Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 99 of 228
Found at i:28702887 original size:51 final size:51
Alignment explanation
Indices: 28702824--28702928 Score: 201
Period size: 51 Copynumber: 2.1 Consensus size: 51
28702814 TATAATTAAG
28702824 TTATGTAAGTTATGTGAGTTATGTAAGTTATGATATGATATATATAAGTTA
1 TTATGTAAGTTATGTGAGTTATGTAAGTTATGATATGATATATATAAGTTA
*
28702875 TTATGTATGTTATGTGAGTTATGTAAGTTATGATATGATATATATAAGTTA
1 TTATGTAAGTTATGTGAGTTATGTAAGTTATGATATGATATATATAAGTTA
28702926 TTA
1 TTA
28702929 AGTTAAGATC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (51 bp):
TTATGTAAGTTATGTGAGTTATGTAAGTTATGATATGATATATATAAGTTA
Found at i:28705091 original size:14 final size:14
Alignment explanation
Indices: 28705068--28705115 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
28705058 CCCCAAAAAT
28705068 CTAAACCTTAAACC
1 CTAAACCTTAAACC
* *
28705082 CTAAATCTTAAAATC
1 CTAAACCTT-AAACC
*
28705097 ATAAACCTTAAACC
1 CTAAACCTTAAACC
28705111 CTAAA
1 CTAAA
28705116 ATAAAATATT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.25
Consensus pattern (14 bp):
CTAAACCTTAAACC
Found at i:28705094 original size:29 final size:29
Alignment explanation
Indices: 28705047--28705115 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
28705037 TATACGGAAA
28705047 TAAACCCTAAACCCCAAAAATC-TAAACCT
1 TAAACCCTAAACCCC-AAAATCATAAACCT
* **
28705076 TAAACCCTAAATCTTAAAATCATAAACCT
1 TAAACCCTAAACCCCAAAATCATAAACCT
28705105 TAAACCCTAAA
1 TAAACCCTAAA
28705116 ATAAAATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 6 0.17
29 30 0.83
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (29 bp):
TAAACCCTAAACCCCAAAATCATAAACCT
Found at i:28705101 original size:22 final size:22
Alignment explanation
Indices: 28705076--28705117 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
28705066 ATCTAAACCT
* *
28705076 TAAACCCTAAATCTTAAAATCA
1 TAAACCCTAAACCCTAAAATCA
*
28705098 TAAACCTTAAACCCTAAAAT
1 TAAACCCTAAACCCTAAAAT
28705118 AAAATATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (22 bp):
TAAACCCTAAACCCTAAAATCA
Found at i:28705485 original size:84 final size:84
Alignment explanation
Indices: 28705351--28705520 Score: 268
Period size: 84 Copynumber: 2.0 Consensus size: 84
28705341 AGCGCCATTA
*
28705351 AAAAACTTAATTCCCTATAGTGAAACGATGACGTTTAAGTCAAATTGGTATCGCAATTTTGCGGC
1 AAAAACTTAATTCCCTATAGTGAAACGACGACGTTTAAGTCAAATTGGTATCGCAATTTTGCGGC
28705416 GTTTATGAAAAACGCCACT
66 GTTTATGAAAAACGCCACT
* * * * * * *
28705435 AAAAACTTGATTCCTTGTAGTGAAACGACGCCGTTTAAGTCAAATTGGTATTGCAGTTTTGCGGT
1 AAAAACTTAATTCCCTATAGTGAAACGACGACGTTTAAGTCAAATTGGTATCGCAATTTTGCGGC
28705500 GTTTATGAAAAACGCCACT
66 GTTTATGAAAAACGCCACT
28705519 AA
1 AA
28705521 TGTATAACCT
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
84 78 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (84 bp):
AAAAACTTAATTCCCTATAGTGAAACGACGACGTTTAAGTCAAATTGGTATCGCAATTTTGCGGC
GTTTATGAAAAACGCCACT
Found at i:28705619 original size:101 final size:101
Alignment explanation
Indices: 28705452--28705643 Score: 276
Period size: 101 Copynumber: 1.9 Consensus size: 101
28705442 TGATTCCTTG
* * * * **
28705452 TAGTGAAACGACGCCGTTTAAGTCAAATTGGTATTGCAGTTTTGCGGTGTTTATGAAAAACGCCA
1 TAGTAAAACGAAGCCGTTTAAGTCAAATTGGTATTGCAATTTTGCAGCATTTATGAAAAACGCCA
*
28705517 CTAATGTATAACCTTTACGGCGTTTTTAATTCCCTA
66 CTAACGTATAACCTTTACGGCGTTTTTAATTCCCTA
* * *
28705553 TAGTAAAACGAAGCCGTTTAAGTCAAATTGGTATTGTAATTTTGCAGCATTTCTGAAAAATGCCA
1 TAGTAAAACGAAGCCGTTTAAGTCAAATTGGTATTGCAATTTTGCAGCATTTATGAAAAACGCCA
* *
28705618 CTAACGTATAACCTTTGCGGTGTTTT
66 CTAACGTATAACCTTTACGGCGTTTT
28705644 CAGTCAAAAT
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
101 79 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (101 bp):
TAGTAAAACGAAGCCGTTTAAGTCAAATTGGTATTGCAATTTTGCAGCATTTATGAAAAACGCCA
CTAACGTATAACCTTTACGGCGTTTTTAATTCCCTA
Found at i:28705788 original size:124 final size:124
Alignment explanation
Indices: 28705567--28705792 Score: 301
Period size: 124 Copynumber: 1.8 Consensus size: 124
28705557 AAAACGAAGC
* ** *
28705567 CGTTTAAGTCAAATTGGTATTGTAATTTTGCAGCATTTCTGAAAAATGCCACTAACGTATAACCT
1 CGTTTAAGTCAAATTGGTATTGCAATTTTGCAGCATTTCAAAAAAAAGCCACTAACGTATAACCT
* ** * *
28705632 TTGCGGTGTTTTCAGTCAAAATACCACTAAAAATTTAATGTTTTGTAGTGAAACAATGA
66 TTACGGCATTTTCAATCAAAACACCACTAAAAATTTAATGTTTTGTAGTGAAACAATGA
* * * *
28705691 CGTTTAAGTCGAATTGGTATTGCAATTTTGCAGCGTTT-AAAAAAAAGCCACTAATGTATCACCT
1 CGTTTAAGTCAAATTGGTATTGCAATTTTGCAGCATTTCAAAAAAAAGCCACTAACGTATAACCT
* *
28705755 TTATGGCATTTTCAATCAAAACGCCACTAAAAAATTTA
66 TTACGGCATTTTCAATCAAAACACCACT-AAAAATTTA
28705793 TTTCCTGTAG
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
123 42 0.49
124 44 0.51
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (124 bp):
CGTTTAAGTCAAATTGGTATTGCAATTTTGCAGCATTTCAAAAAAAAGCCACTAACGTATAACCT
TTACGGCATTTTCAATCAAAACACCACTAAAAATTTAATGTTTTGTAGTGAAACAATGA
Found at i:28705802 original size:123 final size:124
Alignment explanation
Indices: 28705567--28705807 Score: 299
Period size: 123 Copynumber: 2.0 Consensus size: 124
28705557 AAAACGAAGC
* ** *
28705567 CGTTTAAGTCAAATTGGTATTGTAATTTTGCAGCATTTCTGAAAAATGCCACTAACGTATAACCT
1 CGTTTAAGTCAAATTGGTATTGCAATTTTGCAGCATTTCAAAAAAAAGCCACTAACGTATAACCT
* ** * * *
28705632 TTGCGGTGTTTTCAGTCAAAATACCACTAAAAATTTAATGTTTTGTAGTGAAACAATGA
66 TTACGGCATTTTCAATCAAAACACCACTAAAAATTTAATGTTCTGTAGTGAAACAATGA
* * * *
28705691 CGTTTAAGTCGAATTGGTATTGCAATTTTGCAGCGTTT-AAAAAAAAGCCACTAATGTATCACCT
1 CGTTTAAGTCAAATTGGTATTGCAATTTTGCAGCATTTCAAAAAAAAGCCACTAACGTATAACCT
* *
28705755 TTATGGCATTTTCAATCAAAACGCCACTAAAAAATTT-AT-TTCCTGTAGTGAAA
66 TTACGGCATTTTCAATCAAAACACCACT-AAAAATTTAATGTT-CTGTAGTGAAA
28705808 TGGCGTTGTT
Statistics
Matches: 99, Mismatches: 16, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
122 2 0.02
123 54 0.55
124 43 0.43
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (124 bp):
CGTTTAAGTCAAATTGGTATTGCAATTTTGCAGCATTTCAAAAAAAAGCCACTAACGTATAACCT
TTACGGCATTTTCAATCAAAACACCACTAAAAATTTAATGTTCTGTAGTGAAACAATGA
Found at i:28709999 original size:15 final size:15
Alignment explanation
Indices: 28709979--28710009 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
28709969 AAACATGAAA
28709979 TTGTTATGAATATCT
1 TTGTTATGAATATCT
28709994 TTGTTATGAATATCT
1 TTGTTATGAATATCT
28710009 T
1 T
28710010 ATTAAGTGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.13, T:0.55
Consensus pattern (15 bp):
TTGTTATGAATATCT
Found at i:28710348 original size:43 final size:43
Alignment explanation
Indices: 28710293--28710417 Score: 144
Period size: 43 Copynumber: 2.9 Consensus size: 43
28710283 GCTTTTCATT
* *
28710293 AAAA-CGCTGCTAAGGAACATGATCTTTAGTGGCGTTTGTAGG
1 AAAAGCGCCGCTAAAGAACATGATCTTTAGTGGCGTTTGTAGG
* * *
28710335 AAAAGCGCCGCTAAAGATCATGTTCTTTAGTAGCGTTTGTAGG
1 AAAAGCGCCGCTAAAGAACATGATCTTTAGTGGCGTTTGTAGG
* * * * * *
28710378 AAAAGCCCCACTAAATACCATGATCATTAGCGGCGTTTGT
1 AAAAGCGCCGCTAAAGAACATGATCTTTAGTGGCGTTTGT
28710418 GAGAAAAAAC
Statistics
Matches: 69, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
42 4 0.06
43 65 0.94
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGAACATGATCTTTAGTGGCGTTTGTAGG
Found at i:28710424 original size:43 final size:43
Alignment explanation
Indices: 28710310--28710435 Score: 144
Period size: 43 Copynumber: 2.9 Consensus size: 43
28710300 TGCTAAGGAA
* * *
28710310 CATGATCTTTAGTGGCGTTTGTAGGAAAAGCGCCGCTAAAGAT
1 CATGATCTTTAGTGGCGTTTGTAGGAAAAGCCCCACTAAAGAC
* * *
28710353 CATGTTCTTTAGTAGCGTTTGTAGGAAAAGCCCCACTAAATAC
1 CATGATCTTTAGTGGCGTTTGTAGGAAAAGCCCCACTAAAGAC
* * * * *
28710396 CATGATCATTAGCGGCGTTTGTGAGAAAAAACACCACTAA
1 CATGATCTTTAGTGGCGTTTGT-AGGAAAAGCCCCACTAA
28710436 CTTTATCAGA
Statistics
Matches: 69, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
43 55 0.80
44 14 0.20
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (43 bp):
CATGATCTTTAGTGGCGTTTGTAGGAAAAGCCCCACTAAAGAC
Found at i:28714917 original size:14 final size:14
Alignment explanation
Indices: 28714898--28714926 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
28714888 CTAATCTATG
28714898 ATTTCCATCTAACC
1 ATTTCCATCTAACC
28714912 ATTTCCATCTAACC
1 ATTTCCATCTAACC
28714926 A
1 A
28714927 CCAATGATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (14 bp):
ATTTCCATCTAACC
Found at i:28719435 original size:33 final size:33
Alignment explanation
Indices: 28719371--28719435 Score: 76
Period size: 33 Copynumber: 2.0 Consensus size: 33
28719361 ATTCGCGAAA
* * *
28719371 AAGAGGGAGATGGATAGGGTTGATTGTGCAAAG
1 AAGAGGGAGATGGAAAGGGTTGACTGAGCAAAG
* * *
28719404 AAGAGGGAGTTGGAAATGTTTGACTGAGCAAA
1 AAGAGGGAGATGGAAAGGGTTGACTGAGCAAA
28719436 TGAGAGAAAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.35, C:0.05, G:0.38, T:0.22
Consensus pattern (33 bp):
AAGAGGGAGATGGAAAGGGTTGACTGAGCAAAG
Found at i:28719937 original size:5 final size:5
Alignment explanation
Indices: 28719922--28719960 Score: 51
Period size: 5 Copynumber: 7.2 Consensus size: 5
28719912 AAATAAAGTG
28719922 ATAATA ATAAA ATAAA ATAAA ATAATA ATTAAA ATAAA A
1 ATAA-A ATAAA ATAAA ATAAA ATAA-A A-TAAA ATAAA A
28719961 AAATTTGGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 20 0.65
6 8 0.26
7 3 0.10
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (5 bp):
ATAAA
Found at i:28719961 original size:18 final size:18
Alignment explanation
Indices: 28719924--28719960 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
28719914 ATAAAGTGAT
28719924 AATAATAAAATAAAATAA
1 AATAATAAAATAAAATAA
*
28719942 AATAAT-AATTAAAATAA
1 AATAATAAAATAAAATAA
28719959 AA
1 AA
28719961 AAATTTGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (18 bp):
AATAATAAAATAAAATAA
Found at i:28724858 original size:26 final size:27
Alignment explanation
Indices: 28724829--28724885 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
28724819 AGCTGAGCTG
*
28724829 CCAGTA-CAG-AATATGTGACATAGCCA
1 CCAGTAGCAGTAAT-TGTGACAGAGCCA
*
28724855 CCAGTAGCAGTAATTGTGGCAGAGCCA
1 CCAGTAGCAGTAATTGTGACAGAGCCA
28724882 CCAG
1 CCAG
28724886 AAATAATACT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 6 0.22
27 18 0.67
28 3 0.11
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.18
Consensus pattern (27 bp):
CCAGTAGCAGTAATTGTGACAGAGCCA
Found at i:28725109 original size:26 final size:26
Alignment explanation
Indices: 28725076--28725135 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
28725066 TTCCCTACCG
* * *
28725076 GGGTATTTCAGTACTTTACCCATCGA
1 GGGTATTTCAGTAATTTACACATCAA
**
28725102 GGGTATTTTGGTAATTTACACATCAA
1 GGGTATTTCAGTAATTTACACATCAA
28725128 GGGTATTT
1 GGGTATTT
28725136 GGGTCAACAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (26 bp):
GGGTATTTCAGTAATTTACACATCAA
Found at i:28725812 original size:170 final size:172
Alignment explanation
Indices: 28725493--28725819 Score: 480
Period size: 170 Copynumber: 1.9 Consensus size: 172
28725483 TTCTCTGAAT
* * *
28725493 TCTTCAGTACTATCAAATTAGAGTCTTCTCAAATCTAAATCTATGATTTCCATCTAACCATCGAC
1 TCTTCAGTACCATCAAATTAAAGTCTTCTCAAATCTAAATCTATGATTTCCATCTAACCACCGAC
* * *
28725558 GATGCCAAATATAAGAGAATTTATTCCCATTATATAACGTCTTCAAACATGTTTGCGCAACACAA
66 GATGCCAAATATAAGAGAACTTATTCCCATTATATAACATCTTCAAACATGTTTACGCAACACAA
*
28725623 TAAGGACAAGCATAACGTCCATTGGTATTCCAACCAGAGAAC
131 CAAGGACAAGCATAACGTCCATTGGTATTCCAACCAGAGAAC
* ** *
28725665 TCTTCAGTACCATCTAA-TAAAGTCTTCTGGAATCT-AATCTATGATTTCCATCTAACCACCGAT
1 TCTTCAGTACCATCAAATTAAAGTCTTCTCAAATCTAAATCTATGATTTCCATCTAACCACCGAC
** * *
28725728 GATGCCCCATATAAGAGAACTTATTCCCATTATATAACCAT-TTCGAACATGTTTACGCAACATA
66 GATGCCAAATATAAGAGAACTTATTCCCATTATATAA-CATCTTCAAACATGTTTACGCAACACA
*
28725792 ACAAGGACAAGCATAACGTCCTTTGGTA
130 ACAAGGACAAGCATAACGTCCATTGGTA
28725820 CTTAAACCTA
Statistics
Matches: 138, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
170 106 0.77
171 17 0.12
172 15 0.11
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (172 bp):
TCTTCAGTACCATCAAATTAAAGTCTTCTCAAATCTAAATCTATGATTTCCATCTAACCACCGAC
GATGCCAAATATAAGAGAACTTATTCCCATTATATAACATCTTCAAACATGTTTACGCAACACAA
CAAGGACAAGCATAACGTCCATTGGTATTCCAACCAGAGAAC
Found at i:28730750 original size:17 final size:17
Alignment explanation
Indices: 28730728--28730763 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
28730718 ATAAAGTGAT
28730728 AATAATAAATAAAATAA
1 AATAATAAATAAAATAA
*
28730745 AATAATAATTAAAATAA
1 AATAATAAATAAAATAA
28730762 AA
1 AA
28730764 AATTTGGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
AATAATAAATAAAATAA
Found at i:28730764 original size:23 final size:22
Alignment explanation
Indices: 28730703--28730763 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 22
28730693 AGGAATTAAT
* *
28730703 TAATAATT-AAACAAAATAAAG
1 TAATAATTAAAATAAAATAAAA
* *
28730724 TGATAATAATAAATAAAATAAAA
1 TAATAATTA-AAATAAAATAAAA
28730747 TAATAATTAAAATAAAA
1 TAATAATTAAAATAAAA
28730764 AATTTGGGTT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
21 6 0.19
22 8 0.25
23 18 0.56
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.26
Consensus pattern (22 bp):
TAATAATTAAAATAAAATAAAA
Found at i:28735798 original size:28 final size:28
Alignment explanation
Indices: 28735767--28735862 Score: 66
Period size: 28 Copynumber: 3.2 Consensus size: 28
28735757 CCCTTTCCAG
28735767 TATCAGTGTGGGCCTTAGCCCAATACAA
1 TATCAGTGTGGGCCTTAGCCCAATACAA
* * *
28735795 TATCGGAACAGTGCGGGCCTTAGCCTAATATAA
1 TAT-----CAGTGTGGGCCTTAGCCCAATACAA
* * * ** *
28735828 TAACAGTGTAGGCCTAAGCCCGTTACAC
1 TATCAGTGTGGGCCTTAGCCCAATACAA
28735856 TATCAGT
1 TATCAGT
28735863 ATGCTGCAAA
Statistics
Matches: 50, Mismatches: 13, Indels: 10
0.68 0.18 0.14
Matches are distributed among these distances:
28 26 0.52
33 24 0.48
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (28 bp):
TATCAGTGTGGGCCTTAGCCCAATACAA
Found at i:28736249 original size:27 final size:25
Alignment explanation
Indices: 28736194--28736306 Score: 93
Period size: 26 Copynumber: 4.3 Consensus size: 25
28736184 ACCCTTTAGG
*
28736194 GGGTATTTCAGTAATTTTTCCCTAT-A
1 GGGTATTTCAGTAA-TTTACCC-ATGA
*
28736220 GGGGTATTTCAATAATTTACCCATCGA
1 -GGGTATTTCAGTAATTTACCCAT-GA
**
28736247 GGGTATTTTTGTAATTTACCCATTGA
1 GGGTATTTCAGTAATTTACCCA-TGA
** * *
28736273 GGGTATTTTGGTAATTTACACATTA
1 GGGTATTTCAGTAATTTACCCATGA
28736298 CGGGTATTT
1 -GGGTATTT
28736307 GGGTCAACAC
Statistics
Matches: 74, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
25 4 0.05
26 55 0.74
27 15 0.20
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.42
Consensus pattern (25 bp):
GGGTATTTCAGTAATTTACCCATGA
Found at i:28736296 original size:26 final size:26
Alignment explanation
Indices: 28736232--28736306 Score: 107
Period size: 26 Copynumber: 2.9 Consensus size: 26
28736222 GGTATTTCAA
* *
28736232 TAATTTACCCATCGAGGGTATTTTTG
1 TAATTTACCCATTGAGGGTATTTTGG
28736258 TAATTTACCCATTGAGGGTATTTTGG
1 TAATTTACCCATTGAGGGTATTTTGG
*
28736284 TAATTTACACATT-ACGGGTATTT
1 TAATTTACCCATTGA-GGGTATTT
28736307 GGGTCAACAC
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
25 1 0.02
26 44 0.98
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.43
Consensus pattern (26 bp):
TAATTTACCCATTGAGGGTATTTTGG
Found at i:28737188 original size:22 final size:21
Alignment explanation
Indices: 28737163--28737209 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
28737153 AAGTCGGTGC
28737163 AAAAGAAAAAATAAAAACACTGA
1 AAAAGAAAAAA-AAAAACACT-A
* *
28737186 AAAAGAGAAAAAAAAACTCTA
1 AAAAGAAAAAAAAAAACACTA
28737207 AAA
1 AAA
28737210 GACATAGAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.18
22 8 0.36
23 10 0.45
ACGTcount: A:0.74, C:0.09, G:0.09, T:0.09
Consensus pattern (21 bp):
AAAAGAAAAAAAAAAACACTA
Found at i:28743121 original size:28 final size:28
Alignment explanation
Indices: 28743090--28743165 Score: 80
Period size: 33 Copynumber: 2.5 Consensus size: 28
28743080 CCCTTTCTAG
28743090 TATCAGTGTGGGCCTTAGCCCAATACAA
1 TATCAGTGTGGGCCTTAGCCCAATACAA
*
28743118 TATCAAAATAGTGTGGGCCTTAGCCCAATATAA
1 TATC-----AGTGTGGGCCTTAGCCCAATACAA
* *
28743151 TAACAGTGTAGGCCT
1 TATCAGTGTGGGCCT
28743166 AAGCGCGTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
28 14 0.35
33 26 0.65
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (28 bp):
TATCAGTGTGGGCCTTAGCCCAATACAA
Found at i:28743621 original size:26 final size:26
Alignment explanation
Indices: 28743555--28743667 Score: 138
Period size: 26 Copynumber: 4.3 Consensus size: 26
28743545 ACCCTTCTAG
* *
28743555 GGGTATTTTAGTAATTTTTCCCTATAGA
1 GGGTATTTTAGTAA-TTTACCC-ATCGA
*
28743583 -GGTATTTCAGTAATTTACCCATCGA
1 GGGTATTTTAGTAATTTACCCATCGA
* * *
28743608 GGGTATTTTGGTAATTTACGCACCGA
1 GGGTATTTTAGTAATTTACCCATCGA
*
28743634 GGGTATTTTGGTAATTTACCCATCGA
1 GGGTATTTTAGTAATTTACCCATCGA
28743660 GGGTATTT
1 GGGTATTT
28743668 GGGTCAACAC
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
25 4 0.05
26 59 0.79
27 12 0.16
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.40
Consensus pattern (26 bp):
GGGTATTTTAGTAATTTACCCATCGA
Found at i:28746240 original size:40 final size:40
Alignment explanation
Indices: 28746196--28746426 Score: 229
Period size: 40 Copynumber: 5.8 Consensus size: 40
28746186 GGATATAGCT
* * *
28746196 ACTCGTTCAAACGCCTTCGGGACATAGCCCGG-TTATAGTA
1 ACTCGTACAAATGCCTTCGGGACTTAGCCCGGATT-TAGTA
* *
28746236 ACTCGTACAATTGCCTTCGGGACTTAACCCGGATTTAGTA
1 ACTCGTACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* *
28746276 ACTCGCACAAATGCCTTCGGG-CTTAGCCCGGAATTAGTA
1 ACTCGTACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * * *
28746315 TCTCGCACAAATGCCTTCGGG-CTTAGCTCGGAATTAGTA
1 ACTCGTACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * * * * *
28746354 TCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGGTC
1 ACTCGTACAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTA
* *
28746394 ACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 AC-TCGTACAAATGCCTTCGGGACTTAGCCCGGA
28746427 CATCATTCAA
Statistics
Matches: 166, Mismatches: 20, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
38 2 0.01
39 71 0.43
40 80 0.48
41 13 0.08
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
ACTCGTACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:28746320 original size:39 final size:40
Alignment explanation
Indices: 28746203--28746426 Score: 244
Period size: 39 Copynumber: 5.7 Consensus size: 40
28746193 GCTACTCGTT
* * * *
28746203 CAAACGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* * *
28746243 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
28746283 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* *
28746322 CAAATGCCTTCGGG-CTTAGCTCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * * *
28746361 CAAATGCCTTC-GGATCTTAGTCCGG-ATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAAT-TAGTAAC-TCGCA
28746402 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28746427 CATCATTCAA
Statistics
Matches: 160, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
38 2 0.01
39 73 0.46
40 72 0.45
41 13 0.08
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:28746371 original size:78 final size:80
Alignment explanation
Indices: 28746203--28746426 Score: 242
Period size: 79 Copynumber: 2.8 Consensus size: 80
28746193 GCTACTCGTT
* * * *
28746203 CAAACGCCTTCGGGACATAGCCCGGTTATAGTAACTCGTACAATTGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
*
28746268 ATTTAGTAACTCGCA
66 AATTAGTAACTCGCA
* * * *
28746283 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTCGGG-CTTAGCTCG
1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
*
28746345 GAATTAGTATCTCGCA
65 GAATTAGTAACTCGCA
* * * * * *
28746361 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CATAGCCCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCC
28746424 GGA
64 GGA
28746427 CATCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
77 2 0.02
78 33 0.27
79 55 0.45
80 32 0.26
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
AATTAGTAACTCGCA
Found at i:28751152 original size:35 final size:35
Alignment explanation
Indices: 28751112--28751179 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
28751102 TTTTTATATT
28751112 CTTTAAATGTTTATGTAAGTTATGATAATCATTAA
1 CTTTAAATGTTTATGTAAGTTATGATAATCATTAA
*
28751147 CTTTAAATGTTTATGTAAGTTATGATTATCATT
1 CTTTAAATGTTTATGTAAGTTATGATAATCATT
28751180 TTTTTATCAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.49
Consensus pattern (35 bp):
CTTTAAATGTTTATGTAAGTTATGATAATCATTAA
Found at i:28751368 original size:59 final size:59
Alignment explanation
Indices: 28751305--28751941 Score: 857
Period size: 59 Copynumber: 10.8 Consensus size: 59
28751295 TAAATGAATG
* * * * *
28751305 ATTAATCGAAAATTAATTAATAATTCATAGAATTATTATGAAACATAATCATTTATTTA
1 ATTAATCGAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTA
* * *
28751364 ATTAATTGAAAATTGATTAATTATTCATAGAATTATTATGAAATATGATTATTTATTTA
1 ATTAATCGAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTA
28751423 ATTAATC-AAAATTTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTA
1 ATTAATCGAAAA-TTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTA
** * * *
28751482 ATTAATTAAAAATTAATTAATTATTCGTAATATTATTATGAAATATGATTGTTTATTTA
1 ATTAATCGAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTA
* * *
28751541 ATTAATCAAAAATTAATTAATTATTCATAAAATTATTATCAAATATGATTATCTATTTA
1 ATTAATCGAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTA
* * * * * *
28751600 ATTAATCGGAAATTAATTAATTATTCGTAAAATTATTATCAAATATGGTTGTCTATTTA
1 ATTAATCGAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTA
* * * *
28751659 ATTAATCGAAAATTAATTAATTAGTCGTAAAATTATTATGAAATATAATTCTTTATTTA
1 ATTAATCGAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTA
* ** * *
28751718 TTTCTTTGAAAATTAATTAATTAATCATAAAATTATTATGAAATATGATTATTTATTTA
1 ATTAATCGAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTA
* * **
28751777 TTTAATCAAAAATTAATTAATTATTCATAGCATTATTATGAAATATGATTATTTATTTA
1 ATTAATCGAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTA
* * * *
28751836 ATTAATCAAAAATTAATTAATTATTCATAGAATTGTTATGAAATATGATTATTTATATA
1 ATTAATCGAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTA
* **
28751895 ATTAATC-ATAAATTACTTAATTATTTGT-AAATTATTATGAAATATGA
1 ATTAATCGA-AAATTAATTAATTATTCATAAAATTATTATGAAATATGA
28751942 CCCAGCTTTT
Statistics
Matches: 520, Mismatches: 55, Indels: 7
0.89 0.09 0.01
Matches are distributed among these distances:
58 22 0.04
59 494 0.95
60 4 0.01
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (59 bp):
ATTAATCGAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTA
Found at i:28751538 original size:32 final size:31
Alignment explanation
Indices: 28751336--28751891 Score: 154
Period size: 32 Copynumber: 18.8 Consensus size: 31
28751326 AATTCATAGA
* * *
28751336 ATTATTATGAAACATAATCATTTATT-T-A-
1 ATTATTATGAAATATGATTATTTATTCTAAT
* *
28751364 ATTAAT-TGAAA-ATTGATTAATTATTCATAGA-
1 ATTATTATGAAATA-TGATTATTTATTC-TA-AT
28751395 ATTATTATGAAATATGATTATTTATT-TAAT
1 ATTATTATGAAATATGATTATTTATTCTAAT
* * * * * *
28751425 -TAATCA--AAATTTAATTAATTATTCATAAA
1 ATTATTATGAAATATGATTATTTATTC-TAAT
28751454 ATTATTATGAAATATGATTATTTATT-TAAT
1 ATTATTATGAAATATGATTATTTATTCTAAT
* * * *
28751484 -TAATTA-AAAAT-TAATTAATTATTCGTAAT
1 ATTATTATGAAATATGATTATTTATTC-TAAT
*
28751513 ATTATTATGAAATATGATTGTTTATT-TAAT
1 ATTATTATGAAATATGATTATTTATTCTAAT
* * * * * *
28751543 -TAATCA-AAAAT-TAATTAATTATTCATAAA
1 ATTATTATGAAATATGATTATTTATTC-TAAT
* *
28751572 ATTATTATCAAATATGATTATCTATT-T-A-
1 ATTATTATGAAATATGATTATTTATTCTAAT
* ** * * *
28751600 ATTAATCGGAAAT-TAATTAATTATTCGTAAA
1 ATTATTATGAAATATGATTATTTATTC-TAAT
* * * *
28751631 ATTATTATCAAATATGGTTGTCTATT-T-A-
1 ATTATTATGAAATATGATTATTTATTCTAAT
* * * *
28751659 ATTA--ATCGAAA-ATTAATTAATTAGTCGTAAA
1 ATTATTAT-GAAATA-TGATTATTTATTC-TAAT
* *
28751690 ATTATTATGAAATATAATTCTTTATT-T-AT
1 ATTATTATGAAATATGATTATTTATTCTAAT
* * * * *
28751719 -TTCTT-TGAAA-ATTAATTAATTAATCATAAA
1 ATTATTATGAAATA-TGATTATTTATTC-TAAT
28751749 ATTATTATGAAATATGATTATTTATT-T-AT
1 ATTATTATGAAATATGATTATTTATTCTAAT
* * * * **
28751778 -TTA--ATCAAAAATTAATTAATTATTCATAGC
1 ATTATTATGAAATA-TGATTATTTATTC-TAAT
28751808 ATTATTATGAAATATGATTATTTATT-TAAT
1 ATTATTATGAAATATGATTATTTATTCTAAT
* * * * *
28751838 -TAATCA-AAAAT-TAATTAATTATTCATAGA-
1 ATTATTATGAAATATGATTATTTATTC-TA-AT
*
28751867 ATTGTTATGAAATATGATTATTTAT
1 ATTATTATGAAATATGATTATTTAT
28751892 ATAATTAATC
Statistics
Matches: 371, Mismatches: 100, Indels: 110
0.64 0.17 0.19
Matches are distributed among these distances:
26 11 0.03
27 99 0.27
28 37 0.10
29 39 0.11
30 35 0.09
31 38 0.10
32 101 0.27
33 11 0.03
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.46
Consensus pattern (31 bp):
ATTATTATGAAATATGATTATTTATTCTAAT
Found at i:28751562 original size:19 final size:20
Alignment explanation
Indices: 28751538--28751575 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
28751528 GATTGTTTAT
28751538 TTAATTAATCA-AAAATTAA
1 TTAATTAATCATAAAATTAA
*
28751557 TTAATTATTCATAAAATTA
1 TTAATTAATCATAAAATTA
28751576 TTATCAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAATTAATCATAAAATTAA
Found at i:28751680 original size:19 final size:20
Alignment explanation
Indices: 28751656--28751693 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
28751646 GGTTGTCTAT
28751656 TTAATTAATCG-AAAATTAA
1 TTAATTAATCGTAAAATTAA
*
28751675 TTAATTAGTCGTAAAATTA
1 TTAATTAATCGTAAAATTA
28751694 TTATGAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.39
Consensus pattern (20 bp):
TTAATTAATCGTAAAATTAA
Found at i:28754204 original size:23 final size:24
Alignment explanation
Indices: 28754174--28754224 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
28754164 CATGGGTTGC
28754174 TGTTTTTTTTCTC-TTTTCTGGGT
1 TGTTTTTTTTCTCTTTTTCTGGGT
28754197 TGTTTTTTTTCTCTTTTTCTGGGT
1 TGTTTTTTTTCTCTTTTTCTGGGT
28754221 TGTT
1 TGTT
28754225 GTTTCTGGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 13 0.48
24 14 0.52
ACGTcount: A:0.00, C:0.12, G:0.18, T:0.71
Consensus pattern (24 bp):
TGTTTTTTTTCTCTTTTTCTGGGT
Found at i:28754377 original size:25 final size:25
Alignment explanation
Indices: 28754341--28754468 Score: 150
Period size: 25 Copynumber: 5.1 Consensus size: 25
28754331 AAACTTACAC
*
28754341 GGCGATGCAGCAGAGGACTGTCGAT
1 GGCGATGCAGCAGAGGACTATCGAT
*
28754366 GGCGATGTAGCAGAGGACTATCGAT
1 GGCGATGCAGCAGAGGACTATCGAT
* *
28754391 GGCAATGC-GACAGAGGACTTTCGAT
1 GGCGATGCAG-CAGAGGACTATCGAT
** * *
28754416 GATGATGCGGCAGAGGACTATTGAT
1 GGCGATGCAGCAGAGGACTATCGAT
* *
28754441 GGTGATGCAACAGAGGACTATCGAT
1 GGCGATGCAGCAGAGGACTATCGAT
28754466 GGC
1 GGC
28754469 ATTGAAGCAG
Statistics
Matches: 86, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
24 1 0.01
25 84 0.98
26 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.36, T:0.20
Consensus pattern (25 bp):
GGCGATGCAGCAGAGGACTATCGAT
Found at i:28754998 original size:7 final size:7
Alignment explanation
Indices: 28754986--28755012 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
28754976 ACTCTCAAAG
28754986 TTTGCTA
1 TTTGCTA
28754993 TTTGCTA
1 TTTGCTA
28755000 TTTGCTA
1 TTTGCTA
28755007 TTTGCT
1 TTTGCT
28755013 TGGGGATGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.11, C:0.15, G:0.15, T:0.59
Consensus pattern (7 bp):
TTTGCTA
Found at i:28767220 original size:39 final size:39
Alignment explanation
Indices: 28767177--28767356 Score: 254
Period size: 39 Copynumber: 4.6 Consensus size: 39
28767167 CATATTCACT
* * * *
28767177 TTTAAGCATGTATCACATTACACATATAATCACACCAA-A
1 TTTAAGCATATATCACAATACTCATATAATCACA-TAACA
* * *
28767216 TTTAACCATATTTCACAATTCTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
28767255 TTTAAGCATATATCACAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
*
28767294 TTTAATCATATATCACAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* *
28767333 TTCAAACATATATCACAATACTCA
1 TTTAAGCATATATCACAATACTCA
28767357 AAACCATGTT
Statistics
Matches: 127, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
38 2 0.02
39 125 0.98
ACGTcount: A:0.44, C:0.22, G:0.02, T:0.32
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACTCATATAATCACATAACA
Found at i:28767288 original size:17 final size:17
Alignment explanation
Indices: 28767261--28767327 Score: 57
Period size: 17 Copynumber: 3.7 Consensus size: 17
28767251 AACATTTAAG
28767261 CATAT-ATCACAATACT
1 CATATAATCACAATACT
28767277 CATATAATCAC-ATAACATTT
1 CATATAATCACAAT-AC---T
*
28767297 AATCATATATCACAATACT
1 CAT-ATA-ATCACAATACT
28767316 CATATAATCACA
1 CATATAATCACA
28767328 TAACATTCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 15
0.71 0.03 0.26
Matches are distributed among these distances:
16 7 0.17
17 13 0.32
18 3 0.07
19 3 0.07
20 3 0.07
21 3 0.07
22 7 0.17
23 2 0.05
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.31
Consensus pattern (17 bp):
CATATAATCACAATACT
Found at i:28769284 original size:71 final size:70
Alignment explanation
Indices: 28769159--28769372 Score: 227
Period size: 71 Copynumber: 3.0 Consensus size: 70
28769149 AGGATGTGAC
* ** * *
28769159 ATGAGTGTGTCCAGCACTAGTCGGTATAATTGACAAATAAATGCATCTTGCGCTGGTCGATAAAA
1 ATGAGTGTG-CCAGCACTAGTCGGTATAACTGACAAATAAATGCGCCCTACGCTGGTCGATAAAA
28769224 TCAACA
65 TCAACA
* * * *
28769230 ATGAGTGTGCCTAGCACT-GATCGGTATAACTGATAAATAAATGTGCCCTACGCTGGT-TAGCAA
1 ATGAGTGTGCC-AGCACTAG-TCGGTATAACTGACAAATAAATGCGCCCTACGCTGGTCGA-TAA
*
28769293 AAGCGAA-A
63 AATC-AACA
* * *
28769301 ATGAGTGTGCCCAGCACTAGTCAGTATAACCGACAAATAAATGCGCCCTACGTTGGTCGATAAAA
1 ATGAGTGTG-CCAGCACTAGTCGGTATAACTGACAAATAAATGCGCCCTACGCTGGTCGATAAAA
*
28769366 TCGACA
65 TCAACA
28769372 A
1 A
28769373 ATAAATGCTC
Statistics
Matches: 116, Mismatches: 19, Indels: 16
0.77 0.13 0.11
Matches are distributed among these distances:
70 5 0.04
71 105 0.91
72 6 0.05
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (70 bp):
ATGAGTGTGCCAGCACTAGTCGGTATAACTGACAAATAAATGCGCCCTACGCTGGTCGATAAAAT
CAACA
Found at i:28769946 original size:105 final size:105
Alignment explanation
Indices: 28769759--28769975 Score: 317
Period size: 105 Copynumber: 2.1 Consensus size: 105
28769749 TCAGATATAA
* * **
28769759 CCAGCTTTGGAAAAACACTTATTCACTTATAATATCAACATCAAAATCAACATAAGTATTTATCT
1 CCAGCTTTGGAAAAACACTTATTCACCTATAATACCAACATCAAAATCAACATAAACATTTATCT
*
28769824 AATCCTAACACTTAATTTAGCATAAACATAATAGAAATGT
66 AATCCTAACACTTAATTTAACATAAACATAATAGAAATGT
* * ** * * *
28769864 CCAGTTTTGGAAAAACACTTATTCGCCTATAATACCAGTATTAAAATCGACATAAACATTTATTT
1 CCAGCTTTGGAAAAACACTTATTCACCTATAATACCAACATCAAAATCAACATAAACATTTATCT
*
28769929 AATCCTAACATTTAATTTAACATAAACATAATAGAAATGT
66 AATCCTAACACTTAATTTAACATAAACATAATAGAAATGT
28769969 CCAGCTT
1 CCAGCTT
28769976 GGGCAACACT
Statistics
Matches: 98, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
105 98 1.00
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.32
Consensus pattern (105 bp):
CCAGCTTTGGAAAAACACTTATTCACCTATAATACCAACATCAAAATCAACATAAACATTTATCT
AATCCTAACACTTAATTTAACATAAACATAATAGAAATGT
Found at i:28769956 original size:18 final size:17
Alignment explanation
Indices: 28769913--28769957 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
28769903 ATTAAAATCG
28769913 ACATAAACATTTATTTA
1 ACATAAACATTTATTTA
*
28769930 ATCCT-AACATTTAATTTA
1 A-CATAAACATTT-ATTTA
28769948 ACATAAACAT
1 ACATAAACAT
28769958 AATAGAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.38
Consensus pattern (17 bp):
ACATAAACATTTATTTA
Found at i:28770011 original size:23 final size:23
Alignment explanation
Indices: 28769974--28770066 Score: 89
Period size: 23 Copynumber: 4.1 Consensus size: 23
28769964 AATGTCCAGC
* * *
28769974 TTGGGCAACACTTAAAACATGCT
1 TTGGACAACATTTAAAACATACT
** *
28769997 TTGGATGACATTTAAAACATATT
1 TTGGACAACATTTAAAACATACT
*
28770020 TTGGACAACATTTAAAACTTACT
1 TTGGACAACATTTAAAACATACT
* * *
28770043 CT-GACAGCATTTGAAACATACT
1 TTGGACAACATTTAAAACATACT
28770065 TT
1 TT
28770067 TTCTATCATT
Statistics
Matches: 55, Mismatches: 15, Indels: 1
0.77 0.21 0.01
Matches are distributed among these distances:
22 18 0.33
23 37 0.67
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (23 bp):
TTGGACAACATTTAAAACATACT
Found at i:28770962 original size:22 final size:20
Alignment explanation
Indices: 28770937--28770977 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
28770927 TTATTTTCCC
*
28770937 TCTTCTTTCATTTTCTTTTTTT
1 TCTTC-TTC-TTTTCCTTTTTT
28770959 TCTTCTTCTTTTCCTTTTT
1 TCTTCTTCTTTTCCTTTTT
28770978 ACTTCCTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 3 0.17
22 5 0.28
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (20 bp):
TCTTCTTCTTTTCCTTTTTT
Found at i:28777752 original size:38 final size:38
Alignment explanation
Indices: 28777710--28777784 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 38
28777700 CATTGTCAAA
* *
28777710 TTTTAACAATAATAAAAATTACAACATGGGTCAACTAG
1 TTTTAACAATAACAAAAATTACAACATGAGTCAACTAG
* *
28777748 TTTTAATAATAACAAAAATTATAACATGAGTCAACTA
1 TTTTAACAATAACAAAAATTACAACATGAGTCAACTA
28777785 ATTTATAGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.49, C:0.12, G:0.08, T:0.31
Consensus pattern (38 bp):
TTTTAACAATAACAAAAATTACAACATGAGTCAACTAG
Found at i:28787950 original size:23 final size:24
Alignment explanation
Indices: 28787915--28787976 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
28787905 AAATAACAAT
28787915 AATAAATACAACAATGAAAT-A-GA
1 AATAAATA-AACAATGAAATAAGGA
28787938 AATAATATAAAC-AT-AAATAAGGA
1 AATAA-ATAAACAATGAAATAAGGA
*
28787961 AAAAAATAAACAATGA
1 AATAAATAAACAATGA
28787977 CATGTAATGT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
21 4 0.12
22 9 0.27
23 16 0.48
24 4 0.12
ACGTcount: A:0.68, C:0.06, G:0.08, T:0.18
Consensus pattern (24 bp):
AATAAATAAACAATGAAATAAGGA
Found at i:28788592 original size:22 final size:23
Alignment explanation
Indices: 28788564--28788606 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
28788554 AAGGTATCTA
28788564 AAAATTAAATC-TCTAAGATTAC
1 AAAATTAAATCTTCTAAGATTAC
*
28788586 AAAATTATATCTTCTAAGATT
1 AAAATTAAATCTTCTAAGATT
28788607 GCATATCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.37
Consensus pattern (23 bp):
AAAATTAAATCTTCTAAGATTAC
Found at i:28788622 original size:19 final size:19
Alignment explanation
Indices: 28788598--28788651 Score: 108
Period size: 19 Copynumber: 2.8 Consensus size: 19
28788588 AATTATATCT
28788598 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
28788617 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
28788636 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
28788652 CTTGAAGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:28789375 original size:37 final size:38
Alignment explanation
Indices: 28789325--28789415 Score: 112
Period size: 37 Copynumber: 2.4 Consensus size: 38
28789315 TCCACATTAC
* * **
28789325 GTGGTGTGCAGGGTGGATGAACCTATTATGGTTC-TAT
1 GTGGTGTGCAGGGTGGACGAACCTATTATAGCCCTTAT
* * *
28789362 GTGGTGTGCAGGGTAGACGAGCCTTTTATAGCCCTTAT
1 GTGGTGTGCAGGGTGGACGAACCTATTATAGCCCTTAT
28789400 GTGGTGTGCAGGGTGG
1 GTGGTGTGCAGGGTGG
28789416 TCAAATGGTG
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
37 27 0.60
38 18 0.40
ACGTcount: A:0.16, C:0.13, G:0.38, T:0.32
Consensus pattern (38 bp):
GTGGTGTGCAGGGTGGACGAACCTATTATAGCCCTTAT
Found at i:28795759 original size:28 final size:27
Alignment explanation
Indices: 28795700--28795807 Score: 144
Period size: 27 Copynumber: 4.0 Consensus size: 27
28795690 TGAACATCTT
* *
28795700 TAACTCTAATCTCAGCTTCTCATTCTC
1 TAACTCCAATATCAGCTTCTCATTCTC
* *
28795727 TAACTCCAATATCAACTTTTCATTTCTC
1 TAACTCCAATATCAGCTTCTCA-TTCTC
*
28795755 TAACTCCCATATCAGCTTCTCATTCTC
1 TAACTCCAATATCAGCTTCTCATTCTC
* *
28795782 TAACTCCAATCTCAGCCTCTCATTCT
1 TAACTCCAATATCAGCTTCTCATTCT
28795808 GGTGCAACAA
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
27 46 0.66
28 24 0.34
ACGTcount: A:0.24, C:0.34, G:0.03, T:0.39
Consensus pattern (27 bp):
TAACTCCAATATCAGCTTCTCATTCTC
Found at i:28795942 original size:93 final size:93
Alignment explanation
Indices: 28795783--28795992 Score: 285
Period size: 93 Copynumber: 2.3 Consensus size: 93
28795773 CTCATTCTCT
* * * *
28795783 AACTCCAATCTCAGCCTCTCATTCTGGTGCAACAATTGTTCTTTTTCGTTGATCACTTGAATCAA
1 AACTCCAATCTCAGCCTCGCATTCCGGTGCAACAATTGCTCTTCTTCGTTGATCACTTGAATCAA
* * * *
28795848 TTCCAAGTTCTGTTCCCTTTGACACTCA
66 TTCCAAATTCTATTCCATTTCACACTCA
* * * *
28795876 AACTCAAATCTCATCCTCGCATTCCGGTGCAATAATTGCTCTTCTTCGTTGATCGCTTGAATCAA
1 AACTCCAATCTCAGCCTCGCATTCCGGTGCAACAATTGCTCTTCTTCGTTGATCACTTGAATCAA
* * *
28795941 TTTCAAATTCTATTCCATTTCACGCTCT
66 TTCCAAATTCTATTCCATTTCACACTCA
28795969 AACTCCAATCTCAGCCTCGCATTC
1 AACTCCAATCTCAGCCTCGCATTC
28795993 TCCTTCTCCA
Statistics
Matches: 100, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
93 100 1.00
ACGTcount: A:0.23, C:0.30, G:0.11, T:0.36
Consensus pattern (93 bp):
AACTCCAATCTCAGCCTCGCATTCCGGTGCAACAATTGCTCTTCTTCGTTGATCACTTGAATCAA
TTCCAAATTCTATTCCATTTCACACTCA
Found at i:28797670 original size:24 final size:23
Alignment explanation
Indices: 28797643--28797712 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 23
28797633 TGCATAATGC
28797643 TATATATATTGTTATGTAATATTT
1 TATATATATT-TTATGTAATATTT
28797667 TATA-ATAGTTTGTATGT-AT-TTT
1 TATATATA-TTT-TATGTAATATTT
*
28797689 TATATATATAATTATG-AATATTT
1 TATATATAT-TTTATGTAATATTT
28797712 T
1 T
28797713 TCACTTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 13
0.74 0.02 0.25
Matches are distributed among these distances:
22 14 0.36
23 14 0.36
24 11 0.28
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (23 bp):
TATATATATTTTATGTAATATTT
Found at i:28798712 original size:37 final size:36
Alignment explanation
Indices: 28798669--28798738 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
28798659 TAATTAGTTT
* *
28798669 TTTTATATTTTTAATG-ATTTTTAATTTTTAAAAATAG
1 TTTTATATTTTT--TGAAATTTTAAATTTTAAAAATAG
28798706 TTTTATATTTTTTGAAATTTTAAATTTTAAAAA
1 TTTTATATTTTTTGAAATTTTAAATTTTAAAAA
28798739 ATTAATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
35 2 0.07
36 16 0.53
37 12 0.40
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (36 bp):
TTTTATATTTTTTGAAATTTTAAATTTTAAAAATAG
Found at i:28798739 original size:37 final size:36
Alignment explanation
Indices: 28798669--28798740 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 36
28798659 TAATTAGTTT
* *
28798669 TTTTATATTTTTAATGATTTTTAATTTTTAAAAATAG
1 TTTTATATTTTTAA-GATTTTAAATTTTAAAAAATAG
28798706 TTTTATATTTTTTGAA-ATTTTAAATTTTAAAAAAT
1 TTTTATA-TTTTT-AAGATTTTAAATTTTAAAAAAT
28798741 TAATTAAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
37 24 0.77
38 5 0.16
39 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (36 bp):
TTTTATATTTTTAAGATTTTAAATTTTAAAAAATAG
Found at i:28808589 original size:36 final size:39
Alignment explanation
Indices: 28808544--28808630 Score: 108
Period size: 39 Copynumber: 2.3 Consensus size: 39
28808534 GGAGTTGTAA
* * *
28808544 GTGACTATTCATCTATATCAC-T-AA-ATGCTAGGAGTT
1 GTGACTATTCATCTACATAACTTAAATATGATAGGAGTT
* *
28808580 GTGACTATTCATTTACATAACTTAAATATTATAGGAGTT
1 GTGACTATTCATCTACATAACTTAAATATGATAGGAGTT
28808619 GTGACTATTCAT
1 GTGACTATTCAT
28808631 GCATGTGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
36 18 0.42
37 1 0.02
38 2 0.05
39 22 0.51
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (39 bp):
GTGACTATTCATCTACATAACTTAAATATGATAGGAGTT
Found at i:28808672 original size:23 final size:23
Alignment explanation
Indices: 28808646--28808689 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
28808636 TGTGTAACTT
* *
28808646 TTCAGCTTCAAGTCTCTTCACTC
1 TTCAGATTCAAGTCTATTCACTC
*
28808669 TTCATATTCAAGTCTATTCAC
1 TTCAGATTCAAGTCTATTCAC
28808690 ATTTCTAACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.23, C:0.30, G:0.07, T:0.41
Consensus pattern (23 bp):
TTCAGATTCAAGTCTATTCACTC
Found at i:28813193 original size:23 final size:23
Alignment explanation
Indices: 28813167--28813233 Score: 125
Period size: 23 Copynumber: 2.9 Consensus size: 23
28813157 TGTGTAACTT
*
28813167 TTCATCTTCAAGTCTCTTCACTC
1 TTCATATTCAAGTCTCTTCACTC
28813190 TTCATATTCAAGTCTCTTCACTC
1 TTCATATTCAAGTCTCTTCACTC
28813213 TTCATATTCAAGTCTCTTCAC
1 TTCATATTCAAGTCTCTTCAC
28813234 ATTTCTAACT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.21, C:0.31, G:0.04, T:0.43
Consensus pattern (23 bp):
TTCATATTCAAGTCTCTTCACTC
Found at i:28818053 original size:50 final size:51
Alignment explanation
Indices: 28817983--28818166 Score: 176
Period size: 51 Copynumber: 3.6 Consensus size: 51
28817973 TACCATTCGA
* * * * * **
28817983 TACACGTAGTATCCTTCACATAGTACTATACACGTGATCAAA-ATTTTTGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAAGACTTCCGG
* *
28818033 TTCACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAAGCCTTCCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAAGACTTCCGG
* * * * * *
28818084 TACACATAGTAGCCTGCAAATAGTACTACACATGTGACCATTA-TCTAT-CGA
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA-AAGACT-TCCGG
* *
28818135 TACACGTAGTAGCCTACACTTAGTACTACACA
1 TACACGTAGTAGCCTGCACATAGTACTACACA
28818167 TGCGTTTATA
Statistics
Matches: 111, Mismatches: 20, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
50 37 0.33
51 72 0.65
52 2 0.02
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (51 bp):
TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAAGACTTCCGG
Found at i:28821248 original size:23 final size:23
Alignment explanation
Indices: 28821222--28821320 Score: 153
Period size: 23 Copynumber: 4.3 Consensus size: 23
28821212 AGTGTTATTG
28821222 ATCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTACGGCTACAT
**
28821245 ATCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTACGGCTACAT
* *
28821268 TTCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTACGGCTACAT
*
28821291 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTACGGCTACAT
28821314 ATCAGTG
1 ATCAGTG
28821321 AAGCACTTAT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 67 1.00
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTACGGCTACAT
Found at i:28821294 original size:46 final size:46
Alignment explanation
Indices: 28821222--28821320 Score: 171
Period size: 46 Copynumber: 2.2 Consensus size: 46
28821212 AGTGTTATTG
*
28821222 ATCAGTGGTAGCTACGGCTACATATCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTACGGCTACATATCAGTGGTAGCTTCGGCTACAT
* *
28821268 TTCAGTGGTAGCTACGGCTACGTATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTACGGCTACATATCAGTGGTAGCTTCGGCTACAT
28821314 ATCAGTG
1 ATCAGTG
28821321 AAGCACTTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.30
Consensus pattern (46 bp):
ATCAGTGGTAGCTACGGCTACATATCAGTGGTAGCTTCGGCTACAT
Found at i:28822563 original size:49 final size:49
Alignment explanation
Indices: 28822500--28822638 Score: 233
Period size: 49 Copynumber: 2.8 Consensus size: 49
28822490 CAATAAGTGA
*
28822500 TATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTATATGT
1 TATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTATATGT
28822549 TATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTATATGT
1 TATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTATATGT
* * * *
28822598 TATGTGAGTACATGTAAGACCATAGTTGGACTATGGCATCG
1 TATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCG
28822639 AGAAAATAAG
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 85 1.00
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.32
Consensus pattern (49 bp):
TATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTATATGT
Found at i:28823725 original size:62 final size:63
Alignment explanation
Indices: 28823616--28823745 Score: 176
Period size: 62 Copynumber: 2.1 Consensus size: 63
28823606 AACCATCACT
* * * *
28823616 TACACGGCCTGAGCACACACCCGTGTCCCTAGCCTGTGTGACCCTAA-TCCCAAATAGTGAGC
1 TACACAGCCTGAGCACACACCCGTGTCCCTAGCCCGTATGACCCTAATTCCAAAATAGTGAGC
*
28823678 TACACAGCCT-AGACACACACCCGTGTCCCTAGCCCGTATG-CCTCTAATTCCAAAATAGTGAGT
1 TACACAGCCTGAG-CACACACCCGTGTCCCTAGCCCGTATGACC-CTAATTCCAAAATAGTGAGC
28823741 TACAC
1 TACAC
28823746 GGTCCACCAC
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
61 4 0.07
62 38 0.63
63 18 0.30
ACGTcount: A:0.27, C:0.35, G:0.18, T:0.21
Consensus pattern (63 bp):
TACACAGCCTGAGCACACACCCGTGTCCCTAGCCCGTATGACCCTAATTCCAAAATAGTGAGC
Found at i:28827057 original size:18 final size:18
Alignment explanation
Indices: 28827031--28827066 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
28827021 ATTTTGAGTT
*
28827031 AAATGAATCGAGTTATTC
1 AAATGAATCGAATTATTC
*
28827049 AAATTAATCGAATTATTC
1 AAATGAATCGAATTATTC
28827067 GAGTCGAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (18 bp):
AAATGAATCGAATTATTC
Found at i:28828190 original size:42 final size:42
Alignment explanation
Indices: 28827975--28828181 Score: 272
Period size: 42 Copynumber: 4.9 Consensus size: 42
28827965 GCGTTTACAG
* * *
28827975 AAAAAATGCCGCTAAAGGTCATGTTCTTTAGCGGTGCTT-AA
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAAA
* *
28828016 AAAAAACACCGCTAAAGATCATGTTCTTTAGCGGCTCTTAAA
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAAA
* * **
28828058 AAAAAGACGCCGCTAAAGATCTTGTTCTTTAGCGGCGCATGGA
1 AAAAA-ACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAAA
* *
28828101 GAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGA
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAAA
* * *
28828143 CAAAAACGCCGCTAAAAATCATATTCTTTAGCGGCGCTT
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
28828182 TCTTAAAAAA
Statistics
Matches: 146, Mismatches: 18, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
41 34 0.23
42 77 0.53
43 35 0.24
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (42 bp):
AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAAA
Found at i:28828609 original size:21 final size:21
Alignment explanation
Indices: 28828583--28828651 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
28828573 GCTTCTCTCG
*
28828583 CTGCTTCACTCGTTGCAGCCT
1 CTGCTTCACTCGCTGCAGCCT
* *
28828604 CTGCTTCTCTCACTGCAGCCT
1 CTGCTTCACTCGCTGCAGCCT
* *
28828625 CTGCTTCCCTCGCTGCCGCCT
1 CTGCTTCACTCGCTGCAGCCT
28828646 CTGCTT
1 CTGCTT
28828652 TAAGTTGTAG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.06, C:0.43, G:0.17, T:0.33
Consensus pattern (21 bp):
CTGCTTCACTCGCTGCAGCCT
Found at i:28831131 original size:22 final size:22
Alignment explanation
Indices: 28831106--28831148 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
28831096 ACAACAGAAC
* *
28831106 AGGTTTTTAGCGGCGTTTTTTT
1 AGGTCTTTAGCGGCGCTTTTTT
28831128 AGGTCTTTAGCGGCGCTTTTT
1 AGGTCTTTAGCGGCGCTTTTT
28831149 AACGCCACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.14, G:0.28, T:0.49
Consensus pattern (22 bp):
AGGTCTTTAGCGGCGCTTTTTT
Found at i:28831286 original size:42 final size:42
Alignment explanation
Indices: 28831238--28831573 Score: 446
Period size: 42 Copynumber: 8.0 Consensus size: 42
28831228 GCGTTTACAT
28831238 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
* *
28831280 AAAAAAACTCCGCTAAAGATCATGCTCTTTAGCGGCGCTTAG
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
* * *
28831322 AAAAAAAACGCCCCCAAAGATCATGTTTTTTAGCGGCGCTTAG
1 -AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
28831365 -AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
* *
28831406 GAAAAAACGCCGTTAAAGATCATGTTCTTTAGCGGCGCTTAG
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
* *
28831448 GAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTGG
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC-TTAG
* * * * *
28831491 AATAAAACGCCTCTAAA-AGTAATGTTCTATAGCGGCGCTTAT
1 AAAAAAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCGCTTAG
** *
28831533 TCAAAAACGCCGCTAAA-AGT-AGTGTTCTTTAGCGGTGCTTA
1 AAAAAAACGCCGCTAAAGA-TCA-TGTTCTTTAGCGGCGCTTA
28831574 TTTCACAAAC
Statistics
Matches: 263, Mismatches: 26, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
41 39 0.15
42 153 0.58
43 71 0.27
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (42 bp):
AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
Found at i:28831559 original size:85 final size:84
Alignment explanation
Indices: 28831239--28831573 Score: 446
Period size: 85 Copynumber: 4.0 Consensus size: 84
28831229 CGTTTACATA
* * *
28831239 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAACTCCGCTAAAGATCATG
1 AAAAAACGCCTCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATG
* *
28831304 CTCTTTAGCGGCGCTTAGAA
66 TTCTTTAGCGGCGCTTAG-G
* * *
28831324 AAAAAACGCCCCCAAAGATCATGTTTTTTAGCGGCGCTTA-GAAAAAACGCCGCTAAAGATCATG
1 AAAAAACGCCTCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATG
28831388 TTCTTTAGCGGCGCTTAGG
66 TTCTTTAGCGGCGCTTAGG
28831407 AAAAAACGCCGT-TAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCAT
1 AAAAAACGCC-TCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCAT
*
28831471 GTTCTTTAGCGGCGCTTTGG
65 GTTCTTTAGCGGCGCTTAGG
* * ***
28831491 AATAAAACGCCTCTAAA-AGTAATGTTCTATAGCGGCGCTTATTCAAAAACGCCGCTAAA-AGT-
1 AA-AAAACGCCTCTAAAGA-TCATGTTCTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGA-TC
*
28831553 AGTGTTCTTTAGCGGTGCTTA
63 A-TGTTCTTTAGCGGCGCTTA
28831574 TTTCACAAAC
Statistics
Matches: 225, Mismatches: 18, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
83 36 0.16
84 87 0.39
85 102 0.45
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (84 bp):
AAAAAACGCCTCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATG
TTCTTTAGCGGCGCTTAGG
Found at i:28832047 original size:33 final size:33
Alignment explanation
Indices: 28832005--28832118 Score: 147
Period size: 33 Copynumber: 3.5 Consensus size: 33
28831995 GCTTCTATTG
* *
28832005 CTGCTTCTCTCGGTGTTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCGCTGCTTCTCTCGCTGCGGCCT
* **
28832038 CTGCTTCTCTCGCTGCTTCTCTCACTGTAGCCT
1 CTGCTTCTCTCGCTGCTTCTCTCGCTGCGGCCT
* *
28832071 CTGCTTCTCTCACTGCTTCTCTTGCTGCGGCCT
1 CTGCTTCTCTCGCTGCTTCTCTCGCTGCGGCCT
**
28832104 CTTTTTCTCTCGCTG
1 CTGCTTCTCTCGCTG
28832119 TAGCCGCTGC
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 68 1.00
ACGTcount: A:0.03, C:0.38, G:0.18, T:0.41
Consensus pattern (33 bp):
CTGCTTCTCTCGCTGCTTCTCTCGCTGCGGCCT
Found at i:28832055 original size:12 final size:12
Alignment explanation
Indices: 28831993--28832098 Score: 64
Period size: 12 Copynumber: 9.3 Consensus size: 12
28831983 TTTTGAACCT
* *
28831993 CTGCTTCTATTG
1 CTGCTTCTCTCG
28832005 CTGCTTCTCTCG
1 CTGCTTCTCTCG
* *
28832017 GTGTTTCTCTCG
1 CTGCTTCTCTCG
**
28832029 CTGCGGC-CT--
1 CTGCTTCTCTCG
28832038 CTGCTTCTCTCG
1 CTGCTTCTCTCG
*
28832050 CTGCTTCTCTCA
1 CTGCTTCTCTCG
*
28832062 CTG-TAGC-CT--
1 CTGCT-TCTCTCG
*
28832071 CTGCTTCTCTCA
1 CTGCTTCTCTCG
*
28832083 CTGCTTCTCTTG
1 CTGCTTCTCTCG
28832095 CTGC
1 CTGC
28832099 GGCCTCTTTT
Statistics
Matches: 71, Mismatches: 15, Indels: 16
0.70 0.15 0.16
Matches are distributed among these distances:
9 9 0.13
10 5 0.07
11 5 0.07
12 52 0.73
ACGTcount: A:0.04, C:0.37, G:0.18, T:0.42
Consensus pattern (12 bp):
CTGCTTCTCTCG
Found at i:28837674 original size:9 final size:9
Alignment explanation
Indices: 28837660--28837981 Score: 214
Period size: 9 Copynumber: 35.9 Consensus size: 9
28837650 TTTTTATGTA
28837660 TTATGTAAG
1 TTATGTAAG
28837669 TTATGTAAG
1 TTATGTAAG
*
28837678 TTCTGT-A-
1 TTATGTAAG
28837685 TTATGT-A-
1 TTATGTAAG
*
28837692 TTATGTATG
1 TTATGTAAG
**
28837701 CCCCATGTAAG
1 --TTATGTAAG
*
28837712 TAATGTAAG
1 TTATGTAAG
*
28837721 CTATGTAAG
1 TTATGTAAG
*
28837730 TAATGT-A-
1 TTATGTAAG
28837737 TTATGTAAG
1 TTATGTAAG
* *
28837746 TTGTGTACATCA
1 TTATGTA-A--G
*
28837758 TTATGTGAG
1 TTATGTAAG
28837767 TTATGTAAG
1 TTATGTAAG
* *
28837776 TTATTTAAT
1 TTATGTAAG
*
28837785 TTACT-TAAT
1 TTA-TGTAAG
28837794 TTATGTAAG
1 TTATGTAAG
*
28837803 TTATGTTAG
1 TTATGTAAG
* * *
28837812 ATATTTAAT
1 TTATGTAAG
28837821 TTATGTAAG
1 TTATGTAAG
28837830 TTATGTAAG
1 TTATGTAAG
* *
28837839 TTATTTAAT
1 TTATGTAAG
*
28837848 TTACT-TAAT
1 TTA-TGTAAG
28837857 TTATGTAAG
1 TTATGTAAG
* *
28837866 TTATTTAAT
1 TTATGTAAG
*
28837875 TTACT-TAAT
1 TTA-TGTAAG
28837884 TTATGTAAG
1 TTATGTAAG
*
28837893 TTATGCAAG
1 TTATGTAAG
* * *
28837902 ATATTTAAT
1 TTATGTAAG
28837911 TTATGTAAG
1 TTATGTAAG
28837920 TTATGTAAG
1 TTATGTAAG
*
28837929 TTACT-TAAT
1 TTA-TGTAAG
28837938 TTATGTAAG
1 TTATGTAAG
28837947 TTATGTAAG
1 TTATGTAAG
* *
28837956 TTATTTAAT
1 TTATGTAAG
*
28837965 TTTTGTAAG
1 TTATGTAAG
28837974 TTATGTAA
1 TTATGTAA
28837982 TTAACCAAAT
Statistics
Matches: 244, Mismatches: 52, Indels: 34
0.74 0.16 0.10
Matches are distributed among these distances:
7 17 0.07
8 7 0.03
9 203 0.83
10 5 0.02
11 7 0.03
12 5 0.02
ACGTcount: A:0.32, C:0.04, G:0.15, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:28837690 original size:25 final size:25
Alignment explanation
Indices: 28837656--28837752 Score: 72
Period size: 25 Copynumber: 3.8 Consensus size: 25
28837646 TATATTTTTA
*
28837656 TGTATTATGTAAGTTATGTAAGTTC
1 TGTATTATGTAAGTTATGTAAGTAC
* **
28837681 TGTATTATGT-A-TTATGTATGCCCC
1 TGTATTATGTAAGTTATGTAAG-TAC
* * *
28837705 ATGTAAGTAATGTAAGCTATGTAAGTAA
1 -TGT-A-TTATGTAAGTTATGTAAGTAC
*
28837733 TGTATTATGTAAGTTGTGTA
1 TGTATTATGTAAGTTATGTA
28837753 CATCATTATG
Statistics
Matches: 54, Mismatches: 12, Indels: 12
0.69 0.15 0.15
Matches are distributed among these distances:
23 8 0.15
24 2 0.04
25 26 0.48
26 2 0.04
27 8 0.15
28 1 0.02
29 7 0.13
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.43
Consensus pattern (25 bp):
TGTATTATGTAAGTTATGTAAGTAC
Found at i:28837804 original size:27 final size:27
Alignment explanation
Indices: 28837767--28837983 Score: 236
Period size: 27 Copynumber: 7.7 Consensus size: 27
28837757 ATTATGTGAG
*
28837767 TTATGTAAGTTATTTAATTTACTTAAT
1 TTATGTAAGTTATGTAATTTACTTAAT
* *
28837794 TTATGTAAGTTATGTTAGATATTTAATTTATGTAAG
1 TTATGTAAGTTATG-T--A-ATTT-A---CT-TAAT
*
28837830 TTATGTAAGTTATTTAATTTACTTAAT
1 TTATGTAAGTTATGTAATTTACTTAAT
*
28837857 TTATGTAAGTTATTTAATTTACTTAAT
1 TTATGTAAGTTATGTAATTTACTTAAT
* ** *
28837884 TTATGTAAGTTATGCAAGATATTTAAT
1 TTATGTAAGTTATGTAATTTACTTAAT
*
28837911 TTATGTAAGTTATGTAAGTTACTTAAT
1 TTATGTAAGTTATGTAATTTACTTAAT
* *
28837938 TTATGTAAGTTATGTAAGTTATTTAAT
1 TTATGTAAGTTATGTAATTTACTTAAT
*
28837965 TTTTGTAAGTTATGTAATT
1 TTATGTAAGTTATGTAATT
28837984 AACCAAATGT
Statistics
Matches: 164, Mismatches: 17, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
27 132 0.80
28 2 0.01
30 1 0.01
31 5 0.03
32 5 0.03
33 1 0.01
35 2 0.01
36 16 0.10
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.52
Consensus pattern (27 bp):
TTATGTAAGTTATGTAATTTACTTAAT
Found at i:28839405 original size:21 final size:22
Alignment explanation
Indices: 28839387--28839434 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
28839377 TGTAAATTTT
28839387 ATAAGCACCAACTGGAATTTGTCA
1 ATAAG-ACCAACTGGAATTTGT-A
*
28839411 ATTAGACCAACTGGAATTTGTA
1 ATAAGACCAACTGGAATTTGTA
28839433 AT
1 AT
28839435 TTCTAATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 3 0.13
23 16 0.70
24 4 0.17
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.29
Consensus pattern (22 bp):
ATAAGACCAACTGGAATTTGTA
Found at i:28839420 original size:23 final size:22
Alignment explanation
Indices: 28839393--28839435 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
28839383 TTTTATAAGC
28839393 ACCAACTGGAATTTGTCAATTAG
1 ACCAACTGGAATTTGT-AATTAG
28839416 ACCAACTGGAATTTGTAATT
1 ACCAACTGGAATTTGTAATT
28839436 TCTAATTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (22 bp):
ACCAACTGGAATTTGTAATTAG
Found at i:28843108 original size:63 final size:63
Alignment explanation
Indices: 28843009--28843139 Score: 262
Period size: 63 Copynumber: 2.1 Consensus size: 63
28842999 TTTGTCAAAT
28843009 TTGTAGAACTTACTTTCGTAAAGGTTCCATTGATTCATGGTCAAACAGAACATATCGATGTGC
1 TTGTAGAACTTACTTTCGTAAAGGTTCCATTGATTCATGGTCAAACAGAACATATCGATGTGC
28843072 TTGTAGAACTTACTTTCGTAAAGGTTCCATTGATTCATGGTCAAACAGAACATATCGATGTGC
1 TTGTAGAACTTACTTTCGTAAAGGTTCCATTGATTCATGGTCAAACAGAACATATCGATGTGC
28843135 TTGTA
1 TTGTA
28843140 CCCACGATAA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 68 1.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (63 bp):
TTGTAGAACTTACTTTCGTAAAGGTTCCATTGATTCATGGTCAAACAGAACATATCGATGTGC
Found at i:28845854 original size:9 final size:9
Alignment explanation
Indices: 28845840--28846303 Score: 554
Period size: 9 Copynumber: 52.7 Consensus size: 9
28845830 ACCATAAATG
28845840 AGTTATGTA
1 AGTTATGTA
28845849 AGTTATGT-
1 AGTTATGTA
28845857 A-TTATGT-
1 AGTTATGTA
28845864 A-TTATGTA
1 AGTTATGTA
*
28845872 ATTTATGTA
1 AGTTATGTA
*
28845881 AGTTATTTA
1 AGTTATGTA
28845890 AGTTATGTA
1 AGTTATGTA
28845899 AGTTATGTA
1 AGTTATGTA
*
28845908 AGTTATTTA
1 AGTTATGTA
*
28845917 ATTTATGTA
1 AGTTATGTA
28845926 AGTTATGTA
1 AGTTATGTA
*
28845935 AGTTATTTA
1 AGTTATGTA
28845944 AGTTATGTA
1 AGTTATGTA
28845953 AGTTATGTA
1 AGTTATGTA
28845962 AGTTATGTA
1 AGTTATGTA
28845971 AGTTATGTA
1 AGTTATGTA
*
28845980 AGTTATTTA
1 AGTTATGTA
*
28845989 ATTTATGTA
1 AGTTATGTA
28845998 AGTTATGTA
1 AGTTATGTA
*
28846007 AGTTATTTA
1 AGTTATGTA
*
28846016 ATTTATGTA
1 AGTTATGTA
28846025 AGTTATGTA
1 AGTTATGTA
*
28846034 AGTTATGCA
1 AGTTATGTA
*
28846043 AGTTATTTA
1 AGTTATGTA
*
28846052 ATTTATGTA
1 AGTTATGTA
28846061 AGTTATGTA
1 AGTTATGTA
28846070 AGTTATGTA
1 AGTTATGTA
28846079 AGTTATGTA
1 AGTTATGTA
*
28846088 AGTTATTTA
1 AGTTATGTA
*
28846097 ATTTATGTA
1 AGTTATGTA
*
28846106 AGTTATATA
1 AGTTATGTA
28846115 AGTTATGTA
1 AGTTATGTA
*
28846124 AGTTATTTA
1 AGTTATGTA
*
28846133 ATTTATGTA
1 AGTTATGTA
28846142 AGTTATGTA
1 AGTTATGTA
* ** *
28846151 GGCAATAT-
1 AGTTATGTA
28846159 A-TTATGTA
1 AGTTATGTA
* *
28846167 AATAATGTA
1 AGTTATGTA
*
28846176 AGTTA-GGA
1 AGTTATGTA
28846184 AGGTTATGT-
1 A-GTTATGTA
*
28846193 A-TTGTGTA
1 AGTTATGTA
*
28846201 AGTTATTTA
1 AGTTATGTA
28846210 AGTTATGTA
1 AGTTATGTA
*
28846219 AGTTATTTA
1 AGTTATGTA
*
28846228 ATTTATGTA
1 AGTTATGTA
28846237 AGTTATGTA
1 AGTTATGTA
28846246 AGTTATGTA
1 AGTTATGTA
*
28846255 AGTTATTTA
1 AGTTATGTA
*
28846264 ATTTATGTA
1 AGTTATGTA
28846273 AGTTATGTA
1 AGTTATGTA
*
28846282 GGTTATGT-
1 AGTTATGTA
*
28846290 A-TTATGTT
1 AGTTATGTA
28846298 AGTTAT
1 AGTTAT
28846304 TATGTTATTA
Statistics
Matches: 385, Mismatches: 60, Indels: 20
0.83 0.13 0.04
Matches are distributed among these distances:
7 27 0.07
8 8 0.02
9 349 0.91
10 1 0.00
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (9 bp):
AGTTATGTA
Found at i:28846330 original size:29 final size:29
Alignment explanation
Indices: 28846298--28846395 Score: 87
Period size: 29 Copynumber: 3.3 Consensus size: 29
28846288 GTATTATGTT
28846298 AGTTATTATGTTATTATATAAGTTATGCA
1 AGTTATTATGTTATTATATAAGTTATGCA
* *
28846327 AGTTTCTATATATG-T-TTATATATTGTATAT--T
1 AG--T-TAT-TATGTTATTATATA-AGT-TATGCA
28846358 AGTTATTATGTTATTATATAAGTTATGCA
1 AGTTATTATGTTATTATATAAGTTATGCA
*
28846387 AGTTTTTAT
1 AGTTATTAT
28846396 ATATATATAT
Statistics
Matches: 54, Mismatches: 5, Indels: 20
0.68 0.06 0.25
Matches are distributed among these distances:
27 7 0.13
28 6 0.11
29 18 0.33
31 10 0.19
32 6 0.11
33 7 0.13
ACGTcount: A:0.32, C:0.03, G:0.12, T:0.53
Consensus pattern (29 bp):
AGTTATTATGTTATTATATAAGTTATGCA
Found at i:28846404 original size:29 final size:29
Alignment explanation
Indices: 28846312--28846429 Score: 76
Period size: 31 Copynumber: 3.9 Consensus size: 29
28846302 ATTATGTTAT
* *
28846312 TATATAAGTTATGCAAGTTTCTATATATG
1 TATATAAGTTATGCAAGTTTTTATATATA
* * *** * *
28846341 TTTATATATTGTATATTAGTTATTATGT-TA
1 TATATA-AGT-TATGCAAGTTTTTATATATA
28846371 TTATATAAGTTATGCAAGTTTTTATATATA
1 -TATATAAGTTATGCAAGTTTTTATATATA
* * *
28846401 TATATATGTATTATGTAAGTTTATATATA
1 TATATAAG--TTATGCAAGTTTTTATATA
28846430 AGTTATGATA
Statistics
Matches: 64, Mismatches: 19, Indels: 10
0.69 0.20 0.11
Matches are distributed among these distances:
29 24 0.38
30 7 0.11
31 33 0.52
ACGTcount: A:0.35, C:0.03, G:0.11, T:0.52
Consensus pattern (29 bp):
TATATAAGTTATGCAAGTTTTTATATATA
Found at i:28846520 original size:17 final size:18
Alignment explanation
Indices: 28846488--28846521 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
28846478 TGATTGATAA
28846488 ATTTTGAAAAAAATATAG
1 ATTTTGAAAAAAATATAG
*
28846506 ATTTT-AAAAATATATA
1 ATTTTGAAAAAAATATA
28846522 CATTAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (18 bp):
ATTTTGAAAAAAATATAG
Found at i:28848676 original size:334 final size:333
Alignment explanation
Indices: 28848008--28848792 Score: 797
Period size: 334 Copynumber: 2.4 Consensus size: 333
28847998 TTTGTGGCAT
* * * *
28848008 TTTTCTGAAAAA-CGCCACTAAAAATTAAAGTTC-AAACCGAAACGGCGCCGTTTAATTAAGCTT
1 TTTTCT-AAAAAGCGCCACTAAAAATTAAAGTTCTAATCCAAAACGGCGCCGTTTTATTAAGATT
* * * * * * *
28848071 TAATGCACAGTTCTGGCGTTTTTTGTAAAAACG-TAGTAAAAATTAATTTTCTTAAGTTATATGA
65 TAATGCACAGTTCTGGCGTTTTCTGT-TAAACGCCAGTAAAAATTAATTTGCTTAAGCTAAACGA
* * * * * * * *
28848135 GGTCGTTTAGACAATATTTTAAGTCATTTTACGGTGTTTTGTGCAAAAATGCCACTATAAATTAA
129 AGCCGTGTAGACAACATTTTAAGTCACTTTACGGTGTTTGGTGCAAAAACGCCACTAAAAATTAA
* * ** * * * *
28848200 GAGAAACGGCGTCGTTGGATTAATTTAGAGAAAATGATAAGTTAAAAAACTAGTACAAAAACGGC
194 CAAAAACGGCACCATTGAATTAATATAGAGAAAATGATAAATTAAAAAACTAGTACAAAAACGGC
* * * *
28848265 ATCGTTTAGACAAATTTTAAGACAATTTTACAGTGCATCCTGAACAAACGCCGCTATTGCTTGCA
259 ACCGTTTAGACAAATTTTAAGACAACTTTACAGTGCATACTGAACAAACGCCGCTATAGCTTGCA
28848330 CGTTTACGGCG
324 CG-TTACGGCG
* * *
28848341 TTTTCTAAAAAGCGCCACTAAAATTTAAAGTTCTAATCCAAAACGGCACCGTTTTATTAAGATGT
1 TTTTCTAAAAAGCGCCACTAAAAATTAAAGTTCTAATCCAAAACGGCGCCGTTTTATTAAGATTT
* *
28848406 AATGCACATTTCTGGCGTTTTCTGATTAAACGCCAGTAAAAATAAATTTGCTTAAGCTAAACGAA
66 AATGCACAGTTCTGGCGTTTTCTG-TTAAACGCCAGTAAAAATTAATTTGCTTAAGCTAAACGAA
* * * *
28848471 GCCGTGTAGGCAACATTTTATGTCACTTTGCGGTGTTTGGTGTAAAAACGCCAC-AAAAATTAAC
130 GCCGTGTAGACAACATTTTAAGTCACTTTACGGTGTTTGGTGCAAAAACGCCACTAAAAATTAAC
* ** ** * * *
28848535 AAAAATGGCACCATTGAATTAATATAGAGAAAATTCTAAATATAAAAATGT-GTACAGAGACGGT
195 AAAAACGGCACCATTGAATTAATATAGAGAAAATGATAAAT-TAAAAAACTAGTACAAAAACGGC
* * *
28848599 GCCGTTTAG-CAAAATTTTAAGAC-ACTTT-C-GTGGCGTTTATTGAACAAACGCCGCTATAGCT
259 ACCGTTTAGAC-AAATTTTAAGACAACTTTACAGT-GC--ATACTGAACAAACGCCGCTATAGC-
* *
28848660 TGTGTAC-TTGCGGCG
319 T-TGCACGTTACGGCG
* * * * *
28848675 -TTTCTAGACAAGTGCCAC-AAAGAATGAAGGTTCTAATCCAAAACGGCGCCGTTTTGTTAAGAT
1 TTTTCTA-AAAAGCGCCACTAAA-AATTAAAGTTCTAATCCAAAACGGCGCCGTTTTATTAAGAT
* *
28848738 TTAATGCATAGTTCTGGTGTTTTCCT-TTAAAGCGCCAGT-AAAATTAATTTGCTTA
64 TTAATGCACAGTTCTGGCGTTTT-CTGTTAAA-CGCCAGTAAAAATTAATTTGCTTA
28848793 TGTTAGACGT
Statistics
Matches: 372, Mismatches: 65, Indels: 30
0.80 0.14 0.06
Matches are distributed among these distances:
331 2 0.01
332 8 0.02
333 60 0.16
334 218 0.59
335 80 0.22
336 4 0.01
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31
Consensus pattern (333 bp):
TTTTCTAAAAAGCGCCACTAAAAATTAAAGTTCTAATCCAAAACGGCGCCGTTTTATTAAGATTT
AATGCACAGTTCTGGCGTTTTCTGTTAAACGCCAGTAAAAATTAATTTGCTTAAGCTAAACGAAG
CCGTGTAGACAACATTTTAAGTCACTTTACGGTGTTTGGTGCAAAAACGCCACTAAAAATTAACA
AAAACGGCACCATTGAATTAATATAGAGAAAATGATAAATTAAAAAACTAGTACAAAAACGGCAC
CGTTTAGACAAATTTTAAGACAACTTTACAGTGCATACTGAACAAACGCCGCTATAGCTTGCACG
TTACGGCG
Found at i:28849031 original size:83 final size:83
Alignment explanation
Indices: 28848892--28849059 Score: 336
Period size: 83 Copynumber: 2.0 Consensus size: 83
28848882 TGCTAAGTTA
28848892 AAAATCGTGGACAGAAACGGCGTCATTCAACCAAATTTTAAGTCACTTTTGCGGCGTTTCTTGTA
1 AAAATCGTGGACAGAAACGGCGTCATTCAACCAAATTTTAAGTCACTTTTGCGGCGTTTCTTGTA
28848957 CAAACGCCGCTATTGCTT
66 CAAACGCCGCTATTGCTT
28848975 AAAATCGTGGACAGAAACGGCGTCATTCAACCAAATTTTAAGTCACTTTTGCGGCGTTTCTTGTA
1 AAAATCGTGGACAGAAACGGCGTCATTCAACCAAATTTTAAGTCACTTTTGCGGCGTTTCTTGTA
28849040 CAAACGCCGCTATTGCTT
66 CAAACGCCGCTATTGCTT
28849058 AA
1 AA
28849060 GCATTAGCGG
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 85 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.30
Consensus pattern (83 bp):
AAAATCGTGGACAGAAACGGCGTCATTCAACCAAATTTTAAGTCACTTTTGCGGCGTTTCTTGTA
CAAACGCCGCTATTGCTT
Found at i:28850932 original size:112 final size:113
Alignment explanation
Indices: 28850793--28851028 Score: 298
Period size: 112 Copynumber: 2.1 Consensus size: 113
28850783 GCTTTACCGT
* *
28850793 AAACGCCGCTAAAGCCCTGAGCGTTAGCGGCGCTTACCTAAAAACGCCGCTCAATCCCCGAAAGC
1 AAACGCCGCTAAAGCCCTGAGCGTTAGCGGCACTTACCTAAAAACGCCGCTAAATCCCCGAAAGC
* * * * * *
28850858 TCAG-AAATGGCGTCGTTGGGCTTACATTTTTTGTGGCACTTTTTCAA
66 TCAGAAAACGGAGTCGTTGGGATTACATATTTTGCGGCACTTTATCAA
* * *
28850905 AAACGCCGCTAAATG-CCTGAG-GCTTAGCGGCACTTTCTTAAAAACGCCGCTAAATTCCCGAAA
1 AAACGCCGCTAAA-GCCCTGAGCG-TTAGCGGCACTTACCTAAAAACGCCGCTAAATCCCCGAAA
** **
28850968 GCTCAGAAAACGGAGTCGTTGGGATTAGGTATTTTGCGGCACTTTATGGA
64 GCTCAGAAAACGGAGTCGTTGGGATTACATATTTTGCGGCACTTTATCAA
28851018 AAACGCCGCTA
1 AAACGCCGCTA
28851029 CTGCTTATTT
Statistics
Matches: 106, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
111 1 0.01
112 60 0.57
113 45 0.42
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.24
Consensus pattern (113 bp):
AAACGCCGCTAAAGCCCTGAGCGTTAGCGGCACTTACCTAAAAACGCCGCTAAATCCCCGAAAGC
TCAGAAAACGGAGTCGTTGGGATTACATATTTTGCGGCACTTTATCAA
Found at i:28853255 original size:17 final size:18
Alignment explanation
Indices: 28853228--28853261 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
28853218 TTAGGTTAAC
28853228 TAAATTAATTTTCTCAAT
1 TAAATTAATTTTCTCAAT
28853246 TAAA-TAATTTTCTCAA
1 TAAATTAATTTTCTCAA
28853262 CTCAATTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:28856514 original size:21 final size:21
Alignment explanation
Indices: 28856490--28856531 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28856480 TAAGGGGGTT
*
28856490 TAAAGTTAAAAAAACTAAAAA
1 TAAAATTAAAAAAACTAAAAA
* *
28856511 TAAAATTAAACAAAGTAAAAA
1 TAAAATTAAAAAAACTAAAAA
28856532 AGATCATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.71, C:0.05, G:0.05, T:0.19
Consensus pattern (21 bp):
TAAAATTAAAAAAACTAAAAA
Found at i:28861886 original size:24 final size:24
Alignment explanation
Indices: 28861847--28861897 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
28861837 AAATATTTTT
*
28861847 ATTTTTAGGAATATT-AGTTACTA
1 ATTTTTAGGAATATTAAGTAACTA
28861870 ATTTTTAGATGAA-ATTAAGTAACTA
1 ATTTTTAG--GAATATTAAGTAACTA
28861895 ATT
1 ATT
28861898 AAGAATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 8 0.33
24 3 0.12
25 13 0.54
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.45
Consensus pattern (24 bp):
ATTTTTAGGAATATTAAGTAACTA
Found at i:28868980 original size:5 final size:5
Alignment explanation
Indices: 28868970--28868994 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
28868960 ATATAAATTA
28868970 TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT
28868995 ATAAATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:28869209 original size:22 final size:22
Alignment explanation
Indices: 28869175--28869224 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
28869165 TCTTTTAACA
* *
28869175 CATAAACATTCAATTATATTGG
1 CATAATCAATCAATTATATTGG
*
28869197 CATAATCAATCAATTATGTTGG
1 CATAATCAATCAATTATATTGG
28869219 CATAAT
1 CATAAT
28869225 ACATCCATGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (22 bp):
CATAATCAATCAATTATATTGG
Found at i:28870610 original size:92 final size:92
Alignment explanation
Indices: 28870514--28871186 Score: 1098
Period size: 92 Copynumber: 7.3 Consensus size: 92
28870504 AACTTATCTT
*
28870514 CATATACAAATAAATTTCAGCAATGTATAATCAAATACGAATCAATTCGACAACTTATCTTCATA
1 CATATACAAATAAATTTCAGCAATGTATAATCATATACGAATCAATTCGACAACTTATCTTCATA
28870579 TACAAATCAATTTCGATAATATATAAC
66 TACAAATCAATTTCGATAATATATAAC
* **
28870606 CATATACAAATAAATTTCAGCAATGTATAATTATATACGAATCAATTCGGTAACTTATCTTCATA
1 CATATACAAATAAATTTCAGCAATGTATAATCATATACGAATCAATTCGACAACTTATCTTCATA
28870671 TACAAATCAATTTCGATAATATATAAC
66 TACAAATCAATTTCGATAATATATAAC
* * *
28870698 CATATAAAAATAAATTTCAGCAATGTAAAATCAAATACGAATCAATTCGACAACTTATCTTCATA
1 CATATACAAATAAATTTCAGCAATGTATAATCATATACGAATCAATTCGACAACTTATCTTCATA
*
28870763 TAC-CATCAATTTCGATAATATATAAC
66 TACAAATCAATTTCGATAATATATAAC
* *
28870789 CATATACAAATAAATTTCAGCAATGTATAATTATATACGAATCAATTC-AGTAACTTATCTTCAT
1 CATATACAAATAAATTTCAGCAATGTATAATCATATACGAATCAATTCGA-CAACTTATCTTCAT
28870853 ATACAAATCAATTTCGATAATATATAAC
65 ATACAAATCAATTTCGATAATATATAAC
* * *
28870881 CATATAAAAATAAATTTCAGTAATGTATAATCATATACGAATCAATTCGGCAACTTATCTTCATA
1 CATATACAAATAAATTTCAGCAATGTATAATCATATACGAATCAATTCGACAACTTATCTTCATA
28870946 TACAAATCAATTTCGATAATATATAAC
66 TACAAATCAATTTCGATAATATATAAC
* * * * * *
28870973 AATATACAAATAAATTTCATCAATGTATAATTATATACGAATCAATTTGGCAACTTATCTTCTTA
1 CATATACAAATAAATTTCAGCAATGTATAATCATATACGAATCAATTCGACAACTTATCTTCATA
*
28871038 TACAAATCAATTTCGATAATATATGAC
66 TACAAATCAATTTCGATAATATATAAC
* * *
28871065 CATATACAAATAAACTTCAGTAATGTATAATCATATACGAATCAATTTGACAACTTATCTTCATA
1 CATATACAAATAAATTTCAGCAATGTATAATCATATACGAATCAATTCGACAACTTATCTTCATA
28871130 TACAAATCAATTTCGATAATATATAAC
66 TACAAATCAATTTCGATAATATATAAC
* *
28871157 CACATACAAATAAATTTCAGTAATGTATAA
1 CATATACAAATAAATTTCAGCAATGTATAA
28871187 AACAATCAAA
Statistics
Matches: 538, Mismatches: 40, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
90 1 0.00
91 83 0.15
92 454 0.84
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.34
Consensus pattern (92 bp):
CATATACAAATAAATTTCAGCAATGTATAATCATATACGAATCAATTCGACAACTTATCTTCATA
TACAAATCAATTTCGATAATATATAAC
Found at i:28871069 original size:367 final size:368
Alignment explanation
Indices: 28870514--28871186 Score: 1168
Period size: 367 Copynumber: 1.8 Consensus size: 368
28870504 AACTTATCTT
*
28870514 CATATACAAATAAATTTCAGCAATGTATAATCAAATACGAATCAATTCGACAACTTATCTTCATA
1 CATATAAAAATAAATTTCAGCAATGTATAATCAAATACGAATCAATTCGACAACTTATCTTCATA
*
28870579 TACAAATCAATTTCGATAATATATAACCATATACAAATAAATTTCAGCAATGTATAATTATATAC
66 TACAAATCAATTTCGATAATATATAACAATATACAAATAAATTTCAGCAATGTATAATTATATAC
*
28870644 GAATCAATTCGGTAACTTATCTTCATATACAAATCAATTTCGATAATATATAACCATATAAAAAT
131 GAATCAATTCGGCAACTTATCTTCATATACAAATCAATTTCGATAATATATAACCATATAAAAAT
* *
28870709 AAATTTCAGCAATGTAAAATCAAATACGAATCAATTCGACAACTTATCTTCATATAC-CATCAAT
196 AAACTTCAGCAATGTAAAATCAAATACGAATCAATTCGACAACTTATCTTCATATACAAATCAAT
*
28870773 TTCGATAATATATAACCATATACAAATAAATTTCAGCAATGTATAATTATATACGAATCAATTCA
261 TTCGATAATATATAACCACATACAAATAAATTTCAGCAATGTATAATTATATACGAATCAATTCA
28870838 GTAACTTATCTTCATATACAAATCAATTTCGATAATATATAAC
326 GTAACTTATCTTCATATACAAATCAATTTCGATAATATATAAC
* * *
28870881 CATATAAAAATAAATTTCAGTAATGTATAATCATATACGAATCAATTCGGCAACTTATCTTCATA
1 CATATAAAAATAAATTTCAGCAATGTATAATCAAATACGAATCAATTCGACAACTTATCTTCATA
*
28870946 TACAAATCAATTTCGATAATATATAACAATATACAAATAAATTTCATCAATGTATAATTATATAC
66 TACAAATCAATTTCGATAATATATAACAATATACAAATAAATTTCAGCAATGTATAATTATATAC
* * * *
28871011 GAATCAATTTGGCAACTTATCTTCTTATACAAATCAATTTCGATAATATATGACCATATACAAAT
131 GAATCAATTCGGCAACTTATCTTCATATACAAATCAATTTCGATAATATATAACCATATAAAAAT
* * * *
28871076 AAACTTCAGTAATGTATAATCATATACGAATCAATTTGACAACTTATCTTCATATACAAATCAAT
196 AAACTTCAGCAATGTAAAATCAAATACGAATCAATTCGACAACTTATCTTCATATACAAATCAAT
*
28871141 TTCGATAATATATAACCACATACAAATAAATTTCAGTAATGTATAA
261 TTCGATAATATATAACCACATACAAATAAATTTCAGCAATGTATAA
28871187 AACAATCAAA
Statistics
Matches: 286, Mismatches: 19, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
367 236 0.83
368 50 0.17
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.34
Consensus pattern (368 bp):
CATATAAAAATAAATTTCAGCAATGTATAATCAAATACGAATCAATTCGACAACTTATCTTCATA
TACAAATCAATTTCGATAATATATAACAATATACAAATAAATTTCAGCAATGTATAATTATATAC
GAATCAATTCGGCAACTTATCTTCATATACAAATCAATTTCGATAATATATAACCATATAAAAAT
AAACTTCAGCAATGTAAAATCAAATACGAATCAATTCGACAACTTATCTTCATATACAAATCAAT
TTCGATAATATATAACCACATACAAATAAATTTCAGCAATGTATAATTATATACGAATCAATTCA
GTAACTTATCTTCATATACAAATCAATTTCGATAATATATAAC
Found at i:28874971 original size:19 final size:19
Alignment explanation
Indices: 28874947--28875023 Score: 91
Period size: 19 Copynumber: 3.8 Consensus size: 19
28874937 CTTGAAAAGG
*
28874947 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAA
28874966 GATATGCAATCTTAGATAA
1 GATATGCAATCTTAGATAA
*
28874985 GATATACAATCTTAGAAGATAA
1 GATATGCAATCTT---AGATAA
*
28875007 GATATTGTAATCTTAGA
1 GATA-TGCAATCTTAGA
28875024 GATTTAATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
19 30 0.60
20 3 0.06
22 10 0.20
23 7 0.14
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.34
Consensus pattern (19 bp):
GATATGCAATCTTAGATAA
Found at i:28875873 original size:24 final size:24
Alignment explanation
Indices: 28875840--28875956 Score: 100
Period size: 24 Copynumber: 5.0 Consensus size: 24
28875830 AAGTGTATTG
28875840 TATATTATTATTTTAGATTTATCA
1 TATATTATTATTTTAGATTTATCA
* *
28875864 TGTTTTATTATTTGTA-ATTTATCA
1 TATATTATTATTT-TAGATTTATCA
* * *
28875888 -ATAATA-T-TTTTAAATTTATTA
1 TATATTATTATTTTAGATTTATCA
*
28875909 TATACTATTATTTTAGA-TTATCA
1 TATATTATTATTTTAGATTTATCA
** * *
28875932 CGTATGATTATTTTAGAATTATCA
1 TATATTATTATTTTAGATTTATCA
28875956 T
1 T
28875957 CAAAATTTTT
Statistics
Matches: 73, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
20 2 0.03
21 10 0.14
22 6 0.08
23 22 0.30
24 31 0.42
25 2 0.03
ACGTcount: A:0.33, C:0.05, G:0.06, T:0.56
Consensus pattern (24 bp):
TATATTATTATTTTAGATTTATCA
Found at i:28875942 original size:68 final size:69
Alignment explanation
Indices: 28875835--28875998 Score: 183
Period size: 68 Copynumber: 2.4 Consensus size: 69
28875825 TATCTAAGTG
* * * * * *
28875835 TATTGTATATTATTATTTTAGATTTATCATGTTTTATTATTTGTA-ATTTATCAAT-AATATTTT
1 TATTATATATTATTATTTTAGATTTATCACGTATGATTATTT-TAGAATTATC-ATCAAAATTTT
28875898 TAAATT
64 TAAATT
*
28875904 TATTATATACTATTATTTTAGA-TTATCACGTATGATTATTTTAGAATTATCATCAAAATTTTTA
1 TATTATATATTATTATTTTAGATTTATCACGTATGATTATTTTAGAATTATCATCAAAATTTTTA
28875968 AATT
66 AATT
* * *
28875972 T-TATATGTATTATTATTTCAAATTTAT
1 TAT-TATATATTATTATTTTAGATTTAT
28875999 TATATATTAT
Statistics
Matches: 80, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
67 5 0.06
68 51 0.64
69 24 0.30
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.55
Consensus pattern (69 bp):
TATTATATATTATTATTTTAGATTTATCACGTATGATTATTTTAGAATTATCATCAAAATTTTTA
AATT
Found at i:28876096 original size:23 final size:23
Alignment explanation
Indices: 28876069--28876113 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
28876059 AATTGTACAT
*
28876069 TCATATATATTATTTGTTTTAAC
1 TCATATATATTATTTATTTTAAC
*
28876092 TCATATATATTGTTTATTTTAA
1 TCATATATATTATTTATTTTAA
28876114 AATTTTGAAC
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:0.31, C:0.07, G:0.04, T:0.58
Consensus pattern (23 bp):
TCATATATATTATTTATTTTAAC
Found at i:28877627 original size:16 final size:16
Alignment explanation
Indices: 28877602--28877636 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
28877592 TTGTGTTTTG
*
28877602 TTTTGGCTGCATGACA
1 TTTTGACTGCATGACA
*
28877618 TTTTGACTGCATGGCA
1 TTTTGACTGCATGACA
28877634 TTT
1 TTT
28877637 CATCATAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.43
Consensus pattern (16 bp):
TTTTGACTGCATGACA
Found at i:28885400 original size:397 final size:396
Alignment explanation
Indices: 28884656--28885848 Score: 2221
Period size: 397 Copynumber: 3.0 Consensus size: 396
28884646 TTAATTTTTA
28884656 GACTTTATAAATAAATTTCTATGTAAAAATTCAGCCCAAAGAGGCCCATTAAAGGCCTTGGACGA
1 GACTTTATAAATAAATTTCTATGTAAAAATTCAGCCCAAAGAGGCCCATTAAAGGCCTTGGACGA
* *
28884721 AATTCCCTTGAAAATCAATGATTAGGTTTTTTTTTTTAGTTTTCCTATTAGGGTTAGGAAAATTG
66 AATTCCCTTGAAAATCAATAATTAGGTTTTTTTTTTTAGTTTTCCTATTAGGGTTAGGAAAATAG
* *
28884786 TTAGAAGGCCTATATATATGGCTTGGCTAGGCACCCATAGAATATACATTGATTATACTTTGAAA
131 TTAGAAGGCCTATATATATGGCTTGGCCAGCCACCCATAGAATATACATTGATTATACTTTGAAA
*
28884851 TCATATTTTTGTTGAGTGAAAATTCTCTTTGGGTTTTCTCCAAGAATTTTCTCTTGAGTTTTCTT
196 TCAGATTTTTGTTGAGTGAAAATTCTCTTTGGGTTTTCTCCAAGAATTTTCTCTTGAGTTTTCTT
28884916 TGGAAGTAGTTTTAACAATCTTTTTGATTGTGGGAGCCATCTTCAGCCTTCTTCTTGCCATTGTT
261 TGGAAGTAGTTTTAACAATCTTTTTGATTGTGGGAGCCATCTTCAGCCTTCTTCTTGCCATTGTT
*
28884981 CTTCATTGGAGGGGATATTAGAGCCGTTTGAAGGGAGTTGTGAAATCTTTCTCGATTTCAAGGCT
326 CTTCATTGGAGGGGAGATTAGAGCCGTTTGAAGGGAGTTGTGAAATCTTTCTCGATTTCAAGGCT
28885046 TCTTAG
391 TCTTAG
28885052 GACTTTATAAATAAATTTCTATGTAAAAATTCAGCCCAAAGAGGCCCATTAAAGGCCTTGGACGA
1 GACTTTATAAATAAATTTCTATGTAAAAATTCAGCCCAAAGAGGCCCATTAAAGGCCTTGGACGA
* *
28885117 AATTCCCTTGAAAATCAATAATTAGGTTTTTTTTTTTTAGTTTTCCTGTTAGGGCTAGGAAAATA
66 AATTCCCTTGAAAATCAATAATTAGG-TTTTTTTTTTTAGTTTTCCTATTAGGGTTAGGAAAATA
28885182 GTTAGAAGGCCTATATATATGGCTTGGCCAGCCACCCATAGAATATACATTGATTATACTTTGAA
130 GTTAGAAGGCCTATATATATGGCTTGGCCAGCCACCCATAGAATATACATTGATTATACTTTGAA
28885247 ATCAGATTTTTGTTGAGTGAAAATTCTCTTTGGGTTTTCTCCAAGAATTTTCTCTTGAGTTTTCT
195 ATCAGATTTTTGTTGAGTGAAAATTCTCTTTGGGTTTTCTCCAAGAATTTTCTCTTGAGTTTTCT
28885312 TTGGAAGTAGTTTTAACAATCTTTTTGATTGTGGGAGCCATCTTCAGCCTTCTTCTTGCCATTGT
260 TTGGAAGTAGTTTTAACAATCTTTTTGATTGTGGGAGCCATCTTCAGCCTTCTTCTTGCCATTGT
*
28885377 TCTTCATTGGATGGGAGATTAGAGCCGTTTGAAGGGAGTTGTGAAATCTTTCTCGATTTCAAGGC
325 TCTTCATTGGAGGGGAGATTAGAGCCGTTTGAAGGGAGTTGTGAAATCTTTCTCGATTTCAAGGC
28885442 TTCTTAG
390 TTCTTAG
28885449 GACTTTATAAATAAATTTCTATGTAAAAATTCAGCCCAAAGAGGCCCATTAAAGGCCTTGGACGA
1 GACTTTATAAATAAATTTCTATGTAAAAATTCAGCCCAAAGAGGCCCATTAAAGGCCTTGGACGA
**
28885514 AATTCCCTTGAAAATCAATAATTCA--AATTTTTTTTTAGTTTTCCTATTAGGGTTAGGAAAATA
66 AATTCCCTTGAAAATCAATAATT-AGGTTTTTTTTTTTAGTTTTCCTATTAGGGTTAGGAAAATA
28885577 GTTAGAAGGCCTATATATATGGCTTGGCCAGCCACCCATAGAATATACATTGATTATACTTTGAA
130 GTTAGAAGGCCTATATATATGGCTTGGCCAGCCACCCATAGAATATACATTGATTATACTTTGAA
28885642 ATCAGATTTTTGTTGAGTGAAAATTCTCTTTGGGTTTTCTCCAAGAATTTTCTCTTGAGTTTTCT
195 ATCAGATTTTTGTTGAGTGAAAATTCTCTTTGGGTTTTCTCCAAGAATTTTCTCTTGAGTTTTCT
*
28885707 TTGGAAGTAGTTTTAACAATCTTTTT-ATTGTGGGAGCCATCTTCAGCCTTGTTCTTGCCATTGT
260 TTGGAAGTAGTTTTAACAATCTTTTTGATTGTGGGAGCCATCTTCAGCCTTCTTCTTGCCATTGT
* *
28885771 TCTTCATTGGAGGGGAGATTAGAGCTGTTTGAAGGGAGTTGTGAAATCTTTTTCGATTTCAAGGC
325 TCTTCATTGGAGGGGAGATTAGAGCCGTTTGAAGGGAGTTGTGAAATCTTTCTCGATTTCAAGGC
28885836 TTCTTAG
390 TTCTTAG
28885843 GACTTT
1 GACTTT
28885849 TTCTTTATGT
Statistics
Matches: 778, Mismatches: 17, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
394 112 0.14
395 190 0.24
396 90 0.12
397 385 0.49
398 1 0.00
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (396 bp):
GACTTTATAAATAAATTTCTATGTAAAAATTCAGCCCAAAGAGGCCCATTAAAGGCCTTGGACGA
AATTCCCTTGAAAATCAATAATTAGGTTTTTTTTTTTAGTTTTCCTATTAGGGTTAGGAAAATAG
TTAGAAGGCCTATATATATGGCTTGGCCAGCCACCCATAGAATATACATTGATTATACTTTGAAA
TCAGATTTTTGTTGAGTGAAAATTCTCTTTGGGTTTTCTCCAAGAATTTTCTCTTGAGTTTTCTT
TGGAAGTAGTTTTAACAATCTTTTTGATTGTGGGAGCCATCTTCAGCCTTCTTCTTGCCATTGTT
CTTCATTGGAGGGGAGATTAGAGCCGTTTGAAGGGAGTTGTGAAATCTTTCTCGATTTCAAGGCT
TCTTAG
Found at i:28886713 original size:11 final size:11
Alignment explanation
Indices: 28886699--28886733 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
28886689 TGAAAAAATG
28886699 AGAAAATGAAA
1 AGAAAATGAAA
28886710 AGAAAATGAAAA
1 AGAAAATG-AAA
*
28886722 AGAAAAGGAAA
1 AGAAAATGAAA
28886733 A
1 A
28886734 AGAGAGACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.74, C:0.00, G:0.20, T:0.06
Consensus pattern (11 bp):
AGAAAATGAAA
Found at i:28886724 original size:12 final size:12
Alignment explanation
Indices: 28886699--28886736 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
28886689 TGAAAAAATG
28886699 AGAAAATG-AAA
1 AGAAAATGAAAA
28886710 AGAAAATGAAAA
1 AGAAAATGAAAA
*
28886722 AGAAAAGGAAAA
1 AGAAAATGAAAA
28886734 AGA
1 AGA
28886737 GAGACCAAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
11 8 0.32
12 17 0.68
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (12 bp):
AGAAAATGAAAA
Found at i:28888303 original size:12 final size:12
Alignment explanation
Indices: 28888286--28888310 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28888276 AAATTGAGAC
28888286 TATCCCTTCAGA
1 TATCCCTTCAGA
28888298 TATCCCTTCAGA
1 TATCCCTTCAGA
28888310 T
1 T
28888311 CTTGTTGTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.32, G:0.08, T:0.36
Consensus pattern (12 bp):
TATCCCTTCAGA
Found at i:28889503 original size:254 final size:255
Alignment explanation
Indices: 28889065--28890027 Score: 1341
Period size: 253 Copynumber: 3.8 Consensus size: 255
28889055 CAGATTTAAG
* * *
28889065 ACGGCGAATCTTATCTTCCCAAGGTAATAGGGAAACAGATTTAAGCCACTAAGTCATATCTCCCT
1 ACGGCGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACTAAGTCCTATCTCCCT
*
28889130 GAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTCAGCAGTAGTGGAGCAGATCG
66 GAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCG
* *
28889195 AAGACGGTGAATCTTATCTTCCCAAAGTAGTAGGGAAACAGATTTAAGCCACCAATCCTATCTCC
131 AAGACGGCGAATCTTATCTTCCCAAGGTAGTAGGGAAACAGATTTAAGCCACCAATCCTATCTCC
*
28889260 CTGAGTAGCAGTGGAGTAGGCAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAA
196 CTGAGCAGCAGTGGAGTAGGCAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAA
** * * * *
28889320 ACGGCTTATCTTATCTTCCCAAGGTAGTAGGGGAGCAGATTTAAGCCGC-CAGTCCTATCTCCTT
1 ACGGCGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACTAAGTCCTATCTCCCT
*
28889384 GAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGTAGATCG
66 GAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCG
*
28889449 AAGACGGCGAATCTTATCTTCCCAAGGTAATAGGGAAACAGATTTAAGCCACCAATCCTATCTCC
131 AAGACGGCGAATCTTATCTTCCCAAGGTAGTAGGGAAACAGATTTAAGCCACCAATCCTATCTCC
* * *
28889514 CTGACCAGCAGTGGAGTAGGTAGAT-CTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAG
196 CTGAGCAGCAGTGGAGTAGGCAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAA
* * *
28889573 ATGACGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCAC-CAGTCCTATCTCCCT
1 ACGGCGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACTAAGTCCTATCTCCCT
* * * *
28889637 GAGTAGCAATTGAGTAGGTTGAAGATTGTAGATCCTGTCTCTCTAAGCAGTAGTGGAGCAGATCG
66 GAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCG
* * *
28889702 AAGACGGCGAATCTTATCTTCCCGAGGTAGTAGGGAAGCAGATTTAAGCCACTAAGTCCTATCTC
131 AAGACGGCGAATCTTATCTTCCCAAGGTAGTAGGGAAACAGATTTAAGCCACCAA-TCCTATCTC
* *
28889767 CCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGGTCCTGTCTCCCTAAGCAGTAGTGGAGTAGA
195 CCTGAGCAGCAGTGGAGTA-G--G--CA--G-A--TCCTGTCTCCCTAAGCAGTAGTGGAGCAGA
28889832 TC-AAA
250 TCGAAA
* *
28889837 GACGGCGAATC---T-TTCCCGAGGTAGTAGGGAAGTAGATTTAAGCCACTAAGTCCTATCTCCC
1 -ACGGCGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACTAAGTCCTATCTCCC
* * * * *
28889898 TGAGCAGTAGTGGAGTAGGGTGAAGAATGTAGATCCCGTCTCCCTAAGCAGTAGTAGAGCAGATC
65 TGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATC
* ** * * * * *
28889963 AAAGACGATGAAT-TTCATCTTTCCAAGGTAGTAGGGAAGCAGATTTAAACCACCAGTCATATCT
130 GAAGACGGCGAATCTT-ATCTTCCCAAGGTAGTAGGGAAACAGATTTAAGCCACCAATCCTATCT
28890027 C
194 C
28890028 TTTGGCATTA
Statistics
Matches: 632, Mismatches: 61, Indels: 24
0.88 0.09 0.03
Matches are distributed among these distances:
253 201 0.32
254 186 0.29
255 44 0.07
257 1 0.00
259 1 0.00
261 43 0.07
262 116 0.18
264 3 0.00
265 37 0.06
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.25
Consensus pattern (255 bp):
ACGGCGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACTAAGTCCTATCTCCCT
GAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCG
AAGACGGCGAATCTTATCTTCCCAAGGTAGTAGGGAAACAGATTTAAGCCACCAATCCTATCTCC
CTGAGCAGCAGTGGAGTAGGCAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAA
Found at i:28889523 original size:132 final size:132
Alignment explanation
Indices: 28889281--28890027 Score: 1013
Period size: 132 Copynumber: 5.8 Consensus size: 132
28889271 TGGAGTAGGC
* **
28889281 AGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAAACGGCTTATCTTATCTTCCCAAGGTA
1 AGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCAAGGTA
* * * *
28889346 GTAGGGGAGCAGATTTAAGCCGCCAGTCCTATCTCCTTGAGCAGCAGTGGAGTAGGTTGAAGATT
66 GTAGGGAAGCAGATTTAAGCCACCAATCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATT
28889411 GT
131 GT
*
28889413 AGATCCTGTCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACGGCGAATCTTATCTTCCCAAGGTA
1 AGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCAAGGTA
* * *
28889478 ATAGGGAAACAGATTTAAGCCACCAATCCTATCTCCCTGACCAGCAGT-G-G-A-G-T--AG---
66 GTAGGGAAGCAGATTTAAGCCACCAATCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATT
28889533 GT
131 GT
* *
28889535 AGAT-CTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACGAATCTTATCTTCCCAAGGTA
1 AGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCAAGGTA
* * * *
28889599 GTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTGAGTAGCAATTGAGTAGGTTGAAGATT
66 GTAGGGAAGCAGATTTAAGCCACCAATCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATT
28889664 GT
131 GT
* *
28889666 AGATCCTGTCTCTCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCGAGGTA
1 AGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCAAGGTA
*
28889731 GTAGGGAAGCAGATTTAAGCCACTAAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGAT
66 GTAGGGAAGCAGATTTAAGCCACCAA-TCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGAT
28889796 TGT
130 TGT
* * * *
28889799 AGGTCCTGTCTCCCTAAGCAGTAGTGGAGTAGATCAAAGACGGCGAATC---T-TTCCCGAGGTA
1 AGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCAAGGTA
* * * * *
28889860 GTAGGGAAGTAGATTTAAGCCACTAAGTCCTATCTCCCTGAGCAGTAGTGGAGTAGGGTGAAGAA
66 GTAGGGAAGCAGATTTAAGCCACCAA-TCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGAT
28889925 TGT
130 TGT
* * * ** *
28889928 AGATCCCGTCTCCCTAAGCAGTAGTAGAGCAGATCAAAGACGATGAAT-TTCATCTTTCCAAGGT
1 AGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTT-ATCTTCCCAAGGT
* * *
28889992 AGTAGGGAAGCAGATTTAAACCACCAGTCATATCTC
65 AGTAGGGAAGCAGATTTAAGCCACCAATCCTATCTC
28890028 TTTGGCATTA
Statistics
Matches: 548, Mismatches: 50, Indels: 34
0.87 0.08 0.05
Matches are distributed among these distances:
121 99 0.18
122 7 0.01
123 1 0.00
124 1 0.00
125 3 0.01
126 1 0.00
127 1 0.00
128 3 0.01
129 118 0.22
130 2 0.00
131 7 0.01
132 191 0.35
133 114 0.21
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.25
Consensus pattern (132 bp):
AGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCAAGGTA
GTAGGGAAGCAGATTTAAGCCACCAATCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATT
GT
Found at i:28890103 original size:50 final size:50
Alignment explanation
Indices: 28890049--28890227 Score: 288
Period size: 50 Copynumber: 3.6 Consensus size: 50
28890039 AGTGGAACAG
* *
28890049 ATTGAAGCTACAACAGCGAATCTTACTTCTCTGACGTTGCTGTAAAATAT
1 ATTGAAGCTACAACAACGAATCTTACTTCTCCGACGTTGCTGTAAAATAT
* * *
28890099 ATTGAAGCTACAACAGCAAATCTTACTTCTCCGACGTTGCAGTAAAATAT
1 ATTGAAGCTACAACAACGAATCTTACTTCTCCGACGTTGCTGTAAAATAT
*
28890149 ATTGAAGCTACAACAACGAATCTTACTTCTCCGACGTTG-TAGTAAAATAG
1 ATTGAAGCTACAACAACGAATCTTACTTCTCCGACGTTGCT-GTAAAATAT
28890199 ATTGAAGCTACAACAACGAATCTTACTTC
1 ATTGAAGCTACAACAACGAATCTTACTTC
28890228 CCCTGAAGTT
Statistics
Matches: 121, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
50 121 1.00
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (50 bp):
ATTGAAGCTACAACAACGAATCTTACTTCTCCGACGTTGCTGTAAAATAT
Found at i:28890246 original size:50 final size:50
Alignment explanation
Indices: 28890047--28890257 Score: 273
Period size: 50 Copynumber: 4.2 Consensus size: 50
28890037 ACAGTGGAAC
* * *
28890047 AGATTGAAGCTACAACAGCGAATCTTACTTCTCTGACGTTGCT-GTAAAAT
1 AGATTGAAGCTACAACAACGAATCTTACTTCCCCGACGTTG-TAGTAAAAT
* * * * *
28890097 ATATTGAAGCTACAACAGCAAATCTTACTTCTCCGACGTTGCAGTAAAAT
1 AGATTGAAGCTACAACAACGAATCTTACTTCCCCGACGTTGTAGTAAAAT
* *
28890147 ATATTGAAGCTACAACAACGAATCTTACTTCTCCGACGTTGTAGTAAAAT
1 AGATTGAAGCTACAACAACGAATCTTACTTCCCCGACGTTGTAGTAAAAT
*
28890197 AGATTGAAGCTACAACAACGAATCTTACTTCCCCTGAAGTTGTAG-AAAAT
1 AGATTGAAGCTACAACAACGAATCTTACTTCCCC-GACGTTGTAGTAAAAT
*
28890247 CAAATTGAAGC
1 -AGATTGAAGC
28890258 CACTAATCCT
Statistics
Matches: 147, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
50 129 0.88
51 18 0.12
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (50 bp):
AGATTGAAGCTACAACAACGAATCTTACTTCCCCGACGTTGTAGTAAAAT
Found at i:28890680 original size:19 final size:19
Alignment explanation
Indices: 28890656--28890709 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
28890646 CTTAAAAAAG
*
28890656 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAA
28890675 GATATGCAATCTTAGATAA
1 GATATGCAATCTTAGATAA
28890694 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
28890710 AGATAAGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (19 bp):
GATATGCAATCTTAGATAA
Found at i:28890731 original size:23 final size:22
Alignment explanation
Indices: 28890656--28890732 Score: 76
Period size: 19 Copynumber: 3.7 Consensus size: 22
28890646 CTTAAAAAAG
*
28890656 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAA
28890675 GATATGCAATCTT---AGATAA
1 GATATGCAATCTTAGAAGATAA
28890694 GATATGCAATCTTAGAAGATAA
1 GATATGCAATCTTAGAAGATAA
* *
28890716 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
28890733 TATTTAATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 31 0.61
22 8 0.16
23 12 0.24
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAA
Found at i:28891584 original size:24 final size:24
Alignment explanation
Indices: 28891553--28891802 Score: 139
Period size: 24 Copynumber: 10.7 Consensus size: 24
28891543 GTGTATTGTA
*
28891553 TATTATTATTTTAGATTTATCATG
1 TATTATTATTTTAAATTTATCATG
* * *
28891577 TTTTATTATTTGT-TATTTATCA-A
1 TATTATTATTT-TAAATTTATCATG
*
28891600 TATTATTATTTTAAATTCAT--TG
1 TATTATTATTTTAAATTTATCATG
**
28891622 TTAACATTATTTTAAATTTATCATG
1 -TATTATTATTTTAAATTTATCATG
* *
28891647 TA-TATCTATTTCAACTTTATCAT-
1 TATTAT-TATTTTAAATTTATCATG
* * *
28891670 TAATA-T-TTTTAAATTTATTATA
1 TATTATTATTTTAAATTTATCATG
* ** *
28891692 TACTATTATTTTGGATTTATCACG
1 TATTATTATTTTAAATTTATCATG
*
28891716 TATGATTATTTTAGAA-TTATCAT-
1 TATTATTATTTTA-AATTTATCATG
* * *
28891739 CA-AAAT-TTTTAAATTTTAT-ATG
1 TATTATTATTTTAAA-TTTATCATG
* * *
28891761 TATTATTATTTCAAATTTATTATA
1 TATTATTATTTTAAATTTATCATG
*
28891785 TATTATTTATTGTAAATT
1 TATTA-TTATTTTAAATT
28891803 ATCCAATTCA
Statistics
Matches: 170, Mismatches: 37, Indels: 37
0.70 0.15 0.15
Matches are distributed among these distances:
20 2 0.01
21 19 0.11
22 13 0.08
23 45 0.26
24 77 0.45
25 14 0.08
ACGTcount: A:0.33, C:0.06, G:0.05, T:0.56
Consensus pattern (24 bp):
TATTATTATTTTAAATTTATCATG
Found at i:28891726 original size:69 final size:67
Alignment explanation
Indices: 28891506--28891792 Score: 197
Period size: 69 Copynumber: 4.1 Consensus size: 67
28891496 TTTGAATGTT
* * * * * *
28891506 TATACTTATTATTAAATTAATCATTAATATTATCTAAGTGTATTGTATATTATTATTTTAGATTT
1 TATA-TTATT-TT-AATTTATCATTAATATT-TTTAAATTTATTATATACTATTATTTTAGATTT
28891571 ATCATG
62 ATCATG
* * * * * * *
28891577 TTTTATTATTTGTTATTTATCAATATTATTATTTTAAATTCATTGT-TAAC-ATTATTTTAAATT
1 -TATATTATTT-TAATTTATCATTAATA-T-TTTTAAATTTATTATAT-ACTATTATTTTAGATT
28891640 TATCATG
61 TATCATG
* *
28891647 TATATCTATTTCAACTTTATCATTAATATTTTTAAATTTATTATATACTATTATTTTGGATTTAT
1 TATAT-TATTTTAA-TTTATCATTAATATTTTTAAATTTATTATATACTATTATTTTAGATTTAT
*
28891712 CACG
64 CATG
* * * * * * *
28891716 TATGATTATTTTAGAATTATCATCAAAATTTTTAAATTT-TATATGTATTATTATTTCAAATTTA
1 TAT-ATTATTTTA-ATTTATCATTAATATTTTTAAATTTAT-TATATACTATTATTTTAGATTTA
*
28891780 T--TA
63 TCATG
28891783 TATATTATTT
1 TATATTATTT
28891793 ATTGTAAATT
Statistics
Matches: 172, Mismatches: 32, Indels: 28
0.74 0.14 0.12
Matches are distributed among these distances:
66 7 0.04
67 3 0.02
68 16 0.09
69 73 0.42
70 51 0.30
71 18 0.10
72 4 0.02
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.55
Consensus pattern (67 bp):
TATATTATTTTAATTTATCATTAATATTTTTAAATTTATTATATACTATTATTTTAGATTTATCA
TG
Found at i:28891878 original size:23 final size:23
Alignment explanation
Indices: 28891851--28891895 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
28891841 AATTGTACAT
*
28891851 TCATATATATTATTTGTTTTAAC
1 TCATATATATTATTTATTTTAAC
*
28891874 TCATATATATTGTTTATTTTAA
1 TCATATATATTATTTATTTTAA
28891896 AATTTTGAAC
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:0.31, C:0.07, G:0.04, T:0.58
Consensus pattern (23 bp):
TCATATATATTATTTATTTTAAC
Found at i:28903803 original size:75 final size:76
Alignment explanation
Indices: 28903647--28903796 Score: 182
Period size: 75 Copynumber: 2.0 Consensus size: 76
28903637 AAGGTAGTCT
* * * * *
28903647 AAAGTTTATTTATTTAAATTACAAAAAACTCCTAAAATTAAAAATTGAAATAGCAAAAAGGTCAT
1 AAAGTTTATCTATTTAAATTAAAAAAAACTCATAAAATTAAAAATTAAAATAGCAAAAAAGTCAT
28903712 TACATAAATAC
66 TACATAAATAC
* *
28903723 AAAGTTTA-CTATTTAAATTGAAAAAAAAC-CATAAAATTGATAAA-TAAAAT-GACAAAAAATT
1 AAAGTTTATCTATTTAAATT-AAAAAAAACTCATAAAATT-AAAAATTAAAATAG-CAAAAAAGT
28903784 CATTACATAAATA
63 CATTACATAAATA
28903797 TGAAGTTATT
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
74 1 0.02
75 43 0.67
76 20 0.31
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.29
Consensus pattern (76 bp):
AAAGTTTATCTATTTAAATTAAAAAAAACTCATAAAATTAAAAATTAAAATAGCAAAAAAGTCAT
TACATAAATAC
Found at i:28904049 original size:33 final size:32
Alignment explanation
Indices: 28904001--28904179 Score: 137
Period size: 33 Copynumber: 5.4 Consensus size: 32
28903991 AGAAGTAGTA
* * *
28904001 GAGTACGTCAGTGGATACGAGTCGGGAGGAGTG
1 GAGTACGACGGTGGATACG-GCCGGGAGGAGTG
* * *
28904034 GAGTACGACGATGGATATGGACCGGGAGGAATG
1 GAGTACGACGGTGGATACGG-CCGGGAGGAGTG
* * * *
28904067 GAGTACGATGGTGGATACGGGCTGGAAAGAGTG
1 GAGTACGACGGTGGATAC-GGCCGGGAGGAGTG
* * * *
28904100 AAGTACGGCGGTGGATACGGGCCGGAATGAGTG
1 GAGTACGACGGTGGATAC-GGCCGGGAGGAGTG
* *
28904133 GAGTACTGA-GGTGGATACGAGCCGGGATGACTG
1 GAGTAC-GACGGTGGATACG-GCCGGGAGGAGTG
28904166 GAGTACTGA-GGTGG
1 GAGTAC-GACGGTGG
28904180 TTGTGGGCTG
Statistics
Matches: 120, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
32 2 0.02
33 115 0.96
34 3 0.03
ACGTcount: A:0.26, C:0.12, G:0.45, T:0.17
Consensus pattern (32 bp):
GAGTACGACGGTGGATACGGCCGGGAGGAGTG
Found at i:28904171 original size:66 final size:66
Alignment explanation
Indices: 28904011--28904171 Score: 171
Period size: 66 Copynumber: 2.4 Consensus size: 66
28904001 GAGTACGTCA
* * * *
28904011 GTGGATACGAGTCGGGAGGAGTGGAGTACGACGATGGATATGGACCGGGAGGAATGGAGTACGAT
1 GTGGATACGAGCCGGGAAGAGTGGAGTACGACGATGGATACGGACCGGAAGGAATGGAGTACGAT
28904076 G
66 G
* * * * * * * * *
28904077 GTGGATACGGGCTGGAAAGAGTGAAGTACGGCGGTGGATACGGGCCGGAATGAGTGGAGTACTGA
1 GTGGATACGAGCCGGGAAGAGTGGAGTACGACGATGGATACGGACCGGAAGGAATGGAGTAC-GA
28904142 -G
65 TG
* *
28904143 GTGGATACGAGCCGGGATGACTGGAGTAC
1 GTGGATACGAGCCGGGAAGAGTGGAGTAC
28904172 TGAGGTGGTT
Statistics
Matches: 75, Mismatches: 19, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
66 73 0.97
67 2 0.03
ACGTcount: A:0.26, C:0.12, G:0.45, T:0.17
Consensus pattern (66 bp):
GTGGATACGAGCCGGGAAGAGTGGAGTACGACGATGGATACGGACCGGAAGGAATGGAGTACGAT
G
Found at i:28915232 original size:62 final size:61
Alignment explanation
Indices: 28915163--28915308 Score: 159
Period size: 67 Copynumber: 2.3 Consensus size: 61
28915153 AAAAAATTAC
* *** * *
28915163 ATTACTAAAAAAATCAC-AAAACGCTATACTAAACACTAACAATTTGTAACCTAATCTCATAA
1 ATTACTAAAAAAATAACTAAAACAAAATACAAAACACTAACAATTTCTAACCTAA--TCATAA
28915225 ATTACTAATAAAATAAATAACTAAAACAAAATACAAAACACTAACAATTTCTAACCTAATCATAA
1 ATTAC---TAAAA-AAATAACTAAAACAAAATACAAAACACTAACAATTTCTAACCTAATCATAA
* *
28915290 ACTACTAACAAAATAACTA
1 ATTACTAAAAAAATAACTA
28915309 TAAAATTATT
Statistics
Matches: 71, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
61 9 0.13
62 9 0.13
65 15 0.21
66 6 0.08
67 32 0.45
ACGTcount: A:0.55, C:0.19, G:0.01, T:0.25
Consensus pattern (61 bp):
ATTACTAAAAAAATAACTAAAACAAAATACAAAACACTAACAATTTCTAACCTAATCATAA
Found at i:28915239 original size:105 final size:102
Alignment explanation
Indices: 28915052--28915240 Score: 267
Period size: 105 Copynumber: 1.8 Consensus size: 102
28915042 TACATTATAT
28915052 AAAAATTACATTAAAAAAATCACAAAACACATAACTAAACACTAACAATTTATATAACCTAATCA
1 AAAAATTACATTAAAAAAATCACAAAACACATAACTAAACACTAACAATTTATATAACCTAATCA
*
28915117 TAAATTACTAACCAAATAACTATAAAATTATTTTTAA
66 TAAATTACTAACAAAATAACTATAAAATTATTTTTAA
* *
28915154 AAAAATTACATTACTAAAAAAATCACAAAACGC-TATACTAAACACTAACAA-TT-TGTAACCTA
1 AAAAATTACA-T--TAAAAAAATCACAAAACACATA-ACTAAACACTAACAATTTATATAACCTA
*
28915216 ATCTCATAAATTACTAATAAAATAA
62 A--TCATAAATTACTAACAAAATAA
28915241 ATAACTAAAA
Statistics
Matches: 77, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
102 10 0.13
103 10 0.13
104 4 0.05
105 53 0.69
ACGTcount: A:0.55, C:0.16, G:0.01, T:0.28
Consensus pattern (102 bp):
AAAAATTACATTAAAAAAATCACAAAACACATAACTAAACACTAACAATTTATATAACCTAATCA
TAAATTACTAACAAAATAACTATAAAATTATTTTTAA
Found at i:28918059 original size:25 final size:24
Alignment explanation
Indices: 28918001--28918061 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 24
28917991 TTTCCCTTTG
28918001 ATTTTGTTAAAC--AACAGAATTA
1 ATTTTGTTAAACAAAACAGAATTA
** * *
28918023 AAGTTCTGAAACAAAATCAGAATTA
1 ATTTTGTTAAACAAAA-CAGAATTA
28918048 ATTTTGTTAAACAA
1 ATTTTGTTAAACAA
28918062 CAGGGCTAAA
Statistics
Matches: 28, Mismatches: 8, Indels: 3
0.72 0.21 0.08
Matches are distributed among these distances:
22 8 0.29
24 2 0.07
25 18 0.64
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.33
Consensus pattern (24 bp):
ATTTTGTTAAACAAAACAGAATTA
Found at i:28919461 original size:31 final size:31
Alignment explanation
Indices: 28919394--28919480 Score: 106
Period size: 31 Copynumber: 2.8 Consensus size: 31
28919384 TTGAGAAGCC
** ** *
28919394 CTTATTTGAGTTCTTTCAAAAAGGCTTGGTT
1 CTTATTTGAGCACTTTCAAAAAGTTTTGCTT
28919425 CTTATTTGAGCACTTTCAAAAAGTTTTGACTT
1 CTTATTTGAGCACTTTCAAAAAGTTTTG-CTT
28919457 -TTATTTGAGCACTTT-AAAAAGTTT
1 CTTATTTGAGCACTTTCAAAAAGTTT
28919481 GGTCCTCATG
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
30 9 0.18
31 39 0.78
32 2 0.04
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.45
Consensus pattern (31 bp):
CTTATTTGAGCACTTTCAAAAAGTTTTGCTT
Found at i:28922261 original size:27 final size:27
Alignment explanation
Indices: 28922218--28922386 Score: 232
Period size: 27 Copynumber: 6.2 Consensus size: 27
28922208 AGCTTAGGCT
* *
28922218 GTAAAAGTTATCGAAATATCCTC-AAGGG
1 GTAAAAG-TACCGAAATACCCTCGAA-GG
* *
28922246 GTAAAATTATCGAAATACCCTCGAAGG
1 GTAAAAGTACCGAAATACCCTCGAAGG
*
28922273 GTAAAAGTACCGAAATACCTTCGAAGG
1 GTAAAAGTACCGAAATACCCTCGAAGG
* *
28922300 GTAAAATTATCGAAATACCCTCGAAGG
1 GTAAAAGTACCGAAATACCCTCGAAGG
*
28922327 GTAAAAGTACCAAAATACCCTCGAAGG
1 GTAAAAGTACCGAAATACCCTCGAAGG
28922354 GTAAAAGTACCGAAATACCCTCGAAGG
1 GTAAAAGTACCGAAATACCCTCGAAGG
*
28922381 ATAAAA
1 GTAAAA
28922387 AAGGTTTCCA
Statistics
Matches: 127, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
27 119 0.94
28 8 0.06
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.20
Consensus pattern (27 bp):
GTAAAAGTACCGAAATACCCTCGAAGG
Found at i:28922354 original size:81 final size:82
Alignment explanation
Indices: 28922218--28922386 Score: 261
Period size: 81 Copynumber: 2.1 Consensus size: 82
28922208 AGCTTAGGCT
* * * *
28922218 GTAAAAGTTATCGAAATATCCTCAAGGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAAGTAC
1 GTAAAAGTTATCGAAATACCCTCAAGGGGTAAAAGTACCAAAATACCCTCGAAGGGTAAAAGTAC
*
28922283 CGAAATACCTTCGAAGG
66 CGAAATACCCTCGAAGG
28922300 GTAAAA-TTATCGAAATACCCTCGAA-GGGTAAAAGTACCAAAATACCCTCGAAGGGTAAAAGTA
1 GTAAAAGTTATCGAAATACCCTC-AAGGGGTAAAAGTACCAAAATACCCTCGAAGGGTAAAAGTA
28922363 CCGAAATACCCTCGAAGG
65 CCGAAATACCCTCGAAGG
*
28922381 ATAAAA
1 GTAAAA
28922387 AAGGTTTCCA
Statistics
Matches: 80, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
81 72 0.90
82 8 0.10
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.20
Consensus pattern (82 bp):
GTAAAAGTTATCGAAATACCCTCAAGGGGTAAAAGTACCAAAATACCCTCGAAGGGTAAAAGTAC
CGAAATACCCTCGAAGG
Found at i:28928216 original size:16 final size:17
Alignment explanation
Indices: 28928195--28928226 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28928185 CTTTGTCGAA
28928195 TTTCCC-TTTCTTTTTC
1 TTTCCCTTTTCTTTTTC
28928211 TTTCCCTTTTCTTTTT
1 TTTCCCTTTTCTTTTT
28928227 TTTTACTGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTCCCTTTTCTTTTTC
Found at i:28929670 original size:32 final size:32
Alignment explanation
Indices: 28929628--28929764 Score: 177
Period size: 32 Copynumber: 4.3 Consensus size: 32
28929618 TACAAGCCAT
**
28929628 AAGCCATCAGTAGTAGTAATATGATCGACACA
1 AAGCCATCAGTAACAGTAATATGATCGACACA
* * **
28929660 TAGCCATCAGTAACAGTAATATGACCGGTACA
1 AAGCCATCAGTAACAGTAATATGATCGACACA
*
28929692 AAGCCATCAGTAACGGTAATATGATC-AGCACA
1 AAGCCATCAGTAACAGTAATATGATCGA-CACA
* *
28929724 AAGCCATCAGTAACGGTAATACGATCGACACA
1 AAGCCATCAGTAACAGTAATATGATCGACACA
28929756 AAGCCATCA
1 AAGCCATCA
28929765 ATAGCATCGC
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
32 90 0.99
33 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.18, T:0.19
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATCGACACA
Found at i:28929946 original size:24 final size:24
Alignment explanation
Indices: 28929913--28929987 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 24
28929903 CCATGCTCAG
*
28929913 AATCAGTCATACAAATCATAAACA
1 AATCAATCATACAAATCATAAACA
* * *
28929937 AATCAATCATACTAATCACATACA
1 AATCAATCATACAAATCATAAACA
** *
28929961 AATCAATCATTTAAATCATAGACA
1 AATCAATCATACAAATCATAAACA
28929985 AAT
1 AAT
28929988 TAGACATTTA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.52, C:0.20, G:0.03, T:0.25
Consensus pattern (24 bp):
AATCAATCATACAAATCATAAACA
Done.