT
419 GGTTATTGAGCCACTAAAAGAGGCGGCGGAGGAGGGGTCGCCTAAAATTGGAAATTTGTATTTTT
*
61834764 CTTATAATAAAATGATTCTCCTTTGAATATTCCAAGCTGTCCATTAGTTTGACTAGTAAAGTCTA
484 CTTATAATAAAATGATTCTCCTTTGAATATTCCAAGCTGTCCATTAGTTTGAATAGTAAAGTCTA
61834829 TATGAAGTATGGATAGTAATGTCTATGGATATTATTCCAAATCATCAACTTTATCCACCAACATA
549 TATGAAGTATGGATAGTAATGTCTATGGATATTATTCCAAATCATCAACTTTATCCACCAACATA
61834894 GTTGAGCTATTGACACGTGTCTATTTATTTGCTT
614 GTTGAGCTATTGACACGTGTCTATTTATTTGCTT
61834928 AAATCGAGCC
Statistics
Matches: 609, Mismatches: 29, Indels: 59
0.87 0.04 0.08
Matches are distributed among these distances:
662 56 0.09
663 1 0.00
667 135 0.22
668 4 0.01
672 7 0.01
674 3 0.00
676 61 0.10
678 5 0.01
679 6 0.01
680 4 0.01
681 2 0.00
682 246 0.40
683 4 0.01
684 75 0.12
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (654 bp):
TTTTTTAGGAATTATTGTTAAATTGAAACCAGTAAGCATCTATTTTTATTGTTTTCAGAAGATAA
GAATAAATGTGTGTCTTTATATTTGGTTTATTGGCTATAGGTACTCACTATTCACTCTCGTAAGT
TTGAGTCGCAAGCGATTTATGTCATAAGTTCCAACAAAAGATATAAAATAAATGAAAAAGTATCA
AACAAATCAATAATTAATTCATATATATTTTTCACGATTAATTATGCAAGTGTTTTTAATTTAAA
TTTTATTAACCCTTATTCATATTTATTTCGATTATTACTTTATTCTAATTATAAGCGGATGAAAG
TGTAACCCTCTTATACTTCTAAACCCCTAACCATGTTTTCAATTAGAAACACCTTCCATAAAGAA
AAAGAACAGAAGAAGATGAAGATTGATTGGTTATTGAGCCACTAAAAGAGGCGGCGGAGGAGGGG
TCGCCTAAAATTGGAAATTTGTATTTTTCTTATAATAAAATGATTCTCCTTTGAATATTCCAAGC
TGTCCATTAGTTTGAATAGTAAAGTCTATATGAAGTATGGATAGTAATGTCTATGGATATTATTC
CAAATCATCAACTTTATCCACCAACATAGTTGAGCTATTGACACGTGTCTATTTATTTGCTTTTT
TAGG
Found at i:61836285 original size:39 final size:39
Alignment explanation
Indices: 61836239--61836319 Score: 110
Period size: 39 Copynumber: 2.1 Consensus size: 39
61836229 ATAATTTAAA
* **
61836239 TTTATATATT-TCGTATATCATAATATTAATGAATTTGAG
1 TTTATATATTCT-ATATATCATAATATTAACAAATTTGAG
*
61836278 TTTATATATTCTATATATTATAATATTAACAAATTTGAG
1 TTTATATATTCTATATATCATAATATTAACAAATTTGAG
61836317 TTT
1 TTT
61836320 TTTAGTATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
39 36 0.97
40 1 0.03
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (39 bp):
TTTATATATTCTATATATCATAATATTAACAAATTTGAG
Found at i:61836366 original size:15 final size:15
Alignment explanation
Indices: 61836346--61836376 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
61836336 CATTTAGTTT
61836346 TAATTTTGGAAGTGA
1 TAATTTTGGAAGTGA
61836361 TAATTTTGGAAGTGA
1 TAATTTTGGAAGTGA
61836376 T
1 T
61836377 TTCAGTGATG
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:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (15 bp):
TAATTTTGGAAGTGA
Found at i:61839866 original size:21 final size:22
Alignment explanation
Indices: 61839830--61839874 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
61839820 GGTTCCATTT
*
61839830 TTTTCTTTTTTTTTCTGTCTTG
1 TTTTCTTTTATTTTCTGTCTTG
*
61839852 TTTTC-TTTATTTTCTTTCTTG
1 TTTTCTTTTATTTTCTGTCTTG
61839873 TT
1 TT
61839875 CTTTAAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.02, C:0.13, G:0.07, T:0.78
Consensus pattern (22 bp):
TTTTCTTTTATTTTCTGTCTTG
Found at i:61840374 original size:2 final size:2
Alignment explanation
Indices: 61840365--61840394 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
61840355 TATAGTTTTT
61840365 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
61840395 TATTCAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:61845356 original size:6 final size:6
Alignment explanation
Indices: 61845345--61845370 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
61845335 GTAATGGTAG
61845345 CAGTAA CAGTAA CAGTAA CAGTAA CA
1 CAGTAA CAGTAA CAGTAA CAGTAA CA
61845371 ATATTCAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.19, G:0.15, T:0.15
Consensus pattern (6 bp):
CAGTAA
Found at i:61845448 original size:45 final size:45
Alignment explanation
Indices: 61845353--61845457 Score: 142
Period size: 45 Copynumber: 2.3 Consensus size: 45
61845343 AGCAGTAACA
61845353 GTAACAGTAACAGTAACAATATTCAACACACAAAGTGCTGAATCT
1 GTAACAGTAACAGTAACAATATTCAACACACAAAGTGCTGAATCT
* * * *
61845398 ATAACAGTAACGGTAACAGTATTCGACACACAAAGTG-TCGAAT-T
1 GTAACAGTAACAGTAACAATATTCAACACACAAAGTGCT-GAATCT
61845442 GGTAACAGTAACAGTA
1 -GTAACAGTAACAGTA
61845458 GTCGGCATAT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
44 2 0.04
45 50 0.96
ACGTcount: A:0.43, C:0.18, G:0.17, T:0.22
Consensus pattern (45 bp):
GTAACAGTAACAGTAACAATATTCAACACACAAAGTGCTGAATCT
Found at i:61851706 original size:22 final size:20
Alignment explanation
Indices: 61851667--61851722 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 20
61851657 ATTTTATTCT
*
61851667 ATTTTTATTTTTAGAAATTTA
1 ATTTTTATTTTT-TAAATTTA
61851688 ACTTCTTTATTTTTTAAATTTA
1 A-TT-TTTATTTTTTAAATTTA
*
61851710 ATTGTTATTTTTT
1 ATTTTTATTTTTT
61851723 TTGTTATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 9 0.29
21 3 0.10
22 10 0.32
23 9 0.29
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.66
Consensus pattern (20 bp):
ATTTTTATTTTTTAAATTTA
Found at i:61859620 original size:3 final size:3
Alignment explanation
Indices: 61859612--61859642 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
61859602 TTCTAACGCA
61859612 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
61859643 CATTAATCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:61864580 original size:27 final size:27
Alignment explanation
Indices: 61864550--61864601 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
61864540 TTTAATATAT
61864550 ATATATATACCTATATA-AAAAAAACCC
1 ATATATATA-CTATATATAAAAAAACCC
* *
61864577 ATATGTATATTATATATAAAAAAAC
1 ATATATATACTATATATAAAAAAAC
61864602 TATGCGTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.31
Consensus pattern (27 bp):
ATATATATACTATATATAAAAAAACCC
Found at i:61866237 original size:44 final size:45
Alignment explanation
Indices: 61866161--61866258 Score: 144
Period size: 44 Copynumber: 2.2 Consensus size: 45
61866151 AAGACTTGTA
* **
61866161 TCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCACCACCAATACAGGAAGACAAGATCTGCTT
* *
61866206 TCTTCGATCTACTTCA-CGCCAATACATGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCACCACCAATACAGGAAGACAAGATCTGCTT
61866250 TCTTCGATC
1 TCTTCGATC
61866259 GATTCCACTA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 32 0.67
45 16 0.33
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.31
Consensus pattern (45 bp):
TCTTCGATCTACTTCACCACCAATACAGGAAGACAAGATCTGCTT
Found at i:61866385 original size:44 final size:44
Alignment explanation
Indices: 61866337--61866526 Score: 120
Period size: 44 Copynumber: 4.3 Consensus size: 44
61866327 AAAATTCGCC
* * *
61866337 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGGCAAAATCTGTA
1 ATCTTCAATCTACTCCACTACTGCTCAGGGAGGCAAAATCTGTA
* ** * ** *
61866381 ATCTTCAATCTATTCCACTGTTGCCCAGGGAGATATAATTACTG--
1 ATCTTCAATCTACTCCACTACTGCTCAGGGAGGCA-AAAT-CTGTA
* * * **
61866425 -GCTTCAATGTACTCCACTGTAAC--CTCAGGGAGGTAAAATCTGCC
1 ATCTTCAATCTACTCCAC--T-ACTGCTCAGGGAGGCAAAATCTGTA
* * * * *
61866469 ATCTTCGATCTGCTTCACTACTGCTTAGGGAGGCAAGATCTGTA
1 ATCTTCAATCTACTCCACTACTGCTCAGGGAGGCAAAATCTGTA
61866513 ATCTTCAATCTACT
1 ATCTTCAATCTACT
61866527 TCGCCACCAG
Statistics
Matches: 106, Mismatches: 30, Indels: 20
0.68 0.19 0.13
Matches are distributed among these distances:
42 5 0.05
43 18 0.17
44 64 0.60
45 16 0.15
46 3 0.03
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (44 bp):
ATCTTCAATCTACTCCACTACTGCTCAGGGAGGCAAAATCTGTA
Found at i:61866443 original size:132 final size:132
Alignment explanation
Indices: 61866276--61866524 Score: 419
Period size: 132 Copynumber: 1.9 Consensus size: 132
61866266 CTACCGATCG
*
61866276 GGGAGATAGAATAACTGGCTTCAATATACTCCACTGCAACTTCAGGGAGGTAAAAT-TCGCCATC
1 GGGAGATAGAATAACTGGCTTCAATATACTCCACTGCAACCTCAGGGAGGTAAAATCT-GCCATC
61866340 TTCGATCTGCTCCACTACTGCTTAGGGAGGCAAAATCTGTAATCTTCAATCTATTCCACTGTTGC
65 TTCGATCTGCTCCACTACTGCTTAGGGAGGCAAAATCTGTAATCTTCAATCTATTCCACTGTTGC
61866405 CCA
130 CCA
* * * *
61866408 GGGAGATATAATTACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATCT
1 GGGAGATAGAATAACTGGCTTCAATATACTCCACTGCAACCTCAGGGAGGTAAAATCTGCCATCT
* *
61866473 TCGATCTGCTTCACTACTGCTTAGGGAGGCAAGATCTGTAATCTTCAATCTA
66 TCGATCTGCTCCACTACTGCTTAGGGAGGCAAAATCTGTAATCTTCAATCTA
61866525 CTTCGCCACC
Statistics
Matches: 109, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
132 108 0.99
133 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (132 bp):
GGGAGATAGAATAACTGGCTTCAATATACTCCACTGCAACCTCAGGGAGGTAAAATCTGCCATCT
TCGATCTGCTCCACTACTGCTTAGGGAGGCAAAATCTGTAATCTTCAATCTATTCCACTGTTGCC
CA
Found at i:61866687 original size:45 final size:45
Alignment explanation
Indices: 61866611--61867134 Score: 540
Period size: 45 Copynumber: 11.7 Consensus size: 45
61866601 TATCTTTGAT
* * * *
61866611 GAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGAAAAG
1 GAAGACAAGATCTGGTATCTTTGATCTACTTCGCCACCAGAATAG
* *
61866656 GAAGACAAGATCTGGTATCTTTGATCCACTTCGCTACCA-ATATAG
1 GAAGACAAGATCTGGTATCTTTGATCTACTTCGCCACCAGA-ATAG
* * * * * * * *
61866701 GAAGACAGGATATAGTATCTTTGATCTACTTC-ACGCCAGTACAT
1 GAAGACAAGATCTGGTATCTTTGATCTACTTCGCCACCAGAATAG
* * * * *
61866745 GAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGG
1 GAAGACAAGATCTGGTATCTTTGATCTACTTCGCCACCAGAATAG
*
61866790 GAAGACAAGATCTGGTATCTTTGATCTACTTCGCTACCA-ATATAG
1 GAAGACAAGATCTGGTATCTTTGATCTACTTCGCCACCAGA-ATAG
* * * * * *
61866835 GAAGACAGGATCTGGTATCTTTGATCTACTTC-ACGCCAGTACAT
1 GAAGACAAGATCTGGTATCTTTGATCTACTTCGCCACCAGAATAG
* * * *
61866879 GAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGAATAA
1 GAAGACAAGATCTGGTATCTTTGATCTACTTCGCCACCAGAATAG
* *
61866924 GAAGACAAGATCTGGTATCTTTGATCCACTTCGCTACCA-ATATAG
1 GAAGACAAGATCTGGTATCTTTGATCTACTTCGCCACCAGA-ATAG
* * * * * *
61866969 GAAGACAGGATCTAGTATCTTTGATCTACTTC-ACGCCAGTATAT
1 GAAGACAAGATCTGGTATCTTTGATCTACTTCGCCACCAGAATAG
* * * * *
61867013 GAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGG
1 GAAGACAAGATCTGGTATCTTTGATCTACTTCGCCACCAGAATAG
* *
61867058 GAAGACAAGATCTGGTATCTTTGATCAACTTCGCTACCA-ATATAG
1 GAAGACAAGATCTGGTATCTTTGATCTACTTCGCCACCAGA-ATAG
* *
61867103 GAAGCCAGGATCTGGTATCTTTGATCTACTTC
1 GAAGACAAGATCTGGTATCTTTGATCTACTTC
61867135 ACGCCAGTAC
Statistics
Matches: 387, Mismatches: 82, Indels: 20
0.79 0.17 0.04
Matches are distributed among these distances:
44 99 0.26
45 288 0.74
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (45 bp):
GAAGACAAGATCTGGTATCTTTGATCTACTTCGCCACCAGAATAG
Found at i:61866776 original size:89 final size:89
Alignment explanation
Indices: 61866611--61867156 Score: 551
Period size: 89 Copynumber: 6.1 Consensus size: 89
61866601 TATCTTTGAT
* * * * * *
61866611 GAAGACAAGATCT-GTTTTCTTCGATCTACTTCGCCACCAGAAAAGGAAGACAAGATCTGGTATC
1 GAAGACAAGATCTAG-TATCTTTGATCTACTTC-ACACCAGTATATGAAGACAAGATCTGGTATC
* * *
61866675 TTTGATCCACTTCGCTACCAATATAG
64 TTTGATCTACTTCGCCACCAGTATAG
* * * * * *
61866701 GAAGACAGGATATAGTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTT
1 GAAGACAAGATCTAGTATCTTTGATCTACTTCACACCAGTATATGAAGACAAGATCTGGTATCTT
* *
61866766 CGATCTACTTCGCCACCAGTATGG
66 TGATCTACTTCGCCACCAGTATAG
* * * * *
61866790 GAAGACAAGATCTGGTATCTTTGATCTACTTCGCTACCAATATAGGAAGACAGGATCTGGTATCT
1 GAAGACAAGATCTAGTATCTTTGATCTACTTCAC-ACCAGTATATGAAGACAAGATCTGGTATCT
* * * *
61866855 TTGATCTACTTC-ACGCCAGTACAT
65 TTGATCTACTTCGCCACCAGTATAG
* * * * *
61866879 GAAGACAAGATCT-GTTTTCTTCGATCTACTTCGCCACCAGAATAAGAAGACAAGATCTGGTATC
1 GAAGACAAGATCTAG-TATCTTTGATCTACTTC-ACACCAGTATATGAAGACAAGATCTGGTATC
* * *
61866943 TTTGATCCACTTCGCTACCAATATAG
64 TTTGATCTACTTCGCCACCAGTATAG
* * * *
61866969 GAAGACAGGATCTAGTATCTTTGATCTACTTCACGCCAGTATATGAAGACAAGATCTGTTTTCTT
1 GAAGACAAGATCTAGTATCTTTGATCTACTTCACACCAGTATATGAAGACAAGATCTGGTATCTT
* *
61867034 CGATCTACTTCGCCACCAGTATGG
66 TGATCTACTTCGCCACCAGTATAG
* * * * * * *
61867058 GAAGACAAGATCTGGTATCTTTGATCAACTTCGCTACCAATATAGGAAGCCAGGATCTGGTATCT
1 GAAGACAAGATCTAGTATCTTTGATCTACTTCAC-ACCAGTATATGAAGACAAGATCTGGTATCT
* * * *
61867123 TTGATCTACTTC-ACGCCAGTACAT
65 TTGATCTACTTCGCCACCAGTATAG
61867147 GAAGACAAGA
1 GAAGACAAGA
61867157 CTTGCTGAAG
Statistics
Matches: 371, Mismatches: 78, Indels: 15
0.80 0.17 0.03
Matches are distributed among these distances:
88 1 0.00
89 240 0.65
90 128 0.35
91 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (89 bp):
GAAGACAAGATCTAGTATCTTTGATCTACTTCACACCAGTATATGAAGACAAGATCTGGTATCTT
TGATCTACTTCGCCACCAGTATAG
Found at i:61866853 original size:134 final size:134
Alignment explanation
Indices: 61866609--61867156 Score: 979
Period size: 134 Copynumber: 4.1 Consensus size: 134
61866599 ACTATCTTTG
*
61866609 ATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGAAAAGGAAGACAAGATCTGGTAT
1 ATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGAATAGGAAGACAAGATCTGGTAT
*
61866674 CTTTGATCCACTTCGCTACCAATATAGGAAGACAGGATATAGTATCTTTGATCTACTTCACGCCA
66 CTTTGATCCACTTCGCTACCAATATAGGAAGACAGGATCTAGTATCTTTGATCTACTTCACGCCA
61866739 GTAC
131 GTAC
* *
61866743 ATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTAT
1 ATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGAATAGGAAGACAAGATCTGGTAT
* *
61866808 CTTTGATCTACTTCGCTACCAATATAGGAAGACAGGATCTGGTATCTTTGATCTACTTCACGCCA
66 CTTTGATCCACTTCGCTACCAATATAGGAAGACAGGATCTAGTATCTTTGATCTACTTCACGCCA
61866873 GTAC
131 GTAC
*
61866877 ATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGAATAAGAAGACAAGATCTGGTAT
1 ATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGAATAGGAAGACAAGATCTGGTAT
61866942 CTTTGATCCACTTCGCTACCAATATAGGAAGACAGGATCTAGTATCTTTGATCTACTTCACGCCA
66 CTTTGATCCACTTCGCTACCAATATAGGAAGACAGGATCTAGTATCTTTGATCTACTTCACGCCA
*
61867007 GTAT
131 GTAC
* *
61867011 ATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTAT
1 ATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGAATAGGAAGACAAGATCTGGTAT
* * *
61867076 CTTTGATCAACTTCGCTACCAATATAGGAAGCCAGGATCTGGTATCTTTGATCTACTTCACGCCA
66 CTTTGATCCACTTCGCTACCAATATAGGAAGACAGGATCTAGTATCTTTGATCTACTTCACGCCA
61867141 GTAC
131 GTAC
61867145 ATGAAGACAAGA
1 ATGAAGACAAGA
61867157 CTTGCTGAAG
Statistics
Matches: 395, Mismatches: 19, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
134 395 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (134 bp):
ATGAAGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGAATAGGAAGACAAGATCTGGTAT
CTTTGATCCACTTCGCTACCAATATAGGAAGACAGGATCTAGTATCTTTGATCTACTTCACGCCA
GTAC
Found at i:61867474 original size:44 final size:43
Alignment explanation
Indices: 61867417--61867499 Score: 121
Period size: 44 Copynumber: 1.9 Consensus size: 43
61867407 AACCTCTCCA
* * *
61867417 TTTTTTACTCAAAGCTCCCTTTGTAGGGTTTCACATTGGCCTT
1 TTTTTTACTCAAAGCGCCATTTGTAGGCTTTCACATTGGCCTT
*
61867460 TTTTTTGACTCAAAGCGCCATTTGTAGGCTTTCACCTTGG
1 TTTTTT-ACTCAAAGCGCCATTTGTAGGCTTTCACATTGG
61867500 TCCCACCTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
43 6 0.17
44 29 0.83
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.42
Consensus pattern (43 bp):
TTTTTTACTCAAAGCGCCATTTGTAGGCTTTCACATTGGCCTT
Found at i:61875153 original size:27 final size:26
Alignment explanation
Indices: 61875123--61875173 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
61875113 TTTAATATAT
61875123 ATATATATACCTATATAAAAAAAACCC
1 ATATATATA-CTATATAAAAAAAACCC
* * *
61875150 ATATGTATATTATATATAAAAAAC
1 ATATATATACTATATAAAAAAAAC
61875174 TATGCGTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.55, C:0.12, G:0.02, T:0.31
Consensus pattern (26 bp):
ATATATATACTATATAAAAAAAACCC
Found at i:61878070 original size:18 final size:18
Alignment explanation
Indices: 61878047--61878092 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
61878037 TTACTTATAA
*
61878047 ATATTTTTATAATTTTAT
1 ATATTTTTATAATCTTAT
61878065 ATATTTTTATAATCTTAT
1 ATATTTTTATAATCTTAT
*
61878083 GTATTTTTAT
1 ATATTTTTAT
61878093 CAAGAATGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (18 bp):
ATATTTTTATAATCTTAT
Found at i:61885437 original size:39 final size:39
Alignment explanation
Indices: 61885391--61885471 Score: 110
Period size: 39 Copynumber: 2.1 Consensus size: 39
61885381 ATAATTTAAA
* **
61885391 TTTATATATT-TCGTATATCATAATATTAATGAATTTGAG
1 TTTATATATTCT-ATATATCATAATATTAACAAATTTGAG
*
61885430 TTTATATATTCTATATATTATAATATTAACAAATTTGAG
1 TTTATATATTCTATATATCATAATATTAACAAATTTGAG
61885469 TTT
1 TTT
61885472 TTTAGTATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
39 36 0.97
40 1 0.03
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (39 bp):
TTTATATATTCTATATATCATAATATTAACAAATTTGAG
Found at i:61885518 original size:15 final size:15
Alignment explanation
Indices: 61885498--61885528 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
61885488 CATTTAGTTT
61885498 TAATTTTGGAAGTGA
1 TAATTTTGGAAGTGA
61885513 TAATTTTGGAAGTGA
1 TAATTTTGGAAGTGA
61885528 T
1 T
61885529 TTCAGTGATG
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:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (15 bp):
TAATTTTGGAAGTGA
Found at i:61894699 original size:14 final size:12
Alignment explanation
Indices: 61894680--61894726 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
61894670 CCCCTATCTG
61894680 TTATTAGTTATTT
1 TTATTA-TTATTT
61894693 ATTATTAATTATTT
1 -TTATT-ATTATTT
*
61894707 TTACTATTATTT
1 TTATTATTATTT
61894719 TTATTATT
1 TTATTATT
61894727 GTATAATATC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 14 0.47
13 4 0.13
14 11 0.37
15 1 0.03
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (12 bp):
TTATTATTATTT
Found at i:61894931 original size:27 final size:26
Alignment explanation
Indices: 61894877--61894939 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
61894867 TATATATATT
61894877 TAAATACATAT-TACTTTAATTTTCA
1 TAAATACATATATACTTTAATTTTCA
*
61894902 TAAATATATATATACATTTACATTTT-A
1 TAAATACATATATAC-TTTA-ATTTTCA
61894929 T-AATACATATA
1 TAAATACATATA
61894940 CATTTTCCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
25 10 0.30
26 12 0.36
27 6 0.18
28 5 0.15
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (26 bp):
TAAATACATATATACTTTAATTTTCA
Found at i:61894936 original size:18 final size:19
Alignment explanation
Indices: 61894908--61894945 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
61894898 TTCATAAATA
*
61894908 TATATATACATTTACATTT
1 TATATATACATATACATTT
61894927 TATA-ATACATATACATTT
1 TATATATACATATACATTT
61894945 T
1 T
61894946 CCAAACTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (19 bp):
TATATATACATATACATTT
Found at i:61896280 original size:3 final size:3
Alignment explanation
Indices: 61896272--61896314 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
61896262 TTCTAAAGCA
61896272 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
61896315 CATTAACCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:61896665 original size:21 final size:24
Alignment explanation
Indices: 61896623--61896666 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
61896613 AACTATCATT
61896623 TAAATATATATTATCTACTTTAACA
1 TAAATATATATTATCTA-TTTAACA
61896648 TAAATAT-T-TTATCT-TTTAA
1 TAAATATATATTATCTATTTAA
61896667 AAAATACTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 5 0.26
23 6 0.32
24 1 0.05
25 7 0.37
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (24 bp):
TAAATATATATTATCTATTTAACA
Found at i:61901639 original size:22 final size:22
Alignment explanation
Indices: 61901611--61901656 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
61901601 ATAAATAAGA
61901611 TTACTTTTCCCAGCAGATATCT
1 TTACTTTTCCCAGCAGATATCT
61901633 TTACTTTTCCCAGCAGATATCT
1 TTACTTTTCCCAGCAGATATCT
61901655 TT
1 TT
61901657 GTCCTTTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.26, G:0.09, T:0.43
Consensus pattern (22 bp):
TTACTTTTCCCAGCAGATATCT
Found at i:61903298 original size:22 final size:22
Alignment explanation
Indices: 61903244--61903304 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 22
61903234 TTGTACTATA
* *
61903244 CTTTATGTACTTGGTTTCTTTTT
1 CTTTATGTA-ATGCTTTCTTTTT
61903267 -TTTAAT-TAATGCTTTCTTTTT
1 CTTT-ATGTAATGCTTTCTTTTT
61903288 CTTTATGTAATTGCTTT
1 CTTTATGTAA-TGCTTT
61903305 GTATAAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
21 13 0.41
22 11 0.34
23 8 0.25
ACGTcount: A:0.15, C:0.11, G:0.10, T:0.64
Consensus pattern (22 bp):
CTTTATGTAATGCTTTCTTTTT
Found at i:61911722 original size:22 final size:20
Alignment explanation
Indices: 61911688--61911730 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 20
61911678 AGTTCTTTTT
61911688 TATTTCAAAAAATATATATACA
1 TATTTCAAAAAATA-A-ATACA
61911710 TATTT-AAAGAAATAAATACA
1 TATTTCAAA-AAATAAATACA
61911730 T
1 T
61911731 TAAATCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 6 0.30
21 4 0.20
22 10 0.50
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (20 bp):
TATTTCAAAAAATAAATACA
Found at i:61927451 original size:70 final size:69
Alignment explanation
Indices: 61927332--61927468 Score: 247
Period size: 70 Copynumber: 2.0 Consensus size: 69
61927322 TATGAATATT
61927332 TATTTACAGATATTATTATTTTAAAAAATAATATGAAGTACCTAGTGTTTTAAACTGGGTTAAAA
1 TATTTACAGATATTATTATTTTAAAAAATAATATGAAGTACCTAGTGTTTTAAACTGGGTTAAAA
61927397 TAAA
66 TAAA
* *
61927401 TATTTAGAGATATTATTATTTTAAAAAAATACTATGAAGTACCTAGTGTTTTAAACTGGGTTAAA
1 TATTTACAGATATTATTATTTT-AAAAAATAATATGAAGTACCTAGTGTTTTAAACTGGGTTAAA
61927466 ATA
65 ATA
61927469 TTTAAATATA
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
69 21 0.32
70 44 0.68
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.39
Consensus pattern (69 bp):
TATTTACAGATATTATTATTTTAAAAAATAATATGAAGTACCTAGTGTTTTAAACTGGGTTAAAA
TAAA
Found at i:61929287 original size:13 final size:13
Alignment explanation
Indices: 61929269--61929293 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
61929259 TTCAAATAAA
61929269 TTTTAAAATTTAT
1 TTTTAAAATTTAT
61929282 TTTTAAAATTTA
1 TTTTAAAATTTA
61929294 AAAATTATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTAAAATTTAT
Found at i:61929293 original size:20 final size:20
Alignment explanation
Indices: 61929265--61929302 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
61929255 AATATTCAAA
* *
61929265 TAAATTTTAAAATTTATTTT
1 TAAAATTTAAAAATTATTTT
61929285 TAAAATTTAAAAATTATT
1 TAAAATTTAAAAATTATT
61929303 AAAAAAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TAAAATTTAAAAATTATTTT
Found at i:61929309 original size:20 final size:19
Alignment explanation
Indices: 61929286--61929331 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
61929276 ATTTATTTTT
*
61929286 AAAATTTAAAAATTATTAAA
1 AAAATTTAAAAAGTA-TAAA
*
61929306 AAAATATAAAAAGTATAAA
1 AAAATTTAAAAAGTATAAA
*
61929325 AATATTT
1 AAAATTT
61929332 TTAAATTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (19 bp):
AAAATTTAAAAAGTATAAA
Found at i:61931166 original size:29 final size:29
Alignment explanation
Indices: 61931111--61931167 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
61931101 CTGGACCAAA
**
61931111 TTAGTCCCTATACTATTAAATTGATCAAT
1 TTAGTCCCTATACTATTAAAAAGATCAAT
*
61931140 TTAGTCCC-ATATTATTAAAAAGAATCAA
1 TTAGTCCCTATACTATTAAAAAG-ATCAA
61931168 ATAAGGCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (29 bp):
TTAGTCCCTATACTATTAAAAAGATCAAT
Found at i:61938091 original size:23 final size:23
Alignment explanation
Indices: 61938044--61938091 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
61938034 GATTAAAATT
* *
61938044 AAATTGTAATTTTTATAATAGTA
1 AAATTGTAATTTTTAAAAGAGTA
* *
61938067 AAATTTTAATTTTTAAAAGATTA
1 AAATTGTAATTTTTAAAAGAGTA
61938090 AA
1 AA
61938092 TCAAAATGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (23 bp):
AAATTGTAATTTTTAAAAGAGTA
Found at i:61942446 original size:21 final size:21
Alignment explanation
Indices: 61942405--61942447 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
61942395 AATAAAGTAG
*
61942405 ATTATATATTATTTTTATAGT
1 ATTATATATTATATTTATAGT
61942426 ATTATATATTATGATTT-TAGT
1 ATTATATATTAT-ATTTATAGT
61942447 A
1 A
61942448 AATTCATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (21 bp):
ATTATATATTATATTTATAGT
Found at i:61943622 original size:23 final size:22
Alignment explanation
Indices: 61943558--61943622 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 22
61943548 AAAGAGATAG
*
61943558 AATTTTTTATTTATTTCTAATTT
1 AATTTTTTATTTACTT-TAATTT
*
61943581 AA-TTTTTATTTAACGTTAATTTT
1 AATTTTTTATTT-ACTTTAA-TTT
61943604 AATTCTTTTATTTA-TTTAA
1 AATT-TTTTATTTACTTTAA
61943623 AAAAATCACG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
22 12 0.34
23 13 0.37
24 2 0.06
25 8 0.23
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.65
Consensus pattern (22 bp):
AATTTTTTATTTACTTTAATTT
Found at i:61945858 original size:21 final size:21
Alignment explanation
Indices: 61945832--61945873 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
61945822 CAATGAAAAT
*
61945832 TTTTGAACAA-TTTAATGATCA
1 TTTTGAA-AAGTTAAATGATCA
61945853 TTTTGAAAAGTTAAATGATCA
1 TTTTGAAAAGTTAAATGATCA
61945874 AAACAAACAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.40
Consensus pattern (21 bp):
TTTTGAAAAGTTAAATGATCA
Found at i:61958497 original size:45 final size:45
Alignment explanation
Indices: 61958446--61958535 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
61958436 TGGAACCATG
61958446 CCGATATTATATTGCGGTCCCTGGACTCGTTGGGGAGGGAAAACA
1 CCGATATTATATTGCGGTCCCTGGACTCGTTGGGGAGGGAAAACA
61958491 CCGATATTATATTGCGGTCCCTGGACTCGTTGGGGAGGGAAAACA
1 CCGATATTATATTGCGGTCCCTGGACTCGTTGGGGAGGGAAAACA
61958536 GCAGGCTGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.24
Consensus pattern (45 bp):
CCGATATTATATTGCGGTCCCTGGACTCGTTGGGGAGGGAAAACA
Found at i:61959147 original size:30 final size:30
Alignment explanation
Indices: 61959113--61959169 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
61959103 TGCATTTCCA
61959113 TTCTGCTGCTGAATTTGAGGAGCCAAAATG
1 TTCTGCTGCTGAATTTGAGGAGCCAAAATG
61959143 TTCTGCTGCTGAATTTGAGGAGCCAAA
1 TTCTGCTGCTGAATTTGAGGAGCCAAA
61959170 GGATATAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (30 bp):
TTCTGCTGCTGAATTTGAGGAGCCAAAATG
Found at i:61963782 original size:2 final size:2
Alignment explanation
Indices: 61963775--61963818 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
61963765 AATGATTCTA
*
61963775 AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG A- AG AG -G AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
61963815 -G AG A
1 AG AG A
61963819 AACTGGAATC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
1 3 0.08
2 34 0.92
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:61965315 original size:27 final size:27
Alignment explanation
Indices: 61965285--61965336 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
61965275 TTTTAGTCCT
61965285 GTGCCGCCATTCTCATTAGCACCACTG
1 GTGCCGCCATTCTCATTAGCACCACTG
*
61965312 GTGCCGCCATTCTCATTGGCACCAC
1 GTGCCGCCATTCTCATTAGCACCAC
61965337 CTTCAGCCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.17, C:0.38, G:0.19, T:0.25
Consensus pattern (27 bp):
GTGCCGCCATTCTCATTAGCACCACTG
Found at i:61974197 original size:2 final size:2
Alignment explanation
Indices: 61974192--61974216 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
61974182 GCCATATATA
61974192 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
61974217 ATACACTCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:61983727 original size:29 final size:31
Alignment explanation
Indices: 61983656--61983732 Score: 104
Period size: 29 Copynumber: 2.5 Consensus size: 31
61983646 TTAACGACTC
* *
61983656 AGTGACTAAAATGTTACAATACTATAACGTA
1 AGTGACTAAAATGTAACAATACTATAACATA
**
61983687 AGTGACTAAAATGTAAC-ATTTTA-AACATA
1 AGTGACTAAAATGTAACAATACTATAACATA
61983716 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
61983733 CTGAGGTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 22 0.52
30 4 0.10
31 16 0.38
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.29
Consensus pattern (31 bp):
AGTGACTAAAATGTAACAATACTATAACATA
Found at i:61983750 original size:31 final size:29
Alignment explanation
Indices: 61983686--61983754 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
61983676 ACTATAACGT
** *
61983686 AAGTGACTAAAATGTAACATTTTAAACAT
1 AAGTGACTAAAATGTAACATGGTAAACAA
*
61983715 AAGTGACTAAAATGTAACCTGAGGTAAACAA
1 AAGTGACTAAAATGTAACAT--GGTAAACAA
61983746 AAGTGACTA
1 AAGTGACTA
61983755 TTTTAGTAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.56
31 15 0.44
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.25
Consensus pattern (29 bp):
AAGTGACTAAAATGTAACATGGTAAACAA
Found at i:61989032 original size:23 final size:23
Alignment explanation
Indices: 61988994--61989048 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
61988984 TTCTACCATG
* **
61988994 AATTTTTAAAATAAAACTTAATTT
1 AATTTTTAATATAAAAAATAA-TT
61989018 AATTTTTAATA-AAAAAATAATT
1 AATTTTTAATATAAAAAATAATT
61989040 -ATTTTTAAT
1 AATTTTTAAT
61989049 CTAATATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.32
22 2 0.07
23 7 0.25
24 10 0.36
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
AATTTTTAATATAAAAAATAATT
Found at i:61992235 original size:18 final size:20
Alignment explanation
Indices: 61992179--61992281 Score: 64
Period size: 18 Copynumber: 5.5 Consensus size: 20
61992169 ATAAAAAATC
*
61992179 AAATATTAAAAATTAG-AATA
1 AAATA-TAAAAATTAGTAAGA
* *
61992199 AAATATAAAAA--AGAAAAA
1 AAATATAAAAATTAGTAAGA
61992217 AAATATAAAAATT-GT-A-A
1 AAATATAAAAATTAGTAAGA
* *
61992234 AATTGTATAAAATTAGTAAGA
1 AAATATA-AAAATTAGTAAGA
*
61992255 AATTATAAAAA-TA-T-AG-
1 AAATATAAAAATTAGTAAGA
61992271 AAATATAAAAA
1 AAATATAAAAA
61992282 ACTTATAAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 18
0.74 0.06 0.19
Matches are distributed among these distances:
16 10 0.14
17 10 0.14
18 22 0.31
19 11 0.16
20 10 0.14
21 7 0.10
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (20 bp):
AAATATAAAAATTAGTAAGA
Found at i:61992245 original size:27 final size:27
Alignment explanation
Indices: 61992215--61992310 Score: 79
Period size: 27 Copynumber: 3.5 Consensus size: 27
61992205 AAAAAAGAAA
* *
61992215 AAAAATATAAAAATTGTAAAATTGTAT
1 AAAAATATAAAAATTATAAAATTATAT
*
61992242 AAAATTAGTAAGAAATTATAAAA--ATAT
1 AAAAATA-TAA-AAATTATAAAATTATAT
* *
61992269 AGAAATATAAAAAACTTATAAAATTTTAT
1 AAAAATAT-AAAAA-TTATAAAATTATAT
**
61992298 AAAGTTATAAAAA
1 AAAAATATAAAAA
61992311 ATGTAAAGAA
Statistics
Matches: 54, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
26 4 0.07
27 24 0.44
28 8 0.15
29 18 0.33
ACGTcount: A:0.61, C:0.01, G:0.06, T:0.31
Consensus pattern (27 bp):
AAAAATATAAAAATTATAAAATTATAT
Done.