Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 90 of 193
Found at i:29473589 original size:17 final size:18
Alignment explanation
Indices: 29473555--29473590 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
29473545 TGAATTTCTA
29473555 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
29473573 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
29473590 T
1 T
29473591 AACTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:29476261 original size:14 final size:16
Alignment explanation
Indices: 29476232--29476265 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
29476222 TGTGAATTTG
29476232 TTTATATATTTAATTA
1 TTTATATATTTAATTA
29476248 TTTATATA-TT-ATTA
1 TTTATATATTTAATTA
29476262 TTTA
1 TTTA
29476266 AAATTCATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 2 0.11
16 8 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTATATATTTAATTA
Found at i:29480572 original size:2 final size:2
Alignment explanation
Indices: 29480565--29480594 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
29480555 TGCATTTGAA
29480565 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29480595 TAAAGTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29487091 original size:16 final size:16
Alignment explanation
Indices: 29487070--29487114 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
29487060 ACAAGTTGCT
29487070 TCGGGCAGAGGGAGCA
1 TCGGGCAGAGGGAGCA
*
29487086 TCGGGCAGAGGAAGCA
1 TCGGGCAGAGGGAGCA
* *
29487102 TTGGACAGAGGGA
1 TCGGGCAGAGGGA
29487115 CGATCTCGGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.29, C:0.16, G:0.47, T:0.09
Consensus pattern (16 bp):
TCGGGCAGAGGGAGCA
Found at i:29487582 original size:6 final size:6
Alignment explanation
Indices: 29487571--29487608 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
29487561 AATTTATTCA
*
29487571 TAAATT TAAATT TAAA-T TAATCTT TAAATT TAAATT TA
1 TAAATT TAAATT TAAATT TAA-ATT TAAATT TAAATT TA
29487609 GTATAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 4 0.14
6 20 0.71
7 4 0.14
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (6 bp):
TAAATT
Found at i:29489668 original size:59 final size:59
Alignment explanation
Indices: 29489600--29489891 Score: 265
Period size: 59 Copynumber: 5.0 Consensus size: 59
29489590 TTACATTCTC
* * * ** *
29489600 ACCCTAAAACTTCCAAAAATTACAATTTTCACTCCAAAATTCTGAAAATTCCATTTTTG
1 ACCCCAAAACTTCCAAAAATTACCATTTTCACTCCGAAATTCCAAAAATTCCATTTTTA
** * * *
29489659 ACCCCAAAACTTTTGAAAAA-T-CCATTTTTACTCTCGAACTTCTAAAAATTCCATTTTTA
1 ACCCCAAAAC-TTCCAAAAATTACCATTTTCACTC-CGAAATTCCAAAAATTCCATTTTTA
* * * * *
29489718 ACCCCAAAACTTACTAAAATTACCATTTAC-CCCCGAACTTCCAAAAATTCCATTTTTA
1 ACCCCAAAACTTCCAAAAATTACCATTTTCACTCCGAAATTCCAAAAATTCCATTTTTA
* * * *
29489776 ACCCCTAAATTTCCCAAAATTA-CATTTTCA-TCCTTGAAATTCCAAAAATTCCATTTTTG
1 ACCCCAAAACTTCCAAAAATTACCATTTTCACTCC--GAAATTCCAAAAATTCCATTTTTA
* * * * *
29489835 ACCCCAACACTTCC-AAAATTACCATTTT-ACCCCCAAATGTCCAAAAACTCCGTTTTT
1 ACCCCAAAACTTCCAAAAATTACCATTTTCACTCCGAAAT-TCCAAAAATTCCATTTTT
29489892 GATCCCGATT
Statistics
Matches: 192, Mismatches: 31, Indels: 21
0.79 0.13 0.09
Matches are distributed among these distances:
57 12 0.06
58 82 0.43
59 85 0.44
60 13 0.07
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (59 bp):
ACCCCAAAACTTCCAAAAATTACCATTTTCACTCCGAAATTCCAAAAATTCCATTTTTA
Found at i:29489795 original size:30 final size:30
Alignment explanation
Indices: 29489456--29489891 Score: 161
Period size: 29 Copynumber: 14.9 Consensus size: 30
29489446 CCCTAGAGGT
* *
29489456 CCCTAAACCGTCCAAAAATT--ATGTTTTGAC
1 CCCTAAA-CTTCCAAAAATTCCAT-TTTTAAC
* *
29489486 CCC-AAACTTTCC-AAAATTACATTTTT-AG
1 CCCTAAAC-TTCCAAAAATTCCATTTTTAAC
* **
29489514 CCCTAAAACTT-CTAAAATTATATTTTT-AC
1 CCCT-AAACTTCCAAAAATTCCATTTTTAAC
* *
29489543 CCCTAAACTTTCC-AAAATTGCC---TTGAAGGT
1 CCCTAAAC-TTCCAAAAATT-CCATTTTTAA--C
* * * *
29489573 CCCTAAACTTTCAAAAATTACA-TTCTCA-
1 CCCTAAACTTCCAAAAATTCCATTTTTAAC
* * *
29489601 CCCTAAAACTTCCAAAAATTACAATTTTCAC
1 CCCT-AAACTTCCAAAAATTCCATTTTTAAC
* * ** *
29489632 TCC-AAAATTCTGAAAATTCCATTTTTGAC
1 CCCTAAACTTCCAAAAATTCCATTTTTAAC
* **
29489661 CCCAAAACTTTTGAAAAA-TCCATTTTT-A-
1 CCCTAAAC-TTCCAAAAATTCCATTTTTAAC
* * *
29489689 CTCTCGAACTTCTAAAAATTCCATTTTTAAC
1 CCCT-AAACTTCCAAAAATTCCATTTTTAAC
* * *
29489720 CCCAAAACTTACTAAAATTACCA--TTT-AC
1 CCCTAAACTTCCAAAAATT-CCATTTTTAAC
**
29489748 CCCCGAACTTCCAAAAATTCCATTTTTAAC
1 CCCTAAACTTCCAAAAATTCCATTTTTAAC
* * * * *
29489778 CCCTAAATTTCCCAAAATTACA-TTTTCAT
1 CCCTAAACTTCCAAAAATTCCATTTTTAAC
* *
29489807 CCTTGAAA-TTCCAAAAATTCCATTTTTGAC
1 CCCT-AAACTTCCAAAAATTCCATTTTTAAC
29489837 CCC-AACACTTCC-AAAATTACCA-TTTT-AC
1 CCCTAA-ACTTCCAAAAATT-CCATTTTTAAC
* * *
29489865 CCCCAAA-TGTCCAAAAACTCCGTTTTT
1 CCCTAAACT-TCCAAAAATTCCATTTTT
29489892 GATCCCGATT
Statistics
Matches: 312, Mismatches: 57, Indels: 75
0.70 0.13 0.17
Matches are distributed among these distances:
27 6 0.02
28 60 0.19
29 142 0.46
30 89 0.29
31 15 0.05
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (30 bp):
CCCTAAACTTCCAAAAATTCCATTTTTAAC
Found at i:29489802 original size:117 final size:117
Alignment explanation
Indices: 29489600--29489891 Score: 297
Period size: 117 Copynumber: 2.5 Consensus size: 117
29489590 TTACATTCTC
* * * * ** *
29489600 ACCCTAAAACTTCCAAAAATTACAATTTTCACTCCAAAAT-TCTGAAAATTCCATTTTTGACCCC
1 ACCCCAAAACTTCC-AAAATTACCATTTT-ACCCCCAAATGTCCAAAAATTCCATTTTTAACCCC
** * * * *
29489664 AAAACTTTTGAAAAATCCATTTTTA-CTCTCGAACTTCTAAAAATTCCATTTTTA
64 AAAACTTTCCAAAAATACATTTTCATC-CTCGAAATTCCAAAAATTCCATTTTTA
* *
29489718 ACCCCAAAACTTACTAAAATTACCA-TTTACCCCCGAACT-TCCAAAAATTCCATTTTTAACCCC
1 ACCCCAAAACTT-CCAAAATTACCATTTTACCCCC-AAATGTCCAAAAATTCCATTTTTAACCCC
* * * *
29489781 TAAA-TTTCCCAAAATTACATTTTCATCCTTGAAATTCCAAAAATTCCATTTTTG
64 AAAACTTT-CCAAAAATACATTTTCATCCTCGAAATTCCAAAAATTCCATTTTTA
* * *
29489835 ACCCCAACACTTCCAAAATTACCATTTTACCCCCAAATGTCCAAAAACTCCGTTTTT
1 ACCCCAAAACTTCCAAAATTACCATTTTACCCCCAAATGTCCAAAAATTCCATTTTT
29489892 GATCCCGATT
Statistics
Matches: 144, Mismatches: 24, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
116 21 0.15
117 101 0.70
118 21 0.15
119 1 0.01
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (117 bp):
ACCCCAAAACTTCCAAAATTACCATTTTACCCCCAAATGTCCAAAAATTCCATTTTTAACCCCAA
AACTTTCCAAAAATACATTTTCATCCTCGAAATTCCAAAAATTCCATTTTTA
Found at i:29493427 original size:13 final size:13
Alignment explanation
Indices: 29493411--29493435 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29493401 TATAACTTAT
29493411 TTTATAAATTTTG
1 TTTATAAATTTTG
29493424 TTTATAAATTTT
1 TTTATAAATTTT
29493436 TTAAATAATT
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:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTATAAATTTTG
Found at i:29493427 original size:25 final size:25
Alignment explanation
Indices: 29493399--29493447 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
29493389 TTTTAAAATT
* *
29493399 TTTATAACTTATTTTATA-AATTTTG
1 TTTATAAATT-TTTTAAATAATTTTG
29493424 TTTATAAATTTTTTAAATAATTTT
1 TTTATAAATTTTTTAAATAATTTT
29493448 AAAATTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (25 bp):
TTTATAAATTTTTTAAATAATTTTG
Found at i:29495412 original size:29 final size:29
Alignment explanation
Indices: 29495380--29495444 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
29495370 AAAATGAGAC
*
29495380 TTTTGGA-TGCCCGAGGGGC-AAAATGGTAA
1 TTTTGGACT-CCCGA-GGGCAAAAATGGCAA
*
29495409 TTTTGGACTCTCGAGGGCAAAAATGGCAA
1 TTTTGGACTCCCGAGGGCAAAAATGGCAA
29495438 TTTTGGA
1 TTTTGGA
29495445 AAAATTTGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 4 0.12
29 27 0.84
30 1 0.03
ACGTcount: A:0.28, C:0.14, G:0.31, T:0.28
Consensus pattern (29 bp):
TTTTGGACTCCCGAGGGCAAAAATGGCAA
Found at i:29495625 original size:57 final size:59
Alignment explanation
Indices: 29495547--29495679 Score: 155
Period size: 57 Copynumber: 2.3 Consensus size: 59
29495537 TCTGGGAGTG
* * * *
29495547 AAATGGTAATTTTTGGAAGTTTCAGCGTC-AAAATGGAATTTTTGGAA-ATTCGGGGT-CA
1 AAATGG-AATTTTTGAAAGTTT-AGCGGCAAAAATGGAATTTTTGGAAGATTAGGGGTAAA
* * *
29495605 AAATGGAATTTTTGAAAGTTTAGGGGCAAAAATGTAATTTTTGGAAGTTTAGGGGTAAA
1 AAATGGAATTTTTGAAAGTTTAGCGGCAAAAATGGAATTTTTGGAAGATTAGGGGTAAA
*
29495664 AAATGTAATTTTTGAA
1 AAATGGAATTTTTGAA
29495680 GCTTCGGGTT
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
56 4 0.06
57 31 0.48
58 13 0.20
59 16 0.25
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (59 bp):
AAATGGAATTTTTGAAAGTTTAGCGGCAAAAATGGAATTTTTGGAAGATTAGGGGTAAA
Found at i:29495668 original size:30 final size:30
Alignment explanation
Indices: 29495547--29495748 Score: 202
Period size: 29 Copynumber: 6.8 Consensus size: 30
29495537 TCTGGGAGTG
*
29495547 AAATGGTAATTTTTGGAAGTTTCA-GCGTC-A
1 AAAT-GTAATTTTTGGAAGTTT-AGGGGTCAA
* * *
29495577 AAATGGAATTTTTGGAA-ATTCGGGGTC-A
1 AAATGTAATTTTTGGAAGTTTAGGGGTCAA
* *
29495605 AAATGGAATTTTTGAAAGTTTAGGGG-CAA
1 AAATGTAATTTTTGGAAGTTTAGGGGTCAA
*
29495634 AAATGTAATTTTTGGAAGTTTAGGGGTAAA
1 AAATGTAATTTTTGGAAGTTTAGGGGTCAA
* * *
29495664 AAATGTAATTTTT-GAAGCTTCGGGTTCAA
1 AAATGTAATTTTTGGAAGTTTAGGGGTCAA
* * *
29495693 AAATGAAATTTTTGAAAGTTCAAGGGG-CAA
1 AAATGTAATTTTTGGAAGTT-TAGGGGTCAA
29495723 AAATGTAATTTTTGGATAGTTTAGGG
1 AAATGTAATTTTTGGA-AGTTTAGGG
29495749 ACTTTCAGGG
Statistics
Matches: 142, Mismatches: 23, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
28 24 0.17
29 67 0.47
30 44 0.31
31 7 0.05
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (30 bp):
AAATGTAATTTTTGGAAGTTTAGGGGTCAA
Found at i:29495694 original size:59 final size:58
Alignment explanation
Indices: 29495576--29495736 Score: 173
Period size: 59 Copynumber: 2.8 Consensus size: 58
29495566 TTTCAGCGTC
* * * * * *
29495576 AAAATGGAATTTTTGGAA-ATTCGGGGTCAAAATGGAATTTTTGAAAGTTTAGGGGCA
1 AAAATGAAATTTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTGAAAGCTTAGGGGCA
* * *
29495633 AAAATGTAATTTTTGGAAGTTTAGGGGTAAAAAATGTAATTTTTG-AAGCTTCGGGTTCA
1 AAAATGAAATTTTTGGAAGTTTAGGGGT-AAAAATGTAATTTTTGAAAGCTTAGGG-GCA
* * *
29495692 AAAATGAAATTTTTGAAAGTTCAAGGGGCAAAAATGTAATTTTTG
1 AAAATGAAATTTTTGGAAGTT-TAGGGGTAAAAATGTAATTTTTG
29495737 GATAGTTTAG
Statistics
Matches: 88, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
57 17 0.19
58 15 0.17
59 51 0.58
60 5 0.06
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (58 bp):
AAAATGAAATTTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTGAAAGCTTAGGGGCA
Found at i:29497622 original size:18 final size:18
Alignment explanation
Indices: 29497601--29497636 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
29497591 TAAATTCAAT
*
29497601 TTTAAATTTAATCTTTAA
1 TTTAAATTTAAACTTTAA
*
29497619 TTTAGATTTAAACTTTAA
1 TTTAAATTTAAACTTTAA
29497637 AAGAAAAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTAAATTTAAACTTTAA
Found at i:29499624 original size:18 final size:18
Alignment explanation
Indices: 29499601--29499638 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
29499591 GTGGCACGTC
29499601 ACATAGGCTACTTAGTTG
1 ACATAGGCTACTTAGTTG
*
29499619 ACATAGGTTACTTAGTTG
1 ACATAGGCTACTTAGTTG
29499637 AC
1 AC
29499639 CTGTGGTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (18 bp):
ACATAGGCTACTTAGTTG
Found at i:29501567 original size:54 final size:55
Alignment explanation
Indices: 29501503--29501612 Score: 204
Period size: 55 Copynumber: 2.0 Consensus size: 55
29501493 ATCCATGATC
*
29501503 ACCTCTAATTATATTGGAGGAATAT-AAAAATTCATTTTCTTATTTTTTATCTAA
1 ACCTCTAATTATATTGGAGGAATATAAAAAATCCATTTTCTTATTTTTTATCTAA
29501557 ACCTCTAATTATATTGGAGGAATATAAAAAATCCATTTTCTTATTTTTTATCTAA
1 ACCTCTAATTATATTGGAGGAATATAAAAAATCCATTTTCTTATTTTTTATCTAA
29501612 A
1 A
29501613 ATTTAACTTT
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
54 25 0.46
55 29 0.54
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (55 bp):
ACCTCTAATTATATTGGAGGAATATAAAAAATCCATTTTCTTATTTTTTATCTAA
Found at i:29501834 original size:14 final size:15
Alignment explanation
Indices: 29501810--29501839 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
29501800 TTAAATTAGT
29501810 TTTTATTTAAAAATA
1 TTTTATTTAAAAATA
29501825 TTTT-TTTAAAAATA
1 TTTTATTTAAAAATA
29501839 T
1 T
29501840 AATACATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTTATTTAAAAATA
Found at i:29502132 original size:17 final size:17
Alignment explanation
Indices: 29502110--29502161 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
29502100 TAATATAAAA
29502110 ATATATAATTATTTAAT
1 ATATATAATTATTTAAT
29502127 ATATATAA--A---AAT
1 ATATATAATTATTTAAT
*
29502139 ATA-ATTATTATTTAAT
1 ATATATAATTATTTAAT
29502155 ATATATA
1 ATATATA
29502162 TTAATATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 12
0.66 0.05 0.29
Matches are distributed among these distances:
11 3 0.11
12 6 0.22
13 1 0.04
15 1 0.04
16 6 0.22
17 10 0.37
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATATAATTATTTAAT
Found at i:29502149 original size:28 final size:28
Alignment explanation
Indices: 29502102--29502175 Score: 114
Period size: 28 Copynumber: 2.7 Consensus size: 28
29502092 TGATGATTTA
*
29502102 ATATAAAAATAT-ATAATTATTTAATAT
1 ATATAAAAATATAATTATTATTTAATAT
29502129 ATATAAAAATATAATTATTATTTAATAT
1 ATATAAAAATATAATTATTATTTAATAT
**
29502157 ATATATTAATATAATTATT
1 ATATAAAAATATAATTATT
29502176 TTATAACACA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
27 12 0.28
28 31 0.72
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
ATATAAAAATATAATTATTATTTAATAT
Found at i:29502157 original size:16 final size:15
Alignment explanation
Indices: 29502136--29502175 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 15
29502126 TATATATAAA
29502136 AATATAATTATTATTT
1 AATATAATTATTA-TT
29502152 AATAT-A-TA-TATT
1 AATATAATTATTATT
29502164 AATATAATTATT
1 AATATAATTATT
29502176 TTATAACACA
Statistics
Matches: 21, Mismatches: 0, Indels: 7
0.75 0.00 0.25
Matches are distributed among these distances:
12 7 0.33
13 3 0.14
14 4 0.19
15 2 0.10
16 5 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AATATAATTATTATT
Found at i:29502758 original size:14 final size:14
Alignment explanation
Indices: 29502739--29502769 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
29502729 AGCAACTATT
*
29502739 ATTTTAATATTTTA
1 ATTTTAATATTTCA
29502753 ATTTTAATATTTCA
1 ATTTTAATATTTCA
29502767 ATT
1 ATT
29502770 AAAACTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (14 bp):
ATTTTAATATTTCA
Found at i:29503541 original size:19 final size:20
Alignment explanation
Indices: 29503504--29503544 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
29503494 TTTAAAAATT
29503504 AAATAAAGATTATAAATAAA
1 AAATAAAGATTATAAATAAA
* *
29503524 AAATAAATA-TATATATAAA
1 AAATAAAGATTATAAATAAA
29503543 AA
1 AA
29503545 TACGAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (20 bp):
AAATAAAGATTATAAATAAA
Found at i:29503911 original size:18 final size:18
Alignment explanation
Indices: 29503890--29503930 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
29503880 TTAGAAATGT
*
29503890 TTTTTTATCTCAAAATTA
1 TTTTTTATCTCAAAAATA
29503908 TTTTTTATCTCAAAAATA
1 TTTTTTATCTCAAAAATA
29503926 TTTTT
1 TTTTT
29503931 GAAAAACAAT
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:0.32, C:0.10, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTTTATCTCAAAAATA
Found at i:29516628 original size:21 final size:23
Alignment explanation
Indices: 29516586--29516630 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
29516576 TCTTAACAAT
*
29516586 AATTTTAAAAATATATATTTAAA
1 AATTATAAAAATATATATTTAAA
29516609 AATTATAAAAATAT-TA-TTAAA
1 AATTATAAAAATATATATTTAAA
29516630 A
1 A
29516631 GTACTTGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.29
22 2 0.10
23 13 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
AATTATAAAAATATATATTTAAA
Found at i:29519396 original size:4 final size:4
Alignment explanation
Indices: 29519387--29519469 Score: 148
Period size: 4 Copynumber: 20.8 Consensus size: 4
29519377 TCAAGAACTT
* *
29519387 ATAC ATAC ATAC ATAC ATAC ATGC ATGC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
29519435 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
29519470 TTCAAATTGA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 77 1.00
ACGTcount: A:0.48, C:0.24, G:0.02, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:29520273 original size:15 final size:15
Alignment explanation
Indices: 29520250--29520284 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
29520240 GTCAACCACG
*
29520250 TGACTCCTCGACTGT
1 TGACCCCTCGACTGT
29520265 TGACCCCTCGACTGT
1 TGACCCCTCGACTGT
29520280 TGACC
1 TGACC
29520285 TTTGACTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.14, C:0.37, G:0.20, T:0.29
Consensus pattern (15 bp):
TGACCCCTCGACTGT
Found at i:29521697 original size:29 final size:31
Alignment explanation
Indices: 29521665--29521790 Score: 104
Period size: 32 Copynumber: 4.2 Consensus size: 31
29521655 TTCAAATTTG
29521665 ACCCCT-AAACTTTCT-AAAATTTCATTTTA
1 ACCCCTAAAACTTTCTAAAAATTTCATTTTA
*
29521694 A-CCCTCAAAA--TTCTAAAAATTAT-ATTTTG
1 ACCCCT-AAAACTTTCTAAAAATT-TCATTTTA
* *
29521723 ACCCCTAAAA-TTTTTAGAAAAATTGCATTTTA
1 ACCCCTAAAACTTTCT--AAAAATTTCATTTTA
* * *
29521755 ACCCCTAAAACTTTCCAAAATTTTGATTTTA
1 ACCCCTAAAACTTTCTAAAAATTTCATTTTA
*
29521786 CCCCC
1 ACCCC
29521791 CATTTTCCCT
Statistics
Matches: 77, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
28 8 0.10
29 17 0.22
30 11 0.14
31 16 0.21
32 22 0.29
33 3 0.04
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (31 bp):
ACCCCTAAAACTTTCTAAAAATTTCATTTTA
Found at i:29530091 original size:28 final size:27
Alignment explanation
Indices: 29530058--29530148 Score: 71
Period size: 28 Copynumber: 3.2 Consensus size: 27
29530048 CCCAAATTTT
29530058 CCAAAATCTCATTTTGAACCCGATTTCA
1 CCAAAATCTCATTTT-AACCCGATTTCA
* *
29530086 CCAAAAAT-TACCTTTTACCCCGAACTTT--
1 CC-AAAATCT-CATTTTAACCCG-A-TTTCA
*
29530114 CCAAAATCTCATTTTTAACCCTAATTTCA
1 CCAAAATCTCA-TTTTAACCC-GATTTCA
29530143 CCAAAA
1 CCAAAA
29530149 ATTACCATTT
Statistics
Matches: 49, Mismatches: 5, Indels: 17
0.69 0.07 0.24
Matches are distributed among these distances:
27 9 0.18
28 20 0.41
29 17 0.35
30 3 0.06
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (27 bp):
CCAAAATCTCATTTTAACCCGATTTCA
Found at i:29530163 original size:29 final size:29
Alignment explanation
Indices: 29530075--29530163 Score: 75
Period size: 28 Copynumber: 3.1 Consensus size: 29
29530065 CTCATTTTGA
29530075 ACCCG-ATTTCACCAAAAATTACC-TTTT
1 ACCCGAATTTCACCAAAAATTACCATTTT
29530102 ACCCCGAACTTT--CC-AAAA-T-CTCATTTTT
1 A-CCCGAA-TTTCACCAAAAATTAC-CA-TTTT
*
29530130 AACCCTAATTTCACCAAAAATTACCATTTT
1 -ACCCGAATTTCACCAAAAATTACCATTTT
29530160 ACCC
1 ACCC
29530164 CTAAACTTTC
Statistics
Matches: 49, Mismatches: 1, Indels: 22
0.68 0.01 0.31
Matches are distributed among these distances:
25 1 0.02
26 2 0.04
27 8 0.16
28 15 0.31
29 8 0.16
30 11 0.22
31 3 0.06
32 1 0.02
ACGTcount: A:0.34, C:0.31, G:0.02, T:0.33
Consensus pattern (29 bp):
ACCCGAATTTCACCAAAAATTACCATTTT
Found at i:29530177 original size:30 final size:29
Alignment explanation
Indices: 29530086--29530177 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 29
29530076 CCCGATTTCA
*
29530086 CCAAAAATTACC-TTTTACCCCGAACTTT
1 CCAAAAATTACCATTTTACCCCTAACTTT
*
29530114 CC-AAAA-T-CTCATTTTTAACCCTAA-TTT
1 CCAAAAATTAC-CA-TTTTACCCCTAACTTT
29530141 CACCAAAAATTACCATTTTACCCCTAAACTTT
1 --CCAAAAATTACCATTTTACCCCT-AACTTT
29530173 CCAAA
1 CCAAA
29530178 CCCGATTTTA
Statistics
Matches: 51, Mismatches: 3, Indels: 18
0.71 0.04 0.25
Matches are distributed among these distances:
25 1 0.02
26 2 0.04
27 7 0.14
28 12 0.24
29 2 0.04
30 18 0.35
31 5 0.10
32 4 0.08
ACGTcount: A:0.36, C:0.30, G:0.01, T:0.33
Consensus pattern (29 bp):
CCAAAAATTACCATTTTACCCCTAACTTT
Found at i:29530187 original size:57 final size:57
Alignment explanation
Indices: 29530029--29530220 Score: 232
Period size: 57 Copynumber: 3.4 Consensus size: 57
29530019 CAAAACTTCA
* *
29530029 AAAAATTACCATTTTACCCCCCAAATTTTCCAAAATCTCATTTTGAACCC-GATTTCACC
1 AAAAATTACCATTTTA--CCCCAAACTTTCCAAAATCTCATTTT-AACCCTAATTTCACC
*
29530088 AAAAATTACC-TTTTACCCCGAACTTTCCAAAATCTCATTTTTAACCCTAATTTCACC
1 AAAAATTACCATTTTACCCCAAACTTTCCAAAATCTCA-TTTTAACCCTAATTTCACC
* * * *
29530145 AAAAATTACCATTTTACCCCTAAACTTTCC-AAA-CCCGATTTTAACCCTAGTTTTATC
1 AAAAATTACCATTTTACCCC-AAACTTTCCAAAATCTC-ATTTTAACCCTAATTTCACC
29530202 AAAAATTA-CATTTTACCCC
1 AAAAATTACCATTTTACCCC
29530221 GAAAGTTAAA
Statistics
Matches: 120, Mismatches: 8, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
56 36 0.30
57 48 0.40
58 18 0.15
59 18 0.15
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (57 bp):
AAAAATTACCATTTTACCCCAAACTTTCCAAAATCTCATTTTAACCCTAATTTCACC
Found at i:29542831 original size:199 final size:199
Alignment explanation
Indices: 29542296--29542997 Score: 1065
Period size: 198 Copynumber: 3.5 Consensus size: 199
29542286 TTCAACAAAA
** *
29542296 AGAGGCGGTCACCTTCCTGATGA-ATTTAAAGAAGAATACCAACTCAACGCTCAATGCGAACAAA
1 AGAGGCGGTCACCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAATGCGAACAAA
* * * * * *
29542360 TCCTCGTACCCAGGTT-CTGATGAGACACT-A-AGGTAGGTCGAAACAATGAAATGGTTAGATTC
66 T-CTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAACAATAAAATGGTTAGCTTC
* *
29542422 CTGATGAGATACAGAGAAGTGGACCAAATTTGTCTTCCTGAGGAGATCCAAAGAAGCAAATTAAA
130 CTGATGAGATACAAAGAAGTGGACCAAATTTGTCTTCCTGAGGAGATCCAGAGAAGCAAATTAAA
29542487 ACAAC
195 ACAAC
29542492 AGAGGCGGTCACCTTCCTGATGAGATACAGAG-AGAATACCAACTCAACGCTCAATGCGAACAAA
1 AGAGGCGGTCACCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAATGCGAACAAA
* * * *
29542556 TCTCGTACACAGCTTCCTGATGAGACACTGAGAAGCAGGTCAAAACAATAAAATAGTTAGCTTCC
66 TCTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAACAATAAAATGGTTAGCTTCC
29542621 TGATGAGATACAAAGAAGTGGACCAAATTTGTCTTCCTGAGGAGATCCAGAGAAGCAAATTAAAA
131 TGATGAGATACAAAGAAGTGGACCAAATTTGTCTTCCTGAGGAGATCCAGAGAAGCAAATTAAAA
29542686 CAAC
196 CAAC
* *
29542690 AGAGGTGGTCACCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAATGCGAGCAAA
1 AGAGGCGGTCACCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAATGCGAACAAA
* *
29542755 TTTCGAACTCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAACAATAAAATGGTTAGCTTCC
66 TCTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAACAATAAAATGGTTAGCTTCC
*
29542820 TGATAAGATACAAAGAAGTGGACCAAATTTGTCTTCCTGAGGAGAT-CAGAGAAGCAAATTAAAA
131 TGATGAGATACAAAGAAGTGGACCAAATTTGTCTTCCTGAGGAGATCCAGAGAAGCAAATTAAAA
* *
29542884 TAAT
196 CAAC
* * ***
29542888 AGAGGCGGTCACCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACACTCAACGCGGGTGAA
1 AGAGGCGGTCACCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAATGC-GAACAA
* * * *
29542953 TTTTCGAACCCAACTTCCTGATGAGACATTGAGAAGCAGGTCGAA
65 ATCTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAA
29542998 GCCAAAGAAA
Statistics
Matches: 467, Mismatches: 33, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
195 12 0.03
196 69 0.15
197 6 0.01
198 200 0.43
199 180 0.39
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.21
Consensus pattern (199 bp):
AGAGGCGGTCACCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAATGCGAACAAA
TCTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAACAATAAAATGGTTAGCTTCC
TGATGAGATACAAAGAAGTGGACCAAATTTGTCTTCCTGAGGAGATCCAGAGAAGCAAATTAAAA
CAAC
Found at i:29543392 original size:6 final size:6
Alignment explanation
Indices: 29543376--29543421 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
29543366 TTTAAGTTTT
* *
29543376 TTAAAA TTTAAAC TTAATA -TA-AA TTAAAA TTAAAA TTAAAA TTAAA
1 TTAAAA -TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAA
29543422 TGTCCAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
4 1 0.03
5 4 0.12
6 23 0.70
7 5 0.15
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (6 bp):
TTAAAA
Found at i:29543421 original size:23 final size:23
Alignment explanation
Indices: 29543376--29543422 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
29543366 TTTAAGTTTT
* *
29543376 TTAAAATTTAAACTTAATATAAA
1 TTAAAATTTAAAATTAAAATAAA
29543399 TTAAAA-TTAAAATTAAAATTAAA
1 TTAAAATTTAAAATTAAAA-TAAA
29543422 T
1 T
29543423 GTCCAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
TTAAAATTTAAAATTAAAATAAA
Found at i:29545376 original size:29 final size:29
Alignment explanation
Indices: 29545212--29545376 Score: 121
Period size: 29 Copynumber: 5.7 Consensus size: 29
29545202 GATTTCACCA
*
29545212 AAAATTACCATTTTACCCCCAAACTTTCC
1 AAAATTACCATTTTAACCCCAAACTTTCC
**
29545241 AAAATT-CCATTTTTAACCCC-AGTTTTACC
1 AAAATTACCA-TTTTAACCCCAAACTTT-CC
*
29545270 AAAATTACCATTTT-ACCCCTAAACTTTCT
1 AAAATTACCATTTTAACCCC-AAACTTTCC
* *
29545299 AAAA--CCCTATTTTTAA-CCCTAA-TTCTACC
1 AAAATTACC-A-TTTTAACCCCAAACTT-T-CC
* * *
29545328 AAAATTACCGTTTTACCCCCAAACTCTCC
1 AAAATTACCATTTTAACCCCAAACTTTCC
29545357 AAAATT-CCATTTTCAACCCC
1 AAAATTACCATTTT-AACCCC
29545377 GATTTCATCA
Statistics
Matches: 105, Mismatches: 16, Indels: 30
0.70 0.11 0.20
Matches are distributed among these distances:
27 4 0.04
28 22 0.21
29 62 0.59
30 14 0.13
31 3 0.03
ACGTcount: A:0.33, C:0.32, G:0.01, T:0.33
Consensus pattern (29 bp):
AAAATTACCATTTTAACCCCAAACTTTCC
Found at i:29545389 original size:58 final size:58
Alignment explanation
Indices: 29545152--29545399 Score: 272
Period size: 58 Copynumber: 4.3 Consensus size: 58
29545142 AAAACTTTTG
* ** * *
29545152 AAAAATTACCATTTTACCCTCGGACTTTCCAAAATCTCGTTTTTAACACCGATTTCACC
1 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATC-CATTTTTAACCCCGATTTCACC
*
29545211 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCC-AGTTTTACC
1 AAAAATTACCATTTTACCCCCAAACTTTCCAAAA-TCCATTTTTAACCCCGA-TTTCACC
* * * * *
29545270 -AAAATTACCATTTTACCCCTAAACTTTCTAAAACCCTATTTTTAA-CCCTAATTCTACC
1 AAAAATTACCATTTTACCCCCAAACTTTCCAAAATCC-ATTTTTAACCCCGATTTC-ACC
* * * *
29545328 -AAAATTACCGTTTTACCCCCAAACTCTCCAAAATTCCATTTTCAACCCCGATTTCATC
1 AAAAATTACCATTTTACCCCCAAACTTTCCAAAA-TCCATTTTTAACCCCGATTTCACC
29545386 AAAAATTA-CATTTT
1 AAAAATTACCATTTT
29545400 TACCACCGAA
Statistics
Matches: 160, Mismatches: 21, Indels: 17
0.81 0.11 0.09
Matches are distributed among these distances:
57 7 0.04
58 87 0.54
59 64 0.40
60 2 0.01
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.34
Consensus pattern (58 bp):
AAAAATTACCATTTTACCCCCAAACTTTCCAAAATCCATTTTTAACCCCGATTTCACC
Found at i:29545547 original size:20 final size:19
Alignment explanation
Indices: 29545495--29545548 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 19
29545485 CACTAAATAC
29545495 TTGCATTTATTTTAATTAT
1 TTGCATTTATTTTAATTAT
29545514 TATGCACTTGTATTTTATATT-T
1 T-TGCA-TT-TATTTTA-ATTAT
29545536 TTGCATTCTATTT
1 TTGCATT-TATTT
29545549 ATCTGCTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 1 0.03
20 11 0.37
21 6 0.20
22 9 0.30
23 3 0.10
ACGTcount: A:0.22, C:0.09, G:0.07, T:0.61
Consensus pattern (19 bp):
TTGCATTTATTTTAATTAT
Found at i:29548724 original size:99 final size:98
Alignment explanation
Indices: 29548541--29549310 Score: 729
Period size: 99 Copynumber: 7.8 Consensus size: 98
29548531 AGGTTTGAAA
* * * * * * *
29548541 GGGAA-GATTGAGGGCGCAACGACGAATCTGATACCCTGAAGATACGGAGGGAAAGGTTGAGGTC
1 GGGAAGGATTGAGGTCGCAACGGCGAATCTGGTACCATGAAGATATGAAGGGAAAGGTT-AGGCC
* * * * *
29548605 ACAATGGCGAACCCGATACCTTAAAAGATATGAT
65 GCAACGGCGAACCCGGTACCTTAGAAGATGTGAT
* ** * * * *
29548639 AGGAAGGATTGAGACCGCAACGGCGGATCTAGTACCATGAATATATGAATGGAAAGGTTATGGCC
1 GGGAAGGATTGAGGTCGCAACGGCGAATCTGGTACCATGAAGATATGAAGGGAAAGGTTA-GGCC
* * * *
29548704 GTAACGACGAACTCGGTACCTTAGAAGATTTGAT
65 GCAACGGCGAACCCGGTACCTTAGAAGATGTGAT
* * *
29548738 GGGAAGGATTGAGGCCGCAACGGTGAATCTGGTACCATGAAGATATGAAGGGAAAGGTTAAGGTC
1 GGGAAGGATTGAGGTCGCAACGGCGAATCTGGTACCATGAAGATATGAAGGGAAAGGTT-AGGCC
*
29548803 GCAAGGGCGAACCCGGTACCTTAGAAGATGTGAT
65 GCAACGGCGAACCCGGTACCTTAGAAGATGTGAT
* * * * ** * * *
29548837 GAGAAGAATTAAGGTCGCAATGGTAAATCTAGTACCATGAATATATGAAGGGAAAGGTTGAGGCT
1 GGGAAGGATTGAGGTCGCAACGGCGAATCTGGTACCATGAAGATATGAAGGGAAAGGTT-AGGCC
* *
29548902 GCAATGGAGAA-CCGGTACCTTAGAAGATGTGAT
65 GCAACGGCGAACCCGGTACCTTAGAAGATGTGAT
* * * * * * * * *
29548935 AGGAAGGATTGAGGCCGCAACGACAAATTTGGTACTACGAATATATGAAGGGAAAGGTCAAGGCC
1 GGGAAGGATTGAGGTCGCAACGGCGAATCTGGTACCATGAAGATATGAAGGGAAAGGT-TAGGCC
* *
29549000 GCAACGGTGAACCCGGTACTTTAGAAGATGTGAT
65 GCAACGGCGAACCCGGTACCTTAGAAGATGTGAT
* * * * *
29549034 GGGCAGGATTAAGGTCGCAACGGTGAATCTGGTACCATGAAGATCTGAAAGGAAAGGTTGAGGCC
1 GGGAAGGATTGAGGTCGCAACGGCGAATCTGGTACCATGAAGATATGAAGGGAAAGGTT-AGGCC
* * * *
29549099 GCAACGGTGAACTCGGTACCTTAAAAAATGTGAT
65 GCAACGGCGAACCCGGTACCTTAGAAGATGTGAT
* * * *
29549133 GGGAAGGATTGAGGTCACAATGACGAATCTGGTACCATGAAGATATGAAAGGG-AAGGTTAAGGT
1 GGGAAGGATTGAGGTCGCAACGGCGAATCTGGTACCATGAAGATATG-AAGGGAAAGGTT-AGGC
* ** * *
29549197 CGGAACGGCGAACTTGATACCTTAAAAGATGTGAT
64 CGCAACGGCGAACCCGGTACCTTAGAAGATGTGAT
** * * * * * *
29549232 GGGAAAAATCGAGGTCGCAACGAC-AGATCTAGTACCATGAAAATATAAAAGGGAAAGTTTGAGG
1 GGGAAGGATTGAGGTCGCAACGGCGA-ATCTGGTACCATGAAGATAT-GAAGGGAAAGGTT-AGG
*
29549296 CCGTAACGGCGAACC
63 CCGCAACGGCGAACC
29549311 TTGTATCCTA
Statistics
Matches: 552, Mismatches: 110, Indels: 18
0.81 0.16 0.03
Matches are distributed among these distances:
98 87 0.16
99 440 0.80
100 25 0.05
ACGTcount: A:0.35, C:0.15, G:0.31, T:0.20
Consensus pattern (98 bp):
GGGAAGGATTGAGGTCGCAACGGCGAATCTGGTACCATGAAGATATGAAGGGAAAGGTTAGGCCG
CAACGGCGAACCCGGTACCTTAGAAGATGTGAT
Found at i:29548849 original size:50 final size:50
Alignment explanation
Indices: 29548600--29549253 Score: 213
Period size: 49 Copynumber: 13.2 Consensus size: 50
29548590 GGAAAGGTTG
* * * * * * *
29548600 AGGTCACAATGGCGAACCCGATACCTTAAAAGATATGATAGGAAGGATTG
1 AGGTCGCAACGGCGAACCCGGTACCTTAGAAGATATGATGGGAAGAATTA
** * * ** * * * *
29548650 AGACCGCAACGGCGGATCTAGTACCAT-GAATATATGAATGGAAAG-GTTA
1 AGGTCGCAACGGCGAACCCGGTACCTTAGAAGATATG-ATGGGAAGAATTA
* * * * * * * *
29548699 TGGCCGTAACGACGAACTCGGTACCTTAGAAGATTTGATGGGAAGGATTG
1 AGGTCGCAACGGCGAACCCGGTACCTTAGAAGATATGATGGGAAGAATTA
* * * * * * *
29548749 AGGCCGCAACGGTGAATCTGGTACCAT-GAAGATATGAAGGGAA-AGGTTA
1 AGGTCGCAACGGCGAACCCGGTACCTTAGAAGATATGATGGGAAGA-ATTA
* * *
29548798 AGGTCGCAAGGGCGAACCCGGTACCTTAGAAGATGTGATGAGAAGAATTA
1 AGGTCGCAACGGCGAACCCGGTACCTTAGAAGATATGATGGGAAGAATTA
* ** * ** * * * * *
29548848 AGGTCGCAATGGTAAATCTAGTACCAT-GAATATATGAAGGGAA-AGGTTG
1 AGGTCGCAACGGCGAACCCGGTACCTTAGAAGATATGATGGGAAGA-ATTA
* * * * * *
29548897 AGG-CTGCAATGGAGAA-CCGGTACCTTAGAAGATGTGATAGGAAGGATTG
1 AGGTC-GCAACGGCGAACCCGGTACCTTAGAAGATATGATGGGAAGAATTA
* * * *** * * * *
29548946 AGGCCGCAACGACAAATTTGGTA-C-TACGAATATATGAAGGGAA-AGGTCA
1 AGGTCGCAACGGCGAACCCGGTACCTTA-GAAGATATGATGGGAAGA-ATTA
* * * * * *
29548995 AGGCCGCAACGGTGAACCCGGTACTTTAGAAGATGTGATGGGCAGGATTA
1 AGGTCGCAACGGCGAACCCGGTACCTTAGAAGATATGATGGGAAGAATTA
* * * * * ** * *
29549045 AGGTCGCAACGGTGAATCTGGTACCAT-GAAGATCTGAAAGGAA-AGGTTG
1 AGGTCGCAACGGCGAACCCGGTACCTTAGAAGATATGATGGGAAGA-ATTA
* * * * * * * *
29549094 AGGCCGCAACGGTGAACTCGGTACCTTAAAAAATGTGATGGGAAGGATTG
1 AGGTCGCAACGGCGAACCCGGTACCTTAGAAGATATGATGGGAAGAATTA
* * * * * * * *
29549144 AGGTCACAATGACGAATCTGGTACCAT-GAAGATATGAAAGGGAAG-GTTA
1 AGGTCGCAACGGCGAACCCGGTACCTTAGAAGATATG-ATGGGAAGAATTA
* ** * * * * **
29549193 AGGTCGGAACGGCGAACTTGATACCTTAAAAGATGTGATGGGAAAAATCG
1 AGGTCGCAACGGCGAACCCGGTACCTTAGAAGATATGATGGGAAGAATTA
29549243 AGGTCGCAACG
1 AGGTCGCAACG
29549254 ACAGATCTAG
Statistics
Matches: 420, Mismatches: 161, Indels: 46
0.67 0.26 0.07
Matches are distributed among these distances:
48 11 0.03
49 221 0.53
50 185 0.44
51 3 0.01
ACGTcount: A:0.34, C:0.15, G:0.31, T:0.20
Consensus pattern (50 bp):
AGGTCGCAACGGCGAACCCGGTACCTTAGAAGATATGATGGGAAGAATTA
Found at i:29548884 original size:198 final size:198
Alignment explanation
Indices: 29548541--29549394 Score: 833
Period size: 198 Copynumber: 4.3 Consensus size: 198
29548531 AGGTTTGAAA
* * * * * *
29548541 GGGAA-GATTGAGGGCGCAACGACGAATCTGATACCCTGAAGATACGGAGGGAAAGGTTGAGGTC
1 GGGAAGGATTGAGGCCGCAACGACGAATCTGGTACCATGAAGATATGAAGGGAAAGGTTAAGGTC
* * * * * ** **
29548605 ACAATGGCGAACCCGATACCTTAAAAGATATGAT-AGGAAGGATTGAGACCGCAACGGCGGATCT
66 GCAACGGCGAACCCGATACCTTAAAAGATGTGATGA-GAAGAATTAAGGTCGCAACGGCAAATCT
* *
29548669 AGTACCATGAATATATGAATGGAAAGGTT-ATGGCCGTAACGACGAACTCGGTACCTTAGAAGAT
130 AGTACCATGAATATATGAAGGGAAAGGTTGA-GGCCGCAACGACGAACTCGGTACCTTAGAAGAT
*
29548733 TTGAT
194 GTGAT
**
29548738 GGGAAGGATTGAGGCCGCAACGGTGAATCTGGTACCATGAAGATATGAAGGGAAAGGTTAAGGTC
1 GGGAAGGATTGAGGCCGCAACGACGAATCTGGTACCATGAAGATATGAAGGGAAAGGTTAAGGTC
* * * * *
29548803 GCAAGGGCGAACCCGGTACCTTAGAAGATGTGATGAGAAGAATTAAGGTCGCAATGGTAAATCTA
66 GCAACGGCGAACCCGATACCTTAAAAGATGTGATGAGAAGAATTAAGGTCGCAACGGCAAATCTA
* *
29548868 GTACCATGAATATATGAAGGGAAAGGTTGAGGCTGCAATGGA-GAAC-CGGTACCTTAGAAGATG
131 GTACCATGAATATATGAAGGGAAAGGTTGAGGCCGCAA-CGACGAACTCGGTACCTTAGAAGATG
29548931 TGAT
195 TGAT
* * * * * * * *
29548935 AGGAAGGATTGAGGCCGCAACGACAAATTTGGTACTACGAATATATGAAGGGAAAGGTCAAGGCC
1 GGGAAGGATTGAGGCCGCAACGACGAATCTGGTACCATGAAGATATGAAGGGAAAGGTTAAGGTC
* * * * * * * ** *
29549000 GCAACGGTGAACCCGGTACTTTAGAAGATGTGATGGGCAGGATTAAGGTCGCAACGGTGAATCTG
66 GCAACGGCGAACCCGATACCTTAAAAGATGTGATGAGAAGAATTAAGGTCGCAACGGCAAATCTA
* * * ** * *
29549065 GTACCATGAAGATCTGAAAGGAAAGGTTGAGGCCGCAACGGTGAACTCGGTACCTTAAAAAATGT
131 GTACCATGAATATATGAAGGGAAAGGTTGAGGCCGCAACGACGAACTCGGTACCTTAGAAGATGT
29549130 GAT
196 GAT
* * *
29549133 GGGAAGGATTGAGGTCACAATGACGAATCTGGTACCATGAAGATATGAAAGGG-AAGGTTAAGGT
1 GGGAAGGATTGAGGCCGCAACGACGAATCTGGTACCATGAAGATATG-AAGGGAAAGGTTAAGGT
* ** * * ** * *
29549197 CGGAACGGCGAACTTGATACCTTAAAAGATGTGATGGGAAAAATCGAGGTCGCAACGACAGATCT
65 CGCAACGGCGAACCCGATACCTTAAAAGATGTGATGAGAAGAATTAAGGTCGCAACGGCAAATCT
* * * * * * * * *
29549262 AGTACCATGAAAATATAAAAGGGAAAGTTTGAGGCCGTAACGGCGAAC-CTTGTATCCTAAAAAT
130 AGTACCATGAATATAT-GAAGGGAAAGGTTGAGGCCGCAACGACGAACTC-GGTA-CCTTAGAAG
**
29549326 AAAT-AT
192 ATGTGAT
** * * * * *
29549332 ATGAAAGATTGAGGCTGCAATGACAAATCTGATACCATGAAGATATGAAGGGGAAGAGGTTAA
1 GGGAAGGATTGAGGCCGCAACGACGAATCTGGTACCATGAAGATATGAA-GGGAA-AGGTTAA
29549395 AATCACAATG
Statistics
Matches: 543, Mismatches: 101, Indels: 22
0.82 0.15 0.03
Matches are distributed among these distances:
196 1 0.00
197 174 0.32
198 269 0.50
199 82 0.15
200 10 0.02
201 7 0.01
ACGTcount: A:0.35, C:0.15, G:0.30, T:0.20
Consensus pattern (198 bp):
GGGAAGGATTGAGGCCGCAACGACGAATCTGGTACCATGAAGATATGAAGGGAAAGGTTAAGGTC
GCAACGGCGAACCCGATACCTTAAAAGATGTGATGAGAAGAATTAAGGTCGCAACGGCAAATCTA
GTACCATGAATATATGAAGGGAAAGGTTGAGGCCGCAACGACGAACTCGGTACCTTAGAAGATGT
GAT
Found at i:29549170 original size:296 final size:297
Alignment explanation
Indices: 29548541--29549288 Score: 838
Period size: 296 Copynumber: 2.5 Consensus size: 297
29548531 AGGTTTGAAA
* * * * * *
29548541 GGGAA-GATTGAGGGCGCAACGACGAATCTGATACCCTGAAGATACGGAGGGAAAGGTTGAGGTC
1 GGGAAGGATTGAGGTCGCAATGACGAATCTGGTACCATGAAGATATGAAGGGAAAGGTTGAGGTC
* * **
29548605 ACAATGGCGAACCCGATACCTTAAAAGATATGATAGGAAGGATTGAGACCGCAACGGCGGATCTA
66 ACAATGGAGAACCCGATACCTTAAAAGATATGATAGGAAGGATTGAGACCGCAACGACAAATCTA
* * * * * * *
29548670 GTACCATGAATATATGAATGGAAAGGTTATGGCCGTAACGACGAACTCGGTACCTTAGAAGATTT
131 GTACCACGAATATATGAAGGGAAAGGTCAAGGCCGCAACGACGAACCCGGTACCTTAGAAGATGT
* *
29548735 GATGGGAAGGATTGAGGCCGCAACGGTGAATCTGGTACCATGAAGATATGAAGGGAAAGGTTAAG
196 GATGGGAAGGATTAAGGCCGCAACGGTGAATCTGGTACCATGAAGATATGAAAGGAAAGGTTAAG
* * * *
29548800 GTCGCAAGGGCGAACCCGGTACCTTAGAAGATGTGAT
261 GCCGCAACGGCGAACCCGGTACCTTAAAAAATGTGAT
* * * *** * *
29548837 GAGAAGAATTAAGGTCGCAATGGTAAATCTAGTACCATGAATATATGAAGGGAAAGGTTGAGG-C
1 GGGAAGGATTGAGGTCGCAATGACGAATCTGGTACCATGAAGATATGAAGGGAAAGGTTGAGGTC
* * * * * *
29548901 TGCAATGGAGAA-CCGGTACCTTAGAAGATGTGATAGGAAGGATTGAGGCCGCAACGACAAATTT
66 -ACAATGGAGAACCCGATACCTTAAAAGATATGATAGGAAGGATTGAGACCGCAACGACAAATCT
* * ** *
29548965 GGTACTACGAATATATGAAGGGAAAGGTCAAGGCCGCAACGGTGAACCCGGTACTTTAGAAGATG
130 AGTACCACGAATATATGAAGGGAAAGGTCAAGGCCGCAACGACGAACCCGGTACCTTAGAAGATG
* * * *
29549030 TGATGGGCAGGATTAAGGTCGCAACGGTGAATCTGGTACCATGAAGATCTGAAAGGAAAGGTTGA
195 TGATGGGAAGGATTAAGGCCGCAACGGTGAATCTGGTACCATGAAGATATGAAAGGAAAGGTTAA
* *
29549095 GGCCGCAACGGTGAACTCGGTACCTTAAAAAATGTGAT
260 GGCCGCAACGGCGAACCCGGTACCTTAAAAAATGTGAT
* *
29549133 GGGAAGGATTGAGGTCACAATGACGAATCTGGTACCATGAAGATATGAAAGGG-AAGGTTAAGGT
1 GGGAAGGATTGAGGTCGCAATGACGAATCTGGTACCATGAAGATATG-AAGGGAAAGGTTGAGGT
** * * ** * * ** * ** *
29549197 CGGAACGGCGAACTTGATACCTTAAAAGATGTGATGGGAAAAATCGAGGTCGCAACGACAGATCT
65 CACAATGGAGAACCCGATACCTTAAAAGATATGATAGGAAGGATTGAGACCGCAACGACAAATCT
* * *
29549262 AGTACCATGAAAATATAAAAGGGAAAG
130 AGTACCACGAATATAT-GAAGGGAAAG
29549289 TTTGAGGCCG
Statistics
Matches: 369, Mismatches: 77, Indels: 10
0.81 0.17 0.02
Matches are distributed among these distances:
296 248 0.67
297 112 0.30
298 9 0.02
ACGTcount: A:0.35, C:0.15, G:0.31, T:0.20
Consensus pattern (297 bp):
GGGAAGGATTGAGGTCGCAATGACGAATCTGGTACCATGAAGATATGAAGGGAAAGGTTGAGGTC
ACAATGGAGAACCCGATACCTTAAAAGATATGATAGGAAGGATTGAGACCGCAACGACAAATCTA
GTACCACGAATATATGAAGGGAAAGGTCAAGGCCGCAACGACGAACCCGGTACCTTAGAAGATGT
GATGGGAAGGATTAAGGCCGCAACGGTGAATCTGGTACCATGAAGATATGAAAGGAAAGGTTAAG
GCCGCAACGGCGAACCCGGTACCTTAAAAAATGTGAT
Found at i:29549644 original size:38 final size:38
Alignment explanation
Indices: 29549602--29549872 Score: 249
Period size: 38 Copynumber: 6.9 Consensus size: 38
29549592 AAGCTACACA
* *
29549602 CCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCAT
1 CCAATCTTTTACCCCAATCATGGGGCAGATTGAAGCAT
* * *
29549640 CCAATCTTTTACCCTAATCA-GAAGGCAGATTGAAGACACA
1 CCAATCTTTTACCCCAATCATG-GGGCAGATTGAAG-CA-T
* * *
29549680 CCAATCTCTTACCCCAATCATAGGGCGGATTGAAGCAT
1 CCAATCTTTTACCCCAATCATGGGGCAGATTGAAGCAT
* ** *
29549718 TCAATCTTTTACCTTAATCAGGGGGCAGATTGAAGCAT
1 CCAATCTTTTACCCCAATCATGGGGCAGATTGAAGCAT
* * * * *
29549756 CCAATATTTTATCCTAATCA-GAGAGCAGATTGAAAACATCAT
1 CCAATCTTTTACCCCAATCATG-GGGCAGATTG---A-AGCAT
* *
29549798 CCAATCTCTTACCCGAATCATGGGGCAGATTGAAGCAT
1 CCAATCTTTTACCCCAATCATGGGGCAGATTGAAGCAT
* * *
29549836 CCAATTTTTTACCACAACCATGGGGCAGATTTGAAGC
1 CCAATCTTTTACCCCAATCATGGGGCAGA-TTGAAGC
29549873 TATCATCCTA
Statistics
Matches: 187, Mismatches: 35, Indels: 21
0.77 0.14 0.09
Matches are distributed among these distances:
37 2 0.01
38 113 0.60
39 12 0.06
40 29 0.16
41 1 0.01
42 29 0.16
43 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (38 bp):
CCAATCTTTTACCCCAATCATGGGGCAGATTGAAGCAT
Found at i:29549726 original size:78 final size:78
Alignment explanation
Indices: 29549597--29549752 Score: 249
Period size: 78 Copynumber: 2.0 Consensus size: 78
29549587 AAGCGAAGCT
* *
29549597 ACACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGA
1 ACACACCAATCTCTTACCCCAATCATAGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGA
29549662 AGGCAGATTGAAG
66 AGGCAGATTGAAG
* * * *
29549675 ACACACCAATCTCTTACCCCAATCATAGGGCGGATTGAAGCATTCAATCTTTTACCTTAATCAGG
1 ACACACCAATCTCTTACCCCAATCATAGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGA
*
29549740 GGGCAGATTGAAG
66 AGGCAGATTGAAG
29549753 CATCCAATAT
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
78 71 1.00
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (78 bp):
ACACACCAATCTCTTACCCCAATCATAGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGA
AGGCAGATTGAAG
Found at i:29549753 original size:116 final size:118
Alignment explanation
Indices: 29549602--29549872 Score: 368
Period size: 116 Copynumber: 2.3 Consensus size: 118
29549592 AAGCTACACA
* * * *
29549602 CCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGA-AGGC
1 CCAATCTTTTACCACAATCATGGGGCAGATTGAAGCATCCAATATTTTACCCTAATCAGAGA-GC
* *
29549666 AGATTGAAGACA-CA-CCAATCTCTTACCCCAATCATAGGGCGGATTGAAGCAT
65 AGATTGAAAACATCATCCAATCTCTTACCCCAATCATAGGGCAGATTGAAGCAT
* ** * *
29549718 TCAATCTTTTACCTTAATCAGGGGGCAGATTGAAGCATCCAATATTTTATCCTAATCAGAGAGCA
1 CCAATCTTTTACCACAATCATGGGGCAGATTGAAGCATCCAATATTTTACCCTAATCAGAGAGCA
* *
29549783 GATTGAAAACATCATCCAATCTCTTACCCGAATCATGGGGCAGATTGAAGCAT
66 GATTGAAAACATCATCCAATCTCTTACCCCAATCATAGGGCAGATTGAAGCAT
* *
29549836 CCAATTTTTTACCACAACCATGGGGCAGATTTGAAGC
1 CCAATCTTTTACCACAATCATGGGGCAGA-TTGAAGC
29549873 TATCATCCTA
Statistics
Matches: 133, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
116 65 0.49
117 3 0.02
118 58 0.44
119 7 0.05
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (118 bp):
CCAATCTTTTACCACAATCATGGGGCAGATTGAAGCATCCAATATTTTACCCTAATCAGAGAGCA
GATTGAAAACATCATCCAATCTCTTACCCCAATCATAGGGCAGATTGAAGCAT
Found at i:29549864 original size:80 final size:77
Alignment explanation
Indices: 29549618--29549880 Score: 225
Period size: 80 Copynumber: 3.4 Consensus size: 77
29549608 TCTTACCCCG
* * *
29549618 ATCATGGGGCAGATTG--A-AGCATCCAATCTTTTACCCTAATCAGAAGGCAGATTGAAGACACA
1 ATCATGGGGCAGATTGAAACATCATCCAATCTTTTACCCTAATCAG-GGGCAGATTGAAG-CA-T
* *
29549680 CCAATCTCTTACCCCA
63 CCAATATTTTA-CCCA
* * * *
29549696 ATCATAGGGCGGATTGAAGCAT--T-CAATCTTTTACCTTAATCAGGGGGCAGATTGAAGCATCC
1 ATCATGGGGCAGATTGAAACATCATCCAATCTTTTACCCTAATCA-GGGGCAGATTGAAGCATCC
*
29549758 AATATTTTATCCTA
65 AATATTTTA-CCCA
* * *
29549772 ATCA-GAGAGCAGATTGAAAACATCATCCAATCTCTTACCCGAATCATGGGGCAGATTGAAGCAT
1 ATCATG-GGGCAGATTG-AAACATCATCCAATCTTTTACCCTAATCA-GGGGCAGATTGAAGCAT
*
29549836 CCAATTTTTTACCACA
63 CCAATATTTTACC-CA
* *
29549852 ACCATGGGGCAGATTTGAAGCTATCATCC
1 ATCATGGGGCAGA-TTGAAAC-ATCATCC
29549881 TACAAAAGTG
Statistics
Matches: 148, Mismatches: 24, Indels: 23
0.76 0.12 0.12
Matches are distributed among these distances:
76 24 0.16
77 7 0.05
78 44 0.30
79 5 0.03
80 56 0.38
81 12 0.08
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.26
Consensus pattern (77 bp):
ATCATGGGGCAGATTGAAACATCATCCAATCTTTTACCCTAATCAGGGGCAGATTGAAGCATCCA
ATATTTTACCCA
Found at i:29549976 original size:50 final size:50
Alignment explanation
Indices: 29549901--29550053 Score: 155
Period size: 50 Copynumber: 3.1 Consensus size: 50
29549891 AATCTCAACC
* * * * *
29549901 TCCTGAAGTTGCAGCGAAATGGAGTGATGGTTTAACACCAAATCCTATCT
1 TCCTGAAATTGCAGCAAAATGGAGTGAAGCTTCAACACCAAATCCTATCT
* *
29549951 TCCTGAAATTGCAGTAAAATGGAGTGAAGCTTCAACACCAAATTCTATCT
1 TCCTGAAATTGCAGCAAAATGGAGTGAAGCTTCAACACCAAATCCTATCT
* * *** ** * *
29550001 TTCT-AAGTTGCAATGAAATAAAGTGAAGCTTCAACACCAAAGCTTATCT
1 TCCTGAAATTGCAGCAAAATGGAGTGAAGCTTCAACACCAAATCCTATCT
29550050 TCCT
1 TCCT
29550054 AAGTTGTAGT
Statistics
Matches: 86, Mismatches: 17, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
49 40 0.47
50 46 0.53
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (50 bp):
TCCTGAAATTGCAGCAAAATGGAGTGAAGCTTCAACACCAAATCCTATCT
Found at i:29550031 original size:49 final size:49
Alignment explanation
Indices: 29549934--29550059 Score: 162
Period size: 49 Copynumber: 2.6 Consensus size: 49
29549924 GTGATGGTTT
* * **
29549934 AACACCAAATCCTATCTTCCTGAAATTGCAGTAAAATGGAGTGAAGCTTC
1 AACACCAAATCCTATCTTCCT-AAGTTGCAATAAAATAAAGTGAAGCTTC
* * *
29549984 AACACCAAATTCTATCTTTCTAAGTTGCAATGAAATAAAGTGAAGCTTC
1 AACACCAAATCCTATCTTCCTAAGTTGCAATAAAATAAAGTGAAGCTTC
* *
29550033 AACACCAAAGCTTATCTTCCTAAGTTG
1 AACACCAAATCCTATCTTCCTAAGTTG
29550060 TAGTGAAGTG
Statistics
Matches: 65, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
49 46 0.71
50 19 0.29
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (49 bp):
AACACCAAATCCTATCTTCCTAAGTTGCAATAAAATAAAGTGAAGCTTC
Found at i:29550716 original size:21 final size:20
Alignment explanation
Indices: 29550675--29550719 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 20
29550665 GATACTTGCA
29550675 AAAAGAAGAACAGACAGAAGC
1 AAAAGAAGAACAGACA-AAGC
29550696 AAAAGCAAGAACAGAGC-AAGC
1 AAAAG-AAGAACAGA-CAAAGC
29550717 AAA
1 AAA
29550720 TACGAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 12 0.55
22 9 0.41
23 1 0.05
ACGTcount: A:0.62, C:0.16, G:0.22, T:0.00
Consensus pattern (20 bp):
AAAAGAAGAACAGACAAAGC
Found at i:29551537 original size:25 final size:25
Alignment explanation
Indices: 29551483--29551537 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
29551473 GGCCGATGAG
* *
29551483 GAGAAAGGTTTTTTTTTTTTAAAAA
1 GAGAGAGGATTTTTTTTTTTAAAAA
* *
29551508 AAGAGAGGATTTTTTTTTTTAAATA
1 GAGAGAGGATTTTTTTTTTTAAAAA
29551533 GAGAG
1 GAGAG
29551538 TAAAATGAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.44
Consensus pattern (25 bp):
GAGAGAGGATTTTTTTTTTTAAAAA
Found at i:29551964 original size:30 final size:29
Alignment explanation
Indices: 29551904--29552103 Score: 147
Period size: 29 Copynumber: 6.7 Consensus size: 29
29551894 ATATTTTAAG
* * *
29551904 CCTAAACTTTCCCAAAAATTCAAATTTGACC
1 CCTAAACTTT-CTAAAATTTC-ATTTTGACC
29551935 CCTAAACTTTCTAAAATTTCATTTTTGA-C
1 CCTAAACTTTCTAAAATTTCA-TTTTGACC
* * * *
29551964 CCTGATCTTTCCAAACATTTCATTTTCACC
1 CCTAAACTTTCTAAA-ATTTCATTTTGACC
* * *
29551994 TC-GAACTTTCTAAAAATTTCATTTTGACT
1 CCTAAACTTTCT-AAAATTTCATTTTGACC
*
29552023 CC-AAACTTTCTAAAAATTACATTTTGACC
1 CCTAAACTTTCT-AAAATTTCATTTTGACC
* *
29552052 TCC-AAACTTTCTAGAAAAATTGCATTTTAACC
1 -CCTAAACTTTCT---AAAATTTCATTTTGACC
*
29552084 CCTAAAACTTTCCAAAATTT
1 CCT-AAACTTTCTAAAATTT
29552104 TGATTTTACC
Statistics
Matches: 140, Mismatches: 20, Indels: 19
0.78 0.11 0.11
Matches are distributed among these distances:
29 63 0.45
30 41 0.29
31 12 0.09
32 16 0.11
33 8 0.06
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.38
Consensus pattern (29 bp):
CCTAAACTTTCTAAAATTTCATTTTGACC
Found at i:29552020 original size:58 final size:58
Alignment explanation
Indices: 29551907--29552100 Score: 162
Period size: 58 Copynumber: 3.2 Consensus size: 58
29551897 TTTTAAGCCT
* *
29551907 AAACTTTCCCAAAAATT-CAAATTTGACC-CCTAAACTTTCT-AAAATTTCATTTTTGACCC
1 AAACTTT-CCAAAAATTAC-ATTTTCACCTCC-AAACTTTCTAAAAATTTCA-TTTTGACCC
* * * * *
29551966 TGATCTTTCCAAACATTTCATTTTCACCT-CGAACTTTCTAAAAATTTCATTTTGACTCC
1 -AAACTTTCCAAAAATTACATTTTCACCTCCAAACTTTCTAAAAATTTCATTTTGAC-CC
* * * *
29552025 AAACTTTCTAAAAATTACATTTTGACCTCCAAACTTTCTAGAAAAATTGCATTTTAACCCC
1 AAACTTTCCAAAAATTACATTTTCACCTCCAAACTTTCT--AAAAATTTCATTTTGA-CCC
29552086 TAAAACTTTCCAAAA
1 --AAACTTTCCAAAA
29552101 TTTTGATTTT
Statistics
Matches: 108, Mismatches: 16, Indels: 17
0.77 0.11 0.12
Matches are distributed among these distances:
58 37 0.34
59 36 0.33
60 6 0.06
61 16 0.15
62 1 0.01
63 12 0.11
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (58 bp):
AAACTTTCCAAAAATTACATTTTCACCTCCAAACTTTCTAAAAATTTCATTTTGACCC
Found at i:29555018 original size:19 final size:19
Alignment explanation
Indices: 29554994--29555033 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
29554984 TATGGTAATA
29554994 TATTAAT-TTTTTTCTTTTT
1 TATTAATGTTTTTT-TTTTT
29555013 TATTAATGGTTTTTTTTTTT
1 TATTAAT-GTTTTTTTTTTT
29555033 T
1 T
29555034 TTTTATGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 6 0.32
21 6 0.32
ACGTcount: A:0.15, C:0.03, G:0.05, T:0.78
Consensus pattern (19 bp):
TATTAATGTTTTTTTTTTT
Found at i:29555450 original size:15 final size:15
Alignment explanation
Indices: 29555402--29555444 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
29555392 ATGACCTTGT
*
29555402 GAGGTCGATGAGCAA
1 GAGGTCAATGAGCAA
** *
29555417 CCGGGCAATGAGCAA
1 GAGGTCAATGAGCAA
29555432 GAGGTCAATGAGC
1 GAGGTCAATGAGC
29555445 CGGAGGATGA
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.33, C:0.19, G:0.37, T:0.12
Consensus pattern (15 bp):
GAGGTCAATGAGCAA
Found at i:29555805 original size:4 final size:4
Alignment explanation
Indices: 29555796--29555823 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
29555786 CCTACTTTCT
29555796 ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC
29555824 CATCCTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:29565273 original size:7 final size:7
Alignment explanation
Indices: 29565261--29565300 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
29565251 AGTAAAGAAT
*
29565261 TTTCTAA
1 TTTCGAA
*
29565268 TTTCTAA
1 TTTCGAA
29565275 TTT-GAA
1 TTTCGAA
29565281 TTTCGAA
1 TTTCGAA
29565288 TTTCGAA
1 TTTCGAA
29565295 TTTCGA
1 TTTCGA
29565301 CTCCTAAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 5 0.16
7 26 0.84
ACGTcount: A:0.28, C:0.12, G:0.10, T:0.50
Consensus pattern (7 bp):
TTTCGAA
Found at i:29566214 original size:16 final size:16
Alignment explanation
Indices: 29566193--29566243 Score: 84
Period size: 16 Copynumber: 3.2 Consensus size: 16
29566183 TTTCTAGTAT
*
29566193 TTTATTTACTAGCGTG
1 TTTATTTACTAGCGTA
*
29566209 TTTATTTGCTAGCGTA
1 TTTATTTACTAGCGTA
29566225 TTTATTTACTAGCGTA
1 TTTATTTACTAGCGTA
29566241 TTT
1 TTT
29566244 TGCTCTTTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.20, C:0.12, G:0.16, T:0.53
Consensus pattern (16 bp):
TTTATTTACTAGCGTA
Found at i:29572212 original size:6 final size:6
Alignment explanation
Indices: 29572203--29572235 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
29572193 GAGAGAGAGA
29572203 GGAGGG GGA-GG GGAGGGG GGAGGG GGAGGG GGA
1 GGAGGG GGAGGG GGA-GGG GGAGGG GGAGGG GGA
29572236 TGGATCATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.20
6 15 0.60
7 5 0.20
ACGTcount: A:0.18, C:0.00, G:0.82, T:0.00
Consensus pattern (6 bp):
GGAGGG
Found at i:29572221 original size:12 final size:13
Alignment explanation
Indices: 29572206--29572234 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
29572196 AGAGAGAGGA
29572206 GGGGGA-GGGGAG
1 GGGGGAGGGGGAG
29572218 GGGGGAGGGGGAG
1 GGGGGAGGGGGAG
29572231 GGGG
1 GGGG
29572235 ATGGATCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.14, C:0.00, G:0.86, T:0.00
Consensus pattern (13 bp):
GGGGGAGGGGGAG
Found at i:29578103 original size:17 final size:17
Alignment explanation
Indices: 29578081--29578163 Score: 107
Period size: 17 Copynumber: 4.9 Consensus size: 17
29578071 TGAAATGAAG
*
29578081 TTTATTTTAAATTCAAA
1 TTTATTTTAAATTTAAA
29578098 TTTATTTTAAATTTAAA
1 TTTATTTTAAATTTAAA
*
29578115 TTTATTTT-TATTTAAA
1 TTTATTTTAAATTTAAA
*
29578131 TTTAATTTT-AGTTTAAA
1 TTT-ATTTTAAATTTAAA
*
29578148 TTTAATTTAAATTTAA
1 TTTATTTTAAATTTAA
29578164 TATTATGGTA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
16 14 0.24
17 44 0.76
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (17 bp):
TTTATTTTAAATTTAAA
Found at i:29578111 original size:11 final size:11
Alignment explanation
Indices: 29578107--29578164 Score: 64
Period size: 11 Copynumber: 5.3 Consensus size: 11
29578097 ATTTATTTTA
29578107 AATTTAAATTT
1 AATTTAAATTT
**
29578118 -ATTTTTATTT
1 AATTTAAATTT
*
29578128 AAATTTAATTTT
1 -AATTTAAATTT
*
29578140 AGTTTAAATTT
1 AATTTAAATTT
29578151 AATTTAAATTT
1 AATTTAAATTT
29578162 AAT
1 AAT
29578165 ATTATGGTAA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
10 8 0.22
11 22 0.59
12 7 0.19
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:29578112 original size:6 final size:6
Alignment explanation
Indices: 29578086--29578163 Score: 67
Period size: 6 Copynumber: 13.8 Consensus size: 6
29578076 TGAAGTTTAT
* * **
29578086 TTTAAA TTCAAA TTT-AT TTTAAA TTTAAA TTT--A TTTTTA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
29578131 TTT-AA TTTTAG TTTAAA TTT-AA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
29578164 TATTATGGTA
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
4 4 0.07
5 14 0.24
6 40 0.69
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (6 bp):
TTTAAA
Found at i:29578146 original size:39 final size:39
Alignment explanation
Indices: 29578081--29578156 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 39
29578071 TGAAATGAAG
*
29578081 TTTATTTTAAATTCAAATTTATTTTAAATTTAAATTTATT
1 TTTATTTTAAATTCAAATTTAGTTTAAATTT-AATTTATT
* *
29578121 TTTA-TTTAAATTTAATTTTAGTTTAAATTTAATTTA
1 TTTATTTTAAATTCAAATTTAGTTTAAATTTAATTTA
29578157 AATTTAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 6 0.18
39 23 0.70
40 4 0.12
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (39 bp):
TTTATTTTAAATTCAAATTTAGTTTAAATTTAATTTATT
Found at i:29578164 original size:28 final size:28
Alignment explanation
Indices: 29578124--29578181 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
29578114 ATTTATTTTT
* *
29578124 ATTTAAATTTAATTTTA-GTTTAAATTTA
1 ATTTAAATTTAATATTATG-GTAAATTTA
29578152 ATTTAAATTTAATATTATGGTAAATTTA
1 ATTTAAATTTAATATTATGGTAAATTTA
29578180 AT
1 AT
29578182 GTTCATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 26 0.96
29 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.53
Consensus pattern (28 bp):
ATTTAAATTTAATATTATGGTAAATTTA
Found at i:29578225 original size:14 final size:14
Alignment explanation
Indices: 29578206--29578246 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
29578196 AGCCCGAATG
29578206 AAAGGCCCAATTAC
1 AAAGGCCCAATTAC
* *
29578220 AAAGG-CCAAATAG
1 AAAGGCCCAATTAC
29578233 AAA-GCCCAATTAC
1 AAAGGCCCAATTAC
29578246 A
1 A
29578247 TCAGCCCAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
12 1 0.05
13 16 0.73
14 5 0.23
ACGTcount: A:0.49, C:0.24, G:0.15, T:0.12
Consensus pattern (14 bp):
AAAGGCCCAATTAC
Found at i:29578239 original size:26 final size:26
Alignment explanation
Indices: 29578188--29578255 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 26
29578178 TAATGTTCAT
*
29578188 ATTACAAAAGCCCGAATGAAAGGCCCA
1 ATTAC-AAAGCCCAAATGAAAGGCCCA
*
29578215 ATTACAAAGGCCAAATAGAAA-GCCCA
1 ATTACAAAGCCCAAAT-GAAAGGCCCA
*
29578241 ATTACATCAGCCCAA
1 ATTACA-AAGCCCAA
29578256 TTGACCCAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
26 20 0.57
27 15 0.43
ACGTcount: A:0.46, C:0.26, G:0.15, T:0.13
Consensus pattern (26 bp):
ATTACAAAGCCCAAATGAAAGGCCCA
Found at i:29578958 original size:7 final size:7
Alignment explanation
Indices: 29578946--29578987 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
29578936 TCAATATTTG
29578946 TTAATAA
1 TTAATAA
29578953 TTAATAA
1 TTAATAA
29578960 -TAATAA
1 TTAATAA
*
29578966 TTAATAT
1 TTAATAA
29578973 TATAATAA
1 T-TAATAA
29578981 TTAATAA
1 TTAATAA
29578988 AAAGGAAGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 6 0.19
7 19 0.61
8 6 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
TTAATAA
Found at i:29578979 original size:15 final size:13
Alignment explanation
Indices: 29578947--29578987 Score: 64
Period size: 13 Copynumber: 3.0 Consensus size: 13
29578937 CAATATTTGT
29578947 TAATAATTAATAA
1 TAATAATTAATAA
29578960 TAATAATTAATATTA
1 TAATAATTAATA--A
29578975 TAATAATTAATAA
1 TAATAATTAATAA
29578988 AAAGGAAGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 13 0.50
15 13 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TAATAATTAATAA
Found at i:29580033 original size:29 final size:28
Alignment explanation
Indices: 29580001--29580093 Score: 66
Period size: 29 Copynumber: 3.2 Consensus size: 28
29579991 GATTTTACTA
29580001 AAAATTATAATTTTACCCCCAAACTTTCC
1 AAAATTAT-ATTTTACCCCCAAACTTTCC
* *
29580030 AAAATCTCAT-TTTTAACCCC-GA-TTTCACC
1 AAAAT-T-ATATTTTACCCCCAAACTTT--CC
* *
29580059 AAAAATTACCATTTTACCCCTAAACTTTCC
1 -AAAATTA-TATTTTACCCCCAAACTTTCC
29580089 AAAAT
1 AAAAT
29580094 CTCATTTTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 18
0.67 0.08 0.25
Matches are distributed among these distances:
27 3 0.06
28 2 0.04
29 22 0.45
30 16 0.33
31 3 0.06
32 3 0.06
ACGTcount: A:0.38, C:0.28, G:0.01, T:0.33
Consensus pattern (28 bp):
AAAATTATATTTTACCCCCAAACTTTCC
Found at i:29580063 original size:59 final size:59
Alignment explanation
Indices: 29579963--29580122 Score: 241
Period size: 59 Copynumber: 2.7 Consensus size: 59
29579953 CTAGTCCTTG
* * * *
29579963 AACTTTCCAAAATC-CTATTTTTTACCCCGATTTTACTAAAAATTATAATTTTACCCCCA
1 AACTTTCCAAAATCTC-ATTTTTAACCCCGATTTCACCAAAAATTACAATTTTACCCCCA
* *
29580022 AACTTTCCAAAATCTCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCTA
1 AACTTTCCAAAATCTCATTTTTAACCCCGATTTCACCAAAAATTACAATTTTACCCCCA
29580081 AACTTTCCAAAATCTCATTTTTTAACCCCGATTTCACCAAAA
1 AACTTTCCAAAATCTCA-TTTTTAACCCCGATTTCACCAAAA
29580123 TGAACTTTCT
Statistics
Matches: 93, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
59 68 0.73
60 25 0.27
ACGTcount: A:0.34, C:0.28, G:0.02, T:0.36
Consensus pattern (59 bp):
AACTTTCCAAAATCTCATTTTTAACCCCGATTTCACCAAAAATTACAATTTTACCCCCA
Found at i:29580102 original size:29 final size:28
Alignment explanation
Indices: 29580011--29580102 Score: 75
Period size: 29 Copynumber: 3.1 Consensus size: 28
29580001 AAAATTATAA
29580011 TTTTACCCCCAAACTTTCCAAAATCTCAT
1 TTTTA-CCCCAAACTTTCCAAAATCTCAT
*
29580040 TTTTAACCCC-GA-TTTCACCAAAAAT-TACCA-
1 TTTT-ACCCCAAACTTT--CC-AAAATCT--CAT
29580070 TTTTACCCCTAAACTTTCCAAAATCTCAT
1 TTTTACCCC-AAACTTTCCAAAATCTCAT
29580099 TTTT
1 TTTT
29580103 TAACCCCGAT
Statistics
Matches: 50, Mismatches: 2, Indels: 22
0.68 0.03 0.30
Matches are distributed among these distances:
27 3 0.06
28 3 0.06
29 25 0.50
30 13 0.26
31 3 0.06
32 3 0.06
ACGTcount: A:0.32, C:0.30, G:0.01, T:0.37
Consensus pattern (28 bp):
TTTTACCCCAAACTTTCCAAAATCTCAT
Found at i:29580123 original size:30 final size:29
Alignment explanation
Indices: 29580028--29580123 Score: 85
Period size: 30 Copynumber: 3.2 Consensus size: 29
29580018 CCCAAACTTT
29580028 CCAAAATCTCATTTTTAACCCCGATTTCA
1 CCAAAATCTCATTTTTAACCCCGATTTCA
*
29580057 CCAAAAAT-TACCA-TTTT-ACCCCTAAACTTT--
1 CC-AAAATCT--CATTTTTAACCCC--GA-TTTCA
29580087 CCAAAATCTCATTTTTTAACCCCGATTTCA
1 CCAAAATCTCA-TTTTTAACCCCGATTTCA
29580117 CCAAAAT
1 CCAAAAT
29580124 GAACTTTCTA
Statistics
Matches: 53, Mismatches: 2, Indels: 23
0.68 0.03 0.29
Matches are distributed among these distances:
28 5 0.09
29 14 0.26
30 23 0.43
31 8 0.15
32 3 0.06
ACGTcount: A:0.34, C:0.30, G:0.02, T:0.33
Consensus pattern (29 bp):
CCAAAATCTCATTTTTAACCCCGATTTCA
Found at i:29580167 original size:44 final size:44
Alignment explanation
Indices: 29580081--29580165 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 44
29580071 TTTACCCCTA
* * *
29580081 AACTTTCCAAAATCTCATTTTTTAACCCCGATTTCACCAAAATG
1 AACTTTCCAAAATCCCATTTTTAAACCCCAATTTCACCAAAATG
* *
29580125 AACTTTCTAAAATCCCA-TTTTAAACCCTAATTTCACCAAAA
1 AACTTTCCAAAATCCCATTTTTAAACCCCAATTTCACCAAAA
29580166 ATTACCATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 21 0.58
44 15 0.42
ACGTcount: A:0.38, C:0.27, G:0.02, T:0.33
Consensus pattern (44 bp):
AACTTTCCAAAATCCCATTTTTAAACCCCAATTTCACCAAAATG
Found at i:29580174 original size:31 final size:31
Alignment explanation
Indices: 29580139--29580236 Score: 78
Period size: 31 Copynumber: 3.3 Consensus size: 31
29580129 TTCTAAAATC
29580139 CCATTTTAAACCCTAATTTCACCAAAAATTA
1 CCATTTTAAACCCTAATTTCACCAAAAATTA
*** * * *
29580170 CCATTTTGTCCCCGAACTTT---CTAAAA-TC
1 CCATTTTAAACCCTAA-TTTCACCAAAAATTA
* * *
29580198 CCCTTTTTAACCCTGATTTCACCAAAAATTA
1 CCATTTTAAACCCTAATTTCACCAAAAATTA
29580229 CCATTTTA
1 CCATTTTA
29580237 CCCCCGAACT
Statistics
Matches: 46, Mismatches: 16, Indels: 10
0.64 0.22 0.14
Matches are distributed among these distances:
27 3 0.07
28 11 0.24
29 5 0.11
30 5 0.11
31 19 0.41
32 3 0.07
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.36
Consensus pattern (31 bp):
CCATTTTAAACCCTAATTTCACCAAAAATTA
Found at i:29580217 original size:59 final size:59
Alignment explanation
Indices: 29580124--29580293 Score: 243
Period size: 59 Copynumber: 2.9 Consensus size: 59
29580114 TCACCAAAAT
* **
29580124 GAACTTTCTAAAATCCCATTTTAAACCCTAATTTCACCAAAAATTACCATTTTGTCCCC
1 GAACTTTCTAAAATCCCATTTTAAACCCTGATTTCACCAAAAATTACCATTTTACCCCC
* *
29580183 GAACTTTCTAAAATCCCCTTTTTAACCCTGATTTCACCAAAAATTACCATTTTACCCCC
1 GAACTTTCTAAAATCCCATTTTAAACCCTGATTTCACCAAAAATTACCATTTTACCCCC
* * * * *
29580242 GAACTTTCTAAAATCTCATTTTGAACCTTGATCTCACCAAAAATCA-CATTTT
1 GAACTTTCTAAAATCCCATTTTAAACCCTGATTTCACCAAAAATTACCATTTT
29580294 TACCTCGAAA
Statistics
Matches: 100, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
58 6 0.06
59 94 0.94
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (59 bp):
GAACTTTCTAAAATCCCATTTTAAACCCTGATTTCACCAAAAATTACCATTTTACCCCC
Found at i:29580226 original size:103 final size:103
Alignment explanation
Indices: 29580022--29580224 Score: 284
Period size: 103 Copynumber: 2.0 Consensus size: 103
29580012 TTTACCCCCA
* * *
29580022 AACTTTCCAAAATCTCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCTAAACTTT
1 AACTTTCCAAAATCCCATTTTAAACCCCAATTTCACCAAAAATTACCATTTTACCCCTAAACTTT
*
29580087 CCAAAATCTCATTTTTTAACCCCGATTTCACCAAAATG
66 CCAAAATCTCACTTTTTAACCCCGATTTCACCAAAATG
* * * *
29580125 AACTTTCTAAAATCCCATTTTAAACCCTAATTTCACCAAAAATTACCATTTTGTCCCC-GAACTT
1 AACTTTCCAAAATCCCATTTTAAACCCCAATTTCACCAAAAATTACCATTTT-ACCCCTAAACTT
* * *
29580189 TCTAAAATC-CCCTTTTTAACCCTGATTTCACCAAAA
65 TCCAAAATCTCACTTTTTAACCCCGATTTCACCAAAA
29580225 ATTACCATTT
Statistics
Matches: 88, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
102 24 0.27
103 60 0.68
104 4 0.05
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (103 bp):
AACTTTCCAAAATCCCATTTTAAACCCCAATTTCACCAAAAATTACCATTTTACCCCTAAACTTT
CCAAAATCTCACTTTTTAACCCCGATTTCACCAAAATG
Found at i:29580228 original size:162 final size:162
Alignment explanation
Indices: 29579961--29580263 Score: 426
Period size: 162 Copynumber: 1.9 Consensus size: 162
29579951 CTCTAGTCCT
* ** * * * *
29579961 TGAACTTTCCAAAATCCTATTTTTTACCCCGATTTTACTAAAAATTATAATTTTACCCCCAAACT
1 TGAACTTTCCAAAATCCCATTTTAAACCCCAATTTCACCAAAAATTACAATTTTACCCCCAAACT
* *
29580026 TTCCAAAATCTCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCTAAACTTTCCAA
66 TTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCAAACTTTCCAA
29580091 AATCTCATTTTTTAACCCCGATTTCACCAAAA
131 AATCTCATTTTTTAACCCCGATTTCACCAAAA
* * * ** *
29580123 TGAACTTTCTAAAATCCCATTTTAAACCCTAATTTCACCAAAAATTACCATTTTGTCCCCGAACT
1 TGAACTTTCCAAAATCCCATTTTAAACCCCAATTTCACCAAAAATTACAATTTTACCCCCAAACT
* * * * *
29580188 TTCTAAAATCCCCTTTTTAACCCTGATTTCACCAAAAATTACCATTTTACCCCCGAACTTTCTAA
66 TTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCAAACTTTCCAA
29580253 AATCTCATTTT
131 AATCTCATTTT
29580264 GAACCTTGAT
Statistics
Matches: 121, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
162 121 1.00
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.36
Consensus pattern (162 bp):
TGAACTTTCCAAAATCCCATTTTAAACCCCAATTTCACCAAAAATTACAATTTTACCCCCAAACT
TTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCAAACTTTCCAA
AATCTCATTTTTTAACCCCGATTTCACCAAAA
Found at i:29580255 original size:29 final size:29
Alignment explanation
Indices: 29580124--29580255 Score: 74
Period size: 29 Copynumber: 4.5 Consensus size: 29
29580114 TCACCAAAAT
* *
29580124 GAACTTTCTAAAA-TCCCATTTTAAACCC
1 GAACTTTCTAAAATTACCATTTTAACCCC
* * **
29580152 TAA-TTTCACCAAAAATTACCATTTTGTCCCC
1 GAACTTT---CTAAAATTACCATTTTAACCCC
** * *
29580183 GAACTTTCTAAAATCCCCTTTTTAACCCT
1 GAACTTTCTAAAATTACCATTTTAACCCC
* *
29580212 G-A-TTTCACCAAAAATTACCATTTTACCCCC
1 GAACTTT---CTAAAATTACCATTTTAACCCC
29580242 GAACTTTCTAAAAT
1 GAACTTTCTAAAAT
29580256 CTCATTTTGA
Statistics
Matches: 73, Mismatches: 21, Indels: 19
0.65 0.19 0.17
Matches are distributed among these distances:
27 6 0.08
28 3 0.04
29 22 0.30
30 22 0.30
31 14 0.19
32 6 0.08
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (29 bp):
GAACTTTCTAAAATTACCATTTTAACCCC
Found at i:29584816 original size:199 final size:201
Alignment explanation
Indices: 29584476--29585209 Score: 1242
Period size: 201 Copynumber: 3.7 Consensus size: 201
29584466 GGAGTAATTC
* *
29584476 AATCAAAACAGGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAACACCAACTCAACGCTC
1 AATCAAAACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAACACCAACTCAGCGCTC
29584541 AAACACGAGCAAATCTTCGAACCC-GACTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATA
66 AAACACGAGCAAATCTTCGAACCCAG-CTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATA
29584605 AAAAGGTTAGCTTCCTGATGAGACA-A-AGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAG
130 AAAAGGTTAGCTTCCTGATGAGACACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAG
29584668 AAAAGCG
195 AAAAGCG
* * **
29584675 AATCAAAACGAGCAAGGTAGTCATCTTCCTGATGAGATACAGAGAAGAACACCAACTCAGCGCTC
1 AATCAAAACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAACACCAACTCAGCGCTC
*
29584740 AAACACGAGCAAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCAAAGCAATAA
66 AAACACGAGCAAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAA
*
29584805 AAAGGTTAGCTTCCTGATGAGACACAGATAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGA
131 AAAGGTTAGCTTCCTGATGAGACACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGA
*
29584870 GAAGCG
196 AAAGCG
* * *
29584876 AATCAAAACCAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAACACCAGCTCAGCACTC
1 AATCAAAACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAACACCAACTCAGCGCTC
29584941 AAACACGAGCAAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAA
66 AAACACGAGCAAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAA
*
29585006 AAAGGTTAGCTTCCTGATGAGACACAGAGAAGTGGACCAGATTCGTCTTCTTGAGGAGATCCAGA
131 AAAGGTTAGCTTCCTGATGAGACACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGA
29585071 AAAGCG
196 AAAGCG
*
29585077 AATCAAAACAAGCGAGGCGGTCATCTTCCTGATGAGATACGGAGAAGAACACCAACTCAGCGCTC
1 AATCAAAACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAACACCAACTCAGCGCTC
** * * *
29585142 -AATGCGAGCAAATCTTTGAACTCCAGCTTCCTGATGAGACACTGAGAAGTAGGTCGAAGTCAAC
66 AAACACGAGCAAATCTTCGAAC-CCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAG-CAAT
29585206 AAAA
129 AAAA
29585210 CCAATGAAAT
Statistics
Matches: 502, Mismatches: 28, Indels: 7
0.93 0.05 0.01
Matches are distributed among these distances:
199 145 0.29
200 20 0.04
201 330 0.66
202 7 0.01
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (201 bp):
AATCAAAACAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAACACCAACTCAGCGCTC
AAACACGAGCAAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAA
AAAGGTTAGCTTCCTGATGAGACACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGA
AAAGCG
Found at i:29585584 original size:17 final size:17
Alignment explanation
Indices: 29585539--29585645 Score: 92
Period size: 17 Copynumber: 6.3 Consensus size: 17
29585529 CCCAAACCAT
* *
29585539 TTTAAATTTGCTTTGAAA
1 TTTAAATTT-ATTTTAAA
*
29585557 -TTAAGTTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
29585573 TTCAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
**
29585590 TTTAAATTTATTTTTGA
1 TTTAAATTTATTTTAAA
*
29585607 TTTAAATTTAATTTT-AG
1 TTTAAATTT-ATTTTAAA
* * *
29585624 TTTGAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
29585641 TTTAA
1 TTTAA
29585646 TATTATGGTA
Statistics
Matches: 73, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
16 10 0.14
17 58 0.79
18 5 0.07
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:29585610 original size:23 final size:23
Alignment explanation
Indices: 29585584--29585644 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
29585574 TCAAATTTAT
*
29585584 TTTAAATTTAAATTTATTTTTG-A
1 TTTAAATTTAAATTTA-GTTTGAA
*
29585607 TTTAAATTTAATTTTAGTTTGAA
1 TTTAAATTTAAATTTAGTTTGAA
*
29585630 TTT-AATTTAAGTTTA
1 TTTAAATTTAAATTTA
29585645 ATATTATGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 15 0.44
23 19 0.56
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (23 bp):
TTTAAATTTAAATTTAGTTTGAA
Found at i:29587643 original size:58 final size:59
Alignment explanation
Indices: 29587444--29587861 Score: 556
Period size: 59 Copynumber: 7.1 Consensus size: 59
29587434 GCTCTCTAGT
*
29587444 CCCCGAACTTTCCAAAATCTCATTTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
1 CCCCGAACTTTCCAAAATCCCA-TTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
* * * * *
29587504 CCCTGAACTTTCCAAAATCCTATTATTAACCCCGATTTTACCAAAAATTATCATTTTAC
1 CCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
** * * *
29587563 CCCTAAACTTTCCAAAAT-CCATTTTTAGCCTCGATTTTACCAAAAATTACCATTTT-C
1 CCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
* *
29587620 CCCCGACCTTTCTAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
1 CCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
** * * *
29587679 CCCTAAACTTTCCAAAATCCCA-TTTTAACCCCAATTTTACCAAAAATTACCATTTTGC
1 CCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
* * * *
29587737 CCCCAAACTTTTCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACTATTTCAC
1 CCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
* * *
29587796 CCCCGAACTTTCCAAAATCTCATTTTTAACCCTGATCTCACCAAAAATTA-CATATTTAC
1 CCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCAT-TTTAC
*
29587855 CCTCGAA
1 CCCCGAA
29587862 AGTCAAAAAT
Statistics
Matches: 313, Mismatches: 41, Indels: 9
0.86 0.11 0.02
Matches are distributed among these distances:
57 15 0.05
58 123 0.39
59 156 0.50
60 19 0.06
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.33
Consensus pattern (59 bp):
CCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
Found at i:29587787 original size:117 final size:116
Alignment explanation
Indices: 29587449--29587846 Score: 539
Period size: 117 Copynumber: 3.4 Consensus size: 116
29587439 CTAGTCCCCG
* *
29587449 AACTTTCCAAAATCTCATTTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCTGAACTT
1 AACTTTCCAAAATCCCA-TTTTTAACCCCGATTTCACCAAAAATTACCATTTT-CCCC-CAACTT
* * * * *
29587514 TCCAAAATCCTATTATTAACCCCGATTTTACCAAAAATTATCATTTTACCCCTA
63 TTCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCTA
* * * * *
29587568 AACTTTCCAAAAT-CCATTTTTAGCCTCGATTTTACCAAAAATTACCATTTTCCCCCGACCTTTC
1 AACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTCCCCCAACTTTTC
29587632 TAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCTA
66 -AAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCTA
* *
29587684 AACTTTCCAAAATCCCA-TTTTAACCCCAATTTTACCAAAAATTACCATTTTGCCCCCAAACTTT
1 AACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTT-CCCCC-AACTTT
* * **
29587748 TCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACTATTTCACCCCCG
64 TCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCTA
* * *
29587801 AACTTTCCAAAATCTCATTTTTAACCCTGATCTCACCAAAAATTAC
1 AACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTAC
29587847 ATATTTACCC
Statistics
Matches: 248, Mismatches: 26, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
115 5 0.02
116 95 0.38
117 103 0.42
118 32 0.13
119 13 0.05
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.34
Consensus pattern (116 bp):
AACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTCCCCCAACTTTTC
AAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCTA
Found at i:29587887 original size:117 final size:115
Alignment explanation
Indices: 29587444--29587869 Score: 500
Period size: 116 Copynumber: 3.6 Consensus size: 115
29587434 GCTCTCTAGT
*
29587444 CCCCGAACTTTCCAAAATCTCATTTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCTG
1 CCCCAAACTTTCCAAAATCTCA-TTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCC-G
* * * *
29587509 AACTTTCCAAAATCCTATTATTAACCCCGATTTTACCAAAAATTA-TCATTTTAC
64 AA-ATT-CAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACT-ATTTTAC
* * * * *
29587563 CCCTAAACTTTCCAAAATC-CATTTTTAGCCTCGATTTTACCAAAAATTACCATTTTCCCCCGAC
1 CCCCAAACTTTCCAAAATCTCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCGA-
** *
29587627 CTTTCTAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTAC
65 AATTC-AAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACTATTTTAC
* * * * * *
29587679 CCCTAAACTTTCCAAAATCCCA-TTTTAACCCCAATTTTACCAAAAATTACCATTTTGCCCCCAA
1 CCCCAAACTTTCCAAAATCTCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCGAA
*
29587743 ACTTTTCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACTATTTCAC
66 A---TTCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACTATTTTAC
* * *
29587796 CCCCGAACTTTCCAAAATCTCATTTTTAACCCTGATCTCACCAAAAATTA-CATATTTACCCTCG
1 CCCCAAACTTTCCAAAATCTCATTTTTAACCCCGATTTCACCAAAAATTACCAT-TTTACCC-CG
*
29587860 AAAGTCAAAA
64 AAATTCAAAA
29587870 ATTACCATTT
Statistics
Matches: 267, Mismatches: 30, Indels: 23
0.83 0.09 0.07
Matches are distributed among these distances:
115 1 0.00
116 107 0.40
117 104 0.39
118 34 0.13
119 21 0.08
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.33
Consensus pattern (115 bp):
CCCCAAACTTTCCAAAATCTCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCGAA
ATTCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACTATTTTAC
Found at i:29594465 original size:21 final size:21
Alignment explanation
Indices: 29594447--29594494 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
29594437 GGGATTTAAG
*
29594447 GTTTAGAGTTATAAGTTTAGA
1 GTTTAGAGTTACAAGTTTAGA
*
29594468 GTTTAGAGTTACAAGTTCAGA
1 GTTTAGAGTTACAAGTTTAGA
29594489 GTTTAG
1 GTTTAG
29594495 GATCCATGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.31, C:0.04, G:0.25, T:0.40
Consensus pattern (21 bp):
GTTTAGAGTTACAAGTTTAGA
Found at i:29595582 original size:18 final size:20
Alignment explanation
Indices: 29595559--29595596 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
29595549 AAATATCGTT
29595559 AAACTT-TTT-TTAAAATAA
1 AAACTTATTTCTTAAAATAA
*
29595577 AAACTTATTTCTTACAATAA
1 AAACTTATTTCTTAAAATAA
29595597 TTTAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 3 0.18
20 8 0.47
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (20 bp):
AAACTTATTTCTTAAAATAA
Found at i:29597141 original size:4 final size:4
Alignment explanation
Indices: 29597132--29597162 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
29597122 GAATAGAAGG
29597132 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
29597163 AAGGAAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:29597872 original size:29 final size:29
Alignment explanation
Indices: 29597814--29597872 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
29597804 TTAACGGTTC
* * * *
29597814 AGTGATTAAAATGTAATATTTCAAATATA
1 AGTGACTAAAATATAACATTTCAAAAATA
29597843 AGTGACTAAAATATAACATTAT-AAAAATA
1 AGTGACTAAAATATAACATT-TCAAAAATA
29597872 A
1 A
29597873 AAGTAACTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
29 24 0.96
30 1 0.04
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.32
Consensus pattern (29 bp):
AGTGACTAAAATATAACATTTCAAAAATA
Found at i:29598257 original size:2 final size:2
Alignment explanation
Indices: 29598250--29598282 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
29598240 CCTCCTTTTC
*
29598250 AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29598283 AGCCTTGATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:29601440 original size:32 final size:32
Alignment explanation
Indices: 29601404--29601464 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
29601394 GAAGGGTTAT
* *
29601404 TGTATGCTCCTCTGTAGGATTGTTTTTTTCTC
1 TGTATGCTCCTCTGTAGCATCGTTTTTTTCTC
29601436 TGTATGCTCCTCTGTAGCATCGTTTTTTT
1 TGTATGCTCCTCTGTAGCATCGTTTTTTT
29601465 GGTATTTCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.10, C:0.20, G:0.18, T:0.52
Consensus pattern (32 bp):
TGTATGCTCCTCTGTAGCATCGTTTTTTTCTC
Found at i:29606881 original size:29 final size:27
Alignment explanation
Indices: 29606848--29606978 Score: 129
Period size: 28 Copynumber: 4.6 Consensus size: 27
29606838 ACTTAGGGGC
29606848 AAAATGGTAATTTTGATGAAA-TCGAGGGT
1 AAAATGG-AATTTTG--GAAATTCGAGGGT
*
29606877 AAAATGGAATTTTGGAAAGTTCGGGGGT
1 AAAATGGAATTTTGGAAA-TTCGAGGGT
* * *
29606905 AAAATGGTAATTTTTGGTAAAATCAAGGTT
1 AAAATGG-AA-TTTTGG-AAATTCGAGGGT
*
29606935 AAAATGGAATTATGGAAAATTCGAGGGT
1 AAAATGGAATTTTGG-AAATTCGAGGGT
29606963 AAAATGGCAATTTTGG
1 AAAATGG-AATTTTGG
29606979 TAAAATTAGG
Statistics
Matches: 85, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
26 4 0.05
28 42 0.49
29 18 0.21
30 18 0.21
31 3 0.04
ACGTcount: A:0.38, C:0.04, G:0.27, T:0.31
Consensus pattern (27 bp):
AAAATGGAATTTTGGAAATTCGAGGGT
Found at i:29606887 original size:28 final size:29
Alignment explanation
Indices: 29606848--29607064 Score: 123
Period size: 28 Copynumber: 7.5 Consensus size: 29
29606838 ACTTAGGGGC
*
29606848 AAAATGGTAATTTTGATGAAATCGAGGGT
1 AAAATGGTAATTTTGGTGAAATCGAGGGT
*
29606877 AAAATGG-AATTTT-G-GAAAGTTCGGGGGT
1 AAAATGGTAATTTTGGTGAAA--TCGAGGGT
* * *
29606905 AAAATGGTAATTTTTGGTAAAATCAAGGTT
1 AAAATGGTAA-TTTTGGTGAAATCGAGGGT
* *
29606935 AAAATGG-AATTATGG-AAAATTCGAGGGT
1 AAAATGGTAATTTTGGTGAAA-TCGAGGGT
* * *
29606963 AAAATGGCAATTTTGGTAAAAT-TAGGGTT
1 AAAATGGTAATTTTGGTGAAATCGAGGG-T
* * * *
29606992 AAAAATAG-AATTTT--TAAAAAGTTTG-GCAGT
1 -AAAATGGTAATTTTGGT-GAAA--TCGAG-GGT
* *
29607022 AAAATGGTAATTTTGGTGAAATCGGGGGC
1 AAAATGGTAATTTTGGTGAAATCGAGGGT
29607051 AAAATGG-AATTTTG
1 AAAATGGTAATTTTG
29607065 TAAAACTTGG
Statistics
Matches: 149, Mismatches: 19, Indels: 41
0.71 0.09 0.20
Matches are distributed among these distances:
26 4 0.03
27 5 0.03
28 53 0.36
29 42 0.28
30 36 0.24
31 5 0.03
32 4 0.03
ACGTcount: A:0.39, C:0.04, G:0.26, T:0.31
Consensus pattern (29 bp):
AAAATGGTAATTTTGGTGAAATCGAGGGT
Found at i:29606928 original size:58 final size:57
Alignment explanation
Indices: 29606843--29607092 Score: 238
Period size: 58 Copynumber: 4.3 Consensus size: 57
29606833 TGGATACTTA
* * * *
29606843 GGGGCAAAATGGTAATTTTGATGAAATCGAGGGTAAAATGGAATTTTGGAAAGTTCG
1 GGGGTAAAATGGTAATTTTGGTAAAATCGAGGGTAAAATGGAATTTTGAAAAGTTCG
* * *
29606900 GGGGTAAAATGGTAATTTTTGGTAAAATCAAGGTTAAAATGGAATTATGGAAAA-TTCG
1 GGGGTAAAATGGTAA-TTTTGGTAAAATCGAGGGTAAAATGGAATT-TTGAAAAGTTCG
* * * * * *
29606958 AGGGTAAAATGGCAATTTTGGTAAAAT-TAGGGTTAAAAATAGAATTTTTAAAAAGTTTG
1 GGGGTAAAATGGTAATTTTGGTAAAATCGAGGG-T-AAAATGGAA-TTTTGAAAAGTTCG
** * * * *
29607017 GCAGTAAAATGGTAATTTTGGTGAAATCGGGGGCAAAATGGAATTTTGTAAAACTT-G
1 GGGGTAAAATGGTAATTTTGGTAAAATCGAGGGTAAAATGGAATTTTG-AAAAGTTCG
29607074 GGGGTCAAAAT-GTAATTTT
1 GGGGT-AAAATGGTAATTTT
29607093 TAGAAAGTTT
Statistics
Matches: 156, Mismatches: 28, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
56 3 0.02
57 43 0.28
58 75 0.48
59 32 0.21
60 3 0.02
ACGTcount: A:0.38, C:0.04, G:0.27, T:0.31
Consensus pattern (57 bp):
GGGGTAAAATGGTAATTTTGGTAAAATCGAGGGTAAAATGGAATTTTGAAAAGTTCG
Found at i:29607076 original size:28 final size:29
Alignment explanation
Indices: 29606843--29607092 Score: 137
Period size: 29 Copynumber: 8.7 Consensus size: 29
29606833 TGGATACTTA
* *
29606843 GGGG-CAAAATGGTAATTTTGATGAAATCG
1 GGGGTCAAAATGG-AATTTTGGTAAAATCG
* *
29606872 AGGGT-AAAATGGAATTTTGG-AAAGTTCG
1 GGGGTCAAAATGGAATTTTGGTAAA-ATCG
29606900 GGGGT-AAAATGGTAATTTTTGGTAAAATC-
1 GGGGTCAAAATGG-AA-TTTTGGTAAAATCG
** * *
29606929 AAGGTTAAAATGGAATTATGG-AAAATTCG
1 GGGGTCAAAATGGAATTTTGGTAAAA-TCG
* **
29606958 AGGGT-AAAATGGCAATTTTGGTAAAATTA
1 GGGGTCAAAATGG-AATTTTGGTAAAATCG
* * * *
29606987 GGGTTAAAAATAGAATTTT--TAAAAAGTTTG
1 GGGGTCAAAATGGAATTTTGGT-AAAA--TCG
** *
29607017 GCAGT-AAAATGGTAATTTTGGTGAAATCG
1 GGGGTCAAAATGG-AATTTTGGTAAAATCG
*
29607046 GGGG-CAAAATGGAATTTT-GTAAAACTTG
1 GGGGTCAAAATGGAATTTTGGTAAAA-TCG
*
29607074 GGGGTCAAAATGTAATTTT
1 GGGGTCAAAATGGAATTTT
29607093 TAGAAAGTTT
Statistics
Matches: 173, Mismatches: 28, Indels: 40
0.72 0.12 0.17
Matches are distributed among these distances:
27 12 0.07
28 51 0.29
29 68 0.39
30 35 0.20
31 6 0.03
32 1 0.01
ACGTcount: A:0.38, C:0.04, G:0.27, T:0.31
Consensus pattern (29 bp):
GGGGTCAAAATGGAATTTTGGTAAAATCG
Found at i:29607120 original size:30 final size:30
Alignment explanation
Indices: 29607075--29607183 Score: 103
Period size: 30 Copynumber: 3.6 Consensus size: 30
29607065 TAAAACTTGG
* *
29607075 GGGTCAAAATGTAATTTTTAGAAAGTTTTA
1 GGGTCAAAATATAATTTTTAAAAAGTTTTA
* **
29607105 GGGTTAAAATATAA-TTTTAAAGAAGTTTGG
1 GGGTCAAAATATAATTTTTAAA-AAGTTTTA
* * * *
29607135 GGGTCAAAATGTAGTTCTCAAAAAGTTTTA
1 GGGTCAAAATATAATTTTTAAAAAGTTTTA
* *
29607165 GTGTTAAAATATAATTTTT
1 GGGTCAAAATATAATTTTT
29607184 GGATAGTTTA
Statistics
Matches: 59, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
29 6 0.10
30 48 0.81
31 5 0.08
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.39
Consensus pattern (30 bp):
GGGTCAAAATATAATTTTTAAAAAGTTTTA
Found at i:29607120 original size:87 final size:85
Alignment explanation
Indices: 29606848--29607122 Score: 238
Period size: 87 Copynumber: 3.2 Consensus size: 85
29606838 ACTTAGGGGC
* * * *
29606848 AAAATGGTAATTTTGATGAAATCGAGGGTAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGT
1 AAAAT-GTAATTTTGGTGAAATCGAGGGTAAAATGGAATTTTGTAAAATT-GGGGGTAAAATAGT
* * * *
29606913 AATTTTTGGTAAA-ATCAAGGTT
64 AATTTTTAG-AAAGTTTAGGGTT
* * * * *
29606935 AAAATGGAATTATGG-AAAATTCGAGGGTAAAATGGCAATTTTGGTAAAATTAGGGTTAAAAATA
1 AAAATGTAATTTTGGTGAAA-TCGAGGGTAAAATGG-AATTTT-GTAAAATTGGGGGT-AAAATA
*
29606999 G-AATTTTTAAAAAGTTT-GGCAG-T
62 GTAATTTTTAGAAAGTTTAGG--GTT
* *
29607022 AAAATGGTAATTTTGGTGAAATCGGGGGCAAAATGGAATTTTGTAAAACTTGGGGGTCAAAAT-G
1 AAAAT-GTAATTTTGGTGAAATCGAGGGTAAAATGGAATTTTGTAAAA-TTGGGGGT-AAAATAG
29607086 TAATTTTTAGAAAGTTTTAGGGTT
63 TAATTTTTAGAAAG-TTTAGGGTT
*
29607110 AAAATATAATTTT
1 AAAATGTAATTTT
29607123 AAAGAAGTTT
Statistics
Matches: 150, Mismatches: 24, Indels: 28
0.74 0.12 0.14
Matches are distributed among these distances:
85 3 0.02
86 33 0.22
87 66 0.44
88 43 0.29
89 5 0.03
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.33
Consensus pattern (85 bp):
AAAATGTAATTTTGGTGAAATCGAGGGTAAAATGGAATTTTGTAAAATTGGGGGTAAAATAGTAA
TTTTTAGAAAGTTTAGGGTT
Found at i:29608961 original size:12 final size:12
Alignment explanation
Indices: 29608944--29609000 Score: 55
Period size: 11 Copynumber: 4.8 Consensus size: 12
29608934 TTAAATGTAT
29608944 TTTAAATTTAAA
1 TTTAAATTTAAA
29608956 TTTAAATTTAAA
1 TTTAAATTTAAA
* * *
29608968 -ATAAACTTAAT
1 TTTAAATTTAAA
*
29608979 TTTAAA-ATAAA
1 TTTAAATTTAAA
29608990 TTTAAACTTTA
1 TTTAAA-TTTA
29609001 TTGGGCCTAG
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
11 17 0.49
12 16 0.46
13 2 0.06
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:29608969 original size:7 final size:6
Alignment explanation
Indices: 29608944--29609000 Score: 55
Period size: 6 Copynumber: 9.7 Consensus size: 6
29608934 TTAAATGTAT
* * * *
29608944 TTTAAA TTTAAA TTTAAA TTTAAA -ATAAA CTTAAT TTTAAA -ATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
29608990 TTTAAA CTTTA
1 TTTAAA -TTTA
29609001 TTGGGCCTAG
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
5 8 0.20
6 29 0.71
7 4 0.10
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:29608972 original size:17 final size:17
Alignment explanation
Indices: 29608952--29609000 Score: 71
Period size: 17 Copynumber: 2.8 Consensus size: 17
29608942 ATTTTAAATT
29608952 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
29608969 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
29608986 TAAATTTAAACTTTA
1 TAAATTTAAA-TTTA
29609001 TTGGGCCTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 23 0.85
18 4 0.15
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:29616478 original size:47 final size:48
Alignment explanation
Indices: 29616409--29616517 Score: 175
Period size: 47 Copynumber: 2.3 Consensus size: 48
29616399 ATTAAGTTTG
* *
29616409 ATGAATTCATCAAGTCCATCTCAATAGGATCACCC-AAACTTAGGAAT
1 ATGAATTCATTAAGTCCATCTCAATAGGATCACCCAAAACTCAGGAAT
* *
29616456 ATGAATTCATTAAGTTCGTCTCAATAGGATCACCCAAAACTCAGGAAT
1 ATGAATTCATTAAGTCCATCTCAATAGGATCACCCAAAACTCAGGAAT
29616504 ATGAATTCATTAAG
1 ATGAATTCATTAAG
29616518 AATAAGAAAC
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
47 32 0.56
48 25 0.44
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.28
Consensus pattern (48 bp):
ATGAATTCATTAAGTCCATCTCAATAGGATCACCCAAAACTCAGGAAT
Found at i:29619115 original size:14 final size:15
Alignment explanation
Indices: 29619098--29619157 Score: 68
Period size: 17 Copynumber: 3.9 Consensus size: 15
29619088 ATTTATAATT
29619098 ACTTA-TAAACTAGA
1 ACTTATTAAACTAGA
*
29619112 ACTTATTAAACTAAA
1 ACTTATTAAACTAGA
29619127 ACCCTTATTAAACTAGA
1 A--CTTATTAAACTAGA
*
29619144 ATTTTATTAAACTA
1 A-CTTATTAAACTA
29619158 AAGTTTACAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
14 5 0.13
15 9 0.23
16 11 0.28
17 14 0.36
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.35
Consensus pattern (15 bp):
ACTTATTAAACTAGA
Found at i:29619144 original size:32 final size:32
Alignment explanation
Indices: 29619099--29619159 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 32
29619089 TTTATAATTA
29619099 CTTATAAACTAGAA-CTTATTAAACTAAAACC
1 CTTATAAACTAGAATCTTATTAAACTAAAACC
*
29619130 CTTATTAAACTAGAATTTTATTAAACTAAA
1 CTTA-TAAACTAGAATCTTATTAAACTAAA
29619160 GTTTACATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 4 0.15
32 10 0.37
33 13 0.48
ACGTcount: A:0.48, C:0.15, G:0.03, T:0.34
Consensus pattern (32 bp):
CTTATAAACTAGAATCTTATTAAACTAAAACC
Found at i:29620871 original size:58 final size:58
Alignment explanation
Indices: 29620794--29621207 Score: 464
Period size: 58 Copynumber: 7.1 Consensus size: 58
29620784 TGACTTTCAA
* * * * * *
29620794 GGGTGAAAAT-GTAATTTTTGATGAAACCGAGGTTAAAAATGGAATTTTAGAGAGTTTGG
1 GGGT-AAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAG
* * * * *
29620853 GGGTAAAATAGTAATTTTGGTGGTAGAATTGGGGTTAAGAATAGG-GTTTTGAAAAGTTTAG
1 GGGTAAAATGGTAATTTTGGT-G-A-AATCGGGGTTAAAAAT-GGAATTTTGGAAAGTTTAG
* * *
29620914 GGGTAAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAG-TTCG
1 GGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAG
* *
29620971 AGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTGAAAAATGG-ATTTTGGAAAGTTTAA
1 -GGGTAAAATGGTAA-TTTTGGTGAAATCGGGGTT-AAAAATGGAATTTTGGAAAGTTTAG
* * * * *
29621031 GGGTAAAACGGTAATTTTTGGTGAAATTGGGGTTAAAAATGGGATTTT-GAAAATTTTG
1 GGGTAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAG
*
29621089 GGGTAAAATGGTGATTTTGGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAG
1 GGGTAAAATGGTAATTTT-GGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAG
*
29621148 GGGTAAAATGGTAATTTTGGGTGAAATCGGGGTT-AAAATGGAATTTTAGAAAGTTT-G
1 GGGTAAAATGGTAATTTT-GGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAG
29621205 GGG
1 GGG
29621208 ACTAGAGAGC
Statistics
Matches: 307, Mismatches: 35, Indels: 28
0.83 0.09 0.08
Matches are distributed among these distances:
57 13 0.04
58 122 0.40
59 115 0.37
60 12 0.04
61 43 0.14
62 2 0.01
ACGTcount: A:0.34, C:0.02, G:0.31, T:0.33
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAG
Found at i:29621093 original size:117 final size:116
Alignment explanation
Indices: 29620794--29621207 Score: 489
Period size: 117 Copynumber: 3.5 Consensus size: 116
29620784 TGACTTTCAA
* * *
29620794 GGGTGAAAAT-GTAATTTTTGATGAAACCGAGGTTAAAAATGGAATTTT-AGAGAGTTTGGGGGT
1 GGGT-AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGA-AAAGTTT-GGGGT
* * * * *
29620857 AAAATAGTAA-TTTTGGTGGTAGAATTGGGGTTAAGAATAGGGTTTTGAAAAGTTTAG
63 AAAATGGTAATTTTTGGT-G-A-AATCGGGGTTAAAAAT-GGATTTTGGAAAGTTTAG
* * *
29620914 GGGTAAAATGGTAA-TTTTGGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAGTTCGAGGGTAA
1 GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGAAAAGTTTG-GGGTAA
* *
29620978 AATGGTAATTTTTGATGAAATCGGGGTTGAAAAATGGATTTTGGAAAGTTTAA
65 AATGGTAATTTTTGGTGAAATCGGGGTT-AAAAATGGATTTTGGAAAGTTTAG
* * * * *
29621031 GGGTAAAACGGTAATTTTTGGTGAAATTGGGGTTAAAAATGGGATTTTGAAAATTTTGGGGTAAA
1 GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGAAAAGTTTGGGGTAAA
* *
29621096 ATGGTGATTTTGGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAG
66 ATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGG-ATTTTGGAAAGTTTAG
* *
29621148 GGGTAAAATGGTAATTTTGGGTGAAATCGGGGTT-AAAATGGAATTTT-AGAAAGTTTGGGG
1 GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGA-AAAGTTTGGGG
29621208 ACTAGAGAGC
Statistics
Matches: 258, Mismatches: 28, Indels: 20
0.84 0.09 0.07
Matches are distributed among these distances:
115 1 0.00
116 30 0.12
117 114 0.44
118 45 0.17
119 54 0.21
120 14 0.05
ACGTcount: A:0.34, C:0.02, G:0.31, T:0.33
Consensus pattern (116 bp):
GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGAAAAGTTTGGGGTAAA
ATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGATTTTGGAAAGTTTAG
Found at i:29622033 original size:20 final size:19
Alignment explanation
Indices: 29622000--29622038 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
29621990 TATCCCTTAA
*
29622000 AACCTTTTACTCTTATTCTT
1 AACCTGTTACTCTT-TTCTT
*
29622020 AACCTGTTATTCTTTTCTT
1 AACCTGTTACTCTTTTCTT
29622039 TCGTTGGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.18, C:0.23, G:0.03, T:0.56
Consensus pattern (19 bp):
AACCTGTTACTCTTTTCTT
Found at i:29622223 original size:3 final size:3
Alignment explanation
Indices: 29622200--29622281 Score: 78
Period size: 3 Copynumber: 26.7 Consensus size: 3
29622190 TTTCCCTTTT
* * *
29622200 TTA TT- TTA TTA -TG TTA TTTA TTA TTA TTAA TAA CTTCA TTA TTA TTG
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TT-A TTA -TT-A TTA TTA TTA
*
29622247 CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
29622282 CATAAATTAA
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
2 3 0.05
3 53 0.82
4 8 0.12
5 1 0.02
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:29622913 original size:27 final size:27
Alignment explanation
Indices: 29622847--29622916 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
29622837 CATTGGGCCT
*
29622847 ATTTGGGCCA-TTGTAATTGGGCCTTCA
1 ATTTGGG-CATTTGTAATTGGCCCTTCA
*
29622874 ATTTGGATC-TTTGTAATTAGGCCCTT-A
1 ATTTGG-GCATTTGTAATT-GGCCCTTCA
29622901 ATTTGGGCATTTGTAA
1 ATTTGGGCATTTGTAA
29622917 ATGGATTTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
26 1 0.03
27 29 0.81
28 6 0.17
ACGTcount: A:0.21, C:0.14, G:0.23, T:0.41
Consensus pattern (27 bp):
ATTTGGGCATTTGTAATTGGCCCTTCA
Found at i:29623003 original size:17 final size:18
Alignment explanation
Indices: 29622981--29623021 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
29622971 TTTCAAATAT
*
29622981 TTTAAATTTAA-AATGAA
1 TTTAAATTTAATAATAAA
29622998 TTTAAATTTAATAATAAA
1 TTTAAATTTAATAATAAA
29623016 TTTAAA
1 TTTAAA
29623022 CCTAAAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
TTTAAATTTAATAATAAA
Found at i:29623548 original size:25 final size:25
Alignment explanation
Indices: 29623520--29623567 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
29623510 TTATTAAGCA
29623520 TTAAAATAAA-ATAAAATAATATATT
1 TTAAAA-AAATATAAAATAATATATT
*
29623545 TTAAAAAAATTTAAAATAATATA
1 TTAAAAAAATATAAAATAATATA
29623568 AGGTCTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 3 0.14
25 18 0.86
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
TTAAAAAAATATAAAATAATATATT
Found at i:29624225 original size:7 final size:7
Alignment explanation
Indices: 29624215--29624244 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
29624205 TTAATAAATA
29624215 ATATTAT
1 ATATTAT
29624222 ATATTAT
1 ATATTAT
29624229 ATATTAT
1 ATATTAT
29624236 ATATTAT
1 ATATTAT
29624243 AT
1 AT
29624245 GCATTAAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATATTAT
Found at i:29637527 original size:18 final size:18
Alignment explanation
Indices: 29637494--29637528 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29637484 TTGCAATTTG
*
29637494 TCAAAATGTTCACAATAT
1 TCAAAATGGTCACAATAT
*
29637512 TCAAAATGGTCCCAATA
1 TCAAAATGGTCACAATA
29637529 CTAACACTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.29
Consensus pattern (18 bp):
TCAAAATGGTCACAATAT
Found at i:29639951 original size:26 final size:26
Alignment explanation
Indices: 29639902--29639951 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
29639892 TGGTTTCCTT
*
29639902 AATTTTAGTTTCTTATTCTTCAAGTA
1 AATTTTAGTTTCTTATTCTACAAGTA
*
29639928 AATTTTGGTTTCTTAGTT-TACAAG
1 AATTTTAGTTTCTTA-TTCTACAAG
29639952 AATAAACCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 19 0.90
27 2 0.10
ACGTcount: A:0.26, C:0.10, G:0.12, T:0.52
Consensus pattern (26 bp):
AATTTTAGTTTCTTATTCTACAAGTA
Found at i:29640112 original size:29 final size:30
Alignment explanation
Indices: 29640048--29640113 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
29640038 CTCTCATTCT
* *
29640048 AATGAG-TCTAAGGTTAGGAGCTCCATTTG
1 AATGAGTTCTAAGGTTAGGAGCTCCACTTC
*
29640077 ACT-AGTTCTAAGGTTAGGAGCTCC-CTTC
1 AATGAGTTCTAAGGTTAGGAGCTCCACTTC
29640105 AATGAGTTC
1 AATGAGTTC
29640114 CATACGTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
28 6 0.19
29 25 0.81
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (30 bp):
AATGAGTTCTAAGGTTAGGAGCTCCACTTC
Found at i:29652596 original size:23 final size:24
Alignment explanation
Indices: 29652556--29652608 Score: 83
Period size: 23 Copynumber: 2.2 Consensus size: 24
29652546 TTTTTGGGGT
29652556 TGAGAGCTAGAAACATGGAGA-GA
1 TGAGAGCTAGAAACATGGAGAGGA
29652579 TGGAGAGCTA-AAACATGGAGAGGA
1 T-GAGAGCTAGAAACATGGAGAGGA
29652603 TGAGAG
1 TGAGAG
29652609 TTTTTGCAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
23 17 0.61
24 11 0.39
ACGTcount: A:0.42, C:0.08, G:0.38, T:0.13
Consensus pattern (24 bp):
TGAGAGCTAGAAACATGGAGAGGA
Found at i:29667336 original size:25 final size:25
Alignment explanation
Indices: 29667286--29667335 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
29667276 TTCACACAAG
*
29667286 TCTTTTCCCTATTTCTCTCTTCTTT
1 TCTTCTCCCTATTTCTCTCTTCTTT
* *
29667311 TCTTCTCCTTATTTTTCT-TTCTTT
1 TCTTCTCCCTATTTCTCTCTTCTTT
29667335 T
1 T
29667336 TTACGGCTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.04, C:0.28, G:0.00, T:0.68
Consensus pattern (25 bp):
TCTTCTCCCTATTTCTCTCTTCTTT
Found at i:29669421 original size:3 final size:3
Alignment explanation
Indices: 29669413--29669456 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
29669403 TTATGTGTGT
* *
29669413 TTA TTA TTA TTA TTA TTG TCA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
29669457 TTTAATAGCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:29670440 original size:15 final size:16
Alignment explanation
Indices: 29670422--29670454 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
29670412 ATGTAATTAA
29670422 TTAAAATGATAT-CAT
1 TTAAAATGATATACAT
*
29670437 TTAATATGATATACAT
1 TTAAAATGATATACAT
29670453 TT
1 TT
29670455 TACTATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (16 bp):
TTAAAATGATATACAT
Found at i:29675606 original size:60 final size:62
Alignment explanation
Indices: 29675468--29675618 Score: 200
Period size: 60 Copynumber: 2.5 Consensus size: 62
29675458 GCATTTGGTA
* * *
29675468 ACTCACGATGACACAAAGTCATCGGACCTTTAATCCGTAATAGGATTCACTTCTCATTTAAT
1 ACTCACGATGACACATAGTCATCGGACCTATAATCCGTAATAGGATTCACTTCTCATTTAAC
* * *
29675530 ACTCACGATGACACATAGTCATAGGACCTCATAATCTGTAA-ATGATTCA-TT-TCATTTAAC
1 ACTCACGATGACACATAGTCATCGGACCT-ATAATCCGTAATAGGATTCACTTCTCATTTAAC
* *
29675590 ACTTACGATGACACATAGTTATCGGACCT
1 ACTCACGATGACACATAGTCATCGGACCT
29675619 TTTTCATTTA
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
60 34 0.43
61 2 0.03
62 34 0.43
63 9 0.11
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.30
Consensus pattern (62 bp):
ACTCACGATGACACATAGTCATCGGACCTATAATCCGTAATAGGATTCACTTCTCATTTAAC
Found at i:29679844 original size:36 final size:36
Alignment explanation
Indices: 29679760--29679860 Score: 132
Period size: 36 Copynumber: 2.8 Consensus size: 36
29679750 TCGTTATTCG
* *
29679760 TTTTACTCCCTGTTGACCCTAAAAGTCATGATGCTCG
1 TTTTACTCCCTGTTGACCC-AAAGGTCATGATGCTCA
* *
29679797 TTTTACT-CCTGTTGACCCAAAGGTTATTATGCTCA
1 TTTTACTCCCTGTTGACCCAAAGGTCATGATGCTCA
* *
29679832 TTTTTCTCCCTGTTTACCCAAAGGTCATG
1 TTTTACTCCCTGTTGACCCAAAGGTCATG
29679861 CCTGTTACCA
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
35 19 0.35
36 29 0.53
37 7 0.13
ACGTcount: A:0.21, C:0.26, G:0.15, T:0.39
Consensus pattern (36 bp):
TTTTACTCCCTGTTGACCCAAAGGTCATGATGCTCA
Found at i:29685618 original size:6 final size:6
Alignment explanation
Indices: 29685598--29685656 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
29685588 TTAAATGGGT
* * *
29685598 TTTAAA TTT-AT TTTAAA TTTAAA TTTACTCA TTTAAA TTT-AC TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA
*
29685646 TTTAAG TTTAA
1 TTTAAA TTTAA
29685657 TCAAATTTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
5 8 0.19
6 29 0.69
8 5 0.12
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (6 bp):
TTTAAA
Done.