Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 138 of 199
Found at i:41823458 original size:35 final size:35
Alignment explanation
Indices: 41823419--41823490 Score: 90
Period size: 35 Copynumber: 2.1 Consensus size: 35
41823409 ATAAATGGTT
* * * *
41823419 TACTGGCTCTACGGAGTGACATCATGGAAATGATC
1 TACTGGCTCTACAGAGCGACACCATGAAAATGATC
* *
41823454 TACTGGTTCTACAGAGCGACACCATGAAAATGGTC
1 TACTGGCTCTACAGAGCGACACCATGAAAATGATC
41823489 TA
1 TA
41823491 TTGACTCTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.25
Consensus pattern (35 bp):
TACTGGCTCTACAGAGCGACACCATGAAAATGATC
Found at i:41825145 original size:25 final size:25
Alignment explanation
Indices: 41825089--41825136 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
41825079 TTAACAATTT
41825089 ATAGCTCGTGAGAGCATACCGATTC
1 ATAGCTCGTGAGAGCATACCGATTC
41825114 ATAGCTCGTGAGAGCATACCGAT
1 ATAGCTCGTGAGAGCATACCGAT
41825137 CTTCAGCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (25 bp):
ATAGCTCGTGAGAGCATACCGATTC
Found at i:41825176 original size:25 final size:25
Alignment explanation
Indices: 41825091--41825182 Score: 91
Period size: 25 Copynumber: 3.7 Consensus size: 25
41825081 AACAATTTAT
*
41825091 AGCTCGTGA-GAGCATACCGATTCAT
1 AGCTCGT-ATGAGCATACCGATTCAC
*
41825116 AGCTCGTGA-GAGCATACCGA-TCTTC
1 AGCTCGT-ATGAGCATACCGATTC-AC
**
41825141 AGCTCAAATGAGCATACCGATTCAC
1 AGCTCGTATGAGCATACCGATTCAC
*
41825166 AGGTCGTATGAGCATAC
1 AGCTCGTATGAGCATAC
41825183 ATGTACATGA
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
24 3 0.05
25 51 0.91
26 2 0.04
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (25 bp):
AGCTCGTATGAGCATACCGATTCAC
Found at i:41830439 original size:7 final size:7
Alignment explanation
Indices: 41830427--41830477 Score: 68
Period size: 7 Copynumber: 7.4 Consensus size: 7
41830417 TAATTTGAAT
41830427 CCTAAAC
1 CCTAAAC
41830434 CCTAAAC
1 CCTAAAC
**
41830441 TTTAAA-
1 CCTAAAC
41830447 CCTAAAC
1 CCTAAAC
*
41830454 CTTAAAC
1 CCTAAAC
41830461 CCTAAAC
1 CCTAAAC
41830468 CCTAAAC
1 CCTAAAC
41830475 CCT
1 CCT
41830478 GACCTTTTGG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
6 4 0.11
7 33 0.89
ACGTcount: A:0.41, C:0.37, G:0.00, T:0.22
Consensus pattern (7 bp):
CCTAAAC
Found at i:41836419 original size:41 final size:40
Alignment explanation
Indices: 41836345--41836424 Score: 99
Period size: 42 Copynumber: 2.0 Consensus size: 40
41836335 TTGTAATATT
41836345 ATTATTTATACTAAGTATTTAAAAGATAATTAAATATTTAG
1 ATTATTTATACTAAGTATTTAAAAGATAATTAAA-ATTTAG
* * * *
41836386 ATTATTTTATATTAATTATTTACAA-ATATTTAAAATTTA
1 ATTA-TTTATACTAAGTATTTAAAAGATAATTAAAATTTA
41836425 TATTTCATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
40 5 0.15
41 12 0.35
42 17 0.50
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.49
Consensus pattern (40 bp):
ATTATTTATACTAAGTATTTAAAAGATAATTAAAATTTAG
Found at i:41839060 original size:26 final size:26
Alignment explanation
Indices: 41839024--41839086 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
41839014 TAGTGATTAT
41839024 GTGATTATTTAGCAAGCTTTGAGCTG
1 GTGATTATTTAGCAAGCTTTGAGCTG
* *
41839050 GTGATTTTTTAGCAAGCTTTGAGCCG
1 GTGATTATTTAGCAAGCTTTGAGCTG
*
41839076 ATGATTATTTA
1 GTGATTATTTA
41839087 ATAGGCTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.24, C:0.11, G:0.24, T:0.41
Consensus pattern (26 bp):
GTGATTATTTAGCAAGCTTTGAGCTG
Found at i:41840425 original size:21 final size:22
Alignment explanation
Indices: 41840385--41840432 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
41840375 ACGGTTTGAG
* *
41840385 CACACGGGCGTGTGGAGGTAGT
1 CACACGGGCATGTGGAGGTAGC
41840407 CACACGGGCATGT-GAGGTAGC
1 CACACGGGCATGTGGAGGTAGC
41840428 CACAC
1 CACAC
41840433 AGGCTAACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.23, C:0.25, G:0.38, T:0.15
Consensus pattern (22 bp):
CACACGGGCATGTGGAGGTAGC
Found at i:41840974 original size:13 final size:13
Alignment explanation
Indices: 41840956--41840980 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41840946 AACATATTTT
41840956 TTTATTTGTGTAG
1 TTTATTTGTGTAG
41840969 TTTATTTGTGTA
1 TTTATTTGTGTA
41840981 ACACCCGTAA
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:0.16, C:0.00, G:0.20, T:0.64
Consensus pattern (13 bp):
TTTATTTGTGTAG
Found at i:41849026 original size:18 final size:17
Alignment explanation
Indices: 41848985--41849028 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
41848975 GTCGTTCGTG
41848985 TTCAAAACGTTATTCAT
1 TTCAAAACGTTATTCAT
*
41849002 TTACAAATCGTTATTCAAT
1 TT-CAAAACGTTATTC-AT
41849021 TTCAAAAC
1 TTCAAAAC
41849029 ATTTTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 17 0.74
19 4 0.17
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.39
Consensus pattern (17 bp):
TTCAAAACGTTATTCAT
Found at i:41852230 original size:39 final size:39
Alignment explanation
Indices: 41852187--41852265 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
41852177 TTAACTTTTA
* * *
41852187 CGGTTTAATCTTTTTTACTCAATTAAGTATCTAAATGTT
1 CGGTTTAATCCTGTTTACTCAATTAAGTATCTAAACGTT
41852226 CGGTTTAATCCTGTTTACTCAATTAAGTATCTAAACGTT
1 CGGTTTAATCCTGTTTACTCAATTAAGTATCTAAACGTT
41852265 C
1 C
41852266 AAATTTCTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.28, C:0.16, G:0.11, T:0.44
Consensus pattern (39 bp):
CGGTTTAATCCTGTTTACTCAATTAAGTATCTAAACGTT
Found at i:41856477 original size:37 final size:38
Alignment explanation
Indices: 41856420--41856495 Score: 136
Period size: 37 Copynumber: 2.0 Consensus size: 38
41856410 ATTTTTAACG
*
41856420 TTAATTCTGTCCTATTATTTGCCCTAATTGACATAAAA
1 TTAATTCTGTCCCATTATTTGCCCTAATTGACATAAAA
41856458 TTAATTCT-TCCCATTATTTGCCCTAATTGACATAAAA
1 TTAATTCTGTCCCATTATTTGCCCTAATTGACATAAAA
41856495 T
1 T
41856496 CCACCCTCTC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 29 0.78
38 8 0.22
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.42
Consensus pattern (38 bp):
TTAATTCTGTCCCATTATTTGCCCTAATTGACATAAAA
Found at i:41864211 original size:23 final size:23
Alignment explanation
Indices: 41864134--41864243 Score: 104
Period size: 23 Copynumber: 5.0 Consensus size: 23
41864124 TCTGATCAGC
41864134 ATACGACACAT-AAGTGCCTGA-
1 ATACGACACATAAAGTGCCTGAT
****
41864155 A-ACGACACACGGGGTGCCTG--
1 ATACGACACATAAAGTGCCTGAT
* *
41864175 ATACGACATATAAAGTGCTTGAT
1 ATACGACACATAAAGTGCCTGAT
* *
41864198 ATGCGACACGTAAAGTGCCTGAT
1 ATACGACACATAAAGTGCCTGAT
*
41864221 GTACGACACATAAAGTGCCTGAT
1 ATACGACACATAAAGTGCCTGAT
41864244 CGGCAAGGCC
Statistics
Matches: 69, Mismatches: 16, Indels: 6
0.76 0.18 0.07
Matches are distributed among these distances:
20 9 0.13
21 21 0.30
23 39 0.57
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.21
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAT
Found at i:41865251 original size:13 final size:13
Alignment explanation
Indices: 41865233--41865262 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
41865223 AACCTTTAGT
*
41865233 TTTTCTTTTTTTC
1 TTTTCTTTCTTTC
41865246 TTTTCTTTCTTTC
1 TTTTCTTTCTTTC
41865259 TTTT
1 TTTT
41865263 TCCTGCTCTG
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:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTCTTTCTTTC
Found at i:41865492 original size:14 final size:17
Alignment explanation
Indices: 41865473--41865510 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
41865463 ATTTATTTCT
41865473 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
41865487 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
41865504 TAATATA
1 TAATATA
41865511 CTTTATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.38
15 1 0.05
16 4 0.19
17 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:41874578 original size:25 final size:26
Alignment explanation
Indices: 41874550--41874664 Score: 73
Period size: 25 Copynumber: 4.6 Consensus size: 26
41874540 CAAACCAAAC
41874550 AAAGCCTATGTGACATA-TTATCTAG
1 AAAGCCTATGTGACATAGTTATCTAG
* * *
41874575 AAAGCCTTTG-GGC-TAGTTAGCTA-
1 AAAGCCTATGTGACATAGTTATCTAG
* * *
41874598 AAAGGCCTATGTGGCATA-TTATTTGG
1 AAA-GCCTATGTGACATAGTTATCTAG
** * *
41874624 AAAAACTTTGTGACA-AGTTAT-TTG
1 AAAGCCTATGTGACATAGTTATCTAG
41874648 AAATGCCTATGTGACAT
1 AAA-GCCTATGTGACAT
41874665 TATTTTGGAA
Statistics
Matches: 67, Mismatches: 15, Indels: 15
0.69 0.15 0.15
Matches are distributed among these distances:
23 5 0.07
24 20 0.30
25 37 0.55
26 5 0.07
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (26 bp):
AAAGCCTATGTGACATAGTTATCTAG
Found at i:41878428 original size:14 final size:14
Alignment explanation
Indices: 41878409--41878448 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
41878399 TTGATTGGCA
41878409 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
41878423 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
41878437 GGAAAATGTTTT
1 GTAAAATGTTTT
41878449 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:41878457 original size:20 final size:20
Alignment explanation
Indices: 41878432--41878471 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
41878422 CGTAAAATGA
*
41878432 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
41878452 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
41878472 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:41878461 original size:34 final size:35
Alignment explanation
Indices: 41878417--41878483 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
41878407 CAGTAAAATG
*
41878417 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
41878451 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
41878484 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:41878487 original size:14 final size:15
Alignment explanation
Indices: 41878411--41878487 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
41878401 GATTGGCAGT
* *
41878411 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
41878425 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
41878439 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
41878459 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
41878474 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
41878488 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:41878548 original size:32 final size:32
Alignment explanation
Indices: 41878464--41878549 Score: 93
Period size: 33 Copynumber: 2.6 Consensus size: 32
41878454 TCTGTAAAAT
* * *
41878464 GATTTACTGGAAAATATTTTCTGGTGTTTGATT
1 GATTTCCT-GAAAATATTTTCTGCTGTTTGATA
* *
41878497 GA-ATCTGTGTAAAATATTTTCTGCTGTTTGATA
1 GATTTC-CTG-AAAATATTTTCTGCTGTTTGATA
41878530 GATTTCCTGAAAATATTTTC
1 GATTTCCTGAAAATATTTTC
41878550 CGGAAAAGTT
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
32 13 0.30
33 28 0.65
34 2 0.05
ACGTcount: A:0.27, C:0.09, G:0.17, T:0.47
Consensus pattern (32 bp):
GATTTCCTGAAAATATTTTCTGCTGTTTGATA
Found at i:41881016 original size:6 final size:6
Alignment explanation
Indices: 41881005--41881049 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
41880995 TGTCAAGGAT
* * *
41881005 AGGGGA AGGGGA AGGGGA AGGGGA AGGGAA AGGGAA AGGGAA AGG
1 AGGGGA AGGGGA AGGGGA AGGGGA AGGGGA AGGGGA AGGGGA AGG
41881050 AAAATTTTCC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (6 bp):
AGGGGA
Found at i:41881052 original size:17 final size:17
Alignment explanation
Indices: 41881014--41881052 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
41881004 TAGGGGAAGG
* * *
41881014 GGAAGGGGAAGGGGAAG
1 GGAAAGGGAAAGGGAAA
41881031 GGAAAGGGAAAGGGAAA
1 GGAAAGGGAAAGGGAAA
41881048 GGAAA
1 GGAAA
41881053 ATTTTCCTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (17 bp):
GGAAAGGGAAAGGGAAA
Found at i:41893275 original size:29 final size:31
Alignment explanation
Indices: 41893227--41893289 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 31
41893217 GGGTCCAATT
* * *
41893227 TTTTTAAAGTTGCTCGTAT-AGGAGTTAA-A
1 TTTTTAAAATTGATCATATAAGGAGTTAACA
*
41893256 TTTTTAAAATTGATCATATAAGGATTTAACA
1 TTTTTAAAATTGATCATATAAGGAGTTAACA
41893287 TTT
1 TTT
41893290 ACAAAAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 16 0.57
30 8 0.29
31 4 0.14
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.44
Consensus pattern (31 bp):
TTTTTAAAATTGATCATATAAGGAGTTAACA
Found at i:41894224 original size:27 final size:27
Alignment explanation
Indices: 41894194--41894266 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
41894184 ATAGGTGGTG
*
41894194 CCTATCTGGTAGGCGCCACCGGTGACT
1 CCTATCTGATAGGCGCCACCGGTGACT
* *
41894221 CCTATCTAATAGGCGCCACTGGTGACT
1 CCTATCTGATAGGCGCCACCGGTGACT
41894248 CCTA-CTTGATAGGCGCCAC
1 CCTATC-TGATAGGCGCCAC
41894267 TAGTGCTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 1 0.02
27 40 0.98
ACGTcount: A:0.19, C:0.33, G:0.25, T:0.23
Consensus pattern (27 bp):
CCTATCTGATAGGCGCCACCGGTGACT
Found at i:41896299 original size:62 final size:62
Alignment explanation
Indices: 41896217--41896377 Score: 207
Period size: 62 Copynumber: 2.6 Consensus size: 62
41896207 CCGTGAGATT
* * **
41896217 TTATACCACAAATAATGAGTTACACGACCAAGGCACACGCCTGTGTCCCTAGCCATGTGGTC
1 TTATACCACAAACAGTGAGTTACACGACCAAGGCACACGCCCATGTCCCTAGCCATGTGGTC
* * * * *
41896279 TTATACTATAAACAGTGAGTTATAC-AGCCAAAGCACACGCCCATGTCCCTAGCCGTGTGGTC
1 TTATACCACAAACAGTGAGTTACACGA-CCAAGGCACACGCCCATGTCCCTAGCCATGTGGTC
* *
41896341 TTATACCACAAACAGTGAGTTACACGGCCATGGCACA
1 TTATACCACAAACAGTGAGTTACACGACCAAGGCACA
41896378 TATTCGTGTG
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
61 1 0.01
62 81 0.99
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.22
Consensus pattern (62 bp):
TTATACCACAAACAGTGAGTTACACGACCAAGGCACACGCCCATGTCCCTAGCCATGTGGTC
Found at i:41896372 original size:49 final size:50
Alignment explanation
Indices: 41896313--41896414 Score: 125
Period size: 50 Copynumber: 2.1 Consensus size: 50
41896303 CAGCCAAAGC
* *
41896313 ACACGCCCATGTC-CCTAGCCGTGTGGTCTTATACCACAAACAGTGAGTT
1 ACACGCCCATGGCACATAGCCGTGTGGTCTTATACCACAAACAGTGAGTT
* ** * * *
41896362 ACACGGCCATGGCACATATTCGTGTGGTTTTATACCATAAACAGTGCGTT
1 ACACGCCCATGGCACATAGCCGTGTGGTCTTATACCACAAACAGTGAGTT
41896412 ACA
1 ACA
41896415 TTGCCAATTA
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
49 11 0.25
50 33 0.75
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (50 bp):
ACACGCCCATGGCACATAGCCGTGTGGTCTTATACCACAAACAGTGAGTT
Found at i:41913510 original size:44 final size:43
Alignment explanation
Indices: 41913460--41914364 Score: 377
Period size: 44 Copynumber: 20.8 Consensus size: 43
41913450 GATCGCATCT
41913460 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCA
* * *
41913504 AGTCTTATC-CTCCTTAAGTTGCAGTGGGGCAGACTGAAGATGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGAGCAGACT-AAGA-AGCA
** * *
41913549 AACCTTATCTCCCTGAAGTTGCAGTGGAGCAG-GTTA-AAGCCGA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A
* * * * * * * * *
41913592 TAATCCTATCTCTCTAAAGTTGTAGTGGAACGGA-TTA-AAGTCTT
1 -AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A
* * * * * * * *
41913636 GGATCTTATCTCTCTGAAGTTGCAG-AGAGCATA-T-CGCATCT
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
*
41913677 AGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCA
* * *
41913721 AGTCTTATC-CTCCTGAAGTTGCAGTGGGGCAAACTGAAGATGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGAGCAGACT-AAGA-AGCA
** * * *
41913766 AACCTTATCTCCCTAAAGTTGCAGTGGAGCAG-GTTA-AAGCTGA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGC--A
* * * * * ** * * *
41913809 TAATCCTATCTCCCTAAAGTTGTAGTGAAGTGGATTAA-AATCTT
1 -AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGC-A
* * * * * * *
41913853 GGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CGCACCT
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
*
41913894 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGTA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCA
* * *
41913938 GGTCTTATC-CTCCTGAAGTTGCAGT-AAGGCAGACTGAAGATGGCGA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGC-A
*
41913984 A-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTA-AAGCCGA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A
* * * * * ** *
41914026 TAGTCCTATCTCCCTAAAGTTGTAGTGGATCAGATTAA-ATCCTT
1 -AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGC-A
* * * * * * *
41914070 TGATCTTATCTCTCTGAAGTTGCAG-AGAGCAAGA-T-CGCACCT
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGC-AGACTAAGAAGCA
*
41914112 AGCCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGC-
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCA
* * *
41914155 AGTTCTTATC-CTCTTGAAGTTGCAGT-AAGGCAGACTGAAGATGGCGA
1 AG-TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGC-A
*
41914202 A-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAG--GCCAA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A
* * * * *
41914244 TAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAA-AATCA
1 -AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
* * * * * * *
41914287 CAGATCTTATCTCTCTGAAGTTGCAG-AGAACAGA-T-CGCATCT
1 -AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
*
41914329 AGTCTTATCTCCCTGACA-TTGCAGTGGAGTAGACTA
1 AGTCTTATCTCCCTGA-AGTTGCAGTGGAGCAGACTA
41914365 CAGCACTAGT
Statistics
Matches: 651, Mismatches: 144, Indels: 133
0.70 0.16 0.14
Matches are distributed among these distances:
40 60 0.09
41 53 0.08
42 27 0.04
43 42 0.06
44 329 0.51
45 132 0.20
46 7 0.01
47 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (43 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
Found at i:41913749 original size:217 final size:217
Alignment explanation
Indices: 41913374--41914364 Score: 1504
Period size: 217 Copynumber: 4.6 Consensus size: 217
41913364 TTGGTGGCCA
* * * * *
41913374 ATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATTTTGGATCTTATCTCTCTGCAGT
1 ATAATCCTATCTCCCTAAAGTTGTAGTGGAACGGATTAAAATCTTGGATCTTATCTCTCTGAAGT
*
41913439 TGTAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
66 TGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
* **
41913504 AGTCTTATCCTCCTTAAGTTGCAGTGGGGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTT
131 AGTCTTATCCTCCTGAAGTTGCAGTAAGGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTT
*
41913569 GCAGTGGAGCAGGTTAAAGCCG
196 GCAGTGGAGCAGATTAAAGCCG
* *
41913591 ATAATCCTATCTCTCTAAAGTTGTAGTGGAACGGATTAAAGTCTTGGATCTTATCTCTCTGAAGT
1 ATAATCCTATCTCCCTAAAGTTGTAGTGGAACGGATTAAAATCTTGGATCTTATCTCTCTGAAGT
* *
41913656 TGCAGAGAGCATATCGCATCTAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
66 TGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
** * *
41913721 AGTCTTATCCTCCTGAAGTTGCAGTGGGGCAAACTGAAGATGGCAAACCTTATCTCCCTAAAGTT
131 AGTCTTATCCTCCTGAAGTTGCAGTAAGGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTT
* *
41913786 GCAGTGGAGCAGGTTAAAGCTG
196 GCAGTGGAGCAGATTAAAGCCG
*
41913808 ATAATCCTATCTCCCTAAAGTTGTAGT-GAAGTGGATTAAAATCTTGGATCTTATCTCTCTGAAG
1 ATAATCCTATCTCCCTAAAGTTGTAGTGGAA-CGGATTAAAATCTTGGATCTTATCTCTCTGAAG
* *
41913872 TTGCAGAGAGCAGATCGCACCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGT
65 TTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGC
* * *
41913937 AGGTCTTATCCTCCTGAAGTTGCAGTAAGGCAGACTGAAGATGGCGAATCTTATCTCCCTGAAGT
130 AAGTCTTATCCTCCTGAAGTTGCAGTAAGGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGT
41914002 TGCAGTGGAGCAGATTAAAGCCG
195 TGCAGTGGAGCAGATTAAAGCCG
* * * *
41914025 ATAGTCCTATCTCCCTAAAGTTGTAGTGGATCAGATT-AAATCCTTTGATCTTATCTCTCTGAAG
1 ATAATCCTATCTCCCTAAAGTTGTAGTGGAACGGATTAAAAT-CTTGGATCTTATCTCTCTGAAG
* *
41914089 TTGCAGAGAGCAAGATCGCACCTAGCCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAG
65 TTGCAGAGAGC-AGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAG
* * *
41914154 C-AGTTCTTATCCTCTTGAAGTTGCAGTAAGGCAGACTGAAGATGGCGAATCTTATCTCCCTGAA
129 CAAG-TCTTATCCTCCTGAAGTTGCAGTAAGGCAGACTGAAGATGGCAAACCTTATCTCCCTGAA
* *
41914218 GTTGCAGTGGAGCAGATTAAGGCCA
193 GTTGCAGTGGAGCAGATTAAAGCCG
* * * ***
41914243 ATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGT
1 ATAATCCTATCTCCCTAAAGTTGTAGTGGAACGGATTAAAATCTTGGATCTTATCTCTCTGAAGT
* *
41914308 TGCAGAGAACAGATCGCATCTAGTCTTATCTCCCTGACA-TTGCAGTGGAGTAGACTA
66 TGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGA-AGTTGCAGTGGAGCAGACTA
41914365 CAGCACTAGT
Statistics
Matches: 714, Mismatches: 53, Indels: 14
0.91 0.07 0.02
Matches are distributed among these distances:
216 7 0.01
217 505 0.71
218 198 0.28
219 4 0.01
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.28
Consensus pattern (217 bp):
ATAATCCTATCTCCCTAAAGTTGTAGTGGAACGGATTAAAATCTTGGATCTTATCTCTCTGAAGT
TGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
AGTCTTATCCTCCTGAAGTTGCAGTAAGGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTT
GCAGTGGAGCAGATTAAAGCCG
Found at i:41915674 original size:18 final size:18
Alignment explanation
Indices: 41915651--41915691 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
41915641 TTTACCCCAA
41915651 AATTTTGAATTCCAGTTC
1 AATTTTGAATTCCAGTTC
*
41915669 AATTTTGAATTCCAGTTT
1 AATTTTGAATTCCAGTTC
41915687 AATTT
1 AATTT
41915692 AGTCCTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.49
Consensus pattern (18 bp):
AATTTTGAATTCCAGTTC
Found at i:41916084 original size:19 final size:20
Alignment explanation
Indices: 41916043--41916084 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
41916033 ATTTCTATGT
* *
41916043 CATTGTAATATTTATTATTG
1 CATTGTAATATTTAATATAG
*
41916063 CATTGT-ATATTTAATGTAG
1 CATTGTAATATTTAATATAG
41916082 CAT
1 CAT
41916085 CACATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Found at i:41917477 original size:5 final size:5
Alignment explanation
Indices: 41917467--41917497 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
41917457 GTAAATTAAT
41917467 AAATA AAATA AAATA AAATA AAATA AAATA A
1 AAATA AAATA AAATA AAATA AAATA AAATA A
41917498 TAATGATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:41917605 original size:18 final size:18
Alignment explanation
Indices: 41917582--41917630 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
41917572 GATATAAATA
41917582 AATAATAAATAAAATGAT
1 AATAATAAATAAAATGAT
*
41917600 AATAATAAA-AGTAATGAT
1 AATAATAAATA-AAATGAT
41917618 AA-AA-AAATAAAAT
1 AATAATAAATAAAAT
41917631 AAGTGTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
16 6 0.22
17 4 0.15
18 17 0.63
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.24
Consensus pattern (18 bp):
AATAATAAATAAAATGAT
Found at i:41919155 original size:45 final size:44
Alignment explanation
Indices: 41919003--41919209 Score: 149
Period size: 44 Copynumber: 4.7 Consensus size: 44
41918993 ATTTGCTCTG
* *
41919003 CTGTAACTTCAGGGAGATAAAATTAG-TAGCTTCAATCTACTCCA
1 CTGTAACTTCAGGGAGATAAGATT-GCTATCTTCAATCTACTCCA
* * * * **
41919047 CTGCAACTTTC-GGGAAATAAAATT--TATCACTTTAATCTACTTTA
1 CTGTAAC-TTCAGGGAGATAAGATTGCTAT--CTTCAATCTACTCCA
* * *
41919091 CTGTAATTTCAAAGG-GATAAGATCTGCTATCTTCAATCTGCTCCA
1 CTGTAACTTC-AGGGAGATAAGAT-TGCTATCTTCAATCTACTCCA
* *
41919136 CTGTAACTTCAGGGAGATAAGATTTGCTGTCTTCAATCTACT-TA
1 CTGTAACTTCAGGGAGATAAGA-TTGCTATCTTCAATCTACTCCA
* *
41919180 CTGCAACTTCAGAGG-GATGAGATTTGCTAT
1 CTGTAACTTCAG-GGAGATAAGA-TTGCTAT
41919210 GGTAGATTTA
Statistics
Matches: 129, Mismatches: 23, Indels: 22
0.74 0.13 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.02
44 69 0.53
45 51 0.40
46 1 0.01
47 3 0.02
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.34
Consensus pattern (44 bp):
CTGTAACTTCAGGGAGATAAGATTGCTATCTTCAATCTACTCCA
Found at i:41919181 original size:89 final size:89
Alignment explanation
Indices: 41919032--41919209 Score: 207
Period size: 89 Copynumber: 2.0 Consensus size: 89
41919022 AAATTAGTAG
* *
41919032 CTTCAATCTACTCCACTGCAACTTTCGGGAAATAAAATTTATCACTTTAATCTACTTTACTGTAA
1 CTTCAATCTACTCCACTGCAACTTTCGGGAAATAAAATTTATCACTTCAATCTACTTTACTGCAA
*
41919097 TTTCAAAGGGATAAGATCTGCTAT
66 CTTCAAAGGGATAAGATCTGCTAT
* * * * * **
41919121 CTTCAATCTGCTCCACTGTAAC-TTCAGGGAGATAAGATTTGCTGTCTTCAATCTAC-TTACTGC
1 CTTCAATCTACTCCACTGCAACTTTC-GGGAAATAAAATTT-ATCACTTCAATCTACTTTACTGC
* * *
41919184 AACTTCAGAGGGATGAGATTTGCTAT
64 AACTTCAAAGGGATAAGATCTGCTAT
41919210 GGTAGATTTA
Statistics
Matches: 74, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
88 3 0.04
89 60 0.81
90 11 0.15
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (89 bp):
CTTCAATCTACTCCACTGCAACTTTCGGGAAATAAAATTTATCACTTCAATCTACTTTACTGCAA
CTTCAAAGGGATAAGATCTGCTAT
Found at i:41919203 original size:44 final size:44
Alignment explanation
Indices: 41919080--41919209 Score: 154
Period size: 45 Copynumber: 2.9 Consensus size: 44
41919070 TTATCACTTT
* * *
41919080 AATCTACTTTACTGTAATTTCAAAGGGATAAGATCTGCTATCTTC
1 AATCTAC-TTACTGTAACTTCAGAGGGATAAGATTTGCTATCTTC
* * *
41919125 AATCTGCTCCACTGTAACTTCAG-GGAGATAAGATTTGCTGTCTTC
1 AATCTACT-TACTGTAACTTCAGAGG-GATAAGATTTGCTATCTTC
* *
41919170 AATCTACTTACTGCAACTTCAGAGGGATGAGATTTGCTAT
1 AATCTACTTACTGTAACTTCAGAGGGATAAGATTTGCTAT
41919210 GGTAGATTTA
Statistics
Matches: 71, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
44 28 0.39
45 43 0.61
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (44 bp):
AATCTACTTACTGTAACTTCAGAGGGATAAGATTTGCTATCTTC
Found at i:41919345 original size:44 final size:44
Alignment explanation
Indices: 41919266--41919821 Score: 268
Period size: 44 Copynumber: 11.9 Consensus size: 44
41919256 TGACTTATAA
* * * *
41919266 CTTTAATCTATTCCACTGCAATTTCAGGGAAATAAGATTCGCAT
1 CTTTAATCTGTTCCATTGCAACTTCAAGGAAATAAGATTCGCAT
* * * * *
41919310 CTTCAATCTATTCCATTGCAACTTCAAGGAGATAAGATTTGTGGCTTTAAG
1 CTTTAATCTGTTCCATTGCAACTTCAAGGAAATAAGA--T-TCGC----AT
** *
41919361 CTTTAATCTGTTCCACAGCAACTTCAGGGAAATAAGATTCGCAT
1 CTTTAATCTGTTCCATTGCAACTTCAAGGAAATAAGATTCGCAT
* * * * *
41919405 CTTTAATCTGTTTCATTTCAACTTCAAGGAGATAAGATTTGTGGCTTTAAG
1 CTTTAATCTGTTCCATTGCAACTTCAAGGAAATAAGA--T-TCGC----AT
* * * * *
41919456 ATTTAATCTTTTTCACTGCAACTTCAGGGAAATAAGATTCGCAT
1 CTTTAATCTGTTCCATTGCAACTTCAAGGAAATAAGATTCGCAT
* * * * * * * *
41919500 CGTCAATCTGCTCTATTGCAACTTCAAGGAGATAACATTTGTAGCTTTAAA
1 CTTTAATCTGTTCCATTGCAACTTCAAGGAAATAAGA--T-TCGC----AT
* * * * *
41919551 CTTTAATCTGTTCGACTGCAATTTCAGGGAAATAAGATTTGCAT
1 CTTTAATCTGTTCCATTGCAACTTCAAGGAAATAAGATTCGCAT
* * * * *
41919595 CTTTAATTTGCTCCATTGTAACTTCAA-GAAGATAAGATTTGTAGCTTTAA
1 CTTTAATCTGTTCCATTGCAACTTCAAGGAA-ATAAGA--T-TCGC---AT
* * * * * * *
41919645 GTTTAATATGTTCCACTACAACTTCAGGGAAATAATATTTGCAT
1 CTTTAATCTGTTCCATTGCAACTTCAAGGAAATAAGATTCGCAT
* ** * * * * *
41919689 CTTCAATCTACTCCATTTCAACTTCAAGGAGATAAGGTTGTGGCTTTAAG
1 CTTTAATCTGTTCCATTGCAACTTCAAGGAAATAA-GAT-TCGC----AT
*
41919739 CTTTAATCTGTTCCATTGCAACTTCAGGGAAATAAGATTCGCAT
1 CTTTAATCTGTTCCATTGCAACTTCAAGGAAATAAGATTCGCAT
* * *
41919783 CTTCAATCTGCTCCATTGCAACTTCAAGGAGATAAGATT
1 CTTTAATCTGTTCCATTGCAACTTCAAGGAAATAAGATT
41919822 TGTAGCTTTA
Statistics
Matches: 377, Mismatches: 100, Indels: 70
0.69 0.18 0.13
Matches are distributed among these distances:
43 3 0.01
44 181 0.48
45 1 0.00
46 7 0.02
47 15 0.04
48 13 0.03
49 5 0.01
50 56 0.15
51 96 0.25
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (44 bp):
CTTTAATCTGTTCCATTGCAACTTCAAGGAAATAAGATTCGCAT
Found at i:41919365 original size:95 final size:95
Alignment explanation
Indices: 41919250--41919916 Score: 876
Period size: 95 Copynumber: 7.0 Consensus size: 95
41919240 AGAGGTATAG
* * *
41919250 GATTTGTGACTTATAA-CTTTAATCTATTCCACTGCAATTTCAGGGAAATAAGATTCGCATCTTC
1 GATTTGTGGCTT-TAAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCATCTTC
**
41919314 AATCTATTCCATTGCAACTTCAAGGAGATAA
65 AATCTGCTCCATTGCAACTTCAAGGAGATAA
* *
41919345 GATTTGTGGCTTTAAGCTTTAATCTGTTCCACAGCAACTTCAGGGAAATAAGATTCGCATCTTTA
1 GATTTGTGGCTTTAAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCATCTTCA
* * *
41919410 ATCTGTTTCATTTCAACTTCAAGGAGATAA
66 ATCTGCTCCATTGCAACTTCAAGGAGATAA
* * * *
41919440 GATTTGTGGCTTTAAGATTTAATCTTTTTCACTGCAACTTCAGGGAAATAAGATTCGCATCGTCA
1 GATTTGTGGCTTTAAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCATCTTCA
*
41919505 ATCTGCTCTATTGCAACTTCAAGGAGATAA
66 ATCTGCTCCATTGCAACTTCAAGGAGATAA
* * * * * * *
41919535 CATTTGTAGCTTTAAACTTTAATCTGTTCGACTGCAATTTCAGGGAAATAAGATTTGCATCTTTA
1 GATTTGTGGCTTTAAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCATCTTCA
* * *
41919600 ATTTGCTCCATTGTAACTTCAAGAAGATAA
66 ATCTGCTCCATTGCAACTTCAAGGAGATAA
* * * * *
41919630 GATTTGTAGCTTTAAG-TTTAATATGTTCCACTACAACTTCAGGGAAATAATATTTGCATCTTCA
1 GATTTGTGGCTTTAAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCATCTTCA
* *
41919694 ATCTACTCCATTTCAACTTCAAGGAGATAA
66 ATCTGCTCCATTGCAACTTCAAGGAGATAA
* *
41919724 G-GTTGTGGCTTTAAGCTTTAATCTGTTCCATTGCAACTTCAGGGAAATAAGATTCGCATCTTCA
1 GATTTGTGGCTTTAAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCATCTTCA
41919788 ATCTGCTCCATTGCAACTTCAAGGAGATAA
66 ATCTGCTCCATTGCAACTTCAAGGAGATAA
* * * * * * *
41919818 GATTTGTAGCTTTAAGCTTTAATCTGTTCCGCTACAACTTCAAGGAGATAAGACTT-GTAACTTC
1 GATTTGTGGCTTTAAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGA-TTCGCATCTTC
* * *
41919882 AACCTGCTCCACTGTAACTTC-AGAGAGATAA
65 AATCTGCTCCATTGCAACTTCAAG-GAGATAA
41919913 GATT
1 GATT
41919917 CGCCATAATA
Statistics
Matches: 500, Mismatches: 67, Indels: 10
0.87 0.12 0.02
Matches are distributed among these distances:
93 12 0.02
94 145 0.29
95 341 0.68
96 2 0.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (95 bp):
GATTTGTGGCTTTAAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCATCTTCA
ATCTGCTCCATTGCAACTTCAAGGAGATAA
Found at i:41919815 original size:283 final size:285
Alignment explanation
Indices: 41919264--41919916 Score: 929
Period size: 283 Copynumber: 2.3 Consensus size: 285
41919254 TGTGACTTAT
* * * ** *
41919264 AACTTTAATCTATTCCACTGCAATTTCAGGGAAATAAGATTCGCATCTTCAATCTATTCCATTGC
1 AACTTTAATCTGTTCGACTGCAATTTCAGGGAAATAAGATTTGCATCTTCAATCTGCTCCATTGT
* * *
41919329 AACTTCAAGGAGATAAGATTTGTGGCTTTAAGCTTTAATCTGTTCCACAGCAACTTCAGGGAAAT
66 AACTTCAAGAAGATAAGATTTGTAGCTTTAAGCTTTAATATGTTCCACAGCAACTTCAGGGAAAT
* ** * *
41919394 AAGATTCGCATCTTTAATCTGTTTCATTTCAACTTCAAGGAGATAAGATTTGTGGCTTTAAGATT
131 AAGATTCGCATCTTCAATCTACTCCATTTCAACTTCAAGGAGATAAGAGTTGTGGCTTTAAGATT
* * *
41919459 TAATCTTTTTCACTGCAACTTCAGGGAAATAAGATTCGCATCGTCAATCTGCTCTATTGCAACTT
196 TAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCATCGTCAATCTGCTCCATTGCAACTT
41919524 CAAGGAGATAACATTTGTAGCTTTA
261 CAAGGAGATAACATTTGTAGCTTTA
* *
41919549 AACTTTAATCTGTTCGACTGCAATTTCAGGGAAATAAGATTTGCATCTTTAATTTGCTCCATTGT
1 AACTTTAATCTGTTCGACTGCAATTTCAGGGAAATAAGATTTGCATCTTCAATCTGCTCCATTGT
41919614 AACTTCAAGAAGATAAGATTTGTAGCTTTAAG-TTTAATATGTTCCACTA-CAACTTCAGGGAAA
66 AACTTCAAGAAGATAAGATTTGTAGCTTTAAGCTTTAATATGTTCCAC-AGCAACTTCAGGGAAA
* * *
41919677 TAATATTTGCATCTTCAATCTACTCCATTTCAACTTCAAGGAGATAAG-GTTGTGGCTTTAAGCT
130 TAAGATTCGCATCTTCAATCTACTCCATTTCAACTTCAAGGAGATAAGAGTTGTGGCTTTAAGAT
* *
41919741 TTAATCTGTTCCATTGCAACTTCAGGGAAATAAGATTCGCATCTTCAATCTGCTCCATTGCAACT
195 TTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCATCGTCAATCTGCTCCATTGCAACT
*
41919806 TCAAGGAGATAAGATTTGTAGCTTTA
260 TCAAGGAGATAACATTTGTAGCTTTA
* * * * * * * * * *
41919832 AGCTTTAATCTGTTCCG-CTACAACTTCAAGGAGATAAGACTTGTAACTTCAACCTGCTCCACTG
1 AACTTTAATCTGTT-CGACTGCAATTTCAGGGAAATAAGATTTGCATCTTCAATCTGCTCCATTG
41919896 TAACTTC-AGAGAGATAAGATT
65 TAACTTCAAGA-AGATAAGATT
41919917 CGCCATAATA
Statistics
Matches: 328, Mismatches: 37, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
282 3 0.01
283 165 0.50
284 72 0.22
285 88 0.27
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.35
Consensus pattern (285 bp):
AACTTTAATCTGTTCGACTGCAATTTCAGGGAAATAAGATTTGCATCTTCAATCTGCTCCATTGT
AACTTCAAGAAGATAAGATTTGTAGCTTTAAGCTTTAATATGTTCCACAGCAACTTCAGGGAAAT
AAGATTCGCATCTTCAATCTACTCCATTTCAACTTCAAGGAGATAAGAGTTGTGGCTTTAAGATT
TAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGCATCGTCAATCTGCTCCATTGCAACTT
CAAGGAGATAACATTTGTAGCTTTA
Found at i:41930830 original size:21 final size:22
Alignment explanation
Indices: 41930781--41930843 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
41930771 TGAACAAATG
41930781 AATAAAT-AAATATT-AAG-TA
1 AATAAATAAAATATTAAAGATA
*
41930800 AATTAATAAAATATTAAAGATA
1 AATAAATAAAATATTAAAGATA
* *
41930822 AA-AAATAAAATAATAATGATA
1 AATAAATAAAATATTAAAGATA
41930843 A
1 A
41930844 TGTTAATGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 6 0.16
20 7 0.19
21 20 0.54
22 4 0.11
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (22 bp):
AATAAATAAAATATTAAAGATA
Found at i:41935760 original size:22 final size:21
Alignment explanation
Indices: 41935737--41935778 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
41935727 TTCTTTGTAT
* *
41935737 TTTGGGCTTGTACTTTTGTTA
1 TTTGGGCCTGTAATTTTGTTA
41935758 TTTGGGCCTGTAATTTTGTTA
1 TTTGGGCCTGTAATTTTGTTA
41935779 ATGAACTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.12, C:0.10, G:0.24, T:0.55
Consensus pattern (21 bp):
TTTGGGCCTGTAATTTTGTTA
Found at i:41938904 original size:19 final size:19
Alignment explanation
Indices: 41938882--41938918 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
41938872 CAAACAGATA
41938882 GCTTTCATACAATCAAATC
1 GCTTTCATACAATCAAATC
41938901 GCTTTCATACAATCAAAT
1 GCTTTCATACAATCAAAT
41938919 TCAACTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.32
Consensus pattern (19 bp):
GCTTTCATACAATCAAATC
Found at i:41942558 original size:77 final size:75
Alignment explanation
Indices: 41942330--41942560 Score: 304
Period size: 75 Copynumber: 3.1 Consensus size: 75
41942320 TTACGTAAAT
* * * * * * ** *
41942330 AATACAAAGTTTATTATTTAAATTGCAAAAAACTCC-TAAAATTAATAATTGAAATAGTGAAGAA
1 AATACAAAGTTGACTATTTAAATTGAAAAAAAC-CCATAAAATTAATAACTAAAATGGAAAAAAA
41942394 GTCATTACATA
65 GTCATTACATA
* *
41942405 AATAAAAACTTGACTATTTAAATTGCAAAAAAACCCAT-AAATTAATAACTAAAATGGAAAAAAA
1 AATACAAAGTTGACTATTTAAATTG-AAAAAAACCCATAAAATTAATAACTAAAATGGAAAAAAA
41942469 GTCATTACATA
65 GTCATTACATA
41942480 AATACAAAGTTGACTATTTAAATTGAAAAAAAAACCCATAAAATTAATAACTAAAATGGAAAAAA
1 AATACAAAGTTGACTATTTAAATTG--AAAAAAACCCATAAAATTAATAACTAAAATGGAAAAAA
*
41942545 AGTCATTATATA
64 AGTCATTACATA
41942557 AATA
1 AATA
41942561 TGAAGTTATT
Statistics
Matches: 137, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
75 77 0.56
76 20 0.15
77 40 0.29
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.28
Consensus pattern (75 bp):
AATACAAAGTTGACTATTTAAATTGAAAAAAACCCATAAAATTAATAACTAAAATGGAAAAAAAG
TCATTACATA
Found at i:41944888 original size:16 final size:15
Alignment explanation
Indices: 41944864--41944893 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
41944854 TAAAAATCAA
41944864 ATAAAATTACATTAT
1 ATAAAATTACATTAT
41944879 ATAAATATTACATTA
1 ATAAA-ATTACATTA
41944894 AAAAATCACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAAAATTACATTAT
Found at i:41945015 original size:104 final size:97
Alignment explanation
Indices: 41944895--41945209 Score: 328
Period size: 104 Copynumber: 3.1 Consensus size: 97
41944885 ATTACATTAA
*
41944895 AAAATCACAAAACACTAACAATTTATATAACCTAATCATAAATTAGTAAAAAAATAACTAAAAAA
1 AAAA-CACAAAACACTAACAA-TT-TATAACCTAATCATAAATTACTAAAAAAATAACTAAAAAA
41944960 TTATTTTTTTAAAAAATTACATTATTAAAAATCAC
63 TTATTTTTTTAAAAAATTACATTATTAAAAATCAC
* * * *
41944995 AAAACTCTAAACTAAACACTAACAATTTGTAACCTAATCCCATAAATTACTAAGAAAATAAAT-A
1 AAAA--C---ACAAAACACTAACAATTTATAACCTAAT--CATAAATTACTAAAAAAATAACTAA
* * *
41945059 ACAATTACATTTTTTTAAAAGAAATTACATTACTAAAAAATAAC
59 AAAATT--ATTTTTTT-AAA-AAATTACATTA-TTAAAAATCAC
* * * *
41945103 AAAACACAAAACACTATCAATTTATAACCTAATCATAAACTACTAACAAAATAACTATAAAATTA
1 AAAACACAAAACACTAACAATTTATAACCTAATCATAAATTACTAAAAAAATAACTAAAAAATTA
* *
41945168 -TTTTTAAAAAAATTTACATTACTAAAAACTCAC
66 TTTTTTTAAAAAA-TTACATTATTAAAAA-TCAC
*
41945201 AGAACACAA
1 AAAACACAA
41945210 CAATTTATAA
Statistics
Matches: 180, Mismatches: 21, Indels: 30
0.78 0.09 0.13
Matches are distributed among these distances:
97 8 0.04
98 22 0.12
99 5 0.03
100 5 0.03
101 22 0.12
102 15 0.08
103 33 0.18
104 34 0.19
105 8 0.04
106 4 0.02
107 11 0.06
108 13 0.07
ACGTcount: A:0.55, C:0.15, G:0.02, T:0.29
Consensus pattern (97 bp):
AAAACACAAAACACTAACAATTTATAACCTAATCATAAATTACTAAAAAAATAACTAAAAAATTA
TTTTTTTAAAAAATTACATTATTAAAAATCAC
Found at i:41945131 original size:103 final size:98
Alignment explanation
Indices: 41944895--41945209 Score: 327
Period size: 98 Copynumber: 3.1 Consensus size: 98
41944885 ATTACATTAA
* *
41944895 AAAATCACAAAACACTAACAATTTATATAACCTAATCATAAATTAGTAAAAAAATAACTAAAAAA
1 AAAATCACAAAACACTAACAA-TT-TATAACCTAATCATAAATTACTAAAAAAATAA--ATAAAA
*
41944960 TTATTTTTTT-AAAAAATTACATTA-TTAAAAATCAC
62 TTATTTTTTTAAAAAAATTACATTACTAAAAAATCAC
* * *
41944995 AAAACTCTAAACTAAACACTAACAATTTGTAACCTAATCCCATAAATTACTAAGAAAATAAATAA
1 AAAA-TC---ACAAAACACTAACAATTTATAACCTAAT--CATAAATTACTAAAAAAATAAATAA
*
41945060 CAATTACATTTTTTTAAAAGAAATTACATTACTAAAAAATAAC
60 -AATT--ATTTTTTTAAAA-AAATTACATTACTAAAAAATCAC
* * *
41945103 AAAA-CACAAAACACTATCAATTTATAACCTAATCATAAACTACTAACAAAATAACTATAAAATT
1 AAAATCACAAAACACTAACAATTTATAACCTAATCATAAATTACTAAAAAAATAA--ATAAAATT
*
41945167 A--TTTTTAAAAAAATTTACATTACTAAAAACTCAC
64 ATTTTTTTAAAAAAA-TTACATTACTAAAAAATCAC
*
41945201 AGAA-CACAA
1 AAAATCACAA
41945210 CAATTTATAA
Statistics
Matches: 185, Mismatches: 15, Indels: 32
0.80 0.06 0.14
Matches are distributed among these distances:
97 3 0.02
98 35 0.19
100 5 0.03
101 21 0.11
102 17 0.09
103 35 0.19
104 33 0.18
105 8 0.04
106 4 0.02
107 11 0.06
108 13 0.07
ACGTcount: A:0.55, C:0.15, G:0.02, T:0.29
Consensus pattern (98 bp):
AAAATCACAAAACACTAACAATTTATAACCTAATCATAAATTACTAAAAAAATAAATAAAATTAT
TTTTTTAAAAAAATTACATTACTAAAAAATCAC
Found at i:41945263 original size:72 final size:72
Alignment explanation
Indices: 41945180--41945404 Score: 405
Period size: 72 Copynumber: 3.1 Consensus size: 72
41945170 TTTAAAAAAA
*
41945180 TTTACATTACTAAAAACTCACAGAACACAACAATTTATAATAAATTACTAACAAAATATTTAACA
1 TTTACATTACTAAAAACTCACAAAACACAACAATTTATAATAAATTACTAACAAAATATTTAACA
41945245 AAATAAT
66 AAATAAT
*
41945252 TTTACATTACTAAAAACTCACAAAACACAACAATTTATAATAAATTACTAAGAAAATATTTAACA
1 TTTACATTACTAAAAACTCACAAAACACAACAATTTATAATAAATTACTAACAAAATATTTAACA
41945317 AAATAAT
66 AAATAAT
*
41945324 TTTACATTACTAAAAACTCGCAAAACACAACAATTTATAATAAATTACTAACAAAATATTTAACA
1 TTTACATTACTAAAAACTCACAAAACACAACAATTTATAATAAATTACTAACAAAATATTTAACA
* *
41945389 AAACAAA
66 AAATAAT
41945396 TTTACATTA
1 TTTACATTA
41945405 ATACAAAATC
Statistics
Matches: 147, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 147 1.00
ACGTcount: A:0.54, C:0.15, G:0.01, T:0.29
Consensus pattern (72 bp):
TTTACATTACTAAAAACTCACAAAACACAACAATTTATAATAAATTACTAACAAAATATTTAACA
AAATAAT
Found at i:41945275 original size:41 final size:41
Alignment explanation
Indices: 41945230--41945348 Score: 96
Period size: 41 Copynumber: 3.1 Consensus size: 41
41945220 TAAATTACTA
41945230 ACAAAATATTTAACAAAATAATTTTACATTACTAAAAACTC
1 ACAAAATATTTAACAAAATAATTTTACATTACTAAAAACTC
* * * ** *
41945271 ACAAAACA--CAAC--AAT--TTATA-A-TA--AATTACTA
1 ACAAAATATTTAACAAAATAATTTTACATTACTAAAAACTC
*
41945302 AGAAAATATTTAACAAAATAATTTTACATTACTAAAAACTC
1 ACAAAATATTTAACAAAATAATTTTACATTACTAAAAACTC
*
41945343 GCAAAA
1 ACAAAA
41945349 CACAACAATT
Statistics
Matches: 53, Mismatches: 15, Indels: 20
0.60 0.17 0.23
Matches are distributed among these distances:
31 11 0.21
33 5 0.09
34 1 0.02
35 7 0.13
37 7 0.13
38 1 0.02
39 5 0.09
41 16 0.30
ACGTcount: A:0.55, C:0.14, G:0.02, T:0.29
Consensus pattern (41 bp):
ACAAAATATTTAACAAAATAATTTTACATTACTAAAAACTC
Found at i:41945287 original size:34 final size:34
Alignment explanation
Indices: 41945180--41945359 Score: 112
Period size: 34 Copynumber: 5.1 Consensus size: 34
41945170 TTTAAAAAAA
*
41945180 TTTACATTACTAAAAACTCACAGAACACAACAATT
1 TTTACATTACTAAAAACTCACAAAACACAACAA-T
* * *** * *
41945215 TATAATAAATTACTAACAAAAT-ATTTAACAAAATAAT
1 T-T--TACATTACTAA-AAACTCACAAAACACAACAAT
41945252 TTTACATTACTAAAAACTCACAAAACACAACAATT
1 TTTACATTACTAAAAACTCACAAAACACAACAA-T
* * *** * *
41945287 TATAATAAATTACTAAGAAAAT-ATTTAACAAAATAAT
1 T-T--TACATTACTAA-AAACTCACAAAACACAACAAT
*
41945324 TTTACATTACTAAAAACTCGCAAAACACAACAAT
1 TTTACATTACTAAAAACTCACAAAACACAACAAT
41945358 TT
1 TT
41945360 ATAATAAATT
Statistics
Matches: 105, Mismatches: 29, Indels: 23
0.67 0.18 0.15
Matches are distributed among these distances:
33 8 0.08
34 40 0.38
35 3 0.03
36 4 0.04
37 4 0.04
38 38 0.36
39 8 0.08
ACGTcount: A:0.53, C:0.16, G:0.02, T:0.29
Consensus pattern (34 bp):
TTTACATTACTAAAAACTCACAAAACACAACAAT
Found at i:41945394 original size:38 final size:37
Alignment explanation
Indices: 41945203--41945399 Score: 140
Period size: 38 Copynumber: 5.4 Consensus size: 37
41945193 AAACTCACAG
*
41945203 AACACAACAATTTATAATAAATTACTAACAAAATATTT
1 AACAAAACAATTTATAATAAATTACTAA-AAAATATTT
* * * ***
41945241 AACAAAATAA-TT-T--TACATTACTAAAAACTCACAA
1 AACAAAACAATTTATAATAAATTACTAAAAAAT-ATTT
*
41945275 AACACAACAATTTATAATAAATTACTAAGAAAATATTT
1 AACAAAACAATTTATAATAAATTACTAA-AAAATATTT
* * * ****
41945313 AACAAAATAA-TT-T--TACATTACTAAAAACTCGCAA
1 AACAAAACAATTTATAATAAATTACTAAAAAAT-ATTT
*
41945347 AACACAACAATTTATAATAAATTACTAACAAAATATTT
1 AACAAAACAATTTATAATAAATTACTAA-AAAATATTT
41945385 AACAAAACAAATTTA
1 AACAAAAC-AATTTA
41945400 CATTAATACA
Statistics
Matches: 115, Mismatches: 31, Indels: 25
0.67 0.18 0.15
Matches are distributed among these distances:
33 8 0.07
34 37 0.32
35 4 0.03
36 4 0.03
37 4 0.03
38 44 0.38
39 14 0.12
ACGTcount: A:0.56, C:0.14, G:0.01, T:0.29
Consensus pattern (37 bp):
AACAAAACAATTTATAATAAATTACTAAAAAATATTT
Found at i:41945494 original size:60 final size:60
Alignment explanation
Indices: 41945429--41945612 Score: 350
Period size: 60 Copynumber: 3.1 Consensus size: 60
41945419 AATACTAAAC
* *
41945429 TAAACACAACAATTTAAAACATAATCCTAAATTACTAATAAATTAATTTTAAAATAATTA
1 TAAACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
41945489 TAAACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
1 TAAACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
41945549 TAAACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
1 TAAACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
41945609 TAAA
1 TAAA
41945613 AAACAAAAAA
Statistics
Matches: 122, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 122 1.00
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.33
Consensus pattern (60 bp):
TAAACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
Found at i:41945782 original size:3 final size:3
Alignment explanation
Indices: 41945774--41945813 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
41945764 ACATTACCTT
41945774 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
41945814 CTTTTCTCTC
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:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:41945842 original size:9 final size:8
Alignment explanation
Indices: 41945771--41945830 Score: 59
Period size: 9 Copynumber: 7.0 Consensus size: 8
41945761 AATACATTAC
41945771 CTTTTCTT
1 CTTTTCTT
41945779 CTTCTTCTT
1 CTT-TTCTT
41945788 CTTCTTCTT
1 CTT-TTCTT
41945797 CTTCTTCTT
1 CTT-TTCTT
41945806 CTTCTTC-T
1 CTT-TTCTT
41945814 CTTTTCTCT
1 CTTTTCT-T
*
41945823 CCTTTCTT
1 CTTTTCTT
41945831 TCTCTCTTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
7 3 0.06
8 8 0.17
9 37 0.77
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (8 bp):
CTTTTCTT
Found at i:41947481 original size:19 final size:20
Alignment explanation
Indices: 41947436--41947484 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
41947426 GCAAATTACG
*
41947436 TTTTAAAAT-AAAATCATTA
1 TTTTAAAATAAAAAACATTA
* *
41947455 ATTAAAAATAAAAAACATT-
1 TTTTAAAATAAAAAACATTA
41947474 TTTTAAAATAA
1 TTTTAAAATAA
41947485 TACAAAGTGT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (20 bp):
TTTTAAAATAAAAAACATTA
Found at i:41952192 original size:18 final size:18
Alignment explanation
Indices: 41952169--41952205 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
41952159 TCGCTTAACT
41952169 AAATTAAATTTTAAGGAA
1 AAATTAAATTTTAAGGAA
41952187 AAATTAAATTTTAAGGAA
1 AAATTAAATTTTAAGGAA
41952205 A
1 A
41952206 TTGCCTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (18 bp):
AAATTAAATTTTAAGGAA
Found at i:41953599 original size:25 final size:25
Alignment explanation
Indices: 41953504--41953601 Score: 99
Period size: 25 Copynumber: 4.0 Consensus size: 25
41953494 ATTAGGGTCA
**
41953504 CCGAT-TTCAGCTCTTATGAGCTTC
1 CCGATATTCAGCTCGCATGAGCTTC
* *
41953528 CCGATACTCAGCTCGCATGAGCATC
1 CCGATATTCAGCTCGCATGAGCTTC
* *
41953553 CCGTTATTCAGCTCACATGAGCTTC
1 CCGATATTCAGCTCGCATGAGCTTC
* * * *
41953578 CCGCTATTTAGCTCGGAGGAGCTT
1 CCGATATTCAGCTCGCATGAGCTT
41953602 ACTGTTTTCA
Statistics
Matches: 60, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
24 5 0.08
25 55 0.92
ACGTcount: A:0.19, C:0.31, G:0.20, T:0.30
Consensus pattern (25 bp):
CCGATATTCAGCTCGCATGAGCTTC
Found at i:41955320 original size:50 final size:50
Alignment explanation
Indices: 41955079--41955320 Score: 245
Period size: 50 Copynumber: 4.9 Consensus size: 50
41955069 GATAATAACA
* * ** * * *
41955079 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGAATGTTTTTTGTAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCT-CGG
* * * * * ** * *
41955128 TGCCAATGCCATATCCTAGATATGGTCTTACATGAGAGTTCTCATGTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
* * * ** * *
41955178 TGCCCATGCCATGTCCCAAACATGGTCTTACGGGGGACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
41955228 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
*
41955278 TGCCAACGCCATGTCCCATACATGGTCTTACATGGGACCTCTT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTT
41955321 TACCCAAATG
Statistics
Matches: 160, Mismatches: 31, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
48 1 0.01
49 36 0.22
50 123 0.77
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.29
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
Found at i:41956802 original size:17 final size:17
Alignment explanation
Indices: 41956780--41956819 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
41956770 TAGTAATTCA
* *
41956780 GAAGCTTGTTCGGGTTG
1 GAAGCTCGTCCGGGTTG
41956797 GAAGCTCGTCCGGGTTG
1 GAAGCTCGTCCGGGTTG
41956814 GAAGCT
1 GAAGCT
41956820 GATCGAAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.15, C:0.17, G:0.40, T:0.28
Consensus pattern (17 bp):
GAAGCTCGTCCGGGTTG
Found at i:41956866 original size:22 final size:22
Alignment explanation
Indices: 41956841--41956886 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
41956831 TTTCGCACCA
* *
41956841 TCCATCGGTCCTTTTGGTACTT
1 TCCATCGGTCCTTTCGATACTT
41956863 TCCATCGGTCCTTTCGATACTT
1 TCCATCGGTCCTTTCGATACTT
41956885 TC
1 TC
41956887 AGTAAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.11, C:0.30, G:0.15, T:0.43
Consensus pattern (22 bp):
TCCATCGGTCCTTTCGATACTT
Found at i:41960458 original size:25 final size:25
Alignment explanation
Indices: 41960430--41960516 Score: 93
Period size: 25 Copynumber: 3.5 Consensus size: 25
41960420 TGTAAATAGT
* *
41960430 AAGCTCTTCCGAACTGAATAACGGG
1 AAGCTCATGCGAACTGAATAACGGG
* * *
41960455 AAGCTCATGTGAACTAAATAACGAG
1 AAGCTCATGCGAACTGAATAACGGG
* * *
41960480 AAGCTCATGCGAGCTGTATAAAGGG
1 AAGCTCATGCGAACTGAATAACGGG
*
41960505 AAGCTCGTGCGA
1 AAGCTCATGCGA
41960517 GCTGTGGTGT
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.20
Consensus pattern (25 bp):
AAGCTCATGCGAACTGAATAACGGG
Found at i:41966894 original size:25 final size:25
Alignment explanation
Indices: 41966866--41966924 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
41966856 ACTCAACTTG
41966866 CATGAGCTTC-CCATTATTCAGCTCA
1 CATGAGCTTCTCC-TTATTCAGCTCA
41966891 CATGAGCTTCTCCTTATTCAGCTCA
1 CATGAGCTTCTCCTTATTCAGCTCA
* *
41966916 GAGGAGCTT
1 CATGAGCTT
41966925 ACTGTTTACA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 29 0.94
26 2 0.06
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.32
Consensus pattern (25 bp):
CATGAGCTTCTCCTTATTCAGCTCA
Found at i:41968224 original size:4 final size:4
Alignment explanation
Indices: 41968215--41968240 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
41968205 ATATTAGAAT
41968215 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
41968241 AAGGTAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:41977267 original size:43 final size:43
Alignment explanation
Indices: 41977098--41977268 Score: 168
Period size: 43 Copynumber: 4.0 Consensus size: 43
41977088 ATAGGATTCT
* * * *
41977098 GATATGTGATTACGTGTAAGATCACGTATGGGACGTTGGCATC
1 GATATTTGATTTCGTGTAAGACCACGTCTGGGACGTTGGCATC
* * *
41977141 GAT-TTGTGATTTACGTGTAAGACCATGTCTGGGACATCGGCATC
1 GATATT-TGATTT-CGTGTAAGACCACGTCTGGGACGTTGGCATC
** * * *
41977185 G-TATAGGAGTTCGTGTAAGACCCCGTCGGGGACAG-TGGCATC
1 GATATTTGATTTCGTGTAAGACCACGTCTGGGAC-GTTGGCATC
* *
41977227 GATATTTGATTTCATGTAAGACCACGTCTGGGATGTTGGCAT
1 GATATTTGATTTCGTGTAAGACCACGTCTGGGACGTTGGCAT
41977269 TGAATGAGCT
Statistics
Matches: 100, Mismatches: 22, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
42 28 0.28
43 44 0.44
44 28 0.28
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (43 bp):
GATATTTGATTTCGTGTAAGACCACGTCTGGGACGTTGGCATC
Found at i:41982901 original size:22 final size:23
Alignment explanation
Indices: 41982875--41982924 Score: 77
Period size: 22 Copynumber: 2.2 Consensus size: 23
41982865 AAGCTCCATG
41982875 TTCATATATCAT-TATCCAT-ATT
1 TTCATATATCATGTAT-CATCATT
41982897 TTCATATATCATGTATCATCATT
1 TTCATATATCATGTATCATCATT
41982920 TTCAT
1 TTCAT
41982925 CTATTTCAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.58
23 11 0.42
ACGTcount: A:0.30, C:0.18, G:0.02, T:0.50
Consensus pattern (23 bp):
TTCATATATCATGTATCATCATT
Found at i:41986487 original size:3 final size:3
Alignment explanation
Indices: 41986479--41986512 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
41986469 CATGATTACT
41986479 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
41986513 GGATAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:41990025 original size:2 final size:2
Alignment explanation
Indices: 41990018--41990042 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41990008 ACCTTCTAAT
41990018 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 T
41990043 GCAAAATATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41991449 original size:57 final size:58
Alignment explanation
Indices: 41991382--41991503 Score: 165
Period size: 57 Copynumber: 2.1 Consensus size: 58
41991372 TTTTTCAATT
** * * *
41991382 TTCATTTTCATTTTTGTTTTGGAGAAATCCACATTCATTTCCAAATGTTTC-TATTTC
1 TTCATTTTCATTTTCATTTTGGAGAAAACCACAATCATCTCCAAATGTTTCTTATTTC
* *
41991439 TTCATTTTCATTTTCATTTTGGAGAAAACCATAATCATCTCTAAATGTTTCTTATTTC
1 TTCATTTTCATTTTCATTTTGGAGAAAACCACAATCATCTCCAAATGTTTCTTATTTC
*
41991497 TCCATTT
1 TTCATTT
41991504 CACCATTTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
57 44 0.79
58 12 0.21
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.50
Consensus pattern (58 bp):
TTCATTTTCATTTTCATTTTGGAGAAAACCACAATCATCTCCAAATGTTTCTTATTTC
Found at i:42003930 original size:48 final size:48
Alignment explanation
Indices: 42003859--42004002 Score: 164
Period size: 49 Copynumber: 3.0 Consensus size: 48
42003849 GTGGCATGAA
*
42003859 ACTTGAACCCGTGACCGCATAACCACATCAACTGGGAGCTTGAGTTAT
1 ACTTGAACCCGTGACTGCATAACCACATCAACTGGGAGCTTGAGTTAT
* *
42003907 ACTTGAACCCGGGACTGCATAACCACTATCATCTGGGAGTCTT-AGTTAT
1 ACTTGAACCCGTGACTGCATAACCAC-ATCAACTGGGAG-CTTGAGTTAT
* * * * * * *
42003956 ACTTCAGCTCGTGACTGTATAACCATCATGAACTAGGAGCATGAGTT
1 ACTTGAACCCGTGACTGCATAACCA-CATCAACTGGGAGCTTGAGTT
42004003 GCAATACGAC
Statistics
Matches: 80, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
48 26 0.32
49 50 0.62
50 4 0.05
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.26
Consensus pattern (48 bp):
ACTTGAACCCGTGACTGCATAACCACATCAACTGGGAGCTTGAGTTAT
Found at i:42005705 original size:18 final size:18
Alignment explanation
Indices: 42005678--42005714 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
42005668 ATGCGACTGG
* *
42005678 GTTGATAACGAAGAGGGA
1 GTTGAGAACGAAGAAGGA
42005696 GTTGAGAACGAAGAAGGA
1 GTTGAGAACGAAGAAGGA
42005714 G
1 G
42005715 CTAAACTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.41, C:0.05, G:0.41, T:0.14
Consensus pattern (18 bp):
GTTGAGAACGAAGAAGGA
Found at i:42007672 original size:56 final size:53
Alignment explanation
Indices: 42007592--42007840 Score: 249
Period size: 56 Copynumber: 4.7 Consensus size: 53
42007582 GGTAATGAGA
*
42007592 TCCCATGTAAGACCATGTCCGGGACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C-TTGAGA-TATGAGAGG
* * *
42007648 TCCCATGTAAGACCATGTCTGGGACATGACATTGGAATCATTGAGATTATTAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C-TTGAGA-TATGAGAGG
* * *
42007704 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCAC-CGAG--ATGAAAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTTGAGATATGAGAGG
** * * * * **
42007754 TCCCCCGTAAGATCATGTCTAGGACATGGCATGGGCACCT---ATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTTGAGATATGAGAGG
* *
42007804 TCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
42007841 GTACAAGAAA
Statistics
Matches: 163, Mismatches: 27, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
50 73 0.45
53 3 0.02
55 1 0.01
56 86 0.53
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (53 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTTGAGATATGAGAGG
Found at i:42007756 original size:50 final size:50
Alignment explanation
Indices: 42007592--42007889 Score: 224
Period size: 56 Copynumber: 5.7 Consensus size: 50
42007582 GGTAATGAGA
* * *
42007592 TCCCATGTAAGACCATGTCCGGGACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAAAGG
* ** *
42007648 TCCCATGTAAGACCATGTCTGGGACATGACATTGGAATCATTGAGATTATTAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGG---CACCGAGATGA--A-AGG
*
42007704 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAAAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAAAGG
** * * * * * *
42007754 TCCCCCGTAAGATCATGTCTAGGACATGGCATGGGCACCTATATGAGAA-C
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGA-AAGG
* * * * **
42007804 TCCCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACAAGAAACA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAAAGG
* * *
42007853 TCCCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
42007890 TGTATTATCA
Statistics
Matches: 198, Mismatches: 35, Indels: 25
0.77 0.14 0.10
Matches are distributed among these distances:
48 2 0.01
49 36 0.18
50 71 0.36
51 3 0.02
53 11 0.06
56 73 0.37
59 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAAAGG
Found at i:42014129 original size:26 final size:26
Alignment explanation
Indices: 42014083--42014148 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
42014073 GACAAGAATT
* **
42014083 AAAAAGAAATCTAAACCCTAAGATGA-
1 AAAAAAAAATCTAAAAACTAA-ATGAC
*
42014109 AGAAAAAAATCTAAAAACTAAATGAC
1 AAAAAAAAATCTAAAAACTAAATGAC
*
42014135 AAAAAAAAAACTAA
1 AAAAAAAAATCTAA
42014149 GAATGTCCTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
25 4 0.12
26 29 0.88
ACGTcount: A:0.67, C:0.12, G:0.08, T:0.14
Consensus pattern (26 bp):
AAAAAAAAATCTAAAAACTAAATGAC
Found at i:42015431 original size:19 final size:19
Alignment explanation
Indices: 42015393--42015432 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
42015383 AAAATATTAT
* *
42015393 ATTAATTTTATTTAATTTG
1 ATTAATTTAATTTAACTTG
*
42015412 ATTAATTTAATTTTACTTG
1 ATTAATTTAATTTAACTTG
42015431 AT
1 AT
42015433 CAAAGTTCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (19 bp):
ATTAATTTAATTTAACTTG
Found at i:42016476 original size:25 final size:25
Alignment explanation
Indices: 42016461--42016520 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
42016451 TTTGGCTCTC
42016461 ACAAGCTTCCTATTATATGGTTCTT
1 ACAAGCTTCCTATTATATGGTTCTT
*
42016486 ACAAGCTTCCTGTTATATGGTTCTT
1 ACAAGCTTCCTATTATATGGTTCTT
*
42016511 ACGAGCTTCC
1 ACAAGCTTCC
42016521 CGTTAATAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.40
Consensus pattern (25 bp):
ACAAGCTTCCTATTATATGGTTCTT
Found at i:42016525 original size:25 final size:25
Alignment explanation
Indices: 42016446--42016525 Score: 97
Period size: 25 Copynumber: 3.2 Consensus size: 25
42016436 ATAAGCATCT
* * *
42016446 CGTTATTTGGCTCTCACAAGCTTCC
1 CGTTATATGGTTCTTACAAGCTTCC
**
42016471 TATTATATGGTTCTTACAAGCTTCC
1 CGTTATATGGTTCTTACAAGCTTCC
* *
42016496 TGTTATATGGTTCTTACGAGCTTCC
1 CGTTATATGGTTCTTACAAGCTTCC
42016521 CGTTA
1 CGTTA
42016526 ATAGCTCTTC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.19, C:0.24, G:0.16, T:0.41
Consensus pattern (25 bp):
CGTTATATGGTTCTTACAAGCTTCC
Found at i:42016657 original size:27 final size:25
Alignment explanation
Indices: 42016610--42016678 Score: 84
Period size: 27 Copynumber: 2.7 Consensus size: 25
42016600 CTCGATATAT
42016610 GGCTCTTTAGAGCTTCCTGATTAAA
1 GGCTCTTTAGAGCTTCCTGATTAAA
* *
42016635 GGCTCTTTCATGAGCTTCTTGATTAAT
1 GGCTCTTT-A-GAGCTTCCTGATTAAA
* *
42016662 GGCTCTCTGGAGCTTCC
1 GGCTCTTTAGAGCTTCC
42016679 CGATATTGGC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
25 15 0.41
26 1 0.03
27 21 0.57
ACGTcount: A:0.17, C:0.23, G:0.22, T:0.38
Consensus pattern (25 bp):
GGCTCTTTAGAGCTTCCTGATTAAA
Found at i:42016725 original size:24 final size:23
Alignment explanation
Indices: 42016586--42016732 Score: 82
Period size: 24 Copynumber: 6.0 Consensus size: 23
42016576 ACACACCACA
* *
42016586 GCTCTTATGAGCGTCTCGATATATG
1 GCTCTT-TGAGCTTCCCGAT-TATG
* *
42016611 GCTCTTTAGAGCTTCCTGATTAAAG
1 GCTCTTT-GAGCTTCCCGATT-ATG
**
42016636 GCTCTTTCATGAGCTTCTTGATTAATG
1 GCTC-TT--TGAGCTTCCCGATT-ATG
*
42016663 GCTCTCTGGAGCTTCCCGA-TATTG
1 GCTCT-TTGAGCTTCCCGATTA-TG
* * *
42016687 GCTCGCTTGAACTTCCCGATTACG
1 GCTC-TTTGAGCTTCCCGATTATG
42016711 GCTCTTATGAGCTTCCC-ATTAT
1 GCTCTT-TGAGCTTCCCGATTAT
42016733 AAAACTCGAA
Statistics
Matches: 96, Mismatches: 16, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
23 6 0.06
24 34 0.35
25 32 0.33
26 3 0.03
27 20 0.21
28 1 0.01
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.37
Consensus pattern (23 bp):
GCTCTTTGAGCTTCCCGATTATG
Found at i:42021243 original size:16 final size:16
Alignment explanation
Indices: 42021222--42021268 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
42021212 TTAATCACTT
*
42021222 TAATATTAAATTAATA
1 TAATATTAAATTAAAA
* *
42021238 TAATATT-TATCAAAA
1 TAATATTAAATTAAAA
42021253 TAAATATTAAATTAAA
1 T-AATATTAAATTAAA
42021269 TTTAAACATT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
15 6 0.25
16 13 0.54
17 5 0.21
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
TAATATTAAATTAAAA
Found at i:42021302 original size:18 final size:18
Alignment explanation
Indices: 42021253--42021302 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
42021243 TTTATCAAAA
*
42021253 TAAATATTAAATTAAATT
1 TAAATATTAAATAAAATT
*
42021271 TAAACATTAAATAAAATT
1 TAAATATTAAATAAAATT
42021289 T-AATATTAAGATAA
1 TAAATATTAA-ATAA
42021303 TCACTTTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 7 0.25
18 21 0.75
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (18 bp):
TAAATATTAAATAAAATT
Found at i:42023633 original size:17 final size:17
Alignment explanation
Indices: 42023611--42023709 Score: 64
Period size: 17 Copynumber: 5.8 Consensus size: 17
42023601 ATTATTTTAA
42023611 TAATTTAATATTTAATT
1 TAATTTAATATTTAATT
**
42023628 TAATTTAATACGT-ATCT
1 TAATTTAATATTTAAT-T
* *
42023645 TAA--TAGTATTTTA-T
1 TAATTTAATATTTAATT
*
42023659 TAATTTAATATTAAAGTGAT
1 TAATTTAATATTTAA-T--T
42023679 T-ATCTTAATATTTAATT
1 TAAT-TTAATATTTAATT
*
42023696 TAATTTAATGTTTA
1 TAATTTAATATTTA
42023710 TCTACAAGAT
Statistics
Matches: 62, Mismatches: 10, Indels: 20
0.67 0.11 0.22
Matches are distributed among these distances:
14 4 0.06
15 5 0.08
16 10 0.16
17 26 0.42
18 2 0.03
19 3 0.05
20 12 0.19
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (17 bp):
TAATTTAATATTTAATT
Found at i:42032792 original size:24 final size:24
Alignment explanation
Indices: 42032760--42032811 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
42032750 CACCACGAAC
* *
42032760 TTCTAATGCGGTATCGATTCATGT
1 TTCTAATGCGATATCGATTCACGT
* *
42032784 TTCTGATGCGATATCGGTTCACGT
1 TTCTAATGCGATATCGATTCACGT
42032808 TTCT
1 TTCT
42032812 TCTGACGGCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.42
Consensus pattern (24 bp):
TTCTAATGCGATATCGATTCACGT
Found at i:42037127 original size:21 final size:21
Alignment explanation
Indices: 42037101--42037151 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
42037091 GATTGTTTTT
*
42037101 TTTATTGTCTTATTATTATTA
1 TTTATTGTCTTATTACTATTA
* * *
42037122 TTTATTATTTTTTTACTATTA
1 TTTATTGTCTTATTACTATTA
42037143 TCTTATTGT
1 T-TTATTGT
42037152 TTTTACACGA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.22, C:0.06, G:0.04, T:0.69
Consensus pattern (21 bp):
TTTATTGTCTTATTACTATTA
Found at i:42039823 original size:42 final size:42
Alignment explanation
Indices: 42039759--42040012 Score: 314
Period size: 42 Copynumber: 6.0 Consensus size: 42
42039749 AACTTTTGCA
* * *
42039759 GCGTTTACAGAAAAAAATGCCGCTAAAAATCATGTTCTTTAGCG
1 GCGTTTA-A-AAAAAGACGCCGCTAAAGATCATGTTCTTTAGCG
42039803 GCGTTTAAAAAAAGACGCCGCTAAAGATCATGTTCTTTAGCG
1 GCGTTTAAAAAAAGACGCCGCTAAAGATCATGTTCTTTAGCG
* * * *
42039845 GCGCTTAACAAAAGACGCCGCTAAATAACATGTTCTTTAGCG
1 GCGTTTAAAAAAAGACGCCGCTAAAGATCATGTTCTTTAGCG
*
42039887 GCGCTTAAAAAAAAGACGCCGCTAAAGATCATGTTCTTTAGCG
1 GCG-TTTAAAAAAAGACGCCGCTAAAGATCATGTTCTTTAGCG
* * *
42039930 GCGGTTACAAAAAA-TCGCCGCTAAAGATAATGTTCTTTAGCG
1 GCGTTTA-AAAAAAGACGCCGCTAAAGATCATGTTCTTTAGCG
*** *
42039972 GCGCTTGGTAAAAA-ACGCCGCTATAGATCATGTTCTTTAGC
1 GCG-TTTAAAAAAAGACGCCGCTAAAGATCATGTTCTTTAGC
42040013 AGTGCTTTCA
Statistics
Matches: 184, Mismatches: 23, Indels: 8
0.86 0.11 0.04
Matches are distributed among these distances:
42 132 0.72
43 45 0.24
44 7 0.04
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.26
Consensus pattern (42 bp):
GCGTTTAAAAAAAGACGCCGCTAAAGATCATGTTCTTTAGCG
Found at i:42039910 original size:127 final size:126
Alignment explanation
Indices: 42039769--42040012 Score: 355
Period size: 127 Copynumber: 1.9 Consensus size: 126
42039759 GCGTTTACAG
* * *
42039769 AAAAAAATGCCGCTAAAAATCATGTTCTTTAGCGGCGTTTA-AAAAAAGACGCCGCTAAAGATCA
1 AAAAAAACGCCGCTAAAAATCATGTTCTTTAGCGGCGGTTACAAAAAA-ACGCCGCTAAAGATAA
* *
42039833 TGTTCTTTAGCGGCGCTTAACAAAAGACGCCGCTAAATAACATGTTCTTTAGCGGCGCTTAA
65 TGTTCTTTAGCGGCGCTTAACAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAA
* *
42039895 AAAAAAGACGCCGCTAAAGATCATGTTCTTTAGCGGCGGTTACAAAAAATCGCCGCTAAAGATAA
1 AAAAAA-ACGCCGCTAAAAATCATGTTCTTTAGCGGCGGTTACAAAAAAACGCCGCTAAAGATAA
*** * *
42039960 TGTTCTTTAGCGGCGCTTGGTAAAAAACGCCGCTATAGATCATGTTCTTTAGC
65 TGTTCTTTAGCGGCGCTTAACAAAAAACGCCGCTAAAGAACATGTTCTTTAGC
42040013 AGTGCTTTCA
Statistics
Matches: 104, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
126 6 0.06
127 92 0.88
128 6 0.06
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (126 bp):
AAAAAAACGCCGCTAAAAATCATGTTCTTTAGCGGCGGTTACAAAAAAACGCCGCTAAAGATAAT
GTTCTTTAGCGGCGCTTAACAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAA
Found at i:42040034 original size:85 final size:85
Alignment explanation
Indices: 42039771--42040081 Score: 348
Period size: 85 Copynumber: 3.7 Consensus size: 85
42039761 GTTTACAGAA
* * *
42039771 AAAAATGCCGCTAAAAATCATGTTCTTTAGCGGCG-TTTAAAAAAAGACGCCGCTAAAGATCATG
1 AAAAACGCCGCTAAAGATAATGTTCTTTAGCGGCGCTTTAAAAAAAGACGCCGCTAAAGATCATG
*
42039835 TTCTTTAGCGGCGC-TTAAC
66 TTCTTTAGCGGCGCTTTCAC
* *
42039854 AAAAGACGCCGCTAAATA-ACATGTTCTTTAGCGGCGCTTAAAAAAAAGACGCCGCTAAAGATCA
1 AAAA-ACGCCGCTAAAGATA-ATGTTCTTTAGCGGCGCTTTAAAAAAAGACGCCGCTAAAGATCA
* *
42039918 TGTTCTTTAGCGGCGGTTACA-
64 TGTTCTTTAGCGGCGCTTTCAC
*** *
42039939 AAAAATCGCCGCTAAAGATAATGTTCTTTAGCGGCGCTTGGTAAAAA-ACGCCGCTATAGATCAT
1 AAAAA-CGCCGCTAAAGATAATGTTCTTTAGCGGCGCTTTAAAAAAAGACGCCGCTAAAGATCAT
* *
42040003 GTTCTTTAGCAGTGCTTTCATC
65 GTTCTTTAGCGGCGCTTTCA-C
** * * *
42040025 ACGAACGCCGCGGAAAG-TAATGTTCTTTAGCGGCGCTTTTATAAAAA-ACGCCACTAA
1 AAAAACGCCGC-TAAAGATAATGTTCTTTAGCGGCGC-TTTAAAAAAAGACGCCGCTAA
42040082 TTTTGGGATT
Statistics
Matches: 195, Mismatches: 23, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
83 4 0.02
84 60 0.31
85 105 0.54
86 26 0.13
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.26
Consensus pattern (85 bp):
AAAAACGCCGCTAAAGATAATGTTCTTTAGCGGCGCTTTAAAAAAAGACGCCGCTAAAGATCATG
TTCTTTAGCGGCGCTTTCAC
Found at i:42040048 original size:127 final size:127
Alignment explanation
Indices: 42039790--42040059 Score: 321
Period size: 127 Copynumber: 2.1 Consensus size: 127
42039780 GCTAAAAATC
* *
42039790 ATGTTCTTTAGCGGCGTTTAAAAAAAGACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAACA
1 ATGTTCTTTAGCGGCGGTTAAAAAAAGACGCCGCTAAAGATAATGTTCTTTAGCGGCGCTTAACA
* * * * *
42039855 AAAGACGCCGCTAAATAACATGTTCTTTAGCGGCGCTTAAAAAAAAGACGCCGCTAAAGATC
66 AAAAACGCCGCTAAAGAACATGTTCTTTAGCAGCGCTTAAAAAAAAGACGCCGCGAAAGATA
* ***
42039917 ATGTTCTTTAGCGGCGGTTACAAAAAA-TCGCCGCTAAAGATAATGTTCTTTAGCGGCGCTTGGT
1 ATGTTCTTTAGCGGCGGTTA-AAAAAAGACGCCGCTAAAGATAATGTTCTTTAGCGGCGCTTAAC
* * * ** ** *
42039981 AAAAAACGCCGCTATAGATCATGTTCTTTAGCAGTGCTT-TCATCACGAACGCCGCGGAAAG-TA
65 AAAAAACGCCGCTAAAGAACATGTTCTTTAGCAGCGCTTAAAAAAAAG-ACGCCGC-GAAAGATA
42040044 ATGTTCTTTAGCGGCG
1 ATGTTCTTTAGCGGCG
42040060 CTTTTATAAA
Statistics
Matches: 121, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
126 3 0.02
127 108 0.89
128 10 0.08
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (127 bp):
ATGTTCTTTAGCGGCGGTTAAAAAAAGACGCCGCTAAAGATAATGTTCTTTAGCGGCGCTTAACA
AAAAACGCCGCTAAAGAACATGTTCTTTAGCAGCGCTTAAAAAAAAGACGCCGCGAAAGATA
Found at i:42040465 original size:12 final size:12
Alignment explanation
Indices: 42040448--42040496 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
42040438 TTTTGAACCT
42040448 CTGCTTCTCTCG
1 CTGCTTCTCTCG
*
42040460 CTGCTTCTCGCG
1 CTGCTTCTCTCG
**
42040472 CTGCAGCT-T--
1 CTGCTTCTCTCG
42040481 CTGCTTCTCTCG
1 CTGCTTCTCTCG
42040493 CTGC
1 CTGC
42040497 AGCCTCTGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
9 6 0.21
10 1 0.04
12 21 0.75
ACGTcount: A:0.02, C:0.41, G:0.20, T:0.37
Consensus pattern (12 bp):
CTGCTTCTCTCG
Found at i:42040484 original size:21 final size:21
Alignment explanation
Indices: 42040460--42040508 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
42040450 GCTTCTCTCG
*
42040460 CTGCTTCTCGCGCTGCAGCTT
1 CTGCTTCTCGCGCTGCAGCCT
*
42040481 CTGCTTCTCTCGCTGCAGCCT
1 CTGCTTCTCGCGCTGCAGCCT
42040502 CTGCTTC
1 CTGCTTC
42040509 CGTCGTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.04, C:0.41, G:0.20, T:0.35
Consensus pattern (21 bp):
CTGCTTCTCGCGCTGCAGCCT
Found at i:42040539 original size:35 final size:35
Alignment explanation
Indices: 42040493--42040578 Score: 154
Period size: 35 Copynumber: 2.5 Consensus size: 35
42040483 GCTTCTCTCG
42040493 CTGCAGCCTCTGCTTCCGTCGTTGTTACCTCTGCT
1 CTGCAGCCTCTGCTTCCGTCGTTGTTACCTCTGCT
* *
42040528 CTGCAGCCTCTGCTTCCGTCGTTGTTGCCTCTGTT
1 CTGCAGCCTCTGCTTCCGTCGTTGTTACCTCTGCT
42040563 CTGCAGCCTCTGCTTC
1 CTGCAGCCTCTGCTTC
42040579 TCTCGCTACA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 49 1.00
ACGTcount: A:0.05, C:0.37, G:0.21, T:0.37
Consensus pattern (35 bp):
CTGCAGCCTCTGCTTCCGTCGTTGTTACCTCTGCT
Found at i:42040593 original size:35 final size:35
Alignment explanation
Indices: 42040493--42040597 Score: 106
Period size: 35 Copynumber: 3.0 Consensus size: 35
42040483 GCTTCTCTCG
* **
42040493 CTGCAGCCTCTGCTTCCGTCGTTGTTA-CCTCTGCT
1 CTGCAGCCTCTGCTTCCGTCGCT-ACAGCCTCTGCT
* *** *
42040528 CTGCAGCCTCTGCTTCCGTCGTTGTTGCCTCTGTT
1 CTGCAGCCTCTGCTTCCGTCGCTACAGCCTCTGCT
42040563 CTGCAGCCTCTGCTTCTC-TCGCTACAGCCTCTGCT
1 CTGCAGCCTCTGCTTC-CGTCGCTACAGCCTCTGCT
42040598 TCCCTCGTTG
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
34 1 0.02
35 58 0.97
36 1 0.02
ACGTcount: A:0.06, C:0.38, G:0.20, T:0.36
Consensus pattern (35 bp):
CTGCAGCCTCTGCTTCCGTCGCTACAGCCTCTGCT
Found at i:42046224 original size:9 final size:9
Alignment explanation
Indices: 42046207--42046391 Score: 100
Period size: 9 Copynumber: 20.4 Consensus size: 9
42046197 TATGTATTAA
*
42046207 GTAAATTAT
1 GTAAGTTAT
42046216 GTAAGTTAT
1 GTAAGTTAT
*
42046225 GTACGTGTA-
1 GTAAGT-TAT
42046234 -TAAGTTAT
1 GTAAGTTAT
42046242 GTAAGTTAT
1 GTAAGTTAT
*
42046251 GT-A-TTAA
1 GTAAGTTAT
**
42046258 GTAAACTAT
1 GTAAGTTAT
*
42046267 GTAAGTTGT
1 GTAAGTTAT
42046276 GT-A-TTAT
1 GTAAGTTAT
*
42046283 GTAACTTAT
1 GTAAGTTAT
42046292 GTAAGTTAT
1 GTAAGTTAT
** *
42046301 CAAAGTAAT
1 GTAAGTTAT
*
42046310 GTATGTTAT
1 GTAAGTTAT
42046319 GTAAG-T-T
1 GTAAGTTAT
42046326 GTAAGTTAT
1 GTAAGTTAT
*
42046335 -TATGTATTAT
1 GTAAG--TTAT
42046345 GTAAGTTTACAT
1 GTAAG-TT--AT
*
42046357 ATAAGTTTAT
1 GTAAG-TTAT
42046367 GTGATAGTTAT
1 GT-A-AGTTAT
42046378 GTAAGTTTAT
1 GTAAG-TTAT
42046388 GTAA
1 GTAA
42046392 ATATTAATAA
Statistics
Matches: 135, Mismatches: 24, Indels: 33
0.70 0.12 0.17
Matches are distributed among these distances:
7 18 0.13
8 13 0.10
9 63 0.47
10 20 0.15
11 10 0.07
12 11 0.08
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.44
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:42046224 original size:25 final size:25
Alignment explanation
Indices: 42046196--42046300 Score: 124
Period size: 25 Copynumber: 4.2 Consensus size: 25
42046186 TGATATATAT
42046196 TTATGTATTAAGTAAATTATGTAAG
1 TTATGTATTAAGTAAATTATGTAAG
*
42046221 TTATGTACGTGT-A-TAAGTTATGTAAG
1 TTATGTA--T-TAAGTAAATTATGTAAG
*
42046247 TTATGTATTAAGTAAACTATGTAAG
1 TTATGTATTAAGTAAATTATGTAAG
* * *
42046272 TTGTGTATTATGTAACTTATGTAAG
1 TTATGTATTAAGTAAATTATGTAAG
42046297 TTAT
1 TTAT
42046301 CAAAGTAATG
Statistics
Matches: 67, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
23 1 0.01
24 2 0.03
25 42 0.63
26 19 0.28
27 2 0.03
28 1 0.01
ACGTcount: A:0.34, C:0.03, G:0.18, T:0.45
Consensus pattern (25 bp):
TTATGTATTAAGTAAATTATGTAAG
Found at i:42046252 original size:51 final size:50
Alignment explanation
Indices: 42046196--42046300 Score: 147
Period size: 51 Copynumber: 2.1 Consensus size: 50
42046186 TGATATATAT
* * *
42046196 TTATGTATTAAGTAAATTATGTAAGTTATGTACGTGTATAAGTTATGTAAG
1 TTATGTATTAAGTAAACTATGTAAGTTATGTA-GTATATAACTTATGTAAG
* * *
42046247 TTATGTATTAAGTAAACTATGTAAGTTGTGTATTATGTAACTTATGTAAG
1 TTATGTATTAAGTAAACTATGTAAGTTATGTAGTATATAACTTATGTAAG
42046297 TTAT
1 TTAT
42046301 CAAAGTAATG
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
50 18 0.38
51 30 0.62
ACGTcount: A:0.34, C:0.03, G:0.18, T:0.45
Consensus pattern (50 bp):
TTATGTATTAAGTAAACTATGTAAGTTATGTAGTATATAACTTATGTAAG
Found at i:42046324 original size:18 final size:18
Alignment explanation
Indices: 42046207--42046334 Score: 65
Period size: 16 Copynumber: 7.5 Consensus size: 18
42046197 TATGTATTAA
* *
42046207 GTAAATTATGTAAGTTAT
1 GTAAGTTATGTAAGTAAT
* *
42046225 GTACGTGTA--TAAGTTAT
1 GTAAGT-TATGTAAGTAAT
*
42046242 GTAAGTTATGT-ATTAA-
1 GTAAGTTATGTAAGTAAT
** **
42046258 GTAAACTATGTAAGTTGT
1 GTAAGTTATGTAAGTAAT
* *
42046276 GT-A-TTATGTAACTTAT
1 GTAAGTTATGTAAGTAAT
**
42046292 GTAAGTTATCAAAGTAAT
1 GTAAGTTATGTAAGTAAT
*
42046310 GTATGTTATGTAAGT--T
1 GTAAGTTATGTAAGTAAT
42046326 GTAAGTTAT
1 GTAAGTTAT
42046335 TATGTATTAT
Statistics
Matches: 82, Mismatches: 21, Indels: 16
0.69 0.18 0.13
Matches are distributed among these distances:
16 32 0.39
17 20 0.24
18 28 0.34
19 2 0.02
ACGTcount: A:0.34, C:0.03, G:0.20, T:0.43
Consensus pattern (18 bp):
GTAAGTTATGTAAGTAAT
Found at i:42046573 original size:13 final size:13
Alignment explanation
Indices: 42046555--42046712 Score: 115
Period size: 13 Copynumber: 12.0 Consensus size: 13
42046545 TAAATTTTAG
*
42046555 TAAGTAATGTATT
1 TAAGTAATATATT
*
42046568 TAAGTAACATATT
1 TAAGTAATATATT
* *
42046581 TAAGTAAAAAATT
1 TAAGTAATATATT
** *
42046594 TAACCAA-ATTTT
1 TAAGTAATATATT
*
42046606 AGTAAGTAATGTATT
1 --TAAGTAATATATT
*
42046621 TAAGTAACATATT
1 TAAGTAATATATT
*
42046634 TAAGTAATAAATT
1 TAAGTAATATATT
*
42046647 TAACG-AA-ATTTT
1 TAA-GTAATATATT
*
42046659 AGTAAGTAATGTATT
1 --TAAGTAATATATT
*
42046674 TAAGTAATTTATT
1 TAAGTAATATATT
42046687 TAAGTAATATATT
1 TAAGTAATATATT
* *
42046700 CAAGTAACATATT
1 TAAGTAATATATT
42046713 AAGAGTAAAT
Statistics
Matches: 113, Mismatches: 24, Indels: 16
0.74 0.16 0.10
Matches are distributed among these distances:
12 6 0.05
13 90 0.80
14 11 0.10
15 6 0.05
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (13 bp):
TAAGTAATATATT
Found at i:42046694 original size:53 final size:53
Alignment explanation
Indices: 42046546--42046695 Score: 264
Period size: 53 Copynumber: 2.8 Consensus size: 53
42046536 ATATATACTT
*
42046546 AAATTTTAGTAAGTAATGTATTTAAGTAACATATTTAAGTAAAAAATTTAACC
1 AAATTTTAGTAAGTAATGTATTTAAGTAACATATTTAAGTAATAAATTTAACC
*
42046599 AAATTTTAGTAAGTAATGTATTTAAGTAACATATTTAAGTAATAAATTTAACG
1 AAATTTTAGTAAGTAATGTATTTAAGTAACATATTTAAGTAATAAATTTAACC
**
42046652 AAATTTTAGTAAGTAATGTATTTAAGTAATTTATTTAAGTAATA
1 AAATTTTAGTAAGTAATGTATTTAAGTAACATATTTAAGTAATA
42046696 TATTCAAGTA
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 93 1.00
ACGTcount: A:0.45, C:0.03, G:0.11, T:0.41
Consensus pattern (53 bp):
AAATTTTAGTAAGTAATGTATTTAAGTAACATATTTAAGTAATAAATTTAACC
Found at i:42047383 original size:4 final size:4
Alignment explanation
Indices: 42047374--42047452 Score: 158
Period size: 4 Copynumber: 19.8 Consensus size: 4
42047364 AAAAATCTAT
42047374 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
42047422 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
42047453 TTATGCAGTT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 75 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:42047600 original size:6 final size:6
Alignment explanation
Indices: 42047589--42047617 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
42047579 TCAATTCTGT
42047589 ATATAC ATATAC ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATA
42047618 TATAAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:42048925 original size:47 final size:48
Alignment explanation
Indices: 42048838--42048936 Score: 128
Period size: 47 Copynumber: 2.1 Consensus size: 48
42048828 GTTTTGTTAA
* * **
42048838 TTTAGGTAATATTTAAAAAAATTAGATAAAATTATCAATTTCAGT-TT
1 TTTAAGTAATATTTAAAAAAATTAGATAAAAATAAAAATTTCAGTGTT
* * *
42048885 TTTAAGTAATATTTATAAAAATTAGGTAAAAATAAAAATTTTAGTGTT
1 TTTAAGTAATATTTAAAAAAATTAGATAAAAATAAAAATTTCAGTGTT
42048933 TTTA
1 TTTA
42048937 TTTCTTTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
47 38 0.86
48 6 0.14
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.43
Consensus pattern (48 bp):
TTTAAGTAATATTTAAAAAAATTAGATAAAAATAAAAATTTCAGTGTT
Found at i:42048980 original size:9 final size:9
Alignment explanation
Indices: 42048968--42049010 Score: 61
Period size: 9 Copynumber: 4.7 Consensus size: 9
42048958 ATTTTTTTGT
42048968 AATTTTTAC
1 AATTTTTAC
42048977 AATTTTTTTAC
1 AA--TTTTTAC
42048988 AA-TTTTAC
1 AATTTTTAC
42048996 AATTTTTAC
1 AATTTTTAC
42049005 AATTTT
1 AATTTT
42049011 AAATTATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
8 8 0.26
9 14 0.45
11 9 0.29
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (9 bp):
AATTTTTAC
Found at i:42048982 original size:8 final size:8
Alignment explanation
Indices: 42048982--42049015 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
42048972 TTTACAATTT
42048982 TTTTACAA
1 TTTTACAA
42048990 TTTTACAA
1 TTTTACAA
42048998 TTTTTACAA
1 -TTTTACAA
42049007 TTTTA-AA
1 TTTTACAA
42049014 TT
1 TT
42049016 ATTATATTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 4 0.16
8 13 0.52
9 8 0.32
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (8 bp):
TTTTACAA
Found at i:42048982 original size:19 final size:19
Alignment explanation
Indices: 42048971--42049015 Score: 69
Period size: 17 Copynumber: 2.5 Consensus size: 19
42048961 TTTTTGTAAT
42048971 TTTTACAATTTTTTTACAA
1 TTTTACAATTTTTTTACAA
42048990 TTTTACAA--TTTTTACAA
1 TTTTACAATTTTTTTACAA
42049007 TTTTA-AATT
1 TTTTACAATT
42049016 ATTATATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 2 0.08
17 14 0.58
19 8 0.33
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTACAATTTTTTTACAA
Found at i:42049029 original size:21 final size:20
Alignment explanation
Indices: 42049004--42049058 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 20
42048994 ACAATTTTTA
42049004 CAATTTTAAATTATT-ATATT
1 CAATTTTAAATTATTCATA-T
*
42049024 CAAATTATTATA-TATTGCATAT
1 C-AATT-TTAAATTATT-CATAT
42049046 CAATTTTAAATTA
1 CAATTTTAAATTA
42049059 GTAATCTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
20 5 0.18
21 14 0.50
22 6 0.21
23 3 0.11
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (20 bp):
CAATTTTAAATTATTCATAT
Found at i:42049243 original size:7 final size:7
Alignment explanation
Indices: 42049231--42049305 Score: 57
Period size: 7 Copynumber: 11.0 Consensus size: 7
42049221 ACTAATTAAT
42049231 CTAAACC
1 CTAAACC
42049238 CTAAACC
1 CTAAACC
42049245 CTAAACC
1 CTAAACC
*
42049252 AT-AACC
1 CTAAACC
* *
42049258 C-GATCC
1 CTAAACC
*
42049264 CTAACCC
1 CTAAACC
42049271 CT-AACC
1 CTAAACC
*
42049277 CTTAACC
1 CTAAACC
*
42049284 CTTAACCC
1 C-TAAACC
*
42049292 CTAACCC
1 CTAAACC
42049299 CTAAACC
1 CTAAACC
42049306 TTATTTAATA
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
6 13 0.24
7 37 0.67
8 5 0.09
ACGTcount: A:0.35, C:0.47, G:0.01, T:0.17
Consensus pattern (7 bp):
CTAAACC
Found at i:42049248 original size:14 final size:14
Alignment explanation
Indices: 42049231--42049305 Score: 57
Period size: 13 Copynumber: 5.5 Consensus size: 14
42049221 ACTAATTAAT
42049231 CTAAACCCTAAACC
1 CTAAACCCTAAACC
*
42049245 CTAAACCAT-AACC
1 CTAAACCCTAAACC
* * *
42049258 C-GATCCCTAACCC
1 CTAAACCCTAAACC
*
42049271 CT-AACCCTTAACC
1 CTAAACCCTAAACC
* *
42049284 CTTAACCCCTAACCC
1 C-TAAACCCTAAACC
42049299 CTAAACC
1 CTAAACC
42049306 TTATTTAATA
Statistics
Matches: 45, Mismatches: 12, Indels: 8
0.69 0.18 0.12
Matches are distributed among these distances:
12 4 0.09
13 18 0.40
14 14 0.31
15 9 0.20
ACGTcount: A:0.35, C:0.47, G:0.01, T:0.17
Consensus pattern (14 bp):
CTAAACCCTAAACC
Found at i:42049264 original size:89 final size:89
Alignment explanation
Indices: 42049107--42049277 Score: 238
Period size: 89 Copynumber: 1.9 Consensus size: 89
42049097 TATAAAGAAC
** * * *
42049107 TTATTTAATATATAAATTAAAAAGTACTAATTAATCCAAATCTGAAACCCTAACCCAACCCCAAA
1 TTATTTAATATATAAATTAAAAAACACTAATTAATCCAAACCTGAAACCCTAAACCAAACCCAAA
*
42049172 TCCCTAATCCCTAACCCCTAAACT
66 TCCCTAACCCCTAACCCCTAAACT
*
42049196 TTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCT-AAACCCTAAACCATAACCC-
1 TTATTTAATATATAAATTAAAAAACACTAATTAATCCAAA-CCTGAAACCCTAAACCA-AACCCA
*
42049259 GATCCCTAACCCCTAACCC
64 AATCCCTAACCCCTAACCC
42049278 TTAACCCTTA
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
89 66 0.92
90 6 0.08
ACGTcount: A:0.43, C:0.29, G:0.02, T:0.26
Consensus pattern (89 bp):
TTATTTAATATATAAATTAAAAAACACTAATTAATCCAAACCTGAAACCCTAAACCAAACCCAAA
TCCCTAACCCCTAACCCCTAAACT
Found at i:42049291 original size:21 final size:21
Alignment explanation
Indices: 42049265--42049308 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
42049255 ACCCGATCCC
* *
42049265 TAACCCCTAACCCTTAACCCT
1 TAACCCCTAACCCCTAAACCT
42049286 TAACCCCTAACCCCTAAACCT
1 TAACCCCTAACCCCTAAACCT
42049307 TA
1 TA
42049309 TTTAATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.32, C:0.45, G:0.00, T:0.23
Consensus pattern (21 bp):
TAACCCCTAACCCCTAAACCT
Found at i:42049412 original size:7 final size:7
Alignment explanation
Indices: 42049402--42049453 Score: 67
Period size: 7 Copynumber: 8.0 Consensus size: 7
42049392 CTCTTAACAT
42049402 CTAACCC
1 CTAACCC
42049409 CTAA--C
1 CTAACCC
42049414 CTAACCC
1 CTAACCC
42049421 CTAACCC
1 CTAACCC
42049428 CTAA--C
1 CTAACCC
42049433 CTAACCC
1 CTAACCC
42049440 CTAACCC
1 CTAACCC
*
42049447 TTAACCC
1 CTAACCC
42049454 ATAAACCTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
5 10 0.25
7 30 0.75
ACGTcount: A:0.31, C:0.52, G:0.00, T:0.17
Consensus pattern (7 bp):
CTAACCC
Found at i:42049415 original size:109 final size:110
Alignment explanation
Indices: 42049181--42049412 Score: 292
Period size: 110 Copynumber: 2.1 Consensus size: 110
42049171 ATCCCTAATC
*
42049181 CCTAACCCCTAAACTTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCC
1 CCTAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCC
* * * *
42049246 TAAACCATAACCCGATCCCTAACCCCTAACCCTTAACCCTTAACC
66 TAAACCATAACCCAATCCATAAACCCTAACCCTTAACCCTTAACA
* *
42049291 CCTAACCCCTAAACCTTATTTAATATAT-AATTAAAACACACTAATTAATCTAAACCCTAAACTC
1 CCTAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCC
** * *
42049355 T-AACC-TAACACCAAATTTATAAACCTTAAATCCC-TAACTCTTAACA
66 TAAACCATAAC-CC-AATCCATAAACCCT-AA-CCCTTAACCCTTAACA
*
42049401 TCTAACCCCTAA
1 CCTAACCCCTAA
42049413 CCTAACCCCT
Statistics
Matches: 106, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
107 4 0.04
108 6 0.06
109 43 0.41
110 50 0.47
111 3 0.03
ACGTcount: A:0.42, C:0.31, G:0.00, T:0.27
Consensus pattern (110 bp):
CCTAACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACCC
TAAACCATAACCCAATCCATAAACCCTAACCCTTAACCCTTAACA
Found at i:42049419 original size:12 final size:12
Alignment explanation
Indices: 42049402--42049445 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
42049392 CTCTTAACAT
42049402 CTAACCCCTAAC
1 CTAACCCCTAAC
42049414 CTAA--CC---C
1 CTAACCCCTAAC
42049421 CTAACCCCTAAC
1 CTAACCCCTAAC
42049433 CTAACCCCTAAC
1 CTAACCCCTAAC
42049445 C
1 C
42049446 CTTAACCCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
7 5 0.19
9 2 0.07
10 2 0.07
12 18 0.67
ACGTcount: A:0.32, C:0.52, G:0.00, T:0.16
Consensus pattern (12 bp):
CTAACCCCTAAC
Found at i:42049424 original size:19 final size:19
Alignment explanation
Indices: 42049402--42049452 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
42049392 CTCTTAACAT
42049402 CTAACCCCTAACCTAACCC
1 CTAACCCCTAACCTAACCC
42049421 CTAACCCCTAACCTAACCC
1 CTAACCCCTAACCTAACCC
*
42049440 CTAACCCTTAACC
1 CTAACCCCTAACC
42049453 CATAAACCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.31, C:0.51, G:0.00, T:0.18
Consensus pattern (19 bp):
CTAACCCCTAACCTAACCC
Found at i:42049509 original size:14 final size:15
Alignment explanation
Indices: 42049487--42049520 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
42049477 CTTAAACCAG
*
42049487 AATCCCTAA-TCCAT
1 AATCTCTAATTCCAT
42049501 AATCTCTAATTCCAT
1 AATCTCTAATTCCAT
42049516 AATCT
1 AATCT
42049521 ATAAAACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.35
Consensus pattern (15 bp):
AATCTCTAATTCCAT
Found at i:42050558 original size:113 final size:113
Alignment explanation
Indices: 42050066--42050850 Score: 1009
Period size: 113 Copynumber: 6.9 Consensus size: 113
42050056 TTAAATTATT
* * *
42050066 TTAAATCCCTGAGCATTAGCGGCGCTTACATAAAAACGCCACTAAATCCTCGAAAGCTCGGAAAA
1 TTAAAGCCCTGAGCATTAGCGGCGCTTACATAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAA
* * *
42050131 CGGCGTCGTTGGGCTGAAGTATTTTTGCGGTGCTTTCCCAAAAAGGCCG
66 CGGCGTCGTTGGGCTTAGGTA-TTTTGCGGTGCTTTCCCAAAAACGCCG
* * * *
42050180 TTAAAGCCCTGAGCATTAGCGGTGCTTACATAAAAAAGCCACTAAAATCCTCGAAAGCTCGGAAA
1 TTAAAGCCCTGAGCATTAGCGGCGCTTACATAAAAACGCCACT-AAATCCCCGAAAGCTCAGAAA
* * *
42050245 ACGGCGTCGTTGGGCTGAAAGTAGTTTTGCGGTGCTTTCCCACAAAAGGCCG
65 ACGGCGTCGTTGGGCT-TAGGTA-TTTTGCGGTGCTTTCCCA-AAAACGCCG
* * *
42050297 TTAAAGCCCTGAGCATTAGCGGTGCTTACATAAAAAAGCCACTAAATCCTCGAAAGCTCAGAAAA
1 TTAAAGCCCTGAGCATTAGCGGCGCTTACATAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAA
*
42050362 CGGCGTCGTTGGG-TTGAAGTATTTTTGCGGTGCTTTCCCAAAAACGCCG
66 CGGCGTCGTTGGGCTT-AGGTA-TTTTGCGGTGCTTTCCCAAAAACGCCG
* * * *
42050411 CTAAAGCCCTGAGCATTAGTGGTGCTTACATAAAAACGCCACCAAATCCCCGAAAGCTCAGAAAA
1 TTAAAGCCCTGAGCATTAGCGGCGCTTACATAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAA
* *
42050476 CGGCGTCGTTGGGCTTAGGTATTTTGCGGCT-CTTTCCCAAAAATGCTG
66 CGGCGTCGTTGGGCTTAGGTATTTTGCGG-TGCTTTCCCAAAAACGCCG
* ** *
42050524 TTAAAGCCCTGAGCATTAGCGGCGCATATTTAAAAACGCCACTAAATCCCCAAAAGCTCAGAAAA
1 TTAAAGCCCTGAGCATTAGCGGCGCTTACATAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAA
* * *
42050589 CAGCGTTGTTGGGCTTAGGTATTTTGCGGCGCTTTCCCAAAAACGCCG
66 CGGCGTCGTTGGGCTTAGGTATTTTGCGGTGCTTTCCCAAAAACGCCG
* * ** *
42050637 CTAAAGCCCTGAGCATTAGCGGCGCATATTTAAAAACGCCACTAAATCCCCAAAAGCTCAGAAAA
1 TTAAAGCCCTGAGCATTAGCGGCGCTTACATAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAA
* * * * * **
42050702 CGGTGTTGTTGGGCTTAGGTTTTTTTGTGGCGCTTTATCAAAAACGCCG
66 CGGCGTCGTTGGGCTTAGG-TATTTTGCGGTGCTTTCCCAAAAACGCCG
* * * * ** * * *
42050751 CTAAAG-CCTGAACATTAGCGGCGCTTCCTTAAAAACGCTGCTAAATCCCTGGAAGCTCGGAAAA
1 TTAAAGCCCTGAGCATTAGCGGCGCTTACATAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAA
42050815 CGGCGTCGTTGGGCTTAGGTATTTTGCGGTGCTTTC
66 CGGCGTCGTTGGGCTTAGGTATTTTGCGGTGCTTTC
42050851 TGGGAAACGC
Statistics
Matches: 610, Mismatches: 53, Indels: 18
0.90 0.08 0.03
Matches are distributed among these distances:
112 13 0.02
113 268 0.44
114 157 0.26
115 63 0.10
116 57 0.09
117 52 0.09
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.24
Consensus pattern (113 bp):
TTAAAGCCCTGAGCATTAGCGGCGCTTACATAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAA
CGGCGTCGTTGGGCTTAGGTATTTTGCGGTGCTTTCCCAAAAACGCCG
Found at i:42051084 original size:25 final size:24
Alignment explanation
Indices: 42051056--42051102 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
42051046 AATAAAGGAA
* *
42051056 AAATAGATAATAATAATAAATGTGC
1 AAATAAATAAAAATAA-AAATGTGC
42051081 AAATAAATAAAAATAAAAATGT
1 AAATAAATAAAAATAAAAATGT
42051103 AGGCTATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.26
Consensus pattern (24 bp):
AAATAAATAAAAATAAAAATGTGC
Found at i:42052073 original size:10 final size:10
Alignment explanation
Indices: 42052060--42052111 Score: 50
Period size: 10 Copynumber: 4.8 Consensus size: 10
42052050 TGTTATTTCG
42052060 AAATGAAAAA
1 AAATGAAAAA
42052070 AAATGATAAAATA
1 AAATG--AAAA-A
*
42052083 AAATAAAACAA
1 AAATGAAA-AA
*
42052094 AAATGAAATA
1 AAATGAAAAA
42052104 AAATGAAA
1 AAATGAAA
42052112 GTATCACGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 14 0.40
11 11 0.31
12 5 0.14
13 5 0.14
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (10 bp):
AAATGAAAAA
Found at i:42052915 original size:44 final size:44
Alignment explanation
Indices: 42052862--42053164 Score: 177
Period size: 44 Copynumber: 6.8 Consensus size: 44
42052852 TCATCGTTTT
* *
42052862 AATCCGCTCCACTGCAACTTTAGGAAGATAGGATTAGTAGCTTC
1 AATCTGCTCCACTGCAACTTTAGGAAGATAAGATTAGTAGCTTC
* * * *
42052906 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTC
1 AATCTGCTCCACTGCAACTTTAGGAAGATAAGATTAGTAGCTTC
* * *
42052950 AACCTGCTCCACTGCAACTTTAGGAAGATAAGGTT--T-GATAT-
1 AATCTGCTCCACTGCAACTTTAGGAAGATAAGATTAGTAGCT-TC
* * * *
42052991 GATCTGCTCTACTACAACTTTA-GAGAGATAAAACCTGTAATTTA-TAGCTTT
1 AATCTGCTCCACTGCAACTTTAGGA-AGAT--AA---G--A-TTAGTAGCTTC
* * * * *
42053042 AATCTGTTCCACTGCAACTTCAGGAAAATAAGATTTGCTATCTTC
1 AATCTGCTCCACTGCAACTTTAGGAAGATAAGATTAG-TAGCTTC
* * * * * * ** * * *
42053087 AGTCTGCTCCGCTACAACTTCAGGGAGATAGGGCTAATGGCTTT
1 AATCTGCTCCACTGCAACTTTAGGAAGATAAGATTAGTAGCTTC
* * *
42053131 AATCTACTACACTGCAACTTCAGGAAGATAAGAT
1 AATCTGCTCCACTGCAACTTTAGGAAGATAAGAT
42053165 CCACCATAAT
Statistics
Matches: 193, Mismatches: 50, Indels: 32
0.70 0.18 0.12
Matches are distributed among these distances:
40 2 0.01
41 23 0.12
42 2 0.01
43 4 0.02
44 99 0.51
45 31 0.16
46 2 0.01
49 4 0.02
50 2 0.01
51 22 0.11
52 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTTAGGAAGATAAGATTAGTAGCTTC
Found at i:42053200 original size:143 final size:142
Alignment explanation
Indices: 42053028--42053754 Score: 855
Period size: 143 Copynumber: 5.0 Consensus size: 142
42053018 ATAAAACCTG
* * * *
42053028 TAATTTATAGCTTTAATCTGTTCCACTGCAACTTCAGGAAAATAAGATTTGCTATCTTCAGTCTG
1 TAATTTGTAGCTTTAATCTGTTCCACTGCAAC-CCAGGGAAATAAGATTTGCTGTCTTCAGTCTG
* * ** * *
42053093 CTCCGCTACAACTTCAGGGAGATAGGGCTAATGGCTTTAATCTACTACACTGCAACTTCAGGAAG
65 CTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTACACTGCAACTTCAGGAAG
*
42053158 ATAAGATCCACCA
130 ATAAGATCCGCCA
* * * * *
42053171 TAATTTGTAGCTTTAATTTATTCCACTGCAACGCTAGGGAAATAAGATTTGCTGTTTTTAGTCTG
1 TAATTTGTAGCTTTAATCTGTTCCACTGCAAC-CCAGGGAAATAAGATTTGCTGTCTTCAGTCTG
** * *
42053236 CTTGGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGTAACTTCAGGAAG
65 CTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTACACTGCAACTTCAGGAAG
*
42053301 ATAAGATCCGCTA
130 ATAAGATCCGCCA
* * * * * *
42053314 TAACTTGTAACTTTAATCTGTTCCACTACAATGCCAGGGAAATAAGATTCGTTGTCTTCAGTCTG
1 TAATTTGTAGCTTTAATCTGTTCCACTGCAA-CCCAGGGAAATAAGATTTGCTGTCTTCAGTCTG
** *
42053379 CTTGGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCT-CTACTGCAACTTTAGGAA
65 CTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTAC-ACTGCAACTTCAGGAA
*
42053443 GATAAGATCCGCTA
129 GATAAGATCCGCCA
* * * * *
42053457 TAATTTGTAGCTTTAATCTGTTCCACCGCAACGCCAGGGAAA-AAAATATGCTATCTTCAGTTTG
1 TAATTTGTAGCTTTAATCTGTTCCACTGCAAC-CCAGGGAAATAAGATTTGCTGTCTTCAGTCTG
* *
42053521 CTCCGCTGTAACTTTAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTACCTGCTCCACTGC
65 CTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTG-----CTA-------CACTGC
42053586 AACTTCAGGAAGATAAGATCCGCCA
118 AACTTCAGGAAGATAAGATCCGCCA
* * * *
42053611 TAATTTGTGGCTTTAATCTATTCCACTGCAACTCTAGGGAAATAAGATTTGCTGTCTTCAATCTG
1 TAATTTGTAGCTTTAATCTGTTCCACTGCAAC-CCAGGGAAATAAGATTTGCTGTCTTCAGTCTG
* * *
42053676 CTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGTAACTTAAGGAAG
65 CTCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTACACTGCAACTTCAGGAAG
* *
42053741 ATAATATTCGCCA
130 ATAAGATCCGCCA
42053754 T
1 T
42053755 GATGACTTCA
Statistics
Matches: 498, Mismatches: 69, Indels: 34
0.83 0.11 0.06
Matches are distributed among these distances:
142 57 0.11
143 312 0.63
147 2 0.00
150 2 0.00
154 65 0.13
155 60 0.12
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (142 bp):
TAATTTGTAGCTTTAATCTGTTCCACTGCAACCCAGGGAAATAAGATTTGCTGTCTTCAGTCTGC
TCCGCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTACACTGCAACTTCAGGAAGA
TAAGATCCGCCA
Found at i:42053685 original size:45 final size:44
Alignment explanation
Indices: 42053618--42053733 Score: 117
Period size: 45 Copynumber: 2.6 Consensus size: 44
42053608 CCATAATTTG
* ** **
42053618 TGGCTTTAATCTATTCCACTGCAAC-TCTAGGGAAATAAGATTTGC
1 TGGCTTCAATCTGCTCCACTGCAACTTC-AGGGAAATAAG-GCTGC
* * * *
42053663 TGTCTTCAATCTGCTCCGCTGCAACTTCAGGGAGATAAGGCTGG
1 TGGCTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGGCTGC
*
42053707 TGGCTTCAATCTGCTCCACTGTAACTT
1 TGGCTTCAATCTGCTCCACTGCAACTT
42053734 AAGGAAGATA
Statistics
Matches: 58, Mismatches: 12, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
44 26 0.45
45 30 0.52
46 2 0.03
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.32
Consensus pattern (44 bp):
TGGCTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGGCTGC
Found at i:42065815 original size:15 final size:15
Alignment explanation
Indices: 42065795--42065828 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
42065785 CTTGTAACAA
*
42065795 CAAATCAAAAGCAAC
1 CAAATCAAAACCAAC
*
42065810 CAAATCTAAACCAAC
1 CAAATCAAAACCAAC
42065825 CAAA
1 CAAA
42065829 AGCAGTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.29, G:0.03, T:0.09
Consensus pattern (15 bp):
CAAATCAAAACCAAC
Found at i:42066135 original size:21 final size:21
Alignment explanation
Indices: 42066111--42066158 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
42066101 TTTTGAACAA
*
42066111 CTGCTTCGCTCGCTGCAACCT
1 CTGCTTCCCTCGCTGCAACCT
**
42066132 CTGCTTCCCTCGCTGCCGCCT
1 CTGCTTCCCTCGCTGCAACCT
42066153 CTGCTT
1 CTGCTT
42066159 TAAGTTGTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.04, C:0.46, G:0.19, T:0.31
Consensus pattern (21 bp):
CTGCTTCCCTCGCTGCAACCT
Found at i:42070329 original size:90 final size:90
Alignment explanation
Indices: 42070176--42070356 Score: 344
Period size: 90 Copynumber: 2.0 Consensus size: 90
42070166 GACCCTTGGT
*
42070176 ACTCCAATCGGATAAATTGGCATAAGCGAGGAAGTCATTAATGGTCCACATCAAAGCTGCACGTA
1 ACTCCAACCGGATAAATTGGCATAAGCGAGGAAGTCATTAATGGTCCACATCAAAGCTGCACGTA
42070241 AATTAAAGTTCTCCTTTCTCAGCAC
66 AATTAAAGTTCTCCTTTCTCAGCAC
*
42070266 ACTCCAACCGGATAAATTGGCATAAGCGGGGAAGTCATTAATGGTCCACATCAAAGCTGCACGTA
1 ACTCCAACCGGATAAATTGGCATAAGCGAGGAAGTCATTAATGGTCCACATCAAAGCTGCACGTA
42070331 AATTAAAGTTCTCCTTTCTCAGCAC
66 AATTAAAGTTCTCCTTTCTCAGCAC
42070356 A
1 A
42070357 TCGTATGTCT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
90 89 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (90 bp):
ACTCCAACCGGATAAATTGGCATAAGCGAGGAAGTCATTAATGGTCCACATCAAAGCTGCACGTA
AATTAAAGTTCTCCTTTCTCAGCAC
Done.