Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 56 of 82
Found at i:20345368 original size:15 final size:14
Alignment explanation
Indices: 20345344--20345386 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
20345334 TATTTTATAT
20345344 ATTTATTTAATTTA
1 ATTTATTTAATTTA
20345358 ATTTAATTTAATTTAA
1 ATTT-ATTTAATTT-A
*
20345374 ATTT-TTTATTTTA
1 ATTTATTTAATTTA
20345387 TTTGAGTGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 1 0.04
14 11 0.42
15 9 0.35
16 5 0.19
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
ATTTATTTAATTTA
Found at i:20346443 original size:22 final size:23
Alignment explanation
Indices: 20346415--20346458 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
20346405 GGTAGCTAAA
*
20346415 GTCACGCAATGC-CTACAAATAG
1 GTCACGCAATGCTCAACAAATAG
20346437 GTCACGCAATGCTCAACAAATA
1 GTCACGCAATGCTCAACAAATA
20346459 TTCAGTCACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.39, C:0.27, G:0.16, T:0.18
Consensus pattern (23 bp):
GTCACGCAATGCTCAACAAATAG
Found at i:20346503 original size:39 final size:40
Alignment explanation
Indices: 20346437--20346515 Score: 106
Period size: 39 Copynumber: 2.0 Consensus size: 40
20346427 CTACAAATAG
* * *
20346437 GTCACGCAATGCTCAACAAATATTCAGTCACATAACGCCT
1 GTCACACAACGCTAAACAAATATTCAGTCACATAACGCCT
* *
20346477 GTCACACAACGCTAAAC-AATATTCAGTCACGTAATGCCT
1 GTCACACAACGCTAAACAAATATTCAGTCACATAACGCCT
20346516 ATAAACCCAC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
39 20 0.59
40 14 0.41
ACGTcount: A:0.35, C:0.29, G:0.13, T:0.23
Consensus pattern (40 bp):
GTCACACAACGCTAAACAAATATTCAGTCACATAACGCCT
Found at i:20348060 original size:21 final size:21
Alignment explanation
Indices: 20348034--20348074 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
20348024 TACTATTAGT
20348034 AACTTGAGCTTAAACTTTTAC
1 AACTTGAGCTTAAACTTTTAC
20348055 AACTTGAGCTTAAACTTTTA
1 AACTTGAGCTTAAACTTTTA
20348075 AGAGCCACCT
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:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (21 bp):
AACTTGAGCTTAAACTTTTAC
Found at i:20364307 original size:21 final size:21
Alignment explanation
Indices: 20364265--20364307 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
20364255 CTTGTACCGG
*
20364265 TGGTGGAACTAAAGGAGTAAC
1 TGGTGGAACTAAAGGAGGAAC
* * *
20364286 TGGTGGTACTATAGGTGGAAC
1 TGGTGGAACTAAAGGAGGAAC
20364307 T
1 T
20364308 TGACCAGTCG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.09, G:0.35, T:0.26
Consensus pattern (21 bp):
TGGTGGAACTAAAGGAGGAAC
Found at i:20371484 original size:252 final size:251
Alignment explanation
Indices: 20371094--20372820 Score: 1772
Period size: 252 Copynumber: 6.9 Consensus size: 251
20371084 CTTTTATAAT
* * * * *
20371094 ACCTTTATAATATTTTACATTAATTCTTACCGTTTTACGT--TAAGCTTTTTTAAATATTAATTA
1 ACCTTTATAATGTTTTACGTTAATTCTTACCGCTTTACGTCATAA-C-TTTTTAAATAATAATTT
* * ** **
20371157 TCA-CTGTAATTCTTTTTATCTTTACTATTATTCACATATATTTTAAAATTTGTAAATCGTAAAA
64 TCATC-ATAATTCTTTTTATCTTTACTATTATTCACGTATAAATTAAAATTTGTAAGCCGTAAAA
* * * * *
20371221 CACTTTAAACTCAAAAATAACAATTTAAATGTTTAATTTCTCTAAAAATTATGTTTATTAGATAT
128 CACTTTAAACTCGAGAATAAAAATTTAAATGTTTAATTT-TCTAAAAATTATGTTTATTTGACAT
* * * *
20371286 AATTAACTTGTTACATTAAATCTCATATATTTATGTCAATATTTTAAAAATGTTTGTTTC
192 AATTAACTTGTTACGTTAAATCTCACACATTTACGTCAATATTTTAAAAATGTTTGTTTC
*** * * *
20371346 ACCTTTATAATGTTTTACGTTAATTCTTACTATTTTACGTCATAACTTTTCAACTAATAACTTTC
1 ACCTTTATAATGTTTTACGTTAATTCTTACCGCTTTACGTCATAACTTTTTAAATAATAATTTTC
* * * *
20371411 ATTATAATTCCTTTTATCTTTACTATTATTCACATATAAATTAAAATTTGTACGCCGTAAAACAC
66 ATCATAATTCTTTTTATCTTTACTATTATTCACGTATAAATTAAAATTTGTAAGCCGTAAAACAC
* * * * * *
20371476 TGTAAACTCGCGAATAACAATTTAAATGTTTAA-TTTCTAAAAAATTATATTTATTAGACATATT
131 TTTAAACTCGAGAATAAAAATTTAAATGTTTAATTTTCT-AAAAATTATGTTTATTTGACATAAT
* * * *
20371540 TGACTTGTTACATTAAATCTCACACATTTACGTTC-ATATTTTTAAAATGGTTG-TTC
195 TAACTTGTTACGTTAAATCTCACACATTTACG-TCAATATTTTAAAAATGTTTGTTTC
* * * *
20371596 TACCTTTATAATATTTTATGTTAATTCTTACCACTTTACGT--TAGCCTTTTTAAATACA-AATT
1 -ACCTTTATAATGTTTTACGTTAATTCTTACCGCTTTACGTCATA-ACTTTTTAAATA-ATAATT
* * * * * * *
20371658 TTTACCGTAATTATTTTTAT-TCTTACTATTATTTACGCATAAATTAAAATTTGTAAGTCGTAAA
63 TTCATCATAATTCTTTTTATCT-TTACTATTATTCACGTATAAATTAAAATTTGTAAGCCGTAAA
* * * * *
20371722 ACACTTTAAACACAAGAATAAAAAGTTAAATGTTTAATTTCTCCAAAAATTATGTTTATTAGACA
127 ACACTTTAAACTCGAGAATAAAAATTTAAATGTTTAATTT-TCTAAAAATTATGTTTATTTGACA
* * * * * *
20371787 TAATTAAGTTGTTACGTTTAATCTCACACATTTACGTCAATATTTTGAAAATGCTTATTCC
191 TAATTAACTTGTTACGTTAAATCTCACACATTTACGTCAATATTTTAAAAATGTTTGTTTC
* * * * * * *
20371848 ACCTCTATAATGTTTTATGTTAATTCTTACTGCTTTACATCATGACTTTTCAACTAATAATTTTC
1 ACCTTTATAATGTTTTACGTTAATTCTTACCGCTTTACGTCATAACTTTTTAAATAATAATTTTC
* * * *
20371913 ATCATCATTCTTTTTAT-TCTTACTATTATTCATGCATAAATTAAAATTTGTAAGCCGTAAAACG
66 ATCATAATTCTTTTTATCT-TTACTATTATTCACGTATAAATTAAAATTTGTAAGCCGTAAAACA
* * * * *
20371977 TTTTAAA-TATGAGAATAAAAAGTTAAATGTTTAATTTTTTCAAAAATTATGTTTATTTCACATA
130 CTTTAAACT-CGAGAATAAAAATTTAAATGTTTAATTTTCT-AAAAATTATGTTTATTTGACATA
* * * * * * *
20372041 ATTTACTTGTTATGTTAAATCTCACACATTTACATCACTATTTTTAAATTGCTTG-TTC
193 ATTAACTTGTTACGTTAAATCTCACACATTTACGTCAATATTTTAAAAATGTTTGTTTC
* * * * * * *
20372099 TACCATTATAATATTTTATGTTAATTCTTACCGCTTTACCT-AAAAGCTTTTTAAATACTATTTT
1 -ACCTTTATAATGTTTTACGTTAATTCTTACCGCTTTACGTCATAA-CTTTTTAAATAATAATTT
* * * * * *
20372163 TCA-CTGTATTTCTTTTTATCCTCACTATTATTCACGTATAGATCAAAATTTGTAAGCCGTAAAA
64 TCATC-ATAATTCTTTTTATCTTTACTATTATTCACGTATAAATTAAAATTTGTAAGCCGTAAAA
* * * * *
20372227 TATTTTAAACTTGAGAATAACAATTTAAATG-TTAATTTTTTCAAAAATTATGTTTATTTGACAT
128 CACTTTAAACTCGAGAATAAAAATTTAAATGTTTAATTTTCT-AAAAATTATGTTTATTTGACAT
* * * * * * *
20372291 AATTAACTTTTTACGTTAAATATTACATATTTATGTCAATACTTTAAAAATGTTTGTTCC
192 AATTAACTTGTTACGTTAAATCTCACACATTTACGTCAATATTTTAAAAATGTTTGTTTC
* * * * * *
20372351 ACTTTTATAATGTTTTACGCTAATTTTTACCGCTTTACGTCATGACTTTTCAACTAATAATTTTC
1 ACCTTTATAATGTTTTACGTTAATTCTTACCGCTTTACGTCATAACTTTTTAAATAATAATTTTC
* * * * * *
20372416 ATCATAATTTTTTTTATCCTTACTATTATTCATGCATAGATTAAAATTTATAAGCCGTAAAACAC
66 ATCATAATTCTTTTTATCTTTACTATTATTCACGTATAAATTAAAATTTGTAAGCCGTAAAACAC
* * * * *
20372481 TTTAAACAT-GAGAATAAAAAGTCAAATGTTTAATTTTTTTGAAAATTATGTTTATTTGATATAA
131 TTTAAAC-TCGAGAATAAAAATTTAAATGTTTAA-TTTTCTAAAAATTATGTTTATTTGACATAA
* * * * * *
20372545 TTGACTTGTTACATTAAATCTCACACATTTACGTTAATATTTTGAAAGTGTTTATTTC
194 TTAACTTGTTACGTTAAATCTCACACATTTACGTCAATATTTTAAAAATGTTTGTTTC
* * *
20372603 ACATTTATAATGTTTTACGTTAATTCTTACCGCTTTACGTCA-AGGCTTTTTAAATATTAATTTT
1 ACCTTTATAATGTTTTACGTTAATTCTTACCGCTTTACGTCATA-ACTTTTTAAATAATAATTTT
* * * * * *
20372667 CATCATAATT-TTTTTATCCTTATTATTATTCATGTATAGATTAAATTTTGTAAGCCCTAAAACA
65 CATCATAATTCTTTTTATCTTTACTATTATTCACGTATAAATTAAAATTTGTAAGCCGTAAAACA
*
20372731 CTTTAAA-TACGAGAA-GAAAATGTTAAATGTTTAATATTTAC-AAAAATTATGTTTATTTGACA
130 CTTTAAACT-CGAGAATAAAAAT-TTAAATGTTTAAT-TTT-CTAAAAATTATGTTTATTTGACA
20372793 TAATTGAA-TTGTTACGTTAAATCTCACA
191 TAATT-AACTTGTTACGTTAAATCTCACA
20372821 AATTGTCAAT
Statistics
Matches: 1236, Mismatches: 203, Indels: 73
0.82 0.13 0.05
Matches are distributed among these distances:
249 4 0.00
250 107 0.09
251 533 0.43
252 580 0.47
253 9 0.01
254 3 0.00
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (251 bp):
ACCTTTATAATGTTTTACGTTAATTCTTACCGCTTTACGTCATAACTTTTTAAATAATAATTTTC
ATCATAATTCTTTTTATCTTTACTATTATTCACGTATAAATTAAAATTTGTAAGCCGTAAAACAC
TTTAAACTCGAGAATAAAAATTTAAATGTTTAATTTTCTAAAAATTATGTTTATTTGACATAATT
AACTTGTTACGTTAAATCTCACACATTTACGTCAATATTTTAAAAATGTTTGTTTC
Found at i:20372307 original size:503 final size:502
Alignment explanation
Indices: 20371093--20372820 Score: 2107
Period size: 503 Copynumber: 3.4 Consensus size: 502
20371083 ACTTTTATAA
* * * * * *
20371093 TACCTTTATAATATTTTACATTAATTCTTACCGTTTTACGTTAAGCTTTTTTAAATATTAATTAT
1 TACCATTATAATATTTTACGTTAATTCTTACCGCTTTACGTAAAGC-TTTTTAAATACTAATTTT
* * ** **
20371158 CACTGTAATTCTTTTTATCTTTACTATTATTCACATATATTTTAAAATTTGTAAATCGTAAAACA
65 CACTGTAATTCTTTTTATCCTTACTATTATTCACGTATAGATTAAAATTTGTAAGCCGTAAAACA
* * *
20371223 CTTTAAACTCAAAAATAACAATTTAAATGTTTAA-TTTCTCTAAAAATTATGTTTATTAGATATA
130 CTTTAAACTCAAGAATAACAATTTAAATGTTTAATTTTTTC-AAAAATTATGTTTATTAGACATA
* * *
20371287 ATTAACTTGTTACATTAAATCTCATATATTTATGTCAATATTTTAAAAATGTTTGTTTCACCTTT
194 ATTAACTTGTTACGTTAAATCTCACATATTTATGTCAATATTTTAAAAATGTTTGTTCCACCTTT
** * * *
20371352 ATAATGTTTTACGTTAATTCTTACTATTTTACGTCATAACTTTTCAACTAATAACTTTCATTATA
259 ATAATGTTTTACGTTAATTCTTACTGCTTTACGTCATGACTTTTCAACTAATAATTTTCATCATA
* *** * *
20371417 ATTCCTTTTA-TCTTTACTATTATTCACATATAAATTAAAATTTGTACGCCGTAAAACACTGTAA
324 ATTCTTTTTATTC-TTACTATTATTCATGCATAAATTAAAATTTGTAAGCCGTAAAACACTTTAA
* * * * * * *
20371481 ACT-CGCGAATAACAATTTAAATGTTTAA-TTTCTAAAAAATTATATTTATTAGACAT-ATTTGA
388 A-TATGAGAATAAAAAGTTAAATGTTTAATTTTTTAAAAAATTATGTTTATTTGACATAATTT-A
* *
20371543 CTTGTTACATTAAATCTCACACATTTACGTTCATATTTTTAAAATGGTTGTTC
451 CTTGTTACATTAAATCTCACACATTTAC-ATCATATTTTTAAAATGCTTGTTC
* * * * *
20371596 TACCTTTATAATATTTTATGTTAATTCTTACCACTTTACGT-TAGCCTTTTTAAATACAAATTTT
1 TACCATTATAATATTTTACGTTAATTCTTACCGCTTTACGTAAAG-CTTTTTAAATACTAATTTT
* * * * * * * *
20371660 TACCGTAATTATTTTTATTCTTACTATTATTTACGCATAAATTAAAATTTGTAAGTCGTAAAACA
65 CACTGTAATTCTTTTTATCCTTACTATTATTCACGTATAGATTAAAATTTGTAAGCCGTAAAACA
* * * * *
20371725 CTTTAAACACAAGAATAAAAAGTTAAATGTTTAATTTCTCCAAAAATTATGTTTATTAGACATAA
130 CTTTAAACTCAAGAATAACAATTTAAATGTTTAATTTTTTCAAAAATTATGTTTATTAGACATAA
* * * * * * * *
20371790 TTAAGTTGTTACGTTTAATCTCACACATTTACGTCAATATTTTGAAAATGCTTATTCCACCTCTA
195 TTAACTTGTTACGTTAAATCTCACATATTTATGTCAATATTTTAAAAATGTTTGTTCCACCTTTA
* * *
20371855 TAATGTTTTATGTTAATTCTTACTGCTTTACATCATGACTTTTCAACTAATAATTTTCATCATCA
260 TAATGTTTTACGTTAATTCTTACTGCTTTACGTCATGACTTTTCAACTAATAATTTTCATCATAA
**
20371920 TTCTTTTTATTCTTACTATTATTCATGCATAAATTAAAATTTGTAAGCCGTAAAACGTTTTAAAT
325 TTCTTTTTATTCTTACTATTATTCATGCATAAATTAAAATTTGTAAGCCGTAAAACACTTTAAAT
* *
20371985 ATGAGAATAAAAAGTTAAATGTTTAATTTTTTCAAAAATTATGTTTATTTCACATAATTTACTTG
390 ATGAGAATAAAAAGTTAAATGTTTAATTTTTTAAAAAATTATGTTTATTTGACATAATTTACTTG
** *
20372050 TTATGTTAAATCTCACACATTTACATCACTATTTTTAAATTGCTTGTTC
455 TTACATTAAATCTCACACATTTACATCA-TATTTTTAAAATGCTTGTTC
* * *
20372099 TACCATTATAATATTTTATGTTAATTCTTACCGCTTTACCTAAAAGCTTTTTAAATACTATTTTT
1 TACCATTATAATATTTTACGTTAATTCTTACCGCTTTACGT-AAAGCTTTTTAAATACTAATTTT
* * * *
20372164 CACTGTATTTCTTTTTATCCTCACTATTATTCACGTATAGATCAAAATTTGTAAGCCGTAAAATA
65 CACTGTAATTCTTTTTATCCTTACTATTATTCACGTATAGATTAAAATTTGTAAGCCGTAAAACA
* ** *
20372229 TTTTAAACTTGAGAATAACAATTTAAATG-TTAATTTTTTCAAAAATTATGTTTATTTGACATAA
130 CTTTAAACTCAAGAATAACAATTTAAATGTTTAATTTTTTCAAAAATTATGTTTATTAGACATAA
* * * * *
20372293 TTAACTTTTTACGTTAAATATTACATATTTATGTCAATACTTTAAAAATGTTTGTTCCACTTTTA
195 TTAACTTGTTACGTTAAATCTCACATATTTATGTCAATATTTTAAAAATGTTTGTTCCACCTTTA
* * *
20372358 TAATGTTTTACGCTAATTTTTACCGCTTTACGTCATGACTTTTCAACTAATAATTTTCATCATAA
260 TAATGTTTTACGTTAATTCTTACTGCTTTACGTCATGACTTTTCAACTAATAATTTTCATCATAA
* * * * *
20372423 TTTTTTTTATCCTTACTATTATTCATGCATAGATTAAAATTTATAAGCCGTAAAACACTTTAAAC
325 TTCTTTTTATTCTTACTATTATTCATGCATAAATTAAAATTTGTAAGCCGTAAAACACTTTAAAT
* ** * *
20372488 ATGAGAATAAAAAGTCAAATGTTTAATTTTTTTGAAAATTATGTTTATTTGATATAATTGACTTG
390 ATGAGAATAAAAAGTTAAATGTTTAATTTTTTAAAAAATTATGTTTATTTGACATAATTTACTTG
* * * * * *
20372553 TTACATTAAATCTCACACATTTACGTTAATATTTTGAAAGTGTTTATT-
455 TTACATTAAATCTCACACATTTAC-ATCATATTTTTAAAATGCTTGTTC
* * *
20372601 T-CACATTTATAATGTTTTACGTTAATTCTTACCGCTTTACGTCAAGGCTTTTTAAATATTAATT
1 TAC-CA-TTATAATATTTTACGTTAATTCTTACCGCTTTACGT-AAAGCTTTTTAAATACTAATT
* * * * *
20372665 TTCA-TCATAATT-TTTTTATCCTTATTATTATTCATGTATAGATTAAATTTTGTAAGCCCTAAA
63 TTCACT-GTAATTCTTTTTATCCTTACTATTATTCACGTATAGATTAAAATTTGTAAGCCGTAAA
* * * * *
20372728 ACACTTTAAA-TACGAGAAGAA-AATGTTAAATGTTTAATATTTACAAAAATTATGTTTATTTGA
127 ACACTTTAAACT-CAAGAATAACAAT-TTAAATGTTTAATTTTTTCAAAAATTATGTTTATTAGA
20372791 CATAATTGAA-TTGTTACGTTAAATCTCACA
190 CATAATT-AACTTGTTACGTTAAATCTCACA
20372821 AATTGTCAAT
Statistics
Matches: 1049, Mismatches: 159, Indels: 34
0.84 0.13 0.03
Matches are distributed among these distances:
501 6 0.01
502 383 0.37
503 557 0.53
504 101 0.10
505 2 0.00
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (502 bp):
TACCATTATAATATTTTACGTTAATTCTTACCGCTTTACGTAAAGCTTTTTAAATACTAATTTTC
ACTGTAATTCTTTTTATCCTTACTATTATTCACGTATAGATTAAAATTTGTAAGCCGTAAAACAC
TTTAAACTCAAGAATAACAATTTAAATGTTTAATTTTTTCAAAAATTATGTTTATTAGACATAAT
TAACTTGTTACGTTAAATCTCACATATTTATGTCAATATTTTAAAAATGTTTGTTCCACCTTTAT
AATGTTTTACGTTAATTCTTACTGCTTTACGTCATGACTTTTCAACTAATAATTTTCATCATAAT
TCTTTTTATTCTTACTATTATTCATGCATAAATTAAAATTTGTAAGCCGTAAAACACTTTAAATA
TGAGAATAAAAAGTTAAATGTTTAATTTTTTAAAAAATTATGTTTATTTGACATAATTTACTTGT
TACATTAAATCTCACACATTTACATCATATTTTTAAAATGCTTGTTC
Found at i:20374226 original size:24 final size:23
Alignment explanation
Indices: 20374181--20374230 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
20374171 CTAACATTAT
*
20374181 TAACTTAAAATAAATATTTAAACA
1 TAACTTAAAATAAATATATAAA-A
*
20374205 TAACTTAAATTAAACTA-ATAAAA
1 TAACTTAAAATAAA-TATATAAAA
20374228 TAA
1 TAA
20374231 ATAAAAACAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 4 0.17
24 17 0.74
25 2 0.09
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (23 bp):
TAACTTAAAATAAATATATAAAA
Found at i:20374900 original size:20 final size:20
Alignment explanation
Indices: 20374875--20374915 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
20374865 CTTTTATAAT
20374875 GTTTTACGTTAATATTTACC
1 GTTTTACGTTAATATTTACC
20374895 GTTTTACGTTAATATTTACC
1 GTTTTACGTTAATATTTACC
20374915 G
1 G
20374916 CATTACGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.49
Consensus pattern (20 bp):
GTTTTACGTTAATATTTACC
Found at i:20374921 original size:20 final size:20
Alignment explanation
Indices: 20374878--20374923 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
20374868 TTATAATGTT
**
20374878 TTACGTTAATATTTACCGTT
1 TTACGTTAATATTTACCGCA
20374898 TTACGTTAATATTTACCGCA
1 TTACGTTAATATTTACCGCA
20374918 TTACGT
1 TTACGT
20374924 CAAGGCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (20 bp):
TTACGTTAATATTTACCGCA
Found at i:20375316 original size:251 final size:249
Alignment explanation
Indices: 20374930--20375795 Score: 860
Period size: 251 Copynumber: 3.4 Consensus size: 249
20374920 ACGTCAAGGC
** * * *
20374930 TTTTAAATACTAATTTTCATTGTAATTCTTTTTATCCTTACTATTATTCATGTACAGATTAAAAT
1 TTTTAAATACTAATTTTCATCATAATTCTTTTTATCTTTACTATTATTCATGCATAGATTAAAAT
* * * * *
20374995 TTGTAATCCGTAAAACACTTTAAACTCGAGAATAACAATTTAAATCTTTAATTTTTTTAAAAATT
66 TTGTAAGCCGTAAAACACTTTAAACTCAAGAATAACAATTTAAATGTTTAATTTCTCTAAAAATT
*
20375060 ATGTTTATTAGACTTAATTGACTTGTTACGTTAAATCTCACACATTGACGTCAATACTTTTAAAA
131 ATGTTTATTAGACTTAATTGACTTGTTACGTTAAATCTCACACATTTACGTCAATA-TTTTAAAA
* * *
20375125 TGCTTATTCCACATTTGTAATATTTTATGTTAATTCTTACCACTTTATGTCAAACCT
195 TGCTTGTTCCACATTTATAATATTTTATGTTAATTCTTACCA-TTTACGTCAAA-CT
20375182 TTTTAAATACTAATTTTCATCATAATT-TTTTTATCTTTACTATTATTCATGCATAGATTAAAAT
1 TTTTAAATACTAATTTTCATCATAATTCTTTTTATCTTTACTATTATTCATGCATAGATTAAAAT
** * * * * *
20375246 TTGTAAGCCGTACGACACTTTAAATTCAAGAATAACAATATAAATGTGTAATTTCTCAAAAAACT
66 TTGTAAGCCGTAAAACACTTTAAACTCAAGAATAACAATTTAAATGTTTAATTTCTCTAAAAATT
* * * * * *
20375311 ATGTTTATTAGA-TATAATTGACTGGTTACATTGATTCTCACAAATTTATGTCAATATTTTGAAA
131 ATGTTTATTAGACT-TAATTGACTTGTTACGTTAAATCTCACACATTTACGTCAATATTTT-AAA
* * * * * * * *
20375375 ATGTTTGTTTCACCTTTATAATGTTTTATGTTAATTCTTACCGTTTTACGTTACGATT
194 ATGCTTGTTCCACATTTATAATATTTTATGTTAATTCTTACC-ATTTACGTCA-AACT
**
20375433 TTTTAAATACTAATTTTCATGGTAATTCTTTTTATTTTCACCGTAATTCTTTTTATCTTTGTTAT
1 TTTTAAATACT-A-----AT--T--TTC-----A---TCA---TAATTCTTTTTATCTTTACTAT
* * *
20375498 TATTCATGCATAGA-TAAAATTTTGTAAGCTGTAAAATACTTTAAACTCGAA-AATAATAATTTA
45 TATTCATGCATAGATTAAAA-TTTGTAAGCCGTAAAACACTTTAAACTC-AAGAATAACAATTTA
* * * ** *
20375561 AAAGTTTAATTTGTCTAAAAATTATATTTCGTAGACATAATTGACTTGTTACGTTAAATCTCACA
108 AATGTTTAATTTCTCTAAAAATTATGTTTATTAGACTTAATTGACTTGTTACGTTAAATCTCACA
* * * * *
20375626 CATTTACATCAATATTTTTAAAATGCTTGTTCTACTTTTATAATATTTTACGTTAATTCTTATCG
173 CATTTACGTCAATA-TTTTAAAATGCTTGTTCCACATTTATAATATTTTATGTTAATTCTTA-CC
* *
20375691 ATTTACGTGAAGGCT
236 ATTTACGTCAA-ACT
* * * *
20375706 TTTTAAATATTAATTTTCATCATAATTCTTTTTAT-TCTTACTATTTTTCATGTATAAATTAAAA
1 TTTTAAATACTAATTTTCATCATAATTCTTTTTATCT-TTACTATTATTCATGCATAGATTAAAA
* *
20375770 ATTGTAAGCCATAAAACACTTTAAAC
65 TTTGTAAGCCGTAAAACACTTTAAAC
20375796 ATTTAACTTT
Statistics
Matches: 498, Mismatches: 82, Indels: 68
0.77 0.13 0.10
Matches are distributed among these distances:
250 5 0.01
251 193 0.39
252 78 0.16
253 5 0.01
255 3 0.01
257 2 0.00
258 1 0.00
259 1 0.00
261 3 0.01
263 3 0.01
265 1 0.00
266 1 0.00
267 2 0.00
269 3 0.01
272 11 0.02
273 179 0.36
274 7 0.01
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (249 bp):
TTTTAAATACTAATTTTCATCATAATTCTTTTTATCTTTACTATTATTCATGCATAGATTAAAAT
TTGTAAGCCGTAAAACACTTTAAACTCAAGAATAACAATTTAAATGTTTAATTTCTCTAAAAATT
ATGTTTATTAGACTTAATTGACTTGTTACGTTAAATCTCACACATTTACGTCAATATTTTAAAAT
GCTTGTTCCACATTTATAATATTTTATGTTAATTCTTACCATTTACGTCAAACT
Found at i:20375471 original size:21 final size:21
Alignment explanation
Indices: 20375445--20375488 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
20375435 TTAAATACTA
**
20375445 ATTTTCATGGTAATTCTTTTT
1 ATTTTCACCGTAATTCTTTTT
20375466 ATTTTCACCGTAATTCTTTTT
1 ATTTTCACCGTAATTCTTTTT
20375487 AT
1 AT
20375489 CTTTGTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.14, G:0.07, T:0.59
Consensus pattern (21 bp):
ATTTTCACCGTAATTCTTTTT
Found at i:20375604 original size:524 final size:514
Alignment explanation
Indices: 20374409--20375794 Score: 1533
Period size: 521 Copynumber: 2.7 Consensus size: 514
20374399 CGTAAATGCT
* *
20374409 TTTTAAATACTAATTTTTACAGTAATTCTTTTTAT-TCTTACTATTATTCACGCATAGATTAAAA
1 TTTTAAATACTAATTTTCACAGTAATTCTTTTTATCT-TTACTATTATTCATGCATAGATTAAAA
* * * *
20374473 TTTGTAAGCCATAAAATACTTTAAAGTTGAAAATAATAATTTAAATGTTTAATTTCTCCAAAAAT
65 TTTGTAAGCCGTAAAATACTTTAAACTCGAAAATAATAATTTAAATGTTTAATTTCTCTAAAAAT
* *
20374538 TATGTTTATTAGACATAATT-AGCTTTTTACTTTAAATCTCACACATTTACATCAATATTTTGAA
130 TATGTTTATTAGACATAATTGA-CTTGTTACGTTAAATCTCACACATTTACATCAATATTTT-AA
* * * * * *
20374602 AATGCTTGTTCTACCTTTATAATGTTTTATGTTAATTCTTATCTCTTTACGTCATGA-TTTTTCT
193 AATGCTTGTTCTACATTTATAATATTTTATGTTAATTCTTACCACTTTACGTCA-AACTTTTT-A
* * * * *
20374666 ACTAATAATTTTCATCATAATTCTTTTTATCCTTACTATTATTCACGCATAGGTTAAAATTTTTA
256 AATAATAATTTTCATCATAATTCTTTTTATCTTTACTATTATTCATGCATAGATTAAAATTTGTA
** * * * ** * *
20374731 AATCGTAAAACACTTTAAGCATGAGAATAAAAGGTTAAATGTTTATTTTCCCGAATATTATGTTT
321 AGCCGTAAAACACTTTAA--ATAAGAATAAAA-GTTAAATGTGTAATTTCCAAAAAACTATGTTT
* * * * * *
20374796 ATTTGACATAATTGACTTGTTACGTTAAATTTTATACATTTTATCAATATTTTGAAAATGCTTAT
383 ATTAGACATAATTGACTGGTTACATTAAATTTCACAAATTTTATCAATATTTTGAAAATGCTTAT
* * * *
20374861 TCTACTTTTATAATGTTTTACGTTAATATTTACCGTTTTACGTTAATATTTACCGCATTACGTCA
448 TCTACCTTTATAATGTTTTACGTTAATATTTACCGTTTTACGTTAAGATTTACCGAAATACGTCA
20374926 AGG
513 A-G
** * * *
20374929 CTTTTAAATACTAATTTTCATTGTAATTCTTTTTATCCTTACTATTATTCATGTACAGATTAAAA
1 -TTTTAAATACTAATTTTCACAGTAATTCTTTTTATCTTTACTATTATTCATGCATAGATTAAAA
* * * * * * *
20374994 TTTGTAATCCGTAAAACACTTTAAACTCGAGAATAACAATTTAAATCTTTAATTTTTTTAAAAAT
65 TTTGTAAGCCGTAAAATACTTTAAACTCGAAAATAATAATTTAAATGTTTAATTTCTCTAAAAAT
* * *
20375059 TATGTTTATTAGACTTAATTGACTTGTTACGTTAAATCTCACACATTGACGTCAATACTTTTAAA
130 TATGTTTATTAGACATAATTGACTTGTTACGTTAAATCTCACACATTTACATCAATA-TTTTAAA
* * * *
20375124 ATGCTTATTCCACATTTGTAATATTTTATGTTAATTCTTACCACTTTATGTCAAACCTTTTTAAA
194 ATGCTTGTTCTACATTTATAATATTTTATGTTAATTCTTACCACTTTACGTCAAA-CTTTTTAAA
*
20375189 TACTAATTTTCATCATAATT-TTTTTATCTTTACTATTATTCATGCATAGATTAAAATTTGTAAG
258 TAATAATTTTCATCATAATTCTTTTTATCTTTACTATTATTCATGCATAGATTAAAATTTGTAAG
**
20375253 CCGTACGACACTTTAAATTCAAGAATAACAA-TATAAATGTGTAATTTCTCAAAAAACTATGTTT
323 CCGTAAAACACTTTAAA-T-AAGAATAA-AAGT-TAAATGTGTAATTTC-CAAAAAACTATGTTT
* * * *
20375317 ATTAGATATAATTGACTGGTTACATT-GATTCTCACAAATTTATGTCAATATTTTGAAAATGTTT
383 ATTAGACATAATTGACTGGTTACATTAAATT-TCACAAATTT-TATCAATATTTTGAAAATGCTT
* * * ***
20375381 GTT-TCACCTTTATAATGTTTTATGTTAAT-TCTTACCGTTTTACGTTACGATTT-TTTAAATAC
446 ATTCT-ACCTTTATAATGTTTTACGTTAATAT-TTACCGTTTTACGTTAAGATTTACCGAAATAC
20375443 -T-AA-
509 GTCAAG
* * * **
20375446 TTTTCATGGTAATTCTTTTTATTTTCACCGTAATTCTTTTTATCTTTGTTATTATTCATGCATAG
1 TTTT-A----AATAC---TAATTTTCACAGTAATTCTTTTTATCTTTACTATTATTCATGCATAG
* * *
20375511 A-TAAAATTTTGTAAGCTGTAAAATACTTTAAACTCGAAAATAATAATTTAAAAGTTTAATTTGT
58 ATTAAAA-TTTGTAAGCCGTAAAATACTTTAAACTCGAAAATAATAATTTAAATGTTTAATTTCT
* **
20375575 CTAAAAATTATATTTCGTAGACATAATTGACTTGTTACGTTAAATCTCACACATTTACATCAATA
122 CTAAAAATTATGTTTATTAGACATAATTGACTTGTTACGTTAAATCTCACACATTTACATCAATA
* * * * *
20375640 TTTTTAAAATGCTTGTTCTACTTTTATAATATTTTACGTTAATTCTTATCGA-TTTACGTGAAGG
187 -TTTTAAAATGCTTGTTCTACATTTATAATATTTTATGTTAATTCTTA-CCACTTTACGTCAA-A
* * * *
20375704 CTTTTTAAATATTAATTTTCATCATAATTCTTTTTAT-TCTTACTATTTTTCATGTATAAATTAA
249 CTTTTTAAATAATAATTTTCATCATAATTCTTTTTATCT-TTACTATTATTCATGCATAGATTAA
* *
20375768 AAATTGTAAGCCATAAAACACTTTAAA
313 AATTTGTAAGCCGTAAAACACTTTAAA
20375795 CATTTAACTT
Statistics
Matches: 726, Mismatches: 112, Indels: 50
0.82 0.13 0.06
Matches are distributed among these distances:
516 4 0.01
517 1 0.00
518 1 0.00
519 4 0.01
520 77 0.11
521 280 0.39
522 74 0.10
523 5 0.01
524 226 0.31
525 54 0.07
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (514 bp):
TTTTAAATACTAATTTTCACAGTAATTCTTTTTATCTTTACTATTATTCATGCATAGATTAAAAT
TTGTAAGCCGTAAAATACTTTAAACTCGAAAATAATAATTTAAATGTTTAATTTCTCTAAAAATT
ATGTTTATTAGACATAATTGACTTGTTACGTTAAATCTCACACATTTACATCAATATTTTAAAAT
GCTTGTTCTACATTTATAATATTTTATGTTAATTCTTACCACTTTACGTCAAACTTTTTAAATAA
TAATTTTCATCATAATTCTTTTTATCTTTACTATTATTCATGCATAGATTAAAATTTGTAAGCCG
TAAAACACTTTAAATAAGAATAAAAGTTAAATGTGTAATTTCCAAAAAACTATGTTTATTAGACA
TAATTGACTGGTTACATTAAATTTCACAAATTTTATCAATATTTTGAAAATGCTTATTCTACCTT
TATAATGTTTTACGTTAATATTTACCGTTTTACGTTAAGATTTACCGAAATACGTCAAG
Found at i:20375698 original size:273 final size:272
Alignment explanation
Indices: 20375194--20375741 Score: 670
Period size: 273 Copynumber: 2.0 Consensus size: 272
20375184 TTAAATACTA
* *
20375194 ATTTTCATCATAATTTTTTTATCTTTACTATTATTCATGCATAGATTAAAATTTGTAAGCCGTAC
1 ATTTTCACCATAATTTTTTTATCTTTACTATTATTCATGCATAGATTAAAATTTGTAAGCCGTAA
* * * * * *
20375259 GACACTTTAAATTCAAGAATAACAATATAAATGTGTAATTTCTCAAAAAACTATGTTTATTAGAT
66 AACACTTTAAACTCAAGAATAACAATATAAAAGTGTAATTTCTCAAAAAACTATATTTAGTAGAC
* * ** *
20375324 ATAATTGACTGGTTACATTGATTCTCACAAATTTATGTCAATATTTTGAAAATGTTTGTTTCACC
131 ATAATTGACTGGTTACATTAAATCTCACAAATTTACATCAATATTTTGAAAATGCTTGTTTCACC
* * * * * * *
20375389 TTTATAATGTTTTATGTTAATTCTTACCGTTTTACGTTACGATTTTTTAAATACTAATTTTCATG
196 TTTATAATATTTTACGTTAATTCTTACCGATTTACGTGAAGACTTTTTAAATACTAATTTTCATC
*
20375454 GTAATTCTTTTT
261 ATAATTCTTTTT
* ** *
20375466 ATTTTCACCGTAATTCTTTTTATCTTTGTTATTATTCATGCATAGA-TAAAATTTTGTAAGCTGT
1 ATTTTCACCATAATT-TTTTTATCTTTACTATTATTCATGCATAGATTAAAA-TTTGTAAGCCGT
* * * * * * * *
20375530 AAAATACTTTAAACTCGAA-AATAATAATTTAAAAGTTTAATTTGTCTAAAAATTATATTTCGTA
64 AAAACACTTTAAACTC-AAGAATAACAATATAAAAGTGTAATTTCTCAAAAAACTATATTTAGTA
* * * *
20375594 GACATAATTGACTTGTTACGTTAAATCTCACACATTTACATCAATATTTTTAAAATGCTTG-TTC
128 GACATAATTGACTGGTTACATTAAATCTCACAAATTTACATCAATATTTTGAAAATGCTTGTTTC
* * * *
20375658 TACTTTTATAATATTTTACGTTAATTCTTATCGATTTACGTGAAGGCTTTTTAAATATTAATTTT
193 -ACCTTTATAATATTTTACGTTAATTCTTACCGATTTACGTGAAGACTTTTTAAATACTAATTTT
20375723 CATCATAATTCTTTTT
257 CATCATAATTCTTTTT
20375739 ATT
1 ATT
20375742 CTTACTATTT
Statistics
Matches: 231, Mismatches: 41, Indels: 7
0.83 0.15 0.03
Matches are distributed among these distances:
272 21 0.09
273 208 0.90
274 2 0.01
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.46
Consensus pattern (272 bp):
ATTTTCACCATAATTTTTTTATCTTTACTATTATTCATGCATAGATTAAAATTTGTAAGCCGTAA
AACACTTTAAACTCAAGAATAACAATATAAAAGTGTAATTTCTCAAAAAACTATATTTAGTAGAC
ATAATTGACTGGTTACATTAAATCTCACAAATTTACATCAATATTTTGAAAATGCTTGTTTCACC
TTTATAATATTTTACGTTAATTCTTACCGATTTACGTGAAGACTTTTTAAATACTAATTTTCATC
ATAATTCTTTTT
Found at i:20376316 original size:251 final size:250
Alignment explanation
Indices: 20375790--20376849 Score: 1010
Period size: 249 Copynumber: 4.2 Consensus size: 250
20375780 ATAAAACACT
* * * * * * * * *
20375790 TTAAACATTTAACTTTTTATTCTCGTGTTTAAAGTGTTTTATGGTTGACAATTTTTAATGTGTGA
1 TTAAATATTTAAATTTTTATTCTCGAGTTTAAAATGTTTTACGGTTTACAAATTTTAATCTAT-A
* * *
20375855 GTGAATAATAGTAAGGATAAAAAGAATTATGATGAAAATTATTAATTG-AAAATCATGACGT-AA
65 GTGAATAATAATAAGGATAAAAAGAATTATGATGAAAATTATTAATTGAAAAATAATGATGTAAA
* * * * * **
20375918 GCCGTAAGAATTAACGTAAAACATTATAAAGGTGAAACAATG-ATTGTCAAAGTATTGATATAAA
130 GCCATAAAAATTAACGTAAAACATTATAAAGGTGGAACAA-GAATTATCAAAATATTGACGTAAA
* * * *
20375982 TGTGTGAAATTTAATATAACAAGTCAATTATGTCAAATAAATATAATTTTTGAAAAAA
194 TGTGTGAAATTTAACATAACAAGTCAATTATATCAAATAAACATAATTTTTG-GAAAA
** * *
20376040 TTAAACGTTTAACTTTTTCATTCTCGTGTTTAAAATGTTTTACGGTTTACAAATTTTAATCTATA
1 TTAAATATTTAAATTTTT-ATTCTCGAGTTTAAAATGTTTTACGGTTTACAAATTTTAATCTATA
* * * * *
20376105 CGAGAATAATAACAAGGATAAAAATAATTATGATAAAAATTATTAGTTGAAAAATAATGATGTAA
65 -GTGAATAATAATAAGGATAAAAAGAATTATGATGAAAATTATTAATTGAAAAATAATGATGTAA
*** * *
20376170 AGTGGTAAAAATTAACGTAAAACATTATAAAGGTGGAATAAGAATTTTCAAAATATTGACGTAAA
129 AGCCATAAAAATTAACGTAAAACATTATAAAGGTGGAACAAGAATTATCAAAATATTGACGTAAA
* * *
20376235 TGTGTG-AATTTAACATAATAAGTCAATTGTATCTAATAAACATAATTTTTGGAGAAA
194 TGTGTGAAATTTAACATAACAAGTCAATTATATCAAATAAACATAATTTTTGGA-AAA
* * *** * *
20376292 TTAAATATTTAAATTGTTATTCTCGAGTTTAAAGTGTTTTACAAATTGCAAATTTTAATCTGT-G
1 TTAAATATTTAAATTTTTATTCTCGAGTTTAAAATGTTTTACGGTTTACAAATTTTAATCTATAG
* * * * *
20376356 TGAATAATGATAAGGATAAAAAGAATTATGGTGAGAATT-TT-AGT-AAAAAAAACTTTGATGTA
66 TGAATAATAATAAGGATAAAAAGAATTATGATGAAAATTATTAATTGAAAAATAA---TGATGTA
* * * * *
20376418 AAGACATAAGAATTAATGTAAAATATTATAAAGGTGGAACAAAAATTATCAAAATATTGACGT-A
128 AAGCCATAAAAATTAACGTAAAACATTATAAAGGTGGAACAAGAATTATCAAAATATTGACGTAA
* * * * * * * *
20376482 ATGAGTGAGATTTAATAT-TCAAGTTAATTATGTTAAAAAAACATAATTTTTAGGAAAA
193 ATGTGTGAAATTTAACATAACAAGTCAATTATATCAAATAAACATAATTTTT-GGAAAA
* * * ** * * *
20376540 TTAAATATTTAAAGTTTTATT-TTGAGTTTAAAATGTTTTATGACTAACAAATTTTAATGTATGC
1 TTAAATATTTAAATTTTTATTCTCGAGTTTAAAATGTTTTACGGTTTACAAATTTTAATCTAT-A
* * * * *
20376604 GTGAATAATAGTAAGGATAAAAAGAATTATAATGAAAATTATTAATCGAAAAGTCATGATGTAAA
65 GTGAATAATAATAAGGATAAAAAGAATTATGATGAAAATTATTAATTGAAAAATAATGATGTAAA
** * * * * *
20376669 GCCATAAAAATTAATATAAAATATTATAAAGGTAGAATAAGTATTATCAAAATATTGACGAAAAT
130 GCCATAAAAATTAACGTAAAACATTATAAAGGTGGAACAAGAATTATCAAAATATTGACGTAAAT
** * * ** * *
20376734 GTGTGTGATTTAACGTAACAAATCAATTATATCAAAATAAATTTATTTTTTGTTAAAA
195 GTGTGAAATTTAACATAACAAGTCAATTATATC-AAATAAACATAATTTTTG-GAAAA
* * * ** * *
20376792 TTAAATATTTAATTTTTTATTATTGAG-TTAACAACATTTAACGGTTTAAAAATTTTAA
1 TTAAATATTTAAATTTTTATTCTCGAGTTTAA-AATGTTTTACGGTTTACAAATTTTAA
20376850 CTTATAAAAG
Statistics
Matches: 663, Mismatches: 125, Indels: 41
0.80 0.15 0.05
Matches are distributed among these distances:
246 7 0.01
247 33 0.05
248 56 0.08
249 202 0.30
250 35 0.05
251 133 0.20
252 113 0.17
253 84 0.13
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.36
Consensus pattern (250 bp):
TTAAATATTTAAATTTTTATTCTCGAGTTTAAAATGTTTTACGGTTTACAAATTTTAATCTATAG
TGAATAATAATAAGGATAAAAAGAATTATGATGAAAATTATTAATTGAAAAATAATGATGTAAAG
CCATAAAAATTAACGTAAAACATTATAAAGGTGGAACAAGAATTATCAAAATATTGACGTAAATG
TGTGAAATTTAACATAACAAGTCAATTATATCAAATAAACATAATTTTTGGAAAA
Found at i:20377069 original size:68 final size:68
Alignment explanation
Indices: 20376995--20377128 Score: 182
Period size: 68 Copynumber: 2.0 Consensus size: 68
20376985 TTAATTTTCA
* *
20376995 TAAAAATCCTATTGTTCTCCTTGTTAG-TTTTTT-CATTCTAATTAATATTTTTTGGTTAATTAT
1 TAAAAATCCTATTATTCTCCTTGTTAGTTTTTTTGC-TT-TAATTAATATTTTTTGCTTAATTAT
20377058 TTCCT
64 TTCCT
** * *
20377063 TAAAAATTTTGTTATTCTCTTTGTTAGTTTTTTTGCTTTAATTAATATTTTTTGCTTAATTATTT
1 TAAAAATCCTATTATTCTCCTTGTTAGTTTTTTTGCTTTAATTAATATTTTTTGCTTAATTATTT
20377128 C
66 C
20377129 GTTTTAATTA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
68 49 0.84
69 8 0.14
70 1 0.02
ACGTcount: A:0.23, C:0.10, G:0.07, T:0.59
Consensus pattern (68 bp):
TAAAAATCCTATTATTCTCCTTGTTAGTTTTTTTGCTTTAATTAATATTTTTTGCTTAATTATTT
CCT
Found at i:20378075 original size:26 final size:25
Alignment explanation
Indices: 20378029--20378077 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
20378019 CTTAATAAAA
**
20378029 AATTATTTTTCTTTTGTCTTTTTAT
1 AATTATTTTTCTTTTCACTTTTTAT
*
20378054 AATTAGTTTTTTTTTTCACTTTTT
1 AATTA-TTTTTCTTTTCACTTTTT
20378078 TTGAACGTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 5 0.25
26 15 0.75
ACGTcount: A:0.16, C:0.08, G:0.04, T:0.71
Consensus pattern (25 bp):
AATTATTTTTCTTTTCACTTTTTAT
Found at i:20385626 original size:295 final size:288
Alignment explanation
Indices: 20385060--20385638 Score: 843
Period size: 295 Copynumber: 2.0 Consensus size: 288
20385050 CCGTGCTCTT
* * * **
20385060 GACTTTATATTTCAGTTGCAGGTTCATTTAATTTATTTTATTATTAAAATCTGGTGCAGTTGTTG
1 GACTTTATATTTCAGTTGCAGGTTCATTTAACTTAATCTAGCATTAAAATCTGGTGCAGTTGTTG
* * * *
20385125 TGATTGTATGTTCTGCCACTGCTGCTTTTTGTAATAACAGTAATTTGTTCATACTGGCATTTCTG
66 TAATTGTATATTCTGACACTGCTGCTTTTTGTAATAACAGTAATTTGTTCATACTCGCATTTCTG
** * * * *
20385190 CATAATACATCAAGAAAGAGCTTTTTTAGCTCTAAGAAGGTCCAAACACATTATTTACATGATAT
131 CATAATACATCAAGAAAGAGCCCTTTTAGCACTAACAAGGTCCAAACACATTATTTACACGACAT
* ***
20385255 GTAGGCTTCTTGTTTGTTTTATCTTTTGTTATAGATAATTTTATGTGGCAAAAGGACTGCATCTT
196 GTAGGCTTCTTGTTTGTCTTATCTTTTGTTATAGATAATTTTATACAGCAAAAGGACTGCATCTT
20385320 GATTTTCAAGTGTGTCTTCACTGTGCTC
261 GATTTTCAAGTGTGTCTTCACTGTGCTC
*
20385348 GACTTTATATTTCAGTTGCAGGTTCATTTAACTTAATCTAGCATTAAAATCTGGTCCAGGTAGTT
1 GACTTTATATTTCAGTTGCAGGTTCATTTAACTTAATCTAGCATTAAAATCTGGT----GCAGTT
* * * *
20385413 GTTGTAATTGTATATTCTTACATTTGCTGCTTTTTGTAGTAGCAGTAATTTGTTCATACTCGCAT
62 GTTGTAATTGTATATTCTGACA-CTGCTGCTTTTTGTAATAACAGTAATTTGTTCATACTCGCAT
20385478 TTCTGCATAATACATCAAGAAAGAGCCCTTTTAGCACTAACAAGGTCCAAACACACATTATTTAC
126 TTCTGCATAATACATCAAGAAAGAGCCCTTTTAGCACTAACAAGGTCC-AA-ACACATTATTTAC
* * *
20385543 ACGACATTTAGGCTTCTTGTTTGTCTTATCTTTTGTTATTGATAATTTTATACAGTAAAAGGACT
189 ACGACATGTAGGCTTCTTGTTTGTCTTATCTTTTGTTATAGATAATTTTATACAGCAAAAGGACT
*
20385608 GCATCTTGATTTTCAAGTGTGTCTTCTCTGT
254 GCATCTTGATTTTCAAGTGTGTCTTCACTGT
20385639 TGATTTGAAG
Statistics
Matches: 256, Mismatches: 28, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
288 50 0.20
292 23 0.09
293 82 0.32
294 2 0.01
295 99 0.39
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (288 bp):
GACTTTATATTTCAGTTGCAGGTTCATTTAACTTAATCTAGCATTAAAATCTGGTGCAGTTGTTG
TAATTGTATATTCTGACACTGCTGCTTTTTGTAATAACAGTAATTTGTTCATACTCGCATTTCTG
CATAATACATCAAGAAAGAGCCCTTTTAGCACTAACAAGGTCCAAACACATTATTTACACGACAT
GTAGGCTTCTTGTTTGTCTTATCTTTTGTTATAGATAATTTTATACAGCAAAAGGACTGCATCTT
GATTTTCAAGTGTGTCTTCACTGTGCTC
Found at i:20394373 original size:47 final size:47
Alignment explanation
Indices: 20394319--20394412 Score: 136
Period size: 47 Copynumber: 2.0 Consensus size: 47
20394309 GTCATTGAAA
* *
20394319 TGGGGTGTTTGACTTGT-GACTACCTAAGAGTTCAGTATCTATCTGAT
1 TGGGGTGTTTAACTCGTCG-CTACCTAAGAGTTCAGTATCTATCTGAT
* *
20394366 TGGGGTGTTTAACTCGTCGCTGCCTAAGAGTTCAGTATTTATCTGAT
1 TGGGGTGTTTAACTCGTCGCTACCTAAGAGTTCAGTATCTATCTGAT
20394413 ACTGGTCTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
47 41 0.98
48 1 0.02
ACGTcount: A:0.20, C:0.16, G:0.26, T:0.38
Consensus pattern (47 bp):
TGGGGTGTTTAACTCGTCGCTACCTAAGAGTTCAGTATCTATCTGAT
Found at i:20400681 original size:20 final size:20
Alignment explanation
Indices: 20400656--20400695 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
20400646 TCAGATGCTG
*
20400656 ATTTACACATAAAATAAAAT
1 ATTTACACAAAAAATAAAAT
20400676 ATTTACACAAAAAATAAAAT
1 ATTTACACAAAAAATAAAAT
20400696 GCTATGCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (20 bp):
ATTTACACAAAAAATAAAAT
Found at i:20407157 original size:18 final size:18
Alignment explanation
Indices: 20407134--20407169 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
20407124 GACTTATGCG
20407134 ATGATTAGCATGTAATCT
1 ATGATTAGCATGTAATCT
20407152 ATGATTAGCATGTAATCT
1 ATGATTAGCATGTAATCT
20407170 TGTGCCTAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (18 bp):
ATGATTAGCATGTAATCT
Found at i:20410423 original size:15 final size:15
Alignment explanation
Indices: 20410385--20410427 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
20410375 CTTTGCAATG
* *
20410385 CAATGTGATTACAAG
1 CAATGTGATTGCAAA
* *
20410400 TAATATGATTGCAAA
1 CAATGTGATTGCAAA
20410415 CAATGTGATTGCA
1 CAATGTGATTGCA
20410428 GGGAAAATAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.30
Consensus pattern (15 bp):
CAATGTGATTGCAAA
Found at i:20410627 original size:17 final size:17
Alignment explanation
Indices: 20410605--20410637 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
20410595 ATTATTAATT
20410605 TTATATA-ATATCATTTC
1 TTATATATATAT-ATTTC
20410622 TTATATATATATATTT
1 TTATATATATATATTT
20410638 TTAATGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (17 bp):
TTATATATATATATTTC
Found at i:20410696 original size:32 final size:32
Alignment explanation
Indices: 20410647--20410717 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
20410637 TTTAATGTTA
* * *
20410647 TATATGTTATTTTCATTTTTTATTATAATCTTG
1 TATAT-TTATTTTCATTTCTTAATATAATCTTC
* *
20410680 TATATTTTTTTTCATTTCTTAATATAATTTTC
1 TATATTTATTTTCATTTCTTAATATAATCTTC
20410712 TATATT
1 TATATT
20410718 AGATAGTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
32 28 0.85
33 5 0.15
ACGTcount: A:0.25, C:0.07, G:0.03, T:0.65
Consensus pattern (32 bp):
TATATTTATTTTCATTTCTTAATATAATCTTC
Found at i:20413619 original size:27 final size:27
Alignment explanation
Indices: 20413586--20413638 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
20413576 TTATTTTATT
20413586 TTTAAAATATTAATAATTGATAATTTA
1 TTTAAAATATTAATAATTGATAATTTA
20413613 TTTAAAATATTAATAATTGATAATTT
1 TTTAAAATATTAATAATTGATAATTT
20413639 TAATATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (27 bp):
TTTAAAATATTAATAATTGATAATTTA
Found at i:20413654 original size:41 final size:41
Alignment explanation
Indices: 20413608--20413700 Score: 109
Period size: 41 Copynumber: 2.2 Consensus size: 41
20413598 ATAATTGATA
*
20413608 ATTTATTTAAAATATTAATAATTGATAATT-T-TAATATTAAT
1 ATTTATTTAAAAT-TTAATAATTGAT-ATTGTAAAATATTAAT
* * *
20413649 ATTTATTTATAATTTAATTATTTATATTGTAAAATATTAAT
1 ATTTATTTAAAATTTAATAATTGATATTGTAAAATATTAAT
20413690 ATTTTATTTAA
1 A-TTTATTTAA
20413701 TTTAAATATT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
39 3 0.07
40 11 0.25
41 22 0.50
42 8 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (41 bp):
ATTTATTTAAAATTTAATAATTGATATTGTAAAATATTAAT
Found at i:20413693 original size:112 final size:111
Alignment explanation
Indices: 20413471--20413698 Score: 257
Period size: 112 Copynumber: 2.0 Consensus size: 111
20413461 TTTTTATTAG
* *
20413471 ATTTTTTAAATATTAATAATCTAGAATTTAATTAAAATATTAATAATAAATCATTTAAATATTAA
1 ATTTTTAAAATATTAATAATCTAGAATTTAATTAAAATATTAATAATAAATAATTTAAATATTAA
* * * *
20413536 CATTTATTTAATTTAAATATTATTATGATTAATTTTTATTTTATTTT
66 CATTTATTTAATTTAAATATTATTATGATAAAATATTA-TATATTTT
* * ** *
20413583 ATTTTTAAAATATTAATAAT-TGATAATTTATTTAAAATATTAATAATTGATAATTTTAATATTA
1 ATTTTTAAAATATTAATAATCT-AGAATTTAATTAAAATATTAATAATAAATAATTTAAATATTA
* *
20413647 ATATTTATTTATAATTTAATTATT-TATATTG-TAAAATATTA-ATATTTT
65 ACATTTA-TT-TAATTTAAATATTAT-TA-TGATAAAATATTATATATTTT
20413695 ATTT
1 ATTT
20413699 AATTTAAATA
Statistics
Matches: 98, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
111 1 0.01
112 71 0.72
113 3 0.03
114 21 0.21
115 2 0.02
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (111 bp):
ATTTTTAAAATATTAATAATCTAGAATTTAATTAAAATATTAATAATAAATAATTTAAATATTAA
CATTTATTTAATTTAAATATTATTATGATAAAATATTATATATTTT
Found at i:20413771 original size:155 final size:154
Alignment explanation
Indices: 20413527--20413813 Score: 470
Period size: 155 Copynumber: 1.9 Consensus size: 154
20413517 TAAATCATTT
* *
20413527 AAATATTAACATTTATTTAATTTAAATATTATTATGATTAATTTTTATTTTATTTTATTTTTAAA
1 AAATATTAACATTTATTTAATTTAAATATTATGATGATCAATTTTTATTTTATTTTATTTTTAAA
* *
20413592 ATATTAATAATTGATAATTTATTTAAAATATTAATAATTGATAATTTTAATATTAATA-TTTATT
66 ATATTAATAATTGATAATTTATTTAAAATATTAATAATAGATAATTTAAATATTAATATTTTATT
20413656 TATAATTTAATTATTTATATTGTA
131 TATAATTTAATTATTTATATTGTA
*
20413680 AAATATTAATATTTTATTTAATTTAAATATTATGATGATCAATTATTTTATTTTATTTTATTTTT
1 AAATATTAACA-TTTATTTAATTTAAATATTATGATGATCAA-T-TTTTATTTTATTTTATTTTT
* *
20413745 GAAA-ATTAATAATTGATTATTTATTTAAAATATTAATAATAGATAATTTAAATATTAATATTTT
63 AAAATATTAATAATTGATAATTTATTTAAAATATTAATAATAGATAATTTAAATATTAATATTTT
20413809 ATTTA
128 ATTTA
20413814 ATTTAAATTT
Statistics
Matches: 123, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
153 10 0.08
154 28 0.23
155 54 0.44
156 31 0.25
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (154 bp):
AAATATTAACATTTATTTAATTTAAATATTATGATGATCAATTTTTATTTTATTTTATTTTTAAA
ATATTAATAATTGATAATTTATTTAAAATATTAATAATAGATAATTTAAATATTAATATTTTATT
TATAATTTAATTATTTATATTGTA
Found at i:20413885 original size:109 final size:108
Alignment explanation
Indices: 20413648--20414048 Score: 404
Period size: 114 Copynumber: 3.6 Consensus size: 108
20413638 TTAATATTAA
* * *
20413648 TATTTATTTATAAT-TTAATTATTTAT-ATTGTAAAATATTAATATTTTATTTAATTTAAATATT
1 TATTTATTTAAAATATTAATAATTGATAATT-T-AAATATTAATATTTTATTTAATTTAAATATT
* *
20413711 ATGATGATCAATTATTTTATTTTATTTTATTTTTGAAA-ATTAATAATTG
64 ATTATGATTAATT-TTTTATTTTA---TATTTTT-AAATATTAATAATTG
* *
20413760 ATTATTTATTTAAAATATTAATAATAGATAATTTAAATATTAATATTTTATTTAATTTAAATTTT
1 --TATTTATTTAAAATATTAATAATTGATAATTTAAATATTAATATTTTATTTAATTTAAATATT
20413825 ATTATGATTAATTTTTTATTTTAT-TTTTTAAATATTAATAATTGG
64 ATTATGATTAATTTTTTATTTTATATTTTTAAATATTAATAATT-G
* * *
20413870 TAATTTATTTAAAATATTAATAATTGATGATTTAATTATTAATATTGTTTATCTAATTTAAATGA
1 T-ATTTATTTAAAATATTAATAATTGATAATTTAAATATTAATA-T-TTTATTTAATTTAAAT-A
* * * * **
20413935 -TATTATGTTTATTTATTTTTAATTTATTTTGTTTTTAAATAGGAATAATT-
62 TTATTATG---ATTAATTTTTTA-TT-TTATATTTTTAAATATTAATAATTG
*
20413985 TA-TAATTTAAAATATTAATAATTGATAATTTAAATATTAATATTTTATTTATAATTT-AATATT
1 TATTTATTTAAAATATTAATAATTGATAATTTAAATATTAATATTTTA-TT-TAATTTAAATATT
20414048 A
64 A
20414049 ATATTTTATT
Statistics
Matches: 249, Mismatches: 21, Indels: 36
0.81 0.07 0.12
Matches are distributed among these distances:
108 4 0.02
109 54 0.22
110 3 0.01
111 27 0.11
112 7 0.03
113 53 0.21
114 65 0.26
115 13 0.05
116 6 0.02
117 17 0.07
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.56
Consensus pattern (108 bp):
TATTTATTTAAAATATTAATAATTGATAATTTAAATATTAATATTTTATTTAATTTAAATATTAT
TATGATTAATTTTTTATTTTATATTTTTAAATATTAATAATTG
Found at i:20413926 original size:21 final size:22
Alignment explanation
Indices: 20413884--20413927 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
20413874 TTATTTAAAA
*
20413884 TATTAATAATTGATGATTTAAT
1 TATTAATAATTGATGATCTAAT
* *
20413906 TATTAAT-ATTGTTTATCTAAT
1 TATTAATAATTGATGATCTAAT
20413927 T
1 T
20413928 TAAATGATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (22 bp):
TATTAATAATTGATGATCTAAT
Found at i:20414004 original size:23 final size:22
Alignment explanation
Indices: 20413968--20414057 Score: 92
Period size: 23 Copynumber: 3.9 Consensus size: 22
20413958 TTATTTTGTT
**
20413968 TTTAAATAGGAATAATTTATAA
1 TTTAAATATTAATAATTTATAA
*
20413990 TTTAAAATATTAATAATTGATAA
1 TTT-AAATATTAATAATTTATAA
20414013 TTTAAATATTAATATTTTATTTATAA
1 TTTAAATATTAATA----ATTTATAA
*
20414039 TTT-AATATTAATATTTTAT
1 TTTAAATATTAATAATTTAT
20414058 TAAAAATTGG
Statistics
Matches: 58, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
21 5 0.09
22 14 0.24
23 19 0.33
25 10 0.17
26 10 0.17
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (22 bp):
TTTAAATATTAATAATTTATAA
Found at i:20414034 original size:19 final size:20
Alignment explanation
Indices: 20413980--20414048 Score: 72
Period size: 19 Copynumber: 3.4 Consensus size: 20
20413970 TAAATAGGAA
20413980 TAAT-TTATAATTTAAAATAT
1 TAATATTATAATTT-AAATAT
20414000 TAATAATTGATAATTTAAATAT
1 TAAT-ATT-ATAATTTAAATAT
*
20414022 TAATATT-TTATTTATAAT-T
1 TAATATTATAATTTA-AATAT
20414041 TAATATTA
1 TAATATTA
20414049 ATATTTTATT
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
19 14 0.33
20 7 0.16
21 3 0.07
22 12 0.28
23 7 0.16
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (20 bp):
TAATATTATAATTTAAATAT
Found at i:20414050 original size:25 final size:26
Alignment explanation
Indices: 20413982--20414058 Score: 101
Period size: 25 Copynumber: 3.1 Consensus size: 26
20413972 AATAGGAATA
20413982 ATTTATAATTTAAAATATTAATA----
1 ATTTATAATTT-AAATATTAATATTTT
*
20414005 ATTGATAATTTAAATATTAATATTTT
1 ATTTATAATTTAAATATTAATATTTT
20414031 ATTTATAATTT-AATATTAATATTTT
1 ATTTATAATTTAAATATTAATATTTT
20414056 ATT
1 ATT
20414059 AAAAATTGGA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
22 11 0.23
23 10 0.21
25 17 0.35
26 10 0.21
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (26 bp):
ATTTATAATTTAAATATTAATATTTT
Found at i:20414065 original size:25 final size:26
Alignment explanation
Indices: 20414011--20414065 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 26
20414001 AATAATTGAT
* *
20414011 AATTTAAATATTAATATTTTATTTAT
1 AATTTAAATATTAATATTTTATTAAA
20414037 AATTT-AATATTAATATTTTATTAAA
1 AATTTAAATATTAATATTTTATTAAA
20414062 AATT
1 AATT
20414066 GGAATCAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 22 0.81
26 5 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
AATTTAAATATTAATATTTTATTAAA
Found at i:20419261 original size:30 final size:30
Alignment explanation
Indices: 20419227--20419299 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
20419217 CCAATTAGTG
*
20419227 TTTTTTTATTTTTT-AAAAATATAATTATAA
1 TTTTTTTATTTTTTAAAAAAAAT-ATTATAA
** * * *
20419257 TTTTTAAATTATTTAAAAAAAATATTTTAG
1 TTTTTTTATTTTTTAAAAAAAATATTATAA
20419287 TTTTTTTATTTTT
1 TTTTTTTATTTTT
20419300 AGTAATAGCA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
30 26 0.79
31 7 0.21
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (30 bp):
TTTTTTTATTTTTTAAAAAAAATATTATAA
Found at i:20420774 original size:15 final size:15
Alignment explanation
Indices: 20420756--20420830 Score: 63
Period size: 15 Copynumber: 5.3 Consensus size: 15
20420746 TTATTTTATT
20420756 TTTAAATATTAATAA
1 TTTAAATATTAATAA
*
20420771 TTT--ATA--ATTAA
1 TTTAAATATTAATAA
*
20420782 TTAAAATATTAATAA
1 TTTAAATATTAATAA
20420797 -TT-AATAATTAATAA
1 TTTAAAT-ATTAATAA
* *
20420811 TTTAAATATCAATAT
1 TTTAAATATTAATAA
20420826 TTTAA
1 TTTAA
20420831 TATAAATTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
11 6 0.13
13 9 0.19
14 9 0.19
15 20 0.43
16 3 0.06
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTAAATATTAATAA
Found at i:20420788 original size:26 final size:26
Alignment explanation
Indices: 20420759--20420808 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
20420749 TTTTATTTTT
*
20420759 AAATATTAATAATTTATAATTAATTA
1 AAATATTAATAATTAATAATTAATTA
20420785 AAATATTAATAATTAATAATTAAT
1 AAATATTAATAATTAATAATTAAT
20420809 AATTTAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
AAATATTAATAATTAATAATTAATTA
Found at i:20420801 original size:7 final size:7
Alignment explanation
Indices: 20420763--20420812 Score: 61
Period size: 7 Copynumber: 7.4 Consensus size: 7
20420753 ATTTTTAAAT
20420763 ATTAATA
1 ATTAATA
*
20420770 ATTTATA
1 ATTAATA
20420777 ATTAATTA
1 ATTAA-TA
20420785 A--AAT-
1 ATTAATA
20420789 ATTAATA
1 ATTAATA
20420796 ATTAATA
1 ATTAATA
20420803 ATTAATA
1 ATTAATA
20420810 ATT
1 ATT
20420813 TAAATATCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
4 1 0.03
5 1 0.03
6 5 0.14
7 27 0.73
8 3 0.08
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
ATTAATA
Found at i:20420945 original size:8 final size:8
Alignment explanation
Indices: 20420934--20421050 Score: 55
Period size: 8 Copynumber: 14.5 Consensus size: 8
20420924 CATTAAAAAT
20420934 TTAATATA
1 TTAATATA
20420942 TTAATA-A
1 TTAATATA
20420949 TTTAATA-A
1 -TTAATATA
* * *
20420957 ATAAAACA
1 TTAATATA
*
20420965 TTAA-ATT
1 TTAATATA
*
20420972 TTAAAATA
1 TTAATATA
*
20420980 TTAATATT
1 TTAATATA
20420988 TTATATATAA
1 TTA-ATAT-A
*
20420998 TTTAA-ACA
1 -TTAATATA
*
20421006 TTATTAATA
1 TTAAT-ATA
20421015 TTAATATGA
1 TTAATAT-A
*
20421024 TTAAAATA
1 TTAATATA
20421032 TTAA-ATA
1 TTAATATA
*
20421039 TTAATATT
1 TTAATATA
20421047 TTAA
1 TTAA
20421051 ATTTTATAAA
Statistics
Matches: 84, Mismatches: 15, Indels: 20
0.71 0.13 0.17
Matches are distributed among these distances:
7 20 0.24
8 42 0.50
9 18 0.21
10 1 0.01
11 3 0.04
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (8 bp):
TTAATATA
Found at i:20420976 original size:15 final size:16
Alignment explanation
Indices: 20420958--20420990 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
20420948 ATTTAATAAA
20420958 TAAAACATTAA-ATTT
1 TAAAACATTAATATTT
*
20420973 TAAAATATTAATATTT
1 TAAAACATTAATATTT
20420989 TA
1 TA
20420991 TATATAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAAACATTAATATTT
Found at i:20420995 original size:15 final size:15
Alignment explanation
Indices: 20420964--20421052 Score: 55
Period size: 15 Copynumber: 6.0 Consensus size: 15
20420954 TAAATAAAAC
20420964 ATTAA-ATTTTAAAAT
1 ATTAATATTTT-AAAT
*
20420979 ATTAATATTTTATAT
1 ATTAATATTTTAAAT
*
20420994 A-T-A-ATTTAAACATT
1 ATTAATATTTTAA-A-T
20421008 ATTAATA--TTAATAT
1 ATTAATATTTTAA-AT
* *
20421022 GATTAAAATATTAAAT
1 -ATTAATATTTTAAAT
20421038 ATTAATATTTTAAAT
1 ATTAATATTTTAAAT
20421053 TTTATAAATA
Statistics
Matches: 57, Mismatches: 8, Indels: 18
0.69 0.10 0.22
Matches are distributed among these distances:
12 5 0.09
13 2 0.04
14 4 0.07
15 33 0.58
16 8 0.14
17 5 0.09
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (15 bp):
ATTAATATTTTAAAT
Found at i:20421060 original size:24 final size:25
Alignment explanation
Indices: 20421006--20421062 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
20420996 AATTTAAACA
*
20421006 TTATTAATATTAATATGATTAAAAT
1 TTATAAATATTAATATGATTAAAAT
* * *
20421031 AT-TAAATATTAATAT-TTTAAATT
1 TTATAAATATTAATATGATTAAAAT
20421054 TTATAAATA
1 TTATAAATA
20421063 ATTTATTCTT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 7 0.27
24 18 0.69
25 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (25 bp):
TTATAAATATTAATATGATTAAAAT
Found at i:20424333 original size:141 final size:141
Alignment explanation
Indices: 20424079--20424354 Score: 471
Period size: 141 Copynumber: 2.0 Consensus size: 141
20424069 GTTAAAGATG
*
20424079 AAATGGAATTTAGAGATGAGTAGAATTATCATAGAATGCAGCATAAACTGATATGATCTCTAGTA
1 AAATGGAATTTAGAGATGAGTAGAATTATCATAGAACGCAGCATAAACTGATATGATCTCTAGTA
**
20424144 AGCTTTTAGATTAGAGGGTTTGATACTACATTAACCAAATGTTGCCTATGTGCGTGTTATGTCCT
66 AGCTTTTAGATTAGAGGGTTTGATACTACATTAACCAAATGTTGCCTATGTGAATGTTATGTCCT
20424209 GTGTCAGATTA
131 GTGTCAGATTA
** * *
20424220 AAATGGAATTTAGAGATGAGTAGGGTTATCTTAGAACGCAGCATAAACTGATATTATCTCTAGTA
1 AAATGGAATTTAGAGATGAGTAGAATTATCATAGAACGCAGCATAAACTGATATGATCTCTAGTA
**
20424285 AGCTTTTAGATTAGAGGGTTTGATACTACATTAACCAGTTGTTGCCTATGTGAATGTTATGTCCT
66 AGCTTTTAGATTAGAGGGTTTGATACTACATTAACCAAATGTTGCCTATGTGAATGTTATGTCCT
20424350 GTGTC
131 GTGTC
20424355 TATCTGATAC
Statistics
Matches: 126, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
141 126 1.00
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.35
Consensus pattern (141 bp):
AAATGGAATTTAGAGATGAGTAGAATTATCATAGAACGCAGCATAAACTGATATGATCTCTAGTA
AGCTTTTAGATTAGAGGGTTTGATACTACATTAACCAAATGTTGCCTATGTGAATGTTATGTCCT
GTGTCAGATTA
Found at i:20426080 original size:16 final size:16
Alignment explanation
Indices: 20426059--20426089 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
20426049 AAATATAAAA
20426059 AATATATATATATATG
1 AATATATATATATATG
20426075 AATATATATATATAT
1 AATATATATATATAT
20426090 ATTATAAAAT
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:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
AATATATATATATATG
Found at i:20426516 original size:228 final size:227
Alignment explanation
Indices: 20426117--20426574 Score: 907
Period size: 228 Copynumber: 2.0 Consensus size: 227
20426107 AATAATTTTA
20426117 TTAATTAATATACTCTCAGGTCAAGCTCGGGCCTTACAAATCTTTTCCAAAACTCAATCTAAATT
1 TTAATTAATATACTCTCAGGTCAAGCTCGGGCCTTACAAATCTTTTCCAAAACTCAATCTAAATT
20426182 GGACAAGGCCATCGACCTTACAAATCTTTTCCGAAACTCATGACCAAATTTATTAACGATAAATA
66 GGACAAGGCCATCGACCTTACAAATCTTTTCCGAAACTCATGACCAAATTTATTAACGATAAATA
20426247 TTTCAAAAATGGATGACGTTAAAATGATATACGTAATTTTAAATTTAGAAAACATATTATTTTAC
131 TTTCAAAAATGGATGACGTTAAAATGATATACGTAATTTTAAATTTAGAAAACATATTATTTTAC
20426312 TTTAGTTAAATTATGTAATTAGTTTTTATATT
196 TTTAGTTAAATTATGTAATTAGTTTTTATATT
20426344 TTNAATTAATATACTCTCAGGTCAAGCTCGGGCCTTACAAATCTTTTCCAAAACTCAATCTAAAT
1 TT-AATTAATATACTCTCAGGTCAAGCTCGGGCCTTACAAATCTTTTCCAAAACTCAATCTAAAT
20426409 TGGACAAGGCCATCGACCTTACAAATCTTTTCCGAAACTCATGACCAAATTTATTAACGATAAAT
65 TGGACAAGGCCATCGACCTTACAAATCTTTTCCGAAACTCATGACCAAATTTATTAACGATAAAT
20426474 ATTTCAAAAATGGATGACGTTAAAATGATATACGTAATTTTAAATTTAGAAAACATATTATTTTA
130 ATTTCAAAAATGGATGACGTTAAAATGATATACGTAATTTTAAATTTAGAAAACATATTATTTTA
20426539 CTTTAGTTAAATTATGTAATTAGTTTTTATATT
195 CTTTAGTTAAATTATGTAATTAGTTTTTATATT
20426572 TTA
1 TTA
20426575 TAAAAAAATA
Statistics
Matches: 230, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
227 3 0.01
228 227 0.99
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.37
Consensus pattern (227 bp):
TTAATTAATATACTCTCAGGTCAAGCTCGGGCCTTACAAATCTTTTCCAAAACTCAATCTAAATT
GGACAAGGCCATCGACCTTACAAATCTTTTCCGAAACTCATGACCAAATTTATTAACGATAAATA
TTTCAAAAATGGATGACGTTAAAATGATATACGTAATTTTAAATTTAGAAAACATATTATTTTAC
TTTAGTTAAATTATGTAATTAGTTTTTATATT
Found at i:20429443 original size:3 final size:3
Alignment explanation
Indices: 20429435--20429476 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
20429425 ATTTATTCAT
20429435 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
20429477 AACAAGGATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:20443090 original size:29 final size:27
Alignment explanation
Indices: 20443032--20443100 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 27
20443022 GACTTATATT
20443032 TTTTAATTTTTTAATTAATCCATCGATA
1 TTTTAATTTTTTAATTAATCCA-CGATA
*
20443060 TTTTAATTTTGTTCAATCTAATCC-CTATA
1 TTTTAATTTT-TT-AAT-TAATCCACGATA
*
20443089 TTATATATTTTT
1 TTTTA-ATTTTT
20443101 ATTCAATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
28 10 0.29
29 11 0.31
30 8 0.23
31 6 0.17
ACGTcount: A:0.29, C:0.12, G:0.03, T:0.57
Consensus pattern (27 bp):
TTTTAATTTTTTAATTAATCCACGATA
Found at i:20445226 original size:21 final size:21
Alignment explanation
Indices: 20445189--20445229 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20445179 ATGGTAACAG
*
20445189 TATAATGTAGTAAATACTATA
1 TATAATGTAGAAAATACTATA
20445210 TATAATGTA-AAATATACTAT
1 TATAATGTAGAAA-ATACTAT
20445230 GATCTAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (21 bp):
TATAATGTAGAAAATACTATA
Found at i:20474952 original size:2 final size:2
Alignment explanation
Indices: 20474919--20474990 Score: 108
Period size: 2 Copynumber: 36.0 Consensus size: 2
20474909 GCCTGATACA
* * * *
20474919 AT AT AT AA AT AT AA AT AT AA AT AT AA AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20474961 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20474991 TCAAGTCACC
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:20476144 original size:46 final size:45
Alignment explanation
Indices: 20476077--20476168 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 45
20476067 AATTCCAGAC
*
20476077 TAATCTGGCATAAATATATCATGGTGATGTATTAAAGAGGTTTTTT
1 TAATCTGGCATAAATATATCATGGTGAAGTATTAAAGA-GTTTTTT
20476123 TAATCTGGCATAAATATATCATGGTGAAGTATTAAAGAGTTTTTT
1 TAATCTGGCATAAATATATCATGGTGAAGTATTAAAGAGTTTTTT
20476168 T
1 T
20476169 GAGTCTATAC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 8 0.18
46 37 0.82
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.41
Consensus pattern (45 bp):
TAATCTGGCATAAATATATCATGGTGAAGTATTAAAGAGTTTTTT
Found at i:20477912 original size:3 final size:3
Alignment explanation
Indices: 20477906--20477968 Score: 72
Period size: 3 Copynumber: 21.0 Consensus size: 3
20477896 GTAGTATTCG
* * * * * *
20477906 TCT TCT TCT TCT TCT TCC TCC TCT TCT TCC TCT TCC CCT TCC TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
20477954 TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT
20477969 CTTTCGTCCT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (3 bp):
TCT
Found at i:20477921 original size:12 final size:12
Alignment explanation
Indices: 20477906--20477968 Score: 81
Period size: 12 Copynumber: 5.2 Consensus size: 12
20477896 GTAGTATTCG
*
20477906 TCTTCTTCTTCT
1 TCTTCCTCTTCT
*
20477918 TCTTCCTCCTCT
1 TCTTCCTCTTCT
*
20477930 TCTTCCTCTTCC
1 TCTTCCTCTTCT
*
20477942 CCTTCCTCTTCT
1 TCTTCCTCTTCT
*
20477954 TCTTCTTCTTCT
1 TCTTCCTCTTCT
20477966 TCT
1 TCT
20477969 CTTTCGTCCT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 43 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (12 bp):
TCTTCCTCTTCT
Found at i:20478845 original size:33 final size:33
Alignment explanation
Indices: 20478802--20478865 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
20478792 GCAAGATACG
*
20478802 TCATCTTTAATTATAATATATCAACATATCACA
1 TCATCATTAATTATAATATATCAACATATCACA
*
20478835 TCATCATTAATTATAATATATTAACATATCA
1 TCATCATTAATTATAATATATCAACATATCA
20478866 GTTCAATGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.41
Consensus pattern (33 bp):
TCATCATTAATTATAATATATCAACATATCACA
Found at i:20478958 original size:30 final size:29
Alignment explanation
Indices: 20478924--20478990 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 29
20478914 AATAATTGAT
**
20478924 TATAAAAATTGATTTGATTTGAAATAAAAA
1 TATAAAAATT-ATTTGATTCAAAATAAAAA
*
20478954 TATAAAGACTTATTTGATTCAAAATAAAAA
1 TATAAA-AATTATTTGATTCAAAATAAAAA
20478984 TATAAAA
1 TATAAAA
20478991 CTTTAATTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 1 0.03
30 29 0.88
31 3 0.09
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.34
Consensus pattern (29 bp):
TATAAAAATTATTTGATTCAAAATAAAAA
Found at i:20480122 original size:26 final size:26
Alignment explanation
Indices: 20480084--20480137 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
20480074 CCAATAATTT
*
20480084 TAGCTATTTAAACAAATAGTCATGTC
1 TAGCTATTGAAACAAATAGTCATGTC
20480110 TAGCTATTGAAACAAATAGTCATGTC
1 TAGCTATTGAAACAAATAGTCATGTC
20480136 TA
1 TA
20480138 TTGAAAAACC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (26 bp):
TAGCTATTGAAACAAATAGTCATGTC
Found at i:20480141 original size:22 final size:24
Alignment explanation
Indices: 20480087--20480143 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 24
20480077 ATAATTTTAG
*
20480087 CTATTTAAACAAATAGTCATGTCTA
1 CTATTGAAACAAATAGTCATG-CTA
20480112 GCTATTGAAACAAATAGTCATG-T-
1 -CTATTGAAACAAATAGTCATGCTA
20480135 CTATTGAAA
1 CTATTGAAA
20480144 AACCAACCGT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 9 0.30
24 1 0.03
26 20 0.67
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.33
Consensus pattern (24 bp):
CTATTGAAACAAATAGTCATGCTA
Found at i:20487314 original size:12 final size:12
Alignment explanation
Indices: 20487297--20487323 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
20487287 CACTACTACT
20487297 GCTCCCACTCCC
1 GCTCCCACTCCC
20487309 GCTCCCACTCCC
1 GCTCCCACTCCC
20487321 GCT
1 GCT
20487324 ACTCTCACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.63, G:0.11, T:0.19
Consensus pattern (12 bp):
GCTCCCACTCCC
Found at i:20497707 original size:15 final size:15
Alignment explanation
Indices: 20497689--20497732 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
20497679 GTGTTTACAG
20497689 GTAATGTAATTGTAA
1 GTAATGTAATTGTAA
*
20497704 GTAATGTAATTGCAA
1 GTAATGTAATTGTAA
* *
20497719 GCAATGTGATTGTA
1 GTAATGTAATTGTA
20497733 GGAAAAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.36, C:0.05, G:0.23, T:0.36
Consensus pattern (15 bp):
GTAATGTAATTGTAA
Found at i:20498693 original size:24 final size:24
Alignment explanation
Indices: 20498666--20498797 Score: 108
Period size: 24 Copynumber: 5.6 Consensus size: 24
20498656 ACACGCTATG
* *
20498666 ATGTTACACACTATGTACAAAAAT
1 ATGTGACACACCATGTACAAAAAT
** **
20498690 ATGTGACACACCATG-A-TTAGGT
1 ATGTGACACACCATGTACAAAAAT
* * * *
20498712 -TGTTACACACCATGTATAGAAAC
1 ATGTGACACACCATGTACAAAAAT
* *
20498735 ATGTGACACGCCATGTACAAAAAC
1 ATGTGACACACCATGTACAAAAAT
**
20498759 ATGTGACACGTCATGTACAAAAAT
1 ATGTGACACACCATGTACAAAAAT
*
20498783 ATGTGACACGCCATG
1 ATGTGACACACCATG
20498798 GTTAGGTTGT
Statistics
Matches: 86, Mismatches: 19, Indels: 6
0.77 0.17 0.05
Matches are distributed among these distances:
21 13 0.15
22 3 0.03
23 2 0.02
24 68 0.79
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATGTGACACACCATGTACAAAAAT
Found at i:20498917 original size:29 final size:29
Alignment explanation
Indices: 20498804--20498967 Score: 112
Period size: 29 Copynumber: 5.8 Consensus size: 29
20498794 CATGGTTAGG
* * *
20498804 TTGTTACACTCCATGTTGAAAAAAATATTG
1 TTGTTACACGCCATGTTGAAAAAAA-AATA
* *
20498834 TTGTTACACGCCATG-T-ACAAAAACATA
1 TTGTTACACGCCATGTTGAAAAAAAAATA
* * *
20498861 ---TTACAAGCTATAGTT----AAAAAAGA
1 TTGTTACACGCCAT-GTTGAAAAAAAAATA
20498884 TTGTTACACGCCATGTTGAAAAAAAAATA
1 TTGTTACACGCCATGTTGAAAAAAAAATA
* *
20498913 CTGTTGTTACACGCCATGTTGAAAAAATATTA
1 ---TTGTTACACGCCATGTTGAAAAAAAAATA
* *
20498945 TTGTTACACGCCATATTTAAAAA
1 TTGTTACACGCCATGTTGAAAAA
20498968 CATTTTGTTA
Statistics
Matches: 106, Mismatches: 16, Indels: 25
0.72 0.11 0.17
Matches are distributed among these distances:
23 6 0.06
24 9 0.08
25 4 0.04
26 10 0.09
27 1 0.01
28 6 0.06
29 29 0.27
30 14 0.13
32 27 0.25
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (29 bp):
TTGTTACACGCCATGTTGAAAAAAAAATA
Found at i:20498975 original size:27 final size:29
Alignment explanation
Indices: 20498883--20498980 Score: 101
Period size: 32 Copynumber: 3.3 Consensus size: 29
20498873 GTTAAAAAAG
* *
20498883 ATTGTTACACGCCATGTTGAAAAAAAAATACT
1 ATTGTTACACGCCATATTG-AAAAAACAT--T
* * *
20498915 GTTGTTACACGCCATGTTGAAAAAATATT
1 ATTGTTACACGCCATATTGAAAAAACATT
*
20498944 ATTGTTACACGCCATATT-TAAAAACATT
1 ATTGTTACACGCCATATTGAAAAAACATT
20498972 -TTGTTACAC
1 ATTGTTACAC
20498981 TTTAATGTCT
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
27 9 0.15
28 8 0.13
29 17 0.28
31 8 0.13
32 18 0.30
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (29 bp):
ATTGTTACACGCCATATTGAAAAAACATT
Found at i:20500860 original size:29 final size:29
Alignment explanation
Indices: 20500820--20500916 Score: 97
Period size: 29 Copynumber: 3.3 Consensus size: 29
20500810 AAAGAAGAAT
* * *
20500820 TGTATGTGAATAGGTATAAGAAAAGAAAC
1 TGTACGTGAATAGGTACAAGAAAAGAAGC
*
20500849 TGTACGTGAATAGGTACAAGAGAAA-AAGT
1 TGTACGTGAATAGGTACAAGA-AAAGAAGC
* * * *
20500878 TGTACATAAATAGATACAAGAGAAGAAGC
1 TGTACGTGAATAGGTACAAGAAAAGAAGC
*
20500907 TATACGTGAA
1 TGTACGTGAA
20500917 CAAGTATAAG
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
28 2 0.04
29 49 0.91
30 3 0.06
ACGTcount: A:0.47, C:0.07, G:0.24, T:0.22
Consensus pattern (29 bp):
TGTACGTGAATAGGTACAAGAAAAGAAGC
Found at i:20501108 original size:17 final size:18
Alignment explanation
Indices: 20501086--20501120 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
20501076 TTACTTTCAC
*
20501086 TGTTATT-TGTGTGAAGT
1 TGTTATTCTGTGCGAAGT
20501103 TGTTATTCTGTGCGAAGT
1 TGTTATTCTGTGCGAAGT
20501121 AATTGTTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.17, C:0.06, G:0.29, T:0.49
Consensus pattern (18 bp):
TGTTATTCTGTGCGAAGT
Found at i:20502208 original size:19 final size:19
Alignment explanation
Indices: 20502163--20502210 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
20502153 TCATTTGTAC
20502163 TTTTATTAATT-TATTTATA
1 TTTTA-TAATTATATTTATA
*
20502182 -TTTA-AATTATTTTTATA
1 TTTTATAATTATATTTATA
20502199 TTTTATAATTAT
1 TTTTATAATTAT
20502211 GGATAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
16 4 0.16
17 7 0.28
18 8 0.32
19 6 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTATAATTATATTTATA
Found at i:20504903 original size:92 final size:93
Alignment explanation
Indices: 20504746--20505029 Score: 468
Period size: 92 Copynumber: 3.1 Consensus size: 93
20504736 GCAGCACAAA
*
20504746 TAATGTTGTGGAACATGTCCCTCATGTTTTGGCTGCGTCACTACCACTCATACCTAGTTTTTGTA
1 TAATGTTGTGGAACATGTCCCTCATGTTTTGGCTGCATCACTACCACTCATACCTAGTTTTTGTA
*
20504811 TACAGGTTTAGAGAAATG-AATCATTTT
66 TACAGGTTTAAAGAAATGAAATCATTTT
20504838 TAATGTTGTGGAACATGTCCCTCATGTTTTGGCTGCATCACTACCACTCATACCTAGTTTTTGTA
1 TAATGTTGTGGAACATGTCCCTCATGTTTTGGCTGCATCACTACCACTCATACCTAGTTTTTGTA
20504903 TACA-GTTTAAAGAAATGAAATCATTTT
66 TACAGGTTTAAAGAAATGAAATCATTTT
* *
20504930 TAATGTTGTGGAACATGTCCTTCATG--TTGGCTGCATCACTACCACTCATACCTAGTTTTTGCA
1 TAATGTTGTGGAACATGTCCCTCATGTTTTGGCTGCATCACTACCACTCATACCTAGTTTTTGTA
*
20504993 TTCAGTAGTTTTAAAGAAATGAAATCATTTT
66 TACAG--G-TTTAAAGAAATGAAATCATTTT
20505024 TAATGT
1 TAATGT
20505030 CTTTAAAAAA
Statistics
Matches: 182, Mismatches: 5, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
90 39 0.21
91 12 0.07
92 102 0.56
93 1 0.01
94 28 0.15
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (93 bp):
TAATGTTGTGGAACATGTCCCTCATGTTTTGGCTGCATCACTACCACTCATACCTAGTTTTTGTA
TACAGGTTTAAAGAAATGAAATCATTTT
Found at i:20510139 original size:2 final size:2
Alignment explanation
Indices: 20510132--20510166 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
20510122 AAACATGTGC
*
20510132 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20510167 ACATGAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20510726 original size:29 final size:29
Alignment explanation
Indices: 20510684--20510742 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
20510674 TACATTAATC
20510684 ACAGCCCTTCCCTGTACATCCAACATCCA
1 ACAGCCCTTCCCTGTACATCCAACATCCA
20510713 ACAGCCCTTCCCTGTACATCCAACATCCA
1 ACAGCCCTTCCCTGTACATCCAACATCCA
20510742 A
1 A
20510743 TATGACAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.29, C:0.44, G:0.07, T:0.20
Consensus pattern (29 bp):
ACAGCCCTTCCCTGTACATCCAACATCCA
Found at i:20517331 original size:15 final size:15
Alignment explanation
Indices: 20517306--20517345 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
20517296 TATTTCAAAC
20517306 ATAATTAATAA-TTTT
1 ATAATT-ATAATTTTT
20517321 ATAAGTTATAATTTTT
1 ATAA-TTATAATTTTT
20517337 ATAATTATA
1 ATAATTATA
20517346 GACACCTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
ATAATTATAATTTTT
Found at i:20522334 original size:16 final size:16
Alignment explanation
Indices: 20522301--20522368 Score: 63
Period size: 15 Copynumber: 4.4 Consensus size: 16
20522291 TTACTAATCA
20522301 AATAAAATATAA-AAAT
1 AATAAAA-ATAATAAAT
*
20522317 AA-AAAAGTAATGAAAT
1 AATAAAAATAAT-AAAT
20522333 AATAAAAATAATAAAT
1 AATAAAAATAATAAAT
**
20522349 -ATAGCAATAAT-AAT
1 AATAAAAATAATAAAT
20522363 AATAAA
1 AATAAA
20522369 TACAAGAGGG
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
14 6 0.14
15 16 0.38
16 12 0.29
17 8 0.19
ACGTcount: A:0.71, C:0.01, G:0.04, T:0.24
Consensus pattern (16 bp):
AATAAAAATAATAAAT
Found at i:20524184 original size:25 final size:24
Alignment explanation
Indices: 20524149--20524207 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 24
20524139 TAGATAGTAA
* * *
20524149 ATATATTTATATTTAAAGTATATAT
1 ATATATATATACTAAAAGTAT-TAT
*
20524174 ATATATATATACTAAAAGTATTTT
1 ATATATATATACTAAAAGTATTAT
20524198 A-ATATATATA
1 ATATATATATA
20524208 ATAATAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 9 0.30
24 3 0.10
25 18 0.60
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (24 bp):
ATATATATATACTAAAAGTATTAT
Found at i:20524520 original size:337 final size:325
Alignment explanation
Indices: 20523792--20524625 Score: 948
Period size: 337 Copynumber: 2.5 Consensus size: 325
20523782 CATTACGATA
* * * * * * * * *
20523792 GTAATGTTAATACAAAATAAAAAGGAAATACATTTGTATTTAAAGCGTATATGTGCTAAGAGTAT
1 GTAATGTTAACACAAAATATAAAGTAAATATATTTATATTTAAAG-ATATATATACTAAAAGTAT
* * *
20523857 TTTAGTAAATATATAATAGTAATTATATTTCTTATAAATGAACCCAAAGTATATAAAGTATATAT
65 TTTAG---ATATAT-ATAATAATAATATTTCTTATAAATGAACAC-AA-TATATAAAGTATATAT
* *
20523922 ATTAAAAGACATTGCAAG---TTAATAATCATAGTTTCATTAATTAATTTAATTAACTATATGAA
124 ATTAAAAGACATTACAAGTAATTAATAATCATAGTTTCATGAATTAATTTAATTAACTATATGAA
*
20523984 TTTGTCCTTAATTACATGAAATTAAAAAAAAATAACTAGGTTTCAAATCTCACAACTTTCCTTTA
189 TTTGTCCTTAATTACATAAAATTAAAAAAAAATAACTAGGTTTCAAATCTCACAACTTTCCTTTA
* * * * * *
20524049 GATTTATATATTATAAGTTTTTATAAACAAAGGTATATATTGTAATTAATAATTTTATAAGTTAT
254 GATTTATATATTATAAATTTATATAAAAAAAGATATATATTATAATTAATAATTTTATAAATTAT
*
20524114 GATTTTT
319 AATTTTT
20524121 GTAATGTTAACACAAAA-ATAGATAGTAAATATATTTATATTTAAAGTATATATATATATATATA
1 GTAATGTTAACACAAAATATA-A-AGTAAATATATTTATATTTAAAG---------ATATATATA
*
20524185 CTAAAAGTATTTTA-ATATATATAATAATAATA-TTCTTTATAAATGAACTTCATATATATAAAG
55 CTAAAAGTATTTTAGATATATATAATAATAATATTTC-TTATAAATGAAC-ACA-ATATATAAAG
*
20524248 TATATATATTAAAAGACATTACAAGATAATTAATAATTATAGTTTCATGAATTAATTTAATTAAC
117 TATATATATTAAAAGACATTACAAG-TAATTAATAATCATAGTTTCATGAATTAATTTAATTAAC
*
20524313 TATATGAGTTTGTCCTTAATTACATAAAATT-AAAAAAAATAACTAGGTTTCAAACCTATTCTAT
181 TATATGAATTTGTCCTTAATTACATAAAATTAAAAAAAAATAACTAGGTTTC-AA---A-TC---
*
20524377 TCTCGTAAC-TTCTCTTTA-AGTTTATATATTATAAATTTATATAAATAAAAGTATATATATTAT
238 TCAC--AACTTTC-CTTTAGA-TTTATATATTATAAATTTATATAAA-AAAAG-ATATATATTAT
20524440 AATTAATAATTTTATAAATTATAATTTTT
297 AATTAATAATTTTATAAATTATAATTTTT
* *
20524469 GTAATGTTAACACAAAATATAAAGTAAATATGTTTATATTTAAAGTATATATATACTAAAAATAT
1 GTAATGTTAACACAAAATATAAAGTAAATATATTTATATTTAAAG-ATATATATACTAAAAGTAT
* * *
20524534 TTTAGTATATATATAATTGTAATTATATTTCTTATAAATTAACACAATATATAAACTATATATAT
65 TTTAG-ATATATATAA---TAATAATATTTCTTATAAATGAACACAATATATAAAGTATATATAT
20524599 TAAAAGACATTACAAGTTAATTAATAA
126 TAAAAGACATTACAAG-TAATTAATAA
20524626 GGGTAAAATA
Statistics
Matches: 434, Mismatches: 33, Indels: 63
0.82 0.06 0.12
Matches are distributed among these distances:
328 2 0.00
329 17 0.04
330 20 0.05
332 3 0.01
333 56 0.13
334 8 0.02
336 20 0.05
337 65 0.15
338 19 0.04
339 23 0.05
340 1 0.00
341 12 0.03
342 44 0.10
343 2 0.00
344 21 0.05
345 7 0.02
346 31 0.07
347 26 0.06
348 54 0.12
349 3 0.01
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (325 bp):
GTAATGTTAACACAAAATATAAAGTAAATATATTTATATTTAAAGATATATATACTAAAAGTATT
TTAGATATATATAATAATAATATTTCTTATAAATGAACACAATATATAAAGTATATATATTAAAA
GACATTACAAGTAATTAATAATCATAGTTTCATGAATTAATTTAATTAACTATATGAATTTGTCC
TTAATTACATAAAATTAAAAAAAAATAACTAGGTTTCAAATCTCACAACTTTCCTTTAGATTTAT
ATATTATAAATTTATATAAAAAAAGATATATATTATAATTAATAATTTTATAAATTATAATTTTT
Found at i:20535070 original size:30 final size:30
Alignment explanation
Indices: 20535025--20535090 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 30
20535015 GTTAATTTAG
20535025 GGTTAAACGTTTCAATT-GTAACAATTAAA
1 GGTTAAACGTTTCAATTCGTAACAATTAAA
* * *
20535054 GGTTAAACGTTTTCAATTCTTTACAATTAAG
1 GGTTAAACG-TTTCAATTCGTAACAATTAAA
20535085 GGTTAA
1 GGTTAA
20535091 GGTGAGAGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 9 0.28
30 8 0.25
31 15 0.47
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (30 bp):
GGTTAAACGTTTCAATTCGTAACAATTAAA
Found at i:20535305 original size:27 final size:27
Alignment explanation
Indices: 20535275--20535459 Score: 165
Period size: 27 Copynumber: 6.8 Consensus size: 27
20535265 TTAAAATAGT
20535275 GTGTAACAACTAAATTTTCAACATGAC
1 GTGTAACAACTAAATTTTCAACATGAC
* * * **
20535302 GTGTAACAAGTACATTTTTCAATATGGT
1 GTGTAACAACTA-AATTTTCAACATGAC
* * * *
20535330 ATATAACAACTAAATCTTCAAAAT-AGC
1 GTGTAACAACTAAATTTTCAACATGA-C
* *
20535357 ATGTAACAACTAAATTTTCAATATGAC
1 GTGTAACAACTAAATTTTCAACATGAC
* * *
20535384 GTATAACAATTACATTTTTCAACATGAC
1 GTGTAACAACTA-AATTTTCAACATGAC
* * *
20535412 GTGTAACAATTAAATTTTTAACATGAT
1 GTGTAACAACTAAATTTTCAACATGAC
* *
20535439 ATGTAACAACTATATTTTCAA
1 GTGTAACAACTAAATTTTCAA
20535460 TGCGATTTTT
Statistics
Matches: 125, Mismatches: 29, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
27 80 0.64
28 45 0.36
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.35
Consensus pattern (27 bp):
GTGTAACAACTAAATTTTCAACATGAC
Found at i:20535319 original size:55 final size:54
Alignment explanation
Indices: 20535278--20535459 Score: 195
Period size: 55 Copynumber: 3.3 Consensus size: 54
20535268 AAATAGTGTG
* * *
20535278 TAACAACTAAATTTTCAACATGACGTGTAACAAGTACATTTTTCAATATGGTATA
1 TAACAACTAAATTTTCAACATGACGTGTAACAATTA-AATTTTCAATATGATATA
* * * * **
20535333 TAACAACTAAATCTTCAAAAT-AGCATGTAACAACTAAATTTTCAATATGACGTA
1 TAACAACTAAATTTTCAACATGA-CGTGTAACAATTAAATTTTCAATATGATATA
* * * * *
20535387 TAACAATTACATTTTTCAACATGACGTGTAACAATTAAATTTTTAACATGATATG
1 TAACAACTA-AATTTTCAACATGACGTGTAACAATTAAATTTTCAATATGATATA
*
20535442 TAACAACTATATTTTCAA
1 TAACAACTAAATTTTCAA
20535460 TGCGATTTTT
Statistics
Matches: 102, Mismatches: 22, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
54 30 0.29
55 71 0.70
56 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (54 bp):
TAACAACTAAATTTTCAACATGACGTGTAACAATTAAATTTTCAATATGATATA
Found at i:20535410 original size:28 final size:27
Alignment explanation
Indices: 20535219--20535456 Score: 146
Period size: 27 Copynumber: 8.8 Consensus size: 27
20535209 AATTATAGCG
*
20535219 TGACGTGTAACAACT--TTTTT-ATCA
1 TGACGTGTAACAACTAATTTTTCAACA
* * * * *
20535243 TGGCATGTAACAATTAAATTTTTTAAAA
1 TGACGTGTAACAACT-AATTTTTCAACA
* *
20535271 T-AGTGTGTAACAACTAAATTTTCAACA
1 TGA-CGTGTAACAACTAATTTTTCAACA
* *
20535298 TGACGTGTAACAAGTACATTTTTCAATA
1 TGACGTGTAACAACTA-ATTTTTCAACA
*** * * * *
20535326 TGGTATATAACAACTAAATCTTCAAAA
1 TGACGTGTAACAACTAATTTTTCAACA
* * *
20535353 T-AGCATGTAACAACTAAATTTTCAATA
1 TGA-CGTGTAACAACTAATTTTTCAACA
* *
20535380 TGACGTATAACAATTACATTTTTCAACA
1 TGACGTGTAACAACTA-ATTTTTCAACA
*
20535408 TGACGTGTAACAATTAAATTTTT-AACA
1 TGACGTGTAACAACT-AATTTTTCAACA
**
20535435 TGATATGTAACAACTATATTTT
1 TGACGTGTAACAACTA-ATTTT
20535457 CAATGCGATT
Statistics
Matches: 164, Mismatches: 38, Indels: 21
0.74 0.17 0.09
Matches are distributed among these distances:
24 12 0.07
26 1 0.01
27 87 0.53
28 63 0.38
29 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (27 bp):
TGACGTGTAACAACTAATTTTTCAACA
Found at i:20535419 original size:82 final size:82
Alignment explanation
Indices: 20535241--20535460 Score: 271
Period size: 82 Copynumber: 2.7 Consensus size: 82
20535231 ACTTTTTTAT
* * * *
20535241 CATGGCATGTAACAATTAAATTTTTTAAAATAGTGTGTAACAACTAAATTTTCAACATGACGTGT
1 CATGACATGTAACAATTAAA-TTTTTAAAATAGTATGTAACAACTAAATTTTCAATATGACGTAT
20535306 AACAAGTACATTTTTCAA
65 AACAAGTACATTTTTCAA
* ** * * * * *
20535324 TATGGTATATAACAACTAAATCTTCAAAATAGCATGTAACAACTAAATTTTCAATATGACGTATA
1 CATGACATGTAACAATTAAATTTTTAAAATAGTATGTAACAACTAAATTTTCAATATGACGTATA
*
20535389 ACAATTACATTTTTCAA
66 ACAAGTACATTTTTCAA
* * *
20535406 CATGACGTGTAACAATTAAATTTTTAACAT-GATATGTAACAACTATATTTTCAAT
1 CATGACATGTAACAATTAAATTTTTAAAATAG-TATGTAACAACTAAATTTTCAAT
20535461 GCGATTTTTT
Statistics
Matches: 114, Mismatches: 22, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
81 1 0.01
82 97 0.85
83 16 0.14
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (82 bp):
CATGACATGTAACAATTAAATTTTTAAAATAGTATGTAACAACTAAATTTTCAATATGACGTATA
ACAAGTACATTTTTCAA
Found at i:20538454 original size:24 final size:24
Alignment explanation
Indices: 20538428--20538488 Score: 88
Period size: 24 Copynumber: 2.5 Consensus size: 24
20538418 TATACAAATT
20538428 AAAT-TTTTCCTTAAAAAAGCTAATA
1 AAATGTTTTCCTTAAAAAA--TAATA
*
20538453 AAATGTTTTCTTTAAAAAATAATA
1 AAATGTTTTCCTTAAAAAATAATA
20538477 AAATGTTTTCCT
1 AAATGTTTTCCT
20538489 ATCTCTAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
24 16 0.48
25 4 0.12
26 13 0.39
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (24 bp):
AAATGTTTTCCTTAAAAAATAATA
Found at i:20545043 original size:6 final size:6
Alignment explanation
Indices: 20545032--20545057 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
20545022 GATCTTGGAG
20545032 AGTCAT AGTCAT AGTCAT AGTCAT AG
1 AGTCAT AGTCAT AGTCAT AGTCAT AG
20545058 CAGCCAGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (6 bp):
AGTCAT
Found at i:20548140 original size:21 final size:21
Alignment explanation
Indices: 20548099--20548140 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
20548089 CTGTCGCCTG
*
20548099 TGTTTTTAGCTTCTCTGAAAA
1 TGTTTTTAGCTTCTCTCAAAA
*
20548120 TGTTTATTA-CTTTTCTCAAAA
1 TGTTT-TTAGCTTCTCTCAAAA
20548141 CCATTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.26, C:0.14, G:0.10, T:0.50
Consensus pattern (21 bp):
TGTTTTTAGCTTCTCTCAAAA
Found at i:20554492 original size:4 final size:4
Alignment explanation
Indices: 20554483--20554509 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
20554473 ACCAAAATAT
20554483 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
20554510 GTTACCCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:20559403 original size:23 final size:23
Alignment explanation
Indices: 20559377--20559422 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
20559367 ATCCAATAAC
20559377 CTTATCCTAATATAATTAGGAAT
1 CTTATCCTAATATAATTAGGAAT
20559400 CTTATCCTAATATAATTAGGAAT
1 CTTATCCTAATATAATTAGGAAT
20559423 TGTTATTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (23 bp):
CTTATCCTAATATAATTAGGAAT
Found at i:20561412 original size:22 final size:20
Alignment explanation
Indices: 20561369--20561413 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
20561359 AAATTATAAC
* *
20561369 ATTTTTTTCATTTAAAATAT
1 ATTTTTTTAATTTAAAAAAT
20561389 ATTTTTTATAATTTATAAAAAT
1 ATTTTTT-TAATTTA-AAAAAT
20561411 ATT
1 ATT
20561414 AACAAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
21 6 0.29
22 8 0.38
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTTTTTAATTTAAAAAAT
Found at i:20561586 original size:28 final size:28
Alignment explanation
Indices: 20561520--20561586 Score: 66
Period size: 28 Copynumber: 2.5 Consensus size: 28
20561510 TTTTTAGATG
*
20561520 TTAATATTTT--ATTTGTAATTTAAACA
1 TTAATATTTTAAATTTATAATTTAAACA
* ** * *
20561546 TTATTATGATAAATTTATCATTTAAATA
1 TTAATATTTTAAATTTATAATTTAAACA
20561574 TTAATATTTTAAA
1 TTAATATTTTAAA
20561587 ATATTATATT
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
26 7 0.23
28 23 0.77
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (28 bp):
TTAATATTTTAAATTTATAATTTAAACA
Found at i:20561590 original size:16 final size:15
Alignment explanation
Indices: 20561569--20561635 Score: 52
Period size: 16 Copynumber: 4.5 Consensus size: 15
20561559 TTTATCATTT
20561569 AAATATTAATATTTTA
1 AAATATT-ATATTTTA
20561585 AAATATTATATTTT-
1 AAATATTATATTTTA
* *
20561599 -TAT-TTATAATTTA
1 AAATATTATATTTTA
*
20561612 AACATTATTATA-ATTA
1 AA-A-TATTATATTTTA
20561628 AAATATTA
1 AAATATTA
20561636 AAATTGTATA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
12 8 0.19
13 2 0.05
14 5 0.12
15 9 0.21
16 13 0.31
17 5 0.12
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (15 bp):
AAATATTATATTTTA
Found at i:20561635 original size:17 final size:17
Alignment explanation
Indices: 20561602--20561635 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
20561592 ATATTTTTAT
*
20561602 TTATAATTTAAACATTA
1 TTATAATTAAAACATTA
*
20561619 TTATAATTAAAATATTA
1 TTATAATTAAAACATTA
20561636 AAATTGTATA
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TTATAATTAAAACATTA
Found at i:20563559 original size:40 final size:41
Alignment explanation
Indices: 20563480--20563595 Score: 112
Period size: 42 Copynumber: 2.8 Consensus size: 41
20563470 TACAATTATA
* ****
20563480 AAAAAAT-AAAAAATAAAAAAAAAAAAATTAAAGAAAGAAAAT
1 AAAAAATAAAAAAATAGAAAAAAAAAAA--AATCCTAGAAAAT
20563522 AAAAAAT-AAAAAA-AGAAAAAAAAAAAAATCCTNAGAAAAT
1 AAAAAATAAAAAAATAGAAAAAAAAAAAAATCCT-AGAAAAT
* *
20563562 AAAAAATACAAAAAATAGAAATAAACAAAAATCC
1 AAAAAATA-AAAAAATAGAAAAAAAAAAAAATCC
20563596 CTGATGATGG
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
39 2 0.03
40 14 0.22
41 12 0.19
42 19 0.30
43 16 0.25
ACGTcount: A:0.78, C:0.05, G:0.04, T:0.11
Consensus pattern (41 bp):
AAAAAATAAAAAAATAGAAAAAAAAAAAAATCCTAGAAAAT
Found at i:20563567 original size:1 final size:1
Alignment explanation
Indices: 20563479--20563549 Score: 61
Period size: 1 Copynumber: 71.0 Consensus size: 1
20563469 ATACAATTAT
* * ** * * * * *
20563479 AAAAAAATAAAAAATAAAAAAAAAAAAATTAAAGAAAGAAAATAAAAAATAAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
20563544 AAAAAA
1 AAAAAA
20563550 TCCTNAGAAA
Statistics
Matches: 54, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.87, C:0.00, G:0.04, T:0.08
Consensus pattern (1 bp):
A
Found at i:20563569 original size:7 final size:7
Alignment explanation
Indices: 20563480--20563550 Score: 72
Period size: 7 Copynumber: 10.0 Consensus size: 7
20563470 TACAATTATA
20563480 AAAAAAT
1 AAAAAAT
20563487 AAAAAAT
1 AAAAAAT
*
20563494 AAAAAAA
1 AAAAAAT
20563501 AAAAAATT
1 AAAAAA-T
*
20563509 AAAGAA-
1 AAAAAAT
*
20563515 AGAAAAT
1 AAAAAAT
20563522 AAAAAAT
1 AAAAAAT
*
20563529 AAAAAAAG
1 -AAAAAAT
*
20563537 AAAAAAA
1 AAAAAAT
20563544 AAAAAAT
1 AAAAAAT
20563551 CCTNAGAAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
6 4 0.08
7 37 0.71
8 11 0.21
ACGTcount: A:0.86, C:0.00, G:0.04, T:0.10
Consensus pattern (7 bp):
AAAAAAT
Found at i:20563576 original size:43 final size:39
Alignment explanation
Indices: 20563482--20563595 Score: 112
Period size: 35 Copynumber: 2.9 Consensus size: 39
20563472 CAATTATAAA
* *
20563482 AAAATAAAAAATAAAAAAA-AAAAAATTAAAGAA----AG
1 AAAATAAAAAATAAAAAAAGAAAAAA-AAAAAAATCCTAG
20563517 AAAATAAAAAATAAAAAAAGAAAAAAAAAAAAATCCTNAG
1 AAAATAAAAAATAAAAAAAGAAAAAAAAAAAAATCCT-AG
* *
20563557 AAAATAAAAAATACAAAAAATAGAAATAAACAAAAATCC
1 AAAATAAAAAAT--AAAAAA-AGAAAAAAAAAAAAATCC
20563596 CTGATGATGG
Statistics
Matches: 66, Mismatches: 4, Indels: 10
0.82 0.05 0.12
Matches are distributed among these distances:
35 24 0.36
36 6 0.09
40 14 0.21
42 6 0.09
43 16 0.24
ACGTcount: A:0.78, C:0.05, G:0.04, T:0.11
Consensus pattern (39 bp):
AAAATAAAAAATAAAAAAAGAAAAAAAAAAAAATCCTAG
Found at i:20564694 original size:24 final size:24
Alignment explanation
Indices: 20564667--20564743 Score: 57
Period size: 24 Copynumber: 3.2 Consensus size: 24
20564657 TAAATAAAAA
20564667 AAATTAATGACAACTTCTCTAATC
1 AAATTAATGACAACTTCTCTAATC
* * *** * **
20564691 AAATGATTGA-GTTTTCAACTAAAAA
1 AAATTAATGACAACTTC-TCT-AATC
20564716 AAATTAATGACAACTTCTCTAATC
1 AAATTAATGACAACTTCTCTAATC
20564740 AAAT
1 AAAT
20564744 GATTGAGTTT
Statistics
Matches: 34, Mismatches: 16, Indels: 6
0.61 0.29 0.11
Matches are distributed among these distances:
23 3 0.09
24 16 0.47
25 12 0.35
26 3 0.09
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.32
Consensus pattern (24 bp):
AAATTAATGACAACTTCTCTAATC
Found at i:20564732 original size:49 final size:49
Alignment explanation
Indices: 20564661--20564759 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
20564651 CACATCTAAA
20564661 TAAAAAAAATTAATGACAACTTCTCTAATCAAATGATTGAGTTTTCAAC
1 TAAAAAAAATTAATGACAACTTCTCTAATCAAATGATTGAGTTTTCAAC
20564710 TAAAAAAAATTAATGACAACTTCTCTAATCAAATGATTGAGTTTTCAAC
1 TAAAAAAAATTAATGACAACTTCTCTAATCAAATGATTGAGTTTTCAAC
20564759 T
1 T
20564760 GTTCGGATGC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.33
Consensus pattern (49 bp):
TAAAAAAAATTAATGACAACTTCTCTAATCAAATGATTGAGTTTTCAAC
Found at i:20564737 original size:25 final size:25
Alignment explanation
Indices: 20564661--20564737 Score: 59
Period size: 25 Copynumber: 3.1 Consensus size: 25
20564651 CACATCTAAA
20564661 TAAAAAAAATTAATGACAACTTCTC
1 TAAAAAAAATTAATGACAACTTCTC
** * * *** *
20564686 T-AATCAAATGATTGA-GTTTTCAAC
1 TAAAAAAAATTAATGACAACTTC-TC
20564710 TAAAAAAAATTAATGACAACTTCTC
1 TAAAAAAAATTAATGACAACTTCTC
20564735 TAA
1 TAA
20564738 TCAAATGATT
Statistics
Matches: 33, Mismatches: 16, Indels: 6
0.60 0.29 0.11
Matches are distributed among these distances:
23 3 0.09
24 12 0.36
25 15 0.45
26 3 0.09
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.31
Consensus pattern (25 bp):
TAAAAAAAATTAATGACAACTTCTC
Found at i:20569569 original size:31 final size:31
Alignment explanation
Indices: 20569526--20569603 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
20569516 GTGTCAGAGT
*
20569526 TGGCGTGCTATAACATTTTACGTTATATGCA
1 TGGCGTGTTATAACATTTTACGTTATATGCA
20569557 TGGCGTGTTATAACATTTTACGTTATATGCA
1 TGGCGTGTTATAACATTTTACGTTATATGCA
* *
20569588 TGGTGTGTTACAACAT
1 TGGCGTGTTATAACAT
20569604 GATTGACAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.40
Consensus pattern (31 bp):
TGGCGTGTTATAACATTTTACGTTATATGCA
Found at i:20573731 original size:62 final size:62
Alignment explanation
Indices: 20573632--20573765 Score: 196
Period size: 62 Copynumber: 2.2 Consensus size: 62
20573622 GCCCCAATTG
* * * *
20573632 TGGTGACACGCTGAGTGGAAGCAGATATTTGGTATGACACGCTAAGTTCCTGCAGATTTCGA
1 TGGTGACATGCTGAGTGGAAGCAGATACTTGGCATGACACGCTAAGTGCCTGCAGATTTCGA
* * * *
20573694 TGGTGACATGCTGAGTGGAAGCAGATACTTGGCATGACACGTTGAGTGCCTGCAGATTTTGG
1 TGGTGACATGCTGAGTGGAAGCAGATACTTGGCATGACACGCTAAGTGCCTGCAGATTTCGA
20573756 TGGTGACATG
1 TGGTGACATG
20573766 TTGACTTCTT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.28
Consensus pattern (62 bp):
TGGTGACATGCTGAGTGGAAGCAGATACTTGGCATGACACGCTAAGTGCCTGCAGATTTCGA
Found at i:20573732 original size:117 final size:117
Alignment explanation
Indices: 20573519--20573732 Score: 252
Period size: 117 Copynumber: 1.8 Consensus size: 117
20573509 ATCTTGTAGA
* * *
20573519 GACACGCTGAGTGGAAGTAGATACTTGGCGTGACACGCTAAGTGCATGCAGATTTTTGTGGTGAC
1 GACACGCTGAGTGGAAGCAGATACTTGGCATGACACGCTAAGTGCATGCAGATTTTCGTGGTGAC
* *** * **
20573584 ATGCTGACTTCTTTCAGTATTGTGGGGTGACATGGCACGCCCCAATTGTGGT
66 ATGCTGACTGCAAGCAGTACTGTGGCATGACATGGCACGCCCCAATTGTGGT
* * * *
20573636 GACACGCTGAGTGGAAGCAGATATTTGGTATGACACGCTAAGTTCCTGCAGA-TTTCGATGGTGA
1 GACACGCTGAGTGGAAGCAGATACTTGGCATGACACGCTAAGTGCATGCAGATTTTCG-TGGTGA
* *
20573700 CATGCTGAGTGGAAGCAGATACT-TGGCATGACA
65 CATGCTGACTGCAAGCAG-TACTGTGGCATGACA
20573733 CGTTGAGTGC
Statistics
Matches: 79, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
116 4 0.05
117 72 0.91
118 3 0.04
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.27
Consensus pattern (117 bp):
GACACGCTGAGTGGAAGCAGATACTTGGCATGACACGCTAAGTGCATGCAGATTTTCGTGGTGAC
ATGCTGACTGCAAGCAGTACTGTGGCATGACATGGCACGCCCCAATTGTGGT
Found at i:20573763 original size:31 final size:31
Alignment explanation
Indices: 20573631--20573763 Score: 90
Period size: 31 Copynumber: 4.3 Consensus size: 31
20573621 CGCCCCAATT
* *
20573631 GTGGTGACACGCTGAGTGGAAGCAGATATTTG
1 GTGGTGACACGCTGAGTGCATGCAGAT-TTTG
* * * * *
20573663 GT-ATGACACGCTAAGTTCCTGCAGATTTCG
1 GTGGTGACACGCTGAGTGCATGCAGATTTTG
* * * * *
20573693 ATGGTGACATGCTGAGTGGAAGCAGATACTTG
1 GTGGTGACACGCTGAGTGCATGCAGAT-TTTG
** * *
20573725 G-CATGACACGTTGAGTGCCTGCAGATTTTG
1 GTGGTGACACGCTGAGTGCATGCAGATTTTG
20573755 GTGGTGACA
1 GTGGTGACA
20573764 TGTTGACTTC
Statistics
Matches: 70, Mismatches: 28, Indels: 7
0.67 0.27 0.07
Matches are distributed among these distances:
30 8 0.11
31 58 0.83
32 4 0.06
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.27
Consensus pattern (31 bp):
GTGGTGACACGCTGAGTGCATGCAGATTTTG
Found at i:20573818 original size:117 final size:117
Alignment explanation
Indices: 20573694--20573966 Score: 429
Period size: 117 Copynumber: 2.3 Consensus size: 117
20573684 CAGATTTCGA
* * *
20573694 TGGTGACATGCTGAGTGGAAGCAGATACTTGGCATGACACGTTGAGTGCCTGCAGATTTTGGTGG
1 TGGTGACATGTTGAGTGGAAGCAGATACTTGGCGTGACACGTTGAGTGCCTACAGATTTTGGTGG
* * * *
20573759 TGACATGTTGACTTCTTGCAGTATTATGGGGTGACACAGCATGCCCTAATTG
66 TGACAAGCTAACTTCTTGCAGTATTATGGGGTGACACAGCACGCCCTAATTG
*
20573811 TGGTGACATGTTGAGTGGAAGTAGATACTTGGCGTGACACGTTGAGTGCCTACAGATTTTGGTGG
1 TGGTGACATGTTGAGTGGAAGCAGATACTTGGCGTGACACGTTGAGTGCCTACAGATTTTGGTGG
* *
20573876 TGACAAGCTAACTTCTTGCAGTATTGTGGGGTGACACGGCACGCCCTAATTG
66 TGACAAGCTAACTTCTTGCAGTATTATGGGGTGACACAGCACGCCCTAATTG
* * *
20573928 TGATGACACGTTGAGTGAAAGCAGATACTTGGCGTGACA
1 TGGTGACATGTTGAGTGGAAGCAGATACTTGGCGTGACA
20573967 TGCTGACTTG
Statistics
Matches: 142, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
117 142 1.00
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (117 bp):
TGGTGACATGTTGAGTGGAAGCAGATACTTGGCGTGACACGTTGAGTGCCTACAGATTTTGGTGG
TGACAAGCTAACTTCTTGCAGTATTATGGGGTGACACAGCACGCCCTAATTG
Found at i:20573828 original size:179 final size:179
Alignment explanation
Indices: 20573519--20573880 Score: 490
Period size: 179 Copynumber: 2.0 Consensus size: 179
20573509 ATCTTGTAGA
* * *
20573519 GACACGCTGAGTGGAAGTAGATACTTGGCGTGACACGCTAAGTGCATGCAGATTTTTGTGGTGAC
1 GACACGCTGAGTGGAAGCAGATACTTGGCATGACACGCTAAGTGCATGCAGATTTTGGTGGTGAC
* * **
20573584 ATGCTGACTTCTTTCAGTATTGTGGGGTGACATGGCACGCCCCAATTGTGGTGACACGCTGAGTG
66 ATGCTGACTTCTTGCAGTATTATGGGGTGACACAGCACGCCCCAATTGTGGTGACACGCTGAGTG
* * * *
20573649 GAAGCAGATATTTGGTATGACACGCTAAGTTCCTGCAGATTTCGATGGT
131 GAAGCAGATACTTGGCATGACACGCTAAGTGCCTACAGATTTCGATGGT
* * * *
20573698 GACATGCTGAGTGGAAGCAGATACTTGGCATGACACGTTGAGTGCCTGCAGATTTTGGTGGTGAC
1 GACACGCTGAGTGGAAGCAGATACTTGGCATGACACGCTAAGTGCATGCAGATTTTGGTGGTGAC
* * * * *
20573763 ATGTTGACTTCTTGCAGTATTATGGGGTGACACAGCATGCCCTAATTGTGGTGACATGTTGAGTG
66 ATGCTGACTTCTTGCAGTATTATGGGGTGACACAGCACGCCCCAATTGTGGTGACACGCTGAGTG
* * * * * *
20573828 GAAGTAGATACTTGGCGTGACACGTTGAGTGCCTACAGATTTTGGTGGT
131 GAAGCAGATACTTGGCATGACACGCTAAGTGCCTACAGATTTCGATGGT
20573877 GACA
1 GACA
20573881 AGCTAACTTC
Statistics
Matches: 157, Mismatches: 26, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
179 157 1.00
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (179 bp):
GACACGCTGAGTGGAAGCAGATACTTGGCATGACACGCTAAGTGCATGCAGATTTTGGTGGTGAC
ATGCTGACTTCTTGCAGTATTATGGGGTGACACAGCACGCCCCAATTGTGGTGACACGCTGAGTG
GAAGCAGATACTTGGCATGACACGCTAAGTGCCTACAGATTTCGATGGT
Found at i:20576329 original size:145 final size:144
Alignment explanation
Indices: 20576010--20576330 Score: 374
Period size: 145 Copynumber: 2.2 Consensus size: 144
20576000 GTGGAAATAT
** * *
20576010 TGAACACAAACCGTTAGAACCAATCTTACCGATGGGTCGTTAGCACTGTGCGTCTGAGGAGGACC
1 TGAACACAAACCGTTAGAACC-ATCTTACCGATGCCTCGTTAGCACTGTGAGTCTGAGAAGGACC
* * * * * *
20576075 TCTCAGTGATTGAGGAGTTGTCGTCGCATGGTCTAACTGCAAACACAGATATATTATTCAATAAT
65 TATCAGTGATTGAGGAGCTGTCATCGCATGGTCCAACTGCAAACAAAGATATATTAATCAATAAT
* *
20576140 CACATATGGAATTGT
130 CACATATGAAATTGC
* ** * *
20576155 TGAACACAAACCGTTATAACTGTCCTTACCGACT-CCTCGTTAGCATTGTGAGTCTGAGAATGAC
1 TGAACACAAACCGTTAGAACCAT-CTTACCGA-TGCCTCGTTAGCACTGTGAGTCTGAGAAGGAC
* * * * * *
20576219 CTATCGGTGGTTGTGGAGCTGTCATCGCATGGTCCAACTGTAAACAAAGATATGTTAATCGATAA
64 CTATCAGTGATTGAGGAGCTGTCATCGCATGGTCCAACTGCAAACAAAGATATATTAATCAATAA
*
20576284 TTACATATGAAATTGC
129 TCACATATGAAATTGC
*
20576300 TGAGCACAAACCGTTAGAACCATCTTTACCG
1 TGAACACAAACCGTTAGAACCATC-TTACCG
20576331 GCTCTCCACT
Statistics
Matches: 145, Mismatches: 28, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
144 2 0.01
145 142 0.98
146 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (144 bp):
TGAACACAAACCGTTAGAACCATCTTACCGATGCCTCGTTAGCACTGTGAGTCTGAGAAGGACCT
ATCAGTGATTGAGGAGCTGTCATCGCATGGTCCAACTGCAAACAAAGATATATTAATCAATAATC
ACATATGAAATTGC
Found at i:20577789 original size:31 final size:31
Alignment explanation
Indices: 20577725--20578079 Score: 423
Period size: 31 Copynumber: 11.5 Consensus size: 31
20577715 GTTAACCCAT
* *
20577725 AATGTTGTAACATGCCATGC-TATAATGTAA
1 AATGTTGTAACACGCCATGCATATAACGTAA
* *
20577755 AATATTGTAACACGCTATGCATAT-ACAGTAA
1 AATGTTGTAACACGCCATGCATATAAC-GTAA
* * *
20577786 AATATTGT-ACACGCCATGCATGTAACGTCA
1 AATGTTGTAACACGCCATGCATATAACGTAA
* *
20577816 AATGTTGT-ACATGCCATGCATATAATGTAA
1 AATGTTGTAACACGCCATGCATATAACGTAA
* * *
20577846 AATGTTGTAACACGCCATGTATATAACTTTA
1 AATGTTGTAACACGCCATGCATATAACGTAA
* * *
20577877 AATGTTATAACACGCCATACATATAACGTCA
1 AATGTTGTAACACGCCATGCATATAACGTAA
*
20577908 AATGTTGTAACACGCCATGCATATAACGTCA
1 AATGTTGTAACACGCCATGCATATAACGTAA
*
20577939 AATGTTGTAACACGCCACGCATATAACGTAA
1 AATGTTGTAACACGCCATGCATATAACGTAA
* *
20577970 AATATTGTAACACACCATGCATATAACGTAA
1 AATGTTGTAACACGCCATGCATATAACGTAA
*
20578001 AATGTTGTAACACCCCATGCATATAACGTAA
1 AATGTTGTAACACGCCATGCATATAACGTAA
* * * ** *
20578032 AATATTGTAATACACCATGTGTATCAA-GTCA
1 AATGTTGTAACACGCCATGCATAT-AACGTAA
20578063 AATGTTGTAACACGCCA
1 AATGTTGTAACACGCCA
20578080 ACGCTGACAC
Statistics
Matches: 280, Mismatches: 40, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
30 67 0.24
31 211 0.75
32 2 0.01
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.28
Consensus pattern (31 bp):
AATGTTGTAACACGCCATGCATATAACGTAA
Found at i:20578783 original size:47 final size:46
Alignment explanation
Indices: 20578710--20579036 Score: 314
Period size: 47 Copynumber: 7.0 Consensus size: 46
20578700 AAACCTACCG
* * * *
20578710 TGTCATAGATTCCCTCCATGGAGTGTCACAAACTTTGAACGCTGGT
1 TGTCACAGATTCCCTCCATGGCGTGTCACAAACTCTGAACGCTGCT
* * * * * * *
20578756 ATGTCATAGATTTCCTCTATGCCGTGTCATAAACTCTGAACGTTGCCG
1 -TGTCACAGATTCCCTCCATGGCGTGTCACAAACTCTGAACGCTG-CT
* * *
20578804 TGTCACAGATTCCCTCAATGGCGTGTCACAAACTTTGAAC-CTTGTCG
1 TGTCACAGATTCCCTCCATGGCGTGTCACAAACTCTGAACGC-TG-CT
* * *
20578851 TGTCACAGATTCCCTCTATGGCGTGTCACAAACTCTAAACACTAGCT
1 TGTCACAGATTCCCTCCATGGCGTGTCACAAACTCTGAACGCT-GCT
* * * *
20578898 TGTCATAGATTCTCTCCATGTCGTGTCACAAACTCTGAATGCTGACT
1 TGTCACAGATTCCCTCCATGGCGTGTCACAAACTCTGAACGCTG-CT
* * *
20578945 TGTCACAAATTCCCTCCATGGCGTGTCATAAACTCTGAACCCTGCCT
1 TGTCACAGATTCCCTCCATGGCGTGTCACAAACTCTGAACGCTG-CT
* * * * * *
20578992 TTTCACAGATTCCCTCTATGACATGTCACAAACTCTAAACCCTGC
1 TGTCACAGATTCCCTCCATGGCGTGTCACAAACTCTGAACGCTGC
20579037 AGTGTCAAGT
Statistics
Matches: 232, Mismatches: 43, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
46 2 0.01
47 228 0.98
48 2 0.01
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (46 bp):
TGTCACAGATTCCCTCCATGGCGTGTCACAAACTCTGAACGCTGCT
Found at i:20578830 original size:94 final size:93
Alignment explanation
Indices: 20578693--20579025 Score: 348
Period size: 94 Copynumber: 3.6 Consensus size: 93
20578683 GCAGTCTGAC
* * * *
20578693 AAACTCTAAACC-TACCGTGTCATAGATTCCCTCCATGGAGTGTCACAAACTTTGAACGCTGGTA
1 AAACTCTGAACCTTGCCGTGTCACAGATTCCCTCCATGGCGTGTCACAAACTTTGAACGCTGGT-
* * *
20578757 TGTCATAGATTTCCTCTATGCCGTGTCAT
65 TGTCACAGATTCCCTCTATGGCGTGTCAT
* * *
20578786 AAACTCTGAACGTTGCCGTGTCACAGATTCCCTCAATGGCGTGTCACAAACTTTGAAC-CTTGTC
1 AAACTCTGAACCTTGCCGTGTCACAGATTCCCTCCATGGCGTGTCACAAACTTTGAACGCTGGT-
*
20578850 GTGTCACAGATTCCCTCTATGGCGTGTCAC
65 -TGTCACAGATTCCCTCTATGGCGTGTCAT
* * * * * * * * *
20578880 AAACTCTAAACACTAG-CTTGTCATAGATTCTCTCCATGTCGTGTCACAAACTCTGAATGCTGAC
1 AAACTCTGAAC-CTTGCCGTGTCACAGATTCCCTCCATGGCGTGTCACAAACTTTGAACGCTG-G
* *
20578944 TTGTCACAAATTCCCTCCATGGCGTGTCAT
64 TTGTCACAGATTCCCTCTATGGCGTGTCAT
* * * * * *
20578974 AAACTCTGAACCCTGCCTTTTCACAGATTCCCTCTATGACATGTCACAAACT
1 AAACTCTGAACCTTGCCGTGTCACAGATTCCCTCCATGGCGTGTCACAAACT
20579026 CTAAACCCTG
Statistics
Matches: 198, Mismatches: 36, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
93 16 0.08
94 177 0.89
95 4 0.02
96 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (93 bp):
AAACTCTGAACCTTGCCGTGTCACAGATTCCCTCCATGGCGTGTCACAAACTTTGAACGCTGGTT
GTCACAGATTCCCTCTATGGCGTGTCAT
Found at i:20578832 original size:23 final size:23
Alignment explanation
Indices: 20578802--20578880 Score: 68
Period size: 23 Copynumber: 3.4 Consensus size: 23
20578792 TGAACGTTGC
20578802 CGTGTCACAGATTCCCTCAATGG
1 CGTGTCACAGATTCCCTCAATGG
* **** ** *
20578825 CGTGTCACAAACTTTGAACCTTGT
1 CGTGTCACAGA-TTCCCTCAATGG
*
20578849 CGTGTCACAGATTCCCTCTATGG
1 CGTGTCACAGATTCCCTCAATGG
20578872 CGTGTCACA
1 CGTGTCACA
20578881 AACTCTAAAC
Statistics
Matches: 39, Mismatches: 16, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
23 24 0.62
24 15 0.38
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.29
Consensus pattern (23 bp):
CGTGTCACAGATTCCCTCAATGG
Found at i:20578902 original size:141 final size:141
Alignment explanation
Indices: 20578691--20579036 Score: 410
Period size: 141 Copynumber: 2.5 Consensus size: 141
20578681 ATGCAGTCTG
* * * * * * * * *
20578691 ACAAACTCT-AAACCTACCGTGTCATAGATTCCCTCCATGGAGTGTCACAAACTTTGAACGCTGG
1 ACAAACTCTGAACCCTGCCGTGTCACAGATTCCCTCTATGGCGTGTCACAAACTCTAAACACTGC
* * * * *
20578755 TATGTCATAGATT-TCCTCTATGCCGTGTCATAAACTCTGAACGTTGCCGTGTCACAGATTCCCT
66 TATGTCATAGATTCT-CTCCATGCCGTGTCACAAACTCTGAACGCTGACGTGTCACAAATTCCCT
20578819 CAATGGCGTGTC
130 CAATGGCGTGTC
* * *
20578831 ACAAACTTTGAACCTTGTCGTGTCACAGATTCCCTCTATGGCGTGTCACAAACTCTAAACACTAG
1 ACAAACTCTGAACCCTGCCGTGTCACAGATTCCCTCTATGGCGTGTCACAAACTCTAAACACT-G
* * *
20578896 CT-TGTCATAGATTCTCTCCATGTCGTGTCACAAACTCTGAATGCTGACTTGTCACAAATTCCCT
65 CTATGTCATAGATTCTCTCCATGCCGTGTCACAAACTCTGAACGCTGACGTGTCACAAATTCCCT
*
20578960 CCATGGCGTGTC
130 CAATGGCGTGTC
* * * * * *
20578972 ATAAACTCTGAACCCTGCCTTTTCACAGATTCCCTCTATGACATGTCACAAACTCTAAACCCTGC
1 ACAAACTCTGAACCCTGCCGTGTCACAGATTCCCTCTATGGCGTGTCACAAACTCTAAACACTGC
20579037 AGTGTCAAGT
Statistics
Matches: 173, Mismatches: 30, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
140 10 0.06
141 160 0.92
142 3 0.02
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (141 bp):
ACAAACTCTGAACCCTGCCGTGTCACAGATTCCCTCTATGGCGTGTCACAAACTCTAAACACTGC
TATGTCATAGATTCTCTCCATGCCGTGTCACAAACTCTGAACGCTGACGTGTCACAAATTCCCTC
AATGGCGTGTC
Found at i:20579085 original size:23 final size:23
Alignment explanation
Indices: 20579048--20579091 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
20579038 GTGTCAAGTC
*
20579048 GTGTCACACAATCCCACCATGTA
1 GTGTCACACAATCCCAACATGTA
* *
20579071 GTGTCATACATTCCCAACATG
1 GTGTCACACAATCCCAACATG
20579092 CTGTTTCACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.32, G:0.14, T:0.25
Consensus pattern (23 bp):
GTGTCACACAATCCCAACATGTA
Found at i:20580946 original size:2 final size:2
Alignment explanation
Indices: 20580939--20580980 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
20580929 GGCTTAGCAA
20580939 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20580981 TTGTTTTAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20581187 original size:23 final size:23
Alignment explanation
Indices: 20581154--20581259 Score: 149
Period size: 23 Copynumber: 4.6 Consensus size: 23
20581144 GCAATGCCTA
*
20581154 AGTCACACAATGCCTTACTAACT
1 AGTCACGCAATGCCTTACTAACT
* * *
20581177 AGTTATGCAATGCTTTACTAACT
1 AGTCACGCAATGCCTTACTAACT
* *
20581200 AGTCACGCAATGCCTTACTTACA
1 AGTCACGCAATGCCTTACTAACT
*
20581223 AGTCACGCAATGCTTTACTAACT
1 AGTCACGCAATGCCTTACTAACT
20581246 AGTCACGCAATGCC
1 AGTCACGCAATGCC
20581260 ATATCAACCA
Statistics
Matches: 70, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.28
Consensus pattern (23 bp):
AGTCACGCAATGCCTTACTAACT
Found at i:20581233 original size:46 final size:46
Alignment explanation
Indices: 20581154--20581259 Score: 167
Period size: 46 Copynumber: 2.3 Consensus size: 46
20581144 GCAATGCCTA
* * * *
20581154 AGTCACACAATGCCTTACTAACTAGTTATGCAATGCTTTACTAACT
1 AGTCACGCAATGCCTTACTAACAAGTCACGCAATGCTTTACTAACT
*
20581200 AGTCACGCAATGCCTTACTTACAAGTCACGCAATGCTTTACTAACT
1 AGTCACGCAATGCCTTACTAACAAGTCACGCAATGCTTTACTAACT
20581246 AGTCACGCAATGCC
1 AGTCACGCAATGCC
20581260 ATATCAACCA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 55 1.00
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.28
Consensus pattern (46 bp):
AGTCACGCAATGCCTTACTAACAAGTCACGCAATGCTTTACTAACT
Found at i:20581273 original size:46 final size:46
Alignment explanation
Indices: 20581154--20581279 Score: 155
Period size: 46 Copynumber: 2.7 Consensus size: 46
20581144 GCAATGCCTA
* * * * *
20581154 AGTCACACAATGCCTTACTAACTAGTTATGCAATGCTTTACTAACT
1 AGTCACGCAATGCCATACTAACAAGTCACGCAATGCTTTACTAACT
* *
20581200 AGTCACGCAATGCCTTACTTACAAGTCACGCAATGCTTTACTAACT
1 AGTCACGCAATGCCATACTAACAAGTCACGCAATGCTTTACTAACT
* *
20581246 AGTCACGCAATGCCATA-TCAACCAGTCATGCAAT
1 AGTCACGCAATGCCATACT-AACAAGTCACGCAAT
20581280 ATCTAAAAAT
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
45 1 0.01
46 69 0.99
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.28
Consensus pattern (46 bp):
AGTCACGCAATGCCATACTAACAAGTCACGCAATGCTTTACTAACT
Found at i:20581383 original size:22 final size:22
Alignment explanation
Indices: 20581196--20581420 Score: 98
Period size: 22 Copynumber: 10.1 Consensus size: 22
20581186 ATGCTTTACT
**
20581196 AACTAGTCACGCAATGCCTTACT
1 AACTAGTCACGCAATGCC-TAAA
* * * **
20581219 TACAAGTCACGCAATGCTTTACT
1 AACTAGTCACGCAATGC-CTAAA
**
20581242 AACTAGTCACGCAATGCCATATC
1 AACTAGTCACGCAATGCC-TAAA
* * **
20581265 AACCAGTCATGCAATATCTAAA
1 AACTAGTCACGCAATGCCTAAA
* * * *
20581287 AA-TCAGTTATGCAATACTTAAA
1 AACT-AGTCACGCAATGCCTAAA
* * * *
20581309 AATTAGTCATGCAATGCTTACA
1 AACTAGTCACGCAATGCCTAAA
* *
20581331 AACTAATCACGTAATGCCT-AA
1 AACTAGTCACGCAATGCCTAAA
** *
20581352 AGTTAGTCACGCAATGTCTAAA
1 AACTAGTCACGCAATGCCTAAA
**
20581374 AACTAGTCACATAATGTCC-AAA
1 AACTAGTCACGCAATG-CCTAAA
* *
20581396 AA-TCGATTACGCAATGCCTAAA
1 AACTAG-TCACGCAATGCCTAAA
20581418 AAC
1 AAC
20581421 CACCAAAACT
Statistics
Matches: 152, Mismatches: 41, Indels: 18
0.72 0.19 0.09
Matches are distributed among these distances:
21 19 0.12
22 81 0.53
23 52 0.34
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (22 bp):
AACTAGTCACGCAATGCCTAAA
Found at i:20583292 original size:108 final size:108
Alignment explanation
Indices: 20583174--20583376 Score: 327
Period size: 108 Copynumber: 1.9 Consensus size: 108
20583164 AATTTTGAGT
* * *
20583174 AAATTTAAATAAAAGGTAAATTGGGTAAGTGTTGAATAA-TTTCAAAAGAATGTGTATTTGTAAA
1 AAATTGAAATAAAAGGTAAATTGGGTAAGAGTTGAATAATTTTC-AAAGAATATGTATTTGTAAA
* *
20583238 TTGTAAAAGTTGTAACTAAATCAACATATTTTGCTAATTTAAAC
65 TTATAAAAGTTGTAACCAAATCAACATATTTTGCTAATTTAAAC
20583282 AAATTGAAATAAAAGGTAAATTGGGTAAGAGTTGAATAATTTTCAAAGAATATGTATTTGTAAAT
1 AAATTGAAATAAAAGGTAAATTGGGTAAGAGTTGAATAATTTTCAAAGAATATGTATTTGTAAAT
* *
20583347 TATGAAAGTTGTAACCAAATCAACTTATTT
66 TATAAAAGTTGTAACCAAATCAACATATTT
20583377 AGTCATGTTA
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
108 83 0.95
109 4 0.05
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.35
Consensus pattern (108 bp):
AAATTGAAATAAAAGGTAAATTGGGTAAGAGTTGAATAATTTTCAAAGAATATGTATTTGTAAAT
TATAAAAGTTGTAACCAAATCAACATATTTTGCTAATTTAAAC
Found at i:20589273 original size:2 final size:2
Alignment explanation
Indices: 20589217--20589261 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
20589207 ATTTTACTCT
*
20589217 TA TA TA TC TA TA TA TA 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
20589259 TA T
1 TA T
20589262 TAAGATTATA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20596798 original size:21 final size:21
Alignment explanation
Indices: 20596769--20596819 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
20596759 TTGCATTTTT
* *
20596769 AAAAAAAATATAAAATAAAGA
1 AAAAAAAATAAAAAATAAAAA
*
20596790 AAGAAAAATAAAAAATAAAAA
1 AAAAAAAATAAAAAATAAAAA
20596811 AAAAAAAAT
1 AAAAAAAAT
20596820 CCCCAATGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.84, C:0.00, G:0.04, T:0.12
Consensus pattern (21 bp):
AAAAAAAATAAAAAATAAAAA
Found at i:20596803 original size:7 final size:7
Alignment explanation
Indices: 20596771--20596819 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
20596761 GCATTTTTAA
20596771 AAAAAAT
1 AAAAAAT
*
20596778 ATAAAAT
1 AAAAAAT
20596785 AAAGAAA-
1 AAA-AAAT
*
20596792 GAAAAAT
1 AAAAAAT
20596799 AAAAAAT
1 AAAAAAT
*
20596806 AAAAAAA
1 AAAAAAT
20596813 AAAAAAT
1 AAAAAAT
20596820 CCCCAATGAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
6 3 0.09
7 28 0.82
8 3 0.09
ACGTcount: A:0.84, C:0.00, G:0.04, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:20597774 original size:2 final size:2
Alignment explanation
Indices: 20597767--20597872 Score: 135
Period size: 2 Copynumber: 53.0 Consensus size: 2
20597757 CAAAATTTTA
20597767 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
** * * *
20597809 AT AT NCC AA AA AT -T TT CAT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
20597852 -T AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
20597873 TTATGTTAAT
Statistics
Matches: 94, Mismatches: 6, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
1 2 0.02
2 91 0.97
3 1 0.01
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20599775 original size:25 final size:25
Alignment explanation
Indices: 20599739--20599817 Score: 76
Period size: 25 Copynumber: 3.2 Consensus size: 25
20599729 ATTTTTTATT
* *
20599739 TTTAAAAAATTATTATGTATATTTA
1 TTTAAAATATTAATATGTATATTTA
* *
20599764 TTTAAAATATTAATA-ATATA-TAA
1 TTTAAAATATTAATATGTATATTTA
20599787 TTT-AAATATTAATATG-ATTATTGTA
1 TTTAAAATATTAATATGTA-TATT-TA
20599812 TTTAAA
1 TTTAAA
20599818 TTTTAGACGT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
22 12 0.28
23 7 0.16
24 5 0.12
25 17 0.40
26 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (25 bp):
TTTAAAATATTAATATGTATATTTA
Found at i:20599902 original size:21 final size:21
Alignment explanation
Indices: 20599878--20599942 Score: 53
Period size: 21 Copynumber: 3.0 Consensus size: 21
20599868 TATCATTTAA
20599878 ATATTAATATTTTAAAATATT
1 ATATTAATATTTTAAAATATT
** *
20599899 ATATTTTTA-TTTATAAT-TT
1 ATATTAATATTTTAAAATATT
*
20599918 AAATATTAACATTGTTAAAATATT
1 --ATATTAATATT-TTAAAATATT
20599942 A
1 A
20599943 AATATTTTAT
Statistics
Matches: 32, Mismatches: 7, Indels: 9
0.67 0.15 0.19
Matches are distributed among these distances:
19 2 0.06
20 7 0.22
21 13 0.41
22 2 0.06
23 6 0.19
24 2 0.06
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
ATATTAATATTTTAAAATATT
Found at i:20599959 original size:44 final size:42
Alignment explanation
Indices: 20599865--20599982 Score: 164
Period size: 44 Copynumber: 2.8 Consensus size: 42
20599855 ATTATGATAA
* * *
20599865 ATTTATCATTTAAATATTAATATTTTAAAATATTATATTTTT
1 ATTTATAATTTAAATATTAACATTTTAAAATATTAAATTTTT
20599907 ATTTATAATTTAAATATTAACATTGTTAAAATATTAAATATTTT
1 ATTTATAATTTAAATATTAACATT-TTAAAATATTAAAT-TTTT
* * *
20599951 ATTTATAATTAAAATATTAAAATTTTATAATA
1 ATTTATAATTTAAATATTAACATTTTAAAATA
20599983 AAACTATATA
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
42 22 0.32
43 20 0.29
44 26 0.38
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.52
Consensus pattern (42 bp):
ATTTATAATTTAAATATTAACATTTTAAAATATTAAATTTTT
Found at i:20601989 original size:21 final size:21
Alignment explanation
Indices: 20601935--20601997 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
20601925 ATGTATAAAT
* *
20601935 TAAGTTCAAAAGTCATTTAAAA
1 TAAGTTCAAAAATCA-TTCAAA
* * *
20601957 CAACTTTAAAAATCATTCAAA
1 TAAGTTCAAAAATCATTCAAA
*
20601978 TAAGTTCAAAAATCACTCAA
1 TAAGTTCAAAAATCATTCAA
20601998 GCAATTTTGA
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
21 21 0.66
22 11 0.34
ACGTcount: A:0.51, C:0.16, G:0.05, T:0.29
Consensus pattern (21 bp):
TAAGTTCAAAAATCATTCAAA
Found at i:20602295 original size:9 final size:9
Alignment explanation
Indices: 20602268--20602338 Score: 54
Period size: 9 Copynumber: 7.4 Consensus size: 9
20602258 TGCATTTTTT
20602268 AAAAAAATA
1 AAAAAAATA
*
20602277 ATATAAAATA
1 A-AAAAAATA
20602287 AAAAAAATA
1 AAAAAAATA
20602296 AAGAAAGAA-A
1 AA-AAA-AATA
20602306 ATAAAAAATA
1 A-AAAAAATA
*
20602316 CAAAAAATA
1 AAAAAAATA
* *
20602325 GAAATAAACA
1 -AAAAAAATA
20602335 AAAA
1 AAAA
20602339 TCCCTGATGA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
9 23 0.47
10 23 0.47
11 3 0.06
ACGTcount: A:0.80, C:0.03, G:0.04, T:0.13
Consensus pattern (9 bp):
AAAAAAATA
Done.