Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 69 of 228
Found at i:20570752 original size:16 final size:16
Alignment explanation
Indices: 20570731--20570767 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
20570721 AGATGAAAGG
20570731 ACAGGTCAGGCCTGCC
1 ACAGGTCAGGCCTGCC
20570747 ACAGGTCAGGCCTGCC
1 ACAGGTCAGGCCTGCC
*
20570763 GCAGG
1 ACAGG
20570768 CCTGATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.19, C:0.35, G:0.35, T:0.11
Consensus pattern (16 bp):
ACAGGTCAGGCCTGCC
Found at i:20570867 original size:12 final size:13
Alignment explanation
Indices: 20570850--20570878 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
20570840 GGTTTGGCCT
20570850 AAAAAAC-CAAAA
1 AAAAAACTCAAAA
20570862 AAAAAACTCAAAA
1 AAAAAACTCAAAA
20570875 AAAA
1 AAAA
20570879 TGAAATGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.83, C:0.14, G:0.00, T:0.03
Consensus pattern (13 bp):
AAAAAACTCAAAA
Found at i:20572038 original size:19 final size:17
Alignment explanation
Indices: 20572007--20572057 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 17
20571997 CTTGTTGCTA
20572007 TTATTTCTTTATTTTTGT
1 TTATTT-TTTATTTTTGT
*
20572025 TCATATTTTTTATTTTGGT
1 T--TATTTTTTATTTTTGT
20572044 TTA-TTTTTATTTTT
1 TTATTTTTTATTTTT
20572058 TCGGTCATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 10 0.34
17 2 0.07
18 1 0.03
19 11 0.38
20 5 0.17
ACGTcount: A:0.14, C:0.04, G:0.06, T:0.76
Consensus pattern (17 bp):
TTATTTTTTATTTTTGT
Found at i:20572284 original size:3 final size:3
Alignment explanation
Indices: 20572276--20572344 Score: 95
Period size: 3 Copynumber: 23.0 Consensus size: 3
20572266 ATTGTTTGTC
*
20572276 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
20572324 TTT GTT ATTT ATT -TT ATT ATT
1 ATT ATT A-TT ATT ATT ATT ATT
20572345 TATTTCATTT
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
2 2 0.03
3 54 0.92
4 3 0.05
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:20577827 original size:108 final size:109
Alignment explanation
Indices: 20577637--20577859 Score: 304
Period size: 108 Copynumber: 2.1 Consensus size: 109
20577627 AGGACACTTG
* * * *
20577637 TTTTCATCTTATTCATTTTTGTATCTTAGAAAAATTTGCTATCTTGATTAATTTGTTCATTTAAA
1 TTTTCATCTTATTCATTCTCGTATCTCAGAAAAATTTGCTATCTTGATTAATTTATTCATTTAAA
* *
20577702 GCTTTGCTCTCAATAAAATTCCATCTTATCCATTGTGATAATCT
66 GCTTTGCTCTCAATAAAATTCCATCTCATCCATTGTGATAATCA
* * * **
20577746 TTTTCATCTTATTCA-TCTCGTATCTCAGCAAAATTTGCTATCTTGATTTATTTATTTATTTCGA
1 TTTTCATCTTATTCATTCTCGTATCTCAGAAAAATTTGCTATCTTGATTAATTTATTCATTTAAA
** * *
20577810 GCTTTTTTCTCAATAAAATTTCATCTCGTCCATTGTGATAATCA
66 GCTTTGCTCTCAATAAAATTCCATCTCATCCATTGTGATAATCA
20577854 TTTTCA
1 TTTTCA
20577860 AGCATTTTTC
Statistics
Matches: 99, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
108 84 0.85
109 15 0.15
ACGTcount: A:0.26, C:0.17, G:0.08, T:0.49
Consensus pattern (109 bp):
TTTTCATCTTATTCATTCTCGTATCTCAGAAAAATTTGCTATCTTGATTAATTTATTCATTTAAA
GCTTTGCTCTCAATAAAATTCCATCTCATCCATTGTGATAATCA
Found at i:20578367 original size:24 final size:24
Alignment explanation
Indices: 20578332--20578389 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
20578322 ATGTCCCAAA
*
20578332 ATTACAAGTGGATTGAACCTTAAAG
1 ATTAC-AGTGGATTGAACCCTAAAG
*
20578357 ATTACAGTGGATTGAACCCTGAAG
1 ATTACAGTGGATTGAACCCTAAAG
20578381 ATTACAGTG
1 ATTACAGTG
20578390 AGGGCAATCT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 26 0.84
25 5 0.16
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (24 bp):
ATTACAGTGGATTGAACCCTAAAG
Found at i:20578890 original size:88 final size:88
Alignment explanation
Indices: 20578692--20578890 Score: 236
Period size: 88 Copynumber: 2.3 Consensus size: 88
20578682 GGAATGGATT
* *** ** * *
20578692 GTTGAAGATTGTAGATCTTGTCTTCCTGTACCGGTAGTGAAGCAGATTGAAAACATCAGCCTTAT
1 GTTGAAGATTGTAGATCTTGTCTTACTGTACCAACAGTGAAGCAGATAAAAAAAATCAACCTTAT
* *
20578757 CTCCCTAAGCAGTAGTGGAGTAG
66 CTCCCTAAGCAGCAGTGGAGGAG
* * * *
20578780 GTTAAAGATTATAAATCTTGTCTTACTGTACTAACAGTGAAGCAGATAAAAAAAATCAACCTTAT
1 GTTGAAGATTGTAGATCTTGTCTTACTGTACCAACAGTGAAGCAGATAAAAAAAATCAACCTTAT
* *
20578845 CTCCTTGAGCAGCAGTGGAGGAG
66 CTCCCTAAGCAGCAGTGGAGGAG
* *
20578868 GTTGAAGATTGCAGATCCTGTCT
1 GTTGAAGATTGTAGATCTTGTCT
20578891 CCCTAAGCAG
Statistics
Matches: 90, Mismatches: 21, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
88 90 1.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (88 bp):
GTTGAAGATTGTAGATCTTGTCTTACTGTACCAACAGTGAAGCAGATAAAAAAAATCAACCTTAT
CTCCCTAAGCAGCAGTGGAGGAG
Found at i:20579155 original size:21 final size:21
Alignment explanation
Indices: 20579129--20579172 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
20579119 CTGGCATTGT
*
20579129 AGTGGAATAGATTAAAGCTGA
1 AGTGGAACAGATTAAAGCTGA
* *
20579150 AGTGGAGCGGATTAAAGCTGA
1 AGTGGAACAGATTAAAGCTGA
20579171 AG
1 AG
20579173 GCAGCGAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.07, G:0.34, T:0.20
Consensus pattern (21 bp):
AGTGGAACAGATTAAAGCTGA
Found at i:20579268 original size:52 final size:52
Alignment explanation
Indices: 20579153--20579293 Score: 149
Period size: 52 Copynumber: 2.7 Consensus size: 52
20579143 AAGCTGAAGT
* * * * * *
20579153 GGAGCGGATTAAAGCTGAAGGCAGCGAATCCT-ATTTCCTTGGCGTTACAGT
1 GGAGCAGATTAAAGCTGAAGGCAGCGAATCTTGTTTTCCCTGGCATTACAGC
* * * * * *
20579204 GGAACAAATTAAAGATAAAGGTAGCGAATCTTGTTTTCCCTGGCATTGCAGC
1 GGAGCAGATTAAAGCTGAAGGCAGCGAATCTTGTTTTCCCTGGCATTACAGC
* *
20579256 GGAGCAGATTAAAGCTGAAGACAACGAATCTTGTTTTC
1 GGAGCAGATTAAAGCTGAAGGCAGCGAATCTTGTTTTC
20579294 GATTGAAGAC
Statistics
Matches: 70, Mismatches: 19, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
51 25 0.36
52 45 0.64
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (52 bp):
GGAGCAGATTAAAGCTGAAGGCAGCGAATCTTGTTTTCCCTGGCATTACAGC
Found at i:20579407 original size:44 final size:44
Alignment explanation
Indices: 20579312--20579751 Score: 273
Period size: 44 Copynumber: 9.8 Consensus size: 44
20579302 ACAGACTACA
* * * **
20579312 AATCTTATCTCCCTGAAGTTGCGGTGGAGCATATTAAAGCCA-C
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACC
* *
20579355 AGACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACC
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACC
* * * * * *
20579400 AATCTTATCTCCTTGAAG-TACAGTGGTGCAGATTAAAAATAAATC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAT--ACC
* * * *
20579445 AATCTTATCTTCTTGAAGTTGCAGTGGAGTAGATTGAAGTTACC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACC
* * * * **
20579489 AAGTCCTATCTCCCTGAAGTTGCAGTAGAGCGGATT-AAAATGATG
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAT-ACC
* * * * * * *
20579534 AATCCTATAC-CTCGGAAGTTACAGTAGG-TCGGATT-AAGTCTACCATAAC
1 AATCTTAT-CTCCCTGAAGTTGCAGT-GGAGCAGATTGAAG------ATACC
* * *
20579583 AAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAGACAACC
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGA-TACC
*
20579629 AACCTTATCTCCCTGAAGTTGCAGTGGAGCATG-TTGAAGATACC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCA-GATTGAAGATACC
* ** * * **
20579673 AATCTTATCTCCCTGAAGTTACAGTTAAGGAGATTGAAGCTATT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACC
* * ** *
20579717 AATCTTATTTTCCTGAAGTCACAGTGGAGCGGATT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT
20579752 AAAACGGATC
Statistics
Matches: 305, Mismatches: 70, Indels: 43
0.73 0.17 0.10
Matches are distributed among these distances:
43 19 0.06
44 147 0.48
45 87 0.29
46 21 0.07
49 6 0.02
50 22 0.07
51 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACC
Found at i:20579690 original size:89 final size:89
Alignment explanation
Indices: 20579312--20579697 Score: 293
Period size: 89 Copynumber: 4.3 Consensus size: 89
20579302 ACAGACTACA
* * * *
20579312 AATCTTATCTCCCTGAAGTTGCGGTGGAGCATATT-AAAGCCA-CAGACCTTATCTCCCTGAAGT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAACAATCA-ACCTTATCTCCCTGAAGT
*
20579375 TGCAGTGGAGCAGGTTGAAGATACC
65 TGCAGTGGAGCATGTTGAAGATACC
* * * * * * *
20579400 AATCTTATCTCCTTGAAG-TACAGTGGTGCAGATTAAAAATAAATCAATCTTATCTTCTTGAAGT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAA-CAATCAACCTTATCTCCCTGAAGT
* *
20579464 TGCAGTGGAGTA-GATTGAAGTTACC
65 TGCAGTGGAGCATG-TTGAAGATACC
* * * ** * * *
20579489 AAGTCCTATCTCCCTGAAGTTGCAGTAGAGCGGATT-AAAATGATGAATCC-TATAC-CTCGGAA
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAACAATCAA-CCTTAT-CTCCCTGAA
* * * ** *
20579551 GTTACAGTAGGTCGGATTAAGTCT-ACCATAAC
63 GTTGCAGT-GG-AGCA-T--GT-TGAAGATACC
* * * * *
20579583 AAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAGACAACCAACCTTATCTCCCTGAAGT
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAACAATCAACCTTATCTCCCTGAAGT
20579648 TGCAGTGGAGCATGTTGAAGATACC
65 TGCAGTGGAGCATGTTGAAGATACC
*
20579673 AATCTTATCTCCCTGAAGTTACAGT
1 AATCTTATCTCCCTGAAGTTGCAGT
20579698 TAAGGAGATT
Statistics
Matches: 225, Mismatches: 54, Indels: 37
0.71 0.17 0.12
Matches are distributed among these distances:
87 12 0.05
88 21 0.09
89 78 0.35
90 33 0.15
91 14 0.06
92 1 0.00
93 2 0.01
94 41 0.18
95 23 0.10
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (89 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAACAATCAACCTTATCTCCCTGAAGTT
GCAGTGGAGCATGTTGAAGATACC
Found at i:20579697 original size:139 final size:134
Alignment explanation
Indices: 20579312--20579697 Score: 390
Period size: 139 Copynumber: 2.8 Consensus size: 134
20579302 ACAGACTACA
* * * *
20579312 AATCTTATCTCCCTGAAGTTGCGGTGGAGCATATTAAAGCCA-CAGACCTTATCTCCCTGAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCAACCA-ACCTTATCTCCCTGAAGTT
*
20579376 GCAGTGGAGCAGGTTGAAGATACCAATCTTATCTCCTTGAAG-TACAGTGGTGCAGATTAAAAAT
65 GCAGTGGAGCAGGTTGAAGATACCAATCTTATCTCCCTGAAGTTACAGTGGTGCAGATTAAAAAT
*
20579440 AAATC
130 AAAAC
* * * **
20579445 AATCTTATCTTCTTGAAGTTGCAGTGGAGTAGATTGAAGTTACCAAGTCC-TATCTCCCTGAAGT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCAACCAA--CCTTATCTCCCTGAAGT
* * ** * * * *
20579509 TGCAGTAGAGC-GGATT-AAAATGATGAATCCTATAC-CTCGGAAGTTACAGTAGGT-CGGATTA
64 TGCAGTGGAGCAGG-TTGAAGAT-ACCAATCTTAT-CTCCCTGAAGTTACAGT-GGTGCAGATTA
***
20579570 AGTCTACCATAAC
125 AAAATA--A-AAC
* *
20579583 AAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAGACAACCAACCTTATCTCCCTGAAGT
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAG-CAACCAACCTTATCTCCCTGAAGT
*
20579648 TGCAGTGGAGCATGTTGAAGATACCAATCTTATCTCCCTGAAGTTACAGT
64 TGCAGTGGAGCAGGTTGAAGATACCAATCTTATCTCCCTGAAGTTACAGT
20579698 TAAGGAGATT
Statistics
Matches: 200, Mismatches: 36, Indels: 28
0.76 0.14 0.11
Matches are distributed among these distances:
133 41 0.20
134 41 0.20
135 18 0.09
136 3 0.01
137 1 0.00
138 7 0.04
139 79 0.40
140 10 0.05
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (134 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCAACCAACCTTATCTCCCTGAAGTTG
CAGTGGAGCAGGTTGAAGATACCAATCTTATCTCCCTGAAGTTACAGTGGTGCAGATTAAAAATA
AAAC
Found at i:20581260 original size:19 final size:17
Alignment explanation
Indices: 20581229--20581279 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 17
20581219 CTTGCTGTTA
20581229 TTATTTCTTTATTTTTGT
1 TTATTT-TTTATTTTTGT
*
20581247 TCATATTTTTTATTTTGGT
1 T--TATTTTTTATTTTTGT
20581266 TTA-TTTTTATTTTT
1 TTATTTTTTATTTTT
20581280 TTGGTCATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 10 0.34
17 2 0.07
18 1 0.03
19 11 0.38
20 5 0.17
ACGTcount: A:0.14, C:0.04, G:0.06, T:0.76
Consensus pattern (17 bp):
TTATTTTTTATTTTTGT
Found at i:20581482 original size:3 final size:3
Alignment explanation
Indices: 20581474--20581520 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
20581464 ACTGTTTGTC
* *
20581474 ATT ATT ATT ATT ATT ATT ATT ATC ATT -TT TTT ATTT ATT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT
20581518 ATT
1 ATT
20581521 TATTTCATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
2 4 0.11
3 31 0.82
4 3 0.08
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (3 bp):
ATT
Found at i:20581491 original size:12 final size:11
Alignment explanation
Indices: 20581478--20581525 Score: 51
Period size: 12 Copynumber: 4.1 Consensus size: 11
20581468 TTTGTCATTA
20581478 TTATTATTATT
1 TTATTATTATT
*
20581489 ATTATTATCATT
1 -TTATTATTATT
*
20581501 TTTTTATTTATT
1 TTATTA-TTATT
20581513 TTATTATTTATT
1 TTATTA-TTATT
20581525 T
1 T
20581526 CATTTTTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
11 5 0.16
12 26 0.84
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (11 bp):
TTATTATTATT
Found at i:20582460 original size:15 final size:16
Alignment explanation
Indices: 20582426--20582464 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
20582416 ATATGAAATG
*
20582426 AATTGAAAAAAAATTG
1 AATTGAAAAAAAATTA
*
20582442 AATTGAAAAAAGA-TA
1 AATTGAAAAAAAATTA
20582457 AATTGAAA
1 AATTGAAA
20582465 TGAGACTACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.64, C:0.00, G:0.13, T:0.23
Consensus pattern (16 bp):
AATTGAAAAAAAATTA
Found at i:20582571 original size:28 final size:28
Alignment explanation
Indices: 20582539--20582627 Score: 144
Period size: 28 Copynumber: 3.2 Consensus size: 28
20582529 AAAAAAAATT
* *
20582539 AATGAAATGAAATGTT-AAATGAATATGA
1 AATGAAATGTAAT-TTGTAATGAATATGA
20582567 AATGAAATGTAATTTGTAATGAATATGA
1 AATGAAATGTAATTTGTAATGAATATGA
20582595 AATGAAATGTAATTTGTAATGAATATGA
1 AATGAAATGTAATTTGTAATGAATATGA
20582623 AATGA
1 AATGA
20582628 TGATTATGAA
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
27 2 0.03
28 56 0.97
ACGTcount: A:0.49, C:0.00, G:0.18, T:0.33
Consensus pattern (28 bp):
AATGAAATGTAATTTGTAATGAATATGA
Found at i:20582589 original size:17 final size:17
Alignment explanation
Indices: 20582567--20582617 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
20582557 ATGAATATGA
20582567 AATGAAATGTAATTTGT
1 AATGAAATGTAATTTGT
*
20582584 AATG-AA--T-A--TGA
1 AATGAAATGTAATTTGT
20582595 AATGAAATGTAATTTGT
1 AATGAAATGTAATTTGT
20582612 AATGAA
1 AATGAA
20582618 TATGAAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 12
0.65 0.05 0.30
Matches are distributed among these distances:
11 6 0.23
12 2 0.08
13 1 0.04
14 2 0.08
15 1 0.04
16 2 0.08
17 12 0.46
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (17 bp):
AATGAAATGTAATTTGT
Found at i:20582695 original size:18 final size:18
Alignment explanation
Indices: 20582674--20582717 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
20582664 AATTATAAAT
20582674 TGAAATGAAA-ACAAAAAC
1 TGAAATGAAAGA-AAAAAC
*
20582692 TGAAATGAAAGAAAAAAT
1 TGAAATGAAAGAAAAAAC
20582710 TGAAATGA
1 TGAAATGA
20582718 GAAAAACTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 23 0.96
19 1 0.04
ACGTcount: A:0.64, C:0.05, G:0.16, T:0.16
Consensus pattern (18 bp):
TGAAATGAAAGAAAAAAC
Found at i:20582779 original size:22 final size:22
Alignment explanation
Indices: 20582751--20582811 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
20582741 AAATAATAAT
*
20582751 TTAAATGAAATGAAAATGTAAA
1 TTAAATGAAATGAAAATGGAAA
*
20582773 TTAAATGAAATGGAAATGGAAA
1 TTAAATGAAATGAAAATGGAAA
*
20582795 TGAAATGAAAT-AAAATG
1 TTAAATGAAATGAAAATG
20582812 AAAAAAAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
21 5 0.14
22 30 0.86
ACGTcount: A:0.57, C:0.00, G:0.18, T:0.25
Consensus pattern (22 bp):
TTAAATGAAATGAAAATGGAAA
Found at i:20582815 original size:6 final size:5
Alignment explanation
Indices: 20582539--20582814 Score: 72
Period size: 5 Copynumber: 52.4 Consensus size: 5
20582529 AAAAAAAATT
* *
20582539 AATGA AATGA AATGTTA AATGA ATATGA AATGA AATGTA ATTTGT AATGA
1 AATGA AATGA AATG--A AATGA A-ATGA AATGA AATG-A A-ATGA AATGA
* * *
20582589 ATATGA AATGA AATGTA ATTTGT AATGA ATATGA AATG- -ATGA TTATGA
1 A-ATGA AATGA AATG-A A-ATGA AATGA A-ATGA AATGA AATGA -AATGA
* * * **
20582637 AATGG AATGA AAGTTTA AATGA ACAT-A AATTATA AATTGA AATGA AAACA
1 AATGA AATGA AA--TGA AATGA A-ATGA AA-T-GA AA-TGA AATGA AATGA
* *
20582687 AA--A ACTGA AATGA AA-GA AA--A AATTGA AATGA GAA--A AACTTA
1 AATGA AATGA AATGA AATGA AATGA AA-TGA AATGA -AATGA AA-TGA
* * * * *
20582728 AATTTA AATGGA AA-AA TAAT-A ATTTA AATGA AATGAA AATGTA AATTA
1 AA-TGA AAT-GA AATGA -AATGA AATGA AATGA AATG-A AATG-A AATGA
*
20582776 AATGA AATGGA AATGGA AATGA AATGA AATAA AATGA AA
1 AATGA AAT-GA AAT-GA AATGA AATGA AATGA AATGA AA
20582815 AAAAAAGGTT
Statistics
Matches: 209, Mismatches: 29, Indels: 66
0.69 0.10 0.22
Matches are distributed among these distances:
3 10 0.05
4 9 0.04
5 106 0.51
6 66 0.32
7 18 0.09
ACGTcount: A:0.55, C:0.01, G:0.16, T:0.27
Consensus pattern (5 bp):
AATGA
Found at i:20590260 original size:16 final size:16
Alignment explanation
Indices: 20590231--20590265 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
20590221 TACAATCTCT
*
20590231 TTTTACTTTGTTTTAA
1 TTTTAATTTGTTTTAA
*
20590247 TTTTAATTTTTTTTAA
1 TTTTAATTTGTTTTAA
20590263 TTT
1 TTT
20590266 AAACCCCCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTTAATTTGTTTTAA
Found at i:20592299 original size:17 final size:17
Alignment explanation
Indices: 20592277--20592313 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
20592267 GATTTAGTCA
20592277 CTCATGTTATTCATAAT
1 CTCATGTTATTCATAAT
20592294 CTCATGTTATTCATAAT
1 CTCATGTTATTCATAAT
20592311 CTC
1 CTC
20592314 TATATCAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.27, C:0.22, G:0.05, T:0.46
Consensus pattern (17 bp):
CTCATGTTATTCATAAT
Found at i:20593630 original size:17 final size:17
Alignment explanation
Indices: 20593606--20593649 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
20593596 TAATTTAATT
20593606 AACTAAATTAATTTCTC
1 AACTAAATTAATTTCTC
* * *
20593623 AGCTAAATGATTTTCTC
1 AACTAAATTAATTTCTC
20593640 AACTAAATTA
1 AACTAAATTA
20593650 TAATTCTATT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.39
Consensus pattern (17 bp):
AACTAAATTAATTTCTC
Found at i:20595148 original size:27 final size:27
Alignment explanation
Indices: 20595109--20595161 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
20595099 CCATTTACAG
* *
20595109 AAATTTAAACCCAGATTATTAA-ACCCA
1 AAATTCAAACCCA-AATATTAAGACCCA
*
20595136 AAATTCAAGCCCAAATATTAAGACCC
1 AAATTCAAACCCAAATATTAAGACCC
20595162 GAATAGCCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.47, C:0.25, G:0.06, T:0.23
Consensus pattern (27 bp):
AAATTCAAACCCAAATATTAAGACCCA
Found at i:20596597 original size:19 final size:20
Alignment explanation
Indices: 20596563--20596600 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
20596553 TATAATAATA
*
20596563 TTTTAATTGTTATCAATATG
1 TTTTAAATGTTATCAATATG
20596583 TTTTAAATG-TATCAATAT
1 TTTTAAATGTTATCAATAT
20596601 TATTTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.53
Consensus pattern (20 bp):
TTTTAAATGTTATCAATATG
Found at i:20609081 original size:44 final size:44
Alignment explanation
Indices: 20609026--20609116 Score: 112
Period size: 44 Copynumber: 2.1 Consensus size: 44
20609016 AGTGTAAGAA
* * * *
20609026 AGCAGATTAAAG-TCAGAAATCTTATCTCCCTGAGATTATAGCGG
1 AGCAGACTAAAGCT-AGAAATCCTATCTCCCTAAGATTACAGCGG
* *
20609070 AGCAGACTAAAGCTAGTAATCCTATCTCCCTAAGATTACAGTGG
1 AGCAGACTAAAGCTAGAAATCCTATCTCCCTAAGATTACAGCGG
20609114 AGC
1 AGC
20609117 GGATTAAAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
44 39 0.98
45 1 0.03
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (44 bp):
AGCAGACTAAAGCTAGAAATCCTATCTCCCTAAGATTACAGCGG
Found at i:20609241 original size:44 final size:43
Alignment explanation
Indices: 20609170--20609683 Score: 255
Period size: 44 Copynumber: 11.0 Consensus size: 43
20609160 TAGATCACAT
* *
20609170 CAGATTGAAGCCAGAAATCTTAGCTCCCTGAGATTACAGCGGAG
1 CAGATTGAAGCTAG-AATCTTATCTCCCTGAGATTACAGCGGAG
* *
20609214 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCTAG-AATCTTATCTCCCTGAGATTACAGCGGAG
* ** * * *
20609258 CGGATT-AAAATAAAGGATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCG
1 CAGATTGAAGCT--AGAATCTTATCTCCCTGAGA-TTAC---AGCG--GA--G
*
20609309 CATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAG
1 ---CAGATTGAAGCTAG-AATCTTATCTCCCTGAGATTACAGCGGAG
* * *
20609356 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGTAG
1 CAGATTGAAGCTAG-AATCTTATCTCCCTGAGATTACAGCGGAG
* * * * * *
20609400 CAGATTAAAAC-AGAGGATCTTATCTCTCTGAAGTTATAGTAGAGTAGATCGCAT
1 CAGATTGAAGCTAGA--ATCTTATCTCCCTG-AG--AT--T--A-CAG--CGGAG
* *
20609454 CAGATTGAAGCCAGATATCTTATCTCCTTGAGATTACAGCGGAG
1 CAGATTGAAGCTAGA-ATCTTATCTCCCTGAGATTACAGCGGAG
* * * *
20609498 CAGATTGAAGCTAGTAATCCTATCTCCTTGAGATTATAGTGGAG
1 CAGATTGAAGCTAG-AATCTTATCTCCCTGAGATTACAGCGGAG
** ** * * *
20609542 TGGATT-AAAATAAAGGATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCG
1 CAGATTGAAGCT--AGAATCTTATCTCCCTGAGA-TTAC---AGCG--GA--G
20609593 CATCAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGCGGAG
1 ---CAGATTGAAGCTAG-AATCTTATCTCCCTGAGATTACAGCGGAG
* * *
20609640 CAGATTGAAGCTAGTAATCCTATCTTCCTGAGATTACAGTGGAG
1 CAGATTGAAGCTAG-AATCTTATCTCCCTGAGATTACAGCGGAG
20609684 TGGATTAAAA
Statistics
Matches: 359, Mismatches: 65, Indels: 92
0.70 0.13 0.18
Matches are distributed among these distances:
42 1 0.00
43 10 0.03
44 221 0.62
45 7 0.02
46 2 0.01
47 11 0.03
49 10 0.03
51 11 0.03
52 2 0.01
53 6 0.02
54 68 0.19
55 10 0.03
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (43 bp):
CAGATTGAAGCTAGAATCTTATCTCCCTGAGATTACAGCGGAG
Found at i:20609284 original size:142 final size:142
Alignment explanation
Indices: 20609028--20609740 Score: 1210
Period size: 142 Copynumber: 5.0 Consensus size: 142
20609018 TGTAAGAAAG
* * * * *
20609028 CAGATTAAAGTCAGAAATCTTATCTCCCTGAGATTATAGCGGAGCAGACTAAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
* *
20609093 ATCTCCCTAAGATTACAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAATAG
66 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAG
*
20609158 AGTAGATCACAT
131 AGTAGATCGCAT
*
20609170 CAGATTGAAGCCAGAAATCTTAGCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
*
20609235 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
66 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAG
20609300 AGTAGATCGCAT
131 AGTAGATCGCAT
20609312 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
* * * *
20609377 ATCTCCCTGAGATTACAGTGTAGCAGATTAAAACAGAGGATCTTATCTCTCTGAAGTTATAGTAG
66 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAG
20609442 AGTAGATCGCAT
131 AGTAGATCGCAT
* *
20609454 CAGATTGAAGCCAGATATCTTATCTCCTTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
* * * *
20609519 ATCTCCTTGAGATTATAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
66 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAG
20609584 AGTAGATCGCAT
131 AGTAGATCGCAT
*
20609596 CAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
* *
20609661 ATCTTCCTGAGATTACAGTGGAGTGGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAG
66 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAG
*
20609726 AGTAGATCACAT
131 AGTAGATCGCAT
20609738 CAG
1 CAG
20609741 GTCTTATCTC
Statistics
Matches: 537, Mismatches: 34, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
142 537 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (142 bp):
CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
ATCTCCCTGAGATTACAGTGGAGCGGATTAAAACAAAGGATCTTATCTCTCTGAAGTTACAGTAG
AGTAGATCGCAT
Found at i:20609393 original size:98 final size:91
Alignment explanation
Indices: 20609170--20609685 Score: 283
Period size: 98 Copynumber: 5.5 Consensus size: 91
20609160 TAGATCACAT
* * * *
20609170 CAGATTGAAGCCAGAAATCTTAGCTCCCTGAGATTAC---AGCG-GAGCAGATTGAAGCTAGTAA
1 CAGATTGAAGCTAG-AATCTTATCTCCCTGAGATTACAGTAGAGTGAGCAGATTGAAGCTAGAAA
* *
20609231 TCCTATCTCCCTGAGATTACAGTGGAG
65 TCTTATCTCCCTGAGATTACAGCGGAG
* ** * *
20609258 CGGATT-AAAATAAAGGATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCATCAGATTGAA
1 CAGATTGAAGCT--AGAATCTTATCTCCCTGAGA-TTACAGTAGAGT-GA--G---CAGATTGAA
*
20609321 GCCAGAAATCTTATCTCCCTGAGATTACAGCGGAG
57 GCTAGAAATCTTATCTCCCTGAGATTACAGCGGAG
* * * *
20609356 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGT---GT-AGCAGATTAAAAC-AGAGG
1 CAGATTGAAGCTAG-AATCTTATCTCCCTGAGATTACAGTAGAGTGAGCAGATTGAAGCTAGA-A
* * * *
20609416 ATCTTATCTCTCTGAAGTTATAGTAGAGTAGATCGCAT
64 ATCTTATCTCCCTG-AG--AT--T--A-CAG--CGGAG
* * * *
20609454 CAGATTGAAGCCAGATATCTTATCTCCTTGAGATTAC---AGCG-GAGCAGATTGAAGCTAGTAA
1 CAGATTGAAGCTAGA-ATCTTATCTCCCTGAGATTACAGTAGAGTGAGCAGATTGAAGCTAGAAA
* * * *
20609515 TCCTATCTCCTTGAGATTATAGTGGAG
65 TCTTATCTCCCTGAGATTACAGCGGAG
** ** * *
20609542 TGGATT-AAAATAAAGGATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCATCAGATTGAA
1 CAGATTGAAGCT--AGAATCTTATCTCCCTGAGA-TTACAGTAGAGT-GA--G---CAGATTGAA
20609605 GCTAGAAATCTTATCTCCCTGAGATTACAGCGGAG
57 GCTAGAAATCTTATCTCCCTGAGATTACAGCGGAG
* * *
20609640 CAGATTGAAGCTAGTAATCCTATCTTCCTGAGATTACAGTGGAGTG
1 CAGATTGAAGCTAG-AATCTTATCTCCCTGAGATTACAGTAGAGTG
20609686 GATTAAAACA
Statistics
Matches: 318, Mismatches: 61, Indels: 89
0.68 0.13 0.19
Matches are distributed among these distances:
87 9 0.03
88 67 0.21
89 6 0.02
90 3 0.01
91 10 0.03
93 7 0.02
95 7 0.02
96 2 0.01
97 8 0.03
98 189 0.59
99 10 0.03
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (91 bp):
CAGATTGAAGCTAGAATCTTATCTCCCTGAGATTACAGTAGAGTGAGCAGATTGAAGCTAGAAAT
CTTATCTCCCTGAGATTACAGCGGAG
Found at i:20609894 original size:20 final size:20
Alignment explanation
Indices: 20609869--20609909 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
20609859 GCAGTTAAAA
20609869 AGGTTAAAGCCACAATGGCG
1 AGGTTAAAGCCACAATGGCG
20609889 AGGTTAAAGCCACAATGGCG
1 AGGTTAAAGCCACAATGGCG
20609909 A
1 A
20609910 ATCTTACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.20, G:0.29, T:0.15
Consensus pattern (20 bp):
AGGTTAAAGCCACAATGGCG
Found at i:20610255 original size:27 final size:27
Alignment explanation
Indices: 20610216--20610268 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
20610206 CCATTTATAG
* *
20610216 AAATTTAAACCCAGATTATTAA-ACCCA
1 AAATTCAAACCCA-AATATTAAGACCCA
*
20610243 AAATTCAAGCCCAAATATTAAGACCC
1 AAATTCAAACCCAAATATTAAGACCC
20610269 GAATAGCCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.47, C:0.25, G:0.06, T:0.23
Consensus pattern (27 bp):
AAATTCAAACCCAAATATTAAGACCCA
Found at i:20611694 original size:19 final size:20
Alignment explanation
Indices: 20611660--20611697 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
20611650 AATAATAATA
*
20611660 TTTTAATTGTTATCAATATG
1 TTTTAAATGTTATCAATATG
20611680 TTTTAAATG-TATCAATAT
1 TTTTAAATGTTATCAATAT
20611698 TATTTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.53
Consensus pattern (20 bp):
TTTTAAATGTTATCAATATG
Found at i:20617165 original size:236 final size:233
Alignment explanation
Indices: 20616764--20617366 Score: 660
Period size: 236 Copynumber: 2.6 Consensus size: 233
20616754 CTGTCTGGAT
* * * *
20616764 TAAACCTTTTATCGACACATCAAATAGCTTAGG-CAAAGCTGTAAATATATATCTTAGGTTACCT
1 TAAACCTTTTATCGACACATCAAATAGCTT-GGCCAAAGCTATAAATATACAT-GTAAGTTACCT
* * ** *
20616828 GTCCAGGCTAAACCTTTAAAACGACATCATGTTAC-TCATCTGAGCAAAACCTGTGTCACATGTA
64 GTCGA-GCTAAACCTTTAAAACGACATCAAGTTACTTGTTC-GAGCTAAACCTGTGTCACATGTA
* * * * * * *
20616892 TCTTCAAGTTTGCAACAAATGTTGGATCTTAGTAATCATCGGTAATTAACCATATCTGATGCTCG
127 TCTTCAAGTCTGCAAAAAATGTTGAATCTCAGTAATCATCAGTAATTAACCACATCTGATGCTCA
* * ** * *
20616957 TCCGAGCTGAACAGATCCATTTGTGTCAAGTTACCCATCCGGGC
192 TCCAAGCCGAACAGAT--ATTCATGTCAAGTTACCCATACAGGC
20617001 TAAACCTTTTATCGACACAT-AAATAGCTTGGCCAAAGCTATAAATATACATGTCAAGTTACCTG
1 TAAACCTTTTATCGACACATCAAATAGCTTGGCCAAAGCTATAAATATACATGT-AAGTTACCTG
* * * *
20617065 TCTGAGCTAAACCTTTAAAACAATATCAGGTTACTTGTTCGAGCTAAACCTGTGTCACGTGTATC
65 TC-GAGCTAAACCTTTAAAACGACATCAAGTTACTTGTTCGAGCTAAACCTGTGTCACATGTATC
* * * *
20617130 TTCGAGTCTGCAAAAAATGTTGAATCTCGGTAATCATCAGTAATTAACCACATTTGTTGCTCATC
129 TTCAAGTCTGCAAAAAATGTTGAATCTCAGTAATCATCAGTAATTAACCACATCTGATGCTCATC
* * **
20617195 CAAGCCGAACATATATTCATGTCAGGTTACCTGTACAGGC
194 CAAGCCGAACAGATATTCATGTCAAGTTACCCATACAGGC
* * * * **
20617235 TGAACCTTTATATCGACACATCAAATAGTTTGTCTACGGCTAT--ATATACATGTAAGGTTACCC
1 TAAACCTTT-TATCGACACATCAAATAGCTTGGCCAAAGCTATAAATATACATGTAA-GTTA-CC
* * * *
20617298 AT-TCGGGCTAAACCTTTAAAACGAGATCAAGTTACTTGTCCGAGCTAAACCTATGTCACATGTA
63 -TGTCGAGCTAAACCTTTAAAACGACATCAAGTTACTTGTTCGAGCTAAACCTGTGTCACATGTA
20617362 TCTTC
127 TCTTC
20617367 TAGCCAACAA
Statistics
Matches: 311, Mismatches: 46, Indels: 21
0.82 0.12 0.06
Matches are distributed among these distances:
233 2 0.01
234 99 0.32
235 18 0.06
236 168 0.54
237 24 0.08
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (233 bp):
TAAACCTTTTATCGACACATCAAATAGCTTGGCCAAAGCTATAAATATACATGTAAGTTACCTGT
CGAGCTAAACCTTTAAAACGACATCAAGTTACTTGTTCGAGCTAAACCTGTGTCACATGTATCTT
CAAGTCTGCAAAAAATGTTGAATCTCAGTAATCATCAGTAATTAACCACATCTGATGCTCATCCA
AGCCGAACAGATATTCATGTCAAGTTACCCATACAGGC
Found at i:20619647 original size:145 final size:147
Alignment explanation
Indices: 20619341--20619687 Score: 407
Period size: 145 Copynumber: 2.4 Consensus size: 147
20619331 ATTTCAACAT
* * * * * *
20619341 GTGTACCTAATTTTATGGTATATTATAATATATACAATCAACATTATATAATTAAGGTATATTAT
1 GTGTAACTAATTTTATGGTAGATTATAATATATATAATTAGCATTATATAATT-AGGTAGATTAT
** ** * ** *
20619406 TAATGATATATAACCCCATATACAACTATTTTTTTTATAATGTACATTTTTATGTTTTTGATTTG
65 TAATGATATATAACCCCATATACAACTATTGATACTATAATGTACATTTTTATATTAATGATATG
*
20619471 TAAACTTAAACTCTAAGC
130 TAAACTTAAACTCTAAAC
* * *
20619489 ATATAACTAATTTTATGGTAGATTATAATA-ATATAATTAGCGTTATATAATTAGGTAGATTATT
1 GTGTAACTAATTTTATGGTAGATTATAATATATATAATTAGCATTATATAATTAGGTAGATTATT
* * * *
20619553 AATGATATCTAACCCTATATACAATTA-TGATACTATAATGTATATTTTTATATTAATGATATGT
66 AATGATATATAACCCCATATACAACTATTGATACTATAATGTACATTTTTATATTAATGATATGT
*
20619617 -AACTTTATAC-CTTAAAC
131 AAAC-TTAAACTC-TAAAC
*
20619634 GTGTAACTAATTTTATGGTAGATCATAATATATATAATT-GACATTATATAATTA
1 GTGTAACTAATTTTATGGTAGATTATAATATATATAATTAG-CATTATATAATTA
20619688 TGGTTAAGTA
Statistics
Matches: 168, Mismatches: 27, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
144 4 0.02
145 65 0.39
146 55 0.33
147 18 0.11
148 26 0.15
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.44
Consensus pattern (147 bp):
GTGTAACTAATTTTATGGTAGATTATAATATATATAATTAGCATTATATAATTAGGTAGATTATT
AATGATATATAACCCCATATACAACTATTGATACTATAATGTACATTTTTATATTAATGATATGT
AAACTTAAACTCTAAAC
Found at i:20619754 original size:24 final size:24
Alignment explanation
Indices: 20619727--20619790 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 24
20619717 TTATGGAACT
*
20619727 TTTAATTTATTTGAAATTCGTATG
1 TTTAATTTGTTTGAAATTCGTATG
* **
20619751 TTTAAATTGTTCTGAAATTTTTATG
1 TTTAATTTGTT-TGAAATTCGTATG
20619776 TTTAATTTGTTTGAA
1 TTTAATTTGTTTGAA
20619791 TTGTTAATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
24 13 0.38
25 21 0.62
ACGTcount: A:0.28, C:0.03, G:0.12, T:0.56
Consensus pattern (24 bp):
TTTAATTTGTTTGAAATTCGTATG
Found at i:20621036 original size:12 final size:12
Alignment explanation
Indices: 20621019--20621043 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20621009 TATTTTTCCA
20621019 TGTATGTATATT
1 TGTATGTATATT
20621031 TGTATGTATATT
1 TGTATGTATATT
20621043 T
1 T
20621044 ATGTTATTTT
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:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (12 bp):
TGTATGTATATT
Found at i:20622934 original size:19 final size:19
Alignment explanation
Indices: 20622910--20622949 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
20622900 TCTTTGTAAC
20622910 TAAAAAAAATCTCATTCAT
1 TAAAAAAAATCTCATTCAT
20622929 TAAAAAAAATCTCATTCAT
1 TAAAAAAAATCTCATTCAT
20622948 TA
1 TA
20622950 CTCCTATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAAAAAATCTCATTCAT
Found at i:20624780 original size:25 final size:25
Alignment explanation
Indices: 20624746--20624810 Score: 103
Period size: 25 Copynumber: 2.6 Consensus size: 25
20624736 TACAGCATTG
20624746 CTCACACGAGCTGTGAAATAGCCTA
1 CTCACACGAGCTGTGAAATAGCCTA
*
20624771 CTCACACGAGCTGTGAAATAGCCTG
1 CTCACACGAGCTGTGAAATAGCCTA
* *
20624796 TTCACACGAGTTGTG
1 CTCACACGAGCTGTG
20624811 GGTCGGAATG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (25 bp):
CTCACACGAGCTGTGAAATAGCCTA
Found at i:20625856 original size:41 final size:41
Alignment explanation
Indices: 20625811--20625897 Score: 174
Period size: 41 Copynumber: 2.1 Consensus size: 41
20625801 ATAAAACACT
20625811 TAATTTATGTCCATATTTGTCCACTAACATTATAAATGGTC
1 TAATTTATGTCCATATTTGTCCACTAACATTATAAATGGTC
20625852 TAATTTATGTCCATATTTGTCCACTAACATTATAAATGGTC
1 TAATTTATGTCCATATTTGTCCACTAACATTATAAATGGTC
20625893 TAATT
1 TAATT
20625898 ACCATCTAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (41 bp):
TAATTTATGTCCATATTTGTCCACTAACATTATAAATGGTC
Found at i:20632004 original size:21 final size:21
Alignment explanation
Indices: 20631974--20632013 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20631964 AAAAGGAATG
* *
20631974 AAAATGAAAAAATCAAAAATC
1 AAAATAAAAAAAACAAAAATC
20631995 AAAATAAAAAAAACAAAAA
1 AAAATAAAAAAAACAAAAA
20632014 GAAGAGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.80, C:0.07, G:0.03, T:0.10
Consensus pattern (21 bp):
AAAATAAAAAAAACAAAAATC
Found at i:20632040 original size:22 final size:21
Alignment explanation
Indices: 20631980--20632040 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 21
20631970 AATGAAAATG
* *
20631980 AAAAAATCAAAAATCAAAATAA
1 AAAAAATC-AAAATCAAGAGAA
**
20632002 AAAAAA-CAAAAAGAAGAGAA
1 AAAAAATCAAAATCAAGAGAA
20632022 AAGAAAATCAAAATCAAGA
1 AA-AAAATCAAAATCAAGA
20632041 TCAAAATGAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
20 11 0.35
21 5 0.16
22 15 0.48
ACGTcount: A:0.75, C:0.08, G:0.08, T:0.08
Consensus pattern (21 bp):
AAAAAATCAAAATCAAGAGAA
Found at i:20632991 original size:7 final size:7
Alignment explanation
Indices: 20632979--20633042 Score: 82
Period size: 7 Copynumber: 9.4 Consensus size: 7
20632969 AAAAAAAGGG
20632979 ATGAAAA
1 ATGAAAA
20632986 ATGAAAAA
1 ATG-AAAA
20632994 ATG-AAA
1 ATGAAAA
20633000 ATGAAAA
1 ATGAAAA
20633007 ATG-AAA
1 ATGAAAA
20633013 ATGAAAA
1 ATGAAAA
20633020 ATG-AAA
1 ATGAAAA
20633026 ATGAAAA
1 ATGAAAA
20633033 A-GTAAAA
1 ATG-AAAA
20633040 ATG
1 ATG
20633043 GAGAGGCTAA
Statistics
Matches: 51, Mismatches: 0, Indels: 11
0.82 0.00 0.18
Matches are distributed among these distances:
6 19 0.37
7 24 0.47
8 8 0.16
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.16
Consensus pattern (7 bp):
ATGAAAA
Found at i:20633000 original size:6 final size:6
Alignment explanation
Indices: 20632991--20633032 Score: 66
Period size: 6 Copynumber: 6.7 Consensus size: 6
20632981 GAAAAATGAA
20632991 AAAATG AAAATG AAAAATG AAAATG AAAAATG AAAATG AAAA
1 AAAATG AAAATG -AAAATG AAAATG -AAAATG AAAATG AAAA
20633033 AGTAAAAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 22 0.65
7 12 0.35
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (6 bp):
AAAATG
Found at i:20633039 original size:13 final size:13
Alignment explanation
Indices: 20632983--20633033 Score: 93
Period size: 13 Copynumber: 3.8 Consensus size: 13
20632973 AAAGGGATGA
20632983 AAAATGAAAAAATG
1 AAAATG-AAAAATG
20632997 AAAATGAAAAATG
1 AAAATGAAAAATG
20633010 AAAATGAAAAATG
1 AAAATGAAAAATG
20633023 AAAATGAAAAA
1 AAAATGAAAAA
20633034 GTAAAAATGG
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 31 0.84
14 6 0.16
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (13 bp):
AAAATGAAAAATG
Found at i:20634443 original size:80 final size:80
Alignment explanation
Indices: 20634297--20634660 Score: 360
Period size: 80 Copynumber: 4.5 Consensus size: 80
20634287 TAAGCGGTGA
* * * *
20634297 ATCTTATTTTCTCCAGGAGTAGGGAAACAGATTTAAGCTACAAGTCCTATGTCCTTGATCAACAA
1 ATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCCTTGGTCAACAA
20634362 TGGGATAGGTTAAAG
66 TGGGATAGGTTAAAG
*
20634377 ATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCATTGGT-AAGCA
1 ATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCCTTGGTCAA-CA
* *
20634441 ATGAGATAGGTTGAAG
65 ATGGGATAGGTTAAAG
* * *** * *** **
20634457 ATCTTATCTTCCCCAGAAGTAGGGAAACAGATCTAAGCGGTGAA-T-CT-TAT-CTTCCCCAGGA
1 ATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGC-CACAAGTCCTATGTCCTTGGTCAACA
* * * *
20634518 GTAGGGAAACAGATCTAAGCGGTG
65 AT-GGG--ATAGGT-TAA----AG
* *
20634542 AATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGCCACAAGTCCTATGACCCTGGTCAACA
1 -ATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCCTTGGTCAACA
*
20634607 ATGGGATAGGTTGAAG
65 ATGGGATAGGTTAAAG
*
20634623 ATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGC
1 ATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGC
20634661 GGCGAATCTT
Statistics
Matches: 224, Mismatches: 44, Indels: 32
0.75 0.15 0.11
Matches are distributed among these distances:
77 4 0.02
78 5 0.02
79 4 0.02
80 148 0.66
81 5 0.02
85 5 0.02
86 41 0.18
87 2 0.01
88 4 0.02
89 6 0.03
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.26
Consensus pattern (80 bp):
ATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCCTTGGTCAACAA
TGGGATAGGTTAAAG
Found at i:20634521 original size:43 final size:43
Alignment explanation
Indices: 20634457--20634580 Score: 230
Period size: 43 Copynumber: 2.9 Consensus size: 43
20634447 TAGGTTGAAG
*
20634457 ATCTTATCTTCCCCAGAAGTAGGGAAACAGATCTAAGCGGTGA
1 ATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGGTGA
20634500 ATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGGTGA
1 ATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGGTGA
*
20634543 ATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGC
1 ATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGC
20634581 CACAAGTCCT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 79 1.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.24
Consensus pattern (43 bp):
ATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGGTGA
Found at i:20634565 original size:166 final size:166
Alignment explanation
Indices: 20634377--20634703 Score: 566
Period size: 166 Copynumber: 2.0 Consensus size: 166
20634367 TAGGTTAAAG
* *
20634377 ATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGCCACAAGTCCTATGTCATTGGT-AAGCA
1 ATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGCCACAAGTCCTATGACACTGGTCAA-CA
*
20634441 ATGAGATAGGTTGAAGATCTTATCTTCCCCAGAAGTAGGGAAACAGATCTAAGCGGTGAATCTTA
65 ATGAGATAGGTTGAAGATCTTATCTTCCCCAGAAGTAGGGAAACAGATCTAAGCGGCGAATCTTA
*
20634506 TCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGGTGA
130 TCTTCCCCAGGAGTAGGGAAACAAATCTAAGCGGTGA
*
20634543 ATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGCCACAAGTCCTATGACCCTGGTCAACAA
1 ATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGCCACAAGTCCTATGACACTGGTCAACAA
* *
20634608 TGGGATAGGTTGAAGATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGGCGAATCTTAT
66 TGAGATAGGTTGAAGATCTTATCTTCCCCAGAAGTAGGGAAACAGATCTAAGCGGCGAATCTTAT
*
20634673 CTTCCCCAGGAGTAGGGAAACAAATTTAAGC
131 CTTCCCCAGGAGTAGGGAAACAAATCTAAGC
20634704 CACAAGTCCT
Statistics
Matches: 152, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
166 150 0.99
167 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (166 bp):
ATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGCCACAAGTCCTATGACACTGGTCAACAA
TGAGATAGGTTGAAGATCTTATCTTCCCCAGAAGTAGGGAAACAGATCTAAGCGGCGAATCTTAT
CTTCCCCAGGAGTAGGGAAACAAATCTAAGCGGTGA
Found at i:20634630 original size:123 final size:123
Alignment explanation
Indices: 20634253--20634722 Score: 436
Period size: 123 Copynumber: 3.8 Consensus size: 123
20634243 TCATGTTGCG
* * *
20634253 GATCTTATCTTCTCCAGGAGTAGGGAAACAGATCTAAGCGGTGAATCTTATTTTCTCCAGGAGTA
1 GATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGGTGAATCTTATCTTCCCCAGGAGTA
* * * * *
20634318 GGGAAACAGATTTAAGCTACAAGTCCTATGTCCTTGATCAACAATGGGATAGGTTAAA
66 GGGAAACAGATTTAAGCCACAAGTCCTATGACCCTGGTCAACAATGGGATAGGTTGAA
* *** * * ***
20634376 GATCTTATCTTCCCCAGGAGTAGGGAAACAGATTTAAGC-CACAAGTCCTAT-GT-CATTGGTAA
1 GATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGGTGAA-TCTTATCTTCCCCAGG--A
* ** * * * * * ** ** * ** ** ** *
20634438 GCAATGAGATAGGTTGAAGATCTTATCTTCCCCA-GA-AGTAGGGAAACAGAT-CTA-AGCGGTG
63 GTAGGGAAACAGATTTAAG-CCACA-AGT-CCTATGACCCT-GGTCAACA-ATGGGATAG-GTTG
20634499 -A
122 AA
20634500 -ATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGGTGAATCTTATCTTCCCCAGGAGTA
1 GATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGGTGAATCTTATCTTCCCCAGGAGTA
20634564 GGGAAACAGATTTAAGCCACAAGTCCTATGACCCTGGTCAACAATGGGATAGGTTGAA
66 GGGAAACAGATTTAAGCCACAAGTCCTATGACCCTGGTCAACAATGGGATAGGTTGAA
*
20634622 GATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGGCGAATCTTATCTTCCCCAGGAGTA
1 GATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGGTGAATCTTATCTTCCCCAGGAGTA
* *
20634687 GGGAAACAAATTTAAGCCACAAGTCCTATGTCCCTG
66 GGGAAACAGATTTAAGCCACAAGTCCTATGACCCTG
20634723 ACCAGCAGTG
Statistics
Matches: 262, Mismatches: 67, Indels: 36
0.72 0.18 0.10
Matches are distributed among these distances:
120 5 0.02
121 15 0.06
122 9 0.03
123 207 0.79
124 8 0.03
125 13 0.05
126 5 0.02
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.25
Consensus pattern (123 bp):
GATCTTATCTTCCCCAGGAGTAGGGAAACAGATCTAAGCGGTGAATCTTATCTTCCCCAGGAGTA
GGGAAACAGATTTAAGCCACAAGTCCTATGACCCTGGTCAACAATGGGATAGGTTGAA
Found at i:20640062 original size:24 final size:24
Alignment explanation
Indices: 20640035--20640083 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
20640025 CCTTAATTTT
20640035 CTCCCCTAATTCCCACTACACATC
1 CTCCCCTAATTCCCACTACACATC
20640059 CTCCCCTAATTCCCACTACACATC
1 CTCCCCTAATTCCCACTACACATC
20640083 C
1 C
20640084 ACTACTCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.51, G:0.00, T:0.24
Consensus pattern (24 bp):
CTCCCCTAATTCCCACTACACATC
Found at i:20643532 original size:53 final size:53
Alignment explanation
Indices: 20643452--20643558 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
20643442 TTAACCCAAA
20643452 TTTAACAGAAAAGCTGATGTGATTGTCAGTCAACTAACGGTCAACAGCTTTGT
1 TTTAACAGAAAAGCTGATGTGATTGTCAGTCAACTAACGGTCAACAGCTTTGT
20643505 TTTAACAGAAAAGCTGATGTGATTGTCAGTCAACTAACGGTCAACAGCTTTGT
1 TTTAACAGAAAAGCTGATGTGATTGTCAGTCAACTAACGGTCAACAGCTTTGT
20643558 T
1 T
20643559 GATCTGGGCT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.31
Consensus pattern (53 bp):
TTTAACAGAAAAGCTGATGTGATTGTCAGTCAACTAACGGTCAACAGCTTTGT
Found at i:20655247 original size:16 final size:16
Alignment explanation
Indices: 20655223--20655253 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20655213 GTCACGTAAT
*
20655223 ATGACTAAATAACATA
1 ATGAATAAATAACATA
20655239 ATGAATAAATAACAT
1 ATGAATAAATAACAT
20655254 TTTGATATGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.10, G:0.06, T:0.26
Consensus pattern (16 bp):
ATGAATAAATAACATA
Found at i:20656885 original size:15 final size:15
Alignment explanation
Indices: 20656846--20656885 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
20656836 CCAATAAATG
20656846 ATAAAATAAA-ATAAA
1 ATAAAA-AAACATAAA
*
20656861 ATAAAGAAACATAAA
1 ATAAAAAAACATAAA
20656876 ATAAAAAAAC
1 ATAAAAAAAC
20656886 GAGTCAACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 3 0.14
15 19 0.86
ACGTcount: A:0.78, C:0.05, G:0.03, T:0.15
Consensus pattern (15 bp):
ATAAAAAAACATAAA
Found at i:20658736 original size:13 final size:13
Alignment explanation
Indices: 20658718--20658767 Score: 73
Period size: 13 Copynumber: 3.8 Consensus size: 13
20658708 ATGCTATTAA
20658718 TTTTTATAACATT
1 TTTTTATAACATT
*
20658731 TTTTTATAATATT
1 TTTTTATAACATT
*
20658744 ATTTTTATAAAATT
1 -TTTTTATAACATT
20658758 TTTTTATAAC
1 TTTTTATAAC
20658768 CTTAATTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
13 21 0.64
14 12 0.36
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTTATAACATT
Found at i:20658748 original size:27 final size:28
Alignment explanation
Indices: 20658712--20658776 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 28
20658702 CATAATATGC
*
20658712 TATTAATTTTTATAACATTTTTTTATAA
1 TATTAATTTTTATAAAATTTTTTTATAA
20658740 TATT-ATTTTTATAAAATTTTTTTATAA
1 TATTAATTTTTATAAAATTTTTTTATAA
**
20658767 CCTTAATTTT
1 TATTAATTTT
20658777 CTTTTTGCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 24 0.73
28 9 0.27
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.62
Consensus pattern (28 bp):
TATTAATTTTTATAAAATTTTTTTATAA
Found at i:20661534 original size:10 final size:8
Alignment explanation
Indices: 20661519--20661579 Score: 53
Period size: 7 Copynumber: 8.1 Consensus size: 8
20661509 CCAATTCAAA
20661519 AAAAATGTG
1 AAAAATG-G
20661528 CAAAAATGG
1 -AAAAATGG
20661537 AAAAAT-G
1 AAAAATGG
20661544 -AAAATGG
1 AAAAATGG
20661551 -AAAAT-G
1 AAAAATGG
20661557 AAAAA-GG
1 AAAAATGG
*
20661564 AAAAA-GT
1 AAAAATGG
20661571 AAAAATGG
1 AAAAATGG
20661579 A
1 A
20661580 GAGGCTAAGG
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
6 6 0.13
7 23 0.51
8 8 0.18
9 1 0.02
10 7 0.16
ACGTcount: A:0.64, C:0.02, G:0.21, T:0.13
Consensus pattern (8 bp):
AAAAATGG
Found at i:20661547 original size:14 final size:14
Alignment explanation
Indices: 20661530--20661579 Score: 66
Period size: 13 Copynumber: 3.6 Consensus size: 14
20661520 AAAATGTGCA
20661530 AAAATGGAAAAATG
1 AAAATGGAAAAATG
20661544 AAAATGG-AAAATG
1 AAAATGGAAAAATG
* *
20661557 AAAAAGGAAAAAGTA
1 AAAATGGAAAAA-TG
20661572 AAAATGGA
1 AAAATGGA
20661580 GAGGCTAAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 12 0.39
14 11 0.35
15 8 0.26
ACGTcount: A:0.66, C:0.00, G:0.22, T:0.12
Consensus pattern (14 bp):
AAAATGGAAAAATG
Found at i:20662976 original size:88 final size:88
Alignment explanation
Indices: 20662821--20663359 Score: 702
Period size: 88 Copynumber: 6.1 Consensus size: 88
20662811 AGATTAGTGA
**
20662821 AGATCGAAGATACCAGCCTTGCCTCAATCGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTG
1 AGATCGAAGATACCAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTG
*
20662886 CCTTCTTGCGCTGACAGCGAAGC
66 CCTTCCTGCGCTGACAGCGAAGC
* * *
20662909 ATATCAAAGATACCAGCCTCGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTG
1 AGATCGAAGATACCAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTG
* *
20662974 CCTTCCTACGCTGACAGCGAAGT
66 CCTTCCTGCGCTGACAGCGAAGC
* * * * * *
20662997 AGATCAAAGATACTAGCCTTGCCTCCCTCGGTTACAGTAGAGCAGGTTGATGATAGCAGATTTTG
1 AGATCGAAGATACCAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTG
20663062 CCTTCCTGCGCTGACAGCGAAGC
66 CCTTCCTGCGCTGACAGCGAAGC
* * *
20663085 AGATTGAAGATACCAGCCTTGCCTCCCTCGGTTGCAATGGAGCAGATTGAAGATAGCAGATCTTG
1 AGATCGAAGATACCAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTG
* *
20663150 CCTCCCTGCACTGACAGCGAAGC
66 CCTTCCTGCGCTGACAGCGAAGC
* * * * * *
20663173 AGATCGAAGATACCAGCCTTGCTTCCTTGGGTTACAGTGGAGCAGGTTGAAAATTGCAGATCTTG
1 AGATCGAAGATACCAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTG
* *
20663238 CCTTCCTGTGCTGACAGTGAAGC
66 CCTTCCTGCGCTGACAGCGAAGC
* * * * * * * *
20663261 AGATCGAAGACACTAGTCTTTCCTCCTTGGGTTGCAGTGGAGCAGGTTGAATATAAC-GAATCTT
1 AGATCGAAGATACCAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCAG-ATCTT
* ** *
20663325 GCCTTCTTGTACTGACAGTGAAGC
65 GCCTTCCTGCGCTGACAGCGAAGC
*
20663349 AGATTGAAGAT
1 AGATCGAAGAT
20663360 TACAAGTCCT
Statistics
Matches: 396, Mismatches: 54, Indels: 2
0.88 0.12 0.00
Matches are distributed among these distances:
87 1 0.00
88 395 1.00
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (88 bp):
AGATCGAAGATACCAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAAGATAGCAGATCTTG
CCTTCCTGCGCTGACAGCGAAGC
Found at i:20663256 original size:45 final size:45
Alignment explanation
Indices: 20662855--20663359 Score: 290
Period size: 45 Copynumber: 11.4 Consensus size: 45
20662845 CAATCGGTTG
* * *
20662855 CAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCTTGCGCTGA
1 CAGTGAAGCAGATTGAAGATAGCAGATCTTGCCTTCCTGCGCTGA
* * ** * * * * *
20662900 CAGCGAAGCATATCAAAGATACCAG-CCTCGCCTCCCT-CGGTTG-
1 CAGTGAAGCAGATTGAAGATAGCAGATCTTGCCTTCCTGC-GCTGA
* * *
20662943 CAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTACGCTGA
1 CAGTGAAGCAGATTGAAGATAGCAGATCTTGCCTTCCTGCGCTGA
* * ** * * * *
20662988 CAGCGAAGTAGATCAAAGATA-CTAG-CCTTGCCTCCCT-CGGTTA
1 CAGTGAAGCAGATTGAAGATAGC-AGATCTTGCCTTCCTGCGCTGA
* * *
20663031 CAGT-AGAGCAGGTTGATGATAGCAGATTTTGCCTTCCTGCGCTGA
1 CAGTGA-AGCAGATTGAAGATAGCAGATCTTGCCTTCCTGCGCTGA
* * * * *
20663076 CAGCGAAGCAGATTGAAGATACCAG-CCTTGCCTCCCT-CGGTTG-
1 CAGTGAAGCAGATTGAAGATAGCAGATCTTGCCTTCCTGC-GCTGA
* * * *
20663119 CAATGGAGCAGATTGAAGATAGCAGATCTTGCCTCCCTGCACTGA
1 CAGTGAAGCAGATTGAAGATAGCAGATCTTGCCTTCCTGCGCTGA
* * * * * *
20663164 CAGCGAAGCAGATCGAAGATACCAG-CCTTG-CTTCCTTG-GGTTA
1 CAGTGAAGCAGATTGAAGATAGCAGATCTTGCCTTCC-TGCGCTGA
* * * * *
20663207 CAGTGGAGCAGGTTGAAAATTGCAGATCTTGCCTTCCTGTGCTGA
1 CAGTGAAGCAGATTGAAGATAGCAGATCTTGCCTTCCTGCGCTGA
* * * * *
20663252 CAGTGAAGCAGATCGAAGACA-CTAG-TCTTTCC-TCCTTGGGTTG-
1 CAGTGAAGCAGATTGAAGATAGC-AGATCTTGCCTTCC-TGCGCTGA
* * * * * **
20663295 CAGTGGAGCAGGTTGAATATAAC-GAATCTTGCCTTCTTGTACTGA
1 CAGTGAAGCAGATTGAAGATAGCAG-ATCTTGCCTTCCTGCGCTGA
20663340 CAGTGAAGCAGATTGAAGAT
1 CAGTGAAGCAGATTGAAGAT
20663360 TACAAGTCCT
Statistics
Matches: 334, Mismatches: 101, Indels: 50
0.69 0.21 0.10
Matches are distributed among these distances:
42 2 0.01
43 103 0.31
44 104 0.31
45 124 0.37
46 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (45 bp):
CAGTGAAGCAGATTGAAGATAGCAGATCTTGCCTTCCTGCGCTGA
Found at i:20663404 original size:44 final size:43
Alignment explanation
Indices: 20663354--20663484 Score: 147
Period size: 44 Copynumber: 3.0 Consensus size: 43
20663344 GAAGCAGATT
* *
20663354 GAAGATTACAAGTCCTATCTCCCTGGCTAGCAGTGGAATAGGTG
1 GAAGATTGCAAGTCCTATCTCCCTGAC-AGCAGTGGAATAGGTG
* *
20663398 GAAGATTGTAAGT-CTCATCTCCCTGAACAGCAGTGGAATAGGTT
1 GAAGATTGCAAGTCCT-ATCTCCCTG-ACAGCAGTGGAATAGGTG
** * *
20663442 GAAGATTGCAAAACCTAGCTCCCTGACCAGCAGTGAAATAGGT
1 GAAGATTGCAAGTCCTATCTCCCTGA-CAGCAGTGGAATAGGT
20663485 TGGGAAATTA
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
43 3 0.04
44 68 0.92
45 3 0.04
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.24
Consensus pattern (43 bp):
GAAGATTGCAAGTCCTATCTCCCTGACAGCAGTGGAATAGGTG
Found at i:20663740 original size:44 final size:43
Alignment explanation
Indices: 20663626--20663782 Score: 129
Period size: 44 Copynumber: 3.6 Consensus size: 43
20663616 GAAATTATAG
* * * *
20663626 ATCTTATCCCCCTGAAGTTGCAGTGGGGCAGATCGAATATGGC-A-A
1 ATCTTATCTCCCTGAAATTGCAGTGGAGCAGAT-TAA-A--GCAATA
** *
20663671 ATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCAATA
1 ATCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAG-CAATA
* * * *
20663715 ATCCTATCTCCCTGAAATTGTAGTGGAGCGGATTAAAGTAATA
1 ATCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGCAATA
* *
20663758 GATCTTATCTCTCTGAAGTTGCAGT
1 -ATCTTATCTCCCTGAAATTGCAGT
20663783 AGAGTGGATC
Statistics
Matches: 92, Mismatches: 16, Indels: 9
0.79 0.14 0.08
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 6 0.07
44 54 0.59
45 30 0.33
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (43 bp):
ATCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGCAATA
Found at i:20663851 original size:44 final size:45
Alignment explanation
Indices: 20663801--20663895 Score: 120
Period size: 44 Copynumber: 2.1 Consensus size: 45
20663791 TCGCATCAGG
* * * *
20663801 TCTTATCTCCTTGAGGTTGCAGCGGAGCAGACCGAAGA-AGCAGA
1 TCTTATCCCCCTGAAGTTGCAGCGGAGCAGACCGAAGATAGCAAA
* * *
20663845 TCTTATCCCCCTGAAGTTGCAGTGGGGCAGATCGAAGATAGCAAA
1 TCTTATCCCCCTGAAGTTGCAGCGGAGCAGACCGAAGATAGCAAA
20663890 TCTTAT
1 TCTTAT
20663896 TTCCCAGGCG
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 32 0.74
45 11 0.26
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.24
Consensus pattern (45 bp):
TCTTATCCCCCTGAAGTTGCAGCGGAGCAGACCGAAGATAGCAAA
Found at i:20663972 original size:50 final size:50
Alignment explanation
Indices: 20663918--20664026 Score: 130
Period size: 50 Copynumber: 2.2 Consensus size: 50
20663908 GCAGTGGAAC
** * *
20663918 AGATTAAAGCCACAATGGCGAATCTCGCTTCCCCGACATTGCT-GTTAAAA
1 AGATTAAAGCCACAACAGCGAATCTCACTTCCCCGACATTG-TAGCTAAAA
* * * *
20663968 AGATTAAAGCTACAACAGCGAATCTTACTTCCCTGACATTGTAGCTAAAC
1 AGATTAAAGCCACAACAGCGAATCTCACTTCCCCGACATTGTAGCTAAAA
20664018 AGATTAAAG
1 AGATTAAAG
20664027 TTACAGATCC
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
49 1 0.02
50 49 0.98
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.25
Consensus pattern (50 bp):
AGATTAAAGCCACAACAGCGAATCTCACTTCCCCGACATTGTAGCTAAAA
Found at i:20665929 original size:12 final size:13
Alignment explanation
Indices: 20665913--20665961 Score: 66
Period size: 12 Copynumber: 3.8 Consensus size: 13
20665903 TATGCTATTA
20665913 TTTTTTATAACA-
1 TTTTTTATAACAT
*
20665925 TTTTTTATAATAT
1 TTTTTTATAACAT
20665938 TATTTTTATAA-AT
1 T-TTTTTATAACAT
20665951 TTTTTTATAAC
1 TTTTTTATAAC
20665962 CTTAATTTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
12 20 0.61
13 4 0.12
14 9 0.27
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTTTTATAACAT
Found at i:20665954 original size:26 final size:27
Alignment explanation
Indices: 20665908--20665960 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
20665898 CATAATATGC
20665908 TATTATTTTTTATAACATTTTTTATAA
1 TATTATTTTTTATAACATTTTTTATAA
20665935 TATTA-TTTTTATAA-ATTTTTTTATAA
1 TATTATTTTTTATAACA-TTTTTTATAA
20665961 CCTTAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 1 0.04
26 19 0.76
27 5 0.20
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (27 bp):
TATTATTTTTTATAACATTTTTTATAA
Found at i:20665970 original size:26 final size:26
Alignment explanation
Indices: 20665915--20665970 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
20665905 TGCTATTATT
* *
20665915 TTTTATAACATTTTTTATAATATTAT
1 TTTTATAACATTTTTTATAACATTAA
*
20665941 TTTTATAA-ATTTTTTTATAACCTTAA
1 TTTTATAACA-TTTTTTATAACATTAA
20665967 TTTT
1 TTTT
20665971 CTTTTTGCGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 1 0.04
26 25 0.96
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (26 bp):
TTTTATAACATTTTTTATAACATTAA
Found at i:20667272 original size:2 final size:2
Alignment explanation
Indices: 20667260--20667351 Score: 62
Period size: 2 Copynumber: 46.5 Consensus size: 2
20667250 GACTATGAAG
* * * * * * *
20667260 AT AT GT AT AT AT AT AT GT AA AA AT AT GT AT GT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
20667302 AT AT AT A- AA AT GAA AT AT AT AT AT AT AT AT AT A- AA 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
*
20667343 GT AT AT AT A
1 AT AT AT AT A
20667352 AAATATAGGA
Statistics
Matches: 69, Mismatches: 18, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
1 2 0.03
2 66 0.96
3 1 0.01
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (2 bp):
AT
Found at i:20667304 original size:30 final size:29
Alignment explanation
Indices: 20667268--20667358 Score: 91
Period size: 30 Copynumber: 3.2 Consensus size: 29
20667258 AGATATGTAT
*
20667268 ATATATATGTAAAAATATGTATGTATATAA
1 ATATATAT-TAAAAATATGTATATATATAA
* * *
20667298 ATATATA-TATAAA-ATG-AAATATATAT
1 ATATATATTAAAAATATGTATATATATAA
20667324 ATATATATATAAAATATATGTATATATA-AA
1 ATATATAT-TAAAA-ATATGTATATATATAA
20667354 ATATA
1 ATATA
20667359 GGAAATGTAT
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
26 14 0.29
27 3 0.06
28 9 0.18
29 1 0.02
30 16 0.33
31 6 0.12
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (29 bp):
ATATATATTAAAAATATGTATATATATAA
Found at i:20667357 original size:26 final size:25
Alignment explanation
Indices: 20667260--20667358 Score: 85
Period size: 26 Copynumber: 3.8 Consensus size: 25
20667250 GACTATGAAG
* *
20667260 ATATGTATATATATATGTA-AAAAT
1 ATATGTATATATAAATATATAAAAT
*
20667284 ATGTATGTATATAAATATATATATAAAAT
1 A--TATGTATAT--ATAAATATATAAAAT
* * *
20667313 GAAATATATATATATATATATAAAAT
1 -ATATGTATATATAAATATATAAAAT
20667339 ATATGTATATATAAA-ATATA
1 ATATGTATATATAAATATATA
20667359 GGAAATGTAT
Statistics
Matches: 63, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
24 6 0.10
25 12 0.19
26 24 0.38
28 15 0.24
29 5 0.08
30 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (25 bp):
ATATGTATATATAAATATATAAAAT
Found at i:20670425 original size:14 final size:14
Alignment explanation
Indices: 20670399--20670432 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
20670389 GGTTCGTAAC
20670399 AGAAAATAAAAAAA
1 AGAAAATAAAAAAA
20670413 AGTAAAA-AAAAAAA
1 AG-AAAATAAAAAAA
20670427 AGAAAA
1 AGAAAA
20670433 GGAAAAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.21
14 11 0.58
15 4 0.21
ACGTcount: A:0.85, C:0.00, G:0.09, T:0.06
Consensus pattern (14 bp):
AGAAAATAAAAAAA
Found at i:20670432 original size:19 final size:18
Alignment explanation
Indices: 20670401--20670441 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
20670391 TTCGTAACAG
* *
20670401 AAAATAAAAAAAAGTAAA
1 AAAAAAAAAAAAAGGAAA
20670419 AAAAAAAAAGAAAAGGAAA
1 AAAAAAAAA-AAAAGGAAA
20670438 AAAA
1 AAAA
20670442 CAAACTAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.85, C:0.00, G:0.10, T:0.05
Consensus pattern (18 bp):
AAAAAAAAAAAAAGGAAA
Found at i:20670954 original size:15 final size:15
Alignment explanation
Indices: 20670934--20670963 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20670924 ATTTGTGTCA
*
20670934 ATGGTGATTTTGTTG
1 ATGGTGAGTTTGTTG
20670949 ATGGTGAGTTTGTTG
1 ATGGTGAGTTTGTTG
20670964 TGTTATTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.37, T:0.50
Consensus pattern (15 bp):
ATGGTGAGTTTGTTG
Found at i:20679493 original size:9 final size:9
Alignment explanation
Indices: 20679479--20679520 Score: 68
Period size: 9 Copynumber: 4.8 Consensus size: 9
20679469 GCATCTCACA
20679479 TTTTATTTC
1 TTTTATTTC
20679488 TTTTATTTC
1 TTTTATTTC
20679497 TTTTATTTC
1 TTTTATTTC
*
20679506 -TTTATTTA
1 TTTTATTTC
20679514 TTTTATT
1 TTTTATT
20679521 ATTAATATCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 7 0.23
9 24 0.77
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTATTTC
Found at i:20679511 original size:17 final size:18
Alignment explanation
Indices: 20679478--20679520 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
20679468 GGCATCTCAC
20679478 ATTTTATTTCTTTTATTT
1 ATTTTATTTCTTTTATTT
*
20679496 CTTTTATTTC-TTTATTT
1 ATTTTATTTCTTTTATTT
20679513 ATTTTATT
1 ATTTTATT
20679521 ATTAATATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (18 bp):
ATTTTATTTCTTTTATTT
Found at i:20684289 original size:20 final size:22
Alignment explanation
Indices: 20684264--20684311 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
20684254 CGAATCTGTC
20684264 AAAAATAA-T-CAAAATTCACT
1 AAAAATAATTGCAAAATTCACT
* *
20684284 AAAAATAATTGTAAAATTGACT
1 AAAAATAATTGCAAAATTCACT
20684306 AAAAAT
1 AAAAAT
20684312 TAACATGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.33
21 1 0.04
22 15 0.62
ACGTcount: A:0.60, C:0.08, G:0.04, T:0.27
Consensus pattern (22 bp):
AAAAATAATTGCAAAATTCACT
Found at i:20690595 original size:6 final size:6
Alignment explanation
Indices: 20690584--20690611 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
20690574 TGCCTCCCTC
20690584 GGTTTT GGTTTT GGTTTT GGTTTT GGTT
1 GGTTTT GGTTTT GGTTTT GGTTTT GGTT
20690612 ACCCATGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.36, T:0.64
Consensus pattern (6 bp):
GGTTTT
Found at i:20693457 original size:20 final size:22
Alignment explanation
Indices: 20693432--20693478 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
20693422 TACCCTTTGT
20693432 AAAATAA-T-CAAAATTCACTA
1 AAAATAATTGCAAAATTCACTA
* *
20693452 AAAATAATTGTAAAATTGACTA
1 AAAATAATTGCAAAATTCACTA
20693474 AAAAT
1 AAAAT
20693479 TAACATGTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 7 0.30
21 1 0.04
22 15 0.65
ACGTcount: A:0.60, C:0.09, G:0.04, T:0.28
Consensus pattern (22 bp):
AAAATAATTGCAAAATTCACTA
Found at i:20696699 original size:46 final size:46
Alignment explanation
Indices: 20696639--20696755 Score: 216
Period size: 46 Copynumber: 2.5 Consensus size: 46
20696629 CATATCAAAC
* *
20696639 CTTATCTCCTTGAAGTTGCAGTGGAACAGGTTAAAAATAAACCAAT
1 CTTATCTCCCTGAAGTTACAGTGGAACAGGTTAAAAATAAACCAAT
20696685 CTTATCTCCCTGAAGTTACAGTGGAACAGGTTAAAAATAAACCAAT
1 CTTATCTCCCTGAAGTTACAGTGGAACAGGTTAAAAATAAACCAAT
20696731 CTTATCTCCCTGAAGTTACAGTGGA
1 CTTATCTCCCTGAAGTTACAGTGGA
20696756 GCGTTACAGT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 69 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (46 bp):
CTTATCTCCCTGAAGTTACAGTGGAACAGGTTAAAAATAAACCAAT
Found at i:20696763 original size:13 final size:13
Alignment explanation
Indices: 20696745--20696770 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20696735 TCTCCCTGAA
20696745 GTTACAGTGGAGC
1 GTTACAGTGGAGC
20696758 GTTACAGTGGAGC
1 GTTACAGTGGAGC
20696771 AGATTGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.38, T:0.23
Consensus pattern (13 bp):
GTTACAGTGGAGC
Found at i:20696850 original size:44 final size:44
Alignment explanation
Indices: 20696782--20697098 Score: 251
Period size: 44 Copynumber: 7.0 Consensus size: 44
20696772 GATTGAAGAC
* *
20696782 AAGCTACAAATCTTATCTCCCTGAAGTTACAGTGGAGCATATTA
1 AAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTA
* * * * *
20696826 AAGCCACAAACCTTATCTCCCTGAAGTTGCAGTGGAACAGGTGA
1 AAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTA
** * *
20696870 AAAATAAACCAATCTTACCTCCCTGAAGTTGCAGTGGAGCAGATTGAA
1 AAGCT--ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT--A
* *
20696918 GACAGACTACAAATCTTATC-CCCTTAAAGTTG-ATGTGGAGCAGATTG
1 -A-AG-CTACAAATCTTATCTCCC-TGAAGTTGCA-GTGGAGCAGATTA
* * * *
20696965 AAGCGACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTG
1 AAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTA
* * * * * * *
20697009 AAGATTCCAATCTTATCTCTCTGAAGTTGTAGTGGAGTAGATTG
1 AAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTA
* *** * * * *
20697053 AAGATATTGATCCTATCTCCCTGAAGTTGTAGTTGAGCGGATTA
1 AAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTA
20697097 AA
1 AA
20697099 ATGATGAATC
Statistics
Matches: 217, Mismatches: 45, Indels: 22
0.76 0.16 0.08
Matches are distributed among these distances:
44 141 0.65
45 6 0.03
46 33 0.15
48 5 0.02
49 30 0.14
50 1 0.00
51 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (44 bp):
AAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTA
Found at i:20697110 original size:44 final size:45
Alignment explanation
Indices: 20696978--20697112 Score: 134
Period size: 44 Copynumber: 3.1 Consensus size: 45
20696968 CGACAAACCT
* * * ** *
20696978 TATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGAT-TCCAATCT
1 TATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAAATATTGAATCC
* * *
20697022 TATCTCTCTGAAGTTGTAGTGGAGTAGATTGAAGATATTG-ATCC
1 TATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAAATATTGAATCC
* *
20697066 TATCTCCCTGAAGTTGTAGTTGAGCGGATT-AAAATGA-TGAATCC
1 TATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAAAT-ATTGAATCC
20697110 TAT
1 TAT
20697113 ACCTCTGAGG
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
43 6 0.08
44 69 0.91
45 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (45 bp):
TATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAAATATTGAATCC
Found at i:20707309 original size:37 final size:38
Alignment explanation
Indices: 20707201--20707331 Score: 113
Period size: 39 Copynumber: 3.4 Consensus size: 38
20707191 AAAAGATCTT
* * *
20707201 ATTCAATATGATCAGTGGATAATGCTCGTTTGAGCAAAC
1 ATTCAATATAATCAGTAGATATTGCTCGTTTGAGC-AAC
* * * * * *
20707240 ATTTAGTATAATCAATAGACATTGCTCTTTTGAGC-TC
1 ATTCAATATAATCAGTAGATATTGCTCGTTTGAGCAAC
20707277 ATTCAATAT-ATCCAGTAGATATTGCTCGTTTGAGCATAC
1 ATTCAATATAAT-CAGTAGATATTGCTCGTTTGAGCA-AC
* * *
20707316 TTTCAGTAGAATCAGT
1 ATTCAATATAATCAGT
20707332 GGGTATGGCT
Statistics
Matches: 70, Mismatches: 18, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
36 2 0.03
37 28 0.40
39 38 0.54
40 2 0.03
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (38 bp):
ATTCAATATAATCAGTAGATATTGCTCGTTTGAGCAAC
Found at i:20707354 original size:39 final size:39
Alignment explanation
Indices: 20707300--20707405 Score: 169
Period size: 39 Copynumber: 2.7 Consensus size: 39
20707290 AGTAGATATT
*
20707300 GCTCGTTTGAGCATACTTTCAGTAGAATCAGTGGGTATG
1 GCTCGATTGAGCATACTTTCAGTAGAATCAGTGGGTATG
* *
20707339 GCTCGATTGAACATACCTTT-AGTACAATCAGTGGGTATG
1 GCTCGATTGAGCATA-CTTTCAGTAGAATCAGTGGGTATG
20707378 GCTCGATTGAGCATACTTTCAGTAGAAT
1 GCTCGATTGAGCATACTTTCAGTAGAAT
20707406 ATAATATTTA
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
38 4 0.07
39 52 0.87
40 4 0.07
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (39 bp):
GCTCGATTGAGCATACTTTCAGTAGAATCAGTGGGTATG
Found at i:20707420 original size:12 final size:12
Alignment explanation
Indices: 20707403--20707430 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
20707393 CTTTCAGTAG
20707403 AATATAATATTT
1 AATATAATATTT
20707415 AATATAATATTT
1 AATATAATATTT
20707427 AATA
1 AATA
20707431 AAATTATATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
AATATAATATTT
Found at i:20711221 original size:16 final size:18
Alignment explanation
Indices: 20711200--20711232 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
20711190 AAATAAAAAA
20711200 AATTAAA-C-AAATTTAC
1 AATTAAATCTAAATTTAC
20711216 AATTAAATCTAAATTTA
1 AATTAAATCTAAATTTA
20711233 TTCTATTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (18 bp):
AATTAAATCTAAATTTAC
Found at i:20714968 original size:23 final size:24
Alignment explanation
Indices: 20714935--20714994 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
20714925 GTTATTTAAA
*
20714935 AAAATACTCATATTTATATA-ATT
1 AAAATATTCATATTTATATAGATT
* *
20714958 AAAATATTCATATTTTTATAGGTT
1 AAAATATTCATATTTATATAGATT
20714982 AAAATATGTCATA
1 AAAATAT-TCATA
20714995 AATTCTTGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 18 0.56
24 9 0.28
25 5 0.16
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (24 bp):
AAAATATTCATATTTATATAGATT
Found at i:20719774 original size:8 final size:8
Alignment explanation
Indices: 20719757--20719797 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
20719747 TTGTATAAGC
20719757 ATATAT-T
1 ATATATGT
20719764 ATATATGT
1 ATATATGT
20719772 ATATATGT
1 ATATATGT
*
20719780 ATATCTGT
1 ATATATGT
*
20719788 ATATTTGT
1 ATATATGT
20719796 AT
1 AT
20719798 TTTGTATTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
7 6 0.19
8 25 0.81
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.54
Consensus pattern (8 bp):
ATATATGT
Found at i:20719826 original size:18 final size:18
Alignment explanation
Indices: 20719803--20719837 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20719793 TGTATTTTGT
20719803 ATTTGTATATGGGATGAG
1 ATTTGTATATGGGATGAG
* *
20719821 ATTTGTTTATTGGATGA
1 ATTTGTATATGGGATGA
20719838 AGTATTCTGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.46
Consensus pattern (18 bp):
ATTTGTATATGGGATGAG
Found at i:20723458 original size:16 final size:16
Alignment explanation
Indices: 20723439--20723469 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20723429 AAAAGAAGTT
20723439 GTTAAGGTTGTTAGCA
1 GTTAAGGTTGTTAGCA
*
20723455 GTTAGGGTTGTTAGC
1 GTTAAGGTTGTTAGC
20723470 TGCAGCTAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.06, G:0.35, T:0.39
Consensus pattern (16 bp):
GTTAAGGTTGTTAGCA
Found at i:20724717 original size:31 final size:30
Alignment explanation
Indices: 20724659--20724718 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
20724649 TACTAGTAAA
* *
20724659 TATAAAAAAATGATCTAATTTCTTAAATTT
1 TATAAAAAAATGATATAATTTCATAAATTT
20724689 TATAAAAAAATTGATAT-ATATTCATAAATT
1 TATAAAAAAA-TGATATAAT-TTCATAAATT
20724719 AACCAGGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (30 bp):
TATAAAAAAATGATATAATTTCATAAATTT
Found at i:20725185 original size:14 final size:14
Alignment explanation
Indices: 20725166--20725192 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20725156 TAAGTACCCA
20725166 ACCCAAAAATAAAT
1 ACCCAAAAATAAAT
20725180 ACCCAAAAATAAA
1 ACCCAAAAATAAA
20725193 AATCAAATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.22, G:0.00, T:0.11
Consensus pattern (14 bp):
ACCCAAAAATAAAT
Found at i:20725695 original size:24 final size:24
Alignment explanation
Indices: 20725663--20725724 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
20725653 GCAACATTTA
* *
20725663 ATTACAAGCCTAAACTCATCGTTTC
1 ATTA-AAGCATAAACTCACCGTTTC
* *
20725688 ATTTAAGCATAAACTCACCGTTTT
1 ATTAAAGCATAAACTCACCGTTTC
*
20725712 ATTAAAGCTTAAA
1 ATTAAAGCATAAA
20725725 ACCAATTACT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
24 28 0.90
25 3 0.10
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.34
Consensus pattern (24 bp):
ATTAAAGCATAAACTCACCGTTTC
Found at i:20731729 original size:22 final size:23
Alignment explanation
Indices: 20731677--20731722 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
20731667 GTAACCAAAA
* *
20731677 CTCTCTT-CTCTCCTTTTCTTTT
1 CTCTCTTGTTCTCCTTATCTTTT
20731699 CTCTCTTGTTCTCCTTAT-TTTT
1 CTCTCTTGTTCTCCTTATCTTTT
20731721 CT
1 CT
20731723 TTTTTGTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.02, C:0.33, G:0.02, T:0.63
Consensus pattern (23 bp):
CTCTCTTGTTCTCCTTATCTTTT
Found at i:20736244 original size:12 final size:12
Alignment explanation
Indices: 20736227--20736251 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20736217 ATTGATTTTC
20736227 TCATAATCATAG
1 TCATAATCATAG
20736239 TCATAATCATAG
1 TCATAATCATAG
20736251 T
1 T
20736252 AATGTTGAAA
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:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TCATAATCATAG
Found at i:20737768 original size:15 final size:15
Alignment explanation
Indices: 20737748--20737782 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
20737738 TACGTTTTAA
*
20737748 GGGTTATTTATTTTT
1 GGGTTATTTATTTTC
20737763 GGGTTATTTATTTTC
1 GGGTTATTTATTTTC
20737778 GGGTT
1 GGGTT
20737783 TCGTGGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.11, C:0.03, G:0.26, T:0.60
Consensus pattern (15 bp):
GGGTTATTTATTTTC
Found at i:20747288 original size:3 final size:3
Alignment explanation
Indices: 20747280--20747320 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
20747270 GTGAACAAAC
20747280 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
20747321 AGCATCACAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:20748169 original size:10 final size:10
Alignment explanation
Indices: 20748154--20748180 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
20748144 AACACGCGCG
20748154 TTTGCGTGCA
1 TTTGCGTGCA
20748164 TTTGCGTGCA
1 TTTGCGTGCA
20748174 TTTGCGT
1 TTTGCGT
20748181 ACGGCTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.07, C:0.19, G:0.30, T:0.44
Consensus pattern (10 bp):
TTTGCGTGCA
Found at i:20767831 original size:23 final size:24
Alignment explanation
Indices: 20767779--20767831 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
20767769 AAAATCATGG
20767779 TATATTACTATTTCAAAGTTACTA
1 TATATTACTATTTCAAAGTTACTA
* *
20767803 TGTATTATTATTT-AAAGTTATCT-
1 TATATTACTATTTCAAAGTTA-CTA
20767826 TATATT
1 TATATT
20767832 TATTTTATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.34, C:0.08, G:0.06, T:0.53
Consensus pattern (24 bp):
TATATTACTATTTCAAAGTTACTA
Found at i:20771440 original size:27 final size:27
Alignment explanation
Indices: 20771402--20771481 Score: 99
Period size: 27 Copynumber: 3.0 Consensus size: 27
20771392 AACAAGTCGA
*
20771402 GAAAGAAAAGCCTTTGTGGCGAAATGT
1 GAAAGAAAAGCCTTTGTGGCGAAATAT
* *
20771429 GAAAGAAAAGCCTTTTTGGTGAAATAT
1 GAAAGAAAAGCCTTTGTGGCGAAATAT
* * *
20771456 GAAAGGAATGCCTTTGTGTC-AAATAT
1 GAAAGAAAAGCCTTTGTGGCGAAATAT
20771482 TGAATGGATC
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
26 6 0.13
27 39 0.87
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.28
Consensus pattern (27 bp):
GAAAGAAAAGCCTTTGTGGCGAAATAT
Found at i:20772486 original size:19 final size:19
Alignment explanation
Indices: 20772462--20772499 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
20772452 TATCAGATGT
20772462 GTGGTAATAAGTTGTTTAA
1 GTGGTAATAAGTTGTTTAA
20772481 GTGGTAATAAGTTGTTTAA
1 GTGGTAATAAGTTGTTTAA
20772500 CATATATTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (19 bp):
GTGGTAATAAGTTGTTTAA
Found at i:20780005 original size:13 final size:13
Alignment explanation
Indices: 20779987--20780016 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
20779977 AAACTAGATT
*
20779987 TTAACTAAGTAAA
1 TTAACTAAGAAAA
20780000 TTAACTAAGAAAA
1 TTAACTAAGAAAA
20780013 TTAA
1 TTAA
20780017 AAGGTAACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (13 bp):
TTAACTAAGAAAA
Found at i:20781858 original size:16 final size:16
Alignment explanation
Indices: 20781837--20781870 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
20781827 TTACCAATGA
* *
20781837 AATTCTTTTATTTCTC
1 AATTCTTTCACTTCTC
20781853 AATTCTTTCACTTCTC
1 AATTCTTTCACTTCTC
20781869 AA
1 AA
20781871 GCTAAGATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.53
Consensus pattern (16 bp):
AATTCTTTCACTTCTC
Found at i:20784259 original size:29 final size:29
Alignment explanation
Indices: 20784226--20784360 Score: 144
Period size: 29 Copynumber: 4.7 Consensus size: 29
20784216 CAGAGTCTCA
* *
20784226 CCACAAAGGCATCTTTTTAACAGAGATAG
1 CCACAAAGGCTTCCTTTTAACAGAGATAG
* * **
20784255 CCACAAAGGTTTCCTTTTAACATAGACCG
1 CCACAAAGGCTTCCTTTTAACAGAGATAG
* * *
20784284 CCACAAATGCTTCCTTTTAATAGAGAAAG
1 CCACAAAGGCTTCCTTTTAACAGAGATAG
* * * *
20784313 CTACAAAGGCTTCCTTGTAATAAAGATAG
1 CCACAAAGGCTTCCTTTTAACAGAGATAG
*
20784342 CCACAAAGGCATCCTTTTA
1 CCACAAAGGCTTCCTTTTA
20784361 TGAAATTTGG
Statistics
Matches: 86, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 86 1.00
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.27
Consensus pattern (29 bp):
CCACAAAGGCTTCCTTTTAACAGAGATAG
Found at i:20784302 original size:58 final size:58
Alignment explanation
Indices: 20784226--20784360 Score: 162
Period size: 58 Copynumber: 2.3 Consensus size: 58
20784216 CAGAGTCTCA
* * * * * *
20784226 CCACAAAGGCATCTTTTTAACAGAGATAGCCACAAAGGTTTCCTTTTAACATAGACCG
1 CCACAAAGGCATCCTTTTAACAGAGAAAGCCACAAAGGCTTCCTTGTAACAAAGACAG
* * * * * *
20784284 CCACAAATGCTTCCTTTTAATAGAGAAAGCTACAAAGGCTTCCTTGTAATAAAGATAG
1 CCACAAAGGCATCCTTTTAACAGAGAAAGCCACAAAGGCTTCCTTGTAACAAAGACAG
20784342 CCACAAAGGCATCCTTTTA
1 CCACAAAGGCATCCTTTTA
20784361 TGAAATTTGG
Statistics
Matches: 63, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
58 63 1.00
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.27
Consensus pattern (58 bp):
CCACAAAGGCATCCTTTTAACAGAGAAAGCCACAAAGGCTTCCTTGTAACAAAGACAG
Found at i:20787386 original size:31 final size:31
Alignment explanation
Indices: 20787338--20787493 Score: 144
Period size: 31 Copynumber: 5.1 Consensus size: 31
20787328 TAAGTTGCCG
* *
20787338 AAATGATTCGTATATGGTTGA-ACATTGCTGA
1 AAATAATTTGTATATGGTT-ATACATTGCTGA
* *
20787369 AAATAATTTTTATATGGTTATTCATTGCTGA
1 AAATAATTTGTATATGGTTATACATTGCTGA
*
20787400 AATTGAA-TTGTATAT-GTATATA-AGTTGCTG-
1 AAAT-AATTTGTATATGGT-TATACA-TTGCTGA
* *
20787430 AAATGATTCGTATATGGTTGA-ACATTGCTGA
1 AAATAATTTGTATATGGTT-ATACATTGCTGA
* *
20787461 AAATAATTTTTATATGGTTATACATTGTTGA
1 AAATAATTTGTATATGGTTATACATTGCTGA
20787492 AA
1 AA
20787494 TTTAATTGTT
Statistics
Matches: 101, Mismatches: 14, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
29 1 0.01
30 23 0.23
31 75 0.74
32 2 0.02
ACGTcount: A:0.34, C:0.06, G:0.18, T:0.42
Consensus pattern (31 bp):
AAATAATTTGTATATGGTTATACATTGCTGA
Found at i:20787448 original size:92 final size:92
Alignment explanation
Indices: 20787292--20787513 Score: 356
Period size: 92 Copynumber: 2.4 Consensus size: 92
20787282 AAATTGTTTT
* * *
20787292 TGGTTATACATTGCTGATATTGGATTGTATAT-TACATAAGTTGCCGAAATGATTCGTATATGGT
1 TGGTTATACATTGCTGAAATTGAATTGTATATGTATATAAGTTGCCGAAATGATTCGTATATGGT
20787356 TGAACATTGCTGAAAATAATTTTTATA
66 TGAACATTGCTGAAAATAATTTTTATA
* *
20787383 TGGTTATTCATTGCTGAAATTGAATTGTATATGTATATAAGTTGCTGAAATGATTCGTATATGGT
1 TGGTTATACATTGCTGAAATTGAATTGTATATGTATATAAGTTGCCGAAATGATTCGTATATGGT
20787448 TGAACATTGCTGAAAATAATTTTTATA
66 TGAACATTGCTGAAAATAATTTTTATA
* * * *
20787475 TGGTTATACATTGTTGAAATTTAATTGTTTATGAATATA
1 TGGTTATACATTGCTGAAATTGAATTGTATATGTATATA
20787514 GGATGTCGAA
Statistics
Matches: 120, Mismatches: 10, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
91 29 0.24
92 91 0.76
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.43
Consensus pattern (92 bp):
TGGTTATACATTGCTGAAATTGAATTGTATATGTATATAAGTTGCCGAAATGATTCGTATATGGT
TGAACATTGCTGAAAATAATTTTTATA
Found at i:20787557 original size:31 final size:31
Alignment explanation
Indices: 20787522--20787587 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
20787512 TAGGATGTCG
20787522 AATTTGATT-TGTATATGATTATACATTGCCA
1 AATTTGATTCT-TATATGATTATACATTGCCA
* * *
20787553 AATTTGATTCTTATATGGTTATATATTGCCG
1 AATTTGATTCTTATATGATTATACATTGCCA
20787584 AATT
1 AATT
20787588 GCTTGGCATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.30, C:0.09, G:0.14, T:0.47
Consensus pattern (31 bp):
AATTTGATTCTTATATGATTATACATTGCCA
Found at i:20789959 original size:5 final size:5
Alignment explanation
Indices: 20789949--20789973 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
20789939 GGTAATTTGA
20789949 TAAAT TAAAT TAAAT TAAAT TAAAT
1 TAAAT TAAAT TAAAT TAAAT TAAAT
20789974 AAAACAAAAG
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAAAT
Found at i:20803228 original size:22 final size:22
Alignment explanation
Indices: 20803198--20803243 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
20803188 AGAACATTAG
20803198 TGGGCGAGGAAATTGAGAGTAA
1 TGGGCGAGGAAATTGAGAGTAA
*
20803220 TGGGTGAGGAAATTGAGAGTAA
1 TGGGCGAGGAAATTGAGAGTAA
20803242 TG
1 TG
20803244 TACCTTCGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.35, C:0.02, G:0.41, T:0.22
Consensus pattern (22 bp):
TGGGCGAGGAAATTGAGAGTAA
Found at i:20805216 original size:27 final size:27
Alignment explanation
Indices: 20805173--20805493 Score: 349
Period size: 27 Copynumber: 11.9 Consensus size: 27
20805163 AAAATGTCTG
*
20805173 AATACTCTCGAAGGGTAAAATGACCGA
1 AATACCCTCGAAGGGTAAAATGACCGA
* * *
20805200 AATACCC-CTGAATGGTAAAATAACTGA
1 AATACCCTC-GAAGGGTAAAATGACCGA
* *
20805227 AATACCCCCGAAGGGTAAAATGACCAA
1 AATACCCTCGAAGGGTAAAATGACCGA
* * **
20805254 AATACTCTCGAAAGGTAAAATGACTAA
1 AATACCCTCGAAGGGTAAAATGACCGA
* * * **
20805281 AATACCCCCGAAGGGTAAGATAACTAA
1 AATACCCTCGAAGGGTAAAATGACCGA
20805308 AATACCCTCGAAGGGTAAAATGACCGA
1 AATACCCTCGAAGGGTAAAATGACCGA
*
20805335 AATACCCTCGAAGGGTAAAATGACCAA
1 AATACCCTCGAAGGGTAAAATGACCGA
* **
20805362 AATACCCTCGAAGGGTAAAATAATTGA
1 AATACCCTCGAAGGGTAAAATGACCGA
* * * * *
20805389 AATACCCTAGAAAGGTTAAATAACTGA
1 AATACCCTCGAAGGGTAAAATGACCGA
*
20805416 AATACCCTCAAAGGGTAAAATGACCGA
1 AATACCCTCGAAGGGTAAAATGACCGA
* * *
20805443 AATACCCCCGAA-GGTACAATGACCAA
1 AATACCCTCGAAGGGTAAAATGACCGA
* *
20805469 AATAGCTTCGAAGGGTAAAATGACC
1 AATACCCTCGAAGGGTAAAATGACC
20805494 ATTATACCCC
Statistics
Matches: 246, Mismatches: 45, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
26 22 0.09
27 223 0.91
28 1 0.00
ACGTcount: A:0.44, C:0.20, G:0.18, T:0.17
Consensus pattern (27 bp):
AATACCCTCGAAGGGTAAAATGACCGA
Found at i:20805903 original size:28 final size:28
Alignment explanation
Indices: 20805854--20805943 Score: 99
Period size: 28 Copynumber: 3.2 Consensus size: 28
20805844 ATTGCATTGT
* ** *
20805854 ACTGATTACTGAATTGGGCTAAGGGTCAT
1 ACTG-TTACTGTATTGGGCTAAGGCCCAC
* *
20805883 ATTGTTACTGTATTGGACTAAGGCCCAC
1 ACTGTTACTGTATTGGGCTAAGGCCCAC
* *
20805911 ACTGTTACTGTAATGGGCTAAGACCCAC
1 ACTGTTACTGTATTGGGCTAAGGCCCAC
20805939 ACTGT
1 ACTGT
20805944 ACTTTTACTG
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
28 48 0.94
29 3 0.06
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (28 bp):
ACTGTTACTGTATTGGGCTAAGGCCCAC
Found at i:20808306 original size:31 final size:32
Alignment explanation
Indices: 20808262--20808321 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 32
20808252 AGACTTTGTG
** *
20808262 CAAACTTTTCTTTGCTCTTT-ATTCTTTTGAA
1 CAAACTTACCTTTGCTCTTTCATTATTTTGAA
*
20808293 CAAACTTACCTTTGTTCTTTCATTATTTT
1 CAAACTTACCTTTGCTCTTTCATTATTTT
20808322 TTTCTCTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 17 0.71
32 7 0.29
ACGTcount: A:0.20, C:0.20, G:0.05, T:0.55
Consensus pattern (32 bp):
CAAACTTACCTTTGCTCTTTCATTATTTTGAA
Found at i:20822547 original size:35 final size:35
Alignment explanation
Indices: 20822508--20822604 Score: 140
Period size: 35 Copynumber: 2.7 Consensus size: 35
20822498 TCGGTTGGAC
* * *
20822508 TAGCTCTTATGAGCATTAGTGTGTTTTGGAGGGAT
1 TAGCTCTTATGAGCATTGGTGTGTTTCGGAGGAAT
*
20822543 TAGCTCTTATGAGCATTGGTGTGTTTCGGATGAAT
1 TAGCTCTTATGAGCATTGGTGTGTTTCGGAGGAAT
*
20822578 TGGCTCTTATGAGCATCTGGTGTGTTT
1 TAGCTCTTATGAGCAT-TGGTGTGTTT
20822605 GGGTGGTTTG
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
35 46 0.82
36 10 0.18
ACGTcount: A:0.18, C:0.11, G:0.30, T:0.41
Consensus pattern (35 bp):
TAGCTCTTATGAGCATTGGTGTGTTTCGGAGGAAT
Found at i:20825193 original size:109 final size:109
Alignment explanation
Indices: 20824957--20825153 Score: 376
Period size: 109 Copynumber: 1.8 Consensus size: 109
20824947 AGTCATAAAT
20824957 ATGAAAATGTTGTGTGTAAATGCAAATGAATATATAAGCTAGACTTGTGGGTCATTAAAGCATGA
1 ATGAAAATGTTGTGTGTAAATGCAAATGAATATATAAGCTAGACTTGTGGGTCATTAAAGCATGA
*
20825022 ATACGTTGTTTTGTCTTGATGAAATATCATTAATAGATTAATAC
66 ATACGTTGTTTTGGCTTGATGAAATATCATTAATAGATTAATAC
*
20825066 ATGAAAATGTTGTGTGTAAATGCATATGAATATATAAGCTAGACTTGTGGGTCATTAAAGCATGA
1 ATGAAAATGTTGTGTGTAAATGCAAATGAATATATAAGCTAGACTTGTGGGTCATTAAAGCATGA
20825131 ATACGTTGTTTTGGCTTGATGAA
66 ATACGTTGTTTTGGCTTGATGAA
20825154 TTATTGTTAA
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
109 86 1.00
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.36
Consensus pattern (109 bp):
ATGAAAATGTTGTGTGTAAATGCAAATGAATATATAAGCTAGACTTGTGGGTCATTAAAGCATGA
ATACGTTGTTTTGGCTTGATGAAATATCATTAATAGATTAATAC
Found at i:20827417 original size:25 final size:25
Alignment explanation
Indices: 20827386--20827468 Score: 123
Period size: 25 Copynumber: 3.3 Consensus size: 25
20827376 ATGTGCTAAA
** *
20827386 CAGAGAGCACTGACATGCTAA-ATAT
1 CAGAGAGCACCAACGTGCTAATA-AT
20827411 CAGAGAGCACCAACGTGCTAATAAT
1 CAGAGAGCACCAACGTGCTAATAAT
20827436 CAGAGAGCACCAACGTGCTAATAAT
1 CAGAGAGCACCAACGTGCTAATAAT
20827461 CAGAGAGC
1 CAGAGAGC
20827469 GCGCTAAATT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
25 53 0.98
26 1 0.02
ACGTcount: A:0.40, C:0.23, G:0.22, T:0.16
Consensus pattern (25 bp):
CAGAGAGCACCAACGTGCTAATAAT
Found at i:20828421 original size:13 final size:14
Alignment explanation
Indices: 20828395--20828423 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
20828385 TAATATAGGC
20828395 ATTTAAATAAAATA
1 ATTTAAATAAAATA
20828409 ATTTAAA-AAAATA
1 ATTTAAATAAAATA
20828422 AT
1 AT
20828424 CTTGTAGTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATTTAAATAAAATA
Found at i:20831714 original size:21 final size:22
Alignment explanation
Indices: 20831690--20831731 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
20831680 TTATTAAATA
20831690 AAAATAAAAAAAT-ATTTTTCG
1 AAAATAAAAAAATAATTTTTCG
*
20831711 AAAATAAAATAATAATTTTTC
1 AAAATAAAAAAATAATTTTTC
20831732 AAAGTGGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (22 bp):
AAAATAAAAAAATAATTTTTCG
Found at i:20832517 original size:18 final size:18
Alignment explanation
Indices: 20832485--20832530 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
20832475 AATTTATATG
20832485 TTTA-ATTTTTAATTT-A
1 TTTATATTTTTAATTTAA
*
20832501 TTTCTATTTTATAATTTAA
1 TTTATATTTT-TAATTTAA
20832520 TTTATATTTTT
1 TTTATATTTTT
20832531 TTATATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 3 0.12
17 5 0.20
18 7 0.28
19 10 0.40
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTATATTTTTAATTTAA
Found at i:20832535 original size:10 final size:10
Alignment explanation
Indices: 20832520--20832550 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
20832510 TATAATTTAA
20832520 TTTATATTTT
1 TTTATATTTT
20832530 TTTATATTTT
1 TTTATATTTT
20832540 TTTATATTTT
1 TTTATATTTT
20832550 T
1 T
20832551 ATAATTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTATATTTT
Found at i:20832551 original size:18 final size:18
Alignment explanation
Indices: 20832485--20832553 Score: 54
Period size: 18 Copynumber: 3.8 Consensus size: 18
20832475 AATTTATATG
*
20832485 TTTA-ATTTTTA-ATTTA
1 TTTATATTTTTATATTTT
*
20832501 TTTCTA-TTTTATAATTTAAT
1 TTTATATTTTTAT-ATTT--T
*
20832521 TTATATTTTTTTATATTTT
1 TT-TATATTTTTATATTTT
20832540 TTTATATTTTTATA
1 TTTATATTTTTATA
20832554 ATTCTTTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
16 8 0.20
17 1 0.02
18 15 0.37
19 3 0.07
20 2 0.05
21 6 0.15
22 6 0.15
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATATTTTTATATTTT
Done.