Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397257.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_95.0, 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: 12062019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 103452 characters in sequence are not A, C, G, or T
File 12 of 26
Found at i:4356521 original size:16 final size:15
Alignment explanation
Indices: 4356499--4356535 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
4356489 TTATTCAAAC
4356499 TTTTATTATTTTGAT
1 TTTTATTATTTTGAT
*
4356514 TCTTTATTATTTTTAT
1 T-TTTATTATTTTGAT
4356530 TTTTAT
1 TTTTAT
4356536 AATGTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTTATTATTTTGAT
Found at i:4359221 original size:23 final size:24
Alignment explanation
Indices: 4359194--4359241 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
4359184 ATTTTTCTTG
4359194 ATAGACACAACTGTCTA-TTTCTA
1 ATAGACACAACTGTCTATTTTCTA
*
4359217 ATAGACACAATTGTCTATTTTCTA
1 ATAGACACAACTGTCTATTTTCTA
4359241 A
1 A
4359242 CAAATATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (24 bp):
ATAGACACAACTGTCTATTTTCTA
Found at i:4364423 original size:2 final size:2
Alignment explanation
Indices: 4364416--4364453 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
4364406 GTTAGTATTT
4364416 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4364454 TTTAGATATT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:4366688 original size:30 final size:29
Alignment explanation
Indices: 4366652--4366727 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 29
4366642 ATCATTAGTC
*
4366652 ATAAAGGCTTATTTGATCTAAAATAAAAGTA
1 ATAAAGGCTTATTTGATC-AAAATAAAA-AA
* * * *
4366683 A-AAAGGTTTAATTGAACACAATAAAAAA
1 ATAAAGGCTTATTTGATCAAAATAAAAAA
*
4366711 ATAAATGCTTATTTGAT
1 ATAAAGGCTTATTTGAT
4366728 TTTTCTTAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
28 2 0.06
29 19 0.54
30 13 0.37
31 1 0.03
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.32
Consensus pattern (29 bp):
ATAAAGGCTTATTTGATCAAAATAAAAAA
Found at i:4368032 original size:9 final size:9
Alignment explanation
Indices: 4368018--4368045 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
4368008 TTTATTCAAA
4368018 TTTTTAATT
1 TTTTTAATT
4368027 TTTTTAATT
1 TTTTTAATT
4368036 TTTTTAATT
1 TTTTTAATT
4368045 T
1 T
4368046 CTCTATCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTAATT
Found at i:4368126 original size:9 final size:9
Alignment explanation
Indices: 4368112--4368155 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
4368102 GATAAAATTT
4368112 TTATTTATA
1 TTATTTATA
4368121 TTATTTA-A
1 TTATTTATA
4368129 TTAATTTATA
1 TT-ATTTATA
4368139 TTA-TTATTA
1 TTATTTA-TA
4368148 TTATTTAT
1 TTATTTAT
4368156 TTTTTTCAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
8 6 0.19
9 19 0.61
10 6 0.19
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TTATTTATA
Found at i:4368326 original size:15 final size:16
Alignment explanation
Indices: 4368306--4368339 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
4368296 TATTATGTGG
*
4368306 ATTTT-ATTTTTAATA
1 ATTTTAATTTTTAAAA
4368321 ATTTTAATTTTTAAAA
1 ATTTTAATTTTTAAAA
4368337 ATT
1 ATT
4368340 AAAAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTTAATTTTTAAAA
Found at i:4373665 original size:20 final size:20
Alignment explanation
Indices: 4373637--4373675 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4373627 ATTTTCTTGT
*
4373637 CGTACTCCTTCATTCTATTC
1 CGTAATCCTTCATTCTATTC
*
4373657 CGTAATCCTTTATTCTATT
1 CGTAATCCTTCATTCTATT
4373676 ATGGAAGTTT
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:0.18, C:0.28, G:0.05, T:0.49
Consensus pattern (20 bp):
CGTAATCCTTCATTCTATTC
Found at i:4375934 original size:45 final size:45
Alignment explanation
Indices: 4375868--4375964 Score: 110
Period size: 45 Copynumber: 2.2 Consensus size: 45
4375858 NNNNNNNNNN
* *
4375868 CCGTTCTGGTTTACTGTAGATCGCACC-GTCGCACCCGCACCTTT-T
1 CCGTTCTGGTTTACTGCAGATCGCACCACT-GCACCCGCA-CTTTCT
* *
4375913 CCGTTCTGGTTT-GTCGCAGATCGCACCACTGGACCCGCACTTTCT
1 CCGTTCTGGTTTACT-GCAGATCGCACCACTGCACCCGCACTTTCT
4375958 CCGTTCT
1 CCGTTCT
4375965 ATTTTGCTGC
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
44 5 0.11
45 39 0.87
46 1 0.02
ACGTcount: A:0.12, C:0.36, G:0.21, T:0.31
Consensus pattern (45 bp):
CCGTTCTGGTTTACTGCAGATCGCACCACTGCACCCGCACTTTCT
Found at i:4378613 original size:28 final size:28
Alignment explanation
Indices: 4378566--4378619 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
4378556 ATTTGAAATT
*
4378566 TTATTTATATTTGATGTAATATATTTAC
1 TTATTTATATTTGATATAATATATTTAC
* * *
4378594 TTATTTATTTTTGGTATAATTTATTT
1 TTATTTATATTTGATATAATATATTT
4378620 GTTTGTAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (28 bp):
TTATTTATATTTGATATAATATATTTAC
Found at i:4388128 original size:2 final size:2
Alignment explanation
Indices: 4388121--4388147 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4388111 AAGGCAAAGG
4388121 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
4388148 GGAATATATA
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4392382 original size:14 final size:14
Alignment explanation
Indices: 4392342--4392382 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
4392332 ACCTCATGAA
*
4392342 AAAAAAAACTTTATT
1 AAAAAAAAC-TTAAT
4392357 AAAAAAAACTTAAT
1 AAAAAAAACTTAAT
*
4392371 AATAAAAACTTA
1 AAAAAAAACTTA
4392383 GTGAAGAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 15 0.62
15 9 0.38
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (14 bp):
AAAAAAAACTTAAT
Found at i:4392473 original size:15 final size:15
Alignment explanation
Indices: 4392453--4392490 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
4392443 AAAACTTTAT
4392453 AAAAAAACTT-AGTGA
1 AAAAAAACTTGA-TGA
*
4392468 AAAAAATCTTGATGA
1 AAAAAAACTTGATGA
4392483 AAAAAAAC
1 AAAAAAAC
4392491 ATTTTAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 19 0.95
16 1 0.05
ACGTcount: A:0.63, C:0.08, G:0.11, T:0.18
Consensus pattern (15 bp):
AAAAAAACTTGATGA
Found at i:4394000 original size:23 final size:24
Alignment explanation
Indices: 4393974--4394025 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
4393964 TTTTTTCTTC
*
4393974 TTTTTAAGTATTCTT-TCAAGTTA
1 TTTTTAAGTATTCTTATAAAGTTA
** *
4393997 TTTTTATTTGTTCTTATAAAGTTA
1 TTTTTAAGTATTCTTATAAAGTTA
4394021 TTTTT
1 TTTTT
4394026 TCATAATAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.23, C:0.06, G:0.08, T:0.63
Consensus pattern (24 bp):
TTTTTAAGTATTCTTATAAAGTTA
Found at i:4394162 original size:40 final size:42
Alignment explanation
Indices: 4394047--4394172 Score: 175
Period size: 46 Copynumber: 3.0 Consensus size: 42
4394037 TATCAGTGCG
* *
4394047 ATCCTCTAATCTCTCTCACCCTCAAGCTTCACAAAGTCGACG
1 ATCCTATAATCTCTCTCACCCTCAAGCTTCACAAAGTCGACA
*
4394089 ATCCTATAATCTCTCACCCTCACCCTCAAGCTTCACAAAGTTGACA
1 ATCCTATAATCTCT----CTCACCCTCAAGCTTCACAAAGTCGACA
4394135 ATCCTATAAT-T-TCTCACCCTCAAGCTTCACAAAGTCGA
1 ATCCTATAATCTCTCTCACCCTCAAGCTTCACAAAGTCGA
4394173 AGTTCAATTT
Statistics
Matches: 76, Mismatches: 4, Indels: 10
0.84 0.04 0.11
Matches are distributed among these distances:
40 25 0.33
42 13 0.17
44 1 0.01
45 1 0.01
46 36 0.47
ACGTcount: A:0.29, C:0.36, G:0.08, T:0.27
Consensus pattern (42 bp):
ATCCTATAATCTCTCTCACCCTCAAGCTTCACAAAGTCGACA
Found at i:4396150 original size:8 final size:8
Alignment explanation
Indices: 4396137--4396171 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
4396127 TTCTGTCTAC
4396137 TTTTTCTT
1 TTTTTCTT
4396145 TTTTTCTT
1 TTTTTCTT
*
4396153 TCTTTCTT
1 TTTTTCTT
4396161 TTTCTTCTT
1 TTT-TTCTT
4396170 TT
1 TT
4396172 CTTCCTTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTCTT
Found at i:4396186 original size:22 final size:22
Alignment explanation
Indices: 4396136--4396186 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
4396126 CTTCTGTCTA
* *
4396136 CTTTTTCTTTTTTTCTTTCTTT
1 CTTTTTCTTCTTTTCTTTCCTT
4396158 CTTTTTCTTCTTTTC-TTCCTT
1 CTTTTTCTTCTTTTCTTTCCTT
4396179 CTTCTTTC
1 CTT-TTTC
4396187 CCTCGCCGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (22 bp):
CTTTTTCTTCTTTTCTTTCCTT
Found at i:4396216 original size:16 final size:15
Alignment explanation
Indices: 4396196--4396245 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
4396186 CCCTCGCCGA
4396196 TTCTTTCTCCTTTTC
1 TTCTTTCTCCTTTTC
*
4396211 TCTCTTT-TTCTTTTC
1 T-TCTTTCTCCTTTTC
*
4396226 TTCCCTTCTCC-TTTC
1 TT-CTTTCTCCTTTTC
4396241 TTCTT
1 TTCTT
4396246 CCGCCGTCGG
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
14 3 0.11
15 18 0.64
16 7 0.25
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (15 bp):
TTCTTTCTCCTTTTC
Found at i:4405790 original size:12 final size:12
Alignment explanation
Indices: 4405773--4405797 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4405763 TGCTAAGGGA
4405773 GAAGGACGGAAG
1 GAAGGACGGAAG
4405785 GAAGGACGGAAG
1 GAAGGACGGAAG
4405797 G
1 G
4405798 CGGTAGCTTT
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:0.40, C:0.08, G:0.52, T:0.00
Consensus pattern (12 bp):
GAAGGACGGAAG
Found at i:4407746 original size:20 final size:19
Alignment explanation
Indices: 4407723--4407767 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
4407713 AGAGGGGGGG
4407723 AGAGAGAA-AGAGAAGAAAGA
1 AGAGAGAAGA-AGAA-AAAGA
4407743 AGAGAGAAGAAGAAAAAGA
1 AGAGAGAAGAAGAAAAAGA
4407762 ACGAGA
1 A-GAGA
4407768 ATGTTGGGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.26
20 16 0.70
21 1 0.04
ACGTcount: A:0.64, C:0.02, G:0.33, T:0.00
Consensus pattern (19 bp):
AGAGAGAAGAAGAAAAAGA
Found at i:4410145 original size:2 final size:2
Alignment explanation
Indices: 4410138--4410164 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4410128 CTCAAATCTT
4410138 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4410165 GATAGAGAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4411660 original size:2 final size:2
Alignment explanation
Indices: 4411653--4411682 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4411643 GCCAAAATCA
4411653 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
4411683 TACGAAGATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4412545 original size:20 final size:20
Alignment explanation
Indices: 4412501--4412539 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
4412491 GATACCATAT
4412501 CATCAAATTCAATATCACGC
1 CATCAAATTCAATATCACGC
*
4412521 CATCAGATTCAATATCACG
1 CATCAAATTCAATATCACG
4412540 TTATCATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.28, G:0.08, T:0.26
Consensus pattern (20 bp):
CATCAAATTCAATATCACGC
Found at i:4415855 original size:13 final size:13
Alignment explanation
Indices: 4415837--4415866 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4415827 GGTACATAAT
4415837 AATAATAAACAAC
1 AATAATAAACAAC
*
4415850 AATAATAAACAAT
1 AATAATAAACAAC
4415863 AATA
1 AATA
4415867 CTCAATCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.10, G:0.00, T:0.20
Consensus pattern (13 bp):
AATAATAAACAAC
Found at i:4416915 original size:16 final size:17
Alignment explanation
Indices: 4416896--4416939 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
4416886 AATTTTTTAA
4416896 TTAAATAAAA-AATTAT
1 TTAAATAAAATAATTAT
4416912 TTAAGAATAAAATAATTAT
1 TT-A-AATAAAATAATTAT
*
4416931 TTTAATAAA
1 TTAAATAAA
4416940 TTTTTAATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 2 0.08
17 7 0.29
18 7 0.29
19 8 0.33
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
TTAAATAAAATAATTAT
Found at i:4417517 original size:2 final size:2
Alignment explanation
Indices: 4417504--4417556 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
4417494 GCCTTTTATG
*
4417504 TA TA TG 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
4417546 TA TA TA TA TA T
1 TA TA TA TA TA T
4417557 TTGGCTTAGT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4418459 original size:2 final size:2
Alignment explanation
Indices: 4418452--4418500 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
4418442 CAACGTATCC
4418452 TA TA TA TA T- TA TA T- 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
4418492 TA TA TA TA T
1 TA TA TA TA T
4418501 TTGTGTCCCT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:4428289 original size:16 final size:17
Alignment explanation
Indices: 4428268--4428308 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
4428258 TTATTCAAAT
4428268 AACTAAAATTAAA-GAA
1 AACTAAAATTAAATGAA
*
4428284 AACTAAAATTAAATTAA
1 AACTAAAATTAAATGAA
4428301 AACTAAAA
1 AACTAAAA
4428309 AAACGAGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.68, C:0.07, G:0.02, T:0.22
Consensus pattern (17 bp):
AACTAAAATTAAATGAA
Found at i:4432544 original size:12 final size:12
Alignment explanation
Indices: 4432527--4432565 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
4432517 TTTTCAACCA
4432527 CAACATCTTTTT
1 CAACATCTTTTT
*
4432539 CAACATCTTTCT
1 CAACATCTTTTT
* *
4432551 CAACTTTTTTTT
1 CAACATCTTTTT
4432563 CAA
1 CAA
4432566 TGTCTTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.49
Consensus pattern (12 bp):
CAACATCTTTTT
Found at i:4433827 original size:21 final size:21
Alignment explanation
Indices: 4433803--4433843 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4433793 ATTTCTGAAA
*
4433803 AATGCAGCTAAACTTTGAATT
1 AATGCAGATAAACTTTGAATT
*
4433824 AATGCAGATTAACTTTGAAT
1 AATGCAGATAAACTTTGAAT
4433844 GACTACATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (21 bp):
AATGCAGATAAACTTTGAATT
Found at i:4434879 original size:17 final size:16
Alignment explanation
Indices: 4434850--4434883 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
4434840 CTACAAAAAC
*
4434850 ATAAAATTTAACTTAA
1 ATAAAATTAAACTTAA
4434866 ATAATAATTAAACTTAA
1 ATAA-AATTAAACTTAA
4434883 A
1 A
4434884 ATAGAACATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAAAATTAAACTTAA
Found at i:4449261 original size:37 final size:37
Alignment explanation
Indices: 4449211--4449286 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
4449201 TCACTTTATT
*
4449211 CATTGCTTGGCTTTAATTTTGGTTTAGTTTAAAAGAA
1 CATTGCTTGGCTTTAATTTTGGTTTAGTTTAAAAAAA
*
4449248 CATTGCTTGGCTTTAATTTTGGTTTGGTTTAAAAAAA
1 CATTGCTTGGCTTTAATTTTGGTTTAGTTTAAAAAAA
4449285 CA
1 CA
4449287 ATCCTACTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.28, C:0.09, G:0.18, T:0.45
Consensus pattern (37 bp):
CATTGCTTGGCTTTAATTTTGGTTTAGTTTAAAAAAA
Found at i:4456939 original size:32 final size:31
Alignment explanation
Indices: 4456898--4456957 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
4456888 TAGGTTATGC
* * *
4456898 TTAAAAAGTACGTTTACAAAGTATTAAAGGT
1 TTAAAAAGTACATTTAAAAAGTACTAAAGGT
4456929 TTAAAGAAGTACATTTAAAAAGTACTAAA
1 TTAAA-AAGTACATTTAAAAAGTACTAAA
4456958 TATTTTGGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 5 0.20
32 20 0.80
ACGTcount: A:0.50, C:0.07, G:0.13, T:0.30
Consensus pattern (31 bp):
TTAAAAAGTACATTTAAAAAGTACTAAAGGT
Found at i:4462261 original size:33 final size:33
Alignment explanation
Indices: 4462219--4462338 Score: 170
Period size: 33 Copynumber: 3.6 Consensus size: 33
4462209 AATATATTAA
4462219 AAATGAAAATAAAATATATAAGATTTTAATAAT
1 AAATGAAAATAAAATATATAAGATTTTAATAAT
* * **
4462252 AAATGAAAATAAAATATATGACATTAAAAATATATT
1 AAATGAAAATAAAATATATAAGATT-TTAATA-A-T
4462288 AAATGAAAATAAAATATATAAGATTTTAATAAT
1 AAATGAAAATAAAATATATAAGATTTTAATAAT
4462321 AAATG-AAATAAAATATAT
1 AAATGAAAATAAAATATAT
4462339 GACATAAAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
32 13 0.17
33 29 0.38
34 5 0.07
35 5 0.07
36 24 0.32
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.32
Consensus pattern (33 bp):
AAATGAAAATAAAATATATAAGATTTTAATAAT
Found at i:4462307 original size:69 final size:70
Alignment explanation
Indices: 4462182--4462359 Score: 276
Period size: 69 Copynumber: 2.6 Consensus size: 70
4462172 TAGGTAAAAC
* *
4462182 AAATTAAAATAAAATATA--AAATATAAAAATATATTAAAAATGAAAATAAAATATATAAGATTT
1 AAATGAAAATAAAATATATGACAT-TAAAAATATATT-AAAATGAAAATAAAATATATAAGATTT
4462245 TAATAAT
64 TAATAAT
4462252 AAATGAAAATAAAATATATGACATTAAAAATATATT-AAATGAAAATAAAATATATAAGATTTTA
1 AAATGAAAATAAAATATATGACATTAAAAATATATTAAAATGAAAATAAAATATATAAGATTTTA
4462316 ATAAT
66 ATAAT
4462321 AAATG-AAATAAAATATATGACA-TAAAAATATATTTAAAA
1 AAATGAAAATAAAATATATGACATTAAAAATATA-TTAAAA
4462360 ATGATATTAT
Statistics
Matches: 102, Mismatches: 2, Indels: 9
0.90 0.02 0.08
Matches are distributed among these distances:
67 10 0.10
68 19 0.19
69 41 0.40
70 17 0.17
71 12 0.12
72 3 0.03
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (70 bp):
AAATGAAAATAAAATATATGACATTAAAAATATATTAAAATGAAAATAAAATATATAAGATTTTA
ATAAT
Found at i:4462399 original size:29 final size:31
Alignment explanation
Indices: 4462257--4462400 Score: 75
Period size: 32 Copynumber: 4.5 Consensus size: 31
4462247 ATAATAAATG
*
4462257 AAAATA-AAATATATGACATTAAAAATATATTAA
1 AAAATATAAATATATGACA-TAATAATA-A-TAA
* * **
4462290 ATGAAA-ATAAAATATATAAGATTTTAATAATAA
1 A--AAATAT-AAATATATGACATAATAATAATAA
* *
4462323 ATGAAATA-AAATATATGACATAAAAATATATTTA
1 A--AAATATAAATATATGACATAATAATA-A-TAA
*
4462357 AAAATGAT-ATTATATGA-A-AATAATAATAA
1 AAAAT-ATAAATATATGACATAATAATAATAA
4462386 AAAATATAAATATAT
1 AAAATATAAATATAT
4462401 TAAACTTGTA
Statistics
Matches: 86, Mismatches: 15, Indels: 24
0.69 0.12 0.19
Matches are distributed among these distances:
28 2 0.02
29 13 0.15
30 1 0.01
31 6 0.07
32 20 0.23
33 20 0.23
34 6 0.07
35 8 0.09
36 10 0.12
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (31 bp):
AAAATATAAATATATGACATAATAATAATAA
Found at i:4462600 original size:15 final size:15
Alignment explanation
Indices: 4462552--4462620 Score: 93
Period size: 15 Copynumber: 4.6 Consensus size: 15
4462542 TTTTCCCTGT
*
4462552 AATCACATTGCTTGC
1 AATCACATTACTTGC
*
4462567 AATAACATTACTTGC
1 AATCACATTACTTGC
4462582 AATCACATTACTTGC
1 AATCACATTACTTGC
* * *
4462597 AATCACACTACCTGT
1 AATCACATTACTTGC
4462612 AATCACATT
1 AATCACATT
4462621 GCATTGTAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.35, C:0.26, G:0.07, T:0.32
Consensus pattern (15 bp):
AATCACATTACTTGC
Found at i:4463514 original size:2 final size:2
Alignment explanation
Indices: 4463503--4463543 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
4463493 TTTGCAATGT
4463503 TA TA -A 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
4463544 GATTTCAAGG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4463715 original size:37 final size:39
Alignment explanation
Indices: 4463642--4463734 Score: 102
Period size: 37 Copynumber: 2.4 Consensus size: 39
4463632 TTAAAGGAAG
* * * *
4463642 AAGAAATTAGAATAAAATATATAATATAGGAAATTATAGT
1 AAGAAATGAAAATAAAAAATATAATATA-GAAATTATAAT
*
4463682 AAGAAATGAAAATAAAAAATAT-ATATA-AGATTATAAT
1 AAGAAATGAAAATAAAAAATATAATATAGAAATTATAAT
*
4463719 AAGAGATGAAAA-AAAA
1 AAGAAATGAAAATAAAA
4463735 TATGACATTA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
36 4 0.09
37 19 0.40
39 5 0.11
40 19 0.40
ACGTcount: A:0.63, C:0.00, G:0.12, T:0.25
Consensus pattern (39 bp):
AAGAAATGAAAATAAAAAATATAATATAGAAATTATAAT
Found at i:4472027 original size:15 final size:16
Alignment explanation
Indices: 4472007--4472038 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
4471997 TTACAAATCT
4472007 TTGATTTTATTT-TTC
1 TTGATTTTATTTATTC
4472022 TTGATTTTATTTATTC
1 TTGATTTTATTTATTC
4472038 T
1 T
4472039 GTGGGAGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.16, C:0.06, G:0.06, T:0.72
Consensus pattern (16 bp):
TTGATTTTATTTATTC
Found at i:4472397 original size:24 final size:24
Alignment explanation
Indices: 4472348--4472404 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
4472338 AAGATCAATC
*
4472348 AAAATAAAAATGAAAAATAGACAAA
1 AAAAT-AAAATGAAAAAAAGACAAA
*
4472373 AACATAAAATGAAAAAAAGGA-AAA
1 AAAATAAAATGAAAAAAA-GACAAA
4472397 AAAATAAA
1 AAAATAAA
4472405 TAATAAGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 22 0.79
25 6 0.21
ACGTcount: A:0.77, C:0.04, G:0.09, T:0.11
Consensus pattern (24 bp):
AAAATAAAATGAAAAAAAGACAAA
Found at i:4472823 original size:50 final size:50
Alignment explanation
Indices: 4472751--4472850 Score: 148
Period size: 50 Copynumber: 2.0 Consensus size: 50
4472741 AAAAATCCCT
* *
4472751 CCATTGAGGTTTCAATATCTTAAGAATTCC-TCTACCGAGGTTCCAATATC
1 CCATCGAGGTTTCAATATCTTAAGAA-TCCTTCTACCGAGGATCCAATATC
* *
4472801 CCATCGAGGTTTTAATATCTTAAGAATCCTTCTACCGAGGATCTAATATC
1 CCATCGAGGTTTCAATATCTTAAGAATCCTTCTACCGAGGATCCAATATC
4472851 TTAAAAATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
49 3 0.07
50 42 0.93
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (50 bp):
CCATCGAGGTTTCAATATCTTAAGAATCCTTCTACCGAGGATCCAATATC
Found at i:4472840 original size:31 final size:31
Alignment explanation
Indices: 4472803--4473045 Score: 149
Period size: 31 Copynumber: 7.8 Consensus size: 31
4472793 CCAATATCCC
*
4472803 ATCGAGGTTTTAATATCTTAAGAATCCTTCT
1 ATCGAGGTTCTAATATCTTAAGAATCCTTCT
* * *
4472834 ACCGAGGATCTAATATCTTAAAAAT--TTCT
1 ATCGAGGTTCTAATATCTTAAGAATCCTTCT
* * * *
4472863 CCACCGAAGTT-TAAACATCTTAAAAATTTCC-TCT
1 --ATCGAGGTTCT-AATATCTTAAGAA--TCCTTCT
* * * *
4472897 ATTGAGGATCTAATAACTTGAGAATTCC-TC-
1 ATCGAGGTTCTAATATCTTAAGAA-TCCTTCT
* * * * *
4472927 AACTAAGGTTCGAACATCTTAAGAATTCTTCT
1 ATC-GAGGTTCTAATATCTTAAGAATCCTTCT
* * * * *
4472959 ATTGAGGTTCCAACATCTTAAGAATTCTTTT
1 ATCGAGGTTCTAATATCTTAAGAATCCTTCT
*
4472990 ATCGAGGTTCCAATATCTTAAGAATCCCTT-T
1 ATCGAGGTTCTAATATCTTAAGAAT-CCTTCT
*
4473021 ATCGAGGATCTAATATCTTAAGAAT
1 ATCGAGGTTCTAATATCTTAAGAAT
4473046 TACTCCATCA
Statistics
Matches: 166, Mismatches: 34, Indels: 24
0.74 0.15 0.11
Matches are distributed among these distances:
29 4 0.02
30 4 0.02
31 135 0.81
32 18 0.11
33 2 0.01
34 3 0.02
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (31 bp):
ATCGAGGTTCTAATATCTTAAGAATCCTTCT
Found at i:4473060 original size:62 final size:62
Alignment explanation
Indices: 4472817--4473065 Score: 204
Period size: 62 Copynumber: 4.0 Consensus size: 62
4472807 AGGTTTTAAT
* * * *
4472817 ATCTTAAGAATCCTTCTACCGAGGATCTAATATCTTAAAAATTTCTCCACCGAA-GTTTAAAC
1 ATCTTAAGAATCCTTCTATCGAGGATCTAATATCTTAAGAA-TTCTCCATCGAAGGTTCAAAC
* * * * * * *
4472879 ATCTTAAAAATTTCC-TCTATTGAGGATCTAATAACTTGAGAATTC-CTCAACTAAGGTTCGAAC
1 ATCTTAAGAA--TCCTTCTATCGAGGATCTAATATCTTAAGAATTCTC-CATCGAAGGTTCAAAC
* * * * * ** * *
4472942 ATCTTAAGAATTCTTCTATTGAGGTTCCAACATCTTAAGAATTCTTTTATCG-AGGTTCCAAT
1 ATCTTAAGAATCCTTCTATCGAGGATCTAATATCTTAAGAATTC-TCCATCGAAGGTTCAAAC
4473004 ATCTTAAGAATCCCTT-TATCGAGGATCTAATATCTTAAGAATTACTCCATC-AAGGTTACAAA
1 ATCTTAAGAAT-CCTTCTATCGAGGATCTAATATCTTAAGAATT-CTCCATCGAAGGTT-CAAA
4473066 AAGAAACATC
Statistics
Matches: 145, Mismatches: 31, Indels: 21
0.74 0.16 0.11
Matches are distributed among these distances:
61 3 0.02
62 93 0.64
63 46 0.32
64 3 0.02
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.35
Consensus pattern (62 bp):
ATCTTAAGAATCCTTCTATCGAGGATCTAATATCTTAAGAATTCTCCATCGAAGGTTCAAAC
Found at i:4480901 original size:3 final size:3
Alignment explanation
Indices: 4480893--4480932 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
4480883 ACCAAATTTA
4480893 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 A
4480933 CTGCAATATT
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:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:4490547 original size:36 final size:36
Alignment explanation
Indices: 4490460--4490549 Score: 117
Period size: 36 Copynumber: 2.5 Consensus size: 36
4490450 TTAATTGTTT
* * *
4490460 AATTTAATTAATTAGACCCAACAACTTAATTAAACA
1 AATTTAATCAATTAGGCCCAACAACTTAATTAAAAA
* * **
4490496 ATTTTAATCAATTAGGGCCAATGACTTAATTAAAAA
1 AATTTAATCAATTAGGCCCAACAACTTAATTAAAAA
4490532 AATTTAATCAATTAGGCC
1 AATTTAATCAATTAGGCC
4490550 TAAAACTGTT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (36 bp):
AATTTAATCAATTAGGCCCAACAACTTAATTAAAAA
Found at i:4494194 original size:13 final size:13
Alignment explanation
Indices: 4494176--4494202 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4494166 AATTTATTGT
4494176 TAAATTATTAATA
1 TAAATTATTAATA
4494189 TAAATTATTAATA
1 TAAATTATTAATA
4494202 T
1 T
4494203 TTTTAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TAAATTATTAATA
Found at i:4494235 original size:20 final size:20
Alignment explanation
Indices: 4494175--4494238 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
4494165 TAATTTATTG
*
4494175 TTAAATTATTAATATAAATTA
1 TTAAATTATTAA-ATAATTTA
* **
4494196 TTAATATT-TTTAATTTTTTA
1 TTAA-ATTATTAAATAATTTA
*
4494216 TTAAATTATTGAATAATTTA
1 TTAAATTATTAAATAATTTA
4494236 TTA
1 TTA
4494239 TTAACTTGGT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
19 3 0.09
20 21 0.62
21 7 0.21
22 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAAATTATTAAATAATTTA
Found at i:4494495 original size:144 final size:144
Alignment explanation
Indices: 4494213--4494477 Score: 353
Period size: 144 Copynumber: 1.9 Consensus size: 144
4494203 TTTTAATTTT
* * * * * *
4494213 TTATTAAATTATTGAATAATTTATTATTAACTTGGTTATATGATTTTTAATTTTAATTATTTGAA
1 TTATGAAATTATTAAATAATTTATTATTAAATTAGTTATATAATTTTTAATTTTAATCATTTGAA
* * *
4494278 TTATTTTTCTCTATTTGTATTTTTTATTTCTTAATCTTTTAATTTCTATTTTCATTAAAAATTAA
66 TAATTTTTCTCCATTTGTATTTTTTATTTCTTAATCTTTT-ATTTCTATTTTCATTAAAAAATAA
4494343 TACTTTATTATGAAA
130 TACTTTATTATGAAA
*
4494358 TTATGAAATTATTAAATAATTTA-TATTAAATTAGTTATATAATTTTTTATTTTAATCATTTGAA
1 TTATGAAATTATTAAATAATTTATTATTAAATTAGTTATATAATTTTTAATTTTAATCATTTGAA
*
4494422 TAATTTTTCTCCA-TT-TACTTTTTTCATTTTTTAATCTTTT-TCTT-T-TTTTCATTAAA
66 TAATTTTTCTCCATTTGTA-TTTTTT-ATTTCTTAATCTTTTAT-TTCTATTTTCATTAAA
4494478 TATCAATAAT
Statistics
Matches: 107, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
141 11 0.10
142 4 0.04
143 10 0.09
144 61 0.57
145 21 0.20
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.58
Consensus pattern (144 bp):
TTATGAAATTATTAAATAATTTATTATTAAATTAGTTATATAATTTTTAATTTTAATCATTTGAA
TAATTTTTCTCCATTTGTATTTTTTATTTCTTAATCTTTTATTTCTATTTTCATTAAAAAATAAT
ACTTTATTATGAAA
Found at i:4499190 original size:32 final size:32
Alignment explanation
Indices: 4499154--4499214 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
4499144 CAAGCATAGG
*
4499154 TACTTATCCATCATGATTGCCATTTTAACCCA
1 TACTTAGCCATCATGATTGCCATTTTAACCCA
* *
4499186 TACTTAGCCGTCATGGTTGCCATTTTAAC
1 TACTTAGCCATCATGATTGCCATTTTAAC
4499215 ACTCTAAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.25, C:0.26, G:0.11, T:0.38
Consensus pattern (32 bp):
TACTTAGCCATCATGATTGCCATTTTAACCCA
Found at i:4506639 original size:33 final size:34
Alignment explanation
Indices: 4506556--4506656 Score: 118
Period size: 34 Copynumber: 3.0 Consensus size: 34
4506546 AAGGGAAATA
*
4506556 AGCTTTTTATGGGATCAAGCGAAACCCTTACAAT
1 AGCTTTTAATGGGATCAAGCGAAACCCTTACAAT
* *
4506590 AGCTTTTTACAT--GATCAAGTGAAACCCTTATAAT
1 AGC-TTTTA-ATGGGATCAAGCGAAACCCTTACAAT
* *
4506624 A-CTTTTAATGGGATCAAGCAAAACCTTTACAAT
1 AGCTTTTAATGGGATCAAGCGAAACCCTTACAAT
4506657 GGTTTTTCAC
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
31 2 0.04
32 5 0.09
33 19 0.34
34 24 0.43
35 4 0.07
36 2 0.04
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.32
Consensus pattern (34 bp):
AGCTTTTAATGGGATCAAGCGAAACCCTTACAAT
Found at i:4511293 original size:21 final size:21
Alignment explanation
Indices: 4511268--4511340 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
4511258 TGGAAAAAAA
4511268 ATGTATTGATACATTATTAAT
1 ATGTATTGATACATTATTAAT
* *
4511289 ATGTATTGATACATGACT-AT
1 ATGTATTGATACATTATTAAT
** * *
4511309 ATGTATCAATACATTATGAAC
1 ATGTATTGATACATTATTAAT
*
4511330 ATGTATGGATA
1 ATGTATTGATA
4511341 TATTTGAAAC
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 15 0.37
21 26 0.63
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (21 bp):
ATGTATTGATACATTATTAAT
Found at i:4514302 original size:78 final size:77
Alignment explanation
Indices: 4514217--4514373 Score: 269
Period size: 78 Copynumber: 2.0 Consensus size: 77
4514207 AAATCAAATC
4514217 AAAGTATTGCTTCCATTAAAAGATCAAAATAAAACAAACACAATTTTCTAAGCTAATAAAATAAT
1 AAAGTATTGCTTCCATTAAAAGATCAAAATAAAACAAACACAATTTTCTAAGCTAATAAAATAAT
4514282 CACAAATTTGATG
66 CACAAATTT-ATG
* * * *
4514295 AAAGTATTGCTTCCATTTAAAGATCAAAATAAAACAAACACTATTTTCTAAGTTAATCAAATAAT
1 AAAGTATTGCTTCCATTAAAAGATCAAAATAAAACAAACACAATTTTCTAAGCTAATAAAATAAT
4514360 CACAAATTTATG
66 CACAAATTTATG
4514372 AA
1 AA
4514374 GGAATGCGTG
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
77 5 0.07
78 70 0.93
ACGTcount: A:0.49, C:0.14, G:0.07, T:0.30
Consensus pattern (77 bp):
AAAGTATTGCTTCCATTAAAAGATCAAAATAAAACAAACACAATTTTCTAAGCTAATAAAATAAT
CACAAATTTATG
Found at i:4517709 original size:23 final size:23
Alignment explanation
Indices: 4517627--4517703 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
4517617 TTGTATACTG
* *
4517627 GTTAGTAAGGCCTTGCATGACTT
1 GTTAGTAAAGCATTGCATGACTT
*
4517650 GTTAATAAAGCATTGCATGACTT
1 GTTAGTAAAGCATTGCATGACTT
* *
4517673 GTTAGTAAAGCATTACATGACTA
1 GTTAGTAAAGCATTGCATGACTT
4517696 GTTAGTAA
1 GTTAGTAA
4517704 GACATTGTGT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (23 bp):
GTTAGTAAAGCATTGCATGACTT
Found at i:4517770 original size:22 final size:21
Alignment explanation
Indices: 4517745--4517799 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
4517735 ATAGTCACAC
4517745 AATGCCTAAAAACTAATCACGT
1 AATGCCTAAAAAC-AATCACGT
*
4517767 AATGTCC-AAAATCAATCACGT
1 AATG-CCTAAAAACAATCACGT
* *
4517788 AATACTTAAAAA
1 AATGCCTAAAAA
4517800 TCAGTCTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
20 1 0.04
21 15 0.56
22 9 0.33
23 2 0.07
ACGTcount: A:0.49, C:0.20, G:0.07, T:0.24
Consensus pattern (21 bp):
AATGCCTAAAAACAATCACGT
Found at i:4518597 original size:28 final size:29
Alignment explanation
Indices: 4518542--4518598 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
4518532 AACTATAAAT
*
4518542 AATTAAAATTATAAAAAATAATATTTTTG
1 AATTAAAATTATAAAAAACAATATTTTTG
**
4518571 AATTAAAATTATAAAAAACGTTATTTTT
1 AATTAAAATTATAAAAAACAATATTTTT
4518599 CATAATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (29 bp):
AATTAAAATTATAAAAAACAATATTTTTG
Found at i:4522325 original size:75 final size:76
Alignment explanation
Indices: 4522226--4522396 Score: 242
Period size: 75 Copynumber: 2.3 Consensus size: 76
4522216 AAGTTTCAAC
* ** *
4522226 AATTTGTATTAATCAAGGGA-TGGAGATCT-AAACATGC-AACTTGGTTGCTTGAATATTTATAT
1 AATTTGTATTAATCAAGGGATTGGAGATCTAAAAC-T-CTAACTTGATTGCTCAAATATTAATAT
*
4522288 ATAAAGTTTTGAT
64 ATAAAGTTTTGAA
*
4522301 AATTTGTATT-ATGAAGGGATTGGAGATCTAAAACTCTAACTTGATTGCTCAAATATTAATATAT
1 AATTTGTATTAATCAAGGGATTGGAGATCTAAAACTCTAACTTGATTGCTCAAATATTAATATAT
4522365 AAAGTTTTGAA
66 AAAGTTTTGAA
4522376 AATTTGTATTAATCAAGGGAT
1 AATTTGTATTAATCAAGGGAT
4522397 AAATCTAAAA
Statistics
Matches: 85, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
74 9 0.11
75 63 0.74
76 13 0.15
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.38
Consensus pattern (76 bp):
AATTTGTATTAATCAAGGGATTGGAGATCTAAAACTCTAACTTGATTGCTCAAATATTAATATAT
AAAGTTTTGAA
Found at i:4532362 original size:17 final size:17
Alignment explanation
Indices: 4532340--4532382 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
4532330 TATCAAACAA
*
4532340 CCCCAAATTTAATAGAG
1 CCCCAAATCTAATAGAG
*
4532357 CCCCAAATCTAATAGCG
1 CCCCAAATCTAATAGAG
*
4532374 CACCAAATC
1 CCCCAAATC
4532383 AGATCCATTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.40, C:0.33, G:0.09, T:0.19
Consensus pattern (17 bp):
CCCCAAATCTAATAGAG
Found at i:4545971 original size:16 final size:15
Alignment explanation
Indices: 4545932--4545971 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
4545922 AACATAACTT
4545932 AAAATAAAAGCAAAA
1 AAAATAAAAGCAAAA
*
4545947 ACAATTAAAAGCAAATA
1 A-AAATAAAAGCAAA-A
4545964 AAAATAAA
1 AAAATAAA
4545972 TAAACCTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 1 0.05
16 18 0.86
17 2 0.10
ACGTcount: A:0.75, C:0.07, G:0.05, T:0.12
Consensus pattern (15 bp):
AAAATAAAAGCAAAA
Found at i:4547967 original size:3 final size:3
Alignment explanation
Indices: 4547959--4547985 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
4547949 GTAGCATCTT
4547959 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
4547986 GTGAAACGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:4550089 original size:15 final size:15
Alignment explanation
Indices: 4550069--4550106 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
4550059 ACGTTTATAG
*
4550069 CATATGAGATAGGGT
1 CATATGAGATAAGGT
4550084 CATATGAGATAAGGT
1 CATATGAGATAAGGT
4550099 CATATGAG
1 CATATGAG
4550107 TGAAAAAGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.37, C:0.08, G:0.29, T:0.26
Consensus pattern (15 bp):
CATATGAGATAAGGT
Found at i:4555481 original size:22 final size:22
Alignment explanation
Indices: 4555448--4555503 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
4555438 TTAAAATGGC
*
4555448 TTGAATGA-TTTTTTAACTTGT
1 TTGAATGAGTTTTTTAACTTAT
*
4555469 TTGAATAAGTTTTTTAACTTAT
1 TTGAATGAGTTTTTTAACTTAT
4555491 TTGAATGAGTTTT
1 TTGAATGAGTTTT
4555504 GAGCTTTAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
21 7 0.23
22 24 0.77
ACGTcount: A:0.27, C:0.04, G:0.14, T:0.55
Consensus pattern (22 bp):
TTGAATGAGTTTTTTAACTTAT
Found at i:4559002 original size:57 final size:56
Alignment explanation
Indices: 4558915--4559025 Score: 204
Period size: 57 Copynumber: 2.0 Consensus size: 56
4558905 TAGGCAATCA
*
4558915 ATAATTAAAGCAGGGATCTAAATTGCAGATACATATGCATTTTCGGTCATATCATG
1 ATAATTAAAGCAGGGATCTAAATTGCAGATACATATGCATTTTCCGTCATATCATG
4558971 ATAATTTAAAGCAGGGATCTAAATTGCAGATACATATGCATTTTCCGTCATATCA
1 ATAA-TTAAAGCAGGGATCTAAATTGCAGATACATATGCATTTTCCGTCATATCA
4559026 CATTTATCAT
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
56 4 0.08
57 49 0.92
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.32
Consensus pattern (56 bp):
ATAATTAAAGCAGGGATCTAAATTGCAGATACATATGCATTTTCCGTCATATCATG
Found at i:4559401 original size:22 final size:21
Alignment explanation
Indices: 4559374--4559414 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
4559364 TACACATAAA
*
4559374 TACTACTAAAATAAAATTAATC
1 TACTACCAAAA-AAAATTAATC
*
4559396 TACTACCCAAAAAAATTAA
1 TACTACCAAAAAAAATTAA
4559415 CAATACAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.56, C:0.17, G:0.00, T:0.27
Consensus pattern (21 bp):
TACTACCAAAAAAAATTAATC
Found at i:4562540 original size:28 final size:28
Alignment explanation
Indices: 4562509--4562627 Score: 82
Period size: 28 Copynumber: 4.0 Consensus size: 28
4562499 TATAAGTTAT
4562509 AACATATATAATAATATAAACATATTAA
1 AACATATATAATAATATAAACATATTAA
*
4562537 AACATATATGTTTCTATAAATATAAACATA-T-A
1 AACATATA----T-AAT-AATATAAACATATTAA
* *
4562569 TA-ATAGTAAACATATATATAAACATATTATA
1 AACATA-TATA-ATA-ATATAAACATATTA-A
*
4562600 TGACATATATAATAATATAAACATATTA
1 -AACATATATAATAATATAAACATATTA
4562628 TAATATGTCG
Statistics
Matches: 71, Mismatches: 6, Indels: 26
0.69 0.06 0.25
Matches are distributed among these distances:
27 1 0.01
28 21 0.30
29 1 0.01
30 14 0.20
31 7 0.10
32 9 0.13
33 6 0.08
34 12 0.17
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.35
Consensus pattern (28 bp):
AACATATATAATAATATAAACATATTAA
Found at i:4562570 original size:16 final size:17
Alignment explanation
Indices: 4562551--4562586 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
4562541 TATATGTTTC
4562551 TATAAATA-TAAACATA
1 TATAAATAGTAAACATA
4562567 TAT-AATAGTAAACATA
1 TATAAATAGTAAACATA
4562583 TATA
1 TATA
4562587 TAAACATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (17 bp):
TATAAATAGTAAACATA
Found at i:4564147 original size:30 final size:30
Alignment explanation
Indices: 4564087--4564150 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
4564077 TTAAAGCACA
*
4564087 TTTTCATTGAAATTGTGTTCTGAGAACATG
1 TTTTCATTGAAATTGTGTTCAGAGAACATG
** *
4564117 TTTTCATTGGTATTGTGTTTCAGAG-CCATG
1 TTTTCATTGAAATTGTG-TTCAGAGAACATG
4564147 TTTT
1 TTTT
4564151 TTAGATAAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 23 0.79
31 6 0.21
ACGTcount: A:0.20, C:0.11, G:0.20, T:0.48
Consensus pattern (30 bp):
TTTTCATTGAAATTGTGTTCAGAGAACATG
Found at i:4572732 original size:21 final size:21
Alignment explanation
Indices: 4572706--4572747 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
4572696 AACGTATTTG
4572706 ATTTAAAATAAATAT-ATAAAA
1 ATTT-AAATAAATATAATAAAA
*
4572727 ATTTAATTAAATATAATAAAA
1 ATTTAAATAAATATAATAAAA
4572748 TAATAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
ATTTAAATAAATATAATAAAA
Found at i:4577015 original size:21 final size:22
Alignment explanation
Indices: 4576980--4577023 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
4576970 CTCTTAAAGT
4576980 AATTTAAAATAAAATAACATAA
1 AATTTAAAATAAAATAACATAA
* *
4577002 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACATAA
4577023 A
1 A
4577024 TTAATCACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTTAAAATAAAATAACATAA
Found at i:4578120 original size:98 final size:96
Alignment explanation
Indices: 4578018--4578233 Score: 263
Period size: 99 Copynumber: 2.2 Consensus size: 96
4578008 ATTTTTGGAA
* *
4578018 AAGAAAGAAAAGAGGAGAAGAGAGGAAGAGGGAAC-ACACCCAAAGAAAAAAATCCCAAGGAAAG
1 AAGAAAGAAAA-AAGAGAAGAGAGGAAGAGGGAACAAAACCCAAAGAAAAAAA-CCCAAGGAAAG
* * **
4578082 AGGAGGTGTGGCCCATGAAAGAGATGGTCCAAAG
64 AGGAGGTGAGG-CCAGGAAAGAGATGACCCAAAG
* * * *
4578116 AAGAAAGGAAGAAAAGAGAAGGGAGGAAGTGGGAACAAAACCCAGAGAAAGAAACCCAAGGAAAG
1 AAGAAA-GAA-AAAAGAGAAGAGAGGAAGAGGGAACAAAACCCAAAGAAAAAAACCCAAGGAAAG
*
4578181 AGGAGGTGAGGCCAGGAAAGAGGTGACCCAAAG
64 AGGAGGTGAGGCCAGGAAAGAGATGACCCAAAG
4578214 AAGAAAGAAAGAAAAGAGAA
1 AAGAAAG-AA-AAAAGAGAA
4578234 AAAGGGAAGC
Statistics
Matches: 103, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
97 1 0.01
98 42 0.41
99 44 0.43
100 16 0.16
ACGTcount: A:0.51, C:0.12, G:0.33, T:0.04
Consensus pattern (96 bp):
AAGAAAGAAAAAAGAGAAGAGAGGAAGAGGGAACAAAACCCAAAGAAAAAAACCCAAGGAAAGAG
GAGGTGAGGCCAGGAAAGAGATGACCCAAAG
Found at i:4578242 original size:98 final size:100
Alignment explanation
Indices: 4578017--4578242 Score: 289
Period size: 98 Copynumber: 2.3 Consensus size: 100
4578007 CATTTTTGGA
*
4578017 AAAGAAAGAAAAGAGGAGAAGAGAGGAAGAGGGAACACACCCAAAGAAAAAAATCCCAAGGAAAG
1 AAAGAAAGAAAAGA-GA-AAGAGAGGAAGAGGGAACAAACCCAAAGAAAAAAATCCCAAGGAAAG
* * **
4578082 AGGAGGTGTGGCCCATGAAAGAGATGGTCCAAAGAAG
64 AGGAGGTGAGGCCCAGGAAAGAGATGACCCAAAGAAG
* * * * *
4578119 AAAGGAAGAAAAGAG-AAGGGAGGAAGTGGGAACAAAACCCAGAGAAAGAAA-CCCAAGGAAAGA
1 AAAGAAAGAAAAGAGAAAGAGAGGAAGAGGGAAC-AAACCCAAAGAAAAAAATCCCAAGGAAAGA
*
4578182 GGAGGTGAGG-CCAGGAAAGAGGTGACCCAAAGAAG
65 GGAGGTGAGGCCCAGGAAAGAGATGACCCAAAGAAG
*
4578217 AAAGAAAGAAAAGAGAAAAAG-GGAAG
1 AAAGAAAGAAAAGAGAAAGAGAGGAAG
4578243 CCTAACATGG
Statistics
Matches: 108, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
98 40 0.37
99 40 0.37
100 14 0.13
101 1 0.01
102 13 0.12
ACGTcount: A:0.52, C:0.11, G:0.33, T:0.04
Consensus pattern (100 bp):
AAAGAAAGAAAAGAGAAAGAGAGGAAGAGGGAACAAACCCAAAGAAAAAAATCCCAAGGAAAGAG
GAGGTGAGGCCCAGGAAAGAGATGACCCAAAGAAG
Found at i:4587748 original size:28 final size:30
Alignment explanation
Indices: 4587712--4587767 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
4587702 TTATTTAAGA
*
4587712 ATTTAAATTAA-TTTTTATATTTTTATTAC
1 ATTTAAATTAAGTTTTGATATTTTTATTAC
4587741 ATTT-AATTAAGTTTTGATATTTTTATT
1 ATTTAAATTAAGTTTTGATATTTTTATT
4587768 TTGAATCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (30 bp):
ATTTAAATTAAGTTTTGATATTTTTATTAC
Found at i:4596397 original size:27 final size:27
Alignment explanation
Indices: 4596367--4596436 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 27
4596357 AATGACATTC
**
4596367 CAAGTGTGTAATGCATAAGGACGTTCT
1 CAAGTGTGTAACACATAAGGACGTTCT
** * *
4596394 CAAGTGCATCACACATAAGTACGTTCT
1 CAAGTGTGTAACACATAAGGACGTTCT
*
4596421 CAAGTTTGTAACACAT
1 CAAGTGTGTAACACAT
4596437 TAGTGGCATT
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.29
Consensus pattern (27 bp):
CAAGTGTGTAACACATAAGGACGTTCT
Found at i:4596473 original size:27 final size:28
Alignment explanation
Indices: 4596434--4596498 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 28
4596424 GTTTGTAACA
*
4596434 CATTAGTGGCATTC-CAAATGCATAATG
1 CATTAGTGACATTCTCAAATGCATAATG
* **
4596461 CATTAGTGACATTCTCAATTGTGTAATG
1 CATTAGTGACATTCTCAAATGCATAATG
*
4596489 CACTAGTGAC
1 CATTAGTGAC
4596499 GTTATAAGTG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 13 0.41
28 19 0.59
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (28 bp):
CATTAGTGACATTCTCAAATGCATAATG
Found at i:4596708 original size:3 final size:3
Alignment explanation
Indices: 4596702--4596735 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
4596692 AACAACAACT
*
4596702 ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
4596736 ATATATATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:4615776 original size:31 final size:30
Alignment explanation
Indices: 4615736--4615795 Score: 102
Period size: 31 Copynumber: 2.0 Consensus size: 30
4615726 TCAATCAAAT
4615736 TTTTATTTTTATTTCGAATCAAATAAATTA
1 TTTTATTTTTATTTCGAATCAAATAAATTA
*
4615766 TTTTATTTTTTATTTTGAATCAAATAAATT
1 TTTTA-TTTTTATTTCGAATCAAATAAATT
4615796 TAATGATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 5 0.18
31 23 0.82
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (30 bp):
TTTTATTTTTATTTCGAATCAAATAAATTA
Found at i:4615952 original size:21 final size:21
Alignment explanation
Indices: 4615910--4615952 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
4615900 TAATTATTGA
* * *
4615910 TGATAATATAATATGCTAATT
1 TGATAAAATAACATGATAATT
*
4615931 TGATAAAATAACATGATCATT
1 TGATAAAATAACATGATAATT
4615952 T
1 T
4615953 AGTATTTATC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (21 bp):
TGATAAAATAACATGATAATT
Found at i:4616091 original size:30 final size:28
Alignment explanation
Indices: 4616051--4616126 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 28
4616041 TACCATTAGT
*
4616051 TATAAGGGTTTATTTAATCGAAAATAAAAA
1 TATAAAGGTTTATTTAAT-G-AAATAAAAA
* *
4616081 TATAAAGGTTTAATTGAATGTAATAAAAA
1 TATAAAGGTTT-ATTTAATGAAATAAAAA
* **
4616110 AATAAAATTTTATTTAA
1 TATAAAGGTTTATTTAA
4616127 ATTTTTTTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
28 5 0.13
29 16 0.42
30 11 0.29
31 6 0.16
ACGTcount: A:0.51, C:0.01, G:0.11, T:0.37
Consensus pattern (28 bp):
TATAAAGGTTTATTTAATGAAATAAAAA
Found at i:4628054 original size:3 final size:3
Alignment explanation
Indices: 4628033--4628067 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
4628023 AAATAAGTTT
* *
4628033 TAA TAA TGA TAA TAG TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
4628068 GGATTTACAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:4635170 original size:2 final size:2
Alignment explanation
Indices: 4635163--4635190 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4635153 ATGAATTTCC
4635163 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4635191 AGGCCAAGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:4638156 original size:33 final size:32
Alignment explanation
Indices: 4638109--4638194 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 32
4638099 CACCTCCTCC
* *
4638109 ATCTCCATCC-CCTCCACTTCCTTATGTTTATAA
1 ATCTCCA-CCACCTCCAC-TCCATATGTTTACAA
4638142 ATCTCCACCACCT-C-CTCCATATGTTTACAA
1 ATCTCCACCACCTCCACTCCATATGTTTACAA
* *
4638172 GTCTCCACCACCACCACCTCCAT
1 ATCTCCACCACCTCCA-CTCCAT
4638195 CTCCATCACT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
30 24 0.53
31 2 0.04
32 3 0.07
33 16 0.36
ACGTcount: A:0.23, C:0.43, G:0.03, T:0.30
Consensus pattern (32 bp):
ATCTCCACCACCTCCACTCCATATGTTTACAA
Found at i:4638248 original size:48 final size:48
Alignment explanation
Indices: 4638182--4639211 Score: 594
Period size: 48 Copynumber: 21.3 Consensus size: 48
4638172 GTCTCCACCA
*
4638182 CCACCACCTCCATCTCCATCACTC-CCTCCACCTTATGTTTACAAATCT
1 CCACCACCTCCATCTCCATCAC-CACCTCCTCCTTATGTTTACAAATCT
* * * *
4638230 CCACCTCCTCCATCTCCATCCCCACCACCTCCTTATGTTTATAAATCT
1 CCACCACCTCCATCTCCATCACCACCTCCTCCTTATGTTTACAAATCT
* * ** * * *
4638278 CCACCACCACCATCACTTTCACCACCTCCTCCATATGTTTATAAGTCT
1 CCACCACCTCCATCTCCATCACCACCTCCTCCTTATGTTTACAAATCT
* * *
4638326 CCACCACCCCCATCTCCATCACCCCCTCCACCTTATGTTTACAAATCT
1 CCACCACCTCCATCTCCATCACCACCTCCTCCTTATGTTTACAAATCT
* * * * * *
4638374 CCATCTCCTTCATCTCCATCCCCACCACCTCCTTATGTTTATAAATCT
1 CCACCACCTCCATCTCCATCACCACCTCCTCCTTATGTTTACAAATCT
* * * * * * *
4638422 CCACCTCCACCATCACCTTCACCACCAT-CTCCATATGTCTACAAGTCT
1 CCACCACCTCCATCTCCATCACCACC-TCCTCCTTATGTTTACAAATCT
* * *
4638470 CCACCACCTCCATCTCCATCACCACCCCCTCCTTATGTCTACAAATCC
1 CCACCACCTCCATCTCCATCACCACCTCCTCCTTATGTTTACAAATCT
* * * * * * ** * * *
4638518 CCATCTCCTCTATC-CCTATCCCCACCACCTCCATACATATATAAGTCT
1 CCACCACCTCCATCTCC-ATCACCACCTCCTCCTTATGTTTACAAATCT
* * * * *
4638566 CCACCTCCTCCATCTCCATCCCCACCACCTCCTTATATATACAAATCT
1 CCACCACCTCCATCTCCATCACCACCTCCTCCTTATGTTTACAAATCT
* * * * * * * * * * *
4638614 CCACGACCACCATCACCTTCCCCACCTCCTTCGTATGTCTATAAGTCA
1 CCACCACCTCCATCTCCATCACCACCTCCTCCTTATGTTTACAAATCT
* * * * * * * **
4638662 CCACCTCTTCCATCTCCATCTCCACCACCTCCATATGTGTATAGGTCT
1 CCACCACCTCCATCTCCATCACCACCTCCTCCTTATGTTTACAAATCT
** * * * * * * *
4638710 CTTCCACCGCCACCACCATCACCACCTCTTCCATATGTCTACAAGTCT
1 CCACCACCTCCATCTCCATCACCACCTCCTCCTTATGTTTACAAATCT
** * * * ** *
4638758 CCACCACCTCTGTCTCCAACACCTCCTCCTCCCTATGCCTACAAGTCT
1 CCACCACCTCCATCTCCATCACCACCTCCTCCTTATGTTTACAAATCT
* * * * * *
4638806 CCACCTCCTCCATCTCCATCTCCACCACCTCCATATGTATACAAGTCT
1 CCACCACCTCCATCTCCATCACCACCTCCTCCTTATGTTTACAAATCT
** * * * * * * *
4638854 CCACTTCCACCATCACCTTCACCACCTCCTCCCTATGTATACAAGTCA
1 CCACCACCTCCATCTCCATCACCACCTCCTCCTTATGTTTACAAATCT
** * * * **
4638902 CCACTTCTTCCATCTCCATCTCCACCACCTCCTTACATTTACAAATCT
1 CCACCACCTCCATCTCCATCACCACCTCCTCCTTATGTTTACAAATCT
* * * * * * *
4638950 CCACCACCACCATCACCTTCGA-CACCTCCACCATATGTATACAAGTCT
1 CCACCACCTCCATCTCCATC-ACCACCTCCTCCTTATGTTTACAAATCT
* * * * * * * * * *
4638998 CCACCTCCACAATCACCCTCCCCACCTCCTCCATATATCTACAAGTCT
1 CCACCACCTCCATCTCCATCACCACCTCCTCCTTATGTTTACAAATCT
* * * * * * * * * *
4639046 CCACC-TCTACCATCACCCTCCCCACCTCCCCCATACGTCTATAAGTCT
1 CCACCACCT-CCATCTCCATCACCACCTCCTCCTTATGTTTACAAATCT
* * * * * * *
4639094 CCACCACCTCCTTCTCCATCACCTCGTCCTCCATATATCTACAAGTCT
1 CCACCACCTCCATCTCCATCACCACCTCCTCCTTATGTTTACAAATCT
* * * ** * *
4639142 CCACCTCCACCTCCACCATCACCCTCGCCACCTCCTCCTTACATCTATAAATCT
1 CCA---CCACCT---CCATCTCCATCACCACCTCCTCCTTATGTTTACAAATCT
*
4639196 CCACCACCACCATCTC
1 CCACCACCTCCATCTC
4639212 TATACATGTA
Statistics
Matches: 766, Mismatches: 201, Indels: 30
0.77 0.20 0.03
Matches are distributed among these distances:
47 4 0.01
48 715 0.93
49 4 0.01
51 11 0.01
54 32 0.04
ACGTcount: A:0.23, C:0.47, G:0.04, T:0.27
Consensus pattern (48 bp):
CCACCACCTCCATCTCCATCACCACCTCCTCCTTATGTTTACAAATCT
Found at i:4638329 original size:96 final size:96
Alignment explanation
Indices: 4638182--4639149 Score: 713
Period size: 96 Copynumber: 10.1 Consensus size: 96
4638172 GTCTCCACCA
* * * * *
4638182 CCACCACCTCCATCTCCATCACTC-CCTCCACCTTATGTTTACAAATCTCCACCTCCTCCATCTC
1 CCACCTCCTCCATCTCCATCAC-CACCTCCTCCATATGTATACAAGTCTCCACCTCCTCCATCTC
* * * *
4638246 CATCCCCACCACCTCCTTATGTTTATAAATCT
65 CATCCCCACCACCTCCATATGTCTACAAGTCT
* * * ** * * * *
4638278 CCACCACCACCATCACTTTCACCACCTCCTCCATATGTTTATAAGTCTCCACCACCCCCATCTCC
1 CCACCTCCTCCATCTCCATCACCACCTCCTCCATATGTATACAAGTCTCCACCTCCTCCATCTCC
* * * * *
4638343 ATCACCC-CCTCCACCTTATGTTTACAAATCT
66 ATC-CCCACCACCTCCATATGTCTACAAGTCT
* * * * * * * * * *
4638374 CCATCTCCTTCATCTCCATCCCCACCACCTCCTTATGTTTATAAATCTCCACCTCCACCATCACC
1 CCACCTCCTCCATCTCCATCACCACCTCCTCCATATGTATACAAGTCTCCACCTCCTCCATCTCC
* * *
4638439 TTCACCACCATCTCCATATGTCTACAAGTCT
66 ATCCCCACCACCTCCATATGTCTACAAGTCT
* * * * * * * *
4638470 CCACCACCTCCATCTCCATCACCACCCCCTCCTTATGTCTACAAATCCCCATCTCCTCTATC-CC
1 CCACCTCCTCCATCTCCATCACCACCTCCTCCATATGTATACAAGTCTCCACCTCCTCCATCTCC
** * *
4638534 TATCCCCACCACCTCCATACATATATAAGTCT
66 -ATCCCCACCACCTCCATATGTCTACAAGTCT
* * * * * ** * *
4638566 CCACCTCCTCCATCTCCATCCCCACCACCTCCTTATATATACAAATCTCCACGACCACCATCACC
1 CCACCTCCTCCATCTCCATCACCACCTCCTCCATATGTATACAAGTCTCCACCTCCTCCATCTCC
* * * * * *
4638631 TTCCCCACCTCCTTCGTATGTCTATAAGTCA
66 ATCCCCACCACCTCCATATGTCTACAAGTCT
* * * * * * ** * * * *
4638662 CCACCTCTTCCATCTCCATCTCCACCACCTCCATATGTGTATAGGTCTCTTCCACCGCCACCACC
1 CCACCTCCTCCATCTCCATCACCACCTCCTCCATATGTATACAAGTCTCCACCTCCTCCATCTCC
* * *
4638727 ATCACCACCTCTTCCATATGTCTACAAGTCT
66 ATCCCCACCACCTCCATATGTCTACAAGTCT
* ** * * * **
4638758 CCACCACCTCTGTCTCCAACACCTCCTCCTCCCTATGCCTACAAGTCTCCACCTCCTCCATCTCC
1 CCACCTCCTCCATCTCCATCACCACCTCCTCCATATGTATACAAGTCTCCACCTCCTCCATCTCC
* *
4638823 ATCTCCACCACCTCCATATGTATACAAGTCT
66 ATCCCCACCACCTCCATATGTCTACAAGTCT
* * * * * * * *
4638854 CCACTTCCACCATCACCTTCACCACCTCCTCCCTATGTATACAAGTCACCACTTCTTCCATCTCC
1 CCACCTCCTCCATCTCCATCACCACCTCCTCCATATGTATACAAGTCTCCACCTCCTCCATCTCC
* * ** * *
4638919 ATCTCCACCACCTCCTTACATTTACAAATCT
66 ATCCCCACCACCTCCATATGTCTACAAGTCT
* * * * * * * *
4638950 CCACCACCACCATCACCTTCGA-CACCTCCACCATATGTATACAAGTCTCCACCTCCACAATCAC
1 CCACCTCCTCCATCTCCATC-ACCACCTCCTCCATATGTATACAAGTCTCCACCTCCTCCATCTC
* * *
4639014 CCTCCCCACCTCCTCCATATATCTACAAGTCT
65 CATCCCCACCACCTCCATATGTCTACAAGTCT
* * * * * * * * *
4639046 CCACCT-CTACCATCACCCTCCCCACCTCCCCCATACGTCTATAAGTCTCCACCACCTCCTTCTC
1 CCACCTCCT-CCATCTCCATCACCACCTCCTCCATATGTATACAAGTCTCCACCTCCTCCATCTC
* * ** *
4639110 CATCACCTCGTCCTCCATATATCTACAAGTCT
65 CATCCCCACCACCTCCATATGTCTACAAGTCT
4639142 CCACCTCC
1 CCACCTCC
4639150 ACCTCCACCA
Statistics
Matches: 695, Mismatches: 168, Indels: 17
0.79 0.19 0.02
Matches are distributed among these distances:
95 6 0.01
96 682 0.98
97 7 0.01
ACGTcount: A:0.23, C:0.46, G:0.04, T:0.27
Consensus pattern (96 bp):
CCACCTCCTCCATCTCCATCACCACCTCCTCCATATGTATACAAGTCTCCACCTCCTCCATCTCC
ATCCCCACCACCTCCATATGTCTACAAGTCT
Found at i:4638370 original size:144 final size:144
Alignment explanation
Indices: 4638147--4639152 Score: 917
Period size: 144 Copynumber: 6.9 Consensus size: 144
4638137 TATAAATCTC
* * *
4638147 CACCACCTCCTCCATATGTTTACAAGTCTCCACCACCACCACCTCCATCTCCATCACTCCCTCCA
1 CACCACCTCCTCCATATGTCTACAAGTCT------CCACCACCTCCATCTCCATCACCCCCTCCT
* * * *
4638212 CCTTATGTTTACAAATCTCCACCTCCTCCATCTCCATCCCCACCACCTCCTTATGTTTATAAATC
60 CCTTATGTCTACAAATCTCCACCTCCTCCATCTCCATCCCCACCACCTCCATATGTATATAAGTC
* *
4638277 TCCACCACCACCATCACTTT
125 TCCACCTCCACCATCACCTT
* * * *
4638297 CACCACCTCCTCCATATGTTTATAAGTCTCCACCACCCCCATCTCCATCACCCCCTCCACCTTAT
1 CACCACCTCCTCCATATGTCTACAAGTCTCCACCACCTCCATCTCCATCACCCCCTCCTCCTTAT
* * * * * *
4638362 GTTTACAAATCTCCATCTCCTTCATCTCCATCCCCACCACCTCCTTATGTTTATAAATCTCCACC
66 GTCTACAAATCTCCACCTCCTCCATCTCCATCCCCACCACCTCCATATGTATATAAGTCTCCACC
4638427 TCCACCATCACCTT
131 TCCACCATCACCTT
4638441 CACCACCAT-CTCCATATGTCTACAAGTCTCCACCACCTCCATCTCCATCACCACCC-CCTCCTT
1 CACCACC-TCCTCCATATGTCTACAAGTCTCCACCACCTCCATCTCCATCACC-CCCTCCTCCTT
* * * **
4638504 ATGTCTACAAATCCCCATCTCCTCTATC-CCTATCCCCACCACCTCCATACATATATAAGTCTCC
64 ATGTCTACAAATCTCCACCTCCTCCATCTCC-ATCCCCACCACCTCCATATGTATATAAGTCTCC
* * *
4638568 ACCTCCTCCATCTCCAT
128 ACCTCCACCATCACCTT
* * * * * * * * * * * *
4638585 CCCCACCACCTCCTTATATATACAAATCTCCACGACCACCATCACCTTC-CCCACCTCCTTCGTA
1 CACCACCTCCTCCATATGTCTACAAGTCTCCACCACCTCCATCTCCATCACCC-CCTCCTCCTTA
* * * * * * * **
4638649 TGTCTATAAGTCACCACCTCTTCCATCTCCATCTCCACCACCTCCATATGTGTATAGGTCTCTTC
65 TGTCTACAAATCTCCACCTCCTCCATCTCCATCCCCACCACCTCCATATGTATATAAGTCTCCAC
* * * *
4638714 CACCGCCACCACCAT
130 CTCCACCATCACCTT
* ** * * *
4638729 CACCACCTCTTCCATATGTCTACAAGTCTCCACCACCTCTGTCTCCAACACCTCCTCCTCCCTAT
1 CACCACCTCCTCCATATGTCTACAAGTCTCCACCACCTCCATCTCCATCACCCCCTCCTCCTTAT
* * * * *
4638794 GCCTACAAGTCTCCACCTCCTCCATCTCCATCTCCACCACCTCCATATGTATACAAGTCTCCACT
66 GTCTACAAATCTCCACCTCCTCCATCTCCATCCCCACCACCTCCATATGTATATAAGTCTCCACC
4638859 TCCACCATCACCTT
131 TCCACCATCACCTT
* * * ** * * * * *
4638873 CACCACCTCCTCCCTATGTATACAAGTCACCACTTCTTCCATCTCCATCTCCACCACCTCCTTAC
1 CACCACCTCCTCCATATGTCTACAAGTCTCCACCACCTCCATCTCCATCACCCCCTCCTCCTTAT
* * * * * * ** * * *
4638938 ATTTACAAATCTCCACCACCACCATCACCTTCGACACCTCCACCATATGTATACAAGTCTCCACC
66 GTCTACAAATCTCCACCTCCTCCATCTCCATCCCCACCACCTCCATATGTATATAAGTCTCCACC
* *
4639003 TCCACAATCACCCT
131 TCCACCATCACCTT
* * * * * * *
4639017 CCCCACCTCCTCCATATATCTACAAGTCTCCACC-TCTACCATCACCCTC-CCCACCTCCCCCAT
1 CACCACCTCCTCCATATGTCTACAAGTCTCCACCACCT-CCATCTCCATCACCC-CCTCCTCCTT
* * * * * * * ** * * *
4639080 ACGTCTATAAGTCTCCACCACCTCCTTCTCCATCACCTCGTCCTCCATATATCTACAAGTCTCCA
64 ATGTCTACAAATCTCCACCTCCTCCATCTCCATCCCCACCACCTCCATATGTATATAAGTCTCCA
4639145 CCTCCACC
129 CCTCCACC
4639153 TCCACCATCA
Statistics
Matches: 703, Mismatches: 143, Indels: 26
0.81 0.16 0.03
Matches are distributed among these distances:
142 1 0.00
143 9 0.01
144 657 0.93
145 8 0.01
150 28 0.04
ACGTcount: A:0.23, C:0.46, G:0.04, T:0.27
Consensus pattern (144 bp):
CACCACCTCCTCCATATGTCTACAAGTCTCCACCACCTCCATCTCCATCACCCCCTCCTCCTTAT
GTCTACAAATCTCCACCTCCTCCATCTCCATCCCCACCACCTCCATATGTATATAAGTCTCCACC
TCCACCATCACCTT
Found at i:4639189 original size:102 final size:96
Alignment explanation
Indices: 4639024--4639203 Score: 261
Period size: 102 Copynumber: 1.8 Consensus size: 96
4639014 CCTCCCCACC
*
4639024 TCCTCCATATATCTACAAGTCTCCACCTCTACCATCACCCTCCCCACCTCCCCCATACGTCTATA
1 TCCTCCATATATCTACAAGTCTCCACCTCTACCATCACCCTCCCCACCTCCCCCATACATCTATA
*
4639089 AGTCTCCACCACCTCCTTCTCCATCACCTCG
66 AATCTCCACCACCTCCTTCTCCATCACCTCG
* * *
4639120 TCCTCCATATATCTACAAGTCTCCACCTCCACCTCCACCATCACCCTCGCCACCTCCTCCTTACA
1 TCCTCCATATATCTACAAGTCTCCACCT----CT--ACCATCACCCTCCCCACCTCCCCCATACA
4639185 TCTATAAATCTCCACCACC
60 TCTATAAATCTCCACCACC
4639204 ACCATCTCTA
Statistics
Matches: 73, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
96 28 0.38
100 2 0.03
102 43 0.59
ACGTcount: A:0.22, C:0.49, G:0.03, T:0.26
Consensus pattern (96 bp):
TCCTCCATATATCTACAAGTCTCCACCTCTACCATCACCCTCCCCACCTCCCCCATACATCTATA
AATCTCCACCACCTCCTTCTCCATCACCTCG
Found at i:4640510 original size:17 final size:15
Alignment explanation
Indices: 4640490--4640528 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
4640480 AAGTCCCTTT
4640490 AGTTTCGAATTATTTCA
1 AGTTT-GAATTATTT-A
*
4640507 AGTTTGGATTATTTA
1 AGTTTGAATTATTTA
4640522 AGTTTGA
1 AGTTTGA
4640529 TGCATGGATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 7 0.35
16 8 0.40
17 5 0.25
ACGTcount: A:0.28, C:0.05, G:0.18, T:0.49
Consensus pattern (15 bp):
AGTTTGAATTATTTA
Found at i:4640526 original size:15 final size:16
Alignment explanation
Indices: 4640498--4640527 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4640488 TTAGTTTCGA
4640498 ATTATTTCAAGTTTGG
1 ATTATTTCAAGTTTGG
4640514 ATTATTT-AAGTTTG
1 ATTATTTCAAGTTTG
4640528 ATGCATGGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.03, G:0.17, T:0.53
Consensus pattern (16 bp):
ATTATTTCAAGTTTGG
Found at i:4640849 original size:2 final size:2
Alignment explanation
Indices: 4640842--4640884 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
4640832 AGCCCTTCCT
*
4640842 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG 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
4640884 T
1 T
4640885 GTATGTATGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4640889 original size:14 final size:14
Alignment explanation
Indices: 4640842--4640892 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
4640832 AGCCCTTCCT
*
4640842 TATATATATATATA
1 TATATGTATATATA
*
4640856 TATATATATATATA
1 TATATGTATATATA
4640870 TATATGTATATATA
1 TATATGTATATATA
*
4640884 TGTATGTAT
1 TATATGTAT
4640893 GTATTACCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 35 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (14 bp):
TATATGTATATATA
Found at i:4645266 original size:2 final size:2
Alignment explanation
Indices: 4645259--4645286 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4645249 TGCCGTTCAT
4645259 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
4645287 AAATATAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4660406 original size:3 final size:3
Alignment explanation
Indices: 4660398--4660426 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4660388 AAGTTAAAGC
4660398 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4660427 CTATGTGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:4677299 original size:2 final size:2
Alignment explanation
Indices: 4677294--4677334 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
4677284 TATATATATA
4677294 TG TG TG TG TG TG TG TG 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 TG TG TG TG TG TG TG TG T
4677335 TGAGAATATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:4678029 original size:2 final size:2
Alignment explanation
Indices: 4678022--4678063 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
4678012 TATCTATTCT
4678022 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
4678064 ATCAGAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4678161 original size:17 final size:17
Alignment explanation
Indices: 4678139--4678172 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
4678129 GTTGTGCATT
4678139 GTGAAACATTAATATAC
1 GTGAAACATTAATATAC
4678156 GTGAAACATTAATATAC
1 GTGAAACATTAATATAC
4678173 ATATATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (17 bp):
GTGAAACATTAATATAC
Found at i:4680714 original size:30 final size:31
Alignment explanation
Indices: 4680680--4680761 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
4680670 CTCACCACTT
* * *
4680680 CCTCCTTATGTATACAAATCCCCA-CCGCCA
1 CCTCCTTATATATACAAGTCCCCAGCCACCA
*
4680710 CCTCCTTATACATACAAGT-CCCAGCCACCA
1 CCTCCTTATATATACAAGTCCCCAGCCACCA
* *
4680740 CCCCCTTATCTATACAAGTCCC
1 CCTCCTTATATATACAAGTCCC
4680762 TCCACCACTA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 4 0.09
30 37 0.86
31 2 0.05
ACGTcount: A:0.27, C:0.44, G:0.06, T:0.23
Consensus pattern (31 bp):
CCTCCTTATATATACAAGTCCCCAGCCACCA
Found at i:4680876 original size:47 final size:47
Alignment explanation
Indices: 4680743--4681100 Score: 260
Period size: 47 Copynumber: 7.6 Consensus size: 47
4680733 GCCACCACCC
* * * *
4680743 CCTTATCTATACAAGTCCCTCCACCACTAGTACACTCTCC-TCCTCCT
1 CCTTATGTATACAAGTCCCACCACCACCAGTACACTCACCAT-CTCCT
* * * * * *
4680790 CTTTATATGTACAAATCCCCACCACC-CCA-AAGCACTCACCATCACCT
1 CCTTATGTATACAAGT-CCCACCACCACCAGTA-CACTCACCATCTCCT
* * *
4680837 CTTTATGTCTACAAGTCCCACCACCACCAGTACATTCACCATCTCCT
1 CCTTATGTATACAAGTCCCACCACCACCAGTACACTCACCATCTCCT
*** * * *
4680884 CCTTACCAATACAAGTCCCTCCACCACCAATCCACTCACC-TCCTCCT
1 CCTTATGTATACAAGTCCCACCACCACCAGTACACTCACCAT-CTCCT
* ** * *
4680931 CCTTATGTCTATGAGTCCCCACCACCACCAGTACATTCACCACCTCCT
1 CCTTATGTATACAAGT-CCCACCACCACCAGTACACTCACCATCTCCT
* * * * *
4680979 CCTTATCTATACAAGTCCC-CTCCCCACCAGTCCATTCTCC-TCCTCCT
1 CCTTATGTATACAAGTCCCAC-CACCACCAGTACACTCACCAT-CTCCT
** * ** ** * *
4681026 CCTTATGCCTATAAGTCCCACCACTTCCAAAACACTCACCACCACCT
1 CCTTATGTATACAAGTCCCACCACCACCAGTACACTCACCATCTCCT
*
4681073 CCTTATGTATACAAGTCCCCCCACCACC
1 CCTTATGTATACAAGTCCCACCACCACC
4681101 TCCTTACCTA
Statistics
Matches: 236, Mismatches: 63, Indels: 24
0.73 0.20 0.07
Matches are distributed among these distances:
46 12 0.05
47 176 0.75
48 48 0.20
ACGTcount: A:0.25, C:0.45, G:0.05, T:0.25
Consensus pattern (47 bp):
CCTTATGTATACAAGTCCCACCACCACCAGTACACTCACCATCTCCT
Found at i:4680978 original size:95 final size:94
Alignment explanation
Indices: 4680755--4681100 Score: 356
Period size: 94 Copynumber: 3.7 Consensus size: 94
4680745 TTATCTATAC
* * * * * * * * * *
4680755 AAGTCCCTCCACCACTAGTACACTCTCCTCCTCCTCTTTATATGTACAAATCCCCACCACC-CCA
1 AAGTCCCACCACCACCAGTACATTCACCACCTCCTCCTTATCTATACAAGT-CCCTCCACCACCA
** * * *
4680819 AAGCACTCACCAT-CACCTCTTTATGTCTAC
65 ATCCACTCACC-TCCTCCTCCTTATGTCTAT
* * *
4680849 AAGTCCCACCACCACCAGTACATTCACCATCTCCTCCTTACCAATACAAGTCCCTCCACCACCAA
1 AAGTCCCACCACCACCAGTACATTCACCACCTCCTCCTTATCTATACAAGTCCCTCCACCACCAA
4680914 TCCACTCACCTCCTCCTCCTTATGTCTAT
66 TCCACTCACCTCCTCCTCCTTATGTCTAT
*
4680943 GAGTCCCCACCACCACCAGTACATTCACCACCTCCTCCTTATCTATACAAGTCCCCTCC-CCACC
1 AAGT-CCCACCACCACCAGTACATTCACCACCTCCTCCTTATCTATACAAGT-CCCTCCACCACC
* * * *
4681007 AGTCCATTCTCCTCCTCCTCCTTATGCCTAT
64 AATCCACTCACCTCCTCCTCCTTATGTCTAT
** ** * * * *
4681038 AAGTCCCACCACTTCCAAAACACTCACCACCACCTCCTTATGTATACAAGTCCCCCCACCACC
1 AAGTCCCACCACCACCAGTACATTCACCACCTCCTCCTTATCTATACAAGTCCCTCCACCACC
4681101 TCCTTACCTA
Statistics
Matches: 212, Mismatches: 35, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
93 14 0.07
94 113 0.53
95 79 0.37
96 6 0.03
ACGTcount: A:0.25, C:0.46, G:0.05, T:0.24
Consensus pattern (94 bp):
AAGTCCCACCACCACCAGTACATTCACCACCTCCTCCTTATCTATACAAGTCCCTCCACCACCAA
TCCACTCACCTCCTCCTCCTTATGTCTAT
Found at i:4681106 original size:29 final size:30
Alignment explanation
Indices: 4681064--4681130 Score: 109
Period size: 29 Copynumber: 2.3 Consensus size: 30
4681054 AAAACACTCA
**
4681064 CCACCACCTCCTTATGTATACAAGTCCCC-
1 CCACCACCTCCTTACCTATACAAGTCCCCT
4681093 CCACCACCTCCTTACCTATACAAGTCCCCT
1 CCACCACCTCCTTACCTATACAAGTCCCCT
4681123 CCACCACC
1 CCACCACC
4681131 AGTCCACTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 27 0.77
30 8 0.23
ACGTcount: A:0.24, C:0.51, G:0.04, T:0.21
Consensus pattern (30 bp):
CCACCACCTCCTTACCTATACAAGTCCCCT
Found at i:4681163 original size:48 final size:48
Alignment explanation
Indices: 4681099--4681507 Score: 254
Period size: 48 Copynumber: 8.6 Consensus size: 48
4681089 CCCCCCACCA
** * *
4681099 CCTCCTTACCTATACAAGTCCCCTCCACCACCAGTCCACTCTCCTCCT
1 CCTCCTTATGTATACAAGTCCCCACCACCACCAGTCCACTCACCTCCT
* * *** * * *
4681147 CCTCCTTATGTCTACAAGTCCCCACCACCTCCAAAACACACACCGCCA
1 CCTCCTTATGTATACAAGTCCCCACCACCACCAGTCCACTCACCTCCT
* * *
4681195 CCTCCTTATGTATACAAGTCCCCACCACC-CACAGTACATTCACCACCT
1 CCTCCTTATGTATACAAGTCCCCACCACCAC-CAGTCCACTCACCTCCT
* ** * * * * *
4681243 CTTCCTTACATATACAAGT-CCCTCCACCACCTGTTCATTCA-CACCT
1 CCTCCTTATGTATACAAGTCCCCACCACCACCAGTCCACTCACCTCCT
** * *
4681289 CCT-CTTACCTATATAAGT-CCCACCACCACCAGTCCATTCTCTCCTCCCT
1 CCTCCTTATGTATACAAGTCCCCACCACCACCAGTCCA--CTCACCT-CCT
* * *** * *
4681338 CCTCCTTCTTATGTTTACACA-TCCCCACCACCTCCAAAACACTCACCCCCA
1 CCT-C--CTTATGTATACA-AGTCCCCACCACCACCAGTCCACTCACCTCCT
* * *
4681389 CCT-CTTATGTATACAAGTCCCCA--ACCACCA-ACACATTCACC-ACT
1 CCTCCTTATGTATACAAGTCCCCACCACCACCAGTC-CACTCACCTCCT
* *
4681433 CCT-CTTACT-T-TACAAGT-CCCATCCACCACCAGTCCACTCTCCTCTT
1 CCTCCTTA-TGTATACAAGTCCCCA-CCACCACCAGTCCACTCACCTCCT
*
4681479 CCTCCTTATGTCTACAAGTCCCCACCACC
1 CCTCCTTATGTATACAAGTCCCCACCACC
4681508 TCCTTATGTA
Statistics
Matches: 281, Mismatches: 56, Indels: 48
0.73 0.15 0.12
Matches are distributed among these distances:
42 4 0.01
43 7 0.02
44 10 0.04
45 55 0.20
46 14 0.05
47 42 0.15
48 105 0.37
49 10 0.04
51 5 0.02
52 5 0.02
53 9 0.03
54 15 0.05
ACGTcount: A:0.24, C:0.46, G:0.05, T:0.25
Consensus pattern (48 bp):
CCTCCTTATGTATACAAGTCCCCACCACCACCAGTCCACTCACCTCCT
Found at i:4681198 original size:96 final size:95
Alignment explanation
Indices: 4681093--4681418 Score: 284
Period size: 96 Copynumber: 3.4 Consensus size: 95
4681083 ACAAGTCCCC
*
4681093 CCACCACCTCCTTACCTATACAAGTCCCCTCCACCACCAGTCCACTCTCCTCCTCCTCCTTATGT
1 CCACCACCT-CTTACCTATACAAGTCCCCACCACCACCAGTCCACTCTCCTCCTCCTCCTTATGT
* *
4681158 CTACAAGTCCCCACCACCTCCAAAACACACA
65 ATACAAGTCCCCACCACCTCCAAAACACTCA
* ** * * * * * **
4681189 CCGCCACCTCCTTATGTATACAAGTCCCCACCACC-CACAGTACATTCACCACCTCTTCCTTACA
1 CCACCACCT-CTTACCTATACAAGTCCCCACCACCAC-CAGTCCACTCTCCTCCTCCTCCTTATG
* * **** *
4681253 TATACAAGT-CCCTCCACCACCTGTTCATTCA
64 TATACAAGTCCCCACCACCTCCAAAACACTCA
* *
4681284 -CACCTCCTCTTACCTATATAAGT-CCCACCACCACCAGTCCATTCTCTCCTCCCTCCTCCTTCT
1 CCACCACCTCTTACCTATACAAGTCCCCACCACCACCAGTCCA--CTCTCCT-CCTCCT-C--CT
*
4681347 TATGTTTACACA-TCCCCACCACCTCCAAAACACTCA
60 TATGTATACA-AGTCCCCACCACCTCCAAAACACTCA
* **
4681383 CCCCCACCTCTTATGTATACAAGTCCCCAACCACCA
1 CCACCACCTCTTACCTATACAAGTCCCC-ACCACCA
4681419 ACACATTCAC
Statistics
Matches: 172, Mismatches: 45, Indels: 20
0.73 0.19 0.08
Matches are distributed among these distances:
92 15 0.09
93 13 0.08
94 10 0.06
95 20 0.12
96 60 0.35
98 10 0.06
99 16 0.09
100 18 0.10
101 3 0.02
102 7 0.04
ACGTcount: A:0.25, C:0.47, G:0.05, T:0.24
Consensus pattern (95 bp):
CCACCACCTCTTACCTATACAAGTCCCCACCACCACCAGTCCACTCTCCTCCTCCTCCTTATGTA
TACAAGTCCCCACCACCTCCAAAACACTCA
Found at i:4681210 original size:125 final size:124
Alignment explanation
Indices: 4680968--4681223 Score: 415
Period size: 125 Copynumber: 2.1 Consensus size: 124
4680958 CCAGTACATT
* * *
4680968 CACCACCTCCTCCTTATCTATACAAGTCCCCTCCCCACCAGTCCATTCTCCTCCTCCTCCTTATG
1 CACCACCACCTCCTTACCTATACAAGTCCCCTCCCCACCAGTCCACTCTCCTCCTCCTCCTTATG
* * *
4681033 CCTATAAGTCCCACCACTTCCAAAACACTCACCACCACCTCCTTATGTATACAAGTCCC
66 CCTACAAGTCCCACCACCTCCAAAACACACACCACCACCTCCTTATGTATACAAGTCCC
4681092 C-CCACCACCTCCTTACCTATACAAGTCCCCTCCACCACCAGTCCACTCTCCTCCTCCTCCTTAT
1 CACCACCACCTCCTTACCTATACAAGTCCCCTCC-CCACCAGTCCACTCTCCTCCTCCTCCTTAT
* *
4681156 GTCTACAAGTCCCCACCACCTCCAAAACACACACCGCCACCTCCTTATGTATACAAGTCCC
65 GCCTACAAGT-CCCACCACCTCCAAAACACACACCACCACCTCCTTATGTATACAAGTCCC
4681217 CACCACC
1 CACCACC
4681224 CACAGTACAT
Statistics
Matches: 121, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
123 30 0.25
124 38 0.31
125 48 0.40
126 5 0.04
ACGTcount: A:0.24, C:0.48, G:0.05, T:0.23
Consensus pattern (124 bp):
CACCACCACCTCCTTACCTATACAAGTCCCCTCCCCACCAGTCCACTCTCCTCCTCCTCCTTATG
CCTACAAGTCCCACCACCTCCAAAACACACACCACCACCTCCTTATGTATACAAGTCCC
Found at i:4681369 original size:194 final size:185
Alignment explanation
Indices: 4681094--4681462 Score: 496
Period size: 194 Copynumber: 1.9 Consensus size: 185
4681084 CAAGTCCCCC
*
4681094 CACCACCTCCTTACCTATACAAGTCCCCTCCACCACCAGTCCACTCTCCTCCTCCTCCTTATGTC
1 CACCACCTCCTTACCTATACAAGTCCCCACCACCACCAGTCCACTCTCCTCCTCCTCCTTATGTC
*
4681159 TACAAGTCCCCACCACCTCCAAAACACACACCGCCACCTCCTTATGTATACAAGTCCCC-ACCAC
66 TACAAGTCCCCACCACCTCCAAAACACACACCCCCACCT-CTTATGTATACAAGTCCCCAACCA-
* *
4681223 CCACAGTACATTCACCACCTCTTCCTTACATATACAAGTCCC-TCCACCACCTGTTCATTCA
129 CCA-A-CACATTCACCA-CTCCT-CTTAC-TATACAAGTCCCATCCACCACCTGTTCATTCA
* *
4681284 CACCTCCT-CTTACCTATATAAGT-CCCACCACCACCAGTCCATTCTCTCCTCCCTCCTCCTTCT
1 CACCACCTCCTTACCTATACAAGTCCCCACCACCACCAGTCCA--CTCTCCT-CCTCCT-C--CT
* *
4681347 TATGTTTACACA-TCCCCACCACCTCCAAAACACTCACCCCCACCTCTTATGTATACAAGTCCCC
60 TATGTCTACA-AGTCCCCACCACCTCCAAAACACACACCCCCACCTCTTATGTATACAAGTCCCC
*
4681411 AACCACCAACACATTCACCACTCCTCTTACTTTACAAGTCCCATCCACCACC
124 AACCACCAACACATTCACCACTCCTCTTACTATACAAGTCCCATCCACCACC
4681463 AGTCCACTCT
Statistics
Matches: 161, Mismatches: 9, Indels: 19
0.85 0.05 0.10
Matches are distributed among these distances:
188 28 0.17
189 28 0.17
190 18 0.11
191 16 0.10
192 2 0.01
193 22 0.14
194 46 0.29
195 1 0.01
ACGTcount: A:0.25, C:0.46, G:0.04, T:0.24
Consensus pattern (185 bp):
CACCACCTCCTTACCTATACAAGTCCCCACCACCACCAGTCCACTCTCCTCCTCCTCCTTATGTC
TACAAGTCCCCACCACCTCCAAAACACACACCCCCACCTCTTATGTATACAAGTCCCCAACCACC
AACACATTCACCACTCCTCTTACTATACAAGTCCCATCCACCACCTGTTCATTCA
Found at i:4681537 original size:30 final size:27
Alignment explanation
Indices: 4681479--4681534 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
4681469 CTCTCCTCTT
*
4681479 CCTCCTTATGTCTACAAGTCCCCACCA
1 CCTCCTTATGTATACAAGTCCCCACCA
*
4681506 CCTCCTTATGTATACAAGTCTCCACCA
1 CCTCCTTATGTATACAAGTCCCCACCA
4681533 CC
1 CC
4681535 ACCAGTACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.23, C:0.43, G:0.07, T:0.27
Consensus pattern (27 bp):
CCTCCTTATGTATACAAGTCCCCACCA
Found at i:4681552 original size:48 final size:48
Alignment explanation
Indices: 4681500--4681634 Score: 155
Period size: 48 Copynumber: 2.8 Consensus size: 48
4681490 CTACAAGTCC
*
4681500 CCACCACCTCCTTATGTATACAAGTCTCCACCACCACCAGTACATTCA
1 CCACCTCCTCCTTATGTATACAAGTCTCCACCACCACCAGTACATTCA
** ** * *
4681548 CCACCTCCTCCTTACATATACAAGTCTCCTTCACCACCTGTCCATTCA
1 CCACCTCCTCCTTATGTATACAAGTCTCCACCACCACCAGTACATTCA
* * * *
4681596 CCACCTTCTCCTTATGTTTAC-AGAACTCCACCTCCACCA
1 CCACCTCCTCCTTATGTATACAAG-TCTCCACCACCACCA
4681635 TCACATCCTA
Statistics
Matches: 70, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
47 2 0.03
48 68 0.97
ACGTcount: A:0.25, C:0.43, G:0.05, T:0.27
Consensus pattern (48 bp):
CCACCTCCTCCTTATGTATACAAGTCTCCACCACCACCAGTACATTCA
Found at i:4681607 original size:123 final size:117
Alignment explanation
Indices: 4681386--4681617 Score: 288
Period size: 123 Copynumber: 1.9 Consensus size: 117
4681376 ACACTCACCC
*
4681386 CCACCTCTTATGTATACAAGTCCCCAACCACCAACACATTCACCACTCCTCTTACTTTACAAGTC
1 CCACCTCTTATGTATACAAGTCCCCAACCACCAACACATTCACCACTCCTCTTACTATACAAGTC
* *
4681451 CCATCCACCACCAGTCCACTCTCCTCTTCCTCCTTATGTCTACAAGTCCCCA
66 CCATCCACCACCAGTCCACTCACCCCTTCCTCCTTATGTCTACAAGTCCCCA
* **
4681503 CCACCTCCTTATGTATACAAGTCTCCACCACCACCAGTACATTCACCACCTCCTCCTTACATATA
1 CCACCT-CTTATGTATACAAGTC-CC-CAACCACCAACACATTCACCA-CTCCT-CTTAC-TATA
* * * *
4681568 CAAGTCTCC-TTCACCACCTGTCCATTCACCACCTT-CTCCTTATGTTTACA
60 CAAGTC-CCATCCACCACCAGTCCACTCACC-CCTTCCTCCTTATGTCTACA
4681618 GAACTCCACC
Statistics
Matches: 97, Mismatches: 10, Indels: 10
0.83 0.09 0.09
Matches are distributed among these distances:
117 6 0.06
118 16 0.16
119 2 0.02
120 18 0.19
121 5 0.05
122 5 0.05
123 40 0.41
124 5 0.05
ACGTcount: A:0.25, C:0.42, G:0.05, T:0.28
Consensus pattern (117 bp):
CCACCTCTTATGTATACAAGTCCCCAACCACCAACACATTCACCACTCCTCTTACTATACAAGTC
CCATCCACCACCAGTCCACTCACCCCTTCCTCCTTATGTCTACAAGTCCCCA
Found at i:4682517 original size:19 final size:21
Alignment explanation
Indices: 4682480--4682519 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
4682470 TCTTTTTTTT
4682480 TAATTTTTTAAAATATAATAA
1 TAATTTTTTAAAATATAATAA
4682501 TAATTTTTT-AAAT-TAATAA
1 TAATTTTTTAAAATATAATAA
4682520 AAACTAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 4 0.21
21 9 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAATTTTTTAAAATATAATAA
Found at i:4687380 original size:3 final size:3
Alignment explanation
Indices: 4687372--4687401 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
4687362 AAATTTTCAT
4687372 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4687402 CAAAAACTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:4688071 original size:16 final size:15
Alignment explanation
Indices: 4688012--4688069 Score: 57
Period size: 15 Copynumber: 3.7 Consensus size: 15
4688002 TACATTTTAT
*
4688012 TTTATTATTAATATA
1 TTTATAATTAATATA
4688027 TATTAT-ATTAATAT-
1 T-TTATAATTAATATA
4688041 TTTAATACATTAAATATA
1 TTT-ATA-ATT-AATATA
4688059 TTTATAATTAA
1 TTTATAATTAA
4688070 ATTAAATAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 2 0.05
14 3 0.08
15 11 0.30
16 10 0.27
17 8 0.22
18 3 0.08
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTATAATTAATATA
Found at i:4688075 original size:21 final size:19
Alignment explanation
Indices: 4688037--4688077 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
4688027 TATTATATTA
*
4688037 ATATTTTAATACATTAAAT
1 ATATTTTAATAAATTAAAT
4688056 ATATTTATAATTAAATTAAAT
1 ATATTT-TAA-TAAATTAAAT
4688077 A
1 A
4688078 AGTATATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 3 0.16
21 10 0.53
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
ATATTTTAATAAATTAAAT
Found at i:4689344 original size:66 final size:66
Alignment explanation
Indices: 4689262--4689392 Score: 192
Period size: 66 Copynumber: 2.0 Consensus size: 66
4689252 TAAATCTCCA
* * *
4689262 CCTCCTCATCCCAAGTCACCACCACCTCATTACGTCTATAAGTCTCCACCACTC-CCATCACACC
1 CCTCCTCATCCAAAGTCACCACCACCTCATTACATCTATAAATCTCCACCAC-CACCATCACACC
4689326 CG
65 CG
* * *
4689328 CCTCCTCATCCAAAGTCACCACCACCTCATTATATTTATAAATCTCCACCACCATCATCACACCC
1 CCTCCTCATCCAAAGTCACCACCACCTCATTACATCTATAAATCTCCACCACCACCATCACACCC
4689393 ACTGCCGGTT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
65 1 0.02
66 57 0.98
ACGTcount: A:0.27, C:0.46, G:0.04, T:0.23
Consensus pattern (66 bp):
CCTCCTCATCCAAAGTCACCACCACCTCATTACATCTATAAATCTCCACCACCACCATCACACCC
G
Found at i:4689475 original size:33 final size:30
Alignment explanation
Indices: 4689407--4689467 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
4689397 CCGGTTCATT
* *
4689407 CACCACCTCCTCATTACGTCTACAAGTCCC
1 CACCACCACCTCATTACATCTACAAGTCCC
**
4689437 CACCACCACCTCATTACATCTATGAGTCCC
1 CACCACCACCTCATTACATCTACAAGTCCC
4689467 C
1 C
4689468 TGCACCACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.25, C:0.46, G:0.07, T:0.23
Consensus pattern (30 bp):
CACCACCACCTCATTACATCTACAAGTCCC
Found at i:4689570 original size:63 final size:60
Alignment explanation
Indices: 4689473--4689622 Score: 178
Period size: 60 Copynumber: 2.5 Consensus size: 60
4689463 TCCCCTGCAC
* * * *
4689473 CACATCCCAAACCCT-CAAAGCACCTCCTCCTCATTACATCT-ACGAGTCCCCACCACCACCAT
1 CACATCCCAACCCCTACAAATCTCCACCTCCTCATTACAT-TAACGAGT--CC-CCACCACCAT
* *
4689535 CACATCCCAACCCCTACAAATCTCCACCTCCTCATTACGTTAATGAGTCCCCACCACCAT
1 CACATCCCAACCCCTACAAATCTCCACCTCCTCATTACATTAACGAGTCCCCACCACCAT
* *
4689595 CTCTTCCCAACCCCTACAAATCTCCACC
1 CACATCCCAACCCCTACAAATCTCCACC
4689623 ACCATCACAT
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
60 36 0.46
61 2 0.03
62 15 0.19
63 25 0.32
ACGTcount: A:0.28, C:0.48, G:0.04, T:0.20
Consensus pattern (60 bp):
CACATCCCAACCCCTACAAATCTCCACCTCCTCATTACATTAACGAGTCCCCACCACCAT
Found at i:4698683 original size:30 final size:30
Alignment explanation
Indices: 4698638--4698716 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 30
4698628 CCATATCCTC
* * *
4698638 ATAAGTCTCCCCCACCTCCGACC-TACTATT
1 ATAAATCTCCACCACCTCC-ACCTTACTACT
* *
4698668 ATAAATCTCCACCACCACCACCTTATTACT
1 ATAAATCTCCACCACCTCCACCTTACTACT
* *
4698698 ATAAATCCCCTCCACCTCC
1 ATAAATCTCCACCACCTCC
4698717 TTCACCATCA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 3 0.08
30 37 0.93
ACGTcount: A:0.28, C:0.44, G:0.03, T:0.25
Consensus pattern (30 bp):
ATAAATCTCCACCACCTCCACCTTACTACT
Found at i:4698770 original size:48 final size:48
Alignment explanation
Indices: 4698718--4699082 Score: 274
Period size: 48 Copynumber: 7.5 Consensus size: 48
4698708 TCCACCTCCT
* * * *
4698718 TCACCATCACCTCCACCTCCCTACTATTATAAGTCTCCACCTCCACCA
1 TCACCATCACCACCACCTCCATACTATTACAAGTCACCACCTCCACCA
* * * * * *
4698766 TCACCATCACCACCACCACCACCTTATTATTACAAGTCACCTCCACCTCCT
1 TCACCATCACCACCACCTCCA---TACTATTACAAGTCACCACCTCCACCA
* * * * *
4698817 TCACCATCTCCCCCACCTCCGTACCATTACAAGTCACCACCTCCGCCA
1 TCACCATCACCACCACCTCCATACTATTACAAGTCACCACCTCCACCA
* * * * * *
4698865 TCTCC--CAGTCCTCCACCACCATACCATTACAAGTCTCCACCCCCACCA
1 TCACCATCA--CCACCACCTCCATACTATTACAAGTCACCACCTCCACCA
* * * * *
4698913 TCTCCATCACCACCACCTCCTTACTATTACAAGTCACCACCACCTCCT
1 TCACCATCACCACCACCTCCATACTATTACAAGTCACCACCTCCACCA
* *
4698961 TCACC-T-AGTCCACCACCTCCATACTACTACAAGTCACCACCTCCACCG
1 TCACCATCA--CCACCACCTCCATACTATTACAAGTCACCACCTCCACCA
* * * * * *
4699009 TCCCCTAGC-CCACCGCCACCATATTACTACAAGTCACCACCTCCACCA
1 TCACC-ATCACCACCACCTCCATACTATTACAAGTCACCACCTCCACCA
* * *
4699057 TCCCCTAGC-CCACCACCACCATACTA
1 TCACC-ATCACCACCACCTCCATACTA
4699083 CTNNNNNNNN
Statistics
Matches: 255, Mismatches: 50, Indels: 24
0.78 0.15 0.07
Matches are distributed among these distances:
46 2 0.01
47 1 0.00
48 213 0.84
50 2 0.01
51 37 0.15
ACGTcount: A:0.26, C:0.50, G:0.04, T:0.21
Consensus pattern (48 bp):
TCACCATCACCACCACCTCCATACTATTACAAGTCACCACCTCCACCA
Found at i:4698859 original size:24 final size:23
Alignment explanation
Indices: 4698829--4699004 Score: 83
Period size: 24 Copynumber: 7.3 Consensus size: 23
4698819 ACCATCTCCC
4698829 CCACCTCCGTACCATTACAAGTCA
1 CCACCTCC-TACCATTACAAGTCA
* * * *
4698853 CCACCTCC-GCCATCTCCCAGTCCT
1 CCACCTCCTACCAT-TACAAGT-CA
* *
4698877 CCACCACCATACCATTACAAGTCT
1 CCACCTCC-TACCATTACAAGTCA
* * *
4698901 CCACC-CCCACCATCTCCATCA-CCA
1 CCACCTCCTACCAT-TACA--AGTCA
*
4698925 CCACCTCCTTACTATTACAAGTCA
1 CCACCTCC-TACCATTACAAGTCA
* *
4698949 CCACCACCT-CC-TTCACCTAGTCCA
1 CCACCTCCTACCATT-A-CAAGT-CA
* *
4698973 CCACCTCCATACTACTACAAGTCA
1 CCACCTCC-TACCATTACAAGTCA
4698997 CCACCTCC
1 CCACCTCC
4699005 ACCGTCCCCT
Statistics
Matches: 113, Mismatches: 23, Indels: 32
0.67 0.14 0.19
Matches are distributed among these distances:
21 2 0.02
22 11 0.10
23 16 0.14
24 57 0.50
25 16 0.14
26 10 0.09
27 1 0.01
ACGTcount: A:0.26, C:0.49, G:0.05, T:0.20
Consensus pattern (23 bp):
CCACCTCCTACCATTACAAGTCA
Found at i:4698942 original size:96 final size:96
Alignment explanation
Indices: 4698709--4699082 Score: 329
Period size: 96 Copynumber: 3.9 Consensus size: 96
4698699 TAAATCCCCT
* * * * * *
4698709 CCACCTCCTTCACCATCACCTCCACCTCCCTACTATTATAAGTCTCCACCTCCACCATCACCATC
1 CCACCACCATCACCATCACCACCACCTCCATACTATTACAAGTCACCACCTCCACCATCACC--C
** * * *
4698774 ACCACCACCACCACCTTATTATTACAAGTCACCT
64 A-GTCCACCACCACCATACTATTACAAGTCACCA
* * * * * * * *
4698808 CCACCTCCTTCACCATCTCCCCCACCTCCGTACCATTACAAGTCACCACCTCCGCCATCTCCCAG
1 CCACCACCATCACCATCACCACCACCTCCATACTATTACAAGTCACCACCTCCACCATCACCCAG
* * *
4698873 TCCTCCACCACCATACCATTACAAGTCTCCA
66 TCCACCACCACCATACTATTACAAGTCACCA
* * * * * * *
4698904 CCCCCACCATCTCCATCACCACCACCTCCTTACTATTACAAGTCACCACCACCTCCTTCACCTAG
1 CCACCACCATCACCATCACCACCACCTCCATACTATTACAAGTCACCACCTCCACCATCACCCAG
* *
4698969 TCCACCACCTCCATACTACTACAAGTCACCA
66 TCCACCACCACCATACTATTACAAGTCACCA
* * * * * * * *
4699000 CCTCCACCGTCCCCTAGC-CCACCGCCACCATATTACTACAAGTCACCACCTCCACCATC-CCCT
1 CCACCACCATCACC-ATCACCACCACCTCCATACTATTACAAGTCACCACCTCCACCATCACCC-
*
4699063 AGCCCACCACCACCATACTA
64 AGTCCACCACCACCATACTA
4699083 CTNNNNNNNN
Statistics
Matches: 224, Mismatches: 49, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
95 2 0.01
96 164 0.73
97 4 0.02
99 54 0.24
ACGTcount: A:0.25, C:0.50, G:0.04, T:0.21
Consensus pattern (96 bp):
CCACCACCATCACCATCACCACCACCTCCATACTATTACAAGTCACCACCTCCACCATCACCCAG
TCCACCACCACCATACTATTACAAGTCACCA
Found at i:4698957 original size:27 final size:26
Alignment explanation
Indices: 4698919--4699001 Score: 86
Period size: 27 Copynumber: 3.3 Consensus size: 26
4698909 ACCATCTCCA
4698919 TCACCACCACCTCCTTACTATTACAAG
1 TCACCACCACCTCCTTACTA-TACAAG
* *
4698946 TCACCACCACCTCCTT-C-A-CCTAG
1 TCACCACCACCTCCTTACTATACAAG
*
4698969 T--CCACCACCTCCATACTACTACAAG
1 TCACCACCACCTCCTTACTA-TACAAG
4698994 TCACCACC
1 TCACCACC
4699002 TCCACCGTCC
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
21 12 0.27
22 1 0.02
23 5 0.11
25 5 0.11
26 1 0.02
27 21 0.47
ACGTcount: A:0.28, C:0.47, G:0.04, T:0.22
Consensus pattern (26 bp):
TCACCACCACCTCCTTACTATACAAG
Found at i:4698959 original size:144 final size:145
Alignment explanation
Indices: 4698727--4699077 Score: 411
Period size: 144 Copynumber: 2.4 Consensus size: 145
4698717 TTCACCATCA
* * *
4698727 CCTCCACCTCCCTACTATTATAAGTCTCCACCTCCACCATCACCATCACCACCACCACCACCTTA
1 CCTCCACCACCATACTATTACAAGTCTCCACCTCCACCATCACCAT--CCACCACCACCACCTTA
* * * * *
4698792 TTATTACAAGTCACCTCCACCTCCTTCACC-ATCTCCCCCACCTCCGTACCATTACAAGTCACCA
64 CTATTACAAGTCACCACCACCTCCTTCACCTA-CTCCACCACCTCCATACCACTACAAGTCACCA
* *
4698856 CCTCCGCCATCTCCC-AGT
128 CCTCCACCATC-CCCTAGC
* * * *
4698874 CCTCCACCACCATACCATTACAAGTCTCCACCCCCACCATCTCCAT-CACCACCACCTCCTTACT
1 CCTCCACCACCATACTATTACAAGTCTCCACCTCCACCATCACCATCCACCACCACCACCTTACT
* *
4698938 ATTACAAGTCACCACCACCTCCTTCACCTAGTCCACCACCTCCATACTACTACAAGTCACCACCT
66 ATTACAAGTCACCACCACCTCCTTCACCTACTCCACCACCTCCATACCACTACAAGTCACCACCT
*
4699003 CCACCGTCCCCTAGC
131 CCACCATCCCCTAGC
* * * * * * *
4699018 CCACCGCCACCATATTACTACAAGTCACCACCTCCACCATCCCCTAGCCCACCACCACCA
1 CCTCCACCACCATACTATTACAAGTCTCCACCTCCACCATCACC-A-TCCACCACCACCA
4699078 TACTACTNNN
Statistics
Matches: 172, Mismatches: 27, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
143 3 0.02
144 117 0.68
145 2 0.01
147 50 0.29
ACGTcount: A:0.25, C:0.50, G:0.04, T:0.20
Consensus pattern (145 bp):
CCTCCACCACCATACTATTACAAGTCTCCACCTCCACCATCACCATCCACCACCACCACCTTACT
ATTACAAGTCACCACCACCTCCTTCACCTACTCCACCACCTCCATACCACTACAAGTCACCACCT
CCACCATCCCCTAGC
Found at i:4702873 original size:48 final size:48
Alignment explanation
Indices: 4702729--4702882 Score: 157
Period size: 48 Copynumber: 3.2 Consensus size: 48
4702719 AAGATGAATC
* * *
4702729 ACTTTTAGTAATGAGGAGGTGGTGGG-GAAGGAGATGGTGGAGGGGGTG
1 ACTTGTAGTAATAAGGAGGTGG-GGGTGAAGGAGATGGTGGAGGCGGTG
* * * * * * * * *
4702777 ACTTATAATAATAAGGTGGTGGTGGTGATGGGGAAGGAGGTGGCGGTG
1 ACTTGTAGTAATAAGGAGGTGGGGGTGAAGGAGATGGTGGAGGCGGTG
* * *
4702825 ATTTGTAGTAGTAAGGAGGTGGGGGTGAAGGAGATGGTGGAGGTGGTG
1 ACTTGTAGTAATAAGGAGGTGGGGGTGAAGGAGATGGTGGAGGCGGTG
4702873 ACTTGTAGTA
1 ACTTGTAGTA
4702883 NNNNNNNNNN
Statistics
Matches: 81, Mismatches: 24, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
47 2 0.02
48 79 0.98
ACGTcount: A:0.24, C:0.03, G:0.48, T:0.25
Consensus pattern (48 bp):
ACTTGTAGTAATAAGGAGGTGGGGGTGAAGGAGATGGTGGAGGCGGTG
Found at i:4704757 original size:22 final size:22
Alignment explanation
Indices: 4704732--4704777 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
4704722 AACAGTATGA
4704732 AATAGTATGCAACTTCAACAGT
1 AATAGTATGCAACTTCAACAGT
4704754 AATAGTATGCAACTTCAACAGT
1 AATAGTATGCAACTTCAACAGT
4704776 AA
1 AA
4704778 ATTTGGCTTT
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:0.43, C:0.17, G:0.13, T:0.26
Consensus pattern (22 bp):
AATAGTATGCAACTTCAACAGT
Done.