Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 97 of 132
Found at i:29783576 original size:25 final size:25
Alignment explanation
Indices: 29783530--29783578 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
29783520 TAATTTAAAC
* *
29783530 ATAAAATAAATTAATTAAAAAAATT
1 ATAAAATAAATCAATAAAAAAAATT
*
29783555 ATAAAATAAATCAAAAACAAAAAA
1 ATAAAATAAATCAATAA-AAAAAA
29783579 ATATTATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.22
Consensus pattern (25 bp):
ATAAAATAAATCAATAAAAAAAATT
Found at i:29783666 original size:30 final size:30
Alignment explanation
Indices: 29783626--29783687 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
29783616 ACTAACTTAC
*
29783626 AACATACAACATTTAATTAAAAATTAAATT
1 AACAAACAACATTTAATTAAAAATTAAATT
** *
29783656 AACAAACAACATTTCTTTAAAATTTAAATT
1 AACAAACAACATTTAATTAAAAATTAAATT
29783686 AA
1 AA
29783688 AACAAAACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (30 bp):
AACAAACAACATTTAATTAAAAATTAAATT
Found at i:29787358 original size:19 final size:18
Alignment explanation
Indices: 29787336--29787373 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
29787326 AAAATTACAA
29787336 AAAAATTCAAAATATTTAT
1 AAAAATTCAAAA-ATTTAT
*
29787355 AAAAATTCCAAAATTTAT
1 AAAAATTCAAAAATTTAT
29787373 A
1 A
29787374 GTTTTATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAAATTCAAAAATTTAT
Found at i:29788189 original size:29 final size:29
Alignment explanation
Indices: 29788087--29788188 Score: 177
Period size: 29 Copynumber: 3.5 Consensus size: 29
29788077 TTTAATTGTT
29788087 TATTTTTAAAATTAAAAAAAATTATATTA
1 TATTTTTAAAATTAAAAAAAATTATATTA
29788116 TATTTTTAAAATTAAAAAAAATTATATTA
1 TATTTTTAAAATTAAAAAAAATTATATTA
* *
29788145 TATTTTTAAAATTAATAAAAATTAAATTA
1 TATTTTTAAAATTAAAAAAAATTATATTA
*
29788174 AATTTTTAAAATTAA
1 TATTTTTAAAATTAA
29788189 TCAATTATTT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 70 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
TATTTTTAAAATTAAAAAAAATTATATTA
Found at i:29793708 original size:12 final size:13
Alignment explanation
Indices: 29793693--29793722 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
29793683 ATACACTTAA
29793693 AAATATT-AAAAT
1 AAATATTAAAAAT
29793705 AAATATTAAAAAT
1 AAATATTAAAAAT
29793718 AAATA
1 AAATA
29793723 AATTTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAATATTAAAAAT
Found at i:29793713 original size:21 final size:20
Alignment explanation
Indices: 29793689--29793742 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 20
29793679 TCAAATACAC
29793689 TTAAAAATATTAAAATAAAT
1 TTAAAAATATTAAAATAAAT
29793709 ATT-AAAA-A-T-AAATAAAT
1 -TTAAAAATATTAAAATAAAT
29793726 TTAAAATATATTAAAAT
1 TTAAAA-ATATTAAAAT
29793743 CTTTTTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
16 2 0.07
17 11 0.39
18 2 0.07
19 2 0.07
20 5 0.18
21 6 0.21
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
TTAAAAATATTAAAATAAAT
Found at i:29794060 original size:39 final size:39
Alignment explanation
Indices: 29793978--29794050 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 39
29793968 AAAACAGTAA
* *
29793978 AAAAAATC--AAAATAGTAACCAAAACAGTAAAAAATAT
1 AAAAAATCAAAAAATAGCAACCAAAACAATAAAAAATAT
*
29794015 AAAAAATCAAAAAATAGCAATCAAAACAATAAAAAA
1 AAAAAATCAAAAAATAGCAACCAAAACAATAAAAAA
29794051 AAACCAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 8 0.26
39 23 0.74
ACGTcount: A:0.71, C:0.11, G:0.04, T:0.14
Consensus pattern (39 bp):
AAAAAATCAAAAAATAGCAACCAAAACAATAAAAAATAT
Found at i:29797355 original size:51 final size:52
Alignment explanation
Indices: 29797248--29797355 Score: 146
Period size: 51 Copynumber: 2.1 Consensus size: 52
29797238 GTTGGAAGAG
*
29797248 AAAGAGACTAACCCGACTAGTTTTTTTTTTAATTATAATAATATGGGAAAACTT
1 AAAGAGACTAACCCGACTAG--TTTTTTTTAATTATAATAATATGAGAAAACTT
* * * *
29797302 AAAGAGACTAATCCGATTAG-TTTTTTTAATTATAATAATATGATAAAATTT
1 AAAGAGACTAACCCGACTAGTTTTTTTTAATTATAATAATATGAGAAAACTT
29797353 AAA
1 AAA
29797356 TAATAAATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
51 31 0.63
54 18 0.37
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (52 bp):
AAAGAGACTAACCCGACTAGTTTTTTTTAATTATAATAATATGAGAAAACTT
Found at i:29803176 original size:19 final size:19
Alignment explanation
Indices: 29803152--29803203 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
29803142 GAAAGGAATC
*
29803152 AGCAATACTGGCTCACATG
1 AGCAATACTGGCTCACAAG
**
29803171 AGCAATACTGGCTCGTAAG
1 AGCAATACTGGCTCACAAG
*
29803190 AGCAATATTGGCTC
1 AGCAATACTGGCTC
29803204 GTAAGAGTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (19 bp):
AGCAATACTGGCTCACAAG
Found at i:29803203 original size:38 final size:38
Alignment explanation
Indices: 29803152--29803234 Score: 103
Period size: 38 Copynumber: 2.2 Consensus size: 38
29803142 GAAAGGAATC
*
29803152 AGCAATACTGGCTCACATGAGCAATACTGGCTCGTAAG
1 AGCAATACTGGCTCACAAGAGCAATACTGGCTCGTAAG
* ** ** *
29803190 AGCAATATTGGCTCGTAAGAGTGATATTGGCTCGTAAG
1 AGCAATACTGGCTCACAAGAGCAATACTGGCTCGTAAG
29803228 AGCAATA
1 AGCAATA
29803235 AATTGTACTA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (38 bp):
AGCAATACTGGCTCACAAGAGCAATACTGGCTCGTAAG
Found at i:29803204 original size:19 final size:19
Alignment explanation
Indices: 29803170--29803234 Score: 103
Period size: 19 Copynumber: 3.4 Consensus size: 19
29803160 TGGCTCACAT
*
29803170 GAGCAATACTGGCTCGTAA
1 GAGCAATATTGGCTCGTAA
29803189 GAGCAATATTGGCTCGTAA
1 GAGCAATATTGGCTCGTAA
**
29803208 GAGTGATATTGGCTCGTAA
1 GAGCAATATTGGCTCGTAA
29803227 GAGCAATA
1 GAGCAATA
29803235 AATTGTACTA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.32, C:0.15, G:0.28, T:0.25
Consensus pattern (19 bp):
GAGCAATATTGGCTCGTAA
Found at i:29806199 original size:21 final size:21
Alignment explanation
Indices: 29806173--29806229 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
29806163 TTAAACACAT
*
29806173 AGGGGCACCGAAGTGCACTAC
1 AGGGGCACCGAAGTGCAATAC
*
29806194 GGGGGCACCGAAGTGCAATAC
1 AGGGGCACCGAAGTGCAATAC
*
29806215 AGGGGCACCAAAGTG
1 AGGGGCACCGAAGTG
29806230 AAAACAGAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.25, G:0.37, T:0.09
Consensus pattern (21 bp):
AGGGGCACCGAAGTGCAATAC
Found at i:29806241 original size:20 final size:21
Alignment explanation
Indices: 29806197--29806241 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
29806187 GCACTACGGG
* * *
29806197 GGCACCGAAGTGCAATACAGG
1 GGCACCAAAGTGCAAAACAGA
29806218 GGCACCAAAGTG-AAAACAGA
1 GGCACCAAAGTGCAAAACAGA
29806238 GGCA
1 GGCA
29806242 TCTCTTCATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.40, C:0.22, G:0.31, T:0.07
Consensus pattern (21 bp):
GGCACCAAAGTGCAAAACAGA
Found at i:29811575 original size:27 final size:27
Alignment explanation
Indices: 29811540--29811593 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
29811530 TGTCACAGGC
*
29811540 CGTGAATGGCACAAATTACTCCACACT
1 CGTGAATGGAACAAATTACTCCACACT
*
29811567 CGTGTATGGAACAAATTACTCCACACT
1 CGTGAATGGAACAAATTACTCCACACT
29811594 AAGGTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (27 bp):
CGTGAATGGAACAAATTACTCCACACT
Found at i:29812357 original size:20 final size:19
Alignment explanation
Indices: 29812327--29812386 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 19
29812317 AAGGGCATTG
*
29812327 GAGTGCAATACAGGGGCACC
1 GAGTGC-ATACAAGGGCACC
29812347 AGAGTGCATACAAGGGCACC
1 -GAGTGCATACAAGGGCACC
*
29812367 GAAGTGCAAACAAGGGCACC
1 G-AGTGCATACAAGGGCACC
29812387 TCTTCATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
19 1 0.03
20 29 0.81
21 6 0.17
ACGTcount: A:0.35, C:0.25, G:0.32, T:0.08
Consensus pattern (19 bp):
GAGTGCATACAAGGGCACC
Found at i:29819529 original size:21 final size:19
Alignment explanation
Indices: 29819444--29819524 Score: 108
Period size: 19 Copynumber: 4.3 Consensus size: 19
29819434 AAGGAATCAA
** *
29819444 CAATACTGGCTCACACGAG
1 CAATACTGGCTCGTAAGAG
* * *
29819463 TAATACTGGCTCGTGAGAA
1 CAATACTGGCTCGTAAGAG
29819482 CAATACTGGCTCGTAAGAG
1 CAATACTGGCTCGTAAGAG
29819501 CAATACTGGCTCGTAAGAG
1 CAATACTGGCTCGTAAGAG
29819520 CAATA
1 CAATA
29819525 TACTGTGTTG
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 53 1.00
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.21
Consensus pattern (19 bp):
CAATACTGGCTCGTAAGAG
Found at i:29819553 original size:26 final size:26
Alignment explanation
Indices: 29819507--29819616 Score: 123
Period size: 26 Copynumber: 4.2 Consensus size: 26
29819497 AGAGCAATAC
* * *
29819507 TGGCTCGTAAGAGCAATATACTGTGT
1 TGGCTCATAGGAGCAATATACTGTAT
*
29819533 TGGATCATAGGAGCAATATACTGTAT
1 TGGCTCATAGGAGCAATATACTGTAT
* * *
29819559 TGGCTCGTAGGAGCAATATACTATAC
1 TGGCTCATAGGAGCAATATACTGTAT
* *
29819585 TGGCTCATAGAAGCAATTTACTG-AT
1 TGGCTCATAGGAGCAATATACTGTAT
29819610 TGAGCTC
1 TG-GCTC
29819617 GTATGAGCTA
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
25 3 0.04
26 67 0.96
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (26 bp):
TGGCTCATAGGAGCAATATACTGTAT
Found at i:29819576 original size:52 final size:51
Alignment explanation
Indices: 29819507--29819629 Score: 147
Period size: 52 Copynumber: 2.4 Consensus size: 51
29819497 AGAGCAATAC
* ** *
29819507 TGGCTCGTAAGAGCAATATACTGTGTTGGATCATAGGAGCAATATACTGTAT
1 TGGCTCGTAAGAGCAATATACTATACTGGATCATAGAAGCAATATACTG-AT
* * *
29819559 TGGCTCGTAGGAGCAATATACTATACTGGCTCATAGAAGCAATTTACTGAT
1 TGGCTCGTAAGAGCAATATACTATACTGGATCATAGAAGCAATATACTGAT
* *
29819610 TGAGCTCGTATGAGCTATAT
1 TG-GCTCGTAAGAGCAATAT
29819630 TTACTGGAAG
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
51 4 0.07
52 57 0.93
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (51 bp):
TGGCTCGTAAGAGCAATATACTATACTGGATCATAGAAGCAATATACTGAT
Found at i:29823285 original size:13 final size:13
Alignment explanation
Indices: 29823267--29823293 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29823257 AAACTCTAAT
29823267 TAACCTAGAGTTG
1 TAACCTAGAGTTG
29823280 TAACCTAGAGTTG
1 TAACCTAGAGTTG
29823293 T
1 T
29823294 TGTAGTCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (13 bp):
TAACCTAGAGTTG
Found at i:29825973 original size:31 final size:30
Alignment explanation
Indices: 29825948--29826012 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
29825938 ATTTTCGAGG
*
29825948 AATTTGGGGATCAAAATTGAAATTTTTGGAA
1 AATTT-GGGATCAAAATTGAAATTTTCGGAA
* *
29825979 AATTTGGGATTAAAATTGAACTTTT-GGAA
1 AATTTGGGATCAAAATTGAAATTTTCGGAA
29826008 AATTT
1 AATTT
29826013 TGAGGTTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 9 0.28
30 18 0.56
31 5 0.16
ACGTcount: A:0.38, C:0.03, G:0.20, T:0.38
Consensus pattern (30 bp):
AATTTGGGATCAAAATTGAAATTTTCGGAA
Found at i:29825994 original size:30 final size:30
Alignment explanation
Indices: 29825948--29826012 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 30
29825938 ATTTTCGAGG
*
29825948 AATTTGGGGATCAAAATTGAAATTTTTGGAA
1 AATTTGGGGATCAAAATTG-AACTTTTGGAA
*
29825979 AATTT-GGGATTAAAATTGAACTTTTGGAA
1 AATTTGGGGATCAAAATTGAACTTTTGGAA
29826008 AATTT
1 AATTT
29826013 TGAGGTTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 15 0.47
30 12 0.38
31 5 0.16
ACGTcount: A:0.38, C:0.03, G:0.20, T:0.38
Consensus pattern (30 bp):
AATTTGGGGATCAAAATTGAACTTTTGGAA
Found at i:29826063 original size:29 final size:28
Alignment explanation
Indices: 29826011--29826400 Score: 170
Period size: 29 Copynumber: 13.5 Consensus size: 28
29826001 TTTGGAAAAT
* * * *
29826011 TTTGAGGTTGAAAATGTGATTTTTAGAAA
1 TTTGAGGGTAAAAATGT-AATTTTAGAAG
* *
29826040 TTTGAGGGTAAAAATGGTAATTTTGGATG
1 TTTGAGGGTAAAAAT-GTAATTTTAGAAG
* ** *
29826069 TTCG-GGGGCAAAATGGTAATTTTTGGATA-
1 TTTGAGGGTAAAAAT-GTAA-TTTTAGA-AG
* * * *
29826098 TTCGAGGG-AAAAATATGATTTTTGGAAG
1 TTTGAGGGTAAAAATGT-AATTTTAGAAG
* *
29826126 TTTGAGGGCAAAAAT-TAAATTTTAGAAA
1 TTTGAGGGTAAAAATGT-AATTTTAGAAG
** *
29826154 AGTG-GGGTAAAAATGTGATTTTTAGAAG
1 TTTGAGGGTAAAAATGT-AATTTTAGAAG
* * * *
29826182 TTCGAGGGTAATAATGTGATTTTTGAAAG
1 TTTGAGGGTAAAAATGTAATTTTAG-AAG
*
29826211 TTT-AGGGGTAAAAATATAATTTTTAAGAAG
1 TTTGA-GGGTAAAAATGTAA-TTTT-AGAAG
* * *
29826241 TTCG-GGG-AAAAATGTTATTTTGGGAAG
1 TTTGAGGGTAAAAATGTAATTTT-AGAAG
* * *
29826268 TTTGAGGGTAAAAATATGATTTTTGAAAG
1 TTTGAGGGTAAAAATGTAATTTTAG-AAG
*
29826297 TTT-AGAGGCAAAAATGTAAATTTTAAGAAG
1 TTTGAG-GGTAAAAATGT-AATTTT-AGAAG
* * * *
29826327 TTTAAGGGTAAAACTATAAATTTTTTGAAG
1 TTTGAGGGTAAAAATGT-AA-TTTTAGAAG
* *
29826357 TTTGAAGGT-CAAATGTAATTTTAGAGAAG
1 TTTGAGGGTAAAAATGTAATTTT--AGAAG
* *
29826386 TTTAAGGGTCAAAAT
1 TTTGAGGGTAAAAAT
29826401 ATGATTTCTG
Statistics
Matches: 274, Mismatches: 62, Indels: 49
0.71 0.16 0.13
Matches are distributed among these distances:
27 25 0.09
28 72 0.26
29 118 0.43
30 51 0.19
31 8 0.03
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (28 bp):
TTTGAGGGTAAAAATGTAATTTTAGAAG
Found at i:29826204 original size:56 final size:56
Alignment explanation
Indices: 29826106--29826407 Score: 220
Period size: 59 Copynumber: 5.2 Consensus size: 56
29826096 TATTCGAGGG
* *
29826106 AAAAATATGATTTTTGGAAGTTTGAGGGCAAAAAT-TAAATTTTAGAAAAG-T-GGGGT
1 AAAAATATGATTTTTAGAAGTTCGAGGG-AAAAATGT-AATTTTAG-AAAGTTAGGGGT
* * * *
29826162 AAAAATGTGATTTTTAGAAGTTCGAGGGTAATAATGTGATTTTTGAAAGTTTAGGGGT
1 AAAAATATGATTTTTAGAAGTTCGAGGG-AAAAATGTAATTTTAGAAAG-TTAGGGGT
* * * * *
29826220 AAAAATATAATTTTTAAGAAGTTCG-GGGAAAAATGTTATTTTGGGAAGTTTGAGGGT
1 AAAAATATGATTTTT-AGAAGTTCGAGGGAAAAATGTAATTTTAGAAAGTTAG-GGGT
* * *
29826277 AAAAATATGATTTTT-GAAAGTTTAGAGGCAAAAATGTAAATTTTA-AGAAGTTTAAGGGT
1 AAAAATATGATTTTTAG-AAG-TTCGAGGGAAAAATGT-AATTTTAGA-AAG-TTAGGGGT
* * * * * ** *
29826336 AAAACTATAAATTTTTTGAAGTTTGAAGGTCAAATGTAATTTTAGAGAAGTTTAAGGGT
1 AAAAATAT-GATTTTTAGAAGTTCGAGGGAAAAATGTAATTTTAGA-AAG-TTAGGGGT
*
29826395 CAAAATATGATTT
1 AAAAATATGATTT
29826408 CTGAAAAGTT
Statistics
Matches: 199, Mismatches: 32, Indels: 28
0.77 0.12 0.11
Matches are distributed among these distances:
55 5 0.03
56 42 0.21
57 39 0.20
58 42 0.21
59 59 0.30
60 11 0.06
61 1 0.01
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.35
Consensus pattern (56 bp):
AAAAATATGATTTTTAGAAGTTCGAGGGAAAAATGTAATTTTAGAAAGTTAGGGGT
Found at i:29826275 original size:86 final size:86
Alignment explanation
Indices: 29826021--29826328 Score: 312
Period size: 86 Copynumber: 3.6 Consensus size: 86
29826011 TTTGAGGTTG
* * * * *
29826021 AAAATGTGATTTTTAGAAA-TTTGAGGGTAAAAATGGT-AATTTT-GGATGTTCGGGGGCAAAAT
1 AAAATATGATTTTT-GAAAGTTTGAGGGCAAAAAT-GTAAATTTTAAGAAGTTC-GGGGAAAAAT
29826083 GGTAATTTTTGGATA-TTCGAGGG-A
63 -GTAATTTTTGGA-AGTTCGAGGGTA
* *
29826107 AAAATATGATTTTTGGAAGTTTGAGGGCAAAAAT-TAAATTTTAGAAAAG-T-GGGGTAAAAATG
1 AAAATATGATTTTTGAAAGTTTGAGGGCAAAAATGTAAATTTTA-AGAAGTTCGGGG-AAAAATG
* *
29826169 TGATTTTTAGAAGTTCGAGGGTA
64 TAATTTTTGGAAGTTCGAGGGTA
* * * * *
29826192 ATAATGTGATTTTTGAAAGTTT-AGGGGTAAAAATATAATTTTTAAGAAGTTCGGGGAAAAATGT
1 AAAATATGATTTTTGAAAGTTTGA-GGGCAAAAATGTAAATTTTAAGAAGTTCGGGGAAAAATGT
* * *
29826256 TATTTTGGGAAGTTTGAGGGTA
65 AATTTTTGGAAGTTCGAGGGTA
29826278 AAAATATGATTTTTGAAAGTTT-AGAGGCAAAAATGTAAATTTTAAGAAGTT
1 AAAATATGATTTTTGAAAGTTTGAG-GGCAAAAATGTAAATTTTAAGAAGTT
29826329 TAAGGGTAAA
Statistics
Matches: 186, Mismatches: 24, Indels: 24
0.79 0.10 0.10
Matches are distributed among these distances:
83 1 0.01
84 24 0.13
85 48 0.26
86 107 0.58
87 6 0.03
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.35
Consensus pattern (86 bp):
AAAATATGATTTTTGAAAGTTTGAGGGCAAAAATGTAAATTTTAAGAAGTTCGGGGAAAAATGTA
ATTTTTGGAAGTTCGAGGGTA
Found at i:29826290 original size:142 final size:142
Alignment explanation
Indices: 29826021--29826282 Score: 325
Period size: 142 Copynumber: 1.8 Consensus size: 142
29826011 TTTGAGGTTG
* * * * * *
29826021 AAAATGTGATTTTTAGAAATTTGAGGGTAAAAATGGTAATTTTGGATGTTCGGGGGCAAAATGGT
1 AAAATGTGATTTTTAGAAATTCGAGGGTAAAAATGGTAATTTTGAAAGTTAGGGGGAAAAATGAT
* *
29826086 AATTTTTGGATATTCGAGGGAAAAATATGATTTTTGGAAGTTTGAGGGCAAAAATTAAATTTTAG
66 AATTTTTAGATATTCGAGGGAAAAATATGATTTTGGGAAGTTTGAGGGCAAAAATTAAATTTTAG
29826151 AAAAGTGGGGTA
131 AAAAGTGGGGTA
* * * *
29826163 AAAATGTGATTTTTAGAAGTTCGAGGGTAATAAT-GTGATTTTTGAAAGTTTAGGGGTAAAAAT-
1 AAAATGTGATTTTTAGAAATTCGAGGGTAAAAATGGT-AATTTTGAAAG-TTAGGGGGAAAAATG
* * *
29826226 ATAATTTTTAAGA-AGTTCG-GGGAAAAATGTTATTTTGGGAAGTTTGAGGGTAAAAAT
64 ATAATTTTT-AGATA-TTCGAGGGAAAAATATGATTTTGGGAAGTTTGAGGGCAAAAAT
29826283 ATGATTTTTG
Statistics
Matches: 101, Mismatches: 15, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
141 2 0.02
142 82 0.81
143 17 0.17
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.35
Consensus pattern (142 bp):
AAAATGTGATTTTTAGAAATTCGAGGGTAAAAATGGTAATTTTGAAAGTTAGGGGGAAAAATGAT
AATTTTTAGATATTCGAGGGAAAAATATGATTTTGGGAAGTTTGAGGGCAAAAATTAAATTTTAG
AAAAGTGGGGTA
Found at i:29827965 original size:26 final size:26
Alignment explanation
Indices: 29827909--29827966 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
29827899 ATCATTAAGC
* * *
29827909 TTTTAGGGTTTTGTAATTGGGTTAAAT
1 TTTT-GGGTTTTGTAATTGGCTCAAAA
29827936 TTTTGGG-TTTGTAATTGGACTCAAAA
1 TTTTGGGTTTTGTAATTGG-CTCAAAA
29827962 TTTTG
1 TTTTG
29827967 TAATTGGACA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 11 0.41
26 12 0.44
27 4 0.15
ACGTcount: A:0.22, C:0.03, G:0.24, T:0.50
Consensus pattern (26 bp):
TTTTGGGTTTTGTAATTGGCTCAAAA
Found at i:29828000 original size:6 final size:6
Alignment explanation
Indices: 29827981--29828031 Score: 56
Period size: 6 Copynumber: 9.0 Consensus size: 6
29827971 TGGACATTAG
*
29827981 TAAATT TAAA-- TAAATT TAAACT TAAATT TACAA-- TAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TA-AATT TAAATT TAAATT
29828026 TAAATT
1 TAAATT
29828032 CTGTTTGGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
4 6 0.16
5 2 0.05
6 28 0.74
7 2 0.05
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (6 bp):
TAAATT
Found at i:29828019 original size:11 final size:10
Alignment explanation
Indices: 29827981--29828024 Score: 61
Period size: 10 Copynumber: 4.1 Consensus size: 10
29827971 TGGACATTAG
29827981 TAAATTTAAA
1 TAAATTTAAA
29827991 TAAATTTAAA
1 TAAATTTAAA
29828001 CTTAAATTTACAA
1 --TAAATTTA-AA
29828014 TAAATTTAAA
1 TAAATTTAAA
29828024 T
1 T
29828025 TTAAATTCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
10 13 0.42
11 8 0.26
12 8 0.26
13 2 0.06
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (10 bp):
TAAATTTAAA
Found at i:29828019 original size:23 final size:22
Alignment explanation
Indices: 29827981--29828031 Score: 84
Period size: 23 Copynumber: 2.3 Consensus size: 22
29827971 TGGACATTAG
29827981 TAAATTTAAATAAATTTAAACT
1 TAAATTTAAATAAATTTAAACT
*
29828003 TAAATTTACAATAAATTTAAATT
1 TAAATTTA-AATAAATTTAAACT
29828026 TAAATT
1 TAAATT
29828032 CTGTTTGGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 8 0.30
23 19 0.70
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAATTTAAATAAATTTAAACT
Found at i:29828553 original size:39 final size:39
Alignment explanation
Indices: 29828509--29828908 Score: 215
Period size: 39 Copynumber: 10.3 Consensus size: 39
29828499 CCCCATAATT
* *
29828509 GGGGTAAGAGATTGGCTGATGATGATCTACCCCAGGCTC
1 GGGGTAAGAGATTGACTGATGATGATCTGCCCCAGGCTC
* * * * * * * *
29828548 GGGGTAAGAGATCGAATGGCTG-TAATTTGACCTAGCCTC
1 GGGGTAAGAGATTGACT-GATGATGATCTGCCCCAGGCTC
* * * *
29828587 GGGGTAAGAGATTGACTGGTGGTGATCTGTCCTAGGCTC
1 GGGGTAAGAGATTGACTGATGATGATCTGCCCCAGGCTC
* * **
29828626 GGGGTAAGAGATTGAATGGCT-ACAATCTGCCCCAGGCTC
1 GGGGTAAGAGATTGACT-GATGATGATCTGCCCCAGGCTC
* * * *
29828665 GGGGTAAGAGATTGGCTGATGGTGATCTGTCCCAAGCTC
1 GGGGTAAGAGATTGACTGATGATGATCTGCCCCAGGCTC
* * * * ** **
29828704 TGGGTAAGAGATCGAATGGCT-ACAATCTGCCATAGGCTC
1 GGGGTAAGAGATTGACT-GATGATGATCTGCCCCAGGCTC
* * * * *
29828743 GGGGTAAGAGATCGAATGGCTGCA-AAT-TGCCCTAGGCTC
1 GGGGTAAGAGATTGACT-GATG-ATGATCTGCCCCAGGCTC
* * *
29828782 GGGGTAAAAGATTGACTGATGGTGATATGCCCCAGGCTC
1 GGGGTAAGAGATTGACTGATGATGATCTGCCCCAGGCTC
* * * * * * * *
29828821 AGGGCAAGAGATCGAATGGCT-ATAATATGCCCTC-GGCTA
1 GGGGTAAGAGATTGACT-GATGATGATCTGCCC-CAGGCTC
* * *
29828860 GGGGTAAGAGATTGGCTG--GATGGTCTACCCCAGGCTC
1 GGGGTAAGAGATTGACTGATGATGATCTGCCCCAGGCTC
* *
29828897 GAGGTAAAAGAT
1 GGGGTAAGAGAT
29828909 CGAATCTTCA
Statistics
Matches: 274, Mismatches: 74, Indels: 28
0.73 0.20 0.07
Matches are distributed among these distances:
36 1 0.00
37 21 0.08
38 11 0.04
39 227 0.83
40 13 0.05
41 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.23
Consensus pattern (39 bp):
GGGGTAAGAGATTGACTGATGATGATCTGCCCCAGGCTC
Found at i:29828624 original size:78 final size:77
Alignment explanation
Indices: 29828509--29828754 Score: 339
Period size: 78 Copynumber: 3.2 Consensus size: 77
29828499 CCCCATAATT
* ** **
29828509 GGGGTAAGAGATTGGCTGATGATGATCTACCCCAGGCTCGGGGTAAGAGATCGAATGGCTGTAAT
1 GGGGTAAGAGATTGGCTGATGGTGATCTGTCCCAGGCTCGGGGTAAGAGATCGAATGGCTACAAT
* *
29828574 TTGACCTAGCCTC
66 CTG-CCTAGGCTC
* * * *
29828587 GGGGTAAGAGATTGACTGGTGGTGATCTGTCCTAGGCTCGGGGTAAGAGATTGAATGGCTACAAT
1 GGGGTAAGAGATTGGCTGATGGTGATCTGTCCCAGGCTCGGGGTAAGAGATCGAATGGCTACAAT
*
29828652 CTGCCCCAGGCTC
66 CTG-CCTAGGCTC
* *
29828665 GGGGTAAGAGATTGGCTGATGGTGATCTGTCCCAAGCTCTGGGTAAGAGATCGAATGGCTACAAT
1 GGGGTAAGAGATTGGCTGATGGTGATCTGTCCCAGGCTCGGGGTAAGAGATCGAATGGCTACAAT
29828730 CTGCCATAGGCTC
66 CTGCC-TAGGCTC
29828743 GGGGTAAGAGAT
1 GGGGTAAGAGAT
29828755 CGAATGGCTG
Statistics
Matches: 147, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
77 2 0.01
78 145 0.99
ACGTcount: A:0.24, C:0.18, G:0.34, T:0.24
Consensus pattern (77 bp):
GGGGTAAGAGATTGGCTGATGGTGATCTGTCCCAGGCTCGGGGTAAGAGATCGAATGGCTACAAT
CTGCCTAGGCTC
Found at i:29828709 original size:117 final size:117
Alignment explanation
Indices: 29828611--29828871 Score: 355
Period size: 117 Copynumber: 2.2 Consensus size: 117
29828601 ACTGGTGGTG
* *
29828611 ATCTGTCC-TAGGCTCGGGGTAAGAGATTGAATGGCTAC-AATCTGCCCCAGGCTCGGGGTAAGA
1 ATCTG-CCATAGGCTCGGGGTAAGAGATCGAATGGCTACAAAT-TGCCCCAGGCTCGGGGTAAAA
* * * *
29828674 GATTGGCTGATGGTGATCTGTCCCAAGCTCTGGGTAAGAGATCGAATGGCTACA
64 GATTGACTGATGGTGATATGCCCCAAGCTCAGGGTAAGAGATCGAATGGCTACA
* *
29828728 ATCTGCCATAGGCTCGGGGTAAGAGATCGAATGGCTGCAAATTGCCCTAGGCTCGGGGTAAAAGA
1 ATCTGCCATAGGCTCGGGGTAAGAGATCGAATGGCTACAAATTGCCCCAGGCTCGGGGTAAAAGA
* * *
29828793 TTGACTGATGGTGATATGCCCCAGGCTCAGGGCAAGAGATCGAATGGCTATA
66 TTGACTGATGGTGATATGCCCCAAGCTCAGGGTAAGAGATCGAATGGCTACA
* * * *
29828845 ATATGCCCTCGGCTAGGGGTAAGAGAT
1 ATCTGCCATAGGCTCGGGGTAAGAGAT
29828872 TGGCTGGATG
Statistics
Matches: 127, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
116 2 0.02
117 122 0.96
118 3 0.02
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.23
Consensus pattern (117 bp):
ATCTGCCATAGGCTCGGGGTAAGAGATCGAATGGCTACAAATTGCCCCAGGCTCGGGGTAAAAGA
TTGACTGATGGTGATATGCCCCAAGCTCAGGGTAAGAGATCGAATGGCTACA
Found at i:29828787 original size:78 final size:77
Alignment explanation
Indices: 29828509--29828793 Score: 313
Period size: 78 Copynumber: 3.7 Consensus size: 77
29828499 CCCCATAATT
* * * * * **
29828509 GGGGTAAGAGATTGGCTGATGATGATCTACCCCAGGCTCGGGGTAAGAGATCGAATGGCTGTAAT
1 GGGGTAAGAGATTGACTGGTGGTGATCTGCCCTAGGCTCGGGGTAAGAGATCGAATGGCTACAAT
* *
29828574 TTGACCTAGCCTC
66 CTG-CCTAGGCTC
* *
29828587 GGGGTAAGAGATTGACTGGTGGTGATCTGTCCTAGGCTCGGGGTAAGAGATTGAATGGCTACAAT
1 GGGGTAAGAGATTGACTGGTGGTGATCTGCCCTAGGCTCGGGGTAAGAGATCGAATGGCTACAAT
*
29828652 CTGCCCCAGGCTC
66 CTG-CCTAGGCTC
* * * *
29828665 GGGGTAAGAGATTGGCTGATGGTGATCTGTCCC-AAGCTCTGGGTAAGAGATCGAATGGCTACAA
1 GGGGTAAGAGATTGACTGGTGGTGATCTG-CCCTAGGCTCGGGGTAAGAGATCGAATGGCTACAA
29828729 TCTGCCATAGGCTC
65 TCTGCC-TAGGCTC
* * *** *
29828743 GGGGTAAGAGATCGAATGGCTGCAAAT-TGCCCTAGGCTCGGGGTAAAAGAT
1 GGGGTAAGAGATTGACTGG-TGGTGATCTGCCCTAGGCTCGGGGTAAGAGAT
29828794 TGACTGATGG
Statistics
Matches: 173, Mismatches: 30, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
77 5 0.03
78 162 0.94
79 6 0.03
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.24
Consensus pattern (77 bp):
GGGGTAAGAGATTGACTGGTGGTGATCTGCCCTAGGCTCGGGGTAAGAGATCGAATGGCTACAAT
CTGCCTAGGCTC
Found at i:29841216 original size:29 final size:30
Alignment explanation
Indices: 29841160--29841228 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
29841150 ATTTTCGAGG
**
29841160 AATTTGAGGATCAAAATTGAATTTTTTGGA
1 AATTTGAGGATCAAAATTGAAACTTTTGGA
* *
29841190 AATTTTAGGATTAAAATT-AAACTTTTGGAA
1 AATTTGAGGATCAAAATTGAAACTTTTGG-A
29841220 AATTTGAGG
1 AATTTGAGG
29841229 TTGAAAATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 8 0.24
30 25 0.76
ACGTcount: A:0.39, C:0.03, G:0.19, T:0.39
Consensus pattern (30 bp):
AATTTGAGGATCAAAATTGAAACTTTTGGA
Found at i:29841236 original size:30 final size:29
Alignment explanation
Indices: 29841160--29841236 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 29
29841150 ATTTTCGAGG
* **
29841160 AATTTGAGGATCAAAATTGAATTTTTTGGA
1 AATTTGAGG-TTAAAATTGAAACTTTTGGA
*
29841190 AATTTTAGGATTAAAATT-AAACTTTTGGAA
1 AATTTGAGG-TTAAAATTGAAACTTTTGG-A
29841220 AATTTGAGGTTGAAAAT
1 AATTTGAGGTT-AAAAT
29841237 GTGATTTTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
29 10 0.25
30 30 0.75
ACGTcount: A:0.40, C:0.03, G:0.18, T:0.39
Consensus pattern (29 bp):
AATTTGAGGTTAAAATTGAAACTTTTGGA
Found at i:29841264 original size:29 final size:30
Alignment explanation
Indices: 29841218--29841274 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
29841208 AAACTTTTGG
***
29841218 AAAATTTGAGGTTGAAAAT-GTGATTTTCA
1 AAAATTTGAGGGCAAAAATGGTGATTTTCA
29841247 AAAATTTGAGGGCAAAAATGGTGATTTT
1 AAAATTTGAGGGCAAAAATGGTGATTTT
29841275 TGGAAGTTCG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.39, C:0.04, G:0.23, T:0.35
Consensus pattern (30 bp):
AAAATTTGAGGGCAAAAATGGTGATTTTCA
Found at i:29841293 original size:29 final size:28
Alignment explanation
Indices: 29841261--29841439 Score: 119
Period size: 29 Copynumber: 6.1 Consensus size: 28
29841251 TTTGAGGGCA
* * *
29841261 AAAATGGTGATTTTTGGAAGTTCGGGGGCA
1 AAAAT-GTAATTTTTGGAAGTTCAGGGG-T
*
29841291 AAAATGTAATTTTTGGAAAAGTT-TGGTGGTT
1 AAAATGTAATTTTTGG--AAGTTCAGG-GG-T
* * * * * *
29841322 AAATTGTGATTTTCGAAAGTTTAAGGGT
1 AAAATGTAATTTTTGGAAGTTCAGGGGT
* * *
29841350 AATAATGTAATTTTTAGAAGTTTAGGGGA
1 AA-AATGTAATTTTTGGAAGTTCAGGGGT
29841379 AAAATGTAATTTTTGAGAAGTTCAGGGGT
1 AAAATGTAATTTTTG-GAAGTTCAGGGGT
* *
29841408 AAAATTGTGATTTTAGGAAGTTC-GGCGGT
1 AAAA-TGTAATTTTTGGAAGTTCAGG-GGT
29841437 AAA
1 AAA
29841440 TTTTAAGAAG
Statistics
Matches: 119, Mismatches: 22, Indels: 17
0.75 0.14 0.11
Matches are distributed among these distances:
28 17 0.14
29 66 0.55
30 17 0.14
31 19 0.16
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.36
Consensus pattern (28 bp):
AAAATGTAATTTTTGGAAGTTCAGGGGT
Found at i:29841438 original size:87 final size:89
Alignment explanation
Indices: 29841212--29841429 Score: 223
Period size: 89 Copynumber: 2.5 Consensus size: 89
29841202 AAAATTAAAC
* * * * * * *
29841212 TTTTGGAAAATTTGAGGTTG-AAAA-TGTGATTTTCA-AAAATTTGAGGGCAAAAATGGTGATTT
1 TTTTGGAAAAGTT-AGGTGGTAAAATTGTGATTTT-AGAAAGTTTAAGGGTAATAAT-GTAATTT
* *
29841274 TTGGAAGTTCGGGGGCAAAAATGTAAT
63 TTAGAAGTTCAGGGGCAAAAATGTAAT
* * *
29841301 TTTTGGAAAAGTTTGGTGGTTAAATTGTGATTTTCGAAAGTTTAAGGGTAATAATGTAATTTTTA
1 TTTTGGAAAAGTTAGGTGGTAAAATTGTGATTTTAGAAAGTTTAAGGGTAATAATGTAATTTTTA
*
29841366 GAAGTTTAGGGG-AAAAATGTAAT
66 GAAGTTCAGGGGCAAAAATGTAAT
* *
29841389 TTTT-GAGAAGTTCAGG-GGTAAAATTGTGATTTTAGGAAGTT
1 TTTTGGAAAAGTT-AGGTGGTAAAATTGTGATTTTAGAAAGTT
29841430 CGGCGGTAAA
Statistics
Matches: 107, Mismatches: 18, Indels: 10
0.79 0.13 0.07
Matches are distributed among these distances:
87 29 0.27
88 21 0.20
89 33 0.31
90 24 0.22
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.37
Consensus pattern (89 bp):
TTTTGGAAAAGTTAGGTGGTAAAATTGTGATTTTAGAAAGTTTAAGGGTAATAATGTAATTTTTA
GAAGTTCAGGGGCAAAAATGTAAT
Found at i:29841449 original size:22 final size:22
Alignment explanation
Indices: 29841417--29841461 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
29841407 TAAAATTGTG
*
29841417 ATTTTAGGAAGTTCGGCGGTAA
1 ATTTTAAGAAGTTCGGCGGTAA
* *
29841439 ATTTTAAGAAGTTTGGGGGTAA
1 ATTTTAAGAAGTTCGGCGGTAA
29841461 A
1 A
29841462 ACTATAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.33
Consensus pattern (22 bp):
ATTTTAAGAAGTTCGGCGGTAA
Found at i:29842668 original size:14 final size:14
Alignment explanation
Indices: 29842642--29842675 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
29842632 TAATAACGGT
29842642 AATATA-ATAAATA
1 AATATATATAAATA
*
29842655 AATATATATTAATA
1 AATATATATAAATA
29842669 AATATAT
1 AATATAT
29842676 GCATAGGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AATATATATAAATA
Found at i:29843242 original size:22 final size:23
Alignment explanation
Indices: 29843215--29843257 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
29843205 TGGACATTAG
29843215 TAAATTTA-AAAAAATTTAAACT
1 TAAATTTACAAAAAATTTAAACT
*
29843237 TAAATTTACAATAAATTTAAA
1 TAAATTTACAAAAAATTTAAA
29843258 TTTCAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (23 bp):
TAAATTTACAAAAAATTTAAACT
Found at i:29843253 original size:11 final size:10
Alignment explanation
Indices: 29843215--29843274 Score: 54
Period size: 10 Copynumber: 6.0 Consensus size: 10
29843205 TGGACATTAG
29843215 TAAATTTAAA
1 TAAATTTAAA
*
29843225 AAAATTTAAA
1 TAAATTTAAA
29843235 CTTAAATTTACAA
1 --TAAATTTA-AA
29843248 TAAATTTAAA
1 TAAATTTAAA
*
29843258 T---TTCAAA
1 TAAATTTAAA
29843265 TAAATTTAAA
1 TAAATTTAAA
29843275 CTTAAAATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
7 6 0.15
10 17 0.43
11 8 0.20
12 7 0.17
13 2 0.05
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (10 bp):
TAAATTTAAA
Found at i:29843256 original size:17 final size:17
Alignment explanation
Indices: 29843231--29843293 Score: 83
Period size: 17 Copynumber: 3.7 Consensus size: 17
29843221 TAAAAAAATT
*
29843231 TAAACTTAAATTTACAA
1 TAAATTTAAATTTACAA
29843248 TAAATTTAAATTT-CAAA
1 TAAATTTAAATTTAC-AA
* *
29843265 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTACAA
29843282 TAAATTTAAATT
1 TAAATTTAAATT
29843294 CTGTTTGTGT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
16 1 0.03
17 39 0.98
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTTACAA
Found at i:29843257 original size:6 final size:6
Alignment explanation
Indices: 29843226--29843293 Score: 56
Period size: 6 Copynumber: 11.8 Consensus size: 6
29843216 AAATTTAAAA
*
29843226 AAATTT AAACTT AAATTT ACAA--T AAATTT AAATTT CAAA--T AAATTT
1 AAATTT AAATTT AAATTT A-AATTT AAATTT AAATTT -AAATTT AAATTT
* *
29843272 AAACTT AAA-AT AAATTT AAATT
1 AAATTT AAATTT AAATTT AAATT
29843294 CTGTTTGTGT
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
4 5 0.10
5 7 0.14
6 33 0.66
7 5 0.10
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (6 bp):
AAATTT
Found at i:29848054 original size:5 final size:5
Alignment explanation
Indices: 29848044--29848085 Score: 66
Period size: 5 Copynumber: 8.2 Consensus size: 5
29848034 AGTTGATCGT
*
29848044 GGTCG GGTCG GGTCG GGTCG GGTCT GGTCG GGTTCG GGTCG G
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GG-TCG GGTCG G
29848086 ACTTTAACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 29 0.85
6 5 0.15
ACGTcount: A:0.00, C:0.19, G:0.57, T:0.24
Consensus pattern (5 bp):
GGTCG
Found at i:29848485 original size:32 final size:34
Alignment explanation
Indices: 29848449--29848531 Score: 95
Period size: 32 Copynumber: 2.6 Consensus size: 34
29848439 GTAAAAACGC
* *
29848449 ATAAAAATAACATC-AAAATAAC-CAAAACAACA
1 ATAAAAATAACAGCAAAAACAACACAAAACAACA
29848481 ATAAAAATAACAGCAAAAACAACAGCAAAACAAC-
1 ATAAAAATAACAGCAAAAACAACA-CAAAACAACA
*
29848515 --AAAAATAACAACAAAAA
1 ATAAAAATAACAGCAAAAA
29848532 TAGTAACAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
32 29 0.64
33 7 0.16
35 9 0.20
ACGTcount: A:0.71, C:0.18, G:0.02, T:0.08
Consensus pattern (34 bp):
ATAAAAATAACAGCAAAAACAACACAAAACAACA
Found at i:29848524 original size:12 final size:12
Alignment explanation
Indices: 29848451--29848583 Score: 68
Period size: 12 Copynumber: 11.8 Consensus size: 12
29848441 AAAAACGCAT
*
29848451 AAAAATAACATC
1 AAAAATAACAAC
29848463 -AAAATAAC--C
1 AAAAATAACAAC
* *
29848472 -AAAACAACAAT
1 AAAAATAACAAC
*
29848483 AAAAATAACAGC
1 AAAAATAACAAC
29848495 --AAA-AACAAC
1 AAAAATAACAAC
**
29848504 AGCAA-AACAAC
1 AAAAATAACAAC
29848515 AAAAATAACAAC
1 AAAAATAACAAC
**
29848527 AAAAATAGTAAC
1 AAAAATAACAAC
* *
29848539 AAAAA-AATAGC
1 AAAAATAACAAC
* ***
29848550 AACAATGGGAAC
1 AAAAATAACAAC
*
29848562 AAAAACAACAAC
1 AAAAATAACAAC
29848574 AAAAATAACA
1 AAAAATAACA
29848584 GTATCAAAAT
Statistics
Matches: 90, Mismatches: 24, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
9 13 0.14
10 3 0.03
11 27 0.30
12 47 0.52
ACGTcount: A:0.69, C:0.17, G:0.05, T:0.08
Consensus pattern (12 bp):
AAAAATAACAAC
Found at i:29848542 original size:44 final size:43
Alignment explanation
Indices: 29848451--29848583 Score: 122
Period size: 44 Copynumber: 3.0 Consensus size: 43
29848441 AAAAACGCAT
* * * * *
29848451 AAAAATAACATCAAAATAACCAAAACAACAATAAAAATAACAGC
1 AAAAA-AACAGCAAAACAACAAAAACAACAACAAAAATAACAAC
* **
29848495 AAAAACAACAGCAAAACAACAAAAATAACAACAAAAATAGTAAC
1 AAAAA-AACAGCAAAACAACAAAAACAACAACAAAAATAACAAC
* *
29848539 AAAAAAATAGCAACAATGGGAACAAAAACAACAACAAAAATAACA
1 AAAAAAACAGCAA-AA---CAACAAAAACAACAACAAAAATAACA
29848584 GTATCAAAAT
Statistics
Matches: 71, Mismatches: 14, Indels: 5
0.79 0.16 0.06
Matches are distributed among these distances:
43 7 0.10
44 42 0.59
47 22 0.31
ACGTcount: A:0.69, C:0.17, G:0.05, T:0.08
Consensus pattern (43 bp):
AAAAAAACAGCAAAACAACAAAAACAACAACAAAAATAACAAC
Found at i:29848546 original size:14 final size:15
Alignment explanation
Indices: 29848509--29848554 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
29848499 ACAACAGCAA
29848509 AACAAC-AAAA-A-T
1 AACAACAAAAATAGT
29848521 AACAACAAAAATAGT
1 AACAACAAAAATAGT
*
29848536 AACAA-AAAAATAGC
1 AACAACAAAAATAGT
29848550 AACAA
1 AACAA
29848555 TGGGAACAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 6 0.20
13 4 0.13
14 14 0.47
15 6 0.20
ACGTcount: A:0.72, C:0.15, G:0.04, T:0.09
Consensus pattern (15 bp):
AACAACAAAAATAGT
Found at i:29848694 original size:23 final size:21
Alignment explanation
Indices: 29848607--29848705 Score: 84
Period size: 22 Copynumber: 4.8 Consensus size: 21
29848597 AAAAAAAACT
* *
29848607 AAAACAGCAACCAAAATAGTAA
1 AAAATAGC-ACCAAAACAGTAA
29848629 AAAA-A-CACCAAAACA--AGA
1 AAAATAGCACCAAAACAGTA-A
**
29848647 AAAA-A-CATTAAAACAGTAA
1 AAAATAGCACCAAAACAGTAA
29848666 AAAATAGCAACCAAAACAGTAAA
1 AAAATAGC-ACCAAAACAGT-AA
29848689 AAAATAGCACCAAAACA
1 AAAATAGCACCAAAACA
29848706 ACAATATAAT
Statistics
Matches: 65, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
17 1 0.02
18 14 0.22
19 13 0.20
20 3 0.05
21 2 0.03
22 22 0.34
23 10 0.15
ACGTcount: A:0.67, C:0.18, G:0.07, T:0.08
Consensus pattern (21 bp):
AAAATAGCACCAAAACAGTAA
Found at i:29851063 original size:14 final size:14
Alignment explanation
Indices: 29851044--29851072 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
29851034 TATGGATCAC
29851044 TCTCCACTAAAACT
1 TCTCCACTAAAACT
29851058 TCTCCACTAAAACT
1 TCTCCACTAAAACT
29851072 T
1 T
29851073 TCCTCTTGAA
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:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (14 bp):
TCTCCACTAAAACT
Found at i:29866443 original size:18 final size:19
Alignment explanation
Indices: 29866410--29866446 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
29866400 TGGGTAAGCA
29866410 AATTTTGATCGTTTTTAGT
1 AATTTTGATCGTTTTTAGT
*
29866429 AATTTTTAT-GTTTTTAGT
1 AATTTTGATCGTTTTTAGT
29866447 CCGTATCAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.22, C:0.03, G:0.14, T:0.62
Consensus pattern (19 bp):
AATTTTGATCGTTTTTAGT
Found at i:29879550 original size:15 final size:17
Alignment explanation
Indices: 29879524--29879558 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
29879514 TAAAAAATCC
29879524 AAAATTACAAGTC-TAA
1 AAAATTACAAGTCTTAA
29879540 AAAATTA-AAGTCTTAA
1 AAAATTACAAGTCTTAA
29879556 AAA
1 AAA
29879559 CACTTATCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.60, C:0.09, G:0.06, T:0.26
Consensus pattern (17 bp):
AAAATTACAAGTCTTAA
Found at i:29895596 original size:21 final size:21
Alignment explanation
Indices: 29895572--29895628 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
29895562 TGAAGAGTGT
* *
29895572 TGTGGTTGCATCTGATTCTGG
1 TGTGGATGCATCTGATTCTAG
* *
29895593 TGTGGCTGCATCCGATTCTAG
1 TGTGGATGCATCTGATTCTAG
29895614 TGTGGATGCATCTGA
1 TGTGGATGCATCTGA
29895629 GTATGCTGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.14, C:0.18, G:0.32, T:0.37
Consensus pattern (21 bp):
TGTGGATGCATCTGATTCTAG
Found at i:29904142 original size:21 final size:21
Alignment explanation
Indices: 29904115--29904168 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
29904105 AAGTTTTTTA
29904115 GTATCGGTAGAAG-CATGATTT
1 GTATCGGTAGAAGTCAT-ATTT
* *
29904136 GTTTCGGTAGAAGTCATCTTT
1 GTATCGGTAGAAGTCATATTT
29904157 GTATCGGTAGAA
1 GTATCGGTAGAA
29904169 CCATCTCAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 26 0.90
22 3 0.10
ACGTcount: A:0.26, C:0.11, G:0.28, T:0.35
Consensus pattern (21 bp):
GTATCGGTAGAAGTCATATTT
Found at i:29906256 original size:233 final size:233
Alignment explanation
Indices: 29905849--29906314 Score: 686
Period size: 233 Copynumber: 2.0 Consensus size: 233
29905839 TATTCGGCTC
** * * *
29905849 AGAGATCCTGAATTAGATGAATGAAAGTTGGTGGCAGAAATACGAGATTCTTTCACGTGTATGCG
1 AGAGATCCTGAATTAGATGAATGAAAGAGGGTGGCAAAAATACGAGATTCTTTCACGTGCATGCC
*
29905914 ACACATCGGGCGAGGAAGAATCACATTAAGGGCTTACGGGATGATAGGAAGAGATGGATGAGTGA
66 ACACATCGGGCGAGGAAGAATCACATTAAGGGCTTACGGGATGATAGGAAGAGATGGATCAGTGA
* * * *
29905979 TACTCGAGGAATTTGTGAGGTGGCTTATGAGTATTTCAAGGGATTGTTTAAGTCAGAATGTAATA
131 TACTCGAGGAATTTGTGAGATAGCTTATGAGTATTTCAAGGGATTGTTTAAGTCAAAATGTAACA
* * *
29906044 ATCGCTTTGAGAATGTGCTTATCTTTAT-CCTGCATTGT
196 ACCGCTTTGAGAATGTGCTTAGCTTGATCCCT-CATTGT
* *
29906082 AGAGATCCT-ACATTAGATTG-ATGAAAGAGGGTGGCAAAAATATGAGATTCTTTCACGTGCGTG
1 AGAGATCCTGA-ATTAGA-TGAATGAAAGAGGGTGGCAAAAATACGAGATTCTTTCACGTGCATG
* **
29906145 CCACACATCGGGCGAGGAAGAATCACATTGAGGGCTTACGGGATGATAGGGGGAGATGGATCAGT
64 CCACACATCGGGCGAGGAAGAATCACATTAAGGGCTTACGGGATGATAGGAAGAGATGGATCAGT
* * *
29906210 GATATTCGAGGAATTTGTGAGATAGCTTGTGAGTATTTCGAGGGATTGTTTAAGTCAAAATGTAA
129 GATACTCGAGGAATTTGTGAGATAGCTTATGAGTATTTCAAGGGATTGTTTAAGTCAAAATGTAA
*
29906275 CAACCGCTTTGAGCATGTGCTTAGCTTGATCCCTCATTGT
194 CAACCGCTTTGAGAATGTGCTTAGCTTGATCCCTCATTGT
29906315 GTCGCATCGA
Statistics
Matches: 208, Mismatches: 22, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
232 1 0.00
233 202 0.97
234 5 0.02
ACGTcount: A:0.29, C:0.13, G:0.29, T:0.29
Consensus pattern (233 bp):
AGAGATCCTGAATTAGATGAATGAAAGAGGGTGGCAAAAATACGAGATTCTTTCACGTGCATGCC
ACACATCGGGCGAGGAAGAATCACATTAAGGGCTTACGGGATGATAGGAAGAGATGGATCAGTGA
TACTCGAGGAATTTGTGAGATAGCTTATGAGTATTTCAAGGGATTGTTTAAGTCAAAATGTAACA
ACCGCTTTGAGAATGTGCTTAGCTTGATCCCTCATTGT
Found at i:29912703 original size:23 final size:24
Alignment explanation
Indices: 29912676--29912731 Score: 60
Period size: 28 Copynumber: 2.2 Consensus size: 24
29912666 AAGATCCACA
29912676 TAATG-GTACTAGTCATCCATTAC
1 TAATGAGTACTAGTCATCCATTAC
*
29912699 TAATGCAATCTTACTAGTCATCCATTAC
1 TAATG--A--GTACTAGTCATCCATTAC
29912727 TAATG
1 TAATG
29912732 CAATCTAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 5 0.19
28 22 0.81
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (24 bp):
TAATGAGTACTAGTCATCCATTAC
Found at i:29912714 original size:28 final size:28
Alignment explanation
Indices: 29912682--29912737 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
29912672 CACATAATGG
29912682 TACTAGTCATCCATTACTAATGCAATCT
1 TACTAGTCATCCATTACTAATGCAATCT
29912710 TACTAGTCATCCATTACTAATGCAATCT
1 TACTAGTCATCCATTACTAATGCAATCT
29912738 AAGTCATTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.36
Consensus pattern (28 bp):
TACTAGTCATCCATTACTAATGCAATCT
Found at i:29917346 original size:29 final size:29
Alignment explanation
Indices: 29917313--29917420 Score: 99
Period size: 29 Copynumber: 3.5 Consensus size: 29
29917303 AAAATATTAT
29917313 TATAATATAATTAATTTCATTTTAAAACG
1 TATAATATAATTAATTTCATTTTAAAACG
* * * **
29917342 TATAATTTAATTAAATGTATCAAATTAAAATATTAT
1 TATAATATAATT-AAT-T-TC-ATTTTAAA-A--CG
29917378 TATAATATAATTAATTTCATTTTAAAACG
1 TATAATATAATTAATTTCATTTTAAAACG
*
29917407 TATAATTTAATTAA
1 TATAATATAATTAA
29917421 ATGTATCAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
29 24 0.39
30 3 0.05
31 2 0.03
32 8 0.13
33 8 0.13
34 2 0.03
35 3 0.05
36 11 0.18
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (29 bp):
TATAATATAATTAATTTCATTTTAAAACG
Found at i:29917361 original size:65 final size:65
Alignment explanation
Indices: 29917285--29917479 Score: 347
Period size: 65 Copynumber: 3.0 Consensus size: 65
29917275 TAAATTAAAA
29917285 AATTAAATGTATCAAATTAAAATATTATTATAATATAATTAATTTCATTTTAAAACGTATAATTT
1 AATTAAATGTATCAAATTAAAATATTATTATAATATAATTAATTTCATTTTAAAACGTATAATTT
29917350 AATTAAATGTATCAAATTAAAATATTATTATAATATAATTAATTTCATTTTAAAACGTATAATTT
1 AATTAAATGTATCAAATTAAAATATTATTATAATATAATTAATTTCATTTTAAAACGTATAATTT
* * *
29917415 AATTAAATGTATCAAATTAAAACATTATTATAATATAATTAA-TTCTATTTTAGAGCGTATAATT
1 AATTAAATGTATCAAATTAAAATATTATTATAATATAATTAATTTC-ATTTTAAAACGTATAATT
29917479 T
65 T
29917480 CTTTTTGAAT
Statistics
Matches: 126, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
64 3 0.02
65 123 0.98
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (65 bp):
AATTAAATGTATCAAATTAAAATATTATTATAATATAATTAATTTCATTTTAAAACGTATAATTT
Found at i:29924465 original size:17 final size:17
Alignment explanation
Indices: 29924444--29924482 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
29924434 AACAAGTAAC
*
29924444 AAATATAATTATAATAA
1 AAATATAATGATAATAA
* *
29924461 TAATATCATGATAATAA
1 AAATATAATGATAATAA
29924478 AAATA
1 AAATA
29924483 ACAAAATAAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (17 bp):
AAATATAATGATAATAA
Found at i:29926453 original size:50 final size:50
Alignment explanation
Indices: 29926265--29926754 Score: 236
Period size: 50 Copynumber: 9.8 Consensus size: 50
29926255 ATTCGATATT
* * * * * * *
29926265 GTAGCTTTATCCTACTCCACTGCAACTTCAAGGATATAAGATTTGATGTC
1 GTAGCTTCATCTTGCTCCACTGTAACTTTAGGGAGATAAGATTTGATGTC
* * *
29926315 GTAACTTCATCTTGCTCC-CTTGTATCTTTAGGGAGATAAGATTT-ACT-TT
1 GTAGCTTCATCTTGCTCCAC-TGTAACTTTAGGGAGATAAGATTTGA-TGTC
* * * * *
29926364 GTAGCCTTAATC-CGAC-CCATTGCAACTTTAGGG-GTATAAGATTTGATGTG
1 GTAG-CTTCATCTTG-CTCCACTGTAACTTTAGGGAG-ATAAGATTTGATGTC
* * *
29926414 GTAGTTTCATCTTGCTCCACTGTATCTTTAGGGAGATAAGATTTGCT-TC
1 GTAGCTTCATCTTGCTCCACTGTAACTTTAGGGAGATAAGATTTGATGTC
* * * * *
29926463 TATAGTTTCAATC-TGAC-CCACTGCAACTTTA-GGAGTATATGATTTGATGTG
1 -GTAGCTTC-ATCTTG-CTCCACTGTAACTTTAGGGAG-ATAAGATTTGATGTC
* * ** * * *
29926514 GTAGCTTCATCTTCCTCTACTACAACTTTAGAGAGATAAAGATTTGCT-AC
1 GTAGCTTCATCTTGCTCCACTGTAACTTTAGGGAGAT-AAGATTTGATGTC
* * * * * *
29926564 TGTAGTTTTAATC-TGATCCACTGTAACTTCAGGGATATAGGATTTGATGTC
1 -GTAG-CTTCATCTTGCTCCACTGTAACTTTAGGGAGATAAGATTTGATGTC
** * * * *
29926615 GTAGCTTCATCTTGCTTTACTGTAA-TTTCAGGGAGATAAAAATTTGCTTTT
1 GTAGCTTCATCTTGCTCCACTGTAACTTT-AGGGAGAT-AAGATTTGATGTC
** ** * * * *
29926666 GTAGCTTCAATCTAAC-CCACTACAACTTCAGGG-GTATAGGATTTGATTTT
1 GTAGCTTC-ATCTTGCTCCACTGTAACTTTAGGGAG-ATAAGATTTGATGTC
* ** * *
29926716 GTAGTTTCATCTTGCTTTACTGTAACTTCAGAGAGATAA
1 GTAGCTTCATCTTGCTCCACTGTAACTTTAGGGAGATAA
29926755 AAATTTTCTT
Statistics
Matches: 324, Mismatches: 85, Indels: 62
0.69 0.18 0.13
Matches are distributed among these distances:
48 1 0.00
49 57 0.18
50 187 0.58
51 67 0.21
52 12 0.04
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.38
Consensus pattern (50 bp):
GTAGCTTCATCTTGCTCCACTGTAACTTTAGGGAGATAAGATTTGATGTC
Found at i:29926608 original size:101 final size:99
Alignment explanation
Indices: 29926281--29927112 Score: 697
Period size: 101 Copynumber: 8.3 Consensus size: 99
29926271 TTATCCTACT
* * * * * * *
29926281 CCACTGCAACTTCAAGGATATAAGATTTGATGTCGTAACTTCATCTTGCTC-CCTTGTATCTTTA
1 CCACTGCAACTTCAGGGATATAGGATTTGATGTCGTAGCTTCATCTTGCTCTAC-TGCAACTTCA
* * *
29926345 GGGAGATAAGATTTACTTTGTAGCCTT-AATCCGAC
65 GAGAGATAAGATTTGCTTTGTAG-CTTCAATCTGAC
* * * * * * * * * *
29926380 CCATTGCAACTTTAGGGGTATAAGATTTGATGTGGTAGTTTCATCTTGCTCCACTGTATCTTTAG
1 CCACTGCAACTTCAGGGATATAGGATTTGATGTCGTAGCTTCATCTTGCTCTACTGCAACTTCAG
* * *
29926445 GGAGATAAGATTTGCTTCTATAGTTTCAATCTGAC
66 AGAGATAAGATTTGCTT-TGTAGCTTCAATCTGAC
* * * * * *
29926480 CCACTGCAACTTTA-GGAGTATATGATTTGATGTGGTAGCTTCATCTTCCTCTACTACAACTTTA
1 CCACTGCAACTTCAGGGA-TATAGGATTTGATGTCGTAGCTTCATCTTGCTCTACTGCAACTTCA
* * * *
29926544 GAGAGATAAAGATTTGCTACTGTAGTTTTAATCTGAT
65 GAGAGAT-AAGATTTGCT-TTGTAGCTTCAATCTGAC
* * * *
29926581 CCACTGTAACTTCAGGGATATAGGATTTGATGTCGTAGCTTCATCTTGCTTTACTGTAATTTCAG
1 CCACTGCAACTTCAGGGATATAGGATTTGATGTCGTAGCTTCATCTTGCTCTACTGCAACTTCAG
* * *
29926646 GGAGATAAAAATTTGCTTTTGTAGCTTCAATCTAAC
66 AGAGAT-AAGATTTGC-TTTGTAGCTTCAATCTGAC
* * * * * * *
29926682 CCACTACAACTTCAGGGGTATAGGATTTGATTTTGTAGTTTCATCTTGCTTTACTGTAACTTCAG
1 CCACTGCAACTTCAGGGATATAGGATTTGATGTCGTAGCTTCATCTTGCTCTACTGCAACTTCAG
* * * * *
29926747 AGAGATAAAAATTTTCTTTCGTAACTTCAATCCGAT
66 AGAGAT-AAGATTTGCTTT-GTAGCTTCAATCTGAC
* * * * * * *
29926783 CTACTACAACTTCAAGGATATAGGATTTGATGACGTAACTTCAAT-TTGCTCCACTGCATCTTCA
1 CCACTGCAACTTCAGGGATATAGGATTTGATGTCGTAGCTTC-ATCTTGCTCTACTGCAACTTCA
*
29926847 -AGGAGATAAGATTTGCTTTTGTAGCTTTAAT-TCGAC
65 GA-GAGATAAGATTTGC-TTTGTAGCTTCAATCT-GAC
* * * * * **
29926883 CCACTGTAACTTCAGGGGTATAGGATTTGGTTTTGTAGCTTCATCTTGCTCTACAACAACTTCAG
1 CCACTGCAACTTCAGGGATATAGGATTTGATGTCGTAGCTTCATCTTGCTCTACTGCAACTTCAG
* *
29926948 AGAGATAAAGATTTGTCATTGTAGTTTCAATCTGAC
66 AGAGAT-AAGATTTG-CTTTGTAGCTTCAATCTGAC
* * ** * * * *
29926984 CTAATGCAACTTCAGGGGCATATGATTTGATGTCATAACTTCATCTTGCTCTACTGCATCTTCAG
1 CCACTGCAACTTCAGGGATATAGGATTTGATGTCGTAGCTTCATCTTGCTCTACTGCAACTTCAG
* * * * *
29927049 ACAGATAAGATTTACTTTCGTAGCTTTAATCCGAT
66 AGAGATAAGATTTGCTTT-GTAGCTTCAATCTGAC
* *
29927084 CCATTACAACTTCAGTGG-TATAGGATTTG
1 CCACTGCAACTTCAG-GGATATAGGATTTG
29927113 GTGTTGTATT
Statistics
Matches: 597, Mismatches: 116, Indels: 39
0.79 0.15 0.05
Matches are distributed among these distances:
99 80 0.13
100 184 0.31
101 325 0.54
102 8 0.01
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (99 bp):
CCACTGCAACTTCAGGGATATAGGATTTGATGTCGTAGCTTCATCTTGCTCTACTGCAACTTCAG
AGAGATAAGATTTGCTTTGTAGCTTCAATCTGAC
Found at i:29926919 original size:201 final size:200
Alignment explanation
Indices: 29926263--29927120 Score: 775
Period size: 201 Copynumber: 4.3 Consensus size: 200
29926253 GGATTCGATA
* * * * * *
29926263 TTGTAGCTTT-ATCCT-ACTCCACTGCAACTTCAAGGATATAAGATTTGATGTCGTAACTTCATC
1 TTGTAGCTTTAAT-CTGAC-CCACTACAACTTCAGGGGTATAGGATTTGATGTTGTAGCTTCATC
* ** * * * * * * * * * *
29926326 TTGCTC-CCTTGTATCTTTAGGGAGAT-AAGATTTACTTTGTAGCCTT-AATCCGACCCATTGCA
64 TTGCTCTAC-TACAACTTCAGAGAGATAAAGATTTTCTTCGTAG-TTTCAATCTGATCTACTGCA
* * * * ** * * *
29926388 ACTTTAGGGGTATAAGATTTGATGTGGTAGTTTCATCTTGCTCCACTGTATCTTTAGGGAGATAA
127 ACTTCAGGGATATAGGATTTGATGTCGTAACTTCATCTTGCTCCACTGCATCTTCAAGGAGATAA
29926453 GATTTGCTT
192 GATTTGCTT
* * * * * * *
29926462 CTATAG-TTTCAATCTGACCCACTGCAACTTTAGGAGTATATGATTTGATGTGGTAGCTTCATCT
1 TTGTAGCTTT-AATCTGACCCACTACAACTTCAGGGGTATAGGATTTGATGTTGTAGCTTCATCT
* * * * * * *
29926526 TCCTCTACTACAACTTTAGAGAGATAAAGATTTGCTACTGTAGTTTTAATCTGATCCACTGTAAC
65 TGCTCTACTACAACTTCAGAGAGATAAAGATTTTCTTC-GTAGTTTCAATCTGATCTACTGCAAC
* ** * *
29926591 TTCAGGGATATAGGATTTGATGTCGTAGCTTCATCTTGCTTTACTGTAAT-TTCAGGGAGATAAA
129 TTCAGGGATATAGGATTTGATGTCGTAACTTCATCTTGCTCCACTG-CATCTTCAAGGAGAT-AA
*
29926655 AATTTGCTT
192 GATTTGCTT
* * * *
29926664 TTGTAGCTTCAATCTAACCCACTACAACTTCAGGGGTATAGGATTTGATTTTGTAGTTTCATCTT
1 TTGTAGCTTTAATCTGACCCACTACAACTTCAGGGGTATAGGATTTGATGTTGTAGCTTCATCTT
* ** * ** * *
29926729 GCTTTACTGTAACTTCAGAGAGATAAAAATTTTCTTTCGTAACTTCAATCCGATCTACTACAACT
66 GCTCTACTACAACTTCAGAGAGATAAAGATTTTC-TTCGTAGTTTCAATCTGATCTACTGCAACT
* *
29926794 TCAAGGATATAGGATTTGATGACGTAACTTCAAT-TTGCTCCACTGCATCTTCAAGGAGATAAGA
130 TCAGGGATATAGGATTTGATGTCGTAACTTC-ATCTTGCTCCACTGCATCTTCAAGGAGATAAGA
29926858 TTTGCTT
194 TTTGCTT
** * *
29926865 TTGTAGCTTTAAT-TCGACCCACTGTAACTTCAGGGGTATAGGATTTGGTTTTGTAGCTTCATCT
1 TTGTAGCTTTAATCT-GACCCACTACAACTTCAGGGGTATAGGATTTGATGTTGTAGCTTCATCT
* * *
29926929 TGCTCTACAACAACTTCAGAGAGATAAAGATTTGTCATT-GTAGTTTCAATCTGACCTAATGCAA
65 TGCTCTACTACAACTTCAGAGAGATAAAGATTT-TC-TTCGTAGTTTCAATCTGATCTACTGCAA
** * * * *
29926993 CTTCAGGGGCATATGATTTGATGTCATAACTTCATCTTGCTCTACTGCATCTTC-AGACAGATAA
128 CTTCAGGGATATAGGATTTGATGTCGTAACTTCATCTTGCTCCACTGCATCTTCAAG-GAGATAA
*
29927057 GATTTACTT
192 GATTTGCTT
* * * * * *
29927066 TCGTAGCTTTAATCCGATCCATTACAACTTCAGTGGTATAGGATTTGGTGTTGTA
1 TTGTAGCTTTAATCTGACCCACTACAACTTCAGGGGTATAGGATTTGATGTTGTA
29927121 TTGATCCCTC
Statistics
Matches: 539, Mismatches: 102, Indels: 34
0.80 0.15 0.05
Matches are distributed among these distances:
198 3 0.01
199 62 0.12
200 21 0.04
201 286 0.53
202 161 0.30
203 6 0.01
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (200 bp):
TTGTAGCTTTAATCTGACCCACTACAACTTCAGGGGTATAGGATTTGATGTTGTAGCTTCATCTT
GCTCTACTACAACTTCAGAGAGATAAAGATTTTCTTCGTAGTTTCAATCTGATCTACTGCAACTT
CAGGGATATAGGATTTGATGTCGTAACTTCATCTTGCTCCACTGCATCTTCAAGGAGATAAGATT
TGCTT
Found at i:29944930 original size:50 final size:50
Alignment explanation
Indices: 29944875--29945037 Score: 263
Period size: 50 Copynumber: 3.3 Consensus size: 50
29944865 TGAAACAACT
* * * *
29944875 TGGCGAGCGTAAACGTGTAAATAAGCTGACGAACGTAAACATGTGAAAGC
1 TGGCGAGCGTAAACGCGTAAATAAGCTGACGAGCGTAAACGTGTGCAAGC
*
29944925 TGGCGAGCGTAAACGCGTAAATAAGCTGACGAGCGTAAACGTGCGCAAGC
1 TGGCGAGCGTAAACGCGTAAATAAGCTGACGAGCGTAAACGTGTGCAAGC
*
29944975 TGGCGAGCGTAAACGCGTAAATAAGCTGACGAGCATAAACGTGTGCAAGC
1 TGGCGAGCGTAAACGCGTAAATAAGCTGACGAGCGTAAACGTGTGCAAGC
*
29945025 TGGCGAGCTTAAA
1 TGGCGAGCGTAAA
29945038 TGCATAATTA
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 105 1.00
ACGTcount: A:0.34, C:0.19, G:0.30, T:0.17
Consensus pattern (50 bp):
TGGCGAGCGTAAACGCGTAAATAAGCTGACGAGCGTAAACGTGTGCAAGC
Found at i:29944935 original size:24 final size:26
Alignment explanation
Indices: 29944875--29945018 Score: 152
Period size: 26 Copynumber: 5.7 Consensus size: 26
29944865 TGAAACAACT
29944875 TGGCGAGCGTAAACGTGTAAATAAGC
1 TGGCGAGCGTAAACGTGTAAATAAGC
* * * *
29944901 TGACGAACGTAAACATGT-GA-AAGC
1 TGGCGAGCGTAAACGTGTAAATAAGC
*
29944925 TGGCGAGCGTAAACGCGTAAATAAGC
1 TGGCGAGCGTAAACGTGTAAATAAGC
* ***
29944951 TGACGAGCGTAAACGTG--CGCAAGC
1 TGGCGAGCGTAAACGTGTAAATAAGC
*
29944975 TGGCGAGCGTAAACGCGTAAATAAGC
1 TGGCGAGCGTAAACGTGTAAATAAGC
* *
29945001 TGACGAGCATAAACGTGT
1 TGGCGAGCGTAAACGTGT
29945019 GCAAGCTGGC
Statistics
Matches: 92, Mismatches: 22, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
24 37 0.40
25 2 0.02
26 53 0.58
ACGTcount: A:0.35, C:0.19, G:0.30, T:0.17
Consensus pattern (26 bp):
TGGCGAGCGTAAACGTGTAAATAAGC
Found at i:29945031 original size:24 final size:24
Alignment explanation
Indices: 29944875--29945037 Score: 119
Period size: 26 Copynumber: 6.5 Consensus size: 24
29944865 TGAAACAACT
**
29944875 TGGCGAGCGTAAACGTGTAAATAAGC
1 TGGCGAGCGTAAACGTGT--GCAAGC
* * * *
29944901 TGACGAACGTAAACATGTGAAAGC
1 TGGCGAGCGTAAACGTGTGCAAGC
* **
29944925 TGGCGAGCGTAAACGCGTAAATAAGC
1 TGGCGAGCGTAAACGTGT--GCAAGC
* *
29944951 TGACGAGCGTAAACGTGCGCAAGC
1 TGGCGAGCGTAAACGTGTGCAAGC
* **
29944975 TGGCGAGCGTAAACGCGTAAATAAGC
1 TGGCGAGCGTAAACGTGT--GCAAGC
* *
29945001 TGACGAGCATAAACGTGTGCAAGC
1 TGGCGAGCGTAAACGTGTGCAAGC
*
29945025 TGGCGAGCTTAAA
1 TGGCGAGCGTAAA
29945038 TGCATAATTA
Statistics
Matches: 105, Mismatches: 28, Indels: 10
0.73 0.20 0.07
Matches are distributed among these distances:
24 52 0.50
26 53 0.50
ACGTcount: A:0.34, C:0.19, G:0.30, T:0.17
Consensus pattern (24 bp):
TGGCGAGCGTAAACGTGTGCAAGC
Found at i:29945064 original size:100 final size:100
Alignment explanation
Indices: 29944875--29945066 Score: 258
Period size: 100 Copynumber: 1.9 Consensus size: 100
29944865 TGAAACAACT
* *
29944875 TGGCGAGCGTAAACGTGTAAATAAGCTGACGAACGTAAACATGTGAAAGCTGGCGAGCGTAAACG
1 TGGCGAGCGTAAACGCGTAAATAAGCTGACGAACATAAACATGTGAAAGCTGGCGAGCGTAAACG
* * * * *
29944940 CGTAAATAAGCTGACGAGCGTAAACGTGCGCAAGC
66 CATAAATAAACTAACAAGCATAAACGTGCGCAAGC
* * * * *
29944975 TGGCGAGCGTAAACGCGTAAATAAGCTGACGAGCATAAACGTGTGCAAGCTGGCGAGCTTAAATG
1 TGGCGAGCGTAAACGCGTAAATAAGCTGACGAACATAAACATGTGAAAGCTGGCGAGCGTAAACG
* *
29945040 CATAATTAAACTAACAAGTATAAACGT
66 CATAAATAAACTAACAAGCATAAACGT
29945067 ATGAAGTCTT
Statistics
Matches: 78, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
100 78 1.00
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.18
Consensus pattern (100 bp):
TGGCGAGCGTAAACGCGTAAATAAGCTGACGAACATAAACATGTGAAAGCTGGCGAGCGTAAACG
CATAAATAAACTAACAAGCATAAACGTGCGCAAGC
Found at i:29948409 original size:20 final size:20
Alignment explanation
Indices: 29948358--29948410 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
29948348 ATCTTCAAGG
* * *
29948358 TATCGGTAGAACTGTAGTTG
1 TATCGGTAGAAGTGAAGTTC
29948378 TATCGGTAGAAGTGAAGTTC
1 TATCGGTAGAAGTGAAGTTC
*
29948398 TATCAGTAGAAGT
1 TATCGGTAGAAGT
29948411 CTCACTGGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.30, C:0.09, G:0.28, T:0.32
Consensus pattern (20 bp):
TATCGGTAGAAGTGAAGTTC
Found at i:29948567 original size:33 final size:33
Alignment explanation
Indices: 29948523--29948586 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
29948513 TAGATTTCTC
* *
29948523 CCCCTTAAT-AAAAGTCATTTTGAAATTAAGCT
1 CCCCTTAATAAAAAATCATTTTCAAATTAAGCT
*
29948555 CCCCTTATATAAAAAATCATTTTCAATTTAAG
1 CCCCTTA-ATAAAAAATCATTTTCAAATTAAG
29948587 GCGTAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 7 0.26
33 2 0.07
34 18 0.67
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.36
Consensus pattern (33 bp):
CCCCTTAATAAAAAATCATTTTCAAATTAAGCT
Found at i:29951224 original size:20 final size:20
Alignment explanation
Indices: 29951201--29951242 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
29951191 AGAAGCATAC
*
29951201 TTGTATCGGTAGAACTGAAG
1 TTGTATCGCTAGAACTGAAG
*
29951221 TTGTATCGCTAGAAGTGAAG
1 TTGTATCGCTAGAACTGAAG
29951241 TT
1 TT
29951243 CTACCGGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.33
Consensus pattern (20 bp):
TTGTATCGCTAGAACTGAAG
Found at i:29952053 original size:4 final size:4
Alignment explanation
Indices: 29952044--29952079 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
29952034 AAAATGTTAA
*
29952044 AAAT AAAT AAAT AAAT AAAT AAAAT AAAT GAAT AAA
1 AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAA
29952080 AACAAATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:29952067 original size:35 final size:36
Alignment explanation
Indices: 29952027--29952094 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 36
29952017 TGTAAATATC
* *
29952027 ATAAAATAAAATG-TTAAAAATAAAT-AAATAAATAA
1 ATAAAAT-AAATGAATAAAAACAAATAAAATAAATAA
29952062 ATAAAATAAATGAATAAAAACAAATAAAATAAA
1 ATAAAATAAATGAATAAAAACAAATAAAATAAA
29952095 ATAAGGGACT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 5 0.17
35 17 0.59
36 7 0.24
ACGTcount: A:0.74, C:0.01, G:0.03, T:0.22
Consensus pattern (36 bp):
ATAAAATAAATGAATAAAAACAAATAAAATAAATAA
Found at i:29952192 original size:14 final size:13
Alignment explanation
Indices: 29952172--29952219 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
29952162 GGCTGAAATG
*
29952172 TAAATAAAATAAT
1 TAAATAAAATAAA
*
29952185 TGAAATAATATAAA
1 T-AAATAAAATAAA
29952199 TAAATAAAAATAAA
1 TAAAT-AAAATAAA
*
29952213 AAAATAA
1 TAAATAA
29952220 GCGAGGGACT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 7 0.24
14 22 0.76
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (13 bp):
TAAATAAAATAAA
Found at i:29953443 original size:19 final size:20
Alignment explanation
Indices: 29953421--29953460 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
29953411 ATTGAGTTTA
29953421 TTTAAATGTAAATGGA-TTT
1 TTTAAATGTAAATGGACTTT
* *
29953440 TTTAAATTTTAATGGACTTT
1 TTTAAATGTAAATGGACTTT
29953460 T
1 T
29953461 AATTAATTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.33, C:0.03, G:0.12, T:0.53
Consensus pattern (20 bp):
TTTAAATGTAAATGGACTTT
Found at i:29963604 original size:17 final size:17
Alignment explanation
Indices: 29963584--29963625 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
29963574 CTCCCTTGAC
29963584 CTTTAACCTTCCATATT
1 CTTTAACCTTCCATATT
*
29963601 CTTTAACCTTTCATATT
1 CTTTAACCTTCCATATT
29963618 CTTATAAC
1 CTT-TAAC
29963626 TACTTTTTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (17 bp):
CTTTAACCTTCCATATT
Found at i:29963793 original size:3 final size:3
Alignment explanation
Indices: 29963781--29963831 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
29963771 GTTTATAACA
* *
29963781 ATT A-T ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT AAAT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT
29963826 ATT ATT
1 ATT ATT
29963832 TTTAGGGTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.90
4 2 0.05
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:29964294 original size:50 final size:48
Alignment explanation
Indices: 29964240--29964390 Score: 124
Period size: 51 Copynumber: 3.0 Consensus size: 48
29964230 GATCCAGGGG
*
29964240 AAATATTTTGATTTTTTTAAAAATTTCGAAATAAAAGTTTTGATTTTTAA
1 AAATATTTTGA-TTTTTTAAATATTT-GAAATAAAAGTTTTGATTTTTAA
* * ** * * * *
29964290 AAATACAAATCTG-TTTTTTAGTTATTTTAAAGAAAAATTTTAAATTTTTAA
1 AAAT---ATTTTGATTTTTTAAATATTTGAAATAAAAGTTTT-GATTTTTAA
* *
29964341 ATAAAATTTTGATTTTTTAACTATTTTGAAATAAAAGTTTTGATTTTTAA
1 A-AATATTTTGATTTTTTAAATA-TTTGAAATAAAAGTTTTGATTTTTAA
29964391 GTAAAATAGT
Statistics
Matches: 76, Mismatches: 18, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
49 4 0.05
50 32 0.42
51 34 0.45
52 2 0.03
53 4 0.05
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (48 bp):
AAATATTTTGATTTTTTAAATATTTGAAATAAAAGTTTTGATTTTTAA
Found at i:29964339 original size:21 final size:20
Alignment explanation
Indices: 29964314--29964360 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
29964304 TTTTTAGTTA
29964314 TTTTAAAGAAAAATTTTAAAT
1 TTTTAAA-AAAAATTTTAAAT
* * *
29964335 TTTTAAATAAAATTTTGATT
1 TTTTAAAAAAAATTTTAAAT
29964355 TTTTAA
1 TTTTAA
29964361 CTATTTTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (20 bp):
TTTTAAAAAAAATTTTAAAT
Found at i:29964396 original size:50 final size:50
Alignment explanation
Indices: 29964244--29964406 Score: 152
Period size: 50 Copynumber: 3.2 Consensus size: 50
29964234 CAGGGGAAAT
* *
29964244 ATTTTGATTTTTTTAAAAATTTCGAAATAAAAGTTTTGATTTTTAAAAATACAA
1 ATTTTGA-TTTTTTAAATATTTTGAAATAAAAGTTTTGATTTTT--AAATA-AA
* ** * * *
29964298 A-TCTG-TTTTTTAGTTATTTT-AAAGAAAAATTTTAAATTTTTAAATAAA
1 ATTTTGATTTTTTAAATATTTTGAAATAAAAGTTTT-GATTTTTAAATAAA
* *
29964346 ATTTTGATTTTTTAACTATTTTGAAATAAAAGTTTTGATTTTTAAGTAAA
1 ATTTTGATTTTTTAAATATTTTGAAATAAAAGTTTTGATTTTTAAATAAA
**
29964396 ATAGTGATTTT
1 ATTTTGATTTT
29964407 CTTTAAAAAA
Statistics
Matches: 88, Mismatches: 17, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
48 3 0.03
49 8 0.09
50 45 0.51
51 28 0.32
53 3 0.03
54 1 0.01
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (50 bp):
ATTTTGATTTTTTAAATATTTTGAAATAAAAGTTTTGATTTTTAAATAAA
Found at i:29964442 original size:148 final size:142
Alignment explanation
Indices: 29964272--29964689 Score: 534
Period size: 148 Copynumber: 2.9 Consensus size: 142
29964262 ATTTCGAAAT
* * * * *
29964272 AAAAGTTTTGATTTTTAAAAATACAAATCTGTTTTTTAGTTATTTTAAAGAAAAATTTTAAATTT
1 AAAAGTTTAGTTTTTTAAAAATAAAAATCT-TTTTTTAGTCATTTTAAAGAAAAAATTTAAATTT
* * *
29964337 TTAAATAAAATTTTGA-TTTTTTAACTATTTTGAAATAAAAGTTTTGATTTTTAAGTAAAATAGT
65 TTAAACAAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAGT
* *
29964401 GATTTTCTTTAAAAAAA
130 GATATTCATT----AAA
***
29964418 CAGAAAGTTTAGTTTTTTAAAAATAAAAATCTATTTTTTAGTCATTTTATCCAAAAAATTTAAAT
1 -A-AAAGTTTAGTTTTTTAAAAATAAAAATCT-TTTTTTAGTCATTTTAAAGAAAAAATTTAAAT
* *
29964483 TTTTAAACAAAGTTTT-ATTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAGTA
63 TTTTAAACAAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATA
29964547 GTGATATTCATTAAA
128 GTGATATTCATTAAA
* * *
29964562 AAAAGTTTAGATTTTTTAAAAAATAAAAATCTATTTTTAGTGATTTTAAAGAAAAAATTTAAAAT
1 AAAAGTTTAG-TTTTTT-AAAAATAAAAATCTTTTTTTAGTCATTTTAAAGAAAAAATTTAAATT
* *
29964627 TTTAAACAAAGTTTTGATTTTTTTTTAATTATTTCGAAATAAAAGTTTTGATTTTGAAGTAAA
64 TTTAAACAAAGTTTTGA--TTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAA
29964690 GTACTAGTTT
Statistics
Matches: 239, Mismatches: 25, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
142 9 0.04
143 49 0.21
144 18 0.08
146 41 0.17
147 2 0.01
148 120 0.50
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (142 bp):
AAAAGTTTAGTTTTTTAAAAATAAAAATCTTTTTTTAGTCATTTTAAAGAAAAAATTTAAATTTT
TAAACAAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAGTG
ATATTCATTAAA
Found at i:29965309 original size:21 final size:20
Alignment explanation
Indices: 29965285--29965324 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
29965275 ATAATTTTTA
*
29965285 TTTATTCTCATTTCATATTTG
1 TTTATTCTCATGTC-TATTTG
*
29965306 TTTATTTTCATGTCTATTT
1 TTTATTCTCATGTCTATTT
29965325 ATACTTATGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.17, C:0.12, G:0.05, T:0.65
Consensus pattern (20 bp):
TTTATTCTCATGTCTATTTG
Found at i:29966996 original size:26 final size:25
Alignment explanation
Indices: 29966943--29966997 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
29966933 CCTCATGAGC
*
29966943 ATTTATTCGTATGTTTTGTGTTTGA
1 ATTTATTCGTATGTTTTATGTTTGA
*
29966968 ATTTGTTCGTAATGTTTTATGATTT-A
1 ATTTATTCGT-ATGTTTTATG-TTTGA
29966994 ATTT
1 ATTT
29966998 CGTATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 9 0.35
26 14 0.54
27 3 0.12
ACGTcount: A:0.20, C:0.04, G:0.16, T:0.60
Consensus pattern (25 bp):
ATTTATTCGTATGTTTTATGTTTGA
Found at i:29970286 original size:42 final size:42
Alignment explanation
Indices: 29970222--29970304 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
29970212 GGGAAATGAT
* *
29970222 AGAAAATGCATTGTAGTAGGGCAAAATAGATTATCCTTTGAA
1 AGAAAATGCATTGAAGTAGGGCAAAATAGATGATCCTTTGAA
*
29970264 AGAAAATGCATTGAAGTTGGGCAAAATAGATGATCCTTTGA
1 AGAAAATGCATTGAAGTAGGGCAAAATAGATGATCCTTTGA
29970305 GCGCGAAGAG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.28
Consensus pattern (42 bp):
AGAAAATGCATTGAAGTAGGGCAAAATAGATGATCCTTTGAA
Found at i:29971647 original size:24 final size:24
Alignment explanation
Indices: 29971612--29971657 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
29971602 CATACAATAT
29971612 TTAGCCTATACGAGCCCAGAATGG
1 TTAGCCTATACGAGCCCAGAATGG
29971636 TTAGCTCT-TACGAGCCCAGAAT
1 TTAGC-CTATACGAGCCCAGAAT
29971658 CAGAATAACG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (24 bp):
TTAGCCTATACGAGCCCAGAATGG
Found at i:29971672 original size:28 final size:27
Alignment explanation
Indices: 29971639--29971699 Score: 95
Period size: 27 Copynumber: 2.2 Consensus size: 27
29971629 AGAATGGTTA
29971639 GCTCTTACGAGCCCAGAATCAGAATAAC
1 GCTCTTACGAG-CCAGAATCAGAATAAC
**
29971667 GCTCTTTTGAGCCAGAATCAGAATAAC
1 GCTCTTACGAGCCAGAATCAGAATAAC
29971694 GCTCTT
1 GCTCTT
29971700 TTGAGCCTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 22 0.71
28 9 0.29
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (27 bp):
GCTCTTACGAGCCAGAATCAGAATAAC
Found at i:29971688 original size:27 final size:27
Alignment explanation
Indices: 29971651--29971706 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
29971641 TCTTACGAGC
29971651 CCAGAATCAGAATAACGCTCTTTTGAG
1 CCAGAATCAGAATAACGCTCTTTTGAG
29971678 CCAGAATCAGAATAACGCTCTTTTGAG
1 CCAGAATCAGAATAACGCTCTTTTGAG
29971705 CC
1 CC
29971707 TTCAGTCTCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (27 bp):
CCAGAATCAGAATAACGCTCTTTTGAG
Found at i:29980558 original size:25 final size:24
Alignment explanation
Indices: 29980521--29980591 Score: 88
Period size: 25 Copynumber: 2.9 Consensus size: 24
29980511 CTTACGATCC
* * *
29980521 CAGACAGAGTATCACTCTTGCGAG
1 CAGACAGAATATCGCTCTTACGAG
*
29980545 TCAGACTGAATATCGCTCTTACGAG
1 -CAGACAGAATATCGCTCTTACGAG
29980570 CAAGACAGAATATCGCTCTTAC
1 C-AGACAGAATATCGCTCTTAC
29980592 AAGCCAGAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
24 1 0.03
25 39 0.98
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (24 bp):
CAGACAGAATATCGCTCTTACGAG
Found at i:29984298 original size:49 final size:49
Alignment explanation
Indices: 29984235--29984988 Score: 612
Period size: 49 Copynumber: 15.4 Consensus size: 49
29984225 TTCACCATCT
* * * **
29984235 CGGCCTCAATCTTTCCCTTCAAATCTTTAAGGTATAAGGTTCATCGTTG
1 CGGCCTCAATCTTTCCCTTCACATCTCTAAGGTACAAGGTTCGCCGTTG
* * * * * * *
29984284 CGGCTTCAACCTTTCCCTCCACAACTCTATGGTACAAGATTCGCCATTG
1 CGGCCTCAATCTTTCCCTTCACATCTCTAAGGTACAAGGTTCGCCGTTG
* * * *
29984333 CGACCTCAATCTTT-CCTATCATATCTCTAAGGTACAAGGTTCACCGTTA
1 CGGCCTCAATCTTTCCCT-TCACATCTCTAAGGTACAAGGTTCGCCGTTG
* * * *
29984382 TGGCCTCAA-CTTTTCCCTTCACATCT-TCATGGTACAAGATTCGCCATTG
1 CGGCCTCAATC-TTTCCCTTCACATCTCT-AAGGTACAAGGTTCGCCGTTG
* * *
29984431 TGGCCTCAATCTTTCCCATCACATCTCTAAGGTATAAGGTTCGCCGTT-
1 CGGCCTCAATCTTTCCCTTCACATCTCTAAGGTACAAGGTTCGCCGTTG
* * * * * **
29984479 AGGCTTCAACCTTTCCCTTCACATCT-TCATGGTACAAGATTCGCTATTG
1 CGGCCTCAATCTTTCCCTTCACATCTCT-AAGGTACAAGGTTCGCCGTTG
* * *
29984528 CGGCCTCAATCATTCCCATT-ATATCTCTAAGGTACAAGGTTTGCCGTTG
1 CGGCCTCAATCTTTCCC-TTCACATCTCTAAGGTACAAGGTTCGCCGTTG
* * * * * * *
29984577 TGACTTCAATCTTTCCC-TCTACATCT-TCATGGTACAAGATTCGCCATTA
1 CGGCCTCAATCTTTCCCTTC-ACATCTCT-AAGGTACAAGGTTCGCCGTTG
* * *
29984626 CGGCCTCAATTTTTCCCATCACATCTCTAAGGTACAAGGTTCGCCGTGG
1 CGGCCTCAATCTTTCCCTTCACATCTCTAAGGTACAAGGTTCGCCGTTG
* * * * * * * *
29984675 CGACTTCAACCTTTCCCTTCACTTCT-TCATGGTACAAGATTCACCATTG
1 CGGCCTCAATCTTTCCCTTCACATCTCT-AAGGTACAAGGTTCGCCGTTG
** * * * *
29984724 CGATCTCAAGCTTTCCCATCACATCTCTAAGGTACAAGGTTTGCCGTGG
1 CGGCCTCAATCTTTCCCTTCACATCTCTAAGGTACAAGGTTCGCCGTTG
* * * * * * *
29984773 CGGCTTCAACCTTTCCCTTCACATCT-TCATGGTATAAGATTTGCCATTG
1 CGGCCTCAATCTTTCCCTTCACATCTCT-AAGGTACAAGGTTCGCCGTTG
* * ** *
29984822 CGACCTCAATCTTTCCCATCACATCTCTAAGGTACAAGGTTCATCGTAG
1 CGGCCTCAATCTTTCCCTTCACATCTCTAAGGTACAAGGTTCGCCGTTG
** * * * * *
29984871 CAACTTCAACCTTTCCCTTCACATCT-TCATGGTACAAGATTCGCCATTG
1 CGGCCTCAATCTTTCCCTTCACATCTCT-AAGGTACAAGGTTCGCCGTTG
* * *
29984920 TGGCCTCAATCTTTCCCATCACATCTCTAAGATACAAGGTTCGCCGTTG
1 CGGCCTCAATCTTTCCCTTCACATCTCTAAGGTACAAGGTTCGCCGTTG
* *
29984969 CGGCTTCAACCTTTCCCTTC
1 CGGCCTCAATCTTTCCCTTC
29984989 GTATTTCCAG
Statistics
Matches: 542, Mismatches: 142, Indels: 42
0.75 0.20 0.06
Matches are distributed among these distances:
47 2 0.00
48 46 0.08
49 480 0.89
50 14 0.03
ACGTcount: A:0.22, C:0.30, G:0.15, T:0.33
Consensus pattern (49 bp):
CGGCCTCAATCTTTCCCTTCACATCTCTAAGGTACAAGGTTCGCCGTTG
Found at i:29985013 original size:98 final size:98
Alignment explanation
Indices: 29984235--29984988 Score: 1037
Period size: 98 Copynumber: 7.7 Consensus size: 98
29984225 TTCACCATCT
* * * * **
29984235 CGGCCTCAATCTTTCCCTTCAAATCTTTAAGGTATAAGGTTCATCGTTGCGGCTTCAACCTTTCC
1 CGGCCTCAATCTTTCCCATCACATCTCTAAGGTACAAGGTTCGCCGTTGCGGCTTCAACCTTTCC
* *
29984300 CTCCACAAC-TCTATGGTACAAGATTCGCCATTG
66 CTTCACATCTTC-ATGGTACAAGATTCGCCATTG
* * * * ** * *
29984333 CGACCTCAATCTTTCCTATCATATCTCTAAGGTACAAGGTTCACCGTTATGGCCTCAACTTTTCC
1 CGGCCTCAATCTTTCCCATCACATCTCTAAGGTACAAGGTTCGCCGTTGCGGCTTCAACCTTTCC
29984398 CTTCACATCTTCATGGTACAAGATTCGCCATTG
66 CTTCACATCTTCATGGTACAAGATTCGCCATTG
* * *
29984431 TGGCCTCAATCTTTCCCATCACATCTCTAAGGTATAAGGTTCGCCGTT-AGGCTTCAACCTTTCC
1 CGGCCTCAATCTTTCCCATCACATCTCTAAGGTACAAGGTTCGCCGTTGCGGCTTCAACCTTTCC
*
29984495 CTTCACATCTTCATGGTACAAGATTCGCTATTG
66 CTTCACATCTTCATGGTACAAGATTCGCCATTG
* * * * * * *
29984528 CGGCCTCAATCATTCCCATTATATCTCTAAGGTACAAGGTTTGCCGTTGTGACTTCAATCTTTCC
1 CGGCCTCAATCTTTCCCATCACATCTCTAAGGTACAAGGTTCGCCGTTGCGGCTTCAACCTTTCC
*
29984593 C-TCTACATCTTCATGGTACAAGATTCGCCATTA
66 CTTC-ACATCTTCATGGTACAAGATTCGCCATTG
* * *
29984626 CGGCCTCAATTTTTCCCATCACATCTCTAAGGTACAAGGTTCGCCGTGGCGACTTCAACCTTTCC
1 CGGCCTCAATCTTTCCCATCACATCTCTAAGGTACAAGGTTCGCCGTTGCGGCTTCAACCTTTCC
* *
29984691 CTTCACTTCTTCATGGTACAAGATTCACCATTG
66 CTTCACATCTTCATGGTACAAGATTCGCCATTG
** * * *
29984724 CGATCTCAAGCTTTCCCATCACATCTCTAAGGTACAAGGTTTGCCGTGGCGGCTTCAACCTTTCC
1 CGGCCTCAATCTTTCCCATCACATCTCTAAGGTACAAGGTTCGCCGTTGCGGCTTCAACCTTTCC
* *
29984789 CTTCACATCTTCATGGTATAAGATTTGCCATTG
66 CTTCACATCTTCATGGTACAAGATTCGCCATTG
* ** * **
29984822 CGACCTCAATCTTTCCCATCACATCTCTAAGGTACAAGGTTCATCGTAGCAACTTCAACCTTTCC
1 CGGCCTCAATCTTTCCCATCACATCTCTAAGGTACAAGGTTCGCCGTTGCGGCTTCAACCTTTCC
29984887 CTTCACATCTTCATGGTACAAGATTCGCCATTG
66 CTTCACATCTTCATGGTACAAGATTCGCCATTG
* *
29984920 TGGCCTCAATCTTTCCCATCACATCTCTAAGATACAAGGTTCGCCGTTGCGGCTTCAACCTTTCC
1 CGGCCTCAATCTTTCCCATCACATCTCTAAGGTACAAGGTTCGCCGTTGCGGCTTCAACCTTTCC
29984985 CTTC
66 CTTC
29984989 GTATTTCCAG
Statistics
Matches: 579, Mismatches: 73, Indels: 8
0.88 0.11 0.01
Matches are distributed among these distances:
97 89 0.15
98 486 0.84
99 4 0.01
ACGTcount: A:0.22, C:0.30, G:0.15, T:0.33
Consensus pattern (98 bp):
CGGCCTCAATCTTTCCCATCACATCTCTAAGGTACAAGGTTCGCCGTTGCGGCTTCAACCTTTCC
CTTCACATCTTCATGGTACAAGATTCGCCATTG
Found at i:29996959 original size:30 final size:30
Alignment explanation
Indices: 29996909--29997081 Score: 147
Period size: 30 Copynumber: 5.8 Consensus size: 30
29996899 GGAAAAATGG
*
29996909 GGTCAAAA-ATAAAATTTTGGAAAATTTAGA
1 GGTCAAAATAT-AATTTTTGGAAAATTTAGA
* * * *
29996939 GGCCAAATTATAATTTTTGGAAAAATT-GG
1 GGTCAAAATATAATTTTTGGAAAATTTAGA
* * * *
29996968 GGGCCAAATTTAAATTTTTGGAAAGTTTAGA
1 GGTCAAAATAT-AATTTTTGGAAAATTTAGA
** * *
29996999 GGTCAAAACCTAATTTTTAGAAAGTTTA-A
1 GGTCAAAATATAATTTTTGGAAAATTTAGA
*
29997028 GGGTCAAAATATAATTTTTGGAAAGATTAAG-
1 -GGTCAAAATATAATTTTTGGAAA-ATTTAGA
*
29997059 GGTCAAAACATAATTTTTGGAAA
1 GGTCAAAATATAATTTTTGGAAA
29997082 GTTCGTGGGT
Statistics
Matches: 114, Mismatches: 23, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
29 9 0.08
30 92 0.81
31 13 0.11
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (30 bp):
GGTCAAAATATAATTTTTGGAAAATTTAGA
Found at i:29997013 original size:60 final size:59
Alignment explanation
Indices: 29996914--29997081 Score: 176
Period size: 60 Copynumber: 2.8 Consensus size: 59
29996904 AATGGGGTCA
* * * ** **
29996914 AAAATAAAATTTTGGAAAATTTAGAGGCCAAATTATAATTTTTGGAAAAATTGGGGGCC
1 AAAATAAATTTTTGGAAAGTTTAGAGGTCAAAACATAATTTTTGGAAAAATTAAGGGCC
* * * ** *
29996973 AAATTTAAATTTTTGGAAAGTTTAGAGGTCAAAACCTAATTTTTAGAAAGTTTAAGGGTC
1 AAA-ATAAATTTTTGGAAAGTTTAGAGGTCAAAACATAATTTTTGGAAAAATTAAGGGCC
*
29997033 AAAATATAATTTTTGGAAAGATTA-AGGGTCAAAACATAATTTTTGGAAA
1 AAAATA-AATTTTTGGAAAGTTTAGA-GGTCAAAACATAATTTTTGGAAA
29997082 GTTCGTGGGT
Statistics
Matches: 89, Mismatches: 17, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
59 6 0.07
60 83 0.93
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.33
Consensus pattern (59 bp):
AAAATAAATTTTTGGAAAGTTTAGAGGTCAAAACATAATTTTTGGAAAAATTAAGGGCC
Found at i:29997082 original size:30 final size:29
Alignment explanation
Indices: 29996980--29997137 Score: 154
Period size: 30 Copynumber: 5.2 Consensus size: 29
29996970 GCCAAATTTA
* *
29996980 AATTTTTGGAAAGTTTAGAGGTCAAAACCT
1 AATTTTTGGAAAGTTAAG-GGTCAAAACAT
* *
29997010 AATTTTTAGAAAGTTTAAGGGTCAAAATAT
1 AATTTTTGGAAAG-TTAAGGGTCAAAACAT
29997040 AATTTTTGGAAAGATTAAGGGTCAAAACAT
1 AATTTTTGGAAAG-TTAAGGGTCAAAACAT
** * *
29997070 AATTTTTGGAAAGTTCGTGGGTTCAAATCAG
1 AATTTTTGGAAAGTT-AAGGG-TCAAAACAT
** * *
29997101 AATTTTTGGGTAGTTTAGAAGTCAAAACAT
1 AATTTTTGGAAAGTTAAG-GGTCAAAACAT
29997131 AATTTTT
1 AATTTTT
29997138 AAATAAAATA
Statistics
Matches: 106, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
29 2 0.02
30 79 0.75
31 25 0.24
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.36
Consensus pattern (29 bp):
AATTTTTGGAAAGTTAAGGGTCAAAACAT
Found at i:29997126 original size:61 final size:60
Alignment explanation
Indices: 29996980--29997138 Score: 187
Period size: 60 Copynumber: 2.6 Consensus size: 60
29996970 GCCAAATTTA
* * *
29996980 AATTTTTGGAAAGTTTAGAGGTCAAAACCTAATTTTTAGAAAGTTTAAGGGTCAAAATAT
1 AATTTTTGGAAAGTTTAGAGGTCAAAACATAATTTTTAGAAAGTTCAAGGGTCAAAATAG
* * **
29997040 AATTTTTGGAAAGATTA-AGGGTCAAAACATAATTTTTGGAAAGTTCGTGGGTTC-AAATCAG
1 AATTTTTGGAAAGTTTAGA-GGTCAAAACATAATTTTTAGAAAGTTCAAGGG-TCAAAAT-AG
** *
29997101 AATTTTTGGGTAGTTTAGAAGTCAAAACATAATTTTTA
1 AATTTTTGGAAAGTTTAGAGGTCAAAACATAATTTTTA
29997139 AATAAAATAG
Statistics
Matches: 83, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
59 1 0.01
60 47 0.57
61 34 0.41
62 1 0.01
ACGTcount: A:0.38, C:0.07, G:0.19, T:0.36
Consensus pattern (60 bp):
AATTTTTGGAAAGTTTAGAGGTCAAAACATAATTTTTAGAAAGTTCAAGGGTCAAAATAG
Found at i:29999808 original size:29 final size:29
Alignment explanation
Indices: 29999706--29999909 Score: 144
Period size: 30 Copynumber: 6.9 Consensus size: 29
29999696 GCAAATTTAA
* * * *
29999706 AAAAATTAGGAGTTAAAATGTAATTTTAG
1 AAAAGTTAGGGGTTAAAATATAATTTTTG
*
29999735 AAAAGTTTAGGGGATCAAAATA-AGA-TTTTG
1 AAAAG-TTAGGGG-TTAAAATATA-ATTTTTG
** **
29999765 GGAAGTTGAAAGGTTAAAATATAATTTTTG
1 AAAAGTT-AGGGGTTAAAATATAATTTTTG
*
29999795 AAAAGTTAGGGGTTAAAATGTAA-TTTTG
1 AAAAGTTAGGGGTTAAAATATAATTTTTG
* * * *
29999823 AAAAAGTTTGGGGTCAAAATGTAATTTTTA
1 -AAAAGTTAGGGGTTAAAATATAATTTTTG
* * * *
29999853 AAAAGTTTGAGGGCTAAAATTTAATTTTAG
1 AAAAGTTAG-GGGTTAAAATATAATTTTTG
* *
29999883 AAAAGTTTGAGGGTCAAAATATAATTT
1 AAAAGTTAG-GGGTTAAAATATAATTT
29999910 CTAAATAAAA
Statistics
Matches: 140, Mismatches: 26, Indels: 17
0.77 0.14 0.09
Matches are distributed among these distances:
28 5 0.04
29 57 0.41
30 71 0.51
31 7 0.05
ACGTcount: A:0.42, C:0.02, G:0.21, T:0.35
Consensus pattern (29 bp):
AAAAGTTAGGGGTTAAAATATAATTTTTG
Found at i:29999887 original size:59 final size:59
Alignment explanation
Indices: 29999780--29999914 Score: 184
Period size: 59 Copynumber: 2.3 Consensus size: 59
29999770 TTGAAAGGTT
* *
29999780 AAAATATAATTTTTGAAAAGTTAGGGGTTAAAATGTAATTTTGAAAAAGTTTG-GGGTC
1 AAAATATAATTTTTAAAAAGTTAGGGGCTAAAATGTAATTTTGAAAAAGTTTGAGGGTC
* * *
29999838 AAAATGTAATTTTTAAAAAGTTTGAGGGCTAAAATTTAATTTT-AGAAAAGTTTGAGGGTC
1 AAAATATAATTTTTAAAAAGTTAG-GGGCTAAAATGTAATTTTGA-AAAAGTTTGAGGGTC
*
29999898 AAAATATAATTTCTAAA
1 AAAATATAATTTTTAAA
29999915 TAAAAACAGG
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
58 22 0.33
59 25 0.37
60 20 0.30
ACGTcount: A:0.42, C:0.03, G:0.19, T:0.36
Consensus pattern (59 bp):
AAAATATAATTTTTAAAAAGTTAGGGGCTAAAATGTAATTTTGAAAAAGTTTGAGGGTC
Found at i:30001793 original size:38 final size:38
Alignment explanation
Indices: 30001746--30002214 Score: 206
Period size: 39 Copynumber: 12.1 Consensus size: 38
30001736 TTGTCATAGT
* * *
30001746 TTGGTTGCTTCAATCTACCCCATGATAAGGGTAAGAGA
1 TTGGATGCTTCAATCTGCCCCATGATCAGGGTAAGAGA
* *
30001784 TTGGATGCTTCAATATGCCCCATGATCAGGCTAAGAGA
1 TTGGATGCTTCAATCTGCCCCATGATCAGGGTAAGAGA
* * * * *
30001822 TCGGATGCTTCAATCTTCCTCATAATCGGGGTAAGAGA
1 TTGGATGCTTCAATCTGCCCCATGATCAGGGTAAGAGA
* ** * * *
30001860 ATACATGGTTGCAATCTGCCCTATGATCGGGGTAAGAGA
1 TTGGATGCTT-CAATCTGCCCCATGATCAGGGTAAGAGA
* * * * *
30001899 TTGGCTAACTGT-GATCTACCCCATGATCAGGGTAAAAGA
1 TTGGAT-GCT-TCAATCTGCCCCATGATCAGGGTAAGAGA
* * *
30001938 TTGAATGGTTGCAATCTGCCCC-TG-TCGCGGGGTAAGAGA
1 TTGGATGCTT-CAATCTGCCCCATGAT--CAGGGTAAGAGA
* * * * * *
30001977 TTGGTTAACAGT-GATCTGCCCCATGATCGGGGTAAAAGA
1 TTGGAT-GC-TTCAATCTGCCCCATGATCAGGGTAAGAGA
* * * *
30002016 TCGGATGGTTGCAATCTGCCTC-T-ATCGCGGGGTAAGAGA
1 TTGGATGCTT-CAATCTGCCCCATGAT--CAGGGTAAGAGA
* * * * * *
30002055 TTGGCTGACGGT-GATCTGCCCAATGATCGGGGTAAAAGA
1 TTGGATG-C-TTCAATCTGCCCCATGATCAGGGTAAGAGA
* *
30002094 TTGGATGGTTGCAATCTGCCCC-TGTAGC-GAGGTAAGAGA
1 TTGGATGCTT-CAATCTGCCCCATG-ATCAG-GGTAAGAGA
* * * * *
30002133 TTGGCTGACGGT-GATCTACCCCATGATCAGGGTAAAAGA
1 TTGGATG-C-TTCAATCTGCCCCATGATCAGGGTAAGAGA
* * * *
30002172 TCGGATGGTTGCAATTTGCCCC-T-ATCGTGGGGTAAGAGA
1 TTGGATGCTT-CAATCTGCCCCATGATC--AGGGTAAGAGA
30002211 TTGG
1 TTGG
30002215 CTGACGGTGA
Statistics
Matches: 313, Mismatches: 87, Indels: 61
0.68 0.19 0.13
Matches are distributed among these distances:
37 10 0.03
38 77 0.25
39 212 0.68
40 7 0.02
41 7 0.02
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (38 bp):
TTGGATGCTTCAATCTGCCCCATGATCAGGGTAAGAGA
Found at i:30001925 original size:39 final size:39
Alignment explanation
Indices: 30001873--30002328 Score: 228
Period size: 39 Copynumber: 11.7 Consensus size: 39
30001863 CATGGTTGCA
* * * *
30001873 ATCTGCCCTATGATCGGGGTAAGAGATTGGCTAACTGTG
1 ATCTGCCCCATGATCGGGGTAAAAGATTGGATGACTGTG
* * * ** **
30001912 ATCTACCCCATGATCAGGGTAAAAGATTGAATGGTTGCA
1 ATCTGCCCCATGATCGGGGTAAAAGATTGGATGACTGTG
* * * *
30001951 ATCTGCCCC-TG-TCGCGGGGTAAGAGATTGGTTAACAGTG
1 ATCTGCCCCATGAT--CGGGGTAAAAGATTGGATGACTGTG
* ** **
30001990 ATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTTGCA
1 ATCTGCCCCATGATCGGGGTAAAAGATTGGATGACTGTG
* * * *
30002029 ATCTGCCTC-T-ATCGCGGGGTAAGAGATTGGCTGACGGTG
1 ATCTGCCCCATGAT--CGGGGTAAAAGATTGGATGACTGTG
* ** **
30002068 ATCTGCCCAATGATCGGGGTAAAAGATTGGATGGTTGCA
1 ATCTGCCCCATGATCGGGGTAAAAGATTGGATGACTGTG
* * * * *
30002107 ATCTGCCCC-TGTAGCGAGGTAAGAGATTGGCTGACGGTG
1 ATCTGCCCCATG-ATCGGGGTAAAAGATTGGATGACTGTG
* * * ** **
30002146 ATCTACCCCATGATCAGGGTAAAAGATCGGATGGTTGCA
1 ATCTGCCCCATGATCGGGGTAAAAGATTGGATGACTGTG
* * * *
30002185 ATTTGCCCC-T-ATCGTGGGGTAAGAGATTGGCTGACGGTG
1 ATCTGCCCCATGATC--GGGGTAAAAGATTGGATGACTGTG
* * * ** **
30002224 ATCTGCCCCATGATCGAGGTAAAGGATCGGATGGTTGCA
1 ATCTGCCCCATGATCGGGGTAAAAGATTGGATGACTGTG
* * * ** **
30002263 ATCTACCCC-T-ATCGCGAGGTAAGAGCTTGCCTGACAATG
1 ATCTGCCCCATGATCG-G-GGTAAAAGATTGGATGACTGTG
*
30002302 ATCTGTCCCATGATCGGGGTAAAAGAT
1 ATCTGCCCCATGATCGGGGTAAAAGAT
30002329 CGAATGGTTT
Statistics
Matches: 288, Mismatches: 111, Indels: 36
0.66 0.26 0.08
Matches are distributed among these distances:
37 10 0.03
38 7 0.02
39 253 0.88
40 8 0.03
41 10 0.03
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (39 bp):
ATCTGCCCCATGATCGGGGTAAAAGATTGGATGACTGTG
Found at i:30001954 original size:78 final size:78
Alignment explanation
Indices: 30001864--30002371 Score: 643
Period size: 78 Copynumber: 6.5 Consensus size: 78
30001854 AAGAGAATAC
* * * *
30001864 ATGGTTGCAATCTGCCCTAT-GATCGGGGTAAGAGATTGGCTAACTGTGATCTACCCCATGATCA
1 ATGGTTGCAATCTGCCCTATCG-TCGGGGTAAGAGATTGGCTGACGGTGATCTGCCCCATGATCG
* *
30001928 GGGTAAAAGATTGA
65 GGGTAAAAGATCGG
* * * *
30001942 ATGGTTGCAATCTGCCCCTGTCG-CGGGGTAAGAGATTGGTTAACAGTGATCTGCCCCATGATCG
1 ATGGTTGCAATCTG-CCCTATCGTCGGGGTAAGAGATTGGCTGACGGTGATCTGCCCCATGATCG
30002006 GGGTAAAAGATCGG
65 GGGTAAAAGATCGG
*
30002020 ATGGTTGCAATCTGCCTCTATCG-CGGGGTAAGAGATTGGCTGACGGTGATCTGCCCAATGATCG
1 ATGGTTGCAATCTGCC-CTATCGTCGGGGTAAGAGATTGGCTGACGGTGATCTGCCCCATGATCG
*
30002084 GGGTAAAAGATTGG
65 GGGTAAAAGATCGG
* * * * *
30002098 ATGGTTGCAATCTGCCCCTGTAG-CGAGGTAAGAGATTGGCTGACGGTGATCTACCCCATGATCA
1 ATGGTTGCAATCTG-CCCTATCGTCGGGGTAAGAGATTGGCTGACGGTGATCTGCCCCATGATCG
30002162 GGGTAAAAGATCGG
65 GGGTAAAAGATCGG
*
30002176 ATGGTTGCAATTTGCCCCTATCGT-GGGGTAAGAGATTGGCTGACGGTGATCTGCCCCATGATCG
1 ATGGTTGCAATCTG-CCCTATCGTCGGGGTAAGAGATTGGCTGACGGTGATCTGCCCCATGATCG
* *
30002240 AGGTAAAGGATCGG
65 GGGTAAAAGATCGG
* * * * ** *
30002254 ATGGTTGCAATCTACCCCTATCG-CGAGGTAAGAGCTTGCCTGACAATGATCTGTCCCATGATCG
1 ATGGTTGCAATCT-GCCCTATCGTCGGGGTAAGAGATTGGCTGACGGTGATCTGCCCCATGATCG
*
30002318 GGGTAAAAGATCGA
65 GGGTAAAAGATCGG
*
30002332 ATGGTTTCAATCTGCCCCTATCG-CGGGGTAAGAGATTGGC
1 ATGGTTGCAATCTG-CCCTATCGTCGGGGTAAGAGATTGGC
30002372 CAACTGTGAT
Statistics
Matches: 378, Mismatches: 44, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
77 2 0.01
78 368 0.97
79 7 0.02
80 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.25
Consensus pattern (78 bp):
ATGGTTGCAATCTGCCCTATCGTCGGGGTAAGAGATTGGCTGACGGTGATCTGCCCCATGATCGG
GGTAAAAGATCGG
Found at i:30002047 original size:156 final size:155
Alignment explanation
Indices: 30001864--30002381 Score: 725
Period size: 156 Copynumber: 3.3 Consensus size: 155
30001854 AAGAGAATAC
* *
30001864 ATGGTTGCAATCTG-CCCTAT-GATCGGGGTAAGAGATTGGCTAACTGTGATCTACCCCATGATC
1 ATGGTTGCAATCTGCCCCTATCG--CGGGGTAAGAGATTGGCTAACGGTGATCTGCCCCATGATC
* * * *
30001927 AGGGTAAAAGATTGAATGGTTGCAATCTGCCCCTGTCGCGGGGTAAGAGATTGGTTAACAGTGAT
64 -GGGTAAAAGATTGGATGGTTGCAATCTGCCCCTGTCGCGAGGTAAGAGATTGGCTGACAGTGAT
30001992 CTGCCCCATGATCGGGGTAAAAGATCGG
128 CTGCCCCATGATCGGGGTAAAAGATCGG
* * *
30002020 ATGGTTGCAATCTGCCTCTATCGCGGGGTAAGAGATTGGCTGACGGTGATCTGCCCAATGATCGG
1 ATGGTTGCAATCTGCCCCTATCGCGGGGTAAGAGATTGGCTAACGGTGATCTGCCCCATGATC-G
* *
30002085 GGTAAAAGATTGGATGGTTGCAATCTGCCCCTGTAGCGAGGTAAGAGATTGGCTGACGGTGATCT
65 GGTAAAAGATTGGATGGTTGCAATCTGCCCCTGTCGCGAGGTAAGAGATTGGCTGACAGTGATCT
* *
30002150 ACCCCATGATCAGGGTAAAAGATCGG
130 GCCCCATGATCGGGGTAAAAGATCGG
* * *
30002176 ATGGTTGCAATTTGCCCCTATCGTGGGGTAAGAGATTGGCTGACGGTGATCTGCCCCATGATCGA
1 ATGGTTGCAATCTGCCCCTATCGCGGGGTAAGAGATTGGCTAACGGTGATCTGCCCCATGATCG-
* * * * * * *
30002241 GGTAAAGGATCGGATGGTTGCAATCTACCCCTATCGCGAGGTAAGAGCTTGCCTGACAATGATCT
65 GGTAAAAGATTGGATGGTTGCAATCTGCCCCTGTCGCGAGGTAAGAGATTGGCTGACAGTGATCT
* *
30002306 GTCCCATGATCGGGGTAAAAGATCGA
130 GCCCCATGATCGGGGTAAAAGATCGG
* * *
30002332 ATGGTTTCAATCTGCCCCTATCGCGGGGTAAGAGATTGGCCAACTGTGAT
1 ATGGTTGCAATCTGCCCCTATCGCGGGGTAAGAGATTGGCTAACGGTGAT
30002382 GTAACTTCAC
Statistics
Matches: 322, Mismatches: 37, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
155 1 0.00
156 315 0.98
157 5 0.02
158 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (155 bp):
ATGGTTGCAATCTGCCCCTATCGCGGGGTAAGAGATTGGCTAACGGTGATCTGCCCCATGATCGG
GTAAAAGATTGGATGGTTGCAATCTGCCCCTGTCGCGAGGTAAGAGATTGGCTGACAGTGATCTG
CCCCATGATCGGGGTAAAAGATCGG
Found at i:30002255 original size:234 final size:234
Alignment explanation
Indices: 30001846--30002381 Score: 754
Period size: 234 Copynumber: 2.3 Consensus size: 234
30001836 CTTCCTCATA
* * * *
30001846 ATCGGGGTAAGAGAAT-ACATGGTTGCAATCTG-CCCTATGATCGGGGTAAGAGATTGGCTAACT
1 ATCGGGGTAAAAGATTGA-ATGGTTGCAATCTGCCCCTAT-AGCGGGGTAAGAGATTGGCTAACG
* *
30001909 GTGATCTACCCCATGATCAGGGTAAAAGATTGAATGGTTGCAATCTGCCCCTGTCGCGGGGTAAG
64 GTGATCTACCCCATGATCAGGGTAAAAGATCGAATGGTTGCAATCTGCCCCTATCGCGGGGTAAG
* * * *
30001974 AGATTGGTTAACAGTGATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTTGCAATCTGCCTCT
129 AGATTGGCTAACAGTGATCTGCCCCATGATCGAGGTAAAAGATCGGATGGTTGCAATCTACCCCT
* * **
30002039 ATCGCGGGGTAAGAGATTGGCTGACGGTGATCTG-CCCAATG
194 ATCGCGAGGTAAGAGATTGCCTGACAATGATCTGTCCC-ATG
* * * *
30002080 ATCGGGGTAAAAGATTGGATGGTTGCAATCTGCCCCTGTAGCGAGGTAAGAGATTGGCTGACGGT
1 ATCGGGGTAAAAGATTGAATGGTTGCAATCTGCCCCTATAGCGGGGTAAGAGATTGGCTAACGGT
* * *
30002145 GATCTACCCCATGATCAGGGTAAAAGATCGGATGGTTGCAATTTGCCCCTATCGTGGGGTAAGAG
66 GATCTACCCCATGATCAGGGTAAAAGATCGAATGGTTGCAATCTGCCCCTATCGCGGGGTAAGAG
* * *
30002210 ATTGGCTGACGGTGATCTGCCCCATGATCGAGGTAAAGGATCGGATGGTTGCAATCTACCCCTAT
131 ATTGGCTAACAGTGATCTGCCCCATGATCGAGGTAAAAGATCGGATGGTTGCAATCTACCCCTAT
*
30002275 CGCGAGGTAAGAGCTTGCCTGACAATGATCTGTCCCATG
196 CGCGAGGTAAGAGATTGCCTGACAATGATCTGTCCCATG
* * * * *
30002314 ATCGGGGTAAAAGATCGAATGGTTTCAATCTGCCCCTATCGCGGGGTAAGAGATTGGCCAACTGT
1 ATCGGGGTAAAAGATTGAATGGTTGCAATCTGCCCCTATAGCGGGGTAAGAGATTGGCTAACGGT
30002379 GAT
66 GAT
30002382 GTAACTTCAC
Statistics
Matches: 265, Mismatches: 34, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
234 257 0.97
235 8 0.03
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (234 bp):
ATCGGGGTAAAAGATTGAATGGTTGCAATCTGCCCCTATAGCGGGGTAAGAGATTGGCTAACGGT
GATCTACCCCATGATCAGGGTAAAAGATCGAATGGTTGCAATCTGCCCCTATCGCGGGGTAAGAG
ATTGGCTAACAGTGATCTGCCCCATGATCGAGGTAAAAGATCGGATGGTTGCAATCTACCCCTAT
CGCGAGGTAAGAGATTGCCTGACAATGATCTGTCCCATG
Found at i:30011550 original size:88 final size:89
Alignment explanation
Indices: 30011392--30011573 Score: 228
Period size: 88 Copynumber: 2.1 Consensus size: 89
30011382 TTATGAAGTC
* * * * *
30011392 AAAATGTGATTTTAGGAAAATTTGAAGGTTAAAATGTAATTTTTGAAAAGTTTAGGGTCAAAATA
1 AAAATGTGATTTTAGAAAAATTTGAAGGTCAAAATATAATTTTTGAAAAGTTTAGAGCCAAAATA
*
30011457 TAATTTTGGGGAAGTTTAAGGGTT
66 TAATTTTGGAGAAGTTTAAGGGTT
* *
30011481 AAAATGTGATTTTA-AAAAATTT-AGGGGTCAAACTATAATTTTT-AAAAGTTTAAGAGCCAAAA
1 AAAATGTGATTTTAGAAAAATTTGA-AGGTCAAAATATAATTTTTGAAAAGTTT-AGAGCCAAAA
*
30011543 T-TCAATTTTGGAGAAGTTTGAGGGTT
64 TAT-AATTTTGGAGAAGTTTAAGGGTT
30011569 AAAAT
1 AAAAT
30011574 ATAATTTCTA
Statistics
Matches: 81, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
87 10 0.12
88 57 0.70
89 14 0.17
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.36
Consensus pattern (89 bp):
AAAATGTGATTTTAGAAAAATTTGAAGGTCAAAATATAATTTTTGAAAAGTTTAGAGCCAAAATA
TAATTTTGGAGAAGTTTAAGGGTT
Found at i:30011580 original size:30 final size:30
Alignment explanation
Indices: 30011244--30011580 Score: 194
Period size: 30 Copynumber: 11.4 Consensus size: 30
30011234 ACAGGGTCAA
*
30011244 AAAAT-TAAGTTTTGGAGAA-TTTG-GGGTT
1 AAAATGTAA-TTTTGGAAAAGTTTGAGGGTT
** * *
30011272 AAAACATAAGTTTGGAAGAGTTT-AGGGATT
1 AAAATGTAATTTTGGAAAAGTTTGAGGG-TT
* * * *
30011302 AAAATGTAAATTT-AAACAAATTTAAGGGTT
1 AAAATGTAATTTTGGAA-AAGTTTGAGGGTT
* *
30011332 AAAATGTAATTTTGAAAAAGTTTGAGGGTC
1 AAAATGTAATTTTGGAAAAGTTTGAGGGTT
*** * *
30011362 AAAATGTAATTTCATAAAAGTTATGA-AGTC
1 AAAATGTAATTTTGGAAAAGTT-TGAGGGTT
* *
30011392 AAAATGTGATTTTAGGAAAA-TTTGAAGGTT
1 AAAATGTAATTTT-GGAAAAGTTTGAGGGTT
* *
30011422 AAAATGTAATTTTTGAAAAGTTT-AGGGTC
1 AAAATGTAATTTTGGAAAAGTTTGAGGGTT
* ** *
30011451 AAAATATAATTTTGGGGAAGTTTAAGGGTT
1 AAAATGTAATTTTGGAAAAGTTTGAGGGTT
* * * *
30011481 AAAATGTGATTTT-AAAAAATTT-AGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTGA-GGGTT
* * * * * **
30011510 AAACTATAATTTT-TAAAAGTTTAAGAGCC
1 AAAATGTAATTTTGGAAAAGTTTGAGGGTT
*
30011539 AAAAT-TCAATTTTGGAGAAGTTTGAGGGTT
1 AAAATGT-AATTTTGGAAAAGTTTGAGGGTT
*
30011569 AAAATATAATTT
1 AAAATGTAATTT
30011581 CTAAATAAAA
Statistics
Matches: 238, Mismatches: 54, Indels: 32
0.73 0.17 0.10
Matches are distributed among these distances:
28 13 0.05
29 81 0.34
30 129 0.54
31 15 0.06
ACGTcount: A:0.41, C:0.03, G:0.20, T:0.35
Consensus pattern (30 bp):
AAAATGTAATTTTGGAAAAGTTTGAGGGTT
Found at i:30017704 original size:18 final size:18
Alignment explanation
Indices: 30017625--30017694 Score: 70
Period size: 18 Copynumber: 3.8 Consensus size: 18
30017615 TTTATAACTT
* * *
30017625 TATAAAAATACAAAAATA
1 TATAAATATATAAAAAAA
*
30017643 TATAAAAAT-TAAAAAAA
1 TATAAATATATAAAAAAA
*
30017660 GTTATAAATTTATAAAAAAA
1 --TATAAATATATAAAAAAA
30017680 TATAAATATATAAAA
1 TATAAATATATAAAA
30017695 TAACTAAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
17 6 0.14
18 23 0.52
19 7 0.16
20 8 0.18
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.29
Consensus pattern (18 bp):
TATAAATATATAAAAAAA
Found at i:30018144 original size:9 final size:9
Alignment explanation
Indices: 30018132--30018214 Score: 55
Period size: 9 Copynumber: 9.2 Consensus size: 9
30018122 ATATCAATAA
30018132 TTAATAATT
1 TTAATAATT
*
30018141 TTAAAAATT
1 TTAATAATT
*
30018150 TTAAAAATAT
1 TTAATAAT-T
*
30018160 TTTAT-ATT
1 TTAATAATT
*
30018168 TTTAT-ATT
1 TTAATAATT
*
30018176 TTTATAATT
1 TTAATAATT
30018185 TT-ATACATT
1 TTAATA-ATT
*
30018194 TTCAATAATG
1 TT-AATAATT
*
30018204 TTAATAGTT
1 TTAATAATT
30018213 TT
1 TT
30018215 TCGGAATATG
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
8 17 0.27
9 35 0.56
10 8 0.13
11 3 0.05
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (9 bp):
TTAATAATT
Found at i:30018170 original size:8 final size:8
Alignment explanation
Indices: 30018159--30018189 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
30018149 TTTAAAAATA
30018159 TTTTATAT
1 TTTTATAT
30018167 TTTTATAT
1 TTTTATAT
*
30018175 TTTTATAA
1 TTTTATAT
30018183 TTTTATA
1 TTTTATA
30018190 CATTTTCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (8 bp):
TTTTATAT
Found at i:30020438 original size:13 final size:13
Alignment explanation
Indices: 30020420--30020444 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30020410 GGTATACTAT
30020420 TATATATATATAA
1 TATATATATATAA
30020433 TATATATATATA
1 TATATATATATA
30020445 TTCTATTCTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATATATATATAA
Found at i:30023717 original size:30 final size:30
Alignment explanation
Indices: 30023683--30023907 Score: 210
Period size: 30 Copynumber: 7.6 Consensus size: 30
30023673 CAGAGAATTC
*
30023683 GGGGTTAAAATATAATTTTGGAAAAGTTTA
1 GGGGTTAAAATGTAATTTTGGAAAAGTTTA
* *
30023713 GGGGTAAAAATGTAATTTTGG-GAAGTTTA
1 GGGGTTAAAATGTAATTTTGGAAAAGTTTA
** * *
30023742 -GGGTTAAAACATGATTTTGGAGAAGTTTA
1 GGGGTTAAAATGTAATTTTGGAAAAGTTTA
* * * *
30023771 -GGGTTAAAATGTGATATT-GAGAAGGTTTT
1 GGGGTTAAAATGTAATTTTGGA-AAAGTTTA
** * * *
30023800 TAGGTCAAAATGCAATTTTAGAAAAGTTTA
1 GGGGTTAAAATGTAATTTTGGAAAAGTTTA
*
30023830 GGGGTTAAAATGTAATTTTAGAAAAGTTTA
1 GGGGTTAAAATGTAATTTTGGAAAAGTTTA
*
30023860 GGGGTCAAAATGTAATTTTGGAAAA-TTCTA
1 GGGGTTAAAATGTAATTTTGGAAAAGTT-TA
* *
30023890 GGGG-TCAAATGCAATTTT
1 GGGGTTAAAATGTAATTTT
30023908 CAAAGAAAAT
Statistics
Matches: 161, Mismatches: 29, Indels: 11
0.80 0.14 0.05
Matches are distributed among these distances:
28 18 0.11
29 48 0.30
30 93 0.58
31 2 0.01
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.35
Consensus pattern (30 bp):
GGGGTTAAAATGTAATTTTGGAAAAGTTTA
Found at i:30025411 original size:14 final size:15
Alignment explanation
Indices: 30025392--30025425 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
30025382 TTTCAAATGT
*
30025392 ATTGGGC-TAGGTTA
1 ATTGGGCTTAGGGTA
30025406 ATTGGGCTTAGGGTA
1 ATTGGGCTTAGGGTA
30025421 ATTGG
1 ATTGG
30025426 ACATGTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.21, C:0.06, G:0.38, T:0.35
Consensus pattern (15 bp):
ATTGGGCTTAGGGTA
Found at i:30025980 original size:50 final size:50
Alignment explanation
Indices: 30025926--30026396 Score: 293
Period size: 50 Copynumber: 9.7 Consensus size: 50
30025916 CGTCGTTACG
* *
30025926 GCCTCAACC-TTCACCTTCACATCTTCTAAGGTACCGAGTTTGCCGTTGCA
1 GCCTCAACCTTTC-CCTTCACATCTTCTAAGGTACCGAGTTCGCCATTGCA
* * *
30025976 GCCTCAACCTTTCCCTTCATATCTTCGT--GGTATC-AGGTTCGCCATTGCG
1 GCCTCAACCTTTCCCTTCACATCTTC-TAAGGTACCGA-GTTCGCCATTGCA
* * * * * * *
30026025 GCCTCAACCTTTCCCATCATATCTTTTTAGGTACTGGGTTTGCCATTGCA
1 GCCTCAACCTTTCCCTTCACATCTTCTAAGGTACCGAGTTCGCCATTGCA
* * * * * ** * *
30026075 TCTTCAACCTTTCCCTTCATATCTCCGT--GGTACCGGGTTCATCATTACG
1 GCCTCAACCTTTCCCTTCACATCTTC-TAAGGTACCGAGTTCGCCATTGCA
** * * * * *
30026124 GCCTCAACCTTT-CCTATCACATCTGATTAGGTACCGGGTTCACCGTTGCG
1 GCCTCAACCTTTCCCT-TCACATCTTCTAAGGTACCGAGTTCGCCATTGCA
* * * *
30026174 GCCTCAACCTTTCCCATT-ACATCTTCTAAGGTACCAAGTTCACCGTTAC-
1 GCCTCAACCTTTCCC-TTCACATCTTCTAAGGTACCGAGTTCGCCATTGCA
** *
30026223 GACCTCAACCTTTCCCTTCGTATCTTC-ATGGTACC-AGATTCGCCATTGCA
1 G-CCTCAACCTTTCCCTTCACATCTTCTAAGGTACCGAG-TTCGCCATTGCA
30026273 GCCTCAACCTTT-CCTATCACATCTTCTAAGGTACCG-GATTCGCCA-T-C-
1 GCCTCAACCTTTCCCT-TCACATCTTCTAAGGTACCGAG-TTCGCCATTGCA
* * * * * ** * *
30026320 G---CGACC-TTCCCTTCAAATCCTC-AAGGCACCGGGTTCATCGTTACA
1 GCCTCAACCTTTCCCTTCACATCTTCTAAGGTACCGAGTTCGCCATTGCA
*
30026365 GCCTCAACCTTTCCCTTCATATCTTC-AAGGTA
1 GCCTCAACCTTTCCCTTCACATCTTCTAAGGTA
30026397 TTAGATTTGT
Statistics
Matches: 336, Mismatches: 57, Indels: 57
0.75 0.13 0.13
Matches are distributed among these distances:
42 12 0.04
43 12 0.04
44 8 0.02
45 1 0.00
47 1 0.00
48 16 0.05
49 128 0.38
50 149 0.44
51 8 0.02
52 1 0.00
ACGTcount: A:0.20, C:0.33, G:0.15, T:0.32
Consensus pattern (50 bp):
GCCTCAACCTTTCCCTTCACATCTTCTAAGGTACCGAGTTCGCCATTGCA
Found at i:30026095 original size:99 final size:99
Alignment explanation
Indices: 30025921--30026286 Score: 355
Period size: 99 Copynumber: 3.7 Consensus size: 99
30025911 AGGGTCGTCG
* * * * *
30025921 TTACGGCCTCAACC-TTCACCTTCACATCTTCTAAGGTACCGAGTTTGCCGTTGCAGCCTCAACC
1 TTACGGCCTCAACCTTTC-CCATCACATCTTATTAGGTACCGGGTTTGCCATTGCAGCCTCAACC
* * *
30025985 TTTCCCTTCATATCTTCGTGGTATCAGGTTCGCCA
65 TTTCCCTTCATATCTCCGTGGTACCAGGTTCACCA
* * * * * *
30026020 TTGCGGCCTCAACCTTTCCCATCATATCTTTTTAGGTACTGGGTTTGCCATTGCATCTTCAACCT
1 TTACGGCCTCAACCTTTCCCATCACATCTTATTAGGTACCGGGTTTGCCATTGCAGCCTCAACCT
* *
30026085 TTCCCTTCATATCTCCGTGGTACCGGGTTCATCA
66 TTCCCTTCATATCTCCGTGGTACCAGGTTCACCA
* * ** * *
30026119 TTACGGCCTCAACCTTTCCTATCACATCTGATTAGGTACCGGGTTCACCGTTGCGGCCTCAACCT
1 TTACGGCCTCAACCTTTCCCATCACATCTTATTAGGTACCGGGTTTGCCATTGCAGCCTCAACCT
* * * *
30026184 TTCCCATT-ACATCTTC-TAAGGTACCAAGTTCACCG
66 TTCCC-TTCATATCTCCGT--GGTACCAGGTTCACCA
* * ** * * *
30026219 TTACGACCTCAACCTTTCCCTTCGTATCTTCA-T-GGTACCAGATTCGCCATTGCAGCCTCAACC
1 TTACGGCCTCAACCTTTCCCATCACATCTT-ATTAGGTACCGGGTTTGCCATTGCAGCCTCAACC
30026282 TTTCC
65 TTTCC
30026287 TATCACATCT
Statistics
Matches: 218, Mismatches: 44, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
98 1 0.00
99 174 0.80
100 42 0.19
101 1 0.00
ACGTcount: A:0.19, C:0.33, G:0.15, T:0.33
Consensus pattern (99 bp):
TTACGGCCTCAACCTTTCCCATCACATCTTATTAGGTACCGGGTTTGCCATTGCAGCCTCAACCT
TTCCCTTCATATCTCCGTGGTACCAGGTTCACCA
Found at i:30026305 original size:149 final size:147
Alignment explanation
Indices: 30025919--30026396 Score: 381
Period size: 149 Copynumber: 3.3 Consensus size: 147
30025909 CTAGGGTCGT
* * * * *
30025919 CGTTACGGCCTCAACC-TTCACCTTCACATCTTCTAAGGTACCGAGTTTGCCGTTGCAGCCTCAA
1 CGTTACGACCTCAACCTTTC-CCTTCATATCTTC-ATGGTACCGA-TTCGCCATTGCAGCCTCAA
* * * * *
30025983 CCTTTCCCT-TCATATCTTCGT-GGTATCAGGTTCGCCATTGCGGCCTCAACCTTTCCCATCATA
63 CCTTT-CCTATCACATCTTC-TAGGTACCGGGTTCACCATTGCGGCCTCAACCTTTCCCATCACA
* * *** **
30026046 TCTTTTTAGGTACTGGGTTTGC
126 TCTTCTAAGGTACCAAGTTCAC
* * * * * * ** * *
30026068 CATTGC-ATCTTCAACCTTTCCCTTCATATCTCCGTGGTACCGGGTTCATCATTACGGCCTCAAC
1 CGTTACGA-CCTCAACCTTTCCCTTCATATCTTCATGGTACC-GATTCGCCATTGCAGCCTCAAC
* *
30026132 CTTTCCTATCACATCTGAT-TAGGTACCGGGTTCACCGTTGCGGCCTCAACCTTTCCCATTACAT
64 CTTTCCTATCACATCT--TCTAGGTACCGGGTTCACCATTGCGGCCTCAACCTTTCCCATCACAT
30026196 CTTCTAAGGTACCAAGTTCAC
127 CTTCTAAGGTACCAAGTTCAC
*
30026217 CGTTACGACCTCAACCTTTCCCTTCGTATCTTCATGGTACCAGATTCGCCATTGCAGCCTCAACC
1 CGTTACGACCTCAACCTTTCCCTTCATATCTTCATGGTACC-GATTCGCCATTGCAGCCTCAACC
* * * * * *
30026282 TTTCCTATCACATCTTCTAAGGTACCGGATTCGCCA-T-C-G---CGACC-TTCCCTTCAAATCC
65 TTTCCTATCACATCTTCT-AGGTACCGGGTTCACCATTGCGGCCTCAACCTTTCCCATCACATCT
* ** *
30026340 TC-AAGGCACCGGGTTCAT
129 TCTAAGGTACCAAGTTCAC
*
30026358 CGTTAC-AGCCTCAACCTTTCCCTTCATATCTTCAAGGTA
1 CGTTACGA-CCTCAACCTTTCCCTTCATATCTTCATGGTA
30026397 TTAGATTTGT
Statistics
Matches: 263, Mismatches: 55, Indels: 30
0.76 0.16 0.09
Matches are distributed among these distances:
140 1 0.00
141 47 0.18
142 12 0.05
143 4 0.02
146 1 0.00
147 5 0.02
148 34 0.13
149 154 0.59
150 5 0.02
ACGTcount: A:0.19, C:0.33, G:0.15, T:0.32
Consensus pattern (147 bp):
CGTTACGACCTCAACCTTTCCCTTCATATCTTCATGGTACCGATTCGCCATTGCAGCCTCAACCT
TTCCTATCACATCTTCTAGGTACCGGGTTCACCATTGCGGCCTCAACCTTTCCCATCACATCTTC
TAAGGTACCAAGTTCAC
Found at i:30027213 original size:39 final size:40
Alignment explanation
Indices: 30027128--30027245 Score: 157
Period size: 39 Copynumber: 2.9 Consensus size: 40
30027118 TTTGAGTCGT
* *
30027128 CCTTTACGGGTTTTCAACTCAAAATCCCTTTTGGTTTCAAGACGC
1 CCTTTACGGGTTTTCATCTC--AAT-CCTTTT--TTTTAAGACGC
*
30027173 CCTTTGCGGGTTTTCATCTCAATCCTTTTTTTTAA-ACGC
1 CCTTTACGGGTTTTCATCTCAATCCTTTTTTTTAAGACGC
30027212 CCTTTACGGGTTTTCATCTCAATCCTTTTTTTTA
1 CCTTTACGGGTTTTCATCTCAATCCTTTTTTTTA
30027246 GGAAAAATAT
Statistics
Matches: 69, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
39 37 0.54
40 5 0.07
42 6 0.09
43 3 0.04
45 18 0.26
ACGTcount: A:0.18, C:0.25, G:0.13, T:0.44
Consensus pattern (40 bp):
CCTTTACGGGTTTTCATCTCAATCCTTTTTTTTAAGACGC
Found at i:30034649 original size:30 final size:29
Alignment explanation
Indices: 30034615--30034808 Score: 153
Period size: 29 Copynumber: 6.6 Consensus size: 29
30034605 CAGAGAATTC
*
30034615 GGGGTTAAAATATAACTTTGGAAATGTTTA
1 GGGGTTAAAATATAATTTTGGAAA-GTTTA
*
30034645 GGGG-TAAAAGTGTAATTTTAGGAAAGTTT-
1 GGGGTTAAAA-TATAATTTT-GGAAAGTTTA
* * *
30034674 GGGGTCAAAATGTGATTTTGGAGAAGTTT-
1 GGGGTTAAAATATAATTTTGGA-AAGTTTA
** ** *
30034703 GGCATTAAAACGTAATTTTGGGAAGATTTA
1 GGGGTTAAAATATAATTTTGGAAAG-TTTA
* * *
30034733 AGGGTCAAAATATAATTTTAGAAAAGTTTA
1 GGGGTTAAAATATAATTTT-GGAAAGTTTA
*
30034763 GGGGTT-AAATATAATTTTAGAAAAGTTTA
1 GGGGTTAAAATATAATTTT-GGAAAGTTTA
* *
30034792 AGGGTTAAAATGTAATT
1 GGGGTTAAAATATAATT
30034809 ATTAAAGAAA
Statistics
Matches: 134, Mismatches: 22, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
28 6 0.04
29 70 0.52
30 49 0.37
31 9 0.07
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.35
Consensus pattern (29 bp):
GGGGTTAAAATATAATTTTGGAAAGTTTA
Found at i:30034712 original size:59 final size:60
Alignment explanation
Indices: 30034649--30034808 Score: 166
Period size: 59 Copynumber: 2.7 Consensus size: 60
30034639 TGTTTAGGGG
* * * *
30034649 TAAAAGTGTAATTTTAGGAAAGTTT-GGGGTCAAAATGTGATTTTGGAGAAGTTT-GGCAT
1 TAAAA-TGTAATTTTAGGAAAGTTTAAGGGTCAAAATGTAATTTTAGAAAAGTTTAGGCAT
* * * **
30034708 TAAAACGTAATTTT-GGGAAGATTTAAGGGTCAAAATATAATTTTAGAAAAGTTTAGGGGT
1 TAAAATGTAATTTTAGGAAAG-TTTAAGGGTCAAAATGTAATTTTAGAAAAGTTTAGGCAT
* * *
30034768 T-AAATATAATTTTAGAAAAGTTTAAGGGTTAAAATGTAATT
1 TAAAATGTAATTTTAGGAAAGTTTAAGGGTCAAAATGTAATT
30034809 ATTAAAGAAA
Statistics
Matches: 82, Mismatches: 15, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
57 5 0.06
58 11 0.13
59 58 0.71
60 8 0.10
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.36
Consensus pattern (60 bp):
TAAAATGTAATTTTAGGAAAGTTTAAGGGTCAAAATGTAATTTTAGAAAAGTTTAGGCAT
Found at i:30042792 original size:92 final size:94
Alignment explanation
Indices: 30042653--30043296 Score: 296
Period size: 93 Copynumber: 6.8 Consensus size: 94
30042643 GTTAAAACAT
* * **
30042653 CAAATCTTATACCCCCTGAGTTACAGTGGGTCAAATTAAAACAATGAAGTGGATCTCAATGTCCC
1 CAAATCATATACCCCTTGAGTTACAGTGGGTCAAATTAAAACAATGAAGCAGATCTCAATGTCCC
*
30042718 TGAGGTTACAATGGAATGGAGTGAAGCAC
66 TGAGGTTACAATGGAATGGAATGAAGCAC
* * * *
30042747 CAAATCCTATA-CCCTTGAG-TGCAGTGGGTCAAATTAAAGCAATGAAGCAGATCTCAATGTCCT
1 CAAATCATATACCCCTTGAGTTACAGTGGGTCAAATTAAAACAATGAAGCAGATCTCAATGTCCC
* *
30042810 TGAGGTTACAGTGGAGTGGAATGAAGCAC
66 TGAGGTTACAATGGAATGGAATGAAGCAC
* * ** * * * * * ** * ** * *
30042839 CAGATCATATATCCCTAAATTTAGACTAGATCGGATCAAAATGA-GTAA-CAAATTTCAATGTCC
1 CAAATCATATACCCCTTGAGTTACAGTGGGTCAAATTAAAACAATG-AAGCAGATCTCAATGTCC
* * *
30042902 CTAAGGTTATAGTGGAATGG-ATAGAAGCTACAAC
65 CTGAGGTTACAATGGAATGGAAT-GAAG---C-AC
* * * **
30042936 ACTAAAT-ACTATACCCC-TGAGTTACAGTGGGTCGAATTAAAGCAATGAGGTGGATCTCAACT-
1 -C-AAATCA-TATACCCCTTGAGTTACAGTGGGTCAAATTAAAACAATGAAGCAGATCTCAA-TG
* * * * **
30042998 TCCCTAAGGTTACAGTGGAGTGGAATAAATAAC
62 TCCCTGAGGTTACAATGGAATGGAATGAAGCAC
* ** * * * * *
30043031 CAAATCTTATATTCC-TGAGTTGCAGTGGGTCAGATTGAAACAATAAAGTC-GATCT-AACGTCC
1 CAAATCATATACCCCTTGAGTTACAGTGGGTCAAATTAAAACAATGAAG-CAGATCTCAATGTCC
* * * * * * *
30043093 TTGAGGTTACAGTAGAGTGGAGTAAAAGCAT
65 CTGAGGTTACAATGGAATGGAAT-GAAGCAC
* ** * * ** * *
30043124 CAAATCCTAT-CTTCTTGAGGTTACAATGAAGT-GGATCAAAACAA-GTAA-CAGATCTTAATGT
1 CAAATCATATACCCCTTGA-GTTACAGTG-GGTCAAATTAAAACAATG-AAGCAGATCTCAATGT
** * *
30043185 TTCT-ATGGTTACAGTGGAATGGAGTGAAGTTACAACAC
63 CCCTGA-GGTTACAATGGAATGGAATGAAG------CAC
* * * * * *
30043223 CAAATCTTATACCCC-TGAGTTACAGTGGGTCAGACTAAAACAATGAAGTAGATCTCAACGTCCT
1 CAAATCATATACCCCTTGAGTTACAGTGGGTCAAATTAAAACAATGAAGCAGATCTCAATGTCCC
30043287 TGAGGTTACA
66 TGAGGTTACA
30043297 GTGAAGTGGA
Statistics
Matches: 406, Mismatches: 107, Indels: 69
0.70 0.18 0.12
Matches are distributed among these distances:
92 103 0.25
93 112 0.28
94 65 0.16
95 4 0.01
96 1 0.00
97 4 0.01
98 38 0.09
99 73 0.18
100 6 0.01
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (94 bp):
CAAATCATATACCCCTTGAGTTACAGTGGGTCAAATTAAAACAATGAAGCAGATCTCAATGTCCC
TGAGGTTACAATGGAATGGAATGAAGCAC
Found at i:30043252 original size:285 final size:283
Alignment explanation
Indices: 30042642--30043306 Score: 729
Period size: 285 Copynumber: 2.3 Consensus size: 283
30042632 TAATGGACCT
* *
30042642 AGTTAAAACATCAAATCTTATACCCCCTGAGTTACAGTGGGTCAAATTAAAACAATGAAGTGGAT
1 AGTTACAACACCAAATCTTATA-CCCCTGAGTTACAGTGGGTC-AATTAAAACAATGAAGTGGAT
* * * * *
30042707 CTCAA-TGTCCCTGAGGTTACAATGGAATGGAGTGAAGCACCAAATCCTATACCCTTGAGTGCAG
64 CTCAACT-TCCCTGAGGTTACAGTGGAGTGGAATAAAGAACCAAATCCTATACCCTTGAGTGCAG
* * * *
30042771 TGGGTCAAATTAAAGCAATGAAGCAGATCTCAATGTCCTTGAGGTTACAGTGGAGTGGAATGAAG
128 TGGGTCAAATTAAAGCAATAAAGCAGATCTCAACGTCCTTGAGGTTACAGTAGAGTGGAATAAAG
* * * * **
30042836 CACCAGATCATATATCCCTAAATTTAGACTAGATCGGATCAAAATGAGTAACAAATTTCAATGTC
193 CACCAAATCATATATCCCTAAAGTTACAATAGATCGGATCAAAACAAGTAACAAATTTCAATGTC
*
30042901 CCTAAGGTTATAGTGGAATGGATAGA
258 CCTAAGGTTACAGTGGAATGGATAGA
* * * *
30042927 AGCTACAACACTAAATAC-TATACCCCTGAGTTACAGTGGGTCGAATTAAAGCAATGAGGTGGAT
1 AGTTACAACACCAAAT-CTTATACCCCTGAGTTACAGTGGGTC-AATTAAAACAATGAAGTGGAT
* * * *
30042991 CTCAACTTCCCTAAGGTTACAGTGGAGTGGAATAAATAACCAAATCTTATATTCC-TGAGTTGCA
64 CTCAACTTCCCTGAGGTTACAGTGGAGTGGAATAAAGAACCAAATCCTATA-CCCTTGAG-TGCA
* *
30043055 GTGGGTCAGATTGAAA-CAATAAAGTC-GATCT-AACGTCCTTGAGGTTACAGTAGAGTGGAGTA
127 GTGGGTCAAATT-AAAGCAATAAAG-CAGATCTCAACGTCCTTGAGGTTACAGTAGAGTGGAAT-
* * * * * * * *
30043117 AAAGCATCAAATCCTATCTTCTTGAGGTTACAAT-GAAGT-GGATCAAAACAAGTAACAGATCTT
189 AAAGCACCAAATCATATATCCCTAAAGTTACAATAG-A-TCGGATCAAAACAAGTAACAAAT-TT
** *
30043180 -AATGTTTCTATGGTTACAGTGGAATGGAGT-GA
251 CAATGTCCCTAAGGTTACAGTGGAATGGA-TAGA
* *
30043212 AGTTACAACACCAAATCTTATACCCCTGAGTTACAGTGGGTCAGACTAAAACAATGAAGTAGATC
1 AGTTACAACACCAAATCTTATACCCCTGAGTTACAGTGGGTCA-ATTAAAACAATGAAGTGGATC
* * *
30043277 TCAACGTCCTTGAGGTTACAGTGAAGTGGA
65 TCAACTTCCCTGAGGTTACAGTGGAGTGGA
30043307 TGAAAACAAG
Statistics
Matches: 317, Mismatches: 50, Indels: 26
0.81 0.13 0.07
Matches are distributed among these distances:
284 114 0.36
285 194 0.61
286 9 0.03
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (283 bp):
AGTTACAACACCAAATCTTATACCCCTGAGTTACAGTGGGTCAATTAAAACAATGAAGTGGATCT
CAACTTCCCTGAGGTTACAGTGGAGTGGAATAAAGAACCAAATCCTATACCCTTGAGTGCAGTGG
GTCAAATTAAAGCAATAAAGCAGATCTCAACGTCCTTGAGGTTACAGTAGAGTGGAATAAAGCAC
CAAATCATATATCCCTAAAGTTACAATAGATCGGATCAAAACAAGTAACAAATTTCAATGTCCCT
AAGGTTACAGTGGAATGGATAGA
Found at i:30043332 original size:148 final size:148
Alignment explanation
Indices: 30043137--30043448 Score: 405
Period size: 148 Copynumber: 2.1 Consensus size: 148
30043127 ATCCTATCTT
* * *
30043137 CTTGAGGTTACAATGAAGTGGATCAAAACAAGTAACAGATCTTAATGT-TTCTATGGTTACAGTG
1 CTTGAGGTTACAGTGAAGTGGATCAAAACAAGTAACAGATCTCAATGTCCT-TA-GGTTACAGTG
* *
30043201 GAATGGAGTGAAGTTACAACACCAAATCTTATACCCCTG-AGTTACAGTGGGTC-AGACTAAAAC
64 GAATGGAGTGAAGTTACAACACCAAATCCTATACCCCTGAAGTTACAGTGAGTCGA-ACTAAAAC
* *
30043264 AATGAAGTAGATCTCAACGTC
128 AACGAAGTAGATCCCAACGTC
*
30043285 CTTGAGGTTACAGTGAAGTGGATGAAAACAAGTAACAGATCTCAATGTCCTTGAGGTTACAGTGG
1 CTTGAGGTTACAGTGAAGTGGATCAAAACAAGTAACAGATCTCAATGTCCTT-AGGTTACAGTGG
* * * * * *
30043350 AATGGAGTGAAGTTATAACATCGAATCCTATACCCTTGAAGTTGCAGTGAGTCGAATTAAAACAA
65 AATGGAGTGAAGTTACAACACCAAATCCTATACCCCTGAAGTTACAGTGAGTCGAACTAAAACAA
*
30043415 CGAAGTAGATCCCAATGTC
130 CGAAGTAGATCCCAACGTC
* * *
30043434 CCTAAGGTTATAGTG
1 CTTGAGGTTACAGTG
30043449 GAATGCAGAG
Statistics
Matches: 142, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
148 90 0.63
149 51 0.36
150 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.26
Consensus pattern (148 bp):
CTTGAGGTTACAGTGAAGTGGATCAAAACAAGTAACAGATCTCAATGTCCTTAGGTTACAGTGGA
ATGGAGTGAAGTTACAACACCAAATCCTATACCCCTGAAGTTACAGTGAGTCGAACTAAAACAAC
GAAGTAGATCCCAACGTC
Found at i:30055886 original size:17 final size:15
Alignment explanation
Indices: 30055834--30055880 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
30055824 TAAACACTTA
30055834 TGTAATGTAATTTTT
1 TGTAATGTAATTTTT
* *
30055849 TGCAATTGCTTATTTTT
1 TGTAA-TG-TAATTTTT
30055866 TGTAATGTAATTTTT
1 TGTAATGTAATTTTT
30055881 CATGTAACTC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 11 0.42
16 4 0.15
17 11 0.42
ACGTcount: A:0.23, C:0.04, G:0.13, T:0.60
Consensus pattern (15 bp):
TGTAATGTAATTTTT
Found at i:30065366 original size:19 final size:19
Alignment explanation
Indices: 30065342--30065388 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
30065332 ATATTATGAA
*
30065342 AAAATATATATTACAAATG
1 AAAATATAAATTACAAATG
** *
30065361 AAAATATAAATTTTAAATT
1 AAAATATAAATTACAAATG
30065380 AAAATATAA
1 AAAATATAA
30065389 TAAAAAGACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (19 bp):
AAAATATAAATTACAAATG
Done.