Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 200 of 208
Found at i:60788379 original size:33 final size:36
Alignment explanation
Indices: 60788258--60788383 Score: 114
Period size: 39 Copynumber: 3.2 Consensus size: 36
60788248 TAATAGTACG
*
60788258 GTAACAGTATTTGACACACAAAGTGCCGAATCGGTAATAGTAA
1 GTAACAGTATTCGACACACAAAGTGCCGAATC------AGT-A
60788301 CGGTAACAGTATTCGACACACAAAGTGCCGAATCAGTAACA
1 --GTAACAGTATTCGACACACAAAGTGCCGAATCAGT---A
60788342 GTAACAGTATTCGACACACAAAGTGCCGAAT-A-T-
1 GTAACAGTATTCGACACACAAAGTGCCGAATCAGTA
60788375 GTAACAGTA
1 GTAACAGTA
60788384 ACAGTAATAG
Statistics
Matches: 77, Mismatches: 2, Indels: 16
0.81 0.02 0.17
Matches are distributed among these distances:
33 9 0.12
37 1 0.01
38 1 0.01
39 34 0.44
41 1 0.01
45 31 0.40
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.21
Consensus pattern (36 bp):
GTAACAGTATTCGACACACAAAGTGCCGAATCAGTA
Found at i:60788679 original size:40 final size:40
Alignment explanation
Indices: 60788634--60788720 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 40
60788624 AATTCATAAC
* *
60788634 TTCAGTAAATTCACAGTTCAA-TGCAATA-TACATAACAATA
1 TTCAGTAAATTCACAATTCAACT-CAATACT-CAAAACAATA
* *
60788674 TTCAGTAACTTCACAATTCAACTCAGTACTCAAAACAATA
1 TTCAGTAAATTCACAATTCAACTCAATACTCAAAACAATA
60788714 TTCAGTA
1 TTCAGTA
60788721 TTCCATAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
40 39 0.95
41 2 0.05
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.30
Consensus pattern (40 bp):
TTCAGTAAATTCACAATTCAACTCAATACTCAAAACAATA
Found at i:60795338 original size:40 final size:41
Alignment explanation
Indices: 60795260--60795340 Score: 114
Period size: 40 Copynumber: 2.0 Consensus size: 41
60795250 TGTTACTAAA
*
60795260 TACTGCATGATTGCTACTGATACTATGATGGGCTAAGGCCC
1 TACTGCATGATTGATACTGATACTATGATGGGCTAAGGCCC
60795301 TACTGCAT-ATTTGATACTG-TACTGA-GATGGGCTAAGGCCC
1 TACTGCATGA-TTGATACTGATACT-ATGATGGGCTAAGGCCC
60795341 AAACTGTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
40 20 0.54
41 17 0.46
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (41 bp):
TACTGCATGATTGATACTGATACTATGATGGGCTAAGGCCC
Found at i:60796084 original size:15 final size:16
Alignment explanation
Indices: 60796060--60796106 Score: 62
Period size: 15 Copynumber: 3.0 Consensus size: 16
60796050 AAATTCATGA
60796060 AAATG-ATGATATATG
1 AAATGAATGATATATG
*
60796075 AAAT-ATTGATATAATG
1 AAATGAATGATAT-ATG
60796091 AAATGAATGATATATG
1 AAATGAATGATATATG
60796107 TTTATGAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 10 0.37
16 10 0.37
17 7 0.26
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (16 bp):
AAATGAATGATATATG
Found at i:60802472 original size:20 final size:20
Alignment explanation
Indices: 60802447--60802487 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
60802437 ATTTTCTTGC
*
60802447 TATTTTTTT-ACTATTTTGT
1 TATTTTTTTCACTAATTTGT
60802466 TATTTTTTTCACTAATTTGT
1 TATTTTTTTCACTAATTTGT
60802486 TA
1 TA
60802488 CAATTTCACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.68
Consensus pattern (20 bp):
TATTTTTTTCACTAATTTGT
Found at i:60802474 original size:11 final size:11
Alignment explanation
Indices: 60802426--60802493 Score: 50
Period size: 11 Copynumber: 6.4 Consensus size: 11
60802416 TAAAAAAGTA
*
60802426 ATTTTTTTATT
1 ATTTTTTTACT
* *
60802437 ATTTTCTTGCT
1 ATTTTTTTACT
60802448 ATTTTTTTACT
1 ATTTTTTTACT
*
60802459 ATTTTGTTA-T
1 ATTTTTTTACT
*
60802469 -TTTTTTCACT
1 ATTTTTTTACT
* * *
60802479 AATTTGTTACA
1 ATTTTTTTACT
60802490 ATTT
1 ATTT
60802494 CACTATTATG
Statistics
Matches: 42, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
9 6 0.14
10 2 0.05
11 34 0.81
ACGTcount: A:0.19, C:0.09, G:0.04, T:0.68
Consensus pattern (11 bp):
ATTTTTTTACT
Found at i:60802675 original size:18 final size:18
Alignment explanation
Indices: 60802654--60802695 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
60802644 GAAATATTTA
*
60802654 TTTTAATAT-TTTTAGCAT
1 TTTTAATATATTATA-CAT
60802672 TTTTAATATATTATACAT
1 TTTTAATATATTATACAT
60802690 TTTTAA
1 TTTTAA
60802696 AAATTTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTTAATATATTATACAT
Found at i:60805993 original size:2 final size:2
Alignment explanation
Indices: 60805986--60806014 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
60805976 TTTAGATGTG
60805986 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
60806015 TACTAGCCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:60811075 original size:25 final size:25
Alignment explanation
Indices: 60811047--60811317 Score: 136
Period size: 25 Copynumber: 10.8 Consensus size: 25
60811037 AGCATGTAAT
* ** *
60811047 CGGGAAGCTCTTTTGAGCCATGTAA
1 CGGGAAGCTCATGCGAGCCATATAA
* **
60811072 CGGGAAGCTCATGTGAGCTGTATAA
1 CGGGAAGCTCATGCGAGCCATATAA
* *
60811097 TGGGAAGCTCTTGCGAGCCA-ATAA
1 CGGGAAGCTCATGCGAGCCATATAA
*
60811121 TCGGGAAGCTCATACGAGCCATA-AA
1 -CGGGAAGCTCATGCGAGCCATATAA
* * * *
60811146 CGGGAAGCTTATGTGAGCCAAATAT
1 CGGGAAGCTCATGCGAGCCATATAA
* * * * *
60811171 CGGTAATCTTATGAGAGCCATATAT
1 CGGGAAGCTCATGCGAGCCATATAA
* * *
60811196 CGAGAAGCTCGTGAGAGCCATATAA
1 CGGGAAGCTCATGCGAGCCATATAA
** * *
60811221 CCAGAAGCTCAAGAGAGAGCCAT-TAA
1 CGGGAAGCTC-A-TGCGAGCCATATAA
* * * *
60811247 TCGAGAAGCTCATGAGAGCTAAATAA
1 -CGGGAAGCTCATGCGAGCCATATAA
* * * * *
60811273 TGGGAAGCTCGTGAGAGCTA-AGTAT
1 CGGGAAGCTCATGCGAGCCATA-TAA
* *
60811298 CGGGAAGCTCGTGAGAGCCA
1 CGGGAAGCTCATGCGAGCCA
60811318 AATAGTGGGA
Statistics
Matches: 197, Mismatches: 41, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
24 23 0.12
25 148 0.75
26 8 0.04
27 18 0.09
ACGTcount: A:0.32, C:0.19, G:0.28, T:0.21
Consensus pattern (25 bp):
CGGGAAGCTCATGCGAGCCATATAA
Found at i:60811253 original size:27 final size:26
Alignment explanation
Indices: 60811183--60811264 Score: 89
Period size: 27 Copynumber: 3.1 Consensus size: 26
60811173 GTAATCTTAT
*
60811183 GAGAGCCA-TATATCGAGAAGCTC-GT
1 GAGAGCCATTA-ATCGAGAAGCTCAGA
*
60811208 GAGAGCCATATAA-CCAGAAGCTCAAGA
1 GAGAGCCAT-TAATCGAGAAGCTC-AGA
60811235 GAGAGCCATTAATCGAGAAGCTCATGA
1 GAGAGCCATTAATCGAGAAGCTCA-GA
60811262 GAG
1 GAG
60811265 CTAAATAATG
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
25 17 0.35
26 5 0.10
27 26 0.54
ACGTcount: A:0.38, C:0.20, G:0.27, T:0.16
Consensus pattern (26 bp):
GAGAGCCATTAATCGAGAAGCTCAGA
Found at i:60811280 original size:52 final size:52
Alignment explanation
Indices: 60811183--60811321 Score: 142
Period size: 52 Copynumber: 2.7 Consensus size: 52
60811173 GTAATCTTAT
* *
60811183 GAGAGCCATATATCGAGAAGCTCGTGAGAGCCATATAACCAGAAGCTCAAGA
1 GAGAGCCATATATCGAGAAGCTCATGAGAGCCAAATAACCAGAAGCTCAAGA
* *** *
60811235 GAGAGCCAT-TAATCGAGAAGCTCATGAGAGCTAAATAATGGGAAGCTC--GT
1 GAGAGCCATAT-ATCGAGAAGCTCATGAGAGCCAAATAACCAGAAGCTCAAGA
* * *
60811285 GAGAGCTA-AGTATCGGGAAGCTCGTGAGAGCCAAATA
1 GAGAGCCATA-TATCGAGAAGCTCATGAGAGCCAAATA
60811322 GTGGGATACT
Statistics
Matches: 73, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
50 31 0.42
51 2 0.03
52 40 0.55
ACGTcount: A:0.37, C:0.18, G:0.28, T:0.17
Consensus pattern (52 bp):
GAGAGCCATATATCGAGAAGCTCATGAGAGCCAAATAACCAGAAGCTCAAGA
Found at i:60811327 original size:25 final size:24
Alignment explanation
Indices: 60811251--60811327 Score: 100
Period size: 25 Copynumber: 3.1 Consensus size: 24
60811241 CATTAATCGA
*
60811251 GAAGCTCATGAGAGCTAAATAATGG
1 GAAGCTCGTGAGAGCTAAAT-ATGG
*
60811276 GAAGCTCGTGAGAGCTAAGTATCGG
1 GAAGCTCGTGAGAGCTAAATAT-GG
*
60811301 GAAGCTCGTGAGAGCCAAATAGTGG
1 GAAGCTCGTGAGAGCTAAATA-TGG
60811326 GA
1 GA
60811328 TACTCATAAG
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
24 2 0.04
25 43 0.93
26 1 0.02
ACGTcount: A:0.34, C:0.14, G:0.34, T:0.18
Consensus pattern (24 bp):
GAAGCTCGTGAGAGCTAAATATGG
Found at i:60838343 original size:26 final size:25
Alignment explanation
Indices: 60838308--60838362 Score: 83
Period size: 26 Copynumber: 2.2 Consensus size: 25
60838298 TTACAGTATA
60838308 AAAATAAATAAAATAAATAATATTTT
1 AAAATAAATAAAATAAATAAT-TTTT
* *
60838334 AAAATGAATAAAATAATTAATTTTT
1 AAAATAAATAAAATAAATAATTTTT
60838359 AAAA
1 AAAA
60838363 CATATTCCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 8 0.30
26 19 0.70
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (25 bp):
AAAATAAATAAAATAAATAATTTTT
Found at i:60847778 original size:98 final size:98
Alignment explanation
Indices: 60847609--60847804 Score: 374
Period size: 98 Copynumber: 2.0 Consensus size: 98
60847599 ACAAGCTTAT
* *
60847609 GTATTTATACACAAGTACTGCCAATATACACTAGGAAACTAGCAGGAAACTCCTCTTCCTAAAGT
1 GTATTTATACACAAGTACAGCCAATATACACTAGGAAACTAGCAGGAAACTCCTCCTCCTAAAGT
60847674 TTGTCCTAAAATGAAGCTTAAAATCTGGCCTAA
66 TTGTCCTAAAATGAAGCTTAAAATCTGGCCTAA
60847707 GTATTTATACACAAGTACAGCCAATATACACTAGGAAACTAGCAGGAAACTCCTCCTCCTAAAGT
1 GTATTTATACACAAGTACAGCCAATATACACTAGGAAACTAGCAGGAAACTCCTCCTCCTAAAGT
60847772 TTGTCCTAAAATGAAGCTTAAAATCTGGCCTAA
66 TTGTCCTAAAATGAAGCTTAAAATCTGGCCTAA
60847805 AATCAAGGTC
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 96 1.00
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (98 bp):
GTATTTATACACAAGTACAGCCAATATACACTAGGAAACTAGCAGGAAACTCCTCCTCCTAAAGT
TTGTCCTAAAATGAAGCTTAAAATCTGGCCTAA
Found at i:60853035 original size:30 final size:30
Alignment explanation
Indices: 60852999--60853055 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
60852989 CTTCCTGATA
*
60852999 AAACCAACATATAGAACATCATTTTACATG
1 AAACCAACAAATAGAACATCATTTTACATG
60853029 AAACCAACAAATAGAACATCATTTTAC
1 AAACCAACAAATAGAACATCATTTTAC
60853056 TTTTATGTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.49, C:0.21, G:0.05, T:0.25
Consensus pattern (30 bp):
AAACCAACAAATAGAACATCATTTTACATG
Found at i:60854391 original size:31 final size:31
Alignment explanation
Indices: 60854354--60854417 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
60854344 TTGAAAATGG
*
60854354 AAAACACTAAAGAAAATGTGTTCGATTGAAA
1 AAAACACTAAAGAAAACGTGTTCGATTGAAA
* *
60854385 AAAACACTACAGAAAACGTGTTTGATTGAAA
1 AAAACACTAAAGAAAACGTGTTCGATTGAAA
60854416 AA
1 AA
60854418 TTAAAAATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.52, C:0.11, G:0.16, T:0.22
Consensus pattern (31 bp):
AAAACACTAAAGAAAACGTGTTCGATTGAAA
Found at i:60860896 original size:14 final size:15
Alignment explanation
Indices: 60860847--60860898 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
60860837 GTAAAATATA
60860847 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
60860862 TATTAAATATATTAT
1 AATTAAATATATTAT
60860877 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
60860890 AATTTAATA
1 AATTAAATA
60860899 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:60860978 original size:120 final size:120
Alignment explanation
Indices: 60860755--60861006 Score: 429
Period size: 120 Copynumber: 2.1 Consensus size: 120
60860745 NNNNNNNNNN
60860755 ATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAA
1 ATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAA
* *
60860820 TCATAATATATGATACTGTAAAATATAAATTAACATAATTATTATTAAATATATT
66 TCATAATATATGATACTATAAAATATAAATTAACATAATTAATATTAAATATATT
60860875 ATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAA
1 ATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAA
60860940 TCATAATATATGATACTAT-AAATGA-AAACTTGAA-ATAATTAATATTAAATATATT
66 TCATAATATATGATACTATAAAAT-ATAAA-TT-AACATAATTAATATTAAATATATT
*
60860995 TTAATTAAAATA
1 ATAATTAAAATA
60861007 ATTTAAACAT
Statistics
Matches: 126, Mismatches: 3, Indels: 6
0.93 0.02 0.04
Matches are distributed among these distances:
119 7 0.06
120 117 0.93
121 2 0.02
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (120 bp):
ATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAA
TCATAATATATGATACTATAAAATATAAATTAACATAATTAATATTAAATATATT
Found at i:60865779 original size:16 final size:15
Alignment explanation
Indices: 60865759--60865792 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
60865749 AAAATTTAAG
60865759 ATTTTTAAAACATTT
1 ATTTTTAAAACATTT
* *
60865774 ATTTTTACAATATTT
1 ATTTTTAAAACATTT
60865789 ATTT
1 ATTT
60865793 AAAATTTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTTTTAAAACATTT
Found at i:60870619 original size:16 final size:17
Alignment explanation
Indices: 60870594--60870627 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
60870584 ATTTTAATTT
*
60870594 TTTTATAATTAT-AAAA
1 TTTTAAAATTATGAAAA
60870610 TTTTAAAATTATGAAAA
1 TTTTAAAATTATGAAAA
60870627 T
1 T
60870628 ATATTTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
TTTTAAAATTATGAAAA
Found at i:60872007 original size:17 final size:18
Alignment explanation
Indices: 60871985--60872023 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
60871975 AAATTTTATC
*
60871985 AAATTTATTTTA-AAACT
1 AAATTTATTTGATAAACT
60872002 AAATTTATTTGATAAACT
1 AAATTTATTTGATAAACT
60872020 AAAT
1 AAAT
60872024 GTAAAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (18 bp):
AAATTTATTTGATAAACT
Found at i:60872276 original size:8 final size:9
Alignment explanation
Indices: 60872262--60872317 Score: 55
Period size: 8 Copynumber: 6.3 Consensus size: 9
60872252 TTAAGCCTTT
60872262 TATATATTA
1 TATATATTA
60872271 -ATATATTA
1 TATATATTA
*
60872279 -ATATTTTA
1 TATATATTA
60872287 TATATATATA
1 TATATAT-TA
60872297 TATATATTCA
1 TATATATT-A
*
60872307 TTTATA-TA
1 TATATATTA
60872315 TAT
1 TAT
60872318 TGGGTTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
8 18 0.45
9 7 0.17
10 15 0.38
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (9 bp):
TATATATTA
Found at i:60873074 original size:33 final size:35
Alignment explanation
Indices: 60872979--60873075 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 35
60872969 TTAATATTTT
*
60872979 AATATATGAAATATAAATTTTAAATATTT--TTAAGC
1 AATATAT-AAAT-TATATTTTAAATATTTAATTAAGC
* *
60873014 AATAAATATTAATTAT-TTATAAA-ATTTAATT-AG-
1 AAT--ATATAAATTATATTTTAAATATTTAATTAAGC
60873047 AATATATAAATTATATTTTAAATATTTAA
1 AATATATAAATTATATTTTAAATATTTAA
60873076 ATATTTGTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 10 0.20
32 6 0.12
33 13 0.25
34 8 0.16
35 7 0.14
36 3 0.06
37 4 0.08
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (35 bp):
AATATATAAATTATATTTTAAATATTTAATTAAGC
Found at i:60877441 original size:19 final size:19
Alignment explanation
Indices: 60877379--60877442 Score: 51
Period size: 19 Copynumber: 3.3 Consensus size: 19
60877369 AAAATTACAA
*
60877379 AAAATTCAAAGTAATTT-T
1 AAAATTCAAAATAATTTAT
* * *
60877397 CAAATTTTGAAAATAATTTTT
1 -AAA-ATTCAAAATAATTTAT
60877418 AAAATTCAAAAT-ATTTAT
1 AAAATTCAAAATAATTTAT
60877436 AGAAATT
1 A-AAATT
60877443 TTAAATTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
18 6 0.17
19 15 0.42
20 14 0.39
21 1 0.03
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (19 bp):
AAAATTCAAAATAATTTAT
Found at i:60877459 original size:14 final size:16
Alignment explanation
Indices: 60877440--60877471 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
60877430 ATTTATAGAA
60877440 ATTTT-AAA-TTTTAT
1 ATTTTAAAATTTTTAT
60877454 ATTTTAAAATTTTTAT
1 ATTTTAAAATTTTTAT
60877470 AT
1 AT
60877472 GATTTGAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 3 0.19
16 8 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTTAAAATTTTTAT
Found at i:60881752 original size:52 final size:52
Alignment explanation
Indices: 60881681--60881780 Score: 155
Period size: 52 Copynumber: 1.9 Consensus size: 52
60881671 ATCAAGTGAC
** *
60881681 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTAATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGG
* *
60881733 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGACAA
1 AAAGTGATAAGTAATAGCTTCAGCTACACTTATCTGATCAAGTGACAA
60881781 AGTGATAAGT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (52 bp):
AAAGTGATAAGTAATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGG
Found at i:60881801 original size:37 final size:37
Alignment explanation
Indices: 60881754--60881863 Score: 170
Period size: 37 Copynumber: 3.0 Consensus size: 37
60881744 TAATAGCTTC
* *
60881754 GGCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
*
60881791 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
*
60881828 GGCTACACTTATCTGATC-AGGGAC-AAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
60881863 G
1 G
60881864 ATCATACGTA
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
35 12 0.18
36 4 0.06
37 52 0.76
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.26
Consensus pattern (37 bp):
GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
Found at i:60889606 original size:6 final size:5
Alignment explanation
Indices: 60889577--60889612 Score: 63
Period size: 5 Copynumber: 7.0 Consensus size: 5
60889567 ACCCAAGGGA
60889577 GGTGG GGTGG GGTGG GGTGG GGTGGG GGTGG GGTGG
1 GGTGG GGTGG GGTGG GGTGG GGT-GG GGTGG GGTGG
60889613 TTTGGGTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.00, C:0.00, G:0.81, T:0.19
Consensus pattern (5 bp):
GGTGG
Found at i:60889618 original size:16 final size:16
Alignment explanation
Indices: 60889577--60889612 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
60889567 ACCCAAGGGA
60889577 GGTGGGGT-GGGGTGG
1 GGTGGGGTGGGGGTGG
60889592 GGTGGGGTGGGGGTGG
1 GGTGGGGTGGGGGTGG
60889608 GGTGG
1 GGTGG
60889613 TTTGGGTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.00, C:0.00, G:0.81, T:0.19
Consensus pattern (16 bp):
GGTGGGGTGGGGGTGG
Found at i:60890972 original size:22 final size:22
Alignment explanation
Indices: 60890942--60890984 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
60890932 ACACCAAAAC
* * *
60890942 AGGCTTTTAGCGGCGTTTTTTT
1 AGGCCTTTAGAGGCGCTTTTTT
60890964 AGGCCTTTAGAGGCGCTTTTT
1 AGGCCTTTAGAGGCGCTTTTT
60890985 AGCGCCGCTA
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:0.12, C:0.16, G:0.28, T:0.44
Consensus pattern (22 bp):
AGGCCTTTAGAGGCGCTTTTTT
Found at i:60891108 original size:43 final size:43
Alignment explanation
Indices: 60891047--60891271 Score: 299
Period size: 43 Copynumber: 5.2 Consensus size: 43
60891037 CTAAAGAACG
* *
60891047 CGCCACTAAAGACTAAGACCTTTAGCGGCGCTTTTCCCACAAA
1 CGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAA
*
60891090 CGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTACCCACAAA
1 CGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAA
*
60891133 CGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTACCCACAAA
1 CGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAA
* * ** *
60891176 CGCCGCTATAGATCGTGACCTTTAGCAGCGCTTATT-CCACAAA
1 CGCCGCTAAAGACCAAGACCTTTAGCGGCGCTT-TTCCCACAAA
* * ** **
60891219 CGCCGCTAAAGATCATGACCTTTAGCAACGCTTTTGTCACAAA
1 CGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAA
60891262 CGCCGCTAAA
1 CGCCGCTAAA
60891272 AATATAACCT
Statistics
Matches: 167, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
42 2 0.01
43 164 0.98
44 1 0.01
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.20
Consensus pattern (43 bp):
CGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCACAAA
Found at i:60892015 original size:23 final size:23
Alignment explanation
Indices: 60891965--60892016 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
60891955 GTTAGGTGTC
* *
60891965 AGTATAAAGACATGTCAGATATG
1 AGTATGAAGACATGTCAGAGATG
* * *
60891988 GGTATGAAGGCATGTCTGAGATG
1 AGTATGAAGACATGTCAGAGATG
60892011 AGTATG
1 AGTATG
60892017 TTCAATGATT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.31, T:0.27
Consensus pattern (23 bp):
AGTATGAAGACATGTCAGAGATG
Found at i:60895266 original size:6 final size:6
Alignment explanation
Indices: 60895255--60895289 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
60895245 TTATGTTTTT
*
60895255 TAAAAA TAAAAA TAAAAA TACAAA -AAAAA TAAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
60895290 ATTGCATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (6 bp):
TAAAAA
Found at i:60895329 original size:30 final size:29
Alignment explanation
Indices: 60895287--60895402 Score: 144
Period size: 30 Copynumber: 3.9 Consensus size: 29
60895277 AAAAAAATAA
*
60895287 AAAATTGCATTTTGACCCC-AAACTTTTCT
1 AAAATTACATTTTGACCCCAAAAC-TTTCT
60895316 AAAATTTACATTTTGACCCCAAAAACTTTCT
1 AAAA-TTACATTTTGACCCC-AAAACTTTCT
* **
60895347 AAAATTACATTTTTACCCTTAAACTTTCT
1 AAAATTACATTTTGACCCCAAAACTTTCT
*
60895376 CAAAATTACATTTTGACCCCTAAACTT
1 -AAAATTACATTTTGACCCCAAAACTT
60895403 CCGCAAAATT
Statistics
Matches: 77, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
29 13 0.17
30 51 0.66
31 9 0.12
32 4 0.05
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.38
Consensus pattern (29 bp):
AAAATTACATTTTGACCCCAAAACTTTCT
Found at i:60896043 original size:24 final size:24
Alignment explanation
Indices: 60896011--60896081 Score: 115
Period size: 24 Copynumber: 3.0 Consensus size: 24
60896001 GCCATTTTCA
*
60896011 GCAGGCCCAGCGCAACCCAGTAGG
1 GCAGGCCCAGCGCAGCCCAGTAGG
*
60896035 GCAGGCCCAGCGCAGCCCAGCAGG
1 GCAGGCCCAGCGCAGCCCAGTAGG
*
60896059 CCAGGCCCAGCGCAGCCCAGTAG
1 GCAGGCCCAGCGCAGCCCAGTAG
60896082 ACCCAGCGCA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.23, C:0.41, G:0.34, T:0.03
Consensus pattern (24 bp):
GCAGGCCCAGCGCAGCCCAGTAGG
Found at i:60896059 original size:19 final size:19
Alignment explanation
Indices: 60896035--60896102 Score: 66
Period size: 24 Copynumber: 3.4 Consensus size: 19
60896025 ACCCAGTAGG
60896035 GCAGGCCCAGCGCAGCCCAGCA
1 GCAGGCCCAGCGCAG-CC--CA
60896057 GGCCAGGCCCAGCGCAGCCCA
1 -G-CAGGCCCAGCGCAGCCCA
* *
60896078 GTAGACCCAGCGCA-CCCA
1 GCAGGCCCAGCGCAGCCCA
60896096 GCAGGCC
1 GCAGGCC
60896103 AGGCCCACAC
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
18 9 0.22
19 11 0.28
20 1 0.03
21 2 0.05
23 3 0.08
24 14 0.35
ACGTcount: A:0.22, C:0.46, G:0.31, T:0.01
Consensus pattern (19 bp):
GCAGGCCCAGCGCAGCCCA
Found at i:60896078 original size:48 final size:42
Alignment explanation
Indices: 60896012--60896109 Score: 133
Period size: 48 Copynumber: 2.2 Consensus size: 42
60896002 CCATTTTCAG
60896012 CAGGCCCAGCGCAACCCAGTAGGGCAGGCCCAGCGCAGCCCAGCAGGC
1 CAGGCCCAGCGCAACCCAGTA--G-A--CCCAGCGCA-CCCAGCAGGC
*
60896060 CAGGCCCAGCGCAGCCCAGTAGACCCAGCGCACCCAGCAGGC
1 CAGGCCCAGCGCAACCCAGTAGACCCAGCGCACCCAGCAGGC
60896102 CAGGCCCA
1 CAGGCCCA
60896110 CACGCAAGCA
Statistics
Matches: 49, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
42 18 0.37
43 9 0.18
45 1 0.02
46 1 0.02
48 20 0.41
ACGTcount: A:0.23, C:0.44, G:0.31, T:0.02
Consensus pattern (42 bp):
CAGGCCCAGCGCAACCCAGTAGACCCAGCGCACCCAGCAGGC
Found at i:60896349 original size:5 final size:5
Alignment explanation
Indices: 60896341--60896370 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
60896331 TTACTTCAAT
60896341 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
60896371 AATAATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:60896779 original size:20 final size:20
Alignment explanation
Indices: 60896754--60896892 Score: 74
Period size: 20 Copynumber: 7.2 Consensus size: 20
60896744 CCAGTGTTTC
60896754 AAAAATTTTCGTGTTTTTAA
1 AAAAATTTTCGTGTTTTTAA
** *
60896774 AAAAATCTCCCGTG-TTTT-C
1 AAAAAT-TTTCGTGTTTTTAA
** *
60896793 AAAAATTCCCGT-ATTTT--
1 AAAAATTTTCGTGTTTTTAA
* * *
60896810 GAAAATTTTCTTGTTTTCAA
1 AAAAATTTTCGTGTTTTTAA
*
60896830 AAAAATTTTCGTGTTTTAAA
1 AAAAATTTTCGTGTTTTTAA
** * *
60896850 AAAAAAGTTC-TCGTATTTCA
1 AAAAATTTTCGT-GTTTTTAA
* *
60896870 AAAAATTGTCGTGTTTTCAA
1 AAAAATTTTCGTGTTTTTAA
60896890 AAA
1 AAA
60896893 TTGACCGTGT
Statistics
Matches: 89, Mismatches: 23, Indels: 14
0.71 0.18 0.11
Matches are distributed among these distances:
17 8 0.09
18 13 0.15
19 7 0.08
20 55 0.62
21 6 0.07
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (20 bp):
AAAAATTTTCGTGTTTTTAA
Found at i:60896815 original size:56 final size:54
Alignment explanation
Indices: 60896729--60896892 Score: 159
Period size: 56 Copynumber: 2.9 Consensus size: 54
60896719 CAGAAATCTT
* *
60896729 CGTGTTTTAAAAATTCCAGTGTTTCAAAAATTTTCGTGTTTTTAAAAAAATCTCC
1 CGTGTTTTAAAAATTCCAGTATTTCAAAAATTTTCGTGTTTTCAAAAAAAT-TCC
* ** * **
60896784 CGTGTTTTCAAAAATTCCCGTATTTTGAAAATTTTCTTGTTTTCAAAAAAATTTT
1 CGTGTTTT-AAAAATTCCAGTATTTCAAAAATTTTCGTGTTTTCAAAAAAATTCC
*
60896839 CGTGTTTTAAAAAAAAAGTTCTC-GTATTTCAAAAAATTGTCGTGTTTTCAAAAA
1 CGTGTTTT----AAAAA-TTC-CAGTATTTC-AAAAATTTTCGTGTTTTCAAAAA
60896893 TTGACCGTGT
Statistics
Matches: 89, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
55 17 0.19
56 37 0.42
58 5 0.06
59 9 0.10
60 21 0.24
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (54 bp):
CGTGTTTTAAAAATTCCAGTATTTCAAAAATTTTCGTGTTTTCAAAAAAATTCC
Found at i:60896863 original size:22 final size:21
Alignment explanation
Indices: 60896828--60896874 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
60896818 TCTTGTTTTC
* * *
60896828 AAAAAAATTTTCGTGTTTTAA
1 AAAAAAATTCTCGTATTTCAA
60896849 AAAAAAAGTTCTCGTATTTCAA
1 AAAAAAA-TTCTCGTATTTCAA
60896871 AAAA
1 AAAA
60896875 TTGTCGTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.34
Consensus pattern (21 bp):
AAAAAAATTCTCGTATTTCAA
Found at i:60897029 original size:18 final size:17
Alignment explanation
Indices: 60896661--60897033 Score: 234
Period size: 17 Copynumber: 21.1 Consensus size: 17
60896651 TTTAAAAAAA
*
60896661 TCGTGTTTC-AAAATTG
1 TCGTGTTTCAAAAATTT
*
60896677 TCGTGTTTTAAAAATTT
1 TCGTGTTTCAAAAATTT
* *
60896694 TCGCGTTTCTAAAATTT
1 TCGTGTTTCAAAAATTT
* * *
60896711 TCCTGTTTCAGAAATCT
1 TCGTGTTTCAAAAATTT
*
60896728 TCGTGTTTTAAAAA-TT
1 TCGTGTTTCAAAAATTT
*
60896744 CCAGTGTTTCAAAAATTT
1 TC-GTGTTTCAAAAATTT
* *
60896762 TCGTGTTTTTAAAAAAATCTC
1 TCGTG--TTT-CAAAAAT-TT
* *
60896783 CCGTGTTTTCAAAAATTC
1 TCGTG-TTTCAAAAATTT
* * **
60896801 CCGTATTTTGAAAATTT
1 TCGTGTTTCAAAAATTT
*
60896818 TCTTGTTTTCAAAAAAATTT
1 TCGTG-TTTC--AAAAATTT
* *
60896838 TCGTGTTTTAAAAAAAAAGTTC
1 TCGTG-TTT---CAAAAA-TTT
* *
60896860 TCGTATTTCAAAAAATTG
1 TCGTGTTTC-AAAAATTT
*
60896878 TCGTGTTTTCAAAAATTGA
1 TCGTG-TTTCAAAAATT-T
* *
60896897 CCGTGTTTC-AAAATTG
1 TCGTGTTTCAAAAATTT
*
60896913 TCGTGTTTTAAAAATTT
1 TCGTGTTTCAAAAATTT
*
60896930 TCGTGTTTCTAAAATTT
1 TCGTGTTTCAAAAATTT
*
60896947 TCGTATTTCAAAAATTT
1 TCGTGTTTCAAAAATTT
*
60896964 TCATGTTTTC-AAAATTT
1 TCGTG-TTTCAAAAATTT
* *
60896981 TGCGTGTTCCAAAAATCT
1 T-CGTGTTTCAAAAATTT
* *
60896999 TCGTGTTTTAAAAAATTC
1 TCGTG-TTTCAAAAATTT
60897017 TCGTGTTTC-AAAATTT
1 TCGTGTTTCAAAAATTT
60897033 T
1 T
60897034 TTTTTTTGGT
Statistics
Matches: 277, Mismatches: 58, Indels: 44
0.73 0.15 0.12
Matches are distributed among these distances:
16 24 0.09
17 131 0.47
18 56 0.20
19 22 0.08
20 25 0.09
21 13 0.05
22 6 0.02
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (17 bp):
TCGTGTTTCAAAAATTT
Found at i:60903105 original size:12 final size:11
Alignment explanation
Indices: 60903088--60903186 Score: 66
Period size: 11 Copynumber: 8.9 Consensus size: 11
60903078 TATGCCTAAA
60903088 AAAAAAAGAGAC
1 AAAAAAAGA-AC
60903100 -AAAAAA-AAC
1 AAAAAAAGAAC
*
60903109 AAAAAAAACAAC
1 -AAAAAAAGAAC
*
60903121 AAAAAAGGAAC
1 AAAAAAAGAAC
60903132 AAAACAAA-AAC
1 AAAA-AAAGAAC
*
60903143 AAAACAAA-AAA
1 AAAA-AAAGAAC
60903154 AGAAAAAAGAA-
1 A-AAAAAAGAAC
60903165 AAAACAAAGAA-
1 AAAA-AAAGAAC
60903176 AAGAAAAAGAA
1 AA-AAAAAGAA
60903187 AAATCAAGAT
Statistics
Matches: 75, Mismatches: 4, Indels: 17
0.78 0.04 0.18
Matches are distributed among these distances:
9 2 0.03
10 4 0.05
11 57 0.76
12 12 0.16
ACGTcount: A:0.82, C:0.09, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAC
Found at i:60903115 original size:11 final size:11
Alignment explanation
Indices: 60903085--60903189 Score: 70
Period size: 12 Copynumber: 8.9 Consensus size: 11
60903075 TATTATGCCT
*
60903085 AAAAAAAAAAG
1 AAAAAAAAAAC
60903096 AGACAAAAAAAAC
1 A-A-AAAAAAAAC
60903109 AAAAAAAACAAC
1 AAAAAAAA-AAC
**
60903121 AAAAAAGGAAC
1 AAAAAAAAAAC
*
60903132 AAAACAAAAAC
1 AAAAAAAAAAC
60903143 AAAACAAAAAA-
1 AAAA-AAAAAAC
60903154 AGAAAAAAGAAA-
1 A-AAAAAA-AAAC
*
60903166 AAACAAAGAAAAG
1 AAA-AAA-AAAAC
60903179 AAAAAGAAAAA
1 AAAAA-AAAAA
60903190 TCAAGATGAA
Statistics
Matches: 77, Mismatches: 7, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
11 28 0.36
12 35 0.45
13 14 0.18
ACGTcount: A:0.83, C:0.09, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:60903135 original size:19 final size:17
Alignment explanation
Indices: 60903087--60903180 Score: 74
Period size: 16 Copynumber: 5.6 Consensus size: 17
60903077 TTATGCCTAA
60903087 AAAAAAAAGAGACAAAA-
1 AAAAAAAAGA-ACAAAAC
60903104 AAAACAAAA-AA-AACAAC
1 AAAA-AAAAGAACAA-AAC
*
60903121 -AAAAAAGGAACAAAAC
1 AAAAAAAAGAACAAAAC
* *
60903137 AAAAACAA-AACAAAAA
1 AAAAAAAAGAACAAAAC
60903153 AAGAAAAAAGAA-AAAAC
1 AA-AAAAAAGAACAAAAC
*
60903170 AAAGAAAAGAA
1 AAAAAAAAGAA
60903181 AAAGAAAAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
15 5 0.08
16 28 0.45
17 23 0.37
18 6 0.10
ACGTcount: A:0.82, C:0.10, G:0.09, T:0.00
Consensus pattern (17 bp):
AAAAAAAAGAACAAAAC
Found at i:60903140 original size:27 final size:25
Alignment explanation
Indices: 60903102--60903183 Score: 80
Period size: 27 Copynumber: 3.2 Consensus size: 25
60903092 AAAGAGACAA
*
60903102 AAAAAACAAAAAAAACAACAAAAAAGG
1 AAAAAAC-AAAAAAA-AACAAAAAAAG
60903129 AACAAAACAAAAACAAAACAAAAAAAG
1 AA-AAAACAAAAA-AAAACAAAAAAAG
*
60903156 --AAAA-AAGAAAAAACAAAGAAAAG
1 AAAAAACAAAAAAAAACAAA-AAAAG
60903179 AAAAA
1 AAAAA
60903184 GAAAAATCAA
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
22 8 0.17
23 9 0.19
24 4 0.08
25 3 0.06
27 17 0.35
28 7 0.15
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (25 bp):
AAAAAACAAAAAAAAACAAAAAAAG
Found at i:60903141 original size:34 final size:33
Alignment explanation
Indices: 60903085--60903172 Score: 101
Period size: 33 Copynumber: 2.7 Consensus size: 33
60903075 TATTATGCCT
*
60903085 AAAA-AAAAAAGAGACAAA-AAAAACAAAA-AAA
1 AAAACAAAAAAGA-AAAAACAAAAACAAAACAAA
*
60903116 ACAACAAAAAAGGAACAAAACAAAAACAAAACAAA
1 AAAACAAAAAA-GAA-AAAACAAAAACAAAACAAA
*
60903151 AAAAGAAAAAAGAAAAAACAAA
1 AAAACAAAAAAGAAAAAACAAA
60903173 GAAAAGAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
31 3 0.06
32 7 0.15
33 13 0.27
34 13 0.27
35 12 0.25
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (33 bp):
AAAACAAAAAAGAAAAAACAAAAACAAAACAAA
Found at i:60903171 original size:22 final size:22
Alignment explanation
Indices: 60903143--60903189 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 22
60903133 AAACAAAAAC
60903143 AAAACAAA-AAAAGAAAAAAGAA
1 AAAACAAAGAAAAG-AAAAAGAA
60903165 AAAACAAAGAAAAGAAAAAGAA
1 AAAACAAAGAAAAGAAAAAGAA
60903187 AAA
1 AAA
60903190 TCAAGATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.85, C:0.04, G:0.11, T:0.00
Consensus pattern (22 bp):
AAAACAAAGAAAAGAAAAAGAA
Found at i:60904657 original size:78 final size:78
Alignment explanation
Indices: 60904490--60905125 Score: 855
Period size: 78 Copynumber: 8.2 Consensus size: 78
60904480 NNNNNNACAA
**
60904490 AGGTGAGTTGAGCCTCGGT--CATGCCGAGGTATTTCTTTTAAATTTC-CATTTTC-AAAATCAA
1 AGGTGAGTTGAGCCTCGGTCACATGCCGAGGTATTTCTTTTAAATTTCTGTTTTTCAAAAATCAA
* * *
60904551 CCCATACTGCAAG
66 CTCATATTGCGAG
* * * *
60904564 GGGTGAGTTGAGCCTCGGGTCTCATGCCGAGGTA-TTCTTTTATATTTATGTTTTTCAAAAATCA
1 AGGTGAGTTGAGCCTC-GGTCACATGCCGAGGTATTTCTTTTAAATTTCTGTTTTTCAAAAATCA
60904628 ACTCATATTGCGAG
65 ACTCATATTGCGAG
*
60904642 AGGTGAGTTGAGCCTCGGTCACATGCCGAGGTATTTCTTTTATATTTCTGTTTTTCAAAAATCAA
1 AGGTGAGTTGAGCCTCGGTCACATGCCGAGGTATTTCTTTTAAATTTCTGTTTTTCAAAAATCAA
60904707 CTCATATTGCGAG
66 CTCATATTGCGAG
* * * **
60904720 AGGTGAGTTGAGCCTCGGACACATGCTGAGGTATTTCGTTTAAATTTCTGTTCTTT-TTAAATCA
1 AGGTGAGTTGAGCCTCGGTCACATGCCGAGGTATTTCTTTTAAATTTCTGTT-TTTCAAAAATCA
60904784 ACTCATATTGCGAG
65 ACTCATATTGCGAG
** * **
60904798 AGGTGAGTTGAGCCTCGAACACATGCCGAGGTATTTCGTTTAAATTTCTGTTCTTT-TTAAATCA
1 AGGTGAGTTGAGCCTCGGTCACATGCCGAGGTATTTCTTTTAAATTTCTGTT-TTTCAAAAATCA
60904862 ACTCATATTGCGAG
65 ACTCATATTGCGAG
* *
60904876 AGGTGAGTTGAGCCTCGGTCACATGCCGAGGTATTTCTTTTTCAATTTCTATTTTTCAAAAATCA
1 AGGTGAGTTGAGCCTCGGTCACATGCCGAGGTATTTC-TTTTAAATTTCTGTTTTTCAAAAATCA
60904941 ACTCATATTGCGAG
65 ACTCATATTGCGAG
* * * *
60904955 AGGTGAGTTGAGCCTCGGACACATGCCGAAGTA--T-TTTTCAATTCCTGTTTTTCAAAAATCAA
1 AGGTGAGTTGAGCCTCGGTCACATGCCGAGGTATTTCTTTTAAATTTCTGTTTTTCAAAAATCAA
* *
60905017 CTCATACTGCAAG
66 CTCATATTGCGAG
* *
60905030 GGGTGAGTTGAGCCTCGGGTCTCATGCCGAGGTA-TTCTTTTCAAA-TTCTGTTTTTCAAAAATC
1 AGGTGAGTTGAGCCTC-GGTCACATGCCGAGGTATTTCTTTT-AAATTTCTGTTTTTCAAAAATC
60905093 AACTCATATTGCGAG
64 AACTCATATTGCGAG
*
60905108 AGGTGAGTTGAGCATCGG
1 AGGTGAGTTGAGCCTCGG
60905126 GTCGCACGTC
Statistics
Matches: 507, Mismatches: 42, Indels: 23
0.89 0.07 0.04
Matches are distributed among these distances:
74 15 0.03
75 55 0.11
76 26 0.05
77 37 0.07
78 306 0.60
79 68 0.13
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (78 bp):
AGGTGAGTTGAGCCTCGGTCACATGCCGAGGTATTTCTTTTAAATTTCTGTTTTTCAAAAATCAA
CTCATATTGCGAG
Found at i:60905370 original size:30 final size:30
Alignment explanation
Indices: 60905327--60905475 Score: 171
Period size: 30 Copynumber: 5.0 Consensus size: 30
60905317 AAAAAAATAA
*
60905327 AAAATTGCATTTTGACCCC-AAACTTTTCT
1 AAAATTACATTTTGACCCCAAAACTTTTCT
60905356 AAAATTTACATTTTGACCCCAAAAACTTTT-T
1 AAAA-TTACATTTTGACCCC-AAAACTTTTCT
*
60905387 AAAATTACATTTTGACCCCTAAAC-TTTCT
1 AAAATTACATTTTGACCCCAAAACTTTTCT
* *
60905416 CAAAATTACATTTTGACCCCTAAAC-TTCCT
1 -AAAATTACATTTTGACCCCAAAACTTTTCT
* * *
60905446 CAAAATTACGTTTCGGCCCCAAAACTTTTC
1 -AAAATTACATTTTGACCCCAAAACTTTTC
60905476 CTGCATTTGC
Statistics
Matches: 106, Mismatches: 8, Indels: 10
0.85 0.06 0.08
Matches are distributed among these distances:
28 3 0.03
29 9 0.08
30 78 0.74
31 8 0.08
32 8 0.08
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.36
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCAAAACTTTTCT
Found at i:60905838 original size:13 final size:14
Alignment explanation
Indices: 60905812--60905891 Score: 71
Period size: 13 Copynumber: 5.9 Consensus size: 14
60905802 GACCGAACGG
60905812 AGAAG-AAG-AAGA
1 AGAAGAAAGAAAGA
60905824 AGAAGAAA-AAAGA
1 AGAAGAAAGAAAGA
60905837 AGAAAGAAGAGAAAGAA
1 AG-AAGAA-AGAAAG-A
* *
60905854 AGATGGAAGAAA-A
1 AGAAGAAAGAAAGA
60905867 AGAAGAAAGAAAGA
1 AGAAGAAAGAAAGA
*
60905881 A-AAAAAAGAAA
1 AGAAGAAAGAAA
60905892 ATATTTTGTA
Statistics
Matches: 56, Mismatches: 5, Indels: 13
0.76 0.07 0.18
Matches are distributed among these distances:
12 5 0.09
13 28 0.50
14 7 0.12
15 6 0.11
16 7 0.12
17 3 0.05
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.01
Consensus pattern (14 bp):
AGAAGAAAGAAAGA
Found at i:60905845 original size:17 final size:16
Alignment explanation
Indices: 60905812--60905891 Score: 81
Period size: 17 Copynumber: 4.9 Consensus size: 16
60905802 GACCGAACGG
*
60905812 AGAAGAAGAAG-AAGA
1 AGAAAAAGAAGAAAGA
60905827 AGAAAAAAGAAGAAAGA
1 AG-AAAAAGAAGAAAGA
* **
60905844 AGAGAAAGAAAGATGGA
1 AGAAAAAG-AAGAAAGA
60905861 AGAAAAAGAAGAAAGAA
1 AGAAAAAGAAGAAAG-A
*
60905878 AGAAAAAAAAGAAA
1 AGAAAAAGAAGAAA
60905892 ATATTTTGTA
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
15 2 0.04
16 18 0.34
17 33 0.62
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.01
Consensus pattern (16 bp):
AGAAAAAGAAGAAAGA
Found at i:60905845 original size:20 final size:20
Alignment explanation
Indices: 60905814--60905892 Score: 74
Period size: 20 Copynumber: 4.0 Consensus size: 20
60905804 CCGAACGGAG
*
60905814 AAGAAG-AAGAAGAAGAAAA
1 AAGAAGAAAGAAAAAGAAAA
*
60905833 AAGAAGAAAG-AAGAGAAAGA
1 AAGAAGAAAGAAAAAGAAA-A
* * *
60905853 AAGATGGAAGAAAAAGAAGA
1 AAGAAGAAAGAAAAAGAAAA
60905873 AAGAAAGAAA-AAAAAGAAAA
1 AAG-AAGAAAGAAAAAGAAAA
60905893 TATTTTGTAA
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
19 12 0.26
20 25 0.53
21 10 0.21
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.01
Consensus pattern (20 bp):
AAGAAGAAAGAAAAAGAAAA
Found at i:60906041 original size:19 final size:19
Alignment explanation
Indices: 60906014--60906050 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
60906004 AGTAGCCCAA
*
60906014 AAAGAAAAAAAAGAAGAAC
1 AAAGAAAAAAAAAAAGAAC
*
60906033 AAAGCAAAAAAAAAAGAA
1 AAAGAAAAAAAAAAAGAA
60906051 AGTAGGCCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.81, C:0.05, G:0.14, T:0.00
Consensus pattern (19 bp):
AAAGAAAAAAAAAAAGAAC
Found at i:60906098 original size:24 final size:24
Alignment explanation
Indices: 60906066--60906136 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 24
60906056 GCCATTTTCA
60906066 GCAGGCCCAGCGCAGCCCAGTAGG
1 GCAGGCCCAGCGCAGCCCAGTAGG
*
60906090 GCAGGCCCAGCGCAGCCCAGCAGG
1 GCAGGCCCAGCGCAGCCCAGTAGG
*
60906114 CCAGGCCCAGCGCAGCCCAGTAG
1 GCAGGCCCAGCGCAGCCCAGTAG
60906137 ACCCAGCGCA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.21, C:0.41, G:0.35, T:0.03
Consensus pattern (24 bp):
GCAGGCCCAGCGCAGCCCAGTAGG
Found at i:60906112 original size:19 final size:19
Alignment explanation
Indices: 60906064--60906157 Score: 73
Period size: 24 Copynumber: 4.5 Consensus size: 19
60906054 AGGCCATTTT
60906064 CAGCAGGCCCAGCGCAGCC
1 CAGCAGGCCCAGCGCAGCC
60906083 CAGTAGGGCAGGCCCAGCGCAGCCC
1 C---A--GCAGGCCCAGCGCAG-CC
60906108 AGCAGGCCAGGCCCAGCGCAGCC
1 --CA-G-CAGGCCCAGCGCAGCC
* *
60906131 CAGTAGACCCAGCGCA-CC
1 CAGCAGGCCCAGCGCAGCC
60906149 CAGCAGGCC
1 CAGCAGGCC
60906158 AGGCCCACAC
Statistics
Matches: 62, Mismatches: 4, Indels: 19
0.73 0.05 0.22
Matches are distributed among these distances:
18 9 0.15
19 12 0.19
20 1 0.02
21 2 0.03
22 1 0.02
23 4 0.06
24 30 0.48
25 2 0.03
27 1 0.02
ACGTcount: A:0.22, C:0.44, G:0.32, T:0.02
Consensus pattern (19 bp):
CAGCAGGCCCAGCGCAGCC
Found at i:60906398 original size:5 final size:5
Alignment explanation
Indices: 60906390--60906414 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
60906380 TTACTTCAAT
60906390 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
60906415 AATAATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:60906819 original size:18 final size:17
Alignment explanation
Indices: 60906705--60907078 Score: 236
Period size: 17 Copynumber: 21.1 Consensus size: 17
60906695 TTTAAAAAAA
* *
60906705 TCGTG-TTTCAAAATTG
1 TCGTGTTTTAAAAATTT
60906721 TCGTGTTTTAAAAATTT
1 TCGTGTTTTAAAAATTT
*
60906738 TCGCGTTTCT-AAAATTT
1 TCGTGTTT-TAAAAATTT
* * * *
60906755 TCCTGTTTCAGAAATCT
1 TCGTGTTTTAAAAATTT
60906772 TCGTGTTTTAAAAA-TT
1 TCGTGTTTTAAAAATTT
* *
60906788 CCAGTGTTTCAAAAATTT
1 TC-GTGTTTTAAAAATTT
60906806 TCGTGTTTTTAAAAAAATTT
1 TCGTG-TTTT--AAAAATTT
*
60906826 CTCGTGTTTTCAAAAATTC
1 -TCGTGTTTT-AAAAATTT
* * *
60906845 CCGTATTTTGAAAATTT
1 TCGTGTTTTAAAAATTT
*
60906862 TCTTGTTTTCAAAAAAATTT
1 TCGTGTTTT---AAAAATTT
*
60906882 TCGTGTTTTAAAAAAAAAGTTC
1 TCGTGTTTT----AAAAA-TTT
* * *
60906904 TCGTATTTCAAAAAATTG
1 TCGTGTTT-TAAAAATTT
*
60906922 TCGTGTTTTCAAAAATTGA
1 TCGTGTTTT-AAAAATT-T
* * *
60906941 CCGTG-TTTCAAAATTG
1 TCGTGTTTTAAAAATTT
60906957 TCGTGTTTTAAAAATTT
1 TCGTGTTTTAAAAATTT
60906974 TCGTGTTTCT-AAAATTT
1 TCGTGTTT-TAAAAATTT
* * *
60906991 CCGTATTTCAAAAATTT
1 TCGTGTTTTAAAAATTT
* *
60907008 TCATGTTTTCAAAATTT
1 TCGTGTTTTAAAAATTT
** *
60907025 TGCGTGTTCCAAAAATCT
1 T-CGTGTTTTAAAAATTT
*
60907043 TCGTGTTTTAAAAAATTC
1 TCGTGTTTT-AAAAATTT
*
60907061 TCGTGTTTCAAAAATTT
1 TCGTGTTTTAAAAATTT
60907078 T
1 T
60907079 TTTTTTGGTG
Statistics
Matches: 276, Mismatches: 60, Indels: 43
0.73 0.16 0.11
Matches are distributed among these distances:
16 11 0.04
17 141 0.51
18 60 0.22
19 16 0.06
20 27 0.10
21 12 0.04
22 9 0.03
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (17 bp):
TCGTGTTTTAAAAATTT
Found at i:60906823 original size:20 final size:20
Alignment explanation
Indices: 60906798--60906936 Score: 92
Period size: 20 Copynumber: 7.2 Consensus size: 20
60906788 CCAGTGTTTC
60906798 AAAAATTTTCGTGTTTTTAA
1 AAAAATTTTCGTGTTTTTAA
*
60906818 AAAAATTTCTCGTG-TTTT-C
1 AAAAATTT-TCGTGTTTTTAA
** *
60906837 AAAAATTCCCGT-ATTTT--
1 AAAAATTTTCGTGTTTTTAA
* * *
60906854 GAAAATTTTCTTGTTTTCAA
1 AAAAATTTTCGTGTTTTTAA
*
60906874 AAAAATTTTCGTGTTTTAAA
1 AAAAATTTTCGTGTTTTTAA
** * *
60906894 AAAAAAGTTC-TCGTATTTCA
1 AAAAATTTTCGT-GTTTTTAA
* *
60906914 AAAAATTGTCGTGTTTTCAA
1 AAAAATTTTCGTGTTTTTAA
60906934 AAA
1 AAA
60906937 TTGACCGTGT
Statistics
Matches: 89, Mismatches: 23, Indels: 14
0.71 0.18 0.11
Matches are distributed among these distances:
17 8 0.09
18 10 0.11
19 8 0.09
20 57 0.64
21 6 0.07
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.43
Consensus pattern (20 bp):
AAAAATTTTCGTGTTTTTAA
Found at i:60906907 original size:22 final size:21
Alignment explanation
Indices: 60906872--60906918 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
60906862 TCTTGTTTTC
* * *
60906872 AAAAAAATTTTCGTGTTTTAA
1 AAAAAAATTCTCGTATTTCAA
60906893 AAAAAAAGTTCTCGTATTTCAA
1 AAAAAAA-TTCTCGTATTTCAA
60906915 AAAA
1 AAAA
60906919 TTGTCGTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.34
Consensus pattern (21 bp):
AAAAAAATTCTCGTATTTCAA
Found at i:60908092 original size:21 final size:21
Alignment explanation
Indices: 60908066--60908111 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
60908056 TCTTGGATGT
60908066 GGGAAA-TTAGGGATTTTAGGG
1 GGGAAAGTTAGGGA-TTTAGGG
*
60908087 GGGAAAGTTGGGGATTTAGGG
1 GGGAAAGTTAGGGATTTAGGG
60908108 GGGA
1 GGGA
60908112 GGGGGGAGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.26, C:0.00, G:0.50, T:0.24
Consensus pattern (21 bp):
GGGAAAGTTAGGGATTTAGGG
Found at i:60908845 original size:18 final size:19
Alignment explanation
Indices: 60908822--60908872 Score: 70
Period size: 18 Copynumber: 2.7 Consensus size: 19
60908812 AAAATATATA
60908822 TAATATTTT-TGTATTTTT-
1 TAATATTTTAT-TATTTTTG
60908840 TAATATTTTATTATTTTTG
1 TAATATTTTATTATTTTTG
*
60908859 TAATGTTTTATTAT
1 TAATATTTTATTAT
60908873 GGGTTTTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 16 0.53
19 14 0.47
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (19 bp):
TAATATTTTATTATTTTTG
Found at i:60908898 original size:13 final size:13
Alignment explanation
Indices: 60908880--60908904 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
60908870 TATGGGTTTT
60908880 ATAAAAAAATAAC
1 ATAAAAAAATAAC
60908893 ATAAAAAAATAA
1 ATAAAAAAATAA
60908905 AAAATTACCA
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:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (13 bp):
ATAAAAAAATAAC
Found at i:60908961 original size:28 final size:29
Alignment explanation
Indices: 60908909--60908979 Score: 119
Period size: 28 Copynumber: 2.5 Consensus size: 29
60908899 AAATAAAAAA
60908909 TTACCAAAATAT-TATAACTTTTTTTTTAT
1 TTACCAAAATATATATAAC-TTTTTTTTAT
60908938 TTACCAAAATATATATAA-TTTTTTTTAT
1 TTACCAAAATATATATAACTTTTTTTTAT
60908966 TTACCAAAATATAT
1 TTACCAAAATATAT
60908980 CAAAAAAAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
28 24 0.59
29 12 0.29
30 5 0.12
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (29 bp):
TTACCAAAATATATATAACTTTTTTTTAT
Found at i:60909001 original size:16 final size:17
Alignment explanation
Indices: 60908980--60909022 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
60908970 CAAAATATAT
*
60908980 CAAAAAAAGT-AAAAAA
1 CAAAAAAAATAAAAAAA
60908996 CAAAAAAAATAAAAAAA
1 CAAAAAAAATAAAAAAA
60909013 CAGAAAAAAA
1 CA-AAAAAAA
60909023 ACACACTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 9 0.38
17 8 0.33
18 7 0.29
ACGTcount: A:0.84, C:0.07, G:0.05, T:0.05
Consensus pattern (17 bp):
CAAAAAAAATAAAAAAA
Found at i:60909003 original size:17 final size:18
Alignment explanation
Indices: 60908981--60909022 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
60908971 AAAATATATC
60908981 AAAAAAAGT-AAAAAACA-
1 AAAAAAA-TAAAAAAACAG
60908998 AAAAAAATAAAAAAACAG
1 AAAAAAATAAAAAAACAG
60909016 AAAAAAA
1 AAAAAAA
60909023 ACACACTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.04
17 15 0.65
18 7 0.30
ACGTcount: A:0.86, C:0.05, G:0.05, T:0.05
Consensus pattern (18 bp):
AAAAAAATAAAAAAACAG
Found at i:60910438 original size:12 final size:12
Alignment explanation
Indices: 60910421--60910449 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
60910411 GTTTATATGG
60910421 ACGCCGTACCGA
1 ACGCCGTACCGA
60910433 ACGCCGTACCGA
1 ACGCCGTACCGA
60910445 ACGCC
1 ACGCC
60910450 AGAAATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.24, C:0.45, G:0.24, T:0.07
Consensus pattern (12 bp):
ACGCCGTACCGA
Found at i:60911363 original size:15 final size:14
Alignment explanation
Indices: 60911323--60911351 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
60911313 TTTTTGTATC
60911323 AATTTAATTATTCT
1 AATTTAATTATTCT
60911337 AATTTAATTATTCT
1 AATTTAATTATTCT
60911351 A
1 A
60911352 GTTTTAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTTAATTATTCT
Found at i:60913757 original size:18 final size:18
Alignment explanation
Indices: 60913731--60913768 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
60913721 ATCCCAATGA
* *
60913731 TCGCCACCACCTTCTTCT
1 TCGCAACCACATTCTTCT
60913749 TCGCAACCACATTCTTCT
1 TCGCAACCACATTCTTCT
60913767 TC
1 TC
60913769 ACCACCAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.45, G:0.05, T:0.34
Consensus pattern (18 bp):
TCGCAACCACATTCTTCT
Found at i:60913775 original size:18 final size:18
Alignment explanation
Indices: 60913734--60913775 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
60913724 CCAATGATCG
* *
60913734 CCACCACCTTCTTCTTCG
1 CCACCACATTCTTCTTCA
*
60913752 CAACCACATTCTTCTTCA
1 CCACCACATTCTTCTTCA
60913770 CCACCA
1 CCACCA
60913776 ACCATATCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.48, G:0.02, T:0.29
Consensus pattern (18 bp):
CCACCACATTCTTCTTCA
Found at i:60914522 original size:3 final size:3
Alignment explanation
Indices: 60914514--60914584 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
60914504 AGTAACATCT
60914514 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
60914562 TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
60914585 CTATAAAAAA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:60914974 original size:27 final size:27
Alignment explanation
Indices: 60914895--60914975 Score: 126
Period size: 27 Copynumber: 3.0 Consensus size: 27
60914885 TGGTTGGCAG
*
60914895 GACTGGTGCCGCCAACCTGGTTCCCTC
1 GACTGGTGCCGCCAACCTGCTTCCCTC
*
60914922 GACTGGTGCCGCCAACCTGCTTCCCTT
1 GACTGGTGCCGCCAACCTGCTTCCCTC
**
60914949 GTTTGGTGCCGCCAACCTGCTTCCCTC
1 GACTGGTGCCGCCAACCTGCTTCCCTC
60914976 CACCCAGGGA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.10, C:0.41, G:0.23, T:0.26
Consensus pattern (27 bp):
GACTGGTGCCGCCAACCTGCTTCCCTC
Found at i:60915071 original size:27 final size:29
Alignment explanation
Indices: 60915041--60915110 Score: 101
Period size: 28 Copynumber: 2.5 Consensus size: 29
60915031 TTAGTTTTTT
60915041 TATATATTTTGGTAAAT-AAAAAAA-TTA
1 TATATATTTTGGTAAATAAAAAAAAGTTA
*
60915068 TATATTTTTTGGTAAATAAAAAAAAGTTA
1 TATATATTTTGGTAAATAAAAAAAAGTTA
*
60915097 TA-ACATTTTGGTAA
1 TATATATTTTGGTAA
60915111 TTTTTTATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 16 0.42
28 17 0.45
29 5 0.13
ACGTcount: A:0.47, C:0.01, G:0.10, T:0.41
Consensus pattern (29 bp):
TATATATTTTGGTAAATAAAAAAAAGTTA
Found at i:60916860 original size:2 final size:2
Alignment explanation
Indices: 60916853--60916882 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
60916843 TCTTAAATTC
60916853 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60916883 TACATACTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60937888 original size:26 final size:26
Alignment explanation
Indices: 60937859--60937938 Score: 124
Period size: 26 Copynumber: 3.1 Consensus size: 26
60937849 TTATAAGTTT
60937859 ATAACTACTAAGTAATCCTATTGCTC
1 ATAACTACTAAGTAATCCTATTGCTC
* *
60937885 ATAACTACCAAATAATCCTATTGCTC
1 ATAACTACTAAGTAATCCTATTGCTC
* *
60937911 ATAACAACTAAGTAATCCTATTACTC
1 ATAACTACTAAGTAATCCTATTGCTC
60937937 AT
1 AT
60937939 CAAGCTAAGT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.39, C:0.24, G:0.05, T:0.33
Consensus pattern (26 bp):
ATAACTACTAAGTAATCCTATTGCTC
Found at i:60941157 original size:24 final size:24
Alignment explanation
Indices: 60941130--60941175 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
60941120 TATGAAGAAC
60941130 CTTAAATTTAAAAATGATTATAGG
1 CTTAAATTTAAAAATGATTATAGG
60941154 CTTAAATTTAAAAATGATTATA
1 CTTAAATTTAAAAATGATTATA
60941176 AGTGGACCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.48, C:0.04, G:0.09, T:0.39
Consensus pattern (24 bp):
CTTAAATTTAAAAATGATTATAGG
Found at i:60941877 original size:96 final size:96
Alignment explanation
Indices: 60941765--60941981 Score: 256
Period size: 96 Copynumber: 2.2 Consensus size: 96
60941755 TGTTTATTAT
* * * *
60941765 TTTTTAACAAAAAATCAATTAAATTAGGGTTTAAGGTTACTTGAGTAATTTAATTAAAAAATAGT
1 TTTTTAAGAAAAAATCAAATAAATTAGGGTTCAAGGTTACTTGAGTAAATTAATT-AAAAATAGT
*
60941830 TA-AAAATCAGATAATGGTTTAGAGTTAAGGG
65 TATAAAATCAGATAAGGGTTTAGAGTTAAGGG
* * * * * **
60941861 TTTTTAAGGAAAAATCAAATAAATTGGGGTTCAGGGTTACTTGAGTAAATTAATTATATATTTTT
1 TTTTTAAGAAAAAATCAAATAAATTAGGGTTCAAGGTTACTTGAGTAAATTAATTAAAAATAGTT
* * * *
60941926 ATAAAATTAGATTAGGGTTTAGTGTTTAGGG
66 ATAAAATCAGATAAGGGTTTAGAGTTAAGGG
*
60941957 TTTTTAAGTAAAAACTCAAATAAAT
1 TTTTTAAG-AAAAAATCAAATAAAT
60941982 AAGGATTTGG
Statistics
Matches: 101, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
95 7 0.07
96 80 0.79
97 14 0.14
ACGTcount: A:0.41, C:0.04, G:0.17, T:0.38
Consensus pattern (96 bp):
TTTTTAAGAAAAAATCAAATAAATTAGGGTTCAAGGTTACTTGAGTAAATTAATTAAAAATAGTT
ATAAAATCAGATAAGGGTTTAGAGTTAAGGG
Found at i:60945900 original size:18 final size:18
Alignment explanation
Indices: 60945874--60945916 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
60945864 GACTAGAAAA
* * *
60945874 AGGAAACATATAAGAGTT
1 AGGATACATAAAAGAGCT
*
60945892 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGAGCT
60945910 AGGATAC
1 AGGATAC
60945917 GCACCTGGCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.47, C:0.09, G:0.26, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGAGCT
Found at i:60947765 original size:12 final size:12
Alignment explanation
Indices: 60947748--60947804 Score: 59
Period size: 12 Copynumber: 5.0 Consensus size: 12
60947738 CTTTTAAATA
*
60947748 GAAATTTGAGTG
1 GAAATTTGAGAG
60947760 GAAA-TTGAGAG
1 GAAATTTGAGAG
60947771 GAAATTTGAGA-
1 GAAATTTGAGAG
*
60947782 GAATATTAGAGA-
1 GAA-ATTTGAGAG
60947794 GAAA-TTGAGAG
1 GAAATTTGAGAG
60947805 AAAGGATTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
10 5 0.13
11 14 0.36
12 20 0.51
ACGTcount: A:0.44, C:0.00, G:0.32, T:0.25
Consensus pattern (12 bp):
GAAATTTGAGAG
Found at i:60947773 original size:11 final size:11
Alignment explanation
Indices: 60947748--60947804 Score: 55
Period size: 11 Copynumber: 5.0 Consensus size: 11
60947738 CTTTTAAATA
*
60947748 GAAATTTGAGTG
1 GAAA-TTGAGAG
60947760 GAAATTGAGAG
1 GAAATTGAGAG
60947771 GAAATTTGAGA-
1 GAAA-TTGAGAG
60947782 GAATATT-AGAG
1 GAA-ATTGAGAG
60947793 AGAAATTGAGAG
1 -GAAATTGAGAG
60947805 AAAGGATTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
10 3 0.08
11 18 0.46
12 18 0.46
ACGTcount: A:0.44, C:0.00, G:0.32, T:0.25
Consensus pattern (11 bp):
GAAATTGAGAG
Found at i:60947797 original size:23 final size:21
Alignment explanation
Indices: 60947747--60947807 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 21
60947737 TCTTTTAAAT
*
60947747 AGAAATTTGAGTGGAAATTGAG
1 AGAAATTTGAG-AGAAATTGAG
60947769 AGGAAATTTGAGAGAATATTAGAG
1 A-GAAATTTGAGAGAA-ATT-GAG
60947793 AGAAA-TTGAGAGAAA
1 AGAAATTTGAGAGAAA
60947808 GGATTTAGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
21 1 0.03
22 13 0.37
23 17 0.49
24 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.30, T:0.23
Consensus pattern (21 bp):
AGAAATTTGAGAGAAATTGAG
Found at i:60947803 original size:10 final size:10
Alignment explanation
Indices: 60947760--60947807 Score: 60
Period size: 12 Copynumber: 4.4 Consensus size: 10
60947750 AATTTGAGTG
60947760 GAAATTGAGA
1 GAAATTGAGA
60947770 GGAAATTTGAGA
1 -GAAA-TTGAGA
60947782 GAATATTAGAGA
1 GAA-ATT-GAGA
60947794 GAAATTGAGA
1 GAAATTGAGA
60947804 GAAA
1 GAAA
60947808 GGATTTAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
10 8 0.24
11 12 0.35
12 14 0.41
ACGTcount: A:0.50, C:0.00, G:0.29, T:0.21
Consensus pattern (10 bp):
GAAATTGAGA
Found at i:60948703 original size:22 final size:21
Alignment explanation
Indices: 60948678--60948732 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 21
60948668 AATAAGAATA
60948678 ATAAAAACATATTTAAAAATT-T
1 ATAAAAACATA-TT-AAAATTCT
60948700 ATAAAAACATATTAAAATTCT
1 ATAAAAACATATTAAAATTCT
60948721 ATAAAAATCATA
1 ATAAAAA-CATA
60948733 AAAAGTATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 6 0.19
21 10 0.32
22 15 0.48
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAAAAACATATTAAAATTCT
Found at i:60949237 original size:28 final size:27
Alignment explanation
Indices: 60949199--60949436 Score: 93
Period size: 28 Copynumber: 8.6 Consensus size: 27
60949189 TTTTATGATT
*
60949199 TTTTAGTATTTTTATAAGTTTATATCAA
1 TTTTAATATTTTTATAAGTTTATAT-AA
* * *
60949227 TTTTAATATTTTTATAATTTTTTATAGT
1 TTTTAATATTTTTATAAGTTTATATA-A
*
60949255 TTTTATTATTTTTA-AAGAATTCTA-ATAAA
1 TTTTAATATTTTTATAAG--TT-TATAT-AA
* * *
60949284 TTTTTTAATA-TTTAAT-ATTTTAAATAAA
1 --TTTTAATATTTTTATAAGTTTATAT-AA
* * *
60949312 TTTTATTAATTTTAT-AGCTTT-TATTAT
1 TTTTAATATTTTTATAAG-TTTATA-TAA
*
60949339 TTATTAGA-ATTTTTAT-ATTTTA-AT-A
1 TT-TTA-ATATTTTTATAAGTTTATATAA
* * *
60949364 TTTTTATAATATTTATAAGTTTTTATATTA
1 TTTTAAT-ATTTTTATAAG--TTTATATAA
*
60949394 TTTT-ATAATTTTAATAAGTTTATATGAA
1 TTTTAAT-ATTTTTATAAGTTTATAT-AA
60949422 TTTTAATATTTTTAT
1 TTTTAATATTTTTAT
60949437 TTTTATAATA
Statistics
Matches: 159, Mismatches: 27, Indels: 48
0.68 0.12 0.21
Matches are distributed among these distances:
23 1 0.01
24 2 0.01
25 9 0.06
26 9 0.06
27 26 0.16
28 73 0.46
29 20 0.13
30 12 0.08
31 7 0.04
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (27 bp):
TTTTAATATTTTTATAAGTTTATATAA
Found at i:60949246 original size:9 final size:9
Alignment explanation
Indices: 60949188--60949436 Score: 109
Period size: 10 Copynumber: 26.8 Consensus size: 9
60949178 CCAGTTCAAG
*
60949188 TTTTTATGA
1 TTTTTATAA
60949197 TTTTT-TAGTA
1 TTTTTATA--A
60949207 TTTTTATAA
1 TTTTTATAA
*
60949216 GTTTATATCAA
1 -TTTTTAT-AA
*
60949227 TTTTAAT-A
1 TTTTTATAA
60949235 TTTTTATAA
1 TTTTTATAA
*
60949244 TTTTTTATAG
1 -TTTTTATAA
*
60949254 TTTTTATTA
1 TTTTTATAA
*
60949263 TTTTTAAAGAA
1 TTTTT--ATAA
* *
60949274 TTCTAATAAA
1 TTTTTAT-AA
60949284 TTTTT-TAA
1 TTTTTATAA
*
60949292 TATTTA-ATA
1 TTTTTATA-A
*
60949301 TTTTAAATAA
1 TTTT-TATAA
*
60949311 ATTTTATTAA
1 TTTTTA-TAA
*
60949321 -TTTTATAG
1 TTTTTATAA
* *
60949329 CTTTTATTA
1 TTTTTATAA
*
60949338 TTTATTAGAA
1 TTT-TTATAA
60949348 TTTTTAT-A
1 TTTTTATAA
*
60949356 TTTTAAT-A
1 TTTTTATAA
60949364 TTTTTATAA
1 TTTTTATAA
*
60949373 TATTTATAA
1 TTTTTATAA
*
60949382 GTTTTTATAT
1 -TTTTTATAA
60949392 TATTTTATAA
1 T-TTTTATAA
*
60949402 TTTTAATAA
1 TTTTTATAA
*
60949411 GTTTATATGAA
1 -TTTTTAT-AA
*
60949422 TTTTAAT-A
1 TTTTTATAA
60949430 TTTTTAT
1 TTTTTAT
60949437 TTTTATAATA
Statistics
Matches: 179, Mismatches: 39, Indels: 45
0.68 0.15 0.17
Matches are distributed among these distances:
8 38 0.21
9 59 0.33
10 70 0.39
11 12 0.07
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:60949268 original size:37 final size:36
Alignment explanation
Indices: 60949207--60949405 Score: 92
Period size: 37 Copynumber: 5.4 Consensus size: 36
60949197 TTTTTTAGTA
* * *
60949207 TTTTTATAAGTTTATATCAATTTTAATATTTTTATAAT
1 TTTTTAT-AGTTTTTATTATTTTTAA-ATTTTTATAAT
* *
60949245 TTTTTATAGTTTTTATTATTTTTAAAGAATTCTAATAAAT
1 TTTTTATAGTTTTTATTATTTTT--A-AATTTTTAT-AAT
* *
60949285 TTTTTA-A-TATTTAATA-TTTTAAATAAATTTTATTAA-
1 TTTTTATAGTTTTTATTATTTTTAAAT---TTTTA-TAAT
*
60949321 -TTTTATAGCTTTTATTATTTATTAGAATTTTTAT-A-
1 TTTTTATAGTTTTTATTATTT-TTA-AATTTTTATAAT
* * *
60949356 TTTTAATA-TTTTTATAATATTTATAAGTTTTTAT-AT
1 TTTTTATAGTTTTTAT--TATTTTTAAATTTTTATAAT
*
60949392 TATTTTATAATTTT
1 T-TTTTATAGTTTT
60949406 AATAAGTTTA
Statistics
Matches: 125, Mismatches: 17, Indels: 38
0.69 0.09 0.21
Matches are distributed among these distances:
34 3 0.02
35 22 0.18
36 11 0.09
37 44 0.35
38 21 0.17
39 11 0.09
40 13 0.10
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (36 bp):
TTTTTATAGTTTTTATTATTTTTAAATTTTTATAAT
Found at i:60949375 original size:11 final size:10
Alignment explanation
Indices: 60949359--60949450 Score: 51
Period size: 10 Copynumber: 9.9 Consensus size: 10
60949349 TTTTATATTT
60949359 TAATATTTTTA
1 TAATA-TTTTA
60949370 TAATA-TTTA
1 TAATATTTTA
60949379 TAAGT-TTTTA
1 TAA-TATTTTA
*
60949389 TATTATTTTA
1 TAATATTTTA
*
60949399 TAAT-TTTAA
1 TAATATTTTA
*
60949408 T-A-AGTTTA
1 TAATATTTTA
*
60949416 T-ATGAATTT-
1 TAAT-ATTTTA
60949425 TAATATTTT-
1 TAATATTTTA
60949434 T-AT-TTTTA
1 TAATATTTTA
60949442 TAATATTTT
1 TAATATTTT
60949451 TTTGAATTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 21
0.70 0.08 0.23
Matches are distributed among these distances:
7 4 0.06
8 9 0.14
9 21 0.33
10 25 0.39
11 5 0.08
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (10 bp):
TAATATTTTA
Found at i:60949398 original size:20 final size:18
Alignment explanation
Indices: 60949346--60949449 Score: 71
Period size: 19 Copynumber: 5.9 Consensus size: 18
60949336 TATTTATTAG
60949346 AATTTTTAT-AT-TTTA-
1 AATTTTTATAATATTTAT
60949361 ATATTTTTATAATATTTAT
1 A-ATTTTTATAATATTTAT
*
60949380 AAGTTTTTATATTATTTTAT
1 AA-TTTTTATAATA-TTTAT
*
60949400 AATTTTAATAAGT-TTATAT
1 AATTTTTATAA-TATT-TAT
60949419 GAA--TTT-TAATATTT-T
1 -AATTTTTATAATATTTAT
*
60949434 TATTTTTATAATATTT
1 AATTTTTATAATATTT
60949450 TTTTGAATTT
Statistics
Matches: 71, Mismatches: 5, Indels: 24
0.71 0.05 0.24
Matches are distributed among these distances:
14 1 0.01
15 2 0.03
16 13 0.18
17 15 0.21
18 9 0.13
19 21 0.30
20 10 0.14
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
AATTTTTATAATATTTAT
Found at i:60949406 original size:37 final size:36
Alignment explanation
Indices: 60949241--60949449 Score: 119
Period size: 37 Copynumber: 5.7 Consensus size: 36
60949231 AATATTTTTA
* * * *
60949241 TAATTTTTTATAGTTTTTATTATTTTTA-AAGAATTC
1 TAATATTTTATA-TTTTTATAATATTTATAAGAATTT
* * * *
60949277 TAATAAATTTTTTAATATT-TAATATTT-TAAATAAATTT
1 TAAT--ATTTTATATTTTTATAATATTTAT-AA-GAATTT
* * *
60949315 TATTAATTTTATAGCTTTTAT--TATTTATTAGAATTT
1 TAAT-ATTTTATA-TTTTTATAATATTTATAAGAATTT
* *
60949351 TTATATTTTAATATTTTTATAATATTTATAAG-TTTT
1 TAATATTTT-ATATTTTTATAATATTTATAAGAATTT
* * *
60949387 TATATTATTTTATAATTTTAATAA-GTTTATATGAATTT
1 TA-A-TATTTTAT-ATTTTTATAATATTTATAAGAATTT
60949425 TAATATTTT-TATTTTTATAATATTT
1 TAATATTTTATATTTTTATAATATTT
60949450 TTTTGAATTT
Statistics
Matches: 131, Mismatches: 26, Indels: 33
0.69 0.14 0.17
Matches are distributed among these distances:
34 9 0.07
35 15 0.11
36 30 0.23
37 39 0.30
38 37 0.28
39 1 0.01
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (36 bp):
TAATATTTTATATTTTTATAATATTTATAAGAATTT
Found at i:60949464 original size:19 final size:20
Alignment explanation
Indices: 60949402--60949478 Score: 65
Period size: 20 Copynumber: 4.0 Consensus size: 20
60949392 TATTTTATAA
**
60949402 TTTTAATAAGTTTATATGAA-
1 TTTTAATATTTTTAT-TGAAT
60949422 TTTTAATATTTTTATT---T
1 TTTTAATATTTTTATTGAAT
*
60949439 TTATAATATTTTT-TTGAAT
1 TTTTAATATTTTTATTGAAT
60949458 TTTTAATCATTTTTATGTGAA
1 TTTTAAT-ATTTTTAT-TGAA
60949479 AAATATTAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
16 2 0.04
17 12 0.26
19 8 0.17
20 19 0.41
21 1 0.02
22 4 0.09
ACGTcount: A:0.31, C:0.01, G:0.06, T:0.61
Consensus pattern (20 bp):
TTTTAATATTTTTATTGAAT
Found at i:60949742 original size:26 final size:26
Alignment explanation
Indices: 60949713--60949774 Score: 97
Period size: 26 Copynumber: 2.3 Consensus size: 26
60949703 CTTTCCACAA
*
60949713 TTAAAATAAATAATATTAGTTATCAT
1 TTAAAATAAATAATATTAGTCATCAT
60949739 TTAAAATAAATAATATTAGTCATCAT
1 TTAAAATAAATAATATTAGTCATCAT
60949765 TCTAATAATA
1 T-TAA-AATA
60949775 TTAGTTAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
26 26 0.79
27 3 0.09
28 4 0.12
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.40
Consensus pattern (26 bp):
TTAAAATAAATAATATTAGTCATCAT
Found at i:60952927 original size:13 final size:14
Alignment explanation
Indices: 60952903--60952935 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
60952893 GACACCGGAT
60952903 TATTTTTAAATAAG
1 TATTTTTAAATAAG
60952917 TATTTTT-AATAAG
1 TATTTTTAAATAAG
60952930 T-TTTTT
1 TATTTTT
60952936 TTATTGGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.26
13 7 0.37
14 7 0.37
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (14 bp):
TATTTTTAAATAAG
Found at i:60954589 original size:2 final size:2
Alignment explanation
Indices: 60954584--60954620 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
60954574 TATCAAATTA
*
60954584 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
60954621 CTTCCTTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:60958000 original size:16 final size:17
Alignment explanation
Indices: 60957957--60958001 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
60957947 TAATAAATCT
**
60957957 TTAAAAAATCCATAAAA
1 TTAAAAAATTAATAAAA
*
60957974 TTAATAAATTAATAAAA
1 TTAAAAAATTAATAAAA
60957991 -TAAAAAATTAA
1 TTAAAAAATTAA
60958002 ATTGAAAACA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 10 0.42
17 14 0.58
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (17 bp):
TTAAAAAATTAATAAAA
Found at i:60961924 original size:26 final size:27
Alignment explanation
Indices: 60961871--60961927 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
60961861 TATGGTGGAC
60961871 AAAAAAAAATCAAATACCAAGTTAGGG
1 AAAAAAAAATCAAATACCAAGTTAGGG
*
60961898 AAAAAAAACAT-AAGTACCAAGTT-GGG
1 AAAAAAAA-ATCAAATACCAAGTTAGGG
60961924 AAAA
1 AAAA
60961928 TGTGTCAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 7 0.25
27 19 0.68
28 2 0.07
ACGTcount: A:0.60, C:0.11, G:0.16, T:0.14
Consensus pattern (27 bp):
AAAAAAAAATCAAATACCAAGTTAGGG
Found at i:60962428 original size:29 final size:30
Alignment explanation
Indices: 60962395--60962457 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
60962385 ACTACCCAAA
* *
60962395 AAACAACTTTAACCCAAATCC-ACTATCCT
1 AAACAACTTTAACCCAAACCCAACTAGCCT
*
60962424 AAACAGCTTTAACCCAAACCCAACTAGCCT
1 AAACAACTTTAACCCAAACCCAACTAGCCT
60962454 AAAC
1 AAAC
60962458 CCAAAACCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 19 0.63
30 11 0.37
ACGTcount: A:0.43, C:0.35, G:0.03, T:0.19
Consensus pattern (30 bp):
AAACAACTTTAACCCAAACCCAACTAGCCT
Found at i:60974202 original size:44 final size:44
Alignment explanation
Indices: 60974136--60974235 Score: 105
Period size: 44 Copynumber: 2.3 Consensus size: 44
60974126 CCTGCGTCAA
* *
60974136 CAGT-GAAGTAGATTGAAGATTACAAGTCCTATGTCCCTGACCAG
1 CAGTGGAA-TAGATTGAAGATTACAAGTCCTATCTCCCTAACCAG
* * *
60974180 CAGTGGAATAGATTGGAA-ATTACGAGTCTTATCTCCCTAAGCAG
1 CAGTGGAATAGATT-GAAGATTACAAGTCCTATCTCCCTAACCAG
* *
60974224 TAGTGGAGTAGA
1 CAGTGGAATAGA
60974236 CAGAAGAAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
44 41 0.87
45 6 0.13
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (44 bp):
CAGTGGAATAGATTGAAGATTACAAGTCCTATCTCCCTAACCAG
Found at i:60974364 original size:44 final size:44
Alignment explanation
Indices: 60974247--60974653 Score: 194
Period size: 44 Copynumber: 8.8 Consensus size: 44
60974237 AGAAGAAATC
* * * *
60974247 AATCCTATCTCTCTGAGGTCACAGTGGGGCAGACTGAAGTTAGA
1 AATCCTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGTTAGA
* * * *
60974291 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTT-GT
1 AATCCTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAG-TTAGA
* * ***
60974335 AATCCTATCTCCCTGAGGTTATAGTGGAGCGGATT-AAAACA-A
1 AATCCTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGTTAGA
* * * **
60974377 AGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGA
1 A--ATCCTATCTCCCTGAGGTTACAGT---G--GA--G---CAGATTGAAGTTAGA
* * * * * *
60974433 AATCTTATCTCCCTGAGATTACAGCGGAGAAGATTGAAGCTAGT
1 AATCCTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGTTAGA
* * ***
60974477 AATCCTATCTCCCTGAGATTACAGTGGAACAGATT-AAAACA-A
1 AATCCTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGTTAGA
* * * **
60974519 AGGATCTTATCTCTCTGAAGTTACAGTAAAGTAGATCGCATCAGATTGAAGCCAGA
1 A--ATCCTATCTCCCTGAGGTTACAGT---G--GA--G---CAGATTGAAGTTAGA
* * * * *
60974575 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGT
1 AATCCTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGTTAGA
*
60974619 AATCCTATCTCCCTGAGATTACAGTGGAGCAGATT
1 AATCCTATCTCCCTGAGGTTACAGTGGAGCAGATT
60974654 AAAACAAATG
Statistics
Matches: 279, Mismatches: 54, Indels: 60
0.71 0.14 0.15
Matches are distributed among these distances:
42 2 0.01
43 5 0.02
44 192 0.69
45 2 0.01
47 4 0.01
49 8 0.03
51 3 0.01
54 51 0.18
55 8 0.03
56 4 0.01
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (44 bp):
AATCCTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGTTAGA
Found at i:60974641 original size:98 final size:98
Alignment explanation
Indices: 60974463--60974643 Score: 231
Period size: 98 Copynumber: 1.8 Consensus size: 98
60974453 ACAGCGGAGA
* * * * *
60974463 AGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAACAGATTAAAACAAAGGATCTTA
1 AGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAACAGATTAAAACAAAGAATCCTA
*
60974528 TCTCTCTGAAGTTACAGTAAAGTAGATCGCATC
66 TCTCCCTGAAGTTACAGTAAAGTAGATCGCATC
* * * * *
60974561 AGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGC-TAGTAATCCT
1 AGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAACAGATTAAAACAAAG-AATCCT
60974625 ATCTCCCTG-AGATTACAGT
65 ATCTCCCTGAAG-TTACAGT
60974644 GGAGCAGATT
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
97 4 0.06
98 66 0.94
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (98 bp):
AGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAACAGATTAAAACAAAGAATCCTA
TCTCCCTGAAGTTACAGTAAAGTAGATCGCATC
Found at i:60974672 original size:44 final size:44
Alignment explanation
Indices: 60974575--60974696 Score: 138
Period size: 44 Copynumber: 2.8 Consensus size: 44
60974565 TGAAGCCAGA
* * * * *
60974575 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAACAAAT
*
60974619 AATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAACAAAT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAACAAAT
* * * *
60974663 GATCTTATCTCTCTGA-AGTTACAGTAGAGTAGAT
1 AATCTTATCTCCCTGAGA-TTACAGTGGAGCAGAT
60974697 CGCATCAGAT
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
43 1 0.02
44 65 0.98
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAACAAAT
Found at i:60974726 original size:98 final size:98
Alignment explanation
Indices: 60974604--60974812 Score: 355
Period size: 98 Copynumber: 2.1 Consensus size: 98
60974594 TACAGCGGAG
*
60974604 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAACAAATGATCTT
1 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAACAAAGGATCTT
*
60974669 ATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
66 ATCTCTCTGAAGTTACAGCAGAGTAGATCGCAT
* * * *
60974702 CAGATTGAAGCTAGTAATCCTATCTCCTTGAGATTATAGTGGAGCGGATTAAAATAAAGGATCTT
1 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAACAAAGGATCTT
*
60974767 ATCTCTTTGAAGTTACAGCAGAGTAGATCGCAT
66 ATCTCTCTGAAGTTACAGCAGAGTAGATCGCAT
60974800 CAGATTGAAGCTA
1 CAGATTGAAGCTA
60974813 CAACAACAAA
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 104 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (98 bp):
CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAACAAAGGATCTT
ATCTCTCTGAAGTTACAGCAGAGTAGATCGCAT
Found at i:60974784 original size:142 final size:142
Alignment explanation
Indices: 60974288--60974751 Score: 793
Period size: 142 Copynumber: 3.3 Consensus size: 142
60974278 GACTGAAGTT
* *
60974288 AGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTTGTAATCCTATCTCCCTGAGG
1 AGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
* *
60974353 TTATAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
66 TTACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
60974418 CAGATTGAAGCC
131 CAGATTGAAGCC
*
60974430 AGAAATCTTATCTCCCTGAGATTACAGCGGAGAAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
1 AGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
* *
60974495 TTACAGTGGAACAGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAAAGTAGATCGCAT
66 TTACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
60974560 CAGATTGAAGCC
131 CAGATTGAAGCC
60974572 AGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
1 AGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
*
60974637 TTACAGTGGAGCAGATTAAAACAAATGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
66 TTACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
*
60974702 CAGATTGAAGCT
131 CAGATTGAAGCC
* * * * * *
60974714 AGTAATCCTATCTCCTTGAGATTATAGTGGAGCGGATT
1 AGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATT
60974752 AAAATAAAGG
Statistics
Matches: 304, Mismatches: 18, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
142 304 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (142 bp):
AGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA
TTACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
CAGATTGAAGCC
Found at i:60975214 original size:30 final size:29
Alignment explanation
Indices: 60975178--60975239 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
60975168 CTAACGACCT
60975178 AAATCCACTACCCAAAAACAACTTTAACCC
1 AAATCCACTACCC-AAAACAACTTTAACCC
* * *
60975208 AAATCCACTATCCTAAACAGCTTTAACCC
1 AAATCCACTACCCAAAACAACTTTAACCC
60975237 AAA
1 AAA
60975240 CCCAACTAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 17 0.59
30 12 0.41
ACGTcount: A:0.45, C:0.34, G:0.02, T:0.19
Consensus pattern (29 bp):
AAATCCACTACCCAAAACAACTTTAACCC
Found at i:60975232 original size:29 final size:29
Alignment explanation
Indices: 60975178--60975255 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 29
60975168 CTAACGACCT
*
60975178 AAATCCACTACCCAAAAACAACTTTAACCC
1 AAATCCACTACCC-TAAACAACTTTAACCC
* *
60975208 AAATCCACTATCCTAAACAGCTTTAACCC
1 AAATCCACTACCCTAAACAACTTTAACCC
* *
60975237 AAACCCAACTAGCCTAAAC
1 AAATCC-ACTACCCTAAAC
60975256 CCAAAACCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 19 0.45
30 23 0.55
ACGTcount: A:0.44, C:0.36, G:0.03, T:0.18
Consensus pattern (29 bp):
AAATCCACTACCCTAAACAACTTTAACCC
Found at i:60975255 original size:30 final size:29
Alignment explanation
Indices: 60975193--60975255 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
60975183 CACTACCCAA
* *
60975193 AAACAACTTTAACCCAAATCCACTATCCT
1 AAACAACTTTAACCCAAACCCACTAGCCT
*
60975222 AAACAGCTTTAACCCAAACCCAACTAGCCT
1 AAACAACTTTAACCCAAACCC-ACTAGCCT
60975252 AAAC
1 AAAC
60975256 CCAAAACCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 19 0.63
30 11 0.37
ACGTcount: A:0.43, C:0.35, G:0.03, T:0.19
Consensus pattern (29 bp):
AAACAACTTTAACCCAAACCCACTAGCCT
Found at i:60978404 original size:7 final size:7
Alignment explanation
Indices: 60978392--60978417 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
60978382 TTAAATTAAA
60978392 TTAAAAT
1 TTAAAAT
60978399 TTAAAAT
1 TTAAAAT
60978406 TTAAAAT
1 TTAAAAT
60978413 TTAAA
1 TTAAA
60978418 CTCTAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
TTAAAAT
Found at i:60978424 original size:14 final size:14
Alignment explanation
Indices: 60978389--60978426 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
60978379 AAATTAAATT
60978389 AAAT-TAAAATTTA
1 AAATCTAAAATTTA
*
60978402 AAATTTAAAATTTA
1 AAATCTAAAATTTA
*
60978416 AACTCTAAAAT
1 AAATCTAAAAT
60978427 AAACTAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATCTAAAATTTA
Found at i:60981522 original size:41 final size:41
Alignment explanation
Indices: 60981473--60981581 Score: 164
Period size: 41 Copynumber: 2.6 Consensus size: 41
60981463 GACTTTAAGT
*
60981473 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGCTATAAAC
* *
60981514 CTAGCAGGCTACGTGCCGGTGATCTAAATCAGGCTATAAGC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGCTATAAAC
* *
60981555 CTAGCAGGCTAAGTGCCGTTGAATCTG
1 CTAGCAGGCTACGTGCCGGTG-ATCTG
60981582 TTTAAATTAA
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
41 57 0.93
42 4 0.07
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.24
Consensus pattern (41 bp):
CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGCTATAAAC
Found at i:60989257 original size:51 final size:51
Alignment explanation
Indices: 60989181--60989293 Score: 190
Period size: 51 Copynumber: 2.2 Consensus size: 51
60989171 CTAATCAGTA
* *
60989181 ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAGTGATAAGTG
1 ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAATGACAAGTG
* *
60989232 ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAATGACGAGTG
1 ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAATGACAAGTG
60989283 ACAAGTGATAA
1 ACAAGTGATAA
60989294 ATGTGATCCA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (51 bp):
ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAATGACAAGTG
Found at i:60989416 original size:47 final size:48
Alignment explanation
Indices: 60989304--60989442 Score: 199
Period size: 48 Copynumber: 2.9 Consensus size: 48
60989294 ATGTGATCCA
*
60989304 TGTAAGACCATATCTGGGATATGGCATCGATGTGATATGTGATTTCCG
1 TGTAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGATTTCCG
*
60989352 GGTAAGACCATATCTGGGATATGGCATCGGTGTGATATGTG-TTTCCG
1 TGTAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGATTTCCG
* * * *
60989399 TGTAAGATCATAGCTGGGCTATGGCTTCGGTGTGTGATATGTGA
1 TGTAAGACCATATCTGGGATATGGCATC-G-GTGTGATATGTGA
60989443 CGATGTGCAG
Statistics
Matches: 81, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
47 29 0.36
48 40 0.49
49 12 0.15
ACGTcount: A:0.22, C:0.14, G:0.31, T:0.33
Consensus pattern (48 bp):
TGTAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGATTTCCG
Found at i:60995247 original size:68 final size:68
Alignment explanation
Indices: 60995133--60995268 Score: 218
Period size: 68 Copynumber: 2.0 Consensus size: 68
60995123 ATAAAACTTT
* * * *
60995133 CCCTTGTAAGCTTAGTAGTAAATCCAAGTAGCTTATTTGAGTTTTACTTAAAAATGTACTCTAAA
1 CCCTCGTAAGCTTAGCAGTAAAACCAAGTAACTTATTTGAGTTTTACTTAAAAATGTACTCTAAA
60995198 TAG
66 TAG
* *
60995201 CCCTCGTAAGCTTAGCCGTAAAACCAAGTAACTTGTTTGAGTTTTACTTAAAAATGTACTCTAAA
1 CCCTCGTAAGCTTAGCAGTAAAACCAAGTAACTTATTTGAGTTTTACTTAAAAATGTACTCTAAA
60995266 TAG
66 TAG
60995269 GCTAAGAAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 62 1.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (68 bp):
CCCTCGTAAGCTTAGCAGTAAAACCAAGTAACTTATTTGAGTTTTACTTAAAAATGTACTCTAAA
TAG
Found at i:61003534 original size:43 final size:44
Alignment explanation
Indices: 61003481--61003565 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 44
61003471 TTCGGATTCA
* * *
61003481 TTTATATATAT-AGTTGAATCAATTTTAATATATGTTTAATATCC
1 TTTATATATATAAG-TGAATCAAATATAATATAGGTTTAATATCC
61003525 TTTAT-TATATAAGTGAATCAAATATAATATAGGTTTAATAT
1 TTTATATATATAAGTGAATCAAATATAATATAGGTTTAATAT
61003566 AAGAAAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 30 0.81
44 7 0.19
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.47
Consensus pattern (44 bp):
TTTATATATATAAGTGAATCAAATATAATATAGGTTTAATATCC
Found at i:61005808 original size:2 final size:2
Alignment explanation
Indices: 61005801--61005843 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
61005791 ATAGTCAACA
61005801 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61005843 A
1 A
61005844 ACATCAACAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:61010456 original size:2 final size:2
Alignment explanation
Indices: 61010449--61010477 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
61010439 TGAATTAGTC
61010449 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
61010478 TAAATGGTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:61013256 original size:19 final size:22
Alignment explanation
Indices: 61013217--61013259 Score: 65
Period size: 19 Copynumber: 2.1 Consensus size: 22
61013207 ATTATTAATA
61013217 TTATTAAAAAATGTAATTTTAT
1 TTATTAAAAAATGTAATTTTAT
61013239 TTATT-AAAAAT-T-ATTTTAT
1 TTATTAAAAAATGTAATTTTAT
61013258 TT
1 TT
61013260 TCATAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.43
20 1 0.05
21 6 0.29
22 5 0.24
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TTATTAAAAAATGTAATTTTAT
Found at i:61023430 original size:12 final size:12
Alignment explanation
Indices: 61023413--61023437 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
61023403 CTGTGAACTA
61023413 TCAAAATCTCAT
1 TCAAAATCTCAT
61023425 TCAAAATCTCAT
1 TCAAAATCTCAT
61023437 T
1 T
61023438 GTTCATACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (12 bp):
TCAAAATCTCAT
Found at i:61032963 original size:6 final size:6
Alignment explanation
Indices: 61032952--61032976 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
61032942 ATTATTGAAT
61032952 TTTTAA TTTTAA TTTTAA TTTTAA T
1 TTTTAA TTTTAA TTTTAA TTTTAA T
61032977 GATTAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTTAA
Found at i:61037725 original size:30 final size:30
Alignment explanation
Indices: 61037691--61037752 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
61037681 AATAAATGTG
61037691 TTTGTTTTGCATATGATTTTAATTTGAACT
1 TTTGTTTTGCATATGATTTTAATTTGAACT
61037721 TTTGTTTTGCATATGATTTTAATTTGAACT
1 TTTGTTTTGCATATGATTTTAATTTGAACT
61037751 TT
1 TT
61037753 GATGAATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.23, C:0.06, G:0.13, T:0.58
Consensus pattern (30 bp):
TTTGTTTTGCATATGATTTTAATTTGAACT
Found at i:61043718 original size:20 final size:21
Alignment explanation
Indices: 61043671--61043718 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
61043661 AATATTAGTT
*
61043671 TTAAT-TAAAATAATATATTT
1 TTAATATAAAATAATATATTA
*
61043691 TTTA-ATAAAATAATA-ATTA
1 TTAATATAAAATAATATATTA
61043710 TTAATATAA
1 TTAATATAA
61043719 TGACATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TTAATATAAAATAATATATTA
Found at i:61046808 original size:17 final size:17
Alignment explanation
Indices: 61046777--61046831 Score: 51
Period size: 19 Copynumber: 3.1 Consensus size: 17
61046767 AACAAATATT
61046777 AAATTTAAATGAAATAA
1 AAATTTAAATGAAATAA
61046794 AAATATTAAAT-AAATAGA
1 AAAT-TTAAATGAAATA-A
*
61046812 TAAATTAAAAATG-AATAA
1 -AAATT-TAAATGAAATAA
61046830 AA
1 AA
61046832 TTGGTAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
17 11 0.34
18 9 0.28
19 12 0.38
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.27
Consensus pattern (17 bp):
AAATTTAAATGAAATAA
Done.