Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 147 of 216
Found at i:46506093 original size:132 final size:132
Alignment explanation
Indices: 46505853--46506117 Score: 440
Period size: 132 Copynumber: 2.0 Consensus size: 132
46505843 AATAATAGCC
* * *
46505853 ACAATAACTGCAACACTCTTTTCAACCACAACCTGAAATGGTTCGTCCGACTCAACTTGCTTCAC
1 ACAATAACTGCAACACCCTTTTCAACCACAACCTGAAATGGTTCGCCCGACTCAACCTGCTTCAC
* *
46505918 CTGTGCCTACTACGAATCCCCATAAGGTTGATCCTATTCGAGAAATTCAAAAAAGAGGTGTCAAG
66 CTGTGCCTACTACGAATCCCCATAAAGTTGATCCTATTCGAGAAATTCAAAAAAGAGGCGTCAAG
46505983 GA
131 GA
*
46505985 ACAATAACTGCAACACCCTTTTCAACCACAACCTGAAGTGGTTCGCCCGACTCAACCTGCTTCAC
1 ACAATAACTGCAACACCCTTTTCAACCACAACCTGAAATGGTTCGCCCGACTCAACCTGCTTCAC
* * * *
46506050 TTGTGCCTACTATGACTCCCCATAAAGTTGATCCTATTTGAGAAATTCAAAAAAGAGGCGTCAAG
66 CTGTGCCTACTACGAATCCCCATAAAGTTGATCCTATTCGAGAAATTCAAAAAAGAGGCGTCAAG
46506115 GA
131 GA
46506117 A
1 A
46506118 TTCATTGGTG
Statistics
Matches: 123, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
132 123 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (132 bp):
ACAATAACTGCAACACCCTTTTCAACCACAACCTGAAATGGTTCGCCCGACTCAACCTGCTTCAC
CTGTGCCTACTACGAATCCCCATAAAGTTGATCCTATTCGAGAAATTCAAAAAAGAGGCGTCAAG
GA
Found at i:46510462 original size:41 final size:39
Alignment explanation
Indices: 46510405--46510535 Score: 131
Period size: 40 Copynumber: 3.3 Consensus size: 39
46510395 CGATTTCGAG
46510405 TCGATGAGACACTGGGTGTCAATTTACTACTTTGGATTAAT
1 TCGATGAGACACTGGGTGTCAATTTA-TACTTTGGATT-AT
* * * * *
46510446 TCGATGAGGCACTGGGTGCCAA-TT-TACGTTGGTTTAG
1 TCGATGAGACACTGGGTGTCAATTTATACTTTGGATTAT
* * *
46510483 TCGATGAGACACTGGGAGTCAATTTATTACTTCGAATTAT
1 TCGATGAGACACTGGGTGTCAATTTA-TACTTTGGATTAT
* *
46510523 TTGATGAGGCACT
1 TCGATGAGACACT
46510536 CAAACTGGTG
Statistics
Matches: 72, Mismatches: 15, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
37 20 0.28
38 11 0.15
40 21 0.29
41 20 0.28
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.34
Consensus pattern (39 bp):
TCGATGAGACACTGGGTGTCAATTTATACTTTGGATTAT
Found at i:46510496 original size:37 final size:38
Alignment explanation
Indices: 46510403--46510508 Score: 124
Period size: 37 Copynumber: 2.7 Consensus size: 38
46510393 TTCGATTTCG
*
46510403 AGTCGATGAGACACTGGGTGTCAATTTACTACTTTGGATTA
1 AGTCGATGAGACACTGGGTGTCAA-TT--TACGTTGGATTA
* * * *
46510444 ATTCGATGAGGCACTGGGTGCCAATTTACGTTGG-TTT
1 AGTCGATGAGACACTGGGTGTCAATTTACGTTGGATTA
*
46510481 AGTCGATGAGACACTGGGAGTCAATTTA
1 AGTCGATGAGACACTGGGTGTCAATTTA
46510509 TTACTTCGAA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
37 26 0.46
38 7 0.12
40 2 0.04
41 21 0.38
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.32
Consensus pattern (38 bp):
AGTCGATGAGACACTGGGTGTCAATTTACGTTGGATTA
Found at i:46513134 original size:39 final size:40
Alignment explanation
Indices: 46513085--46513179 Score: 115
Period size: 39 Copynumber: 2.4 Consensus size: 40
46513075 TCTAAAGGGG
*
46513085 TACCAAAATTTCTAACACG-TTACCAAAATCTCTAATGGA
1 TACCAAAATTTCTAACACGAATACCAAAATCTCTAATGGA
* *
46513124 TACCAAAATTTCCT-A-ATGAATGCCAAAATCTCTAATGGA
1 TACCAAAATTT-CTAACACGAATACCAAAATCTCTAATGGA
* *
46513163 TACCTACATTTCTAACA
1 TACCAAAATTTCTAACA
46513180 TATACCTACA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
38 4 0.09
39 40 0.85
40 3 0.06
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.29
Consensus pattern (40 bp):
TACCAAAATTTCTAACACGAATACCAAAATCTCTAATGGA
Found at i:46513141 original size:20 final size:19
Alignment explanation
Indices: 46513105--46513166 Score: 88
Period size: 19 Copynumber: 3.2 Consensus size: 19
46513095 TCTAACACGT
46513105 TACCAAAATCTCTAATGGA
1 TACCAAAATCTCTAATGGA
* *
46513124 TACCAAAATTTCCTAATGAA
1 TACCAAAATCT-CTAATGGA
*
46513144 TGCCAAAATCTCTAATGGA
1 TACCAAAATCTCTAATGGA
46513163 TACC
1 TACC
46513167 TACATTTCTA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
19 20 0.56
20 16 0.44
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27
Consensus pattern (19 bp):
TACCAAAATCTCTAATGGA
Found at i:46513176 original size:19 final size:19
Alignment explanation
Indices: 46513024--46513177 Score: 96
Period size: 20 Copynumber: 7.8 Consensus size: 19
46513014 CTTATGCAAC
* *
46513024 ATACTAAAATTTCTAAAGG
1 ATACCAAAATTTCTAATGG
*
46513043 TATACCAAAATATT-TGAA-GAA
1 -ATACCAAAAT-TTCT-AATG-G
* *
46513064 ATATCAAAATTTCTAAAGGG
1 ATACCAAAATTTCT-AATGG
* **
46513084 GTACCAAAATTTCTAACACG
1 ATACCAAAATTTCTAA-TGG
* *
46513104 TTACCAAAATCTCTAATGG
1 ATACCAAAATTTCTAATGG
*
46513123 ATACCAAAATTTCCTAATGA
1 ATACCAAAATTT-CTAATGG
* *
46513143 ATGCCAAAATCTCTAATGG
1 ATACCAAAATTTCTAATGG
* *
46513162 ATACCTACATTTCTAA
1 ATACCAAAATTTCTAA
46513178 CATATACCTA
Statistics
Matches: 104, Mismatches: 23, Indels: 15
0.73 0.16 0.11
Matches are distributed among these distances:
19 33 0.32
20 66 0.63
21 5 0.05
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.30
Consensus pattern (19 bp):
ATACCAAAATTTCTAATGG
Found at i:46513565 original size:19 final size:19
Alignment explanation
Indices: 46513471--46513603 Score: 83
Period size: 19 Copynumber: 7.0 Consensus size: 19
46513461 TCTAACATCT
* *
46513471 TCCATTAAAAATTTGGGTA
1 TCCATTAGAAATTTTGGTA
* *
46513490 TCCCTTACAAATTTTGGT-
1 TCCATTAGAAATTTTGGTA
* *
46513508 TCCCGTTAG-AAGTTTGGTA
1 T-CCATTAGAAATTTTGGTA
* * *
46513527 TCTATTTGAAGTTCTT-GTA
1 TCCATTAGAAATT-TTGGTA
46513546 TCCATTAGAAATTTTGGTA
1 TCCATTAGAAATTTTGGTA
*** ** *
46513565 TTTTGTTACCAATTTTTGTA
1 -TCCATTAGAAATTTTGGTA
46513585 TCCATTAGAAATTTTGGTA
1 TCCATTAGAAATTTTGGTA
46513604 CAATTTATTG
Statistics
Matches: 82, Mismatches: 26, Indels: 12
0.68 0.22 0.10
Matches are distributed among these distances:
18 15 0.18
19 52 0.63
20 15 0.18
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (19 bp):
TCCATTAGAAATTTTGGTA
Found at i:46514307 original size:20 final size:20
Alignment explanation
Indices: 46514284--46514328 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
46514274 TGCATTATAG
*
46514284 ATTTTAGTA-TTAGTTAAAA
1 ATTTTAGTATTTAATTAAAA
*
46514303 AATTTAGTATTTAATTAAAA
1 ATTTTAGTATTTAATTAAAA
46514323 ATTTTA
1 ATTTTA
46514329 AAAATTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (20 bp):
ATTTTAGTATTTAATTAAAA
Found at i:46517346 original size:20 final size:20
Alignment explanation
Indices: 46517303--46517346 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
46517293 CAAAACCATG
* *
46517303 AACCCTAAACCCAAACTTTT
1 AACCCTAAACCCAAACTCTC
46517323 AACCCTAAACCTCAAA-TCTC
1 AACCCTAAACC-CAAACTCTC
46517343 AACC
1 AACC
46517347 TCAAACCCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.41, C:0.39, G:0.00, T:0.20
Consensus pattern (20 bp):
AACCCTAAACCCAAACTCTC
Found at i:46517419 original size:7 final size:7
Alignment explanation
Indices: 46517407--46517511 Score: 51
Period size: 7 Copynumber: 15.3 Consensus size: 7
46517397 TAATTCAAGA
46517407 TTTAGGG
1 TTTAGGG
46517414 TTTAGGG
1 TTTAGGG
*
46517421 TTT-GGA
1 TTTAGGG
*
46517427 TTTAGAG
1 TTTAGGG
*
46517434 TTTAAGG
1 TTTAGGG
*
46517441 TTTCA-AG
1 TTT-AGGG
**
46517448 TTTTTGG
1 TTTAGGG
46517455 TTCT-GGG
1 TT-TAGGG
*
46517462 TTTAGAG
1 TTTAGGG
*
46517469 TTTAAGG
1 TTTAGGG
46517476 TTTA-GG
1 TTTAGGG
46517482 TTT-GGAG
1 TTTAGG-G
46517489 TTT-GGG
1 TTTAGGG
*
46517495 ATTTAGGA
1 -TTTAGGG
46517503 TTTAGGG
1 TTTAGGG
46517510 TT
1 TT
46517512 CTGAGTTCGA
Statistics
Matches: 75, Mismatches: 14, Indels: 18
0.70 0.13 0.17
Matches are distributed among these distances:
6 13 0.17
7 58 0.77
8 4 0.05
ACGTcount: A:0.18, C:0.02, G:0.33, T:0.47
Consensus pattern (7 bp):
TTTAGGG
Found at i:46517430 original size:20 final size:20
Alignment explanation
Indices: 46517405--46517443 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
46517395 TTTAATTCAA
* *
46517405 GATTTAGGGTTTAGGGTTTG
1 GATTTAGAGTTTAAGGTTTG
46517425 GATTTAGAGTTTAAGGTTT
1 GATTTAGAGTTTAAGGTTT
46517444 CAAGTTTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.46
Consensus pattern (20 bp):
GATTTAGAGTTTAAGGTTTG
Found at i:46517489 original size:20 final size:20
Alignment explanation
Indices: 46517407--46517491 Score: 57
Period size: 20 Copynumber: 4.2 Consensus size: 20
46517397 TAATTCAAGA
*
46517407 TTTAGGGTTTAGGGTTTGGA-
1 TTTAAGGTTTA-GGTTTGGAG
**
46517427 TTT-AGAGTTTAAGGTTTCAAG
1 TTTAAG-GTTT-AGGTTTGGAG
** * *
46517448 TTTTTGGTTCTGGGTTTAGAG
1 TTTAAGGTT-TAGGTTTGGAG
46517469 TTTAAGGTTTAGGTTTGGAG
1 TTTAAGGTTTAGGTTTGGAG
46517489 TTT
1 TTT
46517492 GGGATTTAGG
Statistics
Matches: 49, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
19 1 0.02
20 25 0.51
21 21 0.43
22 2 0.04
ACGTcount: A:0.18, C:0.02, G:0.32, T:0.48
Consensus pattern (20 bp):
TTTAAGGTTTAGGTTTGGAG
Found at i:46524105 original size:14 final size:14
Alignment explanation
Indices: 46524086--46524113 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
46524076 CATATTGACT
46524086 CCTAATCTAAATCA
1 CCTAATCTAAATCA
46524100 CCTAATCTAAATCA
1 CCTAATCTAAATCA
46524114 TTATTCAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.29, G:0.00, T:0.29
Consensus pattern (14 bp):
CCTAATCTAAATCA
Found at i:46528193 original size:24 final size:24
Alignment explanation
Indices: 46528151--46528202 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
46528141 AATCAAAGTC
** *
46528151 AAATATATTATGTTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
46528175 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
46528199 AAAT
1 AAAT
46528203 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:46531829 original size:39 final size:40
Alignment explanation
Indices: 46531752--46531858 Score: 119
Period size: 40 Copynumber: 2.7 Consensus size: 40
46531742 TAGCTCCTCG
* * *
46531752 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATATTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATATAAACTCA
* *
46531792 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATATAAACTCA
**
46531831 CACGAATGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
46531859 ATTAGTATCT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
39 25 0.43
40 33 0.57
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATATAAACTCA
Found at i:46531847 original size:40 final size:39
Alignment explanation
Indices: 46531795--46531925 Score: 181
Period size: 40 Copynumber: 3.3 Consensus size: 39
46531785 TAACTCATTC
* *
46531795 AATGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAAAACTCGCACA
* *
46531835 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTA-AAACTCGCACA
*
46531875 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAA-AACTCGCACA
*
46531915 AATACCTTCGG
1 AATGCCTTCGG
46531926 ATCTTACGTC
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
39 3 0.04
40 77 0.96
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGAATTAAAACTCGCACA
Found at i:46531857 original size:79 final size:80
Alignment explanation
Indices: 46531758--46531925 Score: 189
Period size: 80 Copynumber: 2.1 Consensus size: 80
46531748 CTCGTTCAAG
* * * ** * *
46531758 TGCCTTCGGGACATAGCCCGG-TTATATTAACTCATTC-AATGCCTTCGGGACTTAACCCGGATT
1 TGCCTTCGGGACATAACCCGGAAT-TAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGA-A
*
46531821 TTAA-AACTCGCACGAA
64 TTAATAACTCGCACAAA
* * *
46531837 TGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAGGCCTTCGGGACTTAACCCGGAATT
1 TGCCTTCGGGACATAACCCGGAATTAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGAATT
46531902 AATAACTCGCACAAA
66 AATAACTCGCACAAA
*
46531917 TACCTTCGG
1 TGCCTTCGG
46531926 ATCTTACGTC
Statistics
Matches: 74, Mismatches: 12, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
79 31 0.42
80 43 0.58
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (80 bp):
TGCCTTCGGGACATAACCCGGAATTAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGAATT
AATAACTCGCACAAA
Found at i:46539704 original size:39 final size:40
Alignment explanation
Indices: 46539627--46539773 Score: 120
Period size: 40 Copynumber: 3.7 Consensus size: 40
46539617 TAGCTCCTCG
* * *
46539627 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
* *
46539667 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** * * * *
46539706 CACGAATGCCTTCGGGACTTAACCCGGAAT-TAGTATCTCG
1 TTC-AATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** *
46539746 CACAAAGGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
46539774 ATTAATAACT
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 27 0.29
40 65 0.71
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
Found at i:46539784 original size:80 final size:80
Alignment explanation
Indices: 46539673--46539853 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
46539663 CTCATTCAAT
* * *
46539673 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
46539736 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
46539752 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
46539816 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
46539833 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
46539854 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:46539813 original size:40 final size:40
Alignment explanation
Indices: 46539670--46539853 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
46539660 TAACTCATTC
* *
46539670 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
46539710 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
46539750 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
46539790 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
46539831 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
46539854 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:46544142 original size:9 final size:9
Alignment explanation
Indices: 46544129--46544186 Score: 89
Period size: 9 Copynumber: 6.4 Consensus size: 9
46544119 TTTGGTTAAA
*
46544129 AATTAACCA
1 AATTAACCG
46544138 AATTAACCG
1 AATTAACCG
46544147 AATTAACCG
1 AATTAACCG
*
46544156 AATTACCCG
1 AATTAACCG
46544165 AATTAACCG
1 AATTAACCG
*
46544174 AATTAACCA
1 AATTAACCG
46544183 AATT
1 AATT
46544187 GAATCACTAC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 45 1.00
ACGTcount: A:0.47, C:0.22, G:0.07, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:46544336 original size:18 final size:18
Alignment explanation
Indices: 46544293--46544336 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
46544283 TAATTTTATG
**
46544293 ATTGGGTTGGGTTAGGTA
1 ATTGGGTTGGGTTAAATA
*
46544311 ATTTGGTTGGGTTAAATA
1 ATTGGGTTGGGTTAAATA
*
46544329 CTTGGGTT
1 ATTGGGTT
46544337 TAGATTGGGT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.18, C:0.02, G:0.36, T:0.43
Consensus pattern (18 bp):
ATTGGGTTGGGTTAAATA
Found at i:46546490 original size:64 final size:64
Alignment explanation
Indices: 46546363--46546494 Score: 158
Period size: 64 Copynumber: 2.0 Consensus size: 64
46546353 TTACCGTAAA
* * *** *
46546363 ATAAAAAATAGAAATCTTCATTTTTTTAAAAAAAATTGATAAAATTATGTTGATTTGTTTTTCAT
1 ATAAAAAATAGAAATATTCATTTTTTT---AAAAAGTGATAAAATTATGGCCATGTGTTTTTCAT
46546428 TC
63 TC
*
46546430 ATAAAAAATAGAAATTATTCATTTTTTT-AAAAGTGATAGAATTATGGCCATGTGTTTTTCATTC
1 ATAAAAAATAGAAA-TATTCATTTTTTTAAAAAGTGATAAAATTATGGCCATGTGTTTTTCATTC
46546494 A
1 A
46546495 ATACGTTGTT
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
64 31 0.54
67 14 0.25
68 12 0.21
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (64 bp):
ATAAAAAATAGAAATATTCATTTTTTTAAAAAGTGATAAAATTATGGCCATGTGTTTTTCATTC
Found at i:46548383 original size:20 final size:20
Alignment explanation
Indices: 46548346--46548383 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
46548336 TTTTTCTTTC
*
46548346 TTTATATATATATTAAATAA
1 TTTATATATATATAAAATAA
46548366 TTTATATCATATA-AAAAT
1 TTTATAT-ATATATAAAAT
46548384 TAAATATGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTATATATATATAAAATAA
Found at i:46576759 original size:51 final size:50
Alignment explanation
Indices: 46576612--46576796 Score: 217
Period size: 51 Copynumber: 3.6 Consensus size: 50
46576602 GGTGGTTCCG
* * *
46576612 CACATAGTAGCCTACACTTAGTACTGCACATGTGACCAATACCATCCGGTA
1 CACATAGTAGCCTACACATAGTACTACACATGTGACCAA-ACTATCCGGTA
* * *
46576663 CACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAAGCTATCCGGTA
1 CACATAGTAGCCTACACATAGTACTACACATGTGACCAAA-CTATCCGGTA
* * ***
46576714 CACATAGTAGCCTGCACTTAGTACTACACATGTGACCATAACTATCTTATA
1 CACATAGTAGCCTACACATAGTACTACACATGTGACCA-AACTATCCGGTA
* * *
46576765 CTCATAGTAGCATACGCATAGTACTACACATG
1 CACATAGTAGCCTACACATAGTACTACACATG
46576797 AGTTCTCATG
Statistics
Matches: 115, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
50 1 0.01
51 112 0.97
52 2 0.02
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (50 bp):
CACATAGTAGCCTACACATAGTACTACACATGTGACCAAACTATCCGGTA
Found at i:46582073 original size:9 final size:9
Alignment explanation
Indices: 46582059--46582089 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
46582049 GTTAAACGAA
46582059 TCGAGTTAT
1 TCGAGTTAT
*
46582068 TCGAGTTAA
1 TCGAGTTAT
46582077 TCGAGTTAT
1 TCGAGTTAT
46582086 TCGA
1 TCGA
46582090 ATCAACTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:46582159 original size:9 final size:9
Alignment explanation
Indices: 46582142--46582178 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
46582132 TGAGTTTTCA
46582142 AATTCGAAT
1 AATTCGAAT
*
46582151 AACTCGAAT
1 AATTCGAAT
46582160 AATTCGAAT
1 AATTCGAAT
46582169 AATTCGAAT
1 AATTCGAAT
46582178 A
1 A
46582179 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:46582263 original size:30 final size:31
Alignment explanation
Indices: 46582229--46582288 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
46582219 ACCTTTTTAT
*
46582229 TTTTCCCTTAAAACTTTTACT-TCTTCCCAC
1 TTTTCCCCTAAAACTTTTACTCTCTTCCCAC
*
46582259 TTTTCCCCTAAAACTTTTATTCTCTTCCCA
1 TTTTCCCCTAAAACTTTTACTCTCTTCCCA
46582289 TCCCACCTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 19 0.70
31 8 0.30
ACGTcount: A:0.20, C:0.33, G:0.00, T:0.47
Consensus pattern (31 bp):
TTTTCCCCTAAAACTTTTACTCTCTTCCCAC
Found at i:46585339 original size:40 final size:40
Alignment explanation
Indices: 46585102--46585325 Score: 287
Period size: 40 Copynumber: 5.6 Consensus size: 40
46585092 CGAATGATGT
* * * *
46585102 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* *
46585142 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
46585182 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
46585220 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
46585261 CCGGGCTATGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
46585301 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
46585326 AACGAGTAGC
Statistics
Matches: 166, Mismatches: 11, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
39 35 0.21
40 121 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:46585347 original size:119 final size:119
Alignment explanation
Indices: 46585101--46585358 Score: 301
Period size: 119 Copynumber: 2.2 Consensus size: 119
46585091 TCGAATGATG
* *
46585101 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
* **
46585166 GTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
66 GTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
* * * * *
46585220 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTATG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCGGACTAAGAT-CCGAAGGCAT
* * *
46585283 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
64 TTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-CTAAA
* *
46585340 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
46585359 TACGTGATTT
Statistics
Matches: 119, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
118 3 0.03
119 85 0.71
120 31 0.26
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
GTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
Found at i:46593570 original size:40 final size:40
Alignment explanation
Indices: 46593333--46593556 Score: 287
Period size: 40 Copynumber: 5.6 Consensus size: 40
46593323 CGAATGATGT
* * * *
46593333 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* *
46593373 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
46593413 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
46593451 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
46593492 CCGGGCTATGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
46593532 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
46593557 AACGAGTAGC
Statistics
Matches: 166, Mismatches: 11, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
39 35 0.21
40 121 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:46593578 original size:119 final size:119
Alignment explanation
Indices: 46593332--46593589 Score: 301
Period size: 119 Copynumber: 2.2 Consensus size: 119
46593322 TCGAATGATG
* *
46593332 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
* **
46593397 GTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
66 GTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
* * * * *
46593451 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTATG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCGGACTAAGAT-CCGAAGGCAT
* * *
46593514 TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
64 TTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-CTAAA
* *
46593571 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
46593590 TACGTGATTT
Statistics
Matches: 119, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
118 3 0.03
119 85 0.71
120 31 0.26
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
GTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAAA
Found at i:46610296 original size:28 final size:28
Alignment explanation
Indices: 46610252--46610325 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
46610242 ACACACACAG
* *
46610252 GGTTAGCACATAT-GGTTCGCACCTAGT
1 GGTTCGCACATATGGGTTCGCACCTAGA
** *
46610279 GGTTCTTACATATGGGTTTGCACCTAGA
1 GGTTCGCACATATGGGTTCGCACCTAGA
46610307 GGTTCGCACATATAGGGTT
1 GGTTCGCACATAT-GGGTT
46610326 TGCATATACA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
27 10 0.26
28 23 0.61
29 5 0.13
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (28 bp):
GGTTCGCACATATGGGTTCGCACCTAGA
Found at i:46610560 original size:14 final size:14
Alignment explanation
Indices: 46610543--46610619 Score: 66
Period size: 14 Copynumber: 5.5 Consensus size: 14
46610533 CACATACAGA
46610543 GGTTCACTTATAGG
1 GGTTCACTTATAGG
* *
46610557 GGTTC-GTATACAGG
1 GGTTCACT-TATAGG
* * * *
46610571 CGCTCGCCTATAGG
1 GGTTCACTTATAGG
*
46610585 GGTTCACATATAGG
1 GGTTCACTTATAGG
*
46610599 GGCTCACTTATAGG
1 GGTTCACTTATAGG
46610613 GGTTCAC
1 GGTTCAC
46610620 ATACATGGGC
Statistics
Matches: 47, Mismatches: 14, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
13 1 0.02
14 46 0.98
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29
Consensus pattern (14 bp):
GGTTCACTTATAGG
Found at i:46610567 original size:28 final size:27
Alignment explanation
Indices: 46610530--46610633 Score: 118
Period size: 28 Copynumber: 3.7 Consensus size: 27
46610520 CACATTCCAA
*
46610530 GTTCACATACAGAGGTTCACTTATAGGG
1 GTTCACATACAG-GGCTCACTTATAGGG
** * *
46610558 GTTCGTATACAGGCGCTCGCCTATAGGG
1 GTTCACATACAGG-GCTCACTTATAGGG
*
46610586 GTTCACATATAGGGGCTCACTTATAGGG
1 GTTCACATACA-GGGCTCACTTATAGGG
46610614 GTTCACATACATGGGCTCAC
1 GTTCACATACA-GGGCTCAC
46610634 ATGCAAGGAG
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
27 1 0.02
28 59 0.95
29 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (27 bp):
GTTCACATACAGGGCTCACTTATAGGG
Found at i:46610633 original size:14 final size:14
Alignment explanation
Indices: 46610579--46610635 Score: 69
Period size: 14 Copynumber: 4.1 Consensus size: 14
46610569 GGCGCTCGCC
*
46610579 TATAGGGGTTCACA
1 TATAGGGGCTCACA
*
46610593 TATAGGGGCTCACT
1 TATAGGGGCTCACA
*
46610607 TATAGGGGTTCACA
1 TATAGGGGCTCACA
* *
46610621 TACATGGGCTCACA
1 TATAGGGGCTCACA
46610635 T
1 T
46610636 GCAAGGAGGT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 36 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.28
Consensus pattern (14 bp):
TATAGGGGCTCACA
Found at i:46620043 original size:22 final size:23
Alignment explanation
Indices: 46620018--46620067 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
46620008 ATCTCATGAA
*
46620018 TATTTTATGTATA-TCTTTTCCT
1 TATTTTATGTATATTATTTTCCT
46620040 TA-TTTATGTATATTATTTTCCT
1 TATTTTATGTATATTATTTTCCT
46620062 TGATTT
1 T-ATTT
46620068 ATGGGCTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 10 0.42
22 11 0.46
23 1 0.04
24 2 0.08
ACGTcount: A:0.20, C:0.10, G:0.06, T:0.64
Consensus pattern (23 bp):
TATTTTATGTATATTATTTTCCT
Found at i:46620047 original size:21 final size:23
Alignment explanation
Indices: 46620021--46620070 Score: 77
Period size: 21 Copynumber: 2.3 Consensus size: 23
46620011 TCATGAATAT
*
46620021 TTTATGTATA-TCTTTTCCTT-A
1 TTTATGTATATTATTTTCCTTGA
46620042 TTTATGTATATTATTTTCCTTGA
1 TTTATGTATATTATTTTCCTTGA
46620065 TTTATG
1 TTTATG
46620071 GGCTAATTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 10 0.38
22 9 0.35
23 7 0.27
ACGTcount: A:0.20, C:0.10, G:0.08, T:0.62
Consensus pattern (23 bp):
TTTATGTATATTATTTTCCTTGA
Found at i:46625403 original size:4 final size:4
Alignment explanation
Indices: 46625389--46625452 Score: 59
Period size: 4 Copynumber: 17.0 Consensus size: 4
46625379 CAAGCACCGG
*
46625389 AAGA GAGA AAGA AAGGA AAGA AAG- AAG- AAGA GAAG- AAG- AAG- AAGA
1 AAGA AAGA AAGA AA-GA AAGA AAGA AAGA AAGA -AAGA AAGA AAGA AAGA
46625434 AAGA AAGA AAGA AA-A AAGA
1 AAGA AAGA AAGA AAGA AAGA
46625453 TAATGTATTA
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
3 18 0.34
4 28 0.53
5 7 0.13
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:46625426 original size:11 final size:10
Alignment explanation
Indices: 46625388--46625452 Score: 53
Period size: 11 Copynumber: 6.2 Consensus size: 10
46625378 TCAAGCACCG
46625388 GAAGAGAGAAA
1 GAAGA-AGAAA
*
46625399 GAA-AGGAAA
1 GAAGAAGAAA
46625408 GAAAGAAGAAGA
1 G-AAGAAGAA-A
46625420 GAAGAAG-AA
1 GAAGAAGAAA
46625429 GAAGAAAGAAA
1 GAAG-AAGAAA
*
46625440 GAAAGAAAAAA
1 G-AAGAAGAAA
46625451 GA
1 GA
46625453 TAATGTATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
9 10 0.22
10 8 0.18
11 22 0.49
12 5 0.11
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (10 bp):
GAAGAAGAAA
Found at i:46625429 original size:14 final size:13
Alignment explanation
Indices: 46625388--46625452 Score: 55
Period size: 13 Copynumber: 4.9 Consensus size: 13
46625378 TCAAGCACCG
46625388 GAAGAGAGAAAGAA
1 GAAGA-AGAAAGAA
*
46625402 -AGGAAAGAAAGAA
1 GAAG-AAGAAAGAA
46625415 GAAG-AG-AAGAA
1 GAAGAAGAAAGAA
46625426 GAAGAAGAAAGAAA
1 GAAGAAGAAAG-AA
*
46625440 GAAAGAAAAAAGA
1 G-AAGAAGAAAGA
46625453 TAATGTATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
11 9 0.21
12 4 0.10
13 13 0.31
14 7 0.17
15 9 0.21
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAAGAA
Found at i:46625671 original size:52 final size:53
Alignment explanation
Indices: 46625610--46625716 Score: 171
Period size: 52 Copynumber: 2.0 Consensus size: 53
46625600 TTTTTTATAA
* * *
46625610 TTATTTTAAAATTAATTTGTTAGTAATTTAGGA-TATTTTATAAATTTTTGTG
1 TTATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTGTTGTG
*
46625662 TTATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAGTTGTTGTG
1 TTATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTGTTGTG
46625715 TT
1 TT
46625717 TAGTTTAGTA
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
52 32 0.64
53 18 0.36
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (53 bp):
TTATTTTAAAATTAATTTATTAGTAATTTAGGATTATGTTATAAATTGTTGTG
Found at i:46625981 original size:67 final size:65
Alignment explanation
Indices: 46625848--46625971 Score: 149
Period size: 67 Copynumber: 1.9 Consensus size: 65
46625838 AATTTTATAG
* * ** * * ***
46625848 TTATTTTGTTAGTAGTTTATGATTAGGTTATTAATTGTTAGTGTTTTGTGTTTTGTTATAGTTAT
1 TTATTTTGTTAATAATTTATGATTAGGTTACAAATTGTTAGTGTTTAGTATAGGGTTATAGTTAT
46625913 TTATTTTGTTAATAATTTATGGGATTAGGTTACAAATTGTTAGTGTTTAGTATAGGGTT
1 TTATTTTGTTAATAATTTAT--GATTAGGTTACAAATTGTTAGTGTTTAGTATAGGGTT
46625972 TTTTTTATTT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
65 18 0.38
67 30 0.62
ACGTcount: A:0.23, C:0.01, G:0.21, T:0.55
Consensus pattern (65 bp):
TTATTTTGTTAATAATTTATGATTAGGTTACAAATTGTTAGTGTTTAGTATAGGGTTATAGTTAT
Found at i:46626147 original size:103 final size:104
Alignment explanation
Indices: 46625913--46626231 Score: 370
Period size: 103 Copynumber: 3.1 Consensus size: 104
46625903 TTATAGTTAT
* * *
46625913 TTATTTTGTTAATAATTTATGGGATTAGG-T-TACAAATTGTTAGTGTTTAG-TATAGGGTTTTT
1 TTATTTTGTTAGTAATTTAT--GATTAGGTTATATAAATTGTTAGTGTTTAGTTATAGTG-TTTT
* * * *
46625975 TTTATTTTTTTGTGATGTAATGT-TTTTTTTAAA-ATAATTTTATAG
63 GTGA--TTTTT-T-A-GTAATGTATTTTATAAAATATAATTTTATAG
46626020 TTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGTTAT-GTGTTTTGTG
1 TTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGTTATAGTGTTTTGTG
*
46626084 ATTTTTTAGTAATGTATTTTAAAAAATATAATTTTATAG
66 ATTTTTTAGTAATGTATTTTATAAAATATAATTTTATAG
*
46626123 TTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGTT-TAGTATTTTGTG
1 TTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGTTATAGTGTTTTGTG
* * *
46626187 ATTTTTT--TAATGTAATTTTTATATAATGTAATTTTAT-T
66 ATTTTTTAGTAATGT-A-TTTTATAAAATATAATTTTATAG
46626225 TTATTTT
1 TTATTTT
46626232 TCTTTATTTG
Statistics
Matches: 191, Mismatches: 13, Indels: 21
0.85 0.06 0.09
Matches are distributed among these distances:
101 13 0.07
102 17 0.09
103 99 0.52
104 5 0.03
105 7 0.04
106 7 0.04
107 40 0.21
108 3 0.02
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (104 bp):
TTATTTTGTTAGTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGTTATAGTGTTTTGTG
ATTTTTTAGTAATGTATTTTATAAAATATAATTTTATAG
Found at i:46628250 original size:13 final size:13
Alignment explanation
Indices: 46628228--46628261 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
46628218 GTATTCAATT
46628228 CAATCCAATTACC
1 CAATCCAATTACC
*
46628241 CAATCTAATTACC
1 CAATCCAATTACC
*
46628254 CAACCCAA
1 CAATCCAA
46628262 CCCAATCATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.21
Consensus pattern (13 bp):
CAATCCAATTACC
Found at i:46628383 original size:9 final size:9
Alignment explanation
Indices: 46628363--46628456 Score: 125
Period size: 9 Copynumber: 10.4 Consensus size: 9
46628353 TGTATGATTC
*
46628363 AATTAGGTT
1 AATTCGGTT
*
46628372 AATTCGGGT
1 AATTCGGTT
46628381 AATTCGGTT
1 AATTCGGTT
*
46628390 AATTCGTTT
1 AATTCGGTT
*
46628399 AATTCGGGT
1 AATTCGGTT
46628408 AATTCGGTT
1 AATTCGGTT
**
46628417 AATTCGGGC
1 AATTCGGTT
46628426 AATTCGGTT
1 AATTCGGTT
*
46628435 AATTTGGTT
1 AATTCGGTT
46628444 AATTCGGTT
1 AATTCGGTT
46628453 AATT
1 AATT
46628457 TTTAACCAAA
Statistics
Matches: 72, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 72 1.00
ACGTcount: A:0.24, C:0.10, G:0.23, T:0.43
Consensus pattern (9 bp):
AATTCGGTT
Found at i:46629360 original size:79 final size:76
Alignment explanation
Indices: 46629201--46629375 Score: 269
Period size: 79 Copynumber: 2.3 Consensus size: 76
46629191 AATAACTTCA
* *
46629201 TATTTATGTAATGAATTTTTTTTCATTTTATTTATCAATTTTATGTTTTTTTTTGCAATTTAAAT
1 TATTTATGTAATGACTTTTTTGTCATTTTATTTATCAATTTTATGTTTTTTTTTGCAATTTAAAT
* * *
46629266 AGTCAACTTTT
66 AATAAACTTTG
*
46629277 TATTTATGTAATGACTTTTTTGTCATTTTTATTTATCAATTTTATGGTTTATTTTTTTCAATTTA
1 TATTTATGTAATGACTTTTTTGTCA-TTTTATTTATCAATTTTAT-GTTT-TTTTTTGCAATTTA
46629342 AATAATAAACTTTG
63 AATAATAAACTTTG
46629356 TATTTATGTAATGACTTTTT
1 TATTTATGTAATGACTTTTT
46629376 CGCTATTTCA
Statistics
Matches: 90, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
76 23 0.26
77 19 0.21
78 4 0.04
79 44 0.49
ACGTcount: A:0.27, C:0.06, G:0.07, T:0.59
Consensus pattern (76 bp):
TATTTATGTAATGACTTTTTTGTCATTTTATTTATCAATTTTATGTTTTTTTTTGCAATTTAAAT
AATAAACTTTG
Found at i:46632243 original size:41 final size:40
Alignment explanation
Indices: 46632198--46632283 Score: 102
Period size: 41 Copynumber: 2.1 Consensus size: 40
46632188 AAAGATAAAA
46632198 ATATGTTTATATGAATGTA-TATACAATATATATTTGCATGT
1 ATATGTTTAT-TGAATGTAGTATACAA-ATATATTTGCATGT
* * **
46632239 ATATGTTTATTTAATTTAGTTATTGAAATATATTTGCATGT
1 ATATGTTTATTGAATGTAG-TATACAAATATATTTGCATGT
46632280 ATAT
1 ATAT
46632284 ACAATATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
40 6 0.15
41 28 0.72
42 5 0.13
ACGTcount: A:0.35, C:0.03, G:0.12, T:0.50
Consensus pattern (40 bp):
ATATGTTTATTGAATGTAGTATACAAATATATTTGCATGT
Found at i:46654136 original size:21 final size:20
Alignment explanation
Indices: 46654112--46654151 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
46654102 TGATCCCTAT
46654112 AAAATAATTACAAAAATATTC
1 AAAATAATTA-AAAAATATTC
* *
46654133 AAAATATTTATAAAATATT
1 AAAATAATTAAAAAATATT
46654152 TTTCCCTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAATAATTAAAAAATATTC
Found at i:46655961 original size:72 final size:72
Alignment explanation
Indices: 46655810--46655964 Score: 166
Period size: 72 Copynumber: 2.2 Consensus size: 72
46655800 CAAACTTTAC
* * * * * *
46655810 TTGATGCTTCTCACACAAGCTTCAGAGAATTCATAACACGTGCCGAATCTCAAGCCATCGGTAAA
1 TTGATGCTACTCACACAAGCTTCAGAAAATCCACAACACGTGCCGAATCTCAAGCCACCGATAAA
**
46655875 GGATAAT
66 CAATAAT
** * ** * *
46655882 TCAATGCTACTCACACAAGCTTTAGAAAATCCACAACACGTGTTGGATCTCAAGCCACCGATAAT
1 TTGATGCTACTCACACAAGCTTCAGAAAATCCACAACACGTGCCGAATCTCAAGCCACCGATAAA
*
46655947 CAATGAT
66 CAATAAT
46655954 TTGATGCTACT
1 TTGATGCTACT
46655965 TACTGATAGT
Statistics
Matches: 65, Mismatches: 18, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
72 65 1.00
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.26
Consensus pattern (72 bp):
TTGATGCTACTCACACAAGCTTCAGAAAATCCACAACACGTGCCGAATCTCAAGCCACCGATAAA
CAATAAT
Found at i:46662454 original size:5 final size:5
Alignment explanation
Indices: 46662434--46662468 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
46662424 TATACTATAA
46662434 TAATT T-ATT T-ATT TAATT TAATT TAATT TAATT TA
1 TAATT TAATT TAATT TAATT TAATT TAATT TAATT TA
46662469 TACTAGAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 8 0.28
5 21 0.72
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
TAATT
Found at i:46674205 original size:21 final size:23
Alignment explanation
Indices: 46674171--46674214 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
46674161 TAAATTTTTA
46674171 TAATATATAACTTTATAA-AAAT
1 TAATATATAACTTTATAATAAAT
46674193 TAATATA-AACTTTATAATAAAT
1 TAATATATAACTTTATAATAAAT
46674215 AATCTTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (23 bp):
TAATATATAACTTTATAATAAAT
Found at i:46674207 original size:36 final size:37
Alignment explanation
Indices: 46674151--46674225 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 37
46674141 ATTAGGTAAC
* *
46674151 AAAAATAATATAAATTTTTATAATATATAA-CTTTAT
1 AAAAATAATATAAATCTTTATAATAAATAATCTTTAT
46674187 AAAAATTAATATAAA-CTTTATAATAAATAATCTTTAT
1 AAAAA-TAATATAAATCTTTATAATAAATAATCTTTAT
46674224 AA
1 AA
46674226 GAAAAGGTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
36 18 0.51
37 17 0.49
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (37 bp):
AAAAATAATATAAATCTTTATAATAAATAATCTTTAT
Found at i:46674217 original size:21 final size:21
Alignment explanation
Indices: 46674170--46674217 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 21
46674160 ATAAATTTTT
46674170 ATAATATATAACTTTATAAAA
1 ATAATATATAACTTTATAAAA
46674191 ATTAATATA-AACTTTATAATAA
1 A-TAATATATAACTTTATAA-AA
46674213 ATAAT
1 ATAAT
46674218 CTTTATAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (21 bp):
ATAATATATAACTTTATAAAA
Found at i:46679195 original size:26 final size:25
Alignment explanation
Indices: 46679154--46679201 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
46679144 TCTAAAAATG
46679154 ATTTAAAATAATAAAAAATTCAATT
1 ATTTAAAATAATAAAAAATTCAATT
*
46679179 ATTTTAAATAATAAAAAATTCAA
1 ATTTAAAATAATAAAAAATTCAA
46679202 AAAATCATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.35
Consensus pattern (25 bp):
ATTTAAAATAATAAAAAATTCAATT
Found at i:46679273 original size:18 final size:19
Alignment explanation
Indices: 46679208--46679276 Score: 77
Period size: 21 Copynumber: 3.5 Consensus size: 19
46679198 TCAAAAAATC
46679208 ATTAAAAGTTTGTAAATGATT
1 ATTAAAA-TTTGTAAAT-ATT
*
46679229 ATTAAAAAATTGTAAATATTT
1 ATT-AAAATTTGTAAATA-TT
*
46679250 ATTAAAATTTGTAAATA-G
1 ATTAAAATTTGTAAATATT
46679268 ATTAAAATT
1 ATTAAAATT
46679277 ATTTAAAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
18 9 0.21
20 14 0.33
21 16 0.37
22 4 0.09
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (19 bp):
ATTAAAATTTGTAAATATT
Found at i:46679313 original size:29 final size:29
Alignment explanation
Indices: 46679253--46679315 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
46679243 AATATTTATT
*
46679253 AAAATTTGTAAATAGATTAAAATTATTTA
1 AAAATTTGTAAATAGATTAAAATTATTAA
*
46679282 AAAATTT-TAAAGTTGATTTAAAATTA-TAA
1 AAAATTTGTAAA-TAGA-TTAAAATTATTAA
46679311 AAAAT
1 AAAAT
46679316 AATAAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 4 0.13
29 17 0.57
30 9 0.30
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (29 bp):
AAAATTTGTAAATAGATTAAAATTATTAA
Found at i:46679356 original size:19 final size:17
Alignment explanation
Indices: 46679271--46679369 Score: 63
Period size: 19 Copynumber: 5.4 Consensus size: 17
46679261 TAAATAGATT
*
46679271 AAAATTATTTAAAAATTTT
1 AAAATTA-TT-AAAATTTA
*
46679290 AAAGTTGATTTAAAATTATA
1 AAAATT-A-TTAAAATT-TA
* * *
46679310 AAAAATAATAAAAATTA
1 AAAATTATTAAAATTTA
*
46679327 AAAATTGTTAAAATTGTA
1 AAAATTATTAAAATT-TA
*
46679345 AATAATTATTAAAAATTA
1 AA-AATTATTAAAATTTA
46679363 CAAAATT
1 -AAAATT
46679370 CACCCCTAAT
Statistics
Matches: 63, Mismatches: 12, Indels: 11
0.73 0.14 0.13
Matches are distributed among these distances:
17 13 0.21
18 16 0.25
19 25 0.40
20 9 0.14
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (17 bp):
AAAATTATTAAAATTTA
Found at i:46679627 original size:17 final size:17
Alignment explanation
Indices: 46679605--46679642 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
46679595 AATATAATTT
*
46679605 TAAAAAAAATAAAACATA
1 TAAAAAAATTAAAA-ATA
46679623 TAAAAAAATTAAAAATA
1 TAAAAAAATTAAAAATA
46679640 TAA
1 TAA
46679643 TTTTGTTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (17 bp):
TAAAAAAATTAAAAATA
Found at i:46679725 original size:15 final size:16
Alignment explanation
Indices: 46679700--46679758 Score: 61
Period size: 15 Copynumber: 3.8 Consensus size: 16
46679690 ATATTGAATT
46679700 ATTTATAAAAAAAT-AA
1 ATTT-TAAAAAAATAAA
*
46679716 ATTTTAAAAATATAAA
1 ATTTTAAAAAAATAAA
46679732 ATTTT--AAAAATGAAA
1 ATTTTAAAAAAAT-AAA
*
46679747 ATTATAAAAAAA
1 ATTTTAAAAAAA
46679759 AGTAAAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
14 5 0.14
15 15 0.42
16 11 0.31
17 5 0.14
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (16 bp):
ATTTTAAAAAAATAAA
Found at i:46680245 original size:3 final size:3
Alignment explanation
Indices: 46680237--46680272 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
46680227 TTCTCCTTAT
46680237 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
46680273 AATTTCATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:46680971 original size:16 final size:16
Alignment explanation
Indices: 46680933--46680976 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
46680923 TGGTTTATAA
46680933 TTTTTTGGATTTAGGG
1 TTTTTTGGATTTAGGG
*** *
46680949 AGATTTGGGTTTAGGG
1 TTTTTTGGATTTAGGG
46680965 TTTTTTGGATTT
1 TTTTTTGGATTT
46680977 CTTTGTTGAA
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.14, C:0.00, G:0.32, T:0.55
Consensus pattern (16 bp):
TTTTTTGGATTTAGGG
Found at i:46682674 original size:43 final size:43
Alignment explanation
Indices: 46682612--46682706 Score: 129
Period size: 43 Copynumber: 2.2 Consensus size: 43
46682602 CTGAGATATC
* * *
46682612 GCATTGATATGAGACTTCGTGTAAGATCATGTCTGGGAC-ATTG
1 GCATCGATATGAGACTTCGTGTAAGACCATGGCTGGG-CTATTG
* *
46682655 GCATCGATATGTGATTTCGTGTAAGACCATGGCTGGGCTATTG
1 GCATCGATATGAGACTTCGTGTAAGACCATGGCTGGGCTATTG
46682698 GCATCGATA
1 GCATCGATA
46682707 AAGATTACAT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 1 0.02
43 45 0.98
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (43 bp):
GCATCGATATGAGACTTCGTGTAAGACCATGGCTGGGCTATTG
Found at i:46682998 original size:15 final size:15
Alignment explanation
Indices: 46682978--46683008 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
46682968 AAATGTGCTC
46682978 ATTTGGCTATATGGA
1 ATTTGGCTATATGGA
46682993 ATTTGGCTATATGGA
1 ATTTGGCTATATGGA
46683008 A
1 A
46683009 GTATAAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.06, G:0.26, T:0.39
Consensus pattern (15 bp):
ATTTGGCTATATGGA
Found at i:46684647 original size:14 final size:14
Alignment explanation
Indices: 46684619--46684666 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
46684609 TGATGGGAAT
46684619 AATA-AAATATATAA
1 AATATAAATAT-TAA
46684633 AATATAAATATTAA
1 AATATAAATATTAA
*
46684647 AATATCAAAATATTAG
1 AATAT--AAATATTAA
46684663 AATA
1 AATA
46684667 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 12 0.40
15 6 0.20
16 12 0.40
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (14 bp):
AATATAAATATTAA
Found at i:46684647 original size:23 final size:22
Alignment explanation
Indices: 46684616--46684670 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
46684606 CAATGATGGG
*
46684616 AATAATAAAATATATAAAATATA
1 AATAATAAAATAT-CAAAATATA
*
46684639 AATATTAAAATATCAAAATATTA
1 AATAATAAAATATCAAAATA-TA
46684662 GAATAATAA
1 -AATAATAA
46684671 TAATTAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.22
23 14 0.52
24 7 0.26
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (22 bp):
AATAATAAAATATCAAAATATA
Found at i:46684651 original size:8 final size:8
Alignment explanation
Indices: 46684616--46684666 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
46684606 CAATGATGGG
*
46684616 AATAATAA
1 AATATTAA
46684624 AATATATAA
1 AATAT-TAA
46684633 AATA-T-A
1 AATATTAA
46684639 AATATTAA
1 AATATTAA
*
46684647 AATATCAA
1 AATATTAA
*
46684655 AATATTAG
1 AATATTAA
46684663 AATA
1 AATA
46684667 ATAATAATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
6 5 0.14
7 2 0.06
8 22 0.61
9 7 0.19
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:46684657 original size:16 final size:15
Alignment explanation
Indices: 46684620--46684666 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
46684610 GATGGGAATA
46684620 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
46684636 AT-AAATATTAAAAT
1 ATAAAATATTAAAAT
*
46684650 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
46684666 A
1 A
46684667 ATAATAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 8 0.29
15 6 0.21
16 14 0.50
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:46684846 original size:24 final size:22
Alignment explanation
Indices: 46684794--46684877 Score: 80
Period size: 22 Copynumber: 3.7 Consensus size: 22
46684784 TACATATATA
* *
46684794 AAAATAAATACATGATAATA-TT
1 AAAATATATACATAAT-ATAGTT
*
46684816 AAAAATATGTACATAATATAGTGTT
1 -AAAATATATACATAATATA--GTT
*
46684841 AAAATACATACATAATATAGTT
1 AAAATATATACATAATATAGTT
*
46684863 AAGATATATACATAA
1 AAAATATATACATAA
46684878 GATAACATGT
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
22 19 0.37
23 13 0.25
24 17 0.33
25 2 0.04
ACGTcount: A:0.55, C:0.06, G:0.07, T:0.32
Consensus pattern (22 bp):
AAAATATATACATAATATAGTT
Found at i:46684873 original size:22 final size:23
Alignment explanation
Indices: 46684817--46684877 Score: 79
Period size: 24 Copynumber: 2.7 Consensus size: 23
46684807 GATAATATTA
*
46684817 AAAATATGTACATAATATAGTGTT
1 AAAATATATACATAATATAG-GTT
*
46684841 AAAATACATACATAATATA-GTT
1 AAAATATATACATAATATAGGTT
*
46684863 AAGATATATACATAA
1 AAAATATATACATAA
46684878 GATAACATGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 16 0.48
24 17 0.52
ACGTcount: A:0.52, C:0.07, G:0.08, T:0.33
Consensus pattern (23 bp):
AAAATATATACATAATATAGGTT
Found at i:46684927 original size:25 final size:25
Alignment explanation
Indices: 46684899--46685031 Score: 93
Period size: 25 Copynumber: 5.6 Consensus size: 25
46684889 GAAAAAATAT
46684899 ATATATAAATAATATAATATTAAAG
1 ATATATAAATAATATAATATTAAAG
* * * *
46684924 ATATATAAATAAAATAGTATAAAAT
1 ATATATAAATAATATAATATTAAAG
* *
46684949 ATATATATACGTAATATAA-ATTTAA-
1 ATATATA-A-ATAATATAATATTAAAG
** *
46684974 A-ATATACCTAATAT-AT-TAAAAG
1 ATATATAAATAATATAATATTAAAG
*
46684996 A-ATATATATAATATAATATT-AAG
1 ATATATAAATAATATAATATTAAAG
*
46685019 AAATAT-AATAATA
1 ATATATAAATAATA
46685032 ACAAAAAAAG
Statistics
Matches: 84, Mismatches: 17, Indels: 16
0.72 0.15 0.14
Matches are distributed among these distances:
21 4 0.05
22 18 0.21
23 12 0.14
24 10 0.12
25 29 0.35
26 5 0.06
27 6 0.07
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (25 bp):
ATATATAAATAATATAATATTAAAG
Found at i:46684951 original size:52 final size:47
Alignment explanation
Indices: 46684892--46685026 Score: 125
Period size: 52 Copynumber: 2.8 Consensus size: 47
46684882 ACATGTAGAA
46684892 AAAATATATATATAAATAATATAATATTAAAGATATATAAATAAAATAGTAT
1 AAAATATATATAT-AATAATATAATATT-AAGA-ATATAAATAAAATA-T-T
* ** *
46684944 AAAATATATATATACGTAATATAA-ATTTAA-AATATACCTAATATATT
1 AAAATATATATATA-ATAATATAATA-TTAAGAATATAAATAAAATATT
*
46684991 AAAAGA-ATATAT-ATAATATAATATTAAGAAATATAA
1 AAAATATATATATAATAATATAATATTAAG-AATATAA
46685027 TAATAACAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
44 12 0.17
45 1 0.01
46 12 0.17
47 6 0.08
48 1 0.01
49 11 0.15
50 1 0.01
51 4 0.06
52 23 0.32
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (47 bp):
AAAATATATATATAATAATATAATATTAAGAATATAAATAAAATATT
Found at i:46684956 original size:29 final size:28
Alignment explanation
Indices: 46684866--46684957 Score: 66
Period size: 29 Copynumber: 3.3 Consensus size: 28
46684856 TATAGTTAAG
* * *
46684866 ATATATACATAAGATAACAT-GTAGAAAAA
1 ATATATATATAA-ATAAAATAGTA-AAAAT
* *
46684895 ATATATATATAAAT--AATA-TAATATT
1 ATATATATATAAATAAAATAGTAAAAAT
* *
46684920 AAAGATATATAAATAAAATAGTATAAAAT
1 ATATATATATAAATAAAATAGTA-AAAAT
46684949 ATATATATA
1 ATATATATA
46684958 CGTAATATAA
Statistics
Matches: 47, Mismatches: 11, Indels: 10
0.69 0.16 0.15
Matches are distributed among these distances:
25 14 0.30
26 4 0.09
27 4 0.09
28 4 0.09
29 21 0.45
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (28 bp):
ATATATATATAAATAAAATAGTAAAAAT
Found at i:46685024 original size:22 final size:22
Alignment explanation
Indices: 46684960--46685031 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
46684950 TATATATACG
*
46684960 TAATATAA-ATTTA-AAATATA
1 TAATATAATATTAAGAAATATA
* *
46684980 CCTAATATATTA-AAAGAATATATA
1 --TAATATAATATTAAGAA-ATATA
46685004 TAATATAATATTAAGAAATATAA
1 TAATATAATATTAAGAAATAT-A
46685027 TAATA
1 TAATA
46685032 ACAAAAAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
22 21 0.52
23 14 0.35
24 5 0.12
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (22 bp):
TAATATAATATTAAGAAATATA
Found at i:46685660 original size:30 final size:30
Alignment explanation
Indices: 46685510--46685672 Score: 213
Period size: 30 Copynumber: 5.4 Consensus size: 30
46685500 TAGGTACAAG
* *
46685510 TGGTGGTGGAGCAA-GTGTGGTTAGTGGAGT
1 TGGTGGTGGA-AAAGGTGTGGCTAGTGGAGT
* ** * *
46685540 AGGTAATGGAGCAA-GTGTGGCTAGTGGATT
1 TGGTGGTGGA-AAAGGTGTGGCTAGTGGAGT
*
46685570 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
*
46685600 TGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
46685630 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
46685660 TGGTGGTGGAAAA
1 TGGTGGTGGAAAA
46685673 AGCTAAGATT
Statistics
Matches: 119, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
29 2 0.02
30 117 0.98
ACGTcount: A:0.21, C:0.04, G:0.48, T:0.26
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
Found at i:46686581 original size:13 final size:14
Alignment explanation
Indices: 46686533--46686595 Score: 74
Period size: 14 Copynumber: 4.5 Consensus size: 14
46686523 GAGTTGATTT
* *
46686533 TTGAAAAATATAAA
1 TTGAAAAACAGAAA
46686547 TTGGAAAAACAGAAA
1 TT-GAAAAACAGAAA
*
46686562 TTGAAAAGCAGAAA
1 TTGAAAAACAGAAA
*
46686576 TT-AAAAACAGAAT
1 TTGAAAAACAGAAA
46686589 TTGAAAA
1 TTGAAAA
46686596 GACCTCAGCG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
13 11 0.26
14 19 0.45
15 12 0.29
ACGTcount: A:0.60, C:0.05, G:0.14, T:0.21
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:46686669 original size:14 final size:14
Alignment explanation
Indices: 46686650--46686684 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
46686640 GAGTTGATTT
*
46686650 TTGAAAAGCAGAAA
1 TTGAAAAACAGAAA
46686664 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
*
46686678 TGGAAAA
1 TTGAAAA
46686685 CACCTCAGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.60, C:0.06, G:0.20, T:0.14
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:46686864 original size:14 final size:14
Alignment explanation
Indices: 46686845--46686907 Score: 65
Period size: 14 Copynumber: 4.5 Consensus size: 14
46686835 GAGTTGATTT
*
46686845 TTGAAAAATATAAA
1 TTGAAAAATAGAAA
46686859 TTGAAAAAATAGAAA
1 TTG-AAAAATAGAAA
**
46686874 TTGAAAAGCAGAAA
1 TTGAAAAATAGAAA
* *
46686888 TT-AAAAACAGAAT
1 TTGAAAAATAGAAA
46686901 TTGAAAA
1 TTGAAAA
46686908 GACCTCAGTG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
13 11 0.26
14 18 0.43
15 13 0.31
ACGTcount: A:0.62, C:0.03, G:0.13, T:0.22
Consensus pattern (14 bp):
TTGAAAAATAGAAA
Found at i:46686868 original size:15 final size:15
Alignment explanation
Indices: 46686848--46686880 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
46686838 TTGATTTTTG
*
46686848 AAAAATATAAATTGA
1 AAAAATAGAAATTGA
46686863 AAAAATAGAAATTGA
1 AAAAATAGAAATTGA
46686878 AAA
1 AAA
46686881 GCAGAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (15 bp):
AAAAATAGAAATTGA
Found at i:46686880 original size:13 final size:13
Alignment explanation
Indices: 46686864--46686907 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
46686854 ATAAATTGAA
*
46686864 AAAATAGAAATTG
1 AAAACAGAAATTG
*
46686877 AAAAGCAGAAATTA
1 AAAA-CAGAAATTG
*
46686891 AAAACAGAATTTG
1 AAAACAGAAATTG
46686904 AAAA
1 AAAA
46686908 GACCTCAGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.64, C:0.05, G:0.14, T:0.18
Consensus pattern (13 bp):
AAAACAGAAATTG
Found at i:46687058 original size:77 final size:75
Alignment explanation
Indices: 46686890--46687834 Score: 731
Period size: 74 Copynumber: 12.2 Consensus size: 75
46686880 AGCAGAAATT
* * * * *
46686890 AAAAACAGAATTTGAAAAGACCTCAGTGTGTGGCCCGAGACTCAACTCACCTCTCGCAATATAAG
1 AAAAACAGAAATTGAAAATACCTCAGCGTGT-GCCCGAGGCTCAACTCACCTCTCGCAATATGAG
46686955 TTGA-TTTTTG
65 TTGATTTTTTG
* *
46686965 AAAAGCAGAAATTGAAAATGCCTCAGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAG
46687030 TTGATTCTTTTG
65 TTGATT-TTTTG
* ** *
46687042 AAAAGCAGAAATTGAAAACGCCTCAGCGTGTGACTCGAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAG
46687107 TTGATTCTTTTG
65 TTGATT-TTTTG
** * ** *** * * * * * *
46687119 AAAAGTAGAAATTG-AAA-AGCAGAAATTGAAAATACCTCAGTGTGTCCCGAGGCTCAACTCAC-
1 AAAAACAGAAATTGAAAATACCTCAGCGTG----TGCC-C-GAG-G-CTC-A-ACTCACCTCTCG
* *
46687181 C--TCTCGCAATGTGAGTTGATTTTTTTG
56 CAATAT-G-AGT-TGA--T--TTTT--TG
* *
46687208 ATAAAAATAGAATTTGAAAATACCTCAGCGTGT-CCCGAGGCTCAACTCACCTCTCGCAATATGA
1 --AAAAACAGAAATTGAAAATACCTCAGCGTGTGCCCGAGGCTCAACTCACCTCTCGCAATATGA
46687272 GTTGATGTTTTTG
64 GTTGAT-TTTTTG
*** * * ** *
46687285 AAAAACAGAAATTGAAGAACAAAAATGGAAAACA-CCTCAGCGTCTTGAGGTTCAACTCACCTCT
1 AAAAACAGAAATT---G----AAAAT--ACCTCAGCGT--GTG-CCCGAGGCTCAACTCACCTCT
*
46687349 CGCAATATGAGCTGATTTTTTTG
54 CGCAATATGAGTTGA-TTTTTTG
* ** ** * *
46687372 AAAGACAGAAATTGAAAATACCTCAATGTGT-CTTGAGGCTCAACTTATCTCTCGCAATATGAGT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGT
46687436 TGA-TTTTTG
66 TGATTTTTTG
* * * ** * * *
46687445 ACAAACAAAAATTGAAATTACCTCAGC--GT-CTTGAGGTTCAACTCACCTCTTGCAATATGAGC
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGT
*
46687507 TGATTTTTTTT
66 TGA-TTTTTTG
* * **
46687518 AAAAGACAGAAATTGAAAATATCTCAACGTGTGAAACGAGGCTCAACTCACCTCTCGCAATATGA
1 AAAA-ACAGAAATTGAAAATACCTCAGCGTGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGA
*
46687583 GTT-AATTTTTG
64 GTTGATTTTTTG
* *
46687594 ACAAACAGAAATTGAAATTACCTCAGCGTGT-CCCGAGGCTCAACTCACCTCTCGCAATATGAGT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGT
46687658 TGA-TTTTTG
66 TGATTTTTTG
* *
46687667 AAAAACAGAAATTTAAAAATACCTCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAA-TTGAAAATACCTCAGCGTGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAG
46687731 TTGA-TTTTTG
65 TTGATTTTTTG
* *
46687741 AAAAACAGAAATTTAAAAATACCTCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGAAA-TTGAAAATACCTCAGCGTGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAG
*
46687805 TTGATTTTTTTT
65 TTGA-TTTTTTG
**
46687817 ACGAACAGAAATTGAAAA
1 AAAAACAGAAATTGAAAA
46687835 ACAGAAATTG
Statistics
Matches: 712, Mismatches: 103, Indels: 110
0.77 0.11 0.12
Matches are distributed among these distances:
71 33 0.05
73 83 0.12
74 148 0.21
75 137 0.19
76 28 0.04
77 97 0.14
78 33 0.05
79 7 0.01
80 8 0.01
81 3 0.00
82 19 0.03
83 10 0.01
84 18 0.03
85 4 0.01
86 3 0.00
87 54 0.08
88 4 0.01
89 3 0.00
91 12 0.02
92 3 0.00
93 5 0.01
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.28
Consensus pattern (75 bp):
AAAAACAGAAATTGAAAATACCTCAGCGTGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTTTTTG
Found at i:46687135 original size:14 final size:14
Alignment explanation
Indices: 46687116--46687150 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
46687106 GTTGATTCTT
*
46687116 TTGAAAAGTAGAAA
1 TTGAAAAGCAGAAA
46687130 TTGAAAAGCAGAAA
1 TTGAAAAGCAGAAA
46687144 TTGAAAA
1 TTGAAAA
46687151 TACCTCAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.57, C:0.03, G:0.20, T:0.20
Consensus pattern (14 bp):
TTGAAAAGCAGAAA
Found at i:46687196 original size:89 final size:91
Alignment explanation
Indices: 46687039--46687227 Score: 274
Period size: 89 Copynumber: 2.1 Consensus size: 91
46687029 GTTGATTCTT
* *
46687039 TTGAAAAGCAGAAATTGAAAACGCCTCAGCGTGTGACTCGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAGCAGAAATTGAAAACACCTCA-CGTGTGACCCGAGGCTCAACTCACCTCTCGCAATAT
*
46687104 GAGTTGATTCTTTTG-AAAAGTAGAAA
65 GAGTTGATTCTTTTGAAAAAATAGAAA
* * *
46687130 TTGAAAAGCAGAAATTGAAAATACCTCA-GTGTGTCCCGAGGCTCAACTCACCTCTCGCAATGTG
1 TTGAAAAGCAGAAATTGAAAACACCTCACGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATG
* *
46687194 AGTTGATTTTTTTGATAAAAATAGAAT
66 AGTTGATTCTTTTGA-AAAAATAGAAA
46687221 TTGAAAA
1 TTGAAAA
46687228 TACCTCAGCG
Statistics
Matches: 88, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
89 46 0.52
91 42 0.48
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.28
Consensus pattern (91 bp):
TTGAAAAGCAGAAATTGAAAACACCTCACGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATG
AGTTGATTCTTTTGAAAAAATAGAAA
Found at i:46687606 original size:149 final size:146
Alignment explanation
Indices: 46687318--46688210 Score: 852
Period size: 160 Copynumber: 5.9 Consensus size: 146
46687308 AATGGAAAAC
* * *
46687318 ACCTCAGC-GTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTGAAAGACAGAA
1 ACCTCAGCGGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTTT-AAAAACAGAA
* *** * *
46687382 ATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTTATCTCTCGCAATATGAGTTGATTTTTGAC
65 ATTGAAAATACCTCAACGTGTGACGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAC
*
46687447 AAACAAAAATTGAAATT
130 AAACAGAAATTGAAATT
* * *
46687464 ACCTCAGC-GTCTTGAGGTTCAACTCACCTCTTGCAATATGAGCTGATTTTTTTTAAAAGACAGA
1 ACCTCAGCGGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGA-TTTTTTTAAAA-ACAGA
* *
46687528 AATTGAAAATATCTCAACGTGTGAAACGAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTT
64 AATTGAAAATACCTCAACGTGTG--ACGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
46687593 GACAAACAGAAATTGAAATT
127 GACAAACAGAAATTGAAATT
* * *
46687613 ACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAA
1 ACCTCAGCG-GTCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTAAAAACAGAA
* * *
46687677 ATTTAAAAATACCTCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
65 A-TTGAAAATACCTCAACGTGTGAC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
* * *
46687741 AAAAACAGAAATTTAAAAAT
128 ACAAACAGAAA-TTGAAATT
*
46687761 ACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTACGAACAGA
1 ACCTCAGCG-GTCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGA---TTTTT---------
* * *
46687826 AATTGAAAAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAAT
53 --TT-AAAAACAGAAATTGAAAATACCTCAACGTGTGA--CGAGGCTCAACTCACCTCTCGCAAT
46687891 ATGAGTTGATTTTTGACAAACAGAAATTGAAATT
113 ATGAGTTGATTTTTGACAAACAGAAATTGAAATT
* * * *
46687925 ACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGACAAACAGAA
1 ACCTCAGCG-GTCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTAAAAACAGAA
* * *
46687989 ATTGAAATTACCTCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAA
65 ATTGAAAATACCTCAACGTGTGAC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT---
* * *
46688053 AACAGAAATTAAAAACCAGAAATTGAAAAT
126 --------TGACAAA-CAGAAATTGAAATT
* * * * **
46688083 ACCTCAGTGTGTGAGCC-AAGGCTCAACTCACCTCTTGCAATATGAGCT-AATTTTTTATGAACA
1 ACCTCAGCG-GT---CCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTAAAAACA
* * * * *
46688146 TAAATT-AAAACCACCTCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTAGATTT
62 GAAATTGAAAA-TACCTCAACGTGTGAC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
46688209 TT
125 TT
46688211 TTGAAAATCA
Statistics
Matches: 645, Mismatches: 56, Indels: 89
0.82 0.07 0.11
Matches are distributed among these distances:
145 1 0.00
146 86 0.13
147 80 0.12
148 87 0.13
149 90 0.14
151 33 0.05
152 4 0.01
157 5 0.01
158 24 0.04
159 4 0.01
160 98 0.15
161 1 0.00
163 18 0.03
164 64 0.10
165 49 0.08
166 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (146 bp):
ACCTCAGCGGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTTTAAAAACAGAAA
TTGAAAATACCTCAACGTGTGACGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACA
AACAGAAATTGAAATT
Found at i:46687839 original size:14 final size:14
Alignment explanation
Indices: 46687820--46687848 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
46687810 TTTTTTTACG
46687820 AACAGAAATTGAAA
1 AACAGAAATTGAAA
46687834 AACAGAAATTGAAA
1 AACAGAAATTGAAA
46687848 A
1 A
46687849 GACCTCAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.07, G:0.14, T:0.14
Consensus pattern (14 bp):
AACAGAAATTGAAA
Found at i:46687892 original size:91 final size:88
Alignment explanation
Indices: 46687738--46687922 Score: 266
Period size: 91 Copynumber: 2.1 Consensus size: 88
46687728 GAGTTGATTT
* *
46687738 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTTAAAAAGACCTCAGCGTGGCCTGAGGCTCAACTCACCTCTCGCAATATG
* *
46687803 AGTTGATTTTTTTTACGAACAGAAA
66 AGTTGA--TTTTTGACAAACAGAAA
*
46687828 TTGAAAAACAGAAA-TTGAAAAGACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTCGCAAT
1 TTGAAAAACAGAAATTTAAAAAGACCTCAGC--GTG-GCCTGAGGCTCAACTCACCTCTCGCAAT
46687891 ATGAGTTGATTTTTGACAAACAGAAA
63 ATGAGTTGATTTTTGACAAACAGAAA
46687917 TTGAAA
1 TTGAAA
46687923 TTACCTCAGC
Statistics
Matches: 87, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
89 35 0.40
90 14 0.16
91 36 0.41
92 2 0.02
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.26
Consensus pattern (88 bp):
TTGAAAAACAGAAATTTAAAAAGACCTCAGCGTGGCCTGAGGCTCAACTCACCTCTCGCAATATG
AGTTGATTTTTGACAAACAGAAA
Found at i:46687945 original size:164 final size:162
Alignment explanation
Indices: 46687664--46688067 Score: 526
Period size: 164 Copynumber: 2.6 Consensus size: 162
46687654 GAGTTGATTT
* *
46687664 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTTAAAAAGACCTCAGCGTGGCCTGAGGCTCAACTCACCTCTCGCAATATG
46687729 AGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCT
66 AGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCT
* *
46687794 CGCAATATGAGTTGATTTTTTTTACGAACAGAAA
131 CGCAATATGAGTTGA--TTTTTGACAAACAGAAA
*
46687828 TTGAAAAACAGAAA-TTGAAAAGACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTCGCAAT
1 TTGAAAAACAGAAATTTAAAAAGACCTCAGC--GTG-GCCTGAGGCTCAACTCACCTCTCGCAAT
* * * *
46687891 ATGAGTTGATTTTTGACAAACAGAAA-TTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCACC
63 ATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACC
46687955 TCTCGCAATATGAGTTGATTTTTGACAAACAGAAA
128 TCTCGCAATATGAGTTGATTTTTGACAAACAGAAA
*
46687990 TT--------GAAA-TT------ACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTTAAAAAGACCTCAGCGTGGCCTGAGGCTCAACTCACCTCTCGCAATATG
46688040 AGTTGA-TTTT-AAAAACAGAAA-TTAAAAA
66 AGTTGATTTTTGAAAAACAGAAATTTAAAAA
46688068 CCAGAAATTG
Statistics
Matches: 223, Mismatches: 13, Indels: 28
0.84 0.05 0.11
Matches are distributed among these distances:
144 15 0.07
145 6 0.03
146 36 0.16
148 8 0.04
154 6 0.03
162 17 0.08
163 14 0.06
164 67 0.30
165 52 0.23
166 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (162 bp):
TTGAAAAACAGAAATTTAAAAAGACCTCAGCGTGGCCTGAGGCTCAACTCACCTCTCGCAATATG
AGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCT
CGCAATATGAGTTGATTTTTGACAAACAGAAA
Found at i:46687962 original size:73 final size:73
Alignment explanation
Indices: 46687828--46688062 Score: 368
Period size: 73 Copynumber: 3.2 Consensus size: 73
46687818 CGAACAGAAA
* ** *
46687828 TTGAAAAACAGAAATTGAAAAGACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTCGCAATA
1 TTGACAAACAGAAATTGAAATTACCTCAGC--GTG-TCCTGAGGCTCAACTCACCTCTCGCAATA
46687892 TGAGTTGATTT
63 TGAGTTGATTT
*
46687903 TTGACAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
46687968 GTTGATTT
66 GTTGATTT
46687976 TTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
46688041 GTTGA-TT
66 GTTGATTT
*
46688048 TT-AAAAACAGAAATT
1 TTGACAAACAGAAATT
46688063 AAAAACCAGA
Statistics
Matches: 152, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
71 12 0.08
72 5 0.03
73 108 0.71
75 27 0.18
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (73 bp):
TTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTT
Found at i:46688066 original size:13 final size:14
Alignment explanation
Indices: 46688048--46688081 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
46688038 TGAGTTGATT
46688048 TTAAAAA-CAGAAA
1 TTAAAAACCAGAAA
46688061 TTAAAAACCAGAAA
1 TTAAAAACCAGAAA
*
46688075 TTGAAAA
1 TTAAAAA
46688082 TACCTCAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.65, C:0.09, G:0.09, T:0.18
Consensus pattern (14 bp):
TTAAAAACCAGAAA
Found at i:46688164 original size:233 final size:235
Alignment explanation
Indices: 46687591--46688225 Score: 929
Period size: 233 Copynumber: 2.7 Consensus size: 235
46687581 GAGTTAATTT
* * *
46687591 TTGACAAACAGAAATTGAAATTACCTCAGCGTGT--CCCGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTGAGCCGAGGCTCAACTCACCTCTCGCAATAT
46687654 GAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTC
66 GAGTTGATTTTTGAAAAACAGAAA-TTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTC
46687719 TCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCA
130 TCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCA
**
46687784 ACTCACCTCTCGCAATATGAGTTGATTTTTTTTACGAACAGAAA
195 ACTCACCTCTCGCAATATGAGTTGA---TTTTTAAAAACAGAAA
* *
46687828 TTGAAAAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTGAGCCGAGGCTCAACTCACCTCTCGCAATAT
* * * *
46687893 GAGTTGATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCACCTCT
66 GAGTTGATTTTTGAAAAACAGAAATTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCT
* * *
46687958 CGCAATATGAGTTGATTTTTGACAAACAGAAA-TTGAAATTACCTCAGCGTGTCCTGAGGCTCAA
131 CGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAA
46688022 CTCACCTCTCGCAATATGAGTTGA-TTTTAAAAACAGAAA
196 CTCACCTCTCGCAATATGAGTTGATTTTTAAAAACAGAAA
* * *
46688061 TT-AAAAACCAGAAATTGAAAATACCTCAGTGTGTGAGCCAAGGCTCAACTCACCTCTTGCAATA
1 TTGAAAAA-CAGAAATTGAAAATACCTCAGCGTGTGAGCCGAGGCTCAACTCACCTCTCGCAATA
* * * ** * **
46688125 TGAGCTAATTTTTTATGAACATAAATTAAAACCACCTCAGCGTGTCCTGAGGCTCAACTCACCTC
65 TGAGTTGATTTTTGAAAAACAGAAATTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTC
* *
46688190 TCGCAATATGAGTAGATTTTTTTGAAAATCAGAAAT
130 TCGCAATATGAGTTGA--TTTTTGAAAAACAGAAAT
46688226 AAAAACATCA
Statistics
Matches: 360, Mismatches: 32, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
232 5 0.01
233 136 0.38
235 15 0.04
237 84 0.23
238 69 0.19
239 51 0.14
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.28
Consensus pattern (235 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTGAGCCGAGGCTCAACTCACCTCTCGCAATAT
GAGTTGATTTTTGAAAAACAGAAATTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCT
CGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAA
CTCACCTCTCGCAATATGAGTTGATTTTTAAAAACAGAAA
Found at i:46694936 original size:50 final size:50
Alignment explanation
Indices: 46694812--46695060 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
46694802 GATAATAACA
* * ** * *
46694812 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
46694863 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
46694913 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
46694963 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
46695018 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
46695061 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:46694990 original size:100 final size:104
Alignment explanation
Indices: 46694811--46695060 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
46694801 TGATAATAAC
**
46694811 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
46694876 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
46694913 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
46694976 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
46695018 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
46695061 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:46695176 original size:13 final size:13
Alignment explanation
Indices: 46695155--46695186 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
46695145 GCTTGGATCA
*
46695155 TCATCAAATAAAT
1 TCATAAAATAAAT
46695168 TCATAAAATAAAT
1 TCATAAAATAAAT
46695181 TCATAA
1 TCATAA
46695187 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:46695433 original size:30 final size:30
Alignment explanation
Indices: 46695399--46695455 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
46695389 CCTCGACTCT
**
46695399 AACTTTTTTAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
46695429 AACTTTTACATAATTACATTTTTGCCC
1 AACTTTTACAAAATTACAATTTTGCCC
46695456 GGAAATTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.32, C:0.21, G:0.04, T:0.44
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:46702527 original size:50 final size:50
Alignment explanation
Indices: 46702403--46702651 Score: 275
Period size: 50 Copynumber: 4.8 Consensus size: 50
46702393 GATAATAACA
* * ** * *
46702403 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
46702454 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
46702504 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
46702554 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* * *
46702609 ATGCCAATGCCATGCCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
46702652 TTACCCAAAT
Statistics
Matches: 169, Mismatches: 22, Indels: 9
0.85 0.11 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.20
53 2 0.01
54 1 0.01
55 2 0.01
56 38 0.22
ACGTcount: A:0.20, C:0.30, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:46702581 original size:100 final size:104
Alignment explanation
Indices: 46702402--46702651 Score: 348
Period size: 100 Copynumber: 2.4 Consensus size: 104
46702392 TGATAATAAC
**
46702402 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
46702467 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
46702504 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
46702567 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* * *
46702609 ATGCCAATGCCATGCCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
46702652 TTACCCAAAT
Statistics
Matches: 132, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 39 0.30
ACGTcount: A:0.21, C:0.30, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:46702767 original size:13 final size:13
Alignment explanation
Indices: 46702746--46702777 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
46702736 GCTTGGATCA
*
46702746 TCATCAAATAAAT
1 TCATAAAATAAAT
46702759 TCATAAAATAAAT
1 TCATAAAATAAAT
46702772 TCATAA
1 TCATAA
46702778 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:46703024 original size:29 final size:30
Alignment explanation
Indices: 46702987--46703045 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
46702977 GCCCTCGACT
*
46702987 CTAACTTTTT-CAAAATTACAATTTTGCCC
1 CTAAATTTTTACAAAATTACAATTTTGCCC
* * *
46703016 CTAAATTTTTACATAATTGCATTTTTGCCC
1 CTAAATTTTTACAAAATTACAATTTTGCCC
46703046 GGAAATTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.29, C:0.22, G:0.05, T:0.44
Consensus pattern (30 bp):
CTAAATTTTTACAAAATTACAATTTTGCCC
Found at i:46708486 original size:16 final size:15
Alignment explanation
Indices: 46708465--46708512 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
46708455 TGATGGAATA
46708465 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
46708481 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
46708496 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
46708512 A
1 A
46708513 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:46708495 original size:8 final size:8
Alignment explanation
Indices: 46708461--46708512 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
46708451 ACAATGATGG
*
46708461 AATAATAA
1 AATATTAA
46708469 AATATATAA
1 AATAT-TAA
46708478 AATA-TAA
1 AATATTAA
46708485 AATATTAA
1 AATATTAA
*
46708493 AATATCAA
1 AATATTAA
*
46708501 AATATTAG
1 AATATTAA
46708509 AATA
1 AATA
46708513 ATAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:46708512 original size:24 final size:24
Alignment explanation
Indices: 46708460--46708516 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
46708450 AACAATGATG
*
46708460 GAATAATAAAATATATAAAATATA
1 GAATAATAAAATATACAAAATATA
* *
46708484 AAATATTAAAATAT-CAAAATATTA
1 GAATAATAAAATATACAAAATA-TA
46708508 GAATAATAA
1 GAATAATAA
46708517 TAATTAATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (24 bp):
GAATAATAAAATATACAAAATATA
Found at i:46708674 original size:23 final size:22
Alignment explanation
Indices: 46708623--46708676 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
46708613 ATACTACATC
46708623 AATATGTACATAT-ATA--AAA
1 AATATGTACATATAATATTAAA
**
46708642 AATAAATACATGATAATATTAAA
1 AATATGTACAT-ATAATATTAAA
46708665 AATATGTACATA
1 AATATGTACATA
46708677 ATATAGTGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
19 9 0.33
20 2 0.07
21 3 0.11
22 1 0.04
23 12 0.44
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (22 bp):
AATATGTACATATAATATTAAA
Found at i:46708723 original size:22 final size:24
Alignment explanation
Indices: 46708639--46708724 Score: 81
Period size: 25 Copynumber: 3.7 Consensus size: 24
46708629 TACATATATA
* *
46708639 AAAAATAAATACATGATAATA--TT
1 AAAAATATATACATAAT-ATAGGTT
*
46708662 AAAAATATGTACATAATATAGTGTT
1 AAAAATATATACATAATATAG-GTT
*
46708687 AAAAATACATACATAATATA-GTT
1 AAAAATATATACATAATATAGGTT
*
46708710 -AAGATATATACATAA
1 AAAAATATATACATAA
46708725 GATAACATGT
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
22 16 0.30
23 17 0.32
25 20 0.38
ACGTcount: A:0.56, C:0.06, G:0.07, T:0.31
Consensus pattern (24 bp):
AAAAATATATACATAATATAGGTT
Found at i:46708780 original size:25 final size:25
Alignment explanation
Indices: 46708751--46708883 Score: 93
Period size: 25 Copynumber: 5.6 Consensus size: 25
46708741 ATATATATAT
46708751 ATATATAAATAATATAATATTAAAG
1 ATATATAAATAATATAATATTAAAG
* * * *
46708776 ATATATAAATAAAATAGTATAAAAT
1 ATATATAAATAATATAATATTAAAG
* *
46708801 ATATATATACGTAATATAA-ATTTAA-
1 ATATATA-A-ATAATATAATATTAAAG
** *
46708826 A-ATATACCTAATAT-AT-TAAAAG
1 ATATATAAATAATATAATATTAAAG
*
46708848 A-ATATATATAATATAATATT-AAG
1 ATATATAAATAATATAATATTAAAG
*
46708871 AAATAT-AATAATA
1 ATATATAAATAATA
46708884 ACAAAAAAAG
Statistics
Matches: 84, Mismatches: 17, Indels: 16
0.72 0.15 0.14
Matches are distributed among these distances:
21 4 0.05
22 18 0.21
23 12 0.14
24 10 0.12
25 29 0.35
26 5 0.06
27 6 0.07
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (25 bp):
ATATATAAATAATATAATATTAAAG
Found at i:46708781 original size:16 final size:17
Alignment explanation
Indices: 46708743--46708805 Score: 53
Period size: 16 Copynumber: 3.8 Consensus size: 17
46708733 GTAGAAAAAT
*
46708743 ATATATATATATATAAAT
1 ATATATA-ATATATAAAG
46708761 A-ATATAATAT-TAAAG
1 ATATATAATATATAAAG
*
46708776 ATATATAA-ATA-AAAT
1 ATATATAATATATAAAG
*
46708791 AGTATAAAATATATA
1 A-TATATAATATATA
46708806 TATACGTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
15 11 0.30
16 16 0.43
17 8 0.22
18 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (17 bp):
ATATATAATATATAAAG
Found at i:46708806 original size:27 final size:26
Alignment explanation
Indices: 46708740--46708809 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 26
46708730 CATGTAGAAA
* *
46708740 AATATATATATATATATAAATAATAT
1 AATATAAATATATATATAAATAAAAT
* *
46708766 AATATTAA-AGATATATAAATAAAAT
1 AATATAAATATATATATAAATAAAAT
*
46708791 AGTATAAAATATATATATA
1 AATAT-AAATATATATATA
46708810 CGTAATATAA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
25 19 0.54
26 8 0.23
27 8 0.23
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (26 bp):
AATATAAATATATATATAAATAAAAT
Found at i:46708816 original size:52 final size:46
Alignment explanation
Indices: 46708749--46708878 Score: 122
Period size: 46 Copynumber: 2.7 Consensus size: 46
46708739 AAATATATAT
*
46708749 ATATATATAAATAATATAATATTAAAGATATATAAATAAAATAGTATAAA
1 ATATATATATATAATATAATATT-AAGA-ATATAAATAAAATA-T-TAAA
** *
46708799 ATATATATATACGTAATATAA-ATTTAA-AATATACCTAATATATTAAA
1 ATATATATATA--TAATATAATA-TTAAGAATATAAATAAAATATTAAA
*
46708846 AGA-ATATATATAATATAATATTAAGAAATATAA
1 ATATATATATATAATATAATATTAAG-AATATAA
46708879 TAATAACAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
44 12 0.18
45 1 0.01
46 13 0.19
47 6 0.09
48 1 0.01
49 11 0.16
50 11 0.16
51 3 0.04
52 10 0.15
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.35
Consensus pattern (46 bp):
ATATATATATATAATATAATATTAAGAATATAAATAAAATATTAAA
Found at i:46708876 original size:22 final size:22
Alignment explanation
Indices: 46708812--46708883 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
46708802 TATATATACG
*
46708812 TAATATAA-ATTTA-AAATATA
1 TAATATAATATTAAGAAATATA
* *
46708832 CCTAATATATTA-AAAGAATATATA
1 --TAATATAATATTAAGAA-ATATA
46708856 TAATATAATATTAAGAAATATAA
1 TAATATAATATTAAGAAATAT-A
46708879 TAATA
1 TAATA
46708884 ACAAAAAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
22 21 0.52
23 14 0.35
24 5 0.12
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (22 bp):
TAATATAATATTAAGAAATATA
Found at i:46709459 original size:30 final size:30
Alignment explanation
Indices: 46709362--46709491 Score: 138
Period size: 30 Copynumber: 4.3 Consensus size: 30
46709352 TAGGTACAAG
* *
46709362 TGGTGGTGGAGCAAGTGTAGTTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
* ** *
46709392 AGGTAATGGAGCAAGTGTGGCTAGTGGATT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
**
46709422 TAATGGTGGAG-AAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAA-GTGTGGCTAGTGGAGT
* *
46709452 TGGTGGTGGA-AAAGGAGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAA-GTGTGGCTAGTGGAGT
46709482 TGGTGGTGGA
1 TGGTGGTGGA
46709492 AAAAGCTAAG
Statistics
Matches: 83, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
29 2 0.02
30 81 0.98
ACGTcount: A:0.22, C:0.04, G:0.47, T:0.27
Consensus pattern (30 bp):
TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
Found at i:46710226 original size:46 final size:46
Alignment explanation
Indices: 46710176--46710338 Score: 179
Period size: 46 Copynumber: 3.6 Consensus size: 46
46710166 GATATTGTTT
46710176 TGGATTTGTTTGTATTAAATTGTTTGGTTATTGTACATGAAAAAAA
1 TGGATTTGTTTGTATTAAATTGTTTGGTTATTGTACATGAAAAAAA
* ** * **
46710222 TGGATTTCTTTGTATTTTATTGTCT-GCCATGTGT--ATGAAAAAAA
1 TGGATTTGTTTGTATTAAATTGTTTGGTTAT-TGTACATGAAAAAAA
* * * *
46710266 TGGATATGTTTGTATTAAATTGTTTGGTTATTGTACATTATAGAAA
1 TGGATTTGTTTGTATTAAATTGTTTGGTTATTGTACATGAAAAAAA
* * *
46710312 TTGATTTATTTGTATTGAATTGTTTGG
1 TGGATTTGTTTGTATTAAATTGTTTGG
46710339 CTATCTCTAT
Statistics
Matches: 93, Mismatches: 20, Indels: 8
0.77 0.17 0.07
Matches are distributed among these distances:
44 33 0.35
45 6 0.06
46 54 0.58
ACGTcount: A:0.28, C:0.04, G:0.20, T:0.48
Consensus pattern (46 bp):
TGGATTTGTTTGTATTAAATTGTTTGGTTATTGTACATGAAAAAAA
Found at i:46710368 original size:29 final size:28
Alignment explanation
Indices: 46710336--46710535 Score: 109
Period size: 29 Copynumber: 6.9 Consensus size: 28
46710326 TTGAATTGTT
46710336 TGGCTATCTCTATTAAATGGAAGCCTTTG
1 TGGCTATCTCTATTAAA-GGAAGCCTTTG
* * *
46710365 TGGCGATCTCTATTATAAGAAAGCCTTTA
1 TGGCTATCTCTATTA-AAGGAAGCCTTTG
* * * *
46710394 TGGCGACCTCTGTTATAAGAAAGCCTTTG
1 TGGCTATCTCTATTA-AAGGAAGCCTTTG
* * * *
46710423 TGTCAATCTCTATTTTAAA-TATA-TCTTTG
1 TGGCTATCTCTA--TTAAAGGA-AGCCTTTG
* * *
46710452 TGGCTAACTCAATTGAAAGGATGCCTTTG
1 TGGCTATCTCTATT-AAAGGAAGCCTTTG
* * * * **
46710481 TAGCTATCTCTATCAAAATGATGAATTTG
1 TGGCTATCTCTAT-TAAAGGAAGCCTTTG
*
46710510 TGG-TGATCTCTATTAAAGGAATCCTT
1 TGGCT-ATCTCTATTAAAGGAAGCCTT
46710536 GGTGACAAAC
Statistics
Matches: 129, Mismatches: 33, Indels: 19
0.71 0.18 0.10
Matches are distributed among these distances:
27 2 0.02
28 11 0.09
29 108 0.84
30 5 0.04
31 3 0.02
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.38
Consensus pattern (28 bp):
TGGCTATCTCTATTAAAGGAAGCCTTTG
Found at i:46719177 original size:5 final size:5
Alignment explanation
Indices: 46719167--46719244 Score: 65
Period size: 5 Copynumber: 15.6 Consensus size: 5
46719157 TATATATATA
* * *
46719167 ATAAT ATAAT ATTAT ATAAT ATTAT AATAAT ATAAT ATAAT A-ACAT ACTTAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT ATA-AT A-TAAT
46719219 -TAAT -TAAGT A-AAT ATAAT ATAAT ATA
1 ATAAT ATAA-T ATAAT ATAAT ATAAT ATA
46719245 TATTTTAAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
4 9 0.15
5 45 0.75
6 6 0.10
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (5 bp):
ATAAT
Found at i:46719209 original size:8 final size:8
Alignment explanation
Indices: 46719162--46719203 Score: 57
Period size: 8 Copynumber: 5.0 Consensus size: 8
46719152 TGTTTTATAT
46719162 ATATAATA
1 ATATAATA
46719170 ATATAATA
1 ATATAATA
46719178 TTATATAATA
1 --ATATAATA
*
46719188 TTATAATA
1 ATATAATA
46719196 ATATAATA
1 ATATAATA
46719204 TAATAACATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 22 0.73
10 8 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
ATATAATA
Found at i:46719549 original size:19 final size:19
Alignment explanation
Indices: 46719521--46719558 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
46719511 CATTTTTTTA
*
46719521 TTTAATCCATTTAAATCAAT
1 TTTAATCCATAT-AATCAAT
46719541 TTTAA-CCATATAATCAAT
1 TTTAATCCATATAATCAAT
46719559 AAAATTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 5 0.29
20 5 0.29
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTAATCCATATAATCAAT
Found at i:46736235 original size:12 final size:12
Alignment explanation
Indices: 46736220--46736246 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
46736210 GAAAATATTT
46736220 TAAAAAAATAAA
1 TAAAAAAATAAA
46736232 TAAAAAAATAAA
1 TAAAAAAATAAA
46736244 TAA
1 TAA
46736247 TAATATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (12 bp):
TAAAAAAATAAA
Found at i:46736581 original size:8 final size:8
Alignment explanation
Indices: 46736504--46736562 Score: 52
Period size: 8 Copynumber: 7.5 Consensus size: 8
46736494 CATTTTTATT
*
46736504 AAATAAAA
1 AAATATAA
46736512 AAATTATAA
1 AAA-TATAA
46736521 AAACTAT-A
1 AAA-TATAA
46736529 AAATAT--
1 AAATATAA
46736535 AAATATAA
1 AAATATAA
* *
46736543 AACTAAAA
1 AAATATAA
46736551 AAATATAA
1 AAATATAA
46736559 AAAT
1 AAAT
46736563 TTGTTTTAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.14
7 3 0.07
8 23 0.55
9 10 0.24
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (8 bp):
AAATATAA
Found at i:46737448 original size:17 final size:17
Alignment explanation
Indices: 46737426--46737458 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
46737416 ATAGAAAGTC
46737426 AAAGATATGGGTATCAG
1 AAAGATATGGGTATCAG
46737443 AAAGATATGGGTATCA
1 AAAGATATGGGTATCA
46737459 AAATCTGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.27, T:0.24
Consensus pattern (17 bp):
AAAGATATGGGTATCAG
Found at i:46737615 original size:2 final size:2
Alignment explanation
Indices: 46737608--46737648 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
46737598 GGCATTGTTT
46737608 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
46737649 GTAAATTCTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:46740609 original size:17 final size:17
Alignment explanation
Indices: 46740587--46740622 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
46740577 ATAGAAAGTC
*
46740587 AAAGATATGGGTATCAA
1 AAAGATATGAGTATCAA
46740604 AAAGATATGAGTATCAA
1 AAAGATATGAGTATCAA
46740621 AA
1 AA
46740623 TTTGGGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.53, C:0.06, G:0.19, T:0.22
Consensus pattern (17 bp):
AAAGATATGAGTATCAA
Found at i:46740776 original size:2 final size:2
Alignment explanation
Indices: 46740769--46740815 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
46740759 GGCATTGTTT
*
46740769 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TA TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
46740811 TC TC T
1 TC TC T
46740816 GTAAATTCTC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.02, C:0.47, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Done.