Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 70 of 216
Found at i:21029728 original size:45 final size:44
Alignment explanation
Indices: 21029643--21029758 Score: 142
Period size: 45 Copynumber: 2.6 Consensus size: 44
21029633 CCCACAAAAT
* *
21029643 ACAACCAAACATAGCCTCTAAACACAACCAATTTACCCTCCAAAC
1 ACAACCAAACATACCCTC-AAACACAACCAATATACCCTCCAAAC
* * *
21029688 ACAACCAAACATACCCTCCAACACAACCAAATATAGCCTCCAAGC
1 ACAACCAAACATACCCTCAAACACAACC-AATATACCCTCCAAAC
* *
21029733 ACCACCAAATATACCCTTCAAACACA
1 ACAACCAAACATACCC-TCAAACACA
21029759 TCCATTTAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
44 9 0.15
45 44 0.72
46 8 0.13
ACGTcount: A:0.45, C:0.39, G:0.03, T:0.14
Consensus pattern (44 bp):
ACAACCAAACATACCCTCAAACACAACCAATATACCCTCCAAAC
Found at i:21035956 original size:40 final size:41
Alignment explanation
Indices: 21035906--21035995 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 41
21035896 CAAGAGCTAC
* * * * *
21035906 CAATACATTCCCAAAGACACCTAGTGCTTTGGAGAACTAT-
1 CAATAAATTCCCAAAGACACCCAATGCTCTAGAGAACTATA
* *
21035946 CAATAAATTCCCACAGGCACCCAATGCTCTAGAGAACTATA
1 CAATAAATTCCCAAAGACACCCAATGCTCTAGAGAACTATA
21035987 CAATGAAAT
1 CAAT-AAAT
21035996 ACAACAAGTG
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
40 33 0.80
41 4 0.10
42 4 0.10
ACGTcount: A:0.39, C:0.26, G:0.13, T:0.22
Consensus pattern (41 bp):
CAATAAATTCCCAAAGACACCCAATGCTCTAGAGAACTATA
Found at i:21037666 original size:231 final size:231
Alignment explanation
Indices: 21037263--21037727 Score: 894
Period size: 231 Copynumber: 2.0 Consensus size: 231
21037253 TCAGAGTAAG
*
21037263 AATTAAGAATGCTTAGTAAGTTCAAATGGAGTTATTAAACTTACCTTGATCCATTAAAGCATAAA
1 AATTAAGAATGCTTAGTAAGTTCAAACGGAGTTATTAAACTTACCTTGATCCATTAAAGCATAAA
21037328 GAAAATGTCATACATCTTGGCATTCAAAAATGGCCATTCTTGGCACATATTGGCACATCTAAGTA
66 GAAAATGTCATACATCTTGGCATTCAAAAATGGCCATTCTTGGCACATATTGGCACATCTAAGTA
21037393 CATGTCAACATTATCAACTAAATAAGTTAGTCACTTTTACAAATCATGAGAAATATCTAAGACAT
131 CATGTCAACATTATCAACTAAATAAGTTAGTCACTTTTACAAATCATGAGAAATATCTAAGACAT
21037458 TAAGGCACTTCAATACTTATCACATATCACATATCA
196 TAAGGCACTTCAATACTTATCACATATCACATATCA
21037494 AATTAAGAATGCTTAGTAAGTTCAAACGGAGTTATTAAACTTACCTTGATCCATTAAAGCATAAA
1 AATTAAGAATGCTTAGTAAGTTCAAACGGAGTTATTAAACTTACCTTGATCCATTAAAGCATAAA
*
21037559 GAAAATTTCATACATCTTGGCATTCAAAAATGGCCATTCTTGGCACATATTGGCACATCTAAGTA
66 GAAAATGTCATACATCTTGGCATTCAAAAATGGCCATTCTTGGCACATATTGGCACATCTAAGTA
21037624 CATGTCAACATTATCAACTAAATAAGTTAGTCACTTTTACAAATCATGAGAAATATCTAAGACAT
131 CATGTCAACATTATCAACTAAATAAGTTAGTCACTTTTACAAATCATGAGAAATATCTAAGACAT
* *
21037689 TAAGGTAGTTCAATACTTATCACATATCACATATCA
196 TAAGGCACTTCAATACTTATCACATATCACATATCA
21037725 AAT
1 AAT
21037728 ATAAAACATA
Statistics
Matches: 230, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
231 230 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (231 bp):
AATTAAGAATGCTTAGTAAGTTCAAACGGAGTTATTAAACTTACCTTGATCCATTAAAGCATAAA
GAAAATGTCATACATCTTGGCATTCAAAAATGGCCATTCTTGGCACATATTGGCACATCTAAGTA
CATGTCAACATTATCAACTAAATAAGTTAGTCACTTTTACAAATCATGAGAAATATCTAAGACAT
TAAGGCACTTCAATACTTATCACATATCACATATCA
Found at i:21040904 original size:25 final size:25
Alignment explanation
Indices: 21040876--21040940 Score: 60
Period size: 25 Copynumber: 2.6 Consensus size: 25
21040866 CTGTTTTTGA
*
21040876 TAGTATATCCTAAAACTACTATATG
1 TAGTATATACTAAAACTACTATATG
* * *
21040901 TAGTGTATACTGAGACTACTATA-G
1 TAGTATATACTAAAACTACTATATG
**
21040925 ATAGGCTATACTAAAA
1 -TAGTATATACTAAAA
21040941 ACACTCAAGT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
24 1 0.03
25 30 0.97
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (25 bp):
TAGTATATACTAAAACTACTATATG
Found at i:21043675 original size:3 final size:3
Alignment explanation
Indices: 21043662--21043721 Score: 57
Period size: 3 Copynumber: 20.0 Consensus size: 3
21043652 GAAATAAAAT
* * * * * *
21043662 TAA TGA TAA TAA TAT TGA TAA TAA CAA CAA TAA TAA TAA TAA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
21043710 TAT TAA TAA TAA
1 TAA TAA TAA TAA
21043722 AGCTAAAAAA
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:21043684 original size:36 final size:36
Alignment explanation
Indices: 21043642--21043721 Score: 101
Period size: 36 Copynumber: 2.2 Consensus size: 36
21043632 AAACATAAAC
*
21043642 GATAATAACAGA-AATAA-AATTAATGATAATAATATT
1 GATAATAACA-ACAATAATAA-TAATAATAATAATATT
*
21043678 GATAATAACAACAATAATAATAATAATAGTAATATT
1 GATAATAACAACAATAATAATAATAATAATAATATT
*
21043714 AATAATAA
1 GATAATAA
21043722 AGCTAAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
35 1 0.03
36 36 0.92
37 2 0.05
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.30
Consensus pattern (36 bp):
GATAATAACAACAATAATAATAATAATAATAATATT
Found at i:21045110 original size:50 final size:50
Alignment explanation
Indices: 21045055--21045427 Score: 287
Period size: 50 Copynumber: 7.6 Consensus size: 50
21045045 CGATCCTTTA
* *
21045055 AACTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTC
1 AACTGCAATGCCAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTC
* * * ** * * *
21045105 CACTGCAATGCCTGGGAAGTAAGATTCACCATTGTGGCTTCAATCTTTTG
1 AACTGCAATGCCAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTC
* *
21045155 AACTGCAATGTCAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATATGTTC
1 AACTGCAATGCCAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTC
** * * ** * * * *
21045205 CGCTGC-ATCCCCA--AAAGTAAGATTCGCCATTGTGGCTTCGATCTTTTA
1 AACTGCAAT-GCCAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTC
* * * * *
21045253 AATTGCAATGTCGGGGAAGTGAGATTCGTTGTTGTAGCTTCAATCTGTTC
1 AACTGCAATGCCAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTC
* * * ** * *
21045303 CACTGCATTGCCA--GAAGTAAGATTCG-TCGTTAT-GCCTTTGATCTTTTA
1 AACTGCAATGCCAGGGAAGTAAGATTCGCT-GTTGTAG-CTTCAATCTGTTC
* * * * *
21045351 AATTGCAATGTCGGGGAAGTGAGATTCACTGTTGTAGCTTCAATCTGTTC
1 AACTGCAATGCCAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTC
* *
21045401 TACTGCATTGCCA--GAAGTAAGATTCGC
1 AACTGCAATGCCAGGGAAGTAAGATTCGC
21045428 CATTGTGGCT
Statistics
Matches: 236, Mismatches: 77, Indels: 22
0.70 0.23 0.07
Matches are distributed among these distances:
47 2 0.01
48 76 0.32
49 4 0.02
50 152 0.64
51 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (50 bp):
AACTGCAATGCCAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTC
Found at i:21045279 original size:98 final size:98
Alignment explanation
Indices: 21045024--21045453 Score: 572
Period size: 98 Copynumber: 4.4 Consensus size: 98
21045014 GCCGAGGAAA
* * * *
21045024 TAAGATTCACCATTGTGGCTTCGATCCTTTAAACTGCAATGTCAGGGAAGTAAGATCCGCTGTTG
1 TAAGATTCGCCATTGTGGCTTCGATCTTTTAAATTGCAATGTCAGGGAAGTAAGATTCGCTGTTG
***
21045089 TAGCTTCAATCTGTTCCACTGCAATGCCTGGGAAG
66 TAGCTTCAATCTGTTCCACTGC-AT-CCCCAGAAG
* * * *
21045124 TAAGATTCACCATTGTGGCTTCAATCTTTTGAACTGCAATGTCAGGGAAGTAAGATTCGCTGTTG
1 TAAGATTCGCCATTGTGGCTTCGATCTTTTAAATTGCAATGTCAGGGAAGTAAGATTCGCTGTTG
* * *
21045189 TAGCTTCAATATGTTCCGCTGCATCCCCAAAAG
66 TAGCTTCAATCTGTTCCACTGCATCCCCAGAAG
* * *
21045222 TAAGATTCGCCATTGTGGCTTCGATCTTTTAAATTGCAATGTCGGGGAAGTGAGATTCGTTGTTG
1 TAAGATTCGCCATTGTGGCTTCGATCTTTTAAATTGCAATGTCAGGGAAGTAAGATTCGCTGTTG
**
21045287 TAGCTTCAATCTGTTCCACTGCATTGCCAGAAG
66 TAGCTTCAATCTGTTCCACTGCATCCCCAGAAG
* * * * * * * *
21045320 TAAGATTCGTCGTTATGCCTTTGATCTTTTAAATTGCAATGTCGGGGAAGTGAGATTCACTGTTG
1 TAAGATTCGCCATTGTGGCTTCGATCTTTTAAATTGCAATGTCAGGGAAGTAAGATTCGCTGTTG
* **
21045385 TAGCTTCAATCTGTTCTACTGCATTGCCAGAAG
66 TAGCTTCAATCTGTTCCACTGCATCCCCAGAAG
21045418 TAAGATTCGCCATTGTGGCTTCGATCTTTTAAATTG
1 TAAGATTCGCCATTGTGGCTTCGATCTTTTAAATTG
21045454 GAAACTATGG
Statistics
Matches: 295, Mismatches: 35, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
98 212 0.72
99 2 0.01
100 81 0.27
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (98 bp):
TAAGATTCGCCATTGTGGCTTCGATCTTTTAAATTGCAATGTCAGGGAAGTAAGATTCGCTGTTG
TAGCTTCAATCTGTTCCACTGCATCCCCAGAAG
Found at i:21125609 original size:40 final size:40
Alignment explanation
Indices: 21125371--21125595 Score: 280
Period size: 40 Copynumber: 5.7 Consensus size: 40
21125361 TTGAATGATG
* * * * *
21125371 TCCGGGCTAAGTCCCGAGGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
21125411 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGA-TATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGT-TACTAAA
*
21125451 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
21125490 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
21125530 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
21125571 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
21125596 AACGAGTAGC
Statistics
Matches: 164, Mismatches: 14, Indels: 14
0.85 0.07 0.07
Matches are distributed among these distances:
39 34 0.21
40 120 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:21125613 original size:80 final size:80
Alignment explanation
Indices: 21125410--21125628 Score: 243
Period size: 79 Copynumber: 2.8 Consensus size: 80
21125400 AAGTGACCAT
* ** * *
21125410 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGA-TATACTAATTCCGGGCTAAG-CCCGAAGGCA
1 ATCCGGGCTAAG-TCCCGAAGGCATTTGAACGAGT-TACTAAATCCGGGTTAAGTCCCGAAGGCA
21125472 TTGGTGCGAGTTACTAA
64 TTGGTGCGAGTTACTAA
* **
21125489 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATT
*
21125554 TGTGCGAGTTACTATA
66 GGTGCGAGTTACTA-A
* * * *
21125570 A-CCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATATCC-GGTTAAATTCCGAAGG
1 ATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTTA-CTAAATCCGGGTTAAGTCCCGAAGG
21125629 TATGTGATTT
Statistics
Matches: 123, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 60 0.49
80 60 0.49
81 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (80 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATT
GGTGCGAGTTACTAA
Found at i:21128812 original size:46 final size:46
Alignment explanation
Indices: 21128752--21128839 Score: 124
Period size: 46 Copynumber: 1.9 Consensus size: 46
21128742 AAATATGCAG
* * *
21128752 TGTGGGCCTTAGCCCATTACAGT-ATCAGAATCAGAAATAGAATACA
1 TGTGGGCCTAAGCCCAATACAGTGA-CAAAATCAGAAATAGAATACA
*
21128798 TGTGGGCCTAAGCCCAATACAGTGACAAAATCAGTAATAGAA
1 TGTGGGCCTAAGCCCAATACAGTGACAAAATCAGAAATAGAA
21128840 ATGCAACAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
46 36 0.97
47 1 0.03
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (46 bp):
TGTGGGCCTAAGCCCAATACAGTGACAAAATCAGAAATAGAATACA
Found at i:21129110 original size:32 final size:32
Alignment explanation
Indices: 21129055--21129193 Score: 163
Period size: 32 Copynumber: 4.4 Consensus size: 32
21129045 GAATGGCTAC
* **
21129055 AAGCCATAAGT-ACAGTAATATGATTAGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
21129086 AAGCCATCAGTAGCAGTGATATGATCGACACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* ** * *
21129118 CAGCCATCAGTAATGGTAATATGATCGGTACG
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
*
21129150 AAGCCATCAGTAACGGTAATATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
21129182 AAGCCATCAGTA
1 AAGCCATCAGTA
21129194 GTATCGCAGC
Statistics
Matches: 89, Mismatches: 18, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
31 10 0.11
32 79 0.89
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.21
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATCGGCACA
Found at i:21129231 original size:14 final size:14
Alignment explanation
Indices: 21129192--21129231 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 14
21129182 AAGCCATCAG
21129192 TAGTATCGCAGCAA
1 TAGTATCGCAGCAA
21129206 -AGT-T-GCCAGCAA
1 TAGTATCG-CAGCAA
21129218 TAGTATCGCAGCAA
1 TAGTATCGCAGCAA
21129232 AACTGCTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 8
0.73 0.00 0.27
Matches are distributed among these distances:
11 1 0.05
12 7 0.32
13 6 0.27
14 7 0.32
15 1 0.05
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.20
Consensus pattern (14 bp):
TAGTATCGCAGCAA
Found at i:21129366 original size:24 final size:24
Alignment explanation
Indices: 21129338--21129395 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
21129328 ACATTTTCAG
*
21129338 AATCAGTCATACGAATCACAGAA-A
1 AATCAGTCATACCAATCACA-AACA
21129362 AATCAGTCATACCAATCACAAACA
1 AATCAGTCATACCAATCACAAACA
*
21129386 ATTCAGTCAT
1 AATCAGTCAT
21129396 TTAAATCATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 2 0.06
24 29 0.94
ACGTcount: A:0.47, C:0.24, G:0.09, T:0.21
Consensus pattern (24 bp):
AATCAGTCATACCAATCACAAACA
Found at i:21129402 original size:24 final size:24
Alignment explanation
Indices: 21129375--21129446 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 24
21129365 CAGTCATACC
* *
21129375 AATCACAAACAATTCAGTCATTTA
1 AATCACAAACAAATCAATCATTTA
* *
21129399 AATCATAGACAAATCAATCATTTA
1 AATCACAAACAAATCAATCATTTA
* ** *
21129423 CATCACGGACAAATAAATCATTTA
1 AATCACAAACAAATCAATCATTTA
21129447 CACTCGAAAG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.47, C:0.19, G:0.06, T:0.28
Consensus pattern (24 bp):
AATCACAAACAAATCAATCATTTA
Found at i:21129447 original size:24 final size:24
Alignment explanation
Indices: 21129392--21129448 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
21129382 AACAATTCAG
* * *
21129392 TCATTTAAATCATAGACAAATCAA
1 TCATTTACATCACAGACAAATAAA
*
21129416 TCATTTACATCACGGACAAATAAA
1 TCATTTACATCACAGACAAATAAA
21129440 TCATTTACA
1 TCATTTACA
21129449 CTCGAAAGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.46, C:0.19, G:0.05, T:0.30
Consensus pattern (24 bp):
TCATTTACATCACAGACAAATAAA
Found at i:21129577 original size:81 final size:81
Alignment explanation
Indices: 21129492--21129821 Score: 292
Period size: 81 Copynumber: 4.1 Consensus size: 81
21129482 GGCATTACGG
* * *
21129492 TCATTTTACCTTACAGTGGTATTTCGATCATTTAACCCTAT-GGGGGTATTATGGTCATTTTACC
1 TCATTTTACCTTACAG-GGTATTTCGATCATTTTACCCTATCGAGGGTATTATGGTAATTTTACC
* *
21129556 CTAT-GGGGGTTTTTCGA
65 CTATCGAGGGTATTTC-A
* * *
21129573 TCATTTTACCCTACAGGGGTATTACGATTATTTTA-CCTATCGAGGGTATTTCAT--TAATTTTA
1 TCATTTTACCTTACA-GGGTATTTCGATCATTTTACCCTATCGAGGGTA-TT-ATGGTAATTTTA
21129635 -CCTATCGAGGGTATTTCAA
63 CCCTATCGAGGGTATTTC-A
* * *
21129654 TCATTTTACC-CATCGAGGGTATTTCGGTCATTTTACCC-ATCGAGGGTATTTTGGTAATTTTAC
1 TCATTTTACCTTA-C-AGGGTATTTCGATCATTTTACCCTATCGAGGGTATTATGGTAATTTTAC
*
21129717 CC-ATCGAGGGTAATTCA
64 CCTATCGAGGGTATTTCA
* *
21129734 GTCATTTTACCCTT-CAGAGGTAATTTAG-TCATTTTACCCTA-CGAGGGTAATT-TGGTCATTT
1 -TCATTTTA-CCTTACAG-GGT-ATTTCGATCATTTTACCCTATCGAGGGT-ATTATGGTAATTT
* *
21129795 TACCC-CTCGAGGGTAATTCA
61 TACCCTATCGAGGGTATTTCA
21129815 GTCATTT
1 -TCATTT
21129822 AACAAATATT
Statistics
Matches: 212, Mismatches: 19, Indels: 36
0.79 0.07 0.13
Matches are distributed among these distances:
79 1 0.00
80 16 0.08
81 174 0.82
82 19 0.09
83 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.40
Consensus pattern (81 bp):
TCATTTTACCTTACAGGGTATTTCGATCATTTTACCCTATCGAGGGTATTATGGTAATTTTACCC
TATCGAGGGTATTTCA
Found at i:21129633 original size:54 final size:55
Alignment explanation
Indices: 21129509--21129809 Score: 227
Period size: 54 Copynumber: 5.6 Consensus size: 55
21129499 ACCTTACAGT
* * * * *
21129509 GGTATTTC-GATCATTTAACCCTAT-GGGGGTATTAT-GGTCATTTTACCCTAT-GGG
1 GGTATTTCAG-TCATTTTACCCTATCGAGGGTATT-TCGATAATTTTACCC-ATCGAG
* * * *
21129563 GGTTTTTC-GATCATTTTACCCTA-C-AGGGGTATTACGATTATTTTACCTATCGAG
1 GGTATTTCAG-TCATTTTACCCTATCGA-GGGTATTTCGATAATTTTACCCATCGAG
* * * *
21129617 GGTATTTCATTAATTTTA-CCTATCGAGGGTATTTCAATCATTTTACCCATCGAG
1 GGTATTTCAGTCATTTTACCCTATCGAGGGTATTTCGATAATTTTACCCATCGAG
* * *
21129671 GGTATTTCGGTCATTTTACCC-ATCGAGGGTATTTTGGTAATTTTACCCATCGAG
1 GGTATTTCAGTCATTTTACCCTATCGAGGGTATTTCGATAATTTTACCCATCGAG
* * *
21129725 GGTAATTCAGTCATTTTACCCT-TC-AGAGGTAATTTAG-TCATTTTACCC-TACGAG
1 GGTATTTCAGTCATTTTACCCTATCGAG-GGT-ATTTCGATAATTTTACCCAT-CGAG
* *
21129779 GGTAATTT-GGTCATTTTACCC-CTCGAGGGTA
1 GGT-ATTTCAGTCATTTTACCCTATCGAGGGTA
21129810 ATTCAGTCAT
Statistics
Matches: 204, Mismatches: 28, Indels: 31
0.78 0.11 0.12
Matches are distributed among these distances:
53 10 0.05
54 181 0.89
55 13 0.06
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.39
Consensus pattern (55 bp):
GGTATTTCAGTCATTTTACCCTATCGAGGGTATTTCGATAATTTTACCCATCGAG
Found at i:21129799 original size:27 final size:26
Alignment explanation
Indices: 21129490--21129809 Score: 199
Period size: 27 Copynumber: 11.9 Consensus size: 26
21129480 AGGGCATTAC
*
21129490 GGTCATTTTACCTTAC-AGTGGTATTT
1 GGTCATTTTACCCTACGAG-GGTATTT
* * * *
21129516 CGATCATTTAACCCTATGGGGGTATTAT
1 -GGTCATTTTACCCTACGAGGGTATT-T
* * *
21129544 GGTCATTTTACCCTATGGGGGTTTTT
1 GGTCATTTTACCCTACGAGGGTATTT
* *
21129570 CGATCATTTTACCCTAC-AGGGGTATTAC
1 -GGTCATTTTACCCTACGA-GGGTATT-T
* *
21129598 GATTATTTTA-CCTATCGAGGGTATTT
1 GGTCATTTTACCCTA-CGAGGGTATTT
** *
21129624 CATTAATTTTA-CCTATCGAGGGTATTT
1 -GGTCATTTTACCCTA-CGAGGGTATTT
**
21129651 CAATCATTTTACCC-ATCGAGGGTATTT
1 -GGTCATTTTACCCTA-CGAGGGTATTT
21129678 CGGTCATTTTACCC-ATCGAGGGTATTTT
1 -GGTCATTTTACCCTA-CGAGGGTA-TTT
* *
21129706 GGTAATTTTACCC-ATCGAGGGTAATTC
1 GGTCATTTTACCCTA-CGAGGGT-ATTT
* *
21129733 AGTCATTTTACCCTTC-AGAGGTAATTT
1 GGTCATTTTACCCTACGAG-GGT-ATTT
*
21129760 AGTCATTTTACCCTACGAGGGTAATTT
1 GGTCATTTTACCCTACGAGGGT-ATTT
21129787 GGTCATTTTACCCCT-CGAGGGTA
1 GGTCATTTTA-CCCTACGAGGGTA
21129810 ATTCAGTCAT
Statistics
Matches: 248, Mismatches: 30, Indels: 31
0.80 0.10 0.10
Matches are distributed among these distances:
26 8 0.03
27 225 0.91
28 15 0.06
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.39
Consensus pattern (26 bp):
GGTCATTTTACCCTACGAGGGTATTT
Found at i:21129810 original size:27 final size:27
Alignment explanation
Indices: 21129602--21129821 Score: 234
Period size: 27 Copynumber: 8.1 Consensus size: 27
21129592 TATTACGATT
* * *
21129602 ATTTTACCTATCGAGGGT-ATTTCATTA
1 ATTTTACCCATCGAGGGTAATTT-AGTC
* *
21129629 ATTTTACCTATCGAGGGT-ATTTCAATC
1 ATTTTACCCATCGAGGGTAATTT-AGTC
*
21129656 ATTTTACCCATCGAGGGT-ATTTCGGTC
1 ATTTTACCCATCGAGGGTAATTT-AGTC
* * *
21129683 ATTTTACCCATCGAGGGTATTTTGGTA
1 ATTTTACCCATCGAGGGTAATTTAGTC
*
21129710 ATTTTACCCATCGAGGGTAATTCAGTC
1 ATTTTACCCATCGAGGGTAATTTAGTC
*
21129737 ATTTTACCCTTC-AGAGGTAATTTAGTC
1 ATTTTACCCATCGAG-GGTAATTTAGTC
*
21129764 ATTTTACCC-TACGAGGGTAATTTGGTC
1 ATTTTACCCAT-CGAGGGTAATTTAGTC
* *
21129791 ATTTTACCCCTCGAGGGTAATTCAGTC
1 ATTTTACCCATCGAGGGTAATTTAGTC
21129818 ATTT
1 ATTT
21129822 AACAAATATT
Statistics
Matches: 172, Mismatches: 16, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
26 3 0.02
27 163 0.95
28 6 0.03
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (27 bp):
ATTTTACCCATCGAGGGTAATTTAGTC
Found at i:21137671 original size:159 final size:159
Alignment explanation
Indices: 21137431--21137742 Score: 484
Period size: 159 Copynumber: 2.0 Consensus size: 159
21137421 AAAGATACAT
* * * *
21137431 AATTTAAAACATTATGGTTCTAAAGGACCTAAGTGAATATGTGCATACCATGTTTTAATTACAAG
1 AATTTAAAACATTACGGTTCTAAAAGAACTAAGTGAATATGTGCATACCATGTTTTAAATACAAG
*
21137496 TTTTATATGCTTGATGATAAGAATATA-ACATTGTTTATTTATTGAAATTATCGTACGTAGTTAA
66 TTTTATATGCTTGATGATAAGAATA-ACACATTGTTTATTTATTGAAATTATCATACGTAGTTAA
* *
21137560 AATCGATGCCATTCTATTGAAAGATGTGAG
130 AATCGATGCCAGTCTATCGAAAGATGTGAG
* * *
21137590 AATTTAGAACATTACGGTTCTAAAATAACTAAGTGAATATGTGCATACCATGTTTTAAATA-TAG
1 AATTTAAAACATTACGGTTCTAAAAGAACTAAGTGAATATGTGCATACCATGTTTTAAATACAAG
* *
21137654 TTTTTATATGCTTGATGATGAGAATAACACATTGTTTCTTTATTGAAATTATCATACGTAGTTAA
66 -TTTTATATGCTTGATGATAAGAATAACACATTGTTTATTTATTGAAATTATCATACGTAGTTAA
21137719 AATCGATGCCAGTCTATCGAAAGA
130 AATCGATGCCAGTCTATCGAAAGA
21137743 CAAAGGGAAA
Statistics
Matches: 139, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
158 3 0.02
159 136 0.98
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (159 bp):
AATTTAAAACATTACGGTTCTAAAAGAACTAAGTGAATATGTGCATACCATGTTTTAAATACAAG
TTTTATATGCTTGATGATAAGAATAACACATTGTTTATTTATTGAAATTATCATACGTAGTTAAA
ATCGATGCCAGTCTATCGAAAGATGTGAG
Found at i:21139779 original size:32 final size:32
Alignment explanation
Indices: 21139738--21139799 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
21139728 AAGGTTAACA
21139738 TATTTAATATTTATATATAAATATAGGATAGT
1 TATTTAATATTTATATATAAATATAGGATAGT
21139770 TATTTAATATTTATATATAAATATAGGATA
1 TATTTAATATTTATATATAAATATAGGATA
21139800 ATCATGGGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (32 bp):
TATTTAATATTTATATATAAATATAGGATAGT
Found at i:21142631 original size:143 final size:143
Alignment explanation
Indices: 21142373--21142661 Score: 517
Period size: 143 Copynumber: 2.0 Consensus size: 143
21142363 TAAATACGTA
21142373 GTTTGTGCAGTAAATGTTTTTATTTATCATATGTTTTGACTAATATATAGCTTGTACAGGTGGAA
1 GTTTGTGCAGTAAATGTTTTTATTTATCATATGTTTTGACTAATATATAGCTTGTACAGGTGGAA
*
21142438 CCACTGGCTGAGTTACGTGGGAGTACCTGACGAGTTGGAAAACATTAGGCTACTGTTAGATCAAT
66 CCACTGGCCGAGTTACGTGGGAGTACCTGACGAGTTGGAAAACATTAGGCTACTGTTAGATCAAT
*
21142503 GCTCGAAACCAAG
131 ACTCGAAACCAAG
21142516 GTTTGTGCAGTAAATGTTTTTATTTATCATATGTTTTGACTAATATATAGCTTGTACAGGTGGAA
1 GTTTGTGCAGTAAATGTTTTTATTTATCATATGTTTTGACTAATATATAGCTTGTACAGGTGGAA
* * *
21142581 CCA-TGGGCCGAGTTACGTGGGAGTACCTGACGATTTGGAAAACGTTAGGCTGCTGTTAGATCAA
66 CCACT-GGCCGAGTTACGTGGGAGTACCTGACGAGTTGGAAAACATTAGGCTACTGTTAGATCAA
21142645 TACTCGAAACCAAG
130 TACTCGAAACCAAG
21142659 GTT
1 GTT
21142662 AATTACCTAT
Statistics
Matches: 140, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
142 1 0.01
143 139 0.99
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (143 bp):
GTTTGTGCAGTAAATGTTTTTATTTATCATATGTTTTGACTAATATATAGCTTGTACAGGTGGAA
CCACTGGCCGAGTTACGTGGGAGTACCTGACGAGTTGGAAAACATTAGGCTACTGTTAGATCAAT
ACTCGAAACCAAG
Found at i:21147852 original size:9 final size:9
Alignment explanation
Indices: 21147833--21147887 Score: 57
Period size: 8 Copynumber: 6.6 Consensus size: 9
21147823 AAATACTTTC
21147833 AAAATACCCT
1 AAAA-ACCCT
21147843 AAAAACCCT
1 AAAAACCCT
*
21147852 -AAAATCCT
1 AAAAACCCT
21147860 -AAAA-CCT
1 AAAAACCCT
21147867 AAAAACCCT
1 AAAAACCCT
21147876 -AAAA-CCT
1 AAAAACCCT
21147883 AAAAA
1 AAAAA
21147888 AAATAAAAAG
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
7 6 0.15
8 23 0.56
9 8 0.20
10 4 0.10
ACGTcount: A:0.58, C:0.27, G:0.00, T:0.15
Consensus pattern (9 bp):
AAAAACCCT
Found at i:21147887 original size:16 final size:16
Alignment explanation
Indices: 21147833--21147887 Score: 67
Period size: 16 Copynumber: 3.3 Consensus size: 16
21147823 AAATACTTTC
21147833 AAAATACCCTAAAAACCCT
1 AAAA-ACCCT-AAAA-CCT
*
21147852 -AAAATCCTAAAACCT
1 AAAAACCCTAAAACCT
21147867 AAAAACCCTAAAACCT
1 AAAAACCCTAAAACCT
21147883 AAAAA
1 AAAAA
21147888 AAATAAAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
15 3 0.09
16 23 0.70
17 4 0.12
18 3 0.09
ACGTcount: A:0.58, C:0.27, G:0.00, T:0.15
Consensus pattern (16 bp):
AAAAACCCTAAAACCT
Found at i:21147887 original size:24 final size:24
Alignment explanation
Indices: 21147840--21147886 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
21147830 TTCAAAATAC
21147840 CCTAAAAACCCTAAAATCCTAAAA
1 CCTAAAAACCCTAAAATCCTAAAA
21147864 CCTAAAAACCCTAAAA-CCTAAAA
1 CCTAAAAACCCTAAAATCCTAAAA
21147887 AAAATAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.55, C:0.30, G:0.00, T:0.15
Consensus pattern (24 bp):
CCTAAAAACCCTAAAATCCTAAAA
Found at i:21147895 original size:24 final size:24
Alignment explanation
Indices: 21147843--21147895 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
21147833 AAAATACCCT
***
21147843 AAAAACCCTAAAATCCTAAAACCT
1 AAAAACCCTAAAATCCTAAAAAAA
21147867 AAAAACCCTAAAA-CCTAAAAAAA
1 AAAAACCCTAAAATCCTAAAAAAA
21147890 ATAAAA
1 A-AAAA
21147896 AGTCCTAACC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.64, C:0.23, G:0.00, T:0.13
Consensus pattern (24 bp):
AAAAACCCTAAAATCCTAAAAAAA
Found at i:21149025 original size:3 final size:3
Alignment explanation
Indices: 21149017--21149054 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
21149007 GGACTAGATG
*
21149017 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT AAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
21149055 GAAAAAAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:21157218 original size:26 final size:26
Alignment explanation
Indices: 21157184--21157244 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
21157174 CCTTAAATAT
* *
21157184 AATTAAAATAT-ATTAAATTATTTAAC
1 AATTTAAATATGATAAAATT-TTTAAC
*
21157210 AATTTAAATATGATAAAATTTTTAAT
1 AATTTAAATATGATAAAATTTTTAAC
21157236 AATATTAAA
1 AAT-TTAAA
21157245 AAAATCAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 18 0.60
27 12 0.40
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (26 bp):
AATTTAAATATGATAAAATTTTTAAC
Found at i:21160922 original size:51 final size:51
Alignment explanation
Indices: 21160838--21161178 Score: 318
Period size: 51 Copynumber: 6.7 Consensus size: 51
21160828 TATCGATGAA
*
21160838 CACGTGTGTAGTACTGTGTGAAGGCTACTATGTGTACCGATAAATAATTGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAATAATTGT
* * * * * * *
21160889 CACATGTCTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT--TCGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAA-ATAAT-TGT
* * * * * *
21160940 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAATAATTGT
* * * * *
21160991 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTATCGA-AAAGATTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAATAATT-GT
* * *
21161042 CACGTGTGTAGTACTATGTGAAGGCTAGTACGTGAACCG-TAAA-AACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAATAA-TTG-T
* * * *
21161093 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACTG-TAAA-ACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAATAATTG-T
* * *
21161143 CACGTGTGTAGAACTATGTGGAGGCTACTACGTGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTA
21161179 TTGAATGATA
Statistics
Matches: 242, Mismatches: 40, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
50 46 0.19
51 194 0.80
52 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGATAAATAATTGT
Found at i:21161014 original size:102 final size:100
Alignment explanation
Indices: 21160838--21161176 Score: 403
Period size: 102 Copynumber: 3.3 Consensus size: 100
21160828 TATCGATGAA
* * * * *
21160838 CACGTGTGTAGTACTGTGTGAAGGCTACTATGTGTACCGATAAATAATTGTCACATGTCTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATAATGGTCACATGTGTAGTAC
*
21160903 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTCGGT
66 TAAGTGAAGGCTACTATGTGTACCGA-AAGCTT-GGT
* * *
21160940 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATAATGGTCACATGTGTAGTAC
* *
21161005 TAAGTGAAGGCTACTATGTGTATCGAAAAGATTTGGT
66 TAAGTGAAGGCTACTATGTGTACCG-AAAG-CTTGGT
* * *
21161042 CACGTGTGTAGTACTATGTGAAGGCTAGTACGTGAACCG-TAAA-AACTTGATCACGTGTGTAGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATAA--TGGTCACATGTGTAGT
* * * * * *
21161105 ACTATGTGAAGGCTACTACGTGAACTGTAAAACTTGAT
64 ACTAAGTGAAGGCTACTATGTGTACCG-AAAGCTTGGT
* *
21161143 CACGTGTGTAGAACTATGTGGAGGCTACTACGTG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
21161177 TATTGAATGA
Statistics
Matches: 206, Mismatches: 27, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
100 1 0.00
101 39 0.19
102 163 0.79
103 3 0.01
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (100 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATAATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACTATGTGTACCGAAAGCTTGGT
Found at i:21161097 original size:153 final size:153
Alignment explanation
Indices: 21160842--21161128 Score: 398
Period size: 153 Copynumber: 1.9 Consensus size: 153
21160832 GATGAACACG
** *
21160842 TGTGTAGTACTGTGTGAAGGCTACTATGTGTACCGATAAATAATTGTCACATGTCTAGTACTAAG
1 TGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGATAAAGAATTGTCACATGTCTAGTACTAAG
* * * * * *
21160907 TGAAGGCTACAATGTGTACCGAGAAGCTTCGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACG
66 TGAAGGCTACAACGTGAACCGAAAAACTTCGATCACGTGTGTAGTACTATGTGAAGGCTACTACG
21160972 TGAATCGATAAATGATGGTCACA
131 TGAATCGATAAATGATGGTCACA
* * * * *
21160995 TGTGTAGTACTAAGTGAAGGCTACTATGTGTATCGA-AAAGATTTGGTCACGTGTGTAGTACTAT
1 TGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGATAAAGAATT-GTCACATGTCTAGTACTAA
**
21161059 GTGAAGGCTAGTACGTGAACCGTAAAAACTT-GATCACGTGTGTAGTACTATGTGAAGGCTACTA
65 GTGAAGGCTACAACGTGAACCG-AAAAACTTCGATCACGTGTGTAGTACTATGTGAAGGCTACTA
21161123 CGTGAA
129 CGTGAA
21161129 CTGTAAAACT
Statistics
Matches: 116, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
152 6 0.05
153 104 0.90
154 6 0.05
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (153 bp):
TGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGATAAAGAATTGTCACATGTCTAGTACTAAG
TGAAGGCTACAACGTGAACCGAAAAACTTCGATCACGTGTGTAGTACTATGTGAAGGCTACTACG
TGAATCGATAAATGATGGTCACA
Found at i:21163035 original size:23 final size:23
Alignment explanation
Indices: 21163009--21163053 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
21162999 GAGGTGCCTA
*
21163009 ATACGGCACATAAAGTGTCTGAG
1 ATACGACACATAAAGTGTCTGAG
21163032 ATACGACACATAAAGTGTCTGA
1 ATACGACACATAAAGTGTCTGA
21163054 TCGACAAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (23 bp):
ATACGACACATAAAGTGTCTGAG
Found at i:21163999 original size:13 final size:12
Alignment explanation
Indices: 21163983--21164023 Score: 52
Period size: 10 Copynumber: 3.6 Consensus size: 12
21163973 CTTTCTCTGT
21163983 TTCTTTTCTGTTC
1 TTCTTTTCT-TTC
21163996 TTCTTTTCTTTC
1 TTCTTTTCTTTC
21164008 -T-TTTTCTTT-
1 TTCTTTTCTTTC
21164017 TTCTTTT
1 TTCTTTT
21164024 TTGTTTTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 9 0.35
11 5 0.19
12 3 0.12
13 9 0.35
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (12 bp):
TTCTTTTCTTTC
Found at i:21164006 original size:30 final size:28
Alignment explanation
Indices: 21163935--21164017 Score: 78
Period size: 30 Copynumber: 2.9 Consensus size: 28
21163925 ATTTTCCCTC
* **
21163935 TTTCTTTTCTTTCCCTTTTTCTTCCCCTGT
1 TTTCTTTTCTTTCTC-TTTTCTT-TTCTGT
* *
21163965 TTTCGTCTCTTTCTCTGTTTCTTTTCTGT
1 TTTCTTTTCTTTCTCT-TTTCTTTTCTGT
21163994 TCTTCTTTTCTTTCT-TTTTCTTTT
1 T-TTCTTTTCTTTCTCTTTTCTTTT
21164018 TCTTTTTTGT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
28 8 0.18
29 7 0.16
30 29 0.66
ACGTcount: A:0.00, C:0.27, G:0.05, T:0.69
Consensus pattern (28 bp):
TTTCTTTTCTTTCTCTTTTCTTTTCTGT
Found at i:21164255 original size:28 final size:27
Alignment explanation
Indices: 21164223--21164281 Score: 75
Period size: 30 Copynumber: 2.1 Consensus size: 27
21164213 ATTTGTTTCC
*
21164223 TATAA-TATATTATTTTAATCTTAATTAA
1 TATAATTATAATATTTTAAT-TTAA-TAA
21164251 TATAATTTATAATATTTTAATTTAATAA
1 TATAA-TTATAATATTTTAATTTAATAA
21164279 TAT
1 TAT
21164282 TTTTGTAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 11 0.39
29 4 0.14
30 13 0.46
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (27 bp):
TATAATTATAATATTTTAATTTAATAA
Found at i:21164278 original size:16 final size:16
Alignment explanation
Indices: 21164233--21164284 Score: 58
Period size: 15 Copynumber: 3.4 Consensus size: 16
21164223 TATAATATAT
21164233 TATTTTAATCTTAATTAA
1 TATTTTAAT-TTAA-TAA
21164251 TA---TAATTT-ATAA
1 TATTTTAATTTAATAA
21164263 TATTTTAATTTAATAA
1 TATTTTAATTTAATAA
21164279 TATTTT
1 TATTTT
21164285 TGTAATATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
12 5 0.17
13 1 0.03
14 2 0.07
15 10 0.33
16 10 0.33
18 2 0.07
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTTTAATTTAATAA
Found at i:21166572 original size:21 final size:20
Alignment explanation
Indices: 21166539--21166577 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
21166529 ATTTTTACGA
21166539 TTTTAAATATAAAATATTTG
1 TTTTAAATATAAAATATTTG
*
21166559 TTTTATATCATAAAATATT
1 TTTTAAAT-ATAAAATATT
21166578 AAAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (20 bp):
TTTTAAATATAAAATATTTG
Found at i:21170134 original size:2 final size:2
Alignment explanation
Indices: 21170127--21170156 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
21170117 TTATAAATAA
21170127 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
21170157 TTCTTTTTTA
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:21170674 original size:22 final size:22
Alignment explanation
Indices: 21170649--21170690 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
21170639 AAAAAAATAG
21170649 AAAAAAATAAG-AAAAATAATGT
1 AAAAAAA-AAGTAAAAATAATGT
*
21170671 AAAAAAAAAGTAAAAGTAAT
1 AAAAAAAAAGTAAAAATAAT
21170691 AAAAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.17
Consensus pattern (22 bp):
AAAAAAAAAGTAAAAATAATGT
Found at i:21170696 original size:22 final size:21
Alignment explanation
Indices: 21170638--21170696 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
21170628 CAATATAAAG
*
21170638 GAAAAA-AATAGAAAAAAATAA
1 GAAAAATAATA-AAAAAAAAAA
**
21170659 GAAAAATAATGTAAAAAAAAA
1 GAAAAATAATAAAAAAAAAAA
*
21170680 GTAAAAGTAATAAAAAA
1 G-AAAAATAATAAAAAA
21170697 TATTTTTTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 15 0.50
22 15 0.50
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (21 bp):
GAAAAATAATAAAAAAAAAAA
Found at i:21174112 original size:30 final size:29
Alignment explanation
Indices: 21173981--21174114 Score: 78
Period size: 30 Copynumber: 4.5 Consensus size: 29
21173971 TTTTTCTTAC
* * *
21173981 CATTTTATAATTAATGTTAACA-TATTTT
1 CATTATATAATTAATGTAAACACGATTTT
* *
21174009 CA-TAGTATAGTTAATGTAAACATACACATTTT
1 CATTA-TATAATTAATGTAAAC--AC-GATTTT
* * * *
21174041 CATAATATAATTGATGTATAA-ATGCTTTCT
1 CATTATATAATTAATGTA-AACACGATTT-T
*
21174071 CA-TAGTTTAATTAATGTAAACACGATTTCT
1 CATTA-TATAATTAATGTAAACACGATTT-T
21174101 CATTATATAATTAA
1 CATTATATAATTAA
21174115 GCTAAAAATC
Statistics
Matches: 79, Mismatches: 16, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
27 1 0.01
28 16 0.20
29 6 0.08
30 33 0.42
31 2 0.03
32 18 0.23
33 3 0.04
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.43
Consensus pattern (29 bp):
CATTATATAATTAATGTAAACACGATTTT
Found at i:21176134 original size:41 final size:41
Alignment explanation
Indices: 21176089--21176220 Score: 237
Period size: 41 Copynumber: 3.2 Consensus size: 41
21176079 ACTGGCACTT
*
21176089 AGCCTGCTAGACATAAAGTCTGAAATGTTTCACCGGCGTCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGTCA
*
21176130 AGCCTGCTAGACTTAAAGTCTAAAATGTTTCACCGGCGTCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGTCA
*
21176171 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGACA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGTCA
21176212 AGCCTGCTA
1 AGCCTGCTA
21176221 AGCACCGAGC
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 87 1.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (41 bp):
AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGTCA
Found at i:21177884 original size:28 final size:26
Alignment explanation
Indices: 21177852--21177903 Score: 86
Period size: 28 Copynumber: 1.9 Consensus size: 26
21177842 TTTTTAATGT
21177852 TTATTATAACATAATAATATATTATACC
1 TTATTATAACAT-AT-ATATATTATACC
21177880 TTATTATAACATATATATATTATA
1 TTATTATAACATATATATATTATA
21177904 TTAATATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 10 0.42
27 2 0.08
28 12 0.50
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (26 bp):
TTATTATAACATATATATATTATACC
Found at i:21182235 original size:20 final size:20
Alignment explanation
Indices: 21182205--21182242 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
21182195 TATAGATACA
21182205 ATTTTTAATTTTTGTTTAGTT
1 ATTTTTAATTTTT-TTTAGTT
21182226 ATTTTT-ATTTTTTTTAG
1 ATTTTTAATTTTTTTTAG
21182243 GTCATGTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.74
Consensus pattern (20 bp):
ATTTTTAATTTTTTTTAGTT
Found at i:21185267 original size:25 final size:28
Alignment explanation
Indices: 21185238--21185289 Score: 83
Period size: 25 Copynumber: 2.0 Consensus size: 28
21185228 TATATTAGTA
21185238 AAGGTTAATATA-GTA-AAT-TAACAAT
1 AAGGTTAATATATGTATAATATAACAAT
21185263 AAGGTTAATATATGTATAATATAACAA
1 AAGGTTAATATATGTATAATATAACAA
21185290 ATTAAAATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 12 0.50
26 3 0.12
27 3 0.12
28 6 0.25
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.33
Consensus pattern (28 bp):
AAGGTTAATATATGTATAATATAACAAT
Found at i:21187204 original size:41 final size:41
Alignment explanation
Indices: 21187188--21187332 Score: 220
Period size: 41 Copynumber: 3.5 Consensus size: 41
21187178 GACTTTAAGT
*
21187188 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGCTTATAAAC
*
21187229 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGCTTATAAAC
* * *
21187270 CTAGCAGGCTACGTGCCAGTGATCTGAATCAGGC-CATAAGC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCA-GCTTATAAAC
*
21187311 CTAGCAGGCTAAGTGCCGGTGA
1 CTAGCAGGCTACGTGCCGGTGA
21187333 ATATGTTAAA
Statistics
Matches: 97, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
41 96 0.99
42 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.22
Consensus pattern (41 bp):
CTAGCAGGCTACGTGCCGGTGATCTGAATCAGCTTATAAAC
Found at i:21193244 original size:25 final size:28
Alignment explanation
Indices: 21193216--21193267 Score: 74
Period size: 25 Copynumber: 2.0 Consensus size: 28
21193206 TATATTAGTA
21193216 AAGGTTAACATA-GTA-AAT-TAACAAT
1 AAGGTTAACATATGTATAATATAACAAT
*
21193241 AAGGTTAATATATGTATAATATAACAA
1 AAGGTTAACATATGTATAATATAACAA
21193268 ATTAAAATGC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.48
26 3 0.13
27 3 0.13
28 6 0.26
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.31
Consensus pattern (28 bp):
AAGGTTAACATATGTATAATATAACAAT
Found at i:21195180 original size:41 final size:40
Alignment explanation
Indices: 21195151--21195267 Score: 162
Period size: 41 Copynumber: 2.9 Consensus size: 40
21195141 GTGAATTAAT
*
21195151 TCAGACTTTAAGTCTAGCAGGCTACGTGCCGGTGATCTGAA
1 TCAG-CTTTAAGCCTAGCAGGCTACGTGCCGGTGATCTGAA
* *
21195192 TCAGGTTATAAACCTAGCAGGCTACGTGCCGGTGATCTGAA
1 TCAGCTT-TAAGCCTAGCAGGCTACGTGCCGGTGATCTGAA
* *
21195233 TCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGA
1 TCA-GCTTTAAGCCTAGCAGGCTACGTGCCGGTGA
21195268 ATATGTTAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
40 2 0.03
41 63 0.94
42 2 0.03
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (40 bp):
TCAGCTTTAAGCCTAGCAGGCTACGTGCCGGTGATCTGAA
Found at i:21208197 original size:18 final size:18
Alignment explanation
Indices: 21208168--21208211 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
21208158 TGAGTCATGG
* *
21208168 AAGGAAGATGAAA-ATGA
1 AAGGAGGATGAAACATCA
21208185 AAGCGAGGATGAAACATCA
1 AAG-GAGGATGAAACATCA
21208204 AAGGAGGA
1 AAGGAGGA
21208212 AGACGAGGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 3 0.13
18 14 0.61
19 6 0.26
ACGTcount: A:0.52, C:0.07, G:0.32, T:0.09
Consensus pattern (18 bp):
AAGGAGGATGAAACATCA
Found at i:21208305 original size:25 final size:25
Alignment explanation
Indices: 21208259--21208306 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
21208249 ATTTCTTGTC
*
21208259 TTTAGTTTTTATTTCTTTTTAGATG
1 TTTAGTTTTTATTTCTTGTTAGATG
21208284 TTTA-TTTTTATTTCTTAGTTAGA
1 TTTAGTTTTTATTTCTT-GTTAGA
21208307 ATTTTGCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.19, C:0.04, G:0.10, T:0.67
Consensus pattern (25 bp):
TTTAGTTTTTATTTCTTGTTAGATG
Found at i:21216441 original size:44 final size:44
Alignment explanation
Indices: 21216370--21216518 Score: 160
Period size: 45 Copynumber: 3.3 Consensus size: 44
21216360 GATCGAAGTG
* * *
21216370 TGCCATGGTGTCTTTTAATCATGGTCTTATTTATTCTCTTCTTGA
1 TGCCATAGTGTC-TTTAACCATGGTCTTATTTATTCTCTTCGTGA
* *
21216415 TGCCATAGTGTCTTTAACCATGGTCTTATTCATTCTCTATCGTGT
1 TGCCATAGTGTCTTTAACCATGGTCTTATTTATTCTCT-TCGTGA
** *
21216460 TGTAATAGTGTCTTTCAACCATGGTCTT-TTTCATT-TGATTCGTGA
1 TGCCATAGTGTCTTT-AACCATGGTCTTATTT-ATTCT-CTTCGTGA
21216505 TGCCATAG-GTCTTT
1 TGCCATAGTGTCTTT
21216519 CAGCTATGGT
Statistics
Matches: 88, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
44 30 0.34
45 42 0.48
46 16 0.18
ACGTcount: A:0.17, C:0.19, G:0.17, T:0.47
Consensus pattern (44 bp):
TGCCATAGTGTCTTTAACCATGGTCTTATTTATTCTCTTCGTGA
Found at i:21216607 original size:45 final size:45
Alignment explanation
Indices: 21216499--21216661 Score: 226
Period size: 45 Copynumber: 3.7 Consensus size: 45
21216489 TTCATTTGAT
* *
21216499 TCGTGATGCCAT-AGGTCTTTCAG-CTATGGTTTTACTCGATAGAA
1 TCGTGATGCCATAACGTCTTTCAGTC-ATGGTCTTACTCGATAGAA
* *
21216543 -CGTGATGCCATAACGTCTTTTAGTCATGGTCTTGCTCGATAGAA
1 TCGTGATGCCATAACGTCTTTCAGTCATGGTCTTACTCGATAGAA
* *
21216587 TTGTGATGCCATAACATCTTTCAGTCATGGTCTTACTCGATAGAA
1 TCGTGATGCCATAACGTCTTTCAGTCATGGTCTTACTCGATAGAA
*
21216632 TCGTGATGCCATAACGTCTTTCGGT-ATGGT
1 TCGTGATGCCATAACGTCTTTCAGTCATGGT
21216662 GCCATAGTGT
Statistics
Matches: 105, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
43 11 0.10
44 31 0.30
45 63 0.60
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.36
Consensus pattern (45 bp):
TCGTGATGCCATAACGTCTTTCAGTCATGGTCTTACTCGATAGAA
Found at i:21233297 original size:20 final size:20
Alignment explanation
Indices: 21233264--21233308 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
21233254 TTAATTCTTT
* *
21233264 TTAATAATATAAGAATTAAA
1 TTAATAATAGAAGAACTAAA
* *
21233284 TTAATAATGGAAGAACTAAT
1 TTAATAATAGAAGAACTAAA
21233304 TTAAT
1 TTAAT
21233309 CAAAATCATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (20 bp):
TTAATAATAGAAGAACTAAA
Found at i:21235919 original size:22 final size:22
Alignment explanation
Indices: 21235894--21235949 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
21235884 CAAGGGAGCC
21235894 TTGTCTCGAGACA-ATCAAAAAA
1 TTGTCTCGAGACATAT-AAAAAA
* **
21235916 TTGTCTCAAGACATATAGCAAA
1 TTGTCTCGAGACATATAAAAAA
21235938 TTGTCTCGAGAC
1 TTGTCTCGAGAC
21235950 CTTAGGCTCC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 27 0.93
23 2 0.07
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.27
Consensus pattern (22 bp):
TTGTCTCGAGACATATAAAAAA
Found at i:21246056 original size:17 final size:16
Alignment explanation
Indices: 21246034--21246116 Score: 82
Period size: 17 Copynumber: 5.2 Consensus size: 16
21246024 TTAATTATTT
21246034 TTAAAATTTTTAAAAA
1 TTAAAATTTTTAAAAA
* * *
21246050 TTCAAAAATATTATAAA
1 TT-AAAATTTTTAAAAA
*
21246067 --AATATTTTTAAAAA
1 TTAAAATTTTTAAAAA
*
21246081 TTAAAATTATTAAAAAA
1 TTAAAATT-TTTAAAAA
21246098 TTAAAA-TTTTAAAAA
1 TTAAAATTTTTAAAAA
21246113 TTAA
1 TTAA
21246117 TTAAATGTTG
Statistics
Matches: 53, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
14 10 0.19
15 11 0.21
16 8 0.15
17 24 0.45
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (16 bp):
TTAAAATTTTTAAAAA
Found at i:21246077 original size:31 final size:29
Alignment explanation
Indices: 21246039--21246116 Score: 93
Period size: 32 Copynumber: 2.5 Consensus size: 29
21246029 TATTTTTAAA
21246039 ATTTTTAAAAATTCAAAAATATTATAAAAAT
1 ATTTTTAAAAATT-AAAAATATTA-AAAAAT
*
21246070 ATTTTTAAAAATTAAAATTATTAAAAAATT
1 ATTTTTAAAAATTAAAAATATTAAAAAA-T
*
21246100 AAAATTTTAAAAATTAA
1 --ATTTTTAAAAATTAA
21246117 TTAAATGTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
29 5 0.12
30 10 0.24
31 13 0.31
32 14 0.33
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (29 bp):
ATTTTTAAAAATTAAAAATATTAAAAAAT
Found at i:21247192 original size:9 final size:9
Alignment explanation
Indices: 21247178--21247217 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
21247168 AATTTTAATA
21247178 AAAAATTGT
1 AAAAATTGT
*
21247187 AAAAATCGT
1 AAAAATTGT
* *
21247196 AAAAAATAT
1 AAAAATTGT
21247205 AAAAATTGT
1 AAAAATTGT
21247214 AAAA
1 AAAA
21247218 TTTAGAAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.65, C:0.03, G:0.07, T:0.25
Consensus pattern (9 bp):
AAAAATTGT
Found at i:21247199 original size:18 final size:18
Alignment explanation
Indices: 21247176--21247247 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 18
21247166 TAAATTTTAA
*
21247176 TAAAAAATTGTAAAAATCG
1 TAAAAAA-TATAAAAATCG
*
21247195 TAAAAAATATAAAAATTG
1 TAAAAAATATAAAAATCG
** * *
21247213 TAAAATTTAGAAAAATCA
1 TAAAAAATATAAAAATCG
*
21247231 TTAAAAATATATAAAAT
1 TAAAAAATATA-AAAAT
21247248 GCATCAAAAA
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
18 29 0.71
19 12 0.29
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (18 bp):
TAAAAAATATAAAAATCG
Found at i:21247554 original size:19 final size:18
Alignment explanation
Indices: 21247532--21247593 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 18
21247522 TGTCTTTATA
21247532 TTTTATAATCTTTTACAAT
1 TTTTATAAT-TTTTACAAT
*
21247551 TTTTATAAAGTTTTACAATAT
1 TTTTAT-AATTTTTAC-A-AT
* *
21247572 TTTTATGATTTTTATAAT
1 TTTTATAATTTTTACAAT
21247590 TTTT
1 TTTT
21247594 TTCTAATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
18 6 0.17
19 13 0.36
20 9 0.25
21 8 0.22
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (18 bp):
TTTTATAATTTTTACAAT
Found at i:21247584 original size:9 final size:9
Alignment explanation
Indices: 21247532--21247593 Score: 52
Period size: 9 Copynumber: 6.4 Consensus size: 9
21247522 TGTCTTTATA
21247532 TTTTATAAT
1 TTTTATAAT
*
21247541 CTTTTACAAT
1 -TTTTATAAT
*
21247551 TTTTATAAAG
1 TTTTAT-AAT
*
21247561 TTTTACAATAT
1 TTTTA-TA-AT
*
21247572 TTTTATGAT
1 TTTTATAAT
21247581 TTTTATAAT
1 TTTTATAAT
21247590 TTTT
1 TTTT
21247594 TTCTAATTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
9 19 0.46
10 16 0.39
11 6 0.15
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (9 bp):
TTTTATAAT
Found at i:21247584 original size:20 final size:20
Alignment explanation
Indices: 21247532--21247605 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 20
21247522 TGTCTTTATA
21247532 TTTTATAATCTTTTAC-A-AT
1 TTTTATAAT-TTTTACAATAT
*
21247551 TTTTATAAAGTTTTACAATAT
1 TTTTAT-AATTTTTACAATAT
* * *
21247572 TTTTATGATTTTTATAATTT
1 TTTTATAATTTTTACAATAT
*
21247592 TTTTCTAATTTTTA
1 TTTTATAATTTTTA
21247606 TTTTTATTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
19 12 0.27
20 25 0.56
21 8 0.18
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTTATAATTTTTACAATAT
Found at i:21258197 original size:9 final size:10
Alignment explanation
Indices: 21258155--21258199 Score: 51
Period size: 9 Copynumber: 4.8 Consensus size: 10
21258145 TATTCTAATC
21258155 TATT-TTTTA
1 TATTATTTTA
*
21258164 TATT-TATTA
1 TATTATTTTA
*
21258173 CATTATTTTA
1 TATTATTTTA
21258183 TATTATTTT-
1 TATTATTTTA
21258192 TATTATTT
1 TATTATTT
21258200 ATTAATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
9 19 0.61
10 12 0.39
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (10 bp):
TATTATTTTA
Found at i:21287000 original size:19 final size:19
Alignment explanation
Indices: 21286978--21287018 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
21286968 TGGTTTTTAA
21286978 TTTTTCCATCTTTTCTTTT
1 TTTTTCCATCTTTTCTTTT
**
21286997 TTTTTCTTTCTTTTCTTTT
1 TTTTTCCATCTTTTCTTTT
21287016 TTT
1 TTT
21287019 CATCTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTTCCATCTTTTCTTTT
Found at i:21294606 original size:90 final size:86
Alignment explanation
Indices: 21294503--21294694 Score: 217
Period size: 90 Copynumber: 2.2 Consensus size: 86
21294493 TCATAAAAAT
* *
21294503 GCCACTAAAGAACATGATCTTTAACAGTGCTTTTTCTACAAACG-TCGCTAAA-AACATGGTCTT
1 GCCACTAAAGAACATGATCTATAACAGTG-TTTTTCTACAAACGCT-GCTAAAGAACATGATCTT
*
21294566 TAGTTTAGCGGCGTTTTTTCTACAAAC
64 TAG--CAGC-G-GTTTTTTCTACAAAC
* * * * * *
21294593 GCCACTAATGAACATGGTCTATAGCGGTGTTTTTTTACAAATGCTGCTAAAGAACATGATCTTTA
1 GCCACTAAAGAACATGATCTATAACAGTGTTTTTCTACAAACGCTGCTAAAGAACATGATCTTTA
*
21294658 GCAGCGTTTTTTTCTACAAAC
66 GCAGCGGTTTTTTCTACAAAC
*
21294679 GCCACTAAAGATCATG
1 GCCACTAAAGAACATG
21294695 TTTTATAGCG
Statistics
Matches: 88, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
86 28 0.32
87 1 0.01
88 3 0.03
89 18 0.20
90 38 0.43
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (86 bp):
GCCACTAAAGAACATGATCTATAACAGTGTTTTTCTACAAACGCTGCTAAAGAACATGATCTTTA
GCAGCGGTTTTTTCTACAAAC
Found at i:21294648 original size:42 final size:43
Alignment explanation
Indices: 21294503--21294710 Score: 177
Period size: 42 Copynumber: 4.7 Consensus size: 43
21294493 TCATAAAAAT
* * * * *
21294503 GCCACTAAAGAACATGATCTTTAACAGTGCTTTTTCTACAAAC
1 GCCACTAAAGAACATGATCTATAGCGGCGTTTTTTCTACAAAC
* * *
21294546 GTCGCTAAA-AACATGGTCTTTAGTTTAGCGGCGTTTTTTCTACAAAC
1 GCCACTAAAGAACATGATC--TA---TAGCGGCGTTTTTTCTACAAAC
* * * *
21294593 GCCACTAATGAACATGGTCTATAGCGGTGTTTTTT-TACAAAT
1 GCCACTAAAGAACATGATCTATAGCGGCGTTTTTTCTACAAAC
** * *
21294635 GCTGCTAAAGAACATGATCTTTAGCAGCGTTTTTTTCTACAAAC
1 GCCACTAAAGAACATGATCTATAGCGGCG-TTTTTTCTACAAAC
* * *
21294679 GCCACTAAAGATCATGTTTTATAGCGGCGTTT
1 GCCACTAAAGAACATGATCTATAGCGGCGTTT
21294711 GTAGGAAAAG
Statistics
Matches: 129, Mismatches: 28, Indels: 16
0.75 0.16 0.09
Matches are distributed among these distances:
42 36 0.28
43 29 0.22
44 29 0.22
46 2 0.02
47 24 0.19
48 9 0.07
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (43 bp):
GCCACTAAAGAACATGATCTATAGCGGCGTTTTTTCTACAAAC
Found at i:21294702 original size:86 final size:86
Alignment explanation
Indices: 21294569--21294746 Score: 225
Period size: 86 Copynumber: 2.1 Consensus size: 86
21294559 TGGTCTTTAG
* * * ***
21294569 TTTAGCGGCGTTTTTTCTACAAACGCCACTAATGAACATGGTCTATAGCGGTGTTT-TTTTACAA
1 TTTAGCAGCGTTTTTTCTACAAACGCCACTAAAGAACATGGTCTATAGCGGCGTTTGTAGGA-AA
*
21294633 A-TGCTGCTAAAGAACATGATC
65 AGTGCCGCTAAAGAACATGATC
* * *
21294654 TTTAGCAGCGTTTTTTTCTACAAACGCCACTAAAGATCATGTTTTATAGCGGCGTTTGTAGGAAA
1 TTTAGCAGCG-TTTTTTCTACAAACGCCACTAAAGAACATGGTCTATAGCGGCGTTTGTAGGAAA
*
21294719 AGTGCCGCTAAAGACCATGATC
65 AGTGCCGCTAAAGAACATGATC
21294741 TTTAGC
1 TTTAGC
21294747 GGGGTTTGTG
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
85 9 0.11
86 44 0.56
87 26 0.33
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (86 bp):
TTTAGCAGCGTTTTTTCTACAAACGCCACTAAAGAACATGGTCTATAGCGGCGTTTGTAGGAAAA
GTGCCGCTAAAGAACATGATC
Found at i:21294762 original size:43 final size:42
Alignment explanation
Indices: 21294683--21294766 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 42
21294673 ACAAACGCCA
* *
21294683 CTAAAGATCATGTTTTATAGCGGCGTTTGTAGGAAAAGTGCCG
1 CTAAAGACCATGTCTTATAGCGGCGTTTGTAGGAAAA-TGCCG
*
21294726 CTAAAGACCATGATCTT-TAGCGGGGTTTGT-GAGAAAATGCC
1 CTAAAGACCATG-TCTTATAGCGGCGTTTGTAG-GAAAATGCC
21294767 ATTAACTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
42 5 0.14
43 28 0.78
44 3 0.08
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (42 bp):
CTAAAGACCATGTCTTATAGCGGCGTTTGTAGGAAAATGCCG
Found at i:21303200 original size:25 final size:25
Alignment explanation
Indices: 21303166--21303231 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
21303156 AAAAACTTAC
*
21303166 ACGGCGATGCAGCAGAGGACTATTG
1 ACGGCGATGCAGCAGAGGACTATCG
* * *
21303191 ACGGCAATGCAGTAGAGGACTGTCG
1 ACGGCGATGCAGCAGAGGACTATCG
*
21303216 ACGGCGATGTAGCAGA
1 ACGGCGATGCAGCAGA
21303232 TGTTGGGGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.29, C:0.20, G:0.36, T:0.15
Consensus pattern (25 bp):
ACGGCGATGCAGCAGAGGACTATCG
Found at i:21305531 original size:28 final size:29
Alignment explanation
Indices: 21305500--21305555 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
21305490 TATTATTATT
*
21305500 TATATAAATATATAAATTA-ATTATAAAG
1 TATATAAATAAATAAATTACATTATAAAG
* * *
21305528 TATATTATTAAATTAATTACATTATAAA
1 TATATAAATAAATAAATTACATTATAAA
21305556 TATTATATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (29 bp):
TATATAAATAAATAAATTACATTATAAAG
Found at i:21306332 original size:18 final size:18
Alignment explanation
Indices: 21306309--21306351 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
21306299 ATGTGAGGTA
21306309 AGTATTAATATTAGTATT
1 AGTATTAATATTAGTATT
*
21306327 AGTATTATTATTAGTATT
1 AGTATTAATATTAGTATT
*
21306345 ATTATTA
1 AGTATTA
21306352 TGAGTGGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
AGTATTAATATTAGTATT
Found at i:21306352 original size:6 final size:6
Alignment explanation
Indices: 21306309--21306351 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
21306299 ATGTGAGGTA
* * *
21306309 AGTATT AATATT AGTATT AGTATT ATTATT AGTATT ATTATT A
1 AGTATT AGTATT AGTATT AGTATT AGTATT AGTATT AGTATT A
21306352 TGAGTGGGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.53
Consensus pattern (6 bp):
AGTATT
Found at i:21306536 original size:24 final size:25
Alignment explanation
Indices: 21306504--21306563 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 25
21306494 CGGATTAATT
21306504 ATTG-ATTGAAAG-GTGGAAAAA-TG
1 ATTGAATTGAAAGTGT-GAAAAAGTG
21306527 ATTGAATTGAAAGTGTGAAAAAGTGTG
1 ATTGAATTGAAAGTGTGAAAAA--GTG
21306554 ATTGAATTGA
1 ATTGAATTGA
21306564 GAATATATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.12
24 14 0.44
25 2 0.06
27 12 0.38
ACGTcount: A:0.42, C:0.00, G:0.28, T:0.30
Consensus pattern (25 bp):
ATTGAATTGAAAGTGTGAAAAAGTG
Found at i:21306766 original size:37 final size:39
Alignment explanation
Indices: 21306707--21306802 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
21306697 CGGATAGATT
* * * *
21306707 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
21306744 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
21306783 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
21306803 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:21312825 original size:28 final size:29
Alignment explanation
Indices: 21312794--21312849 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
21312784 TATTATTATT
*
21312794 TATATAAATATATAAATTA-ATTATAAAG
1 TATATAAATAAATAAATTACATTATAAAG
* * *
21312822 TATATTATTAAATTAATTACATTATAAA
1 TATATAAATAAATAAATTACATTATAAA
21312850 TATTATATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (29 bp):
TATATAAATAAATAAATTACATTATAAAG
Found at i:21313620 original size:18 final size:18
Alignment explanation
Indices: 21313597--21313639 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
21313587 ATGTGAGGTA
21313597 AGTATTAATATTAGTATT
1 AGTATTAATATTAGTATT
*
21313615 AGTATTATTATTAGTATT
1 AGTATTAATATTAGTATT
*
21313633 ATTATTA
1 AGTATTA
21313640 TGAGTGGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
AGTATTAATATTAGTATT
Found at i:21313640 original size:6 final size:6
Alignment explanation
Indices: 21313597--21313639 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
21313587 ATGTGAGGTA
* * *
21313597 AGTATT AATATT AGTATT AGTATT ATTATT AGTATT ATTATT A
1 AGTATT AGTATT AGTATT AGTATT AGTATT AGTATT AGTATT A
21313640 TGAGTGGGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.53
Consensus pattern (6 bp):
AGTATT
Found at i:21313832 original size:24 final size:25
Alignment explanation
Indices: 21313800--21313859 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 25
21313790 CGGATTAATT
21313800 ATTG-ATTGAAAG-GTGGAAAAA-TG
1 ATTGAATTGAAAGTGT-GAAAAAGTG
21313823 ATTGAATTGAAAGTGTGAAAAAGTGTG
1 ATTGAATTGAAAGTGTGAAAAA--GTG
21313850 ATTGAATTGA
1 ATTGAATTGA
21313860 GAATATATGT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.12
24 14 0.44
25 2 0.06
27 12 0.38
ACGTcount: A:0.42, C:0.00, G:0.28, T:0.30
Consensus pattern (25 bp):
ATTGAATTGAAAGTGTGAAAAAGTG
Found at i:21314072 original size:39 final size:39
Alignment explanation
Indices: 21313962--21314096 Score: 114
Period size: 39 Copynumber: 3.4 Consensus size: 39
21313952 GACCTCGAGT
* * *
21313962 CGATGAGACACTGGGTGTC-ACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCAAC--TATTACTTCGGCTAG-TC
** ** *
21314003 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
* *
21314041 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAACTATTACTTCG-GCTAGTC
*
21314080 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
21314097 CCATTCTGGT
Statistics
Matches: 75, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
38 19 0.25
39 35 0.47
40 4 0.05
41 15 0.20
42 2 0.03
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
Found at i:21315768 original size:6 final size:7
Alignment explanation
Indices: 21315749--21315776 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
21315739 GTAGTGATTC
21315749 TTAAAAA
1 TTAAAAA
21315756 TTAAAAA
1 TTAAAAA
21315763 TTAAAAA
1 TTAAAAA
21315770 TTAAAAA
1 TTAAAAA
21315777 AAAACCTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
TTAAAAA
Found at i:21316162 original size:40 final size:39
Alignment explanation
Indices: 21316087--21316226 Score: 129
Period size: 40 Copynumber: 3.5 Consensus size: 39
21316077 CAAAAGGTCA
* * * *
21316087 AGCATTAGCG-GCGTTTCTAAAACAAACGTCGCTATAGGTTG
1 AGCATTAGCGCGC-TTT-TCAAA-AAACGCCACTATAGATTG
** *
21316128 AGCATTAGCTGCGCTTTTTGAAAAACGCCACTATAGATCG
1 AGCATTAGC-GCGCTTTTCAAAAAACGCCACTATAGATTG
* * *
21316168 AGCATTAGCAGTGCTTTTCAAAAAATGCCGCTATAGATTG
1 AGCATTAGC-GCGCTTTTCAAAAAACGCCACTATAGATTG
21316208 AGCATTAGCGACGCTTTTC
1 AGCATTAGCG-CGCTTTTC
21316227 GGAAAACACC
Statistics
Matches: 82, Mismatches: 14, Indels: 7
0.80 0.14 0.07
Matches are distributed among these distances:
39 1 0.01
40 63 0.77
41 12 0.15
42 4 0.05
43 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (39 bp):
AGCATTAGCGCGCTTTTCAAAAAACGCCACTATAGATTG
Found at i:21316331 original size:40 final size:40
Alignment explanation
Indices: 21316272--21316360 Score: 117
Period size: 40 Copynumber: 2.2 Consensus size: 40
21316262 AGCTTTAGTG
* * * *
21316272 GCATTAGCGGCGCTTTTTAAAAATCG-CAGCAATAGATCGA
1 GCATTAGCGACGATATTTAAAAAACGCCA-CAATAGATCGA
*
21316312 GCATTAGCGACGATATTTAAAAAACGCCACTATAGATCGA
1 GCATTAGCGACGATATTTAAAAAACGCCACAATAGATCGA
21316352 GCATTAGCG
1 GCATTAGCG
21316361 GCACTTTTTG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
40 41 0.95
41 2 0.05
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (40 bp):
GCATTAGCGACGATATTTAAAAAACGCCACAATAGATCGA
Found at i:21316387 original size:143 final size:146
Alignment explanation
Indices: 21316129--21316711 Score: 436
Period size: 143 Copynumber: 3.9 Consensus size: 146
21316119 TATAGGTTGA
* * * * *
21316129 GCATTAGCTGCGCTTTTTGAAAAA-CGCCA-CTATAGATCGAGCATTAGC-AGTGCTTTTCAAAA
1 GCATTAGCAGCGCTTTTTAAAAAATCG-CAGCAATAGATCGAGCATTAGCGA-CGATTTTCAAAA
* * * * * **
21316191 AATGCCGCTATAGATTGAGCATTAGCGACGCTTTTCGGAAAACACCGCAAAAAAGTTGAGCAAAA
64 AACGCCACTATAGATCGAGCATTAGCGGCACTTTTCGGAAAATGCCGCAAAAAAGTTGAGCAAAA
21316256 CA-AG-TGAGCTTTAGTG
129 CATAGTTGAGCTTTAGTG
*
21316272 GCATTAGCGGCGCTTTTT-AAAAATCGCAGCAATAGATCGAGCATTAGCGACGATATTT-AAAAA
1 GCATTAGCAGCGCTTTTTAAAAAATCGCAGCAATAGATCGAGCATTAGCGACGAT-TTTCAAAAA
*
21316335 ACGCCACTATAGATCGAGCATTAGCGGCACTTTTTGGAAAATGCCGCAAAAAAGTTGAGCAAAAT
65 ACGCCACTATAGATCGAGCATTAGCGGCACTTTTCGGAAAATGCCGCAAAAAAGTTGAGC-AAA-
*
21316400 GACATCGTTTGTTGTTGAGCTTTAGTG
128 -ACA-------TAGTTGAGCTTTAGTG
* * * * * *
21316427 GCATTAGCAGTGCTTTTTAAAAAAT-GCTGCAATAAATCGAGAATTAGCGGC-ACTTTGTCGAAA
1 GCATTAGCAGCGCTTTTTAAAAAATCGCAGCAATAGATCGAGCATTAGCGACGA-TTT-TCAAAA
* * *
21316490 AACGCCTCTATAGATCGAGCATTAGCGGCACTTTTCGAAAAAATGCCACAAAAAAGTTGAGCAAA
64 AACGCCACTATAGATCGAGCATTAGCGGCACTTTTCG-GAAAATGCCGCAAAAAAGTTGAGCAAA
*
21316555 ACGACGTTGTTTGTTGTTGAGCTTTAGTG
128 AC-A---------TAGTTGAGCTTTAGTG
* * * * * * * * *
21316584 GCATTAGCTGTGCTTTTTTAAAAAA-CGTC-GAAATGGATTGAGAATTAGCGGCGCTTGTT-GAA
1 GCATTAGCAGCGC-TTTTTAAAAAATCG-CAGCAATAGATCGAGCATTAGCGACGATT-TTCAAA
* * * * * * * *
21316646 AAATGCCGCTATAGATCGAGCATTAGTGGCGCTTTTTGTAAAACGCCGTAAAAAAGTTGAG-AAA
63 AAACGCCACTATAGATCGAGCATTAGCGGCACTTTTCGGAAAATGCCGCAAAAAAGTTGAGCAAA
21316710 AC
128 AC
21316712 GACCTCGTTT
Statistics
Matches: 371, Mismatches: 40, Indels: 46
0.81 0.09 0.10
Matches are distributed among these distances:
142 7 0.02
143 96 0.26
144 7 0.02
146 3 0.01
154 6 0.02
155 58 0.16
156 66 0.18
157 92 0.25
158 34 0.09
159 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.27
Consensus pattern (146 bp):
GCATTAGCAGCGCTTTTTAAAAAATCGCAGCAATAGATCGAGCATTAGCGACGATTTTCAAAAAA
CGCCACTATAGATCGAGCATTAGCGGCACTTTTCGGAAAATGCCGCAAAAAAGTTGAGCAAAACA
TAGTTGAGCTTTAGTG
Found at i:21316587 original size:157 final size:155
Alignment explanation
Indices: 21316260--21316746 Score: 590
Period size: 157 Copynumber: 3.1 Consensus size: 155
21316250 GCAAAACAAG
* * * * *
21316260 TGAGCTTTAGTGGCATTAGCGGCGCTTTTT-AAAAATCGCAGCAATAGATCGAGCATTAGCGACG
1 TGAGCTTTAGTGGCATTAGCAGTGCTTTTTAAAAAAT-GCTGCAATAGATCGAGAATTAGCGGC-
* *
21316324 A-TATT-TAAAAAACGCCACTATAGATCGAGCATTAGCGGCACTTTTTGGAAAATGCCGCAAAAA
64 ACT-TTGTGAAAAACGCCACTATAGATCGAGCATTAGCGGCACTTTTTGAAAAATGCCGCAAAAA
*
21316387 AGTTGAGCAAAATGACATCGTTTGTTGT
128 AGTTGAGCAAAACGACATCGTTTGTTGT
*
21316415 TGAGCTTTAGTGGCATTAGCAGTGCTTTTTAAAAAATGCTGCAATAAATCGAGAATTAGCGGCAC
1 TGAGCTTTAGTGGCATTAGCAGTGCTTTTTAAAAAATGCTGCAATAGATCGAGAATTAGCGGCAC
* * *
21316480 TTTGTCGAAAAACGCCTCTATAGATCGAGCATTAGCGGCACTTTTCGAAAAAATGCCACAAAAAA
66 TTTGT-GAAAAACGCCACTATAGATCGAGCATTAGCGGCACTTTTTG-AAAAATGCCGCAAAAAA
* *
21316545 GTTGAGCAAAACGACGTTGTTTGTTGT
129 GTTGAGCAAAACGACATCGTTTGTTGT
* * * * *
21316572 TGAGCTTTAGTGGCATTAGCTGTGCTTTTTTAAAAAACG-TCGAAATGGATTGAGAATTAGCGGC
1 TGAGCTTTAGTGGCATTAGCAGTGC-TTTTTAAAAAATGCT-GCAATAGATCGAGAATTAGCGGC
* * * * * * * *
21316636 GC-TTGTTGAAAAATGCCGCTATAGATCGAGCATTAGTGGCGCTTTTTGTAAAACGCCGTAAAAA
64 ACTTTG-TGAAAAACGCCACTATAGATCGAGCATTAGCGGCACTTTTTGAAAAATGCCGCAAAAA
* *
21316700 AGTTGAG-AAAACGACCTCGTTTGTTCT
128 AGTTGAGCAAAACGACATCGTTTGTTGT
*
21316727 CGAGCTTTAGTGGCATTAGC
1 TGAGCTTTAGTGGCATTAGC
21316747 GTCATTTTTA
Statistics
Matches: 290, Mismatches: 34, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
154 3 0.01
155 88 0.30
156 63 0.22
157 103 0.36
158 33 0.11
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (155 bp):
TGAGCTTTAGTGGCATTAGCAGTGCTTTTTAAAAAATGCTGCAATAGATCGAGAATTAGCGGCAC
TTTGTGAAAAACGCCACTATAGATCGAGCATTAGCGGCACTTTTTGAAAAATGCCGCAAAAAAGT
TGAGCAAAACGACATCGTTTGTTGT
Found at i:21316814 original size:21 final size:22
Alignment explanation
Indices: 21316785--21316846 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
21316775 ATCATTTTAT
21316785 TTTAGGGTTTAGGGTTTATTA-
1 TTTAGGGTTTAGGGTTTATTAG
* **
21316806 TTTAAGGTTTAATGTTTA-TAG
1 TTTAGGGTTTAGGGTTTATTAG
21316827 TTTAGGGTTTTAGGGTTTAT
1 TTTAGGG-TTTAGGGTTTAT
21316847 GATATAATGT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
20 2 0.06
21 21 0.66
22 9 0.28
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.53
Consensus pattern (22 bp):
TTTAGGGTTTAGGGTTTATTAG
Found at i:21316888 original size:14 final size:14
Alignment explanation
Indices: 21316871--21316915 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
21316861 TATTTTGGGA
21316871 TTAGAGTTT-TGAGT
1 TTAGAGTTTATG-GT
*
21316885 TTAGGGTTTATGGT
1 TTAGAGTTTATGGT
21316899 TTAGAGTTTATGGT
1 TTAGAGTTTATGGT
21316913 TTA
1 TTA
21316916 TGGTTTTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 26 0.93
15 2 0.07
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (14 bp):
TTAGAGTTTATGGT
Found at i:21316893 original size:7 final size:7
Alignment explanation
Indices: 21316883--21316921 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
21316873 AGAGTTTTGA
*
21316883 GTTTAGG
1 GTTTATG
21316890 GTTTATG
1 GTTTATG
21316897 GTTTA-G
1 GTTTATG
21316903 AGTTTATG
1 -GTTTATG
21316911 GTTTATG
1 GTTTATG
21316918 GTTT
1 GTTT
21316922 TATAGTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
6 1 0.03
7 27 0.93
8 1 0.03
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (7 bp):
GTTTATG
Found at i:21316905 original size:21 final size:21
Alignment explanation
Indices: 21316876--21316921 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
21316866 TGGGATTAGA
*
21316876 GTTTTGAGTTTAGGGTTTATG
1 GTTTAGAGTTTAGGGTTTATG
*
21316897 GTTTAGAGTTTATGGTTTATG
1 GTTTAGAGTTTAGGGTTTATG
21316918 GTTT
1 GTTT
21316922 TATAGTTAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.15, C:0.00, G:0.30, T:0.54
Consensus pattern (21 bp):
GTTTAGAGTTTAGGGTTTATG
Found at i:21317166 original size:14 final size:14
Alignment explanation
Indices: 21317127--21317207 Score: 60
Period size: 14 Copynumber: 5.9 Consensus size: 14
21317117 AAGGTTTAAG
21317127 GTTTATGATTTAGT
1 GTTTATGATTTAGT
*
21317141 G-TTAAGAGTTTAGT
1 GTTTATGA-TTTAGT
* *
21317155 GTTTACGATTTAGG
1 GTTTATGATTTAGT
* *
21317169 GTGTA-GGTTTA-T
1 GTTTATGATTTAGT
*
21317181 GGTTTATGGTTTAGT
1 -GTTTATGATTTAGT
*
21317196 GTTTAGGATTTA
1 GTTTATGATTTA
21317208 TGGTTTAGTG
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
13 14 0.26
14 33 0.62
15 6 0.11
ACGTcount: A:0.21, C:0.01, G:0.28, T:0.49
Consensus pattern (14 bp):
GTTTATGATTTAGT
Found at i:21317184 original size:7 final size:7
Alignment explanation
Indices: 21317174--21317228 Score: 62
Period size: 7 Copynumber: 7.9 Consensus size: 7
21317164 TTAGGGTGTA
21317174 GGTTTAT
1 GGTTTAT
21317181 GGTTTAT
1 GGTTTAT
21317188 GGTTTA-
1 GGTTTAT
21317194 GTGTTTA-
1 G-GTTTAT
21317201 GGATTTAT
1 GG-TTTAT
21317209 GGTTTAGT
1 GGTTTA-T
21317217 GG-TTAT
1 GGTTTAT
21317223 GGTTTA
1 GGTTTA
21317229 GGGGTTAGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
6 5 0.12
7 33 0.77
8 5 0.12
ACGTcount: A:0.16, C:0.00, G:0.31, T:0.53
Consensus pattern (7 bp):
GGTTTAT
Found at i:21317199 original size:21 final size:21
Alignment explanation
Indices: 21317113--21317237 Score: 96
Period size: 21 Copynumber: 6.0 Consensus size: 21
21317103 ATATTTTGAG
* *
21317113 GTTTAAGGTTTAAGGTTTA-T
1 GTTTATGGTTTAGGGTTTAGT
* *
21317133 GATTTA-GTGTTAAGAGTTTAGT
1 G-TTTATG-GTTTAGGGTTTAGT
* * *
21317155 GTTTACGATTTAGGGTGTAG-
1 GTTTATGGTTTAGGGTTTAGT
*
21317175 GTTTATGGTTTATGGTTTAGT
1 GTTTATGGTTTAGGGTTTAGT
*
21317196 GTTTA-GGATTTATGGTTTAGT
1 GTTTATGG-TTTAGGGTTTAGT
* *
21317217 GGTTATGGTTTAGGGGTTAGT
1 GTTTATGGTTTAGGGTTTAGT
21317238 TGTAACAGCC
Statistics
Matches: 84, Mismatches: 14, Indels: 13
0.76 0.13 0.12
Matches are distributed among these distances:
20 20 0.24
21 59 0.70
22 5 0.06
ACGTcount: A:0.20, C:0.01, G:0.31, T:0.48
Consensus pattern (21 bp):
GTTTATGGTTTAGGGTTTAGT
Found at i:21317234 original size:14 final size:14
Alignment explanation
Indices: 21317177--21317235 Score: 57
Period size: 14 Copynumber: 4.2 Consensus size: 14
21317167 GGGTGTAGGT
* *
21317177 TTATGGTTTATGGT
1 TTATGGTTTAGGGG
**
21317191 TTA-GTGTTTAGGAT
1 TTATG-GTTTAGGGG
*
21317205 TTATGGTTTAGTGG
1 TTATGGTTTAGGGG
21317219 TTATGGTTTAGGGG
1 TTATGGTTTAGGGG
21317233 TTA
1 TTA
21317236 GTTGTAACAG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
13 1 0.03
14 35 0.95
15 1 0.03
ACGTcount: A:0.17, C:0.00, G:0.32, T:0.51
Consensus pattern (14 bp):
TTATGGTTTAGGGG
Found at i:21318665 original size:26 final size:26
Alignment explanation
Indices: 21318630--21318681 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
21318620 AAATGAAAAG
*
21318630 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
21318656 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
21318682 TTTAGTGGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.13, C:0.23, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:21318694 original size:105 final size:104
Alignment explanation
Indices: 21318448--21318713 Score: 430
Period size: 104 Copynumber: 2.6 Consensus size: 104
21318438 TGTATATAAA
** * *
21318448 AGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTTATTGGTGGTGCTAAGTGCGTGATCCACCATATCTT
*
21318513 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
21318552 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATC
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTT-ATTGGTGGTGCTAAGTGCG-TGATCCACCATATC
21318616 TTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATT-CCCCG
64 TTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
21318655 AGGGGTTGCTAAGTGCTGATTCCCCGATTTAGTGGTGGTGCTAAGTGCGGGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTTATTGGTGGTGCTAAGTGCGTGATCCACCA
21318714 ATAACGGCTA
Statistics
Matches: 152, Mismatches: 7, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
102 26 0.17
103 35 0.23
104 51 0.34
105 39 0.26
106 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.30, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTTATTGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:21319957 original size:29 final size:28
Alignment explanation
Indices: 21319924--21319986 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 28
21319914 GGGTGTTACA
21319924 TTAGGGGCTTAGGGTTTAAAGTTTA-TGAT
1 TTAGGGGCTTAGGGTTT-AAGTTTAGTG-T
*
21319953 TTAGGGGCTTAGGGTTTATGTTTAGTGT
1 TTAGGGGCTTAGGGTTTAAGTTTAGTGT
21319981 TTAGGG
1 TTAGGG
21319987 TCTGATTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 13 0.41
29 19 0.59
ACGTcount: A:0.19, C:0.03, G:0.35, T:0.43
Consensus pattern (28 bp):
TTAGGGGCTTAGGGTTTAAGTTTAGTGT
Found at i:21322720 original size:43 final size:43
Alignment explanation
Indices: 21322662--21322865 Score: 300
Period size: 43 Copynumber: 4.7 Consensus size: 43
21322652 AGAAATAAAT
* * *
21322662 GCCGCTAAAGGCCAAGACCTTTAGCGGCGCTTTTCCCGCAAAC
1 GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTCCCCACAAAC
*
21322705 ACCGCTAAAGACCAAGACCTTTAGCGGCGCTTTCCCCACAAAC
1 GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTCCCCACAAAC
* *
21322748 GCCGCTAAAGGCCAAGACCTTTAGCGGCGCCTTCCCCACAAAC
1 GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTCCCCACAAAC
* * * *
21322791 GCCGCTAAAGACCAAGATCTTTAGCGACGCTTTCACCACAAAT
1 GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTCCCCACAAAC
* *
21322834 GCCGCTAAAGACCATGACCTTTAGCGACGCTT
1 GCCGCTAAAGACCAAGACCTTTAGCGGCGCTT
21322866 CTACCACAAA
Statistics
Matches: 146, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 146 1.00
ACGTcount: A:0.27, C:0.35, G:0.20, T:0.18
Consensus pattern (43 bp):
GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTCCCCACAAAC
Found at i:21322872 original size:43 final size:42
Alignment explanation
Indices: 21322662--21322927 Score: 293
Period size: 43 Copynumber: 6.2 Consensus size: 42
21322652 AGAAATAAAT
* *
21322662 GCCGCTAAAGGCCAAGACCTTTAGCGGCGCTTTTCCCGCAAAC
1 GCCGCTAAAGACCAAGACCTTTAGCGGCGC-TTTCCCACAAAC
*
21322705 ACCGCTAAAGACCAAGACCTTTAGCGGCGCTTTCCCCACAAAC
1 GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTT-CCCACAAAC
* *
21322748 GCCGCTAAAGGCCAAGACCTTTAGCGGCGCCTTCCCCACAAAC
1 GCCGCTAAAGACCAAGACCTTTAGCGGCG-CTTTCCCACAAAC
* * *
21322791 GCCGCTAAAGACCAAGATCTTTAGCGACGCTTTCACCACAAAT
1 GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTC-CCACAAAC
* * *
21322834 GCCGCTAAAGACCATGACCTTTAGCGACGCTTCTACCACAAAC
1 GCCGCTAAAGACCAAGACCTTTAGCGGCGCTT-TCCCACAAAC
* * * * * * *
21322877 -CCTACTATAGA-TAAAACCTTTAGCGGCGCTCCTCGCAAAAAC
1 GCC-GCTAAAGACCAAGACCTTTAGCGGCGCT-TTCCCACAAAC
21322919 GCCGCTAAA
1 GCCGCTAAA
21322928 AATATAACCT
Statistics
Matches: 189, Mismatches: 27, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
42 35 0.19
43 150 0.79
44 4 0.02
ACGTcount: A:0.29, C:0.35, G:0.18, T:0.18
Consensus pattern (42 bp):
GCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTCCCACAAAC
Found at i:21327503 original size:21 final size:21
Alignment explanation
Indices: 21327466--21327521 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
21327456 ACCCTTGAAA
* *
21327466 CCCTAAATCCCTAACTCTTAGC
1 CCCTAAA-CCTTAACTCTTAAC
* *
21327488 CCCTAACCCTTAACTCTTAAT
1 CCCTAAACCTTAACTCTTAAC
21327509 CCCTAAACCTTAA
1 CCCTAAACCTTAA
21327522 ATCATAACAC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 23 0.79
22 6 0.21
ACGTcount: A:0.30, C:0.39, G:0.02, T:0.29
Consensus pattern (21 bp):
CCCTAAACCTTAACTCTTAAC
Found at i:21327755 original size:25 final size:25
Alignment explanation
Indices: 21327726--21327773 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
21327716 TATATGAAAT
*
21327726 TATTTAATATATAAATTAAAAAACA
1 TATTTAAAATATAAATTAAAAAACA
21327751 TATTTAAAATATAAATTAAAAAA
1 TATTTAAAATATAAATTAAAAAA
21327774 TAATTAATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (25 bp):
TATTTAAAATATAAATTAAAAAACA
Found at i:21327863 original size:7 final size:7
Alignment explanation
Indices: 21327829--21327893 Score: 58
Period size: 7 Copynumber: 8.9 Consensus size: 7
21327819 AACCCTAAAT
21327829 CCCTAAC
1 CCCTAAC
* *
21327836 TCTTAAC
1 CCCTAAC
21327843 CCCATAAC
1 CCC-TAAC
**
21327851 ATCTAAC
1 CCCTAAC
21327858 CCCTAAAC
1 CCCT-AAC
21327866 CCCTAAC
1 CCCTAAC
21327873 CCCTAAC
1 CCCTAAC
*
21327880 CACTAAC
1 CCCTAAC
21327887 CACCTAA
1 C-CCTAA
21327894 ACCTTAAATC
Statistics
Matches: 45, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
7 29 0.64
8 16 0.36
ACGTcount: A:0.35, C:0.46, G:0.00, T:0.18
Consensus pattern (7 bp):
CCCTAAC
Found at i:21327871 original size:15 final size:15
Alignment explanation
Indices: 21327853--21327896 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
21327843 CCCATAACAT
*
21327853 CTAACCCCTAAACCC
1 CTAACCCCTAAACCA
21327868 CTAACCCCT-AACCA
1 CTAACCCCTAAACCA
21327882 CTAACCACCTAAACC
1 CTAACC-CCTAAACC
21327897 TTAAATCTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 10 0.38
15 12 0.46
16 4 0.15
ACGTcount: A:0.36, C:0.50, G:0.00, T:0.14
Consensus pattern (15 bp):
CTAACCCCTAAACCA
Found at i:21327945 original size:15 final size:15
Alignment explanation
Indices: 21327909--21327949 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
21327899 AAATCTCAAC
21327909 CCTTAAA-CCATAAT
1 CCTTAAATCCATAAT
*
21327923 CCCT-AATCCATAAT
1 CCTTAAATCCATAAT
21327937 CCTTAAATCCATA
1 CCTTAAATCCATA
21327950 CTCCCTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 2 0.09
14 13 0.57
15 8 0.35
ACGTcount: A:0.39, C:0.32, G:0.00, T:0.29
Consensus pattern (15 bp):
CCTTAAATCCATAAT
Found at i:21327962 original size:22 final size:22
Alignment explanation
Indices: 21327889--21327965 Score: 70
Period size: 22 Copynumber: 3.6 Consensus size: 22
21327879 CCACTAACCA
21327889 CCTAAACCTTAAATCTCA-AC-C
1 CCTAAACCTTAAATC-CATACTC
* * * *
21327910 CTTAAACCAT-AATCCCTAATC
1 CCTAAACCTTAAATCCATACTC
* *
21327931 CATAATCCTTAAATCCATACTC
1 CCTAAACCTTAAATCCATACTC
21327953 CCTAAACCTTAAA
1 CCTAAACCTTAAA
21327966 ACAGTAACTC
Statistics
Matches: 42, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
19 1 0.02
20 5 0.12
21 16 0.38
22 20 0.48
ACGTcount: A:0.39, C:0.34, G:0.00, T:0.27
Consensus pattern (22 bp):
CCTAAACCTTAAATCCATACTC
Found at i:21328370 original size:41 final size:40
Alignment explanation
Indices: 21328324--21328624 Score: 259
Period size: 41 Copynumber: 7.5 Consensus size: 40
21328314 GCGCTTCATA
* * *
21328324 AAAAACGTCGCTAAAGCCCCTACCATTAGTGGCGCTTTTCC
1 AAAAACGCCGCTAAAG-CCCTAGCATTAGCGGCGCTTTTCC
* *
21328365 AAAAACGCCGCTAAAG----ACCATTAGCGGCGATTTTCC
1 AAAAACGCCGCTAAAGCCCTAGCATTAGCGGCGCTTTTCC
* * * ** *
21328401 AAAAAACGCTGCTAAAAACTCGGGCATTAGCGGCGCTTCTCC
1 -AAAAACGCCGCT-AAAGCCCTAGCATTAGCGGCGCTTTTCC
* * * * *
21328443 AAAAACGCCGCTAAAGACTTGGGCATTAGCGGCGCTTCTCT
1 AAAAACGCCGCTAAAGCCCT-AGCATTAGCGGCGCTTTTCC
* ** **
21328484 AAAAACGCCACTAAAAACCTAGACATTAGCGGCGCTTTTAA
1 AAAAACGCCGCTAAAGCCCTAG-CATTAGCGGCGCTTTTCC
* *
21328525 AAAAACGCCGCTAAAGACCTGGGCATTAGCGGCGCTTTTCC
1 AAAAACGCCGCTAAAGCCCT-AGCATTAGCGGCGCTTTTCC
* * **
21328566 AGAAACGCCGCTAAAGACCCGAGCATTAGCGGCGCTTTTTT
1 AAAAACGCCGCTAAAG-CCCTAGCATTAGCGGCGCTTTTCC
*
21328607 AAAAATGCCGCTAAAGCC
1 AAAAACGCCGCTAAAGCC
21328625 ACGAAAGGTC
Statistics
Matches: 214, Mismatches: 36, Indels: 21
0.79 0.13 0.08
Matches are distributed among these distances:
36 18 0.08
37 11 0.05
38 3 0.01
40 6 0.03
41 157 0.73
42 19 0.09
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.20
Consensus pattern (40 bp):
AAAAACGCCGCTAAAGCCCTAGCATTAGCGGCGCTTTTCC
Found at i:21328516 original size:82 final size:81
Alignment explanation
Indices: 21328308--21328622 Score: 304
Period size: 82 Copynumber: 3.9 Consensus size: 81
21328298 TAAAATGATT
* * ** * *
21328308 TTAGCGGCGCTTCAT-AAAAAACGTCGCTAAAGCCCCTA-CCATTAGTGGCGCTTTTCCAAAAAC
1 TTAGCGGCGCTT-TTCAAAAAACGCCGCTAAA-AACCTAGACATTAGCGGCGCTTTTCCAAAAAC
21328371 GCCGCTAAAGAC----CA
64 GCCGCTAAAGACTGGGCA
* * * * *
21328385 TTAGCGGCGATTTTCCAAAAAACGCTGCTAAAAA-CTCGGGCATTAGCGGCGCTTCTCCAAAAAC
1 TTAGCGGCGCTTTT-CAAAAAACGCCGCTAAAAACCT-AGACATTAGCGGCGCTTTTCCAAAAAC
21328449 GCCGCTAAAGACTTGGGCA
64 GCCGCTAAAGAC-TGGGCA
* * * **
21328468 TTAGCGGCGCTTCTCTAAAAACGCCACTAAAAACCTAGACATTAGCGGCGCTTTTAAAAAAACGC
1 TTAGCGGCGCTTTTCAAAAAACGCCGCTAAAAACCTAGACATTAGCGGCGCTTTTCCAAAAACGC
21328533 CGCTAAAGACCTGGGCA
66 CGCTAAAGA-CTGGGCA
* * * * ** *
21328550 TTAGCGGCGCTTTTCCAGAAACGCCGCTAAAGACC-CGAGCATTAGCGGCGCTTTTTTAAAAATG
1 TTAGCGGCGCTTTTCAAAAAACGCCGCTAAAAACCTAGA-CATTAGCGGCGCTTTTCCAAAAACG
21328614 CCGCTAAAG
65 CCGCTAAAG
21328623 CCACGAAAGG
Statistics
Matches: 197, Mismatches: 29, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
76 3 0.02
77 11 0.06
78 48 0.24
81 2 0.01
82 116 0.59
83 17 0.09
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (81 bp):
TTAGCGGCGCTTTTCAAAAAACGCCGCTAAAAACCTAGACATTAGCGGCGCTTTTCCAAAAACGC
CGCTAAAGACTGGGCA
Found at i:21328572 original size:123 final size:124
Alignment explanation
Indices: 21328308--21328621 Score: 347
Period size: 123 Copynumber: 2.6 Consensus size: 124
21328298 TAAAATGATT
* * * * * * * *
21328308 TTAGCGGCGCTTCAT-AAAAAACGTCGCTAAAGCCCCTACCATTAGTGGCGCTTTTCCAAAAACG
1 TTAGCGGCGCTTC-TCCAAAAACGCCGCTAAAGACCCGAGCATTAGCGGCGCTTCTCTAAAAACG
* * * *
21328372 CCGCTAAAGA-C----CATTAGCGGCGATTTTCCAAAAAACGCTGCTAAAAACTCGGGCA
65 CCACTAAAAACCTAGACATTAGCGGCGATTTTCAAAAAAACGCCGCTAAAAACTCGGGCA
** *
21328427 TTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGACTTGGGCATTAGCGGCGCTTCTCTAAAAACGC
1 TTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGACCCGAGCATTAGCGGCGCTTCTCTAAAAACGC
* *
21328492 CACTAAAAACCTAGACATTAGCGGCGCTTTT-AAAAAAACGCCGCTAAAGAC-CTGGGCA
66 CACTAAAAACCTAGACATTAGCGGCGATTTTCAAAAAAACGCCGCTAAAAACTC-GGGCA
* * * * *
21328550 TTAGCGGCGCTTTTCCAGAAACGCCGCTAAAGACCCGAGCATTAGCGGCGCTTTTTTAAAAATGC
1 TTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGACCCGAGCATTAGCGGCGCTTCTCTAAAAACGC
*
21328615 CGCTAAA
66 CACTAAA
21328622 GCCACGAAAG
Statistics
Matches: 162, Mismatches: 26, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
118 1 0.01
119 59 0.36
120 1 0.01
122 1 0.01
123 85 0.52
124 15 0.09
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (124 bp):
TTAGCGGCGCTTCTCCAAAAACGCCGCTAAAGACCCGAGCATTAGCGGCGCTTCTCTAAAAACGC
CACTAAAAACCTAGACATTAGCGGCGATTTTCAAAAAAACGCCGCTAAAAACTCGGGCA
Found at i:21330740 original size:14 final size:14
Alignment explanation
Indices: 21330721--21330750 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
21330711 GTTTTTTCAT
21330721 AAACGCCGCTAAAG
1 AAACGCCGCTAAAG
21330735 AAACGCCGCTAAAG
1 AAACGCCGCTAAAG
21330749 AA
1 AA
21330751 CGGTACTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.27, G:0.20, T:0.07
Consensus pattern (14 bp):
AAACGCCGCTAAAG
Found at i:21331231 original size:3 final size:3
Alignment explanation
Indices: 21331223--21331276 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
21331213 TAGTTTACCC
21331223 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
21331271 ATA ATA
1 ATA ATA
21331277 TCCAGTCAAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:21332976 original size:16 final size:17
Alignment explanation
Indices: 21332955--21332988 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
21332945 TCTTTTCAAA
21332955 TTTAAA-TTAAACTATT
1 TTTAAATTTAAACTATT
*
21332971 TTTAAATTTAAATTATT
1 TTTAAATTTAAACTATT
21332988 T
1 T
21332989 ACGCTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTAAATTTAAACTATT
Found at i:21334309 original size:17 final size:16
Alignment explanation
Indices: 21334275--21334304 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21334265 TAAAATATAT
21334275 CAAAAAAAACTAAAAA
1 CAAAAAAAACTAAAAA
21334291 CAAAAAAAA-TAAAA
1 CAAAAAAAACTAAAA
21334305 GAACAGGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.83, C:0.10, G:0.00, T:0.07
Consensus pattern (16 bp):
CAAAAAAAACTAAAAA
Found at i:21334490 original size:4 final size:4
Alignment explanation
Indices: 21334481--21334550 Score: 58
Period size: 4 Copynumber: 17.5 Consensus size: 4
21334471 GGGGAAGAAG
* *
21334481 AAGA AAGA AAGG AAGA AAG- AA-A AAGA AGGAA AATGA AAGAA CAAGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAG-A AA-GA AAG-A -AAGA
21334527 AAGA AAG- AA-A AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AA
21334551 AGGAAAGGGG
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
3 8 0.15
4 35 0.65
5 7 0.13
6 4 0.07
ACGTcount: A:0.73, C:0.01, G:0.24, T:0.01
Consensus pattern (4 bp):
AAGA
Found at i:21334506 original size:10 final size:10
Alignment explanation
Indices: 21334475--21334557 Score: 73
Period size: 10 Copynumber: 8.3 Consensus size: 10
21334465 AGGAGAGGGG
*
21334475 AAGAAGAAGA
1 AAGAAAAAGA
21334485 AAGAAAGGAAGA
1 AAGAAA--AAGA
21334497 AAGAAAAAGA
1 AAGAAAAAGA
* *
21334507 AGGAAAATGA
1 AAGAAAAAGA
*
21334517 AAGAACAAGA
1 AAGAAAAAGA
21334527 AAG--AAAGA
1 AAGAAAAAGA
21334535 AA-AAGAAAGA
1 AAGAA-AAAGA
*
21334545 AAGAAAAGGA
1 AAGAAAAAGA
21334555 AAG
1 AAG
21334558 GGGAAGAAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
8 6 0.10
10 41 0.69
11 2 0.03
12 10 0.17
ACGTcount: A:0.71, C:0.01, G:0.27, T:0.01
Consensus pattern (10 bp):
AAGAAAAAGA
Found at i:21334547 original size:14 final size:14
Alignment explanation
Indices: 21334481--21334557 Score: 75
Period size: 14 Copynumber: 5.2 Consensus size: 14
21334471 GGGGAAGAAG
21334481 AAGAAAGAAAGGAAGA
1 AAGAAAGAAA--AAGA
*
21334497 AAGAAA-AAGAAGGAA
1 AAGAAAGAA-AAAG-A
*
21334512 AATGAAAGAACAAGA
1 AA-GAAAGAAAAAGA
21334527 AAGAAAGAAAAAGA
1 AAGAAAGAAAAAGA
*
21334541 AAGAAAGAAAAGGA
1 AAGAAAGAAAAAGA
21334555 AAG
1 AAG
21334558 GGGAAGAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
14 29 0.56
15 8 0.15
16 13 0.25
17 2 0.04
ACGTcount: A:0.71, C:0.01, G:0.26, T:0.01
Consensus pattern (14 bp):
AAGAAAGAAAAAGA
Found at i:21334566 original size:38 final size:38
Alignment explanation
Indices: 21334485--21334557 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
21334475 AAGAAGAAGA
* * *
21334485 AAGAAAGGAAGAAAGAAAAAGAAGGAAAATGAAAGAAC
1 AAGAAAGAAAGAAAGAAAAAGAAAGAAAAGGAAAGAAC
21334523 AAGAAAGAAAGAAA-AAGAAAGAAAGAAAAGGAAAG
1 AAGAAAGAAAGAAAGAA-AAAGAAAGAAAAGGAAAG
21334558 GGGAAGAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 2 0.06
38 29 0.94
ACGTcount: A:0.71, C:0.01, G:0.26, T:0.01
Consensus pattern (38 bp):
AAGAAAGAAAGAAAGAAAAAGAAAGAAAAGGAAAGAAC
Found at i:21335350 original size:18 final size:17
Alignment explanation
Indices: 21335323--21335358 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
21335313 TATTTTGGTA
21335323 TTTTTTTAATATTTTAT
1 TTTTTTTAATATTTTAT
*
21335340 TTTTTTGTAATGTTTTAT
1 TTTTTT-TAATATTTTAT
21335358 T
1 T
21335359 ATGGGTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (17 bp):
TTTTTTTAATATTTTAT
Found at i:21335426 original size:28 final size:27
Alignment explanation
Indices: 21335395--21335537 Score: 151
Period size: 28 Copynumber: 5.5 Consensus size: 27
21335385 AAATAAAAAA
21335395 TTACCAAAATATTATAAATTTTTTTTAT
1 TTACCAAAATA-TATAAATTTTTTTTAT
* *
21335423 TTACCGAAATATAT--A-TATTTTTAT
1 TTACCAAAATATATAAATTTTTTTTAT
21335447 TTACCAAAATATTATAAATTTTTTTTAT
1 TTACCAAAATA-TATAAATTTTTTTTAT
*
21335475 TTACC--GA-A-AT--ATTTTTTTTAT
1 TTACCAAAATATATAAATTTTTTTTAT
* *
21335496 TTACCAATATATATATAATTTTGTTTAT
1 TTACCAAAATATATA-AATTTTTTTTAT
21335524 TTACCAAAATATAT
1 TTACCAAAATATAT
21335538 CAAAAAAAAC
Statistics
Matches: 96, Mismatches: 8, Indels: 22
0.76 0.06 0.17
Matches are distributed among these distances:
21 16 0.17
23 3 0.03
24 19 0.20
25 7 0.07
26 1 0.01
27 4 0.04
28 46 0.48
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.52
Consensus pattern (27 bp):
TTACCAAAATATATAAATTTTTTTTAT
Found at i:21335435 original size:52 final size:52
Alignment explanation
Indices: 21335378--21335486 Score: 155
Period size: 52 Copynumber: 2.1 Consensus size: 52
21335368 ATACAAAAAT
21335378 AATATAAAAATAAAAAATTACCAAAATATTATAAATTTTTTTTATTTACCGA
1 AATATAAAAATAAAAAATTACCAAAATATTATAAATTTTTTTTATTTACCGA
* * **** *
21335430 AATATATATATTTTTATTTACCAAAATATTATAAATTTTTTTTATTTACCGA
1 AATATAAAAATAAAAAATTACCAAAATATTATAAATTTTTTTTATTTACCGA
21335482 AATAT
1 AATAT
21335487 TTTTTTTATT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (52 bp):
AATATAAAAATAAAAAATTACCAAAATATTATAAATTTTTTTTATTTACCGA
Found at i:21335497 original size:49 final size:52
Alignment explanation
Indices: 21335395--21335537 Score: 222
Period size: 52 Copynumber: 2.8 Consensus size: 52
21335385 AAATAAAAAA
21335395 TTACCAAAATATTATAAATTTTTTTTATTTACCGAAATATATATATTTTTAT
1 TTACCAAAATATTATAAATTTTTTTTATTTACCGAAATATATATATTTTTAT
21335447 TTACCAAAATATTATAAATTTTTTTTATTTACCGAAATAT-T-T-TTTTTAT
1 TTACCAAAATATTATAAATTTTTTTTATTTACCGAAATATATATATTTTTAT
* * *
21335496 TTACCAATATA-TATATAATTTTGTTTATTTACCAAAATATAT
1 TTACCAAAATATTATA-AATTTTTTTTATTTACCGAAATATAT
21335538 CAAAAAAAAC
Statistics
Matches: 86, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
48 4 0.05
49 39 0.45
50 2 0.02
51 1 0.01
52 40 0.47
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.52
Consensus pattern (52 bp):
TTACCAAAATATTATAAATTTTTTTTATTTACCGAAATATATATATTTTTAT
Found at i:21335504 original size:19 final size:20
Alignment explanation
Indices: 21335464--21335507 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
21335454 AATATTATAA
21335464 ATTTTTTTTATTTACCGAAAT
1 ATTTTTTTTATTTACC-AAAT
21335485 ATTTTTTTTATTTACCAATAT
1 ATTTTTTTTATTTACCAA-AT
21335506 AT
1 AT
21335508 ATATAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.59
Consensus pattern (20 bp):
ATTTTTTTTATTTACCAAAT
Found at i:21340439 original size:3 final size:3
Alignment explanation
Indices: 21340431--21340462 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
21340421 CTTAATACCT
21340431 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
21340463 CTATAAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Done.