Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 56 of 216
Found at i:16503855 original size:23 final size:24
Alignment explanation
Indices: 16503813--16503871 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 24
16503803 ACGATTTTGG
16503813 TTCTTCTTT-TTTCCAGTTTT-TTT
1 TTCTTCTTTCTTTCCA-TTTTATTT
16503836 TTCTTCTTTCTTTCTC-TTTTATTT
1 TTCTTCTTTCTTTC-CATTTTATTT
*
16503860 TTCCTTGTTTCT
1 TT-CTTCTTTCT
16503872 AAAAGCAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
23 13 0.42
24 9 0.29
25 9 0.29
ACGTcount: A:0.03, C:0.20, G:0.03, T:0.73
Consensus pattern (24 bp):
TTCTTCTTTCTTTCCATTTTATTT
Found at i:16504406 original size:17 final size:18
Alignment explanation
Indices: 16504381--16504427 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
16504371 ATATTATCAA
* *
16504381 TATTGTTATTGCGTTAT-
1 TATTATTATTACGTTATC
* *
16504398 TATTATTATAATGTTATC
1 TATTATTATTACGTTATC
16504416 TATTATTATTAC
1 TATTATTATTAC
16504428 ATATATTTAT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.28, C:0.06, G:0.09, T:0.57
Consensus pattern (18 bp):
TATTATTATTACGTTATC
Found at i:16504737 original size:10 final size:9
Alignment explanation
Indices: 16504700--16504755 Score: 53
Period size: 10 Copynumber: 6.2 Consensus size: 9
16504690 TTTATTAATG
*
16504700 TATTTTGTT
1 TATTTTATT
*
16504709 TATATT-TT
1 TATTTTATT
16504717 TATTTTATT
1 TATTTTATT
16504726 TATTTGTATT
1 TATTT-TATT
*
16504736 TATTTCTATA
1 TATTT-TATT
16504746 TATTTT-TT
1 TATTTTATT
16504754 TA
1 TA
16504756 GATACCTATA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
8 10 0.25
9 13 0.32
10 17 0.43
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.73
Consensus pattern (9 bp):
TATTTTATT
Found at i:16508717 original size:9 final size:9
Alignment explanation
Indices: 16508700--16508736 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
16508690 TGAGTTTTCG
16508700 AATTCGAAT
1 AATTCGAAT
*
16508709 AACTCGAAT
1 AATTCGAAT
16508718 AATTCGAAT
1 AATTCGAAT
16508727 AATTCGAAT
1 AATTCGAAT
16508736 A
1 A
16508737 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:16509127 original size:17 final size:16
Alignment explanation
Indices: 16509089--16509123 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
16509079 ACTCCCCTTA
16509089 TTTATTCCCTCAAACT
1 TTTATTCCCTCAAACT
16509105 TTTATTCCC-CAAAACT
1 TTTATTCCCTC-AAACT
16509121 TTT
1 TTT
16509124 TATTTTTCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 1 0.06
16 17 0.94
ACGTcount: A:0.26, C:0.29, G:0.00, T:0.46
Consensus pattern (16 bp):
TTTATTCCCTCAAACT
Found at i:16510774 original size:30 final size:31
Alignment explanation
Indices: 16510730--16510809 Score: 101
Period size: 30 Copynumber: 2.6 Consensus size: 31
16510720 AATGAGTAAC
*
16510730 AAAAGAATAGTTTAGGTACC-ACTTGTGACAAA
1 AAAAG-ATAGTTTAGGTACCAACTTGAGA-AAA
16510762 AAAAGA-AGTTTAGGTACCAACTTGAGAAAA
1 AAAAGATAGTTTAGGTACCAACTTGAGAAAA
* *
16510792 AAAATATTGTTTAGGTAC
1 AAAAGATAGTTTAGGTAC
16510810 TAATTTGTGA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
30 20 0.47
31 18 0.42
32 5 0.12
ACGTcount: A:0.45, C:0.10, G:0.19, T:0.26
Consensus pattern (31 bp):
AAAAGATAGTTTAGGTACCAACTTGAGAAAA
Found at i:16510794 original size:31 final size:30
Alignment explanation
Indices: 16510738--16510795 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 30
16510728 ACAAAAGAAT
* *
16510738 AGTTTAGGTACCACTTGTGACAAAAAAAGA
1 AGTTTAGGTACCACTTGAGAAAAAAAAAGA
16510768 AGTTTAGGTACCAACTTGAGAAAAAAAA
1 AGTTTAGGTACC-ACTTGAGAAAAAAAA
16510796 TATTGTTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 12 0.48
31 13 0.52
ACGTcount: A:0.47, C:0.12, G:0.19, T:0.22
Consensus pattern (30 bp):
AGTTTAGGTACCACTTGAGAAAAAAAAAGA
Found at i:16511680 original size:5 final size:5
Alignment explanation
Indices: 16511659--16511694 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
16511649 ATCATTACTA
*
16511659 AAAAT AAAATT ACAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAA-T AAAAT AAAAT AAAAT AAAAT AAAAT
16511695 GAGCATGGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 24 0.86
6 4 0.14
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:16513459 original size:26 final size:26
Alignment explanation
Indices: 16513423--16513473 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
16513413 GAAACAAATT
* *
16513423 AAGAAGCCAACGAAGGATTACCCACC
1 AAGAAGCCAACAAAGGATCACCCACC
*
16513449 AAGAAGCCAACAAAGGGTCACCCAC
1 AAGAAGCCAACAAAGGATCACCCAC
16513474 TTTCCAAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.43, C:0.31, G:0.20, T:0.06
Consensus pattern (26 bp):
AAGAAGCCAACAAAGGATCACCCACC
Found at i:16522135 original size:5 final size:5
Alignment explanation
Indices: 16522120--16522152 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
16522110 GCAACCCTCA
16522120 TTTATT TTTAT TTTA- TTTAT TTTAT TTTAT TTT
1 TTTA-T TTTAT TTTAT TTTAT TTTAT TTTAT TTT
16522153 GAATTTTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.15
5 18 0.69
6 4 0.15
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:16522140 original size:9 final size:10
Alignment explanation
Indices: 16522120--16522152 Score: 50
Period size: 9 Copynumber: 3.3 Consensus size: 10
16522110 GCAACCCTCA
16522120 TTTATTTTTAT
1 TTTA-TTTTAT
16522131 TTTA-TTTAT
1 TTTATTTTAT
16522140 TTTATTTTAT
1 TTTATTTTAT
16522150 TTT
1 TTT
16522153 GAATTTTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.43
10 8 0.38
11 4 0.19
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTATTTTAT
Found at i:16522144 original size:14 final size:15
Alignment explanation
Indices: 16522119--16522151 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
16522109 GGCAACCCTC
16522119 ATTTATTTTTATTTT
1 ATTTATTTTTATTTT
16522134 ATTTA-TTTTATTTT
1 ATTTATTTTTATTTT
16522148 ATTT
1 ATTT
16522152 TGAATTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
ATTTATTTTTATTTT
Found at i:16522160 original size:17 final size:16
Alignment explanation
Indices: 16522125--16522171 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
16522115 CCTCATTTAT
16522125 TTTTATTTTATTT--A
1 TTTTATTTTATTTGAA
16522139 TTTTATTTTATTTTGAA
1 TTTTATTTTA-TTTGAA
*
16522156 TTTTAGTTTAGTTTGA
1 TTTTATTTTA-TTTGA
16522172 GAATTAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 10 0.36
15 3 0.11
17 15 0.54
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.70
Consensus pattern (16 bp):
TTTTATTTTATTTGAA
Found at i:16524132 original size:31 final size:31
Alignment explanation
Indices: 16524097--16524155 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
16524087 AGTTGAGAAG
* *
16524097 AAACTGTGTTCGATTCAAAAAGTTTATTCAA
1 AAACTGCGTTCGATTCAAAAAATTTATTCAA
*
16524128 AAACTGCGTTTGATTCAAAAAATTTATT
1 AAACTGCGTTCGATTCAAAAAATTTATT
16524156 TGAAAAGTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (31 bp):
AAACTGCGTTCGATTCAAAAAATTTATTCAA
Found at i:16526186 original size:15 final size:15
Alignment explanation
Indices: 16526150--16526191 Score: 68
Period size: 16 Copynumber: 2.8 Consensus size: 15
16526140 TATATATATT
16526150 TTAAACATAAAAAAC
1 TTAAACATAAAAAAC
16526165 TTAAAACATAAAAAAC
1 TT-AAACATAAAAAAC
16526181 TTAAAC-TAAAA
1 TTAAACATAAAA
16526192 CTAAAAACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.19
15 6 0.23
16 15 0.58
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (15 bp):
TTAAACATAAAAAAC
Found at i:16526199 original size:19 final size:21
Alignment explanation
Indices: 16526161--16526207 Score: 71
Period size: 19 Copynumber: 2.3 Consensus size: 21
16526151 TAAACATAAA
16526161 AAACTTAAAACATAAAAAACTT
1 AAAC-TAAAACATAAAAAACTT
16526183 AAACTAAAAC-T-AAAAACTT
1 AAACTAAAACATAAAAAACTT
16526202 AAACTA
1 AAACTA
16526208 GTATATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.56
20 1 0.04
21 6 0.24
22 4 0.16
ACGTcount: A:0.64, C:0.15, G:0.00, T:0.21
Consensus pattern (21 bp):
AAACTAAAACATAAAAAACTT
Found at i:16527512 original size:49 final size:50
Alignment explanation
Indices: 16527457--16527567 Score: 145
Period size: 49 Copynumber: 2.2 Consensus size: 50
16527447 ATCCCTTTCT
* *
16527457 CTCTTCCCCACCATCCTTCCCCCTCCCTTGATTCTCT-CT-CCCTCTCCCC
1 CTCTTCCCCACCATCCTTCCCCCTACCTTGATTCTCTGCTAACCT-TCCCC
* * * *
16527506 CTCTTCCCCACCATCCTTCCTCCTACTTTGATTCTTTGCTAACCTTCTCC
1 CTCTTCCCCACCATCCTTCCCCCTACCTTGATTCTCTGCTAACCTTCCCC
16527556 CTCTTCCCCACC
1 CTCTTCCCCACC
16527568 GTCCCTTTGC
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
49 33 0.61
50 18 0.33
51 3 0.06
ACGTcount: A:0.09, C:0.53, G:0.03, T:0.35
Consensus pattern (50 bp):
CTCTTCCCCACCATCCTTCCCCCTACCTTGATTCTCTGCTAACCTTCCCC
Found at i:16529354 original size:110 final size:111
Alignment explanation
Indices: 16529217--16529418 Score: 343
Period size: 110 Copynumber: 1.8 Consensus size: 111
16529207 ACATCTTTTT
*
16529217 TTTTTTGCTTAAGAATATATTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAACACCTCACCC
1 TTTTTTGCTTAAGAATATATTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAACACCCCACCC
* *
16529282 CGGTTACTTAGCCCAACATACTCCTAATTTATTATATTTATATATA
66 CGGTTACTCAGCCCAACACACTCCTAATTTATTATATTTATATATA
*
16529328 TTTTTT-CTTAAGAATATATTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCACCC
1 TTTTTTGCTTAAGAATATATTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAACACCCCACCC
* *
16529392 TGGTTACTCAGCCCAACACATTCCTAA
66 CGGTTACTCAGCCCAACACACTCCTAA
16529419 AAATTTTTTG
Statistics
Matches: 85, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
110 79 0.93
111 6 0.07
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (111 bp):
TTTTTTGCTTAAGAATATATTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAACACCCCACCC
CGGTTACTCAGCCCAACACACTCCTAATTTATTATATTTATATATA
Found at i:16530584 original size:4 final size:4
Alignment explanation
Indices: 16530568--16530656 Score: 68
Period size: 4 Copynumber: 22.8 Consensus size: 4
16530558 TATCCAAACA
16530568 AAAT AAAGT -AAT AAAT -AAT AAAAT AAAGT GAAAT AAAGT -AAT AAAT
1 AAAT AAA-T AAAT AAAT AAAT -AAAT AAA-T -AAAT AAA-T AAAT AAAT
16530614 AAAT -AAT AAAT -AAT AAAT -AAT AAAT -AAT AAAT -AAT AAAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAA
16530657 AATAAAAATA
Statistics
Matches: 71, Mismatches: 0, Indels: 28
0.72 0.00 0.28
Matches are distributed among these distances:
3 20 0.28
4 38 0.54
5 10 0.14
6 3 0.04
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:16530588 original size:7 final size:7
Alignment explanation
Indices: 16530569--16530667 Score: 96
Period size: 7 Copynumber: 13.3 Consensus size: 7
16530559 ATCCAAACAA
16530569 AATAAAGT
1 AATAAA-T
16530577 AATAAAT
1 AATAAAT
16530584 AATAAAAT
1 AAT-AAAT
16530592 AAAGTGAAAT
1 -AA-T-AAAT
16530602 AA-AGTAAT
1 AATA--AAT
16530610 AAATAAAT
1 -AATAAAT
16530618 AATAAAT
1 AATAAAT
16530625 AATAAAT
1 AATAAAT
16530632 AATAAAT
1 AATAAAT
16530639 AATAAAT
1 AATAAAT
16530646 AATAAAAT
1 AAT-AAAT
16530654 AA-AAAT
1 AATAAAT
16530660 AA-AAAT
1 AATAAAT
16530666 AA
1 AA
16530668 AGAAAAATAA
Statistics
Matches: 82, Mismatches: 1, Indels: 18
0.81 0.01 0.18
Matches are distributed among these distances:
6 13 0.16
7 35 0.43
8 22 0.27
9 6 0.07
10 6 0.07
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (7 bp):
AATAAAT
Found at i:16530602 original size:30 final size:28
Alignment explanation
Indices: 16530568--16530678 Score: 112
Period size: 25 Copynumber: 4.1 Consensus size: 28
16530558 TATCCAAACA
16530568 AAATAAAGTAATAAATAATAAAATAAAGT
1 AAATAAAGTAATAAATAATAAAATAAA-T
*
16530597 GAAATAAAGTAATAAATAA-ATAATAAAT
1 -AAATAAAGTAATAAATAATAAAATAAAT
16530625 -AATAAA-TAATAAATAAT-AAAT-AAT
1 AAATAAAGTAATAAATAATAAAATAAAT
*
16530649 AAAATAAA--AATAAA-AATAAAGAAAAAT
1 -AAATAAAGTAATAAATAATAAA-ATAAAT
16530676 AAA
1 AAA
16530679 AATTGGGTTG
Statistics
Matches: 72, Mismatches: 3, Indels: 16
0.79 0.03 0.18
Matches are distributed among these distances:
24 6 0.08
25 21 0.29
26 16 0.22
27 3 0.04
28 1 0.01
29 7 0.10
30 18 0.25
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.23
Consensus pattern (28 bp):
AAATAAAGTAATAAATAATAAAATAAAT
Found at i:16530680 original size:7 final size:7
Alignment explanation
Indices: 16530607--16530680 Score: 60
Period size: 7 Copynumber: 10.1 Consensus size: 7
16530597 GAAATAAAGT
16530607 AATAAATA
1 AATAAA-A
*
16530615 AATAATA
1 AATAAAA
*
16530622 AATAATA
1 AATAAAA
*
16530629 AATAATA
1 AATAAAA
*
16530636 AATAATA
1 AATAAAA
16530643 AATAATAA
1 AATAA-AA
16530651 AAT-AAA
1 AATAAAA
16530657 AATAAAA
1 AATAAAA
*
16530664 ATAAAGAAA
1 A-ATA-AAA
16530673 AATAAAA
1 AATAAAA
16530680 A
1 A
16530681 TTGGGTTGCC
Statistics
Matches: 58, Mismatches: 4, Indels: 9
0.82 0.06 0.13
Matches are distributed among these distances:
6 5 0.09
7 36 0.62
8 13 0.22
9 4 0.07
ACGTcount: A:0.77, C:0.00, G:0.01, T:0.22
Consensus pattern (7 bp):
AATAAAA
Found at i:16534305 original size:10 final size:10
Alignment explanation
Indices: 16534290--16534318 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
16534280 CTAAATTTTA
16534290 AAAGATAAAT
1 AAAGATAAAT
16534300 AAAGATAAAT
1 AAAGATAAAT
16534310 AAAGATAAA
1 AAAGATAAA
16534319 AGCTAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.17
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:16535391 original size:30 final size:30
Alignment explanation
Indices: 16535357--16535413 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
16535347 TAGGGGATGG
16535357 AAAATGGTAGCTCCGTTAAGTCTGTAATGA
1 AAAATGGTAGCTCCGTTAAGTCTGTAATGA
* * *
16535387 AAAATGGTAGCTCTGTTACGTTTGTAA
1 AAAATGGTAGCTCCGTTAAGTCTGTAA
16535414 CAGATTATGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (30 bp):
AAAATGGTAGCTCCGTTAAGTCTGTAATGA
Found at i:16537153 original size:14 final size:15
Alignment explanation
Indices: 16537128--16537160 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
16537118 CGAATTTATC
*
16537128 TATTTTTAAATATTT
1 TATTTTTAAATAATT
16537143 TATTTTT-AATAATT
1 TATTTTTAAATAATT
16537157 TATT
1 TATT
16537161 CAATCGAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTTTTAAATAATT
Found at i:16540277 original size:2 final size:2
Alignment explanation
Indices: 16540270--16540299 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16540260 GGCTCTGAGT
16540270 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
16540300 AATTGGTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:16546388 original size:375 final size:375
Alignment explanation
Indices: 16545695--16546394 Score: 1105
Period size: 375 Copynumber: 1.9 Consensus size: 375
16545685 AATGTTAATG
* * *
16545695 CCTCATTTTGCTTATGATTGAAATCTAATGGACCAATTAGCTTATTGCTGAGGGTGTCTAATTGT
1 CCTCATTTTGCTTATGACTGAAAGCTAATGGACCAATTAGCTTATTGCTGAGGGTGTCTAATTAT
** * *
16545760 TTCAATAGGGGTTGAATGTTTAAGAGTATCTTTTGAAGCTTAACCAATTGTGGTGTGTGTTAATT
66 TTCAATAGGGGCCGAATGTATAAGAGCATCTTTTGAAGCTTAACCAATTGTGGTGTGTGTTAATT
*
16545825 GTGATGCTTTCCGGTTGTGTTGGAAGTGTAAATGAAATGGGTAAATGAATGTAAGTTGTCCTTTA
131 GTGATGCTTGCCGGTTGTGTTGGAAGTGTAAATGAAATGGGTAAATGAATGTAAGTTGTCCTTTA
* *
16545890 TATGGTCGAATGTGTTATGTGATAACTTGGGATGTTTTCCAAAAGTGCCATGCCAATTCTATACT
196 TATGGCCGAATGTGTTATGTGATAACTTGGGATGTTTGCCAAAAGTGCCATGCCAATTCTATACT
* ** * * *
16545955 ATGTGTTTACTTAAGTTGATTGAATGTGTCTATTGGTTTGCTTGCTATAAACGAATATGCATAAT
261 ATGTGTTCACTTAAGTTGACCGAATGTGTCTATTGGCTTACTTGATATAAACGAATATGCATAAT
16546020 CTGCTAATGTATGCTACTGTATTGCTATTACATTTTCACTGAATGCTCAT
326 CTGCTAATGTATGCTACTGTATTGCTATTACATTTTCACTGAATGCTCAT
* * * * *
16546070 CCTCATTTTTCTTATGACTGAAAGCTAATTGACTAGTTAGCTTATTGCTGAGGGTGTTTAATTAT
1 CCTCATTTTGCTTATGACTGAAAGCTAATGGACCAATTAGCTTATTGCTGAGGGTGTCTAATTAT
*
16546135 TTCAATAGGGGCCGAATGTATAAGAGCATCTTTTGAAGCTTAACCGATTGTGGTGTGTGTTAATT
66 TTCAATAGGGGCCGAATGTATAAGAGCATCTTTTGAAGCTTAACCAATTGTGGTGTGTGTTAATT
* * *
16546200 GT-ACTGCTTGCCGGTTGTGTTGGAAGTGTAAATGAAATGGTTGAATGAATGTAAGTTGTCTTTT
131 GTGA-TGCTTGCCGGTTGTGTTGGAAGTGTAAATGAAATGGGTAAATGAATGTAAGTTGTCCTTT
* * *
16546264 ATATGGCCGAATGTGTTATGTGATAAGTTGGGATGTTTGCCAAAAGTGCGATGCCTATTCTATAC
195 ATATGGCCGAATGTGTTATGTGATAACTTGGGATGTTTGCCAAAAGTGCCATGCCAATTCTATAC
* * *
16546329 TATGTGTTCACTTAAGTTGGCCGAATGTGTCTATTGGCTTACTTGATATAAATGAATATGCGTAA
260 TATGTGTTCACTTAAGTTGACCGAATGTGTCTATTGGCTTACTTGATATAAACGAATATGCATAA
16546394 T
325 T
16546395 ATATTGTATT
Statistics
Matches: 293, Mismatches: 31, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
374 1 0.00
375 292 1.00
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (375 bp):
CCTCATTTTGCTTATGACTGAAAGCTAATGGACCAATTAGCTTATTGCTGAGGGTGTCTAATTAT
TTCAATAGGGGCCGAATGTATAAGAGCATCTTTTGAAGCTTAACCAATTGTGGTGTGTGTTAATT
GTGATGCTTGCCGGTTGTGTTGGAAGTGTAAATGAAATGGGTAAATGAATGTAAGTTGTCCTTTA
TATGGCCGAATGTGTTATGTGATAACTTGGGATGTTTGCCAAAAGTGCCATGCCAATTCTATACT
ATGTGTTCACTTAAGTTGACCGAATGTGTCTATTGGCTTACTTGATATAAACGAATATGCATAAT
CTGCTAATGTATGCTACTGTATTGCTATTACATTTTCACTGAATGCTCAT
Found at i:16546786 original size:23 final size:20
Alignment explanation
Indices: 16546760--16546808 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 20
16546750 TGACCACATC
16546760 ATTGGTAGCATTGTCTGCATCTT
1 ATTGGTAGC-TTGTCTGCA--TT
* *
16546783 ATTGGAAGCTTGTTTGCATT
1 ATTGGTAGCTTGTCTGCATT
16546803 ATTGGT
1 ATTGGT
16546809 GATTTATCGT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 7 0.30
22 8 0.35
23 8 0.35
ACGTcount: A:0.18, C:0.12, G:0.24, T:0.45
Consensus pattern (20 bp):
ATTGGTAGCTTGTCTGCATT
Found at i:16562481 original size:25 final size:25
Alignment explanation
Indices: 16562450--16562497 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
16562440 GCTGTAAATG
16562450 GTAAGCTCCTCCGAGCTAAATAATA
1 GTAAGCTCCTCCGAGCTAAATAATA
*
16562475 GTAAGCTCCTCCGAGCTGAATAA
1 GTAAGCTCCTCCGAGCTAAATAA
16562498 CGATAAGTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (25 bp):
GTAAGCTCCTCCGAGCTAAATAATA
Found at i:16579335 original size:51 final size:51
Alignment explanation
Indices: 16579255--16579413 Score: 221
Period size: 51 Copynumber: 3.1 Consensus size: 51
16579245 AAAAGATTCA
* *
16579255 TTCAATCAACAGCATAGTTTCCTACATCATCAACCAATATATATATCACAT
1 TTCAACCAACAACATAGTTTCCTACATCATCAACCAATATATATATCACAT
* *
16579306 TTCAACCCACAATATAGTTTCCT-CTATCATCAACCAATATATATATCACAT
1 TTCAACCAACAACATAGTTTCCTAC-ATCATCAACCAATATATATATCACAT
* * *
16579357 TTCAACCAACAACATAGTTTTCTACATCATCAACGAATACATATATATTACAT
1 TTCAACCAACAACATAGTTTCCTACATCATCAACCAAT--ATATATATCACAT
16579410 TTCA
1 TTCA
16579414 TACATGTTGA
Statistics
Matches: 95, Mismatches: 9, Indels: 6
0.86 0.08 0.05
Matches are distributed among these distances:
50 1 0.01
51 77 0.81
52 1 0.01
53 16 0.17
ACGTcount: A:0.39, C:0.25, G:0.03, T:0.33
Consensus pattern (51 bp):
TTCAACCAACAACATAGTTTCCTACATCATCAACCAATATATATATCACAT
Found at i:16583780 original size:18 final size:18
Alignment explanation
Indices: 16583752--16583787 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
16583742 TAAAGGTTAT
16583752 TAAAGTAAATT-AGTAAA
1 TAAAGTAAATTAAGTAAA
16583769 TAAAGATAAATTAAGTAAA
1 TAAAG-TAAATTAAGTAAA
16583788 ACAAAACATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 6 0.35
19 6 0.35
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.28
Consensus pattern (18 bp):
TAAAGTAAATTAAGTAAA
Found at i:16588571 original size:61 final size:61
Alignment explanation
Indices: 16588497--16588713 Score: 247
Period size: 61 Copynumber: 3.6 Consensus size: 61
16588487 TTGAAAAGAT
* * * * * *
16588497 TCGCCACATAGGCTTACCT-TGCCTGAGTTATGCAACAAAGGCATTCATTAACATTCAATAC
1 TCGCCACAAAGGCTTTCCTGT-CCAGAGTTTTGCCACAAAGGCATTCATTAACATTCAGTAC
* * * *
16588558 TCGCCACAAAGGCTTTCCTGTCCAGAGTTTTGCCACAAAAGCATTCTTTAACATCCAGTAA
1 TCGCCACAAAGGCTTTCCTGTCCAGAGTTTTGCCACAAAGGCATTCATTAACATTCAGTAC
* * * * *
16588619 TCGCCACAATGGCTTTCCTGTCCAGAGTTTTTCCAGAAAGGCGTTCCTTAACATTCAGTAC
1 TCGCCACAAAGGCTTTCCTGTCCAGAGTTTTGCCACAAAGGCATTCATTAACATTCAGTAC
* * * *
16588680 TCACCACAATGGCTTTCCTATCTAGAGTTTTGCC
1 TCGCCACAAAGGCTTTCCTGTCCAGAGTTTTGCC
16588714 TCCCTCTCCG
Statistics
Matches: 133, Mismatches: 22, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
61 132 0.99
62 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.30
Consensus pattern (61 bp):
TCGCCACAAAGGCTTTCCTGTCCAGAGTTTTGCCACAAAGGCATTCATTAACATTCAGTAC
Found at i:16591193 original size:35 final size:35
Alignment explanation
Indices: 16591112--16591197 Score: 109
Period size: 35 Copynumber: 2.5 Consensus size: 35
16591102 GAATTCTGTT
* * **
16591112 GGGACAGTAAACACAGAACAAAGATGAAGTCCTTC
1 GGGACAGTAAACACGGAACAAAGATGAAGCCCGCC
* *
16591147 AGGACATTAAACACGGAACAAAGATGAAGCCCGCC
1 GGGACAGTAAACACGGAACAAAGATGAAGCCCGCC
*
16591182 GGGATAGTAAACACGG
1 GGGACAGTAAACACGG
16591198 GTAAGCCTAC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.42, C:0.21, G:0.26, T:0.12
Consensus pattern (35 bp):
GGGACAGTAAACACGGAACAAAGATGAAGCCCGCC
Found at i:16597277 original size:63 final size:63
Alignment explanation
Indices: 16597178--16597299 Score: 217
Period size: 63 Copynumber: 1.9 Consensus size: 63
16597168 AATAAAAAAG
* * *
16597178 AAGTAACCAAAATGCAATACAAAGAGAAAAACCCTCTGAATGCACCACTTCACCATATATAAT
1 AAGTAACCAAAATACAATACAAAGAGAAAAACCCTCTAAATGCACCACTTAACCATATATAAT
16597241 AAGTAACCAAAATACAATACAAAGAGAAAAACCCTCTAAATGCACCACTTAACCATATA
1 AAGTAACCAAAATACAATACAAAGAGAAAAACCCTCTAAATGCACCACTTAACCATATA
16597300 CATATATATA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.50, C:0.24, G:0.08, T:0.18
Consensus pattern (63 bp):
AAGTAACCAAAATACAATACAAAGAGAAAAACCCTCTAAATGCACCACTTAACCATATATAAT
Found at i:16598223 original size:43 final size:43
Alignment explanation
Indices: 16598155--16598290 Score: 132
Period size: 43 Copynumber: 3.1 Consensus size: 43
16598145 TGTGGCCAAA
16598155 CCGTGTAG-AATTCAAAAATAAGGTCACACGATTGTGTCGCCAGG
1 CCGTGT-GCAATTC-AAAATAAGGTCACACGATTGTGTCGCCAGG
** * ** *
16598199 CCGTGTGCAATTTGAAATAAGGTCACACGGTCATGTCGTCAGG
1 CCGTGTGCAATTCAAAATAAGGTCACACGATTGTGTCGCCAGG
* * * * *
16598242 CCATGTGCAATTCAAAATAAGGTTAGAC-AGCTGTTTCGCCAGG
1 CCGTGTGCAATTCAAAATAAGGTCACACGA-TTGTGTCGCCAGG
16598285 CCGTGT
1 CCGTGT
16598291 AACAACCTGT
Statistics
Matches: 72, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
43 62 0.86
44 10 0.14
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (43 bp):
CCGTGTGCAATTCAAAATAAGGTCACACGATTGTGTCGCCAGG
Found at i:16599052 original size:26 final size:26
Alignment explanation
Indices: 16598990--16599042 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
16598980 ATGCTTAGTA
16598990 AGCTCGTATATCGTAAACTTAAACTT
1 AGCTCGTATATCGTAAACTTAAACTT
16599016 AGCTCGTATATCGTAAACTTAAACTT
1 AGCTCGTATATCGTAAACTTAAACTT
16599042 A
1 A
16599043 CCGAATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (26 bp):
AGCTCGTATATCGTAAACTTAAACTT
Found at i:16604021 original size:17 final size:17
Alignment explanation
Indices: 16604001--16604040 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
16603991 TGTACAATAC
*
16604001 TAAAATAAAAAATTAAA
1 TAAAATAAAAAATAAAA
* *
16604018 TAAAATTATAAATAAAA
1 TAAAATAAAAAATAAAA
16604035 TAAAAT
1 TAAAAT
16604041 TTAAACATGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
TAAAATAAAAAATAAAA
Found at i:16604041 original size:17 final size:16
Alignment explanation
Indices: 16604010--16604045 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
16604000 CTAAAATAAA
*
16604010 AAATTAAATAAAATTAT
1 AAATAAAATAAAATT-T
16604027 AAATAAAATAAAATTT
1 AAATAAAATAAAATTT
16604043 AAA
1 AAA
16604046 CATGTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATAAAATAAAATTT
Found at i:16606915 original size:5 final size:5
Alignment explanation
Indices: 16606905--16606948 Score: 88
Period size: 5 Copynumber: 8.8 Consensus size: 5
16606895 GATATGTCAT
16606905 ATCTA ATCTA ATCTA ATCTA ATCTA ATCTA ATCTA ATCTA ATCT
1 ATCTA ATCTA ATCTA ATCTA ATCTA ATCTA ATCTA ATCTA ATCT
16606949 TTACAAGATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.39, C:0.20, G:0.00, T:0.41
Consensus pattern (5 bp):
ATCTA
Found at i:16609092 original size:22 final size:22
Alignment explanation
Indices: 16609066--16609134 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
16609056 AGCAAAACTA
16609066 CATGCCACCCCCAAAATATATG
1 CATGCCACCCCCAAAATATATG
* *** *
16609088 CATGCTACAAAGCAAAA-CTA--
1 CATGCCAC-CCCCAAAATATATG
16609108 CATGCCACCCCCAAAATATATG
1 CATGCCACCCCCAAAATATATG
16609130 CATGC
1 CATGC
16609135 TACAAAACAA
Statistics
Matches: 33, Mismatches: 10, Indels: 8
0.65 0.20 0.16
Matches are distributed among these distances:
19 5 0.15
20 9 0.27
22 14 0.42
23 5 0.15
ACGTcount: A:0.39, C:0.33, G:0.10, T:0.17
Consensus pattern (22 bp):
CATGCCACCCCCAAAATATATG
Found at i:16609110 original size:42 final size:42
Alignment explanation
Indices: 16609051--16609145 Score: 181
Period size: 42 Copynumber: 2.3 Consensus size: 42
16609041 AGAACTTAGT
16609051 TACAAAGCAAAACTACATGCCACCCCCAAAATATATGCATGC
1 TACAAAGCAAAACTACATGCCACCCCCAAAATATATGCATGC
16609093 TACAAAGCAAAACTACATGCCACCCCCAAAATATATGCATGC
1 TACAAAGCAAAACTACATGCCACCCCCAAAATATATGCATGC
*
16609135 TACAAAACAAA
1 TACAAAGCAAA
16609146 CACATGTGAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.46, C:0.29, G:0.08, T:0.16
Consensus pattern (42 bp):
TACAAAGCAAAACTACATGCCACCCCCAAAATATATGCATGC
Found at i:16610253 original size:14 final size:14
Alignment explanation
Indices: 16610234--16610273 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
16610224 TTGATTGCCA
16610234 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
16610248 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
16610262 GGAAAATGTTTT
1 GTAAAATGTTTT
16610274 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:16610282 original size:20 final size:20
Alignment explanation
Indices: 16610257--16610296 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
16610247 CGTAAAATGA
*
16610257 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
16610277 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
16610297 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:16610286 original size:34 final size:35
Alignment explanation
Indices: 16610242--16610308 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
16610232 CAGTAAAATG
*
16610242 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
16610276 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
16610309 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:16610312 original size:14 final size:15
Alignment explanation
Indices: 16610236--16610312 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
16610226 GATTGCCAGT
* *
16610236 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
16610250 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
16610264 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
16610284 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
16610299 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
16610313 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:16610491 original size:22 final size:24
Alignment explanation
Indices: 16610466--16610516 Score: 56
Period size: 26 Copynumber: 2.2 Consensus size: 24
16610456 TTATTTATAA
16610466 ATAAATAA-A-TCAA-ATT-AAAT
1 ATAAATAATACTCAATATTAAAAT
16610486 ATATAATAATACTCAATTATTAAAAT
1 ATA-AATAATACTCAA-TATTAAAAT
16610512 ATAAA
1 ATAAA
16610517 AGCATTGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
20 3 0.12
21 5 0.20
22 1 0.04
23 4 0.16
25 5 0.20
26 7 0.28
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (24 bp):
ATAAATAATACTCAATATTAAAAT
Found at i:16613586 original size:16 final size:16
Alignment explanation
Indices: 16613565--16613596 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
16613555 CATAAACCCT
16613565 AACCTTAAAAACCTAA
1 AACCTTAAAAACCTAA
*
16613581 AACCTTAAAACCCTAA
1 AACCTTAAAAACCTAA
16613597 TTAATAAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.28, G:0.00, T:0.19
Consensus pattern (16 bp):
AACCTTAAAAACCTAA
Found at i:16613605 original size:22 final size:22
Alignment explanation
Indices: 16613580--16613624 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
16613570 TAAAAACCTA
* *
16613580 AAACCTTAAAACCCTAATTAAT
1 AAACCCTAAAACCCTAATAAAT
*
16613602 AAACCCTGAAACCCTAATAAAT
1 AAACCCTAAAACCCTAATAAAT
16613624 A
1 A
16613625 CATGGGAAAA
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:0.51, C:0.24, G:0.02, T:0.22
Consensus pattern (22 bp):
AAACCCTAAAACCCTAATAAAT
Found at i:16613614 original size:30 final size:29
Alignment explanation
Indices: 16613549--16613606 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
16613539 TTTAATCAAT
*
16613549 TAAAACCAT-AAACCCTAACCTTAAAAACC
1 TAAAACCTTAAAACCCTAA-CTTAAAAACC
16613578 TAAAACCTTAAAACCCTAA-TTAATAAACC
1 TAAAACCTTAAAACCCTAACTTAA-AAACC
16613607 CTGAAACCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 4 0.15
29 13 0.50
30 9 0.35
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.21
Consensus pattern (29 bp):
TAAAACCTTAAAACCCTAACTTAAAAACC
Found at i:16614598 original size:30 final size:29
Alignment explanation
Indices: 16614560--16614616 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
16614550 ATTAGTGAGT
* *
16614560 TGTAAAAATTGAATCAAATCAAAATTTTG
1 TGTAAAAATCGAATCAAAGCAAAATTTTG
* *
16614589 TGTATAAAATCGTATGAAAGCAAAATTT
1 TGTA-AAAATCGAATCAAAGCAAAATTT
16614617 ACATATTGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 4 0.17
30 19 0.83
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.33
Consensus pattern (29 bp):
TGTAAAAATCGAATCAAAGCAAAATTTTG
Found at i:16615127 original size:18 final size:18
Alignment explanation
Indices: 16615095--16615142 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
16615085 GTCTTAATTG
*
16615095 TTAAAAATTTAAAAA-ACT
1 TTAAATATTTAAAAATA-T
16615113 TTAAATTATTTAAAAATAT
1 TTAAA-TATTTAAAAATAT
16615132 TTAAATATTTA
1 TTAAATATTTA
16615143 TTTTTCAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 11 0.41
19 15 0.56
20 1 0.04
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAAATATTTAAAAATAT
Found at i:16622781 original size:19 final size:20
Alignment explanation
Indices: 16622757--16622796 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
16622747 AGTGCCTCTT
16622757 TTTGCATT-CAT-ATCATGCA
1 TTTGCATTACATCAT-ATGCA
16622776 TTTGCATTACATCATATGCA
1 TTTGCATTACATCATATGCA
16622796 T
1 T
16622797 CAAGTTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.42
20 9 0.47
21 2 0.11
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.42
Consensus pattern (20 bp):
TTTGCATTACATCATATGCA
Found at i:16630999 original size:44 final size:44
Alignment explanation
Indices: 16630870--16631172 Score: 134
Period size: 44 Copynumber: 7.0 Consensus size: 44
16630860 TTAAGTAATT
* *
16630870 ATTGTAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATC-AA-
1 ATTGTAAATCTTATCTCCCTAAACAGTAGTGGAGTAGATCGAAG
* * ** * * * *** *
16630912 A-AGCACCAGCCTTATCTCCCTCAGCAGCAGCAAAGTAGTTCGAAG
1 ATTGTA--AATCTTATCTCCCTAAACAGTAGTGGAGTAGATCGAAG
* *
16630957 ATTGTAAATCTTATCTCCCTAAACAGTAGTGGAGCAAATCGAA-
1 ATTGTAAATCTTATCTCCCTAAACAGTAGTGGAGTAGATCGAAG
* ** * * * * *
16631000 A--GCACCAGCCTTATCTCCCTAAGCAGCAGCGGAGTAGGTCAAAG
1 ATTGTA--AATCTTATCTCCCTAAACAGTAGTGGAGTAGATCGAAG
* *
16631044 ATTGTAGATCTGATCTCCCTAAACAGTAGTGGAGTAGATCGAA-
1 ATTGTAAATCTTATCTCCCTAAACAGTAGTGGAGTAGATCGAAG
*** * ** ** ** * **
16631087 AGCATCAGCCTTATCTCCCTAAACAACAGCAGAGTAGGTTAAAG
1 ATTGTAAATCTTATCTCCCTAAACAGTAGTGGAGTAGATCGAAG
* * * * *
16631131 ATTGTAGATCTTATCTCCCTGAGCAATAGTGGAGCAGATCGA
1 ATTGTAAATCTTATCTCCCTAAACAGTAGTGGAGTAGATCGA
16631173 CAGCACCAGC
Statistics
Matches: 173, Mismatches: 77, Indels: 20
0.64 0.29 0.07
Matches are distributed among these distances:
41 4 0.02
42 1 0.01
43 80 0.46
44 83 0.48
45 1 0.01
46 4 0.02
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.24
Consensus pattern (44 bp):
ATTGTAAATCTTATCTCCCTAAACAGTAGTGGAGTAGATCGAAG
Found at i:16631020 original size:43 final size:43
Alignment explanation
Indices: 16630879--16631456 Score: 211
Period size: 43 Copynumber: 13.3 Consensus size: 43
16630869 TATTGTAGAT
* *
16630879 CTTATCTCCCTAAACAGTAGTGGAGCAGATCAAAAGCACCAGC
1 CTTATCTCCCTAAACAGTAGTGGAGTAGATCGAAAGCACCAGC
* * * *** * * **
16630922 CTTATCTCCCTCAGCAGCAGCAAAGTAGTTCGAAGATTGTA--AAT
1 CTTATCTCCCTAAACAGTAGTGGAGTAGATCGAA-A--GCACCAGC
* *
16630966 CTTATCTCCCTAAACAGTAGTGGAGCAAATCGAAAGCACCAGC
1 CTTATCTCCCTAAACAGTAGTGGAGTAGATCGAAAGCACCAGC
* * * * ** *
16631009 CTTATCTCCCTAAGCAGCAGCGGAGTAGGTC-AAAG-ATTGTAGAT
1 CTTATCTCCCTAAACAGTAGTGGAGTAGATCGAAAGCA--CCAG-C
* *
16631053 CTGATCTCCCTAAACAGTAGTGGAGTAGATCGAAAGCATCAGC
1 CTTATCTCCCTAAACAGTAGTGGAGTAGATCGAAAGCACCAGC
** ** * * ** *
16631096 CTTATCTCCCTAAACAACAGCAGAGTAGGT-TAAAG-ATTGTAGAT
1 CTTATCTCCCTAAACAGTAGTGGAGTAGATCGAAAGCA--CCAG-C
* * * * *
16631140 CTTATCTCCCTGAGCAATAGTGGAGCAGATCGACAGCACCAGC
1 CTTATCTCCCTAAACAGTAGTGGAGTAGATCGAAAGCACCAGC
* * * ** * * ** *
16631183 CTTATCTCCTTGAGCAACAGCGGAGTAGGTC-AAAG-ATTGTAGAT
1 CTTATCTCCCTAAACAGTAGTGGAGTAGATCGAAAGCA--CCAG-C
* * *
16631227 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAAGCACCAGC
1 CTTATCTCCCTAAACAGTAGTGGAGTAGATCGAAAGCACCAGC
* * * * * ** * **** *
16631270 CTTAGCTCCTTGAGCAGCAGCAGAGTAGGTC-AAAGGTTGTAGAT
1 CTTATCTCCCTAAACAGTAGTGGAGTAGATCGAAA-GCACCAG-C
* *
16631314 CTTATCTACCTAAACAGTAGTGGAGCAGATCGAAAGCACCAGC
1 CTTATCTCCCTAAACAGTAGTGGAGTAGATCGAAAGCACCAGC
* * * * ** * * * **** *
16631357 CTTAGCTCCTTGAGCAACAGCGGAGTAGGTCGAAGGTTGTAGAT
1 CTTATCTCCCTAAACAGTAGTGGAGTAGATCGAAAGCACCAG-C
* * * *
16631401 CTTATCTACTTAAACAGTAGTGGAGCAGATCGAAAGCACCAAC
1 CTTATCTCCCTAAACAGTAGTGGAGTAGATCGAAAGCACCAGC
16631444 CTTATCTCCCTAA
1 CTTATCTCCCTAA
16631457 GCAACAGCAG
Statistics
Matches: 367, Mismatches: 144, Indels: 48
0.66 0.26 0.09
Matches are distributed among these distances:
41 5 0.01
42 14 0.04
43 172 0.47
44 157 0.43
45 14 0.04
46 5 0.01
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.23
Consensus pattern (43 bp):
CTTATCTCCCTAAACAGTAGTGGAGTAGATCGAAAGCACCAGC
Found at i:16631538 original size:87 final size:87
Alignment explanation
Indices: 16630870--16631526 Score: 920
Period size: 87 Copynumber: 7.6 Consensus size: 87
16630860 TTAAGTAATT
* *
16630870 ATTGTAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCAAAAGCACCAGCCTTATCTCCCTCA
1 ATTGTAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAAGCACCAGCCTTATCTCCCTAA
* * * *
16630935 GCAGCAGCAAAGTAGTTCGAAG
66 GCAACAGCAGAGTAGGTCAAAG
* *
16630957 ATTGTAAATCTTATCTCCCTAAACAGTAGTGGAGCAAATCGAAAGCACCAGCCTTATCTCCCTAA
1 ATTGTAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAAGCACCAGCCTTATCTCCCTAA
* *
16631022 GCAGCAGCGGAGTAGGTCAAAG
66 GCAACAGCAGAGTAGGTCAAAG
* * *
16631044 ATTGTAGATCTGATCTCCCTAAACAGTAGTGGAGTAGATCGAAAGCATCAGCCTTATCTCCCTAA
1 ATTGTAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAAGCACCAGCCTTATCTCCCTAA
* *
16631109 ACAACAGCAGAGTAGGTTAAAG
66 GCAACAGCAGAGTAGGTCAAAG
* * * * * *
16631131 ATTGTAGATCTTATCTCCCTGAGCAATAGTGGAGCAGATCGACAGCACCAGCCTTATCTCCTTGA
1 ATTGTAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAAGCACCAGCCTTATCTCCCTAA
*
16631196 GCAACAGCGGAGTAGGTCAAAG
66 GCAACAGCAGAGTAGGTCAAAG
* * * * *
16631218 ATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAAGCACCAGCCTTAGCTCCTTGA
1 ATTGTAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAAGCACCAGCCTTATCTCCCTAA
*
16631283 GCAGCAGCAGAGTAGGTCAAAG
66 GCAACAGCAGAGTAGGTCAAAG
* * * * *
16631305 GTTGTAGATCTTATCTACCTAAACAGTAGTGGAGCAGATCGAAAGCACCAGCCTTAGCTCCTTGA
1 ATTGTAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAAGCACCAGCCTTATCTCCCTAA
* *
16631370 GCAACAGCGGAGTAGGTCGAAG
66 GCAACAGCAGAGTAGGTCAAAG
* * * *
16631392 GTTGTAGATCTTATCTACTTAAACAGTAGTGGAGCAGATCGAAAGCACCAACCTTATCTCCCTAA
1 ATTGTAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAAGCACCAGCCTTATCTCCCTAA
*
16631457 GCAACAGCAGAATAGGTCGAAA-
66 GCAACAGCAGAGTAGGTC-AAAG
* *
16631479 ATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAAGCAC
1 ATTGTAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAAGCAC
16631527 AGATCTTATC
Statistics
Matches: 513, Mismatches: 56, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
87 511 1.00
88 2 0.00
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (87 bp):
ATTGTAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAAGCACCAGCCTTATCTCCCTAA
GCAACAGCAGAGTAGGTCAAAG
Found at i:16636008 original size:18 final size:18
Alignment explanation
Indices: 16635987--16636024 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
16635977 ATTTATTTTA
*
16635987 TTATATCGTTTTATCTAT
1 TTATATCGTTTTATATAT
*
16636005 TTATATCTTTTTATATAT
1 TTATATCGTTTTATATAT
16636023 TT
1 TT
16636025 TCAAACTCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.08, G:0.03, T:0.66
Consensus pattern (18 bp):
TTATATCGTTTTATATAT
Found at i:16640723 original size:42 final size:42
Alignment explanation
Indices: 16640662--16640761 Score: 155
Period size: 42 Copynumber: 2.4 Consensus size: 42
16640652 CTATATGAAC
* * *
16640662 GGCACTAAGTGTGCAAAATTAAAATAATGATGTTGGATAATA
1 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGAATAACA
* *
16640704 GGCACTAAGTGTGCGAAATTAAAATGATGATGTTGAATAACG
1 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGAATAACA
16640746 GGCACTAAGTGTGCGA
1 GGCACTAAGTGTGCGA
16640762 TACCGAGAGC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.26
Consensus pattern (42 bp):
GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGAATAACA
Found at i:16644326 original size:8 final size:8
Alignment explanation
Indices: 16644297--16644334 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
16644287 AATATTTCAT
16644297 AAAAAAAG
1 AAAAAAAG
*
16644305 AAGAAAA-
1 AAAAAAAG
*
16644312 AAGAAAAG
1 AAAAAAAG
16644320 AAAAAAAG
1 AAAAAAAG
16644328 AAAAAAA
1 AAAAAAA
16644335 AGGCCAAGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:16645287 original size:44 final size:45
Alignment explanation
Indices: 16645183--16645707 Score: 218
Period size: 44 Copynumber: 11.6 Consensus size: 45
16645173 AATCCTATAC
*
16645183 CCCTGAAGTTGCAGTGG-G-ATGGATTGAAGATCATAGCAAACCTTATCT
1 CCCTGAAGTTGCAGTGGAGCA--GATTGAAG---ATAGCAAATCTTATCT
* *
16645231 CCCTGAAGTTGCAGTGGAGCAGGTTGAAGATA-CAACTCTTATCT
1 CCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCT
* * * * * *
16645275 CCCTAAAGTTGCAATGGAGCAGACTAAAGATAGCAAATTTTATTT
1 CCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCT
* * * *
16645320 CCCTGAAGTTGCAGTAGAACAGATTGAAGCTATAAATTGCAGATTTTATCT
1 CCCTGAAGTTGCAGTGGAGCAGATTGAAG--AT--A--GCAAATCTTATCT
* * * * *
16645371 CTCTGAAGTTGCAGTAGAGCAGA-T---CATAGCAAACCTTTTCT
1 CCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCT
* * * * * *
16645412 CCCTGAAGTTGTAGTAGAGCAGACTGAAAATAGCGAATCTTATTT
1 CCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCT
* * * * * * *
16645457 CCCTAAAGTTGCAATGAAACAGATTAAAGCTATA-AATTACGGATCCTATCT
1 CCCTGAAGTTGCAGTGGAGCAGATTGAAG--ATAGCA--A---ATCTTATCT
* * * * *
16645508 CTCTAAAGTTGCAGTAGAGCAGA-T---CATATCAAA-CTTTATCT
1 CCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATC-TTATCT
* ** * * *
16645549 CCCTGAAGTTGCAGTGGAACA-AGTAAAAAATAACCCAATCTTATCT
1 CCCTGAAGTTGCAGTGGAGCAGA-TTGAAGAT-AGCAAATCTTATCT
* * ** * *
16645595 CCCTGAAGTTGCGGTGGAGCAGATTAAAGCCA-CAAAACCTATCT
1 CCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCT
* * ** * * ** *
16645639 ACCTAAAGTTGCAGCAGAGCAGATTAAAGCTA-TTAATCCTATCT
1 CCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCT
* *
16645683 CCTTGAAGTTGCAGTGGAGCGGATT
1 CCCTGAAGTTGCAGTGGAGCAGATT
16645708 AAAACGATGA
Statistics
Matches: 361, Mismatches: 86, Indels: 64
0.71 0.17 0.13
Matches are distributed among these distances:
40 2 0.01
41 53 0.15
42 1 0.00
43 1 0.00
44 101 0.28
45 75 0.21
46 34 0.09
47 7 0.02
48 25 0.07
49 2 0.01
50 3 0.01
51 57 0.16
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (45 bp):
CCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCT
Found at i:16645579 original size:137 final size:137
Alignment explanation
Indices: 16645264--16645624 Score: 431
Period size: 137 Copynumber: 2.6 Consensus size: 137
16645254 TTGAAGATAC
* * * *
16645264 AACTCTTATCTCCCTAAAGTTGCAATGGAGCAGACTAAAGATAGCAAATTTTATTTCCCTGAAGT
1 AACT-TTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAAATAGCAAATCTTATTTCCCTGAAGT
* * ** *
16645329 TGCAGT-AGAACAGATTGAAGCTATAAATTGCAGATTTTATCTCTCTGAAGTTGCAGTAGAGCAG
65 TGCAGTGA-AACAGATTAAAGCTATAAATTACAGATCCTATCTCTCTAAAGTTGCAGTAGAGCAG
16645393 ATCATAGCA
129 ATCATAGCA
* * * * *
16645402 AACCTTT-TCTCCCTGAAGTTGTAGTAGAGCAGACTGAAAATAGCGAATCTTATTTCCCTAAAGT
1 AA-CTTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAAATAGCAAATCTTATTTCCCTGAAGT
* *
16645466 TGCAATGAAACAGATTAAAGCTATAAATTACGGATCCTATCTCTCTAAAGTTGCAGTAGAGCAGA
65 TGCAGTGAAACAGATTAAAGCTATAAATTACAGATCCTATCTCTCTAAAGTTGCAGTAGAGCAGA
*
16645531 TCATATCA
130 TCATAGCA
* * * * *
16645539 AACTTTATCTCCCTGAAGTTGCAGTGGAACA-AGTAAAAAATAACCCAATCTTATCTCCCTGAAG
1 AACTTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAAAAT-AGCAAATCTTATTTCCCTGAAG
* * *
16645603 TTGCGGTGGAGCAGATTAAAGC
64 TTGCAGTGAAACAGATTAAAGC
16645625 CACAAAACCT
Statistics
Matches: 188, Mismatches: 30, Indels: 10
0.82 0.13 0.04
Matches are distributed among these distances:
136 6 0.03
137 139 0.74
138 41 0.22
139 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (137 bp):
AACTTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAAATAGCAAATCTTATTTCCCTGAAGTT
GCAGTGAAACAGATTAAAGCTATAAATTACAGATCCTATCTCTCTAAAGTTGCAGTAGAGCAGAT
CATAGCA
Found at i:16649916 original size:20 final size:20
Alignment explanation
Indices: 16649893--16649934 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
16649883 AAATATTTCT
*
16649893 AAAATACAAAA-AAATATTGA
1 AAAACACAAAACAAA-ATTGA
16649913 AAAACACAAAACAAAATTGA
1 AAAACACAAAACAAAATTGA
16649933 AA
1 AA
16649935 TATTGAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.71, C:0.10, G:0.05, T:0.14
Consensus pattern (20 bp):
AAAACACAAAACAAAATTGA
Found at i:16653489 original size:88 final size:87
Alignment explanation
Indices: 16653336--16653496 Score: 202
Period size: 88 Copynumber: 1.8 Consensus size: 87
16653326 TTAAGGGTGT
* * * *
16653336 AAAAAACCCTCAAACTTTTTTAAAAGAGCAATTAAGCCTCTATTTTTTTTCCACTCGATGAGGTA
1 AAAAAACCCTCAAACTTTTTTAAAAAAACAATTAAGCCCCTATTTTTTTTCCACTCAATGAGGTA
16653401 CTTGAACTTTTAAAATATAAAA
66 CTTGAACTTTTAAAATATAAAA
**
16653423 AAAAAAGCCCTCAAA-TTTTTTCAAAAAAACAATTAAGCCCCT-TTTATTTTTGTACTCAATTG-
1 AAAAAA-CCCTCAAACTTTTTT-AAAAAAACAATTAAGCCCCTATTT-TTTTTCCACTCAA-TGA
*
16653485 GGTACTTTAACT
62 GGTACTTGAACT
16653497 GTCAAAATGT
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
87 15 0.24
88 46 0.73
89 2 0.03
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (87 bp):
AAAAAACCCTCAAACTTTTTTAAAAAAACAATTAAGCCCCTATTTTTTTTCCACTCAATGAGGTA
CTTGAACTTTTAAAATATAAAA
Found at i:16653655 original size:28 final size:29
Alignment explanation
Indices: 16653623--16653686 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 29
16653613 AATAAAATCA
16653623 ATAAAAATTATTAAAT-TTTAAT-AAAAA-T
1 ATAAAAA-TATTAAATATTT-ATCAAAAATT
* *
16653651 ATAAAGATATTTAATATTTATCAAAAATT
1 ATAAAAATATTAAATATTTATCAAAAATT
16653680 ATAAAAA
1 ATAAAAA
16653687 CCATAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
27 9 0.30
28 14 0.47
29 7 0.23
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (29 bp):
ATAAAAATATTAAATATTTATCAAAAATT
Found at i:16653661 original size:27 final size:29
Alignment explanation
Indices: 16653631--16653684 Score: 69
Period size: 27 Copynumber: 1.9 Consensus size: 29
16653621 CAATAAAAAT
16653631 TATTAAAT-TTTAAT-AAAAA-TATAAAGA
1 TATTAAATATTT-ATCAAAAATTATAAAGA
*
16653658 TATTTAATATTTATCAAAAATTATAAA
1 TATTAAATATTTATCAAAAATTATAAA
16653685 AACCATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 9 0.39
28 8 0.35
29 6 0.26
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (29 bp):
TATTAAATATTTATCAAAAATTATAAAGA
Found at i:16653663 original size:21 final size:20
Alignment explanation
Indices: 16653622--16653666 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
16653612 AAATAAAATC
*
16653622 AATAAAAATTATTAAATTTT
1 AATAAAAATTATAAAATTTT
16653642 AATAAAAA-TATAAAGATATTT
1 AATAAAAATTATAAA-AT-TTT
16653663 AATA
1 AATA
16653667 TTTATCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 5 0.23
20 10 0.45
21 7 0.32
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
AATAAAAATTATAAAATTTT
Found at i:16653987 original size:9 final size:9
Alignment explanation
Indices: 16653969--16654032 Score: 60
Period size: 9 Copynumber: 6.9 Consensus size: 9
16653959 ATTATATAAT
16653969 TTTTTCTATA
1 TTTTT-TATA
16653979 TTTTTTATA
1 TTTTTTATA
16653988 -TTTTTATA
1 TTTTTTATA
16653996 TTTTTT-TA
1 TTTTTTATA
*
16654004 CGATTTTTATAA
1 --TTTTTTAT-A
16654016 TTTTTTATA
1 TTTTTTATA
*
16654025 ATTTTTAT
1 TTTTTTAT
16654033 CATCTTTTGT
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
8 10 0.22
9 17 0.37
10 17 0.37
11 1 0.02
12 1 0.02
ACGTcount: A:0.23, C:0.03, G:0.02, T:0.72
Consensus pattern (9 bp):
TTTTTTATA
Found at i:16654001 original size:19 final size:18
Alignment explanation
Indices: 16653978--16654032 Score: 74
Period size: 19 Copynumber: 2.9 Consensus size: 18
16653968 TTTTTTCTAT
16653978 ATTTTTTATATTTTTATA
1 ATTTTTTATATTTTTATA
* *
16653996 TTTTTTTACGATTTTTATA
1 ATTTTTTA-TATTTTTATA
16654015 ATTTTTTATAATTTTTAT
1 ATTTTTTAT-ATTTTTAT
16654033 CATCTTTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
18 7 0.23
19 24 0.77
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (18 bp):
ATTTTTTATATTTTTATA
Found at i:16654040 original size:10 final size:9
Alignment explanation
Indices: 16653970--16654032 Score: 58
Period size: 8 Copynumber: 6.8 Consensus size: 9
16653960 TTATATAATT
*
16653970 TTTTCTATAT
1 TTTT-TATAA
16653980 TTTTTAT-A
1 TTTTTATAA
16653988 TTTTTAT-A
1 TTTTTATAA
*
16653996 TTTTTTTACGA
1 TTTTTATA--A
16654007 TTTTTATAA
1 TTTTTATAA
16654016 TTTTTTATAA
1 -TTTTTATAA
16654026 TTTTTAT
1 TTTTTAT
16654033 CATCTTTTGT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
8 14 0.30
9 11 0.24
10 13 0.28
11 8 0.17
ACGTcount: A:0.24, C:0.03, G:0.02, T:0.71
Consensus pattern (9 bp):
TTTTTATAA
Found at i:16654040 original size:19 final size:19
Alignment explanation
Indices: 16653978--16654040 Score: 51
Period size: 19 Copynumber: 3.3 Consensus size: 19
16653968 TTTTTTCTAT
*
16653978 ATTTTT-TATATTTTTAT-
1 ATTTTTATACATTTTTATC
* *
16653995 ATTTTTTTACGATTTTTATA
1 ATTTTTATAC-ATTTTTATC
16654015 ATTTTTTATA-ATTTTTATC
1 A-TTTTTATACATTTTTATC
16654034 ATCTTTT
1 AT-TTTT
16654041 GTCATATGTC
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
17 6 0.16
18 3 0.08
19 21 0.55
20 1 0.03
21 7 0.18
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.70
Consensus pattern (19 bp):
ATTTTTATACATTTTTATC
Found at i:16654664 original size:3 final size:3
Alignment explanation
Indices: 16654651--16654684 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
16654641 CTTAATGAAT
*
16654651 ATA AGTA ATA ATA ATA ATA ACA ATA ATA ATA ATA
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16654685 GTGCATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:16655830 original size:16 final size:18
Alignment explanation
Indices: 16655809--16655846 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
16655799 GATTGATATT
16655809 GAAATGAA-A-AAGATGA
1 GAAATGAATATAAGATGA
*
16655825 GAAATGAATATGAGATGA
1 GAAATGAATATAAGATGA
16655843 GAAA
1 GAAA
16655847 ATATTGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 1 0.05
18 10 0.53
ACGTcount: A:0.58, C:0.00, G:0.26, T:0.16
Consensus pattern (18 bp):
GAAATGAATATAAGATGA
Found at i:16655868 original size:43 final size:43
Alignment explanation
Indices: 16655804--16655889 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 43
16655794 TATGCGATTG
16655804 ATATTGAAATGAAAAAGATGAGAAATGAATATGAGATGAGAAA
1 ATATTGAAATGAAAAAGATGAGAAATGAATATGAGATGAGAAA
* *
16655847 ATATTGAAAT-AGAAAATATGAGAAATGACTATGAGATGAGAAA
1 ATATTGAAATGA-AAAAGATGAGAAATGAATATGAGATGAGAAA
16655890 TGAGATATGA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
42 1 0.03
43 39 0.98
ACGTcount: A:0.55, C:0.01, G:0.22, T:0.22
Consensus pattern (43 bp):
ATATTGAAATGAAAAAGATGAGAAATGAATATGAGATGAGAAA
Found at i:16656868 original size:30 final size:30
Alignment explanation
Indices: 16656802--16656868 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
16656792 GTGTCTCAGC
* *
16656802 CGTGTGAGGCACATGGCCTTGCCACACGAG
1 CGTGTGAGGCACACGGCCTGGCCACACGAG
* * *
16656832 CATGTGAGGCACACGGCCTGGTCGCACGAG
1 CGTGTGAGGCACACGGCCTGGCCACACGAG
*
16656862 TGTGTGA
1 CGTGTGA
16656869 CCCCTGAAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.19, C:0.27, G:0.36, T:0.18
Consensus pattern (30 bp):
CGTGTGAGGCACACGGCCTGGCCACACGAG
Found at i:16657232 original size:49 final size:49
Alignment explanation
Indices: 16657160--16657256 Score: 176
Period size: 49 Copynumber: 2.0 Consensus size: 49
16657150 TCTAGAAGGG
* *
16657160 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACTAAGTTTAGCAATGT
1 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACCAAGTTTAGAAATGT
16657209 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACCAAGTTTAGAAATG
1 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACCAAGTTTAGAAATG
16657257 CATAGCATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.42, C:0.06, G:0.27, T:0.25
Consensus pattern (49 bp):
ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACCAAGTTTAGAAATGT
Found at i:16662103 original size:43 final size:42
Alignment explanation
Indices: 16662020--16662103 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 42
16662010 AAACATATAA
**
16662020 TTTTTAAAAATTATAAAAAAATTGCACTTGATTTTTTATAATC
1 TTTTTAAAAATTATAAAAAAATTGCAC-AAATTTTTTATAATC
*
16662063 TTTTTAGAAATTATAAAAAAAATTGCA-AAATTTTTGTATAA
1 TTTTTAAAAATTAT-AAAAAAATTGCACAAATTTTT-TATAA
16662104 ATATTATGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 6 0.17
43 18 0.50
44 12 0.33
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (42 bp):
TTTTTAAAAATTATAAAAAAATTGCACAAATTTTTTATAATC
Found at i:16663559 original size:9 final size:9
Alignment explanation
Indices: 16663541--16663577 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
16663531 TATAGTTTGA
*
16663541 TATTCAAAT
1 TATTCGAAT
16663550 TATTCGAAT
1 TATTCGAAT
*
16663559 TATTCGAGT
1 TATTCGAAT
16663568 TATTCGAAT
1 TATTCGAAT
16663577 T
1 T
16663578 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:16663815 original size:29 final size:30
Alignment explanation
Indices: 16663749--16663805 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
16663739 CATGCAAACT
16663749 ATTTTTTTTCATAATTTTATATATTTTTTAC
1 ATTTTTTTTCA-AATTTTATATATTTTTTAC
*
16663780 TTTTTTTTTC-AATTTTATA-ATTTTTT
1 ATTTTTTTTCAAATTTTATATATTTTTT
16663806 GTAATTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 7 0.28
29 9 0.36
31 9 0.36
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (30 bp):
ATTTTTTTTCAAATTTTATATATTTTTTAC
Found at i:16663861 original size:41 final size:39
Alignment explanation
Indices: 16663785--16663899 Score: 108
Period size: 41 Copynumber: 2.8 Consensus size: 39
16663775 TTTACTTTTT
** * *
16663785 TTTTCAATTTTATAATTTTTTGTAATTTTTTATATTCTA
1 TTTTCAATTTTATAATTTTTAATAAATTTTAATATTCTA
*
16663824 TTTTCAATTTTATACTATTTTTAATAAATTTTAATATTTTGA
1 TTTTCAATTTTATA--ATTTTTAATAAATTTTAATATTCT-A
*
16663866 TTTTTGGC-ATTTTATAATTTTTAA-AAATTCTAAT
1 -TTTT--CAATTTTATAATTTTTAATAAATTTTAAT
16663900 TTTTTTTATA
Statistics
Matches: 64, Mismatches: 6, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
39 14 0.22
41 28 0.44
42 9 0.14
43 4 0.06
44 8 0.12
45 1 0.02
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.61
Consensus pattern (39 bp):
TTTTCAATTTTATAATTTTTAATAAATTTTAATATTCTA
Found at i:16663938 original size:26 final size:26
Alignment explanation
Indices: 16663875--16663953 Score: 113
Period size: 26 Copynumber: 3.0 Consensus size: 26
16663865 ATTTTTGGCA
*
16663875 TTTTATAATTTTTAAAAATTCTAATTTT
1 TTTTATAATTTTTAAAAATTCTAA--AT
16663903 TTTTATAATTTTTAAAAATTCTAAAT
1 TTTTATAATTTTTAAAAATTCTAAAT
* *
16663929 TTTTATAATTTTTGAAAATTTTAAA
1 TTTTATAATTTTTAAAAATTCTAAA
16663954 ATTCTAATTT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
26 24 0.50
28 24 0.50
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (26 bp):
TTTTATAATTTTTAAAAATTCTAAAT
Found at i:16664357 original size:22 final size:23
Alignment explanation
Indices: 16664326--16664369 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
16664316 TGTATAGATC
16664326 TATATCATTT-TATTTATAAATTG
1 TATATCATTTATA-TTATAAATTG
16664349 TATAT-ATTTATATTATAAATT
1 TATATCATTTATATTATAAATT
16664370 ATAAAAGGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (23 bp):
TATATCATTTATATTATAAATTG
Found at i:16665164 original size:19 final size:19
Alignment explanation
Indices: 16665129--16665166 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
16665119 AAAAATAAAA
*
16665129 TAAAATAATTTTTAAAATT
1 TAAAATAATTTTAAAAATT
16665148 TAAAAT-ATTTATAAAAATT
1 TAAAATAATTT-TAAAAATT
16665167 CCAATATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TAAAATAATTTTAAAAATT
Found at i:16668537 original size:18 final size:20
Alignment explanation
Indices: 16668496--16668537 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
16668486 TCTTTTAACA
**
16668496 AAAATTACAAAATAATTTTT
1 AAAATTACAAAATAATTTAC
16668516 AAAATTA-AAAAT-ATTTAC
1 AAAATTACAAAATAATTTAC
16668534 AAAA
1 AAAA
16668538 ATTCTAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.40
19 5 0.25
20 7 0.35
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAATTACAAAATAATTTAC
Found at i:16668538 original size:19 final size:21
Alignment explanation
Indices: 16668493--16668540 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
16668483 CTCTCTTTTA
16668493 ACAAAAATTACAAAATAATTT
1 ACAAAAATTACAAAATAATTT
**
16668514 -TTAAAATTA-AAAAT-ATTT
1 ACAAAAATTACAAAATAATTT
16668532 ACAAAAATT
1 ACAAAAATT
16668541 CTAAAATTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
18 4 0.18
19 11 0.50
20 7 0.32
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.33
Consensus pattern (21 bp):
ACAAAAATTACAAAATAATTT
Found at i:16674735 original size:22 final size:21
Alignment explanation
Indices: 16674709--16675043 Score: 305
Period size: 22 Copynumber: 15.2 Consensus size: 21
16674699 AGCAATTATC
*
16674709 CAACATTCAGACAGCATTTAAT
1 CAACATT-GGACAGCATTTAAT
* *
16674731 TAACATTTGGACAACATTTAAT
1 CAACA-TTGGACAGCATTTAAT
* *
16674753 CAACAATTGGACAACATTAAAT
1 CAAC-ATTGGACAGCATTTAAT
16674775 CAACATTTGGACAGCATTTAAT
1 CAACA-TTGGACAGCATTTAAT
16674797 CAACAATTGGACAGCATTTAAT
1 CAAC-ATTGGACAGCATTTAAT
*
16674819 CAACAATTCGACAGCA-TTAATT
1 CAAC-ATTGGACAGCATTTAA-T
* *
16674841 CAACATTTGAACAACATTTAAT
1 CAACA-TTGGACAGCATTTAAT
*
16674863 CAACAATTGGACAGTA-TTAATT
1 CAAC-ATTGGACAGCATTTAA-T
* *
16674885 CAACATCTGAACAACATTTAAT
1 CAACAT-TGGACAGCATTTAAT
*
16674907 CAACAATTGGACAGCATTCAAT
1 CAAC-ATTGGACAGCATTTAAT
* *
16674929 CAATATTTGGATAGCATTTAAT
1 CAACA-TTGGACAGCATTTAAT
* * *
16674951 CAACAATTCGACGGCATTAAAT
1 CAAC-ATTGGACAGCATTTAAT
*
16674973 CAACATTTGGACAACATTTAAT
1 CAACA-TTGGACAGCATTTAAT
* *
16674995 CAACAATTGGACAACATTCAAT
1 CAAC-ATTGGACAGCATTTAAT
* *
16675017 CAATATTTAGACAGCATTTAAT
1 CAACA-TTGGACAGCATTTAAT
16675039 CAACA
1 CAACA
16675044 ATTTTTACTT
Statistics
Matches: 258, Mismatches: 38, Indels: 34
0.78 0.12 0.10
Matches are distributed among these distances:
21 15 0.06
22 226 0.88
23 17 0.07
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (21 bp):
CAACATTGGACAGCATTTAAT
Found at i:16674782 original size:44 final size:44
Alignment explanation
Indices: 16674709--16675046 Score: 392
Period size: 44 Copynumber: 7.7 Consensus size: 44
16674699 AGCAATTATC
** * * * *
16674709 CAACATTCAGACAGCATTTAATTAACATTTGGACAACATTTAAT
1 CAACATTTGGACAACATTTAATCAACAATTGGACAGCATTTAAT
* * *
16674753 CAACAATTGGACAACATTAAATCAACATTTGGACAGCATTTAAT
1 CAACATTTGGACAACATTTAATCAACAATTGGACAGCATTTAAT
* * *
16674797 CAACAATTGGACAGCATTTAATCAACAATTCGACAGCA-TTAATT
1 CAACATTTGGACAACATTTAATCAACAATTGGACAGCATTTAA-T
* *
16674841 CAACATTTGAACAACATTTAATCAACAATTGGACAGTA-TTAATT
1 CAACATTTGGACAACATTTAATCAACAATTGGACAGCATTTAA-T
* * *
16674885 CAACATCTGAACAACATTTAATCAACAATTGGACAGCATTCAAT
1 CAACATTTGGACAACATTTAATCAACAATTGGACAGCATTTAAT
* * * * * *
16674929 CAATATTTGGATAGCATTTAATCAACAATTCGACGGCATTAAAT
1 CAACATTTGGACAACATTTAATCAACAATTGGACAGCATTTAAT
* *
16674973 CAACATTTGGACAACATTTAATCAACAATTGGACAACATTCAAT
1 CAACATTTGGACAACATTTAATCAACAATTGGACAGCATTTAAT
* * *
16675017 CAATATTTAGACAGCATTTAATCAACAATT
1 CAACATTTGGACAACATTTAATCAACAATT
16675047 TTTACTTCAA
Statistics
Matches: 255, Mismatches: 37, Indels: 4
0.86 0.12 0.01
Matches are distributed among these distances:
43 4 0.02
44 248 0.97
45 3 0.01
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (44 bp):
CAACATTTGGACAACATTTAATCAACAATTGGACAGCATTTAAT
Found at i:16675902 original size:43 final size:42
Alignment explanation
Indices: 16675832--16675938 Score: 108
Period size: 42 Copynumber: 2.5 Consensus size: 42
16675822 CAATGTCAAC
* * * * *
16675832 GTCCCAAACATGGTCTTT-CATGTAATCAAATAATGATACCACT
1 GTCCCAGACATGGT-TTTACATGCAATCAAAT-ACGACACCAAT
* * *
16675875 GTCCCAGACAGGGTTTTACATGCAATCATATACGACGCCAAT
1 GTCCCAGACATGGTTTTACATGCAATCAAATACGACACCAAT
*
16675917 GTCCCAGACATGGTCTTACATG
1 GTCCCAGACATGGTTTTACATG
16675939 TAAATCTCGA
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
42 30 0.57
43 23 0.43
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (42 bp):
GTCCCAGACATGGTTTTACATGCAATCAAATACGACACCAAT
Found at i:16682015 original size:22 final size:22
Alignment explanation
Indices: 16681990--16682051 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
16681980 CCAACATTCA
* *
16681990 GACAACATTTAATTAACATTTG
1 GACAACATTTAATCAACAATTG
16682012 GACAACATTTAATCAACAATTG
1 GACAACATTTAATCAACAATTG
* *
16682034 GACAACAATCAATCAACA
1 GACAACATTTAATCAACA
16682052 TCATTTAATC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.47, C:0.19, G:0.08, T:0.26
Consensus pattern (22 bp):
GACAACATTTAATCAACAATTG
Found at i:16682038 original size:44 final size:44
Alignment explanation
Indices: 16681990--16682261 Score: 276
Period size: 44 Copynumber: 6.4 Consensus size: 44
16681980 CCAACATTCA
* *
16681990 GACAACATTTAATTAACATTTGGACAACATTTAATCAACAATTG
1 GACAACATTTAATCAACAATTGGACAACATTTAATCAACAATTG
* *
16682034 GACAACAATCAATCAAC-A-T------CATTTAATCAACAATTG
1 GACAACATTTAATCAACAATTGGACAACATTTAATCAACAATTG
* * *
16682070 GACAACATTAAATCAACATTTGGACAGCATTTAATCAACAATTG
1 GACAACATTTAATCAACAATTGGACAACATTTAATCAACAATTG
* * * *
16682114 GACAGCATTTAATCAACAATTCGACAGCA-TTAATTCAACATTTG
1 GACAACATTTAATCAACAATTGGACAACATTTAA-TCAACAATTG
* * * *
16682158 AACAACATTTAATCAACAACTGGACAACATTAAATCAACATTTG
1 GACAACATTTAATCAACAATTGGACAACATTTAATCAACAATTG
* * * *
16682202 GACAACATTTAATCAACAATTAGACAACATTCAATCAATATTTG
1 GACAACATTTAATCAACAATTGGACAACATTTAATCAACAATTG
*
16682246 GATAGA-ATTTAATCAA
1 GACA-ACATTTAATCAA
16682262 TAAATTTTAC
Statistics
Matches: 193, Mismatches: 24, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
36 32 0.17
38 1 0.01
42 1 0.01
43 4 0.02
44 151 0.78
45 4 0.02
ACGTcount: A:0.44, C:0.18, G:0.09, T:0.28
Consensus pattern (44 bp):
GACAACATTTAATCAACAATTGGACAACATTTAATCAACAATTG
Found at i:16682062 original size:36 final size:36
Alignment explanation
Indices: 16682017--16682088 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
16682007 ATTTGGACAA
*
16682017 CATTTAATCAACAATTGGACAACAATCAATCAACAT
1 CATTTAATCAACAATTGGACAACAATAAATCAACAT
*
16682053 CATTTAATCAACAATTGGACAACATTAAATCAACAT
1 CATTTAATCAACAATTGGACAACAATAAATCAACAT
16682089 TTGGACAGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.47, C:0.21, G:0.06, T:0.26
Consensus pattern (36 bp):
CATTTAATCAACAATTGGACAACAATAAATCAACAT
Found at i:16682083 original size:22 final size:22
Alignment explanation
Indices: 16682053--16682261 Score: 242
Period size: 22 Copynumber: 9.5 Consensus size: 22
16682043 CAATCAACAT
16682053 CATTTAATCAACAATTGGACAA
1 CATTTAATCAACAATTGGACAA
* * *
16682075 CATTAAATCAACATTTGGACAG
1 CATTTAATCAACAATTGGACAA
*
16682097 CATTTAATCAACAATTGGACAG
1 CATTTAATCAACAATTGGACAA
* *
16682119 CATTTAATCAACAATTCGACAG
1 CATTTAATCAACAATTGGACAA
* *
16682141 CA-TTAATTCAACATTTGAACAA
1 CATTTAA-TCAACAATTGGACAA
*
16682163 CATTTAATCAACAACTGGACAA
1 CATTTAATCAACAATTGGACAA
* *
16682185 CATTAAATCAACATTTGGACAA
1 CATTTAATCAACAATTGGACAA
*
16682207 CATTTAATCAACAATTAGACAA
1 CATTTAATCAACAATTGGACAA
* * * *
16682229 CATTCAATCAATATTTGGATAGA
1 CATTTAATCAACAATTGGACA-A
16682252 -ATTTAATCAA
1 CATTTAATCAA
16682262 TAAATTTTAC
Statistics
Matches: 159, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
21 4 0.03
22 150 0.94
23 5 0.03
ACGTcount: A:0.44, C:0.18, G:0.09, T:0.29
Consensus pattern (22 bp):
CATTTAATCAACAATTGGACAA
Found at i:16682163 original size:11 final size:10
Alignment explanation
Indices: 16682149--16682232 Score: 51
Period size: 11 Copynumber: 7.7 Consensus size: 10
16682139 AGCATTAATT
16682149 CAACATTTGAA
1 CAACATTT-AA
16682160 CAACATTTAA
1 CAACATTTAA
* **
16682170 TCAACAACTGGA
1 -CAAC-ATTTAA
*
16682182 CAACATTAAA
1 CAACATTTAA
*
16682192 TCAACATTTGGA
1 -CAACATTT-AA
16682204 CAACATTTAA
1 CAACATTTAA
*
16682214 TCAACAATTAGA
1 -CAACATTTA-A
16682226 CAACATT
1 CAACATT
16682233 CAATCAATAT
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
10 6 0.11
11 45 0.80
12 5 0.09
ACGTcount: A:0.46, C:0.20, G:0.07, T:0.26
Consensus pattern (10 bp):
CAACATTTAA
Found at i:16683148 original size:42 final size:44
Alignment explanation
Indices: 16683088--16683196 Score: 134
Period size: 44 Copynumber: 2.5 Consensus size: 44
16683078 ACGATAACAC
* * * *
16683088 TGTCCCAAACAGGGTCTTACACGT-AA--TCATATACGACGCCAA
1 TGTCCCAGACATGGTCTTACACGTAAATCTCAAAT-CGAAGCCAA
*
16683130 TGTTCCAGACATGGTCTTACACGTAAATCTCAAATCGAAGCCAA
1 TGTCCCAGACATGGTCTTACACGTAAATCTCAAATCGAAGCCAA
*
16683174 TGTCCCAGACGTGGTCTTACACG
1 TGTCCCAGACATGGTCTTACACG
16683197 ATGTCAAATT
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
42 21 0.37
43 2 0.04
44 29 0.51
45 5 0.09
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (44 bp):
TGTCCCAGACATGGTCTTACACGTAAATCTCAAATCGAAGCCAA
Found at i:16683183 original size:44 final size:42
Alignment explanation
Indices: 16683040--16683196 Score: 147
Period size: 43 Copynumber: 3.7 Consensus size: 42
16683030 CTCATACAAT
* * * *
16683040 GCCAATGTCCCAGACGTGGTCTTTCATGTAATCAAACAACGATA
1 GCCAATGTCCCAGACATGGTCTTACACGTAATCAAA-TACGA-A
* * * * * *
16683084 -ACACTGTCCCAAACAGGGTCTTACACGTAATCATATACGAC
1 GCCAATGTCCCAGACATGGTCTTACACGTAATCAAATACGAA
*
16683125 GCCAATGTTCCAGACATGGTCTTACACGTAAATCTCAAAT-CGAA
1 GCCAATGTCCCAGACATGGTCTTACACGT-AA--TCAAATACGAA
*
16683169 GCCAATGTCCCAGACGTGGTCTTACACG
1 GCCAATGTCCCAGACATGGTCTTACACG
16683197 ATGTCAAATT
Statistics
Matches: 90, Mismatches: 19, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
42 27 0.30
43 29 0.32
44 29 0.32
45 5 0.06
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (42 bp):
GCCAATGTCCCAGACATGGTCTTACACGTAATCAAATACGAA
Found at i:16690602 original size:21 final size:22
Alignment explanation
Indices: 16690578--16690622 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
16690568 AGAAAAAGAG
16690578 AAATACAAAAAAG-AATAG-ATC
1 AAAT-CAAAAAAGAAATAGAATC
*
16690599 AAATCAAAAAGGAAATAGAATC
1 AAATCAAAAAAGAAATAGAATC
16690621 AA
1 AA
16690623 CAATTTGCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 9 0.43
22 5 0.24
ACGTcount: A:0.67, C:0.09, G:0.11, T:0.13
Consensus pattern (22 bp):
AAATCAAAAAAGAAATAGAATC
Found at i:16693509 original size:35 final size:34
Alignment explanation
Indices: 16693422--16693725 Score: 359
Period size: 35 Copynumber: 9.0 Consensus size: 34
16693412 GTCCAAAAAG
* * *
16693422 AAATAATACATGAACAGGAGAGATTCCCTGCAAG
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAC
*
16693456 AAATGAT--GTGAACAGGAGAGATTCCCTGCAAC
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAC
*
16693488 AGAATAATGCGTGAACAGGAGAGATTCCCTGCAAG
1 A-AATAATGCGTGAACAGGAGAGATTCCCTGCAAC
* * * *
16693523 AAATGAT--GTGAACAGTAAAGATTCCCTGCAATA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAA-C
* * *
16693556 AAATAATGTGTGAACAGTAAAGATTCCCTGCAAC
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAC
*
16693590 AAAATAATGTGTGAACAGGAGAGATTCCCTGCAAC
1 -AAATAATGCGTGAACAGGAGAGATTCCCTGCAAC
*
16693625 AAAATAATGCGTGAACAGGAGAGATTCCCTGCAAG
1 -AAATAATGCGTGAACAGGAGAGATTCCCTGCAAC
* *
16693660 AAATGAT--GTGAACAGGAAAGATTCCCTGCAAC
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAC
* *
16693692 AGAATAATGCGTGAACAGGAAATATTCCCTGCAA
1 A-AATAATGCGTGAACAGGAGAGATTCCCTGCAA
16693726 GAAAAGACAA
Statistics
Matches: 240, Mismatches: 20, Indels: 19
0.86 0.07 0.07
Matches are distributed among these distances:
32 70 0.29
33 16 0.07
34 17 0.07
35 137 0.57
ACGTcount: A:0.40, C:0.17, G:0.22, T:0.20
Consensus pattern (34 bp):
AAATAATGCGTGAACAGGAGAGATTCCCTGCAAC
Found at i:16693531 original size:67 final size:67
Alignment explanation
Indices: 16693422--16693729 Score: 454
Period size: 67 Copynumber: 4.6 Consensus size: 67
16693412 GTCCAAAAAG
* * *
16693422 AAATAATACATGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAGAGATTCCCTGCAA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCAA
16693487 CA
66 CA
* *
16693489 GAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGTAAAGATTCCCTGCAA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCAA
*
16693554 TA
66 CA
* * * * * *
16693556 AAATAATGTGTGAACAGTAAAGATTCCCTGCAACAAAATAATGTGTGAACAGGAGAGATTCCCTG
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAA-GAAATGA--TGTGAACAGGAAAGATTCCCTG
16693621 CAACA
63 CAACA
16693626 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCAA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCAA
16693691 CA
66 CA
* * *
16693693 GAATAATGCGTGAACAGGAAATATTCCCTGCAAGAAA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAA
16693730 AGACAAGTGA
Statistics
Matches: 214, Mismatches: 24, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
67 150 0.70
68 5 0.02
69 5 0.02
70 54 0.25
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.19
Consensus pattern (67 bp):
AAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCAA
CA
Found at i:16693665 original size:137 final size:134
Alignment explanation
Indices: 16693422--16693730 Score: 474
Period size: 137 Copynumber: 2.3 Consensus size: 134
16693412 GTCCAAAAAG
* * * * *
16693422 AAATAATACATGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAGAGATTCCCTGCAA
1 AAATAATGCGTGAACAGGAAAGATTCCCTGCAAAAAATAATGTGAACAGGAGAGATTCCCTGCAA
* *
16693487 CAGAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGTAAAGATTCCCTGC
66 CAAAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGC
*
16693552 AATA
131 AACA
* *
16693556 AAATAATGTGTGAACAGTAAAGATTCCCTGCAACAAAATAATGTGTGAACAGGAGAGATTCCCTG
1 AAATAATGCGTGAACAGGAAAGATTCCCTGCAA-AAAATAA--TGTGAACAGGAGAGATTCCCTG
16693621 CAACAAAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCC
63 CAACAAAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCC
16693686 TGCAACA
128 TGCAACA
* *
16693693 GAATAATGCGTGAACAGGAAATATTCCCTGCAAGAAAA
1 AAATAATGCGTGAACAGGAAAGATTCCCTGCAA-AAAA
16693731 GACAAGTGAA
Statistics
Matches: 157, Mismatches: 15, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
134 28 0.18
135 5 0.03
137 124 0.79
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.19
Consensus pattern (134 bp):
AAATAATGCGTGAACAGGAAAGATTCCCTGCAAAAAATAATGTGAACAGGAGAGATTCCCTGCAA
CAAAATAATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGC
AACA
Found at i:16694004 original size:14 final size:13
Alignment explanation
Indices: 16693977--16694014 Score: 67
Period size: 14 Copynumber: 2.8 Consensus size: 13
16693967 AATTTCCAAA
16693977 TTTTCAAATTAAG
1 TTTTCAAATTAAG
16693990 TTTTCAAACTTAAG
1 TTTTCAAA-TTAAG
16694004 TTTTCAAATTA
1 TTTTCAAATTA
16694015 CAAATATCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (13 bp):
TTTTCAAATTAAG
Found at i:16708493 original size:23 final size:23
Alignment explanation
Indices: 16708445--16708493 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
16708435 ATATTATAAT
* * *
16708445 ATTACTTATATTCAGAATGTATC
1 ATTACTGATATTCAAAATGTAGC
16708468 ATTACTGATATTCAAATATG-AGC
1 ATTACTGATATTCAAA-ATGTAGC
16708491 ATT
1 ATT
16708494 CATCTTTGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 19 0.86
24 3 0.14
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (23 bp):
ATTACTGATATTCAAAATGTAGC
Found at i:16708853 original size:26 final size:24
Alignment explanation
Indices: 16708824--16708885 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 24
16708814 TTGTTTTCAT
16708824 ATTTTAAATATAGTATTTTATTTAAA
1 ATTTTAAATATA-TATTTTA-TTAAA
16708850 ATTTAGTAAATATATATTTTATTAAA
1 ATTT--TAAATATATATTTTATTAAA
*
16708876 ATTTCAAATA
1 ATTTTAAATA
16708886 GAAATAATCG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
24 5 0.15
26 13 0.39
27 7 0.21
28 8 0.24
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (24 bp):
ATTTTAAATATATATTTTATTAAA
Found at i:16708871 original size:27 final size:27
Alignment explanation
Indices: 16708828--16708879 Score: 88
Period size: 26 Copynumber: 1.9 Consensus size: 27
16708818 TTTCATATTT
16708828 TAAATATAGTATTTTATTTAAAATTTAG
1 TAAATATAGTATTTTA-TTAAAATTTAG
16708856 TAAATATA-TATTTTATTAAAATTT
1 TAAATATAGTATTTTATTAAAATTT
16708880 CAAATAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 9 0.38
27 7 0.29
28 8 0.33
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (27 bp):
TAAATATAGTATTTTATTAAAATTTAG
Found at i:16713110 original size:17 final size:18
Alignment explanation
Indices: 16713088--16713121 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
16713078 GAAAATATAT
16713088 ATATAATCTA-AAAAAAC
1 ATATAATCTATAAAAAAC
*
16713105 ATATAATTTATAAAAAA
1 ATATAATCTATAAAAAA
16713122 ATTAATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
ATATAATCTATAAAAAAC
Found at i:16713246 original size:22 final size:22
Alignment explanation
Indices: 16713221--16713272 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 22
16713211 AAAAATTTCT
*
16713221 TTTAAAATATAT-TTTATAAAAA
1 TTTAAAATATATAATTAT-AAAA
16713243 TTTAAAATATATAATTATAAAA
1 TTTAAAATATATAATTATAAAA
16713265 TTCTAAAA
1 TT-TAAAA
16713273 AGGTATACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 18 0.67
23 9 0.33
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
TTTAAAATATATAATTATAAAA
Found at i:16715611 original size:22 final size:22
Alignment explanation
Indices: 16715586--16715628 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
16715576 GAGATCCCCT
* *
16715586 AGAAAAAGTATAGAAAACTAAG
1 AGAAAAACTAGAGAAAACTAAG
*
16715608 AGAAAACCTAGAGAAAACTAA
1 AGAAAAACTAGAGAAAACTAA
16715629 ATCTAAAACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.63, C:0.09, G:0.16, T:0.12
Consensus pattern (22 bp):
AGAAAAACTAGAGAAAACTAAG
Found at i:16724546 original size:12 final size:12
Alignment explanation
Indices: 16724529--16724554 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16724519 CAAAATAGGC
16724529 TTTTAGCGGCGT
1 TTTTAGCGGCGT
16724541 TTTTAGCGGCGT
1 TTTTAGCGGCGT
16724553 TT
1 TT
16724555 GGATAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTTAGCGGCGT
Found at i:16724613 original size:40 final size:39
Alignment explanation
Indices: 16724561--16724670 Score: 139
Period size: 40 Copynumber: 2.8 Consensus size: 39
16724551 GTTTGGATAA
**
16724561 AAAACGCCGCTAAAGATCGAGCATTAGCGGCACTTTTTGG
1 AAAACGCCGCTAAAGAT-GAGCATTAGCGGCACTTCATGG
* * *
16724601 AAAACGCTGCTAAAGATTGAGCATTAGTGGCGCTTCATGG
1 AAAACGCCGCTAAAGA-TGAGCATTAGCGGCACTTCATGG
* *
16724641 AAAACGCCGCTAAATATAAGCATTAGCGGC
1 AAAACGCCGCTAAAGATGAGCATTAGCGGC
16724671 GTTTTTCAGA
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
39 12 0.20
40 47 0.78
41 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.22
Consensus pattern (39 bp):
AAAACGCCGCTAAAGATGAGCATTAGCGGCACTTCATGG
Found at i:16724797 original size:41 final size:41
Alignment explanation
Indices: 16724734--16725055 Score: 473
Period size: 41 Copynumber: 7.9 Consensus size: 41
16724724 CTTTCGGAGA
* *
16724734 TTTAGTGGCGTTTTTCAGAAAGCGCCGCTAATGCTCGGGTC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGGGTC
* * ** *
16724775 TTTAGCGGTGTTTTTGATAAAGCGCCGCTAAAACTAGGGTC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGGGTC
* * * *
16724816 TTTAGCGGCATTTTTGGGGAAGCGCCGCTAATGCTCTGGTC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGGGTC
*
16724857 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCTGGTC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGGGTC
* *
16724898 TTTAGCGGCGTTTTTGAGAAAGCGCCACTAATGCTCTGGTC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGGGTC
* *
16724939 TTTAGCAGCGTTTTTGAGAAAGCACCGCTAATGCTCGGGTC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGGGTC
16724980 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGGGTC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGGGTC
* * *
16725021 TTTAGTGGCGTTTTTGATAAAGCGTCGCTAATGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCT
16725056 TAGGGATTTA
Statistics
Matches: 252, Mismatches: 29, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 252 1.00
ACGTcount: A:0.19, C:0.20, G:0.29, T:0.32
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGGGTC
Found at i:16725243 original size:14 final size:14
Alignment explanation
Indices: 16725224--16725263 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
16725214 TATCACTATA
*
16725224 GTTTAGGGTTTTTG
1 GTTTAGGGTTTATG
*
16725238 GTTTAGGGTATATG
1 GTTTAGGGTTTATG
*
16725252 GTTTAGAGTTTA
1 GTTTAGGGTTTA
16725264 ATGTTTAAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (14 bp):
GTTTAGGGTTTATG
Found at i:16725322 original size:14 final size:14
Alignment explanation
Indices: 16725287--16725335 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
16725277 ACCATTTTAA
* *
16725287 GGTTTATGGATTAC
1 GGTTTAGGGATTAT
16725301 GAGTTTAGGGATTAT
1 G-GTTTAGGGATTAT
*
16725316 GGTTTAGGGTTTAT
1 GGTTTAGGGATTAT
16725330 GGTTTA
1 GGTTTA
16725336 AATACTGGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
14 19 0.61
15 12 0.39
ACGTcount: A:0.20, C:0.02, G:0.33, T:0.45
Consensus pattern (14 bp):
GGTTTAGGGATTAT
Found at i:16725463 original size:16 final size:16
Alignment explanation
Indices: 16725444--16725476 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16725434 TAGTATTTTC
16725444 TAATTTA-TATATTAAT
1 TAATTTATTATA-TAAT
16725460 TAATTTATTATATAAT
1 TAATTTATTATATAAT
16725476 T
1 T
16725477 GTAAAAGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TAATTTATTATATAAT
Found at i:16726123 original size:24 final size:25
Alignment explanation
Indices: 16726090--16726137 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
16726080 TTAAAATGAA
16726090 TTTTAAAATATTT-TAAACTTTTAT
1 TTTTAAAATATTTATAAACTTTTAT
* *
16726114 TTTTATAATATTTATATACTTTTA
1 TTTTAAAATATTTATAAACTTTTA
16726138 AAGAAAAGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (25 bp):
TTTTAAAATATTTATAAACTTTTAT
Found at i:16728029 original size:7 final size:7
Alignment explanation
Indices: 16728017--16728042 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
16728007 GGACATGTGA
16728017 TGTTAGT
1 TGTTAGT
16728024 TGTTAGT
1 TGTTAGT
16728031 TGTTAGT
1 TGTTAGT
16728038 TGTTA
1 TGTTA
16728043 ATCGTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.27, T:0.58
Consensus pattern (7 bp):
TGTTAGT
Found at i:16730178 original size:43 final size:43
Alignment explanation
Indices: 16730139--16730296 Score: 212
Period size: 43 Copynumber: 3.7 Consensus size: 43
16730129 AAAAAAGAGT
* *
16730139 CGCTAAAGG-CCTTGA-CTTATAGCGGCGTTTGTGGGAAAAGTGC
1 CGCTAAAGGTCC-TGATC-TATAGCGGCGTTTTTGGGAAAAGCGC
*
16730182 CGCTAAAGGTCCTGAGCTATAGCGGCGTTTTTGGGAAAAGCGC
1 CGCTAAAGGTCCTGATCTATAGCGGCGTTTTTGGGAAAAGCGC
* * * *
16730225 CGGTAAAGGTCTTGATCTATAGTGGCGTTTTTGAGAAAAGCGC
1 CGCTAAAGGTCCTGATCTATAGCGGCGTTTTTGGGAAAAGCGC
*
16730268 TGCTAAAGGTCCTGATCTATAGCGGCGTT
1 CGCTAAAGGTCCTGATCTATAGCGGCGTT
16730297 GACAACAGTG
Statistics
Matches: 102, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
43 99 0.97
44 3 0.03
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.27
Consensus pattern (43 bp):
CGCTAAAGGTCCTGATCTATAGCGGCGTTTTTGGGAAAAGCGC
Found at i:16734074 original size:20 final size:18
Alignment explanation
Indices: 16734000--16734098 Score: 60
Period size: 19 Copynumber: 5.3 Consensus size: 18
16733990 ATAATATTGT
*
16734000 TTTAATAGTTTAATATTAA
1 TTTAATA-TTAAATATTAA
* * *
16734019 ATTAA-ATTTAATACTTAT
1 TTTAATATTAAATA-TTAA
* **
16734037 TTTAATAGTATTTTATTAA
1 TTTAATATTA-AATATTAA
16734056 TTTAATATTAAAGTGATT-A
1 TTTAATATTAAA-T-ATTAA
16734075 TCTTAATATTAAAT-TTAA
1 T-TTAATATTAAATATTAA
16734093 TTTAAT
1 TTTAAT
16734099 GTTTATCTTG
Statistics
Matches: 62, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
17 14 0.23
18 10 0.16
19 22 0.35
20 16 0.26
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (18 bp):
TTTAATATTAAATATTAA
Found at i:16735885 original size:21 final size:20
Alignment explanation
Indices: 16735840--16735886 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
16735830 ATTTAAATAA
*
16735840 TTTTAATTTTAATTATTAAT
1 TTTTAATTTTAATAATTAAT
*
16735860 ATTTATATTTTAA-AATTATAT
1 TTTTA-ATTTTAATAATTA-AT
16735881 TTTTAA
1 TTTTAA
16735887 GAAGTTAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTAATTTTAATAATTAAT
Found at i:16745457 original size:40 final size:40
Alignment explanation
Indices: 16745402--16745481 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
16745392 TAGAAGGCAA
* *
16745402 TCGACAACAACTTGATTAACAGATTTGGAGTGACCGTATT
1 TCGACAACAACTTGATCAACAGATTTAGAGTGACCGTATT
* *
16745442 TCGACAACAACTTGATCAATAGATTTAGAGTGACTGTATT
1 TCGACAACAACTTGATCAACAGATTTAGAGTGACCGTATT
16745482 CTGATAACGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (40 bp):
TCGACAACAACTTGATCAACAGATTTAGAGTGACCGTATT
Found at i:16746166 original size:12 final size:12
Alignment explanation
Indices: 16746149--16746186 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
16746139 TTTTTAACGA
*
16746149 TTTTTAATAAAT
1 TTTTTAAAAAAT
16746161 TTTTTAAAAAAT
1 TTTTTAAAAAAT
*
16746173 TTTATAAAAAAT
1 TTTTTAAAAAAT
16746185 TT
1 TT
16746187 ATGGTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TTTTTAAAAAAT
Found at i:16746257 original size:24 final size:24
Alignment explanation
Indices: 16746211--16746257 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
16746201 CTTCTATTAA
*
16746211 TTATTATAAATTTTAATGATTTTT
1 TTATTATAAATTTTAATCATTTTT
*
16746235 TTATTATAAATTTTTATC-TTTTT
1 TTATTATAAATTTTAATCATTTTT
16746258 AATAATTCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (24 bp):
TTATTATAAATTTTAATCATTTTT
Found at i:16747331 original size:26 final size:26
Alignment explanation
Indices: 16747296--16747346 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
16747286 ACCAATATCG
* *
16747296 CAGCATAGCTGCCAGTAGTAAAAATA
1 CAGCAGAGCTGCCAATAGTAAAAATA
* *
16747322 CAGCAGAGCTGTCAATAGTCAAAAT
1 CAGCAGAGCTGCCAATAGTAAAAAT
16747347 GGCTAAGAGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.20
Consensus pattern (26 bp):
CAGCAGAGCTGCCAATAGTAAAAATA
Found at i:16747466 original size:32 final size:32
Alignment explanation
Indices: 16747394--16747662 Score: 206
Period size: 32 Copynumber: 8.4 Consensus size: 32
16747384 AAGAATGGCT
* * *
16747394 ACAAGCCATAAGT-ACAGTAATGTGATTGGCAC
1 ACAA-CCATCAGTAACAGTAATATGATCGGCAC
* *
16747426 A-AAGCCATCAGTAGCAGTGATATGATCGGCAC
1 ACAA-CCATCAGTAACAGTAATATGATCGGCAC
* * * *
16747458 ACAACCATCAGTAACGGTAACATGATCAGCAT
1 ACAACCATCAGTAACAGTAATATGATCGGCAC
* * *
16747490 AAAACCATCAGTAACAGTGATATGATCAGCAC
1 ACAACCATCAGTAACAGTAATATGATCGGCAC
* *
16747522 ACAGCCATCAGTAACAGTGAA-ATGATTGGCAC
1 ACAACCATCAGTAACAGT-AATATGATCGGCAC
* ** **
16747554 ACAGCCATTGGTAATGGTAATATGATCGGCAC
1 ACAACCATCAGTAACAGTAATATGATCGGCAC
* * * *
16747586 AAAACCATCAGTAACGGTATTATGATCGACAC
1 ACAACCATCAGTAACAGTAATATGATCGGCAC
** * * *
16747618 A-AATCCATCAGTAATGGTACTACGGTCGGCAC
1 ACAA-CCATCAGTAACAGTAATATGATCGGCAC
16747650 A-AAGCCATCAGTA
1 ACAA-CCATCAGTA
16747663 GCATCGCAGC
Statistics
Matches: 193, Mismatches: 39, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
31 14 0.07
32 176 0.91
33 3 0.02
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (32 bp):
ACAACCATCAGTAACAGTAATATGATCGGCAC
Done.