Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 177 of 210
Found at i:52831354 original size:40 final size:36
Alignment explanation
Indices: 52831294--52831379 Score: 93
Period size: 40 Copynumber: 2.3 Consensus size: 36
52831284 AAACTAGTAT
* * *
52831294 TATTATTATGGTTAGTTATTATTTTTAGTA-AAACCC
1 TATTATTATTGTTAGTTATTATTTTGAGTATAAA-AC
52831330 TAATTATTATTGTTAGTTACTATTATTTTGAGTATAAAAC
1 T-ATTATTATTGTTAG-T--TATTATTTTGAGTATAAAAC
52831370 TATTATTATT
1 TATTATTATT
52831380 TTTATTGTGT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
36 1 0.02
37 13 0.31
38 1 0.02
39 9 0.21
40 15 0.36
41 3 0.07
ACGTcount: A:0.33, C:0.06, G:0.09, T:0.52
Consensus pattern (36 bp):
TATTATTATTGTTAGTTATTATTTTGAGTATAAAAC
Found at i:52836492 original size:159 final size:158
Alignment explanation
Indices: 52836075--52836847 Score: 669
Period size: 159 Copynumber: 4.8 Consensus size: 158
52836065 AAGTTGAAAA
* * *
52836075 AAAAAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTCGTATTTTTCTCTCGGCATTTTATT
1 AAAAAAGTTAGTAAAACACTCCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATT
*
52836140 ACTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATG-TT---
66 ACTTTAAAAAATATCATAATTTCTAATTTTATAATTTTATATTATTTCAGTGCATTATGTTTGAA
* *
52836201 ATTTCTTTATTAATTTAGTGT-ATTTTTT
131 ATTT-TTTATTAATTTAGTCTGAATTTTT
** * * *
52836229 AAATTAATTTAGTGTAAAAAAAACCCAAC-CCTTA-TTCCTGCCCTTTGCTCGTATTATTTTT-T
1 AAA--AA---AGT-T-AGTAAAA--C-ACTCCTTACTT-CGGCCATTTGTTCGTATT-TTTTTCT
* * * *
52836291 -CGAATTTTATTACTTCCAAAAAAATAT-ATTATTTTCGT-ATTTTATTATTTTATATTATTTCA
54 CCGCATTTTATTACTT--TAAAAAATATCA-TAATTTC-TAATTTTATAATTTTATATTATTTCA
* * ** *
52836353 GTACATTTTGTTTGAAATTTTTCTATTAATTTTTTCCGAATTTTT
115 GTGCATTATGTTTGAAATTTTT-TATTAATTTAGTCTGAATTTTT
* *
52836398 AAAAAAGTTAGTAAAACACTCTTTACTTCAGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATT
1 AAAAAAGTTAGTAAAACACTCCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATT
*
52836463 ACTTTAAAAAATATCATAATTTCTAATTTTATAATTTTATATTATTTCAGTGCATTGTGTTTGAA
66 ACTTTAAAAAATATCATAATTTCTAATTTTATAATTTTATATTATTTCAGTGCATTATGTTTGAA
* *
52836528 A---TTTATTAATTTAGTGTG-TTTTTT
131 ATTTTTTATTAATTTAGTCTGAATTTTT
* * * * * * * *
52836552 AAATTAATTTAGTGTAAAGAAAAC-CCTTA-TTCCTGCCCTTTGCTCGTATTATTTTCTCC-AAT
1 AAA-AAAGTTA--GT-AA-AACACTCCTTACTT-CGGCCATTTGTTCGTATTTTTTTCTCCGCAT
* * * *
52836614 TTTATTACTTCCAATGAAAATAT-ATTATTT-TCATATTTTATTATTTTATATTATTTCAGTACA
60 TTTATTACTT-TAA--AAAATATCATAATTTCT-A-ATTTTATAATTTTATATTATTTCAGTGCA
* * * *
52836677 TTTTGTTAGAAATATTTGTATTAA-TTATTTCTGAATTTTT
120 TTATGTTTGAAAT-TTTTTATTAATTTA-GTCTGAATTTTT
* *
52836717 AAAAATGTTAGTAAAACACT-CTTACTTCGGTCATTTGTTCGT-TTTTTTATCT--GCATTTTAT
1 AAAAAAGTTAGTAAAACACTCCTTACTTCGGCCATTTGTTCGTATTTTTT-TCTCCGCATTTTAT
* * *
52836778 TACTTTAAAAGATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATATTTGA
65 TACTTTAAAAAATATCATAATTTCTAATTTTATAATTTTATATTATTTCAGTGCATTATGTTTGA
52836843 AATTT
130 AATTT
52836848 ATTAAATATA
Statistics
Matches: 493, Mismatches: 75, Indels: 101
0.74 0.11 0.15
Matches are distributed among these distances:
154 11 0.02
155 18 0.04
156 46 0.09
157 23 0.05
158 36 0.07
159 91 0.18
160 89 0.18
161 25 0.05
162 22 0.04
163 26 0.05
164 68 0.14
165 11 0.02
167 4 0.01
168 14 0.03
169 9 0.02
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (158 bp):
AAAAAAGTTAGTAAAACACTCCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATT
ACTTTAAAAAATATCATAATTTCTAATTTTATAATTTTATATTATTTCAGTGCATTATGTTTGAA
ATTTTTTATTAATTTAGTCTGAATTTTT
Found at i:52836657 original size:16 final size:15
Alignment explanation
Indices: 52836636--52836665 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
52836626 AATGAAAATA
52836636 TATTATTTTCATATTT
1 TATTATTTT-ATATTT
52836652 TATTATTTTATATT
1 TATTATTTTATATT
52836666 ATTTCAGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTATTTTATATTT
Found at i:52836671 original size:160 final size:156
Alignment explanation
Indices: 52836132--52836689 Score: 533
Period size: 160 Copynumber: 3.5 Consensus size: 156
52836122 TTCTCTCGGC
* * * *
52836132 ATTTTATTACTT-TAAAAAATATCA-TAATTTCTAATTTTATAATTTTACATTATTTCAGTGCAT
1 ATTTTATTACTTCCAAAAAATAT-ATTATTTTCT-ATTTTATAATTTTATATTATTTCAGTACAT
* *** *
52836195 TATGTTAT-TTCTTTATTAATTTAGTGTATTTTTTAAATTAATTTAGTGTAAAAAAAACCCAACC
64 TTTGTT-TGAAATTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGTGT---AAAAA---AACC
* *
52836259 CTTATTCCTGCCCTTTGCTCGTATTATTTTTTCGA
122 CTTATTCCTGCCCTTTGCTCGTATTATTTTCTCCA
*
52836294 ATTTTATTACTTCCAAAAAAATATATTATTTTCGTATTTTATTATTTTATATTATTTCAGTACAT
1 ATTTTATTACTTCC-AAAAAATATATTATTTTC-TATTTTATAATTTTATATTATTTCAGTACAT
** ** * * * * *
52836359 TTTGTTTGAAATTTTTCTATTAATTTTTTCCGAATTTTTAAA-AAAGTTA--GT-AAAACACTCT
64 TTTGTTTGAAA---TT-TATTAATTTAGTGTG-TTTTTTAAATTAATTTAGTGTAAAAAAAC-CC
* * * * *
52836420 TTACTT-CAGCCATTTGTTCGTATTTTTTTCTCCGC
123 TTA-TTCCTGCCCTTTGCTCGTATTATTTTCTCC-A
* * *
52836455 ATTTTATTACTT-TAAAAAATATCA-TAATTTCTAATTTTATAATTTTATATTATTTCAGTGCAT
1 ATTTTATTACTTCCAAAAAATAT-ATTATTTTCT-ATTTTATAATTTTATATTATTTCAGTACAT
*
52836518 TGTGTTTGAAATTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGTGTAAAGAAAACCCTTATT
64 TTTGTTTGAAATTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGTGTAAA-AAAACCCTTATT
52836583 CCTGCCCTTTGCTCGTATTATTTTCTCCA
128 CCTGCCCTTTGCTCGTATTATTTTCTCCA
*
52836612 ATTTTATTACTTCCAATGAAAATATATTATTTTCATATTTTATTATTTTATATTATTTCAGTACA
1 ATTTTATTACTTCCAA--AAAATATATTATTTTC-TATTTTATAATTTTATATTATTTCAGTACA
*
52836677 TTTTGTTAGAAAT
63 TTTTGTTTGAAAT
52836690 ATTTGTATTA
Statistics
Matches: 319, Mismatches: 51, Indels: 54
0.75 0.12 0.13
Matches are distributed among these distances:
154 8 0.03
155 16 0.05
156 2 0.01
157 16 0.05
158 32 0.10
159 60 0.19
160 77 0.24
161 15 0.05
162 16 0.05
163 2 0.01
164 47 0.15
165 1 0.00
166 2 0.01
167 2 0.01
168 15 0.05
169 8 0.03
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.51
Consensus pattern (156 bp):
ATTTTATTACTTCCAAAAAATATATTATTTTCTATTTTATAATTTTATATTATTTCAGTACATTT
TGTTTGAAATTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGTGTAAAAAAACCCTTATTCCT
GCCCTTTGCTCGTATTATTTTCTCCA
Found at i:52836960 original size:316 final size:313
Alignment explanation
Indices: 52836075--52836857 Score: 1088
Period size: 323 Copynumber: 2.5 Consensus size: 313
52836065 AAGTTGAAAA
* *
52836075 AAAAAAGTTAGTAAAACACTCTTTACTTCGGCCATTTGTTCGTATTTTTCTCTCGGCATTTTATT
1 AAAAAAGTTAGTAAAACACTCTTTACTTCAGCCATTTGTTCGTATTTTTTTCTC-GCATTTTATT
* *
52836140 ACTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATGTTAT-T
65 ACTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATATT-TGA
** * * * *
52836204 TCTTTATTAATTTAGTGTATTTTTTAAATTAATTTAGTGTAAAAAAAACCCAACCCTTATTCCTG
129 AATTTATTAATATAATGTGTTTTTTAAATTAATTTAGTGT--AAAGAA---AACCCTTATT-CTG
* * * ** *
52836269 CCCTTTGCTCGTATTATTTTTTCGAATTTTATTACTTCCAAAAAAATATATTATTTTCGTATTTT
188 CCCTTTGCTCGTATTATTTTCTCCAATTATATTA-TT--ATGAAAATATATTATTTTCATATTTT
* * *
52836334 ATTATTTTATATTATTTCAGTACATTTTGTTTGAAATTTTTCTATTAATTTTTTCCGAATTTTT
250 ATTATTTTATATTATTTCAGTACATTTTGTTAGAAATATTTCTATTAATTATTTCCGAATTTTT
52836398 AAAAAAGTTAGTAAAACACTCTTTACTTCAGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATT
1 AAAAAAGTTAGTAAAACACTCTTTACTTCAGCCATTTGTTCGTATTTTTTTCT-CGCATTTTATT
* * *
52836463 ACTTTAAAAAATATCATAATTTCTAATTTTATAATTTTATATTATTTCAGTGCATTGTGTTTGAA
65 ACTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATATTTGAA
* *
52836528 ATTTATTAATTTAGTGTGTTTTTTAAATTAATTTAGTGTAAAGAAAACCCTTATTCCTGCCCTTT
130 ATTTATTAATATAATGTGTTTTTTAAATTAATTTAGTGTAAAGAAAACCCTTATT-CTGCCCTTT
*
52836593 GCTCGTATTATTTTCTCCAATTTTATTACTTCCAATGAAAATATATTATTTTCATATTTTATTAT
194 GCTCGTATTATTTTCTCCAATTATATTA-TT---ATGAAAATATATTATTTTCATATTTTATTAT
* *
52836658 TTTATATTATTTCAGTACATTTTGTTAGAAATATTTGTATTAATTATTTCTGAATTTTT
255 TTTATATTATTTCAGTACATTTTGTTAGAAATATTTCTATTAATTATTTCCGAATTTTT
* * *
52836717 AAAAATGTTAGTAAAACACTC-TTACTTCGGTCATTTGTTCGT-TTTTTTATCT-GCATTTTATT
1 AAAAAAGTTAGTAAAACACTCTTTACTTCAGCCATTTGTTCGTATTTTTT-TCTCGCATTTTATT
*
52836779 ACTTTAAAAGATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATATTTGAA
65 ACTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATATTTGAA
52836844 ATTTATTAAATATA
130 ATTTATT-AATATA
52836858 CCATTTTTTT
Statistics
Matches: 427, Mismatches: 28, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
316 78 0.18
317 11 0.03
318 71 0.17
319 103 0.24
321 5 0.01
322 1 0.00
323 157 0.37
324 1 0.00
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (313 bp):
AAAAAAGTTAGTAAAACACTCTTTACTTCAGCCATTTGTTCGTATTTTTTTCTCGCATTTTATTA
CTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTGCATTATATTTGAAA
TTTATTAATATAATGTGTTTTTTAAATTAATTTAGTGTAAAGAAAACCCTTATTCTGCCCTTTGC
TCGTATTATTTTCTCCAATTATATTATTATGAAAATATATTATTTTCATATTTTATTATTTTATA
TTATTTCAGTACATTTTGTTAGAAATATTTCTATTAATTATTTCCGAATTTTT
Found at i:52837211 original size:22 final size:22
Alignment explanation
Indices: 52837181--52837325 Score: 83
Period size: 22 Copynumber: 6.6 Consensus size: 22
52837171 AAAAAAATTA
52837181 CCTTTTTTTCTTTCCCTCTTCT
1 CCTTTTTTTCTTTCCCTCTTCT
**
52837203 CCTTATTTTT-TTTTTCTCTTCT
1 CCTT-TTTTTCTTTCCCTCTTCT
* *
52837225 CCTTTCTTTTTCTTTCCTTCTTTT
1 CC-TT-TTTTTCTTTCCCTCTTCT
* * *
52837249 TCTTTCTTTC-TT-CTTCTTCT
1 CCTTTTTTTCTTTCCCTCTTCT
52837269 CCTTTCCTTTTCTTT--C-CTTCT
1 CCTTT--TTTTCTTTCCCTCTTCT
52837290 --TTTTCTTTCTTTCCTCTCCTT-T
1 CCTTTT-TTTCTTTCC-CT-CTTCT
52837312 CCTTTTCTTTCTTT
1 CCTTTT-TTTCTTT
52837326 TTCTTTCTTT
Statistics
Matches: 96, Mismatches: 13, Indels: 26
0.71 0.10 0.19
Matches are distributed among these distances:
17 1 0.01
18 7 0.07
19 3 0.03
20 11 0.11
21 8 0.08
22 26 0.27
23 19 0.20
24 21 0.22
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (22 bp):
CCTTTTTTTCTTTCCCTCTTCT
Found at i:52837239 original size:10 final size:10
Alignment explanation
Indices: 52837227--52837350 Score: 82
Period size: 10 Copynumber: 12.8 Consensus size: 10
52837217 TCTCTTCTCC
52837227 TTTCTTT-TT
1 TTTCTTTCTT
*
52837236 CTTTCCTTCTT
1 -TTTCTTTCTT
52837247 TTTCTTTCTT
1 TTTCTTTCTT
52837257 TCTTC-TTCTT
1 T-TTCTTTCTT
* * *
52837267 CTCCTTTCCT
1 TTTCTTTCTT
52837277 TTTCTTTC--
1 TTTCTTTCTT
*
52837285 CTTCTTT-TT
1 TTTCTTTCTT
*
52837294 CTTTCTTTCCT
1 -TTTCTTTCTT
* * *
52837305 CTCCTTTCCT
1 TTTCTTTCTT
52837315 TTTCTTTCTT
1 TTTCTTTCTT
52837325 TTTCTTTC--
1 TTTCTTTCTT
52837333 TTTCTTTCTT
1 TTTCTTTCTT
*
52837343 CTTCTTTC
1 TTTCTTTC
52837351 CCTCTCATTC
Statistics
Matches: 89, Mismatches: 16, Indels: 18
0.72 0.13 0.15
Matches are distributed among these distances:
8 14 0.16
9 2 0.02
10 67 0.75
11 6 0.07
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTCTTTCTT
Found at i:52837269 original size:44 final size:44
Alignment explanation
Indices: 52837219--52837348 Score: 182
Period size: 44 Copynumber: 3.1 Consensus size: 44
52837209 TTTTTTTTTC
52837219 TCTTCTCCTTTCTTTTTCTTTCCTTCTTTTTCTTTCTTTCTTCT
1 TCTTCTCCTTTCTTTTTCTTTCCTTCTTTTTCTTTCTTTCTTCT
* *
52837263 TCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCT
1 TCTTCTCCTTTCTTTTTCTTTCCTTCTTTTTCTTTCTTTCTTCT
* *
52837307 CCTT-TCCTTT-TCTTTCTTT--TTC--TTTCTTTCTTTCTTCT
1 TCTTCTCCTTTCTTTTTCTTTCCTTCTTTTTCTTTCTTTCTTCT
52837345 TCTT
1 TCTT
52837349 TCCCTCTCAT
Statistics
Matches: 79, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
38 18 0.23
40 3 0.04
42 7 0.09
43 6 0.08
44 45 0.57
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (44 bp):
TCTTCTCCTTTCTTTTTCTTTCCTTCTTTTTCTTTCTTTCTTCT
Found at i:52837290 original size:38 final size:39
Alignment explanation
Indices: 52837226--52837351 Score: 151
Period size: 38 Copynumber: 3.4 Consensus size: 39
52837216 TTCTCTTCTC
* *
52837226 CTTTCTTTTTCTTTCC--TTCTTT-TTCTTTCTTTC-TT
1 CTTTCTTCTCCTTTCCTTTTCTTTCTTCTTTCTTTCTTT
52837261 C-TTCTTCTCCTTTCCTTTTCTTTCCTTC-TT-TTTCTTT
1 CTTTCTTCTCCTTTCCTTTTCTTT-CTTCTTTCTTTCTTT
*
52837298 CTTTCCTCTCCTTTCCTTTTCTTTCTT-TTTCTTTCTTT
1 CTTTCTTCTCCTTTCCTTTTCTTTCTTCTTTCTTTCTTT
*
52837336 CTTTCTTCTTCTTTCC
1 CTTTCTTCTCCTTTCC
52837352 CTCTCATTCT
Statistics
Matches: 78, Mismatches: 5, Indels: 13
0.81 0.05 0.14
Matches are distributed among these distances:
34 12 0.15
35 1 0.01
36 10 0.13
37 10 0.13
38 45 0.58
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (39 bp):
CTTTCTTCTCCTTTCCTTTTCTTTCTTCTTTCTTTCTTT
Found at i:52837333 original size:82 final size:82
Alignment explanation
Indices: 52837197--52837348 Score: 220
Period size: 82 Copynumber: 1.9 Consensus size: 82
52837187 TTTCTTTCCC
* *
52837197 TCTTCTCCTTATTTTTTTTTTCTCTTCTCCTTTCTTTTTCTTTCCTTCTTTTTCTTTCTTTCTTC
1 TCTTCTCCTTATTTTTTTTTTCTCCTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCTTC
52837262 TTCTTCTCCTTTCCTTT
66 TTCTTCTCCTTTCCTTT
* *
52837279 TCTT-TCCTTCTTTTTCTTTCTT-TCCTCTCCTTTCCTTTTCTTT-CTTTTTCTTTCTTTCTTTC
1 TCTTCTCCTTATTTTT-TTT-TTCTCCTCTCCTTTCCTTTTCTTTCCTTCTT-TTTCTTTCTTTC
52837341 TTCTTCTT
63 TTCTTCTT
52837349 TCCCTCTCAT
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
81 15 0.24
82 46 0.73
83 2 0.03
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.70
Consensus pattern (82 bp):
TCTTCTCCTTATTTTTTTTTTCTCCTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCTTC
TTCTTCTCCTTTCCTTT
Found at i:52838313 original size:8 final size:7
Alignment explanation
Indices: 52838288--52838384 Score: 63
Period size: 7 Copynumber: 13.4 Consensus size: 7
52838278 CCTATACTTT
52838288 AACCCTA
1 AACCCTA
52838295 AACCCTA
1 AACCCTA
52838302 AACCCTTA
1 AACCC-TA
52838310 AACCC-A
1 AACCCTA
*
52838316 TAACCTTA
1 -AACCCTA
*
52838324 AGCCACTA
1 AACC-CTA
*
52838332 ACCCCTA
1 AACCCTA
*
52838339 GACCCT-
1 AACCCTA
*
52838345 AAGCCTA
1 AACCCTA
52838352 TAACCCCTA
1 -AA-CCCTA
52838361 AACCCTA
1 AACCCTA
* *
52838368 AGCCCTC
1 AACCCTA
*
52838375 ACCCCTA
1 AACCCTA
52838382 AAC
1 AAC
52838385 ACTTAACATG
Statistics
Matches: 69, Mismatches: 14, Indels: 14
0.71 0.14 0.14
Matches are distributed among these distances:
6 5 0.07
7 43 0.62
8 17 0.25
9 4 0.06
ACGTcount: A:0.36, C:0.43, G:0.04, T:0.16
Consensus pattern (7 bp):
AACCCTA
Found at i:52838320 original size:29 final size:28
Alignment explanation
Indices: 52838287--52838384 Score: 74
Period size: 29 Copynumber: 3.4 Consensus size: 28
52838277 CCCTATACTT
52838287 TAACCCTAAACCCTAAACCCTTAAACCC
1 TAACCCTAAACCCTAAACCCTTAAACCC
* * * *
52838315 ATAACCTTAAGCCACT-AACCCCTAGACCC
1 -TAACCCTAAACC-CTAAACCCTTAAACCC
* *
52838344 TAAGCCTATAACCCCTAAACCC-TAAGCCC
1 TAACCCTA-AA-CCCTAAACCCTTAAACCC
*
52838373 TCACCCCTAAAC
1 T-AACCCTAAAC
52838385 ACTTAACATG
Statistics
Matches: 53, Mismatches: 11, Indels: 11
0.71 0.15 0.15
Matches are distributed among these distances:
28 7 0.13
29 32 0.60
30 14 0.26
ACGTcount: A:0.36, C:0.43, G:0.04, T:0.17
Consensus pattern (28 bp):
TAACCCTAAACCCTAAACCCTTAAACCC
Found at i:52838348 original size:22 final size:22
Alignment explanation
Indices: 52838290--52838384 Score: 90
Period size: 22 Copynumber: 4.4 Consensus size: 22
52838280 TATACTTTAA
* *
52838290 CCCTAAACCCTAAACC-CTTAAA
1 CCCTAAACCCTAAGCCAC-TAAC
*
52838312 CCC-ATAACCTTAAGCCACTAAC
1 CCCTA-AACCCTAAGCCACTAAC
*
52838334 CCCTAGACCCTAAGCCTA-TAAC
1 CCCTAAACCCTAAGCC-ACTAAC
*
52838356 CCCTAAACCCTAAGCC-CTCAC
1 CCCTAAACCCTAAGCCACTAAC
52838377 CCCTAAAC
1 CCCTAAAC
52838385 ACTTAACATG
Statistics
Matches: 61, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
21 12 0.20
22 46 0.75
23 3 0.05
ACGTcount: A:0.35, C:0.44, G:0.04, T:0.17
Consensus pattern (22 bp):
CCCTAAACCCTAAGCCACTAAC
Found at i:52838443 original size:13 final size:13
Alignment explanation
Indices: 52838403--52838447 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
52838393 TGTAAATTGA
*
52838403 AAACGTACACCAT
1 AAACCTACACCAT
52838416 AAACACTGA-ACCAT
1 AAAC-CT-ACACCAT
52838430 AAACCTACACCAT
1 AAACCTACACCAT
52838443 AAACC
1 AAACC
52838448 GTAAACACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 1 0.04
13 16 0.57
14 10 0.36
15 1 0.04
ACGTcount: A:0.49, C:0.33, G:0.04, T:0.13
Consensus pattern (13 bp):
AAACCTACACCAT
Found at i:52838558 original size:22 final size:24
Alignment explanation
Indices: 52838533--52838578 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
52838523 TATCTATAAC
52838533 CCTAACC-CTTAAACCAT-AATAG
1 CCTAACCTCTTAAACCATGAATAG
*
52838555 CCTAACCTGTTAAACCATGAATAG
1 CCTAACCTCTTAAACCATGAATAG
52838579 TAATTAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.33
23 9 0.43
24 5 0.24
ACGTcount: A:0.39, C:0.28, G:0.09, T:0.24
Consensus pattern (24 bp):
CCTAACCTCTTAAACCATGAATAG
Found at i:52839123 original size:125 final size:125
Alignment explanation
Indices: 52838896--52839338 Score: 721
Period size: 125 Copynumber: 3.5 Consensus size: 125
52838886 ATTAGTGGCA
* * **
52838896 TTTCTAGATAAACGCCACTAGTGCCACTACAGGTCAAAGTTAAACGACGGTGTTCTGCTTAATTA
1 TTTCCAGATAAACGCCGCTAGTGCCACTACAGGTCAAAGTTAAACGACGACGTTCTGCTTAATTA
* *
52838961 TTTGCT-GAGCATTAGTGGCGTTTTTT-AGTAAGCGCCGCAAATGTTAGATCTTTACCGACG
66 TTTG-TGGAGCATTAGTGGCGTTTTTTGA-TAAGCGCCGCAAATGCTAGATCTTTACCGGCG
*
52839021 TTTCCAGATAAATGCCGCTAGTGCCACTACAGGTCAAAGTTAAACGACGACGTTCTGCTTAATTA
1 TTTCCAGATAAACGCCGCTAGTGCCACTACAGGTCAAAGTTAAACGACGACGTTCTGCTTAATTA
*
52839086 TTTGTGGAGCATTAGTGGCGTTTTTTGATAAGAGCCGCAAATGCTAGATCTTTACCGGCG
66 TTTGTGGAGCATTAGTGGCGTTTTTTGATAAGCGCCGCAAATGCTAGATCTTTACCGGCG
52839146 TTTCCAGATAAACGCCGCTAGTGCCACTACAGGTCAAAGTTAAACGACGGA-GTTCTGCTTAATT
1 TTTCCAGATAAACGCCGCTAGTGCCACTACAGGTCAAAGTTAAACGAC-GACGTTCTGCTTAATT
* * *
52839210 ATTTGCGGAGCATTAGTGGCATTTTTTGATAAGCGCCGCAAATGCTAGATCTTTACTGGCG
65 ATTTGTGGAGCATTAGTGGCGTTTTTTGATAAGCGCCGCAAATGCTAGATCTTTACCGGCG
* *
52839271 TTTCCAGATAAACGTCGCTAGTGCCACTACAGGTCAAAGTTAAACGACGGCGTTCTGCTTAATTA
1 TTTCCAGATAAACGCCGCTAGTGCCACTACAGGTCAAAGTTAAACGACGACGTTCTGCTTAATTA
52839336 TTT
66 TTT
52839339 ACGGCGCTTT
Statistics
Matches: 299, Mismatches: 15, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
124 2 0.01
125 294 0.98
126 3 0.01
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.31
Consensus pattern (125 bp):
TTTCCAGATAAACGCCGCTAGTGCCACTACAGGTCAAAGTTAAACGACGACGTTCTGCTTAATTA
TTTGTGGAGCATTAGTGGCGTTTTTTGATAAGCGCCGCAAATGCTAGATCTTTACCGGCG
Found at i:52841474 original size:29 final size:29
Alignment explanation
Indices: 52841415--52841475 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
52841405 ATATTCCCCT
* *
52841415 TAATTTTTAAGGCTAAACTAGGATCTTTC
1 TAATTTTTAAGGCTAAACTAGAATCTCTC
* *
52841444 TAATTTTTATGGCTCAACTAGTAATC-CTC
1 TAATTTTTAAGGCTAAACTAG-AATCTCTC
52841473 TAA
1 TAA
52841476 CCCCTTAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 24 0.89
30 3 0.11
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.41
Consensus pattern (29 bp):
TAATTTTTAAGGCTAAACTAGAATCTCTC
Found at i:52848124 original size:12 final size:13
Alignment explanation
Indices: 52848107--52848135 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
52848097 ATGGTAAAGC
52848107 AAAATAAAAA-TA
1 AAAATAAAAATTA
52848119 AAAATAAAAATTA
1 AAAATAAAAATTA
52848132 AAAA
1 AAAA
52848136 AATCTTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAATAAAAATTA
Found at i:52861663 original size:19 final size:19
Alignment explanation
Indices: 52861639--52861677 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
52861629 GCAAATACTT
52861639 TAAAA-TTAGAAAAGAAATA
1 TAAAATTTAGAAAA-AAATA
*
52861658 TAAAATTTATAAAAAAATA
1 TAAAATTTAGAAAAAAATA
52861677 T
1 T
52861678 TATTAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (19 bp):
TAAAATTTAGAAAAAAATA
Found at i:52861705 original size:21 final size:20
Alignment explanation
Indices: 52861648--52861705 Score: 55
Period size: 22 Copynumber: 2.8 Consensus size: 20
52861638 TTAAAATTAG
*
52861648 AAAAGAAATATA-AAATTTAT
1 AAAA-AAATATATAATTTTAT
52861668 AAAAAAATATTATTAATTTTAT
1 AAAAAAATA-TA-TAATTTTAT
*
52861690 CAAAATAATATATAAT
1 -AAAAAAATATATAAT
52861706 AAATAATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
19 5 0.16
20 6 0.19
21 4 0.12
22 9 0.28
23 8 0.25
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (20 bp):
AAAAAAATATATAATTTTAT
Found at i:52862680 original size:22 final size:23
Alignment explanation
Indices: 52862646--52862704 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 23
52862636 TATATTTGGT
*
52862646 TAAAAATTAAAAATGATTTGAAAA
1 TAAAAATT-AAAATGATGTGAAAA
* *
52862670 TGAAAA-TAAAAT-ATGTGAAAT
1 TAAAAATTAAAATGATGTGAAAA
52862691 TAAAAATTAAAATG
1 TAAAAATTAAAATG
52862705 TTTTCTAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 12 0.41
22 11 0.38
23 1 0.03
24 5 0.17
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (23 bp):
TAAAAATTAAAATGATGTGAAAA
Found at i:52863283 original size:21 final size:22
Alignment explanation
Indices: 52863237--52863283 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
52863227 TATAAAAAAA
*
52863237 TTAAAAAATAAAATTGATTTTC
1 TTAAAAAATAAAAATGATTTTC
*
52863259 -TAAAAATTAAAAAT-ATTTTC
1 TTAAAAAATAAAAATGATTTTC
52863279 TTAAA
1 TTAAA
52863284 TCAAATGGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (22 bp):
TTAAAAAATAAAAATGATTTTC
Found at i:52871209 original size:25 final size:25
Alignment explanation
Indices: 52871181--52871228 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
52871171 TCCAAGCTGA
*
52871181 ATAACGGGAAG-ATCATGTGAGCTAT
1 ATAACAGGAAGCA-CATGTGAGCTAT
52871206 ATAACAGGAAGCACATGTGAGCT
1 ATAACAGGAAGCACATGTGAGCT
52871229 GTGGTGTGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 20 0.95
26 1 0.05
ACGTcount: A:0.38, C:0.15, G:0.27, T:0.21
Consensus pattern (25 bp):
ATAACAGGAAGCACATGTGAGCTAT
Found at i:52874235 original size:20 final size:19
Alignment explanation
Indices: 52874205--52874245 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
52874195 TTTTAAAAAA
* *
52874205 TTTAAAATTTTCATACTTT
1 TTTAAAATTTTAATAATTT
52874224 TTTAATAATTTTAATAATTT
1 TTTAA-AATTTTAATAATTT
52874244 TT
1 TT
52874246 AATTTTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTAAAATTTTAATAATTT
Found at i:52874251 original size:27 final size:26
Alignment explanation
Indices: 52874190--52874259 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 26
52874180 ATTCTAGTAA
* *
52874190 TTAA-TTTTTAAAAAATTTAAAATTT
1 TTAATTTTTTAATAATTTTAAAATTT
*
52874215 TCATACTTTTTTAATAATTTTAATAATTT
1 T--TAATTTTTTAATAATTTTAA-AATTT
*
52874244 TTAATTTTTAAATAAT
1 TTAATTTTTTAATAAT
52874260 AGTTTTGATA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
25 1 0.03
27 15 0.42
28 14 0.39
29 6 0.17
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (26 bp):
TTAATTTTTTAATAATTTTAAAATTT
Found at i:52874257 original size:18 final size:18
Alignment explanation
Indices: 52874222--52874273 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 18
52874212 TTTTCATACT
52874222 TTTTTAATAATTTTAATAA
1 TTTTTAAT-ATTTTAATAA
52874241 TTTTTAAT-TTTTAAATAA
1 TTTTTAATATTTT-AATAA
*
52874259 TAGTTTTGATATTTT
1 T--TTTTAATATTTT
52874274 TTGAATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 8 0.29
20 6 0.21
21 4 0.14
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (18 bp):
TTTTTAATATTTTAATAA
Found at i:52874275 original size:30 final size:31
Alignment explanation
Indices: 52874226--52874286 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
52874216 CATACTTTTT
52874226 TAATAATTTTAATAATTTTT-AATTTTTAAA
1 TAATAATTTTAATAATTTTTGAATTTTTAAA
* * *
52874256 TAATAGTTTTGATATTTTTTGAATTTTTAAA
1 TAATAATTTTAATAATTTTTGAATTTTTAAA
52874287 ATTAATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 17 0.63
31 10 0.37
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (31 bp):
TAATAATTTTAATAATTTTTGAATTTTTAAA
Found at i:52879743 original size:13 final size:13
Alignment explanation
Indices: 52879725--52879751 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
52879715 CACTCAACTC
52879725 TTGTAATAGGAAT
1 TTGTAATAGGAAT
52879738 TTGTAATAGGAAT
1 TTGTAATAGGAAT
52879751 T
1 T
52879752 CAGTGGTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.22, T:0.41
Consensus pattern (13 bp):
TTGTAATAGGAAT
Found at i:52880477 original size:48 final size:48
Alignment explanation
Indices: 52880370--52880486 Score: 159
Period size: 48 Copynumber: 2.4 Consensus size: 48
52880360 GTGGGTTGGG
*
52880370 GGGA-GGGGGGGAGAGCATTGAAAAAATGATAATGGAGGATTAAATGA
1 GGGAGGGGGGGGAGAGCATTGAAAAAAGGATAATGGAGGATTAAATGA
* *
52880417 GGGTAGGAGGGGGTGAGCATTG-AAAAAGGATAATGGAGGATTAAATGA
1 GGG-AGGGGGGGGAGAGCATTGAAAAAAGGATAATGGAGGATTAAATGA
52880465 GGG-GGCCGGGGGGAGAGCATTG
1 GGGAGG--GGGGGGAGAGCATTG
52880487 GAACAAATTA
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
46 2 0.03
47 3 0.05
48 42 0.69
49 14 0.23
ACGTcount: A:0.34, C:0.04, G:0.45, T:0.16
Consensus pattern (48 bp):
GGGAGGGGGGGGAGAGCATTGAAAAAAGGATAATGGAGGATTAAATGA
Found at i:52880561 original size:13 final size:14
Alignment explanation
Indices: 52880525--52880569 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
52880515 ATTGAATTAT
52880525 TAATATTTTAATATA
1 TAATATTTTAA-ATA
52880540 TTAA-ATATTTAAATA
1 -TAATAT-TTTAAATA
52880555 TAATATTTTAAATA
1 TAATATTTTAAATA
52880569 T
1 T
52880570 TTAATATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 12 0.44
15 7 0.26
16 8 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TAATATTTTAAATA
Found at i:52880565 original size:22 final size:21
Alignment explanation
Indices: 52880533--52880587 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 21
52880523 ATTAATATTT
*
52880533 TAATATATTAAATATTTAAATA
1 TAATATTTTAAATATTT-AATA
52880555 TAATATTTTAAATATTTAATA
1 TAATATTTTAAATATTTAATA
* *
52880576 TAAAAATTTAAA
1 TAATATTTTAAA
52880588 AAATATTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 14 0.47
22 16 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TAATATTTTAAATATTTAATA
Found at i:52880579 original size:13 final size:12
Alignment explanation
Indices: 52880541--52880595 Score: 55
Period size: 13 Copynumber: 4.8 Consensus size: 12
52880531 TTTAATATAT
52880541 TAAATATTTAAA
1 TAAATATTTAAA
52880553 TATAATATTT---
1 TA-AATATTTAAA
52880563 TAAATATTTAATA
1 TAAATATTTAA-A
*
52880576 TAAAAATTTAAA
1 TAAATATTTAAA
52880588 -AAATATTT
1 TAAATATTT
52880596 TAATTATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
9 7 0.19
10 2 0.06
11 7 0.19
12 3 0.08
13 17 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAAATATTTAAA
Found at i:52880905 original size:16 final size:16
Alignment explanation
Indices: 52880884--52880946 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 16
52880874 TGAATTACTG
*
52880884 ATTATAGCTCTATTCC
1 ATTACAGCTCTATTCC
* * * *
52880900 ATTATAGTTTTATTAC
1 ATTACAGCTCTATTCC
* *
52880916 ATTACAGTTCTATTTC
1 ATTACAGCTCTATTCC
*
52880932 ATTACAGCCCTATTC
1 ATTACAGCTCTATTC
52880947 TATTCCAGTG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.27, C:0.21, G:0.06, T:0.46
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:52883593 original size:17 final size:17
Alignment explanation
Indices: 52883571--52883626 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
52883561 TTTTTGAGAA
*
52883571 ACACGGGCGTGTGTCGT
1 ACACGGGCGTGTGTCGC
52883588 ACAC-GG-GTG-GTC-C
1 ACACGGGCGTGTGTCGC
*
52883601 ACACGGGCGTGTGCCGC
1 ACACGGGCGTGTGTCGC
52883618 ACACGGGCG
1 ACACGGGCG
52883627 GTCCACACAG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
13 4 0.12
14 5 0.15
15 6 0.18
16 4 0.12
17 14 0.42
ACGTcount: A:0.14, C:0.30, G:0.41, T:0.14
Consensus pattern (17 bp):
ACACGGGCGTGTGTCGC
Found at i:52883607 original size:30 final size:30
Alignment explanation
Indices: 52883571--52883647 Score: 118
Period size: 30 Copynumber: 2.6 Consensus size: 30
52883561 TTTTTGAGAA
* * *
52883571 ACACGGGCGTGTGTCGTACACGGGTGGTCC
1 ACACGGGCGTGTGCCGCACACGGGCGGTCC
52883601 ACACGGGCGTGTGCCGCACACGGGCGGTCC
1 ACACGGGCGTGTGCCGCACACGGGCGGTCC
*
52883631 ACACAGGCGTGTGCCGC
1 ACACGGGCGTGTGCCGC
52883648 TTAAGAAATG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.14, C:0.32, G:0.39, T:0.14
Consensus pattern (30 bp):
ACACGGGCGTGTGCCGCACACGGGCGGTCC
Found at i:52883872 original size:21 final size:20
Alignment explanation
Indices: 52883848--52883898 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
52883838 CGTGTCTCTC
*
52883848 AGCCACACGACCCTGTATCTT
1 AGCCACACGA-CCTGTACCTT
* *
52883869 AGCCACACAGACTTGTCCCTT
1 AGCCACAC-GACCTGTACCTT
52883890 AGCCACACG
1 AGCCACACG
52883899 GTCATGTATC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 1 0.04
21 23 0.88
22 2 0.08
ACGTcount: A:0.25, C:0.39, G:0.16, T:0.20
Consensus pattern (20 bp):
AGCCACACGACCTGTACCTT
Found at i:52886865 original size:14 final size:13
Alignment explanation
Indices: 52886828--52886880 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 13
52886818 TGGAAATTCC
52886828 ATTAGGTTAATTTA
1 ATTA-GTTAATTTA
*
52886842 GGTTAGTTAATTTA
1 -ATTAGTTAATTTA
*
52886856 ATTAGTTTAATTAA
1 ATTAG-TTAATTTA
52886870 ATTA-TTAATTT
1 ATTAGTTAATTT
52886881 GGATCTGCAC
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
12 6 0.18
13 4 0.12
14 20 0.61
15 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (13 bp):
ATTAGTTAATTTA
Found at i:52888769 original size:20 final size:21
Alignment explanation
Indices: 52888717--52888770 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
52888707 TGTTCAAGCT
*
52888717 TTTTATGATTTTTT-TTATAA
1 TTTTATGATTTTTTAATATAA
* *
52888737 GTTTAT-ATATTTTAATAT-A
1 TTTTATGATTTTTTAATATAA
52888756 TTTTATGATTTTTTA
1 TTTTATGATTTTTTA
52888771 TAAGTACGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.67
Consensus pattern (21 bp):
TTTTATGATTTTTTAATATAA
Found at i:52890756 original size:43 final size:43
Alignment explanation
Indices: 52890706--52890794 Score: 133
Period size: 43 Copynumber: 2.1 Consensus size: 43
52890696 ATATGAAGTT
* * *
52890706 TTTCGCTAAGCCCTGACGTTAATTGTGAAAAGATATAATACTC
1 TTTCGCTAAGCCCTAACATTAATTATGAAAAGATATAATACTC
* *
52890749 TTTCGCTAAGCCCTAACATTAATTATGAAAAGATATACTATTC
1 TTTCGCTAAGCCCTAACATTAATTATGAAAAGATATAATACTC
52890792 TTT
1 TTT
52890795 TGTAGTGGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (43 bp):
TTTCGCTAAGCCCTAACATTAATTATGAAAAGATATAATACTC
Found at i:52902083 original size:33 final size:33
Alignment explanation
Indices: 52902041--52902195 Score: 117
Period size: 33 Copynumber: 4.6 Consensus size: 33
52902031 ATATAAAGGG
52902041 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
52902074 GGTTGCTAAGTGCTGA-TCCCAACGTATTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCCC--CG-A--TT-CAT-T---GGT
*
52902116 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * *
52902143 GATTGCTAAGTGCTCATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
52902176 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
52902196 ACCATATCTT
Statistics
Matches: 96, Mismatches: 9, Indels: 34
0.69 0.06 0.24
Matches are distributed among these distances:
27 20 0.21
28 2 0.02
31 2 0.02
32 6 0.06
33 35 0.36
34 2 0.02
35 1 0.01
37 2 0.02
38 2 0.02
39 1 0.01
41 1 0.01
42 18 0.19
43 4 0.04
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:52902123 original size:75 final size:76
Alignment explanation
Indices: 52901964--52902137 Score: 253
Period size: 75 Copynumber: 2.3 Consensus size: 76
52901954 ATTCCCCCAA
* * ** *
52901964 GGGGTTGCTAAGT-CTGATTCTCTGACTCATTGGTGGTTGCTAAGTGCTGATTTCACCGTATCTT
1 GGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATCCCAACGTATCTT
*
52902028 TGAATATAAAG
66 TAAATATAAAG
*
52902039 GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCAACGTAT-TT
1 GGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATCCCAACGTATCTT
* *
52902103 TAAATGTGAAG
66 TAAATATAAAG
52902114 GGGGTTGCTAAGTGCTGATTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
52902138 CAAGGGATTG
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
75 47 0.53
76 42 0.47
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.34
Consensus pattern (76 bp):
GGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATCCCAACGTATCTT
TAAATATAAAG
Found at i:52902149 original size:102 final size:103
Alignment explanation
Indices: 52902043--52902239 Score: 315
Period size: 102 Copynumber: 1.9 Consensus size: 103
52902033 ATAAAGGGGG
* * *
52902043 TTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATCCCAACGTAT-TTTAAA
1 TTGCTAAGTGCTCATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCAACATATCTTTAAA
*
52902107 TGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGA
66 TGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCAAGGGA
* * *
52902145 TTGCTAAGTGCTCATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATCTTTGAA
1 TTGCTAAGTGCTCATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCAACATATCTTTAAA
*
52902210 TGTGAAAGGGGTTGCTAAGTTCTGATTCCC
66 TGTGAAAGGGGTTGCTAAGTGCTGATTCCC
52902240 TGAATCACTG
Statistics
Matches: 86, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
102 53 0.62
103 33 0.38
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.33
Consensus pattern (103 bp):
TTGCTAAGTGCTCATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCAACATATCTTTAAA
TGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCAAGGGA
Found at i:52902237 original size:178 final size:177
Alignment explanation
Indices: 52901934--52902265 Score: 522
Period size: 178 Copynumber: 1.9 Consensus size: 177
52901924 ATTGAATATA
* * * * * *
52901934 AAGGGGGTTGCTAAGTGTTGATTCCCCCAAGGGGTTGCTAAGTCTGATTCTCTGACTCATTGGTG
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGATTGCTAAGTCTCATTCCCCGAATCATTGGTG
* *
52901999 GTTGCTAAGTGCTGATTTCACCGTATCTTTGAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCG
66 GTTGCTAAGTGCTGATTCCACCATATCTTTGAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCG
* *
52902064 ATTCATTGGTGGTTGCTAAGTGCTGATCCCAACGTATTTTAAATGTG
131 AATCACTGGTGGTTGCTAAGTGCTGATCCCAACGTATTTTAAATGTG
52902111 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGATTGCTAAGTGCTCATTCCCCGAATCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGATTGCTAAGT-CTCATTCCCCGAATCATTGGT
* *
52902176 GGTTGCTAAGTGCTGATTCCACCATATCTTTGAATGTGAAA-GGGGTTGCTAAGTTCTGATTCCC
65 GGTTGCTAAGTGCTGATTCCACCATATCTTTGAATAT-AAAGGGGGTTGCTAAGTGCTGATTCCC
*
52902240 TGAATCACTGGTGGTTGCTAAGTGCT
129 CGAATCACTGGTGGTTGCTAAGTGCT
52902266 AAATCCACCG
Statistics
Matches: 140, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
177 41 0.29
178 96 0.69
179 3 0.02
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (177 bp):
AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGATTGCTAAGTCTCATTCCCCGAATCATTGGTG
GTTGCTAAGTGCTGATTCCACCATATCTTTGAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCG
AATCACTGGTGGTTGCTAAGTGCTGATCCCAACGTATTTTAAATGTG
Found at i:52903943 original size:43 final size:43
Alignment explanation
Indices: 52903889--52903977 Score: 124
Period size: 43 Copynumber: 2.1 Consensus size: 43
52903879 ATATGAAGTT
* * * *
52903889 TTTCGCTAAGCCTTGACGTTAATTGTGAAAAGATATAATATTC
1 TTTCGCTAAGCCCTAACATTAATTATGAAAAGATATAATATTC
* *
52903932 TTTCGCTAAGCCCTAACATTGATTATGAAAAGATATACTATTC
1 TTTCGCTAAGCCCTAACATTAATTATGAAAAGATATAATATTC
52903975 TTT
1 TTT
52903978 TGTGGTGGAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (43 bp):
TTTCGCTAAGCCCTAACATTAATTATGAAAAGATATAATATTC
Found at i:52909687 original size:213 final size:213
Alignment explanation
Indices: 52909313--52909746 Score: 751
Period size: 213 Copynumber: 2.0 Consensus size: 213
52909303 TAGAAGTGTG
* * *
52909313 TTGCCCTCCACACTGAAAGAACTTGATATAAACAAGTGTCCAAAGCTAGAGTCCATATCCCAAGA
1 TTGCCCACCACACTGAAAGAACTTGAAATAAACAAGTGTCCAAAACTAGAGTCCATATCCCAAGA
* **
52909378 AATTCAAGATAACTCTTCTCTTGAATCTATTAAAATCTGTGGATGTGATATGCTTAAGGGTTTAC
66 AATTCAAGATAACTCTTCTCTTGAATCTATTAAAATCTGTGAATGCCATATGCTTAAGGGTTTAC
*
52909443 CTCAAGGATTGAACAAGCTCAATCATTGCAAGAGATTAGTCATAAAGGATTGTTCAAATTTGATT
131 CTCAAGGATTGAACAAGCTCAAGCATTGCAAGAGATTAGTCATAAAGGATTGTTCAAATTTGATT
52909508 TCCTTAGGAGAGAGTGGT
196 TCCTTAGGAGAGAGTGGT
* * *
52909526 TTGCCCACCACACTGGAAGTACTTGAAATAAAGAAGTGTCCAAAACTAGAGTCCATATCCCAAGA
1 TTGCCCACCACACTGAAAGAACTTGAAATAAACAAGTGTCCAAAACTAGAGTCCATATCCCAAGA
*
52909591 AATTCAAGATAACTCTTCTCTTGAATCTATTGAAATCTGTGAATGCCATATGCTTAAGGGTTTAC
66 AATTCAAGATAACTCTTCTCTTGAATCTATTAAAATCTGTGAATGCCATATGCTTAAGGGTTTAC
* *
52909656 CTCAAGGATTGAACAAGCTCAAGCATTGCAAGAGATTAGTCATAGAGTATTGTTCAAATTTGATT
131 CTCAAGGATTGAACAAGCTCAAGCATTGCAAGAGATTAGTCATAAAGGATTGTTCAAATTTGATT
52909721 TCCTTAGGAGAGAGTGGT
196 TCCTTAGGAGAGAGTGGT
52909739 TTGCCCAC
1 TTGCCCAC
52909747 TACAAACCTT
Statistics
Matches: 208, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
213 208 1.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.29
Consensus pattern (213 bp):
TTGCCCACCACACTGAAAGAACTTGAAATAAACAAGTGTCCAAAACTAGAGTCCATATCCCAAGA
AATTCAAGATAACTCTTCTCTTGAATCTATTAAAATCTGTGAATGCCATATGCTTAAGGGTTTAC
CTCAAGGATTGAACAAGCTCAAGCATTGCAAGAGATTAGTCATAAAGGATTGTTCAAATTTGATT
TCCTTAGGAGAGAGTGGT
Found at i:52913642 original size:15 final size:17
Alignment explanation
Indices: 52913622--52913659 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
52913612 TTTCATATAT
*
52913622 TTTTTAAT-T-TAGTAA
1 TTTTTAATATCTAATAA
52913637 TTTTTAATATCTAATAA
1 TTTTTAATATCTAATAA
52913654 TTTTTA
1 TTTTTA
52913660 TAATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 8 0.40
16 1 0.05
17 11 0.55
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (17 bp):
TTTTTAATATCTAATAA
Found at i:52913668 original size:10 final size:9
Alignment explanation
Indices: 52913430--52913667 Score: 51
Period size: 9 Copynumber: 25.6 Consensus size: 9
52913420 CAATTCAAGT
52913430 TTTTTATAA
1 TTTTTATAA
52913439 TTTTTATAA
1 TTTTTATAA
* *
52913448 GTTTATAACAA
1 -TTT-TTATAA
* *
52913459 TTTTAATAC
1 TTTTTATAA
* *
52913468 TTTTGA-AT
1 TTTTTATAA
*
52913476 TTTTTATAT
1 TTTTTATAA
52913485 TTTTTAT-A
1 TTTTTATAA
* *
52913493 TTTATAAAA
1 TTTTTATAA
* *
52913502 TTTTAATACG
1 TTTTTATA-A
52913512 TTTTTATACA
1 TTTTTATA-A
* *
52913522 CTTTTAAAA
1 TTTTTATAA
*
52913531 TATTTTAAATAT
1 T-TTTT--ATAA
*
52913543 TTTTTATTA
1 TTTTTATAA
*
52913552 CTTTTATAA
1 TTTTTATAA
* *
52913561 TTTATTAGAT
1 TTT-TTATAA
* *
52913571 TTTATTAGAT
1 TTT-TTATAA
*
52913581 TTCCTTTATCA
1 TT--TTTATAA
52913592 -TTTTATAA
1 TTTTTATAA
*
52913600 CTTTATATCAA
1 -TTTTTAT-AA
*
52913611 TTTTCATATA
1 TTTTTATA-A
52913621 TTTTT-TAA
1 TTTTTATAA
52913629 --TTTAGTAA
1 TTTTTA-TAA
52913637 -TTTT-TAA
1 TTTTTATAA
* *
52913644 TATCTAATAA
1 T-TTTTATAA
52913654 TTTTTATAA
1 TTTTTATAA
52913663 TTTTT
1 TTTTT
52913668 TTCTGATTTT
Statistics
Matches: 168, Mismatches: 40, Indels: 42
0.67 0.16 0.17
Matches are distributed among these distances:
6 3 0.02
7 3 0.02
8 21 0.12
9 64 0.38
10 60 0.36
11 13 0.08
12 4 0.02
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (9 bp):
TTTTTATAA
Found at i:52916442 original size:10 final size:9
Alignment explanation
Indices: 52916377--52916530 Score: 62
Period size: 9 Copynumber: 16.3 Consensus size: 9
52916367 CCAGTTCAAG
*
52916377 TTTTTATACT
1 TTTTTATA-A
*
52916387 TTTTTCTAA
1 TTTTTATAA
52916396 TTTTTATAA
1 TTTTTATAA
*
52916405 GTTTATATCAA
1 -TTTTTAT-AA
* *
52916416 TTTTAATAC
1 TTTTTATAA
*
52916425 TTTTTA-AT
1 TTTTTATAA
52916433 TTTTTATAA
1 TTTTTATAA
52916442 TTTTT-T-A
1 TTTTTATAA
52916449 TTTTTATAAAA
1 TTTTTAT--AA
* *
52916460 TTTTAATATG
1 TTTTTATA-A
52916470 TTTTTATACA
1 TTTTTATA-A
* *
52916480 CTTTTAAAA
1 TTTTTATAA
*
52916489 TATTTTAAATAT
1 T-TTTT--ATAA
*
52916501 TTTTTATTA
1 TTTTTATAA
* *
52916510 CTTTTATTA
1 TTTTTATAA
*
52916519 CTTTTATAA
1 TTTTTATAA
52916528 TTT
1 TTT
52916531 ATTAGATTTT
Statistics
Matches: 108, Mismatches: 25, Indels: 23
0.69 0.16 0.15
Matches are distributed among these distances:
7 6 0.06
8 9 0.08
9 42 0.39
10 35 0.32
11 13 0.12
12 3 0.03
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:52916446 original size:18 final size:18
Alignment explanation
Indices: 52916425--52916463 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
52916415 ATTTTAATAC
* *
52916425 TTTTTAATTTTT-TATAA
1 TTTTTTATTTTTATAAAA
52916442 TTTTTTATTTTTATAAAA
1 TTTTTTATTTTTATAAAA
52916460 TTTT
1 TTTT
52916464 AATATGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTTATTTTTATAAAA
Found at i:52916494 original size:21 final size:21
Alignment explanation
Indices: 52916447--52916494 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
52916437 TATAATTTTT
*
52916447 TATTTTTATAAAATTTTAATA
1 TATTTTTATAAAATTTTAAAA
* * *
52916468 TGTTTTTATACACTTTTAAAA
1 TATTTTTATAAAATTTTAAAA
52916489 TATTTT
1 TATTTT
52916495 AAATATTTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.58
Consensus pattern (21 bp):
TATTTTTATAAAATTTTAAAA
Found at i:52916494 original size:31 final size:30
Alignment explanation
Indices: 52916450--52916516 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 30
52916440 AATTTTTTAT
52916450 TTTTATAAAATTTT-AATATGTTTTTATACAC
1 TTTTATAAAATTTTAAATAT-TTTTTAT-CAC
*
52916481 TTTTA-AAATATTTTAAATATTTTTTATTAC
1 TTTTATAAA-ATTTTAAATATTTTTTATCAC
52916511 TTTTAT
1 TTTTAT
52916517 TACTTTTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
30 10 0.31
31 17 0.53
32 5 0.16
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.60
Consensus pattern (30 bp):
TTTTATAAAATTTTAAATATTTTTTATCAC
Found at i:52916616 original size:16 final size:14
Alignment explanation
Indices: 52916585--52916639 Score: 56
Period size: 16 Copynumber: 3.6 Consensus size: 14
52916575 CAATTTTCAT
52916585 ATATTTTTAATTTA
1 ATATTTTTAATTTA
52916599 ATATTTTTAATATCTA
1 ATATTTTTAAT-T-TA
*
52916615 ATTTTTTATAATTTTA
1 ATATTTT-TAA-TTTA
52916631 ATAATTTTT
1 AT-ATTTTT
52916640 TATGAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
14 11 0.32
15 1 0.03
16 13 0.38
17 8 0.24
18 1 0.03
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (14 bp):
ATATTTTTAATTTA
Found at i:52918362 original size:6 final size:6
Alignment explanation
Indices: 52918344--52918385 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
52918334 CTAAGTCCTT
* * *
52918344 TACAGA TATAGA TAAAGA TACAGA TACAGA TACAGT TACAGA
1 TACAGA TACAGA TACAGA TACAGA TACAGA TACAGA TACAGA
52918386 GACAAATATG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.50, C:0.12, G:0.17, T:0.21
Consensus pattern (6 bp):
TACAGA
Found at i:52919868 original size:43 final size:43
Alignment explanation
Indices: 52919756--52919869 Score: 126
Period size: 43 Copynumber: 2.7 Consensus size: 43
52919746 AGTGTTTCTG
* * * *
52919756 TGTAAGACCACGTCTAGGACGTTGGCATCGACTTGTGTTTTCG
1 TGTAAGACCACGTCTAGGACGTTGGCATCGACTAGTGATTACA
*
52919799 TGTAAGAACC-TGTCTAGGACAG-TGGCATCGA-TCAGTGATTACA
1 TGTAAG-ACCACGTCTAGGAC-GTTGGCATCGACT-AGTGATTACA
*
52919842 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTAGGACGTTGGCAT
52919870 TGTACGAGCT
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
42 5 0.08
43 50 0.85
44 4 0.07
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (43 bp):
TGTAAGACCACGTCTAGGACGTTGGCATCGACTAGTGATTACA
Found at i:52920576 original size:40 final size:38
Alignment explanation
Indices: 52920521--52920637 Score: 155
Period size: 40 Copynumber: 3.0 Consensus size: 38
52920511 CGTTTAGATA
*
52920521 AAAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTT
1 AAAAAACGCCACTAAAAAT-AAGCATTAGCGGCGCTTTT
* *
52920560 AATAAAACGCCACTAAAGATAGAGTATTAGCGGCGCTTTTT
1 AA-AAAACGCCACTAAAAATA-AGCATTAGCGGCGC-TTTT
*
52920601 AAAAAACGCCACTAAAAATGAGCATTAGCGGCG-TTTT
1 AAAAAACGCCACTAAAAATAAGCATTAGCGGCGCTTTT
52920638 CCATAAAGCG
Statistics
Matches: 69, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
37 4 0.06
39 15 0.22
40 44 0.64
41 6 0.09
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (38 bp):
AAAAAACGCCACTAAAAATAAGCATTAGCGGCGCTTTT
Found at i:52920813 original size:41 final size:41
Alignment explanation
Indices: 52920691--52920815 Score: 205
Period size: 41 Copynumber: 3.0 Consensus size: 41
52920681 CTGAGTTTTG
* *
52920691 AGGGCATTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTA
1 AGGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
*
52920732 AGGGCTTTAGCGGCGTTTTTGAAGAAGCGCTGCTAATGCTC
1 AGGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
* *
52920773 AGGGCTTTAGCGGCGTTTATGAGGAAGCGCCGCTAATGCTC
1 AGGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
52920814 AG
1 AG
52920816 ATTTATCATA
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 78 1.00
ACGTcount: A:0.22, C:0.20, G:0.33, T:0.26
Consensus pattern (41 bp):
AGGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
Found at i:52921781 original size:14 final size:15
Alignment explanation
Indices: 52921762--52921806 Score: 67
Period size: 14 Copynumber: 3.1 Consensus size: 15
52921752 AGGACAGTTA
52921762 TAAGGGTT-GGGGTT
1 TAAGGGTTAGGGGTT
52921776 TAAGGGTTAGGGG-T
1 TAAGGGTTAGGGGTT
*
52921790 TAGGGGTTAGGGGTT
1 TAAGGGTTAGGGGTT
52921805 TA
1 TA
52921807 CGGTTTATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 21 0.75
15 7 0.25
ACGTcount: A:0.18, C:0.00, G:0.49, T:0.33
Consensus pattern (15 bp):
TAAGGGTTAGGGGTT
Found at i:52921791 original size:7 final size:7
Alignment explanation
Indices: 52921765--52921804 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
52921755 ACAGTTATAA
52921765 GGGTT-G
1 GGGTTAG
*
52921771 GGGTTTAA
1 GGG-TTAG
52921779 GGGTTAG
1 GGGTTAG
52921786 GGGTTAG
1 GGGTTAG
52921793 GGGTTAG
1 GGGTTAG
52921800 GGGTT
1 GGGTT
52921805 TACGGTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
6 3 0.10
7 24 0.80
8 3 0.10
ACGTcount: A:0.12, C:0.00, G:0.55, T:0.33
Consensus pattern (7 bp):
GGGTTAG
Found at i:52921811 original size:14 final size:14
Alignment explanation
Indices: 52921764--52921811 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
52921754 GACAGTTATA
52921764 AGGGTT-GGGGTTT
1 AGGGTTAGGGGTTT
52921777 AAGGGTTAGGGG-TT
1 -AGGGTTAGGGGTTT
52921791 AGGGGTTAGGGGTTT
1 A-GGGTTAGGGGTTT
*
52921806 ACGGTT
1 AGGGTT
52921812 TATGTTTTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 1 0.03
14 22 0.73
15 7 0.23
ACGTcount: A:0.15, C:0.02, G:0.50, T:0.33
Consensus pattern (14 bp):
AGGGTTAGGGGTTT
Found at i:52922898 original size:17 final size:17
Alignment explanation
Indices: 52922873--52922912 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
52922863 TCACTGGACT
*
52922873 GAAACCCTAGATGAGAA
1 GAAATCCTAGATGAGAA
52922890 GAAATCCTAGATGAGAA
1 GAAATCCTAGATGAGAA
52922907 GAAATC
1 GAAATC
52922913 GGAGGAAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.47, C:0.15, G:0.23, T:0.15
Consensus pattern (17 bp):
GAAATCCTAGATGAGAA
Found at i:52924569 original size:23 final size:23
Alignment explanation
Indices: 52924530--52924774 Score: 219
Period size: 23 Copynumber: 10.7 Consensus size: 23
52924520 NNNNNNNNNN
* *
52924530 GTTTAAGTGCTGCAAATTTAAGT
1 GTTTAAATGCTGCAAATTGAAGT
* *
52924553 GTTTAAATGTTGTAAATTGAAGT
1 GTTTAAATGCTGCAAATTGAAGT
* *
52924576 GTTTAAGTGCTGCAAATTGCAGT
1 GTTTAAATGCTGCAAATTGAAGT
*
52924599 GTTTAAGTGCTGCAAATTGAAGT
1 GTTTAAATGCTGCAAATTGAAGT
* **
52924622 GCTTAGTTGCTGCAAATTG-AGAT
1 GTTTAAATGCTGCAAATTGAAG-T
* * *
52924645 GTTT-TATCGCTG-TAATTGAGGT
1 GTTTAAAT-GCTGCAAATTGAAGT
* * **
52924667 GTATAAATGTTGTTAATTGATA-T
1 GTTTAAATGCTGCAAATTGA-AGT
* *
52924690 GTTTAAGTGCTGCAAATTTAAGT
1 GTTTAAATGCTGCAAATTGAAGT
* *
52924713 GTTTAAATGCTGTAAATTGACGT
1 GTTTAAATGCTGCAAATTGAAGT
*
52924736 GTTTAAGTGCTGCAAATTGAAGT
1 GTTTAAATGCTGCAAATTGAAGT
*
52924759 GTTTTAAGTGCTGCAA
1 G-TTTAAATGCTGCAA
52924775 CTTGTTTTAG
Statistics
Matches: 180, Mismatches: 34, Indels: 15
0.79 0.15 0.07
Matches are distributed among these distances:
22 16 0.09
23 150 0.83
24 14 0.08
ACGTcount: A:0.29, C:0.08, G:0.24, T:0.39
Consensus pattern (23 bp):
GTTTAAATGCTGCAAATTGAAGT
Found at i:52924600 original size:46 final size:45
Alignment explanation
Indices: 52924530--52924774 Score: 244
Period size: 46 Copynumber: 5.3 Consensus size: 45
52924520 NNNNNNNNNN
* * * *
52924530 GTTTAAGTGCTGCAAATTTAAGTGTTTAAATGTTGTAAATTGAAGT
1 GTTTAAGTGCTGCAAA-TTGAGTGTTTAAGTGCTGCAAATTGAAGT
52924576 GTTTAAGTGCTGCAAATTGCAGTGTTTAAGTGCTGCAAATTGAAGT
1 GTTTAAGTGCTGCAAATTG-AGTGTTTAAGTGCTGCAAATTGAAGT
* * * *
52924622 GCTT-AGTTGCTGCAAATTGAGATGTTTTA-TCGCTG-TAATTGAGGT
1 GTTTAAG-TGCTGCAAATTGAG-TGTTTAAGT-GCTGCAAATTGAAGT
* * * ** * *
52924667 GTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTAAGT
1 GTTTAAGTGCTGCAAATTGA-GTGTTTAAGTGCTGCAAATTGAAGT
* *
52924713 GTTTAAATGCTGTAAATTGACGTGTTTAAGTGCTGCAAATTGAAGT
1 GTTTAAGTGCTGCAAATTGA-GTGTTTAAGTGCTGCAAATTGAAGT
52924759 GTTTTAAGTGCTGCAA
1 G-TTTAAGTGCTGCAA
52924775 CTTGTTTTAG
Statistics
Matches: 163, Mismatches: 27, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
45 37 0.23
46 114 0.70
47 12 0.07
ACGTcount: A:0.29, C:0.08, G:0.24, T:0.39
Consensus pattern (45 bp):
GTTTAAGTGCTGCAAATTGAGTGTTTAAGTGCTGCAAATTGAAGT
Found at i:52924762 original size:114 final size:114
Alignment explanation
Indices: 52924551--52924764 Score: 308
Period size: 114 Copynumber: 1.9 Consensus size: 114
52924541 GCAAATTTAA
* * *
52924551 GTGTTTAAATGTTGTAAATTGAAGTGTTTAAGTGCTGCAAATTGCAGTGTTTAAGTGCTGCAAAT
1 GTGTATAAATGTTGTAAATTGAAGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAATGCTGCAAAT
52924616 TGAAGTGCTTAGTTGCTGCAAATTGAGATGTTTTATCGCTGTAATTGAG
66 TGAAGTGCTTAGTTGCTGCAAATTGAGATGTTTTATCGCTGTAATTGAG
* * *
52924665 GTGTATAAATGTTGTTAATTGATA-TGTTTAAGTGCTGCAAATTTAAGTGTTTAAATGCTGTAAA
1 GTGTATAAATGTTGTAAATTGA-AGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAATGCTGCAAA
* *
52924729 TTGACGTGTTTAAG-TGCTGCAAATTGA-AGTGTTTTA
65 TTGAAGTGCTT-AGTTGCTGCAAATTGAGA-TGTTTTA
52924765 AGTGCTGCAA
Statistics
Matches: 89, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
113 1 0.01
114 85 0.96
115 3 0.03
ACGTcount: A:0.29, C:0.07, G:0.24, T:0.40
Consensus pattern (114 bp):
GTGTATAAATGTTGTAAATTGAAGTGTTTAAGTGCTGCAAATTGAAGTGTTTAAATGCTGCAAAT
TGAAGTGCTTAGTTGCTGCAAATTGAGATGTTTTATCGCTGTAATTGAG
Found at i:52925417 original size:43 final size:43
Alignment explanation
Indices: 52925370--52925684 Score: 452
Period size: 43 Copynumber: 7.3 Consensus size: 43
52925360 TTTTCGTGAC
* * * * * *
52925370 CTTTAGTGGCGTTTTTGGGAAAAGCACCACTAAAGGTTTTGGT
1 CTTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCTTGGT
52925413 CTTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCTTGGT
1 CTTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCTTGGT
* * *
52925456 CTTTAGCAGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGT
1 CTTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCTTGGT
* * *
52925499 CTTTAGCGGCGTTTGCGGGAGAAGCGTCGCTAAAGGTCCTGGT
1 CTTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCTTGGT
52925542 CTTTAGCGGCGTTT-TCGGGAGAAGCGCCGCTAAAGGTCTTGGT
1 CTTTAGCGGCGTTTGT-GGGAGAAGCGCCGCTAAAGGTCTTGGT
* *
52925585 TTTTAGCGGCGTTTGCGGGAGAAGCGCCGCTAAAGGTCTTGGT
1 CTTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCTTGGT
* * **
52925628 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTAAT
1 CTTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCTTGGT
52925671 CTTTAGCGGCGTTT
1 CTTTAGCGGCGTTT
52925685 TTTCCGGCGC
Statistics
Matches: 246, Mismatches: 24, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
43 246 1.00
ACGTcount: A:0.18, C:0.19, G:0.34, T:0.29
Consensus pattern (43 bp):
CTTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCTTGGT
Found at i:52928227 original size:21 final size:20
Alignment explanation
Indices: 52928204--52928273 Score: 56
Period size: 19 Copynumber: 3.5 Consensus size: 20
52928194 TTTCAATACA
52928204 TTTTTATAAAATTTTACAA-
1 TTTTTATAAAATTTTACAAT
* *
52928223 TATTTA-AATAATTTATTAGAAT
1 TTTTTATAA-AA-TT-TTACAAT
*
52928245 TTTCTTATAAAA-TTTATAAT
1 TTT-TTATAAAATTTTACAAT
52928265 TTTTTATAA
1 TTTTTATAA
52928274 TTTTTATAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
18 2 0.05
19 13 0.32
20 11 0.27
21 6 0.15
22 2 0.05
23 5 0.12
24 2 0.05
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (20 bp):
TTTTTATAAAATTTTACAAT
Found at i:52928277 original size:9 final size:9
Alignment explanation
Indices: 52928257--52928334 Score: 77
Period size: 9 Copynumber: 8.3 Consensus size: 9
52928247 TCTTATAAAA
52928257 TTTATAATTT
1 TTTATAA-TT
52928267 TTTATAATT
1 TTTATAATT
52928276 TTTATAACTT
1 TTTATAA-TT
*
52928286 TATATCAATT
1 TTTAT-AATT
* *
52928296 TTCAGAATT
1 TTTATAATT
52928305 TTTATAATT
1 TTTATAATT
52928314 TTTGAT-ATT
1 TTT-ATAATT
*
52928323 TTTATCATT
1 TTTATAATT
52928332 TTT
1 TTT
52928335 TGAAAAAAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
8 2 0.03
9 35 0.60
10 19 0.33
11 2 0.03
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (9 bp):
TTTATAATT
Found at i:52929513 original size:2 final size:2
Alignment explanation
Indices: 52929506--52929534 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
52929496 CTTTTATAAT
52929506 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
52929535 TTGGATCCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52930668 original size:17 final size:17
Alignment explanation
Indices: 52930631--52930668 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
52930621 GTTAAAATGT
*
52930631 AATTTTATTATTTTAAT
1 AATTTTATTATTTTAAA
52930648 AATTTATATTA-TTTAAA
1 AATTT-TATTATTTTAAA
52930665 AATT
1 AATT
52930669 AAATTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
AATTTTATTATTTTAAA
Found at i:52930947 original size:12 final size:12
Alignment explanation
Indices: 52930926--52930960 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
52930916 TCTTTTAAAG
52930926 TTACAAATATAA
1 TTACAAATATAA
*
52930938 TTACAGATATAA
1 TTACAAATATAA
*
52930950 TTACAATTATA
1 TTACAAATATA
52930961 GCTATAGATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.37
Consensus pattern (12 bp):
TTACAAATATAA
Found at i:52935722 original size:66 final size:66
Alignment explanation
Indices: 52935608--52935743 Score: 236
Period size: 66 Copynumber: 2.1 Consensus size: 66
52935598 GCAACCTCAC
* * *
52935608 TTCTCTCCAGTGCTTGATTATCGAAAATTGCCCAAACCTGAAGACTCTTCCGGGAAACAATATGC
1 TTCTCTCCAGTGCTTGACTATCGAAAATTGCCCAAACCTCAAGACTCTTCCAGGAAACAATATGC
52935673 T
66 T
*
52935674 TTCTCTCCAGTGCTTGACTATCGAAAATTGCCCAAACCTCAAGTCTCTTCCAGGAAACAATATGC
1 TTCTCTCCAGTGCTTGACTATCGAAAATTGCCCAAACCTCAAGACTCTTCCAGGAAACAATATGC
52935739 T
66 T
52935740 TTCT
1 TTCT
52935744 TCGCTTTTCG
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (66 bp):
TTCTCTCCAGTGCTTGACTATCGAAAATTGCCCAAACCTCAAGACTCTTCCAGGAAACAATATGC
T
Found at i:52937116 original size:25 final size:25
Alignment explanation
Indices: 52937082--52937133 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
52937072 CTCGATGATA
52937082 GTTAAGCTAGAGTTATGTATTTATT
1 GTTAAGCTAGAGTTATGTATTTATT
*
52937107 GTTACGCTAGAGTTATGTATTTATT
1 GTTAAGCTAGAGTTATGTATTTATT
52937132 GT
1 GT
52937134 GATAATGTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.06, G:0.21, T:0.48
Consensus pattern (25 bp):
GTTAAGCTAGAGTTATGTATTTATT
Found at i:52939254 original size:93 final size:93
Alignment explanation
Indices: 52939077--52939451 Score: 470
Period size: 93 Copynumber: 4.0 Consensus size: 93
52939067 TGATTGTCCA
* * * * ** * *
52939077 CCAAAATTCTCTACATCTCTTGAGATGGAAATCATAGGCAAGGCATTTACTGCACAAGAACTATC
1 CCAACATTCTCCACATCTCTTGGGATGGAAATCATAGGCAAAGCATTTACCCCACAAGCACTCTC
* * *
52939142 TAT-AGTTTGCATCAAGGCAGTCTTTTCT
66 T-TCATTTTGTATCAGGGCAGTCTTTTCT
* * * *
52939170 CCAACATTCTCCACATCTCTTGGGTTGGAAGTTATAGGCAAAGCATTTACCCCACAGGCACTCTC
1 CCAACATTCTCCACATCTCTTGGGATGGAAATCATAGGCAAAGCATTTACCCCACAAGCACTCTC
52939235 TTCATTTTGTATCAGGGCAGTCTTTTCT
66 TTCATTTTGTATCAGGGCAGTCTTTTCT
* * * * *
52939263 GCAACATTCTCCATATCTCTCGGGATGGAAATTATAGGCAAAGCATTTGCCCCACAAGCACTAC-
1 CCAACATTCTCCACATCTCTTGGGATGGAAATCATAGGCAAAGCATTTACCCCACAAGCACT-CT
52939327 CTTCATTTTGTATCAGGGCAGTCTTTTCT
65 CTTCATTTTGTATCAGGGCAGTCTTTTCT
* *
52939356 CCAACATTCTCCACATCTCTTGGGATGGAAATCATAGGCAAAGCATTTAACCAACAAGCAC-CAT
1 CCAACATTCTCCACATCTCTTGGGATGGAAATCATAGGCAAAGCATTTACCCCACAAGCACTC-T
* *
52939420 CTTCATTTTGTA-CTGGGTCATTCTTTTCT
65 CTTCATTTTGTATCAGGG-CAGTCTTTTCT
52939449 CCA
1 CCA
52939452 GCTGGTATTT
Statistics
Matches: 246, Mismatches: 31, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
91 1 0.00
92 5 0.02
93 239 0.97
94 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (93 bp):
CCAACATTCTCCACATCTCTTGGGATGGAAATCATAGGCAAAGCATTTACCCCACAAGCACTCTC
TTCATTTTGTATCAGGGCAGTCTTTTCT
Found at i:52942779 original size:21 final size:20
Alignment explanation
Indices: 52942753--52942807 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 20
52942743 AACAGCGGTG
*
52942753 GCGGTGAGATTAGTTACTGTA
1 GCGGTGATATTAG-TACTGTA
52942774 GCGGTGATATTGAGTACTGTA
1 GCGGTGATATT-AGTACTGTA
52942795 GCGGTGATATTAG
1 GCGGTGATATTAG
52942808 AAACAATGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 2 0.06
21 28 0.88
22 2 0.06
ACGTcount: A:0.24, C:0.09, G:0.35, T:0.33
Consensus pattern (20 bp):
GCGGTGATATTAGTACTGTA
Found at i:52943122 original size:22 final size:22
Alignment explanation
Indices: 52943071--52943122 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
52943061 TTTTATAGTT
*
52943071 ATAATTAAATATTTTTTATAACA
1 ATAA-TAAATATTATTTATAACA
* *
52943094 ATGATAAATATTATTT-TCACAA
1 ATAATAAATATTATTTATAAC-A
52943116 ATAATAA
1 ATAATAA
52943123 CATTATACTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 3 0.12
22 18 0.75
23 3 0.12
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (22 bp):
ATAATAAATATTATTTATAACA
Found at i:52953194 original size:29 final size:29
Alignment explanation
Indices: 52953128--52953183 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
52953118 CACGTTATCC
* *
52953128 AAATGCTTTTTAATTTAGACAACGTGTCT
1 AAATGCATTTGAATTTAGACAACGTGTCT
* *
52953157 AGATGCATTTGAATTTGGACAACGTGT
1 AAATGCATTTGAATTTAGACAACGTGT
52953184 TCAAATTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (29 bp):
AAATGCATTTGAATTTAGACAACGTGTCT
Found at i:52953499 original size:25 final size:26
Alignment explanation
Indices: 52953471--52953522 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
52953461 GCTTGGTTTC
*
52953471 TGTAGTATATAATATATATAG-ATTT
1 TGTAGTATATAATATATAAAGTATTT
*
52953496 TGTAGTATATATTATATAAAGTATTT
1 TGTAGTATATAATATATAAAGTATTT
52953522 T
1 T
52953523 CAAATAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (26 bp):
TGTAGTATATAATATATAAAGTATTT
Found at i:52956167 original size:10 final size:10
Alignment explanation
Indices: 52956154--52956218 Score: 53
Period size: 10 Copynumber: 6.6 Consensus size: 10
52956144 TTTTATGATT
52956154 TTTTTTATCA
1 TTTTTTATCA
*
52956164 -TTTTTATAA
1 TTTTTTATCA
* *
52956173 GTTTATATCA
1 TTTTTTATCA
* * *
52956183 ATTTTCATAA
1 TTTTTTATCA
52956193 TTTTTTAT-A
1 TTTTTTATCA
52956202 TTTTTTTATCA
1 -TTTTTTATCA
52956213 TTTTTT
1 TTTTTT
52956219 GAAAAAAAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
9 9 0.21
10 33 0.77
11 1 0.02
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.68
Consensus pattern (10 bp):
TTTTTTATCA
Found at i:52958662 original size:17 final size:17
Alignment explanation
Indices: 52958642--52958675 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
52958632 TATTCATATA
* *
52958642 GTTCTCTTATTTAGATG
1 GTTCTCATAGTTAGATG
52958659 GTTCTCATAGTTAGATG
1 GTTCTCATAGTTAGATG
52958676 CAAAATCAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.47
Consensus pattern (17 bp):
GTTCTCATAGTTAGATG
Found at i:52960007 original size:19 final size:17
Alignment explanation
Indices: 52959983--52960025 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
52959973 AAAAAATATT
52959983 TAAAAATTCATATTTTTGA
1 TAAAAATTCAT-TTTTT-A
*
52960002 TAAAAATACATTTTTTA
1 TAAAAATTCATTTTTTA
52960019 -AAAAATT
1 TAAAAATT
52960026 TATTAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 1 0.05
18 5 0.23
19 10 0.45
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (17 bp):
TAAAAATTCATTTTTTA
Found at i:52969550 original size:30 final size:29
Alignment explanation
Indices: 52969514--52969576 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 29
52969504 TCCTTCTTTC
*
52969514 GCAAACCCAACTCCGTAAGGAGAAATGCT
1 GCAAACCCAACTCCATAAGGAGAAATGCT
52969543 AGCAAACCCAACTCCATAAGGAGAAATGCT
1 -GCAAACCCAACTCCATAAGGAGAAATGCT
52969573 GCAA
1 GCAA
52969577 CATATACAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.41, C:0.27, G:0.19, T:0.13
Consensus pattern (29 bp):
GCAAACCCAACTCCATAAGGAGAAATGCT
Found at i:52972691 original size:2 final size:2
Alignment explanation
Indices: 52972686--52972725 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
52972676 TATGCAGATG
52972686 TA TA TA TA T- TA TA -A TA 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 TA TA TA TA
52972726 CATACGGTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:52972899 original size:3 final size:3
Alignment explanation
Indices: 52972891--52972930 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
52972881 GAAATAAAAC
*
52972891 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
52972931 CATTATTGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:52978516 original size:35 final size:35
Alignment explanation
Indices: 52978476--52978555 Score: 101
Period size: 35 Copynumber: 2.3 Consensus size: 35
52978466 AATTTTTTTG
*
52978476 TAATTTTTATAAGTTTATATCAATTTTAATACTTT
1 TAATTTTTATAAGTTTATATCAATTTTAATACCTT
* ** *
52978511 TAATTTTTTTATTTTTATATTAATTTTAATACCTT
1 TAATTTTTATAAGTTTATATCAATTTTAATACCTT
52978546 T--TTTTTATAA
1 TAATTTTTATAA
52978556 AATTTTACAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
33 7 0.18
35 31 0.82
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.62
Consensus pattern (35 bp):
TAATTTTTATAAGTTTATATCAATTTTAATACCTT
Found at i:52978637 original size:21 final size:22
Alignment explanation
Indices: 52978596--52978639 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
52978586 AATTTTATAA
* *
52978596 TTTATTAAATTTATTAGAATTT
1 TTTATAAAATTTATTAAAATTT
52978618 TTTATAAAATTTA-TAAAATTT
1 TTTATAAAATTTATTAAAATTT
52978639 T
1 T
52978640 ATAATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
TTTATAAAATTTATTAAAATTT
Found at i:52978645 original size:29 final size:28
Alignment explanation
Indices: 52978588--52978678 Score: 94
Period size: 29 Copynumber: 3.1 Consensus size: 28
52978578 TTGTTATTAA
* *
52978588 TTTTAT-AATTTATTAAATTTATTAGAATT
1 TTTTATAAATTTA-TAAAATT-TTATAATT
52978617 TTTTATAAAATTTATAAAATTTTATAATT
1 TTTTAT-AAATTTATAAAATTTTATAATT
* *
52978646 TTTTATAACTTTATATCAATTTTCATAATT
1 TTTTATAAATTTATA-AAATTTT-ATAATT
52978676 TTT
1 TTT
52978679 AATATTTTTA
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
28 8 0.15
29 25 0.46
30 15 0.28
31 6 0.11
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.58
Consensus pattern (28 bp):
TTTTATAAATTTATAAAATTTTATAATT
Found at i:52978687 original size:19 final size:19
Alignment explanation
Indices: 52978588--52978728 Score: 71
Period size: 19 Copynumber: 7.4 Consensus size: 19
52978578 TTGTTATTAA
52978588 TTTTATAATTTATT-A-AAT
1 TTTTATAATTT-TTAATAAT
* * *
52978606 TTATTAGAATTTTTTATAAA
1 TT-TTATAATTTTTAATAAT
* *
52978626 ATTTATAAAATTTT-ATAATT
1 TTTTAT-AATTTTTAATAA-T
*
52978646 TTTTATAA-CTTTATATCAAT
1 TTTTATAATTTTTA-AT-AAT
*
52978666 TTTCATAATTTTTAAT-A-
1 TTTTATAATTTTTAATAAT
* *
52978683 TTTT-TAATATCTAATAAT
1 TTTTATAATTTTTAATAAT
* *
52978701 TTTTATAATTTTTTATCAT
1 TTTTATAATTTTTAATAAT
52978720 TTTTCATAA
1 TTTT-ATAA
52978729 AAGATATTAT
Statistics
Matches: 93, Mismatches: 17, Indels: 24
0.69 0.13 0.18
Matches are distributed among these distances:
16 9 0.10
17 4 0.04
18 12 0.13
19 32 0.34
20 30 0.32
21 6 0.06
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.58
Consensus pattern (19 bp):
TTTTATAATTTTTAATAAT
Found at i:52978713 original size:10 final size:10
Alignment explanation
Indices: 52978588--52978728 Score: 74
Period size: 10 Copynumber: 13.8 Consensus size: 10
52978578 TTGTTATTAA
52978588 TTTTATAATT
1 TTTTATAATT
*
52978598 TATTA-AATT
1 TTTTATAATT
* *
52978607 TATTAGAATT
1 TTTTATAATT
*
52978617 TTTTATAA-A
1 TTTTATAATT
* **
52978626 ATTTATAAAA
1 TTTTATAATT
52978636 TTTTATAATT
1 TTTTATAATT
*
52978646 TTTTATAACT
1 TTTTATAATT
*
52978656 TTATATCAA-T
1 TTTTAT-AATT
*
52978666 TTTCATAATT
1 TTTTATAATT
*
52978676 TTTAAT-ATT
1 TTTTATAATT
52978685 TTTAATATCTAATAAT
1 TTT--TA--TAAT--T
52978701 TTTTATAATT
1 TTTTATAATT
*
52978711 TTTTATCATT
1 TTTTATAATT
*
52978721 TTTCATAA
1 TTTTATAA
52978729 AAGATATTAT
Statistics
Matches: 103, Mismatches: 17, Indels: 22
0.73 0.12 0.15
Matches are distributed among these distances:
9 24 0.23
10 63 0.61
11 3 0.03
12 4 0.04
13 1 0.01
14 4 0.04
16 4 0.04
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.58
Consensus pattern (10 bp):
TTTTATAATT
Found at i:52983768 original size:66 final size:66
Alignment explanation
Indices: 52983662--52983860 Score: 353
Period size: 66 Copynumber: 3.0 Consensus size: 66
52983652 GCAACCTCAC
* *
52983662 TTCTCTCCAGTGCTTGACTATCGGAAATTGCCCAAACCTCAAGACTCTTCCGGGAAACAATATGC
1 TTCTCTCCAGCGCTTGACTATCGCAAATTGCCCAAACCTCAAGACTCTTCCGGGAAACAATATGC
52983727 T
66 T
*
52983728 TTCTCTCCAGCGCTTGACTATCGCAAATTGCCCACACCTCAAGACTCTTCCGGGAAACAATATGC
1 TTCTCTCCAGCGCTTGACTATCGCAAATTGCCCAAACCTCAAGACTCTTCCGGGAAACAATATGC
52983793 T
66 T
* *
52983794 TTCTCTCCAGCGCTTGACTATTGCAAATTGCCCAAACCTCAAGACTCTTCCAGGAAACAATATGC
1 TTCTCTCCAGCGCTTGACTATCGCAAATTGCCCAAACCTCAAGACTCTTCCGGGAAACAATATGC
52983859 T
66 T
52983860 T
1 T
52983861 CCTTCGCTTT
Statistics
Matches: 127, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 127 1.00
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (66 bp):
TTCTCTCCAGCGCTTGACTATCGCAAATTGCCCAAACCTCAAGACTCTTCCGGGAAACAATATGC
T
Found at i:52986299 original size:30 final size:30
Alignment explanation
Indices: 52986263--52986321 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
52986253 TCCTTCTTTT
*
52986263 GCAAACCCAACTCCGTAAGGAGAAATGCTC
1 GCAAACCCAACTCCATAAGGAGAAATGCTC
52986293 GCAAACCCAACTCCATAAGGAGAAATGCT
1 GCAAACCCAACTCCATAAGGAGAAATGCT
52986322 GAAACATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.39, C:0.29, G:0.19, T:0.14
Consensus pattern (30 bp):
GCAAACCCAACTCCATAAGGAGAAATGCTC
Found at i:52988768 original size:2 final size:2
Alignment explanation
Indices: 52988763--52988801 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
52988753 TCCAAAAAAG
52988763 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
52988802 ATAACCTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:52992057 original size:131 final size:131
Alignment explanation
Indices: 52991880--52992141 Score: 524
Period size: 131 Copynumber: 2.0 Consensus size: 131
52991870 AAGTAAAATA
52991880 ATTTTAGACAATTAGACTTGGATATAAAAGAGATTATAACAAAATAACAAGCAGCCTGCCAATTT
1 ATTTTAGACAATTAGACTTGGATATAAAAGAGATTATAACAAAATAACAAGCAGCCTGCCAATTT
52991945 AAACAGCAAATACAGTGATAAAACCTCAAAAACTAAACAAAGCAAAATTACCAAAAGTAGTAGCT
66 AAACAGCAAATACAGTGATAAAACCTCAAAAACTAAACAAAGCAAAATTACCAAAAGTAGTAGCT
52992010 C
131 C
52992011 ATTTTAGACAATTAGACTTGGATATAAAAGAGATTATAACAAAATAACAAGCAGCCTGCCAATTT
1 ATTTTAGACAATTAGACTTGGATATAAAAGAGATTATAACAAAATAACAAGCAGCCTGCCAATTT
52992076 AAACAGCAAATACAGTGATAAAACCTCAAAAACTAAACAAAGCAAAATTACCAAAAGTAGTAGCT
66 AAACAGCAAATACAGTGATAAAACCTCAAAAACTAAACAAAGCAAAATTACCAAAAGTAGTAGCT
52992141 C
131 C
52992142 CAAAAAGTGC
Statistics
Matches: 131, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
131 131 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (131 bp):
ATTTTAGACAATTAGACTTGGATATAAAAGAGATTATAACAAAATAACAAGCAGCCTGCCAATTT
AAACAGCAAATACAGTGATAAAACCTCAAAAACTAAACAAAGCAAAATTACCAAAAGTAGTAGCT
C
Found at i:52993919 original size:93 final size:93
Alignment explanation
Indices: 52993752--52994126 Score: 495
Period size: 93 Copynumber: 4.0 Consensus size: 93
52993742 TGATTGTCCA
* * * * * * *
52993752 CCAAAATTCTCTACATCTCTTGAGATGGAAATCATAGGCAAGGCATTTACCGCACAAGAACTATC
1 CCAACATTCTCCACATCTCTTGGGATGGAAATCATAGGCAAAGCATTTACCCCACAAGCACTCTC
* * *
52993817 TTTAGTTTGTATCAAGGCAGTCTTTTCT
66 TTCATTTTGTATCAGGGCAGTCTTTTCT
* * * *
52993845 CCAACATTCTCCACATCTCTTGGGTTGGAAGTTATAGGCATAGCATTTACCCCACAAGCACTCTC
1 CCAACATTCTCCACATCTCTTGGGATGGAAATCATAGGCAAAGCATTTACCCCACAAGCACTCTC
52993910 TTCATTTTGTATCAGGGCAGTCTTTTCT
66 TTCATTTTGTATCAGGGCAGTCTTTTCT
* * *
52993938 GCAACATTCTCCATATCTCTTGGGATGGAAATTATAGGCAAAGCATTTACCCCACAAGCACTAC-
1 CCAACATTCTCCACATCTCTTGGGATGGAAATCATAGGCAAAGCATTTACCCCACAAGCACT-CT
*
52994002 CTTCATTTTGTATCAGGGCAGTCTTTTCC
65 CTTCATTTTGTATCAGGGCAGTCTTTTCT
* *
52994031 CCAACATTCTCCACATCTCTTGGGATGGAAATCATAGGCAAAGCATTTAACCAACAAGCAC-CAT
1 CCAACATTCTCCACATCTCTTGGGATGGAAATCATAGGCAAAGCATTTACCCCACAAGCACTC-T
* * *
52994095 CTTCATTTTTTA-CTGGGTCACTCTTTTCT
65 CTTCATTTTGTATCAGGG-CAGTCTTTTCT
52994124 CCA
1 CCA
52994127 GCTGGTATTT
Statistics
Matches: 249, Mismatches: 29, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
91 1 0.00
92 4 0.02
93 243 0.98
94 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (93 bp):
CCAACATTCTCCACATCTCTTGGGATGGAAATCATAGGCAAAGCATTTACCCCACAAGCACTCTC
TTCATTTTGTATCAGGGCAGTCTTTTCT
Found at i:52996059 original size:24 final size:25
Alignment explanation
Indices: 52996032--52996079 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
52996022 AGAGGAAATT
52996032 TTAAAGAACATAAAA-GAAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAAA
** *
52996056 TTAAATTACTTAAAACGAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAA
52996080 TATAGGGATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (25 bp):
TTAAAGAACATAAAACGAAAAAAAA
Found at i:53010560 original size:14 final size:16
Alignment explanation
Indices: 53010541--53010572 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
53010531 TGCCTTTCTG
53010541 ATTA-TTTTAA-ATAA
1 ATTATTTTTAATATAA
53010555 ATTATTTTTAATATAA
1 ATTATTTTTAATATAA
53010571 AT
1 AT
53010573 GCGTTGCATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.25
15 6 0.38
16 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTATTTTTAATATAA
Found at i:53015408 original size:22 final size:22
Alignment explanation
Indices: 53015383--53015452 Score: 140
Period size: 22 Copynumber: 3.2 Consensus size: 22
53015373 TAAGACAAGT
53015383 AAAGAAATTATTACAGGAGATG
1 AAAGAAATTATTACAGGAGATG
53015405 AAAGAAATTATTACAGGAGATG
1 AAAGAAATTATTACAGGAGATG
53015427 AAAGAAATTATTACAGGAGATG
1 AAAGAAATTATTACAGGAGATG
53015449 AAAG
1 AAAG
53015453 GGAAAGGTTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.51, C:0.04, G:0.23, T:0.21
Consensus pattern (22 bp):
AAAGAAATTATTACAGGAGATG
Found at i:53017453 original size:2 final size:2
Alignment explanation
Indices: 53017448--53017482 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
53017438 ACACACACAC
53017448 AT AT AT AT 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 AT AT AT AT A
53017483 ATAATAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53023546 original size:46 final size:46
Alignment explanation
Indices: 53023479--53023573 Score: 163
Period size: 46 Copynumber: 2.1 Consensus size: 46
53023469 AGGTTAATAT
*
53023479 TTATTTATTTTTTTAGATAATTCTAAAGAGTTTTATTAGGATTCAA
1 TTATTTATTTTCTTAGATAATTCTAAAGAGTTTTATTAGGATTCAA
* *
53023525 TTATTTATTTTCTTAGATAATTTTAAAGAGTTTTATTAGGGTTCAA
1 TTATTTATTTTCTTAGATAATTCTAAAGAGTTTTATTAGGATTCAA
53023571 TTA
1 TTA
53023574 CTCTTGTCTT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.32, C:0.04, G:0.12, T:0.53
Consensus pattern (46 bp):
TTATTTATTTTCTTAGATAATTCTAAAGAGTTTTATTAGGATTCAA
Found at i:53024073 original size:22 final size:22
Alignment explanation
Indices: 53024048--53024095 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
53024038 TCAAAAACAC
*
53024048 TTTTCATCGGTTTCGTCAATTT
1 TTTTCATCGGTTTCATCAATTT
*
53024070 TTTTCATCGGTTTCATCGATTT
1 TTTTCATCGGTTTCATCAATTT
53024092 TTTT
1 TTTT
53024096 TAAAAAAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.12, C:0.17, G:0.12, T:0.58
Consensus pattern (22 bp):
TTTTCATCGGTTTCATCAATTT
Found at i:53029739 original size:23 final size:23
Alignment explanation
Indices: 53029708--53029785 Score: 65
Period size: 23 Copynumber: 3.4 Consensus size: 23
53029698 TATTTATTTA
*
53029708 TTTTTTTAGATAATTTTAAAGAG
1 TTTTATTAGATAATTTTAAAGAG
*
53029731 TTTTATTAGGATTCAATTATT---TA-
1 TTTTATTA-GA-T-AATT-TTAAAGAG
*
53029754 TTTTCTTAGATAATTTTAAAGAG
1 TTTTATTAGATAATTTTAAAGAG
53029777 TTTTATTAG
1 TTTTATTAG
53029786 GGTTCAATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 16
0.67 0.08 0.25
Matches are distributed among these distances:
19 2 0.05
20 4 0.10
21 1 0.02
22 3 0.07
23 22 0.52
24 3 0.07
25 1 0.02
26 4 0.10
27 2 0.05
ACGTcount: A:0.32, C:0.03, G:0.12, T:0.54
Consensus pattern (23 bp):
TTTTATTAGATAATTTTAAAGAG
Found at i:53029767 original size:46 final size:46
Alignment explanation
Indices: 53029701--53029795 Score: 172
Period size: 46 Copynumber: 2.1 Consensus size: 46
53029691 AGGTTATTAT
*
53029701 TTATTTATTTTTTTAGATAATTTTAAAGAGTTTTATTAGGATTCAA
1 TTATTTATTTTCTTAGATAATTTTAAAGAGTTTTATTAGGATTCAA
*
53029747 TTATTTATTTTCTTAGATAATTTTAAAGAGTTTTATTAGGGTTCAA
1 TTATTTATTTTCTTAGATAATTTTAAAGAGTTTTATTAGGATTCAA
53029793 TTA
1 TTA
53029796 CTCTTGTCTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.32, C:0.03, G:0.12, T:0.54
Consensus pattern (46 bp):
TTATTTATTTTCTTAGATAATTTTAAAGAGTTTTATTAGGATTCAA
Found at i:53032329 original size:3 final size:3
Alignment explanation
Indices: 53032317--53032377 Score: 106
Period size: 3 Copynumber: 20.7 Consensus size: 3
53032307 AATGAAAACC
*
53032317 ATA A-A ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
53032364 ATA ATA ATA ATA AT
1 ATA ATA ATA ATA AT
53032378 GAAAGTCAAG
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
2 2 0.04
3 53 0.96
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:53042066 original size:23 final size:23
Alignment explanation
Indices: 53042012--53042056 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
53042002 AATTTACTTC
53042012 AAATATATAAT--TTATATATTT
1 AAATATATAATGGTTATATATTT
53042033 AAATATATAATGGTTATAT-TTT
1 AAATATATAATGGTTATATATTT
53042055 AA
1 AA
53042057 TATTTTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 11 0.50
22 5 0.23
23 6 0.27
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (23 bp):
AAATATATAATGGTTATATATTT
Found at i:53042225 original size:22 final size:23
Alignment explanation
Indices: 53042197--53042244 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
53042187 AGTTGATTGC
* *
53042197 ATTAAAGGATGAGAGG-TGAAGT
1 ATTAAAGGATGAAAGGAGGAAGT
53042219 ATTAAAGGATGAAAGGAGGAAGT
1 ATTAAAGGATGAAAGGAGGAAGT
53042242 ATT
1 ATT
53042245 TTCGAAACCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.23
Consensus pattern (23 bp):
ATTAAAGGATGAAAGGAGGAAGT
Found at i:53043433 original size:26 final size:25
Alignment explanation
Indices: 53043378--53043433 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
53043368 TTTTAGGGAT
**
53043378 AATTTTTTAGAATTAAAATTCCGCC
1 AATTTTTTAGAATTAAAATTCAACC
* * *
53043403 TATTTTTTAGAATTCAAATTTAACTC
1 AATTTTTTAGAATTAAAATTCAAC-C
53043429 AATTT
1 AATTT
53043434 CTACCACATA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.46
Consensus pattern (25 bp):
AATTTTTTAGAATTAAAATTCAACC
Found at i:53050694 original size:25 final size:26
Alignment explanation
Indices: 53050666--53050723 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 26
53050656 AAAAAAAGAG
*
53050666 AAAATTTTAAAGAACATAAAA-GAAA
1 AAAATATTAAAGAACATAAAACGAAA
* ** *
53050691 AAAAAATTAAATTACTTAAAACGAAA
1 AAAATATTAAAGAACATAAAACGAAA
53050717 AAAATAT
1 AAAATAT
53050724 AGAAATCAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.22
Consensus pattern (26 bp):
AAAATATTAAAGAACATAAAACGAAA
Found at i:53054646 original size:16 final size:18
Alignment explanation
Indices: 53054619--53054651 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
53054609 TATAATTCGG
53054619 TTGAGAAAATT-ATTTAA
1 TTGAGAAAATTAATTTAA
53054636 TTGAG-AAATTAATTTA
1 TTGAGAAAATTAATTTA
53054652 TTTAGCAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAA
Found at i:53056014 original size:28 final size:29
Alignment explanation
Indices: 53055961--53056016 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
53055951 CGCGAAAAAT
*
53055961 GGCCCATTCCGGTAAATAATTAAAAAACC
1 GGCCCATTCCAGTAAATAATTAAAAAACC
*
53055990 GGCCCATTTCAGTAAAT-ATTGAAAAAA
1 GGCCCATTCCAGTAAATAATT-AAAAAA
53056017 AGGGCTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (29 bp):
GGCCCATTCCAGTAAATAATTAAAAAACC
Found at i:53057466 original size:21 final size:20
Alignment explanation
Indices: 53057418--53057467 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
53057408 TTTTAAAATA
53057418 TTTTTAAAATTCTTTTTTAT
1 TTTTTAAAATTCTTTTTTAT
*
53057438 TTTTTAAAATT-TTTTTGTGT
1 TTTTTAAAATTCTTTTT-TAT
53057458 TTATTTAAAA
1 TT-TTTAAAA
53057468 AACGGGTTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 5 0.19
20 15 0.56
21 7 0.26
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (20 bp):
TTTTTAAAATTCTTTTTTAT
Found at i:53059559 original size:24 final size:24
Alignment explanation
Indices: 53059525--53059576 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
53059515 TTTCTAGAAG
*
53059525 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGTATAATAT
*
53059549 ATTTAGCATTTATTAGTATAATTT
1 ATTTAGCATTTATTAGTATAATAT
53059573 ATTT
1 ATTT
53059577 GACCTATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.56
Consensus pattern (24 bp):
ATTTAGCATTTATTAGTATAATAT
Found at i:53060639 original size:25 final size:27
Alignment explanation
Indices: 53060606--53060655 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
53060596 ATTATGATAT
* *
53060606 GCAAGTAAAA-AT-AATAAGAGTCACA
1 GCAAATAAAAGATAAATAAAAGTCACA
53060631 GCAAATAAAAGATAAATAAAAGTCA
1 GCAAATAAAAGATAAATAAAAGTCA
53060656 AATTAATTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 9 0.43
26 2 0.10
27 10 0.48
ACGTcount: A:0.60, C:0.10, G:0.14, T:0.16
Consensus pattern (27 bp):
GCAAATAAAAGATAAATAAAAGTCACA
Found at i:53061083 original size:10 final size:10
Alignment explanation
Indices: 53061054--53061084 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
53061044 ATATGTAAGT
*
53061054 ATGTATATAT
1 ATGTATATAA
53061064 ATGTATATAA
1 ATGTATATAA
53061074 ATGTATATAA
1 ATGTATATAA
53061084 A
1 A
53061085 AATTATGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (10 bp):
ATGTATATAA
Found at i:53061182 original size:33 final size:33
Alignment explanation
Indices: 53061118--53061183 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
53061108 AAAAAATATA
*
53061118 TAAAAATATGTGTATATATATTTTTACAAAAGT
1 TAAAAATATGTGTATATATATTTATACAAAAGT
53061151 TAAAAATATGTACGTATATATA-TTATA-AAAAGT
1 TAAAAATATGT--GTATATATATTTATACAAAAGT
53061184 ATGTATATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 17 0.57
34 4 0.13
35 9 0.30
ACGTcount: A:0.48, C:0.03, G:0.09, T:0.39
Consensus pattern (33 bp):
TAAAAATATGTGTATATATATTTATACAAAAGT
Found at i:53061190 original size:18 final size:18
Alignment explanation
Indices: 53061164--53061204 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
53061154 AAATATGTAC
53061164 GTATATATATTATAAAAA
1 GTATATATATTATAAAAA
*
53061182 GTATGTATATTATAAAAA
1 GTATATATATTATAAAAA
53061200 -TATAT
1 GTATAT
53061205 GCATGTGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (18 bp):
GTATATATATTATAAAAA
Found at i:53061333 original size:26 final size:27
Alignment explanation
Indices: 53061282--53061333 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
53061272 TAATAAGGTA
*
53061282 AGTAATAATAAATACAATAATAGTAAT
1 AGTAATAATAAATAAAATAATAGTAAT
*
53061309 AGTAATATTAAA-AAAATAATAGTAA
1 AGTAATAATAAATAAAATAATAGTAA
53061334 AAATAATGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.29
Consensus pattern (27 bp):
AGTAATAATAAATAAAATAATAGTAAT
Found at i:53061987 original size:2 final size:2
Alignment explanation
Indices: 53061982--53062024 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
53061972 TATATATATA
53061982 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
53062024 T
1 T
53062025 ACGATTAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:53062413 original size:13 final size:13
Alignment explanation
Indices: 53062395--53062421 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
53062385 TTTTCTGATT
53062395 TGATGCTTTGGGC
1 TGATGCTTTGGGC
53062408 TGATGCTTTGGGC
1 TGATGCTTTGGGC
53062421 T
1 T
53062422 ATTAGGGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.15, G:0.37, T:0.41
Consensus pattern (13 bp):
TGATGCTTTGGGC
Found at i:53073404 original size:12 final size:13
Alignment explanation
Indices: 53073382--53073418 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
53073372 TTTGATATTG
53073382 TTCTCTTTTTTTT
1 TTCTCTTTTTTTT
53073395 TTCT-TTTTTTTT
1 TTCTCTTTTTTTT
*
53073407 TTCCCTTTTTTT
1 TTCTCTTTTTTT
53073419 ACTATTAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTCTCTTTTTTTT
Found at i:53075353 original size:15 final size:16
Alignment explanation
Indices: 53075333--53075370 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
53075323 GAAAAATTAT
53075333 AAACTAAATAAATA-A
1 AAACTAAATAAATACA
53075348 AAACT-AATAAATACA
1 AAACTAAATAAATACA
*
53075363 TAACTAAA
1 AAACTAAA
53075371 AGGTAACACC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 8 0.40
15 10 0.50
16 2 0.10
ACGTcount: A:0.68, C:0.11, G:0.00, T:0.21
Consensus pattern (16 bp):
AAACTAAATAAATACA
Found at i:53076113 original size:20 final size:20
Alignment explanation
Indices: 53076084--53076124 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
53076074 TGACTATCTT
53076084 AGTAAAAAATTCC-ACAAAA
1 AGTAAAAAATTCCAACAAAA
53076103 AGTACAAAAATTCCAACAAAA
1 AGTA-AAAAATTCCAACAAAA
53076124 A
1 A
53076125 AAAAAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 4 0.20
20 9 0.45
21 7 0.35
ACGTcount: A:0.63, C:0.17, G:0.05, T:0.15
Consensus pattern (20 bp):
AGTAAAAAATTCCAACAAAA
Found at i:53076754 original size:24 final size:24
Alignment explanation
Indices: 53076727--53076809 Score: 66
Period size: 24 Copynumber: 3.3 Consensus size: 24
53076717 ATAGTTTCTT
53076727 TCTATATAAATTATTTAAAAAATC
1 TCTATATAAATTATTTAAAAAATC
53076751 TCTATAT---TT-TTTAAAAAAATAGTTTC
1 TCTATATAAATTATTT--AAAAA-A---TC
53076777 TTTCTATATAAATTATTTAAAAAATC
1 --TCTATATAAATTATTTAAAAAATC
53076803 TCTATAT
1 TCTATAT
53076810 TTTTTAAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 24
0.66 0.00 0.34
Matches are distributed among these distances:
20 3 0.06
21 2 0.04
22 5 0.11
23 1 0.02
24 14 0.30
26 4 0.09
28 7 0.15
29 1 0.02
30 5 0.11
31 2 0.04
32 3 0.06
ACGTcount: A:0.43, C:0.08, G:0.01, T:0.47
Consensus pattern (24 bp):
TCTATATAAATTATTTAAAAAATC
Done.