Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 241 of 345
Found at i:70939077 original size:27 final size:27
Alignment explanation
Indices: 70938893--70939101 Score: 283
Period size: 27 Copynumber: 7.7 Consensus size: 27
70938883 GGGTATTTTA
* *
70938893 GTAATTTTGTAAATCGAGGGTAAAACG
1 GTAATTCTATAAATCGAGGGTAAAACG
*
70938920 GTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAACG
* *
70938947 GTAATTCTGTAAATCGAGGGTAAAACA
1 GTAATTCTATAAATCGAGGGTAAAACG
* *
70938974 GTAATTTTATAAATCGAGGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAACG
* * *
70939001 GTAATTCTATAAATTGAAGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAACG
*
70939028 GTAATTCTATAAATAGAGGGTAAAACG
1 GTAATTCTATAAATCGAGGGTAAAACG
*
70939055 GTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTATAAATCGAGGGTAAAACG
* * *
70939082 GTAATTTTACAAATTGAGGG
1 GTAATTCTATAAATCGAGGG
70939102 CATTTCAGTA
Statistics
Matches: 160, Mismatches: 22, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 160 1.00
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (27 bp):
GTAATTCTATAAATCGAGGGTAAAACG
Found at i:70941877 original size:2 final size:2
Alignment explanation
Indices: 70941870--70941897 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
70941860 CACCAAACAG
70941870 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
70941898 GTGGCGAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:70949307 original size:27 final size:26
Alignment explanation
Indices: 70949259--70949318 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
70949249 GCGAGGCTGC
*
70949259 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
70949286 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
*
70949312 CATATAT
1 CAGATAT
70949319 ATATATATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:70949320 original size:2 final size:2
Alignment explanation
Indices: 70949313--70949338 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
70949303 CCACCAGAAC
70949313 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
70949339 GTGGCGAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:70949419 original size:27 final size:26
Alignment explanation
Indices: 70949371--70949422 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
70949361 GCGAGGCTGC
*
70949371 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
70949397 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
70949423 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:70953542 original size:43 final size:44
Alignment explanation
Indices: 70953440--70953554 Score: 146
Period size: 43 Copynumber: 2.6 Consensus size: 44
70953430 TAGGATTTCG
*
70953440 TGTAAGACCACGTCTGGGACGTTGGCATCGACTTCTGTTTTACA
1 TGTAAGACCACGTCTGGGACGTTGGCATCGACTTCTGTATTACA
* * * *
70953484 TGTAAAACCATGTCTGGGACAG-TGGTATCGA-TGTTTG-ATTACA
1 TGTAAGACCACGTCTGGGAC-GTTGGCATCGACT-TCTGTATTACA
70953527 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
70953555 TGTATATGTT
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
42 1 0.02
43 29 0.48
44 29 0.48
45 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.30
Consensus pattern (44 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGACTTCTGTATTACA
Found at i:70960760 original size:18 final size:18
Alignment explanation
Indices: 70960737--70960808 Score: 74
Period size: 18 Copynumber: 3.9 Consensus size: 18
70960727 CATGGGATTT
70960737 TGATATACATGAT-TGATA
1 TGATATACATGATATG-TA
70960755 TGATATGCACATGATATGTA
1 TGATAT--ACATGATATGTA
**
70960775 TGATATGTATGATATGTA
1 TGATATACATGATATGTA
**
70960793 TGATATGTATGATATG
1 TGATATACATGATATG
70960809 CACATGATGT
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
18 32 0.65
20 15 0.31
21 2 0.04
ACGTcount: A:0.35, C:0.04, G:0.21, T:0.40
Consensus pattern (18 bp):
TGATATACATGATATGTA
Found at i:70960768 original size:20 final size:20
Alignment explanation
Indices: 70960743--70960799 Score: 75
Period size: 18 Copynumber: 3.0 Consensus size: 20
70960733 ATTTTGATAT
70960743 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGATATGC
70960763 ACATGATATGTATGATATG-
1 ACATGATATGTATGATATGC
*
70960782 -TATGATATGTATGATATG
1 ACATGATATGTATGATATG
70960800 TATGATATGC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
18 17 0.49
20 16 0.46
21 2 0.06
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.39
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:70960777 original size:9 final size:9
Alignment explanation
Indices: 70960765--70960808 Score: 88
Period size: 9 Copynumber: 4.9 Consensus size: 9
70960755 TGATATGCAC
70960765 ATGATATGT
1 ATGATATGT
70960774 ATGATATGT
1 ATGATATGT
70960783 ATGATATGT
1 ATGATATGT
70960792 ATGATATGT
1 ATGATATGT
70960801 ATGATATG
1 ATGATATG
70960809 CACATGATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.43
Consensus pattern (9 bp):
ATGATATGT
Found at i:70960818 original size:18 final size:18
Alignment explanation
Indices: 70960743--70960820 Score: 55
Period size: 18 Copynumber: 4.6 Consensus size: 18
70960733 ATTTTGATAT
70960743 ACATGATTGATATGATATGC
1 ACATGA-TG-TATGATATGC
70960763 ACATGA--TATG-TATG-
1 ACATGATGTATGATATGC
*
70960777 --AT-ATGTATGATATGT
1 ACATGATGTATGATATGC
*
70960792 ATGAT-ATGTATGATATGC
1 A-CATGATGTATGATATGC
70960810 ACATGATGTAT
1 ACATGATGTAT
70960821 TCATAAATGC
Statistics
Matches: 48, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
11 1 0.02
12 2 0.04
13 4 0.08
14 4 0.08
15 4 0.08
16 4 0.08
17 2 0.04
18 21 0.44
20 6 0.12
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (18 bp):
ACATGATGTATGATATGC
Found at i:70960818 original size:27 final size:27
Alignment explanation
Indices: 70960765--70960820 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
70960755 TGATATGCAC
* *
70960765 ATGATATGTATGATATGTATGATATGT
1 ATGATATGTATGATATGCATCATATGT
70960792 ATGATATGTATGATATGCA-CATGATGT
1 ATGATATGTATGATATGCATCAT-ATGT
70960819 AT
1 AT
70960821 TCATAAATGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 2 0.08
27 24 0.92
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.41
Consensus pattern (27 bp):
ATGATATGTATGATATGCATCATATGT
Found at i:70960895 original size:26 final size:26
Alignment explanation
Indices: 70960866--70960937 Score: 128
Period size: 26 Copynumber: 2.8 Consensus size: 26
70960856 GAGGAAATGC
70960866 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
70960892 AAAAGGGCTTATGCCCCAGCTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
70960918 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
70960938 ATTAAAGAGG
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
25 9 0.20
26 35 0.80
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:70969016 original size:20 final size:20
Alignment explanation
Indices: 70968991--70969029 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
70968981 ATTTTGATAT
70968991 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGATATGC
70969011 ACATGATATGTATGATATG
1 ACATGATATGTATGATATG
70969030 TATGATATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.36
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:70969019 original size:29 final size:29
Alignment explanation
Indices: 70968985--70969043 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
70968975 CATGGGATTT
70968985 TGATATACATGAT-TGATATGATATGCACA
1 TGATATACATGATATG-TATGATATGCACA
**
70969014 TGATATGTATGATATGTATGATATGCACA
1 TGATATACATGATATGTATGATATGCACA
70969043 T
1 T
70969044 AATGTATTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 25 0.93
30 2 0.07
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.37
Consensus pattern (29 bp):
TGATATACATGATATGTATGATATGCACA
Found at i:70969025 original size:9 final size:9
Alignment explanation
Indices: 70969013--70969038 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
70969003 TGATATGCAC
70969013 ATGATATGT
1 ATGATATGT
70969022 ATGATATGT
1 ATGATATGT
70969031 ATGATATG
1 ATGATATG
70969039 CACATAATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (9 bp):
ATGATATGT
Found at i:70969033 original size:4 final size:5
Alignment explanation
Indices: 70968993--70969038 Score: 53
Period size: 5 Copynumber: 9.6 Consensus size: 5
70968983 TTTGATATAC
*
70968993 ATGAT -TGAT ATGAT ATGCAC ATGAT ATG-T ATGAT ATG-T ATGAT ATG
1 ATGAT ATGAT ATGAT ATG-AT ATGAT ATGAT ATGAT ATGAT ATGAT ATG
70969039 CACATAATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
4 12 0.34
5 19 0.54
6 4 0.11
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.39
Consensus pattern (5 bp):
ATGAT
Found at i:70969126 original size:27 final size:26
Alignment explanation
Indices: 70969096--70969219 Score: 162
Period size: 26 Copynumber: 4.8 Consensus size: 26
70969086 GAGGAAGTGC
*
70969096 AAAAGGGCTTATGCCCCAGTTTATTAA
1 AAAAGGGCTTATGCCCCAGTTTATT-G
70969123 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* * * *
70969149 AAAAGGGTTTATGGCCTAATTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
70969175 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
70969200 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
70969220 ATTAAAGAGG
Statistics
Matches: 86, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
25 30 0.35
26 31 0.36
27 25 0.29
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:70969851 original size:18 final size:18
Alignment explanation
Indices: 70969828--70969874 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
70969818 CTTAGGACGC
*
70969828 GTTTTCAAAACGACATTT
1 GTTTTCCAAACGACATTT
70969846 GTTTTCCAAACGACATTT
1 GTTTTCCAAACGACATTT
70969864 GTTTTCCAAAC
1 GTTTTCCAAAC
70969875 AACACAACGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (18 bp):
GTTTTCCAAACGACATTT
Found at i:70974648 original size:13 final size:13
Alignment explanation
Indices: 70974630--70974661 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
70974620 GTACAGAATT
*
70974630 CACACGGTCAGGG
1 CACACGGCCAGGG
70974643 CACACGGCCAGGG
1 CACACGGCCAGGG
70974656 CACACG
1 CACACG
70974662 CCCATGTCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.25, C:0.38, G:0.34, T:0.03
Consensus pattern (13 bp):
CACACGGCCAGGG
Found at i:70977347 original size:47 final size:47
Alignment explanation
Indices: 70977293--70977461 Score: 293
Period size: 47 Copynumber: 3.6 Consensus size: 47
70977283 CCATTCTTGG
*
70977293 CATGGTCTTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTATCTTACCAAATGCCATGTTCCAAA
* *
70977340 CATGGTCTTACATGGTATCCTTGTTTTACCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTATCTTACCAAATGCCATGTTCCAAA
* *
70977387 CATGGTCTTACATGGTATCCTTGTCTTACCAAACGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTATCTTACCAAATGCCATGTTCCAAA
70977434 CATGGTCTTACATGGTATCCTTATCTTA
1 CATGGTCTTACATGGTATCCTTATCTTA
70977462 GTGCTAATGC
Statistics
Matches: 116, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 116 1.00
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.36
Consensus pattern (47 bp):
CATGGTCTTACATGGTATCCTTATCTTACCAAATGCCATGTTCCAAA
Found at i:70984107 original size:40 final size:40
Alignment explanation
Indices: 70984048--70984255 Score: 229
Period size: 40 Copynumber: 5.2 Consensus size: 40
70984038 CATTGGAATG
* * *
70984048 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTCATT
**
70984088 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTCATT
* * * **
70984128 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTCATT
* * *
70984168 AAATCCGGGTTAAGACCCGAAGGCAATTGTGCGAGTCACT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTCATT
* ** * * *
70984208 ATAACCGGGCTTCGTCCCGAAGGCATTTGAGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTCATT
70984248 ATATCCGG
1 ATATCCGG
70984256 TTAAATTCCG
Statistics
Matches: 141, Mismatches: 25, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
39 3 0.02
40 136 0.96
41 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTCATT
Found at i:70992131 original size:40 final size:40
Alignment explanation
Indices: 70992072--70992279 Score: 229
Period size: 40 Copynumber: 5.2 Consensus size: 40
70992062 CATTGGAATG
* * *
70992072 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTCATT
**
70992112 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTCATT
* * * **
70992152 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTCATT
* * *
70992192 AAATCCGGGTTAAGACCCGAAGGCAATTGTGCGAGTCACT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTCATT
* ** * * *
70992232 ATAACCGGGCTTCGTCCCGAAGGCATTTGAGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTCATT
70992272 ATATCCGG
1 ATATCCGG
70992280 TTAAATTCCG
Statistics
Matches: 141, Mismatches: 25, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
39 3 0.02
40 136 0.96
41 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTCATT
Found at i:70999755 original size:2 final size:2
Alignment explanation
Indices: 70999748--70999781 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
70999738 GTTGTAAGCT
70999748 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
70999782 CATACATGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:71004063 original size:99 final size:94
Alignment explanation
Indices: 71003934--71004113 Score: 218
Period size: 99 Copynumber: 1.9 Consensus size: 94
71003924 CCATCAAGTC
* * *
71003934 GATGACATGTACCAGACATGGTATTACACTGACTATCGAAATCG-AGGCTAACGCCATGTCCCAG
1 GATGACATGTACCAGACACGGTATTACACTGAC-A-C-AAATCGTA-GCCAAC-ACATGTCCCAG
*
71003998 ACATGGTCTTGCACTAGCTCTCACATATCCTTACT
61 ACAT-GTCTTACACTAGCTCTCACATATCCTTACT
* * * **
71004033 GATGCCATGTCCCAGACACGGTCTTACACTGACACATCTCGTAGCCAACACATGTCCCAGACATG
1 GATGACATGTACCAGACACGGTATTACACTGACACAAATCGTAGCCAACACATGTCCCAGACATG
71004098 TCTTACACTAGCTCTC
66 TCTTACACTAGCTCTC
71004114 GTCTCAAGGC
Statistics
Matches: 71, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
94 16 0.23
95 14 0.20
96 9 0.13
97 2 0.03
98 1 0.01
99 29 0.41
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (94 bp):
GATGACATGTACCAGACACGGTATTACACTGACACAAATCGTAGCCAACACATGTCCCAGACATG
TCTTACACTAGCTCTCACATATCCTTACT
Found at i:71005832 original size:19 final size:20
Alignment explanation
Indices: 71005803--71005840 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
71005793 CAATGATTCA
*
71005803 ATGGACATGAAACTCTTGAC
1 ATGGACATGAAAATCTTGAC
71005823 ATGG-CATGAAAATCTTGA
1 ATGGACATGAAAATCTTGA
71005841 GATGATATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (20 bp):
ATGGACATGAAAATCTTGAC
Found at i:71005850 original size:19 final size:19
Alignment explanation
Indices: 71005806--71005850 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
71005796 TGATTCAATG
*
71005806 GACATGAAACTCTTGACAT
1 GACATGAAAATCTTGACAT
* *
71005825 GGCATGAAAATCTTGAGAT
1 GACATGAAAATCTTGACAT
*
71005844 GATATGA
1 GACATGA
71005851 TAATGACTTG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (19 bp):
GACATGAAAATCTTGACAT
Found at i:71008129 original size:43 final size:42
Alignment explanation
Indices: 71007991--71008158 Score: 153
Period size: 44 Copynumber: 3.9 Consensus size: 42
71007981 TAGGACTCCA
*
71007991 ATATGTGATTTTGTGTAAGACCAC-GTCTGGGACATTGGCATCG
1 ATAT-TGATTTCGTGTAAGACC-CTGTCTGGGACATTGGCATCG
* *
71008034 AT-TTGAGATTTACGTTTAAGACCATGTCTGGGACATTGGCATCG
1 ATATT--GATTT-CGTGTAAGACCCTGTCTGGGACATTGGCATCG
* * *
71008078 -TATTTGATTTCGTGTAAGACCCTATCTGGGATAATGGCATCG
1 ATA-TTGATTTCGTGTAAGACCCTGTCTGGGACATTGGCATCG
* * * *
71008120 ATAGTTGATTACATGTAAGACCCTTTTCTGGGACGTTGG
1 ATA-TTGATTTCGTGTAAGACCC-TGTCTGGGACATTGG
71008159 TATTGTACGA
Statistics
Matches: 102, Mismatches: 15, Indels: 15
0.77 0.11 0.11
Matches are distributed among these distances:
41 1 0.01
42 28 0.27
43 32 0.31
44 39 0.38
45 2 0.02
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.35
Consensus pattern (42 bp):
ATATTGATTTCGTGTAAGACCCTGTCTGGGACATTGGCATCG
Found at i:71017356 original size:20 final size:21
Alignment explanation
Indices: 71017333--71017380 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
71017323 ATCAGCTCAC
*
71017333 TTGAGCTCG-TTTTAGCTCGT
1 TTGAGCTCGAATTTAGCTCGT
71017353 TTGAGCT-GAATTTAGCTCGT
1 TTGAGCTCGAATTTAGCTCGT
*
71017373 TTCAGCTC
1 TTGAGCTC
71017381 ATTCCTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.15, C:0.21, G:0.23, T:0.42
Consensus pattern (21 bp):
TTGAGCTCGAATTTAGCTCGT
Found at i:71017621 original size:13 final size:13
Alignment explanation
Indices: 71017603--71017627 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
71017593 AATAGTTGTG
71017603 TGTTATTTAATTA
1 TGTTATTTAATTA
71017616 TGTTATTTAATT
1 TGTTATTTAATT
71017628 TTGTAGGTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:71022155 original size:13 final size:13
Alignment explanation
Indices: 71022137--71022161 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
71022127 AATAGTTGTG
71022137 TGTTATTTAATTA
1 TGTTATTTAATTA
71022150 TGTTATTTAATT
1 TGTTATTTAATT
71022162 TTGTAGGTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:71025156 original size:19 final size:19
Alignment explanation
Indices: 71025132--71025171 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
71025122 AGCTCCCATG
71025132 TAGCTCCACACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
***
71025151 TAGCTCGGGACCAGCTCAT
1 TAGCTCCACACCAGCTCAT
71025170 TA
1 TA
71025172 TTAGCTCACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (19 bp):
TAGCTCCACACCAGCTCAT
Found at i:71026437 original size:14 final size:14
Alignment explanation
Indices: 71026415--71026462 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
71026405 ACCTAAACCG
* *
71026415 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
71026429 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
71026443 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
71026457 ACCATT
1 ACCATT
71026463 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:71028460 original size:18 final size:18
Alignment explanation
Indices: 71028439--71028488 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
71028429 AAACTCTTTT
71028439 TCATTCTCTTTTTCAATC
1 TCATTCTCTTTTTCAATC
* *
71028457 TCATTTTCTTTTTCACTC
1 TCATTCTCTTTTTCAATC
*
71028475 TCAATCTCTTTTTC
1 TCATTCTCTTTTTC
71028489 TTTTTCTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.14, C:0.28, G:0.00, T:0.58
Consensus pattern (18 bp):
TCATTCTCTTTTTCAATC
Found at i:71028546 original size:42 final size:42
Alignment explanation
Indices: 71028492--71028588 Score: 142
Period size: 42 Copynumber: 2.3 Consensus size: 42
71028482 CTTTTTCTTT
* * *
71028492 TTCTTTCA-TTTCTTTGTTTCTTTTCTCAATTTCATTCAAGA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCAATTTCATTCAAAA
*
71028533 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCAATTTCATTCAAAA
*
71028575 TCCTCTCATTTTCT
1 TTCTCTCATTTTCT
71028589 CTCATAATCT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 7 0.14
42 43 0.86
ACGTcount: A:0.15, C:0.24, G:0.04, T:0.57
Consensus pattern (42 bp):
TTCTCTCATTTTCTTTGTTTCTTCTCTCAATTTCATTCAAAA
Found at i:71028643 original size:15 final size:14
Alignment explanation
Indices: 71028623--71028664 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
71028613 TTTCTTTTGA
*
71028623 TCTCTTTTTGCTTT
1 TCTCTTCTTGCTTT
71028637 TCGTCTTCTT-CTTT
1 TC-TCTTCTTGCTTT
71028651 TCTC-TCTTGCTTT
1 TCTCTTCTTGCTTT
71028664 T
1 T
71028665 TACAATAGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 4 0.16
13 7 0.28
14 8 0.32
15 6 0.24
ACGTcount: A:0.00, C:0.26, G:0.07, T:0.67
Consensus pattern (14 bp):
TCTCTTCTTGCTTT
Found at i:71032174 original size:12 final size:12
Alignment explanation
Indices: 71032132--71032184 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
71032122 ATGAAAAAAC
*
71032132 AAAAAAAA-ATG
1 AAAAAAAATCTG
* *
71032143 AAAAAAAATTTC
1 AAAAAAAATCTG
71032155 AAACAAAAATTCTG
1 AAA-AAAAA-TCTG
71032169 AAAAAAAATCTG
1 AAAAAAAATCTG
71032181 AAAA
1 AAAA
71032185 TTTGAACATA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
11 8 0.23
12 12 0.34
13 10 0.29
14 5 0.14
ACGTcount: A:0.70, C:0.08, G:0.06, T:0.17
Consensus pattern (12 bp):
AAAAAAAATCTG
Found at i:71037540 original size:15 final size:14
Alignment explanation
Indices: 71037509--71037565 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
71037499 AAGAGAAAAT
71037509 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
71037525 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
71037540 AAAGAAAATGGAATAA
1 AAAGAAAA--GAAGAA
71037556 AAAGAAAAGA
1 AAAGAAAAGA
71037566 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 6 0.16
15 9 0.24
16 17 0.46
17 5 0.14
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:71037636 original size:11 final size:12
Alignment explanation
Indices: 71037613--71037642 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
71037603 TTGAGAGAAC
71037613 TTGAAAAAGCCT
1 TTGAAAAAGCCT
71037625 TTGAAAAA-CCT
1 TTGAAAAAGCCT
71037636 TTGAAAA
1 TTGAAAA
71037643 GCAAAAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:71037660 original size:12 final size:12
Alignment explanation
Indices: 71037645--71037669 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
71037635 TTTGAAAAGC
71037645 AAAAAGAAAATG
1 AAAAAGAAAATG
71037657 AAAAAGAAAATG
1 AAAAAGAAAATG
71037669 A
1 A
71037670 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:71037666 original size:18 final size:18
Alignment explanation
Indices: 71037639--71037694 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
71037629 AAAACCTTTG
71037639 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
71037658 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
71037676 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
71037693 AA
1 AA
71037695 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:71037681 original size:30 final size:31
Alignment explanation
Indices: 71037645--71037726 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
71037635 TTTGAAAAGC
*
71037645 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
71037675 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
71037705 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
71037727 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:71040061 original size:30 final size:30
Alignment explanation
Indices: 71039966--71040062 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
71039956 AGCTCACTCC
* *
71039966 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTT-AGCTCACGAGCTAAAGCT
* * * **
71039996 TAGCTCAACTTCAGCTTAGGAG-TTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAG-CT
* *
71040026 CAGCTCAACTTTAGCTCACAAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAAGCT
71040056 TAGCTCA
1 TAGCTCA
71040063 TTTTAGTTTA
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
29 2 0.04
30 40 0.82
31 7 0.14
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAAGCT
Found at i:71043465 original size:46 final size:46
Alignment explanation
Indices: 71043293--71043465 Score: 185
Period size: 46 Copynumber: 3.7 Consensus size: 46
71043283 AACCCGCCCC
***
71043293 TAAGTGAACTCGGACTCAACTCAACGAGCTT-GGGTGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAG-TTCGGACATTCGCATCCA
* *
71043339 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
71043387 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
*
71043432 TAAGTGAACTCGGGCTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
71043466 AGCTCAACCA
Statistics
Matches: 105, Mismatches: 12, Indels: 20
0.77 0.09 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 57 0.54
47 28 0.27
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:71044982 original size:28 final size:28
Alignment explanation
Indices: 71044921--71045018 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 28
71044911 TCACAAATTG
** * *
71044921 GCACTAAGTGTGCGGGTTCAAATTATACA
1 GCACTAAGTGTGCAAGTTC-GATTATATA
*
71044950 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCAAGTTCGATTATATA
* *
71044978 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCAAGTTCGATTATAT-A
71045006 GCACTAAGTGTGC
1 GCACTAAGTGTGC
71045019 GGGCTTATGG
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.02
28 43 0.72
29 16 0.27
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCAAGTTCGATTATATA
Found at i:71046807 original size:30 final size:30
Alignment explanation
Indices: 71046771--71046849 Score: 131
Period size: 30 Copynumber: 2.6 Consensus size: 30
71046761 ACTTTAAAAA
*
71046771 AATTACACTTTTGTCCCTAAAATTTTGCAT
1 AATTACACTTTTGCCCCTAAAATTTTGCAT
* *
71046801 AATTACACTTTTGCCCCTAAACTTTTGTAT
1 AATTACACTTTTGCCCCTAAAATTTTGCAT
71046831 AATTACACTTTTGCCCCTA
1 AATTACACTTTTGCCCCTA
71046850 GGCTCGGGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.28, C:0.24, G:0.06, T:0.42
Consensus pattern (30 bp):
AATTACACTTTTGCCCCTAAAATTTTGCAT
Found at i:71050681 original size:40 final size:40
Alignment explanation
Indices: 71050602--71050759 Score: 151
Period size: 40 Copynumber: 4.0 Consensus size: 40
71050592 TTCGAATGAT
* * * *
71050602 ATCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAAGTGACTAA
1 ATCCGGACTAAGAT-CCGAAGGCATTCGTGC-GAGTTACTAA
* *
71050642 ATCCGGACTAAGATCCGACGGCATACGTGCGAGTTACTAA
1 ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
* * * *
71050682 ATCCGGACTAAGATCCGAAGGCTTTCGAGCAAGCTACTAA
1 ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
** *
71050722 ATCCGGGTTGAG-TCCCGAAGGCATTCGTGCGAGTTACT
1 ATCCGGACTAAGAT-CCGAAGGCATTCGTGCGAGTTACT
71050760 GTAACCGGGC
Statistics
Matches: 96, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
39 1 0.01
40 89 0.93
41 6 0.06
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
Found at i:71050780 original size:80 final size:80
Alignment explanation
Indices: 71050602--71050789 Score: 206
Period size: 80 Copynumber: 2.3 Consensus size: 80
71050592 TTCGAATGAT
* *
71050602 ATCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAATCCGGACTAAGATCCGACGGCATA
1 ATCCGGGCTAAGTCCCGAAGGCTTTGAGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATA
71050667 CGTGCGAGTTACTAA
66 CGTGCGAGTTACTAA
* ** *
71050682 ATCCGGACTAAGAT-CCGAAGGCTTTCGAGC-AAGCT-ACTAAATCCGGGTTGAG-TCCCGAAGG
1 ATCCGGGCTAAG-TCCCGAAGGCTTT-GAGCTAAG-TGACTAAATCCGGACTAAGAT-CCGAAGG
* *
71050743 CATTCGTGCGAGTTACTGTA
62 CATACGTGCGAGTTACT-AA
*
71050763 A-CCGGGCTATGTCCCGAAGGCATTTGA
1 ATCCGGGCTAAGTCCCGAAGGC-TTTGA
71050790 ATGTGTAGCC
Statistics
Matches: 91, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
79 2 0.02
80 79 0.87
81 10 0.11
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (80 bp):
ATCCGGGCTAAGTCCCGAAGGCTTTGAGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATA
CGTGCGAGTTACTAA
Found at i:71058728 original size:40 final size:40
Alignment explanation
Indices: 71058649--71058806 Score: 151
Period size: 40 Copynumber: 4.0 Consensus size: 40
71058639 TTCGAATGAT
* * * *
71058649 ATCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAAGTGACTAA
1 ATCCGGACTAAGAT-CCGAAGGCATTCGTGC-GAGTTACTAA
* *
71058689 ATCCGGACTAAGATCCGACGGCATACGTGCGAGTTACTAA
1 ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
* * * *
71058729 ATCCGGACTAAGATCCGAAGGCTTTCGAGCAAGCTACTAA
1 ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
** *
71058769 ATCCGGGTTGAG-TCCCGAAGGCATTCGTGCGAGTTACT
1 ATCCGGACTAAGAT-CCGAAGGCATTCGTGCGAGTTACT
71058807 GTAACCGGGC
Statistics
Matches: 96, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
39 1 0.01
40 89 0.93
41 6 0.06
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
ATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAA
Found at i:71058827 original size:80 final size:80
Alignment explanation
Indices: 71058649--71058836 Score: 206
Period size: 80 Copynumber: 2.3 Consensus size: 80
71058639 TTCGAATGAT
* *
71058649 ATCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAATCCGGACTAAGATCCGACGGCATA
1 ATCCGGGCTAAGTCCCGAAGGCTTTGAGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATA
71058714 CGTGCGAGTTACTAA
66 CGTGCGAGTTACTAA
* ** *
71058729 ATCCGGACTAAGAT-CCGAAGGCTTTCGAGC-AAGCT-ACTAAATCCGGGTTGAG-TCCCGAAGG
1 ATCCGGGCTAAG-TCCCGAAGGCTTT-GAGCTAAG-TGACTAAATCCGGACTAAGAT-CCGAAGG
* *
71058790 CATTCGTGCGAGTTACTGTA
62 CATACGTGCGAGTTACT-AA
*
71058810 A-CCGGGCTATGTCCCGAAGGCATTTGA
1 ATCCGGGCTAAGTCCCGAAGGC-TTTGA
71058837 ATGTGTAGCC
Statistics
Matches: 91, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
79 2 0.02
80 79 0.87
81 10 0.11
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (80 bp):
ATCCGGGCTAAGTCCCGAAGGCTTTGAGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATA
CGTGCGAGTTACTAA
Found at i:71062523 original size:14 final size:14
Alignment explanation
Indices: 71062476--71062523 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
71062466 GTACGAATGG
*
71062476 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
71062490 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
71062504 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
71062518 ATTGGT
1 AATGGT
71062524 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:71065102 original size:13 final size:13
Alignment explanation
Indices: 71065084--71065108 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
71065074 TAACCTACAA
71065084 AATTAAATAACAT
1 AATTAAATAACAT
71065097 AATTAAATAACA
1 AATTAAATAACA
71065109 CACAACTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (13 bp):
AATTAAATAACAT
Found at i:71078020 original size:27 final size:27
Alignment explanation
Indices: 71077990--71078051 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
71077980 GGGCAAAATG
71077990 GTAATTTTACCCCACAAGGGTATTTCA
1 GTAATTTTACCCCACAAGGGTATTTCA
* * *
71078017 GTAATTTTACCCTACAGGGGTATTTTA
1 GTAATTTTACCCCACAAGGGTATTTCA
71078044 GTAATTTT
1 GTAATTTT
71078052 TCAAACCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.40
Consensus pattern (27 bp):
GTAATTTTACCCCACAAGGGTATTTCA
Found at i:71078065 original size:54 final size:54
Alignment explanation
Indices: 71078007--71078157 Score: 151
Period size: 54 Copynumber: 2.8 Consensus size: 54
71077997 TACCCCACAA
** * * *
71078007 GGGTATTTCAGTAATTTTACCCTAC-AGGGGTATTTTAGTAATTTTTCAAACCAT
1 GGGTATTTCAGTAATTTTA-CAAACAAAGGGTATTTTAGTAATTTTACAAACCAG
** * *
71078061 GGGTATTTTGGTAATTTTATAAACAAAGGGTATTTTAGTAATTTTACAAACTAG
1 GGGTATTTCAGTAATTTTACAAACAAAGGGTATTTTAGTAATTTTACAAACCAG
** * * * *
71078115 GGGTATTTTGGTGATTTTATAAACTAAGGGTATTTTGGTAATT
1 GGGTATTTCAGTAATTTTACAAACAAAGGGTATTTTAGTAATT
71078158 CTGTAAATTG
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
53 2 0.02
54 82 0.98
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (54 bp):
GGGTATTTCAGTAATTTTACAAACAAAGGGTATTTTAGTAATTTTACAAACCAG
Found at i:71078123 original size:81 final size:81
Alignment explanation
Indices: 71078005--71078157 Score: 211
Period size: 81 Copynumber: 1.9 Consensus size: 81
71077995 TTTACCCCAC
** *
71078005 AAGGGTATTTCAGTAATTTTACCCTACAGGGGTATTTTAGTAATTTT-TCAAACCATGGGTATTT
1 AAGGGTATTTCAGTAATTTTACCAAACAGGGGTATTTTAGTAATTTTAT-AAACCAAGGGTATTT
71078069 TGGTAATTTTATAAACA
65 TGGTAATTTTATAAACA
* * * *
71078086 AAGGGTATTTTAGTAATTTTA-CAAACTAGGGGTATTTTGGTGATTTTATAAACTAAGGGTATTT
1 AAGGGTATTTCAGTAATTTTACCAAAC-AGGGGTATTTTAGTAATTTTATAAACCAAGGGTATTT
71078150 TGGTAATT
65 TGGTAATT
71078158 CTGTAAATTG
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
80 3 0.05
81 59 0.94
82 1 0.02
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.42
Consensus pattern (81 bp):
AAGGGTATTTCAGTAATTTTACCAAACAGGGGTATTTTAGTAATTTTATAAACCAAGGGTATTTT
GGTAATTTTATAAACA
Found at i:71078173 original size:27 final size:27
Alignment explanation
Indices: 71078034--71078157 Score: 160
Period size: 27 Copynumber: 4.6 Consensus size: 27
71078024 TACCCTACAG
* * *
71078034 GGGTATTTTAGTAATTTT-TCAAACCAT
1 GGGTATTTTGGTAATTTTAT-AAACTAA
*
71078061 GGGTATTTTGGTAATTTTATAAACAAA
1 GGGTATTTTGGTAATTTTATAAACTAA
* * *
71078088 GGGTATTTTAGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTATAAACTAA
*
71078115 GGGTATTTTGGTGATTTTATAAACTAA
1 GGGTATTTTGGTAATTTTATAAACTAA
71078142 GGGTATTTTGGTAATT
1 GGGTATTTTGGTAATT
71078158 CTGTAAATTG
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
27 83 0.99
28 1 0.01
ACGTcount: A:0.31, C:0.06, G:0.20, T:0.44
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTATAAACTAA
Found at i:71078173 original size:54 final size:54
Alignment explanation
Indices: 71078034--71078159 Score: 180
Period size: 54 Copynumber: 2.3 Consensus size: 54
71078024 TACCCTACAG
* * * *
71078034 GGGTATTTTAGTAATTTTTCAAACCATGGGTATTTTGGTAATTTTATAAACAAA
1 GGGTATTTTAGTAATTCTACAAACTAGGGGTATTTTGGTAATTTTATAAACAAA
* * *
71078088 GGGTATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTGATTTTATAAACTAA
1 GGGTATTTTAGTAATTCTACAAACTAGGGGTATTTTGGTAATTTTATAAACAAA
*
71078142 GGGTATTTTGGTAATTCT
1 GGGTATTTTAGTAATTCT
71078160 GTAAATTGAG
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 65 1.00
ACGTcount: A:0.30, C:0.06, G:0.20, T:0.44
Consensus pattern (54 bp):
GGGTATTTTAGTAATTCTACAAACTAGGGGTATTTTGGTAATTTTATAAACAAA
Found at i:71079784 original size:20 final size:21
Alignment explanation
Indices: 71079729--71079777 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
71079719 AAAAAGGAAT
* *
71079729 GAGCTGAAACGAGCTAAATTC
1 GAGCTCAAACGAGCTAAAATC
71079750 GAGCTCAAACGAGCTAAAAT-
1 GAGCTCAAACGAGCTAAAATC
71079770 GAGCTCAA
1 GAGCTCAA
71079778 GTGAGCTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.16
Consensus pattern (21 bp):
GAGCTCAAACGAGCTAAAATC
Found at i:71081934 original size:30 final size:29
Alignment explanation
Indices: 71081879--71081942 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
71081869 TTTTTCAATT
* *
71081879 TCTTTTTCACTCTCAAATTTCTTTTCGTTC
1 TCTTTTTCAATCTCAAATCTCTTTTC-TTC
*
71081909 TCTTTTTCAATCTC-AATCTCATTTTCTTT
1 TCTTTTTCAATCTCAAATCTC-TTTTCTTC
71081938 TCTTT
1 TCTTT
71081943 GTTTTTCTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 12 0.40
30 18 0.60
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (29 bp):
TCTTTTTCAATCTCAAATCTCTTTTCTTC
Found at i:71081957 original size:19 final size:20
Alignment explanation
Indices: 71081933--71081973 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
71081923 AATCTCATTT
71081933 TCTTTTCTTTGTTT-TTCTC
1 TCTTTTCTTTGTTTCTTCTC
71081952 TCTTTTCTTTGTTTCTTCTC
1 TCTTTTCTTTGTTTCTTCTC
71081972 TC
1 TC
71081974 GATTTCATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.00, C:0.24, G:0.05, T:0.71
Consensus pattern (20 bp):
TCTTTTCTTTGTTTCTTCTC
Found at i:71084538 original size:29 final size:29
Alignment explanation
Indices: 71084472--71084528 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
71084462 GATTCAAAGA
*
71084472 TGGGTTTATGGATATGAAGTTTATGTAGT
1 TGGGTTTATGGATATAAAGTTTATGTAGT
*
71084501 TGGGTTTATGGATATAAAGTTTTTGTAG
1 TGGGTTTATGGATATAAAGTTTATGTAG
71084529 GTTTGGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.46
Consensus pattern (29 bp):
TGGGTTTATGGATATAAAGTTTATGTAGT
Found at i:71087745 original size:30 final size:28
Alignment explanation
Indices: 71087692--71087747 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
71087682 TTCTTCCACG
* *
71087692 CTTTCTTTTTGCTCACTCTCTTTTTCAA
1 CTTTCTTTTTGCACACACTCTTTTTCAA
71087720 CTTTACTTTCTTGCACACACTCTTTTTC
1 CTTT-CTTT-TTGCACACACTCTTTTTC
71087748 TTTTTCGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 4 0.17
30 16 0.67
ACGTcount: A:0.12, C:0.30, G:0.04, T:0.54
Consensus pattern (28 bp):
CTTTCTTTTTGCACACACTCTTTTTCAA
Found at i:71088793 original size:12 final size:12
Alignment explanation
Indices: 71088778--71088812 Score: 63
Period size: 11 Copynumber: 3.0 Consensus size: 12
71088768 TTAGATTTTG
71088778 TTTTTTTTTGAA
1 TTTTTTTTTGAA
71088790 -TTTTTTTTGAA
1 TTTTTTTTTGAA
71088801 TTTTTTTTTGAA
1 TTTTTTTTTGAA
71088813 ACTTACTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:71088822 original size:23 final size:23
Alignment explanation
Indices: 71088778--71088822 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
71088768 TTAGATTTTG
** **
71088778 TTTTTTTTTGAATTTTTTTTGAA
1 TTTTTTTTTGAAACTTACTTGAA
71088801 TTTTTTTTTGAAACTTACTTGA
1 TTTTTTTTTGAAACTTACTTGA
71088823 TGAGTCACAG
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:0.20, C:0.04, G:0.09, T:0.67
Consensus pattern (23 bp):
TTTTTTTTTGAAACTTACTTGAA
Found at i:71089094 original size:29 final size:29
Alignment explanation
Indices: 71089028--71089084 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
71089018 GATTCAAAGA
*
71089028 TGGGTTTATGGATATGAAGTTTATGTAGT
1 TGGGTTTATGGATATAAAGTTTATGTAGT
*
71089057 TGGGTTTATGGATATAAAGTTTTTGTAG
1 TGGGTTTATGGATATAAAGTTTATGTAG
71089085 GTTTGGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.46
Consensus pattern (29 bp):
TGGGTTTATGGATATAAAGTTTATGTAGT
Found at i:71092028 original size:13 final size:13
Alignment explanation
Indices: 71092010--71092034 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
71092000 TAACCTACAA
71092010 AATTAAATAACAT
1 AATTAAATAACAT
71092023 AATTAAATAACA
1 AATTAAATAACA
71092035 CACAACTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (13 bp):
AATTAAATAACAT
Found at i:71092282 original size:21 final size:21
Alignment explanation
Indices: 71092258--71092297 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
71092248 GAAAAAGGAA
71092258 TGAGCT-GAAACAAGCTAAATT
1 TGAGCTCG-AACAAGCTAAATT
*
71092279 TGAGCTCGAACGAGCTAAA
1 TGAGCTCGAACAAGCTAAA
71092298 ACGAGCTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.20
Consensus pattern (21 bp):
TGAGCTCGAACAAGCTAAATT
Found at i:71102196 original size:11 final size:12
Alignment explanation
Indices: 71102177--71102209 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
71102167 TTCTTTTCGT
*
71102177 TCTCTTTTTCAA
1 TCTCATTTTCAA
71102189 TCTC-TTTTCAA
1 TCTCATTTTCAA
71102200 TCTCATTTTC
1 TCTCATTTTC
71102210 TTTTTCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.15, C:0.27, G:0.00, T:0.58
Consensus pattern (12 bp):
TCTCATTTTCAA
Found at i:71102244 original size:12 final size:12
Alignment explanation
Indices: 71102229--71102259 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
71102219 TTTTTTTTGC
71102229 TTTTCAAAGGCT
1 TTTTCAAAGGCT
71102241 TTTTCAAAGGCT
1 TTTTCAAAGGCT
71102253 TTTTCAA
1 TTTTCAA
71102260 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:71102317 original size:5 final size:5
Alignment explanation
Indices: 71102307--71102363 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
71102297 CTCTTGCCTC
*
71102307 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
71102354 TCTTT TCTTT
1 TCTTT TCTTT
71102364 ATTTTCCCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:71102347 original size:15 final size:14
Alignment explanation
Indices: 71102307--71102363 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
71102297 CTCTTGCCTC
*
71102307 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
71102322 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
71102337 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
71102354 TCTTTTCTTT
1 TCTTTTCTTT
71102364 ATTTTCCCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:71106567 original size:30 final size:30
Alignment explanation
Indices: 71106533--71106610 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 30
71106523 TAAACTAAAA
* ** *
71106533 TGAGCTAAGCTTTAGCTTGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCCTAAGCTAAAGT
* * * *
71106563 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCCTAAGCTAAAGT
*
71106593 TGAGCTAAGGTTTAGCTC
1 TGAGCTAAGATTTAGCTC
71106611 ATGAGTTGGA
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCCTAAGCTAAAGT
Found at i:71109834 original size:29 final size:29
Alignment explanation
Indices: 71109801--71109860 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
71109791 ATAACCAAAC
* *
71109801 CTACAAAAACTTTATATCCATAAATCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
71109830 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
71109859 CT
1 CT
71109861 TTGAATCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:71109853 original size:15 final size:15
Alignment explanation
Indices: 71109807--71109854 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
71109797 AAACCTACAA
*
71109807 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
71109822 AAA-TCCATCTACAT
1 AAACTTCATATCCAT
71109836 AAACTTCATATCCAT
1 AAACTTCATATCCAT
71109851 AAAC
1 AAAC
71109855 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:71110120 original size:13 final size:13
Alignment explanation
Indices: 71110086--71110120 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
71110076 AAAAAAAAAA
71110086 AAAAAAAAATTTC
1 AAAAAAAAATTTC
* *
71110099 AAACAAAAATTTG
1 AAAAAAAAATTTC
71110112 AAAAAAAAA
1 AAAAAAAAA
71110121 CAAATCTGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.17
Consensus pattern (13 bp):
AAAAAAAAATTTC
Found at i:71110526 original size:20 final size:20
Alignment explanation
Indices: 71110483--71110526 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
71110473 TGTGGTAAGG
* ** *
71110483 TATTCATTTTTGTTTTGTTT
1 TATTCATTTTTCTTTTCATC
71110503 TATTCATTTTTCTTTTCATC
1 TATTCATTTTTCTTTTCATC
71110523 TATT
1 TATT
71110527 AATCATGTCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.11, G:0.05, T:0.70
Consensus pattern (20 bp):
TATTCATTTTTCTTTTCATC
Found at i:71111195 original size:30 final size:28
Alignment explanation
Indices: 71111159--71111214 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
71111149 AAGCGAAAAA
* *
71111159 GAAAAAGAGTGTGTGCAAGAAAGTAAAGTT
1 GAAAAAGAGAGTGAGCAA-AAAG-AAAGTT
71111189 GAAAAAGAGAGTGAGCAAAAAGAAAG
1 GAAAAAGAGAGTGAGCAAAAAGAAAG
71111215 CGTGGAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 4 0.17
30 16 0.67
ACGTcount: A:0.54, C:0.04, G:0.30, T:0.12
Consensus pattern (28 bp):
GAAAAAGAGAGTGAGCAAAAAGAAAGTT
Found at i:71114736 original size:29 final size:29
Alignment explanation
Indices: 71114703--71114762 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
71114693 ATAACCAAAC
* *
71114703 CTACAAAAACTTTATATCCATAAATCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
71114732 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
71114761 CT
1 CT
71114763 TTGAATCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:71114755 original size:15 final size:15
Alignment explanation
Indices: 71114709--71114756 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
71114699 AAACCTACAA
*
71114709 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
71114724 AAA-TCCATCTACAT
1 AAACTTCATATCCAT
71114738 AAACTTCATATCCAT
1 AAACTTCATATCCAT
71114753 AAAC
1 AAAC
71114757 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:71115308 original size:30 final size:31
Alignment explanation
Indices: 71115254--71115313 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
71115244 CTTTTGTTTC
* *
71115254 AATTTCTTTTTCATCTTTTTTTTCACTCTCA
1 AATTTCTTTTTCATCTTCTTTTTCAATCTCA
**
71115285 AATTTCTTTTTGTTC-TCTTTTTCAATCTC
1 AATTTCTTTTTCATCTTCTTTTTCAATCTC
71115314 TTTTTAATCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 12 0.48
31 13 0.52
ACGTcount: A:0.15, C:0.22, G:0.02, T:0.62
Consensus pattern (31 bp):
AATTTCTTTTTCATCTTCTTTTTCAATCTCA
Found at i:71115313 original size:12 final size:12
Alignment explanation
Indices: 71115298--71115331 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
71115288 TTCTTTTTGT
71115298 TCTCTTTTTCAA
1 TCTCTTTTTCAA
71115310 TCTCTTTTT-AA
1 TCTCTTTTTCAA
*
71115321 TCTCATTTTCA
1 TCTCTTTTTCA
71115332 TTTTCATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.18, C:0.24, G:0.00, T:0.59
Consensus pattern (12 bp):
TCTCTTTTTCAA
Found at i:71115426 original size:5 final size:5
Alignment explanation
Indices: 71115416--71115472 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
71115406 CTCTTGCCTC
*
71115416 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
71115463 TCTTT TCTTT
1 TCTTT TCTTT
71115473 ATTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:71115456 original size:15 final size:14
Alignment explanation
Indices: 71115416--71115472 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
71115406 CTCTTGCCTC
*
71115416 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
71115431 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
71115446 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
71115463 TCTTTTCTTT
1 TCTTTTCTTT
71115473 ATTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:71115482 original size:21 final size:20
Alignment explanation
Indices: 71115414--71115483 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 20
71115404 GCCTCTTGCC
71115414 TCTCTTTTCTTTTTATTTCATTT
1 TCTCTTTTC-TTTT-TTT-ATTT
**
71115437 TCT-TTTTCTTCTTTTGCTTT
1 TCTCTTTTCTT-TTTTTATTT
71115457 T-TCTTTTCTTTTCTTTATTT
1 TCTCTTTTCTTTT-TTTATTT
71115477 TCTCTTT
1 TCTCTTT
71115484 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
19 3 0.08
20 17 0.44
21 9 0.23
22 7 0.18
23 3 0.08
ACGTcount: A:0.04, C:0.19, G:0.01, T:0.76
Consensus pattern (20 bp):
TCTCTTTTCTTTTTTTATTT
Found at i:71118574 original size:26 final size:26
Alignment explanation
Indices: 71118521--71118575 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
71118511 TTAGTATGTT
*
71118521 TTTTAATGTATCTAGTGAGGATATAA
1 TTTTAATGTATCTAGTGAGGACATAA
* *
71118547 TTTTAATGTGTCTAGTTTAGGACA-AA
1 TTTTAATGTATCTAG-TGAGGACATAA
71118573 TTT
1 TTT
71118576 ATTAGCTGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 19 0.76
27 6 0.24
ACGTcount: A:0.31, C:0.05, G:0.18, T:0.45
Consensus pattern (26 bp):
TTTTAATGTATCTAGTGAGGACATAA
Found at i:71120299 original size:17 final size:17
Alignment explanation
Indices: 71120277--71120318 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
71120267 TCTTTTAGAG
71120277 GGTGCATGGACAGCT-AA
1 GGTGCATGGACA-CTCAA
71120294 GGTGCATGGACACTCAA
1 GGTGCATGGACACTCAA
*
71120311 GATGCATG
1 GGTGCATG
71120319 AATCGGTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 2 0.09
17 21 0.91
ACGTcount: A:0.29, C:0.19, G:0.33, T:0.19
Consensus pattern (17 bp):
GGTGCATGGACACTCAA
Found at i:71122319 original size:20 final size:20
Alignment explanation
Indices: 71122292--71122329 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
71122282 AGACACATTA
71122292 ATAAACATATAAT-TAAATT
1 ATAAACATATAATATAAATT
*
71122311 ATAACACATTTAATATAAA
1 ATAA-ACATATAATATAAA
71122330 CTTAGCTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 8 0.50
21 4 0.25
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (20 bp):
ATAAACATATAATATAAATT
Found at i:71122541 original size:20 final size:20
Alignment explanation
Indices: 71122488--71122533 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
71122478 GCTGAAATGA
*
71122488 AGCTAAAATGAGCTCAATCG
1 AGCTGAAATGAGCTCAATCG
*
71122508 AGCTGAAATAAGCTCAAGT-G
1 AGCTGAAATGAGCTCAA-TCG
71122528 AGCTGA
1 AGCTGA
71122534 TTTGAGCTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (20 bp):
AGCTGAAATGAGCTCAATCG
Found at i:71122552 original size:30 final size:31
Alignment explanation
Indices: 71122472--71122553 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
71122462 GAAATTAAGT
*
71122472 AATTGAGCTGAAATGAAGCTAAAATGAGCTC
1 AATTGAGCTGAAATGAAGCTCAAATGAGCTC
* * *
71122503 AATCGAGCTGAAAT-AAGCTCAAGTGAGCTG
1 AATTGAGCTGAAATGAAGCTCAAATGAGCTC
* *
71122533 ATTTGAGCTG-AATGGAGCTCA
1 AATTGAGCTGAAATGAAGCTCA
71122554 GGGAGCTAGA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 3 0.07
30 27 0.63
31 13 0.30
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.23
Consensus pattern (31 bp):
AATTGAGCTGAAATGAAGCTCAAATGAGCTC
Found at i:71122860 original size:29 final size:29
Alignment explanation
Indices: 71122794--71122850 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
71122784 GATTCAAAGA
*
71122794 TGGGTTTATGGATATGAAGTTTATGTAGT
1 TGGGTTTATGGATATAAAGTTTATGTAGT
*
71122823 TGGGTTTATGGATATAAAGTTTTTGTAG
1 TGGGTTTATGGATATAAAGTTTATGTAG
71122851 GTTTGGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.46
Consensus pattern (29 bp):
TGGGTTTATGGATATAAAGTTTATGTAGT
Found at i:71126037 original size:30 final size:28
Alignment explanation
Indices: 71125984--71126039 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
71125974 TTCTTCCACG
* *
71125984 CTTTCTTTTTGCTCACTCTCTTTTTCAA
1 CTTTCTTTTTGCACACACTCTTTTTCAA
71126012 CTTTACTTTCTTGCACACACTCTTTTTC
1 CTTT-CTTT-TTGCACACACTCTTTTTC
71126040 TTTTTCGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 4 0.17
30 16 0.67
ACGTcount: A:0.12, C:0.30, G:0.04, T:0.54
Consensus pattern (28 bp):
CTTTCTTTTTGCACACACTCTTTTTCAA
Found at i:71127416 original size:29 final size:29
Alignment explanation
Indices: 71127350--71127406 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
71127340 GATTCAAAGA
*
71127350 TGGGTTTATGGATATGAAGTTTATGTAGT
1 TGGGTTTATGGATATAAAGTTTATGTAGT
*
71127379 TGGGTTTATGGATATAAAGTTTTTGTAG
1 TGGGTTTATGGATATAAAGTTTATGTAG
71127407 GTTTGGTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.46
Consensus pattern (29 bp):
TGGGTTTATGGATATAAAGTTTATGTAGT
Found at i:71131691 original size:19 final size:19
Alignment explanation
Indices: 71131664--71131754 Score: 66
Period size: 19 Copynumber: 4.9 Consensus size: 19
71131654 TTATTCCAGC
*
71131664 AACTAAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
*
71131683 AACTTAATTAACTAACATG
1 AACTTAATTAACTAAGATG
* * *
71131702 AA--TAATTTATTCCAGCAT-
1 AACTTAATTAACT-AAG-ATG
71131720 --CTTAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
* *
71131737 AACTCAATTAAGTAAGAT
1 AACTTAATTAACTAAGAT
71131755 AAGTAATTTA
Statistics
Matches: 54, Mismatches: 11, Indels: 14
0.68 0.14 0.18
Matches are distributed among these distances:
16 2 0.04
17 9 0.17
18 8 0.15
19 35 0.65
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.32
Consensus pattern (19 bp):
AACTTAATTAACTAAGATG
Found at i:71131714 original size:54 final size:54
Alignment explanation
Indices: 71131654--71131782 Score: 188
Period size: 54 Copynumber: 2.4 Consensus size: 54
71131644 CATCATTAAA
* *
71131654 TTATTCCAGCAACTAAATTAACTAAGATGAACTTAATTAACTAACATGAA-TAAT
1 TTATTCCAGCAACTTAATTAACTAAGATGAACTCAATTAACTAACAT-AAGTAAT
* * *
71131708 TTATTCCAGCATCTTAATTAACTAAGATGAACTCAATTAAGTAAGATAAGTAAT
1 TTATTCCAGCAACTTAATTAACTAAGATGAACTCAATTAACTAACATAAGTAAT
*
71131762 TTATTCCAGCAATTTAATTAA
1 TTATTCCAGCAACTTAATTAA
71131783 TTAAACTAAG
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
53 2 0.03
54 65 0.97
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (54 bp):
TTATTCCAGCAACTTAATTAACTAAGATGAACTCAATTAACTAACATAAGTAAT
Found at i:71136796 original size:12 final size:12
Alignment explanation
Indices: 71136767--71136803 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
71136757 TTATACAAGT
*
71136767 TTGAAAAAAAAT
1 TTGAAAAAAAAA
71136779 TCTGAAAAAAAAA
1 T-TGAAAAAAAAA
71136792 TTGAAAAAAAAA
1 TTGAAAAAAAAA
71136804 AGTGATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.70, C:0.03, G:0.08, T:0.19
Consensus pattern (12 bp):
TTGAAAAAAAAA
Found at i:71139930 original size:19 final size:19
Alignment explanation
Indices: 71139906--71139945 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
71139896 AGCTCCCATG
71139906 TAGCTC-CACACCAGCTCAT
1 TAGCTCGCA-ACCAGCTCAT
*
71139925 TAGCTCGGAACCAGCTCAT
1 TAGCTCGCAACCAGCTCAT
71139944 TA
1 TA
71139946 TCAGCTCACG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.28, C:0.35, G:0.15, T:0.23
Consensus pattern (19 bp):
TAGCTCGCAACCAGCTCAT
Found at i:71150662 original size:11 final size:10
Alignment explanation
Indices: 71150646--71150690 Score: 63
Period size: 10 Copynumber: 4.2 Consensus size: 10
71150636 ATACAAGTTA
71150646 AAAAAAATTCG
1 AAAAAAATT-G
71150657 AAAAAAAATTG
1 -AAAAAAATTG
71150668 AAAAAAATTTG
1 AAAAAAA-TTG
71150679 AAAAAAATTG
1 AAAAAAATTG
71150689 AA
1 AA
71150691 GTGAAAACTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 12 0.38
11 11 0.34
12 9 0.28
ACGTcount: A:0.69, C:0.02, G:0.09, T:0.20
Consensus pattern (10 bp):
AAAAAAATTG
Found at i:71150662 original size:12 final size:11
Alignment explanation
Indices: 71150645--71150690 Score: 67
Period size: 11 Copynumber: 4.2 Consensus size: 11
71150635 TATACAAGTT
71150645 AAAAAAAATTCG
1 AAAAAAAATT-G
71150657 AAAAAAAATTG
1 AAAAAAAATTG
*
71150668 AAAAAAATTTG
1 AAAAAAAATTG
71150679 -AAAAAAATTG
1 AAAAAAAATTG
71150689 AA
1 AA
71150691 GTGAAAACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
10 9 0.29
11 12 0.39
12 10 0.32
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.20
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:71150671 original size:21 final size:21
Alignment explanation
Indices: 71150646--71150690 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
71150636 ATACAAGTTA
71150646 AAAAAAATTCGAAAAAAAATTG
1 AAAAAAATTCG-AAAAAAATTG
*
71150668 AAAAAAATTTGAAAAAAATTG
1 AAAAAAATTCGAAAAAAATTG
71150689 AA
1 AA
71150691 GTGAAAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.69, C:0.02, G:0.09, T:0.20
Consensus pattern (21 bp):
AAAAAAATTCGAAAAAAATTG
Found at i:71153565 original size:30 final size:30
Alignment explanation
Indices: 71153531--71153591 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
71153521 TCCTTAACTC
71153531 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
71153561 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
71153591 A
1 A
71153592 GGCTCAGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:71155180 original size:16 final size:14
Alignment explanation
Indices: 71155159--71155227 Score: 66
Period size: 16 Copynumber: 4.4 Consensus size: 14
71155149 ACATTCTTGT
71155159 AAAAGAGAAAACAAAG
1 AAAAGA-AAAA-AAAG
71155175 AAAAGAAAAGAAAAAG
1 AAAAG-AAA-AAAAAG
*
71155191 CAAAAGAAGAAAAAG
1 -AAAAGAAAAAAAAG
71155206 AAAACGAAATAAAAAG
1 AAAA-GAAA-AAAAAG
71155222 AAAAGA
1 AAAAGA
71155228 GAGGCAAGAG
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
14 4 0.09
15 11 0.24
16 23 0.50
17 8 0.17
ACGTcount: A:0.77, C:0.04, G:0.17, T:0.01
Consensus pattern (14 bp):
AAAAGAAAAAAAAG
Found at i:71155185 original size:21 final size:20
Alignment explanation
Indices: 71155159--71155229 Score: 74
Period size: 20 Copynumber: 3.4 Consensus size: 20
71155149 ACATTCTTGT
71155159 AAAAGAGAAAACAAAGAAAAG
1 AAAAGAGAAAACAAA-AAAAG
*
71155180 AAAAGA-AAAAGCAAAAGAAG
1 AAAAGAGAAAA-CAAAAAAAG
71155200 AAAA-AGAAAACGAAATAAAAAG
1 AAAAGAGAAAAC--AA-AAAAAG
71155222 AAAAGAGA
1 AAAAGAGA
71155230 GGCAAGAGGC
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
19 2 0.05
20 16 0.38
21 12 0.29
22 9 0.21
23 3 0.07
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.01
Consensus pattern (20 bp):
AAAAGAGAAAACAAAAAAAG
Found at i:71155195 original size:6 final size:5
Alignment explanation
Indices: 71155171--71155227 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
71155161 AAGAGAAAAC
*
71155171 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAACGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
71155218 AAAGA AAAGA
1 AAAGA AAAGA
71155228 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:71155300 original size:6 final size:6
Alignment explanation
Indices: 71155289--71155317 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
71155279 AAAAGCCTTT
71155289 GAAAAA GAAAAA GAAAAA GAAAAA GAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAA
71155318 TGAGATTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:71155328 original size:12 final size:12
Alignment explanation
Indices: 71155313--71155352 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
71155303 AAAAGAAAAA
*
71155313 GAAAATGAGATT
1 GAAAAAGAGATT
*
71155325 GAAAAAGAGAAT
1 GAAAAAGAGATT
*
71155337 GAAAAAGAGTTT
1 GAAAAAGAGATT
71155349 GAAA
1 GAAA
71155353 GAGAAAAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.25, T:0.17
Consensus pattern (12 bp):
GAAAAAGAGATT
Found at i:71155328 original size:18 final size:18
Alignment explanation
Indices: 71155287--71155340 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
71155277 GAAAAAGCCT
*
71155287 TTGAAAAAGAAAAAGAAA
1 TTGAAAAAGAAAATGAAA
** *
71155305 AAGAAAAAGAAAATGAGA
1 TTGAAAAAGAAAATGAAA
*
71155323 TTGAAAAAGAGAATGAAA
1 TTGAAAAAGAAAATGAAA
71155341 AAGAGTTTGA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.69, C:0.00, G:0.20, T:0.11
Consensus pattern (18 bp):
TTGAAAAAGAAAATGAAA
Found at i:71155350 original size:24 final size:24
Alignment explanation
Indices: 71155301--71155363 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
71155291 AAAAGAAAAA
*
71155301 GAAAAAGAAAAAGAAAATGAGATT
1 GAAAAAGAAAAAGAAAAAGAGATT
* * *
71155325 GAAAAAGAGAATGAAAAAGAGTTT
1 GAAAAAGAAAAAGAAAAAGAGATT
*
71155349 GAAAGAGAAAAAGAA
1 GAAAAAGAAAAAGAA
71155364 TGTGAACAAG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.65, C:0.00, G:0.24, T:0.11
Consensus pattern (24 bp):
GAAAAAGAAAAAGAAAAAGAGATT
Found at i:71155392 original size:18 final size:19
Alignment explanation
Indices: 71155350--71155394 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
71155340 AAAGAGTTTG
71155350 AAAGAGAAAAAGAATGTGAA
1 AAAGA-AAAAAGAATGTGAA
* *
71155370 CAAGAAAAAAGAGTG-GAA
1 AAAGAAAAAAGAATGTGAA
71155388 AAAGAAA
1 AAAGAAA
71155395 TTGAGTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 9 0.41
19 9 0.41
20 4 0.18
ACGTcount: A:0.67, C:0.02, G:0.24, T:0.07
Consensus pattern (19 bp):
AAAGAAAAAAGAATGTGAA
Found at i:71159268 original size:12 final size:14
Alignment explanation
Indices: 71159240--71159275 Score: 58
Period size: 12 Copynumber: 2.7 Consensus size: 14
71159230 ATACAAGTTT
71159240 GAAAAAAAAATTCC
1 GAAAAAAAAATTCC
71159254 GAAAAAAAAA-T-C
1 GAAAAAAAAATTCC
71159266 GAAAAAAAAA
1 GAAAAAAAAA
71159276 GTGATTTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 11 0.50
13 1 0.05
14 10 0.45
ACGTcount: A:0.75, C:0.08, G:0.08, T:0.08
Consensus pattern (14 bp):
GAAAAAAAAATTCC
Found at i:71168063 original size:46 final size:46
Alignment explanation
Indices: 71167994--71168121 Score: 193
Period size: 46 Copynumber: 2.8 Consensus size: 46
71167984 GATATTTGGG
* *
71167994 CATCCGAGCTTGTTGAGTCGAGTCCGAGTTCACTTATGGATGCGAA
1 CATCCGAGCTAGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
** *
71168040 TGTCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
1 CATCCGAGCTAGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
* *
71168086 CATCTGAGCTAGTTGAGTTGAGTCCTAGTTCACTTA
1 CATCCGAGCTAGTTGAGTTGAGTCCGAGTTCACTTA
71168122 CGGGCAGGTT
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 73 1.00
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.31
Consensus pattern (46 bp):
CATCCGAGCTAGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
Found at i:71170881 original size:19 final size:20
Alignment explanation
Indices: 71170845--71170882 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
71170835 TATCTTGCTC
*
71170845 AATTCAGCTCATTTGAGCTT
1 AATTCAGCTCAGTTGAGCTT
71170865 AATTCAGCTC-GTTGAGCT
1 AATTCAGCTCAGTTGAGCT
71170883 AGATTTAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (20 bp):
AATTCAGCTCAGTTGAGCTT
Found at i:71177542 original size:21 final size:20
Alignment explanation
Indices: 71177505--71177554 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
71177495 ATCAGCTCAC
71177505 TTGAGCTCAATTCAGCTCGT
1 TTGAGCTCAATTCAGCTCGT
* * *
71177525 TTGAGTTCGAATTTAGCTTGT
1 TTGAGCTC-AATTCAGCTCGT
*
71177546 TTCAGCTCA
1 TTGAGCTCA
71177555 TTCCTACTAC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (20 bp):
TTGAGCTCAATTCAGCTCGT
Found at i:71180467 original size:18 final size:17
Alignment explanation
Indices: 71180446--71180502 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
71180436 TTTTTCAAAC
71180446 TCATTTTCTTTTCTTTCT
1 TCATTTTCTTTTCTTT-T
* * *
71180464 TCATTCTCACTCTCTTTT
1 TCATTTTC-TTTTCTTTT
*
71180482 TCAATTTTCTTTTCTTGT
1 TC-ATTTTCTTTTCTTTT
71180500 TCA
1 TCA
71180503 CATTCTTTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
17 1 0.03
18 18 0.60
19 11 0.37
ACGTcount: A:0.11, C:0.25, G:0.02, T:0.63
Consensus pattern (17 bp):
TCATTTTCTTTTCTTTT
Found at i:71183895 original size:16 final size:15
Alignment explanation
Indices: 71183874--71183918 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
71183864 ATATATTGAA
*
71183874 AAAAATAAAAGAATT
1 AAAAATAAAAGAAAT
*
71183889 CAAAAATAAAAAAAAT
1 -AAAAATAAAAGAAAT
*
71183905 AAAAAAAAAAGAAA
1 AAAAATAAAAGAAA
71183919 AAGAAGTGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.82, C:0.02, G:0.04, T:0.11
Consensus pattern (15 bp):
AAAAATAAAAGAAAT
Found at i:71184321 original size:10 final size:10
Alignment explanation
Indices: 71184308--71184353 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
71184298 AGCTCACTTG
71184308 AGCTCGTTTT
1 AGCTCGTTTT
* *
71184318 AGCTTGTTTG
1 AGCTCGTTTT
*
71184328 AGCTCGAATTT
1 AGCTCG-TTTT
71184339 AGCTCGTTTT
1 AGCTCGTTTT
71184349 AGCTC
1 AGCTC
71184354 ATTCCTTTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
10 21 0.72
11 8 0.28
ACGTcount: A:0.15, C:0.20, G:0.22, T:0.43
Consensus pattern (10 bp):
AGCTCGTTTT
Found at i:71184341 original size:21 final size:20
Alignment explanation
Indices: 71184305--71184353 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
71184295 ATCAGCTCAC
* *
71184305 TTGAGCTCGTTTTAGCTTGT
1 TTGAGCTCGATTTAGCTCGT
71184325 TTGAGCTCGAATTTAGCTCGT
1 TTGAGCTCG-ATTTAGCTCGT
*
71184346 TTTAGCTC
1 TTGAGCTC
71184354 ATTCCTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.14, C:0.18, G:0.22, T:0.45
Consensus pattern (20 bp):
TTGAGCTCGATTTAGCTCGT
Found at i:71186579 original size:18 final size:18
Alignment explanation
Indices: 71186556--71186628 Score: 59
Period size: 18 Copynumber: 4.4 Consensus size: 18
71186546 GAAAGAAAAA
71186556 GAAAAAGAGATTGAGAGT
1 GAAAAAGAGATTGAGAGT
* * *
71186574 GAAAAAGAAAATGAGATT
1 GAAAAAGAGATTGAGAGT
71186592 GAAAAA-A-A--GA-A-T
1 GAAAAAGAGATTGAGAGT
* *
71186604 GAAAAAGAGTTTGAGAGA
1 GAAAAAGAGATTGAGAGT
71186622 GAAAAAG
1 GAAAAAG
71186629 CATGTGAACA
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
12 7 0.16
13 2 0.05
14 2 0.05
16 3 0.07
17 2 0.05
18 28 0.64
ACGTcount: A:0.59, C:0.00, G:0.27, T:0.14
Consensus pattern (18 bp):
GAAAAAGAGATTGAGAGT
Found at i:71186582 original size:24 final size:24
Alignment explanation
Indices: 71186549--71186628 Score: 92
Period size: 24 Copynumber: 3.3 Consensus size: 24
71186539 AAGAAATGAA
71186549 AGAAAAAGAAAAAGAGATTGAGAG
1 AGAAAAAGAAAAAGAGATTGAGAG
* *
71186573 TGAAAAAGAAAATGAGATTGA-A-
1 AGAAAAAGAAAAAGAGATTGAGAG
* *
71186595 AAAAAGAATGAAAAAGAGTTTGAGAG
1 AGAAA-AA-GAAAAAGAGATTGAGAG
71186621 AGAAAAAG
1 AGAAAAAG
71186629 CATGTGAACA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
22 3 0.07
23 3 0.07
24 32 0.71
25 3 0.07
26 4 0.09
ACGTcount: A:0.61, C:0.00, G:0.26, T:0.12
Consensus pattern (24 bp):
AGAAAAAGAAAAAGAGATTGAGAG
Found at i:71191254 original size:13 final size:13
Alignment explanation
Indices: 71191236--71191260 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
71191226 TAACCTACAA
71191236 AATTAAATAACAT
1 AATTAAATAACAT
71191249 AATTAAATAACA
1 AATTAAATAACA
71191261 CACAACTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (13 bp):
AATTAAATAACAT
Found at i:71191518 original size:10 final size:10
Alignment explanation
Indices: 71191485--71191533 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
71191475 AAAAAGGAAT
*
71191485 GAGCTGAAAC
1 GAGCTCAAAC
71191495 GAGCT-AAATTC
1 GAGCTCAAA--C
71191506 GAGCTCAAAC
1 GAGCTCAAAC
*
71191516 GAGCTAAAAC
1 GAGCTCAAAC
71191526 GAGCTCAA
1 GAGCTCAA
71191534 GTGAGCTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 3 0.09
10 22 0.65
11 6 0.18
12 3 0.09
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:71191540 original size:20 final size:21
Alignment explanation
Indices: 71191485--71191533 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
71191475 AAAAAGGAAT
* *
71191485 GAGCTGAAACGAGCTAAATTC
1 GAGCTCAAACGAGCTAAATAC
71191506 GAGCTCAAACGAGCTAAA-AC
1 GAGCTCAAACGAGCTAAATAC
71191526 GAGCTCAA
1 GAGCTCAA
71191534 GTGAGCTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.14
Consensus pattern (21 bp):
GAGCTCAAACGAGCTAAATAC
Done.