Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
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: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 96 of 141
Found at i:31147801 original size:50 final size:50
Alignment explanation
Indices: 31147720--31148002 Score: 208
Period size: 50 Copynumber: 5.7 Consensus size: 50
31147710 TTGGCATTAC
* ** *
31147720 AGTGGAATAGATTGAAGCCACAACGATGAATCTTACTTCCCTAGCGGTGT
1 AGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCCTAACGGTGT
* * ** ** *
31147770 AGTGGAACAGATTGAAGCTACGACGGCGAATCTTGTTTCTCC-AACATTGC
1 AGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTC-CCTAACGGTGT
** * * *
31147820 AGTTAAATAGATTGAAGCCACAACTGCGAATCTTACTTCCCTATCGGTGT
1 AGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCCTAACGGTGT
* * * * * ** ** **
31147870 AGTAGAACAGATTGAAGCTACGACGGTGAATTTTGTTTCCCTAACATTAC
1 AGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCCTAACGGTGT
** * * * *** *
31147920 AGTTAAATAGATTGAAGCCACAACTGTGAATCTTACTTCCCTGGTGGTCT
1 AGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCCTAACGGTGT
* *
31147970 AGTGGAACAGATTGAAGCTACGACGGCGAATCT
1 AGTGGAACAGATTGAAGCCACAACGGCGAATCT
31148003 GGTTTCCCCG
Statistics
Matches: 170, Mismatches: 61, Indels: 4
0.72 0.26 0.02
Matches are distributed among these distances:
49 2 0.01
50 166 0.98
51 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (50 bp):
AGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCCTAACGGTGT
Found at i:31147855 original size:100 final size:99
Alignment explanation
Indices: 31147725--31148042 Score: 476
Period size: 100 Copynumber: 3.2 Consensus size: 99
31147715 ATTACAGTGG
31147725 AATAGATTGAAGCCACAAC-GATGAATCTTACTTCCCTAGCGGTGTAGTGGAACAGATTGAAGCT
1 AATAGATTGAAGCCACAACTG-TGAATCTTACTTCCCTAGCGGTGTAGTGGAACAGATTGAAGCT
31147789 ACGACGGCGAATCTTGTTTCTCCAACATTGCAGTTA
65 ACGACGGCGAATCTTGTTTC-CCAACATTGCAGTTA
* * *
31147825 AATAGATTGAAGCCACAACTGCGAATCTTACTTCCCTATCGGTGTAGTAGAACAGATTGAAGCTA
1 AATAGATTGAAGCCACAACTGTGAATCTTACTTCCCTAGCGGTGTAGTGGAACAGATTGAAGCTA
* * *
31147890 CGACGGTGAATTTTGTTTCCCTAACATTACAGTTA
66 CGACGGCGAATCTTGTTTCCC-AACATTGCAGTTA
* * *
31147925 AATAGATTGAAGCCACAACTGTGAATCTTACTTCCCTGGTGGTCTAGTGGAACAGATTGAAGCTA
1 AATAGATTGAAGCCACAACTGTGAATCTTACTTCCCTAGCGGTGTAGTGGAACAGATTGAAGCTA
* * *
31147990 CGACGGCGAATCTGGTTTCCCCGACATTGTAGTTA
66 CGACGGCGAATCTTGTTT-CCCAACATTGCAGTTA
*
31148025 AATAGATTAAAGCCACAA
1 AATAGATTGAAGCCACAA
31148043 TGGCAAATCT
Statistics
Matches: 196, Mismatches: 19, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
99 2 0.01
100 190 0.97
101 4 0.02
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (99 bp):
AATAGATTGAAGCCACAACTGTGAATCTTACTTCCCTAGCGGTGTAGTGGAACAGATTGAAGCTA
CGACGGCGAATCTTGTTTCCCAACATTGCAGTTA
Found at i:31148032 original size:50 final size:50
Alignment explanation
Indices: 31147778--31148037 Score: 180
Period size: 50 Copynumber: 5.2 Consensus size: 50
31147768 GTAGTGGAAC
* *
31147778 AGATTGAAGCTACGACGGCGAATCTTGTTTCTCCAACATTGCAGTTAAAT
1 AGATTGAAGCTACGACGGCGAATCTTGTTTCCCCAACATTGTAGTTAAAT
* * * ** * * ** *
31147828 AGATTGAAGCCACAACTGCGAATCTTACTTCCCTATCGGTGTAG-TAGAAC
1 AGATTGAAGCTACGACGGCGAATCTTGTTTCCCCAACATTGTAGTTA-AAT
* * * **
31147878 AGATTGAAGCTACGACGGTGAATTTTGTTTCCCTAACATTACAGTTAAAT
1 AGATTGAAGCTACGACGGCGAATCTTGTTTCCCCAACATTGTAGTTAAAT
* * * * ** ****** * ** *
31147928 AGATTGAAGCCACAACTGTGAATCTTACTTCCCTGGTGGTCTAGTGGAAC
1 AGATTGAAGCTACGACGGCGAATCTTGTTTCCCCAACATTGTAGTTAAAT
* *
31147978 AGATTGAAGCTACGACGGCGAATCTGGTTTCCCCGACATTGTAGTTAAAT
1 AGATTGAAGCTACGACGGCGAATCTTGTTTCCCCAACATTGTAGTTAAAT
*
31148028 AGATTAAAGC
1 AGATTGAAGC
31148038 CACAATGGCA
Statistics
Matches: 150, Mismatches: 58, Indels: 4
0.71 0.27 0.02
Matches are distributed among these distances:
49 2 0.01
50 146 0.97
51 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (50 bp):
AGATTGAAGCTACGACGGCGAATCTTGTTTCCCCAACATTGTAGTTAAAT
Found at i:31148076 original size:200 final size:200
Alignment explanation
Indices: 31147714--31148089 Score: 524
Period size: 200 Copynumber: 1.9 Consensus size: 200
31147704 ATCTCTTTGG
* *
31147714 CATTACAGTGGAATAGATTGAAGCCACAACGATGAATCTTACTTCCCTAGCGGTGTAGTGGAACA
1 CATTACAGTGAAATAGATTGAAGCCACAACGATGAATCTTACTTCCCTAGCGGTCTAGTGGAACA
* * *
31147779 GATTGAAGCTACGACGGCGAATCTTGTTTCTCCAACATTGCAGTTAAATAGATTGAAGCCACAAC
66 GATTGAAGCTACGACGGCGAATCTGGTTTCCCCAACATTGCAGTTAAATAGATTAAAGCCACAAC
* * * ** * *
31147844 TGCGAATCTTACTTCCCTATCGGTGTAGTAGAACAGATTGAAGCTACGACGGTGAATTTTGTTTC
131 TGCAAATCTTACTTCCCTAGCAGTACAGTAGAACAAATTAAAGCTACGACGGTGAATTTTGTTTC
31147909 CCTAA
196 CCTAA
* * *
31147914 CATTACAGTTAAATAGATTGAAGCCACAACTG-TGAATCTTACTTCCCTGGTGGTCTAGTGGAAC
1 CATTACAGTGAAATAGATTGAAGCCACAAC-GATGAATCTTACTTCCCTAGCGGTCTAGTGGAAC
* *
31147978 AGATTGAAGCTACGACGGCGAATCTGGTTTCCCCGACATTGTAGTTAAATAGATTAAAGCCACAA
65 AGATTGAAGCTACGACGGCGAATCTGGTTTCCCCAACATTGCAGTTAAATAGATTAAAGCCACAA
* * *
31148043 -TGGCAAATCTTA-TCTCCTTGGCATTACAGTAGAACAAATTAAAGCTA
130 CT-GCAAATCTTACT-TCCCTAGCAGTACAGTAGAACAAATTAAAGCTA
31148090 AAGGTAGCGA
Statistics
Matches: 153, Mismatches: 20, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
199 2 0.01
200 150 0.98
201 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.28
Consensus pattern (200 bp):
CATTACAGTGAAATAGATTGAAGCCACAACGATGAATCTTACTTCCCTAGCGGTCTAGTGGAACA
GATTGAAGCTACGACGGCGAATCTGGTTTCCCCAACATTGCAGTTAAATAGATTAAAGCCACAAC
TGCAAATCTTACTTCCCTAGCAGTACAGTAGAACAAATTAAAGCTACGACGGTGAATTTTGTTTC
CCTAA
Found at i:31148078 original size:100 final size:99
Alignment explanation
Indices: 31147725--31148111 Score: 401
Period size: 100 Copynumber: 3.9 Consensus size: 99
31147715 ATTACAGTGG
* * *
31147725 AATAGATTGAAGCCACAAC-GATG-AATCTTACTTCCCTAGCGGTGTAGTGGAACAGATTGAAGC
1 AATAGATTGAAGCCACAACTG--GCAATCTTACTTCCCTGGCGGT-CAGTAGAACAGATTGAAGC
*
31147788 TACGACGGCGAATCTTGTTTCTCCAACATTGCAGTTA
63 TACGACGGCGAATCTTGTTTCCCCAACATTGCAGTTA
** *
31147825 AATAGATTGAAGCCACAACT-GCGAATCTTACTTCCCTATCGGTGTAGTAGAACAGATTGAAGCT
1 AATAGATTGAAGCCACAACTGGC-AATCTTACTTCCCTGGCGGT-CAGTAGAACAGATTGAAGCT
* * * *
31147889 ACGACGGTGAATTTTGTTTCCCTAACATTACAGTTA
64 ACGACGGCGAATCTTGTTTCCCCAACATTGCAGTTA
* *
31147925 AATAGATTGAAGCCACAACTGTG-AATCTTACTTCCCTGGTGGTCTAGTGGAACAGATTGAAGCT
1 AATAGATTGAAGCCACAACTG-GCAATCTTACTTCCCTGGCGGTC-AGTAGAACAGATTGAAGCT
* * *
31147989 ACGACGGCGAATCTGGTTTCCCCGACATTGTAGTTA
64 ACGACGGCGAATCTTGTTTCCCCAACATTGCAGTTA
* * ** * *
31148025 AATAGATTAAAGCCACAA-TGGCAAATCTTA-TCTCCTTGGCATTACAGTAGAACAAATTAAAGC
1 AATAGATTGAAGCCACAACTGGC-AATCTTACT-TCCCTGGCGGT-CAGTAGAACAGATTGAAGC
* *
31148088 TA-AAGGTAGCGAATCTTGTTTCCC
63 TACGACG--GCGAATCTTGTTTCCC
31148112 TGGCATTGCA
Statistics
Matches: 245, Mismatches: 30, Indels: 23
0.82 0.10 0.08
Matches are distributed among these distances:
98 2 0.01
99 5 0.02
100 221 0.90
101 16 0.07
102 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.28
Consensus pattern (99 bp):
AATAGATTGAAGCCACAACTGGCAATCTTACTTCCCTGGCGGTCAGTAGAACAGATTGAAGCTAC
GACGGCGAATCTTGTTTCCCCAACATTGCAGTTA
Found at i:31148942 original size:22 final size:22
Alignment explanation
Indices: 31148882--31148939 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 22
31148872 AATCTTTAAG
31148882 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
31148901 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
31148923 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
31148940 GATTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.39
22 8 0.24
23 12 0.36
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:31149186 original size:23 final size:23
Alignment explanation
Indices: 31149142--31149186 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
31149132 TCTTATTTTG
* *
31149142 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
31149165 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
31149187 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:31157199 original size:7 final size:7
Alignment explanation
Indices: 31157173--31157211 Score: 62
Period size: 7 Copynumber: 5.6 Consensus size: 7
31157163 GTGATGTGAG
31157173 AAAATGA
1 AAAATGA
31157180 AAAGATG-
1 AAA-ATGA
31157187 AAAATGA
1 AAAATGA
31157194 AAAATGA
1 AAAATGA
31157201 AAAATGA
1 AAAATGA
31157208 AAAA
1 AAAA
31157212 GTAAAAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 3 0.10
7 24 0.80
8 3 0.10
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (7 bp):
AAAATGA
Found at i:31157199 original size:21 final size:21
Alignment explanation
Indices: 31157173--31157219 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
31157163 GTGATGTGAG
*
31157173 AAAATGAAAAGATGAAAATG-A
1 AAAATGAAAA-ATGAAAAAGTA
31157194 AAAATGAAAAATGAAAAAGTA
1 AAAATGAAAAATGAAAAAGTA
31157215 AAAAT
1 AAAAT
31157220 AGAGAGGCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (21 bp):
AAAATGAAAAATGAAAAAGTA
Found at i:31157217 original size:14 final size:14
Alignment explanation
Indices: 31157173--31157219 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
31157163 GTGATGTGAG
*
31157173 AAAATG-AAAAGATG
1 AAAATGAAAAAG-TA
31157187 AAAATGAAAAA-TGA
1 AAAATGAAAAAGT-A
31157201 AAAATGAAAAAGTA
1 AAAATGAAAAAGTA
31157215 AAAAT
1 AAAAT
31157220 AGAGAGGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
13 1 0.03
14 23 0.79
15 5 0.17
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (14 bp):
AAAATGAAAAAGTA
Found at i:31159795 original size:44 final size:44
Alignment explanation
Indices: 31159728--31160879 Score: 1030
Period size: 44 Copynumber: 26.0 Consensus size: 44
31159718 GCTAAAAAGC
*** * *
31159728 AGCAGATCTTGTCTTCATGTATTGGTGTGAAGTATATCAAAGAT
1 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGAT
*** ***
31159772 AGCAGATCTTGTCTTCCCATATTGGTGGTGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCATGTATT-GACATGAAGTAGATCGAAGAT
***
31159817 AATGGATCTTGTCTTCATGTATTGACATGAAGTAGATC-AGAGAT
1 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGA-AGAT
* *
31159861 AGCAGATCTTATCTTCATGTATTGACATGAAGTAGATCGAAGGT
1 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGAT
*** * *
31159905 AATGGGTCTTGTCTTCATGTATTGACATAAAGTAGATC-AGAGAT
1 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGA-AGAT
* * *
31159949 AACAAATTTTGTCTTCATGTATTGACATGAAGTAGATC-AGAGAT
1 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGA-AGAT
* * * ***
31159993 AGCAGATATTGTCTTCCCAT-AATGGTGGTGAAGTAGATCGAAGA-
1 AGCAGATCTTGTCTT--CATGTATTGACATGAAGTAGATCGAAGAT
* * *
31160037 A-CATGGATCCTATCTTCATGTATTGACATGGAGTAGATC-AGAGAT
1 AGCA--GATCTTGTCTTCATGTATTGACATGAAGTAGATCGA-AGAT
*
31160082 AGCAGATCTTGTCTTCATGTATTGACATGAACTAGATC-AGAGAT
1 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGA-AGAT
* * *
31160126 AGTAGATCTTATCTTCATGTATTGACATGAAGTAGATCGAATAT
1 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGAT
*
31160170 -G-ATGGATCTTGTCTTCATGTATTGACATGAAGTAAATC-AGAGAT
1 AGCA--GATCTTGTCTTCATGTATTGACATGAAGTAGATCGA-AGAT
* * *
31160214 AGCAGATCTTGTCTTCATGTACT-AGCGTGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCATGTATTGA-CATGAAGTAGATCGAAGAT
** * * *
31160258 AATAGATCTTGTCTTCATGTACT-AGCGTGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCATGTATTGA-CATGAAGTAGATCGAAGAT
** * * *
31160302 AATAGATCTTGTCTTCATGTACT-AGCGTGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCATGTATTGA-CATGAAGTAGATCGAAGAT
** * * *
31160346 AATAGATCTTGTCTTCATGTACT-AGCGTGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCATGTATTGA-CATGAAGTAGATCGAAGAT
* * * * *
31160390 AGCAAATCTTGTCTTTATGTATTGGCGTGAAGTAGATCGAAGAA
1 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGAT
* * * * * * * *
31160434 AACAGATCTTGTCTTCCTCTACTGGCAGCGAAGTAGATCAAATAT
1 AGCAGATCTTGTCTTCATGTATTGACA-TGAAGTAGATCGAAGAT
* *
31160479 AACAGATCTTGTCTTCATGTATTGACATGAAATAGATCGAAGAT
1 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGAT
* * * **
31160523 AGCAGATCATGTCTTCATGTATTGGCTTGGTGTAGATCGAAGAAT
1 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAG-AT
* *
31160568 GGCAGATCTTGTCTTCATGTATTGACACGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGAT
* *** ***
31160612 AGCAAATCTTGTCTTCCCATATTGGTGGTGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCATGTATT-GACATGAAGTAGATCGAAGAT
***
31160657 AATGGATCTTGTCTTCATGTATTGACATGAAGTAGATC-AGAGAT
1 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGA-AGAT
31160701 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGAT
* *** *
31160745 AGCAGATCTTGTCTTTCCA--TACTGGTGGTGAAGAAGATCGAAGAT
1 AGCAGATCTTGTC-TT-CATGTA-TTGACATGAAGTAGATCGAAGAT
***
31160790 AATGGATCTTGTCTTCATGTATTGACATGAAGTAGATC-AGAGAT
1 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGA-AGAT
* * *
31160834 AGCAGATCTTGTCTTCCTGTA-TCAGCAGTGAAGTAGATCAAAGAT
1 AGCAGATCTTGTCTTCATGTATTGA-CA-TGAAGTAGATCGAAGAT
31160879 A
1 A
31160880 CAAGTCTTAT
Statistics
Matches: 925, Mismatches: 147, Indels: 71
0.81 0.13 0.06
Matches are distributed among these distances:
42 1 0.00
43 17 0.02
44 678 0.73
45 219 0.24
46 10 0.01
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (44 bp):
AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGAT
Found at i:31160635 original size:133 final size:133
Alignment explanation
Indices: 31159728--31160879 Score: 1012
Period size: 133 Copynumber: 8.7 Consensus size: 133
31159718 GCTAAAAAGC
*** * * ***
31159728 AGCAGATCTTGTCTTCATGTATTGGTGTGAAGTATATCAAAG-ATAGCAGATCTTGTCTTCCCAT
1 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGAATAGCAGATCTTGTCTTCATGT
*** **
31159792 ATTGGTGGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATC-A
66 ATT-GACATGAAGTAGATCGAAGATAACAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGA
31159856 GAGAT
130 -AGAT
* *
31159861 AGCAGATCTTATCTTCATGTATTGACATGAAGTAGATCGAAGGTAAT-G--GGTCTTGTCTTCAT
1 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAA-G-AATAGCAGATCTTGTCTTCAT
* * *
31159923 GTATTGACATAAAGTAGATC-AGAGATAACAAATTTTGTCTTCATGTATTGACATGAAGTAGATC
64 GTATTGACATGAAGTAGATCGA-AGATAACAGATCTTGTCTTCATGTATTGACATGAAGTAGATC
31159987 -AGAGAT
128 GA-AGAT
* * * *** * * *
31159993 AGCAGATATTGTCTTCCCAT-AATGGTGGTGAAGTAGATCGAAGAACATG--GATCCTATCTTCA
1 AGCAGATCTTGTCTT--CATGTATTGACATGAAGTAGATCGAAGAATA-GCAGATCTTGTCTTCA
* * *
31160055 TGTATTGACATGGAGTAGATC-AGAGATAGCAGATCTTGTCTTCATGTATTGACATGAACTAGAT
63 TGTATTGACATGAAGTAGATCGA-AGATAACAGATCTTGTCTTCATGTATTGACATGAAGTAGAT
31160119 C-AGAGAT
127 CGA-AGAT
* * *
31160126 AGTAGATCTTATCTTCATGTATTGACATGAAGTAGATCGAA-TAT-G-ATGGATCTTGTCTTCAT
1 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGAATAGCA--GATCTTGTCTTCAT
* * * *
31160188 GTATTGACATGAAGTAAATC-AGAGATAGCAGATCTTGTCTTCATGTACT-AGCGTGAAGTAGAT
64 GTATTGACATGAAGTAGATCGA-AGATAACAGATCTTGTCTTCATGTATTGA-CATGAAGTAGAT
*
31160251 CGAAGAA
127 CGAAGAT
** * * **
31160258 AATAGATCTTGTCTTCATGTACT-AGCGTGAAGTAGATCGAAGAA-AATAGATCTTGTCTTCATG
1 AGCAGATCTTGTCTTCATGTATTGA-CATGAAGTAGATCGAAGAATAGCAGATCTTGTCTTCATG
* * * * * *
31160321 TACT-AGCGTGAAGTAGATCGAAGAAAATAGATCTTGTCTTCATGTACT-AGCGTGAAGTAGATC
65 TATTGA-CATGAAGTAGATCGAAGATAACAGATCTTGTCTTCATGTATTGA-CATGAAGTAGATC
*
31160384 GAAGAA
128 GAAGAT
* * * * * * *
31160390 AGCAAATCTTGTCTTTATGTATTGGCGTGAAGTAGATCGAAGAA-AACAGATCTTGTCTTCCTCT
1 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGAATAGCAGATCTTGTCTTCATGT
* * * * * *
31160454 ACTGGCAGCGAAGTAGATCAAATATAACAGATCTTGTCTTCATGTATTGACATGAAATAGATCGA
66 ATTGACA-TGAAGTAGATCGAAGATAACAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGA
31160519 AGAT
130 AGAT
* * * ** *
31160523 AGCAGATCATGTCTTCATGTATTGGCTTGGTGTAGATCGAAGAATGGCAGATCTTGTCTTCATGT
1 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGAATAGCAGATCTTGTCTTCATGT
* * * *** ***
31160588 ATTGACACGAAGTAGATCGAAGATAGCAAATCTTGTCTTCCCATATTGGTGGTGAAGTAGATCGA
66 ATTGACATGAAGTAGATCGAAGATAACAGATCTTGTCTTCATGTATT-GACATGAAGTAGATCGA
31160653 AGAT
130 AGAT
***
31160657 AATGGATCTTGTCTTCATGTATTGACATGAAGTAGATC--AGAGATAGCAGATCTTGTCTTCATG
1 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGA-ATAGCAGATCTTGTCTTCATG
* * *** *
31160720 TATTGACATGAAGTAGATCGAAGATAGCAGATCTTGTCTTTCCA--TACTGGTGGTGAAGAAGAT
65 TATTGACATGAAGTAGATCGAAGATAACAGATCTTGTC-TT-CATGTA-TTGACATGAAGTAGAT
31160783 CGAAGAT
127 CGAAGAT
*** *
31160790 AATGGATCTTGTCTTCATGTATTGACATGAAGTAGATC--AGAGATAGCAGATCTTGTCTTCCTG
1 AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGA-ATAGCAGATCTTGTCTTCATG
* *
31160853 TA-TCAGCAGTGAAGTAGATCAAAGATA
65 TATTGA-CA-TGAAGTAGATCGAAGATA
31160880 CAAGTCTTAT
Statistics
Matches: 862, Mismatches: 125, Indels: 63
0.82 0.12 0.06
Matches are distributed among these distances:
129 1 0.00
131 10 0.01
132 330 0.38
133 423 0.49
134 94 0.11
135 2 0.00
136 2 0.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (133 bp):
AGCAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGAATAGCAGATCTTGTCTTCATGT
ATTGACATGAAGTAGATCGAAGATAACAGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAA
GAT
Found at i:31161809 original size:13 final size:14
Alignment explanation
Indices: 31161791--31161819 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
31161781 TATATATATA
31161791 TTCTTTTA-TTCTT
1 TTCTTTTATTTCTT
31161804 TTCTTTTATTTCTT
1 TTCTTTTATTTCTT
31161818 TT
1 TT
31161820 AAACGAATAA
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:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (14 bp):
TTCTTTTATTTCTT
Found at i:31166302 original size:18 final size:18
Alignment explanation
Indices: 31166279--31166330 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
31166269 AAAATGTGAG
* *
31166279 AAATGATGTTCATATTTT
1 AAATGATGTTCACATTTC
31166297 AAATGATGTTCACATTTC
1 AAATGATGTTCACATTTC
31166315 AAATGATGTTCACATT
1 AAATGATGTTCACATT
31166331 GATGGAAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (18 bp):
AAATGATGTTCACATTTC
Found at i:31168808 original size:13 final size:13
Alignment explanation
Indices: 31168755--31168820 Score: 71
Period size: 13 Copynumber: 5.1 Consensus size: 13
31168745 CTTAAATCAA
*
31168755 ACTTTTCAAAAGT
1 ACTTTTCAAAAGC
31168768 A-TTTCTCAAAAGC
1 ACTTT-TCAAAAGC
* **
31168781 ACTTTTCCACTGC
1 ACTTTTCAAAAGC
*
31168794 ACTTTTTAAAAGC
1 ACTTTTCAAAAGC
31168807 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
31168820 A
1 A
31168821 ATGCTAAACT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
12 3 0.07
13 36 0.86
14 3 0.07
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.35
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:31170482 original size:52 final size:51
Alignment explanation
Indices: 31170404--31170507 Score: 163
Period size: 52 Copynumber: 2.0 Consensus size: 51
31170394 CGAAGCAATC
*
31170404 TAATCACCCATAAAAAGATTTGATTTACTCTACCCTTCTATCTCTTGAATT
1 TAATCACCCATAAAAAGATTTGATTTACTCTACCCTTCTATCTCCTGAATT
* * *
31170455 TAATCACCCATAATCAAGATTTGATTTACTTTACTCTTCTATCTCCTGAATT
1 TAATCACCCATAA-AAAGATTTGATTTACTCTACCCTTCTATCTCCTGAATT
31170507 T
1 T
31170508 TATTTACTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
51 13 0.27
52 35 0.73
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.41
Consensus pattern (51 bp):
TAATCACCCATAAAAAGATTTGATTTACTCTACCCTTCTATCTCCTGAATT
Found at i:31177487 original size:48 final size:48
Alignment explanation
Indices: 31177416--31177519 Score: 156
Period size: 48 Copynumber: 2.2 Consensus size: 48
31177406 CATGAGAGGC
* * *
31177416 TCGATGTCGCAATATAGCAAGCGAAGTAGAA-AAAGTACAAAACTATCT
1 TCGATGTCGCAACATAGAAAGCGAAAT-GAAGAAAGTACAAAACTATCT
*
31177464 TCGATGTCGCAACATAGAAAGCGAAATGAAGAAAGTACGAAACTATCT
1 TCGATGTCGCAACATAGAAAGCGAAATGAAGAAAGTACAAAACTATCT
31177512 TCGATGTC
1 TCGATGTC
31177520 ACGACACACA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
47 3 0.06
48 48 0.94
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.21
Consensus pattern (48 bp):
TCGATGTCGCAACATAGAAAGCGAAATGAAGAAAGTACAAAACTATCT
Found at i:31195204 original size:15 final size:15
Alignment explanation
Indices: 31195175--31195207 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
31195165 GATAGGGTGA
31195175 GAAAATAAATAATTG
1 GAAAATAAATAATTG
31195190 GAAAA-AAATAGATTG
1 GAAAATAAATA-ATTG
31195205 GAA
1 GAA
31195208 TGAGTTATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.61, C:0.00, G:0.18, T:0.21
Consensus pattern (15 bp):
GAAAATAAATAATTG
Found at i:31198715 original size:21 final size:22
Alignment explanation
Indices: 31198625--31198720 Score: 70
Period size: 22 Copynumber: 4.4 Consensus size: 22
31198615 TACACCACAC
* *
31198625 TAGTAGGCACCGAAGTGCTTAAG
1 TAGTAGGCACCGAAGTAC-TAAA
* * ** * *
31198648 CAGTAGGCACCAAAGTGTTGAG
1 TAGTAGGCACCGAAGTACTAAA
* * *
31198670 TAGTAGGTATCGAAGTGCTAAA
1 TAGTAGGCACCGAAGTACTAAA
31198692 TAGTAGGCACCGAAGTAC-AAA
1 TAGTAGGCACCGAAGTACTAAA
31198713 TAGT-GGCA
1 TAGTAGGCA
31198721 AGAAAGTACA
Statistics
Matches: 59, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 4 0.07
21 7 0.12
22 33 0.56
23 15 0.25
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.21
Consensus pattern (22 bp):
TAGTAGGCACCGAAGTACTAAA
Found at i:31199964 original size:25 final size:25
Alignment explanation
Indices: 31199936--31199991 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
31199926 TTTTCCAAAT
*
31199936 AGGCTTCACAGAGATTTCACCACAA
1 AGGCTTCACAGAGAATTCACCACAA
*
31199961 AGGCTTCATAGAGAATTCACCACAA
1 AGGCTTCACAGAGAATTCACCACAA
*
31199986 AAGCTT
1 AGGCTT
31199992 GGTTTGGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.38, C:0.25, G:0.16, T:0.21
Consensus pattern (25 bp):
AGGCTTCACAGAGAATTCACCACAA
Found at i:31202209 original size:50 final size:49
Alignment explanation
Indices: 31202106--31202282 Score: 192
Period size: 50 Copynumber: 3.4 Consensus size: 49
31202096 GGGAATGAGA
*
31202106 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGC-TTGGGA-C--TGAG---ATGAGAGG
* *
31202162 TCCCATGTAAGACCATGTCTGGGGCATGGCTTTGGGACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGC-TTGGGACTGAGATGAGAGG
* * * **
31202212 TCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACTGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCTTGGG-ACTGAGATGAGAGG
*
31202262 TCCCATGTAAGACCATATCTG
1 TCCCATGTAAGACCATGTCTG
31202283 AGATATGTCA
Statistics
Matches: 107, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
49 4 0.04
50 65 0.61
53 3 0.03
55 1 0.01
56 34 0.32
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.24
Consensus pattern (49 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCTTGGGACTGAGATGAGAGG
Found at i:31205011 original size:22 final size:22
Alignment explanation
Indices: 31204983--31205026 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
31204973 TTTTGAACCA
31204983 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
31205005 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
31205027 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:31210550 original size:50 final size:50
Alignment explanation
Indices: 31210431--31210555 Score: 142
Period size: 50 Copynumber: 2.5 Consensus size: 50
31210421 TCATTGAGAT
* * * * *
31210431 TATGAGAGGTCCCAGGTAAGACCATGTCTGGGACCTGGCGTTGGCACCGA
1 TATGAGAGGTCCCACGTAAGACCATGTCTAGGACCTGGCATGGGCACCAA
* * * *
31210481 GATGCGAGGTCCCCCGTAAGACCATGTCTAGGACGTGGCATGGGCACCAA
1 TATGAGAGGTCCCACGTAAGACCATGTCTAGGACCTGGCATGGGCACCAA
** *
31210531 TATGAGAACTCCCATGTAAGACCAT
1 TATGAGAGGTCCCACGTAAGACCAT
31210556 ATCTGGGATA
Statistics
Matches: 60, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 60 1.00
ACGTcount: A:0.26, C:0.26, G:0.30, T:0.19
Consensus pattern (50 bp):
TATGAGAGGTCCCACGTAAGACCATGTCTAGGACCTGGCATGGGCACCAA
Found at i:31214812 original size:25 final size:24
Alignment explanation
Indices: 31214778--31214829 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 24
31214768 ATATGTTTAC
31214778 TTTTTAAA-TTTATTAAATAATATA
1 TTTTTAAATTTTATTAAA-AATATA
*
31214802 TTTTTATAATTTTTTTAAAAATATA
1 TTTTTA-AATTTTATTAAAAATATA
31214827 TTT
1 TTT
31214830 ACTAATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 6 0.24
25 11 0.44
26 8 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTTTAAATTTTATTAAAAATATA
Found at i:31215371 original size:22 final size:23
Alignment explanation
Indices: 31215321--31215364 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
31215311 GTTCTTTTGG
31215321 TAAAATATCATTTAGAAACATTA
1 TAAAATATCATTTAGAAACATTA
*
31215344 TAAAATAT-ATTTAGAACCATT
1 TAAAATATCATTTAGAAACATT
31215365 CTCAAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36
Consensus pattern (23 bp):
TAAAATATCATTTAGAAACATTA
Found at i:31218004 original size:75 final size:75
Alignment explanation
Indices: 31217881--31218029 Score: 280
Period size: 75 Copynumber: 2.0 Consensus size: 75
31217871 CCAAGCTATT
* *
31217881 TCCTAGCAACTTATAACAAATTTCAAGTTAGGACGTTGGAACACACCATTACTAACCTTTATGAA
1 TCCTAGCAACTTATAACAAATTTCAAGTTAGGAAGTTGGAAAACACCATTACTAACCTTTATGAA
31217946 GCTTTCTCTC
66 GCTTTCTCTC
31217956 TCCTAGCAACTTATAACAAATTTCAAGTTAGGAAGTTGGAAAACACCATTACTAACCTTTATGAA
1 TCCTAGCAACTTATAACAAATTTCAAGTTAGGAAGTTGGAAAACACCATTACTAACCTTTATGAA
31218021 GCTTTCTCT
66 GCTTTCTCT
31218030 ATCTAAATTC
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.32
Consensus pattern (75 bp):
TCCTAGCAACTTATAACAAATTTCAAGTTAGGAAGTTGGAAAACACCATTACTAACCTTTATGAA
GCTTTCTCTC
Found at i:31218582 original size:8 final size:8
Alignment explanation
Indices: 31218569--31218593 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
31218559 TTGTGAAGAC
31218569 TACACTTT
1 TACACTTT
31218577 TACACTTT
1 TACACTTT
31218585 TACACTTT
1 TACACTTT
31218593 T
1 T
31218594 CCTAGCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (8 bp):
TACACTTT
Found at i:31220190 original size:23 final size:23
Alignment explanation
Indices: 31220161--31220282 Score: 174
Period size: 23 Copynumber: 5.3 Consensus size: 23
31220151 ATAAGTGCCA
*
31220161 CACTGATATGTAACCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
31220184 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
31220207 CACTGAAATGTAGCCGAAGATAC
1 CACTGATATGTAGCCGAAGCTAC
*
31220230 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
31220253 CACTGA-ATTGTAGCCAAAGCTAC
1 CACTGATA-TGTAGCCGAAGCTAC
31220276 CACTGAT
1 CACTGAT
31220283 TAATAACATT
Statistics
Matches: 87, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
22 1 0.01
23 86 0.99
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:31220231 original size:46 final size:46
Alignment explanation
Indices: 31220161--31220282 Score: 199
Period size: 46 Copynumber: 2.7 Consensus size: 46
31220151 ATAAGTGCCA
* *
31220161 CACTGATATGTAACCGAAGCTACCACTGATATGTAGCCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
*
31220207 CACTGAAATGTAGCCGAAGATACCACTGATATGTAGCCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
* *
31220253 CACTGAATTGTAGCCAAAGCTACCACTGAT
1 CACTGAAATGTAGCCGAAGCTACCACTGAT
31220283 TAATAACATT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 70 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (46 bp):
CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
Found at i:31220526 original size:18 final size:17
Alignment explanation
Indices: 31220500--31220538 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
31220490 ATTTTCCTTC
31220500 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
31220517 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
31220535 CACA
1 CACA
31220539 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:31222435 original size:183 final size:176
Alignment explanation
Indices: 31222092--31222450 Score: 453
Period size: 177 Copynumber: 2.0 Consensus size: 176
31222082 CATCAGTACT
* *
31222092 ACTACTATTATTAAATATCATATTATCATTTTTTACAAATAAACAATATTAAAAAAATAATATAT
1 ACTACTATTATTAAATATCATATTATCATATTTTACAAATAAACAAGATTAAAAAAATAATATAT
* ** * *
31222157 AAACATGAAATGAAATGAAAAAAAGGAGGTTGTTCATTATTTTTGTTCTTAAAAAAAAGGGAAAA
66 AAAAATGAAATGAAATGAAAAAAAAAAGGTTGTTCATTACTTTTGTTCTTAAAAAAAAGGAAAAA
31222222 AAACACAACTACAAGCATTCTATTTCTTTTTTTTT-TTTTCTTCTA
131 AAACACAACTACAAGCATTCTATTTCTTTTTTTTTCTTTTCTTCTA
* * *
31222267 ACTATTATTATTAAATATCATTATTATCAATATTTTACAAATAAATAAGATTAAAACAAT-ATAT
1 ACTACTATTATTAAATATCA-TATTATC-ATATTTTACAAATAAACAAGATTAAAAAAATAATAT
31222331 ATACATGAAATGAAATGAAA-GAACAAAAAAAAAGGCTT-TTCA-TACTTTT-TTCTT-AAAAAA
64 ATA-A--AAATGAAATGAAATG-A-AAAAAAAAAGG-TTGTTCATTACTTTTGTTCTTAAAAAAA
31222391 AGGTAAAAAAAAAACCCAACAACTACAAGCATTCTATTTCTTTTTTTTTCTTTTCTTCTA
123 AGG---AAAAAAAA--C-ACAACTACAAGCATTCTATTTCTTTTTTTTTCTTTTCTTCTA
31222451 TCTTTTTTTT
Statistics
Matches: 159, Mismatches: 10, Indels: 21
0.84 0.05 0.11
Matches are distributed among these distances:
175 19 0.12
176 14 0.09
177 37 0.23
178 6 0.04
179 19 0.12
180 20 0.13
181 2 0.01
182 1 0.01
183 31 0.19
184 10 0.06
ACGTcount: A:0.45, C:0.11, G:0.06, T:0.37
Consensus pattern (176 bp):
ACTACTATTATTAAATATCATATTATCATATTTTACAAATAAACAAGATTAAAAAAATAATATAT
AAAAATGAAATGAAATGAAAAAAAAAAGGTTGTTCATTACTTTTGTTCTTAAAAAAAAGGAAAAA
AAACACAACTACAAGCATTCTATTTCTTTTTTTTTCTTTTCTTCTA
Found at i:31222619 original size:22 final size:21
Alignment explanation
Indices: 31222579--31222619 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
31222569 CTCCCCTTTC
* *
31222579 TAAAATAAAGGTTTCTTTTTT
1 TAAAAAAAAGGTTTATTTTTT
*
31222600 TAAAAAAAAGGTTTAATTTT
1 TAAAAAAAAGGTTTATTTTT
31222620 AGGAAAAGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.46
Consensus pattern (21 bp):
TAAAAAAAAGGTTTATTTTTT
Found at i:31222714 original size:8 final size:8
Alignment explanation
Indices: 31222701--31222728 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
31222691 ATTTTAAAGG
31222701 AAATTTTA
1 AAATTTTA
31222709 AAATTTTA
1 AAATTTTA
31222717 AAATTTTA
1 AAATTTTA
31222725 AAAT
1 AAAT
31222729 AAAGTTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
AAATTTTA
Found at i:31223498 original size:10 final size:10
Alignment explanation
Indices: 31223483--31223556 Score: 67
Period size: 10 Copynumber: 7.1 Consensus size: 10
31223473 CACTTGTATG
31223483 ATTTTTATTT
1 ATTTTTATTT
31223493 ATTTTTATTT
1 ATTTTTATTT
*
31223503 ATTCTTATTT
1 ATTTTTATTT
*
31223513 CGTTTTTATTT
1 -ATTTTTATTT
*
31223524 ATTTTCATATAT
1 ATTTT--TATTT
* *
31223536 ATTTATATAT
1 ATTTTTATTT
*
31223546 ATTTATATTT
1 ATTTTTATTT
31223556 A
1 A
31223557 CACATTCCCC
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
10 38 0.70
11 8 0.15
12 8 0.15
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.69
Consensus pattern (10 bp):
ATTTTTATTT
Found at i:31243450 original size:4 final size:4
Alignment explanation
Indices: 31243441--31243510 Score: 70
Period size: 4 Copynumber: 17.5 Consensus size: 4
31243431 GTGCCCCAAT
* * *
31243441 TTCA TTCA TTCA TCCA TCCA TTCA TTCA -TCTA TTCA TTCA TTCA TCCA
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA TTC-A TTCA TTCA TTCA TTCA
* * *
31243489 TTCG TTCA CTCA TTCG TTCA TT
1 TTCA TTCA TTCA TTCA TTCA TT
31243511 TGTTTATTCA
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
3 2 0.04
4 50 0.93
5 2 0.04
ACGTcount: A:0.21, C:0.30, G:0.03, T:0.46
Consensus pattern (4 bp):
TTCA
Found at i:31243491 original size:16 final size:16
Alignment explanation
Indices: 31243441--31243501 Score: 86
Period size: 16 Copynumber: 3.8 Consensus size: 16
31243431 GTGCCCCAAT
31243441 TTCATTCATTCATCCA
1 TTCATTCATTCATCCA
* *
31243457 TCCATTCATTCATCTA
1 TTCATTCATTCATCCA
31243473 TTCATTCATTCATCCA
1 TTCATTCATTCATCCA
* *
31243489 TTCGTTCACTCAT
1 TTCATTCATTCAT
31243502 TCGTTCATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.23, C:0.31, G:0.02, T:0.44
Consensus pattern (16 bp):
TTCATTCATTCATCCA
Found at i:31253847 original size:42 final size:42
Alignment explanation
Indices: 31253783--31254127 Score: 519
Period size: 42 Copynumber: 8.2 Consensus size: 42
31253773 AAGGAAAACA
31253783 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
31253825 TTCATTACATTTAGAGGTCCAGGTGTGGAGGTCCATTCACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
31253867 TTCAGTGCATATAGAGACCCAGGTGTGGAGGTCCATTCACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
31253909 TCCATTGCATTTAGAGGCCCAGATGTGGAGGTTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
*
31253951 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCTTTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
31253993 TTCATTGCATATAAAGACCCAGGTGTGGAGGTCCATTCACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
**
31254035 TTCATTGCATTTAGAGGCCCAAATGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
31254077 TTCATTGTATTTAGAGGCCCAGGTGTGGAGGTCCAATTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
31254119 TTCATTGCA
1 TTCATTGCA
31254128 CTGTATATGA
Statistics
Matches: 268, Mismatches: 35, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 268 1.00
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
Found at i:31254011 original size:126 final size:126
Alignment explanation
Indices: 31253785--31254127 Score: 578
Period size: 126 Copynumber: 2.7 Consensus size: 126
31253775 GGAAAACATT
* * *
31253785 CATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTACATTTAGAGGTCCAGGTG
1 CATTGCATTTAGAGGCCCAGATGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTG
* * *
31253850 TGGAGGTCCATTCACTTTTCAGTGCATATAGAGACCCAGGTGTGGAGGTCCATTCACTTTC
66 TGGAGGTCCATTTACTTTTCATTGCATATAAAGACCCAGGTGTGGAGGTCCATTCACTTTC
*
31253911 CATTGCATTTAGAGGCCCAGATGTGGAGGTTCATTTACTTTTCATTGCATTTAGAGGCCCAGGTG
1 CATTGCATTTAGAGGCCCAGATGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTG
* *
31253976 TGGAGGTCCTTTTACTTTTCATTGCATATAAAGACCCAGGTGTGGAGGTCCATTCACTTTT
66 TGGAGGTCCATTTACTTTTCATTGCATATAAAGACCCAGGTGTGGAGGTCCATTCACTTTC
* *
31254037 CATTGCATTTAGAGGCCCAAATGTGGAGGTCCATTTACTTTTCATTGTATTTAGAGGCCCAGGTG
1 CATTGCATTTAGAGGCCCAGATGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTG
*
31254102 TGGAGGTCCAATTACTTTTCATTGCA
66 TGGAGGTCCATTTACTTTTCATTGCA
31254128 CTGTATATGA
Statistics
Matches: 203, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
126 203 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (126 bp):
CATTGCATTTAGAGGCCCAGATGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGGTG
TGGAGGTCCATTTACTTTTCATTGCATATAAAGACCCAGGTGTGGAGGTCCATTCACTTTC
Found at i:31255207 original size:150 final size:149
Alignment explanation
Indices: 31254986--31255391 Score: 559
Period size: 150 Copynumber: 2.7 Consensus size: 149
31254976 TAAAAAAAAA
* * *
31254986 GAGAAAGTTTAGATTTT-AACAAATAAAAATATATTTTTTTTAGTTATTTTAAAGGAAGGTTTAA
1 GAGAAAGTTTAGATTTTGAA-AAATAAAAATAT-TTTTTTTTAGTCATTTTAAAAGAAAGTTTAA
* * *
31255050 AATTTTAAAACAAAGTTTTGATTTTTTTTAACTATTTCAAAGTAAAAGGTTTAATCTTTAAGAAA
64 AATTTTAAAACAAAGTTTTGATTTTTTTTAACTATTTCAAAATAAAAGCTTTAACCTTTAAGAAA
31255115 AATAGTGTTTTTTTTT-AAA-G
129 AATAGT-TTTTTTTTTAAAAGG
*
31255135 GAGAAAGTTTAGATTTTGAAAACTAAAAATATGTATTTTTTTAGTCATTTTAAAAGAAAGTTTAA
1 GAGAAAGTTTAGATTTTGAAAAATAAAAATAT-T-TTTTTTTAGTCATTTTAAAAGAAAGTTTAA
* *
31255200 AATTTTAAAACAAAATTTTGATTTTTTTTTTTAGCTATTTCAAAATAAAAGCTTTAACCTTTAAG
64 AATTTTAAAACAAAGTTTTGA---TTTTTTTTAACTATTTCAAAATAAAAGCTTTAACCTTTAAG
31255265 AAAAATAGTTTTTTTTTTAAAAAAAAGG
126 AAAAATAGTTTTTTTTTT----AAAAGG
* * *
31255293 GAGAAAGTTTAGATTTTGAAAAATAAAAATA-TTTTTTTAAGTCATTTTAAATGAAAGTTTATAA
1 GAGAAAGTTTAGATTTTGAAAAATAAAAATATTTTTTTTTAGTCATTTTAAAAGAAAGTTTAAAA
*
31255357 TTTTAAAATAAAGTTTTGATTTTTTTTAACTATTT
66 TTTTAAAACAAAGTTTTGATTTTTTTTAACTATTT
31255392 TGAAATAAGG
Statistics
Matches: 229, Mismatches: 17, Indels: 19
0.86 0.06 0.07
Matches are distributed among these distances:
149 29 0.13
150 49 0.21
152 24 0.10
153 46 0.20
155 46 0.20
156 1 0.00
157 3 0.01
158 31 0.14
ACGTcount: A:0.41, C:0.04, G:0.11, T:0.44
Consensus pattern (149 bp):
GAGAAAGTTTAGATTTTGAAAAATAAAAATATTTTTTTTTAGTCATTTTAAAAGAAAGTTTAAAA
TTTTAAAACAAAGTTTTGATTTTTTTTAACTATTTCAAAATAAAAGCTTTAACCTTTAAGAAAAA
TAGTTTTTTTTTTAAAAGG
Found at i:31255229 original size:53 final size:54
Alignment explanation
Indices: 31255127--31255227 Score: 129
Period size: 53 Copynumber: 1.9 Consensus size: 54
31255117 TAGTGTTTTT
*
31255127 TTTTAAAGGAGAAAGTTTAGATTTTGAAAACTAAAAATATGTATTTTTTTAGTCA
1 TTTTAAA-GAGAAAGTTTAAATTTTGAAAACTAAAAATATGTATTTTTTTAGTCA
* *
31255182 TTTTAAA-AGAAAGTTTAAAATTTT-AAAAC-AAAATTTTG-ATTTTTTT
1 TTTTAAAGAGAAAGTTT-AAATTTTGAAAACTAAAAATATGTATTTTTTT
31255228 TTTTAGCTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
51 8 0.19
52 7 0.17
53 14 0.33
54 6 0.14
55 7 0.17
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.45
Consensus pattern (54 bp):
TTTTAAAGAGAAAGTTTAAATTTTGAAAACTAAAAATATGTATTTTTTTAGTCA
Found at i:31256034 original size:10 final size:10
Alignment explanation
Indices: 31256001--31256067 Score: 55
Period size: 10 Copynumber: 6.4 Consensus size: 10
31255991 ACTAGTATAA
31256001 TTTTATTTAT
1 TTTTATTTAT
* *
31256011 TCTTATTTCGT
1 TTTTATTT-AT
31256022 TTTTATTTAT
1 TTTTATTTAT
*
31256032 TTTCATGTCTAT
1 TTTTAT-T-TAT
*
31256044 TTATATTTAT
1 TTTTATTTAT
31256054 TTATTA-TTAT
1 TT-TTATTTAT
31256064 TTTT
1 TTTT
31256068 TACACATTTC
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
9 2 0.04
10 24 0.53
11 12 0.27
12 7 0.16
ACGTcount: A:0.19, C:0.06, G:0.03, T:0.72
Consensus pattern (10 bp):
TTTTATTTAT
Found at i:31263793 original size:24 final size:23
Alignment explanation
Indices: 31263750--31263796 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
31263740 ATTTATTTTA
*
31263750 AAAATAATATATTATTAAATAAT
1 AAAATAATATATTATAAAATAAT
31263773 AAAATAAT-TAATCTATAAAATAAT
1 AAAATAATAT-AT-TATAAAATAAT
31263797 GAATTAAGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 1 0.05
23 10 0.48
24 10 0.48
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (23 bp):
AAAATAATATATTATAAAATAAT
Found at i:31272022 original size:17 final size:17
Alignment explanation
Indices: 31271978--31272025 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
31271968 ATACTTACAG
*
31271978 AAGAGTTCGCCAAACCA
1 AAGAGTTCGCCAAAACA
* ***
31271995 CAGAACACGCCAAAACA
1 AAGAGTTCGCCAAAACA
31272012 AAGAGTTCGCCAAA
1 AAGAGTTCGCCAAA
31272026 TGACGCATCA
Statistics
Matches: 22, Mismatches: 9, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.08
Consensus pattern (17 bp):
AAGAGTTCGCCAAAACA
Found at i:31272580 original size:14 final size:14
Alignment explanation
Indices: 31272561--31272600 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
31272551 TTGTTTGGCA
*
31272561 GTAAAATGTTTTCC
1 GTAAAATGATTTCC
*
31272575 GTAAAATGATTTCT
1 GTAAAATGATTTCC
*
31272589 GGAAAATGATTT
1 GTAAAATGATTT
31272601 ACTTTTCTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.40
Consensus pattern (14 bp):
GTAAAATGATTTCC
Found at i:31272609 original size:20 final size:20
Alignment explanation
Indices: 31272584--31272623 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
31272574 CGTAAAATGA
31272584 TTTCTGGAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
*
31272604 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
31272624 GGAAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.10, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:31272613 original size:34 final size:34
Alignment explanation
Indices: 31272569--31272634 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 34
31272559 CAGTAAAATG
31272569 TTTTCCGTAAAATGATTT-CTGGAAAATGATTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAAT-ATTTAC
*
31272603 TTTTCTGTAAAATGATTTACTGGAAAATATTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTT
31272635 TCTGCTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 21 0.70
35 9 0.30
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (34 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTAC
Found at i:31272840 original size:72 final size:72
Alignment explanation
Indices: 31272723--31273010 Score: 558
Period size: 72 Copynumber: 4.0 Consensus size: 72
31272713 ATAATAATAT
31272723 TATCCAAATACATAATTAATGGTACACCACATAGTAATAACATTGTCCAAGTGAATAATATTACA
1 TATCCAAATACATAATTAATGGTACACCACATAGTAATAACATTGTCCAAGTGAATAATATTACA
31272788 TCACATA
66 TCACATA
31272795 TATCCAAATACATAATTAATGGTACACCACATAGTAATAACATTGTCCAAGTGAATAATATTACA
1 TATCCAAATACATAATTAATGGTACACCACATAGTAATAACATTGTCCAAGTGAATAATATTACA
31272860 TCACATA
66 TCACATA
31272867 TATCCAAATACATAATTAATGGTACACCACATAGTAATAACATTGTCCAAGTGAATAATATTACA
1 TATCCAAATACATAATTAATGGTACACCACATAGTAATAACATTGTCCAAGTGAATAATATTACA
31272932 TCACATA
66 TCACATA
*
31272939 TATCCAAATACATAATTAATGGTACACCACATAGTAATAACATTGTCCAAGTGCATAATATTACA
1 TATCCAAATACATAATTAATGGTACACCACATAGTAATAACATTGTCCAAGTGAATAATATTACA
*
31273004 CCACATA
66 TCACATA
31273011 AATGTATCAA
Statistics
Matches: 214, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 214 1.00
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.29
Consensus pattern (72 bp):
TATCCAAATACATAATTAATGGTACACCACATAGTAATAACATTGTCCAAGTGAATAATATTACA
TCACATA
Found at i:31282716 original size:14 final size:14
Alignment explanation
Indices: 31282697--31282724 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
31282687 TGGAAAAGGT
31282697 GGAAAATATTTTCC
1 GGAAAATATTTTCC
31282711 GGAAAATATTTTCC
1 GGAAAATATTTTCC
31282725 ACCAAACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
GGAAAATATTTTCC
Found at i:31287636 original size:30 final size:30
Alignment explanation
Indices: 31287581--31287642 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
31287571 CACTAAGCAA
31287581 GTTTCATATACATGTATCATCCATTT-CAT
1 GTTTCATATACATGTATCATCCATTTCCAT
31287610 GTTTCAATATATCATGTAAT-AT-CATTTCCAT
1 GTTTC-ATATA-CATGT-ATCATCCATTTCCAT
31287641 GT
1 GT
31287643 ATTTCATGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
29 5 0.17
30 10 0.34
31 12 0.41
32 2 0.07
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (30 bp):
GTTTCATATACATGTATCATCCATTTCCAT
Found at i:31287878 original size:50 final size:49
Alignment explanation
Indices: 31287801--31287918 Score: 148
Period size: 49 Copynumber: 2.4 Consensus size: 49
31287791 GTATGCCCAA
* *
31287801 ACGAGCTGTGAATCA-GTATGCTCTCACGAGCTGTAAACCGGTAAGCTCAT
1 ACGAGCTGAGAAT-AGGTAAGCTCTCACGAGCTG-AAACCGGTAAGCTCAT
* **
31287851 ATGAGCTGAGAATAGGTAAGCTCTCACGAGCTGAAATTGGTAAGCTCAT
1 ACGAGCTGAGAATAGGTAAGCTCTCACGAGCTGAAACCGGTAAGCTCAT
* *
31287900 ACGAACTGAGAATCGGTAA
1 ACGAGCTGAGAATAGGTAA
31287919 TCCCTAATGA
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
49 31 0.53
50 28 0.47
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.23
Consensus pattern (49 bp):
ACGAGCTGAGAATAGGTAAGCTCTCACGAGCTGAAACCGGTAAGCTCAT
Found at i:31287903 original size:24 final size:25
Alignment explanation
Indices: 31287801--31287918 Score: 109
Period size: 25 Copynumber: 4.8 Consensus size: 25
31287791 GTATGCCCAA
* * *
31287801 ACGAGCTGTGAATCAGTATGCTC-T
1 ACGAGCTGAGAATCGGTAAGCTCAT
*
31287825 CACGAGCTGTA-AACCGGTAAGCTCAT
1 -ACGAGCTG-AGAATCGGTAAGCTCAT
* *
31287851 ATGAGCTGAGAATAGGTAAGCTC-T
1 ACGAGCTGAGAATCGGTAAGCTCAT
*
31287875 CACGAGCTGA-AATTGGTAAGCTCAT
1 -ACGAGCTGAGAATCGGTAAGCTCAT
*
31287900 ACGAACTGAGAATCGGTAA
1 ACGAGCTGAGAATCGGTAA
31287919 TCCCTAATGA
Statistics
Matches: 76, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
24 22 0.29
25 53 0.70
26 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.23
Consensus pattern (25 bp):
ACGAGCTGAGAATCGGTAAGCTCAT
Found at i:31289775 original size:18 final size:18
Alignment explanation
Indices: 31289744--31289778 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31289734 ACTTAGTTGT
* *
31289744 TTTCTTCTTTCCCTTAGC
1 TTTCTACTTCCCCTTAGC
31289762 TTTCTACTTCCCCTTAG
1 TTTCTACTTCCCCTTAG
31289779 AGGACAAGGT
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:0.09, C:0.34, G:0.06, T:0.51
Consensus pattern (18 bp):
TTTCTACTTCCCCTTAGC
Found at i:31298317 original size:18 final size:18
Alignment explanation
Indices: 31298294--31298334 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
31298284 TTTAGATTAA
31298294 TTAGAGTTCTAGTACACT
1 TTAGAGTTCTAGTACACT
* *
31298312 TTAGAGTTTTAGTATACT
1 TTAGAGTTCTAGTACACT
31298330 TTAGA
1 TTAGA
31298335 ATTTTATTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.44
Consensus pattern (18 bp):
TTAGAGTTCTAGTACACT
Found at i:31298339 original size:18 final size:18
Alignment explanation
Indices: 31298303--31298340 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
31298293 ATTAGAGTTC
*
31298303 TAGTACACTTTAGAGTTT
1 TAGTACACTTTAGAATTT
*
31298321 TAGTATACTTTAGAATTT
1 TAGTACACTTTAGAATTT
31298339 TA
1 TA
31298341 TTTGGGAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.08, G:0.13, T:0.47
Consensus pattern (18 bp):
TAGTACACTTTAGAATTT
Found at i:31298970 original size:25 final size:22
Alignment explanation
Indices: 31298917--31298970 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 22
31298907 AAAAAAAGTG
31298917 ATAAAAATATAGAAAAAGAAAA
1 ATAAAAATATAGAAAAAGAAAA
31298939 A-AGAAAATATGATGAAAAAAGAAAA
1 ATA-AAAATAT-A-G-AAAAAGAAAA
31298964 ATAAAAA
1 ATAAAAA
31298971 AATATTCTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
21 1 0.04
22 8 0.30
23 1 0.04
24 1 0.04
25 15 0.56
26 1 0.04
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.13
Consensus pattern (22 bp):
ATAAAAATATAGAAAAAGAAAA
Found at i:31305336 original size:64 final size:64
Alignment explanation
Indices: 31305256--31305376 Score: 181
Period size: 64 Copynumber: 1.9 Consensus size: 64
31305246 GAAAAAAAAA
* ** *
31305256 TTTTTGGTGCTGGCCTATCAATGGCCGGCACCAGTA-TATGAAAAACAAATTTTGGGAAATTTT
1 TTTTTGGTGCTAGCCTATCAATGGCCGGCACCACCAGTATGAAAAAAAAATTTTGGGAAATTTT
*
31305319 TTTTTGTGTGCTAGCCTATCAATGGCTGGCACCACCAGTATGAAAAAAAAATTTTGGG
1 TTTTTG-GTGCTAGCCTATCAATGGCCGGCACCACCAGTATGAAAAAAAAATTTTGGG
31305377 TGCTGGCCTG
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
63 6 0.12
64 26 0.51
65 19 0.37
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (64 bp):
TTTTTGGTGCTAGCCTATCAATGGCCGGCACCACCAGTATGAAAAAAAAATTTTGGGAAATTTT
Found at i:31305414 original size:114 final size:114
Alignment explanation
Indices: 31305205--31305414 Score: 321
Period size: 114 Copynumber: 1.8 Consensus size: 114
31305195 AAAAAATAAA
* * *
31305205 TTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCAGTACGAAAAAAAAATTTTTGGTGCTGGC
1 TTTTTGGGTGCTAGCCTATCAATGGCCGGCACCACCAGTACGAAAAAAAAATTTTGGGTGCTGGC
**
31305270 CTATCAATGGCCGGCACCAGTATATGAAAAACAAATTTTGGGAAATTTT
66 CTATCAATGGCCGGCACCAGTATACAAAAAACAAATTTTGGGAAATTTT
* * *
31305319 TTTTTGTGTGCTAGCCTATCAATGGCTGGCACCACCAGTATGAAAAAAAAATTTTGGGTGCTGGC
1 TTTTTGGGTGCTAGCCTATCAATGGCCGGCACCACCAGTACGAAAAAAAAATTTTGGGTGCTGGC
* * *
31305384 CTGTCAATGGTCGGCAGCAGTATACAAAAAA
66 CTATCAATGGCCGGCACCAGTATACAAAAAA
31305415 AATAGGTGTT
Statistics
Matches: 85, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
114 85 1.00
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.28
Consensus pattern (114 bp):
TTTTTGGGTGCTAGCCTATCAATGGCCGGCACCACCAGTACGAAAAAAAAATTTTGGGTGCTGGC
CTATCAATGGCCGGCACCAGTATACAAAAAACAAATTTTGGGAAATTTT
Found at i:31306302 original size:21 final size:22
Alignment explanation
Indices: 31306261--31306303 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
31306251 TTGTATTTTA
*
31306261 TTGTGTATGTAAATTTAATTTG
1 TTGTGTATGTAAACTTAATTTG
31306283 TTGTGTA-GTAATACTT-ATTTG
1 TTGTGTATGTAA-ACTTAATTTG
31306304 AATTATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.26, C:0.02, G:0.19, T:0.53
Consensus pattern (22 bp):
TTGTGTATGTAAACTTAATTTG
Found at i:31309568 original size:52 final size:52
Alignment explanation
Indices: 31309485--31309600 Score: 171
Period size: 52 Copynumber: 2.2 Consensus size: 52
31309475 AGCCAATACC
* * *
31309485 AAATTTTTTTTTGTACTAGTGGTGCCGGCCATTGACAGGCCAGCACCCAAAA
1 AAATTTTTTTTTGTACTACTGGTGCCAGCCATTGACAAGCCAGCACCCAAAA
*
31309537 AAATTTTGTTTTTGTA-TACTGGTGCTAGCCATTGACAAGCCAGCACCCAAAA
1 AAATTTT-TTTTTGTACTACTGGTGCCAGCCATTGACAAGCCAGCACCCAAAA
*
31309589 AATTTTTTTTTT
1 AAATTTTTTTTT
31309601 TAAATTTTTG
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
51 5 0.09
52 45 0.78
53 8 0.14
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (52 bp):
AAATTTTTTTTTGTACTACTGGTGCCAGCCATTGACAAGCCAGCACCCAAAA
Found at i:31310098 original size:28 final size:30
Alignment explanation
Indices: 31310059--31310118 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
31310049 CATTTATCAT
31310059 AAAAATAAATA-TT-ATTATCATAAAAATA
1 AAAAATAAATATTTAATTATCATAAAAATA
* *
31310087 AAAAATATATATTTAATTATCATAAATATA
1 AAAAATAAATATTTAATTATCATAAAAATA
31310117 AA
1 AA
31310119 TATTATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 10 0.36
29 2 0.07
30 16 0.57
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (30 bp):
AAAAATAAATATTTAATTATCATAAAAATA
Found at i:31317919 original size:16 final size:16
Alignment explanation
Indices: 31317898--31317929 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
31317888 ATTAAAGACA
*
31317898 GAATTTTGGTCTTCTT
1 GAATTTTGATCTTCTT
31317914 GAATTTTGATCTTCTT
1 GAATTTTGATCTTCTT
31317930 ACAAGTACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.12, G:0.16, T:0.56
Consensus pattern (16 bp):
GAATTTTGATCTTCTT
Found at i:31321678 original size:29 final size:30
Alignment explanation
Indices: 31321623--31321681 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
31321613 ATCTCAAAAT
* *
31321623 TATACATGAACTTTGATTTAATGTGCAATTG
1 TATACATGAACTTTAATTT-AGGTGCAATTG
31321654 TATACATGAACTTTAATTT-GGTGCAATT
1 TATACATGAACTTTAATTTAGGTGCAATT
31321682 ATTCAATTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
31 18 0.69
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.42
Consensus pattern (30 bp):
TATACATGAACTTTAATTTAGGTGCAATTG
Found at i:31323823 original size:2 final size:2
Alignment explanation
Indices: 31323816--31323853 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
31323806 AAACTGCCAT
31323816 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
31323854 CCAGTGTTGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:31327481 original size:21 final size:19
Alignment explanation
Indices: 31327459--31327513 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
31327449 TAAAAAAATA
31327459 TATAAAT-TTTTGTAATTTT
1 TATAAATATTTTG-AATTTT
31327478 TATAAATATTTTGAA-TTT
1 TATAAATATTTTGAATTTT
*
31327496 TAAAAATTATTTTGAATT
1 TATAAA-TATTTTGAATT
31327514 CTTTGTTGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
18 8 0.25
19 18 0.56
20 6 0.19
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:31331522 original size:21 final size:21
Alignment explanation
Indices: 31331473--31331532 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
31331463 ATGCTTTTAC
* *
31331473 ATCAGAATT-AGATTATACTT
1 ATCAAAATTCAGATCATACTT
* *
31331493 ATCATAATTCCGATCATACTT
1 ATCAAAATTCAGATCATACTT
* *
31331514 ATTAAAATTCAGATTATAC
1 ATCAAAATTCAGATCATAC
31331533 AGAGCATATA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 8 0.25
21 24 0.75
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (21 bp):
ATCAAAATTCAGATCATACTT
Found at i:31332454 original size:3 final size:3
Alignment explanation
Indices: 31332448--31332488 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
31332438 AAAACAAATC
*
31332448 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAA AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
31332489 AAGGTAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:31334820 original size:25 final size:25
Alignment explanation
Indices: 31334742--31334813 Score: 90
Period size: 25 Copynumber: 2.9 Consensus size: 25
31334732 CAAGCCTATT
* *
31334742 TTCACAGGTCGTGTGAGCATATTGA
1 TTCACAGCTCGTGTGAGCATACTGA
* * * *
31334767 TTTACAACTCGTGTAAGCATACCGA
1 TTCACAGCTCGTGTGAGCATACTGA
31334792 TTCACAGCTCGTGTGAGCATAC
1 TTCACAGCTCGTGTGAGCATAC
31334814 ATGTTCAAGA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (25 bp):
TTCACAGCTCGTGTGAGCATACTGA
Found at i:31344094 original size:103 final size:103
Alignment explanation
Indices: 31343908--31344105 Score: 231
Period size: 103 Copynumber: 1.9 Consensus size: 103
31343898 TTTTGTAAGT
* * * * * **
31343908 TTTGTGAGAAATATAATGCTATTTTGGTACCGTTTTTAAGATGGGGTATTGATATTTTTGAAAAT
1 TTTGTGAAAAATAGAATGCCATTTTGGTACCGCTTTTAAGATAGGGTATTGATATTCATGAAAAT
*
31343973 ATCAATACTTTACCAAAAGGTATCAATACTGAATTGGG
66 ATCAATACTTGACCAAAAGGTATCAATACTGAATTGGG
* *
31344011 TTTGTGAAAAATAGAATGCCGTTTTGGTATCGCTTTTAAGA-AGGGTATTGATAATTCAT-AAAA
1 TTTGTGAAAAATAGAATGCCATTTTGGTACCGCTTTTAAGATAGGGTATTGAT-ATTCATGAAAA
* * *
31344074 TATTAATA-TTGGGCCGAAAAGGTATCGATACT
65 TATCAATACTT-GACC-AAAAGGTATCAATACT
31344106 TTTTGGCCTG
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
101 2 0.03
102 23 0.29
103 54 0.68
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (103 bp):
TTTGTGAAAAATAGAATGCCATTTTGGTACCGCTTTTAAGATAGGGTATTGATATTCATGAAAAT
ATCAATACTTGACCAAAAGGTATCAATACTGAATTGGG
Found at i:31345782 original size:5 final size:5
Alignment explanation
Indices: 31345761--31345796 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
31345751 TAAAAGAAAG
*
31345761 AAGAA CAAGAA AGGAA AAGAA AAGAA AAGAA AAGAA
1 AAGAA -AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA
31345797 TAAAGGGGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.75, C:0.03, G:0.22, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:31345872 original size:3 final size:3
Alignment explanation
Indices: 31345864--31345889 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
31345854 AACCAATCAA
31345864 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
31345890 CTAAAGGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:31347908 original size:538 final size:538
Alignment explanation
Indices: 31346890--31347957 Score: 1572
Period size: 538 Copynumber: 2.0 Consensus size: 538
31346880 GGATGATTAA
* *
31346890 TTTTCCAGCCAAGGACAGTCCAAATGATGACTATTTTATTTACTTTATATTTAATTTTTATCCAA
1 TTTTCCACCCAAGGACAGTCCAAATGATGACTATTTTATTCACTTTATATTTAATTTTTATCCAA
* * * * * *
31346955 AATTAATTGGGTTCAAACTTAATATAAAGCTTGAAAGAGAAAGTGGTCCAGTATGTTAAATATAG
66 AATTAATTAGGTTCAAAATTAATATAAAGCCTGAAAGAGAAAATGGCCCAGTATGCTAAATATAG
*
31347020 AAGACTAATCCACCAAGCAAATTGGCAGTCCAAAATCGTCCCTATAGTAGATCCAATCAGTTATT
131 AAGACTAATCCACCAAGCAAATTGGCAGTCCAAAATCATCCCTATAGTAGATCCAATCAGTTATT
* * * *
31347085 TTTGCTGATTTTTATGCTTGCAAAATAGCCCTTGAGCTATCCCTAAATTCTATTCAAGCCCCTTC
196 TTTGCTGATTTTTATACTTGCAAAATAACCCTTGAGCTATCCCTAAATCCTATTCAAGCCCCTCC
*
31347150 ACTTTCTATGCCTTTGAATATTTGCCCCAAGCTAAATATAACAAAGTTTGAATTATTCAAACTTG
261 ACTTTCTATGCCTTTGAATATTTGCCCCAAGCTAAATATAACAAAGTTTGAATTATTCAAAATTG
* *
31347215 CTCCTTTCATGGCCAGCCAAGGAAGAGTGTATGACTGCTAATTATTTGCTATTTTTAGTAGCCAC
326 CTCCTTTCATGGCCAGCCAAGGAAGAGTGTATGACTACTAATTATTTGCTATTTTTAGCAGCCAC
* * *
31347280 TCCCACCTATAAATACCCCCTTTGTCACCTCACTCAACACACCTTCATCTCCCACAAATTTCTTA
391 TCCCACCTATAAATACCCCATTTGTCACCTCACTCAACACACATTCATCTCCCACAAATCTCTTA
* * * *
31347345 TTTCCTCTTTTTCGTTTCCCTTTGTTTTTCCCATTTCCCTTATCCATTTCCTTGTTGATTTTCCC
456 TTTCCTCTTTTCCGTTTCACTTTG-TTTTCCCATTTCCCTTATCCATTTCCTTGTCGATTTCCCC
*
31347410 TCTTGGTAAAGCTGAATAT
520 TCTTGGAAAAGCTGAATAT
** * *
31347429 TTTTCCACCCAAGGATGGTCCAAATTATGATTATTTTATTCACTTTATATTTAATTTTTATCCAA
1 TTTTCCACCCAAGGACAGTCCAAATGATGACTATTTTATTCACTTTATATTTAATTTTTATCCAA
**
31347494 AATTAATTAGGTT-AGAAATTAATATAAAGCCT-AAAGGAGAAAATGGCCCAGTATGCTATGTAT
66 AATTAATTAGGTTCA-AAATTAATATAAAGCCTGAAA-GAGAAAATGGCCCAGTATGCTAAATAT
* * * *
31347557 AGAAGATTGATCCACCAAGCAAATTTGCAGTCCAAAA-CATCCCTATAGTTGATCCAATCAGTTT
129 AGAAGACTAATCCACCAAGCAAATTGGCAGTCCAAAATCATCCCTATAGTAGATCCAATCAG-TT
**
31347621 ATTTTT-CTGATTTTTATACTTTTAAAATAACCCTTGAGCTATCCCTAAATCCTATTCAAGCCCC
193 ATTTTTGCTGATTTTTATACTTGCAAAATAACCCTTGAGCTATCCCTAAATCCTATTCAAGCCCC
* * *
31347685 TCCATTTTCTATGCCTTTGAATATTTTCCCCAAGCTAAATATAGCAAAGTTTGAATTATTCAAAA
258 TCCACTTTCTATGCCTTTGAATATTTGCCCCAAGCTAAATATAACAAAGTTTGAATTATTCAAAA
* ** * * *
31347750 TTGCTTCTTTTGTGG-CTGACCAAGGAAGAGTGTATGGCTACTAATTATTTTCTATTTTTAGCAG
323 TTGCTCCTTTCATGGCCAG-CCAAGGAAGAGTGTATGACTACTAATTATTTGCTATTTTTAGCAG
* ** * *
31347814 CCACTCCCACCTATAAATACCCCATTTGTTATGTCATTCAACACACATTCATTTCCCACAAATCT
387 CCACTCCCACCTATAAATACCCCATTTGTCACCTCACTCAACACACATTCATCTCCCACAAATCT
* *
31347879 CTTATTTCCT-TTCTTCCGTTTCACTTTGTTTTCCCATTTCCCTTGTCCATTTTCTTGTCGATTT
452 CTTATTTCCTCTT-TTCCGTTTCACTTTGTTTTCCCATTTCCCTTATCCATTTCCTTGTCGATTT
31347943 CCCCTCTTGGAAAAG
516 CCCCTCTTGGAAAAG
31347958 AGCTTCCATC
Statistics
Matches: 472, Mismatches: 52, Indels: 12
0.88 0.10 0.02
Matches are distributed among these distances:
537 50 0.11
538 272 0.58
539 150 0.32
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.37
Consensus pattern (538 bp):
TTTTCCACCCAAGGACAGTCCAAATGATGACTATTTTATTCACTTTATATTTAATTTTTATCCAA
AATTAATTAGGTTCAAAATTAATATAAAGCCTGAAAGAGAAAATGGCCCAGTATGCTAAATATAG
AAGACTAATCCACCAAGCAAATTGGCAGTCCAAAATCATCCCTATAGTAGATCCAATCAGTTATT
TTTGCTGATTTTTATACTTGCAAAATAACCCTTGAGCTATCCCTAAATCCTATTCAAGCCCCTCC
ACTTTCTATGCCTTTGAATATTTGCCCCAAGCTAAATATAACAAAGTTTGAATTATTCAAAATTG
CTCCTTTCATGGCCAGCCAAGGAAGAGTGTATGACTACTAATTATTTGCTATTTTTAGCAGCCAC
TCCCACCTATAAATACCCCATTTGTCACCTCACTCAACACACATTCATCTCCCACAAATCTCTTA
TTTCCTCTTTTCCGTTTCACTTTGTTTTCCCATTTCCCTTATCCATTTCCTTGTCGATTTCCCCT
CTTGGAAAAGCTGAATAT
Found at i:31355253 original size:39 final size:39
Alignment explanation
Indices: 31355167--31355253 Score: 104
Period size: 39 Copynumber: 2.2 Consensus size: 39
31355157 TCTTGAGCGT
* * * *
31355167 CCTGCTGCACACGCACCAACCCCGTATCTTGCCTTGCTC
1 CCTGCTGCTCACGCACCAAACCCGCATCCTGCCTTGCTC
* *
31355206 CCTACTGCTCACGCACCAAACCTGCATCCTGCCTTGC-C
1 CCTGCTGCTCACGCACCAAACCCGCATCCTGCCTTGCTC
31355244 CACTGCTGCT
1 C-CTGCTGCT
31355254 ACTACTACTT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
38 2 0.05
39 38 0.95
ACGTcount: A:0.16, C:0.46, G:0.15, T:0.23
Consensus pattern (39 bp):
CCTGCTGCTCACGCACCAAACCCGCATCCTGCCTTGCTC
Found at i:31361765 original size:12 final size:12
Alignment explanation
Indices: 31361744--31361806 Score: 58
Period size: 12 Copynumber: 5.3 Consensus size: 12
31361734 CAGATTCAAT
31361744 AAAA-AAAATCA
1 AAAACAAAATCA
31361755 AAAACAAAATCA
1 AAAACAAAATCA
*
31361767 AAAACAAAA-AA
1 AAAACAAAATCA
*
31361778 AAAGAAAAAATCA
1 AAA-ACAAAATCA
** *
31361791 AAGTCAAAAGCA
1 AAAACAAAATCA
31361803 AAAA
1 AAAA
31361807 AGAGAAATCA
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
11 8 0.20
12 29 0.73
13 3 0.08
ACGTcount: A:0.78, C:0.11, G:0.05, T:0.06
Consensus pattern (12 bp):
AAAACAAAATCA
Found at i:31361780 original size:30 final size:31
Alignment explanation
Indices: 31361744--31361835 Score: 84
Period size: 30 Copynumber: 2.9 Consensus size: 31
31361734 CAGATTCAAT
31361744 AAAAAAAATCAAAAA-CAAAATCAAAAACAA
1 AAAAAAAATCAAAAATCAAAATCAAAAACAA
* *
31361774 AAAAAAAGA--AAAAATCAAAGTCAAAAGCAA
1 AAAAAAA-ATCAAAAATCAAAATCAAAAACAA
31361804 AAAAGAGAAATCAATCAAAGTCAAAAT-AAAAA
1 AAAA-A-AAATCAA--AAA-TCAAAATCAAAAA
31361836 TATGAAAAGC
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
29 5 0.10
30 24 0.49
31 3 0.06
32 2 0.04
33 2 0.04
35 7 0.14
36 6 0.12
ACGTcount: A:0.74, C:0.11, G:0.07, T:0.09
Consensus pattern (31 bp):
AAAAAAAATCAAAAATCAAAATCAAAAACAA
Found at i:31362232 original size:15 final size:14
Alignment explanation
Indices: 31362208--31362263 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 14
31362198 AATGGATTTC
31362208 AAAAA-AAAAAGATG
1 AAAAAGAAAAA-ATG
*
31362222 AAAAAG-GAAAATG
1 AAAAAGAAAAAATG
*
31362235 AAAAATAAAAAAATG
1 AAAAA-GAAAAAATG
*
31362250 AAAAAGTAAAAATG
1 AAAAAGAAAAAATG
31362264 GAGAGGCTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 8 0.24
14 15 0.44
15 11 0.32
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11
Consensus pattern (14 bp):
AAAAAGAAAAAATG
Found at i:31362250 original size:28 final size:27
Alignment explanation
Indices: 31362208--31362260 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
31362198 AATGGATTTC
*
31362208 AAAAAAAAAAGATGAAAAAGGAAAATG
1 AAAAAAAAAAAATGAAAAAGGAAAATG
*
31362235 AAAAATAAAAAAATGAAAAAGTAAAA
1 AAAAA-AAAAAAATGAAAAAGGAAAA
31362261 ATGGAGAGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.09
Consensus pattern (27 bp):
AAAAAAAAAAAATGAAAAAGGAAAATG
Found at i:31363706 original size:44 final size:44
Alignment explanation
Indices: 31363640--31364040 Score: 262
Period size: 44 Copynumber: 8.7 Consensus size: 44
31363630 AGAAATGGTG
31363640 AATCTTATCTCCCTGATG-TTACAGTGGAGCAGATTGAAGTCAGA
1 AATCTTATCTCCCTGA-GATTACAGTGGAGCAGATTGAAGTCAGA
* *
31363684 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAG-CTAGT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGTC-AGA
* * * *
31363728 AATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAAT-A-A
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGTCAGA
*
31363770 AGGATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCATCAGATTGAAGTCAGA
1 A--ATCTTATCTCCCTGAGA-TTACAGT---G--GA--G---CAGATTGAAGTCAGA
* *
31363826 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAG-CTAGT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGTC-AGA
* * ** * *
31363870 AATCCTATCTCCCTGAGATTACAGTGAAGTGGATTAAAAT-A-A
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGTCAGA
* * *
31363912 AGGATCTTATCTCTCT-AAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGA
1 A--ATCTTATCTCCCTGAGA-TTACAGT---G--GA--G---CAGATTGAAGTCAGA
*** * *
31363968 AATCTTATCTCCCTGAGATTACAACAGAGCAGATTGAAGCCAGT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGTCAGA
*
31364012 AATCCTATCTCCCTGAGATTACAGTGGAG
1 AATCTTATCTCCCTGAGATTACAGTGGAG
31364041 TGGATTAAAA
Statistics
Matches: 277, Mismatches: 43, Indels: 74
0.70 0.11 0.19
Matches are distributed among these distances:
42 2 0.01
43 8 0.03
44 193 0.70
47 4 0.01
49 7 0.03
51 3 0.01
54 51 0.18
55 5 0.02
56 4 0.01
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.27
Consensus pattern (44 bp):
AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGTCAGA
Found at i:31363836 original size:142 final size:142
Alignment explanation
Indices: 31363669--31364094 Score: 771
Period size: 142 Copynumber: 3.0 Consensus size: 142
31363659 TACAGTGGAG
31363669 CAGATTGAAGTCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGTCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
*
31363734 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
66 ATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
31363799 AGTAGATCGCAT
131 AGTAGATCGCAT
31363811 CAGATTGAAGTCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGTCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
* *
31363876 ATCTCCCTGAGATTACAGTGAAGTGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAG
66 ATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
31363941 AGTAGATCGCAT
131 AGTAGATCGCAT
* * * *
31363953 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAACAGAGCAGATTGAAGCCAGTAATCCT
1 CAGATTGAAGTCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
* *
31364018 ATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAAATGATCATATCTCTCTGAAGTTACAGTAG
66 ATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
31364083 AGTAGATCGCAT
131 AGTAGATCGCAT
31364095 TAGGTTTTTT
Statistics
Matches: 273, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
142 273 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (142 bp):
CAGATTGAAGTCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
ATCTCCCTGAGATTACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
AGTAGATCGCAT
Found at i:31363892 original size:98 final size:97
Alignment explanation
Indices: 31363713--31363894 Score: 217
Period size: 98 Copynumber: 1.9 Consensus size: 97
31363703 TACAGCGGAG
* * * * *
31363713 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTT
1 CAGATTGAAGCTAGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATTAAAAT-AAGAATCCT
*
31363778 ATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
65 ATCTCCCTGAAGTTACAGTAGAGTAGATCGCAT
* **
31363811 CAGATTGAAG-TCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT-AGTAATC
1 CAGATTGAAGCT-AGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATT-AAAATAAG-AATC
31363874 CTATCTCCCTG-AGATTACAGT
63 CTATCTCCCTGAAG-TTACAGT
31363895 GAAGTGGATT
Statistics
Matches: 71, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
97 5 0.07
98 63 0.89
99 3 0.04
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (97 bp):
CAGATTGAAGCTAGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATTAAAATAAGAATCCTA
TCTCCCTGAAGTTACAGTAGAGTAGATCGCAT
Found at i:31364217 original size:50 final size:50
Alignment explanation
Indices: 31364163--31364862 Score: 300
Period size: 50 Copynumber: 14.0 Consensus size: 50
31364153 TCCCAAGTGG
* * *
31364163 TGCAGTGGAACAGATTAAAGCCACAACAGCGAATCATGCTTCCCCGACAT
1 TGCAGTGAAAAAGATTAAAGCCACAACAGCGAATCTTGCTTCCCCGACAT
* * * * *
31364213 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTAC-TCCGCAGGAGA-
1 TGCAGTGAAAAAGATTAAAGCCACAACAGCGAATCTTGCTTCC-C-CGACAT
** * * * * *
31364263 TGCAACGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
1 TGCAGTGAAAAAGATTAAAGCCACAACAGCGAATCTTGCTTCCCCGACAT
* * * * * * *
31364313 TGCAGTTAAAAATATTAACGCTACAACAGCGAATCTTAC-TCCCCAGGCAA
1 TGCAGTGAAAAAGATTAAAGCCACAACAGCGAATCTTGCTTCCCC-GACAT
* * * * * * * *
31364363 TGTAGCGGAACATATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
1 TGCAGTGAAAAAGATTAAAGCCACAACAGCGAATCTTGCTTCCCCGACAT
* * * * * * *
31364413 TGTAGTTAAAAATATTAAAGCTACAACAACGAATCTTAC-TCCCCAGGCGA-
1 TGCAGTGAAAAAGATTAAAGCCACAACAGCGAATCTTGCTTCCCC-GAC-AT
* * * * *** * *
31364463 TGTAGCGGAACAGATTAAAGCCACATTGGTGAATCTTGCTTCCTCGACAT
1 TGCAGTGAAAAAGATTAAAGCCACAACAGCGAATCTTGCTTCCCCGACAT
* * * * * ** * * *
31364513 TGCAGTTAAAAAGATTAAAGCTATAACGGTGAATCTT-AATCGCCAGGCAA
1 TGCAGTGAAAAAGATTAAAGCCACAACAGCGAATCTTGCTTC-CCCGACAT
* * * * * * * **
31364563 TGCAGCGGAACAGATTAAAGCCATAACGGTGAATCTTGCTTTCTTGACAT
1 TGCAGTGAAAAAGATTAAAGCCACAACAGCGAATCTTGCTTCCCCGACAT
* * *** * * * ** * *
31364613 TGCAGTTAAAAAGACTAAAGCCACAGTGGCGAGTGTTACTTCCTTGGCAC
1 TGCAGTGAAAAAGATTAAAGCCACAACAGCGAATCTTGCTTCCCCGACAT
* * ** * * * * *
31364663 AGCAGTGGAGTAGATTAAAACCACTACGGCGTATCTTGCTTCCCCGAAAT
1 TGCAGTGAAAAAGATTAAAGCCACAACAGCGAATCTTGCTTCCCCGACAT
* * * * * * *
31364713 TGCAGTTAAAAAGACTAAAGCCACAACGGCGAGTGTTACTT-CCCTAGCGA-
1 TGCAGTGAAAAAGATTAAAGCCACAACAGCGAATCTTGCTTCCCCGA-C-AT
**** * * * * * *
31364763 TGCAGTGGGGCAGATTAAAGCCACGACGGCGTATCTTGCTTTCTCGATAT
1 TGCAGTGAAAAAGATTAAAGCCACAACAGCGAATCTTGCTTCCCCGACAT
* * * * *
31364813 TGCAGTTAAAAAGATCAAAGCTACAACAGCGAATCTTACTTCCTCGACAT
1 TGCAGTGAAAAAGATTAAAGCCACAACAGCGAATCTTGCTTCCCCGACAT
31364863 CACAGTTAAA
Statistics
Matches: 460, Mismatches: 174, Indels: 32
0.69 0.26 0.05
Matches are distributed among these distances:
49 24 0.05
50 415 0.90
51 21 0.05
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (50 bp):
TGCAGTGAAAAAGATTAAAGCCACAACAGCGAATCTTGCTTCCCCGACAT
Found at i:31364342 original size:100 final size:100
Alignment explanation
Indices: 31364163--31364852 Score: 732
Period size: 100 Copynumber: 6.9 Consensus size: 100
31364153 TCCCAAGTGG
* * * * *
31364163 TGCAGTGGAACAGATTAAAGCCACAACAGCGAATCATGCTTCCCCGACATTGCAGTTAAAAAGAT
1 TGCAGCGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGAT
31364228 TAAAGCTACAACAGCGAATCTTACTCCGCAGG-AGA
66 TAAAGCTACAACAGCGAATCTTACTCC-CAGGCAGA
* *
31364263 TGCAACGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAATAT
1 TGCAGCGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGAT
*
31364328 TAACGCTACAACAGCGAATCTTACTCCCCAGGCA-A
66 TAAAGCTACAACAGCGAATCTTACT-CCCAGGCAGA
* * * *
31364363 TGTAGCGGAACATATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGTAGTTAAAAATAT
1 TGCAGCGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGAT
*
31364428 TAAAGCTACAACAACGAATCTTACTCCCCAGGC-GA
66 TAAAGCTACAACAGCGAATCTTACT-CCCAGGCAGA
* * *
31364463 TGTAGCGGAACAGATTAAAGCCACATTGGTGAATCTTGCTTCCTCGACATTGCAGTTAAAAAGAT
1 TGCAGCGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGAT
* * * *
31364528 TAAAGCTATAACGGTGAATCTTAATCGCCAGGCA-A
66 TAAAGCTACAACAGCGAATCTTACTC-CCAGGCAGA
* * * ** *
31364563 TGCAGCGGAACAGATTAAAGCCATAACGGTGAATCTTGCTTTCTTGACATTGCAGTTAAAAAGAC
1 TGCAGCGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGAT
* *** * * ** *
31364628 TAAAGCCACAGTGGCGAGTGTTACTTCCTTGGCACA
66 TAAAGCTACAACAGCGAATCTTAC-TCCCAGGCAGA
* ** * * * *
31364664 -GCAGTGGAGTAGATTAAAACCAC-TACGGCGTATCTTGCTTCCCCGAAATTGCAGTTAAAAAGA
1 TGCAGCGGAACAGATTAAAGCCACAT-CGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGA
* * * * *
31364727 CTAAAGCCACAACGGCGAGTGTTACTTCCCTA-GC-GA
65 TTAAAGCTACAACAGCGAATCTTAC-TCCC-AGGCAGA
* ** * * * * *
31364763 TGCAGTGGGGCAGATTAAAGCCACGA-CGGCGTATCTTGCTTTCTCGATATTGCAGTTAAAAAGA
1 TGCAGCGGAACAGATTAAAGCCAC-ATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGA
*
31364827 TCAAAGCTACAACAGCGAATCTTACT
65 TTAAAGCTACAACAGCGAATCTTACT
31364853 TCCTCGACAT
Statistics
Matches: 508, Mismatches: 70, Indels: 25
0.84 0.12 0.04
Matches are distributed among these distances:
99 3 0.01
100 499 0.98
101 6 0.01
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (100 bp):
TGCAGCGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGAT
TAAAGCTACAACAGCGAATCTTACTCCCAGGCAGA
Found at i:31365204 original size:10 final size:10
Alignment explanation
Indices: 31365189--31365217 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
31365179 AAAAATAATT
31365189 AAATGTCCAA
1 AAATGTCCAA
31365199 AAATGTCCAA
1 AAATGTCCAA
31365209 AAATGTCCA
1 AAATGTCCA
31365218 GTTACAAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.48, C:0.21, G:0.10, T:0.21
Consensus pattern (10 bp):
AAATGTCCAA
Found at i:31365396 original size:27 final size:28
Alignment explanation
Indices: 31365365--31365437 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 28
31365355 CCTGCGCCGC
*
31365365 TGCCACG-CACGCCTCTCCCTACGTACG
1 TGCCACGCCACGCCTCTCCCAACGTACG
*
31365392 TGCCACGTCCGCGCCTCTCCCAACGTACG
1 TGCCACG-CCACGCCTCTCCCAACGTACG
*
31365421 TGCCACGTCCGCGCCTC
1 TGCCACG-CCACGCCTC
31365438 AGTACATGCC
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
27 7 0.17
29 35 0.83
ACGTcount: A:0.12, C:0.49, G:0.21, T:0.18
Consensus pattern (28 bp):
TGCCACGCCACGCCTCTCCCAACGTACG
Found at i:31365409 original size:29 final size:29
Alignment explanation
Indices: 31365374--31365437 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
31365364 CTGCCACGCA
*
31365374 CGCCTCTCCCTACGTACGTGCCACGTCCG
1 CGCCTCTCCCAACGTACGTGCCACGTCCG
31365403 CGCCTCTCCCAACGTACGTGCCACGTCCG
1 CGCCTCTCCCAACGTACGTGCCACGTCCG
31365432 CGCCTC
1 CGCCTC
31365438 AGTACATGCC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.11, C:0.50, G:0.20, T:0.19
Consensus pattern (29 bp):
CGCCTCTCCCAACGTACGTGCCACGTCCG
Found at i:31373886 original size:50 final size:51
Alignment explanation
Indices: 31373818--31373922 Score: 167
Period size: 50 Copynumber: 2.1 Consensus size: 51
31373808 GACCACTTAT
* *
31373818 CACTTGTCCCTGATCAGATAAGTGTAG-CTAAGCTACCACTTATCACTTGC
1 CACTTGTCACTGATCAGATAAGTGTAGCCGAAGCTACCACTTATCACTTGC
* *
31373868 CACTTGTCAGTGATCAGATAAGTGTAGCCGAAGCTACCACTTATCACTTGT
1 CACTTGTCACTGATCAGATAAGTGTAGCCGAAGCTACCACTTATCACTTGC
31373919 CACT
1 CACT
31373923 AATCAGAAGT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
50 25 0.50
51 25 0.50
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.30
Consensus pattern (51 bp):
CACTTGTCACTGATCAGATAAGTGTAGCCGAAGCTACCACTTATCACTTGC
Found at i:31377813 original size:49 final size:49
Alignment explanation
Indices: 31377758--31377951 Score: 209
Period size: 49 Copynumber: 4.0 Consensus size: 49
31377748 TTCGTTTTCT
*
31377758 CGATGCCATAGTCCAACTATGGTCTTACACGTAATCACAAATCACATAC
1 CGATGCCATAGTCCAACTATGGTCTTACACGGAATCACAAATCACATAC
* * * *
31377807 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCACTTAC
1 CGATGCCATAGTCCAACTATGGTCTTACACGGAATCACAAATCACATAC
* *
31377856 CGATGCCATAG-CTCAGCTATGGTCTTACACGGAATCACATATCAC--AC
1 CGATGCCATAGTC-CAACTATGGTCTTACACGGAATCACAAATCACATAC
* * **
31377903 TGATGCCATA-TCCCAGA-TATGATCTTACACAAAAATCACATAATCACAT
1 CGATGCCATAGT-CCA-ACTATGGTCTTACAC-GGAATCACA-AATCACAT
31377952 TTCCACATGT
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
47 25 0.20
48 9 0.07
49 92 0.73
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.25
Consensus pattern (49 bp):
CGATGCCATAGTCCAACTATGGTCTTACACGGAATCACAAATCACATAC
Found at i:31377949 original size:98 final size:97
Alignment explanation
Indices: 31377758--31377949 Score: 253
Period size: 98 Copynumber: 2.0 Consensus size: 97
31377748 TTCGTTTTCT
*
31377758 CGATGCCATAGTCCAACTATGGTCTTACACGTAATCACAAATCACATACCGATGCCATAGCCCAG
1 CGATGCCATAGTCCAACTATGGTCTTACACGGAATCACAAATCACA-ACCGATGCCATAGCCCAG
* * **
31377823 CTATGGTCTTACACGGAATCACATATCACTTAC
65 ATATGATCTTACACAAAATCACATATCACTTAC
* * * *
31377856 CGATGCCATAG-CTCAGCTATGGTCTTACACGGAATCACATATCAC-ACTGATGCCATATCCCAG
1 CGATGCCATAGTC-CAACTATGGTCTTACACGGAATCACAAATCACAACCGATGCCATAGCCCAG
31377919 ATATGATCTTACACAAAAATCACATAATCAC
65 ATATGATCTTACAC-AAAATCACAT-ATCAC
31377950 ATTTCCACAT
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
96 28 0.34
97 9 0.11
98 45 0.55
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (97 bp):
CGATGCCATAGTCCAACTATGGTCTTACACGGAATCACAAATCACAACCGATGCCATAGCCCAGA
TATGATCTTACACAAAATCACATATCACTTAC
Found at i:31379986 original size:44 final size:44
Alignment explanation
Indices: 31379923--31380910 Score: 1658
Period size: 44 Copynumber: 22.6 Consensus size: 44
31379913 AACCGTTACA
31379923 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
1 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
31379967 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
1 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
31380011 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
1 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
31380055 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
1 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
31380099 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
1 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
31380143 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
1 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
31380187 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
1 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
31380231 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
1 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
31380275 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
1 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
31380319 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
1 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
31380363 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
1 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
31380407 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
1 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
31380451 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
1 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
31380495 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
1 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
31380539 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
1 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
31380583 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
1 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
31380627 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
1 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
31380671 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
1 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
* ** * *
31380715 CGGTGGAATCAGCACTTAGCAACCACCTTATAATC-AATGAT-A
1 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
* *** *
31380757 CGG-GGAATCAGCACATAGCAACC-CCTTTCACAATC-AAGGAT-A
1 CGGTGGAATCAGCACTTAGCAACCACC--TCATGTTCAAAGGATCC
* * ** * *
31380799 CGGTGGAATCAACACTTAGCAACCACCTTATAATC-AATGAT-A
1 CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
* * *** *
31380841 CGG-AGAATCAGCACATAGCAACC-CCTTTCACAATC-AAGGAT-A
1 CGGTGGAATCAGCACTTAGCAACCACC--TCATGTTCAAAGGATCC
31380883 CGGTGGAATCAGCACTTAGCAACCACCT
1 CGGTGGAATCAGCACTTAGCAACCACCT
31380911 TATAATCAAT
Statistics
Matches: 914, Mismatches: 22, Indels: 18
0.96 0.02 0.02
Matches are distributed among these distances:
40 4 0.00
41 36 0.04
42 49 0.05
43 41 0.04
44 784 0.86
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.20
Consensus pattern (44 bp):
CGGTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCC
Found at i:31383103 original size:51 final size:51
Alignment explanation
Indices: 31383027--31383324 Score: 587
Period size: 51 Copynumber: 5.8 Consensus size: 51
31383017 NNNNNNNNNN
31383027 ATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTGCCACTTTTCACTG
1 ATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTGCCACTTTTCACTG
31383078 ATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTGCCACTTTTCACTG
1 ATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTGCCACTTTTCACTG
31383129 ATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTGCCACTTTTCACTG
1 ATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTGCCACTTTTCACTG
31383180 ATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTGCCACTTTTCACTG
1 ATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTGCCACTTTTCACTG
31383231 ATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTGCCACTTTTCACTG
1 ATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTGCCACTTTTCACTG
*
31383282 ATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTGTCACT
1 ATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTGCCACT
31383325 AACCAGAAGT
Statistics
Matches: 246, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 246 1.00
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (51 bp):
ATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTGCCACTTTTCACTG
Found at i:31386273 original size:12 final size:13
Alignment explanation
Indices: 31386243--31386270 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
31386233 TATTTTAATA
31386243 TTTATTAAATTTT
1 TTTATTAAATTTT
31386256 TTTATTAAATTTT
1 TTTATTAAATTTT
31386269 TT
1 TT
31386271 ATTTTAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTATTAAATTTT
Found at i:31386382 original size:15 final size:15
Alignment explanation
Indices: 31386359--31386396 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
31386349 ATATATATAC
*
31386359 ATAATATTA-TTTCAA
1 ATAAAATTAGTTTC-A
31386374 ATAAAATTAGTTTCA
1 ATAAAATTAGTTTCA
31386389 ATAAAATT
1 ATAAAATT
31386397 TAATTATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (15 bp):
ATAAAATTAGTTTCA
Found at i:31392321 original size:25 final size:25
Alignment explanation
Indices: 31392293--31392347 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
31392283 AACTGTCCTT
* *
31392293 GATAGTATATCCTAAAACTGCTATA
1 GATAGTATATACTAAAACTACTATA
* *
31392318 GATAGTATATACTGAGACTACTATA
1 GATAGTATATACTAAAACTACTATA
31392343 GATAG
1 GATAG
31392348 ACCATACTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (25 bp):
GATAGTATATACTAAAACTACTATA
Found at i:31396036 original size:24 final size:23
Alignment explanation
Indices: 31395985--31396037 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
31395975 CAATACAGTC
31395985 ATTTTTCTCTCCATCTTTCTAACG
1 ATTTTTCTCTCCATC-TTCTAACG
*
31396009 -TTTTCTCTCTCCCATC-TCTACCG
1 ATTTT-TCTCT-CCATCTTCTAACG
31396032 ATTTTT
1 ATTTTT
31396038 TTCTTCCTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
23 11 0.44
24 9 0.36
25 5 0.20
ACGTcount: A:0.13, C:0.32, G:0.04, T:0.51
Consensus pattern (23 bp):
ATTTTTCTCTCCATCTTCTAACG
Found at i:31398132 original size:18 final size:19
Alignment explanation
Indices: 31398092--31398135 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
31398082 AAATAAAACC
31398092 TTTTGAAATTGAATAATGA
1 TTTTGAAATTGAATAATGA
31398111 -TTTGTAAA-TGAATAAT-A
1 TTTTG-AAATTGAATAATGA
31398128 TTTTGAAA
1 TTTTGAAA
31398136 ACGAACGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 4 0.17
18 16 0.70
19 3 0.13
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (19 bp):
TTTTGAAATTGAATAATGA
Found at i:31405947 original size:29 final size:28
Alignment explanation
Indices: 31405908--31405976 Score: 77
Period size: 31 Copynumber: 2.4 Consensus size: 28
31405898 CAAAATTTGA
31405908 CATATATAATTATA-TCAAATTAAAATT
1 CATATATAATTATAGTCAAATTAAAATT
*
31405935 CATATATTAAATTATATGTTAAATTAAAATT
1 CATATA-T-AATTATA-GTCAAATTAAAATT
* *
31405966 AATGTATAATT
1 CATATATAATT
31405977 TTAAAAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
27 6 0.17
28 1 0.03
29 11 0.31
30 1 0.03
31 16 0.46
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.43
Consensus pattern (28 bp):
CATATATAATTATAGTCAAATTAAAATT
Found at i:31415208 original size:29 final size:29
Alignment explanation
Indices: 31415137--31415209 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 29
31415127 ATAAAAATAA
*
31415137 AATTTTTCATAAAAAATTTAAAAAAAGTATTT
1 AATTTTTC--AAAAAATTTAAAAAAAG-ACTT
*
31415169 AACTTTT-AAAAAATTATAAAAAAA-ACTT
1 AATTTTTCAAAAAATT-TAAAAAAAGACTT
31415197 AATTTTTCAAAAA
1 AATTTTTCAAAAA
31415210 TATATATTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
28 9 0.25
29 13 0.36
30 8 0.22
32 6 0.17
ACGTcount: A:0.56, C:0.05, G:0.01, T:0.37
Consensus pattern (29 bp):
AATTTTTCAAAAAATTTAAAAAAAGACTT
Found at i:31415215 original size:29 final size:30
Alignment explanation
Indices: 31415137--31415215 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 30
31415127 ATAAAAATAA
* * *
31415137 AATTTTTCATAAAAAATTTAAAAAAAGTATTT
1 AATTTTTCA-AAAATATATAAAAAAAG-ACTT
* *
31415169 AACTTTTAAAAAAT-TATAAAAAAA-ACTT
1 AATTTTTCAAAAATATATAAAAAAAGACTT
31415197 AATTTTTCAAAAATATATA
1 AATTTTTCAAAAATATATA
31415216 TTCTAGAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
28 15 0.38
29 4 0.10
30 9 0.23
31 4 0.10
32 7 0.18
ACGTcount: A:0.56, C:0.05, G:0.01, T:0.38
Consensus pattern (30 bp):
AATTTTTCAAAAATATATAAAAAAAGACTT
Found at i:31420058 original size:35 final size:35
Alignment explanation
Indices: 31420000--31420071 Score: 90
Period size: 35 Copynumber: 2.1 Consensus size: 35
31419990 ATAAATGTTT
* * *
31420000 TACTAGCTCTACGGAGTGGCACCATGGAAATAGTC
1 TACTAGCTCTACGAAGTGACACCATGAAAATAGTC
* * *
31420035 TACTGGCTCTATGAAGTGACACCATGAAAATGGTC
1 TACTAGCTCTACGAAGTGACACCATGAAAATAGTC
31420070 TA
1 TA
31420072 TTGACTTAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.25
Consensus pattern (35 bp):
TACTAGCTCTACGAAGTGACACCATGAAAATAGTC
Found at i:31420540 original size:28 final size:28
Alignment explanation
Indices: 31420497--31420571 Score: 105
Period size: 28 Copynumber: 2.7 Consensus size: 28
31420487 GAAAAGGGAA
*
31420497 GTCCGCCAAGGACTATCTTAGGTGAAAT
1 GTCCGCCAAGGACTATCTTAGATGAAAT
* * *
31420525 GTTCGCCAAGGACTATCTTATATGGAAT
1 GTCCGCCAAGGACTATCTTAGATGAAAT
*
31420553 GTCCGCCAAGCACTATCTT
1 GTCCGCCAAGGACTATCTT
31420572 GACTACTAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (28 bp):
GTCCGCCAAGGACTATCTTAGATGAAAT
Found at i:31423385 original size:21 final size:22
Alignment explanation
Indices: 31423360--31423408 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
31423350 TTAAGGCTTG
*
31423360 TAATTGACCTAATTAGGCCAAC
1 TAATTAACCTAATTAGGCCAAC
*
31423382 -AATTAACCTAATTAGGGCAAC
1 TAATTAACCTAATTAGGCCAAC
31423403 TAATTA
1 TAATTA
31423409 TGCCTAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (22 bp):
TAATTAACCTAATTAGGCCAAC
Found at i:31426154 original size:23 final size:24
Alignment explanation
Indices: 31426105--31426155 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
31426095 NNNNTAATTA
* * *
31426105 AATTTTTAAATAATATATCTTTAT
1 AATTTTAAAAAAAAATATCTTTAT
*
31426129 AATTTTAAAAAAAAATAT-TTTCT
1 AATTTTAAAAAAAAATATCTTTAT
31426152 AATT
1 AATT
31426156 AAATGAGAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (24 bp):
AATTTTAAAAAAAAATATCTTTAT
Found at i:31426414 original size:16 final size:16
Alignment explanation
Indices: 31426393--31426426 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31426383 CACAATCATT
* *
31426393 TAAATATTATTAAAAC
1 TAAATAATAGTAAAAC
31426409 TAAATAATAGTAAAAC
1 TAAATAATAGTAAAAC
31426425 TA
1 TA
31426427 TCAAATATCA
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:0.59, C:0.06, G:0.03, T:0.32
Consensus pattern (16 bp):
TAAATAATAGTAAAAC
Found at i:31428666 original size:42 final size:42
Alignment explanation
Indices: 31428590--31428669 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
31428580 AACTATGGGG
* *
31428590 ACTTCTACCCAGACATCTTGTCTGATATATCGATACAATTCC
1 ACTTCTACCCAGACATCTTGTCAGATATACCGATACAATTCC
* * * *
31428632 ACTTCTACCCATACATCTTGTGAGTTGTACCGATACAA
1 ACTTCTACCCAGACATCTTGTCAGATATACCGATACAA
31428670 GTCTGTCTGC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.29, C:0.28, G:0.11, T:0.33
Consensus pattern (42 bp):
ACTTCTACCCAGACATCTTGTCAGATATACCGATACAATTCC
Found at i:31429098 original size:16 final size:16
Alignment explanation
Indices: 31429059--31429099 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
31429049 ATCTTAGCCT
*
31429059 TTGTAAAAGATAAAGA
1 TTGTAAATGATAAAGA
* *
31429075 TTGTAAATGATAGATA
1 TTGTAAATGATAAAGA
31429091 TTGTAAATG
1 TTGTAAATG
31429100 TTATACCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.20, T:0.34
Consensus pattern (16 bp):
TTGTAAATGATAAAGA
Found at i:31431441 original size:6 final size:6
Alignment explanation
Indices: 31431430--31431463 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
31431420 AATAAACGAG
31431430 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
31431464 GAAGTTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:31431481 original size:24 final size:24
Alignment explanation
Indices: 31431430--31431504 Score: 62
Period size: 24 Copynumber: 3.1 Consensus size: 24
31431420 AATAAACGAG
* * *
31431430 AAAAATAAAAATAAAAATAAAAAT-
1 AAAAAT-AAAAGAAAATTAAAATTA
**
31431454 AAAAATAAAAGAAGTTTAAAATTA
1 AAAAATAAAAGAAAATTAAAATTA
* **
31431478 AAAACTAAATTAAAATTAAAATTA
1 AAAAATAAAAGAAAATTAAAATTA
31431502 AAA
1 AAA
31431505 TAAAGTAAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
23 12 0.30
24 28 0.70
ACGTcount: A:0.73, C:0.01, G:0.03, T:0.23
Consensus pattern (24 bp):
AAAAATAAAAGAAAATTAAAATTA
Found at i:31448909 original size:26 final size:26
Alignment explanation
Indices: 31448880--31448939 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
31448870 CGAAATCATT
*
31448880 TGGAAATGAATTTAGGTTTCCAAAAA
1 TGGAAATGAATGTAGGTTTCCAAAAA
**
31448906 TGGAAATGAATGTAGGTTTCCAAGTA
1 TGGAAATGAATGTAGGTTTCCAAAAA
31448932 TGGAAATG
1 TGGAAATG
31448940 GAAATGATTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.30
Consensus pattern (26 bp):
TGGAAATGAATGTAGGTTTCCAAAAA
Found at i:31450049 original size:5 final size:5
Alignment explanation
Indices: 31450039--31450067 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
31450029 GGAGTTAATA
31450039 AATTG AATTG AATTG AATTG AATTG AATT
1 AATTG AATTG AATTG AATTG AATTG AATT
31450068 ATCGTTTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.41
Consensus pattern (5 bp):
AATTG
Found at i:31458469 original size:11 final size:11
Alignment explanation
Indices: 31458455--31458498 Score: 58
Period size: 11 Copynumber: 4.3 Consensus size: 11
31458445 AAATGATATT
*
31458455 TTATTATTTTA
1 TTATTAATTTA
31458466 TTATTAA--T-
1 TTATTAATTTA
31458474 TTATTAATTTA
1 TTATTAATTTA
31458485 TTATTAATTTA
1 TTATTAATTTA
31458496 TTA
1 TTA
31458499 ATTTATTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
8 7 0.24
9 1 0.03
10 1 0.03
11 20 0.69
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TTATTAATTTA
Found at i:31458478 original size:19 final size:19
Alignment explanation
Indices: 31458454--31458505 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
31458444 TAAATGATAT
*
31458454 TTTATTATTTTATTATTAA
1 TTTATTAATTTATTATTAA
31458473 TTTATTAATTTATTATTAA
1 TTTATTAATTTATTATTAA
31458492 TTTATTAATTTATT
1 TTTATTAATTTATT
31458506 TAGTATATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTATTAATTTATTATTAA
Found at i:31458496 original size:8 final size:8
Alignment explanation
Indices: 31458466--31458505 Score: 53
Period size: 8 Copynumber: 4.6 Consensus size: 8
31458456 TATTATTTTA
31458466 TTATTAAT
1 TTATTAAT
31458474 TTATTAATTT
1 TTATTAA--T
31458484 ATTATTAAT
1 -TTATTAAT
31458493 TTATTAAT
1 TTATTAAT
31458501 TTATT
1 TTATT
31458506 TAGTATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 20 0.69
9 1 0.03
10 1 0.03
11 7 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
TTATTAAT
Found at i:31467086 original size:17 final size:18
Alignment explanation
Indices: 31467059--31467092 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
31467049 TAGTGTGATA
31467059 TAACTCCGAACAAGCTTC
1 TAACTCCGAACAAGCTTC
*
31467077 TAAC-CCGAACGAGCTT
1 TAACTCCGAACAAGCTT
31467093 TCAATGCACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.32, C:0.32, G:0.15, T:0.21
Consensus pattern (18 bp):
TAACTCCGAACAAGCTTC
Found at i:31476297 original size:50 final size:50
Alignment explanation
Indices: 31476175--31476346 Score: 173
Period size: 50 Copynumber: 3.3 Consensus size: 50
31476165 TATCCCTGAT
* * * *
31476175 ATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCTATGTCCCAGAC
1 ATGGTCTTACATGGGAGCTCTCATATCGGTGCCAACGCCATGTCCCAGAC
* * * *
31476225 ATGGTCTTACATAGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGGC
1 ATGGTCTTACATGGGAGCTCTCATATCGGTGCCAACGCCATGTCCCAGAC
* * ** *
31476275 ATGGTCTTACATGGGAGGTCTCATAATGTCAATGATGCCATTGCCATGTCCCAGAT
1 ATGGTCTTACATGGGAGCTCTCAT-A--TC---GGTGCCAACGCCATGTCCCAGAC
31476331 ATGGTCTTACATGGGA
1 ATGGTCTTACATGGGA
31476347 TCTCATTCCC
Statistics
Matches: 99, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
50 63 0.64
53 2 0.02
56 34 0.34
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (50 bp):
ATGGTCTTACATGGGAGCTCTCATATCGGTGCCAACGCCATGTCCCAGAC
Found at i:31478684 original size:95 final size:96
Alignment explanation
Indices: 31478526--31478717 Score: 377
Period size: 95 Copynumber: 2.0 Consensus size: 96
31478516 TGTAAGTGAA
31478526 GAATAAATATGAAAGCTTGTTTCTATTTTATTTAATTTTAACTTTAATTACTAATTACCCAAATT
1 GAATAAATATGAAAGCTTGTTTCTATTTTATTTAATTTTAACTTTAATTACTAATTACCCAAATT
31478591 AACCTTAAAAATTAATCAAAATTTCAATAAT
66 AACCTTAAAAATTAATCAAAATTTCAATAAT
31478622 GAATAAATATG-AAGCTTGTTTCTATTTTATTTAATTTTAACTTTAATTACTAATTACCCAAATT
1 GAATAAATATGAAAGCTTGTTTCTATTTTATTTAATTTTAACTTTAATTACTAATTACCCAAATT
31478686 AACCTTAAAAATTAATCAAAATTTCAATAAT
66 AACCTTAAAAATTAATCAAAATTTCAATAAT
31478717 G
1 G
31478718 CCAAACCATG
Statistics
Matches: 96, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
95 85 0.89
96 11 0.11
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (96 bp):
GAATAAATATGAAAGCTTGTTTCTATTTTATTTAATTTTAACTTTAATTACTAATTACCCAAATT
AACCTTAAAAATTAATCAAAATTTCAATAAT
Found at i:31482572 original size:29 final size:28
Alignment explanation
Indices: 31482535--31482600 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 28
31482525 TAGATAATGA
31482535 AAAAGGATAGCTTCGGCTATCTAATGTG
1 AAAAGGATAGCTTCGGCTATCTAATGTG
31482563 AAAAGCGATAGCTTCGGCTATCTAATGTG
1 AAAAG-GATAGCTTCGGCTATCTAATGTG
31482592 AAAACGGAT
1 AAAA-GGAT
31482601 GGTGACGACC
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
28 5 0.14
29 30 0.83
30 1 0.03
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (28 bp):
AAAAGGATAGCTTCGGCTATCTAATGTG
Found at i:31483353 original size:22 final size:22
Alignment explanation
Indices: 31483325--31483369 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
31483315 GACTTTAGTA
31483325 TGAGATGACAGAGAATCAGTGC
1 TGAGATGACAGAGAATCAGTGC
31483347 TGAGATGACAGAGAATCAGTGC
1 TGAGATGACAGAGAATCAGTGC
31483369 T
1 T
31483370 AAAAAGTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.13, G:0.31, T:0.20
Consensus pattern (22 bp):
TGAGATGACAGAGAATCAGTGC
Found at i:31483514 original size:50 final size:50
Alignment explanation
Indices: 31483430--31483705 Score: 392
Period size: 50 Copynumber: 5.5 Consensus size: 50
31483420 ATTTGGGTAA
* * * * *
31483430 AGAGATCCAATGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAGACG
1 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATG
*
31483480 AGAGGTCTCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATG
* *
31483530 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATG
31483580 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATG
* * * *
31483630 AGAGATCCC-TCGTAAGACCATGTTTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCAT-GTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATG
* ** *
31483680 GGAGGTCCCCCGTTAGACCATGTTTG
1 AGAGGTCCCATGTAAGACCATGTTTG
31483706 TAACATCCCG
Statistics
Matches: 205, Mismatches: 19, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
49 1 0.00
50 204 1.00
ACGTcount: A:0.24, C:0.21, G:0.33, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATG
Found at i:31484525 original size:50 final size:50
Alignment explanation
Indices: 31484443--31484733 Score: 282
Period size: 50 Copynumber: 5.8 Consensus size: 50
31484433 TTTTGGGTAA
* * *
31484443 AGAGATCCCATGTAAGATCATGTCTGGTACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
*
31484493 AGAGGTCCCATGTTAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* * * *
31484543 AGAGGTCTCATTTAAGACCATGTCTAGGACATGGCGTTGCCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* ** * *
31484593 ATAGGTCCCCCGTAAGACCATGTCTGGGACATGGC-ATGGACACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGG-CACCGAGATG
** * ** * * * * *
31484643 AGAACTCCCATGTAAGTCCACATCTAGGATATGGCATTGGCA--GTAAAGG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCG-AGATG
* ** * * *
31484692 AAACATCCCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
31484734 TGTTATTATC
Statistics
Matches: 196, Mismatches: 42, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
48 1 0.01
49 36 0.18
50 156 0.80
51 3 0.02
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:31489801 original size:155 final size:155
Alignment explanation
Indices: 31489614--31489925 Score: 624
Period size: 155 Copynumber: 2.0 Consensus size: 155
31489604 ATAACATCTT
31489614 AATTTTTTGCCTAGTCAGAACAGTGGTTTCGAGACCACAAATTCGATGAGGAAAAATTTATTTCT
1 AATTTTTTGCCTAGTCAGAACAGTGGTTTCGAGACCACAAATTCGATGAGGAAAAATTTATTTCT
31489679 TCTTATATTTTTATGGTCTACGATTTCACTGAATGATTTTGTGAAAATTTCGTTCGAAAATTTCG
66 TCTTATATTTTTATGGTCTACGATTTCACTGAATGATTTTGTGAAAATTTCGTTCGAAAATTTCG
31489744 ACGTTTGGGCACTCAATTTAGTAAA
131 ACGTTTGGGCACTCAATTTAGTAAA
31489769 AATTTTTTGCCTAGTCAGAACAGTGGTTTCGAGACCACAAATTCGATGAGGAAAAATTTATTTCT
1 AATTTTTTGCCTAGTCAGAACAGTGGTTTCGAGACCACAAATTCGATGAGGAAAAATTTATTTCT
31489834 TCTTATATTTTTATGGTCTACGATTTCACTGAATGATTTTGTGAAAATTTCGTTCGAAAATTTCG
66 TCTTATATTTTTATGGTCTACGATTTCACTGAATGATTTTGTGAAAATTTCGTTCGAAAATTTCG
31489899 ACGTTTGGGCACTCAATTTAGTAAA
131 ACGTTTGGGCACTCAATTTAGTAAA
31489924 AA
1 AA
31489926 GGACTAAATT
Statistics
Matches: 157, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
155 157 1.00
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.38
Consensus pattern (155 bp):
AATTTTTTGCCTAGTCAGAACAGTGGTTTCGAGACCACAAATTCGATGAGGAAAAATTTATTTCT
TCTTATATTTTTATGGTCTACGATTTCACTGAATGATTTTGTGAAAATTTCGTTCGAAAATTTCG
ACGTTTGGGCACTCAATTTAGTAAA
Found at i:31490586 original size:50 final size:49
Alignment explanation
Indices: 31490509--31490742 Score: 279
Period size: 50 Copynumber: 4.7 Consensus size: 49
31490499 TAAAGAGATC
*
31490509 CCATGTAAGATCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGT
1 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGT
* *
31490558 CTTATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATGAGAGGT
1 C-CATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGT
* *
31490608 CCCATGAAAGAACATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGT
1 -CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGT
** * * * * **
31490658 CCCCGTAAGACCATGTCTGGGACATGACATGGGCACCGATATGAGAACT
1 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGT
* * * * *
31490707 CCCATGTAAGACAATATCTAGGATATGGCATTGGCA
1 -CCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
31490743 GTAAAGGAAA
Statistics
Matches: 157, Mismatches: 25, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
49 40 0.25
50 116 0.74
51 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (49 bp):
CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGT
Done.