Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, whole genome shotgun sequence
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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 129 of 190
Found at i:20671914 original size:7 final size:8
Alignment explanation
Indices: 20671857--20671924 Score: 70
Period size: 8 Copynumber: 8.8 Consensus size: 8
20671847 GATAAAGTGA
20671857 AAAAAATG
1 AAAAAATG
*
20671865 AAAAAA-C
1 AAAAAATG
20671872 AAAAAAT-
1 AAAAAATG
20671879 AAAAAATG
1 AAAAAATG
**
20671887 AGAAATGTG
1 A-AAAAATG
20671896 AAAAAATG
1 AAAAAATG
*
20671904 AAAAAATA
1 AAAAAATG
20671912 AAAAAAT-
1 AAAAAATG
20671919 AAAAAA
1 AAAAAA
20671925 AGAGAGAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
7 19 0.37
8 26 0.51
9 6 0.12
ACGTcount: A:0.78, C:0.01, G:0.09, T:0.12
Consensus pattern (8 bp):
AAAAAATG
Found at i:20673202 original size:22 final size:22
Alignment explanation
Indices: 20673177--20673242 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
20673167 CCTAAAATTT
20673177 TTGAATGAGAACCTTTGAAATA
1 TTGAATGAGAACCTTTGAAATA
* * * * *
20673199 TTGAATGTGAA-ATACTAAAATTT
1 TTGAATGAGAACCT-TTGAAA-TA
20673222 TTGAATGAGAACCTTTGAAAT
1 TTGAATGAGAACCTTTGAAAT
20673243 TTTGGTTGTG
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
21 1 0.03
22 15 0.47
23 15 0.47
24 1 0.03
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.35
Consensus pattern (22 bp):
TTGAATGAGAACCTTTGAAATA
Found at i:20673242 original size:23 final size:23
Alignment explanation
Indices: 20673171--20673245 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
20673161 TGAAACCCTA
20673171 AAATTTTTGAATGAGAACCTTTG
1 AAATTTTTGAATGAGAACCTTTG
* * * * *
20673194 AAA-TATTGAATGTGAA-ATACTA
1 AAATTTTTGAATGAGAACCT-TTG
20673216 AAATTTTTGAATGAGAACCTTTG
1 AAATTTTTGAATGAGAACCTTTG
20673239 AAATTTT
1 AAATTTT
20673246 GGTTGTGAAT
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
21 1 0.03
22 15 0.38
23 22 0.56
24 1 0.03
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.39
Consensus pattern (23 bp):
AAATTTTTGAATGAGAACCTTTG
Found at i:20673342 original size:17 final size:16
Alignment explanation
Indices: 20673322--20673408 Score: 77
Period size: 17 Copynumber: 5.2 Consensus size: 16
20673312 AACCGAAAAC
20673322 TCTTGCAAATCTTCAAT
1 TCTTGCAAATCTT-AAT
20673339 TCTTGCAAATC-TAAGT
1 TCTTGCAAATCTTAA-T
***
20673355 TCTTATGAATCTTCAAT
1 TCTTGCAAATCTT-AAT
*
20673372 TCTTGCAAATCTTTGAGT
1 TCTTGCAAATC-TT-AAT
*
20673390 TCTTGCAAACCTTAAT
1 TCTTGCAAATCTTAAT
20673406 TCT
1 TCT
20673409 AGTGAATTTT
Statistics
Matches: 56, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
15 2 0.04
16 15 0.27
17 23 0.41
18 16 0.29
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.43
Consensus pattern (16 bp):
TCTTGCAAATCTTAAT
Found at i:20673559 original size:34 final size:35
Alignment explanation
Indices: 20673505--20673601 Score: 85
Period size: 34 Copynumber: 2.8 Consensus size: 35
20673495 GAGAACGTCT
* * *
20673505 AATTTTTGCGAATCTCCAATTCTTACAAATT-TGAA
1 AATTCTTGCAAATCTTCAATTCTTACAAATTAT-AA
* * *
20673540 AA-TCTTGCAAATCTTCAATTTTTTC-GATTATAA
1 AATTCTTGCAAATCTTCAATTCTTACAAATTATAA
*
20673573 AATTCTTGCAAATC-TCTAATTCTTGCAAA
1 AATTCTTGCAAATCTTC-AATTCTTACAAA
20673602 AAAATCTTCT
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
33 9 0.18
34 37 0.76
35 3 0.06
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.41
Consensus pattern (35 bp):
AATTCTTGCAAATCTTCAATTCTTACAAATTATAA
Found at i:20673640 original size:17 final size:17
Alignment explanation
Indices: 20673570--20673662 Score: 77
Period size: 17 Copynumber: 5.7 Consensus size: 17
20673560 TTTTCGATTA
*
20673570 TAAAATTCTTGCAAATC
1 TAAAATTCTTGTAAATC
** *
20673587 TCTAATTCTTGCAAA--
1 TAAAATTCTTGTAAATC
* *
20673602 -AAAA-TCTTCTAAATT
1 TAAAATTCTTGTAAATC
* *
20673617 TACAATTTTTGTAAATC
1 TAAAATTCTTGTAAATC
*
20673634 TAAAATTCTTGTGAATC
1 TAAAATTCTTGTAAATC
20673651 TAAAATTCTTGT
1 TAAAATTCTTGT
20673663 GAATTTTCAT
Statistics
Matches: 59, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
13 7 0.12
14 2 0.03
16 3 0.05
17 47 0.80
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.42
Consensus pattern (17 bp):
TAAAATTCTTGTAAATC
Found at i:20673698 original size:17 final size:18
Alignment explanation
Indices: 20673676--20673709 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20673666 TTTTCATTTT
20673676 TTGCGAA-CTTAAAAATC
1 TTGCGAATCTTAAAAATC
*
20673693 TTGCGAATCTTTAAAAT
1 TTGCGAATCTTAAAAAT
20673710 TTACGAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTGCGAATCTTAAAAATC
Found at i:20674370 original size:14 final size:14
Alignment explanation
Indices: 20674351--20674381 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
20674341 CTAAGGGATT
20674351 AGAGTGAAAAATAC
1 AGAGTGAAAAATAC
20674365 AGAGTGAAAAATAC
1 AGAGTGAAAAATAC
20674379 AGA
1 AGA
20674382 ATTCATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.58, C:0.06, G:0.23, T:0.13
Consensus pattern (14 bp):
AGAGTGAAAAATAC
Found at i:20675543 original size:122 final size:116
Alignment explanation
Indices: 20675412--20675628 Score: 319
Period size: 122 Copynumber: 1.8 Consensus size: 116
20675402 ACAAGAAACA
* *
20675412 TTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATGAAAATTTCAAAAAAAAAATTTTT
1 TTTTTAAGGAAAAGTTGAAAGTACCAATTTTCCTTGAAAATAAAAATTTC----AAAAAA-TTTT
*
20675477 TTGGAGAAAAAGTTGAAAGTATC-AATTTTCCTTGAAGATAAAATTTTCAAAAAATCT
61 TTGAAG-AAAAGTTGAAAGTATCAAATTTT-CTTGAAGATAAAATTTTCAAAAAATCT
* *
20675534 TTTTTAAGGAAAAGTTGAAAGTACCAATTTTTCTTGAAAATAAAAATTTCATAAAATTTTTTGAA
1 TTTTTAAGGAAAAGTTGAAAGTACCAATTTTCCTTGAAAATAAAAATTTCAAAAAATTTTTTGAA
20675599 GAAAAGTTGAAAGTATCAAATTTTCTTGAA
66 GAAAAGTTGAAAGTATCAAATTTTCTTGAA
20675629 TAAAGGCATT
Statistics
Matches: 89, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
116 22 0.25
117 15 0.17
118 5 0.06
122 47 0.53
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.36
Consensus pattern (116 bp):
TTTTTAAGGAAAAGTTGAAAGTACCAATTTTCCTTGAAAATAAAAATTTCAAAAAATTTTTTGAA
GAAAAGTTGAAAGTATCAAATTTTCTTGAAGATAAAATTTTCAAAAAATCT
Found at i:20675562 original size:59 final size:57
Alignment explanation
Indices: 20675412--20675628 Score: 249
Period size: 59 Copynumber: 3.7 Consensus size: 57
20675402 ACAAGAAACA
*
20675412 TTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATGAAAATTTCAAAAAAAAAATT
1 TTTTTAAGGAAAAGTTGAAAGTACCAATTTTCCTTGAAAAT-AAAATTTC----AAAAAATT
* * * *
20675474 TTTTTGGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAGATAAAATTTTCAAAAAATCT
1 TTTTT-AAGGAAAAGTTGAAAGTACCAATTTTCCTTGAAAATAAAA-TTTCAAAAAAT-T
* *
20675534 TTTTTAAGGAAAAGTTGAAAGTACCAATTTTTCTTGAAAATAAAAATTTCATAAAATT
1 TTTTTAAGGAAAAGTTGAAAGTACCAATTTTCCTTGAAAAT-AAAATTTCAAAAAATT
* *
20675592 TTTTGAA-GAAAAGTTGAAAGTATCAAATTTT-CTTGAA
1 TTTTTAAGGAAAAGTTGAAAGTA-CCAATTTTCCTTGAA
20675629 TAAAGGCATT
Statistics
Matches: 139, Mismatches: 11, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
57 21 0.15
58 14 0.10
59 48 0.35
60 10 0.07
62 9 0.06
63 37 0.27
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.36
Consensus pattern (57 bp):
TTTTTAAGGAAAAGTTGAAAGTACCAATTTTCCTTGAAAATAAAATTTCAAAAAATT
Found at i:20678474 original size:3 final size:3
Alignment explanation
Indices: 20678466--20678506 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
20678456 AAAACTCTGT
20678466 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
20678507 TTGTGCCGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:20683014 original size:89 final size:90
Alignment explanation
Indices: 20682903--20683076 Score: 280
Period size: 89 Copynumber: 1.9 Consensus size: 90
20682893 AATTACAAAG
* * * *
20682903 GGTCAGAAAATCAAATAAGAGAATCGAGCAAAAATAGTAAACTAGTGGATTTAATTATCCTCTT-
1 GGTCAAAAAATCAAATAAGAGAATCCAACAAAAATAGTAAACTAGTGGATTTAATTACCCTCTTA
20682967 AAAG-AAAAGACGTAGTGGATTACAC
66 AAAGAAAAAG-CGTAGTGGATTACAC
*
20682992 GGTCAAAAAATCAAATAAGAGAATCCAACAAAAATAGTAAACTAGTGGATTTAATTGCCCTCTTA
1 GGTCAAAAAATCAAATAAGAGAATCCAACAAAAATAGTAAACTAGTGGATTTAATTACCCTCTTA
20683057 AAAGAAAAAGCGTAGTGGAT
66 AAAGAAAAAGCGTAGTGGAT
20683077 AGAATAAGGG
Statistics
Matches: 78, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
89 59 0.76
90 14 0.18
91 5 0.06
ACGTcount: A:0.46, C:0.13, G:0.18, T:0.23
Consensus pattern (90 bp):
GGTCAAAAAATCAAATAAGAGAATCCAACAAAAATAGTAAACTAGTGGATTTAATTACCCTCTTA
AAAGAAAAAGCGTAGTGGATTACAC
Found at i:20684534 original size:16 final size:16
Alignment explanation
Indices: 20684513--20684555 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
20684503 ATTATTTTTT
*
20684513 AAATATAAATATTTAA
1 AAATATAAATATATAA
* *
20684529 AAATATCATTATATAA
1 AAATATAAATATATAA
*
20684545 ATATATAAATA
1 AAATATAAATA
20684556 AAAAATTAAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
AAATATAAATATATAA
Found at i:20690723 original size:25 final size:26
Alignment explanation
Indices: 20690666--20690724 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
20690656 AGGTTACATA
* * *
20690666 TATGTTATATATGATGAATACTTATG
1 TATGCTATATAAGATGAATACTCATG
*
20690692 TGTGCTATATAAGATGAATAC-CATG
1 TATGCTATATAAGATGAATACTCATG
20690717 TATGCTAT
1 TATGCTAT
20690725 GTTGGTTTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 10 0.36
26 18 0.64
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.41
Consensus pattern (26 bp):
TATGCTATATAAGATGAATACTCATG
Found at i:20695258 original size:14 final size:14
Alignment explanation
Indices: 20695225--20695258 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
20695215 TTTTAATATG
*
20695225 TAAATATTATATTT
1 TAAAAATTATATTT
*
20695239 TTAAAATTATATTT
1 TAAAAATTATATTT
20695253 TAAAAA
1 TAAAAA
20695259 ATTCTTTAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAAAAATTATATTT
Found at i:20702220 original size:327 final size:327
Alignment explanation
Indices: 20701499--20702244 Score: 839
Period size: 327 Copynumber: 2.3 Consensus size: 327
20701489 TCCTGAGAAT
* * *
20701499 ACTATTTTTTATTGAAAATCTGGTGAAAAACATTTGTATTTGCAGTGGTTGACTTTTCTTTCAAG
1 ACTATCTTTTATTGAAAATCTGGTGAAAAACACTTGTATTTGCAGTGGTTGA-TTATCTTTCAAG
* * * * *
20701564 ATTTTTATTGGTTTCAAGAAAGAGATTTGAGTGTAAAAAGGAATAACTTTAAGGCATATTAAAAA
65 ACTTGTATTGGTTCCAAGATAGAGATTTGAGTGTAAAAAGGAATAACTTTAAGGCATACTAAAAA
* ** * * *
20701629 TGTCACATTCATCAATAGTAGTATCCAACAGGGGTTGAAACAAATAACATTATAGTACAATGAAA
130 TCTCACATTCATCAATAACAGTATACAACAAGGATTGAAACAAATAACATTATAGTACAATGAAA
* * * * *
20701694 CATTATTTGATATCAACTTATACTTTTGAAATCAATCCATTAAACTCTTTTGATGAAGGTTTGGA
195 CATCAGTTGATATCAACTTACACTTTTGAAATCAATCCATTAAACACTTTTAATGAAGGTTTGGA
*
20701759 AATACCTTTCTTAGTCACAGTTTGGGCAGCAAAAAATGTTTAAAAAACTTGCTTTTATAAAGAAA
260 AATACCTTTCTTAGT-ACAGTTTGGGCAACAAAAAATGTTTAAAAAACTTGCTTTTATAAAGAAA
20701824 ATTA
324 ATTA
* * * * * *
20701828 ACTATTTTTTATTG-AAATCTAGTCAAAAACACTTGTATTTAC-GAAGGTTGACTATCTTT-AAG
1 ACTATCTTTTATTGAAAATCTGGTGAAAAACACTTGTATTTGCAG-TGGTTGATTATCTTTCAAG
* *
20701890 ACTTGTATTGGTTCCAAGATAGAGATTTGAGTGTCAAAAGGAAATAA-TTTCAAGGCATACTATA
65 ACTTGTATTGGTTCCAAGATAGAGATTTGAGTGTAAAAAGG-AATAACTTT-AAGGCATACTAAA
* * * * * * **
20701954 GATACT-ACTTTCATGAGTAACGGTATACAACAAGGATTGAATA-GAATAGTATTAT-GATACAA
128 AAT-CTCACATTCATCAATAACAGTATACAACAAGGATTGAA-ACAAATAACATTATAG-TACAA
* * *
20702016 TGAAGCATCAGTTGATATCACCTTACAC-TTTGAAAATCAATCCATTGAACACTTTTAATG-AGG
190 TGAAACATCAGTTGATATCAACTTACACTTTTG-AAATCAATCCATTAAACACTTTTAATGAAGG
** * * *
20702079 TTTTGGAAATACCTTTCTTAGT-CAGTTT-TTCAATAAACAATGTTTAAAGAACTTGCTTTTATA
254 -TTTGGAAATACCTTTCTTAGTACAGTTTGGGCAACAAAAAATGTTTAAAAAACTTGCTTTTATA
*
20702142 AAGAGAATTA
318 AAGAAAATTA
** * * *
20702152 TTTGTCTTTTATTGAAAATTTGGTGAAAAACACTTGTATTTGCAGTGGTTGATTGGTCTTTCAAG
1 ACTATCTTTTATTGAAAATCTGGTGAAAAACACTTGTATTTGCAGTGGTTGATT-ATCTTTCAAG
** *
20702217 ACTTGTATTGAATCTAAGATAGAGATTT
65 ACTTGTATTGGTTCCAAGATAGAGATTT
20702245 AAGGAAAAAT
Statistics
Matches: 348, Mismatches: 57, Indels: 26
0.81 0.13 0.06
Matches are distributed among these distances:
324 48 0.14
325 37 0.11
326 56 0.16
327 161 0.46
328 32 0.09
329 14 0.04
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (327 bp):
ACTATCTTTTATTGAAAATCTGGTGAAAAACACTTGTATTTGCAGTGGTTGATTATCTTTCAAGA
CTTGTATTGGTTCCAAGATAGAGATTTGAGTGTAAAAAGGAATAACTTTAAGGCATACTAAAAAT
CTCACATTCATCAATAACAGTATACAACAAGGATTGAAACAAATAACATTATAGTACAATGAAAC
ATCAGTTGATATCAACTTACACTTTTGAAATCAATCCATTAAACACTTTTAATGAAGGTTTGGAA
ATACCTTTCTTAGTACAGTTTGGGCAACAAAAAATGTTTAAAAAACTTGCTTTTATAAAGAAAAT
TA
Found at i:20708228 original size:22 final size:22
Alignment explanation
Indices: 20708197--20708239 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
20708187 ATTAAAAATT
*
20708197 TAAAAATAATAATAAATAATAG
1 TAAAAATAATAATAAAAAATAG
* *
20708219 TAAAATTAATAGTAAAAAATA
1 TAAAAATAATAATAAAAAATA
20708240 CTTAAAATCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (22 bp):
TAAAAATAATAATAAAAAATAG
Found at i:20708239 original size:10 final size:11
Alignment explanation
Indices: 20708199--20708239 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
20708189 TAAAAATTTA
*
20708199 AAAATAATAAT
1 AAAATAATAGT
20708210 -AAATAATAGT
1 AAAATAATAGT
20708220 AAAATTAATAGT
1 AAAA-TAATAGT
20708232 AAAA-AATA
1 AAAATAATA
20708240 CTTAAAATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 13 0.48
11 3 0.11
12 11 0.41
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (11 bp):
AAAATAATAGT
Found at i:20709581 original size:267 final size:267
Alignment explanation
Indices: 20709106--20709641 Score: 946
Period size: 267 Copynumber: 2.0 Consensus size: 267
20709096 TACGGTAAGG
**
20709106 AAGAGGAAGCAGATATGAAAGGTAGGGATTTAAATTATGATAGCGATCACATTTTCAGTTGCATC
1 AAGAGGAAGCAGATATGAAAGGTAGGGATTTAAATTACAATAGCGATCACATTTTCAGTTGCATC
* *
20709171 ATATTTGTCATGATTTTGGATATAACAGAGACCTTCGCAGTCATTGTGCTTATTGCAATCGTGAA
66 ATATTTGTCATGATTTTGGATATAACAGAGACCTTCGCAATCATTGTGCCTATTGCAATCGTGAA
20709236 TTTTTTTGAATTTTGCTCAACTTGCTATAAAACATAATAATTTTAATTATCAGTCATAAAAACTC
131 TTTTTTTGAATTTTGCTCAACTTGCTATAAAACATAATAATTTTAATTATCAGTCATAAAAACTC
*
20709301 TTATTTTATGATTTTTAAAGTAATTTATATCACATTATGTGTTTTAGTTATTTAAGAAAAAATAT
196 TTATTTTATGATTTTTAAAGTAATTTATATCACATCATGTGTTTTAGTTATTTAAGAAAAAATAT
20709366 TTATAGT
261 TTATAGT
* *
20709373 AAGAGGAAGCAGATGTGAAAGGTAGGGATTTAAATTACAATAGCGATCACATTTTCAGTTGCGTC
1 AAGAGGAAGCAGATATGAAAGGTAGGGATTTAAATTACAATAGCGATCACATTTTCAGTTGCATC
* *
20709438 GTATTTGTCATGATTTTGGATATAACGGAGACCTTCGCAATCATTGTGCCTATTGCAATCGTGAA
66 ATATTTGTCATGATTTTGGATATAACAGAGACCTTCGCAATCATTGTGCCTATTGCAATCGTGAA
*
20709503 TTTTTTTGAATTTTGCTCAACTTGCTATAAAACATAATAATTTTAATTATTAGTCATAAAAACTC
131 TTTTTTTGAATTTTGCTCAACTTGCTATAAAACATAATAATTTTAATTATCAGTCATAAAAACTC
* * * *
20709568 TTATTTTATGATTTTTAAAGTAATTTATATCATATCATTTGTTTTATTTATTTTAGAAAAAATAT
196 TTATTTTATGATTTTTAAAGTAATTTATATCACATCATGTGTTTTAGTTATTTAAGAAAAAATAT
20709633 TTATAGT
261 TTATAGT
20709640 AA
1 AA
20709642 AATATTCATA
Statistics
Matches: 255, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
267 255 1.00
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (267 bp):
AAGAGGAAGCAGATATGAAAGGTAGGGATTTAAATTACAATAGCGATCACATTTTCAGTTGCATC
ATATTTGTCATGATTTTGGATATAACAGAGACCTTCGCAATCATTGTGCCTATTGCAATCGTGAA
TTTTTTTGAATTTTGCTCAACTTGCTATAAAACATAATAATTTTAATTATCAGTCATAAAAACTC
TTATTTTATGATTTTTAAAGTAATTTATATCACATCATGTGTTTTAGTTATTTAAGAAAAAATAT
TTATAGT
Found at i:20721601 original size:16 final size:16
Alignment explanation
Indices: 20721580--20721623 Score: 88
Period size: 16 Copynumber: 2.8 Consensus size: 16
20721570 TGAAAGGATG
20721580 CAAGACATTCAACTAC
1 CAAGACATTCAACTAC
20721596 CAAGACATTCAACTAC
1 CAAGACATTCAACTAC
20721612 CAAGACATTCAA
1 CAAGACATTCAA
20721624 TATCAAGAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.45, C:0.30, G:0.07, T:0.18
Consensus pattern (16 bp):
CAAGACATTCAACTAC
Found at i:20724094 original size:12 final size:13
Alignment explanation
Indices: 20724077--20724131 Score: 60
Period size: 12 Copynumber: 4.3 Consensus size: 13
20724067 TTGGGATAGG
20724077 TTAGGGTTTA-GT
1 TTAGGGTTTATGT
20724089 TTAGGGTTTATG-
1 TTAGGGTTTATGT
* *
20724101 TTAAGGTTTTTGTT
1 TTAGGGTTTATG-T
*
20724115 TTAGGGTTTATGG
1 TTAGGGTTTATGT
20724128 TTAG
1 TTAG
20724132 TATTGTGGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
12 20 0.57
13 5 0.14
14 10 0.29
ACGTcount: A:0.16, C:0.00, G:0.31, T:0.53
Consensus pattern (13 bp):
TTAGGGTTTATGT
Found at i:20724154 original size:13 final size:13
Alignment explanation
Indices: 20724060--20724400 Score: 105
Period size: 13 Copynumber: 26.5 Consensus size: 13
20724050 TCAAGTTGCT
20724060 TTTAGGTTT-GGG
1 TTTAGGTTTAGGG
*
20724072 -ATAGG-TTAGGG
1 TTTAGGTTTAGGG
20724083 TTTA-GTTTAGGG
1 TTTAGGTTTAGGG
* * *
20724095 TTTATGTTAAGGT
1 TTTAGGTTTAGGG
* *
20724108 TTTTGTTTTAGGG
1 TTTAGGTTTAGGG
**
20724121 TTTATGG-TTAGTA
1 TTTA-GGTTTAGGG
20724134 TTGT-GGTTTAGGG
1 TT-TAGGTTTAGGG
**
20724147 TTTAGGTTTACAG
1 TTTAGGTTTAGGG
*
20724160 TTTGACGTTTA-GG
1 TTT-AGGTTTAGGG
* *
20724173 TTTTGGTTT-CGG
1 TTTAGGTTTAGGG
* *
20724185 TTTCA-ATTTCA-GT
1 TTT-AGGTTT-AGGG
*
20724198 TTTAGTTTTA-GG
1 TTTAGGTTTAGGG
*
20724210 TTTGGGTTT--GG
1 TTTAGGTTTAGGG
20724221 TTTAAGGTTTAGGG
1 TTT-AGGTTTAGGG
20724235 TTTAGAG-TTA-GG
1 TTTAG-GTTTAGGG
*
20724247 TTTAAGGTTTAGGA
1 TTT-AGGTTTAGGG
*
20724261 TTTAAAGTTTTA--G
1 TTT--AGGTTTAGGG
20724274 TTTAGGGTTTAGGG
1 TTTA-GGTTTAGGG
*
20724288 TTT-GAATTT-GAGG
1 TTTAG-GTTTAG-GG
*
20724301 TTT-GTTTTTAGGG
1 TTTAG-GTTTAGGG
* *
20724314 TTTGAGATTTAGGA
1 TTT-AGGTTTAGGG
20724328 TTTAGGTTTAGGG
1 TTTAGGTTTAGGG
* *
20724341 TTT-GGATTTAAGA
1 TTTAGG-TTTAGGG
* *
20724354 TTTGGGATTTAGGA
1 TTTAGG-TTTAGGG
*
20724368 TTTTGGTTTAGGG
1 TTTAGGTTTAGGG
20724381 TTTAGGGTTT-GGG
1 TTTA-GGTTTAGGG
20724394 ATTTAGG
1 -TTTAGG
20724401 GTTTTAGTTT
Statistics
Matches: 249, Mismatches: 46, Indels: 67
0.69 0.13 0.19
Matches are distributed among these distances:
10 2 0.01
11 14 0.06
12 57 0.23
13 113 0.45
14 55 0.22
15 8 0.03
ACGTcount: A:0.18, C:0.01, G:0.32, T:0.49
Consensus pattern (13 bp):
TTTAGGTTTAGGG
Found at i:20724156 original size:6 final size:6
Alignment explanation
Indices: 20724138--20724400 Score: 81
Period size: 7 Copynumber: 40.3 Consensus size: 6
20724128 TTAGTATTGT
* * * *
20724138 GGTTTA GGGTTTA GGTTTA CAGTTTGA CGTTTA GGTTTT GGTTTC GGTTTCA
1 GGTTTA -GGTTTA GGTTTA -GGTTT-A GGTTTA GGTTTA GGTTTA GGTTT-A
* * * *
20724190 -ATTTCA GTTTTA GTTTTA GGTTTG GGTTT- GGTTTAA GGTTTA GGGTTTA
1 GGTTT-A GGTTTA GGTTTA GGTTTA GGTTTA GGTTT-A GGTTTA -GGTTTA
*
20724239 GAG-TTA GGTTTAA GGTTTA GGATTTAAA GTTTTA -GTTTA GGGTTTA
1 G-GTTTA GGTTT-A GGTTTA GG-TTT--A GGTTTA GGTTTA -GGTTTA
* * *
20724285 GGGTTT- GAATTTGA GGTTT- GTTTTTA GGGTTTGA GATTTA GGATTTA
1 -GGTTTA G-GTTT-A GGTTTA G-GTTTA -GGTTT-A GGTTTA GG-TTTA
* * *
20724332 GGTTTA GGGTTT- GGATTTAA GATTTG GGATTTA GGATTTT GGTTTA GGGTTTA
1 GGTTTA -GGTTTA GG-TTT-A GGTTTA GG-TTTA GG-TTTA GGTTTA -GGTTTA
*
20724385 GGGTTTG GGATTTA GG
1 -GGTTTA GG-TTTA GG
20724401 GTTTTAGTTT
Statistics
Matches: 200, Mismatches: 26, Indels: 60
0.70 0.09 0.21
Matches are distributed among these distances:
5 14 0.07
6 75 0.38
7 101 0.50
8 8 0.04
9 2 0.01
ACGTcount: A:0.18, C:0.02, G:0.32, T:0.48
Consensus pattern (6 bp):
GGTTTA
Found at i:20724223 original size:18 final size:19
Alignment explanation
Indices: 20724202--20724237 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
20724192 TTCAGTTTTA
*
20724202 GTTTTAGGTTT-GGGTTTG
1 GTTTAAGGTTTAGGGTTTG
20724220 GTTTAAGGTTTAGGGTTT
1 GTTTAAGGTTTAGGGTTT
20724238 AGAGTTAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.11, C:0.00, G:0.36, T:0.53
Consensus pattern (19 bp):
GTTTAAGGTTTAGGGTTTG
Found at i:20724247 original size:19 final size:19
Alignment explanation
Indices: 20724138--20724404 Score: 85
Period size: 20 Copynumber: 13.6 Consensus size: 19
20724128 TTAGTATTGT
20724138 GGTTTAGGGTTTAGGTTTA
1 GGTTTAGGGTTTAGGTTTA
* * *
20724157 CAGTTT-GACGTTTAGGTTTT
1 -GGTTTAG-GGTTTAGGTTTA
* *
20724177 GGTTT-CGGTTTCA-ATTTCA
1 GGTTTAGGGTTT-AGGTTT-A
* * *
20724196 GTTTTA-GTTTTAGGTTTG
1 GGTTTAGGGTTTAGGTTTA
20724214 GGTTT--GGTTTAAGGTTTA
1 GGTTTAGGGTTT-AGGTTTA
*
20724232 GGGTTTAGAG-TTAGGTTTAA
1 -GGTTTAGGGTTTAGGTTT-A
* *
20724252 GGTTTAGGATTTAAAGTTTTA
1 GGTTTAGGGTTT--AGGTTTA
20724273 -GTTTAGGGTTTAGGGTTT-
1 GGTTTAGGGTTTA-GGTTTA
* *
20724291 GAATTT-GAGGTTT-GTTTTTA
1 G-GTTTAG-GGTTTAG-GTTTA
*
20724311 GGGTTT-GAGATTTAGGATTTA
1 -GGTTTAG-GGTTTAGG-TTTA
20724332 GGTTTAGGGTTT-GGATTTAA
1 GGTTTAGGGTTTAGG-TTT-A
* *
20724352 GATTT-GGGATTTAGGATTTT
1 GGTTTAGGG-TTTAGG-TTTA
*
20724372 GGTTTAGGGTTTAGGGTTTG
1 GGTTTAGGGTTTA-GGTTTA
20724392 GGATTTAGGGTTT
1 GG-TTTAGGGTTT
20724405 TAGTTTGGGG
Statistics
Matches: 187, Mismatches: 31, Indels: 57
0.68 0.11 0.21
Matches are distributed among these distances:
17 4 0.02
18 20 0.11
19 52 0.28
20 76 0.41
21 30 0.16
22 5 0.03
ACGTcount: A:0.18, C:0.02, G:0.32, T:0.48
Consensus pattern (19 bp):
GGTTTAGGGTTTAGGTTTA
Found at i:20724253 original size:26 final size:26
Alignment explanation
Indices: 20724219--20724343 Score: 98
Period size: 27 Copynumber: 4.7 Consensus size: 26
20724209 GTTTGGGTTT
20724219 GGTTTAAGGTTTAGGGTTTAGAGTTA
1 GGTTTAAGGTTTAGGGTTTAGAGTTA
* *
20724245 GGTTTAAGGTTTAGGATTTAAAGTTTTA
1 GGTTTAAGGTTTAGGGTTTAGAG--TTA
* *
20724273 -GTTTAGGGTTTAGGGTTT-GAATTTGA
1 GGTTTAAGGTTTAGGGTTTAG-AGTT-A
* *
20724299 GGTTT--GTTTTTAGGGTTTGAGATTTA
1 GGTTTAAG-GTTTAGGGTTT-AGAGTTA
20724325 GGATTT-AGGTTTAGGGTTT
1 GG-TTTAAGGTTTAGGGTTT
20724344 GGATTTAAGA
Statistics
Matches: 81, Mismatches: 8, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
25 3 0.04
26 35 0.43
27 38 0.47
28 5 0.06
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (26 bp):
GGTTTAAGGTTTAGGGTTTAGAGTTA
Found at i:20724355 original size:26 final size:26
Alignment explanation
Indices: 20724225--20724366 Score: 92
Period size: 27 Copynumber: 5.3 Consensus size: 26
20724215 GTTTGGTTTA
* * *
20724225 AGGTTTAGGGTTTAGAGTT-AGGTTT
1 AGGTTTAGGGTTTGGATTTAAGATTT
* ** *
20724250 AAGGTTTAGGATTTAAAGTTTTAG-TTT
1 -AGGTTTAGGGTTTGGA-TTTAAGATTT
* * *
20724277 AGGGTTTAGGGTTTGAATTTGAGGTTT
1 A-GGTTTAGGGTTTGGATTTAAGATTT
* *
20724304 -GTTTTTAGGGTTTGAGATTTAGGATTT
1 AG-GTTTAGGGTTTG-GATTTAAGATTT
20724331 AGGTTTAGGGTTTGGATTTAAGATTT
1 AGGTTTAGGGTTTGGATTTAAGATTT
*
20724357 GGGATTTAGG
1 AGG-TTTAGG
20724367 ATTTTGGTTT
Statistics
Matches: 94, Mismatches: 14, Indels: 15
0.76 0.11 0.12
Matches are distributed among these distances:
25 1 0.01
26 44 0.47
27 46 0.49
28 3 0.03
ACGTcount: A:0.22, C:0.00, G:0.32, T:0.46
Consensus pattern (26 bp):
AGGTTTAGGGTTTGGATTTAAGATTT
Found at i:20724421 original size:7 final size:7
Alignment explanation
Indices: 20724204--20724404 Score: 85
Period size: 7 Copynumber: 30.4 Consensus size: 7
20724194 CAGTTTTAGT
20724204 TTTA-GG
1 TTTAGGG
20724210 TTT-GGG
1 TTTAGGG
20724216 TTT--GG
1 TTTAGGG
*
20724221 TTTAAGG
1 TTTAGGG
20724228 TTTAGGG
1 TTTAGGG
*
20724235 TTTAGAG
1 TTTAGGG
20724242 -TTA-GG
1 TTTAGGG
*
20724247 TTTAAGG
1 TTTAGGG
*
20724254 TTTAGGA
1 TTTAGGG
* *
20724261 TTTAAAGT
1 TTT-AGGG
20724269 TTTA--G
1 TTTAGGG
20724274 TTTAGGG
1 TTTAGGG
20724281 TTTAGGG
1 TTTAGGG
**
20724288 TTT-GAA
1 TTTAGGG
20724294 TTT-GAGG
1 TTTAG-GG
**
20724301 TTT-GTT
1 TTTAGGG
20724307 TTTAGGG
1 TTTAGGG
*
20724314 TTT-GAGA
1 TTTAG-GG
*
20724321 TTTAGGA
1 TTTAGGG
20724328 TTTA-GG
1 TTTAGGG
20724334 TTTAGGG
1 TTTAGGG
*
20724341 TTT-GGA
1 TTTAGGG
* *
20724347 TTTAAGA
1 TTTAGGG
20724354 TTT-GGG
1 TTTAGGG
*
20724360 ATTTAGGA
1 -TTTAGGG
*
20724368 TTT-TGG
1 TTTAGGG
20724374 TTTAGGG
1 TTTAGGG
20724381 TTTAGGG
1 TTTAGGG
20724388 TTT-GGG
1 TTTAGGG
20724394 ATTTAGGG
1 -TTTAGGG
20724402 TTT
1 TTT
20724405 TAGTTTGGGG
Statistics
Matches: 150, Mismatches: 26, Indels: 37
0.70 0.12 0.17
Matches are distributed among these distances:
5 10 0.07
6 41 0.27
7 88 0.59
8 11 0.07
ACGTcount: A:0.19, C:0.00, G:0.33, T:0.48
Consensus pattern (7 bp):
TTTAGGG
Found at i:20731913 original size:10 final size:9
Alignment explanation
Indices: 20731887--20731911 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
20731877 TTTAAAAAGA
20731887 TTTTTTTAT
1 TTTTTTTAT
20731896 TTTTTTTAT
1 TTTTTTTAT
20731905 TTTTTTT
1 TTTTTTT
20731912 TACTAAGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:20732069 original size:35 final size:33
Alignment explanation
Indices: 20732023--20732087 Score: 94
Period size: 35 Copynumber: 1.9 Consensus size: 33
20732013 AAAAATTCTA
*
20732023 AAAAATAAAAATAAAATTAAAATAAGTAAAAAATC
1 AAAAATAAAAATAAAA-TAAAAAAAG-AAAAAATC
*
20732058 AAAAATTAAAATAAAATAAAAAAAGAAAAA
1 AAAAATAAAAATAAAATAAAAAAAGAAAAA
20732088 CCTACGATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 5 0.18
34 8 0.29
35 15 0.54
ACGTcount: A:0.78, C:0.02, G:0.03, T:0.17
Consensus pattern (33 bp):
AAAAATAAAAATAAAATAAAAAAAGAAAAAATC
Found at i:20732072 original size:29 final size:28
Alignment explanation
Indices: 20732021--20732076 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 28
20732011 GGAAAAATTC
20732021 TAAAAAATAAAAATAAAATTAAAATAAG
1 TAAAAAATAAAAATAAAATTAAAATAAG
20732049 TAAAAAATCAAAAATTAAAA-TAAAATAA
1 TAAAAAAT-AAAAA-TAAAATTAAAATAA
20732077 AAAAAGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 8 0.31
29 13 0.50
30 5 0.19
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (28 bp):
TAAAAAATAAAAATAAAATTAAAATAAG
Found at i:20732086 original size:24 final size:23
Alignment explanation
Indices: 20732024--20732086 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 23
20732014 AAAATTCTAA
*
20732024 AAAAT-AAAAATAAAATTAAAAT
1 AAAATAAAAAAAAAAATTAAAAT
*
20732046 -AAGTAAAAAATCAAAAATTAAAAT
1 AAAATAAAAAA--AAAAATTAAAAT
20732070 AAAATAAAAAAAGAAAA
1 AAAATAAAAAAA-AAAA
20732087 ACCTACGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
21 3 0.09
22 5 0.15
23 1 0.03
24 15 0.45
25 9 0.27
ACGTcount: A:0.78, C:0.02, G:0.03, T:0.17
Consensus pattern (23 bp):
AAAATAAAAAAAAAAATTAAAAT
Found at i:20732086 original size:25 final size:24
Alignment explanation
Indices: 20732035--20732087 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
20732025 AAATAAAAAT
* *
20732035 AAAATTAAAATAAGTAAAAAATCA
1 AAAATTAAAATAAATAAAAAAACA
*
20732059 AAAATTAAAATAAAATAAAAAAAGA
1 AAAATTAAAAT-AAATAAAAAAACA
20732084 AAAA
1 AAAA
20732088 CCTACGATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.77, C:0.02, G:0.04, T:0.17
Consensus pattern (24 bp):
AAAATTAAAATAAATAAAAAAACA
Found at i:20732353 original size:13 final size:13
Alignment explanation
Indices: 20732335--20732359 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20732325 CAAACCTTAT
20732335 CAAAAAATTCAAC
1 CAAAAAATTCAAC
20732348 CAAAAAATTCAA
1 CAAAAAATTCAA
20732360 AGTTCATCCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.20, G:0.00, T:0.16
Consensus pattern (13 bp):
CAAAAAATTCAAC
Found at i:20732911 original size:5 final size:5
Alignment explanation
Indices: 20732901--20732993 Score: 73
Period size: 5 Copynumber: 17.8 Consensus size: 5
20732891 ATATGATAAC
* * *
20732901 AATAT AATAT ACTAT GAGA- AATAT AATAT AATA- ATATAAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT A-AT-AT AATAT AATAT
* *
20732951 ACTAGT AATAAC AATAT AATAT AATAT AATAT ATACTAT AATA
1 AATA-T AAT-AT AATAT AATAT AATAT AATAT A-A-TAT AATA
20732994 ACAATAAAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
4 3 0.04
5 50 0.71
6 11 0.16
7 6 0.09
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.35
Consensus pattern (5 bp):
AATAT
Found at i:20732936 original size:8 final size:8
Alignment explanation
Indices: 20732923--20732994 Score: 58
Period size: 8 Copynumber: 8.5 Consensus size: 8
20732913 TATGAGAAAT
20732923 ATAATATA
1 ATAATATA
20732931 ATAATATA
1 ATAATATA
20732939 ATAATATA
1 ATAATATA
20732947 ATATACTAGTA
1 ATA-A-TA-TA
*
20732958 ATAACA-A
1 ATAATATA
20732965 TATAATATA
1 -ATAATATA
20732974 AT-ATAATA
1 ATAAT-ATA
*
20732982 TATACTATA
1 -ATAATATA
20732991 ATAA
1 ATAA
20732995 CAATAAAAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 16
0.72 0.06 0.22
Matches are distributed among these distances:
7 3 0.06
8 32 0.62
9 8 0.15
10 4 0.08
11 5 0.10
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.36
Consensus pattern (8 bp):
ATAATATA
Found at i:20732968 original size:17 final size:16
Alignment explanation
Indices: 20732946--20732999 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 16
20732936 ATAATAATAT
20732946 AATATACTAGTAATAAC
1 AATATACTA-TAATAAC
*
20732963 AATATAATATAATATA-
1 AATATACTATAATA-AC
20732979 ATATATACTATAATAAC
1 A-ATATACTATAATAAC
20732996 AATA
1 AATA
20733000 AAAATCACCA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
16 10 0.31
17 22 0.69
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.33
Consensus pattern (16 bp):
AATATACTATAATAAC
Found at i:20733335 original size:59 final size:58
Alignment explanation
Indices: 20733179--20733395 Score: 178
Period size: 55 Copynumber: 3.8 Consensus size: 58
20733169 AACAGGTGAC
* ** * ** * *
20733179 CAAGACTGAACCATGAGTCAAGAAAATGATCTGGATTAAGCTAAGATCAAGCGA-C-T
1 CAAGATTGAACCACAAGTCTAGAAAATGATCTAAACTAAGCCAAGATCAAGCGAGCAT
* * * *
20733235 -AAGATTGAACCATAAGTCTAGAAAA-CAACTTAAACTGAGCCAAGATCAAGCGAGCAAT
1 CAAGATTGAACCACAAGTCTAGAAAATGATC-TAAACTAAGCCAAGATCAAGCGAGC-AT
* * * * * *
20733293 CGAGATTGAACCACAAGTTTAGAAAATGATCTGAATTAAGCCAAGATC--GAGTG-AT
1 CAAGATTGAACCACAAGTCTAGAAAATGATCTAAACTAAGCCAAGATCAAGCGAGCAT
* * *
20733348 CAAGATTGAACCACAAGCCAAGAAAGTGATCTAAACTAAGCCAAGATC
1 CAAGATTGAACCACAAGTCTAGAAAATGATCTAAACTAAGCCAAGATC
20733396 GAATGATTAG
Statistics
Matches: 128, Mismatches: 27, Indels: 13
0.76 0.16 0.08
Matches are distributed among these distances:
54 2 0.02
55 83 0.65
56 1 0.01
57 3 0.02
58 1 0.01
59 36 0.28
60 2 0.02
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.19
Consensus pattern (58 bp):
CAAGATTGAACCACAAGTCTAGAAAATGATCTAAACTAAGCCAAGATCAAGCGAGCAT
Found at i:20733372 original size:55 final size:55
Alignment explanation
Indices: 20733299--20733500 Score: 210
Period size: 55 Copynumber: 3.7 Consensus size: 55
20733289 CAATCGAGAT
** * * *
20733299 TGAACCACAAGTTTAGAAAATGATCTGAATTAAGCCAAGATCGAGTGATCAAGAT
1 TGAACCACAAGTCAAGAAAATGATCTGAACTAAGCCAAGATCGAATGATCAAGAC
* * * * *
20733354 TGAACCACAAGCCAAGAAAGTGATCTAAACTAAGCCAAGATCGAATGATTAGGAC
1 TGAACCACAAGTCAAGAAAATGATCTGAACTAAGCCAAGATCGAATGATCAAGAC
* * * * * * *
20733409 TGAGCCACAAGTCAAAAAAATGATCT-AGA-TGAGTCAAGATCAAATGACCGAGAC
1 TGAACCACAAGTCAAGAAAATGATCTGA-ACTAAGCCAAGATCGAATGATCAAGAC
* *
20733463 TAAACCACAAGTCAAGAAAATGATCTGAACTGAGCCAA
1 TGAACCACAAGTCAAGAAAATGATCTGAACTAAGCCAA
20733501 AATTAGATGA
Statistics
Matches: 119, Mismatches: 25, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
54 43 0.36
55 76 0.64
ACGTcount: A:0.44, C:0.18, G:0.19, T:0.18
Consensus pattern (55 bp):
TGAACCACAAGTCAAGAAAATGATCTGAACTAAGCCAAGATCGAATGATCAAGAC
Found at i:20733524 original size:109 final size:110
Alignment explanation
Indices: 20733356--20733558 Score: 248
Period size: 109 Copynumber: 1.9 Consensus size: 110
20733346 ATCAAGATTG
* * * * *
20733356 AACCACAAGCCAAGAAAGTGATCTAAACTAAGCCAAGATCGAATGATTAGGACTGAGCCACAAGT
1 AACCACAAGCCAAGAAAATGATCTAAACTAAGCCAAAATAGAATGACTAGGACTAAGCCACAAGT
*
20733421 CAAAAAAATGATCTAGA-TGAGTCAAGATCAAATGACCGAGACTA
66 CAAAAAAATGATCTAGACTGAGCCAAGATCAAATGACCGAGACTA
* * * * *
20733465 AACCACAAGTCAAGAAAATGATCTGAACTGAGCCAAAATTAG-ATGACTGGGATTAAGCCACAAG
1 AACCACAAGCCAAGAAAATGATCTAAACTAAGCCAAAA-TAGAATGACTAGGACTAAGCCACAAG
** * *
20733529 TCTGAAAGATGATCTGGACTGAGCCAAGAT
65 TCAAAAAAATGATCTAGACTGAGCCAAGAT
20733559 AAAAAATGAG
Statistics
Matches: 77, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
109 65 0.84
110 12 0.16
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.18
Consensus pattern (110 bp):
AACCACAAGCCAAGAAAATGATCTAAACTAAGCCAAAATAGAATGACTAGGACTAAGCCACAAGT
CAAAAAAATGATCTAGACTGAGCCAAGATCAAATGACCGAGACTA
Found at i:20734389 original size:17 final size:18
Alignment explanation
Indices: 20734367--20734412 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
20734357 TTTTTTTGCT
20734367 TTTTGTTTTTGCT-TTTA
1 TTTTGTTTTTGCTGTTTA
*
20734384 TTTTGTTTTTG-TGTTTT
1 TTTTGTTTTTGCTGTTTA
*
20734401 TTTTTTTTTTGC
1 TTTTGTTTTTGC
20734413 ACAACTCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 1 0.04
17 24 0.96
ACGTcount: A:0.02, C:0.04, G:0.13, T:0.80
Consensus pattern (18 bp):
TTTTGTTTTTGCTGTTTA
Found at i:20734713 original size:10 final size:10
Alignment explanation
Indices: 20734694--20734727 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
20734684 TGCCCCATCA
20734694 ATTTTCTTTC
1 ATTTTCTTTC
*
20734704 ATTTTTTTTC
1 ATTTTCTTTC
20734714 -TTTTCTTTC
1 ATTTTCTTTC
20734723 ATTTT
1 ATTTT
20734728 TCTCTTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (10 bp):
ATTTTCTTTC
Found at i:20734722 original size:9 final size:9
Alignment explanation
Indices: 20734695--20734774 Score: 53
Period size: 9 Copynumber: 9.0 Consensus size: 9
20734685 GCCCCATCAA
20734695 TTTTCTTTC
1 TTTTCTTTC
*
20734704 ATTTTTTTTC
1 -TTTTCTTTC
20734714 TTTTCTTTC
1 TTTTCTTTC
*
20734723 -ATT-TTTC
1 TTTTCTTTC
*
20734730 TCTTTATTTC
1 T-TTTCTTTC
20734740 TTTTACTTT-
1 TTTT-CTTTC
*
20734749 TTCTCTTT-
1 TTTTCTTTC
20734757 TTTTCTTT-
1 TTTTCTTTC
20734765 TTTTCCTTTC
1 TTTT-CTTTC
20734775 ATCATTTTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
7 4 0.07
8 17 0.30
9 20 0.35
10 16 0.28
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTCTTTC
Found at i:20734729 original size:16 final size:15
Alignment explanation
Indices: 20734695--20734769 Score: 59
Period size: 16 Copynumber: 4.9 Consensus size: 15
20734685 GCCCCATCAA
20734695 TTTTC-TTTCATTT-T
1 TTTTCTTTTC-TTTCT
20734709 TTTTCTTTTCTTTCAT
1 TTTTCTTTTCTTTC-T
*
20734725 TTTTCTCTTTATTTCT
1 TTTTCT-TTTCTTTCT
*
20734741 TTTACTTTTTCTCTT-T
1 TTTTC-TTTTCT-TTCT
20734757 TTTTCTTTT-TTTC
1 TTTTCTTTTCTTTC
20734770 CTTTCATCAT
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
13 2 0.04
14 9 0.18
15 8 0.16
16 21 0.42
17 10 0.20
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTCTTTTCTTTCT
Found at i:20734739 original size:17 final size:15
Alignment explanation
Indices: 20734695--20734758 Score: 60
Period size: 14 Copynumber: 4.3 Consensus size: 15
20734685 GCCCCATCAA
*
20734695 TTTTCTTTCATTT-T
1 TTTTCTTTTATTTCT
*
20734709 TTTTCTTTTCTTTCAT
1 TTTTCTTTTATTTC-T
20734725 TTTTCTCTTTATTTCT
1 TTTTCT-TTTATTTCT
* *
20734741 TTTACTTTT-TCTCT
1 TTTTCTTTTATTTCT
20734755 TTTT
1 TTTT
20734759 TTCTTTTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
14 18 0.44
15 3 0.07
16 13 0.32
17 7 0.17
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTCTTTTATTTCT
Found at i:20734752 original size:22 final size:21
Alignment explanation
Indices: 20734715--20734765 Score: 75
Period size: 22 Copynumber: 2.4 Consensus size: 21
20734705 TTTTTTTTCT
*
20734715 TTTCTTTCATTTTTCTCTTTA
1 TTTCTTTTATTTTTCTCTTTA
*
20734736 TTTCTTTTACTTTTTCTCTTTT
1 TTTCTTTTA-TTTTTCTCTTTA
20734758 TTTCTTTT
1 TTTCTTTT
20734766 TTTCCTTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 8 0.30
22 19 0.70
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTCTTTTATTTTTCTCTTTA
Found at i:20734768 original size:8 final size:8
Alignment explanation
Indices: 20734706--20734769 Score: 60
Period size: 8 Copynumber: 8.0 Consensus size: 8
20734696 TTTCTTTCAT
20734706 TTTTTTTC
1 TTTTTTTC
20734714 TTTTCTTTC
1 TTTT-TTTC
*
20734723 ATTTTTCTC
1 -TTTTTTTC
*
20734732 TTTATTTC
1 TTTTTTTC
*
20734740 --TTTTAC
1 TTTTTTTC
*
20734746 TTTTTCTC
1 TTTTTTTC
20734754 TTTTTTTC
1 TTTTTTTC
20734762 TTTTTTTC
1 TTTTTTTC
20734770 CTTTCATCAT
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
6 4 0.09
8 29 0.66
9 7 0.16
10 4 0.09
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTTTC
Found at i:20734768 original size:40 final size:39
Alignment explanation
Indices: 20734696--20734773 Score: 95
Period size: 40 Copynumber: 2.0 Consensus size: 39
20734686 CCCCATCAAT
* *
20734696 TTTCTTTCATTTTTTTTCTTTTCTTTCATTTTTCTCTTTA
1 TTTCTTTCACTTTTTCTCTTTTCTTTCATTTTTC-CTTTA
* *
20734736 TTTCTTTTACTTTTTCTCTTTT-TTTCTTTTTTTCCTTT
1 TTTCTTTCACTTTTTCTCTTTTCTTTC-ATTTTTCCTTT
20734774 CATCATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
39 8 0.24
40 25 0.76
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (39 bp):
TTTCTTTCACTTTTTCTCTTTTCTTTCATTTTTCCTTTA
Found at i:20739648 original size:19 final size:19
Alignment explanation
Indices: 20739606--20739663 Score: 53
Period size: 21 Copynumber: 2.9 Consensus size: 19
20739596 AATTCAATCG
* *
20739606 AAAAATTCAAAATTCATCCTA
1 AAAAATCCAAAATT--TCCAA
20739627 AAAAATCCAAAATTTCCAA
1 AAAAATCCAAAATTTCCAA
* *
20739646 AAATATCTCAAATTTTCC
1 AAAAATC-CAAAATTTCC
20739664 CAGATTTTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 10 0.31
20 9 0.28
21 13 0.41
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAATCCAAAATTTCCAA
Found at i:20740148 original size:3 final size:3
Alignment explanation
Indices: 20740142--20740282 Score: 56
Period size: 3 Copynumber: 49.7 Consensus size: 3
20740132 AAGGAAAGAA
* * * *
20740142 AAT AAT AAT AAT TAT AAC AAT AAT AAT -AT ACT -AT AAG AA- ATAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
* *
20740185 AAT -AT AAT AAT AAT AAT -AT AAT -GT ACT AAT -AT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
20740228 -AT ACT AGACT AGACT AGT TAT AAT AAT -AT AAT -AT AAT -AT AAT -AT
1 AAT AAT A-A-T A-A-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
20740272 AAC AAT AAT AA
1 AAT AAT AAT AA
20740283 AAATCACCAA
Statistics
Matches: 104, Mismatches: 18, Indels: 32
0.68 0.12 0.21
Matches are distributed among these distances:
2 23 0.22
3 73 0.70
4 1 0.01
5 7 0.07
ACGTcount: A:0.57, C:0.05, G:0.04, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:20740186 original size:19 final size:19
Alignment explanation
Indices: 20740164--20740233 Score: 79
Period size: 19 Copynumber: 3.6 Consensus size: 19
20740154 TATAACAATA
20740164 ATAATATACT-ATAAGAAAT
1 ATAATATACTAATAA-AAAT
* *
20740183 ATAATATAATAATAATAAT
1 ATAATATACTAATAAAAAT
*
20740202 ATAATGTACTAATATAATAAT
1 ATAATATACTAATA-AA-AAT
20740223 ATAATATACTA
1 ATAATATACTA
20740234 GACTAGACTA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
19 24 0.57
20 5 0.12
21 13 0.31
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.36
Consensus pattern (19 bp):
ATAATATACTAATAAAAAT
Found at i:20740188 original size:5 final size:5
Alignment explanation
Indices: 20740164--20740273 Score: 59
Period size: 5 Copynumber: 21.8 Consensus size: 5
20740154 TATAACAATA
* *
20740164 ATAAT ATACT ATAAG A-AAT ATAAT AT-A- ATAAT AATAAT ATAATGT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT ATAA--T
* * * * * *
20740209 ACTAAT AT-A- ATAAT ATAAT ATACT AGACT AGACT AGTTAT AATAAT
1 A-TAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A-TAAT -ATAAT
20740255 ATAAT ATAAT ATAAT ATAA
1 ATAAT ATAAT ATAAT ATAA
20740274 CAATAATAAA
Statistics
Matches: 84, Mismatches: 10, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
3 4 0.05
4 7 0.08
5 56 0.67
6 11 0.13
7 3 0.04
8 3 0.04
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (5 bp):
ATAAT
Found at i:20740220 original size:21 final size:22
Alignment explanation
Indices: 20740143--20740233 Score: 74
Period size: 21 Copynumber: 4.5 Consensus size: 22
20740133 AGGAAAGAAA
* *
20740143 ATAATA-A-TAATTATAACAAT
1 ATAATATACTAATAATAATAAT
*
20740163 AATAATATACT-ATAA-GA-AAT
1 -ATAATATACTAATAATAATAAT
20740183 AT-A-ATA-TAATAATAATAAT
1 ATAATATACTAATAATAATAAT
*
20740202 ATAATGTACTAAT-ATAATAAT
1 ATAATATACTAATAATAATAAT
20740223 ATAATATACTA
1 ATAATATACTA
20740234 GACTAGACTA
Statistics
Matches: 57, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
16 1 0.02
17 7 0.12
18 2 0.04
19 7 0.12
20 4 0.07
21 27 0.47
22 8 0.14
23 1 0.02
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.35
Consensus pattern (22 bp):
ATAATATACTAATAATAATAAT
Found at i:20740227 original size:32 final size:31
Alignment explanation
Indices: 20740180--20740270 Score: 96
Period size: 32 Copynumber: 2.9 Consensus size: 31
20740170 TACTATAAGA
20740180 AATATAAT-ATAATAATAATAATATAAT-GTACT
1 AATATAATAAT-ATAAT-ATAATATAATAG-ACT
* * *
20740212 AATATAATAATATAATATACTAGACTAGACT
1 AATATAATAATATAATATAATATAATAGACT
*
20740243 AGTTATAATAATATAATATAATATAATA
1 A-ATATAATAATATAATATAATATAATA
20740271 TAACAATAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
31 11 0.22
32 36 0.73
33 2 0.04
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.36
Consensus pattern (31 bp):
AATATAATAATATAATATAATATAATAGACT
Found at i:20744723 original size:34 final size:34
Alignment explanation
Indices: 20744685--20744753 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
20744675 TGAGACCATA
20744685 TACATTAGAATGAGTTAATTTTAATATATTTTCT
1 TACATTAGAATGAGTTAATTTTAATATATTTTCT
20744719 TACATTAGAATGAGTTAATTTTAATATATTTTCT
1 TACATTAGAATGAGTTAATTTTAATATATTTTCT
20744753 T
1 T
20744754 TCTTCTTAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.51
Consensus pattern (34 bp):
TACATTAGAATGAGTTAATTTTAATATATTTTCT
Found at i:20749650 original size:2 final size:2
Alignment explanation
Indices: 20749643--20749670 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20749633 GAACCAAACA
20749643 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
20749671 CCTAATGGCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20750559 original size:14 final size:15
Alignment explanation
Indices: 20750540--20750568 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20750530 ACGTGTAACC
20750540 TTTTTTATT-ATAAA
1 TTTTTTATTGATAAA
20750554 TTTTTTATTGATAAA
1 TTTTTTATTGATAAA
20750569 ATTAAATTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
TTTTTTATTGATAAA
Found at i:20752847 original size:17 final size:18
Alignment explanation
Indices: 20752815--20752852 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
20752805 TTCCATACTT
*
20752815 TTATACATTTTAATACAA
1 TTATACATTCTAATACAA
20752833 TTATAC-TTCTAATACAA
1 TTATACATTCTAATACAA
20752850 TTA
1 TTA
20752853 GATAAACTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (18 bp):
TTATACATTCTAATACAA
Found at i:20759704 original size:122 final size:124
Alignment explanation
Indices: 20759545--20759783 Score: 315
Period size: 122 Copynumber: 1.9 Consensus size: 124
20759535 TTGTTTGGGA
* * *
20759545 TTATTAAAGGTGTCTTCTATAGAAAATGCCTTTAATATTAC-ACTACTAAAATTTTAAGA-GGTT
1 TTATTAAAGGTGTCTTCTATAGAAAACGCCTTCAATA-TACTACTACTAAAATTTTAAGATAGTT
* * * *
20759608 ATTGAAGGTGTTTCTTCTAGAAAAATGCCTTGACTAATTCATTTT-ATTTTTGAAGAAAT
65 AGTGAAGGCGTTTATTCTAGAAAAATGCCTTCACTAATTCATTTTAATTTTTGAAGAAAT
* * * *
20759667 TTATTGAATGTGTCTTCTA-ATGAAAACGCCTTCAATATACTAGTACTCAAATTTTAAGATAGTT
1 TTATTAAAGGTGTCTTCTATA-GAAAACGCCTTCAATATACTACTACTAAAATTTTAAGATAGTT
* *
20759731 AGTGAATGCGTTTATTCTAGGAAAATGCCTTCACTAATTCATTTTAATTTTTG
65 AGTGAAGGCGTTTATTCTAGAAAAATGCCTTCACTAATTCATTTTAATTTTTG
20759784 TACATAATTA
Statistics
Matches: 100, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
121 4 0.04
122 47 0.47
123 42 0.42
124 7 0.07
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (124 bp):
TTATTAAAGGTGTCTTCTATAGAAAACGCCTTCAATATACTACTACTAAAATTTTAAGATAGTTA
GTGAAGGCGTTTATTCTAGAAAAATGCCTTCACTAATTCATTTTAATTTTTGAAGAAAT
Found at i:20759931 original size:187 final size:185
Alignment explanation
Indices: 20759679--20761206 Score: 1627
Period size: 187 Copynumber: 8.1 Consensus size: 185
20759669 ATTGAATGTG
* * * *
20759679 TCTTCTAATG-AAAACGCCTTCAATATACTAGTACTCAAATTTTAAGATAGTTAGTGAATGCGTT
1 TCTTCTACTGAAAAATGCCTTCAATATAC-AGTACTCAAATTTTAAGATGGTTAGTGAAGGCGTT
20759743 TATTCTAGGAAAATGCCTTCACTAATTCATTTTAATTTTTGTACATAATTATTGAAGGTATTTTT
65 TATTCTAGGAAAATGCCTTCACTAATTCATTTTAATTTTTGTACATAATTATTGAAGGTATTTTT
* *
20759808 TGATAACAAATGCCTTCTATAATTTCTTTTAAAAAAATTTTGAGATTATTAAAGGCG
130 TTATAACAAATGCCTTCTATAATTTCTTTT-AAAAAATTTTGAGATTATTAAAGGCA
* * *
20759865 TCTTCTACTAAAAAATGCCTTCAATATATCAGTACTCAAATTTTAATATGGTTAATGAAGGCGTT
1 TCTTCTACTGAAAAATGCCTTCAATATA-CAGTACTCAAATTTTAAGATGGTTAGTGAAGGCGTT
* * * * *
20759930 TATTTTAGAAAAATGCCTTCACTAATTCATTTTAATTTTTGTGCATAATTATTAAAGGTGTTTTT
65 TATTCTAGGAAAATGCCTTCACTAATTCATTTTAATTTTTGTACATAATTATTGAAGGTATTTTT
* * *
20759995 TTATAACAAATGTCTTCAATAATTTCTTTCT-AAAAATTTTTAGGATTATTAAAGGCA
130 TTATAACAAATGCCTTCTATAATTTCTTT-TAAAAAATTTTGA-GATTATTAAAGGCA
* * * * ** *
20760052 TCTTATAGTGAAAAACGCCTTCAATATATCAGTACTTAAATTTTAAGATGGTTAGTGAAATCATT
1 TCTTCTACTGAAAAATGCCTTCAATATA-CAGTACTCAAATTTTAAGATGGTTAGTGAAGGCGTT
* ** * * * ** * *
20760117 TATTTCAAAAAAAATACCTTTAATAATTTC-TTTTAAAATTTGTATATAATTATTGAAGGCATTT
65 TA-TTCTAGGAAAATGCCTTCACTAA-TTCATTTTAATTTTTGTACATAATTATTGAAGGTATTT
20760181 TTTTATAACAAATGCCTT-TAATAAATTT-TTTTAAAAAACTTTTGAAAGAATTTATTGAAA-GC
128 TTTTATAACAAATGCCTTCT-AT-AATTTCTTTTAAAAAA-TTTTG--AG-A-TTATT-AAAGGC
20760243 A
185 A
* * * * ** * *
20760244 TCTTCTAGTG-AAAATGCCTTTAATAAACCAATACTCAAATTTTAAGACAGTTAGTGAAAGTGTT
1 TCTTCTACTGAAAAATGCCTTCAATATA-CAGTACTCAAATTTTAAGATGGTTAGTGAAGGCGTT
* * *
20760308 TATTCTAGGAAAACGCTTTCACTAATTCATTTTAATTTTTGTATATAATTATTGAAGGTATTTTT
65 TATTCTAGGAAAATGCCTTCACTAATTCATTTTAATTTTTGTACATAATTATTGAAGGTATTTTT
* ** * * * *
20760373 TGATAACAAACACTTTCCATAATTTTCTTTTAAAAAATTTTAAAATTATTAAAGGCA
130 TTATAACAAATGCCTTCTATAA-TTTCTTTTAAAAAATTTTGAGATTATTAAAGGCA
* * * * *
20760430 TATTCTACTAAAAAATGCCTTCAATATACCAGTACTCAAATTTTAAGACGGTTAGTAAAGGCATT
1 TCTTCTACTGAAAAATGCCTTCAATATA-CAGTACTCAAATTTTAAGATGGTTAGTGAAGGCGTT
* * * * *
20760495 GATTCTAGGAAAATGCCTTTACTAATTCATTTTAATTTTTATTCATAATTATTGAAGGCATTTTT
65 TATTCTAGGAAAATGCCTTCACTAATTCATTTTAATTTTTGTACATAATTATTGAAGGTATTTTT
* * * * * *
20760560 TGATAACAAATGCCCTT-AATAATTTCCTTCT-AAAATTTTTAAGATTATTAAAGGTA
130 TTATAACAAATG-CCTTCTATAATTT-CTTTTAAAAAATTTTGAGATTATTAAAGGCA
* * * * * *
20760616 TCTTAC-AGTGAAAGATACATTTAATATACCAGTACTCAAATTTTAAGAT-GTTAGTGAAGGCAT
1 TCTT-CTACTGAAAAATGCCTTCAATATA-CAGTACTCAAATTTTAAGATGGTTAGTGAAGGCGT
* * * *
20760679 TTATTTCATA--AAAATACCTTCAATAATTCCTTTTAAATTTTGTACATAATTATTGAAGGTATT
64 TTA-TTC-TAGGAAAATGCCTTCACTAATTCATTTTAATTTTTGTACATAATTATTGAAGGTATT
* * *
20760742 TTTTTATAACAAACGCCTT-TAATAATTTCCTTTTAAAAAATTTTGAAAGAATTTGTTAAAGACA
127 TTTTTATAACAAATGCCTTCT-ATAATTT-CTTTTAAAAAATTTTG--AG-A-TTATTAAAGGCA
* * ** * * *
20760806 TCTGCTAGTGAAAAACACTTTTAATATACTAGTACTCAAATTTTAAGATGGTTAATGAAGGCGTT
1 TCTTCTACTGAAAAATGCCTTCAATATAC-AGTACTCAAATTTTAAGATGGTTAGTGAAGGCGTT
* * *
20760871 TATTTTAGGAAAATGCCTTCACTAATTCGTTTTAATTTTTGTGCATAATTATTGAAGGTATTTTT
65 TATTCTAGGAAAATGCCTTCACTAATTCATTTTAATTTTTGTACATAATTATTGAAGGTATTTTT
**
20760936 TTATAACAAATGCCTTCTATAATTGT-TTTTAAAAACATTTT-AGGATTATTAAAGGTG
130 TTATAACAAATGCCTTCTATAATT-TCTTTTAAAAA-ATTTTGA-GATTATTAAAGGCA
* * * *
20760993 TATTCTACTGAAAAACGCCTTCAATATACTAGTACTCAAATTTTAAGATGGTTATTGAAGGTGTT
1 TCTTCTACTGAAAAATGCCTTCAATATAC-AGTACTCAAATTTTAAGATGGTTAGTGAAGGCGTT
* * * *
20761058 TATTCTAGG-AAATACCTTCACTAATTCGTTTTAATTTTTGTGCATAATT-TTGAAGGCATTTTT
65 TATTCTAGGAAAATGCCTTCACTAATTCATTTTAATTTTTGTACATAATTATTGAAGG---TATT
* *
20761121 TTTTTATAACAAACGCCTTCTATAATTTTCTTTTAAAAAATTTTTGA-ATTATTAAAGGTA
127 TTTTTATAACAAATGCCTTCTATAA-TTTCTTTTAAAAAA-TTTTGAGATTATTAAAGGCA
20761181 TCTTCTACTGAAAAATGCCTTCAATA
1 TCTTCTACTGAAAAATGCCTTCAATA
20761207 ATTTATTATA
Statistics
Matches: 1135, Mismatches: 159, Indels: 94
0.82 0.11 0.07
Matches are distributed among these distances:
184 4 0.00
185 95 0.08
186 147 0.13
187 402 0.35
188 146 0.13
189 38 0.03
190 132 0.12
191 149 0.13
192 19 0.02
193 3 0.00
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (185 bp):
TCTTCTACTGAAAAATGCCTTCAATATACAGTACTCAAATTTTAAGATGGTTAGTGAAGGCGTTT
ATTCTAGGAAAATGCCTTCACTAATTCATTTTAATTTTTGTACATAATTATTGAAGGTATTTTTT
TATAACAAATGCCTTCTATAATTTCTTTTAAAAAATTTTGAGATTATTAAAGGCA
Found at i:20764538 original size:63 final size:63
Alignment explanation
Indices: 20764405--20764538 Score: 137
Period size: 63 Copynumber: 2.1 Consensus size: 63
20764395 TAACAAAATG
* ** * *
20764405 TTATTGAAGGCATTTTAAACCAAAACCGCATTCAATAATTTCACTTAAAAAATATTGTATGGA
1 TTATTGAAGGCATTTTAAACAAAAACCGCATTCAATAATACCACTTAAAAAATATTGAATAGA
* ** * * *
20764468 TTTTTGAAGGCATTTTAAA-AAAAATTGCCTTTAATAATACCAAC-TAAAAATTAATTGAATAGA
1 TTATTGAAGGCATTTTAAACAAAAACCGCATTCAATAATACC-ACTTAAAAAAT-ATTGAATAGA
20764531 TTATTGAA
1 TTATTGAA
20764539 AGCGCTTTCG
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
62 22 0.39
63 35 0.61
ACGTcount: A:0.43, C:0.11, G:0.10, T:0.35
Consensus pattern (63 bp):
TTATTGAAGGCATTTTAAACAAAAACCGCATTCAATAATACCACTTAAAAAATATTGAATAGA
Found at i:20777942 original size:18 final size:18
Alignment explanation
Indices: 20777919--20777954 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
20777909 ATATTAACTC
20777919 TTGATGCCTTCCATTAAT
1 TTGATGCCTTCCATTAAT
*
20777937 TTGATGCTTTCCATTAAT
1 TTGATGCCTTCCATTAAT
20777955 ATAAACAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.19, G:0.11, T:0.47
Consensus pattern (18 bp):
TTGATGCCTTCCATTAAT
Found at i:20783521 original size:5 final size:5
Alignment explanation
Indices: 20783513--20783549 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
20783503 AAAGAAAAAC
20783513 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
20783550 ATACAATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:20784105 original size:12 final size:12
Alignment explanation
Indices: 20784088--20784113 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20784078 TAATTATCAA
20784088 TAATATAAAAGT
1 TAATATAAAAGT
20784100 TAATATAAAAGT
1 TAATATAAAAGT
20784112 TA
1 TA
20784114 TCCCCCAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.35
Consensus pattern (12 bp):
TAATATAAAAGT
Found at i:20785676 original size:21 final size:21
Alignment explanation
Indices: 20785650--20785691 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
20785640 AACTAATACC
* *
20785650 TAAGTTCTGTAGTAGTTATCA
1 TAAGTTCTATAATAGTTATCA
20785671 TAAGTTCTATAATAGTTATCA
1 TAAGTTCTATAATAGTTATCA
20785692 AGCCTTGCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (21 bp):
TAAGTTCTATAATAGTTATCA
Found at i:20786284 original size:15 final size:15
Alignment explanation
Indices: 20786264--20786294 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
20786254 AAGCTGTACC
20786264 TTTCGTTGAGTAGGG
1 TTTCGTTGAGTAGGG
20786279 TTTCGTTGAGTAGGG
1 TTTCGTTGAGTAGGG
20786294 T
1 T
20786295 CAGAAAGGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.06, G:0.39, T:0.42
Consensus pattern (15 bp):
TTTCGTTGAGTAGGG
Found at i:20797598 original size:19 final size:20
Alignment explanation
Indices: 20797552--20797599 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
20797542 CTTTGACCAT
* *
20797552 TTGACTTTTGACCTTTAACT
1 TTGAATTTTGACCTTTAACC
*
20797572 TTTAATTTTGA-CTTTAACC
1 TTGAATTTTGACCTTTAACC
*
20797591 TTGCATTTT
1 TTGAATTTT
20797600 TTAATAATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.21, C:0.17, G:0.08, T:0.54
Consensus pattern (20 bp):
TTGAATTTTGACCTTTAACC
Found at i:20802819 original size:62 final size:62
Alignment explanation
Indices: 20802753--20802985 Score: 201
Period size: 61 Copynumber: 3.8 Consensus size: 62
20802743 ATCTCATTTA
* *
20802753 AAAAATTGAAGGAGATTATTCAAGGTAATTTTAGCTAAAAACACCTTTAATAATCCACTCAT
1 AAAAATTGAAGGGGATTATTCAAGGTAATTTTGGCTAAAAACACCTTTAATAATCCACTCAT
* * ** *
20802815 AAAAATTGAAGGGGATTATTCAA-G-ACATTTTGGCCAAATATGCCTTTAATAACTCCA-T-TT
1 AAAAATTGAAGGGGATTATTCAAGGTA-ATTTTGGCTAAAAACACCTTTAATAA-TCCACTCAT
** * * ** *
20802875 AATATTTTGTAA-GGGATTATTCAAGGTATTTTTTGACTAAAATATGCCTTCAATAATCTC-CTC
1 AA-AAATTG-AAGGGGATTATTCAAGGTA-ATTTTGGCTAAAA-ACACCTTTAATAATC-CACTC
20802938 AT
61 AT
** *
20802940 -AAAATTGAAGGGGATTATTCAAGGTGTTTTTGGCTATAAACACCTT
1 AAAAATTGAAGGGGATTATTCAAGGTAATTTTGGCTAAAAACACCTT
20802986 GACAACCCCA
Statistics
Matches: 137, Mismatches: 23, Indels: 23
0.75 0.13 0.13
Matches are distributed among these distances:
60 4 0.03
61 44 0.32
62 42 0.31
63 31 0.23
64 15 0.11
65 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (62 bp):
AAAAATTGAAGGGGATTATTCAAGGTAATTTTGGCTAAAAACACCTTTAATAATCCACTCAT
Found at i:20802997 original size:124 final size:123
Alignment explanation
Indices: 20802761--20803030 Score: 287
Period size: 124 Copynumber: 2.2 Consensus size: 123
20802751 TAAAAAATTG
* *
20802761 AAGGAGATTATTCAAGGTAATTTTAGCTAAAAACACCTTTAATAATCCACTCATAAAAATTGAAG
1 AAGG-GATTATTCAAGGTATTTTTAGCTAAAAACACCTTCAATAATCCACTCATAAAAATTGAAG
** * * * *
20802826 GGGATTATTCAAGACATTTTGGCCAAATATGCCTTTAATAACTCCATTTAATATTTTGT
65 GGGATTATTCAAGACATTTTGGCCAAATACACCTTTAACAACCCCATTCAATATTTTCT
* **
20802885 AAGGGATTATTCAAGGTATTTTTTGACTAAAATATGCCTTCAATAATCTC-CTCAT-AAAATTGA
1 AAGGGATTATTCAAGGTATTTTTAG-CTAAAA-ACACCTTCAATAATC-CACTCATAAAAATTGA
*** * * *
20802948 AGGGGATTATTCAAGGTGTTTTTGGCTATAA-ACACC-TTGACAACCCCATTCAATTTTTTCT
63 AGGGGATTATTCAA-GACATTTTGGCCA-AATACACCTTTAACAACCCCATTCAATATTTTCT
* *
20803009 AAAGGATTATTCAAGGTGTTTT
1 AAGGGATTATTCAAGGTATTTT
20803031 CTCACAAAAA
Statistics
Matches: 122, Mismatches: 19, Indels: 10
0.81 0.13 0.07
Matches are distributed among these distances:
123 19 0.16
124 71 0.58
125 29 0.24
126 3 0.02
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.36
Consensus pattern (123 bp):
AAGGGATTATTCAAGGTATTTTTAGCTAAAAACACCTTCAATAATCCACTCATAAAAATTGAAGG
GGATTATTCAAGACATTTTGGCCAAATACACCTTTAACAACCCCATTCAATATTTTCT
Found at i:20807229 original size:62 final size:64
Alignment explanation
Indices: 20807144--20807285 Score: 157
Period size: 62 Copynumber: 2.3 Consensus size: 64
20807134 ATAAAAATGG
* ** * *
20807144 GAGGGGATTATTAAAGGCA-TTTTTGGCATAAAATACCTTGAATATTCCCCTT-TAAAAAA-TTA
1 GAGGGGATTATTCAAGGCATTTTTTACCA-AAAATACCTTGAATAATCCACTTATAAAAAATTTA
* * * **
20807206 GAGGGGATTATTCCATGCGTTTTTTACCAAAAATGTCTTGAATAATCCACTTATAAAAAATTTA
1 GAGGGGATTATTCAAGGCATTTTTTACCAAAAATACCTTGAATAATCCACTTATAAAAAATTTA
20807270 -AGGGGATTATTCAAGG
1 GAGGGGATTATTCAAGG
20807286 TGTTTTTAGC
Statistics
Matches: 65, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
62 34 0.52
63 28 0.43
64 3 0.05
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.34
Consensus pattern (64 bp):
GAGGGGATTATTCAAGGCATTTTTTACCAAAAATACCTTGAATAATCCACTTATAAAAAATTTA
Found at i:20807495 original size:12 final size:13
Alignment explanation
Indices: 20807480--20807511 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
20807470 TTTTTGACAT
20807480 TTTTTAT-AAAAA
1 TTTTTATAAAAAA
20807492 TTTTTATAAAAAA
1 TTTTTATAAAAAA
20807505 TTTTTAT
1 TTTTTAT
20807512 GGATTATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTTATAAAAAA
Found at i:20807794 original size:94 final size:93
Alignment explanation
Indices: 20807634--20807821 Score: 313
Period size: 94 Copynumber: 2.0 Consensus size: 93
20807624 TAAGATTTTC
*
20807634 TAAAGATTATTCAAGGTGTTTTCTAGCAAAAAATGCCTTCAATAATCCACCGTCCTTACCTTATG
1 TAAAGATTATTCAAGGTGTTTTCTAGCAAAAAATACCTTCAATAATCCACCGTCCTTACCTTATG
* *
20807699 CTCCCATGTCTTTGGAATGAAAACCTTT
66 CTCCCAAGTCTTGGGAATGAAAACCTTT
**
20807727 TAAAGATTATTCAAGGTGTTTTTCTAGCAAAAAATACCTTCAATAATCCGTCGTCCTTACCTTAT
1 TAAAGATTATTCAAGGTG-TTTTCTAGCAAAAAATACCTTCAATAATCCACCGTCCTTACCTTAT
*
20807792 GCTCCCAAGTCTTGGGAATGAAAATCTTT
65 GCTCCCAAGTCTTGGGAATGAAAACCTTT
20807821 T
1 T
20807822 TAAAAAATCT
Statistics
Matches: 88, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
93 18 0.20
94 70 0.80
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.35
Consensus pattern (93 bp):
TAAAGATTATTCAAGGTGTTTTCTAGCAAAAAATACCTTCAATAATCCACCGTCCTTACCTTATG
CTCCCAAGTCTTGGGAATGAAAACCTTT
Found at i:20813407 original size:54 final size:54
Alignment explanation
Indices: 20813269--20813436 Score: 162
Period size: 55 Copynumber: 3.1 Consensus size: 54
20813259 AATATAATAA
* * * * *
20813269 AAAATTAAAACATATAAGTTTATACTGACAATCTCTAACTGTCGGTATAGATAA-
1 AAAATTAAAACATATAAGTTTATACTGACAGTATCTAACTATC-ATATAGGTAAG
* *
20813323 AGAAATTAAAGCATATAA-TTCTATACTGACAGTATCTAACCATCATATAGGTAAG
1 A-AAATTAAAACATATAAGTT-TATACTGACAGTATCTAACTATCATATAGGTAAG
* * * * *
20813378 AAAATTAAAAAATACAAGTTTATATTGACAG-ATGCTAAGTATCAGTATATGTAAG
1 AAAATTAAAACATATAAGTTTATACTGACAGTAT-CTAACTATCA-TATAGGTAAG
20813433 AAAA
1 AAAA
20813437 ATTACAAGTC
Statistics
Matches: 94, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
53 2 0.02
54 42 0.45
55 50 0.53
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.30
Consensus pattern (54 bp):
AAAATTAAAACATATAAGTTTATACTGACAGTATCTAACTATCATATAGGTAAG
Found at i:20816241 original size:37 final size:35
Alignment explanation
Indices: 20816200--20816321 Score: 111
Period size: 37 Copynumber: 3.3 Consensus size: 35
20816190 CATCGTAGGT
*
20816200 AAAAAAAATAAAGATGATCGGGACAACACCAATGATA
1 AAAAAAAATAAAGATGATCGGGATAACACCAA-G-TA
* * *
20816237 AAAAAAAATAAATATGACCGAGATAACATCACAAGTA
1 AAAAAAAATAAAGATGATCGGGATAACA-C-CAAGTA
**
20816274 AAAAAAAA-ATAAGATGATTAGGATAACACCATAGGTTA
1 AAAAAAAATA-AAGATGATCGGGATAACACCA-A-G-TA
20816312 AAAAAAAATA
1 AAAAAAAATA
20816322 TGATCGAGAC
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
35 2 0.03
36 3 0.04
37 48 0.70
38 12 0.17
39 4 0.06
ACGTcount: A:0.60, C:0.11, G:0.13, T:0.16
Consensus pattern (35 bp):
AAAAAAAATAAAGATGATCGGGATAACACCAAGTA
Found at i:20816241 original size:71 final size:72
Alignment explanation
Indices: 20816166--20816649 Score: 279
Period size: 72 Copynumber: 6.7 Consensus size: 72
20816156 ATCGTAAGTC
* * ** *
20816166 AAAAAATAAAGATGACCGAGACATCATCGTAGGTAAAAAAAATAAAGATGATCGGGACAACACCA
1 AAAAAATAAATATGACCGAGACAACATCACAAGTAAAAAAAATAAAGATGATCGGGACAACACCA
20816231 AT-GATAAA
66 ATAGAT--A
* * ** *
20816239 AAAAAATAAATATGACCGAGATAACATCACAAGTAAAAAAAAAATAAGATGATTAGGATAACACC
1 AAAAAATAAATATGACCGAGACAACATCACAAGTAAAAAAAATA-AAGATGATCGGGACAACACC
* *
20816304 -ATAGGTT
65 AATAGATA
* * ** * ** * ** *
20816311 AAAAAA-AAATATGATCGAGACAATATCGTAAGT-CAAAAAATAATCATGACCGAAACAATACCA
1 AAAAAATAAATATGACCGAGACAACATCACAAGTAAAAAAAATAAAGATGATCGGGACAACACCA
* *
20816374 ATGGTTA
66 ATAGATA
* * * * * * * *
20816381 GAAAAATAAATATGATCGAGACAACACCACAGGTCAAAAAAATAAAAACGATTGGGACAACACC-
1 AAAAAATAAATATGACCGAGACAACATCACAAGTAAAAAAAATAAAGATGATCGGGACAACACCA
*
20816445 ATAGGTCAA
66 ATAGAT--A
* * * ** * * * * *
20816454 AAAAAACAAATATGACTGAGACAACATCGCAAGT-CTAAAAATAAATATGATCGAGATAGCATCA
1 AAAAAATAAATATGACCGAGACAACATCACAAGTAAAAAAAATAAAGATGATCGGGACAACACCA
* *
20816518 AT-GGTCT
66 ATAGAT-A
* * * ** * * * *
20816525 GAAAAATAAATATGACCAAGATAACATCTTAAGTCAGAAAAATAAAGATGATCAGGACAATACC-
1 AAAAAATAAATATGACCGAGACAACATCACAAGTAAAAAAAATAAAGATGATCGGGACAACACCA
*
20816589 ATAGGTAAAA
66 ATA-G--ATA
* *
20816599 AAAAAATAAATATGACC-AGGACAACATCATAAGT--CAAAAATAAAGATGATC
1 AAAAAATAAATATGACCGA-GACAACATCACAAGTAAAAAAAATAAAGATGATC
20816650 AAGACAATTC
Statistics
Matches: 308, Mismatches: 89, Indels: 29
0.72 0.21 0.07
Matches are distributed among these distances:
69 11 0.04
70 16 0.05
71 77 0.25
72 85 0.28
73 71 0.23
74 48 0.16
ACGTcount: A:0.53, C:0.14, G:0.15, T:0.18
Consensus pattern (72 bp):
AAAAAATAAATATGACCGAGACAACATCACAAGTAAAAAAAATAAAGATGATCGGGACAACACCA
ATAGATA
Found at i:20816277 original size:36 final size:36
Alignment explanation
Indices: 20815704--20816776 Score: 194
Period size: 36 Copynumber: 30.1 Consensus size: 36
20815694 TCTTTTTTGT
* * * **
20815704 AAAATAAAGAATGACCGAAACAACACCACAAGTTGAA
1 AAAATAAA-TATGACCGAGACAACATCACAAGTAAAA
* * * * * *
20815741 AAAATAAAGATGACCAATACAACACCACAGGTCAAA
1 AAAATAAATATGACCGAGACAACATCACAAGTAAAA
* * * * * *
20815777 AAAACAAATATGACTGGGACAATACCACAAGTCAAA
1 AAAATAAATATGACCGAGACAACATCACAAGTAAAA
* ** * * *
20815813 AAAATAAAGATGATAGGGACAATCCT-ACAAGTCAAA
1 AAAATAAATATGACCGAGACAA-CATCACAAGTAAAA
* * * * *
20815849 AAAATAAAGATAATCGAGATAACA-CTA-AATGGTCAAA
1 AAAATAAATATGACCGAGACAACATC-ACAA--GTAAAA
** * * *
20815886 AAAATAAATATGACTAAGACAACATCGCAGGT-CAA
1 AAAATAAATATGACCGAGACAACATCACAAGTAAAA
* * ** *
20815921 AAGATAAAGAT-ATTGAGACAACA-CA-ATAG-ATCAA
1 AAAATAAATATGACCGAGACAACATCACA-AGTA-AAA
* * * *
20815955 AAAATAAAGATGACCAAGACAATA-C-CAATGGTAGAA
1 AAAATAAATATGACCGAGACAACATCACAA--GTAAAA
* * ** * * *
20815991 AAAATAAATATGATCGAAATGACACCATAAGTCAAA
1 AAAATAAATATGACCGAGACAACATCACAAGTAAAA
* * ** *
20816027 AAAATAAATATGACTTG-GACAACACCGTAAGT-CAA
1 AAAATAAATATGAC-CGAGACAACATCACAAGTAAAA
* ** ** * ** *
20816062 AAAATAAAGAAAACTAAAACAACATCGTAAGTCAAA
1 AAAATAAATATGACCGAGACAACATCACAAGTAAAA
* * *
20816098 AAAATAAAGATGA-CGAGACAATA-C-CAACGGTCAAGA
1 AAAATAAATATGACCGAGACAACATCACAA--GT-AAAA
** * * ** *
20816134 AAAGCAAATATGTCAG-GACAACATCGTAAGT-CAA
1 AAAATAAATATGACCGAGACAACATCACAAGTAAAA
* * ** *
20816168 AAAATAAAGATGACCGAGACATCATCGTAGGTAAAA
1 AAAATAAATATGACCGAGACAACATCACAAGTAAAA
* * *
20816204 AAAATAAAGATGATCGGGACAACA-C-CAATGATAAAAA
1 AAAATAAATATGACCGAGACAACATCACAA-G-T-AAAA
*
20816241 AAAATAAATATGACCGAGATAACATCACAAGTAAAA
1 AAAATAAATATGACCGAGACAACATCACAAGTAAAA
* * ** * * * * *
20816277 AAAAAATAAGATGA-TTAGGATAACACCATAGGT-TAA
1 AAAATA-AATATGACCGA-GACAACATCACAAGTAAAA
* * ** *
20816313 AAAA-AAATATGATCGAGACAATATCGTAAGT-CAA
1 AAAATAAATATGACCGAGACAACATCACAAGTAAAA
* * * *
20816347 AAAAT-AATCATGACCGAAACAATA-C-CAATGGTTAGA
1 AAAATAAAT-ATGACCGAGACAACATCACAA--GTAAAA
* * * *
20816383 AAAATAAATATGATCGAGACAACACCACAGGTCAAA
1 AAAATAAATATGACCGAGACAACATCACAAGTAAAA
* * ** * * * *
20816419 AAAATAAAAACGATTGGGACAACACCATAGGTCAAAA
1 AAAATAAATATGACCGAGACAACATCACAAGT-AAAA
* * * **
20816456 AAAACAAATATGACTGAGACAACATCGCAAGT-CTA
1 AAAATAAATATGACCGAGACAACATCACAAGTAAAA
* * * * ***
20816491 AAAATAAATATGATCGAGATAGCATCA-ATGGTCTGA
1 AAAATAAATATGACCGAGACAACATCACA-AGTAAAA
* * ** * *
20816527 AAAATAAATATGACCAAGATAACATCTTAAGTCAGA
1 AAAATAAATATGACCGAGACAACATCACAAGTAAAA
* * * * * *
20816563 AAAATAAAGATGATC-AGGACAATACCATAGGTAAAAAA
1 AAAATAAATATGACCGA-GACAACATCACAAGT--AAAA
* *
20816601 AAAATAAATATGACC-AGGACAACATCATAAGT--CA
1 AAAATAAATATGACCGA-GACAACATCACAAGTAAAA
* * * * *
20816635 AAAATAAAGATGATCAAGAC-A-AT-TCAAGTTAAA
1 AAAATAAATATGACCGAGACAACATCACAAGTAAAA
* * * * *
20816668 AAAATAAAGATGA-TGGGACAACA-CA-GATTAAAA
1 AAAATAAATATGACCGAGACAACATCACAAGTAAAA
* * * *
20816701 AAAATAAATATGGCC-AGGACAATA-CTGCAAGT-CAA
1 AAAATAAATATGACCGA-GACAACATC-ACAAGTAAAA
* * * *
20816736 AAAATAAATATAACCGGGACAACACCACATGTAAAA
1 AAAATAAATATGACCGAGACAACATCACAAGTAAAA
20816772 AAAAT
1 AAAAT
20816777 GACTGGGACA
Statistics
Matches: 763, Mismatches: 209, Indels: 129
0.69 0.19 0.12
Matches are distributed among these distances:
31 4 0.01
32 6 0.01
33 38 0.05
34 91 0.12
35 141 0.18
36 330 0.43
37 111 0.15
38 39 0.05
39 3 0.00
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.17
Consensus pattern (36 bp):
AAAATAAATATGACCGAGACAACATCACAAGTAAAA
Found at i:20816339 original size:144 final size:141
Alignment explanation
Indices: 20816148--20816656 Score: 423
Period size: 144 Copynumber: 3.5 Consensus size: 141
20816138 CAAATATGTC
* * * * * * * *
20816148 AGGACAACATCGTAAGTCAAAAAATAAAGATGACCGAGAC-ATCATCGTAGGTAAAAAAAATAAA
1 AGGACAACACCATAGGTAAAAAAACAAATATGA-CGAGACAAT-ATCGTAAGT-CAAAAAATAAA
* * * *
20816212 GATGATCGGGACAACACCAATGATAAAAAAAAATAAATATGACCGAGATAACATCACAAGTAAAA
63 CATGATCGAGACAACACCAATGGT-AAGAAAAATAAATATGACCGAGATAACATCACAAGTAAAA
20816277 AAAAAATAAGATGATT
127 AAAAAA-AAGATGATT
* * *
20816293 AGGATAACACCATAGGTTAAAAAA-AAATATGATCGAGACAATATCGTAAGTCAAAAAATAATCA
1 AGGACAACACCATAGGTAAAAAAACAAATATGA-CGAGACAATATCGTAAGTCAAAAAATAAACA
* * * * * * * *
20816357 TGACCGAAACAATACCAATGGTTAGAAAAATAAATATGATCGAGACAACACCACAGGTCAAAAAA
65 TGATCGAGACAACACCAATGGTAAGAAAAATAAATATGACCGAGATAACATCACAAGT-AAAAAA
* *
20816422 ATAAAA-ACGATT
129 AAAAAAGATGATT
* * * *
20816434 GGGACAACACCATAGGTCAAAAAAAACAAATATGACTGAGACAACATCGCAAGTCTAAAAATAAA
1 AGGACAACACCATAGGT--AAAAAAACAAATATGAC-GAGACAATATCGTAAGTCAAAAAATAAA
* * * * ** * ** * *
20816499 TATGATCGAGATAGCATCAATGGTCTGAAAAATAAATATGACCAAGATAACATCTTAAGTCAGAA
63 CATGATCGAGACAACACCAATGGTAAGAAAAATAAATATGACCGAGATAACATCACAAGTAAAAA
* *
20816564 AAATAAAGATGATC
128 AAAAAAAGATGATT
* * * * *
20816578 AGGACAATACCATAGGTAAAAAAAAAATAAATATGACCAGGACAACATCATAAGTC-AAAAATAA
1 AGGACAACACCATAGGT---AAAAAAACAAATATGACGA-GACAATATCGTAAGTCAAAAAATAA
* *
20816642 AGATGATCAAGACAA
62 ACATGATCGAGACAA
20816657 TTCAAGTTAA
Statistics
Matches: 291, Mismatches: 64, Indels: 19
0.78 0.17 0.05
Matches are distributed among these distances:
141 20 0.07
142 32 0.11
143 51 0.18
144 136 0.47
145 52 0.18
ACGTcount: A:0.53, C:0.14, G:0.15, T:0.18
Consensus pattern (141 bp):
AGGACAACACCATAGGTAAAAAAACAAATATGACGAGACAATATCGTAAGTCAAAAAATAAACAT
GATCGAGACAACACCAATGGTAAGAAAAATAAATATGACCGAGATAACATCACAAGTAAAAAAAA
AAAAGATGATT
Found at i:20816538 original size:215 final size:214
Alignment explanation
Indices: 20816167--20816569 Score: 456
Period size: 215 Copynumber: 1.9 Consensus size: 214
20816157 TCGTAAGTCA
* * ** * *
20816167 AAAAATAAAGATGACCGAGACATCATCGTAGGTAAAAAAAATAAAGATGATCGGGACAACACCAA
1 AAAAATAAAGATGACCGAGACAACACCACAGGTAAAAAAAATAAAAACGATCGGGACAACACCAA
* * *
20816232 TGATAAAAAAAAATAAATATGACCGAGATAACATCACAAGTAAAAAAAAAATAAGATGATTAGGA
66 TGATAAAAAAAAACAAATATGACCGAGACAACATCACAAGTAAAAAAAAAAT-A-ATGATGAGGA
* * * *
20816297 TAACACCATAGGTTAAAAAAAAATATGATCGAGACAATATCGTAAGTCA-AAAAATAATCATGAC
129 TAACACAATAGGTTAAAAAAAAATATGACCAAGACAACATCGTAAGTCAGAAAAATAATCATGAC
20816361 CGAAACAATACCAATGGTTAG
194 CGAAACAATACCAATGGTTAG
* * * *
20816382 AAAAATAAATATGATCGAGACAACACCACAGGTCAAAAAAATAAAAACGATTGGGACAACACC-A
1 AAAAATAAAGATGACCGAGACAACACCACAGGTAAAAAAAATAAAAACGATCGGGACAACACCAA
* * * * * *
20816446 TAGGTCAAAAAAAACAAATATGACTGAGACAACATCGCAAGTCTAAAAATAAAT-ATGATCGA-G
66 T-GATAAAAAAAAACAAATATGACCGAGACAACATCACAAGT-AAAAAAAAAATAATGAT-GAGG
* * * *
20816509 ATAGCATCAAT-GGTCTGAAAAATAAATATGACCAAGATAACATCTTAAGTCAGAAAAATAA
128 ATAACA-CAATAGGT-T-AAAAAAAAATATGACCAAGACAACATCGTAAGTCAGAAAAATAA
20816570 AGATGATCAG
Statistics
Matches: 154, Mismatches: 27, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
213 14 0.09
214 7 0.05
215 116 0.75
216 17 0.11
ACGTcount: A:0.53, C:0.14, G:0.15, T:0.18
Consensus pattern (214 bp):
AAAAATAAAGATGACCGAGACAACACCACAGGTAAAAAAAATAAAAACGATCGGGACAACACCAA
TGATAAAAAAAAACAAATATGACCGAGACAACATCACAAGTAAAAAAAAAATAATGATGAGGATA
ACACAATAGGTTAAAAAAAAATATGACCAAGACAACATCGTAAGTCAGAAAAATAATCATGACCG
AAACAATACCAATGGTTAG
Found at i:20816638 original size:38 final size:38
Alignment explanation
Indices: 20816526--20816638 Score: 122
Period size: 38 Copynumber: 3.0 Consensus size: 38
20816516 CAATGGTCTG
* * * *
20816526 AAAAATAAATATGACCAAGATAACATCTTAAGTC--AG
1 AAAAATAAATATGACCAGGACAACATCATAAGTCAAAA
* * * * * *
20816562 AAAAATAAAGATGATCAGGACAATACCATAGGTAAAAA
1 AAAAATAAATATGACCAGGACAACATCATAAGTCAAAA
20816600 AAAAATAAATATGACCAGGACAACATCATAAGTCAAAA
1 AAAAATAAATATGACCAGGACAACATCATAAGTCAAAA
20816638 A
1 A
20816639 TAAAGATGAT
Statistics
Matches: 59, Mismatches: 16, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
36 25 0.42
38 34 0.58
ACGTcount: A:0.57, C:0.13, G:0.12, T:0.18
Consensus pattern (38 bp):
AAAAATAAATATGACCAGGACAACATCATAAGTCAAAA
Found at i:20816816 original size:36 final size:34
Alignment explanation
Indices: 20816665--20816826 Score: 97
Period size: 35 Copynumber: 4.8 Consensus size: 34
20816655 AATTCAAGTT
* * * *
20816665 AAAAAAATAAAGATGA-TGGGACAACACAGATTA
1 AAAAAAATAAATATGACTGGGACAACACACAATC
* ** * *
20816698 AAAAAAATAAATATGGCCAGGACAATACTGCAAGTC
1 AAAAAAATAAATATGACTGGGACAACAC-ACAA-TC
* *
20816734 -AAAAAATAAATATAACCGGGACAACAC-C-A-C
1 AAAAAAATAAATATGACTGGGACAACACACAATC
**
20816764 ATGTAAAA-AAA-ATGACTGGGACAACACTAACAATC
1 A-AAAAAATAAATATGACTGGGACAACAC--ACAATC
20816799 AAAAAAATAAATATGACTAGGG-CAACAC
1 AAAAAAATAAATATGACT-GGGACAACAC
20816827 CGTGGGTTAG
Statistics
Matches: 97, Mismatches: 19, Indels: 23
0.70 0.14 0.17
Matches are distributed among these distances:
30 15 0.15
31 3 0.03
32 5 0.05
33 16 0.16
34 13 0.13
35 29 0.30
36 13 0.13
37 3 0.03
ACGTcount: A:0.54, C:0.16, G:0.15, T:0.15
Consensus pattern (34 bp):
AAAAAAATAAATATGACTGGGACAACACACAATC
Found at i:20816964 original size:34 final size:37
Alignment explanation
Indices: 20816926--20817114 Score: 126
Period size: 36 Copynumber: 5.3 Consensus size: 37
20816916 ATATCATCGA
*
20816926 GACAACACCACA-GGTCAA-AA-ATAAAGATGA-CTAG
1 GACAACACCACACGATCAAGAAGATAAAGATGATC-AG
*
20816960 GACAACACTACACGATCAAGAAGATAAAGATGATCAG
1 GACAACACCACACGATCAAGAAGATAAAGATGATCAG
* * * * *
20816997 GACAACACCA-ATAGTTGAA-AAGAAAAAGATGATCAT
1 GACAACACCACA-CGATCAAGAAGATAAAGATGATCAG
** * * * * * *
20817033 GATGACACTA-ACGGTCAAAAAGATAAATATGACCAA
1 GACAACACCACACGATCAAGAAGATAAAGATGATCAG
*
20817069 GACAACACCA-ACGATCAGGAAG-TAAAAGATGATCAG
1 GACAACACCACACGATCAAGAAGAT-AAAGATGATCAG
* *
20817105 AATAACACCA
1 GACAACACCA
20817115 ACATTCAAAA
Statistics
Matches: 119, Mismatches: 29, Indels: 12
0.74 0.18 0.08
Matches are distributed among these distances:
34 11 0.09
35 10 0.08
36 72 0.61
37 25 0.21
38 1 0.01
ACGTcount: A:0.50, C:0.19, G:0.17, T:0.14
Consensus pattern (37 bp):
GACAACACCACACGATCAAGAAGATAAAGATGATCAG
Found at i:20816990 original size:37 final size:34
Alignment explanation
Indices: 20816908--20817006 Score: 103
Period size: 34 Copynumber: 2.8 Consensus size: 34
20816898 CAACGGTCTA
* * *
20816908 AAAAATAAATATCATC-GAGACAACACCACAGGTC
1 AAAAATAAAGATGATCAG-GACAACACCACAGATC
*
20816942 AAAAATAAAGATGA-CTAGGACAACACTACACGATC
1 AAAAATAAAGATGATC-AGGACAACACCACA-GATC
20816977 AAGAAGATAAAGATGATCAGGACAACACCA
1 AA-AA-ATAAAGATGATCAGGACAACACCA
20817007 ATAGTTGAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
33 1 0.02
34 23 0.43
35 6 0.11
36 2 0.04
37 21 0.39
38 1 0.02
ACGTcount: A:0.52, C:0.20, G:0.15, T:0.13
Consensus pattern (34 bp):
AAAAATAAAGATGATCAGGACAACACCACAGATC
Found at i:20817221 original size:58 final size:58
Alignment explanation
Indices: 20817121--20817232 Score: 149
Period size: 58 Copynumber: 1.9 Consensus size: 58
20817111 ACCAACATTC
*
20817121 AAAAAATAGAAATGATTGAGACAACACTAATAGTCGAGAAGATAAAGATGATCGGTTG
1 AAAAAATAGAAATGATTGAGACAACACTAATAGTAGAGAAGATAAAGATGATCGGTTG
**
20817179 AAAAAATA-AAGATGATTGAGGTAACACTAAT-GATA-AGAAAGATAAAGATGATCG
1 AAAAAATAGAA-ATGATTGAGACAACACTAATAG-TAGAG-AAGATAAAGATGATCG
20817233 AGACAACACA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
57 5 0.10
58 43 0.90
ACGTcount: A:0.51, C:0.07, G:0.21, T:0.21
Consensus pattern (58 bp):
AAAAAATAGAAATGATTGAGACAACACTAATAGTAGAGAAGATAAAGATGATCGGTTG
Found at i:20817241 original size:36 final size:36
Alignment explanation
Indices: 20817184--20817260 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 36
20817174 GGTTGAAAAA
* ** *
20817184 ATAAAGATGATTGAGGTAACACTAATGAT-AAGAAAG
1 ATAAAGATGATCGAGACAACACAAATGATCAAG-AAG
*
20817220 ATAAAGATGATCGAGACAACACAAATGGTCAAGAAG
1 ATAAAGATGATCGAGACAACACAAATGATCAAGAAG
20817256 ATAAA
1 ATAAA
20817261 AGTGATTAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
36 32 0.91
37 3 0.09
ACGTcount: A:0.52, C:0.09, G:0.21, T:0.18
Consensus pattern (36 bp):
ATAAAGATGATCGAGACAACACAAATGATCAAGAAG
Found at i:20819528 original size:136 final size:139
Alignment explanation
Indices: 20819254--20819539 Score: 309
Period size: 136 Copynumber: 2.1 Consensus size: 139
20819244 AACTTCTTTA
* *
20819254 TTTTTTTTTGGAAACATTTGACTTCAACTTTCTTCTTTTTCAAAGTCTATCTCTCTTTGTTATTT
1 TTTTTTTTTGGAAACATTTGACTTCAACTTTCTTCTTTTTCAAAGTCTATCTCTCTTTGTAACTT
* * * **
20819319 GGGACTAAAGCTTTATTCACTTTTTATCCTCGGACTCTCATCTTTGAGGTGCATGTCATTTTTTC
66 GGGACTAAAGCCTTATTCACTTTTTAGCCTCAGACTCTCATCTTCAAGGTGCATGTCATTTTTTC
*
20819384 TTTGTTCTT
131 TTTATTCTT
* * * *
20819393 TTTTTTTTTGGAAACATTTTATTTCAA-TTT-TT-TTTTTCTTGAATTCTATCTCAT-TTT-TAA
1 TTTTTTTTTGGAAACATTTGACTTCAACTTTCTTCTTTTTC--AAAGTCTATCTC-TCTTTGTAA
* * *
20819453 CTTGGGAGTAAAGCCTTATTCACTTTTT-GCCAT-AGACTTTCATCTTCAAGGTGTATGTC-TTT
63 CTTGGGACTAAAGCCTTATTCACTTTTTAGCC-TCAGACTCTCATCTTCAAGGTGCATGTCATTT
*
20819515 CTTTTTTTATTCTT
127 -TTTCTTTATTCTT
20819529 TGTTTCTTTTT
1 T-TTT-TTTTT
20819540 TTTTTTTAAA
Statistics
Matches: 124, Mismatches: 16, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
135 3 0.02
136 41 0.33
137 33 0.27
138 21 0.17
139 26 0.21
ACGTcount: A:0.18, C:0.16, G:0.11, T:0.55
Consensus pattern (139 bp):
TTTTTTTTTGGAAACATTTGACTTCAACTTTCTTCTTTTTCAAAGTCTATCTCTCTTTGTAACTT
GGGACTAAAGCCTTATTCACTTTTTAGCCTCAGACTCTCATCTTCAAGGTGCATGTCATTTTTTC
TTTATTCTT
Found at i:20819954 original size:408 final size:407
Alignment explanation
Indices: 20819517--20820379 Score: 939
Period size: 417 Copynumber: 2.1 Consensus size: 407
20819507 ATGTCTTTCT
* * *
20819517 TTTTTTATTC-TTTGTTTCTTT-TTTTTTTTTAAATATTTGATTTTAACTTTAACATTCTTCAAT
1 TTTTTTATTCATTT-TTTCTTTCTTTTTTTTGAAATATTTGACTTCAACTTTAACATTCTTCAAT
* ** * *
20819580 TTTATCTTCTTTTTTTTGCTTGGGATTCTAACTGAAA-TCTTATTCACTTTTTGCC-CTGAACTC
65 TCTATC-TCCCTTTTTTACTTGGGATTCTAACTGAAACT-TTATTCACTTTTTGCCTCAG-ACTC
* **
20819643 TCATTTTCGAA-GTGCATGTC-TTTCCTTTTTTACTTTTTTTAATTATTTTTTAATGAATGAATC
127 TC-TTCTCGAAGGTGCATGTCTTTTCCTTTTTT-C-TTTTTT--TTATTTTTTAATGAACAAATC
* * *
20819706 GTATTTAGACAATGAATATTCAGACAATCAT-AA-ATA-A-TT-CTTTC-TCTTAAAAACTTATT
187 ATATTTAGACAATGAATATTCAGACAATCATGAACA-ACATTTAATTTCTTCTTAAAAACTGATT
** * ** * * * * *
20819765 CCATTGATACTTTTGATCCTTTCGAGTTTGTTGTACTGGGCATTGCCCTTTATATATTAGTGTTC
251 CCATTGATACCCTTGATCCTTTCGAATTCATTATACTAGGCATTGCCCTCTATAAATTAGTATTC
* * * * * * *
20819830 TTTTACATTTAAGCGACTTTTTTAGGTTTTCCACTTAAATCCTTCTTTTGACTCAAACTGCCCTT
316 CTTTACATCTAAGCAACCTTTTTAGGTTTTCAACTTAAATCCTTCCTTTGACTCAAACTACCCTT
*
20819895 TTTGGGTTTTCAGTCATGAATTCTCCTTTA
381 TTTGGGTTTTCAGTCATGAATCCTCC---A
* * * *
20819925 TTTTTTATTCATCTTTTT-TTTCTTTTTTTTGGAATTTTTGGCTTCAACTTTAACATTCTTGAAT
1 TTTTTTATTCAT-TTTTTCTTTCTTTTTTTTGAAATATTTGACTTCAACTTTAACATTCTTCAAT
* * * * *
20819989 TCTATCTCCCTTTTTTACTTGGGATTCTAATTGCAACTTTATTTACTTTTTGTCTCAGATTCTCT
65 TCTATCTCCCTTTTTTACTTGGGATTCTAACTGAAACTTTATTCACTTTTTGCCTCAGACTCTCT
* * *
20820054 TCTCTAAGGTGCATGTCTTTTTTTCTTTTTTCTTTTTTTTCTTTTTTAATGAACAAATCATATTT
130 TCTCGAAGGTGCATGTC--TTTTCCTTTTTTCTTTTTTTTATTTTTTAATGAACAAATCATATTT
* * *
20820119 AGATAATGAATATTTAGACAATCATGAACAACATTTAGAAATTTCATTTCTTAAAAACTGATTCT
193 AGACAATGAATATTCAGACAATCATGAACAACATTT---AATTTC--TTCTTAAAAACTGATTCC
*
20820184 ATTGATACCCTTGATCCTTTCGAATTCATTATACTAGGCATTGCCCTCTATAAATTGGTATTCCT
253 ATTGATACCCTTGATCCTTTCGAATTCATTATACTAGGCATTGCCCTCTATAAATTAGTATTCCT
* * *
20820249 TTGCATCTAAGCAACCTTTTTAGGTTTTCAACTTAGATCCTTCCTTTGACTCAAACTACCTTTTT
318 TTACATCTAAGCAACCTTTTTAGGTTTTCAACTTAAATCCTTCCTTTGACTCAAACTACCCTTTT
*
20820314 TGGGTTTTCAGTCATGAGTCCTCCA
383 TGGGTTTTCAGTCATGAATCCTCCA
* *
20820339 TTTTTTATTCA-TTTTTC--CCTTTTTTTAGAAATATTTGACTT
1 TTTTTTATTCATTTTTTCTTTCTTTTTTTTGAAATATTTGACTT
20820380 TAATTTTTCA
Statistics
Matches: 377, Mismatches: 57, Indels: 39
0.80 0.12 0.08
Matches are distributed among these distances:
407 52 0.14
408 69 0.18
409 55 0.15
410 5 0.01
411 29 0.08
412 5 0.01
414 16 0.04
417 146 0.39
ACGTcount: A:0.23, C:0.17, G:0.10, T:0.50
Consensus pattern (407 bp):
TTTTTTATTCATTTTTTCTTTCTTTTTTTTGAAATATTTGACTTCAACTTTAACATTCTTCAATT
CTATCTCCCTTTTTTACTTGGGATTCTAACTGAAACTTTATTCACTTTTTGCCTCAGACTCTCTT
CTCGAAGGTGCATGTCTTTTCCTTTTTTCTTTTTTTTATTTTTTAATGAACAAATCATATTTAGA
CAATGAATATTCAGACAATCATGAACAACATTTAATTTCTTCTTAAAAACTGATTCCATTGATAC
CCTTGATCCTTTCGAATTCATTATACTAGGCATTGCCCTCTATAAATTAGTATTCCTTTACATCT
AAGCAACCTTTTTAGGTTTTCAACTTAAATCCTTCCTTTGACTCAAACTACCCTTTTTGGGTTTT
CAGTCATGAATCCTCCA
Found at i:20824218 original size:144 final size:145
Alignment explanation
Indices: 20824023--20824403 Score: 418
Period size: 144 Copynumber: 2.6 Consensus size: 145
20824013 GACTTTAAAG
* * * * *
20824023 CACCAAAAATCATGAAATATTATAAAATTAAAATCTAAAAAATTTCGTGAAAATTTGATCTCGAA
1 CACCAAAAATCATGAAATATTATAAAATTAAGATATGAAAAGTTTCATGAAAATTTGATCTCGAA
* * ** * *
20824088 AAGGATAAATTACAAAAATA-CTTTTAAGGGATATTTTGGTAATTTTACACCTCTT-GAGGT-CT
66 AAGGCTAAATTACAAAAATACCTTTAAAAAG-TATTTTGGTAATTTCACACAT-TTCGAGGTAC-
20824150 TGCTATGATTTCAAAT-T
128 TGCTATGATTTCAAATGT
* * * *
20824167 CACCAAAAATCATGAAACATTATTAAATTAAGATATGAAAAGTTTCATGAAAATCTGAGCTC-AA
1 CACCAAAAATCATGAAATATTATAAAATTAAGATATGAAAAGTTTCATGAAAATTTGATCTCGAA
* * *
20824231 GAAGGCCAAATTACGAAAATACCTTTAAAAATGTATTTTGGTAATTTCACACATTTCGGGGTACT
66 -AAGGCTAAATTACAAAAATACCTTTAAAAA-GTATTTTGGTAATTTCACACATTTCGAGGTACT
* *
20824296 GTTGTGATTTCAAATGT
129 GCTATGATTTCAAATGT
* ** **
20824313 -ACCAAAAATTATGAAATATTATAAAATTAAGATATGAAAAGTTTCACAAAAATTCAATCAT-G-
1 CACCAAAAATCATGAAATATTATAAAATTAAGATATGAAAAGTTTCATGAAAATTTGATC-TCGA
*
20824375 AAAGGCTAAATTACAAAAATACCCTTAAA
65 AAAGGCTAAATTACAAAAATACCTTTAAA
20824404 GACATAGTGT
Statistics
Matches: 197, Mismatches: 32, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
143 2 0.01
144 97 0.49
145 94 0.48
146 4 0.02
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (145 bp):
CACCAAAAATCATGAAATATTATAAAATTAAGATATGAAAAGTTTCATGAAAATTTGATCTCGAA
AAGGCTAAATTACAAAAATACCTTTAAAAAGTATTTTGGTAATTTCACACATTTCGAGGTACTGC
TATGATTTCAAATGT
Found at i:20824327 original size:145 final size:144
Alignment explanation
Indices: 20824023--20824358 Score: 394
Period size: 145 Copynumber: 2.3 Consensus size: 144
20824013 GACTTTAAAG
* * * * * * *
20824023 CACCAAAAATCATGAAATATTATAAAATTAAAATCTAAAAAATTTCGTGAAAATTTGATCTCGAA
1 CACCAAAAATCATGAAATATTATAAAATTAAGATATGAAAAGTTTCATGAAAATCTGAGCTCGAA
* * * * *
20824088 AAGGATAAATTACAAAAATACTTTTAAGGGATATTTTGGTAATTTTACACCTCTTGAGGTCTTGC
66 AAGGACAAATTACAAAAATACTTTAAAAGGATATTTTGGTAATTTCACACATCTTGAGGTCTTGC
20824153 TATGATTTCAAATT
131 TATGATTTCAAATT
* *
20824167 CACCAAAAATCATGAAACATTATTAAATTAAGATATGAAAAGTTTCATGAAAATCTGAGCTC-AA
1 CACCAAAAATCATGAAATATTATAAAATTAAGATATGAAAAGTTTCATGAAAATCTGAGCTCGAA
* * * *
20824231 GAAGGCCAAATTACGAAAATACCTTTAAAAATG-TATTTTGGTAATTTCACACAT-TTCGGGGTA
66 -AAGGACAAATTACAAAAATA-CTTT-AAAAGGATATTTTGGTAATTTCACACATCTT-GAGGT-
* *
20824294 C-TGTTGTGATTTCAAATGT
126 CTTGCTATGATTTCAAAT-T
*
20824313 -ACCAAAAATTATGAAATATTATAAAATTAAGATATGAAAAGTTTCA
1 CACCAAAAATCATGAAATATTATAAAATTAAGATATGAAAAGTTTCA
20824359 CAAAAATTCA
Statistics
Matches: 163, Mismatches: 23, Indels: 11
0.83 0.12 0.06
Matches are distributed among these distances:
143 2 0.01
144 72 0.44
145 84 0.52
146 5 0.03
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.33
Consensus pattern (144 bp):
CACCAAAAATCATGAAATATTATAAAATTAAGATATGAAAAGTTTCATGAAAATCTGAGCTCGAA
AAGGACAAATTACAAAAATACTTTAAAAGGATATTTTGGTAATTTCACACATCTTGAGGTCTTGC
TATGATTTCAAATT
Found at i:20829666 original size:2 final size:2
Alignment explanation
Indices: 20829654--20829693 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
20829644 GCAGGGCCGC
*
20829654 AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
20829694 GATGGGTGGC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:20830039 original size:51 final size:50
Alignment explanation
Indices: 20829959--20830055 Score: 149
Period size: 51 Copynumber: 1.9 Consensus size: 50
20829949 TTAGTATAGT
* *
20829959 AGTTTACTTGTCTCTCACCTTTTTTTAAAAAATATATTCTTTTCCTATGAG
1 AGTTTACTTGTCTCTCACCTTTTTCTAAAAAATATA-TATTTTCCTATGAG
* *
20830010 AGTTTACTTGTCTCTGACCTTTTTCTAAAATATATATATTTTCCTA
1 AGTTTACTTGTCTCTCACCTTTTTCTAAAAAATATATATTTTCCTA
20830056 GCGGCAAGGG
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
50 9 0.21
51 33 0.79
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.49
Consensus pattern (50 bp):
AGTTTACTTGTCTCTCACCTTTTTCTAAAAAATATATATTTTCCTATGAG
Found at i:20832728 original size:14 final size:14
Alignment explanation
Indices: 20832702--20832734 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
20832692 TATATTTAAA
20832702 AAATAAAATTTATT
1 AAATAAAATTTATT
20832716 AAATAAAATTTATT
1 AAATAAAATTTATT
*
20832730 TAATA
1 AAATA
20832735 TAATATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AAATAAAATTTATT
Found at i:20835937 original size:21 final size:23
Alignment explanation
Indices: 20835899--20835946 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
20835889 AATAAAAATA
*
20835899 ATAATAAATTTAATTA-TT-ATG
1 ATAATAAAATTAATTATTTAATG
20835920 ATAATAAAATT-ATATATTTAATG
1 ATAATAAAATTAAT-TATTTAATG
20835943 ATAA
1 ATAA
20835947 GATTAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 2 0.09
21 12 0.52
22 2 0.09
23 7 0.30
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (23 bp):
ATAATAAAATTAATTATTTAATG
Found at i:20836080 original size:15 final size:15
Alignment explanation
Indices: 20836060--20836092 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
20836050 ATATAGATAA
20836060 TTATTA-TTATATATT
1 TTATTATTTA-ATATT
20836075 TTATTATTTAATATT
1 TTATTATTTAATATT
20836090 TTA
1 TTA
20836093 AATTTTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATTATTTAATATT
Found at i:20836097 original size:7 final size:7
Alignment explanation
Indices: 20836081--20836112 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
20836071 TATTTTATTA
20836081 TTTAATAT
1 TTTAA-AT
20836089 TTTAAAT
1 TTTAAAT
20836096 TTTAAAT
1 TTTAAAT
20836103 TTTAAAT
1 TTTAAAT
20836110 TTT
1 TTT
20836113 TTATTCAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.79
8 5 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
TTTAAAT
Found at i:20841292 original size:32 final size:32
Alignment explanation
Indices: 20841253--20841334 Score: 105
Period size: 31 Copynumber: 2.6 Consensus size: 32
20841243 TTACATTTTT
*
20841253 ATTTTAAACTTTAGTTTAGTCCAAGTTATTTC
1 ATTTTAAACTTTAGTTTAGTCCAAGTCATTTC
*
20841285 ATTTTAAACCTTT--TTTAATCCAAGTCATTTC
1 ATTTTAAA-CTTTAGTTTAGTCCAAGTCATTTC
* *
20841316 TTTTTAGACTTTAGTTTAG
1 ATTTTAAACTTTAGTTTAG
20841335 AAGAGATCCT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
30 4 0.10
31 22 0.52
32 12 0.29
33 4 0.10
ACGTcount: A:0.27, C:0.13, G:0.09, T:0.51
Consensus pattern (32 bp):
ATTTTAAACTTTAGTTTAGTCCAAGTCATTTC
Found at i:20844792 original size:31 final size:31
Alignment explanation
Indices: 20844757--20844820 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
20844747 TTTTACCATT
*
20844757 TAAGCATTGTA-TCAAGAGATAATTTCATATA
1 TAAGCATAGTACT-AAGAGATAATTTCATATA
20844788 TAAGCATAGTACTAAGAGATAATTTCATATA
1 TAAGCATAGTACTAAGAGATAATTTCATATA
20844819 TA
1 TA
20844821 TATAATTGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.34
Consensus pattern (31 bp):
TAAGCATAGTACTAAGAGATAATTTCATATA
Found at i:20844827 original size:16 final size:16
Alignment explanation
Indices: 20844806--20844836 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20844796 GTACTAAGAG
*
20844806 ATAATTTCATATATAT
1 ATAATTGCATATATAT
20844822 ATAATTGCATATATA
1 ATAATTGCATATATA
20844837 AACATAGCAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (16 bp):
ATAATTGCATATATAT
Found at i:20844852 original size:47 final size:47
Alignment explanation
Indices: 20844775--20844871 Score: 158
Period size: 47 Copynumber: 2.1 Consensus size: 47
20844765 GTATCAAGAG
* * * *
20844775 ATAATTTCATATATAAGCATAGTACTAAGAGATAATTTCATATATAT
1 ATAATTGCATATATAAACATAGCACCAAGAGATAATTTCATATATAT
20844822 ATAATTGCATATATAAACATAGCACCAAGAGATAATTTCATATATAT
1 ATAATTGCATATATAAACATAGCACCAAGAGATAATTTCATATATAT
20844869 ATA
1 ATA
20844872 TATATATATA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.35
Consensus pattern (47 bp):
ATAATTGCATATATAAACATAGCACCAAGAGATAATTTCATATATAT
Found at i:20844916 original size:31 final size:31
Alignment explanation
Indices: 20844878--20844944 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
20844868 TATATATATA
*
20844878 TATATATGAAATTATCTCTTTG-TGCTATGTT
1 TATATATGAAATTATCTC-TTGATGCAATGTT
20844909 TATATATGAAATTATCTCTTGATGCAATGTT
1 TATATATGAAATTATCTCTTGATGCAATGTT
20844940 TATAT
1 TATAT
20844945 GGTAAAACAC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
30 3 0.09
31 31 0.91
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.49
Consensus pattern (31 bp):
TATATATGAAATTATCTCTTGATGCAATGTT
Found at i:20854218 original size:12 final size:13
Alignment explanation
Indices: 20854200--20854231 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
20854190 TTTATTTACT
20854200 TTTATTTTTTTCA
1 TTTATTTTTTTCA
20854213 -TTA-TTTTTTCA
1 TTTATTTTTTTCA
20854224 TTTATTTT
1 TTTATTTT
20854232 ATATATTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
11 8 0.47
12 6 0.35
13 3 0.18
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTATTTTTTTCA
Found at i:20858501 original size:18 final size:18
Alignment explanation
Indices: 20858477--20858512 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
20858467 ATAAATAAAT
20858477 TTTAAAAAAG-AATTTCA
1 TTTAAAAAAGAAATTTCA
20858494 TTTAAAAAAGAAATTTCA
1 TTTAAAAAAGAAATTTCA
20858512 T
1 T
20858513 GAATTCATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.36
Consensus pattern (18 bp):
TTTAAAAAAGAAATTTCA
Found at i:20858881 original size:22 final size:22
Alignment explanation
Indices: 20858855--20858900 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
20858845 TATTGAGTGC
20858855 TTAATGGATATTGGTATATGCT
1 TTAATGGATATTGGTATATGCT
20858877 TTAATGGATATTGGTATATGCT
1 TTAATGGATATTGGTATATGCT
20858899 TT
1 TT
20858901 GTTGATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.04, G:0.22, T:0.48
Consensus pattern (22 bp):
TTAATGGATATTGGTATATGCT
Found at i:20862044 original size:16 final size:16
Alignment explanation
Indices: 20862025--20862059 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
20862015 TGTGATAACA
20862025 TATCTTTAACAATTGG
1 TATCTTTAACAATTGG
20862041 TATCTTTAACAATTGG
1 TATCTTTAACAATTGG
20862057 TAT
1 TAT
20862060 GAGCCTGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.46
Consensus pattern (16 bp):
TATCTTTAACAATTGG
Found at i:20862458 original size:21 final size:22
Alignment explanation
Indices: 20862419--20862472 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
20862409 CTTCTTGTAT
20862419 GCTTATAACAATTGATAT-AAGA
1 GCTTA-AACAATTGATATAAAGA
* *
20862441 GCTTAAACATTTGGTATAAAGA
1 GCTTAAACAATTGATATAAAGA
*
20862463 GTTTAAACAA
1 GCTTAAACAA
20862473 AAATGAGGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.31
Consensus pattern (22 bp):
GCTTAAACAATTGATATAAAGA
Found at i:20866174 original size:23 final size:23
Alignment explanation
Indices: 20866147--20866191 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
20866137 AAAAATTTAT
20866147 AAATAATAA-ACACACATTAAAAC
1 AAAT-ATAATACACACATTAAAAC
**
20866170 AAATATAATACTTACATTAAAA
1 AAATATAATACACACATTAAAA
20866192 TAAGTTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.24
Consensus pattern (23 bp):
AAATATAATACACACATTAAAAC
Found at i:20870064 original size:20 final size:20
Alignment explanation
Indices: 20870036--20870077 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
20870026 CATGCTTTCA
* * *
20870036 AATCTTTAATCTTTTGCTTT
1 AATCGTTAAACTTTTACTTT
20870056 AATCGTTAAACTTTTACTTT
1 AATCGTTAAACTTTTACTTT
20870076 AA
1 AA
20870078 AATCTTGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.14, G:0.05, T:0.52
Consensus pattern (20 bp):
AATCGTTAAACTTTTACTTT
Found at i:20872832 original size:2 final size:2
Alignment explanation
Indices: 20872827--20872851 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20872817 AAAAAAGGGG
20872827 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
20872852 CATGGACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20880947 original size:25 final size:25
Alignment explanation
Indices: 20880914--20880965 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
20880904 GGTTTCTTTC
20880914 AAAGCCATTGAGGTTGACCAAGCCA
1 AAAGCCATTGAGGTTGACCAAGCCA
* * *
20880939 AAAGGCATTGAGGTTGATCGAGCCA
1 AAAGCCATTGAGGTTGACCAAGCCA
20880964 AA
1 AA
20880966 TTAAGGTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.27, T:0.17
Consensus pattern (25 bp):
AAAGCCATTGAGGTTGACCAAGCCA
Found at i:20883551 original size:15 final size:16
Alignment explanation
Indices: 20883533--20883562 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
20883523 TAATTGTTAA
20883533 TCAAATA-AAGTGATT
1 TCAAATATAAGTGATT
20883548 TCAAATATAAGTGAT
1 TCAAATATAAGTGAT
20883563 AAGATCACCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.33
Consensus pattern (16 bp):
TCAAATATAAGTGATT
Found at i:20884459 original size:23 final size:23
Alignment explanation
Indices: 20884432--20884476 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
20884422 AAAAATTTAT
20884432 AAATAATAA-ACACACATTAAAAC
1 AAAT-ATAATACACACATTAAAAC
*
20884455 AAATATAATACTCACATTAAAA
1 AAATATAATACACACATTAAAA
20884477 TAAGTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.62, C:0.16, G:0.00, T:0.22
Consensus pattern (23 bp):
AAATATAATACACACATTAAAAC
Found at i:20889955 original size:16 final size:18
Alignment explanation
Indices: 20889934--20889969 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
20889924 AAATTTAAAA
20889934 TTCTTTTC-TA-TTATTT
1 TTCTTTTCTTATTTATTT
20889950 TTCTTTTCTTATTTATTT
1 TTCTTTTCTTATTTATTT
20889968 TT
1 TT
20889970 TCTAACATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 2 0.11
18 8 0.44
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (18 bp):
TTCTTTTCTTATTTATTT
Found at i:20891547 original size:13 final size:14
Alignment explanation
Indices: 20891516--20891547 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
20891506 TAGGACTTTG
20891516 TTTTAGGGTTTACA
1 TTTTAGGGTTTACA
20891530 TTTTAGGGTTTA-A
1 TTTTAGGGTTTACA
20891543 TTTTA
1 TTTTA
20891548 AAGTTTCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.22, C:0.03, G:0.19, T:0.56
Consensus pattern (14 bp):
TTTTAGGGTTTACA
Found at i:20891560 original size:13 final size:13
Alignment explanation
Indices: 20891517--20891598 Score: 58
Period size: 13 Copynumber: 6.2 Consensus size: 13
20891507 AGGACTTTGT
* *
20891517 TTTAGGGTTTACAT
1 TTTAAGGTTT-CAA
*
20891531 TTTAGGGTTT-AA
1 TTTAAGGTTTCAA
*
20891543 TTTTAAAGTTTCAA
1 -TTTAAGGTTTCAA
* *
20891557 TTTAAGGTTTTAG
1 TTTAAGGTTTCAA
*
20891570 TTTACGGTTTCAA
1 TTTAAGGTTTCAA
*
20891583 TTTCAAGGTTTAAA
1 TTT-AAGGTTTCAA
20891597 TT
1 TT
20891599 CGTAAATTCA
Statistics
Matches: 54, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
12 1 0.02
13 31 0.57
14 22 0.41
ACGTcount: A:0.27, C:0.06, G:0.17, T:0.50
Consensus pattern (13 bp):
TTTAAGGTTTCAA
Found at i:20891568 original size:27 final size:27
Alignment explanation
Indices: 20891529--20891598 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 27
20891519 TAGGGTTTAC
* *
20891529 ATTTTAGGGTTTAATTTTAAAGTTTCA
1 ATTTAAGGTTTTAATTTTAAAGTTTCA
* **
20891556 ATTTAAGGTTTT-AGTTTACGGTTTCA
1 ATTTAAGGTTTTAATTTTAAAGTTTCA
*
20891582 ATTTCAAGGTTTAAATT
1 ATTT-AAGGTTTTAATT
20891599 CGTAAATTCA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
26 15 0.44
27 17 0.50
28 2 0.06
ACGTcount: A:0.29, C:0.06, G:0.16, T:0.50
Consensus pattern (27 bp):
ATTTAAGGTTTTAATTTTAAAGTTTCA
Found at i:20891757 original size:15 final size:15
Alignment explanation
Indices: 20891736--20891772 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
20891726 TAAAAAATAT
20891736 TTTTTATTTA-TTTA
1 TTTTTATTTACTTTA
20891750 TCTTTTA-TTACTTTA
1 T-TTTTATTTACTTTA
20891765 TTTTTATT
1 TTTTTATT
20891773 ATAATTCTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTATTTACTTTA
Found at i:20891771 original size:14 final size:13
Alignment explanation
Indices: 20891736--20891774 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
20891726 TAAAAAATAT
20891736 TTTTTATTTATTTA
1 TTTTTA-TTATTTA
20891750 TCTTTTATTACTTTA
1 T-TTTTATTA-TTTA
20891765 TTTTTATTAT
1 TTTTTATTAT
20891775 AATTCTCCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 1 0.04
14 12 0.52
15 10 0.43
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTTATTATTTA
Found at i:20892338 original size:64 final size:65
Alignment explanation
Indices: 20892246--20892368 Score: 185
Period size: 64 Copynumber: 1.9 Consensus size: 65
20892236 AAATTAAATG
* ** * *
20892246 GGATTATTGAAGGTGTTTTTGGCTAAAAATACCTTCAATAATCCATTCAAAAAA-TTTTGGACAA
1 GGATTATTAAAGGTGTTTTCAGCCAAAAATACCTTCAATAATCCATACAAAAAAGTTTTGGACAA
*
20892310 GGATTATTAAAGGTGTTTTCAGCCAAAAATATCTTCAATAATCCATACAAAAAAGTTTT
1 GGATTATTAAAGGTGTTTTCAGCCAAAAATACCTTCAATAATCCATACAAAAAAGTTTT
20892369 TGTATGGATT
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
64 48 0.92
65 4 0.08
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (65 bp):
GGATTATTAAAGGTGTTTTCAGCCAAAAATACCTTCAATAATCCATACAAAAAAGTTTTGGACAA
Found at i:20892726 original size:369 final size:369
Alignment explanation
Indices: 20892043--20892732 Score: 891
Period size: 369 Copynumber: 1.9 Consensus size: 369
20892033 AGTATAAGGG
** * * *
20892043 ACTTTTACTGATGGATTTTTAATACCGTCAAAATATATCATACTTATACTAACACTTTATTTAAC
1 ACTTTTACTGATAAATTTTTAATACCATCAAAATATACCATACTTATACCAACACTTTATTTAAC
* * * ** * * * * *
20892108 CGTCGGTATAAATAAAGTTTTTTTGATGGTATATGACTATTTATCAGTATAAATATGTTATATAT
66 CATCGATAGAAATAAACCTTTTATGATGGTATATAACTATCTATCAATATAAATATGTTATACAT
* * * * * * * *
20892173 TGATGGTCATTAATGTAACTATCAGTATAGGCTCAAAACAGAAAAAAACTATTAGTTTACAAAAA
131 TAACGGTCATTAACGTAACCATCAGTACAAGCTCAAAACAAAAAAAAACTATTAGCTTACAAAAA
* * * * *
20892238 ATTAAATGGGATTATTGAAGGTGTTTTTGGCTAAAAATACCTTCAATAATCCATTCAAAAAATTT
196 ACTAAATGGGATTATTGAAGGAGTTTTTGACTAAAAACACCTTCAATAATCCATACAAAAAATTT
** * * *
20892303 TGGACAAGGATTATTAAAGGTGTTTTCAGCCAAAAATATCTTCAATAATCCATACAAAAAAGTTT
261 TGGACAAGGATTATTAAAGGCATTTTCAGCCAAAAACACCTTAAATAATCCATACAAAAAAGTTT
20892368 TTGTATGGATTATTTACTGCAGTCAAATTTTATCAGTAAAAGAA
326 TTGTATGGATTATTTACTGCAGTCAAATTTTATCAGTAAAAGAA
* * * *
20892412 ACTTTTACTGATAAATTTTTAGTACCATCAAAATATACCCTATTTATACCAATACTTTATTTAAC
1 ACTTTTACTGATAAATTTTTAATACCATCAAAATATACCATACTTATACCAACACTTTATTTAAC
*
20892477 CATCGATAGAAATAAACCTTTTATGATGGTATATAACTATCTGTCAATATAAATATGTTATACAT
66 CATCGATAGAAATAAACCTTTTATGATGGTATATAACTATCTATCAATATAAATATGTTATACAT
* * * *
20892542 TAACGGTTATTAACGTAACCGTTAGTACAAGCTCAAAACAAAAAAAAAACTATTGGCTTACAAAA
131 TAACGGTCATTAACGTAACCATCAGTACAAGCTCAAAAC-AAAAAAAAACTATTAGCTTACAAAA
*
20892607 AACTAAATGGGATTATTGAAGGAGTTTTTGACTAAAAACACCTTCAATAATTCATAC-AAAAATT
195 AACTAAATGGGATTATTGAAGGAGTTTTTGACTAAAAACACCTTCAATAATCCATACAAAAAATT
* ** * * *
20892671 TT-G-CAGGGGATTATTAAAGGCATTTTTTGTCAGAAACGCCTTAAATAATTCCATACAAAAAA
260 TTGGACA-AGGATTATTAAAGGCATTTTCAGCCAAAAACACCTTAAATAA-TCCATACAAAAAA
20892733 TTGAATATGA
Statistics
Matches: 269, Mismatches: 49, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
367 2 0.01
368 32 0.12
369 162 0.60
370 73 0.27
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (369 bp):
ACTTTTACTGATAAATTTTTAATACCATCAAAATATACCATACTTATACCAACACTTTATTTAAC
CATCGATAGAAATAAACCTTTTATGATGGTATATAACTATCTATCAATATAAATATGTTATACAT
TAACGGTCATTAACGTAACCATCAGTACAAGCTCAAAACAAAAAAAAACTATTAGCTTACAAAAA
ACTAAATGGGATTATTGAAGGAGTTTTTGACTAAAAACACCTTCAATAATCCATACAAAAAATTT
TGGACAAGGATTATTAAAGGCATTTTCAGCCAAAAACACCTTAAATAATCCATACAAAAAAGTTT
TTGTATGGATTATTTACTGCAGTCAAATTTTATCAGTAAAAGAA
Found at i:20893353 original size:62 final size:60
Alignment explanation
Indices: 20893253--20893419 Score: 226
Period size: 62 Copynumber: 2.7 Consensus size: 60
20893243 TTTGTTAAGG
20893253 GATTATTCAAGGCATTTTTGGTCAAAAACGCTTTGAATAATCCTATTCAATTTCTTATAAAA
1 GATTATTCAAGGCATTTTTGGT-AAAAACGC-TTGAATAATCCTATTCAATTTCTTATAAAA
* * * *
20893315 GATTATTCAAGGTATTTTTGGCTAAAAACGCTTGGAATAATCCTATTCAATTTTTTGTAAGA
1 GATTATTCAAGGCATTTTTGG-TAAAAACGCTT-GAATAATCCTATTCAATTTCTTATAAAA
* *
20893377 GATTATTCAAGGCATTTCTAGGTAAAAATGCCTTGAATAATCC
1 GATTATTCAAGGCATTT-TTGGTAAAAACG-CTTGAATAATCC
20893420 CAAAAAAAAT
Statistics
Matches: 94, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
61 2 0.02
62 85 0.90
63 7 0.07
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (60 bp):
GATTATTCAAGGCATTTTTGGTAAAAACGCTTGAATAATCCTATTCAATTTCTTATAAAA
Found at i:20893539 original size:121 final size:121
Alignment explanation
Indices: 20893314--20893584 Score: 316
Period size: 121 Copynumber: 2.2 Consensus size: 121
20893304 TTCTTATAAA
* * * * *
20893314 AGATTATTCAAGGTATTTTTGGCTAAAAACGCTTGGAATAATCCTATTCAATTTTTTGTAAGAGA
1 AGATTATTCAAGGCATTTTTGGCTAAAAACGCTTGAAATAACCCCATTCAATTTTTTATAAGAGA
** ** *
20893379 TTATTCAAGGCATTTCTAGGTAAAAATGCCTTGAATAATCCCAAAAAAAATGGCAGG
66 TTATTCAAAACATTTCTAGCCAAAAATACCTTGAATAAT-CCAAAAAAAATGGCAGG
* *
20893436 AGATTATTCAAGGCATTTTTGG-TCAGAAACGCCTT-AAATAACCCCATTTAA-TTTTTATAAGG
1 AGATTATTCAAGGCATTTTTGGCT-AAAAACG-CTTGAAATAACCCCATTCAATTTTTTATAA-G
* * *
20893498 GGA-TATTCAAAACATTTCTAGCCAAAAATACCTTGAATAATCCTAAAAAAATGGTAGG
63 AGATTATTCAAAACATTTCTAGCCAAAAATACCTTGAATAATCCAAAAAAAATGGCAGG
* * *
20893556 GGATTATTCAATGCATTTTTGGCCAAAAA
1 AGATTATTCAAGGCATTTTTGGCTAAAAA
20893585 ATACCTTGAG
Statistics
Matches: 126, Mismatches: 19, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
120 39 0.31
121 42 0.33
122 42 0.33
123 3 0.02
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (121 bp):
AGATTATTCAAGGCATTTTTGGCTAAAAACGCTTGAAATAACCCCATTCAATTTTTTATAAGAGA
TTATTCAAAACATTTCTAGCCAAAAATACCTTGAATAATCCAAAAAAAATGGCAGG
Done.