Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007884.1 Hibiscus syriacus cultivar Beakdansim tig00110264_pilon, whole genome shotgun sequence
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: 2814991
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 13
Found at i:478109 original size:14 final size:14
Alignment explanation
Indices: 478090--478174 Score: 62
Period size: 14 Copynumber: 5.4 Consensus size: 14
478080 TTTCATTTCG
478090 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
478104 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
478123 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
478137 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
478156 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
478170 CGTTG
1 CGTTG
478175 AGATAGTCAT
Statistics
Matches: 57, Mismatches: 4, Indels: 20
0.70 0.05 0.25
Matches are distributed among these distances:
14 25 0.44
16 6 0.11
17 6 0.11
19 20 0.35
ACGTcount: A:0.08, C:0.25, G:0.22, T:0.45
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:478119 original size:33 final size:33
Alignment explanation
Indices: 478077--478199 Score: 210
Period size: 33 Copynumber: 3.7 Consensus size: 33
478067 TGTTTGGATA
478077 GATTTTCATTTCGCGTTGCGATTCTCTCGTTGC
1 GATTTTCATTTCGCGTTGCGATTCTCTCGTTGC
478110 GATTTTCATTTCGCGTTGCGATTCTCTCGTTGC
1 GATTTTCATTTCGCGTTGCGATTCTCTCGTTGC
*
478143 GATTTTCATTTCGCGTTGCGATTCTCTCGTTGA
1 GATTTTCATTTCGCGTTGCGATTCTCTCGTTGC
**
478176 GATAGTCATTTCCGCGTTGCGATT
1 GATTTTCATTT-CGCGTTGCGATT
478200 TTCATTCTCT
Statistics
Matches: 86, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
33 74 0.86
34 12 0.14
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.44
Consensus pattern (33 bp):
GATTTTCATTTCGCGTTGCGATTCTCTCGTTGC
Found at i:480257 original size:21 final size:21
Alignment explanation
Indices: 480233--480299 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
480223 TCATTCCTCG
480233 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
480254 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
480275 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
480296 AGAG
1 AGAG
480300 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:480257 original size:42 final size:42
Alignment explanation
Indices: 480181--480299 Score: 102
Period size: 42 Copynumber: 2.8 Consensus size: 42
480171 GAATCGTCTG
* * * *
480181 TCATCCCTC-AAGA-GTCCACTCCTATCATTGAAGAGGCCCCTA
1 TCAT-CCTCGAAGAGGTCC-CTCCCACCATTCAAGAGGCCACTA
* *
480223 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCA-TCCTCGAAGAGGT-CCCTCCCACCATTCAAGAGGCCACTA
* *
480265 TCATCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 TCATCCTCGAAGAGGTCCCTCCCACCATTCAAGAG
480300 CCCGATTCAC
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
41 4 0.06
42 54 0.86
43 5 0.08
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATCCTCGAAGAGGTCCCTCCCACCATTCAAGAGGCCACTA
Found at i:481885 original size:19 final size:19
Alignment explanation
Indices: 481777--481878 Score: 177
Period size: 19 Copynumber: 5.4 Consensus size: 19
481767 AAAACAGACT
*
481777 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
481796 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
481815 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
481834 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
481853 ATCGCAATGTGAAATAAAA
1 ATCGCAATGCGAAATGAAA
481872 ATCGCAA
1 ATCGCAA
481879 CACGAAACTA
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 80 1.00
ACGTcount: A:0.48, C:0.17, G:0.20, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:481911 original size:19 final size:19
Alignment explanation
Indices: 481889--482085 Score: 234
Period size: 19 Copynumber: 10.8 Consensus size: 19
481879 CACGAAACTA
*
481889 ATTTCGCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
*
481908 ATTTTCGTATTGCGA--TTC
1 A-TTTCGCATTGCGATTTTC
*
481926 A-CTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
481942 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
* *
481961 ATTTCGCATTGTGATTCTC
1 ATTTCGCATTGCGATTTTC
481980 --TT-G--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
*
481994 ATTTCGCATTGCGATTTTT
1 ATTTCGCATTGCGATTTTC
482013 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
** *
482032 ATTTCGCATTAAGAATTTC
1 ATTTCGCATTGCGATTTTC
482051 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
482070 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
482086 CTCTCATTGC
Statistics
Matches: 151, Mismatches: 16, Indels: 22
0.80 0.08 0.12
Matches are distributed among these distances:
14 15 0.10
16 10 0.07
17 6 0.04
18 4 0.03
19 105 0.70
20 11 0.07
ACGTcount: A:0.16, C:0.19, G:0.17, T:0.48
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Found at i:481988 original size:52 final size:52
Alignment explanation
Indices: 481889--482138 Score: 275
Period size: 52 Copynumber: 4.7 Consensus size: 52
481879 CACGAAACTA
* * *
481889 ATTTCGCGTTGCGATTTTCATTTTCGTATTGCGATTCACTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCA-TTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* *
481942 ATTTCGCATTGCGATTTTCATTTCGCATTGTGATTCTCTTGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* * ** *
481994 ATTTCGCATTGCGATTTTTATTTCGCATTGCGATTTTCATTTCGCATTAAGAATTTC
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTC
* **
482051 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCATTGCGATAGTC
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* ** *
482103 ATTTCCGCGTTGCGATAGTCAATTCCGCATTGCGAT
1 ATTT-CGCATTGCGATTTTC-ATTTCGCATTGCGAT
482139 AGTCAAATGA
Statistics
Matches: 166, Mismatches: 24, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
52 69 0.42
53 31 0.19
54 20 0.12
55 6 0.04
57 40 0.24
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.45
Consensus pattern (52 bp):
ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:482117 original size:20 final size:20
Alignment explanation
Indices: 482090--482144 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
482080 GCGATTCTCT
*
482090 CATTGCGATAGTCATTTCCG
1 CATTGCGATAGTCAATTCCG
*
482110 CGTTGCGATAGTCAATTCCG
1 CATTGCGATAGTCAATTCCG
482130 CATTGCGATAGTCAA
1 CATTGCGATAGTCAA
482145 ATGAATGTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.31
Consensus pattern (20 bp):
CATTGCGATAGTCAATTCCG
Found at i:483778 original size:24 final size:24
Alignment explanation
Indices: 483744--483797 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
483734 CTGAAAAATC
483744 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
483768 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
483792 ATCAAA
1 ATCAAA
483798 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:484678 original size:20 final size:19
Alignment explanation
Indices: 484655--484919 Score: 190
Period size: 20 Copynumber: 13.2 Consensus size: 19
484645 ATCTCGTTGT
*
484655 GATTTACAGATTCGCATTGC
1 GATTTAC-GATACGCATTGC
*
484675 GATTTACGTATTCGCATTGC
1 GATTTACG-ATACGCATTGC
* *
484695 GATTTACGTATTCGCATTAC
1 GATTTACG-ATACGCATTGC
*
484715 GATTTACAGATACGTATTGC
1 GATTTAC-GATACGCATTGC
*
484735 GATTTACGGATACGTATTGC
1 GATTTAC-GATACGCATTGC
*
484755 GATTTACAGATACGCGTTGC
1 GATTTAC-GATACGCATTGC
* * *
484775 GATTTACGTATTCTCTTTGC
1 GATTTACG-ATACGCATTGC
*
484795 GATTTACGGATACGCGTTGC
1 GATTTAC-GATACGCATTGC
* * *
484815 GATTTACGTATTCTCTTTGC
1 GATTTACG-ATACGCATTGC
* *
484835 TATTTACGGATACGCGTTGC
1 GATTTAC-GATACGCATTGC
* *
484855 GATTTTACG-TATTGTCGTTGC
1 GA-TTTACGATA-CG-CATTGC
*
484876 GATTTACGGATACGCGTTGC
1 GATTTAC-GATACGCATTGC
* *
484896 GATTTTACGGATACTCGTTGC
1 GA-TTTAC-GATACGCATTGC
484917 GAT
1 GAT
484920 AGTCAGAATC
Statistics
Matches: 208, Mismatches: 25, Indels: 24
0.81 0.10 0.09
Matches are distributed among these distances:
19 5 0.02
20 164 0.79
21 37 0.18
22 2 0.01
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.38
Consensus pattern (19 bp):
GATTTACGATACGCATTGC
Found at i:484699 original size:40 final size:40
Alignment explanation
Indices: 484649--484900 Score: 301
Period size: 40 Copynumber: 6.3 Consensus size: 40
484639 GTCAGAATCT
* * *
484649 CGTTGTGATTTACAG-ATTCGCATTGCGATTTACGTATTCG
1 CGTTGCGATTTAC-GTATTCGCATTGCGATTTACGGATACG
* * *
484689 CATTGCGATTTACGTATTCGCATTACGATTTACAGATACG
1 CGTTGCGATTTACGTATTCGCATTGCGATTTACGGATACG
** * * * *
484729 TATTGCGATTTACGGATACGTATTGCGATTTACAGATACG
1 CGTTGCGATTTACGTATTCGCATTGCGATTTACGGATACG
* *
484769 CGTTGCGATTTACGTATTCTCTTTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATTCGCATTGCGATTTACGGATACG
* * *
484809 CGTTGCGATTTACGTATTCTCTTTGCTATTTACGGATACG
1 CGTTGCGATTTACGTATTCGCATTGCGATTTACGGATACG
*
484849 CGTTGCGATTTTACGTATT-GTCGTTGCGATTTACGGATACG
1 CGTTGCGA-TTTACGTATTCG-CATTGCGATTTACGGATACG
484890 CGTTGCGATTT
1 CGTTGCGATTT
484901 TACGGATACT
Statistics
Matches: 186, Mismatches: 23, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
39 1 0.01
40 149 0.80
41 36 0.19
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (40 bp):
CGTTGCGATTTACGTATTCGCATTGCGATTTACGGATACG
Found at i:484725 original size:60 final size:60
Alignment explanation
Indices: 484655--484919 Score: 230
Period size: 60 Copynumber: 4.4 Consensus size: 60
484645 ATCTCGTTGT
* * * *
484655 GATTTACAGATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTAC
1 GATTTACAGATACGCATTGCGATTTACGGATACGCATTGCGATTTACGTATTCGCATTGC
* * * *
484715 GATTTACAGATACGTATTGCGATTTACGGATACGTATTGCGATTTACAG-ATACGCGTTGC
1 GATTTACAGATACGCATTGCGATTTACGGATACGCATTGCGATTTAC-GTATTCGCATTGC
* * * * * *
484775 GATTTAC-GTATTCTCTTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCTCTTTGC
1 GATTTACAG-ATACGCATTGCGATTTACGGATACGCATTGCGATTTACGTATTCGCATTGC
* * * * * * * * *
484835 TATTTACGGATACGCGTTGCGATTTTACGTAT-TGTCGTTGCGATTTACGGATACGCGTTGC
1 GATTTACAGATACGCATTGCGA-TTTACGGATACG-CATTGCGATTTACGTATTCGCATTGC
* * *
484896 GATTTTACGGATACTCGTTGCGAT
1 GA-TTTACAGATACGCATTGCGAT
484920 AGTCAGAATC
Statistics
Matches: 169, Mismatches: 29, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
59 2 0.01
60 114 0.67
61 34 0.20
62 19 0.11
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.38
Consensus pattern (60 bp):
GATTTACAGATACGCATTGCGATTTACGGATACGCATTGCGATTTACGTATTCGCATTGC
Found at i:484954 original size:20 final size:20
Alignment explanation
Indices: 484931--484976 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
484921 GTCAGAATCA
*
484931 CGTTGCGATTTAT-ATGTTCG
1 CGTTGCGATTT-TCATATTCG
*
484951 CGTTACGATTTTCATATTCG
1 CGTTGCGATTTTCATATTCG
484971 CGTTGC
1 CGTTGC
484977 AATTATGGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.15, C:0.20, G:0.22, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCATATTCG
Found at i:486590 original size:20 final size:20
Alignment explanation
Indices: 486565--486610 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
486555 TGTAAATCGC
486565 AACACATAAGTCAAATTCGA
1 AACACATAAGTCAAATTCGA
*
486585 AACACATAAGTCAAATTCGC
1 AACACATAAGTCAAATTCGA
486605 AACACA
1 AACACA
486611 ATTCGAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.50, C:0.24, G:0.09, T:0.17
Consensus pattern (20 bp):
AACACATAAGTCAAATTCGA
Found at i:487197 original size:20 final size:20
Alignment explanation
Indices: 487162--487215 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
487152 AAATCGCAAC
*
487162 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
*
487181 GCGGTTTTCATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
487201 GCGATTTTCATTTTC
1 GCGATTTTCATTTTC
487216 AGAAACTACT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 7 0.23
20 24 0.77
ACGTcount: A:0.09, C:0.19, G:0.22, T:0.50
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Found at i:488799 original size:39 final size:39
Alignment explanation
Indices: 488745--488819 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
488735 ATACCAGGAG
* *
488745 CCATCACCTGATCGAGCCTCTTCTCCACCATCACCTATT
1 CCATCACATCATCGAGCCTCTTCTCCACCATCACCTATT
488784 CCATCACATCATCGAGCCTCTTCTCCACCATCACCT
1 CCATCACATCATCGAGCCTCTTCTCCACCATCACCT
488820 CATGATAAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.21, C:0.45, G:0.07, T:0.27
Consensus pattern (39 bp):
CCATCACATCATCGAGCCTCTTCTCCACCATCACCTATT
Found at i:489393 original size:21 final size:21
Alignment explanation
Indices: 489339--489454 Score: 117
Period size: 21 Copynumber: 5.5 Consensus size: 21
489329 GATTCACCTT
**
489339 TCATCGTTCAAGAGGCATCTC
1 TCATCGTTCAAGAGGCCCCTC
489360 -CTATCGTTCAAGAGGCCCCTC
1 TC-ATCGTTCAAGAGGCCCCTC
* * *
489381 TCATTGTTTAAGATGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * *
489402 CCACCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTC
*
489423 TCATCGTTCAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* *
489444 CCACCGTTCAA
1 TCATCGTTCAA
489455 AAGCCCGATT
Statistics
Matches: 76, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
20 1 0.01
21 74 0.97
22 1 0.01
ACGTcount: A:0.21, C:0.35, G:0.18, T:0.26
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:489443 original size:42 final size:41
Alignment explanation
Indices: 489339--489454 Score: 142
Period size: 42 Copynumber: 2.8 Consensus size: 41
489329 GATTCACCTT
* * *
489339 TCATCGTTCAAGAGGCATCTCCTATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGC-CCTCCCACCGTTCAAGAGGCCCCTC
* * * *
489381 TCATTGTTTAAGATGCCCCTCCCACCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGA-GGCCCTCCCACCGTTCAAGAGGCCCCTC
489423 TCATCGTTCAAGAGGTCCCTCCCACCGTTCAA
1 TCATCGTTCAAGAGG-CCCTCCCACCGTTCAA
489455 AAGCCCGATT
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
41 1 0.02
42 59 0.95
43 2 0.03
ACGTcount: A:0.21, C:0.35, G:0.18, T:0.26
Consensus pattern (41 bp):
TCATCGTTCAAGAGGCCCTCCCACCGTTCAAGAGGCCCCTC
Found at i:490894 original size:14 final size:14
Alignment explanation
Indices: 490875--490911 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
490865 GCTTGTTTAA
490875 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
490889 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
490903 TTGATTTGT
1 TTGATTTGT
490912 TTAATTGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:490903 original size:78 final size:77
Alignment explanation
Indices: 490782--490974 Score: 304
Period size: 78 Copynumber: 2.5 Consensus size: 77
490772 TGGAGTACAC
*
490782 TTTTTTTGCTTGTTTAATTGAATTT-T-ACA-TTGATTTGTAAAAGTTGATTTGTTTAA-TGTAT
1 TTTTTTTGCTTGTTTAATTG-ATTTGTAAAAGTTGATTTGTAAAAGTTGATTTGTTTAATTG-AT
490843 GAGGAAATAAGAAT
64 GAGGAAATAAGAAT
490857 TATTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTAAAAGTTGATTTGTTTAATTGATG
1 T-TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTAAAAGTTGATTTGTTTAATTGATG
* *
490922 TGTAAATAAGAAT
65 AGGAAATAAGAAT
490935 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGT
1 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGT
490975 TGTTTTAAAT
Statistics
Matches: 110, Mismatches: 3, Indels: 8
0.91 0.02 0.07
Matches are distributed among these distances:
75 5 0.05
76 20 0.18
77 41 0.37
78 42 0.38
79 2 0.02
ACGTcount: A:0.28, C:0.02, G:0.18, T:0.52
Consensus pattern (77 bp):
TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTAAAAGTTGATTTGTTTAATTGATGA
GGAAATAAGAAT
Found at i:491340 original size:19 final size:19
Alignment explanation
Indices: 491280--491391 Score: 84
Period size: 19 Copynumber: 5.7 Consensus size: 19
491270 ACTAAAACCT
* *
491280 GTTGCGAAATT-AAATTCGT
1 GTTGCGAATTTGAAATTC-A
** *
491299 GTTGCGAATTCAAAAATCGA
1 GTTGCGAATTTGAAATTC-A
*
491319 GTTGTGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
491338 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
* *
491357 GTGTTACGAATTTGGAAA-TCGC
1 --GTTGCGAATTT-GAAATTC-A
491379 GTTGCGAATTTGA
1 GTTGCGAATTTGA
491392 CTTCTGTGTT
Statistics
Matches: 76, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
19 30 0.39
20 30 0.39
21 12 0.16
22 4 0.05
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.35
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:491368 original size:21 final size:20
Alignment explanation
Indices: 491280--491470 Score: 96
Period size: 20 Copynumber: 9.6 Consensus size: 20
491270 ACTAAAACCT
*
491280 GTTGCGAAATT-AAATTC-G
1 GTTGCGAATTTGAAATTCAG
** *
491298 TGTTGCGAATTCAAAAATC-G
1 -GTTGCGAATTTGAAATTCAG
*
491318 AGTTGTGAATTTGAAATTCA-
1 -GTTGCGAATTTGAAATTCAG
491338 GTTGCGAATTTGAAATTCAG
1 GTTGCGAATTTGAAATTCAG
*
491358 TGTTACGAATTTGGAAA-TC-G
1 -GTTGCGAATTT-GAAATTCAG
* *
491378 CGTTGCGAATTTG-ACTTCTG
1 -GTTGCGAATTTGAAATTCAG
*
491398 TGTTGCG-ATTTACAAATTC-G
1 -GTTGCGAATTT-GAAATTCAG
* *
491418 CGTTGCGAATTTGGAAA-CCGG
1 -GTTGCGAATTT-GAAATTCAG
* * * *
491439 GTTGCGAAATTGGAGTTCAC
1 GTTGCGAATTTGAAATTCAG
491459 GTTGCGAATTTG
1 GTTGCGAATTTG
491471 TTGGTCATTT
Statistics
Matches: 133, Mismatches: 27, Indels: 23
0.73 0.15 0.13
Matches are distributed among these distances:
18 1 0.01
19 36 0.27
20 68 0.51
21 24 0.18
22 4 0.03
ACGTcount: A:0.27, C:0.13, G:0.25, T:0.35
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCAG
Found at i:491368 original size:40 final size:41
Alignment explanation
Indices: 491324--491430 Score: 123
Period size: 40 Copynumber: 2.7 Consensus size: 41
491314 ATCGAGTTGT
*
491324 GAATTT-GAAATTC-AGTTGCGAATTTGAAATTCAGTGTTAC
1 GAATTTAGAAATTCGCGTTGCGAATTTG-AATTCAGTGTTAC
* * * *
491364 GAATTTGGAAA-TCGCGTTGCGAATTTGACTTCTGTGTTGC
1 GAATTTAGAAATTCGCGTTGCGAATTTGAATTCAGTGTTAC
*
491404 G-ATTTACAAATTCGCGTTGCGAATTTG
1 GAATTTAGAAATTCGCGTTGCGAATTTG
491431 GAAACCGGGT
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
39 7 0.12
40 35 0.60
41 16 0.28
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.37
Consensus pattern (41 bp):
GAATTTAGAAATTCGCGTTGCGAATTTGAATTCAGTGTTAC
Found at i:491376 original size:60 final size:58
Alignment explanation
Indices: 491280--491470 Score: 170
Period size: 60 Copynumber: 3.2 Consensus size: 58
491270 ACTAAAACCT
* *** *
491280 GTTGCGAAATT-AAATTCGTGTTGCGAATTCAAAAATCGAGTTGTGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCGTGTTGCGAATTTGGAAATCGAGTTGCGAATTTG-AATTCA
* * * *
491338 GTTGCGAATTTGAAATTCAGTGTTACGAATTTGGAAATCGCGTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGAAATTC-GTGTTGCGAATTTGGAAATCGAGTTGCGAATTTGAATTC--A
* * * * * *
491399 GTTGCG-ATTTACAAATTCGCGTTGCGAATTTGGAAACCGGGTTGCGAAATTGGAGTTCA
1 GTTGCGAATTT-GAAATTCGTGTTGCGAATTTGGAAATCGAGTTGCG-AATTTGAATTCA
491458 CGTTGCGAATTTG
1 -GTTGCGAATTTG
491471 TTGGTCATTT
Statistics
Matches: 107, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
58 10 0.09
59 10 0.09
60 62 0.58
61 25 0.23
ACGTcount: A:0.27, C:0.13, G:0.25, T:0.35
Consensus pattern (58 bp):
GTTGCGAATTTGAAATTCGTGTTGCGAATTTGGAAATCGAGTTGCGAATTTGAATTCA
Found at i:494513 original size:37 final size:37
Alignment explanation
Indices: 494437--494513 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
494427 TTTTTATATT
*
494437 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
494474 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
494511 TTT
1 TTT
494514 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:494696 original size:19 final size:18
Alignment explanation
Indices: 494654--494696 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
494644 CAGTAATCCT
**
494654 ATTCCCTGGTAATCTTTT
1 ATTCCCTGGTAATCTTAC
494672 ATTTCCACTGGTAATCTTAC
1 A-TTCC-CTGGTAATCTTAC
494692 ATTCC
1 ATTCC
494697 GTGAACCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 8 0.38
20 12 0.57
ACGTcount: A:0.21, C:0.26, G:0.09, T:0.44
Consensus pattern (18 bp):
ATTCCCTGGTAATCTTAC
Found at i:495505 original size:5 final size:5
Alignment explanation
Indices: 495495--495535 Score: 64
Period size: 5 Copynumber: 8.2 Consensus size: 5
495485 ATCCTCTTTC
* *
495495 ACTAT ACTAT ACTAT ACTAT ACCAT ATTAT ACTAT ACTAT A
1 ACTAT ACTAT ACTAT ACTAT ACTAT ACTAT ACTAT ACTAT A
495536 TTTATTTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (5 bp):
ACTAT
Found at i:499869 original size:23 final size:23
Alignment explanation
Indices: 499853--499900 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
499843 TTTGGATTTG
*
499853 TCCAGATATTTGGTTTGAACTTA
1 TCCAGAGATTTGGTTTGAACTTA
499876 TCCAGAGATTTGGTTTGAACTTA
1 TCCAGAGATTTGGTTTGAACTTA
499899 TC
1 TC
499901 GAAAAGAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.42
Consensus pattern (23 bp):
TCCAGAGATTTGGTTTGAACTTA
Found at i:502511 original size:29 final size:28
Alignment explanation
Indices: 502457--502530 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 28
502447 TTATAGGGTT
*
502457 TAAATTACAAAAATATAAATCAGTAAAC
1 TAAATTAAAAAAATATAAATCAGTAAAC
* *
502485 TAAATTGAAAAAAATATAAAAT-TGTAAAT
1 TAAATT-AAAAAAATAT-AAATCAGTAAAC
*
502514 TAAAATTAAAATAATAT
1 T-AAATTAAAAAAATAT
502531 TTTTTTGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
28 6 0.15
29 24 0.62
30 9 0.23
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (28 bp):
TAAATTAAAAAAATATAAATCAGTAAAC
Found at i:505543 original size:174 final size:173
Alignment explanation
Indices: 505111--506317 Score: 1249
Period size: 174 Copynumber: 6.9 Consensus size: 173
505101 CAGATTACAA
* * ** * * * *
505111 AACCTCAAGATATAAAAAATGAAACTTTGAATGAAGAGGTTTCATCTGATGTCGATGGGGGTGAT
1 AACCTCAAGATACAAAAAATGATAC-TACAACGAAGTGGTTTCATCTGATGTTGATGGGGGTAAT
* * * *
505176 AAGATGACTTCAGACTTGAGAACCATGCCTGTTGAGACTGACGACTTGAGTACAGAGAAGCAGGA
65 AGGATGACTTCAGACTTGAGAACCATGCCTGTTGGGACTGATGACTTGAGTACAGAGAAACAGGA
* *
505241 ATCTGAAGGATGCTCTGGTTATGACTCAAAATCACACTTGCAGATTCAGG
130 ATCTGAAGGATGCTCTGGTTATGA-T-----TCACACTTGCAGACTAAGG
* * * ** * * * * *
505291 AACCTCTAGATATAAAAGATGATACTACAGATAAAGTCGTTTCATTTGATGTTGTTGGAGATAAT
1 AACCTCAAGATACAAAAAATGATACTACA-ACGAAGTGGTTTCATCTGATGTTGATGGGGGTAAT
* * * * * *
505356 AGGATGGCTTCAGACTTGGGAACCTTCCCTGTTGGGACCGATGATTTGAGTGA-AGAGAAACAGG
65 AGGATGACTTCAGACTTGAGAACCATGCCTGTTGGGACTGATGACTTGAGT-ACAGAGAAACAGG
* * * * * *
505420 AGTGTGAGGGATGCTCTGGTTTTGATTCCCACTTGCAGACTAAGA
129 AATCTGAAGGATGCTCTGGTTATGATTCACACTTGCAGACTAAGG
* * * * * * *
505465 AACCACAAGATATAAAAAATGTTGCTACATACGGAGTGGTTTCATCTGAAGTTGATGGGGTTAAT
1 AACCTCAAGATACAAAAAATGATACTACA-ACGAAGTGGTTTCATCTGATGTTGATGGGGGTAAT
* * * * * *
505530 ATGATGACTTCAGACTTGAGAACCATACCTGTCGGTAGTGATGACTCGAGTACAGAGAAACAGGA
65 AGGATGACTTCAGACTTGAGAACCATGCCTGTTGGGACTGATGACTTGAGTACAGAGAAACAGGA
* * *
505595 ATGTGAAGGATG-TCCTCGTTATGATTTACACTTGCAGACTAAGG
130 ATCTGAAGGATGCT-CTGGTTATGATTCACACTTGCAGACTAAGG
* * *
505639 AACCTCAAGATACAAAAGATGATACTACAAACAAAGTAGTTTCATCTGATGTTGATGGGGGTAAT
1 AACCTCAAGATACAAAAAATGATACTAC-AACGAAGTGGTTTCATCTGATGTTGATGGGGGTAAT
** *
505704 AGGATGACTTCAGACGAGAGAACCATGCCTGTTGGGACTGATGACTTGAGTACAGAGAAACATGA
65 AGGATGACTTCAGACTTGAGAACCATGCCTGTTGGGACTGATGACTTGAGTACAGAGAAACAGGA
* *
505769 ATCTGAAGCATGCTCTGGTTATGATTCACACTTGCAGACTAATG
130 ATCTGAAGGATGCTCTGGTTATGATTCACACTTGCAGACTAAGG
* * ** * * * *
505813 AACCTCAAGATACGATACCTGATACTATGAAAGAAGCGGTTTCTTCTGATGTTGATGGGGGTAAT
1 AACCTCAAGATACAAAAAATGATACTA-CAACGAAGTGGTTTCATCTGATGTTGATGGGGGTAAT
* ** * * * *
505878 AGGTTGACTTCAGACACGAGAACGATGACTGTTGGGACTGATGATTTGAGTACCGAGAAACAGGA
65 AGGATGACTTCAGACTTGAGAACCATGCCTGTTGGGACTGATGACTTGAGTACAGAGAAACAGGA
* *
505943 ATCTGAAGGATGCTCTGTTTATGATTCACACTTGCAGACTAATG
130 ATCTGAAGGATGCTCTGGTTATGATTCACACTTGCAGACTAAGG
* * ** * *
505987 AATCTCAAGATACAAAACATGATGGTATGAGA-GAAGTGGTTTCACCTGATGTTGATGGGGGTAA
1 AACCTCAAGATACAAAAAATGATACTA-CA-ACGAAGTGGTTTCATCTGATGTTGATGGGGGTAA
* * ** ** * *
506051 TAGGTTGACTTTAGACTCAAGAATAATGCTTGTTGGGACTGATGATTTGAGTACAGAGAAACATG
64 TAGGATGACTTCAGACTTGAGAACCATGCCTGTTGGGACTGATGACTTGAGTACAGAGAAACA-G
* * *
506116 G-ATCTGAAGGATGCTATGGTTATGATTCACATTTGCAGACTACGG
128 GAATCTGAAGGATGCTCTGGTTATGATTCACACTTGCAGACTAAGG
* * * * * **
506161 AACCTCAAGTTATAGAAAATTACACTACAATCCCAGTGGTTTCATCTGATG-T--TGGGGGTAAT
1 AACCTCAAGATACAAAAAATGATACTACAA-CGAAGTGGTTTCATCTGATGTTGATGGGGGTAAT
* * * * * *
506223 AGGATGACTTCAGACTTGAGAACCATTCCTATTGGGCCTGATGACCTGAGTACAGAGAAACCGGG
65 AGGATGACTTCAGACTTGAGAACCATGCCTGTTGGGACTGATGACTTGAGTACAGAGAAACAGGA
506288 ATCTGAAGGATGCTCTGGTTATGATTCACA
130 ATCTGAAGGATGCTCTGGTTATGATTCACA
506318 ATTTGAGGAT
Statistics
Matches: 857, Mismatches: 158, Indels: 33
0.82 0.15 0.03
Matches are distributed among these distances:
170 2 0.00
171 88 0.10
172 1 0.00
173 4 0.00
174 632 0.74
175 5 0.01
179 3 0.00
180 121 0.14
181 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (173 bp):
AACCTCAAGATACAAAAAATGATACTACAACGAAGTGGTTTCATCTGATGTTGATGGGGGTAATA
GGATGACTTCAGACTTGAGAACCATGCCTGTTGGGACTGATGACTTGAGTACAGAGAAACAGGAA
TCTGAAGGATGCTCTGGTTATGATTCACACTTGCAGACTAAGG
Found at i:510088 original size:183 final size:183
Alignment explanation
Indices: 509778--510820 Score: 1576
Period size: 183 Copynumber: 5.7 Consensus size: 183
509768 TTGTCGGTTT
* * * *
509778 GTGTCGATACTGTATAAAAATGTATCGATCCATAACAATATAATAGGT--AAAAAATGTCAAAAT
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAAATGACAAAAT
* * * *
509841 CGGTCTATAAATGACAAAACCGGTAAAGCGCTACCAGATATGTTGAAAGTGTTGATATATTAATA
66 CGGTCTATAAATGACAAAACCGGCAAAGCGCTACCGGATATGTTGAAAGTGTCGATACATTAATA
509906 TAAGTATCGACACATTTGGAATTTAAAAGAGGAGCAGTAATGACGCCTATAAA
131 TAAGTATCGACACATTTGGAATTTAAAAGAGGAGCAGTAATGACGCCTATAAA
* * *
509959 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACATGTAAAAAAAATGCCAAAAT
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAAATGACAAAAT
510024 CGGTCTATAAATGACAAAACCGGCAAAGCGCTACCGGATATGTTGAAAGTGTCGATACATTAATA
66 CGGTCTATAAATGACAAAACCGGCAAAGCGCTACCGGATATGTTGAAAGTGTCGATACATTAATA
* *
510089 TAAGTATCGACACCTTTGGAATTTAAAAGAGGAGCAGTAATGGCGCCTATAAA
131 TAAGTATCGACACATTTGGAATTTAAAAGAGGAGCAGTAATGACGCCTATAAA
*
510142 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAATGAC-AAAT
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAAATGACAAAAT
* * * *
510206 CCGGTCTATAAATGACAAAACCGGCAAAGCGTTACCAGATATGTTGAAAGTATCGATACATAAAT
66 -CGGTCTATAAATGACAAAACCGGCAAAGCGCTACCGGATATGTTGAAAGTGTCGATACATTAAT
* * * * * *
510271 ATAAATATTGACACCTTTCGAATTTAAAAGAGGAGAAGTAAT-AGCACCTATAAA
130 ATAAGTATCGACACATTTGGAATTTAAAAGAGGAGCAGTAATGA-CGCCTATAAA
*
510325 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGT-AAAAAAATGCCAAAAT
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAAATGACAAAAT
* *
510389 CGGTTTATAAATGACAAAACCGGCAAAGCGCTACCGGATATGTTTAAAGTGTCGATACATTAATA
66 CGGTCTATAAATGACAAAACCGGCAAAGCGCTACCGGATATGTTGAAAGTGTCGATACATTAATA
*
510454 TAAGTATCGACACATTTGGAATTTAAAAGAGGAGCAGTAATGGCGCCTATAAA
131 TAAGTATCGACACATTTGGAATTTAAAAGAGGAGCAGTAATGACGCCTATAAA
* * * * *
510507 GCGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAATAGGTAACAAAAATGACAAAAC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAAATGACAAAAT
* * * * *
510572 CGGTCTATAAATGACAAAACCGGTAAAGCGCTACTGTATATGTTGAAGGTGTGGATACATTAATA
66 CGGTCTATAAATGACAAAACCGGCAAAGCGCTACCGGATATGTTGAAAGTGTCGATACATTAATA
* * * *
510637 TAAGTATCGACACTTTTGAAATTTAAAAGAAGAGCAATAAT-AGCGCCTATAAA
131 TAAGTATCGACACATTTGGAATTTAAAAGAGGAGCAGTAATGA-CGCCTATAAA
* * * *
510690 GTGTCTATATTTTATAAAAATACATCGATCCATAACAATATAACAGGTAAAATAAAATGAAAAAA
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAA-AAAATGACAAAA
* *
510755 CCGGTCTATAAATGACAAAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATACATTAAT
65 TCGGTCTATAAATGACAAAACCGGCAAAGCGCTACCGGATATGTTGAAAGTGTCGATACATTAAT
510820 A
130 A
510821 AGTAGGCGTA
Statistics
Matches: 782, Mismatches: 71, Indels: 15
0.90 0.08 0.02
Matches are distributed among these distances:
181 43 0.05
182 163 0.21
183 503 0.64
184 73 0.09
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (183 bp):
GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAAATGACAAAAT
CGGTCTATAAATGACAAAACCGGCAAAGCGCTACCGGATATGTTGAAAGTGTCGATACATTAATA
TAAGTATCGACACATTTGGAATTTAAAAGAGGAGCAGTAATGACGCCTATAAA
Found at i:510824 original size:365 final size:364
Alignment explanation
Indices: 509780--510820 Score: 1660
Period size: 365 Copynumber: 2.8 Consensus size: 364
509770 GTCGGTTTGT
* * *
509780 GTCGATACTGTATAAAAATGTATCGATCCATAACAATATAATAGGT-AAAAAATGTCAAAATCGG
1 GTCGATACTTTATAAAAATGTATCGATCCATAACAATATAATAGGTAAAAAAATGACAAAACCGG
* *
509844 TCTATAAATGACAAAACCGGTAAAGCGCTACCAGATATGTTGAAAGTGTTGATATATTAATATAA
66 TCTATAAATGACAAAACCGGTAAAGCGCTACCAGATATGTTGAAAGTGTCGATACATTAATATAA
* *
509909 GTATCGACACATTTGGAATTTAAAAGAGGAGCAGTAAT-GACGCCTATAAAGTGTCGATACTTTA
131 GTATCGACAC-TTTTGAATTTAAAAGAGGAGCAATAATAG-CGCCTATAAAGTGTCGATACTTTA
* *
509973 TAAAAATATATTGATCCATAACAATATAACATGTAAAAAAAATGCCAAAATCGGTCTATAAATGA
194 TAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAAATGCCAAAATCGGTCTATAAATGA
*
510038 CAAAACCGGCAAAGCGCTACCGGATATGTTGAAAGTGTCGATACATTAATATAAGTATCGACACC
259 CAAAACCGGCAAAGCGCTACCGGATATGTTGAAAGTGTCGATACATTAATATAAGTATCGACACA
*
510103 TTTGGAATTTAAAAGAGGAGCAGTAATGGCGCCTATAAAGT
324 TTTGGAATTTAAAAGAGGAGCAGTAATGGCGCCTATAAAGC
* *
510144 GTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAATGACAAATCCG
1 GTCGATACTTTATAAAAATGTATCGATCCATAACAATATAATAGGT-AAAAAAATGACAAAACCG
* * * *
510209 GTCTATAAATGACAAAACCGGCAAAGCGTTACCAGATATGTTGAAAGTATCGATACATAAATATA
65 GTCTATAAATGACAAAACCGGTAAAGCGCTACCAGATATGTTGAAAGTGTCGATACATTAATATA
* * * *
510274 AATATTGACACCTTTCGAATTTAAAAGAGGAG-AAGTAATAGCACCTATAAAGTGTCGATACTTT
130 AGTATCGACA-CTTTTGAATTTAAAAGAGGAGCAA-TAATAGCGCCTATAAAGTGTCGATACTTT
*
510338 ATAAAAATATATCGATCCATAACAATATAACAGGT-AAAAAAATGCCAAAATCGGTTTATAAATG
193 ATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAAATGCCAAAATCGGTCTATAAATG
*
510402 ACAAAACCGGCAAAGCGCTACCGGATATGTTTAAAGTGTCGATACATTAATATAAGTATCGACAC
258 ACAAAACCGGCAAAGCGCTACCGGATATGTTGAAAGTGTCGATACATTAATATAAGTATCGACAC
510467 ATTTGGAATTTAAAAGAGGAGCAGTAATGGCGCCTATAAAGC
323 ATTTGGAATTTAAAAGAGGAGCAGTAATGGCGCCTATAAAGC
510509 GTCGATACTTTATAAAAATGTATCGATCCATAACAATATAATAGGTAACAAAAATGACAAAACCG
1 GTCGATACTTTATAAAAATGTATCGATCCATAACAATATAATAGGTAA-AAAAATGACAAAACCG
* * *
510574 GTCTATAAATGACAAAACCGGTAAAGCGCTA-CTGTATATGTTGAAGGTGTGGATACATTAATAT
65 GTCTATAAATGACAAAACCGGTAAAGCGCTACCAG-ATATGTTGAAAGTGTCGATACATTAATAT
* * *
510638 AAGTATCGACACTTTTGAAATTTAAAAGAAGAGCAATAATAGCGCCTATAAAGTGTCTATATTTT
129 AAGTATCGACACTTTTG-AATTTAAAAGAGGAGCAATAATAGCGCCTATAAAGTGTCGATACTTT
* ** *
510703 ATAAAAATACATCGATCCATAACAATATAACAGGTAAAATAAAATGAAAAAACCGGTCTATAAAT
193 ATAAAAATATATCGATCCATAACAATATAACAGGTAAAA-AAAATGCCAAAATCGGTCTATAAAT
*
510768 GACAAAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATACATTAATA
257 GACAAAACCGGCAAAGCGCTACCGGATATGTTGAAAGTGTCGATACATTAATA
510821 AGTAGGCGTA
Statistics
Matches: 621, Mismatches: 45, Indels: 19
0.91 0.07 0.03
Matches are distributed among these distances:
364 53 0.09
365 330 0.53
366 164 0.26
367 74 0.12
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (364 bp):
GTCGATACTTTATAAAAATGTATCGATCCATAACAATATAATAGGTAAAAAAATGACAAAACCGG
TCTATAAATGACAAAACCGGTAAAGCGCTACCAGATATGTTGAAAGTGTCGATACATTAATATAA
GTATCGACACTTTTGAATTTAAAAGAGGAGCAATAATAGCGCCTATAAAGTGTCGATACTTTATA
AAAATATATCGATCCATAACAATATAACAGGTAAAAAAAATGCCAAAATCGGTCTATAAATGACA
AAACCGGCAAAGCGCTACCGGATATGTTGAAAGTGTCGATACATTAATATAAGTATCGACACATT
TGGAATTTAAAAGAGGAGCAGTAATGGCGCCTATAAAGC
Found at i:510901 original size:21 final size:21
Alignment explanation
Indices: 510875--510929 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
510865 TAGCTTATCG
*
510875 AAAGTATCGACACCTGACATA
1 AAAGTATCGACACATGACATA
510896 AAAGTATCGACACATGACATA
1 AAAGTATCGACACATGACATA
510917 AAAGTATCGACAC
1 AAAGTATCGACAC
510930 TTGTGTAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.45, C:0.22, G:0.15, T:0.18
Consensus pattern (21 bp):
AAAGTATCGACACATGACATA
Found at i:513832 original size:19 final size:18
Alignment explanation
Indices: 513808--513863 Score: 71
Period size: 16 Copynumber: 3.2 Consensus size: 18
513798 ATGTAGGGGA
513808 AATTTTGTATATGATTCAT
1 AATTTTGTATATGATT-AT
513827 AATTTTGTATAT--TTAT
1 AATTTTGTATATGATTAT
* *
513843 AATTTTGTATGTGATTGT
1 AATTTTGTATATGATTAT
513861 AAT
1 AAT
513864 AGGTTATATG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
16 13 0.39
17 2 0.06
18 6 0.18
19 12 0.36
ACGTcount: A:0.30, C:0.02, G:0.12, T:0.55
Consensus pattern (18 bp):
AATTTTGTATATGATTAT
Found at i:515034 original size:18 final size:18
Alignment explanation
Indices: 515007--515077 Score: 106
Period size: 18 Copynumber: 3.9 Consensus size: 18
514997 GAGTAGAATT
* *
515007 TGTCCTGAAGGACCACTA
1 TGTCCCGAAGAACCACTA
*
515025 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGAACCACTA
*
515043 TGTCCTGAAGAACCACTA
1 TGTCCCGAAGAACCACTA
515061 TGTCCCGAAGAACCACT
1 TGTCCCGAAGAACCACT
515078 CATAATCCTT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 49 1.00
ACGTcount: A:0.30, C:0.31, G:0.20, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGAACCACTA
Found at i:515058 original size:36 final size:36
Alignment explanation
Indices: 515007--515077 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
514997 GAGTAGAATT
* *
515007 TGTCCTGAAGGACCACTATGTCCCGAAGGACCACTA
1 TGTCCTGAAGAACCACTATGTCCCGAAGAACCACTA
515043 TGTCCTGAAGAACCACTATGTCCCGAAGAACCACT
1 TGTCCTGAAGAACCACTATGTCCCGAAGAACCACT
515078 CATAATCCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.30, C:0.31, G:0.20, T:0.20
Consensus pattern (36 bp):
TGTCCTGAAGAACCACTATGTCCCGAAGAACCACTA
Found at i:517784 original size:2 final size:2
Alignment explanation
Indices: 517777--517836 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
517767 CACTCTTGCT
517777 TA TA TA TA 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 TA TA TA TA
517819 -A TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
517837 CTTATTCGCT
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 56 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:519123 original size:18 final size:18
Alignment explanation
Indices: 519065--519165 Score: 126
Period size: 18 Copynumber: 6.0 Consensus size: 18
519055 GCATAGAATT
* *
519065 TGTCCCGTAGGACCATTG
1 TGTCCCGAAGGACCACTG
519083 TGTCCCGAAGGACCAC--
1 TGTCCCGAAGGACCACTG
519099 --T---GAAGGACCACTG
1 TGTCCCGAAGGACCACTG
519112 TGTCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTG
519130 TGTCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTG
*
519148 TGTCCCAAAGGACCACTG
1 TGTCCCGAAGGACCACTG
519166 ATAATCCCTC
Statistics
Matches: 73, Mismatches: 3, Indels: 14
0.81 0.03 0.16
Matches are distributed among these distances:
11 10 0.14
14 1 0.01
15 1 0.01
18 61 0.84
ACGTcount: A:0.24, C:0.32, G:0.27, T:0.18
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTG
Found at i:524087 original size:87 final size:87
Alignment explanation
Indices: 523989--524151 Score: 281
Period size: 87 Copynumber: 1.9 Consensus size: 87
523979 AAATAGGTCA
* *
523989 ATATAAACGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAACGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTAATAATATTT
* *
524054 TCGGTTAAATGCCTATTTTATT
66 CCGATTAAATGCCTATTTTATT
*
524076 ATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTAATAATATTT
1 ATATAAACGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTAATAATATTT
524141 CCGATTAAATG
66 CCGATTAAATG
524152 ATATAACATA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.40
Consensus pattern (87 bp):
ATATAAACGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTAATAATATTT
CCGATTAAATGCCTATTTTATT
Found at i:524123 original size:23 final size:23
Alignment explanation
Indices: 524073--524117 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
524063 TGCCTATTTT
* *
524073 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAACGCTACCTAATAC
524096 ATTATATAAACGCTACCTAATA
1 ATTATATAAACGCTACCTAATA
524118 TGTTATTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (23 bp):
ATTATATAAACGCTACCTAATAC
Found at i:525048 original size:50 final size:50
Alignment explanation
Indices: 524969--525069 Score: 166
Period size: 50 Copynumber: 2.0 Consensus size: 50
524959 TAAAAAATAT
* * *
524969 TCCTGGGACAATTTTAGGAGATGCTCACCATATGCCCTTTAGCCATTATC
1 TCCTGGGAAAATTTTAGGAGATGCACACCATATGCCCTTTAGCCATAATC
*
525019 TCCTGGGAAAATTTTAGGAGATGCACACCATATGTCCTTTAGCCATAATC
1 TCCTGGGAAAATTTTAGGAGATGCACACCATATGCCCTTTAGCCATAATC
525069 T
1 T
525070 AGCTACTTCT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.32
Consensus pattern (50 bp):
TCCTGGGAAAATTTTAGGAGATGCACACCATATGCCCTTTAGCCATAATC
Found at i:526057 original size:32 final size:30
Alignment explanation
Indices: 525999--526062 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
525989 AATTTTAAAA
525999 TATTAAAATAAATAATATTTACTAATAAATT
1 TATTAAAATAAATAATATTTACTAAT-AATT
* *
526030 TATTAAATATAAAATTATTTTTA-TAATAATT
1 TATTAAA-AT-AAATAATATTTACTAATAATT
526061 TA
1 TA
526063 GAGTTATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 13 0.45
32 6 0.21
33 10 0.34
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (30 bp):
TATTAAAATAAATAATATTTACTAATAATT
Found at i:526897 original size:39 final size:38
Alignment explanation
Indices: 526813--527004 Score: 188
Period size: 39 Copynumber: 4.8 Consensus size: 38
526803 GTACACGCCA
*
526813 AAGATGCATTGCACTCCATACGTCTCTCTCCTTTCTCCCC-G
1 AAGACGCATTGCACTCCATACGTCTCTC-CC---CTCCCCTG
* *
526854 AAGACGCATTGCACTCCATGCGTCTCTCCCCTCCCCATA
1 AAGACGCATTGCACTCCATACGTCTCTCCCCTCCCC-TG
** * *
526893 AAGACATATTGCATTCCATTCGTCTCTCCCCTTTCCCCTCG
1 AAGACGCATTGCACTCCATACGTCTCTCCCC--TCCCCT-G
* ** * *
526934 AAGACGCATTGCACTCTACGCGTCCCTCCCCTCACCCGG
1 AAGACGCATTGCACTCCATACGTCTCTCCCCTC-CCCTG
526973 AAGACGCATTGCACTCCATACGTCTCTCCCCT
1 AAGACGCATTGCACTCCATACGTCTCTCCCCT
527005 ACATGCACTC
Statistics
Matches: 125, Mismatches: 20, Indels: 14
0.79 0.13 0.09
Matches are distributed among these distances:
37 6 0.05
39 58 0.46
40 6 0.05
41 55 0.44
ACGTcount: A:0.19, C:0.42, G:0.13, T:0.27
Consensus pattern (38 bp):
AAGACGCATTGCACTCCATACGTCTCTCCCCTCCCCTG
Found at i:526945 original size:80 final size:80
Alignment explanation
Indices: 526819--527004 Score: 250
Period size: 80 Copynumber: 2.3 Consensus size: 80
526809 GCCAAAGATG
* * *
526819 CATTGCACTCCATACGTCTCTCTCCTTTCTCCCCGAAGACGCATTGCACTCCATGCGTCTCTCCC
1 CATTGCACTCCATACGTCTCTCCCCTTTCTCCCCGAAGACGCATTGCACTCCACGCGTCCCTCCC
*
526884 CTC-CCCATAAAGACA
66 CTCACCC-GAAAGACA
* * * *
526899 TATTGCATTCCATTCGTCTCTCCCCTTTC-CCCTCGAAGACGCATTGCACTCTACGCGTCCCTCC
1 CATTGCACTCCATACGTCTCTCCCCTTTCTCCC-CGAAGACGCATTGCACTCCACGCGTCCCTCC
* *
526963 CCTCACCCGGAAGACG
65 CCTCACCCGAAAGACA
526979 CATTGCACTCCATACGTCTCTCCCCT
1 CATTGCACTCCATACGTCTCTCCCCT
527005 ACATGCACTC
Statistics
Matches: 91, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
79 3 0.03
80 85 0.93
81 3 0.03
ACGTcount: A:0.18, C:0.43, G:0.12, T:0.27
Consensus pattern (80 bp):
CATTGCACTCCATACGTCTCTCCCCTTTCTCCCCGAAGACGCATTGCACTCCACGCGTCCCTCCC
CTCACCCGAAAGACA
Found at i:527220 original size:18 final size:18
Alignment explanation
Indices: 527199--527240 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
527189 GGGGCATCGG
527199 GGAGAAGAAAAAAAAAAA
1 GGAGAAGAAAAAAAAAAA
* *
527217 GGAGAAGGAGAAAAAAAA
1 GGAGAAGAAAAAAAAAAA
*
527235 GAAGAA
1 GGAGAA
527241 AGGAAGGAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (18 bp):
GGAGAAGAAAAAAAAAAA
Found at i:527233 original size:24 final size:24
Alignment explanation
Indices: 527199--527282 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 24
527189 GGGGCATCGG
*
527199 GGAGAAGAAAAAAAAAAAGGAGAA
1 GGAGAAAAAAAAAAAAAAGGAGAA
*
527223 GGAGAAAAAAAAGAAGAAA-G-GAA
1 GGAGAAAAAAAA-AAAAAAGGAGAA
* *
527246 GGAAGAAGGAAAAAAAAGAAGGAAGAA
1 GG-AGAA-AAAAAAAAAAAAGG-AGAA
527273 GGA-AAAAAAA
1 GGAGAAAAAAA
527283 GGAAAAAGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
23 5 0.10
24 24 0.50
25 13 0.27
26 1 0.02
27 5 0.10
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (24 bp):
GGAGAAAAAAAAAAAAAAGGAGAA
Found at i:527237 original size:30 final size:29
Alignment explanation
Indices: 527207--527262 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
527197 GGGGAGAAGA
527207 AAAAAAAAAAGG-AGAAGGAGAAAAAAAAG
1 AAAAAAAAAAGGAAGAAGGA-AAAAAAAAG
* **
527236 AAGAAAGGAAGGAAGAAGGAAAAAAAA
1 AAAAAAAAAAGGAAGAAGGAAAAAAAA
527263 GAAGGAAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 16 0.70
30 7 0.30
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (29 bp):
AAAAAAAAAAGGAAGAAGGAAAAAAAAAG
Found at i:527268 original size:20 final size:20
Alignment explanation
Indices: 527243--527283 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
527233 AAGAAGAAAG
527243 GAAGGAAGAAGGAAAAAAAA
1 GAAGGAAGAAGGAAAAAAAA
527263 GAAGGAAGAAGGAAAAAAAA
1 GAAGGAAGAAGGAAAAAAAA
527283 G
1 G
527284 GAAAAAGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (20 bp):
GAAGGAAGAAGGAAAAAAAA
Found at i:527278 original size:48 final size:48
Alignment explanation
Indices: 527201--527300 Score: 127
Period size: 48 Copynumber: 2.1 Consensus size: 48
527191 GGCATCGGGG
527201 AGAAGAAAAAAAAAAAGGAGAAGGAGAAAAAAAA-GAAGAAAGGAAG-GA
1 AGAAGAAAAAAAAAAAGGAGAAGGAGAAAAAAAAGGAA-AAA-GAAGAGA
*
527249 AGAAGGAAAAAAAAGAAGGAAGAA-G-GAAAAAAAAGGAAAAAGAAGAGA
1 AGAA-GAAAAAAAAAAAGG-AGAAGGAGAAAAAAAAGGAAAAAGAAGAGA
527297 AGAA
1 AGAA
527301 AATAATCAAG
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
47 4 0.09
48 22 0.47
49 17 0.36
50 4 0.09
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (48 bp):
AGAAGAAAAAAAAAAAGGAGAAGGAGAAAAAAAAGGAAAAAGAAGAGA
Found at i:527291 original size:20 final size:20
Alignment explanation
Indices: 527243--527293 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
527233 AAGAAGAAAG
*
527243 GAAGGAAGAAGGAAAAAAAA
1 GAAGAAAGAAGGAAAAAAAA
*
527263 GAAGGAAGAAGGAAAAAAAA
1 GAAGAAAGAAGGAAAAAAAA
527283 GGAA-AAAGAAG
1 -GAAGAAAGAAG
527294 AGAAGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 26 0.90
21 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (20 bp):
GAAGAAAGAAGGAAAAAAAA
Found at i:528911 original size:23 final size:24
Alignment explanation
Indices: 528876--528920 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
528866 AGTCAACTCA
528876 AGTCAACTCGTTGACT-TTGATCG
1 AGTCAACTCGTTGACTGTTGATCG
528899 AGTCAACAT-GTTGACTGTTGAT
1 AGTCAAC-TCGTTGACTGTTGAT
528921 TGTTGACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (24 bp):
AGTCAACTCGTTGACTGTTGATCG
Found at i:530824 original size:19 final size:19
Alignment explanation
Indices: 530802--530843 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
530792 TTTTGAAATT
530802 TGATATATG-TTATGATCTC
1 TGATATATGATT-TGATCTC
* *
530821 TGATTTCTGATTTGATCTC
1 TGATATATGATTTGATCTC
530840 TGAT
1 TGAT
530844 CTCTATTCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.21, C:0.12, G:0.17, T:0.50
Consensus pattern (19 bp):
TGATATATGATTTGATCTC
Found at i:532089 original size:62 final size:64
Alignment explanation
Indices: 531972--532109 Score: 158
Period size: 62 Copynumber: 2.2 Consensus size: 64
531962 AACACTAATT
* ** * *
531972 GCATTCGATGTTTTAATAAAGCCAGAGTGTATCGATGCATAGGATGTGTACCGGTAC-AAAA-A
1 GCATTCGATGTTTCAATAAAAACAGAGTGTACCGATGCATAGGATGTGCACCGGTACAAAAATA
* * *
532034 GCATTCGATGTTTCAATAAAAATAGGAGTGTACCGATGCAT-GGTTGTGCATCGGTACATAAAAT
1 GCATTCGATGTTTCAATAAAAACA-GAGTGTACCGATGCATAGGATGTGCACCGGTACA-AAAAT
532098 A
64 A
532099 GC-TTCGATGTT
1 GCATTCGATGTT
532110 GTGTGTGCAT
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
62 33 0.52
63 15 0.23
64 13 0.20
65 3 0.05
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (64 bp):
GCATTCGATGTTTCAATAAAAACAGAGTGTACCGATGCATAGGATGTGCACCGGTACAAAAATA
Found at i:534227 original size:13 final size:13
Alignment explanation
Indices: 534204--534236 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
534194 ATGGGAAACG
534204 TTTTG-AAAACAA
1 TTTTGAAAAACAA
534216 TTTTGAAAAACAA
1 TTTTGAAAAACAA
534229 TATTTGAA
1 T-TTTGAA
534237 TAATCATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.26
13 8 0.42
14 6 0.32
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.36
Consensus pattern (13 bp):
TTTTGAAAAACAA
Found at i:534768 original size:23 final size:23
Alignment explanation
Indices: 534742--534809 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 23
534732 TCAATACACA
534742 TTCAAGGAATGTATCGGTGCACT
1 TTCAAGGAATGTATCGGTGCACT
* * *
534765 TTCATA-G--TGTATTGATGCACA
1 TTCA-AGGAATGTATCGGTGCACT
* *
534786 TTCAAGGAATGCATCGGTACACT
1 TTCAAGGAATGTATCGGTGCACT
534809 T
1 T
534810 CCACAATGTA
Statistics
Matches: 33, Mismatches: 8, Indels: 8
0.67 0.16 0.16
Matches are distributed among these distances:
20 1 0.03
21 16 0.48
23 15 0.45
24 1 0.03
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (23 bp):
TTCAAGGAATGTATCGGTGCACT
Found at i:534786 original size:44 final size:43
Alignment explanation
Indices: 534738--534827 Score: 126
Period size: 44 Copynumber: 2.1 Consensus size: 43
534728 TGTATCAATA
* * * * *
534738 CACATTCAAGGAATGTATCGGTGCACTTTCATAGTGTATTGATG
1 CACATTCAAGGAATGCATCGGTACACTTCCACAATGTA-TGATG
534782 CACATTCAAGGAATGCATCGGTACACTTCCACAATGTATGATG
1 CACATTCAAGGAATGCATCGGTACACTTCCACAATGTATGATG
534825 CAC
1 CAC
534828 TTTGCACAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
43 8 0.20
44 33 0.80
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (43 bp):
CACATTCAAGGAATGCATCGGTACACTTCCACAATGTATGATG
Found at i:540559 original size:64 final size:63
Alignment explanation
Indices: 540427--540581 Score: 170
Period size: 64 Copynumber: 2.4 Consensus size: 63
540417 CTTGGAGTGT
* * * ** *
540427 ATCGGTACACTAATTGCATTCGATGTTTTAATAAAGCCAGAGTATATCGATGCATAGGATGTGT
1 ATCGGTACACAAAATGCATTCGATGTTTCAATAAAAACAGAGTATATCGATGCATA-GATGTGC
* * *
540491 ATCGGTACACAAAATGCATTCGATGTTTCAATAAAAATAGGAGTGTATCGATGCATTA-CTGTGC
1 ATCGGTACACAAAATGCATTCGATGTTTCAATAAAAACA-GAGTATATCGATGCA-TAGATGTGC
*
540555 ATCGGTACATAAAATAGC-TTCGATGTT
1 ATCGGTACACAAAAT-GCATTCGATGTT
540582 GTGTGTGCAT
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
64 60 0.77
65 16 0.21
66 2 0.03
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.32
Consensus pattern (63 bp):
ATCGGTACACAAAATGCATTCGATGTTTCAATAAAAACAGAGTATATCGATGCATAGATGTGC
Found at i:541992 original size:16 final size:16
Alignment explanation
Indices: 541964--542004 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
541954 AGGTATATTT
541964 TATAATATATAATA-TAA
1 TATAAT-TATAATACT-A
541981 TATAATTATAATACTA
1 TATAATTATAATACTA
541997 TATAATTA
1 TATAATTA
542005 ATTTAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TATAATTATAATACTA
Found at i:543897 original size:4 final size:4
Alignment explanation
Indices: 543888--543920 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
543878 AAAAATTTAA
543888 ATAC ATAC ATAC ATAC ATAC ATAC A-A- ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
543921 TATGATTACT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 1 0.04
3 2 0.07
4 24 0.89
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:551163 original size:20 final size:20
Alignment explanation
Indices: 551120--551167 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
551110 TCTAAATCAT
* *
551120 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATTCCATTTTGC
551140 TTTTCAAAA-TCCATTTTAGC
1 TTTTCAAAATTCCATTTT-GC
551160 TTTT-AAAA
1 TTTTCAAAA
551168 GAAAATCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.50
Consensus pattern (20 bp):
TTTTCAAAATTCCATTTTGC
Found at i:551186 original size:24 final size:23
Alignment explanation
Indices: 551145--551190 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
551135 TTTGGTTTTC
*
551145 AAAATCCATTTTAGCTTTTAAAAG
1 AAAATCCATTTTAAC-TTTAAAAG
551169 AAAAT-CATTTTCAACTTTAAAA
1 AAAATCCATTTT-AACTTTAAAA
551191 TTAGAAATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.46, C:0.13, G:0.04, T:0.37
Consensus pattern (23 bp):
AAAATCCATTTTAACTTTAAAAG
Found at i:553054 original size:26 final size:27
Alignment explanation
Indices: 553002--553056 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 27
552992 TAACTTTCTC
553002 CTCTTTTCTCTTCTTCCTTCCTCTTTT
1 CTCTTTTCTCTTCTTCCTTCCTCTTTT
* * *
553029 CTCTTTTCT-TTTTTCCTTCTTTTTTT
1 CTCTTTTCTCTTCTTCCTTCCTCTTTT
553055 CT
1 CT
553057 TCTTCCTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 16 0.64
27 9 0.36
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (27 bp):
CTCTTTTCTCTTCTTCCTTCCTCTTTT
Found at i:553065 original size:26 final size:27
Alignment explanation
Indices: 553002--553070 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
552992 TAACTTTCTC
553002 CTCTTTTCTCTTC-TTCCTTCCTCTTTT
1 CTCTTTTCT-TTCTTTCCTTCCTCTTTT
553029 CTCTTTTCTTT-TTTCCTT-CT-TTTT
1 CTCTTTTCTTTCTTTCCTTCCTCTTTT
*
553053 TTCTTCTTCCTTTCTTTC
1 CTCTT-TT-CTTTCTTTC
553071 TTACTTCTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
24 8 0.22
25 4 0.11
26 12 0.32
27 13 0.35
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (27 bp):
CTCTTTTCTTTCTTTCCTTCCTCTTTT
Found at i:554828 original size:28 final size:29
Alignment explanation
Indices: 554797--554855 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
554787 AATAATTTTA
554797 TTTT-TGT-AATTTGTAAATCATTAAT-TTG
1 TTTTATGTAAATTTGT--ATCATTAATCTTG
*
554825 TTTTATTTAAATTTGTATCATTAATCTTG
1 TTTTATGTAAATTTGTATCATTAATCTTG
554854 TT
1 TT
554856 ACATTTAGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 13 0.48
29 7 0.26
30 7 0.26
ACGTcount: A:0.27, C:0.05, G:0.08, T:0.59
Consensus pattern (29 bp):
TTTTATGTAAATTTGTATCATTAATCTTG
Found at i:554861 original size:29 final size:29
Alignment explanation
Indices: 554804--554867 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
554794 TTATTTTTGT
**
554804 AATTTGTAAATCATTAATTTGTTTTATTTA
1 AATTTGT-AATCATTAATTTGTTACATTTA
554834 AATTTGT-ATCATTAATCTTGTTACATTTA
1 AATTTGTAATCATTAAT-TTGTTACATTTA
*
554863 GATTT
1 AATTT
554868 TTATGTATGC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 9 0.30
29 14 0.47
30 7 0.23
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.55
Consensus pattern (29 bp):
AATTTGTAATCATTAATTTGTTACATTTA
Found at i:559716 original size:24 final size:24
Alignment explanation
Indices: 559684--559771 Score: 97
Period size: 24 Copynumber: 3.7 Consensus size: 24
559674 GATATCAAAA
* *
559684 ATCAAAACAGAATTCAGAACATAT
1 ATCAGAACAGAATTCAGATCATAT
* *
559708 ATCAGAACAGAA-TCTAGATCAGAA
1 ATCAGAACAGAATTC-AGATCATAT
* *
559732 ATCAGAACAGAATTCAGGTCATGT
1 ATCAGAACAGAATTCAGATCATAT
*
559756 ATCAGAACAAAATTCA
1 ATCAGAACAGAATTCA
559772 AGTCGAAAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
23 2 0.04
24 49 0.92
25 2 0.04
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.20
Consensus pattern (24 bp):
ATCAGAACAGAATTCAGATCATAT
Found at i:559748 original size:12 final size:12
Alignment explanation
Indices: 559689--559748 Score: 61
Period size: 12 Copynumber: 5.0 Consensus size: 12
559679 CAAAAATCAA
559689 AACAGAATTCAG
1 AACAGAATTCAG
*
559701 AACA-TATATCAG
1 AACAGAAT-TCAG
559713 AACAGAA-TCTAG
1 AACAGAATTC-AG
* *
559725 ATCAGAAATCAG
1 AACAGAATTCAG
559737 AACAGAATTCAG
1 AACAGAATTCAG
559749 GTCATGTATC
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
11 4 0.10
12 32 0.82
13 3 0.08
ACGTcount: A:0.50, C:0.17, G:0.15, T:0.18
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:559782 original size:48 final size:47
Alignment explanation
Indices: 559681--559785 Score: 122
Period size: 48 Copynumber: 2.2 Consensus size: 47
559671 CGAGATATCA
* * *
559681 AAAATCAAAACAGAATTCAGAACATATATCAGAACAGAATCTAGATC
1 AAAATCAGAACAGAATTCAGAACATATATCAGAACAAAATCAAGATC
** *
559728 AGAAATCAGAACAGAATTCAGGTCATGTATCAGAACAAAATTCAAG-TC
1 A-AAATCAGAACAGAATTCAGAACATATATCAGAACAAAA-TCAAGATC
559776 GAAAATCAGA
1 -AAAATCAGA
559786 TAAAATATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
47 1 0.02
48 43 0.88
49 5 0.10
ACGTcount: A:0.50, C:0.16, G:0.14, T:0.19
Consensus pattern (47 bp):
AAAATCAGAACAGAATTCAGAACATATATCAGAACAAAATCAAGATC
Found at i:559783 original size:24 final size:24
Alignment explanation
Indices: 559703--559785 Score: 62
Period size: 24 Copynumber: 3.5 Consensus size: 24
559693 GAATTCAGAA
* * *
559703 CATATATCAGAACAGAA-TCTAGAT
1 CATAAATCAGAACAAAATTCAAG-T
* * *
559727 CAGAAATCAGAACAGAATTCAGGT
1 CATAAATCAGAACAAAATTCAAGT
**
559751 CATGTATCAGAACAAAATTCAAGT
1 CATAAATCAGAACAAAATTCAAGT
559775 CGA-AAATCAGA
1 C-ATAAATCAGA
559786 TAAAATATTT
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
24 42 0.91
25 4 0.09
ACGTcount: A:0.47, C:0.17, G:0.16, T:0.20
Consensus pattern (24 bp):
CATAAATCAGAACAAAATTCAAGT
Found at i:564827 original size:1 final size:1
Alignment explanation
Indices: 564821--564868 Score: 51
Period size: 1 Copynumber: 48.0 Consensus size: 1
564811 GGAAAGAAAT
* * * * *
564821 AAAAAAAACAAAAACAAAATAAAAAAAAAACAAAAACAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
564869 GAAAGAAATT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.90, C:0.08, G:0.00, T:0.02
Consensus pattern (1 bp):
A
Found at i:564835 original size:6 final size:6
Alignment explanation
Indices: 564824--564867 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
564814 AAGAAATAAA
*
564824 AAAAAC AAAAAC -AAAAT AAAAA- AAAAAC AAAAAC AAAAA- AAAAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAA
564868 AGAAAGAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
5 14 0.40
6 21 0.60
ACGTcount: A:0.89, C:0.09, G:0.00, T:0.02
Consensus pattern (6 bp):
AAAAAC
Found at i:564849 original size:16 final size:15
Alignment explanation
Indices: 564821--564866 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 15
564811 GGAAAGAAAT
*
564821 AAAAAAAACAAAAAC
1 AAAAAAAAAAAAAAC
564836 AAAATAAAAAAAAAAC
1 AAAA-AAAAAAAAAAC
564852 AAAAACAAAAAAAAA
1 AAAAA-AAAAAAAAA
564867 AAGAAAGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 5 0.18
16 23 0.82
ACGTcount: A:0.89, C:0.09, G:0.00, T:0.02
Consensus pattern (15 bp):
AAAAAAAAAAAAAAC
Found at i:564849 original size:22 final size:21
Alignment explanation
Indices: 564821--564868 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 21
564811 GGAAAGAAAT
564821 AAAAAAAACAAAAACAAAATAA
1 AAAAAAAACAAAAACAAAA-AA
564843 AAAAAAAACAAAAACAAAAAA
1 AAAAAAAACAAAAACAAAAAA
564864 AAAAA
1 AAAAA
564869 GAAAGAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 7 0.27
22 19 0.73
ACGTcount: A:0.90, C:0.08, G:0.00, T:0.02
Consensus pattern (21 bp):
AAAAAAAACAAAAACAAAAAA
Found at i:565327 original size:263 final size:266
Alignment explanation
Indices: 564858--565382 Score: 948
Period size: 263 Copynumber: 2.0 Consensus size: 266
564848 AAACAAAAAC
*
564858 AAAAAAAAAAAGAAAGAAATTACTTAGGATTAAGTTTAGGTGGAAGATAGACTAAGGGAGTTGAG
1 AAAAAAAAAAAGAAAGAAATTACTTAGGATTAAGTTTAGGTGGAAGATAGACTAAGGGAGTTGAA
564923 AAACACTTATTATAGTCAACCTCACACAAACACTTAGGAATTTTGTTTTTAGACCGATATTTTTG
66 AAACACTTATTATAGTCAACCTCACACAAACACTTAGGAATTTTGTTTTTAGACCGATATTTTTG
*
564988 CACTACTTTTGCTGAATGAGTCTATGAAGCTTGAACAAATGGAAGATTTCAGAGAATCTAAATAG
131 CACTACTTTTGCTGAATGAGTCTATGAAGCTTGAACAAATGGAAGATTTCAGAGAACCTAAATAG
* * *
565053 AAGTTTTCTAAAA-GACAAGCAATTAAATATGCTAGTTGCTTCATTTTATTTGTATCCGATTGGA
196 AAGTGTTCTAAAATGACAAGCAATCAAATATGCTAGTTGCTTCATTTTATATGTATCCGATTGGA
565117 ATACTG
261 ATACTG
*
565123 AAAAAAACAAA-AAA-AAATTACTTAGGATTAAGTTTAGGTGGAAGATAGACTAAGGGAGTTGAA
1 AAAAAAAAAAAGAAAGAAATTACTTAGGATTAAGTTTAGGTGGAAGATAGACTAAGGGAGTTGAA
*
565186 AAACACTTATTATAGTCAACCTCACACAAGCACTTAGGAATTTTGTTTTTAGACCGATATTTTTG
66 AAACACTTATTATAGTCAACCTCACACAAACACTTAGGAATTTTGTTTTTAGACCGATATTTTTG
*
565251 CACTACTTTTGCTGAATGAGTCTATGAAGCTTGAACAAATGGAAGATTTTAGAGAACCTAAATAG
131 CACTACTTTTGCTGAATGAGTCTATGAAGCTTGAACAAATGGAAGATTTCAGAGAACCTAAATAG
*
565316 AAGTGTTCTAAAATGACAAGCAATCGAATATGCTAGTTGCTTCATTTTATATGTATCCGATTGGA
196 AAGTGTTCTAAAATGACAAGCAATCAAATATGCTAGTTGCTTCATTTTATATGTATCCGATTGGA
565381 AT
261 AT
565383 GCTAAGCCAA
Statistics
Matches: 250, Mismatches: 9, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
263 187 0.75
264 53 0.21
265 10 0.04
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.31
Consensus pattern (266 bp):
AAAAAAAAAAAGAAAGAAATTACTTAGGATTAAGTTTAGGTGGAAGATAGACTAAGGGAGTTGAA
AAACACTTATTATAGTCAACCTCACACAAACACTTAGGAATTTTGTTTTTAGACCGATATTTTTG
CACTACTTTTGCTGAATGAGTCTATGAAGCTTGAACAAATGGAAGATTTCAGAGAACCTAAATAG
AAGTGTTCTAAAATGACAAGCAATCAAATATGCTAGTTGCTTCATTTTATATGTATCCGATTGGA
ATACTG
Found at i:567108 original size:42 final size:42
Alignment explanation
Indices: 567061--567161 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 42
567051 GTTTAATGCT
* * * *
567061 TGATTAAATCCTTCGGGTTATTAGTAAGTCTTTTGAGCATGA
1 TGATTAAATCATTCGGGTCACTAGTAAGTCTTTCGAGCATGA
* *
567103 TGATTAAATCATTCGGGTCCCTAGTAAGTCTTTCGAGCATGG
1 TGATTAAATCATTCGGGTCACTAGTAAGTCTTTCGAGCATGA
* *
567145 TGATTAAGTTATTCGGG
1 TGATTAAATCATTCGGG
567162 CCATCCGTAA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.38
Consensus pattern (42 bp):
TGATTAAATCATTCGGGTCACTAGTAAGTCTTTCGAGCATGA
Found at i:567172 original size:42 final size:42
Alignment explanation
Indices: 567061--567183 Score: 124
Period size: 42 Copynumber: 2.9 Consensus size: 42
567051 GTTTAATGCT
* * *
567061 TGATTAAATCCTTCGGGT-TATTAGTAAGTCTTTTGAGCATGA
1 TGATTAAATCATTCGGGTCCA-TAGTAAGTCTTTCGAGCATGA
* *
567103 TGATTAAATCATTCGGGTCCCTAGTAAGTCTTTCGAGCATGG
1 TGATTAAATCATTCGGGTCCATAGTAAGTCTTTCGAGCATGA
* * * * *
567145 TGATTAAGTTATTCGGG-CCATCCGTAAGACTCTCGAGCA
1 TGATTAAATCATTCGGGTCCAT-AGTAAGTCTTTCGAGCA
567184 GGATACTTTT
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
41 3 0.04
42 65 0.96
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (42 bp):
TGATTAAATCATTCGGGTCCATAGTAAGTCTTTCGAGCATGA
Found at i:585734 original size:113 final size:112
Alignment explanation
Indices: 585513--585719 Score: 312
Period size: 113 Copynumber: 1.9 Consensus size: 112
585503 CAATTTTGGG
* * * *
585513 GCAACAATAGTGGCGTTTTTTGAAAAAAATATCGCAATAGGTCCATCTATAGTGGTGTTTATTGG
1 GCAACAATAGTGGCGTTTTTTGAAAAAAACACCGCAATAGGTCCATCTATAGTGATGTTTATTGA
585578 AAAAACGCCACTATATATATATACTTTTTTGGCATTTTTTTGGGCTGC
66 AAAAACGCCAC-ATATATATATACTTTTTTGGCATTTTTTTGGGCTGC
* * *
585626 GCAATAATAGTGGCTTTTTTTTG-AAAAAACGCCGCAATAGGTCCAT-TATAGTGATGTTTATTG
1 GCAACAATAGTGGC-GTTTTTTGAAAAAAACACCGCAATAGGTCCATCTATAGTGATGTTTATTG
585689 AAAAAACGCCAC-TATATATATACTTTTTTGG
65 AAAAAACGCCACATATATATATACTTTTTTGG
585720 GGCCTTTTTT
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
110 19 0.22
112 27 0.31
113 33 0.38
114 7 0.08
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (112 bp):
GCAACAATAGTGGCGTTTTTTGAAAAAAACACCGCAATAGGTCCATCTATAGTGATGTTTATTGA
AAAAACGCCACATATATATATACTTTTTTGGCATTTTTTTGGGCTGC
Found at i:585987 original size:14 final size:14
Alignment explanation
Indices: 585970--586065 Score: 58
Period size: 14 Copynumber: 6.9 Consensus size: 14
585960 TTGAATTGAA
585970 TAAATTTTAAACTT
1 TAAATTTTAAACTT
*
585984 TAAATTCTAAA--T
1 TAAATTTTAAACTT
* *
585996 TAAATTGAATAAATTT
1 TAAATT--TTAAACTT
* *
586012 TAAACTTTAAATTT
1 TAAATTTTAAACTT
586026 TAAA--TTAAA-TT
1 TAAATTTTAAACTT
586037 GAATAAATTTTAAACTT
1 ---TAAATTTTAAACTT
*
586054 TAAATTCTAAAC
1 TAAATTTTAAAC
586066 CTATCAAATG
Statistics
Matches: 67, Mismatches: 5, Indels: 20
0.73 0.05 0.22
Matches are distributed among these distances:
11 2 0.03
12 12 0.18
14 40 0.60
16 11 0.16
17 2 0.03
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (14 bp):
TAAATTTTAAACTT
Found at i:586002 original size:35 final size:35
Alignment explanation
Indices: 585937--586064 Score: 201
Period size: 35 Copynumber: 3.7 Consensus size: 35
585927 AGATAAGATC
*
585937 ATAAA-TTTAAA-TTATAAA-T-TAAATTGAATTGA
1 ATAAATTTTAAACTT-TAAATTCTAAATTAAATTGA
585969 ATAAATTTTAAACTTTAAATTCTAAATTAAATTGA
1 ATAAATTTTAAACTTTAAATTCTAAATTAAATTGA
*
586004 ATAAATTTTAAACTTTAAATTTTAAATTAAATTGA
1 ATAAATTTTAAACTTTAAATTCTAAATTAAATTGA
586039 ATAAATTTTAAACTTTAAATTCTAAA
1 ATAAATTTTAAACTTTAAATTCTAAA
586065 CCTATCAAAT
Statistics
Matches: 89, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
32 5 0.06
33 10 0.11
34 3 0.03
35 71 0.80
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (35 bp):
ATAAATTTTAAACTTTAAATTCTAAATTAAATTGA
Found at i:586718 original size:32 final size:34
Alignment explanation
Indices: 586677--586756 Score: 101
Period size: 35 Copynumber: 2.4 Consensus size: 34
586667 TTTAAATAGT
*
586677 TATTATTTTTTATATT-AAT-ATATTTATGTAAA
1 TATTATTTTTTATATTAAATAATATTTATATAAA
* *
586709 TATTATTTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTATATT-AAATAATATTTATATAAA
586744 TATTATTTATTTA
1 TATTATTT-TTTA
586757 GAATTATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
32 15 0.38
34 3 0.08
35 19 0.47
36 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (34 bp):
TATTATTTTTTATATTAAATAATATTTATATAAA
Found at i:586720 original size:34 final size:33
Alignment explanation
Indices: 586644--586751 Score: 94
Period size: 35 Copynumber: 3.1 Consensus size: 33
586634 AGTGGTAAGA
* *
586644 ATTTATTTTTATGTTAGTAT-TTT-TTTAAATAGTT
1 ATTT-TTTTTAT-TTAATATATTTATATAAATA-TT
*
586678 ATTATTTTTTATATTAATATATTTATGTAAATATT
1 ATT-TTTTTTAT-TTAATATATTTATATAAATATT
* *
586713 ATTTTTTTTATTAAAATAATATTTATATAATTATT
1 ATTTTTTTTATT-TAAT-ATATTTATATAAATATT
586748 ATTT
1 ATTT
586752 ATTTAGAATT
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
33 1 0.02
34 27 0.43
35 28 0.44
36 7 0.11
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (33 bp):
ATTTTTTTTATTTAATATATTTATATAAATATT
Found at i:588508 original size:21 final size:21
Alignment explanation
Indices: 588478--588525 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
588468 GCAGGGGTAC
* *
588478 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
588499 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
588520 ATGCCA
1 ATGCCA
588526 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:588555 original size:21 final size:21
Alignment explanation
Indices: 588529--588618 Score: 121
Period size: 21 Copynumber: 4.3 Consensus size: 21
588519 TATGCCATCT
* *
588529 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
588550 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
588571 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
588592 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
588613 CCGCAG
1 CCGCAG
588619 CTTTCAAACG
Statistics
Matches: 65, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
20 2 0.03
21 61 0.94
22 2 0.03
ACGTcount: A:0.19, C:0.37, G:0.26, T:0.19
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:591387 original size:13 final size:13
Alignment explanation
Indices: 591369--591395 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
591359 TACATAAATA
591369 TATTTAATATAAT
1 TATTTAATATAAT
591382 TATTTAATATAAT
1 TATTTAATATAAT
591395 T
1 T
591396 TAATATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTTAATATAAT
Found at i:592221 original size:13 final size:13
Alignment explanation
Indices: 592203--592236 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
592193 GTGTTAGGAC
592203 GGCCACAGTGGAG
1 GGCCACAGTGGAG
592216 GGCCACAGTGGAG
1 GGCCACAGTGGAG
*
592229 GGACACAG
1 GGCCACAG
592237 CTCCATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.26, C:0.24, G:0.44, T:0.06
Consensus pattern (13 bp):
GGCCACAGTGGAG
Found at i:596707 original size:31 final size:31
Alignment explanation
Indices: 596633--596708 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
596623 TTAACTTGGG
*
596633 GTGACTACATCTTAATTAAATAAAAATGAAA
1 GTGACTACATCTTAATTAAATAAAAACGAAA
*
596664 ATGA-TCACATCTTAATTAAATAAAAACGAAA
1 GTGACT-ACATCTTAATTAAATAAAAACGAAA
*
596695 GTGACTATATCTTA
1 GTGACTACATCTTA
596709 TGTTTTTTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 1 0.03
31 37 0.95
32 1 0.03
ACGTcount: A:0.49, C:0.12, G:0.09, T:0.30
Consensus pattern (31 bp):
GTGACTACATCTTAATTAAATAAAAACGAAA
Found at i:597533 original size:28 final size:27
Alignment explanation
Indices: 597502--597587 Score: 100
Period size: 28 Copynumber: 3.1 Consensus size: 27
597492 GATTGGGATG
* *
597502 AATATAAATGAACGAACATAAGCGAACA
1 AATATAAATAAACGAACATAA-TGAACA
* *
597530 AATATAAATAAACAAACATGAATAAACA
1 AATATAAATAAACGAACAT-AATGAACA
*
597558 AACATAAATAAACGAACATAAATGAACA
1 AATATAAATAAACGAACAT-AATGAACA
597586 AA
1 AA
597588 GTACCAAATG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
28 47 0.96
29 2 0.04
ACGTcount: A:0.64, C:0.13, G:0.08, T:0.15
Consensus pattern (27 bp):
AATATAAATAAACGAACATAATGAACA
Found at i:597543 original size:14 final size:14
Alignment explanation
Indices: 597526--597587 Score: 88
Period size: 14 Copynumber: 4.4 Consensus size: 14
597516 AACATAAGCG
*
597526 AACAAATATAAATA
1 AACAAACATAAATA
*
597540 AACAAACATGAATA
1 AACAAACATAAATA
597554 AACAAACATAAATA
1 AACAAACATAAATA
* *
597568 AACGAACATAAATG
1 AACAAACATAAATA
597582 AACAAA
1 AACAAA
597588 GTACCAAATG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 42 1.00
ACGTcount: A:0.68, C:0.13, G:0.05, T:0.15
Consensus pattern (14 bp):
AACAAACATAAATA
Found at i:598777 original size:23 final size:23
Alignment explanation
Indices: 598751--598836 Score: 91
Period size: 23 Copynumber: 3.7 Consensus size: 23
598741 TACGCGTTCT
598751 TTCGGGACAATTCTATGTGGTCA
1 TTCGGGACAATTCTATGTGGTCA
* ** * *
598774 TTCGAGACCTTTCTACGTGGTCC
1 TTCGGGACAATTCTATGTGGTCA
* * *
598797 TTCGGGACAATACTATCTGGTCT
1 TTCGGGACAATTCTATGTGGTCA
*
598820 TTCGGGACATTTCTATG
1 TTCGGGACAATTCTATG
598837 CGCAGTTTAT
Statistics
Matches: 48, Mismatches: 15, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (23 bp):
TTCGGGACAATTCTATGTGGTCA
Found at i:599008 original size:2 final size:2
Alignment explanation
Indices: 599003--599047 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
598993 TATATATATA
* *
599003 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG CG TG CG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
599045 TG T
1 TG T
599048 ACATACATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.04, G:0.49, T:0.47
Consensus pattern (2 bp):
TG
Found at i:603071 original size:20 final size:20
Alignment explanation
Indices: 603043--603105 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
603033 AGGGTCTGGG
**
603043 TATCAATACTGGATGAACAA
1 TATCAATACCAGATGAACAA
* * *
603063 TATCGATACCAGATGAGCAG
1 TATCAATACCAGATGAACAA
603083 TATCAATACCAGATGAAC-A
1 TATCAATACCAGATGAACAA
603102 TATC
1 TATC
603106 GATATCATAA
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
19 4 0.11
20 31 0.89
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (20 bp):
TATCAATACCAGATGAACAA
Found at i:604100 original size:23 final size:23
Alignment explanation
Indices: 604074--604159 Score: 91
Period size: 23 Copynumber: 3.7 Consensus size: 23
604064 GCGGTACTTT
*
604074 GGGACAATTCTACGTGGTTCTTC
1 GGGACAATTCTACGTGGTCCTTC
* * *
604097 GGGACATTTCTACGCGGTCCTTT
1 GGGACAATTCTACGTGGTCCTTC
* *
604120 GGGACAATACTATGTGGTCCTTC
1 GGGACAATTCTACGTGGTCCTTC
* * *
604143 GAGACATTTCTATGTGG
1 GGGACAATTCTACGTGG
604160 CATTTCGGTG
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.34
Consensus pattern (23 bp):
GGGACAATTCTACGTGGTCCTTC
Found at i:604137 original size:46 final size:46
Alignment explanation
Indices: 604058--604154 Score: 140
Period size: 46 Copynumber: 2.1 Consensus size: 46
604048 GAGTCGAGGG
* * * *
604058 TTCTGCGCGGTACTTTGGGACAATTCTACGTGGTTCTTCGGGACAT
1 TTCTACGCGGTACTTTGGGACAATACTACGTGGTCCTTCGAGACAT
* *
604104 TTCTACGCGGTCCTTTGGGACAATACTATGTGGTCCTTCGAGACAT
1 TTCTACGCGGTACTTTGGGACAATACTACGTGGTCCTTCGAGACAT
604150 TTCTA
1 TTCTA
604155 TGTGGCATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.18, C:0.23, G:0.25, T:0.35
Consensus pattern (46 bp):
TTCTACGCGGTACTTTGGGACAATACTACGTGGTCCTTCGAGACAT
Found at i:606076 original size:2 final size:2
Alignment explanation
Indices: 606069--606149 Score: 69
Period size: 2 Copynumber: 42.0 Consensus size: 2
606059 TTCCTTTATT
* * * *
606069 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TT TA TG TA TA TT TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
606110 TA T- TT TA TT TA T- TA TA CA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
606150 ATCATCGTTA
Statistics
Matches: 64, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
1 3 0.05
2 61 0.95
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (2 bp):
TA
Found at i:607876 original size:10 final size:10
Alignment explanation
Indices: 607861--607894 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
607851 TTCATTTACC
607861 ATTTATTTTT
1 ATTTATTTTT
607871 ATTTATTTTT
1 ATTTATTTTT
* *
607881 ATCTATTTCT
1 ATTTATTTTT
607891 ATTT
1 ATTT
607895 TACTAACGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:617925 original size:12 final size:12
Alignment explanation
Indices: 617908--617941 Score: 54
Period size: 10 Copynumber: 3.0 Consensus size: 12
617898 AGGAGCATCT
617908 TCAAAAAAAAAA
1 TCAAAAAAAAAA
617920 TC--AAAAAAAA
1 TCAAAAAAAAAA
617930 TCAAAAAAAAAA
1 TCAAAAAAAAAA
617942 AATCATCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 10 0.50
12 10 0.50
ACGTcount: A:0.82, C:0.09, G:0.00, T:0.09
Consensus pattern (12 bp):
TCAAAAAAAAAA
Found at i:617927 original size:10 final size:10
Alignment explanation
Indices: 617912--617939 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
617902 GCATCTTCAA
617912 AAAAAAAATC
1 AAAAAAAATC
617922 AAAAAAAATC
1 AAAAAAAATC
617932 AAAAAAAA
1 AAAAAAAA
617940 AAAATCATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.86, C:0.07, G:0.00, T:0.07
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:618317 original size:105 final size:105
Alignment explanation
Indices: 618135--618594 Score: 911
Period size: 105 Copynumber: 4.4 Consensus size: 105
618125 AGGTTTCACC
*
618135 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTACAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
618200 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
618240 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
618305 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
618345 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
618410 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
618450 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
618515 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
618555 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
618595 TGAACAATAC
Statistics
Matches: 354, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 354 1.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
Found at i:620418 original size:48 final size:44
Alignment explanation
Indices: 620339--620441 Score: 111
Period size: 48 Copynumber: 2.2 Consensus size: 44
620329 CTACTATTAT
*
620339 TATATACTATATTTTCATTATTATTATATTTTATTCCTTTATTTATATA
1 TATATA-TATATTTTCATTATTATTATATTTTA-T--TTTA-TTATACA
*
620388 TATATATATATTTT-ATGTA-TATTTTTATTTTATTTTATTATACA
1 TATATATATATTTTCAT-TATTA-TTATATTTTATTTTATTATACA
620432 TATATATATA
1 TATATATATA
620442 CATATATCGT
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
44 16 0.32
45 4 0.08
47 5 0.10
48 19 0.38
49 6 0.12
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.61
Consensus pattern (44 bp):
TATATATATATTTTCATTATTATTATATTTTATTTTATTATACA
Found at i:620853 original size:17 final size:17
Alignment explanation
Indices: 620809--620865 Score: 57
Period size: 16 Copynumber: 3.5 Consensus size: 17
620799 TATACGTACA
*
620809 TATTTGATTATAGTTATT
1 TATTT-ATTTTAGTTATT
620827 TATTTATTTTAGTT-TT
1 TATTTATTTTAGTTATT
* *
620843 TTTTTAGTTT--TTATT
1 TATTTATTTTAGTTATT
620858 TATTTATT
1 TATTTATT
620866 ACTATTATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
14 2 0.06
15 8 0.24
16 10 0.30
17 8 0.24
18 5 0.15
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (17 bp):
TATTTATTTTAGTTATT
Found at i:622187 original size:18 final size:18
Alignment explanation
Indices: 622164--622198 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
622154 AACTTTAATC
*
622164 GAACAAATGAACGAACAT
1 GAACAAATAAACGAACAT
*
622182 GAACAACTAAACGAACA
1 GAACAAATAAACGAACA
622199 AAATTTCTTG
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:0.57, C:0.20, G:0.14, T:0.09
Consensus pattern (18 bp):
GAACAAATAAACGAACAT
Found at i:622215 original size:107 final size:107
Alignment explanation
Indices: 622029--622259 Score: 435
Period size: 107 Copynumber: 2.2 Consensus size: 107
622019 ATGAGGATAT
*
622029 GTTCATGTTCATTTGTTTAACTTTAATCGAACAAATGAACGAACATGAACAACTAAATGAACAAA
1 GTTCATGTTCATTTGTTTAACTTTAATCGAACAAATGAACGAACATGAACAACTAAACGAACAAA
622094 ATTTCTTGTTCGTTCATTAAGAAATGTAGTTTGTTTGTGTTC
66 ATTTCTTGTTCGTTCATTAAGAAATGTAGTTTGTTTGTGTTC
* *
622136 GTTCATGTCCGTTTGTTTAACTTTAATCGAACAAATGAACGAACATGAACAACTAAACGAACAAA
1 GTTCATGTTCATTTGTTTAACTTTAATCGAACAAATGAACGAACATGAACAACTAAACGAACAAA
622201 ATTTCTTGTTCGTTCATTAAGAAATGTAGTTTGTTTGTGTTC
66 ATTTCTTGTTCGTTCATTAAGAAATGTAGTTTGTTTGTGTTC
622243 GTTCATGTTCATTTGTT
1 GTTCATGTTCATTTGTT
622260 AAAATGATAA
Statistics
Matches: 119, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
107 119 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.39
Consensus pattern (107 bp):
GTTCATGTTCATTTGTTTAACTTTAATCGAACAAATGAACGAACATGAACAACTAAACGAACAAA
ATTTCTTGTTCGTTCATTAAGAAATGTAGTTTGTTTGTGTTC
Found at i:625475 original size:35 final size:35
Alignment explanation
Indices: 625426--625670 Score: 303
Period size: 35 Copynumber: 7.0 Consensus size: 35
625416 GTTAATAAGA
*
625426 AGAACGAAAGGAAGCATCACACTTTCGATTCAAGT
1 AGAACGGAAGGAAGCATCACACTTTCGATTCAAGT
* *
625461 CGAACGGAATGAAGCATCACACTTTCGATTCAAGT
1 AGAACGGAAGGAAGCATCACACTTTCGATTCAAGT
* * * * **
625496 CGAACAGAA-TAAGATATTGCACTTTCGATTCAAGT
1 AGAACGGAAGGAAG-CATCACACTTTCGATTCAAGT
* ** *
625531 AGAACGAAAGGAAAAATCATACTTTCGATTCAAGT
1 AGAACGGAAGGAAGCATCACACTTTCGATTCAAGT
625566 AGAACGGAAGGAAGCATCACACTTTCGATTCAAGT
1 AGAACGGAAGGAAGCATCACACTTTCGATTCAAGT
* * *
625601 AGAATGAAAGGAAGCATCACACTTTTGATTCAAGT
1 AGAACGGAAGGAAGCATCACACTTTCGATTCAAGT
* **
625636 CGAACGGAAGGAAGCATTGCACTTTCGATTCAAGT
1 AGAACGGAAGGAAGCATCACACTTTCGATTCAAGT
625671 GTTTATCTTT
Statistics
Matches: 178, Mismatches: 30, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
34 3 0.02
35 173 0.97
36 2 0.01
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.23
Consensus pattern (35 bp):
AGAACGGAAGGAAGCATCACACTTTCGATTCAAGT
Found at i:626800 original size:15 final size:16
Alignment explanation
Indices: 626776--626818 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
626766 ATTTTAACTC
626776 AAAA-TAAAATAA-TA
1 AAAATTAAAATAATTA
*
626790 ACAATTAAAATAATTA
1 AAAATTAAAATAATTA
626806 AAAATTAAAATAA
1 AAAATTAAAATAA
626819 ATATTAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 3 0.12
15 8 0.32
16 14 0.56
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATTAAAATAATTA
Found at i:628286 original size:182 final size:183
Alignment explanation
Indices: 627905--628505 Score: 915
Period size: 182 Copynumber: 3.3 Consensus size: 183
627895 CGATACAAAT
* * *
627905 AAAATGTATCGATCCATAATAGTATAACAGGTAAAAATATGATC-AAACCGGT-T-TAATTATGA
1 AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGA-CAAAACCGGTCTCGAA--ATGA
* * * *
627967 TAAAACCGGTAAAACACTACCTAATATGTTTAAAGTATCGATTCCATTGAAATAAGTATTGACAC
63 CAAAACCGGTAAAGCGCTACCTAATATGTTTAAAGTATCGATTCCATTGAAATAAGTATCGACAC
*
628032 TTATGGAATTTAAAAGAGAAGCAATAATAGCGCCTATAAAGTGTCGATACTTTATA
128 TTATGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTATA
*
628088 AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAAAAAACCGGTCTCGAAATGACAA
1 AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAA
* * * * * *
628153 AACCTGTAAAGCGTTACCTAATATGTTGAAAGTATCGA-TAC-TTTAATATAAGTATCGAAACTT
66 AACCGGTAAAGCGCTACCTAATATGTTTAAAGTATCGATTCCATTGAA-ATAAGTATCGACACTT
* *
628216 TTGGAATTTAAAAGAAAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTATA
130 ATGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTATA
*
628270 AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACAGGTCTCGAAATGACAA
1 AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAA
*
628335 AATCGGTAAAGCGCTACCTAATATGTTTAAAGTATCGATTCCATTGAAATAAGTATCGACACTTA
66 AACCGGTAAAGCGCTACCTAATATGTTTAAAGTATCGATTCCATTGAAATAAGTATCGACACTTA
* *
628400 TGAAATTTAAAAGAGAAGCAGTAATAGCGCCAATAAAGTGTCGATACTTTATAA
131 TGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTAT-A
* *
628454 AAAATGTATCGATCCATAACAATGTAACAGGTAAAAATATGACAAAATCGGT
1 AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGT
628506 AAAGCGCTAC
Statistics
Matches: 378, Mismatches: 33, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
181 4 0.01
182 164 0.43
183 153 0.40
184 55 0.15
185 2 0.01
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (183 bp):
AAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAA
AACCGGTAAAGCGCTACCTAATATGTTTAAAGTATCGATTCCATTGAAATAAGTATCGACACTTA
TGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTATA
Found at i:630543 original size:22 final size:23
Alignment explanation
Indices: 630492--630545 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
630482 ATGTTTTTGT
630492 TTTA-TATATAAAATGATAGTATA
1 TTTATTATATAAAATGATAG-ATA
630515 TTTATTATATAAAATGATA-A-A
1 TTTATTATATAAAATGATAGATA
630536 TTTAATTATA
1 TTT-ATTATA
630546 AATTTAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.14
22 7 0.24
23 4 0.14
24 14 0.48
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (23 bp):
TTTATTATATAAAATGATAGATA
Found at i:630548 original size:12 final size:12
Alignment explanation
Indices: 630531--630560 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
630521 ATATAAAATG
630531 ATAAATTTAATT
1 ATAAATTTAATT
630543 ATAAATTTAATT
1 ATAAATTTAATT
630555 ATAAAT
1 ATAAAT
630561 ACAGGTTGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATAAATTTAATT
Found at i:630818 original size:18 final size:17
Alignment explanation
Indices: 630786--630821 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
630776 GAAGGTTATT
*
630786 GGCAAGGAGGTAGAGGA
1 GGCAAGGAGGCAGAGGA
630803 GGCAATGGAGGCAGAGGA
1 GGCAA-GGAGGCAGAGGA
630821 G
1 G
630822 AATAAAGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.33, C:0.08, G:0.53, T:0.06
Consensus pattern (17 bp):
GGCAAGGAGGCAGAGGA
Found at i:632934 original size:66 final size:66
Alignment explanation
Indices: 632846--633088 Score: 432
Period size: 66 Copynumber: 3.7 Consensus size: 66
632836 TTGTATCTGA
* * *
632846 ATGTAATTATGTTTGAGGTGAGAAAAGTTAGCAATAGGTTGTTGTACATGTTTCTTATACATGTT
1 ATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGATTGTTGTACATGTTTCTTATACATGTT
632911 G
66 G
632912 ATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGATTGTTGTACATGTTTCTTATACATGTT
1 ATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGATTGTTGTACATGTTTCTTATACATGTT
632977 G
66 G
* *
632978 ATGTGATTATGTATGAGATGAGAAAAGTTAGCAATAGGTTGTTGTACATGTTTCTTATACATGTT
1 ATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGATTGTTGTACATGTTTCTTATACATGTT
633043 G
66 G
*
633044 ATGTAATTATGTATGAGATGAGAAAAGTTAGTAATAGATTGTTGT
1 ATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGATTGTTGT
633089 TGAATGTAAT
Statistics
Matches: 169, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 169 1.00
ACGTcount: A:0.32, C:0.05, G:0.23, T:0.40
Consensus pattern (66 bp):
ATGTAATTATGTATGAGATGAGAAAAGTTAGCAATAGATTGTTGTACATGTTTCTTATACATGTT
G
Found at i:633106 original size:48 final size:48
Alignment explanation
Indices: 633039--633176 Score: 242
Period size: 48 Copynumber: 2.9 Consensus size: 48
633029 TTCTTATACA
633039 TGTTG-ATGTAATTATGTATGAGATGAGAAAAGTTAGTAATAGATTGT
1 TGTTGAATGTAATTATGTATGAGATGAGAAAAGTTAGTAATAGATTGT
633086 TGTTGAATGTAATTATGTATGAGATGAGAAAAGTTAGTAATAGATTGT
1 TGTTGAATGTAATTATGTATGAGATGAGAAAAGTTAGTAATAGATTGT
* * *
633134 TGCTGAATGTAATTATGTGTGAGATGAGAAAAGTTAGCAATAG
1 TGTTGAATGTAATTATGTATGAGATGAGAAAAGTTAGTAATAG
633177 GGTGTTCTAC
Statistics
Matches: 87, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
47 5 0.06
48 82 0.94
ACGTcount: A:0.37, C:0.01, G:0.26, T:0.36
Consensus pattern (48 bp):
TGTTGAATGTAATTATGTATGAGATGAGAAAAGTTAGTAATAGATTGT
Found at i:634050 original size:201 final size:200
Alignment explanation
Indices: 633703--635065 Score: 1725
Period size: 201 Copynumber: 6.8 Consensus size: 200
633693 AATACGTAAA
* * *
633703 CATAAAGTGTCGATACATTTATTAAAAGTATCGATCCTC-AAAATATCGAAACCAATAATTATAA
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCC-CAAAAACATCGAAACCCATAATTATAA
* * * * * * * *
633767 TGTAATAGGTAAATTTT-CAATGTAACCGGTAGAAATATATCGGTTTTATGAGAGAATAGGTCTA
65 TGTAATAGGT-AATTTTGCAATGTAACCGGTATAAATATACCGGTTTAATTAGAAAACATGTCAA
* * *
633831 CAGAATGTATCGACACTTTTGAAATTTGTGTCGATATTTTTTGTCCAGAATGAATGCCTAAACGA
129 CATAATGTATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCC-AAACGA
633896 GGTGCACG
193 GGTGCACG
*
633904 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATACT
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAAT
* * *
633969 GTAATAGGTAATTTTGCAATGTAACCGATAAAAATATATCGGTTTAATTAGAAAACATGTCAACA
66 GTAATAGGTAATTTTGCAATGTAACCGGTATAAATATACCGGTTTAATTAGAAAACATGTCAACA
* * * * *
634034 TAATGTATCAACACTTTTTAAATTTGTGTCGATACATTTTGCCCAGAATGAATGTCAAACTAGGT
131 TAATGTATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGAGGT
634099 GCACG
196 GCACG
* ** * * * * *
634104 CATAAAGTGTTGATACATTTA-AAATTGTATCGATCCTAAAAACATTGAAACCGATACTTACAAT
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAAT
* * * * * * * * * * * *
634168 GTAATAAGTAAATTTACAATGTTACCGATAGAAATATACCAGTTTTATGAGAGAATATGTCTACA
66 GTAATAGGTAATTTTGCAATGTAACCGGTATAAATATACCGGTTTAATTAGAAAACATGTCAACA
* * * *
634233 TAATATATCGATACTTTTTAAATTTGTGTCGATACTTTTTGCCCAGAATGAATGCCCAAATGAGG
131 TAATGTATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATG-CCAAACGAGG
634298 TGCACG
195 TGCACG
* *
634304 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAATCATCGAAACTCATAATTATAAT
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAAT
* *
634369 GTAATAGGCAATTTTGCAATGTAACCGGTATAAATATACCAGTTTAATTAGAAAACA-GTTCAAC
66 GTAATAGGTAATTTTGCAATGTAACCGGTATAAATATACCGGTTTAATTAGAAAACATG-TCAAC
* * * * *
634433 ATAATGTATCGATACTTTTTAAATTTGTGTCGATACTTGTTGTCCAAAAATGAATGACAAACTAG
130 ATAATGTATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCC-AGAATGAATGCCAAACGAG
*
634498 CTGCACG
194 GTGCACG
*
634505 CATAAAGTGTCGATACA-TT-T--AAATTATCGATCCCAAAAACATCGAAACCCATAATTATAAT
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAAT
* * * *
634566 GTAAAAGGTAATTTTTGCAATGTAACTGGTATAAATATATCTGG-TTAATTAGAAAACATGTTAA
66 GTAATAGGTAA-TTTTGCAATGTAACCGGTATAAATATA-CCGGTTTAATTAGAAAACATGTCAA
634630 CATAATGTATCGACACTTTTTAAATTTGTGTCGATAC---TTGTCCAGAATGAATGCCCAAACGA
129 CATAATGTATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATG-CCAAACGA
* *
634692 AGTGCATG
193 GGTGCACG
* * *
634700 CATAAAGTCTCGATACATTTATAAAAAGTATCGATCCCAAAATCATCAAAACCCA-AATTAT-A-
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAAT
* * * *
634762 -TAATAGGTAACTTTGTAATGTAACCGATATAAATATACCAGTTTAATTAGAAAACATGTCAACA
66 GTAATAGGTAATTTTGCAATGTAACCGGTATAAATATACCGGTTTAATTAGAAAACATGTCAACA
* * * * * *
634826 TAATGTATCGACATTTTTTATATTTGTGTCGATACTTGTTGTCCAGAAATGAATGACAAACTAGC
131 TAATGTATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAG-AATGAATGCCAAACGAGG
634891 TGCACG
195 TGCACG
* ** * *
634897 CATAAAGTGTCGATACATTT-GAAATTGTATAGATCCCAAAAACATCGAAATCCATAATTATAAT
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAAT
* * * * *
634961 GTAATAGGTAATTTTGCAATATAACCGGTAAAAATATACCGGATTAATTAGAAAACGTGTTAACA
66 GTAATAGGTAATTTTGCAATGTAACCGGTATAAATATACCGGTTTAATTAGAAAACATGTCAACA
*
635026 TAATGTATCGACACTTTTTAAATTTGTTTCGATACTTTTT
131 TAATGTATCGACACTTTTTAAATTTGTGTCGATACTTTTT
635066 TAAAATTACG
Statistics
Matches: 1005, Mismatches: 134, Indels: 47
0.85 0.11 0.04
Matches are distributed among these distances:
193 2 0.00
194 86 0.09
195 42 0.04
196 29 0.03
197 93 0.09
198 94 0.09
199 170 0.17
200 167 0.17
201 313 0.31
202 9 0.01
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.32
Consensus pattern (200 bp):
CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAAT
GTAATAGGTAATTTTGCAATGTAACCGGTATAAATATACCGGTTTAATTAGAAAACATGTCAACA
TAATGTATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGAGGT
GCACG
Found at i:635411 original size:18 final size:16
Alignment explanation
Indices: 635371--635413 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
635361 TTCTCAAAGC
635371 TCTTCTCAACCAAACT
1 TCTTCTCAACCAAACT
*
635387 T-TTCTCAACGACAACCT
1 TCTTCTCAAC--CAAACT
635404 TCTTCTCAAC
1 TCTTCTCAAC
635414 TAATCCCTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 8 0.35
16 1 0.04
17 6 0.26
18 8 0.35
ACGTcount: A:0.28, C:0.37, G:0.02, T:0.33
Consensus pattern (16 bp):
TCTTCTCAACCAAACT
Found at i:638372 original size:3 final size:3
Alignment explanation
Indices: 638364--638394 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
638354 TTAATTCGAG
*
638364 ATA ATA ATA ATA ATG ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
638395 ATATTATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:638383 original size:15 final size:15
Alignment explanation
Indices: 638363--638392 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
638353 GTTAATTCGA
638363 GATAATAATAATAAT
1 GATAATAATAATAAT
638378 GATAATAATAATAAT
1 GATAATAATAATAAT
638393 AAATATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (15 bp):
GATAATAATAATAAT
Found at i:643897 original size:14 final size:14
Alignment explanation
Indices: 643878--643905 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
643868 CATGATACTG
643878 ATCTTGAATGTGTT
1 ATCTTGAATGTGTT
643892 ATCTTGAATGTGTT
1 ATCTTGAATGTGTT
643906 TCAGGTTGTT
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:0.21, C:0.07, G:0.21, T:0.50
Consensus pattern (14 bp):
ATCTTGAATGTGTT
Found at i:647420 original size:2 final size:2
Alignment explanation
Indices: 647413--647458 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
647403 ACCATATAAC
647413 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
647455 AT AT
1 AT AT
647459 CATGTAAAAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:647791 original size:29 final size:30
Alignment explanation
Indices: 647749--647820 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
647739 CCCGAAGGAC
*
647749 CTATCCAGAGGTCACAAAG-ACCCCGGTAA
1 CTATCCAGAGGTCACAAAGAACCCCGGCAA
* *
647778 CTATCCAGAGGTCATAAAGAACCTCGGCAA
1 CTATCCAGAGGTCACAAAGAACCCCGGCAA
* *
647808 CTGTCCATAGGTC
1 CTATCCAGAGGTC
647821 CCGACGAACC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 18 0.49
30 19 0.51
ACGTcount: A:0.32, C:0.29, G:0.21, T:0.18
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCCCGGCAA
Found at i:647844 original size:31 final size:31
Alignment explanation
Indices: 647806--647870 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
647796 GAACCTCGGC
*
647806 AACTGTCCATAGGTCCCGACGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
647837 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
647868 AAC
1 AAC
647871 CCTCGACTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.32, C:0.28, G:0.22, T:0.18
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAGAACCTAGGTA
Found at i:648944 original size:64 final size:63
Alignment explanation
Indices: 648866--649006 Score: 169
Period size: 64 Copynumber: 2.2 Consensus size: 63
648856 TCTTTAACAT
* *
648866 GTGCATCGATGCACTACC-CATGCATCGATACACAAATTACCTTCGATGTTTTCAT-TTTAAAGG
1 GTGCATCGATGCACT-CCTCATGCATCGATACACAAATTACATTCGATG-TTTCATCTTTAAAGA
* * * * * *
648929 GATGCATCGATGCACTCCTTATGCATCGATGCACCATTTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
648993 GTGCATCGATGCAC
1 GTGCATCGATGCAC
649007 ATTCAATGTG
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
63 21 0.31
64 46 0.69
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
Found at i:649789 original size:24 final size:24
Alignment explanation
Indices: 649745--649790 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
649735 GTTACAGTTA
*
649745 TAGTCTGTTATAACTTATGGTTGT
1 TAGTCTGTTATAACTGATGGTTGT
*
649769 TAGT-TGTTATAGCTGAGTGGTT
1 TAGTCTGTTATAACTGA-TGGTT
649791 ATGCCGTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.20, C:0.07, G:0.26, T:0.48
Consensus pattern (24 bp):
TAGTCTGTTATAACTGATGGTTGT
Done.