Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 348 of 427
Found at i:101241539 original size:136 final size:133
Alignment explanation
Indices: 101241399--101241655 Score: 304
Period size: 136 Copynumber: 1.9 Consensus size: 133
101241389 ATAATATAAA
* * *
101241399 AAAATAAAATATAAAAATAGTATAATTAAAAAAATAAAAT-CTGAAAATAAAAAAATATGAACAA
1 AAAATAAAATACAAAAATAATATAATTAAAAAAATAAAATAC-G-----AAAAAAATACGAACAA
* * **
101241463 GGTGCCAAAGTCA-GGTTACTTATTAAATTAATATAAA-AAAACTTAAATAATACATTTGAATGA
60 AGTGCCAAAATCAGGGTTACTTATTAAAAAAATATAAATAAAACTTAAATAATACATTTGAATGA
101241526 TTTTATGCT
125 TTTTATGCT
* * * * * *
101241535 AAAATAAAATACCAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
1 AAAATAAAATACAAAAATAATATAATTAAAAAAATAAAATACGAAAAAAATACGAACAAAGTGCC
* *
101241600 AAAATCAGGGTTATTTATTAAAAAAATATAAATAATACTTAAATAATACATTTGAA
66 AAAATCAGGGTTACTTATTAAAAAAATATAAATAAAACTTAAATAATACATTTGAA
101241656 GCATTATGTA
Statistics
Matches: 103, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
131 24 0.23
132 21 0.20
133 22 0.21
136 35 0.34
137 1 0.01
ACGTcount: A:0.56, C:0.07, G:0.08, T:0.29
Consensus pattern (133 bp):
AAAATAAAATACAAAAATAATATAATTAAAAAAATAAAATACGAAAAAAATACGAACAAAGTGCC
AAAATCAGGGTTACTTATTAAAAAAATATAAATAAAACTTAAATAATACATTTGAATGATTTTAT
GCT
Found at i:101241642 original size:153 final size:151
Alignment explanation
Indices: 101241485--101242394 Score: 633
Period size: 153 Copynumber: 6.1 Consensus size: 151
101241475 AGGTTACTTA
* ** ** *
101241485 TTAAATTAATATA-AAAAAACTTAAATAATACATTTGAATGATTTTATGCTAAAATAAAATACCA
1 TTAAA-TAATATATAAAAAACTTAAAT-ATAC-TTTGAA-AATAATATGAAAAAATAAAATACGA
101241549 AAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT-AAAATCAGGGTTA
62 AAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCTCAAAATCAGGGTTA
*
101241613 TTTATTAAAAAAATATAAATAATAC
127 TTTATTAAAAAAATATAAAAAATAC
* *** * *
101241638 TTAAATAATACATTTGAAGCATT--ATGTAC--T-AAAATAATAT-AAAGAAATAAAATACGAAA
1 TTAAATAATATATAAAAAAC-TTAAATATACTTTGAAAATAATATGAAA-AAATAAAATACGAAA
* * * *
101241697 ATAATATATATTAAAAAATAATATACGAAAATAAAAAAATTACGAAGAGAGT-ATCAAAATCAGG
64 ATAATATATTTTAAAAAATAATATACG-----AAAAAAA-TACGAATAAAGTGCTCAAAATCAGG
* * *
101241761 GTTATTTAGTAAAAAACCCTTAATATAAAGAAACAG
123 GTTATTTA-TTAAAAA-----AATATAAA-AAATAC
* * * * ** *
101241797 TT-AAT--TA-AT---ACATTTGAATTTTTTTTGCTAAAATAATAT-AAAAAATAAAATA-AAAA
1 TTAAATAATATATAAAAAACTTAAATATACTTTG--AAAATAATATGAAAAAATAAAATACGAAA
*
101241853 ATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT-AAAATCAGGGATATT
64 ATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCTCAAAATCAGGGTTATT
*
101241917 TATTGAAAAAATATAAAAAATA-
129 TATTAAAAAAATATAAAAAATAC
* *** * * *
101241939 TTGAAATAATACATTTGAAACATT--ATGTAC--T-AAAATAATATGAAGAAATAAAATACAAAA
1 TT-AAATAATATATAAAAAAC-TTAAATATACTTTGAAAATAATATGAAAAAATAAAATACGAAA
* *
101241999 ATAATATATTTTAAAAAATAAGATAC-AAAAAAATACGAAAAAAGTG-TCAAAATCAGGGTTATT
64 ATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCTCAAAATCAGGGTTATT
** * *
101242062 TATTAAATTAGTATAAAAAACAC
129 TATTAAAAAAATATAAAAAATAC
* * * * * ** *
101242085 TTACATAATATACATAATACATTTGAAACATTTTTTGCTAAAATAATAT-AAAAAATAAAATAGG
1 TTAAATAATAT--ATAAAAAACTT-AAATATACTTTG--AAAATAATATGAAAAAATAAAATACG
*
101242149 AAAATAATATATTTTAAAAAATAATATACG-AAAAAATATGAATAAAGTGCT-AAAATCAGGGTT
61 AAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCTCAAAATCAGGGTT
** *
101242212 ATTTATTAAAAAAATATTTAAAACAC
126 ATTTATTAAAAAAATATAAAAAATAC
* * * * *
101242238 TTAAATAATATATTTAAAATA-TT--ATGTAC--T-AAAATAAGGGTTTTAAAATTAA-ATAATA
1 TTAAATAATATA--TAAAAAACTTAAATATACTTTGAAAATAA---TATGAAAA--AATAAAATA
* * *
101242296 CGAAATTAATATA-TTTAAAAAA-AAGATACGAAAAAAATACGAA-AAAGTG-TCAAAATCAGTG
59 CGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCTCAAAATCAGGG
**
101242357 TTATTTATTAAATTAATATAAAAAATAC
124 TTATTTATTAAAAAAATATAAAAAATAC
*
101242385 TTACATAATA
1 TTAAATAATA
101242395 CATTTAAAAC
Statistics
Matches: 606, Mismatches: 91, Indels: 126
0.74 0.11 0.15
Matches are distributed among these distances:
142 2 0.00
143 4 0.01
144 29 0.05
145 70 0.12
146 81 0.13
147 66 0.11
148 25 0.04
149 28 0.05
150 30 0.05
151 25 0.04
152 38 0.06
153 122 0.20
154 13 0.02
155 3 0.00
156 31 0.05
157 10 0.02
158 24 0.04
159 5 0.01
ACGTcount: A:0.55, C:0.06, G:0.08, T:0.31
Consensus pattern (151 bp):
TTAAATAATATATAAAAAACTTAAATATACTTTGAAAATAATATGAAAAAATAAAATACGAAAAT
AATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCTCAAAATCAGGGTTATTTA
TTAAAAAAATATAAAAAATAC
Found at i:101241716 original size:30 final size:29
Alignment explanation
Indices: 101241670--101241730 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 29
101241660 TATGTACTAA
101241670 AATAATATAAAGAAATAAAATACGAAAAT
1 AATAATATAAAGAAATAAAATACGAAAAT
*
101241699 AATATATATTAAA-AAATAATATACGAAAAT
1 AATA-ATA-TAAAGAAATAAAATACGAAAAT
101241729 AA
1 AA
101241731 AAAAATTACG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 4 0.14
30 21 0.72
31 4 0.14
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.25
Consensus pattern (29 bp):
AATAATATAAAGAAATAAAATACGAAAAT
Found at i:101241843 original size:12 final size:12
Alignment explanation
Indices: 101241826--101241860 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
101241816 TTTTTTTGCT
101241826 AAAATAATATAA
1 AAAATAATATAA
*
101241838 AAAATAAAATAA
1 AAAATAATATAA
101241850 AAAATAATATA
1 AAAATAATATA
101241861 TTTTAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:101241865 original size:302 final size:288
Alignment explanation
Indices: 101241535--101242444 Score: 1154
Period size: 302 Copynumber: 3.1 Consensus size: 288
101241525 ATTTTATGCT
*
101241535 AAAATAAAATACCAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
1 AAAATAAAATACAAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
*
101241600 AAAATCAGGGTTATTTATTAAAAAAATATAAATAATACTTAAATAATACATTTGAAGCATTATGT
66 AAAATCAGGGTTATTTATTAAAAAAATATAAA-AATACTTAAATAATACATTTGAAACATTATGT
*
101241665 ACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATATTAAAAAATAATATACGAAAATA
130 ACTAAAATAATATAAAGAAATAAAATACGAAAATAATATAT-TTAAAAAATAAGATACG-----A
* * *
101241730 AAAAAATTACGAAGAGAGTATCAAAATCAGGGTTATTTAGTAAAAAACCCTTAATATAAAGAAAC
189 AAAAAA-TACGAA-AAAGTGTCAAAATCAGGGTTATTTA-T--TAAA---TTAATATAAA-AAAC
* **
101241795 AGTTA-ATTAATACATTTGAATTTTTTTTGCTAAAATAATATAA
245 ACTTACATTAATACATTTGAAAATTTTTTGCTAAAATAATATAA
101241838 AAAATAAAATA-AAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
1 AAAATAAAATACAAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
* *
101241902 AAAATCAGGGATATTTATTGAAAAAATATAAAAAATA-TTGAAATAATACATTTGAAACATTATG
66 AAAATCAGGGTTATTTATTAAAAAAATAT-AAAAATACTT-AAATAATACATTTGAAACATTATG
* *
101241966 TACTAAAATAATATGAAGAAATAAAATACAAAAATAATATATTTTAAAAAATAAGATAC-AAAAA
129 TACTAAAATAATATAAAGAAATAAAATACGAAAATAATATA-TTTAAAAAATAAGATACGAAAAA
*
101242030 AATACGAAAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAGTATAAAAAACACTTACATAATA
193 AATACG-AAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAATATAAAAAACACTTAC-----A
101242095 TACATAATACATTTGAAACATTTTTTGCTAAAATAATATAA
252 T---TAATACATTTGAAA-ATTTTTTGCTAAAATAATATAA
** *
101242136 AAAATAAAATAGGAAAATAATATATTTTAAAAAATAATATACG-AAAAAATATGAATAAAGTGCT
1 AAAATAAAATACAAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
* * * * *
101242200 AAAATCAGGGTTATTTATTAAAAAAATATTTAAAACACTTAAATAATATATTTAAAATATTATGT
66 AAAATCAGGGTTATTTATTAAAAAAATA-TAAAAATACTTAAATAATACATTTGAAACATTATGT
* * * *
101242265 ACTAAAATAAGGGTTTTAA-AATTAAATAATACGAAATTAATATATTTAAAAAA-AAGATACGAA
130 ACTAAAATAA---TATAAAGAAAT-AA-AATACGAAAATAATATATTTAAAAAATAAGATACGAA
* *
101242328 AAAAATACGAAAAAGTGTCAAAATCAGTGTTATTTATTAAATTAATATAAAAAATACTTACA-TA
190 AAAAATACGAAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAATATAAAAAACACTTACATTA
*
101242392 ATACATTT-AAAACATTTTTGCTAAAATAATATAA
255 ATACATTTGAAAA-TTTTTTGCTAAAATAATATAA
* *
101242426 AAAATAATATACGAAAATA
1 AAAATAAAATACAAAAATA
101242445 TTTTACTTAT
Statistics
Matches: 549, Mismatches: 34, Indels: 61
0.85 0.05 0.09
Matches are distributed among these distances:
288 8 0.01
289 10 0.02
290 40 0.07
291 10 0.02
292 3 0.01
294 3 0.01
295 28 0.05
296 9 0.02
297 13 0.02
298 115 0.21
299 33 0.06
300 59 0.11
301 28 0.05
302 175 0.32
303 15 0.03
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.30
Consensus pattern (288 bp):
AAAATAAAATACAAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
AAAATCAGGGTTATTTATTAAAAAAATATAAAAATACTTAAATAATACATTTGAAACATTATGTA
CTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTAAAAAATAAGATACGAAAAAAAT
ACGAAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAATATAAAAAACACTTACATTAATACAT
TTGAAAATTTTTTGCTAAAATAATATAA
Found at i:101247129 original size:15 final size:16
Alignment explanation
Indices: 101247110--101247171 Score: 56
Period size: 15 Copynumber: 3.8 Consensus size: 16
101247100 TACCTTCTTT
101247110 TTTTCTTCTCCTTCT-
1 TTTTCTTCTCCTTCTA
*
101247125 TTTTCTTCCTTCTCTTCTC
1 TTTTCTT-C-TC-CTTCTA
* *
101247144 CTTTCTT-TCCTTTTA
1 TTTTCTTCTCCTTCTA
101247159 TTTTCTTCTCCTT
1 TTTTCTTCTCCTT
101247172 GCTGCTGAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
15 17 0.45
16 8 0.21
17 2 0.05
18 5 0.13
19 6 0.16
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTCTTCTCCTTCTA
Found at i:101248826 original size:2 final size:2
Alignment explanation
Indices: 101248819--101248845 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
101248809 TAAATTAAAG
101248819 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
101248846 GGATGTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:101250592 original size:35 final size:34
Alignment explanation
Indices: 101250546--101250784 Score: 158
Period size: 35 Copynumber: 6.8 Consensus size: 34
101250536 AATTATTCGC
101250546 CAGTTTATCTGACTAGCGCTGGGCGCTACTTTTGT
1 CAGTTTATCTGACTAGCGCTGGGCGC-ACTTTTGT
* * * *
101250581 CAGTTTATCTGACTAGTGCTGGGCACACATTCGT
1 CAGTTTATCTGACTAGCGCTGGGCGCACTTTTGT
* * * * *
101250615 CGGTTTATCCGACTAACGCTGGGCGCAAATATTGT
1 CAGTTTATCTGACTAGCGCTGGGCGC-ACTTTTGT
** ** * * *
101250650 TGGTTTATCCAATTAGAGCTGGGCTCACTAATTATTCGT
1 CAGTTTATCTGACTAGCGCTGGGCGCAC---TT-TT-GT
* ** *
101250689 CAGTTTATCCGACTAGCGCTAGGTGCAAAC-TCTGT
1 CAGTTTATCTGACTAGCGCT-GG-GCGCACTTTTGT
* *
101250724 CAGTTTATCTGACTAGTGCTGGGCACACATTTT-T
1 CAGTTTATCTGACTAGCGCTGGGCGCAC-TTTTGT
* *
101250758 CTGTTTATCTGACTAGCACTGGGCGCA
1 CAGTTTATCTGACTAGCGCTGGGCGCA
101250785 AACTCTTTCG
Statistics
Matches: 157, Mismatches: 37, Indels: 21
0.73 0.17 0.10
Matches are distributed among these distances:
33 5 0.03
34 54 0.34
35 70 0.45
36 1 0.01
37 2 0.01
38 2 0.01
39 17 0.11
40 2 0.01
41 4 0.03
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (34 bp):
CAGTTTATCTGACTAGCGCTGGGCGCACTTTTGT
Found at i:101250739 original size:143 final size:136
Alignment explanation
Indices: 101250489--101250786 Score: 375
Period size: 143 Copynumber: 2.1 Consensus size: 136
101250479 CGATTCGTTT
*
101250489 GACTAACGCTGGACGCAAATATCGTTGGTTTATCCAACGGCTCACTAAATTATTCGCCAGTTTAT
1 GACTAACGCTGGGCGCAAATATCGTTGGTTTATCCAACGGCTCACTAAATTATTCGCCAGTTTAT
* * * *
101250554 CTGACTAGCGCTGGGCGCTACTTTTGTCAGTTTATCTGACTAGTGCTGGGCACACATTCGTCGGT
66 CCGACTAGCGCTAGGCGCAACTTCTGTCAGTTTATCTGACTAGTGCTGGGCACACATTCGTCGGT
101250619 TTATCC
131 TTATCC
* *
101250625 GACTAACGCTGGGCGCAAATATTGTTGGTTTATCCAATTAGAGCTGGGCTCACT-AATTATTCGT
1 GACTAACGCTGGGCGCAAATATCGTTGGTTTATCC----A-A-C--GGCTCACTAAATTATTCGC
*
101250689 CAGTTTATCCGACTAGCGCTAGGTGCAAAC-TCTGTCAGTTTATCTGACTAGTGCTGGGCACACA
58 CAGTTTATCCGACTAGCGCTAGGCGC-AACTTCTGTCAGTTTATCTGACTAGTGCTGGGCACACA
** * *
101250753 TTTTTCTGTTTATCT
122 TTCGTCGGTTTATCC
* *
101250768 GACTAGCACTGGGCGCAAA
1 GACTAACGCTGGGCGCAAA
101250787 CTCTTTCGCG
Statistics
Matches: 139, Mismatches: 14, Indels: 11
0.85 0.09 0.07
Matches are distributed among these distances:
136 33 0.24
140 1 0.01
141 1 0.01
142 1 0.01
143 93 0.67
144 10 0.07
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.32
Consensus pattern (136 bp):
GACTAACGCTGGGCGCAAATATCGTTGGTTTATCCAACGGCTCACTAAATTATTCGCCAGTTTAT
CCGACTAGCGCTAGGCGCAACTTCTGTCAGTTTATCTGACTAGTGCTGGGCACACATTCGTCGGT
TTATCC
Found at i:101250745 original size:74 final size:74
Alignment explanation
Indices: 101250527--101250788 Score: 242
Period size: 69 Copynumber: 3.7 Consensus size: 74
101250517 TTTATCCAAC
* * *
101250527 GGCTCACTAAATTATTCGCCAGTTTATCTGACTAGCGCTGGGCGC-TACTTTTGTCAGTTTATCT
1 GGCTCACT-AATTATTCGTCAGTTTATCCGACTAGCGCTGGGCGCAAAC-TTTGTCAGTTTATCT
101250591 GACTAGTGCTG
64 GACTAGTGCTG
* * * ** **
101250602 GG--CAC--A-CATTCGTCGGTTTATCCGACTAACGCTGGGCGCAAA-TATTGTTGGTTTATCCA
1 GGCTCACTAATTATTCGTCAGTTTATCCGACTAGCGCTGGGCGCAAACT-TTGTCAGTTTATCTG
* *
101250661 ATTAGAGCTG
65 ACTAGTGCTG
* * *
101250671 GGCTCACTAATTATTCGTCAGTTTATCCGACTAGCGCTAGGTGCAAACTCTGTCAGTTTATCTGA
1 GGCTCACTAATTATTCGTCAGTTTATCCGACTAGCGCTGGGCGCAAACTTTGTCAGTTTATCTGA
101250736 CTAGTGCTG
66 CTAGTGCTG
* * * *
101250745 GGCACAC--ATT-TT--TCTGTTTATCTGACTAGCACTGGGCGCAAACT
1 GGCTCACTAATTATTCGTCAGTTTATCCGACTAGCGCTGGGCGCAAACT
101250789 CTTTCGCGAA
Statistics
Matches: 149, Mismatches: 30, Indels: 22
0.74 0.15 0.11
Matches are distributed among these distances:
68 1 0.01
69 76 0.51
70 2 0.01
71 5 0.03
72 3 0.02
73 4 0.03
74 55 0.37
75 3 0.02
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (74 bp):
GGCTCACTAATTATTCGTCAGTTTATCCGACTAGCGCTGGGCGCAAACTTTGTCAGTTTATCTGA
CTAGTGCTG
Found at i:101256032 original size:52 final size:52
Alignment explanation
Indices: 101255954--101256052 Score: 171
Period size: 52 Copynumber: 1.9 Consensus size: 52
101255944 TCTTTACTTG
101255954 TCCACTTTTTAACAGGTAATTTTGGCAATTCCATAGATACTGTTGAATATCA
1 TCCACTTTTTAACAGGTAATTTTGGCAATTCCATAGATACTGTTGAATATCA
* * *
101256006 TCCACTTTTTAATAGGTTATTTTGGCAATTCCCTAGATACTGTTGAA
1 TCCACTTTTTAACAGGTAATTTTGGCAATTCCATAGATACTGTTGAA
101256053 CACCATTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.40
Consensus pattern (52 bp):
TCCACTTTTTAACAGGTAATTTTGGCAATTCCATAGATACTGTTGAATATCA
Found at i:101256250 original size:21 final size:20
Alignment explanation
Indices: 101256226--101256264 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
101256216 GAAACTGAGT
*
101256226 CATTAGAGTTGAAATTGAAAC
1 CATTAGA-TTGAAAATGAAAC
*
101256247 CATTATATTGAAAATGAA
1 CATTAGATTGAAAATGAA
101256265 TCTACAATCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (20 bp):
CATTAGATTGAAAATGAAAC
Found at i:101257526 original size:23 final size:23
Alignment explanation
Indices: 101257469--101257517 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
101257459 GTGAAGGGGA
*
101257469 ATTAAAATGAAAAACTTCAAAAT
1 ATTAAAATAAAAAACTTCAAAAT
101257492 ATTAAAATAAAAAACTTCAAAAT
1 ATTAAAATAAAAAACTTCAAAAT
101257515 ATT
1 ATT
101257518 TCTTAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.61, C:0.08, G:0.02, T:0.29
Consensus pattern (23 bp):
ATTAAAATAAAAAACTTCAAAAT
Found at i:101258686 original size:16 final size:16
Alignment explanation
Indices: 101258665--101258695 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
101258655 AATTCCAATT
101258665 TTGTCCATAAAATTTC
1 TTGTCCATAAAATTTC
101258681 TTGTCCATAAAATTT
1 TTGTCCATAAAATTT
101258696 TAGATTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.16, G:0.06, T:0.45
Consensus pattern (16 bp):
TTGTCCATAAAATTTC
Found at i:101260492 original size:32 final size:32
Alignment explanation
Indices: 101260417--101260497 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 32
101260407 AAAATTTAGT
* *
101260417 TTGTTGGATTTTGAAATTATTATGTCTTGAAT
1 TTGTTGGATATTGAAATTATTATGTCTTGAAC
** * *
101260449 TTGTTACATATTGAATTTATTATGT-TTTAAGC
1 TTGTTGGATATTGAAATTATTATGTCTTGAA-C
*
101260481 TTGTTGGATATTAAAAT
1 TTGTTGGATATTGAAAT
101260498 GATTGACAAT
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
31 4 0.11
32 34 0.89
ACGTcount: A:0.28, C:0.04, G:0.16, T:0.52
Consensus pattern (32 bp):
TTGTTGGATATTGAAATTATTATGTCTTGAAC
Found at i:101260942 original size:36 final size:36
Alignment explanation
Indices: 101260902--101260975 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
101260892 TATTTTTTTT
101260902 ACTTGTTATTCTAATTGTGTATAATATCCAACAGGC
1 ACTTGTTATTCTAATTGTGTATAATATCCAACAGGC
101260938 ACTTGTTATTCTAATTGTGTATAATATCCAACAGGC
1 ACTTGTTATTCTAATTGTGTATAATATCCAACAGGC
101260974 AC
1 AC
101260976 ACAAGAAGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.38
Consensus pattern (36 bp):
ACTTGTTATTCTAATTGTGTATAATATCCAACAGGC
Found at i:101261824 original size:14 final size:14
Alignment explanation
Indices: 101261790--101261824 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
101261780 AATAATTTAA
*
101261790 AATATAAATTTATT
1 AATATATATTTATT
101261804 AATATATATTTATT
1 AATATATATTTATT
101261818 AATATAT
1 AATATAT
101261825 GTAAAAACAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
AATATATATTTATT
Found at i:101264448 original size:15 final size:15
Alignment explanation
Indices: 101264430--101264461 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
101264420 TCCTTTTATG
101264430 ATTGGAAGGTTTAAT
1 ATTGGAAGGTTTAAT
101264445 ATTGGAAGGTTTAAT
1 ATTGGAAGGTTTAAT
101264460 AT
1 AT
101264462 GCAAATATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.25, T:0.41
Consensus pattern (15 bp):
ATTGGAAGGTTTAAT
Found at i:101272140 original size:3 final size:3
Alignment explanation
Indices: 101272132--101272218 Score: 174
Period size: 3 Copynumber: 29.0 Consensus size: 3
101272122 AATACTCTAA
101272132 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
101272180 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
101272219 AATCAAGTAA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 84 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:101280725 original size:9 final size:9
Alignment explanation
Indices: 101280693--101280762 Score: 50
Period size: 9 Copynumber: 7.1 Consensus size: 9
101280683 TTAATCCTAG
*
101280693 TTTTAATAA
1 TTTTTATAA
101280702 TTTTATATAA
1 TTTT-TATAA
* *
101280712 CTTTTGTAA
1 TTTTTATAA
101280721 TTTTTAATAGA
1 TTTTT-ATA-A
*
101280732 TTTTATTTAA
1 TTTT-TATAA
101280742 TTTTTATAA
1 TTTTTATAA
101280751 TGTTTTTATAA
1 --TTTTTATAA
101280762 T
1 T
101280763 CCTTTCATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
9 17 0.35
10 14 0.29
11 16 0.33
12 1 0.02
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:101280737 original size:30 final size:30
Alignment explanation
Indices: 101280692--101280762 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
101280682 ATTAATCCTA
*
101280692 GTTTTAATAATTTTATATAACTTTTGTAAT
1 GTTTTAATAATTTTATATAACTTTTATAAT
* *
101280722 -TTTTAATAGATTTTATTTAATTTTTATAAT
1 GTTTTAATA-ATTTTATATAACTTTTATAAT
*
101280752 GTTTTTATAAT
1 GTTTTAATAAT
101280763 CCTTTCATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
29 8 0.23
30 20 0.57
31 7 0.20
ACGTcount: A:0.32, C:0.01, G:0.06, T:0.61
Consensus pattern (30 bp):
GTTTTAATAATTTTATATAACTTTTATAAT
Found at i:101280762 original size:20 final size:19
Alignment explanation
Indices: 101280693--101280762 Score: 54
Period size: 19 Copynumber: 3.5 Consensus size: 19
101280683 TTAATCCTAG
*
101280693 TTTTAATAATTTTATATAA-
1 TTTTTATAATTTT-TATAAT
* *
101280712 CTTTTGTAATTTTTAATAGAT
1 TTTTTATAATTTTT-ATA-AT
101280733 TTTATT-TAATTTTTATAAT
1 TTT-TTATAATTTTTATAAT
101280752 GTTTTTATAAT
1 -TTTTTATAAT
101280763 CCTTTCATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
18 1 0.02
19 17 0.41
20 11 0.27
21 10 0.24
22 2 0.05
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.61
Consensus pattern (19 bp):
TTTTTATAATTTTTATAAT
Found at i:101280823 original size:19 final size:18
Alignment explanation
Indices: 101280793--101280835 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
101280783 CTTAGTAATA
101280793 TTTATATTTAT-ATTTTT
1 TTTATATTTATAATTTTT
101280810 TTCTATATTTTATAATTTTT
1 TT-TATA-TTTATAATTTTT
101280830 TTTATA
1 TTTATA
101280836 ATCTTTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 2 0.09
18 4 0.17
19 9 0.39
20 8 0.35
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATATTTATAATTTTT
Found at i:101285724 original size:18 final size:17
Alignment explanation
Indices: 101285689--101285740 Score: 70
Period size: 18 Copynumber: 3.0 Consensus size: 17
101285679 TAAAAAGTAA
101285689 TTTATTTAAAAATA-TT
1 TTTATTTAAAAATATTT
*
101285705 TTTATATTAAAAGTATTT
1 TTTAT-TTAAAAATATTT
101285723 TTTATCTTAAAAATATTT
1 TTTAT-TTAAAAATATTT
101285741 GTTAACAACA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
16 5 0.16
17 8 0.26
18 18 0.58
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (17 bp):
TTTATTTAAAAATATTT
Found at i:101288288 original size:18 final size:19
Alignment explanation
Indices: 101288265--101288300 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
101288255 GTATGAGATT
101288265 ATGCACTT-ATGTGCCAGG
1 ATGCACTTCATGTGCCAGG
*
101288283 ATGCACTTCGTGTGCCAG
1 ATGCACTTCATGTGCCAG
101288301 ATATGCACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.19, C:0.25, G:0.28, T:0.28
Consensus pattern (19 bp):
ATGCACTTCATGTGCCAGG
Found at i:101290845 original size:63 final size:63
Alignment explanation
Indices: 101290733--101290854 Score: 163
Period size: 63 Copynumber: 1.9 Consensus size: 63
101290723 TGACAAACCT
* * * * *
101290733 TGTAACCCACTGTTCATGAATTAGAGACACACGGGCTAGGGATATGGGCGTGTGCCCAGACCG
1 TGTAACCCACTGTTCATGAATTAGAGACACACGAGCCAGGGACACGGGCGGGTGCCCAGACCG
* * * *
101290796 TGTAACTCATTGTTCATGACTTAGAGACACACGAGCCAGGGACACGGGCGGGTGTCCAG
1 TGTAACCCACTGTTCATGAATTAGAGACACACGAGCCAGGGACACGGGCGGGTGCCCAG
101290855 GCCATGTGAC
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
63 50 1.00
ACGTcount: A:0.25, C:0.24, G:0.30, T:0.20
Consensus pattern (63 bp):
TGTAACCCACTGTTCATGAATTAGAGACACACGAGCCAGGGACACGGGCGGGTGCCCAGACCG
Found at i:101291675 original size:316 final size:316
Alignment explanation
Indices: 101291102--101291688 Score: 1129
Period size: 316 Copynumber: 1.9 Consensus size: 316
101291092 TACTGGATAG
101291102 TTGATTATCTAAACATATATTGAATGTTATGACTATAATGATATTGAGCTCTAAATATGAATTGT
1 TTGATTATCTAAACATATATTGAATGTTATGACTATAATGATATTGAGCTCTAAATATGAATTGT
*
101291167 ATCTGAATAACTGTGTACATTCTTGACATCTGACATTTATAATTTGCACCCGCATTGTATGGAAA
66 ATCTAAATAACTGTGTACATTCTTGACATCTGACATTTATAATTTGCACCCGCATTGTATGGAAA
* *
101291232 ATGTGTTAAGGGGGAGTGATCTGTTTTGGTTTAGTAGTTAAGCCACATGCTATATCTGAATCTGG
131 ATGTGTTAAGAGGGAGTGATCTGTTTTGGTTTAGTAGTTAAGCCACATGATATATCTGAATCTGG
101291297 CCTTTTATCGCAACTTGATCTGGAAGTTAGTTTGTAATCATATCGAACGTGTCGTACTGACACTA
196 CCTTTTATCGCAACTTGATCTGGAAGTTAGTTTGTAATCATATCGAACGTGTCGTACTGACACTA
101291362 TTGGTGTATAGGGCTGGATGGGTATTAAATTCCCTTAATGGAATGTTGGGTTGGTC
261 TTGGTGTATAGGGCTGGATGGGTATTAAATTCCCTTAATGGAATGTTGGGTTGGTC
101291418 TTGATTATCTAAACATATATTGAATGTTATGACTATAATGATATTGAGCTCTAAATATGAATTGT
1 TTGATTATCTAAACATATATTGAATGTTATGACTATAATGATATTGAGCTCTAAATATGAATTGT
*
101291483 ATCTAAATAACTGTGTACATTCTTGACATCTGACATTTATAATTTGCATCCGCATTGTATGGAAA
66 ATCTAAATAACTGTGTACATTCTTGACATCTGACATTTATAATTTGCACCCGCATTGTATGGAAA
101291548 ATGTGTTAAGAGGGAGTGATCTGTTTTGGTTTAGTAGTTAAGCCACATGATATATCTGAATCTGG
131 ATGTGTTAAGAGGGAGTGATCTGTTTTGGTTTAGTAGTTAAGCCACATGATATATCTGAATCTGG
*
101291613 CCTTTTATCGCAACTTGATCTGGAAGTTAGTTTGTAATCATATCGAATGTGTCGTACTGACACTA
196 CCTTTTATCGCAACTTGATCTGGAAGTTAGTTTGTAATCATATCGAACGTGTCGTACTGACACTA
101291678 TTGGTGTATAG
261 TTGGTGTATAG
101291689 CGGATGGGGT
Statistics
Matches: 266, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
316 266 1.00
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.38
Consensus pattern (316 bp):
TTGATTATCTAAACATATATTGAATGTTATGACTATAATGATATTGAGCTCTAAATATGAATTGT
ATCTAAATAACTGTGTACATTCTTGACATCTGACATTTATAATTTGCACCCGCATTGTATGGAAA
ATGTGTTAAGAGGGAGTGATCTGTTTTGGTTTAGTAGTTAAGCCACATGATATATCTGAATCTGG
CCTTTTATCGCAACTTGATCTGGAAGTTAGTTTGTAATCATATCGAACGTGTCGTACTGACACTA
TTGGTGTATAGGGCTGGATGGGTATTAAATTCCCTTAATGGAATGTTGGGTTGGTC
Found at i:101293826 original size:22 final size:23
Alignment explanation
Indices: 101293801--101293846 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
101293791 CAACCAAATC
101293801 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
101293823 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
101293846 A
1 A
101293847 GATAACGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:101307477 original size:37 final size:37
Alignment explanation
Indices: 101307427--101307502 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
101307417 AACCTTGTTG
*
101307427 CTGCCATATCTGAATGGACTGATCTATAAAAATTGAA
1 CTGCCATATCTGAATGGAATGATCTATAAAAATTGAA
101307464 CTGCCATATCTGAATGGAATGATCTATAAAAATTGAA
1 CTGCCATATCTGAATGGAATGATCTATAAAAATTGAA
101307501 CT
1 CT
101307503 AGCTCTGATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (37 bp):
CTGCCATATCTGAATGGAATGATCTATAAAAATTGAA
Found at i:101309180 original size:17 final size:18
Alignment explanation
Indices: 101309152--101309185 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
101309142 AAAGTTGAAT
*
101309152 TTAATATATTAATAATAA
1 TTAATATATTAACAATAA
101309170 TTAAT-TATTAACAATA
1 TTAATATATTAACAATA
101309186 TAGTTATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAATATATTAACAATAA
Found at i:101315994 original size:47 final size:47
Alignment explanation
Indices: 101315876--101316051 Score: 235
Period size: 47 Copynumber: 3.7 Consensus size: 47
101315866 GTGCGAGTGA
* * * *
101315876 TACCTTGATTTGGCTACAGGCCATGGTATAGATATTTTGGAGATGAGT
1 TACCTTGATTTGGCTACAGGCCATGGTATAGGTACTCTGG-GATAAGT
** * *
101315924 TACCTTGATTTGGCTATGGGCCATGGTATAGGTGCTCCGGGATAAGT
1 TACCTTGATTTGGCTACAGGCCATGGTATAGGTACTCTGGGATAAGT
* *
101315971 TACCTTGATTTGGCTACAAGCCATGGTATAGGTCCTCTGGGATAAGT
1 TACCTTGATTTGGCTACAGGCCATGGTATAGGTACTCTGGGATAAGT
* *
101316018 TACCTTGATTTGGCTTCGGGCCATGGTATAGGTA
1 TACCTTGATTTGGCTACAGGCCATGGTATAGGTA
101316052 TTTATCGATT
Statistics
Matches: 111, Mismatches: 17, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
47 78 0.70
48 33 0.30
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.34
Consensus pattern (47 bp):
TACCTTGATTTGGCTACAGGCCATGGTATAGGTACTCTGGGATAAGT
Found at i:101316046 original size:94 final size:95
Alignment explanation
Indices: 101315876--101316050 Score: 273
Period size: 94 Copynumber: 1.9 Consensus size: 95
101315866 GTGCGAGTGA
* * * *
101315876 TACCTTGATTTGGCTACAGGCCATGGTATAGATATTTTGGAGATGAGTTACCTTGATTTGGCTAT
1 TACCTTGATTTGGCTACAAGCCATGGTATAGATACTCTGGAGATAAGTTACCTTGATTTGGCTAT
101315941 GGGCCATGGTATAGGTGCTCCGGGATAAGT
66 GGGCCATGGTATAGGTGCTCCGGGATAAGT
* *
101315971 TACCTTGATTTGGCTACAAGCCATGGTATAGGTCCTCTGG-GATAAGTTACCTTGATTTGGCT-T
1 TACCTTGATTTGGCTACAAGCCATGGTATAGATACTCTGGAGATAAGTTACCTTGATTTGGCTAT
101316034 CGGGCCATGGTATAGGT
66 -GGGCCATGGTATAGGT
101316051 ATTTATCGAT
Statistics
Matches: 73, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
93 1 0.01
94 37 0.51
95 35 0.48
ACGTcount: A:0.21, C:0.17, G:0.29, T:0.34
Consensus pattern (95 bp):
TACCTTGATTTGGCTACAAGCCATGGTATAGATACTCTGGAGATAAGTTACCTTGATTTGGCTAT
GGGCCATGGTATAGGTGCTCCGGGATAAGT
Found at i:101319896 original size:23 final size:23
Alignment explanation
Indices: 101319848--101319897 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
101319838 TACTTTTCTA
* * * *
101319848 TATTATTTCTTTAGATTTATCGT
1 TATTATTTCTTTACAATAATCAT
101319871 TATTATTTCTTTACAATAATCAT
1 TATTATTTCTTTACAATAATCAT
101319894 TATT
1 TATT
101319898 CCAATTGATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.28, C:0.10, G:0.04, T:0.58
Consensus pattern (23 bp):
TATTATTTCTTTACAATAATCAT
Found at i:101329320 original size:125 final size:126
Alignment explanation
Indices: 101329097--101329345 Score: 374
Period size: 125 Copynumber: 2.0 Consensus size: 126
101329087 AAGGCCAAGC
* *
101329097 AGGAACTATTGTAGAAAAAGAGCGTTCACGTGGAAGCTTTTTTCAATAATTTTGCTGACAGTGCA
1 AGGAACTACTGTAGAAAAAGAGCATTCACGTGGAAGCTTTTTTCAATAATTTTGCTGACAGTGCA
* * * * * * *
101329162 TCTTACTTGAAGCGTTTTTGACACTATTTTTTCAGAATCGTCTTCTCAAAATTATTTTTTT
66 TCCTACTTGAAACATTTTTGACACTATCTTTTCAGAATCATCTTCACAAAATAATTTTTTT
* * *
101329223 AGGAACTACTGTAGAAAAAGAGCATTCACGTGGGAGC-TTTTTCAGTAATTTTGCTGATAGTGCA
1 AGGAACTACTGTAGAAAAAGAGCATTCACGTGGAAGCTTTTTTCAATAATTTTGCTGACAGTGCA
*
101329287 TCCTACTTGAAACATTTTTGACATTATCTTTTCAGAATCATCTTCACAAAATAATTTTT
66 TCCTACTTGAAACATTTTTGACACTATCTTTTCAGAATCATCTTCACAAAATAATTTTT
101329346 CTGAAACTAC
Statistics
Matches: 110, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
125 76 0.69
126 34 0.31
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (126 bp):
AGGAACTACTGTAGAAAAAGAGCATTCACGTGGAAGCTTTTTTCAATAATTTTGCTGACAGTGCA
TCCTACTTGAAACATTTTTGACACTATCTTTTCAGAATCATCTTCACAAAATAATTTTTTT
Found at i:101329547 original size:34 final size:33
Alignment explanation
Indices: 101329470--101329558 Score: 146
Period size: 33 Copynumber: 2.7 Consensus size: 33
101329460 AAACTAAAGC
*
101329470 CTAATTTAATTAATTTATTTAAAACCCCTAAAT
1 CTAATTTAATTAATTTATTTAAAACCCCTAAAA
101329503 CTAATTTAATTAATTTATTTAAAACCCCTAAAA
1 CTAATTTAATTAATTTATTTAAAACCCCTAAAA
101329536 CTTAATTTAATT-ATTT-TTTAAAA
1 C-TAATTTAATTAATTTATTTAAAA
101329559 AAAACTCTAA
Statistics
Matches: 54, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
32 7 0.13
33 37 0.69
34 10 0.19
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (33 bp):
CTAATTTAATTAATTTATTTAAAACCCCTAAAA
Found at i:101331227 original size:33 final size:33
Alignment explanation
Indices: 101331183--101331245 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
101331173 TTTAGAGGAG
*
101331183 CGAATCGAATGATTCTGGTGTTTGCTATCGGAA
1 CGAATCAAATGATTCTGGTGTTTGCTATCGGAA
101331216 CGAATCAAATGATTCTGGTGTTTGCTATCG
1 CGAATCAAATGATTCTGGTGTTTGCTATCG
101331246 CGTCTATGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (33 bp):
CGAATCAAATGATTCTGGTGTTTGCTATCGGAA
Found at i:101334476 original size:20 final size:20
Alignment explanation
Indices: 101334453--101334490 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
101334443 CACATCCAAA
*
101334453 TACAAAATTTTAAAAATCTT
1 TACAAAATATTAAAAATCTT
*
101334473 TACAAAATATTGAAAATC
1 TACAAAATATTAAAAATC
101334491 GCGAATAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TACAAAATATTAAAAATCTT
Found at i:101341767 original size:14 final size:14
Alignment explanation
Indices: 101341748--101341777 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
101341738 GAATAGTTTT
101341748 GAAGAAGAAAAATA
1 GAAGAAGAAAAATA
*
101341762 GAAGAAGAAGAATA
1 GAAGAAGAAAAATA
101341776 GA
1 GA
101341778 GGAGGTGGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (14 bp):
GAAGAAGAAAAATA
Found at i:101342361 original size:20 final size:20
Alignment explanation
Indices: 101342338--101342375 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
101342328 CACATCCAAA
*
101342338 TACAAAATTTTAAAAATCTT
1 TACAAAATATTAAAAATCTT
*
101342358 TACAAAATATTGAAAATC
1 TACAAAATATTAAAAATC
101342376 GCGAATAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TACAAAATATTAAAAATCTT
Found at i:101356121 original size:17 final size:18
Alignment explanation
Indices: 101356080--101356122 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
101356070 GTCTGTGTGA
*
101356080 ACCCACACACCCGTGTAG
1 ACCCACACACCCGTATAG
101356098 ACCCACACACCCGTAT-G
1 ACCCACACACCCGTATAG
*
101356115 GCCCACAC
1 ACCCACAC
101356123 GGCCTAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.28, C:0.49, G:0.14, T:0.09
Consensus pattern (18 bp):
ACCCACACACCCGTATAG
Found at i:101361863 original size:28 final size:28
Alignment explanation
Indices: 101361798--101361898 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
101361788 ATAGTGAATC
*
101361798 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
101361827 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
101361855 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
101361885 CGCACACTTAGTGC
1 CGCACACTTAGTGC
101361899 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:101369796 original size:28 final size:28
Alignment explanation
Indices: 101369731--101369831 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
101369721 ATAGTGAATC
*
101369731 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
101369760 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
101369788 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
101369818 CGCACACTTAGTGC
1 CGCACACTTAGTGC
101369832 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:101373272 original size:93 final size:93
Alignment explanation
Indices: 101373159--101373330 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
101373149 CGCCCATAAG
* *
101373159 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
101373224 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
101373252 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
101373317 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
101373331 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:101373327 original size:46 final size:46
Alignment explanation
Indices: 101373152--101373327 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
101373142 TGTAACCCGC
* * *
101373152 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
101373198 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
101373248 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
101373291 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
101373328 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:101378874 original size:39 final size:40
Alignment explanation
Indices: 101378777--101378955 Score: 184
Period size: 40 Copynumber: 4.5 Consensus size: 40
101378767 TCGAATGGTG
* * *
101378777 TCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
101378818 TCCGGG-TCAACTCCCGAAGGCATTTGTGCGAGTTACCAAA
1 TCCGGGCT-AAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * * *
101378858 -ACGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * * *
101378897 TCCGGGCTAATTCCCGAAGGCAATTGTGCGAATCACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
101378938 -CCGGGCTATGTCCCGAAG
1 TCCGGGCTAAGTCCCGAAG
101378956 ACAATCGAGC
Statistics
Matches: 114, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
39 32 0.28
40 55 0.48
41 27 0.24
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:101378916 original size:79 final size:80
Alignment explanation
Indices: 101378779--101378955 Score: 205
Period size: 80 Copynumber: 2.2 Consensus size: 80
101378769 GAATGGTGTC
* * *
101378779 CGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAATCCGGGTCAACTCCCGAAGGCATTTG
1 CGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGACTAAATCCGGGTCAACTCCCGAAGGCAATTG
101378844 TGCGAGTTACCAAAA
66 TGCGAGTTACCAAAA
* * * * *
101378859 CGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGG-CTAATTCCCGAAGGCAATT
1 CGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGACTAAATCCGGGTC-AACTCCCGAAGGCAATT
* * * *
101378922 GTGCGAATCACTATAAC
65 GTGCGAGTTACCA-AAA
*
101378939 CGGGCTATGTCCCGAAG
1 CGGGCTAAGTCCCGAAG
101378956 ACAATCGAGC
Statistics
Matches: 81, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 1 0.01
79 39 0.48
80 41 0.51
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.24
Consensus pattern (80 bp):
CGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGACTAAATCCGGGTCAACTCCCGAAGGCAATTG
TGCGAGTTACCAAAA
Found at i:101378976 original size:40 final size:40
Alignment explanation
Indices: 101378898--101378981 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 40
101378888 GTTATTAAAT
* * *
101378898 CCGGGCTAATTCCCGAAGGCAATTGTGCGAATCACTATAA
1 CCGGGCTAATTCCCGAAGACAATCGAGCGAATCACTATAA
* * *
101378938 CCGGGCT-ATGTCCCGAAGACAATCGAGCGAGTCGCTATAT
1 CCGGGCTAAT-TCCCGAAGACAATCGAGCGAATCACTATAA
101378978 CCGG
1 CCGG
101378982 TTAAATTCCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
39 2 0.05
40 35 0.95
ACGTcount: A:0.26, C:0.27, G:0.26, T:0.20
Consensus pattern (40 bp):
CCGGGCTAATTCCCGAAGACAATCGAGCGAATCACTATAA
Found at i:101378981 original size:80 final size:79
Alignment explanation
Indices: 101378812--101378981 Score: 180
Period size: 80 Copynumber: 2.1 Consensus size: 79
101378802 GTGCTAAGTG
* * * * *
101378812 ACTAAATCCGGG-TCAACTCCCGAAGGCATTTGTGCGAGTTACCAAAACGGGTTAAGTCCCGAAG
1 ACTAAATCCGGGCT-AATTCCCGAAGGCAATTGTGCGAATCACCAAAACGGGCTAAGTCCCGAAG
* * * *
101378876 GCATTCGTGCGAGTT
65 ACAATCGAGCGAGTC
* * * *
101378891 ATTAAATCCGGGCTAATTCCCGAAGGCAATTGTGCGAATCACTATAACCGGGCTATGTCCCGAAG
1 ACTAAATCCGGGCTAATTCCCGAAGGCAATTGTGCGAATCACCA-AAACGGGCTAAGTCCCGAAG
101378956 ACAATCGAGCGAGTC
65 ACAATCGAGCGAGTC
* *
101378971 GCTATATCCGG
1 ACTAAATCCGG
101378982 TTAAATTCCG
Statistics
Matches: 73, Mismatches: 16, Indels: 3
0.79 0.17 0.03
Matches are distributed among these distances:
79 36 0.49
80 37 0.51
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.22
Consensus pattern (79 bp):
ACTAAATCCGGGCTAATTCCCGAAGGCAATTGTGCGAATCACCAAAACGGGCTAAGTCCCGAAGA
CAATCGAGCGAGTC
Found at i:101386982 original size:39 final size:40
Alignment explanation
Indices: 101386858--101387035 Score: 137
Period size: 40 Copynumber: 4.5 Consensus size: 40
101386848 TCGAATGGTG
* * * *
101386858 TCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTG-TGAGTTACTAAA
* * * *
101386899 T-CGGGTCAACTCCCGAAGGCATTTGTGCGAGTTACCAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGAGTTACTAAA
* * *
101386938 ACCGGGTTAAGTCCCGAA-GCATTCGTGTGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGAGTTACTAAA
* * * * * * *
101386977 TCCGGGCTAATTCCTGAAGGCAATTGTGCGAATCACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGAGTTACTA-AA
* *
101387018 -CCGGGCTATGTCCCGAAG
1 TCCGGGTTAAGTCCCGAAG
101387036 ACAATCGAGC
Statistics
Matches: 106, Mismatches: 28, Indels: 7
0.75 0.20 0.05
Matches are distributed among these distances:
39 39 0.37
40 64 0.60
41 3 0.03
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGTGAGTTACTAAA
Found at i:101389251 original size:43 final size:43
Alignment explanation
Indices: 101389205--101389368 Score: 183
Period size: 43 Copynumber: 3.8 Consensus size: 43
101389195 TCACATATCG
* *
101389205 ATGCCACTGTCCCACACAGGGTCTTACATG-AAGTCGATTAACG
1 ATGCCACTGTCCCACACAGGGTCTTACATGTAA-TCGATAAACA
* *
101389248 ATGCCGA-TGTCCCACACATGGTCTTACACGTAATCG-TAATACA
1 ATGCC-ACTGTCCCACACAGGGTCTTACATGTAATCGATAA-ACA
* * * *
101389291 ATGTCACTGTCCTACACAGGGTCTTACATGTAATC-ACAATGCA
1 ATGCCACTGTCCCACACAGGGTCTTACATGTAATCGATAA-ACA
*
101389334 ATTCCACTGTCCCACACAGGGTCTTACATGTAATC
1 ATGCCACTGTCCCACACAGGGTCTTACATGTAATC
101389369 ACATCTCGAT
Statistics
Matches: 103, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
42 3 0.03
43 97 0.94
44 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (43 bp):
ATGCCACTGTCCCACACAGGGTCTTACATGTAATCGATAAACA
Found at i:101389369 original size:43 final size:42
Alignment explanation
Indices: 101389185--101389371 Score: 166
Period size: 43 Copynumber: 4.4 Consensus size: 42
101389175 AGATACGGTT
* * * *
101389185 TTACGTGTTATCACATATCGATGCCACTGTCCCACACAGGGTC
1 TTACATGTAATCACA-ATCAATTCCACTGTCCCACACAGGGTC
* * * *
101389228 TTACATG-AAGTCGATTAA-CGATGCCGA-TGTCCCACACATGGTC
1 TTACATGTAA-TC-A-CAATCAATTCC-ACTGTCCCACACAGGGTC
* ** *
101389271 TTACACGTAATCGTAATACAATGT-CACTGTCCTACACAGGGTC
1 TTACATGTAATCACAAT-CAAT-TCCACTGTCCCACACAGGGTC
101389314 TTACATGTAATCACAATGCAATTCCACTGTCCCACACAGGGTC
1 TTACATGTAATCACAAT-CAATTCCACTGTCCCACACAGGGTC
101389357 TTACATGTAATCACA
1 TTACATGTAATCACA
101389372 TCTCGATAAC
Statistics
Matches: 119, Mismatches: 15, Indels: 20
0.77 0.10 0.13
Matches are distributed among these distances:
41 3 0.03
42 3 0.03
43 107 0.90
44 5 0.04
45 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (42 bp):
TTACATGTAATCACAATCAATTCCACTGTCCCACACAGGGTC
Found at i:101391366 original size:44 final size:44
Alignment explanation
Indices: 101391260--101391367 Score: 135
Period size: 44 Copynumber: 2.5 Consensus size: 44
101391250 TCCTAGACAG
* * * *
101391260 GGTCTTACATGAAAAATAGAAATCGATGCCAATGTCATAGACGT
1 GGTCTTACACGCAAAACAGAAATCGATGCCAACGTCATAGACGT
* * * *
101391304 GGTCTTACTCACAGAACAGAAATTGATGCCAACGTCATAGACGT
1 GGTCTTACACGCAAAACAGAAATCGATGCCAACGTCATAGACGT
*
101391348 GGTCTTACAGGCAAAACAGA
1 GGTCTTACACGCAAAACAGA
101391368 TAACGGATAT
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.22
Consensus pattern (44 bp):
GGTCTTACACGCAAAACAGAAATCGATGCCAACGTCATAGACGT
Found at i:101397951 original size:25 final size:25
Alignment explanation
Indices: 101397917--101397967 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
101397907 GCACATTTCA
101397917 AAATATTCACCAAAATCAAAAACTG
1 AAATATTCACCAAAATCAAAAACTG
101397942 AAATATTCACCAAAATCAAAAACTG
1 AAATATTCACCAAAATCAAAAACTG
101397967 A
1 A
101397968 GGCATGGGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.57, C:0.20, G:0.04, T:0.20
Consensus pattern (25 bp):
AAATATTCACCAAAATCAAAAACTG
Found at i:101403692 original size:8 final size:8
Alignment explanation
Indices: 101403679--101403722 Score: 61
Period size: 8 Copynumber: 5.4 Consensus size: 8
101403669 TTTTAGTTCT
*
101403679 TTTATATG
1 TTTATATA
101403687 TTTATATA
1 TTTATATA
101403695 TTTATATA
1 TTTATATA
*
101403703 TTATATATT
1 TT-TATATA
101403712 TTTATATA
1 TTTATATA
101403720 TTT
1 TTT
101403723 TAAAAATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
8 25 0.78
9 7 0.22
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (8 bp):
TTTATATA
Found at i:101403708 original size:15 final size:15
Alignment explanation
Indices: 101403688--101403718 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
101403678 TTTTATATGT
101403688 TTATATATTTATATA
1 TTATATATTTATATA
*
101403703 TTATATATTTTTATA
1 TTATATATTTATATA
101403718 T
1 T
101403719 ATTTTAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTATATATTTATATA
Found at i:101404566 original size:25 final size:25
Alignment explanation
Indices: 101404535--101404584 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
101404525 TATTTCAATA
* *
101404535 TTTTATATATTT-TAATTGTATATAT
1 TTTTATAAATTTAT-ATTATATATAT
101404560 TTTTATAAATTTATATTATATATAT
1 TTTTATAAATTTATATTATATATAT
101404585 AATAGTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (25 bp):
TTTTATAAATTTATATTATATATAT
Found at i:101405879 original size:31 final size:31
Alignment explanation
Indices: 101405844--101405902 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
101405834 TTAAAATTTT
*
101405844 TATATGATATTATACATTTA-ATCAAAATTCA
1 TATATAATATTA-ACATTTATATCAAAATTCA
* *
101405875 TATATAATTTTAATATTTATATCAAAAT
1 TATATAATATTAACATTTATATCAAAAT
101405903 AATAATTAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 6 0.25
31 18 0.75
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (31 bp):
TATATAATATTAACATTTATATCAAAATTCA
Found at i:101406804 original size:19 final size:19
Alignment explanation
Indices: 101406782--101406819 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
101406772 TTTTATGAGC
*
101406782 ATTTTCATTTTTATTTTAA
1 ATTTTCATTTTGATTTTAA
*
101406801 ATTTTGATTTTGATTTTAA
1 ATTTTCATTTTGATTTTAA
101406820 TTATTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (19 bp):
ATTTTCATTTTGATTTTAA
Found at i:101407486 original size:21 final size:18
Alignment explanation
Indices: 101407448--101407500 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
101407438 GGAAGAATAA
101407448 AGAAATGAAAAAAAAAAG
1 AGAAATGAAAAAAAAAAG
101407466 AGAATATGAAGAAAAACAAAG
1 AGAA-ATGAA-AAAAA-AAAG
101407487 A-AAA-GAAAAAAAAA
1 AGAAATGAAAAAAAAA
101407501 GTGTTCATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
16 2 0.06
17 5 0.16
18 7 0.22
19 6 0.19
20 7 0.22
21 5 0.16
ACGTcount: A:0.77, C:0.02, G:0.15, T:0.06
Consensus pattern (18 bp):
AGAAATGAAAAAAAAAAG
Found at i:101408697 original size:29 final size:29
Alignment explanation
Indices: 101408665--101408747 Score: 157
Period size: 29 Copynumber: 2.9 Consensus size: 29
101408655 GTGACGAGAT
*
101408665 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
101408694 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
101408723 TGGCACTAAGTGTGCATGCTGGAAA
1 TGGCACTAAGTGTGCATGCTGGAAA
101408748 AAAAATACGG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.29, C:0.14, G:0.30, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:101410565 original size:61 final size:61
Alignment explanation
Indices: 101410500--101410626 Score: 164
Period size: 61 Copynumber: 2.1 Consensus size: 61
101410490 ACGTACATAG
* ** * **
101410500 TCTATCAAATTGGTTTTAATTCTAAATAATTTAAAAAATTTAACCCTCCACATTTATGAAT
1 TCTATCAAATTGCTCCTAATTCTAAATAATTCAAAAAATTTAACCCTCCACATTTACAAAT
* * * *
101410561 TCTATCAATTTGCTCCTAATTCTTAATAATTCAATAAATTTAACCCTTCACATTTACAAAT
1 TCTATCAAATTGCTCCTAATTCTAAATAATTCAAAAAATTTAACCCTCCACATTTACAAAT
101410622 TCTAT
1 TCTAT
101410627 TAATGTCTAA
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 56 1.00
ACGTcount: A:0.37, C:0.18, G:0.03, T:0.42
Consensus pattern (61 bp):
TCTATCAAATTGCTCCTAATTCTAAATAATTCAAAAAATTTAACCCTCCACATTTACAAAT
Found at i:101411240 original size:15 final size:15
Alignment explanation
Indices: 101411213--101411251 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
101411203 CTGAGTACGA
101411213 GGTAAGTTT-GTATGT
1 GGTAA-TTTCGTATGT
101411228 GGTAATTTCGTATGT
1 GGTAATTTCGTATGT
101411243 GGTAATTTC
1 GGTAATTTC
101411252 ATTATAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 3 0.13
15 20 0.87
ACGTcount: A:0.21, C:0.05, G:0.28, T:0.46
Consensus pattern (15 bp):
GGTAATTTCGTATGT
Found at i:101423637 original size:30 final size:30
Alignment explanation
Indices: 101423579--101423643 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
101423569 TTCAGTTTAA
* * *
101423579 AATTATTTGATTGATTTTCAATTACCAAAT
1 AATTATTTCATTGATTTTCAATCACCAAAC
*
101423609 AATTATTTCATTGATTTTTC-ATCCCCAAAC
1 AATTATTTCATTGA-TTTTCAATCACCAAAC
101423639 AATTA
1 AATTA
101423644 GAATTGTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (30 bp):
AATTATTTCATTGATTTTCAATCACCAAAC
Found at i:101431542 original size:16 final size:16
Alignment explanation
Indices: 101431521--101431551 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
101431511 CATTTAAGAT
101431521 AGAAGGAAAATGAAAG
1 AGAAGGAAAATGAAAG
101431537 AGAAGGAAAATGAAA
1 AGAAGGAAAATGAAA
101431552 ACGAAAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.29, T:0.06
Consensus pattern (16 bp):
AGAAGGAAAATGAAAG
Found at i:101443075 original size:15 final size:16
Alignment explanation
Indices: 101443055--101443092 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
101443045 TAATTAATGA
101443055 TATATAAATAT-AATT
1 TATATAAATATGAATT
101443070 TATAT-AATATGAATT
1 TATATAAATATGAATT
101443085 TATGATAA
1 TAT-ATAA
101443093 TTAAATTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 5 0.25
15 12 0.60
16 2 0.10
17 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (16 bp):
TATATAAATATGAATT
Found at i:101443101 original size:29 final size:28
Alignment explanation
Indices: 101443035--101443102 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 28
101443025 TTTATTTGTT
101443035 TTAAATTATATAATTAATGATATATAAA
1 TTAAATTATATAATTAATGATATATAAA
* *
101443063 TATAATTTATATAA-T-ATGAATTTATGATAA
1 T-TAAATTATATAATTAATG-ATATAT-A-AA
101443093 TTAAATTATA
1 TTAAATTATA
101443103 ATGATATTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
27 3 0.09
28 7 0.21
29 20 0.61
30 3 0.09
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (28 bp):
TTAAATTATATAATTAATGATATATAAA
Found at i:101443561 original size:9 final size:9
Alignment explanation
Indices: 101443547--101443592 Score: 58
Period size: 9 Copynumber: 5.1 Consensus size: 9
101443537 AATTATTAAT
*
101443547 ATAAAACAA
1 ATAAAATAA
101443556 ATAAAATAA
1 ATAAAATAA
101443565 AT-AAATAA
1 ATAAAATAA
101443573 ATAAAAGTAA
1 ATAAAA-TAA
*
101443583 ATAGAATAA
1 ATAAAATAA
101443592 A
1 A
101443593 ACGAAAGTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
8 8 0.24
9 17 0.52
10 8 0.24
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (9 bp):
ATAAAATAA
Found at i:101443568 original size:18 final size:19
Alignment explanation
Indices: 101443547--101443585 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
101443537 AATTATTAAT
101443547 ATAAAACAAATAAAA-TAA
1 ATAAAACAAATAAAAGTAA
*
101443565 AT-AAATAAATAAAAGTAA
1 ATAAAACAAATAAAAGTAA
101443583 ATA
1 ATA
101443586 GAATAAAACG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (19 bp):
ATAAAACAAATAAAAGTAA
Found at i:101444634 original size:27 final size:27
Alignment explanation
Indices: 101444596--101444695 Score: 110
Period size: 27 Copynumber: 3.6 Consensus size: 27
101444586 TTTAATGCCT
101444596 TATTGGTGTGTTTGGGAGGATATAATA
1 TATTGGTGTGTTTGGGAGGATATAATA
* *
101444623 TATTGGTGTGTTTGGGAGGCTATATTA
1 TATTGGTGTGTTTGGGAGGATATAATA
* ** * *
101444650 TACTGGTGTGTTACGGAGGATTTAAAA
1 TATTGGTGTGTTTGGGAGGATATAATA
101444677 TATTCCAGGTGTGTTTGGG
1 TATT---GGTGTGTTTGGG
101444696 CTAGATATTC
Statistics
Matches: 58, Mismatches: 12, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
27 48 0.83
30 10 0.17
ACGTcount: A:0.22, C:0.05, G:0.33, T:0.40
Consensus pattern (27 bp):
TATTGGTGTGTTTGGGAGGATATAATA
Found at i:101445649 original size:19 final size:19
Alignment explanation
Indices: 101445625--101445662 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
101445615 ATACCAATGG
101445625 CTAACTCTACATTCATTTC
1 CTAACTCTACATTCATTTC
101445644 CTAACTCTACATTCATTTC
1 CTAACTCTACATTCATTTC
101445663 ACAGAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.32, G:0.00, T:0.42
Consensus pattern (19 bp):
CTAACTCTACATTCATTTC
Found at i:101452531 original size:56 final size:56
Alignment explanation
Indices: 101452464--101452575 Score: 172
Period size: 56 Copynumber: 2.0 Consensus size: 56
101452454 TACAAATTGC
* * *
101452464 TTAACATTTGGTATACATGGCTGTTGGTTAGAAAAGATAACAATT-GATATACAAAT
1 TTAACAGTTGGTATACATGGCTGCTAGTTAGAAAAGATAACAATTGGATA-ACAAAT
*
101452520 TTAACAGTTGGTATACATGGCTGCTAGTTAGAAAAGATAACAGTTGGATAACAAAT
1 TTAACAGTTGGTATACATGGCTGCTAGTTAGAAAAGATAACAATTGGATAACAAAT
101452576 AGCATGATAA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
56 47 0.92
57 4 0.08
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (56 bp):
TTAACAGTTGGTATACATGGCTGCTAGTTAGAAAAGATAACAATTGGATAACAAAT
Found at i:101453802 original size:83 final size:84
Alignment explanation
Indices: 101453714--101453891 Score: 270
Period size: 83 Copynumber: 2.1 Consensus size: 84
101453704 TAGAAATAAC
*
101453714 TCATTGCATGCATATTAAAAAATAGGCAAC-AC-ACCAACAATCATTGCATGCATATTAAAAAAT
1 TCATTGCATGCATATTAAAAAATAGGCAACAACTACCAACAATCATTGCATACATATTAAAAAA-
101453777 AGTCAACAGCTTTCCAACAA
65 AGTCAACAGCTTTCCAACAA
* * *
101453797 TCATTGCATGCATATTAAAAAATAGTCAACAACTTTCCAATAATCATTGCATACATATTAAAAAA
1 TCATTGCATGCATATTAAAAAATAGGCAACAAC-TACCAACAATCATTGCATACATATTAAAAAA
*
101453862 AGTCAATAGCTTTCCAACAA
65 AGTCAACAGCTTTCCAACAA
*
101453882 TCACTGCATG
1 TCATTGCATG
101453892 TGATCAGCAA
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
83 29 0.34
84 2 0.02
85 28 0.33
86 27 0.31
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.27
Consensus pattern (84 bp):
TCATTGCATGCATATTAAAAAATAGGCAACAACTACCAACAATCATTGCATACATATTAAAAAAA
GTCAACAGCTTTCCAACAA
Found at i:101453808 original size:43 final size:43
Alignment explanation
Indices: 101453714--101453891 Score: 265
Period size: 43 Copynumber: 4.2 Consensus size: 43
101453704 TAGAAATAAC
* *
101453714 TCATTGCATGCATATTAAAAAATAGGCAACA-C--ACCAACAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
101453754 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
* *
101453797 TCATTGCATGCATATTAAAAAATAGTCAACAACTTTCCAATAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
* *
101453840 TCATTGCATACATATTAAAAAA-AGTCAATAGCTTTCCAACAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
*
101453882 TCACTGCATG
1 TCATTGCATG
101453892 TGATCAGCAA
Statistics
Matches: 125, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
40 30 0.24
41 1 0.01
42 25 0.20
43 69 0.55
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.27
Consensus pattern (43 bp):
TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
Found at i:101453890 original size:85 final size:83
Alignment explanation
Indices: 101453718--101453891 Score: 260
Period size: 85 Copynumber: 2.1 Consensus size: 83
101453708 AATAACTCAT
*
101453718 TGCATGCATATTAAAAAATAGGCAACACACCAACAATCATTGCATGCATATTAAAAAATAGTCAA
1 TGCATGCATATTAAAAAATAGGCAACACACCAACAATCATTGCATACATATTAAAAAATAGTCAA
*
101453783 CAGCTTTCCAACAATCAT
66 CAGCTTTCCAACAATCAC
* * *
101453801 TGCATGCATATTAAAAAATAGTCAACAACTTTCCAATAATCATTGCATACATATTAAAAAA-AGT
1 TGCATGCATATTAAAAAATAGGCAAC-AC--ACCAACAATCATTGCATACATATTAAAAAATAGT
*
101453865 CAATAGCTTTCCAACAATCAC
63 CAACAGCTTTCCAACAATCAC
101453886 TGCATG
1 TGCATG
101453892 TGATCAGCAA
Statistics
Matches: 82, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
83 25 0.30
84 2 0.02
85 28 0.34
86 27 0.33
ACGTcount: A:0.44, C:0.21, G:0.09, T:0.26
Consensus pattern (83 bp):
TGCATGCATATTAAAAAATAGGCAACACACCAACAATCATTGCATACATATTAAAAAATAGTCAA
CAGCTTTCCAACAATCAC
Found at i:101455591 original size:15 final size:15
Alignment explanation
Indices: 101455546--101455592 Score: 85
Period size: 15 Copynumber: 3.1 Consensus size: 15
101455536 ATGCATCACT
101455546 ATCACTACCAGACAC
1 ATCACTACCAGACAC
*
101455561 TTCACTACCAGACAC
1 ATCACTACCAGACAC
101455576 ATCACTACCAGACAC
1 ATCACTACCAGACAC
101455591 AT
1 AT
101455593 TTTCTTCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.38, C:0.38, G:0.06, T:0.17
Consensus pattern (15 bp):
ATCACTACCAGACAC
Found at i:101455973 original size:62 final size:63
Alignment explanation
Indices: 101455875--101456262 Score: 485
Period size: 62 Copynumber: 6.2 Consensus size: 63
101455865 TAGGAGCCTG
* * **
101455875 GATACAAACAATGACAGATATACACAATAAACATCAGTTTAATAATGTA-TAATTTAATGGCA
1 GATACAAACAATGGCAGATATACACAATAAACATCAGTTTAATAATGCATTAATACAATGGCA
* * * **
101455937 GATACAAACAATGGAAGATATACACAATAAATATCAGTTTAATAATGTA-TAATTTAATGGCA
1 GATACAAACAATGGCAGATATACACAATAAACATCAGTTTAATAATGCATTAATACAATGGCA
* **
101455999 GATACAAACAATGGCAGATATACACAATAAACATCAGTTTAATAATGTA-TAATTTAATGGCA
1 GATACAAACAATGGCAGATATACACAATAAACATCAGTTTAATAATGCATTAATACAATGGCA
* * * *
101456061 GATACAAACAATGGCAGATATACACAATAAACATCAATTTGATAATGACATTCATACAATGACA
1 GATACAAACAATGGCAGATATACACAATAAACATCAGTTTAATAATG-CATTAATACAATGGCA
* * * * * *
101456125 GATACAAGCAATGGCAGATATACACAATAAAGATCAATTTGATAATGGCATTCATACAATGACA
1 GATACAAACAATGGCAGATATACACAATAAACATCAGTTTAATAAT-GCATTAATACAATGGCA
* * * * *
101456189 GATACAAACAATAGCAGATACACACAATAAAGATCAGTTTGATAATGGCATTCATACAATGGCA
1 GATACAAACAATGGCAGATATACACAATAAACATCAGTTTAATAAT-GCATTAATACAATGGCA
101456253 GATACAAACA
1 GATACAAACA
101456263 CATCAAAATC
Statistics
Matches: 304, Mismatches: 19, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
62 164 0.54
63 1 0.00
64 138 0.45
65 1 0.00
ACGTcount: A:0.47, C:0.14, G:0.13, T:0.25
Consensus pattern (63 bp):
GATACAAACAATGGCAGATATACACAATAAACATCAGTTTAATAATGCATTAATACAATGGCA
Found at i:101456027 original size:124 final size:125
Alignment explanation
Indices: 101455875--101456262 Score: 535
Period size: 124 Copynumber: 3.1 Consensus size: 125
101455865 TAGGAGCCTG
*
101455875 GATACAAACAATGACAGATATACACAATAAACATCAGTTTAATAATGTATAATTTAATGGCAGAT
1 GATACAAACAATGGCAGATATACACAATAAACATCAGTTTAATAATGTATAATTTAATGGCAGAT
* * * * * **
101455940 ACAAACAATGGAAGATATACACAATAAATATCAGTTTAATAATGTA-TAATTTAATGGCA
66 ACAAACAATGGCAGATATACACAATAAACATCAGTTTGATAATGCATTCATACAATGGCA
101455999 GATACAAACAATGGCAGATATACACAATAAACATCAGTTTAATAATGTATAATTTAATGGCAGAT
1 GATACAAACAATGGCAGATATACACAATAAACATCAGTTTAATAATGTATAATTTAATGGCAGAT
* *
101456064 ACAAACAATGGCAGATATACACAATAAACATCAATTTGATAATGACATTCATACAATGACA
66 ACAAACAATGGCAGATATACACAATAAACATCAGTTTGATAATG-CATTCATACAATGGCA
* * * * * * ** *
101456125 GATACAAGCAATGGCAGATATACACAATAAAGATCAATTTGATAATGGCATTCATACAATGACAG
1 GATACAAACAATGGCAGATATACACAATAAACATCAGTTTAATAAT-GTA-TAATTTAATGGCAG
* * *
101456190 ATACAAACAATAGCAGATACACACAATAAAGATCAGTTTGATAATGGCATTCATACAATGGCA
64 ATACAAACAATGGCAGATATACACAATAAACATCAGTTTGATAAT-GCATTCATACAATGGCA
101456253 GATACAAACA
1 GATACAAACA
101456263 CATCAAAATC
Statistics
Matches: 234, Mismatches: 25, Indels: 6
0.88 0.09 0.02
Matches are distributed among these distances:
124 104 0.44
125 1 0.00
126 51 0.22
127 2 0.01
128 75 0.32
129 1 0.00
ACGTcount: A:0.47, C:0.14, G:0.13, T:0.25
Consensus pattern (125 bp):
GATACAAACAATGGCAGATATACACAATAAACATCAGTTTAATAATGTATAATTTAATGGCAGAT
ACAAACAATGGCAGATATACACAATAAACATCAGTTTGATAATGCATTCATACAATGGCA
Found at i:101456172 original size:34 final size:34
Alignment explanation
Indices: 101456070--101456174 Score: 89
Period size: 32 Copynumber: 3.2 Consensus size: 34
101456060 AGATACAAAC
*
101456070 AATGGCAGATATACACAATAAACATCAATTTGAT
1 AATGGCAGATATACACAATAAAGATCAATTTGAT
* * * *
101456104 AAT-G-ACAT-TCATACAATGACAGATACAA---G-C
1 AATGGCAGATAT-ACACAAT-AAAGAT-CAATTTGAT
101456134 AATGGCAGATATACACAATAAAGATCAATTTGAT
1 AATGGCAGATATACACAATAAAGATCAATTTGAT
101456168 AATGGCA
1 AATGGCA
101456175 TTCATACAAT
Statistics
Matches: 52, Mismatches: 9, Indels: 20
0.64 0.11 0.25
Matches are distributed among these distances:
30 6 0.12
31 8 0.15
32 18 0.35
33 7 0.13
34 13 0.25
ACGTcount: A:0.47, C:0.15, G:0.14, T:0.24
Consensus pattern (34 bp):
AATGGCAGATATACACAATAAAGATCAATTTGAT
Found at i:101456182 original size:34 final size:34
Alignment explanation
Indices: 101456080--101456182 Score: 85
Period size: 34 Copynumber: 3.1 Consensus size: 34
101456070 AATGGCAGAT
* *
101456080 ATACACAATAAACATCAATTTGATAATGACATTC
1 ATACACAATAAAGATCAATTTGATAATGGCATTC
* * *
101456114 AT--ACAATGACAGATACAA---G-CAATGGCAGAT-
1 ATACACAAT-AAAGAT-CAATTTGATAATGGCA-TTC
101456144 ATACACAATAAAGATCAATTTGATAATGGCATTC
1 ATACACAATAAAGATCAATTTGATAATGGCATTC
101456178 ATACA
1 ATACA
101456183 ATGACAGATA
Statistics
Matches: 51, Mismatches: 8, Indels: 20
0.65 0.10 0.25
Matches are distributed among these distances:
30 11 0.22
31 7 0.14
32 10 0.20
33 6 0.12
34 17 0.33
ACGTcount: A:0.47, C:0.17, G:0.12, T:0.25
Consensus pattern (34 bp):
ATACACAATAAAGATCAATTTGATAATGGCATTC
Found at i:101456206 original size:16 final size:16
Alignment explanation
Indices: 101456187--101456217 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
101456177 CATACAATGA
101456187 CAGATACAAACAATAG
1 CAGATACAAACAATAG
*
101456203 CAGATACACACAATA
1 CAGATACAAACAATA
101456218 AAGATCAGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.23, G:0.10, T:0.13
Consensus pattern (16 bp):
CAGATACAAACAATAG
Found at i:101456428 original size:18 final size:17
Alignment explanation
Indices: 101456401--101456434 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
101456391 AAATAACCCT
*
101456401 AAATCGAAATCTAAATTA
1 AAATCAAAATC-AAATTA
101456419 AAATCAAAATCAAATT
1 AAATCAAAATCAAATT
101456435 CTAATCCTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.59, C:0.12, G:0.03, T:0.26
Consensus pattern (17 bp):
AAATCAAAATCAAATTA
Found at i:101457114 original size:31 final size:29
Alignment explanation
Indices: 101457075--101457147 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 29
101457065 GGTAACTGTT
*
101457075 AGTTAGTGACTGTTTTGTCACTTTTTTATA
1 AGTTAGTGACTGTTTTGTCACTTTTTGA-A
** *
101457105 ACGTTAGTGACCATTTTGTTACTTTTTGAA
1 A-GTTAGTGACTGTTTTGTCACTTTTTGAA
101457135 AGTTAAGTGACTG
1 AGTT-AGTGACTG
101457148 AAATGAAACC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
29 3 0.09
30 9 0.26
31 23 0.66
ACGTcount: A:0.23, C:0.11, G:0.19, T:0.47
Consensus pattern (29 bp):
AGTTAGTGACTGTTTTGTCACTTTTTGAA
Found at i:101475476 original size:39 final size:37
Alignment explanation
Indices: 101475431--101475527 Score: 103
Period size: 39 Copynumber: 2.6 Consensus size: 37
101475421 TAATTATGTA
101475431 AATATATATAATTTAATTATTAATTATTATTTTTATTT
1 AATATATATAATTTAATTATTAATTATTA-TTTTATTT
* * *
101475469 AAGTATATAGATATTT-ATTATTTATTATTATTCTA-TT
1 AA-TATATATA-ATTTAATTATTAATTATTATTTTATTT
101475506 AA-AT-TATAATTTATATTATTAA
1 AATATATATAATTTA-ATTATTAA
101475528 ATTTTGATTA
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
33 4 0.08
34 3 0.06
35 9 0.18
37 4 0.08
38 6 0.12
39 20 0.40
40 4 0.08
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (37 bp):
AATATATATAATTTAATTATTAATTATTATTTTATTT
Found at i:101475525 original size:20 final size:20
Alignment explanation
Indices: 101475492--101475548 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
101475482 TTTATTATTT
101475492 ATTATTATTCTATTAAATTATA
1 ATTATTA-T-TATTAAATTATA
* *
101475514 ATT-TATATTATTAAATTTTG
1 ATTAT-TATTATTAAATTATA
101475534 ATTATTATTATTAAA
1 ATTATTATTATTAAA
101475549 AATAAATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
20 23 0.74
21 3 0.10
22 5 0.16
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
ATTATTATTATTAAATTATA
Found at i:101475805 original size:3 final size:3
Alignment explanation
Indices: 101475792--101475822 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
101475782 AATAAGATAT
*
101475792 TTA TAA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
101475823 AAAGTTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:101475847 original size:13 final size:14
Alignment explanation
Indices: 101475829--101475866 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
101475819 TTATAAAGTT
101475829 AATAAAATAAAAG-
1 AATAAAATAAAAGA
* *
101475842 AATAAAAGAAATGA
1 AATAAAATAAAAGA
101475856 AATAAAATAAA
1 AATAAAATAAA
101475867 GTAAAGAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (14 bp):
AATAAAATAAAAGA
Found at i:101477002 original size:44 final size:45
Alignment explanation
Indices: 101476931--101477031 Score: 116
Period size: 44 Copynumber: 2.3 Consensus size: 45
101476921 ACTGTTACTA
* * ** * *
101476931 TTACCGTTATTGTTCCCTATTCGACACTTTGTGT-TTCGAA-ACTG
1 TTACCGTTACTGTTACAGATTCAACACTTTGTGTGTT-GAATAATG
101476975 TTACCGTTACTGTTACAGATTCAACACTTTGTGTGTTGAATAATG
1 TTACCGTTACTGTTACAGATTCAACACTTTGTGTGTTGAATAATG
*
101477020 TTACTGTTACTG
1 TTACCGTTACTG
101477032 CTACTGCTAC
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
44 32 0.67
45 16 0.33
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.43
Consensus pattern (45 bp):
TTACCGTTACTGTTACAGATTCAACACTTTGTGTGTTGAATAATG
Found at i:101481226 original size:229 final size:229
Alignment explanation
Indices: 101480825--101481284 Score: 848
Period size: 229 Copynumber: 2.0 Consensus size: 229
101480815 TCGGAACCGA
*
101480825 GTTACAGATCATTACTAGAATTTACAGAACAATTACAGTTAATTCATGTCATTTATTATTCATAT
1 GTTACAGAGCATTACTAGAATTTACAGAACAATTACAGTTAATTCATGTCATTTATTATTCATAT
* *
101480890 TCGAAACCAATCATATTTAATCGTATTGTCCCTTATATGGACCCTCGAGGCCCCATTTAAGTACT
66 TCGAAACCAATCATATTTAATCATATTGTCCCTTATATGGACCCTCAAGGCCCCATTTAAGTACT
* * *
101480955 AGAAACAGGTCGGGACTATATCGGAAACTCGGAGAATTTTTTGTGAAATTTCAAAATTTTTCTTA
131 AGAAACAGGTCGGGACTATATCAGAAACTCAGAGAATTTTTTGAGAAATTTCAAAATTTTTCTTA
101481020 TGTACAGGGATCACACGCCCGTGTCTTAAGCCGT
196 TGTACAGGGATCACACGCCCGTGTCTTAAGCCGT
101481054 GTTACAGAGCATTACTAGAATTTACAGAACAATTACAGTTAATTCATGTCATTTATTATTCATAT
1 GTTACAGAGCATTACTAGAATTTACAGAACAATTACAGTTAATTCATGTCATTTATTATTCATAT
101481119 TCGAAACCAATCATATTTAATCATATTGTCCCTTATATGGACCCTCAAGGCCCCATTTAAGTACT
66 TCGAAACCAATCATATTTAATCATATTGTCCCTTATATGGACCCTCAAGGCCCCATTTAAGTACT
*
101481184 AGAAATAGGTCGGGACTATATCAGAAACTCAGAGAATTTTTTGAGAAATTTCAAAATTTTTCTTA
131 AGAAACAGGTCGGGACTATATCAGAAACTCAGAGAATTTTTTGAGAAATTTCAAAATTTTTCTTA
*
101481249 TGTACAGGGGTCACACGCCCGTGTCTTAAGCCGT
196 TGTACAGGGATCACACGCCCGTGTCTTAAGCCGT
101481283 GT
1 GT
101481285 GCGCATTCGA
Statistics
Matches: 223, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
229 223 1.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (229 bp):
GTTACAGAGCATTACTAGAATTTACAGAACAATTACAGTTAATTCATGTCATTTATTATTCATAT
TCGAAACCAATCATATTTAATCATATTGTCCCTTATATGGACCCTCAAGGCCCCATTTAAGTACT
AGAAACAGGTCGGGACTATATCAGAAACTCAGAGAATTTTTTGAGAAATTTCAAAATTTTTCTTA
TGTACAGGGATCACACGCCCGTGTCTTAAGCCGT
Found at i:101487728 original size:16 final size:16
Alignment explanation
Indices: 101487707--101487739 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
101487697 AAATAACAAT
101487707 AAAGCAATCTTGCACA
1 AAAGCAATCTTGCACA
101487723 AAAGCAATCTTGCACA
1 AAAGCAATCTTGCACA
101487739 A
1 A
101487740 TCAATGACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.24, G:0.12, T:0.18
Consensus pattern (16 bp):
AAAGCAATCTTGCACA
Found at i:101488468 original size:41 final size:41
Alignment explanation
Indices: 101488423--101488505 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
101488413 AAGGCAAGAG
101488423 ATGGTTATTATGCCAACCAAAAAAGAACAAGGACAAGCCTT
1 ATGGTTATTATGCCAACCAAAAAAGAACAAGGACAAGCCTT
101488464 ATGGTTATTATGCCAACCAAAAAAGAACAAGGACAAGCCTT
1 ATGGTTATTATGCCAACCAAAAAAGAACAAGGACAAGCCTT
101488505 A
1 A
101488506 CTCTCGATGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.45, C:0.19, G:0.17, T:0.19
Consensus pattern (41 bp):
ATGGTTATTATGCCAACCAAAAAAGAACAAGGACAAGCCTT
Found at i:101493374 original size:22 final size:20
Alignment explanation
Indices: 101493346--101493387 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
101493336 TATTTTTTAA
101493346 AATATTTATATTATATTATTTT
1 AATATTTA-ATT-TATTATTTT
*
101493368 AATATTTAATTTTTTATTTT
1 AATATTTAATTTATTATTTT
101493388 TTTATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 3 0.16
22 8 0.42
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
AATATTTAATTTATTATTTT
Found at i:101493390 original size:23 final size:22
Alignment explanation
Indices: 101493335--101493391 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
101493325 CTCGTCCATA
*
101493335 TTATTTTTTAAAATATTTATATT
1 TTATTTTTT-TAATATTTATATT
* * *
101493358 ATATTATTTTAATATTTAATTTT
1 TTATTTTTTTAATATTT-ATATT
101493381 TTATTTTTTTA
1 TTATTTTTTTA
101493392 TTGAAAATTT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
22 7 0.26
23 20 0.74
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTATTTTTTTAATATTTATATT
Found at i:101493761 original size:25 final size:23
Alignment explanation
Indices: 101493733--101493791 Score: 82
Period size: 25 Copynumber: 2.5 Consensus size: 23
101493723 ATATTTTTTA
101493733 TTTTATTTAACATTAATATAATTAT
1 TTTTATTTAACATTAATATAA-T-T
* *
101493758 TTTTATTTAATATTATTATAATT
1 TTTTATTTAACATTAATATAATT
101493781 TTTTATTTAAC
1 TTTTATTTAAC
101493792 TAGATTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 11 0.35
24 1 0.03
25 19 0.61
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTTATTTAACATTAATATAATT
Found at i:101497667 original size:13 final size:13
Alignment explanation
Indices: 101497649--101497673 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
101497639 ACATTTGTGA
101497649 AAAATAAAAAAAT
1 AAAATAAAAAAAT
101497662 AAAATAAAAAAA
1 AAAATAAAAAAA
101497674 ACACACAGAT
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAATAAAAAAAT
Found at i:101497822 original size:34 final size:34
Alignment explanation
Indices: 101497778--101497845 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
101497768 AGGAATAGAC
*
101497778 TATGTCTATTTATAGGCTTGTAAATCCATATTCT
1 TATGTCTATTTATAGGCTTGTAAAGCCATATTCT
*
101497812 TATGTTTATTTATAGGCTTGTAAAGCCATATTCT
1 TATGTCTATTTATAGGCTTGTAAAGCCATATTCT
101497846 AGTAAGACTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.47
Consensus pattern (34 bp):
TATGTCTATTTATAGGCTTGTAAAGCCATATTCT
Found at i:101500228 original size:2 final size:2
Alignment explanation
Indices: 101500223--101500263 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
101500213 TTTCAGGAGT
*
101500223 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
101500264 TACATAAACC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:101503068 original size:26 final size:27
Alignment explanation
Indices: 101503003--101503061 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
101502993 TGTTTTTTTA
* * *
101503003 ATTTTTTAAAAATAGAAAATGGAAACT
1 ATTTTTTAAAAATAAAAAATAGAAAAT
*
101503030 ATTTTTTGAAAATAAAAAATAGAAAAT
1 ATTTTTTAAAAATAAAAAATAGAAAAT
101503057 ATTTT
1 ATTTT
101503062 CAAAAATCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (27 bp):
ATTTTTTAAAAATAAAAAATAGAAAAT
Found at i:101503470 original size:24 final size:24
Alignment explanation
Indices: 101503424--101503471 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
101503414 TGTCAATGAA
* *
101503424 TTTATTAGATAATGATACGTCATT
1 TTTATAAGATAATGATACATCATT
*
101503448 TTTATAAGATAATGATATATCATT
1 TTTATAAGATAATGATACATCATT
101503472 GACAAAGATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (24 bp):
TTTATAAGATAATGATACATCATT
Found at i:101506909 original size:31 final size:31
Alignment explanation
Indices: 101506864--101506932 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
101506854 TTTAAATTAG
*
101506864 TTGATTCAAGTTAAATAAGTCA-TTTGAGTTA
1 TTGAGTCAAGTTAAATAAGT-ATTTTGAGTTA
*
101506895 TTGAGTCAATTTAAATAAGTATTTTGAGTTA
1 TTGAGTCAAGTTAAATAAGTATTTTGAGTTA
101506926 TTCGAGT
1 TT-GAGT
101506933 TGAATTTGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 1 0.03
31 29 0.85
32 4 0.12
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.43
Consensus pattern (31 bp):
TTGAGTCAAGTTAAATAAGTATTTTGAGTTA
Found at i:101507391 original size:15 final size:15
Alignment explanation
Indices: 101507367--101507396 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
101507357 GCCAACAAGG
101507367 TTTTAATTTAAATTT
1 TTTTAATTTAAATTT
*
101507382 TTTTATTTTAAATTT
1 TTTTAATTTAAATTT
101507397 AAACCAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTAATTTAAATTT
Found at i:101516090 original size:47 final size:48
Alignment explanation
Indices: 101515975--101516226 Score: 208
Period size: 47 Copynumber: 5.2 Consensus size: 48
101515965 TGCACATAGT
* * ** * *
101515975 CACATATCA-CACATCGAAGCCATAGCCCAGCCATGGTCTTATACGG-AT
1 CACATATCATCAC--CGATGCCATATCCCAGATATGGTATTATACGGAAG
* * * * * **
101516023 CACATATCA-CTCTGATGCCATATCCCAAATATGGTCTTACATAGAAG
1 CACATATCATCACCGATGCCATATCCCAGATATGGTATTATACGGAAG
101516070 CACATAT-ATCACCGATGCCATATCCCAGATATGGTATTATACGGAAG
1 CACATATCATCACCGATGCCATATCCCAGATATGGTATTATACGGAAG
* * * *
101516117 CACATGATCTCATCATACCGGTGCCATAGCCCAGCTATGGTATTATACGGGAG
1 CACAT-A--TCATC--ACCGATGCCATATCCCAGATATGGTATTATACGGAAG
* * * *
101516170 AACATATCAT-ACCGATGCCATATCCCAGATATGGTCTTATACGAAAAT
1 CACATATCATCACCGATGCCATATCCCAGATATGGTATTATACG-GAAG
101516218 CACATATCA
1 CACATATCA
101516227 CATGTTGCCA
Statistics
Matches: 164, Mismatches: 31, Indels: 18
0.77 0.15 0.08
Matches are distributed among these distances:
46 24 0.15
47 73 0.45
48 21 0.13
50 5 0.03
51 3 0.02
52 1 0.01
53 37 0.23
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (48 bp):
CACATATCATCACCGATGCCATATCCCAGATATGGTATTATACGGAAG
Found at i:101516723 original size:21 final size:21
Alignment explanation
Indices: 101516699--101516739 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
101516689 CACTTTATCT
101516699 AGACATGATAAACTACTTCAC
1 AGACATGATAAACTACTTCAC
101516720 AGACATGATAAACTACTTCA
1 AGACATGATAAACTACTTCA
101516740 TAGTTTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.22, G:0.10, T:0.24
Consensus pattern (21 bp):
AGACATGATAAACTACTTCAC
Found at i:101526166 original size:2 final size:2
Alignment explanation
Indices: 101526159--101526192 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
101526149 TTAAATTATG
*
101526159 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
101526193 AAATAAAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:101526223 original size:19 final size:20
Alignment explanation
Indices: 101526190--101526229 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
101526180 ATATATATAT
101526190 ATAAAATAAAGAAAAT-AAA
1 ATAAAATAAAGAAAATGAAA
101526209 ATAAAATAACA-AAAATGAAA
1 ATAAAATAA-AGAAAATGAAA
101526229 A
1 A
101526230 ATGAACAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.15
Consensus pattern (20 bp):
ATAAAATAAAGAAAATGAAA
Found at i:101526479 original size:30 final size:30
Alignment explanation
Indices: 101526445--101526529 Score: 152
Period size: 30 Copynumber: 2.8 Consensus size: 30
101526435 TTTGATGGTA
*
101526445 TAGGTGCAAGTGGGAGACAAGGTGGTGGAG
1 TAGGTGCAAGTGGGAGGCAAGGTGGTGGAG
*
101526475 TAGGTGTAAGTGGGAGGCAAGGTGGTGGAG
1 TAGGTGCAAGTGGGAGGCAAGGTGGTGGAG
101526505 TAGGTGCAAGTGGGAGGCAAGGTGG
1 TAGGTGCAAGTGGGAGGCAAGGTGG
101526530 CTAAGGTTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.25, C:0.06, G:0.52, T:0.18
Consensus pattern (30 bp):
TAGGTGCAAGTGGGAGGCAAGGTGGTGGAG
Found at i:101527936 original size:12 final size:12
Alignment explanation
Indices: 101527903--101527959 Score: 50
Period size: 12 Copynumber: 5.0 Consensus size: 12
101527893 GTCAATTTGT
*
101527903 GTATTATTTTAA
1 GTATTATTTTTA
*
101527915 GAATTA-TTTTA
1 GTATTATTTTTA
101527926 GTATTATTTTTA
1 GTATTATTTTTA
101527938 -T-TTA-TTTTA
1 GTATTATTTTTA
*
101527947 ATATTTATTTTTA
1 GTA-TTATTTTTA
101527960 TGTTTTTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
9 5 0.14
10 4 0.11
11 10 0.27
12 13 0.35
13 5 0.14
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (12 bp):
GTATTATTTTTA
Found at i:101527944 original size:21 final size:20
Alignment explanation
Indices: 101527918--101527984 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
101527908 ATTTTAAGAA
101527918 TTATTTTAGTATTATTTTTAT
1 TTATTTTA-TATTATTTTTAT
101527939 TTATTTTAATATTTATTTTTAT
1 TTATTTT-ATA-TTATTTTTAT
* *
101527961 GT-TTTTA-AATATATTTTAT
1 TTATTTTATATTAT-TTTTAT
101527980 TTATT
1 TTATT
101527985 ATATTTTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
18 3 0.08
19 8 0.21
20 3 0.08
21 13 0.33
22 12 0.31
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (20 bp):
TTATTTTATATTATTTTTAT
Found at i:101527986 original size:26 final size:25
Alignment explanation
Indices: 101527950--101528007 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 25
101527940 TATTTTAATA
*
101527950 TTTATTT-TTATGTTTTTAAATATAT
1 TTTATTTATTATATTTTTAAAT-TAT
*
101527975 TTTATTTATTATATTTTTAAATTTT
1 TTTATTTATTATATTTTTAAATTAT
101528000 TTTATTTA
1 TTTATTTA
101528008 ATAAAATAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 17 0.57
26 13 0.43
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.71
Consensus pattern (25 bp):
TTTATTTATTATATTTTTAAATTAT
Found at i:101532360 original size:15 final size:18
Alignment explanation
Indices: 101532325--101532368 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
101532315 TCTCCAGCCT
101532325 ATACCAAAAACAACACTA
1 ATACCAAAAACAACACTA
*
101532343 ATACCAAAAACAACAATA
1 ATACCAAAAACAACACTA
101532361 ATACCAAA
1 ATACCAAA
101532369 GGTATGTATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.64, C:0.25, G:0.00, T:0.11
Consensus pattern (18 bp):
ATACCAAAAACAACACTA
Found at i:101532695 original size:14 final size:15
Alignment explanation
Indices: 101532678--101532706 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
101532668 ACACGTAAAT
101532678 ATATTAAATT-AATA
1 ATATTAAATTCAATA
101532692 ATATTAAATTCAATA
1 ATATTAAATTCAATA
101532707 TAACTATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
ATATTAAATTCAATA
Found at i:101536346 original size:26 final size:26
Alignment explanation
Indices: 101536317--101536370 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
101536307 TGACTCCAAA
**
101536317 TTTAAAATTTAAAATTTGTTTCAATC
1 TTTAAAATTTAAAATTTGGCTCAATC
* *
101536343 TTTAAAGTTTAAATTTTGGCTCAATC
1 TTTAAAATTTAAAATTTGGCTCAATC
101536369 TT
1 TT
101536371 GGTGGAGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.50
Consensus pattern (26 bp):
TTTAAAATTTAAAATTTGGCTCAATC
Found at i:101546132 original size:16 final size:16
Alignment explanation
Indices: 101546098--101546136 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
101546088 GATCTCCACT
***
101546098 GAGCTTCTAATCTGCC
1 GAGCTTCTAATCCAAC
101546114 GAGCTTCTAATCCAAC
1 GAGCTTCTAATCCAAC
101546130 GAGCTTC
1 GAGCTTC
101546137 CGATATACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.23, C:0.31, G:0.18, T:0.28
Consensus pattern (16 bp):
GAGCTTCTAATCCAAC
Found at i:101546804 original size:33 final size:33
Alignment explanation
Indices: 101546762--101546898 Score: 106
Period size: 33 Copynumber: 4.3 Consensus size: 33
101546752 GAGGTGTACA
* * *
101546762 TTTCTTTTTCAAATGGTACACAGAAAGTATACC
1 TTTCCTTTTCAAATGATACACACAAAGTATACC
*
101546795 TTTCCTTTTCAAATGATATACACAAAGTATA--
1 TTTCCTTTTCAAATGATACACACAAAGTATACC
* * **
101546826 ---CCTTTTCAAGTG-TACACACAAAGTGTATA
1 TTTCCTTTTCAAATGATACACACAAAGTATACC
** ** * *
101546855 TAGCCTTTTCATGTGGTATACACAAAGTATACC
1 TTTCCTTTTCAAATGATACACACAAAGTATACC
101546888 TTTCCTTTTCA
1 TTTCCTTTTCA
101546899 CATTCGATAG
Statistics
Matches: 84, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
27 13 0.15
28 11 0.13
32 11 0.13
33 49 0.58
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (33 bp):
TTTCCTTTTCAAATGATACACACAAAGTATACC
Found at i:101546849 original size:27 final size:27
Alignment explanation
Indices: 101546798--101546890 Score: 96
Period size: 28 Copynumber: 3.2 Consensus size: 27
101546788 GTATACCTTT
*
101546798 CCTTTTCAAATGATATACACAAAGTATA
1 CCTTTTCAAGTG-TATACACAAAGTATA
*
101546826 CCTTTTCAAGTGTACACACAAAGTGTATATA
1 CCTTTTCAAGTGTATACACAAA--G--TATA
*
101546857 GCCTTTTCATGTGGTATACACAAAGTATA
1 -CCTTTTCAAGT-GTATACACAAAGTATA
101546886 CCTTT
1 CCTTT
101546891 CCTTTTCACA
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
27 9 0.16
28 16 0.29
29 5 0.09
31 5 0.09
32 10 0.18
33 10 0.18
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.34
Consensus pattern (27 bp):
CCTTTTCAAGTGTATACACAAAGTATA
Found at i:101546849 original size:60 final size:61
Alignment explanation
Indices: 101546767--101546890 Score: 151
Period size: 60 Copynumber: 2.0 Consensus size: 61
101546757 GTACATTTCT
* * **
101546767 TTTTCAAATGGTACACAGAAAGTATACCTTTCCTTTTCAAATGATATACACAAAGTATACC
1 TTTTCAAATGGTACACACAAAGTATACATAGCCTTTTCAAATGATATACACAAAGTATACC
* * * ** *
101546828 TTTTCAAGT-GTACACACAAAGTGTATATAGCCTTTTCATGTGGTATACACAAAGTATACC
1 TTTTCAAATGGTACACACAAAGTATACATAGCCTTTTCAAATGATATACACAAAGTATACC
101546888 TTT
1 TTT
101546891 CCTTTTCACA
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
60 45 0.85
61 8 0.15
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (61 bp):
TTTTCAAATGGTACACACAAAGTATACATAGCCTTTTCAAATGATATACACAAAGTATACC
Found at i:101546852 original size:93 final size:95
Alignment explanation
Indices: 101546755--101546965 Score: 234
Period size: 93 Copynumber: 2.2 Consensus size: 95
101546745 TACACTCGAG
* *
101546755 GTGTACATTTCTTTTTCAAATGGTACACAGAAAGTATACCTTTCCTTTTCA-AAT-GATATACAC
1 GTGTACATTTCCTTTTCAAATGGTACACACAAAGTATACCTTTCCTTTTCACAATCGATA-AC-C
101546818 AAAG-TATACCTTTTCA-A-GTGTACACACAAA
64 AAAGCTATACCTTTTCACATG-GTACACACAAA
* ** ** * * * *
101546848 GTGTATATAGCCTTTTCATGTGGTATACACAAAGTATACCTTTCCTTTTCACATTCGATAGCCGA
1 GTGTACATTTCCTTTTCAAATGGTACACACAAAGTATACCTTTCCTTTTCACAATCGATAACCAA
* *
101546913 AGCTATCCCTTTTCACATGGTACACACAAG
66 AGCTATACCTTTTCACATGGTACACACAAA
101546943 GTGTACATTTCCTTTTCATAATG
1 GTGTACATTTCCTTTTCA-AATG
101546966 AGATCAAAAG
Statistics
Matches: 94, Mismatches: 18, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
93 47 0.50
94 14 0.15
95 30 0.32
96 3 0.03
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (95 bp):
GTGTACATTTCCTTTTCAAATGGTACACACAAAGTATACCTTTCCTTTTCACAATCGATAACCAA
AGCTATACCTTTTCACATGGTACACACAAA
Found at i:101547760 original size:21 final size:22
Alignment explanation
Indices: 101547714--101547756 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
101547704 TGTAAAAGTG
*
101547714 ATTTCTCTATCAATAACCTTTC
1 ATTTCTCTATCAATAAACTTTC
101547736 ATTT-TCTATC-ATAAACTTTC
1 ATTTCTCTATCAATAAACTTTC
101547756 A
1 A
101547757 ATTTACAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 6 0.30
22 4 0.20
ACGTcount: A:0.30, C:0.23, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTTCTCTATCAATAAACTTTC
Found at i:101557663 original size:13 final size:13
Alignment explanation
Indices: 101557645--101557670 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
101557635 GAAGTAATCG
101557645 CACACGGGCGTGT
1 CACACGGGCGTGT
101557658 CACACGGGCGTGT
1 CACACGGGCGTGT
101557671 TCCTGTCGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.38, T:0.15
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:101559173 original size:66 final size:66
Alignment explanation
Indices: 101559067--101559200 Score: 268
Period size: 66 Copynumber: 2.0 Consensus size: 66
101559057 AAAATTATAC
101559067 AAAAATCACTTTACAAAATAGTCCTATTTCAACATCAAGCTTCAAACTAAACCATTATAAACTAA
1 AAAAATCACTTTACAAAATAGTCCTATTTCAACATCAAGCTTCAAACTAAACCATTATAAACTAA
101559132 A
66 A
101559133 AAAAATCACTTTACAAAATAGTCCTATTTCAACATCAAGCTTCAAACTAAACCATTATAAACTAA
1 AAAAATCACTTTACAAAATAGTCCTATTTCAACATCAAGCTTCAAACTAAACCATTATAAACTAA
101559198 A
66 A
101559199 AA
1 AA
101559201 GCTTCAAGAG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.49, C:0.21, G:0.03, T:0.27
Consensus pattern (66 bp):
AAAAATCACTTTACAAAATAGTCCTATTTCAACATCAAGCTTCAAACTAAACCATTATAAACTAA
A
Found at i:101562241 original size:14 final size:13
Alignment explanation
Indices: 101562204--101562242 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
101562194 TTATTAAAAT
101562204 AATT-TTATAATTA
1 AATTATTAT-ATTA
101562217 AATTATTATATTAA
1 AATTATTATATT-A
101562231 AATTATTATATT
1 AATTATTATATT
101562243 TTTATACTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.29
14 17 0.71
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATTATTATATTA
Done.