Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 91 of 290
Found at i:30609200 original size:46 final size:46
Alignment explanation
Indices: 30609025--30609200 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
30609015 TGTAACCCGC
* * *
30609025 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
30609071 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
30609121 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
30609164 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
30609201 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 64 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:30611117 original size:22 final size:22
Alignment explanation
Indices: 30611089--30611132 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
30611079 TTCTACCTGA
*
30611089 TTTGACAGCATAGTAATTGAGT
1 TTTGACAGCATAGTAACTGAGT
30611111 TTTGACAGCATAGTAACTGAGT
1 TTTGACAGCATAGTAACTGAGT
30611133 CGATGTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.34
Consensus pattern (22 bp):
TTTGACAGCATAGTAACTGAGT
Found at i:30630140 original size:17 final size:19
Alignment explanation
Indices: 30630118--30630155 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
30630108 TTTCTGTTGA
30630118 TGACATT-TC-CAACTCTT
1 TGACATTGTCACAACTCTT
30630135 TGACATTGGTCACAACTCTT
1 TGACATT-GTCACAACTCTT
30630155 T
1 T
30630156 ACGTATGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
19 2 0.11
20 9 0.50
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (19 bp):
TGACATTGTCACAACTCTT
Found at i:30644484 original size:27 final size:27
Alignment explanation
Indices: 30644454--30644688 Score: 182
Period size: 27 Copynumber: 8.7 Consensus size: 27
30644444 CCCCGAATTA
*
30644454 TAAAATTACTAAAGTACCCCTAAATTT-
1 TAAAATTACTAAA-TACCCCTCAATTTG
*
30644481 TAAAATTACTGAAATACCCC-CGGA-TTG
1 TAAAATTACT-AAATACCCCTC-AATTTG
* **
30644508 TAAAATTATCGAAATACCCCTGGA-TTG
1 TAAAATTA-CTAAATACCCCTCAATTTG
* *
30644535 TAAAATTACCAAAATA-CCCTCGATTTG
1 TAAAATTA-CTAAATACCCCTCAATTTG
*
30644562 TAAAATTACCAAAATACCCC-CAATTTG
1 TAAAATTA-CTAAATACCCCTCAATTTG
* *
30644589 TAAAATTATCGAAATA-CCCTTAATTTG
1 TAAAATTA-CTAAATACCCCTCAATTTG
*
30644616 TAAAATTACTAAAATA-CCCTTAATTTG
1 TAAAATTACT-AAATACCCCTCAATTTG
** *
30644643 TAAAATTACTGAAAT-GTCCTCAGTTTG
1 TAAAATTACT-AAATACCCCTCAATTTG
*
30644670 TAAAATTATCGAAATACCC
1 TAAAATTA-CTAAATACCC
30644689 TTGTAGTGTA
Statistics
Matches: 177, Mismatches: 19, Indels: 23
0.81 0.09 0.11
Matches are distributed among these distances:
26 12 0.07
27 156 0.88
28 9 0.05
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (27 bp):
TAAAATTACTAAATACCCCTCAATTTG
Found at i:30644512 original size:54 final size:55
Alignment explanation
Indices: 30644438--30644657 Score: 224
Period size: 54 Copynumber: 4.1 Consensus size: 55
30644428 TGGGCCACAC
* *
30644438 GAAATACCCCGAA-TTATAAAATTACTAAAGTACCCCTAAATTT-TAAAATTACT
1 GAAATACCCCGAATTTGTAAAATTACTAAAATACCCCTAAATTTGTAAAATTACT
* * ** *
30644491 GAAATACCCCCGGA-TTGTAAAATTA-TCGAAATACCCCTGGA-TTGTAAAATTACC
1 GAAATA-CCCCGAATTTGTAAAATTACT-AAAATACCCCTAAATTTGTAAAATTACT
* * *
30644545 AAAATACCCTCG-ATTTGTAAAATTACCAAAATACCCC-CAATTTGTAAAATTA-T
1 GAAATACCC-CGAATTTGTAAAATTACTAAAATACCCCTAAATTTGTAAAATTACT
** *
30644598 CGAAATACCCTTAATTTGTAAAATTACTAAAATA-CCCTTAATTTGTAAAATTACT
1 -GAAATACCCCGAATTTGTAAAATTACTAAAATACCCCTAAATTTGTAAAATTACT
30644653 GAAAT
1 GAAAT
30644658 GTCCTCAGTT
Statistics
Matches: 138, Mismatches: 18, Indels: 21
0.78 0.10 0.12
Matches are distributed among these distances:
53 17 0.12
54 120 0.87
55 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.30
Consensus pattern (55 bp):
GAAATACCCCGAATTTGTAAAATTACTAAAATACCCCTAAATTTGTAAAATTACT
Found at i:30644577 original size:81 final size:80
Alignment explanation
Indices: 30644437--30644718 Score: 327
Period size: 81 Copynumber: 3.5 Consensus size: 80
30644427 ATGGGCCACA
* *
30644437 CGAAATACCCC-GAATTATAAAATTACTAAAGTACCCCTAAATTT-TAAAATTACTGAAATACCC
1 CGAAATACCCCTGAATTGTAAAATTACTAAAATA-CCCTAAATTTGTAAAATTACTGAAATACCC
30644500 CCGGATTGTAAAATTAT
65 CC-GATTGTAAAATTAT
* * ** **
30644517 CGAAATACCCCTGGATTGTAAAATTACCAAAATACCCTCGATTTGTAAAATTACCAAAATACCCC
1 CGAAATACCCCTGAATTGTAAAATTACTAAAATACCCTAAATTTGTAAAATTACTGAAATACCCC
*
30644582 CAATTTGTAAAATTAT
66 CGA-TTGTAAAATTAT
* * *
30644598 CGAAATA-CCCTTAATTTGTAAAATTACTAAAATACCCTTAATTTGTAAAATTACTGAAATGTCC
1 CGAAATACCCCTGAA-TTGTAAAATTACTAAAATACCCTAAATTTGTAAAATTACTGAAAT-ACC
* * *
30644662 TCAGTTTGTAAAATTAT
64 CCCGATTGTAAAATTAT
* * *
30644679 CGAAATACCCTTGTAGTGTAAAATTACTAAAATAACCCTA
1 CGAAATACCCCTGAATTGTAAAATTACTAAAAT-ACCCTA
30644719 TAAGGTAAAA
Statistics
Matches: 169, Mismatches: 26, Indels: 12
0.82 0.13 0.06
Matches are distributed among these distances:
80 25 0.15
81 132 0.78
82 12 0.07
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (80 bp):
CGAAATACCCCTGAATTGTAAAATTACTAAAATACCCTAAATTTGTAAAATTACTGAAATACCCC
CGATTGTAAAATTAT
Found at i:30644670 original size:54 final size:54
Alignment explanation
Indices: 30644454--30644717 Score: 218
Period size: 54 Copynumber: 4.9 Consensus size: 54
30644444 CCCCGAATTA
* * * * *
30644454 TAAAATTACTAAAGTACCCCTAAATTT-TAAAATTACTGAAATACCCCCGGATTG
1 TAAAATTACTAAAATA-CCCTTAATTTGTAAAATTACTGAAATACCCTCAGTTTG
* ** **
30644508 TAAAATTA-TCGAAATACCCCTGGA-TTGTAAAATTACCAAAATACCCTC-GATTTG
1 TAAAATTACT-AAAATA-CCCTTAATTTGTAAAATTACTGAAATACCCTCAG-TTTG
* ** * *
30644562 TAAAATTACCAAAATACCCCCAATTTGTAAAATTA-TCGAAATACCCTTAATTTG
1 TAAAATTACTAAAATACCCTTAATTTGTAAAATTACT-GAAATACCCTCAGTTTG
**
30644616 TAAAATTACTAAAATACCCTTAATTTGTAAAATTACTGAAATGTCCTCAGTTTG
1 TAAAATTACTAAAATACCCTTAATTTGTAAAATTACTGAAATACCCTCAGTTTG
* * * *
30644670 TAAAATTA-TCGAAATACCCTT-GTAGTGTAAAATTACTAAAATAACCCT
1 TAAAATTACT-AAAATACCCTTAAT-TTGTAAAATTACTGAAAT-ACCCT
30644718 ATAAGGTAAA
Statistics
Matches: 169, Mismatches: 30, Indels: 21
0.77 0.14 0.10
Matches are distributed among these distances:
53 10 0.06
54 155 0.92
55 4 0.02
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.32
Consensus pattern (54 bp):
TAAAATTACTAAAATACCCTTAATTTGTAAAATTACTGAAATACCCTCAGTTTG
Found at i:30644698 original size:27 final size:28
Alignment explanation
Indices: 30644437--30644704 Score: 179
Period size: 27 Copynumber: 10.0 Consensus size: 28
30644427 ATGGGCCACA
* *
30644437 CGAAATACCC-CGAA-TTATAAAATTA-
1 CGAAATACCCTTGAATTTGTAAAATTAT
* * *
30644462 CTAAAGTACCCCTAAATTT-TAAAATTA-
1 CGAAA-TACCCTTGAATTTGTAAAATTAT
** *
30644489 CTGAAATACCCCCGGA-TTGTAAAATTAT
1 C-GAAATACCCTTGAATTTGTAAAATTAT
* * *
30644517 CGAAATACCCCTGGA-TTGTAAAATTAC
1 CGAAATACCCTTGAATTTGTAAAATTAT
* * *
30644544 CAAAATACCCTCG-ATTTGTAAAATTAC
1 CGAAATACCCTTGAATTTGTAAAATTAT
* **
30644571 CAAAATACCC-CCAATTTGTAAAATTAT
1 CGAAATACCCTTGAATTTGTAAAATTAT
30644598 CGAAATACCCTT-AATTTGTAAAATTA-
1 CGAAATACCCTTGAATTTGTAAAATTAT
*
30644624 CTAAAATACCCTT-AATTTGTAAAATTA-
1 C-GAAATACCCTTGAATTTGTAAAATTAT
** * *
30644651 CTGAAATGTCC-TCAGTTTGTAAAATTAT
1 C-GAAATACCCTTGAATTTGTAAAATTAT
* *
30644679 CGAAATACCCTTGTA-GTGTAAAATTA
1 CGAAATACCCTTGAATTTGTAAAATTA
30644705 CTAAAATAAC
Statistics
Matches: 203, Mismatches: 27, Indels: 24
0.80 0.11 0.09
Matches are distributed among these distances:
25 4 0.02
26 11 0.05
27 180 0.89
28 8 0.04
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (28 bp):
CGAAATACCCTTGAATTTGTAAAATTAT
Found at i:30645173 original size:27 final size:27
Alignment explanation
Indices: 30645143--30645231 Score: 83
Period size: 27 Copynumber: 3.3 Consensus size: 27
30645133 CCTTGTGAAA
*
30645143 ATCATATTTACCAGTGGCTATGTGCCT
1 ATCATATTTACCAGTGGCTATGTGCCG
** * *
30645170 ATCATATTTA-TTGATGACTCTGTGCCG
1 ATCATATTTACCAG-TGGCTATGTGCCG
*
30645197 ATCATATTTACCCA-TGGCTGTGTGCCG
1 ATCATATTTA-CCAGTGGCTATGTGCCG
*
30645224 ATTATATT
1 ATCATATT
30645232 ACCGTCGCTG
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
26 1 0.02
27 48 0.98
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.39
Consensus pattern (27 bp):
ATCATATTTACCAGTGGCTATGTGCCG
Found at i:30649267 original size:45 final size:45
Alignment explanation
Indices: 30649217--30649304 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 45
30649207 AAACATGTGT
*
30649217 CACATACATCATGAACTCAGACCACAACTCAATGAGTTCAGATGG
1 CACATACATCATGAACTCAGACCACAACCCAATGAGTTCAGATGG
* * *
30649262 CACATATATCATGAACTCAGACCACAACCCGATGAGTTTAGAT
1 CACATACATCATGAACTCAGACCACAACCCAATGAGTTCAGAT
30649305 CACATAGTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.38, C:0.26, G:0.15, T:0.22
Consensus pattern (45 bp):
CACATACATCATGAACTCAGACCACAACCCAATGAGTTCAGATGG
Found at i:30656876 original size:56 final size:56
Alignment explanation
Indices: 30656805--30657004 Score: 303
Period size: 56 Copynumber: 3.6 Consensus size: 56
30656795 GGCATCGACT
* * *
30656805 TGTGATTCCAATATATGTGTGCGAGTAAGATCAAGTTTTATACGTTGGCATTGATA
1 TGTGATTCCGATATATGTGTGCGAGTAAGACCACGTTTTATACGTTGGCATTGATA
*
30656861 TGTGATTCCGGTATATGTGTGCGAGTAAGACCACGTTTTATACGTTGGCATTGATA
1 TGTGATTCCGATATATGTGTGCGAGTAAGACCACGTTTTATACGTTGGCATTGATA
* *
30656917 TGTGATTCCGGTATATGTGTGCGAGTAAGACCACGTTTTATACGTTGGCATCGATA
1 TGTGATTCCGATATATGTGTGCGAGTAAGACCACGTTTTATACGTTGGCATTGATA
* * *
30656973 TGTGACTT-CGATATATGTTTTCAAGTAAGACC
1 TGTGA-TTCCGATATATGTGTGCGAGTAAGACC
30657005 CTGTCTGGGA
Statistics
Matches: 134, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
56 132 0.99
57 2 0.01
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (56 bp):
TGTGATTCCGATATATGTGTGCGAGTAAGACCACGTTTTATACGTTGGCATTGATA
Found at i:30657022 original size:112 final size:112
Alignment explanation
Indices: 30656795--30657035 Score: 292
Period size: 112 Copynumber: 2.2 Consensus size: 112
30656785 ATTTATATGA
* *
30656795 GGCATCGACT-TGTGATTCCAATATATGTGTGCGAGTAAGATCAAGTTTTATACGTTGGCATTGA
1 GGCATCGA-TATGTGATTCCAATATATGTGTGCGAGTAAGACCAAGTTTTATACGTTGGCATCGA
* * * * *
30656859 TATGTGATTCCGGTATATGTGTGCGAGTAAGACCACGTTTTATACGTT
65 TATGTGATTCCGATATATGTGTGCAAGTAAGACCACGTCTGAGACGTT
* ** *
30656907 GGCATTGATATGTGATTCCGGTATATGTGTGCGAGTAAGACCACGTTTTATACGTTGGCATCGAT
1 GGCATCGATATGTGATTCCAATATATGTGTGCGAGTAAGACCAAGTTTTATACGTTGGCATCGAT
* * *
30656972 ATGTGACTT-CGATATATGTTTTCAAGTAAGACC-CTGTCTGGGACAG-T
66 ATGTGA-TTCCGATATATGTGTGCAAGTAAGACCAC-GTCTGAGAC-GTT
30657019 GGCATCGATATGTGATT
1 GGCATCGATATGTGATT
30657036 ACATATAAGA
Statistics
Matches: 110, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
111 2 0.02
112 105 0.95
113 3 0.03
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (112 bp):
GGCATCGATATGTGATTCCAATATATGTGTGCGAGTAAGACCAAGTTTTATACGTTGGCATCGAT
ATGTGATTCCGATATATGTGTGCAAGTAAGACCACGTCTGAGACGTT
Found at i:30660353 original size:38 final size:39
Alignment explanation
Indices: 30660302--30660394 Score: 145
Period size: 38 Copynumber: 2.4 Consensus size: 39
30660292 ATTATACTCA
30660302 GTTGTACTTCGGTACCCCTGAATGCACATACGTGC-CCT
1 GTTGTACTTCGGTACCCCTGAATGCACATACGTGCTCCT
* *
30660340 GTTGTACTTCGGTACCCCTTAATGCACATATGTGCTCCT
1 GTTGTACTTCGGTACCCCTGAATGCACATACGTGCTCCT
*
30660379 GTTGTACGTC-GTACCC
1 GTTGTACTTCGGTACCC
30660395 ATGATTCACA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
38 39 0.76
39 12 0.24
ACGTcount: A:0.17, C:0.30, G:0.20, T:0.32
Consensus pattern (39 bp):
GTTGTACTTCGGTACCCCTGAATGCACATACGTGCTCCT
Found at i:30661525 original size:21 final size:20
Alignment explanation
Indices: 30661494--30661538 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
30661484 ACCCCTACAG
*
30661494 TTTTGAAAATTTTCATT-GTT
1 TTTTGAAAATTCT-ATTAGTT
30661514 TTTTGAAAAATTCTATTAGTT
1 TTTTG-AAAATTCTATTAGTT
30661535 TTTT
1 TTTT
30661539 TTATTTAGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.27, C:0.04, G:0.09, T:0.60
Consensus pattern (20 bp):
TTTTGAAAATTCTATTAGTT
Found at i:30665080 original size:42 final size:42
Alignment explanation
Indices: 30664974--30665128 Score: 193
Period size: 42 Copynumber: 3.7 Consensus size: 42
30664964 TACCATACCA
* * * *
30664974 ATGCCATATCCTAGATATGGTCTTACATGAAATCTCGTATCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAGTCTCATATCG
* * * * * *
30665016 AGGACAATAGCCCAGCTATGGTCTTACACGAAGTCTAATATTG
1 ATG-CCATATCCCAGATATGGTCTTACACGAAGTCTCATATCG
*
30665059 ATGCCATATCCCAGATATGGTCTTACACGAAGTCTCATATCA
1 ATGCCATATCCCAGATATGGTCTTACACGAAGTCTCATATCG
*
30665101 ATTCCATATCCCAGATATGGTCTTACAC
1 ATGCCATATCCCAGATATGGTCTTACAC
30665129 ATAATCTCAG
Statistics
Matches: 94, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
42 62 0.66
43 32 0.34
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAGTCTCATATCG
Found at i:30665320 original size:23 final size:25
Alignment explanation
Indices: 30665286--30665335 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 25
30665276 TTACCACAAT
30665286 TATATCAATTAA-GCAT-TTAAACA
1 TATATCAATTAATGCATATTAAACA
*
30665309 TATAT-AATTTAATGCTTATTAAACA
1 TATATCAA-TTAATGCATATTAAACA
30665334 TA
1 TA
30665336 CGACAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 2 0.09
23 9 0.39
24 3 0.13
25 9 0.39
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (25 bp):
TATATCAATTAATGCATATTAAACA
Found at i:30668238 original size:24 final size:24
Alignment explanation
Indices: 30668198--30668247 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
30668188 ATATATCACA
*
30668198 ATTATAACATTACATAATATAAAT
1 ATTATAACATTACATAAAATAAAT
* *
30668222 ATTATAAACATT-TATAAAATAGAT
1 ATTAT-AACATTACATAAAATAAAT
30668246 AT
1 AT
30668248 ATAGTTAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (24 bp):
ATTATAACATTACATAAAATAAAT
Found at i:30669240 original size:20 final size:18
Alignment explanation
Indices: 30669193--30669299 Score: 60
Period size: 19 Copynumber: 5.8 Consensus size: 18
30669183 CAAGGTAAAC
30669193 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
30669210 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
** *
30669230 ATTAAATTAATAAAATACT
1 ATTAAATTAAT-ATTTAAT
*
30669249 ATTAAGA-TAAGTATTAAAT
1 ATTAA-ATTAA-TATTTAAT
* *
30669268 -TTAATTTAATATTAAACT
1 ATTAAATTAATATTTAA-T
*
30669286 ATTAAAATAATATT
1 ATTAAATTAATATT
30669300 ATTTTTAGAA
Statistics
Matches: 69, Mismatches: 11, Indels: 18
0.70 0.11 0.18
Matches are distributed among these distances:
17 15 0.22
18 9 0.13
19 27 0.39
20 18 0.26
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:30671231 original size:23 final size:23
Alignment explanation
Indices: 30671201--30671286 Score: 88
Period size: 23 Copynumber: 3.8 Consensus size: 23
30671191 TACCGATATA
30671201 TCAGCTCATAAGAGCTTACTATT
1 TCAGCTCATAAGAGCTTACTATT
**
30671224 TCAGCTCATTGGAGCTTACTATT
1 TCAGCTCATAAGAGCTTACTATT
* *
30671247 T-AGCTTGATAA-AGCTTACCATT
1 TCAGC-TCATAAGAGCTTACTATT
*
30671269 TTAGCTCA-ATAGAGCTTA
1 TCAGCTCATA-AGAGCTTA
30671287 TTGTTCATCA
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
21 1 0.02
22 17 0.33
23 34 0.65
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (23 bp):
TCAGCTCATAAGAGCTTACTATT
Found at i:30679394 original size:29 final size:28
Alignment explanation
Indices: 30679358--30679435 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
30679348 TCATGAGATT
30679358 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
30679388 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
30679415 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
30679436 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:30679653 original size:174 final size:174
Alignment explanation
Indices: 30679388--30679715 Score: 620
Period size: 174 Copynumber: 1.9 Consensus size: 174
30679378 AAATTGTACA
30679388 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
* *
30679453 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
30679518 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
* *
30679562 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
30679627 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
30679692 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
30679716 ACCTTGAGTT
Statistics
Matches: 150, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 150 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:30687468 original size:93 final size:93
Alignment explanation
Indices: 30687361--30687531 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
30687351 GCCCCTAAGT
* *
30687361 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
30687426 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
30687454 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
30687519 CGAGTTCGGATGC
66 CGAGTTCGGATGC
30687532 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:30687528 original size:46 final size:46
Alignment explanation
Indices: 30687356--30687528 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
30687346 AACCCGCCCC
* * *
30687356 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
*
30687402 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
30687450 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
30687495 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
30687529 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 61 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:30687985 original size:30 final size:30
Alignment explanation
Indices: 30687951--30688010 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
30687941 ATTTAATACG
30687951 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
30687981 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
30688011 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:30690837 original size:23 final size:23
Alignment explanation
Indices: 30690744--30690879 Score: 75
Period size: 23 Copynumber: 5.8 Consensus size: 23
30690734 GGATTCATCA
30690744 CAGCTCG-TATGAGCTTACTGATATGT
1 CAGCTCGATA-GAGCTTACTG-T-T-T
* *
30690770 CAGCTTG-TAAGAGCTTACTATTT
1 CAGCTCGAT-AGAGCTTACTGTTT
* * **
30690793 TAGCTC-ATTAAAGCTTGTTGTTT
1 CAGCTCGA-TAGAGCTTACTGTTT
* *
30690816 CAGCT-TATTGGAGCTTACTG-TT
1 CAGCTCGA-TAGAGCTTACTGTTT
*
30690838 CAGCTCGATAGAGCTTACCGTTT
1 CAGCTCGATAGAGCTTACTGTTT
* *
30690861 CAGCTCAATAAAGCTTACT
1 CAGCTCGATAGAGCTTACT
30690880 ATTCATCAGC
Statistics
Matches: 85, Mismatches: 19, Indels: 15
0.71 0.16 0.13
Matches are distributed among these distances:
22 17 0.20
23 48 0.56
24 2 0.02
25 1 0.01
26 16 0.19
27 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (23 bp):
CAGCTCGATAGAGCTTACTGTTT
Found at i:30693526 original size:43 final size:39
Alignment explanation
Indices: 30693450--30693565 Score: 142
Period size: 39 Copynumber: 2.9 Consensus size: 39
30693440 ACACATGTAC
* *
30693450 CATACCAATACCATATCCCAAATATGGTCTTACATGGGATCT
1 CATACCGATACCATATCCCAAATATGGTCTTACA---AATCT
* **
30693492 CATACCGATACCAATAGCCCATCTATGGTCTTACAAATCT
1 CATACCGATACC-ATATCCCAAATATGGTCTTACAAATCT
*
30693532 CATATCGATACCATATCCCAAATATGGTCTTACA
1 CATACCGATACCATATCCCAAATATGGTCTTACA
30693566 CGTAATCTCA
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
39 19 0.30
40 15 0.23
42 11 0.17
43 19 0.30
ACGTcount: A:0.34, C:0.28, G:0.10, T:0.28
Consensus pattern (39 bp):
CATACCGATACCATATCCCAAATATGGTCTTACAAATCT
Found at i:30696491 original size:49 final size:48
Alignment explanation
Indices: 30696433--30696602 Score: 162
Period size: 49 Copynumber: 3.5 Consensus size: 48
30696423 AGTCGATGAT
30696433 ATGTCCCAGACAGGTCTTACACTAACTTTCATATATCGAGGCCGATGTC
1 ATGTCCCAGACAGGTCTTACACTAACTTTCATATATCGAGGCCGATG-C
* * * ** * * * *
30696482 ATGTTCCAGACAGGTCTTGCATTGGCTCTCATCTATCGATGTCGATGCC
1 ATGTCCCAGACAGGTCTTACACTAACTTTCATATATCGAGGCCGATG-C
* * * * *
30696531 ATGTCCTAGACAGGTCTTACACTAGA-TTGCATATCTCGTGGCTGATGC
1 ATGTCCCAGACAGGTCTTACACTA-ACTTTCATATATCGAGGCCGATGC
* *
30696579 ATGTCCCAGATATGTCTTACACTA
1 ATGTCCCAGACAGGTCTTACACTA
30696603 GCTCTCGTCT
Statistics
Matches: 93, Mismatches: 27, Indels: 3
0.76 0.22 0.02
Matches are distributed among these distances:
48 22 0.24
49 71 0.76
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (48 bp):
ATGTCCCAGACAGGTCTTACACTAACTTTCATATATCGAGGCCGATGC
Found at i:30696542 original size:98 final size:97
Alignment explanation
Indices: 30696379--30696651 Score: 254
Period size: 98 Copynumber: 2.8 Consensus size: 97
30696369 GTACGATGTT
* ** *
30696379 GATGCCATGTTCCAAACATGGTCTTACATTGGCT-TACA-C-ATCTAA-GTCGATGATATGTCCC
1 GATG-CATGTTCCAGACA-GGTCTTACATTGGCTCT-CATCTATC-AATGTCGATGCCATGTCCT
*
30696440 AGACAGGTCTTACACTA-ACTTTCATATATCGAGGCC
62 AGACAGGTCTTACACTAGA-TTGCATATATCGAGGCC
* *
30696476 GATGTCATGTTCCAGACAGGTCTTGCATTGGCTCTCATCTATCGATGTCGATGCCATGTCCTAGA
1 GATG-CATGTTCCAGACAGGTCTTACATTGGCTCTCATCTATCAATGTCGATGCCATGTCCTAGA
* * *
30696541 CAGGTCTTACACTAGATTGCATATCTCGTGGCT
65 CAGGTCTTACACTAGATTGCATATATCGAGGCC
* * * * * * *
30696574 GATGCATGTCCCAGATATGTCTTACACTAGCTCTCGTCT-T-AATATCGATGCCATGTCCTTAGA
1 GATGCATGTTCCAGACAGGTCTTACATTGGCTCTCATCTATCAATGTCGATGCCATGTCC-TAGA
** *
30696637 CTTGTTTTACACTAG
65 CAGGTCTTACACTAG
30696652 CACACATCCA
Statistics
Matches: 147, Mismatches: 23, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
95 16 0.11
96 33 0.22
97 47 0.32
98 50 0.34
99 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.33
Consensus pattern (97 bp):
GATGCATGTTCCAGACAGGTCTTACATTGGCTCTCATCTATCAATGTCGATGCCATGTCCTAGAC
AGGTCTTACACTAGATTGCATATATCGAGGCC
Found at i:30701134 original size:37 final size:37
Alignment explanation
Indices: 30701071--30701183 Score: 99
Period size: 37 Copynumber: 3.1 Consensus size: 37
30701061 ATTCCAAAAA
*
30701071 TAATATTATTTTAATAGTTTAATATTAAATTAA-ATT
1 TAATATTATCTTAATAGTTTAATATTAAATTAATATT
* *
30701107 TAATACTTATCTTAATAGTATT-TTATTAATTTAATATT
1 TAATA-TTATCTTAATAGT-TTAATATTAAATTAATATT
* * * *
30701145 AAAGTGATTATCTTAATA-TTAAAT-TTAATTTAATGTT
1 TAA-T-ATTATCTTAATAGTTTAATATTAAATTAATATT
30701182 TA
1 TA
30701184 TCTTGTAGAT
Statistics
Matches: 63, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
36 5 0.08
37 36 0.57
38 9 0.14
39 12 0.19
40 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (37 bp):
TAATATTATCTTAATAGTTTAATATTAAATTAATATT
Found at i:30703099 original size:31 final size:31
Alignment explanation
Indices: 30703056--30703114 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
30703046 GCATATTGTG
*
30703056 CACTCCCTTACTAGAAGCGAATCAATAAGTC
1 CACTCCCATACTAGAAGCGAATCAATAAGTC
* *
30703087 CACTCCCATACTAGAAGTGATTCAATAA
1 CACTCCCATACTAGAAGCGAATCAATAA
30703115 TTTTTCCCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (31 bp):
CACTCCCATACTAGAAGCGAATCAATAAGTC
Found at i:30704412 original size:133 final size:133
Alignment explanation
Indices: 30704202--30704443 Score: 358
Period size: 133 Copynumber: 1.8 Consensus size: 133
30704192 GCTGGTGAGT
* ** *
30704202 ATGTAAAACAGTAAAAAAACAATTTACCTTATAATCGGAGTGCATACACTGTAATAAAAACAATT
1 ATGTAAAACAGTAAAAAAACAATTGACCTTATAATCGGAGTGCATACACCATAAGAAAAACAATT
** * * *
30704267 TTGTCTTTGTTAGGACAGATGAAGGTTCGTTATGAACTGAATAGGGCGAGTATGAGTAACCAGGG
66 TCATCTTTGTTAGGACAGATGAAGGTTCATTACGAACCGAATAGGGCGAGTATGAGTAACCAGGG
30704332 AGC
131 AGC
* * * *
30704335 ATGTAAAACGGTACAGAAACAATTGACCTTATAATTGGAGTGCATACACCATAAGAAAAACAATT
1 ATGTAAAACAGTAAAAAAACAATTGACCTTATAATCGGAGTGCATACACCATAAGAAAAACAATT
*
30704400 TCATCTTTGTTAGGATAGATGAAGGTTCATTACGAACCGAATAG
66 TCATCTTTGTTAGGACAGATGAAGGTTCATTACGAACCGAATAG
30704444 CTAAAAAAAA
Statistics
Matches: 95, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
133 95 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (133 bp):
ATGTAAAACAGTAAAAAAACAATTGACCTTATAATCGGAGTGCATACACCATAAGAAAAACAATT
TCATCTTTGTTAGGACAGATGAAGGTTCATTACGAACCGAATAGGGCGAGTATGAGTAACCAGGG
AGC
Found at i:30706177 original size:22 final size:22
Alignment explanation
Indices: 30706143--30706198 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
30706133 TTTATTTATC
30706143 TATTTA-ATATTATAT-TCAATT
1 TATTTATATATTATATCT-AATT
*
30706164 TATTTATATATTATATCTATTT
1 TATTTATATATTATATCTAATT
30706186 TATTATATATATT
1 TATT-TATATATT
30706199 CTAAATATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 6 0.19
22 16 0.52
23 9 0.29
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.61
Consensus pattern (22 bp):
TATTTATATATTATATCTAATT
Found at i:30706184 original size:9 final size:8
Alignment explanation
Indices: 30706167--30706258 Score: 52
Period size: 9 Copynumber: 11.8 Consensus size: 8
30706157 TTCAATTTAT
30706167 TTATA-TA
1 TTATATTA
30706174 TTATATCTA
1 TTATAT-TA
*
30706183 TTTTATTA
1 TTATATTA
*
30706191 TATATATTC
1 T-TATATTA
* *
30706200 TAAATATTT
1 T-TATATTA
*
30706209 TATATATTT
1 T-TATATTA
*
30706218 TTATATTT
1 TTATATTA
30706226 TTATATTA
1 TTATATTA
30706234 --ATATTA
1 TTATATTA
30706240 TT-T-TTA
1 TTATATTA
30706246 -TATATTA
1 TTATATTA
30706253 TTATAT
1 TTATAT
30706259 ATATATTTAT
Statistics
Matches: 70, Mismatches: 7, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
5 1 0.01
6 10 0.14
7 9 0.13
8 22 0.31
9 28 0.40
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (8 bp):
TTATATTA
Found at i:30706224 original size:8 final size:8
Alignment explanation
Indices: 30706203--30706258 Score: 58
Period size: 8 Copynumber: 6.5 Consensus size: 8
30706193 TATATTCTAA
30706203 ATATTTTAT
1 ATATTTT-T
30706212 ATATTTTT
1 ATATTTTT
30706220 ATATTTTT
1 ATATTTTT
**
30706228 ATATTAAT
1 ATATTTTT
30706236 ATTATTTTT
1 A-TATTTTT
30706245 ATATATTATT
1 ATAT-TT-TT
30706255 ATAT
1 ATAT
30706259 ATATATTTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
8 19 0.47
9 15 0.38
10 6 0.15
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
ATATTTTT
Found at i:30706227 original size:18 final size:18
Alignment explanation
Indices: 30706166--30706258 Score: 57
Period size: 19 Copynumber: 4.9 Consensus size: 18
30706156 ATTCAATTTA
30706166 TTTATATATTATATCTAT-TT
1 TTTATATATT-T-T-TATATT
* *
30706186 TATTATATATATTCTAAATAT
1 T-TTATATAT-TTTTATAT-T
30706207 TTTATATATTTTTATA-T
1 TTTATATATTTTTATATT
**
30706224 TTT-TATATTAATATTATT
1 TTTATATATTTTTA-TATT
*
30706242 TTTATATATTATTATAT
1 TTTATATATTTTTATAT
30706259 ATATATTTAT
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
16 8 0.14
17 6 0.10
18 7 0.12
19 16 0.27
20 10 0.17
21 11 0.19
22 1 0.02
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTATATATTTTTATATT
Found at i:30706233 original size:57 final size:57
Alignment explanation
Indices: 30706153--30706284 Score: 146
Period size: 57 Copynumber: 2.3 Consensus size: 57
30706143 TATTTAATAT
* * *
30706153 TATATTCAATTTATTTATATATT-ATATCTA-TTTTATTATATATATTCTAAATAT-TTTA
1 TATATTC-TTTTATTTTTATATTAATAT-TATTTTTA-TATAT-TATTATAAATATATTTA
*
30706211 TATATT-TTTATATTTTTATATTAATATTATTTTTATATATTATTATATATATATTTA
1 TATATTCTTT-TATTTTTATATTAATATTATTTTTATATATTATTATAAATATATTTA
*
30706268 TTTATTCTTTTATTTTT
1 TATATTCTTTTATTTTT
30706285 GACATAAATT
Statistics
Matches: 64, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
56 12 0.19
57 34 0.53
58 18 0.28
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (57 bp):
TATATTCTTTTATTTTTATATTAATATTATTTTTATATATTATTATAAATATATTTA
Found at i:30706263 original size:16 final size:15
Alignment explanation
Indices: 30706170--30706265 Score: 64
Period size: 14 Copynumber: 6.9 Consensus size: 15
30706160 AATTTATTTA
*
30706170 TATATTATAT-CTAT
1 TATATTATATATTAT
*
30706184 TTTATTATATA-TAT
1 TATATTATATATTAT
* * *
30706198 TCTA-AATATTTTA-
1 TATATTATATATTAT
* *
30706211 TATATTTTTATATTTT
1 TATA-TTATATATTAT
30706227 TATATTA-ATATTAT
1 TATATTATATATTAT
30706241 T-T-TTATATATTAT
1 TATATTATATATTAT
30706254 TATA-TATATATT
1 TATATTATATATT
30706266 TATTTATTCT
Statistics
Matches: 63, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
12 3 0.05
13 16 0.25
14 33 0.52
15 7 0.11
16 4 0.06
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (15 bp):
TATATTATATATTAT
Found at i:30706264 original size:27 final size:24
Alignment explanation
Indices: 30706208--30706270 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 24
30706198 TCTAAATATT
30706208 TTATA-TATTTTTATATTTTTATA
1 TTATATTATTTTTATATTTTTATA
30706231 TTAATATTATTTTTATATATTATTATA
1 TT-ATATTATTTTTATAT-TT-TTATA
30706258 TATATATTTATTT
1 T-TATA-TTATTT
30706271 ATTCTTTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
23 2 0.06
24 3 0.09
25 11 0.32
26 2 0.06
27 9 0.26
28 7 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
TTATATTATTTTTATATTTTTATA
Found at i:30706272 original size:16 final size:16
Alignment explanation
Indices: 30706161--30706272 Score: 61
Period size: 14 Copynumber: 7.6 Consensus size: 16
30706151 ATTATATTCA
30706161 ATTTATTTATATATTAT
1 ATTTATTTATATA-TAT
*
30706178 ATCTATTT-TAT-TAT
1 ATTTATTTATATATAT
*
30706192 ATATATTCTA-A-ATAT
1 ATTTATT-TATATATAT
* * *
30706207 -TTTATATATTTTTAT
1 ATTTATTTATATATAT
30706222 A-TT-TTTATAT-TA-
1 ATTTATTTATATATAT
30706234 ATATTATTT-T-TATAT
1 AT-TTATTTATATATAT
30706249 A-TTA-TTATATATAT
1 ATTTATTTATATATAT
30706263 ATTTATTTAT
1 ATTTATTTAT
30706273 TCTTTTATTT
Statistics
Matches: 72, Mismatches: 8, Indels: 31
0.65 0.07 0.28
Matches are distributed among these distances:
12 3 0.04
13 9 0.12
14 29 0.40
15 17 0.24
16 7 0.10
17 7 0.10
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (16 bp):
ATTTATTTATATATAT
Found at i:30708942 original size:25 final size:26
Alignment explanation
Indices: 30708901--30708970 Score: 83
Period size: 25 Copynumber: 2.8 Consensus size: 26
30708891 TCATGTACAT
*
30708901 GTATGCTCA-TACAAGCTGTGA-ATTG
1 GTATGCTCACT-CAAGCTGTGAGATCG
*
30708926 GTATGCTCACTCGAGCTGT-AGATCG
1 GTATGCTCACTCAAGCTGTGAGATCG
*
30708951 GTATGCTCACACAAGCTGTG
1 GTATGCTCACTCAAGCTGTG
30708971 GGTCAGAACG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
24 1 0.03
25 36 0.95
26 1 0.03
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (26 bp):
GTATGCTCACTCAAGCTGTGAGATCG
Found at i:30713049 original size:16 final size:16
Alignment explanation
Indices: 30713028--30713060 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
30713018 GATGTCCCCG
30713028 ATACTAGTTCAATAGC
1 ATACTAGTTCAATAGC
30713044 ATACTAGTTCAATAGC
1 ATACTAGTTCAATAGC
30713060 A
1 A
30713061 AACTCAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.30
Consensus pattern (16 bp):
ATACTAGTTCAATAGC
Found at i:30716676 original size:25 final size:25
Alignment explanation
Indices: 30716622--30716705 Score: 69
Period size: 25 Copynumber: 3.4 Consensus size: 25
30716612 GTATGCTTAT
* ** *
30716622 ACGAGCTTTAAATCAATATGCTCAC
1 ACGAGCTGTAAATCGGTATACTCAC
* * * *
30716647 TCGAGCTGTAGATTGGTATACTCTC
1 ACGAGCTGTAAATCGGTATACTCAC
* *
30716672 ACGAGCTATAAATCGGTATGCTCAC
1 ACGAGCTGTAAATCGGTATACTCAC
*
30716697 ACAAGCTGT
1 ACGAGCTGT
30716706 GGGTCGGAAC
Statistics
Matches: 43, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.29
Consensus pattern (25 bp):
ACGAGCTGTAAATCGGTATACTCAC
Found at i:30738384 original size:18 final size:18
Alignment explanation
Indices: 30738353--30738397 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
30738343 TATTTAAGAA
30738353 ATTAATAT--AATAATAT
1 ATTAATATAAAATAATAT
30738369 ATTAATATAAAATAATAT
1 ATTAATATAAAATAATAT
* *
30738387 AATAAAATAAA
1 ATTAATATAAA
30738398 GCATATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 8 0.32
18 17 0.68
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
ATTAATATAAAATAATAT
Found at i:30753584 original size:47 final size:47
Alignment explanation
Indices: 30753458--30753796 Score: 355
Period size: 47 Copynumber: 7.7 Consensus size: 47
30753448 GTTATACGTG
* * * *
30753458 TAACGTGGTACTAAGTGGATATACCACGATTACACATATTGATACAT
1 TAACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCAT
* * *
30753505 GTAACATGGTGCTAAGTGGATATGCCATGGTTACATATATTGATTCAT
1 -TAACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCAT
* * *
30753553 TAGCGTGGTGCTAGGTGGATATACCACGGTTA-A-ACA-TG------
1 TAACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCAT
*
30753591 TAACGTGGTGCTAAGTGGATATGCCA-----ACATATATTGATTCAT
1 TAACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCAT
*
30753633 TAACGTGGTGCTAAGTGGATATACCACGGTTA-A-ACA-TG------
1 TAACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCAT
* *
30753671 TAACGCGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCAT
1 TAACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCAT
* **
30753718 TAACGTGGTGCTAAGTTGATATGTCACGGTTACATATATTGATTCAT
1 TAACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCAT
30753765 TAACGTGGTGCTAAGTGGATATACCACGGTTA
1 TAACGTGGTGCTAAGTGGATATACCACGGTTA
30753797 AACATGTAAC
Statistics
Matches: 240, Mismatches: 28, Indels: 47
0.76 0.09 0.15
Matches are distributed among these distances:
33 1 0.00
34 1 0.00
35 2 0.01
36 2 0.01
38 53 0.22
39 1 0.00
40 2 0.01
41 2 0.01
42 25 0.10
44 4 0.02
45 4 0.02
46 2 0.01
47 101 0.42
48 40 0.17
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.32
Consensus pattern (47 bp):
TAACGTGGTGCTAAGTGGATATACCACGGTTACATATATTGATTCAT
Found at i:30753603 original size:85 final size:84
Alignment explanation
Indices: 30753501--30753749 Score: 389
Period size: 80 Copynumber: 3.0 Consensus size: 84
30753491 ACATATTGAT
* *
30753501 ACATGTAACATGGTGCTAAGTGGATATGCCATGGTTACATATATTGATTCATTAGCGTGGTGCTA
1 ACATGTAACGTGGTGCTAAGTGGATATGCCA-GGTTACATATATTGATTCATTAACGTGGTGCTA
*
30753566 GGTGGATATACCACGGTTAA
65 AGTGGATATACCACGGTTAA
30753586 ACATGTAACGTGGTGCTAAGTGGATATGCCA----ACATATATTGATTCATTAACGTGGTGCTAA
1 ACATGTAACGTGGTGCTAAGTGGATATGCCAGGTTACATATATTGATTCATTAACGTGGTGCTAA
30753647 GTGGATATACCACGGTTAA
66 GTGGATATACCACGGTTAA
*
30753666 ACATGTAACGCGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACGTGGTGCTA
1 ACATGTAACGTGGTGCTAAGTGGATATGCCA-GGTTACATATATTGATTCATTAACGTGGTGCTA
* **
30753731 AGTTGATATGTCACGGTTA
65 AGTGGATATACCACGGTTA
30753750 CATATATTGA
Statistics
Matches: 152, Mismatches: 7, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
80 77 0.51
85 75 0.49
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (84 bp):
ACATGTAACGTGGTGCTAAGTGGATATGCCAGGTTACATATATTGATTCATTAACGTGGTGCTAA
GTGGATATACCACGGTTAA
Found at i:30753609 original size:38 final size:40
Alignment explanation
Indices: 30753556--30753824 Score: 212
Period size: 38 Copynumber: 6.5 Consensus size: 40
30753546 GATTCATTAG
*
30753556 CGTGGTGCTAGGTGGATATACCACGGTTA-A-ACATGTAA
1 CGTGGTGCTAAGTGGATATACCACGGTTACATACATGTAA
* * * *
30753594 CGTGGTGCTAAGTGGATATGCCAAC-ATATATTGATTCAT-TAA
1 CGTGGTGCTAAGTGGATATACC-ACGGT-TA--CATACATGTAA
30753636 CGTGGTGCTAAGTGGATATACCACGGTTA-A-ACATGTAA
1 CGTGGTGCTAAGTGGATATACCACGGTTACATACATGTAA
* * *
30753674 CGCGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAA
1 CGTGGTGCTAAGTGGATATACCACGGTTACATACA-TG------TAA
* ** *
30753721 CGTGGTGCTAAGTTGATATGTCACGGTTACATATATTGATTCATTAA
1 CGTGGTGCTAAGTGGATATACCACGGTTACATACA-TG------TAA
30753768 CGTGGTGCTAAGTGGATATACCACGGTTA-A-ACATGTAA
1 CGTGGTGCTAAGTGGATATACCACGGTTACATACATGTAA
30753806 CGTGGTGCTAAGTGGATAT
1 CGTGGTGCTAAGTGGATAT
30753825 GCTATGGTTA
Statistics
Matches: 197, Mismatches: 17, Indels: 34
0.79 0.07 0.14
Matches are distributed among these distances:
37 3 0.02
38 74 0.38
39 5 0.03
40 2 0.01
41 6 0.03
42 26 0.13
43 3 0.02
44 2 0.01
45 2 0.01
46 1 0.01
47 73 0.37
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (40 bp):
CGTGGTGCTAAGTGGATATACCACGGTTACATACATGTAA
Found at i:30753798 original size:212 final size:213
Alignment explanation
Indices: 30753424--30753826 Score: 637
Period size: 212 Copynumber: 1.9 Consensus size: 213
30753414 ATAAAAAAAT
* * * * *
30753424 GTGGTACTAAGTGGGTACACCATGGTTATACGTGTAACGTGGTACTAAGTGGATATACCACGATT
1 GTGGTACTAAGTGGATACACCACGGTTAAACATGTAACGCGGTACTAAGTGGATATACCACGATT
*
30753489 ACACATATTGATACATGTAACATGGTGCTAAGTGGATATGCCATGGTTACATATATTGATTCATT
66 ACACATATTGATACATGTAACATGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATT
* *
30753554 AGCGTGGTGCTAGGTGGATATACCACGGTTAAACATGTAACGTGGTGCTAAGTGGATATGCCAAC
131 AACGTGGTGCTAAGTGGATATACCACGGTTAAACATGTAACGTGGTGCTAAGTGGATATGCCAAC
30753619 ATATATTGATTCATTAAC
196 ATATATTGATTCATTAAC
* * * * *
30753637 GTGGTGCTAAGTGGATATACCACGGTTAAACATGTAACGCGGTGCTAAGTGGATATGCCACGGTT
1 GTGGTACTAAGTGGATACACCACGGTTAAACATGTAACGCGGTACTAAGTGGATATACCACGATT
* * * * *
30753702 ACATATATTGATTCAT-TAACGTGGTGCTAAGTTGATATGTCACGGTTACATATATTGATTCATT
66 ACACATATTGATACATGTAACATGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATT
30753766 AACGTGGTGCTAAGTGGATATACCACGGTTAAACATGTAACGTGGTGCTAAGTGGATATGC
131 AACGTGGTGCTAAGTGGATATACCACGGTTAAACATGTAACGTGGTGCTAAGTGGATATGC
30753827 TATGGTTATA
Statistics
Matches: 172, Mismatches: 18, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
212 103 0.60
213 69 0.40
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (213 bp):
GTGGTACTAAGTGGATACACCACGGTTAAACATGTAACGCGGTACTAAGTGGATATACCACGATT
ACACATATTGATACATGTAACATGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATT
AACGTGGTGCTAAGTGGATATACCACGGTTAAACATGTAACGTGGTGCTAAGTGGATATGCCAAC
ATATATTGATTCATTAAC
Found at i:30763861 original size:8 final size:8
Alignment explanation
Indices: 30763850--30763894 Score: 54
Period size: 8 Copynumber: 5.4 Consensus size: 8
30763840 TTTAAGAAAT
30763850 TAATATAA
1 TAATATAA
*
30763858 TAATATAT
1 TAATATAA
30763866 TAATATAAAA
1 TAATAT--AA
30763876 TAATATAA
1 TAATATAA
*
30763884 TAATAAAA
1 TAATATAA
30763892 TAA
1 TAA
30763895 AGCATATAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
8 25 0.78
10 7 0.22
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
TAATATAA
Found at i:30763879 original size:18 final size:16
Alignment explanation
Indices: 30763848--30763894 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 16
30763838 TATTTAAGAA
30763848 ATTAATATAATAATAT
1 ATTAATATAATAATAT
30763864 ATTAATATAAAATAATAT
1 ATTAATAT--AATAATAT
* *
30763882 AATAATAAAATAA
1 ATTAATATAATAA
30763895 AGCATATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 13 0.48
18 14 0.52
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTAATATAATAATAT
Found at i:30769929 original size:24 final size:24
Alignment explanation
Indices: 30769883--30769941 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
30769873 TAAAGTTGAA
30769883 TAATTAAATTA-ATCTAACAAAAT
1 TAATTAAATTATATCTAACAAAAT
*
30769906 TAATTAAATTATATCTAACCAAAT
1 TAATTAAATTATATCTAACAAAAT
30769930 TAATTAAATTAT
1 TAATTAAATTAT
30769942 GTCGATTTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 11 0.32
24 23 0.68
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (24 bp):
TAATTAAATTATATCTAACAAAAT
Found at i:30776419 original size:48 final size:48
Alignment explanation
Indices: 30776337--30776715 Score: 497
Period size: 48 Copynumber: 7.9 Consensus size: 48
30776327 ATACTAGGGT
* *
30776337 TATGTGAGCCAGTGTAAGACCATGTTCGGGACATGGCATCAGCCTCGA
1 TATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCGA
* * * * * *
30776385 TATGTGAGTCAGTGTAAGACCATATTTGGAACATGACATCGGCATTGA
1 TATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCGA
* *
30776433 TATGAGAGCCAGTATAAGACCATGTTTGGGACATGGCATCGGCCTCGA
1 TATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCGA
* * * *
30776481 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATTGGCATTGA
1 TATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCGA
* * **
30776529 TATGAGAGCTAGTGTAAGACCATGTTTGGGACATGGCATTAGCCTCGA
1 TATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCGA
* * * *
30776577 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCAGCATTGA
1 TATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCGA
* * * *
30776625 TAGGTGAGCTAGTGTAAGACCATGTTTAGGACATGGCATCGGCCTCTA
1 TATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCGA
* * *
30776673 CATGTGGGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGC
1 TATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGC
30776716 ATCTTACCCT
Statistics
Matches: 285, Mismatches: 46, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 285 1.00
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (48 bp):
TATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCGA
Found at i:30776509 original size:96 final size:96
Alignment explanation
Indices: 30776337--30776717 Score: 573
Period size: 96 Copynumber: 4.0 Consensus size: 96
30776327 ATACTAGGGT
* * *
30776337 TATGTGAGCCAGTGTAAGACCATGTTCGGGACATGGCATCAGCCTCGATATGTGAGTCAGTGTAA
1 TATGAGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCAGCCTCGATATGTGAGCCAGTGTAA
* *
30776402 GACCATATTTGGAACATGACATCGGCATTGA
66 GACCATGTTTGGAACATGGCATCGGCATTGA
* *
30776433 TATGAGAGCCAGTATAAGACCATGTTTGGGACATGGCATCGGCCTCGATATGTGAGCCAGTGTAA
1 TATGAGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCAGCCTCGATATGTGAGCCAGTGTAA
*
30776498 GACCATGTTTGGAACATGGCATTGGCATTGA
66 GACCATGTTTGGAACATGGCATCGGCATTGA
* *
30776529 TATGAGAGCTAGTGTAAGACCATGTTTGGGACATGGCATTAGCCTCGATATGTGAGCCAGTGTAA
1 TATGAGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCAGCCTCGATATGTGAGCCAGTGTAA
*
30776594 GACCATGTTTGGAACATGGCATCAGCATTGA
66 GACCATGTTTGGAACATGGCATCGGCATTGA
* * * * * * * * *
30776625 TAGGTGAGCTAGTGTAAGACCATGTTTAGGACATGGCATCGGCCTCTACATGTGGGCTAGTGTAA
1 TATGAGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCAGCCTCGATATGTGAGCCAGTGTAA
*
30776690 GACCATGTTTGGGACATGGCATCGGCAT
66 GACCATGTTTGGAACATGGCATCGGCAT
30776718 CTTACCCTTT
Statistics
Matches: 260, Mismatches: 25, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
96 260 1.00
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.27
Consensus pattern (96 bp):
TATGAGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCAGCCTCGATATGTGAGCCAGTGTAA
GACCATGTTTGGAACATGGCATCGGCATTGA
Found at i:30780365 original size:50 final size:50
Alignment explanation
Indices: 30780305--30780409 Score: 122
Period size: 50 Copynumber: 2.1 Consensus size: 50
30780295 TAACTAGCCA
* * * * * *
30780305 TATGTGATGATATATTGAGCCTT-GTATATTCGGTCTTATAGGTATGTACT
1 TATGTAATGATATAATGA-ACTTGGTATATCCGGTCATATAGGTAAGTACT
* *
30780355 TATGTAATGATATAATGAATTTGGTATATCCGGTCATATAGGTAAGTATT
1 TATGTAATGATATAATGAACTTGGTATATCCGGTCATATAGGTAAGTACT
30780405 TATGT
1 TATGT
30780410 GGTGTTCCAA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
49 2 0.04
50 44 0.96
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.43
Consensus pattern (50 bp):
TATGTAATGATATAATGAACTTGGTATATCCGGTCATATAGGTAAGTACT
Found at i:30780735 original size:21 final size:21
Alignment explanation
Indices: 30780710--30780750 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
30780700 CATTGATTTA
30780710 GTAAATTAGTTTATGAAATTC
1 GTAAATTAGTTTATGAAATTC
30780731 GTAAATTAGTTTATGAAATT
1 GTAAATTAGTTTATGAAATT
30780751 AGAATATGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.44
Consensus pattern (21 bp):
GTAAATTAGTTTATGAAATTC
Found at i:30781450 original size:39 final size:39
Alignment explanation
Indices: 30781396--30781526 Score: 192
Period size: 39 Copynumber: 3.4 Consensus size: 39
30781386 GCATGATATT
30781396 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGC
1 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGC
* *
30781435 TGGAAACATTTCCGGAGTTGAGGTCCGCAGGCTACGTGC
1 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGC
* ** *
30781474 TAGAAACATATCCGGACTTGAGGTTTGCAGGCTACATGC
1 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGC
*
30781513 TGG-AATATATCCGG
1 TGGAAACATATCCGG
30781527 TCCTAAAGTC
Statistics
Matches: 82, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
38 10 0.12
39 72 0.88
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.24
Consensus pattern (39 bp):
TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGC
Found at i:30781541 original size:78 final size:78
Alignment explanation
Indices: 30781398--30781554 Score: 190
Period size: 78 Copynumber: 2.0 Consensus size: 78
30781388 ATGATATTTG
* * ** * *
30781398 GAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGCTGGAAACATTTCCGGAGTTGAGGTCCGC
1 GAAACATATCCGGACTTGAGGTCCGCAGGCTACATGCTGGAAACATATCCGGACCTAAAGTCCGC
30781463 AGGCTACGTGCTA
66 AGGCTACGTGCTA
** * *
30781476 GAAACATATCCGGACTTGAGGTTTGCAGGCTACATGCTGG-AATATATCCGGTCCTAAAGTCCCG
1 GAAACATATCCGGACTTGAGGTCCGCAGGCTACATGCTGGAAACATATCCGGACCTAAAGT-CCG
**
30781540 CAGGCTTTGTGCTA
65 CAGGCTACGTGCTA
30781554 G
1 G
30781555 TAGCTGGATT
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
77 13 0.20
78 53 0.80
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (78 bp):
GAAACATATCCGGACTTGAGGTCCGCAGGCTACATGCTGGAAACATATCCGGACCTAAAGTCCGC
AGGCTACGTGCTA
Found at i:30788279 original size:21 final size:21
Alignment explanation
Indices: 30788254--30788294 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
30788244 CATTGATTTA
30788254 GTAAATTAGTTTATGAAATTC
1 GTAAATTAGTTTATGAAATTC
30788275 GTAAATTAGTTTATGAAATT
1 GTAAATTAGTTTATGAAATT
30788295 AGAATATGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.44
Consensus pattern (21 bp):
GTAAATTAGTTTATGAAATTC
Found at i:30788994 original size:39 final size:39
Alignment explanation
Indices: 30788940--30789057 Score: 191
Period size: 39 Copynumber: 3.0 Consensus size: 39
30788930 GCATGATAAT
*
30788940 TGGAAACATATCCGGACTTGAGGTCCACAGGCTACGTGC
1 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGC
* * *
30788979 TGGAAACATATCCGGAGTTGAGGTCCGCAGGCTACATGT
1 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGC
*
30789018 TGGAAACATATCCGGACTTGAGGTCCGCATGCTACGTGC
1 TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGC
30789057 T
1 T
30789058 AGAATATATC
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 71 1.00
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.23
Consensus pattern (39 bp):
TGGAAACATATCCGGACTTGAGGTCCGCAGGCTACGTGC
Found at i:30789088 original size:78 final size:78
Alignment explanation
Indices: 30788939--30789089 Score: 198
Period size: 78 Copynumber: 1.9 Consensus size: 78
30788929 TGCATGATAA
* * * *
30788939 TTGGAAACATATCCGGACTTGAGGTCCACAGGCTACGTGCTGGAAACATATCCGGAGTTGAGGTC
1 TTGGAAACATATCCGGACTTGAGGTCCACAGGCTACGTGCTAGAAACATATCCGGAGCTAAAGTC
*
30789004 CGCAGGCTACATG
66 CACAGGCTACATG
* * *
30789017 TTGGAAACATATCCGGACTTGAGGTCCGCATGCTACGTGCTAG-AATATATCC-GAGCCTAAAGT
1 TTGGAAACATATCCGGACTTGAGGTCCACAGGCTACGTGCTAGAAACATATCCGGAG-CTAAAGT
30789080 CCCACAGGCT
65 -CCACAGGCT
30789090 TTGTGCTAGT
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
76 3 0.05
77 12 0.19
78 48 0.76
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (78 bp):
TTGGAAACATATCCGGACTTGAGGTCCACAGGCTACGTGCTAGAAACATATCCGGAGCTAAAGTC
CACAGGCTACATG
Found at i:30790725 original size:12 final size:12
Alignment explanation
Indices: 30790690--30790731 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
30790680 CAGTGGTATG
*
30790690 TGAGTTTCCGGG
1 TGAGTTTCCGGA
30790702 TGAGTTTCCGGA
1 TGAGTTTCCGGA
*
30790714 TGTGTTTCCGGA
1 TGAGTTTCCGGA
*
30790726 AGAGTT
1 TGAGTT
30790732 ACCCGGACTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.14, C:0.14, G:0.36, T:0.36
Consensus pattern (12 bp):
TGAGTTTCCGGA
Found at i:30794806 original size:48 final size:48
Alignment explanation
Indices: 30794724--30795153 Score: 536
Period size: 48 Copynumber: 9.0 Consensus size: 48
30794714 ATACTAGGGT
* * *
30794724 TATGTGAGCCAGTGTAAGACCATGTTCGGGACATGGCATCAGCCTCGA
1 TATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCATCGA
* * * * *
30794772 TATGTGAGCCAGTGTAAGACCATATTTGGAACATGACATCGACATTGA
1 TATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCATCGA
* * *
30794820 TATGAGAGCCAGTGTAAGACCATGTTTGGGACATGGCATTGGCCTCGA
1 TATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCATCGA
* * * * * *
30794868 TATGTGAGCCAGTGTAAGACCATATTTGGAACATGACATCGACATTGT
1 TATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCATCGA
* * *
30794916 TATGAGAGCCAGTGTAAGACCATGTTTGGGACATGGCATTGGCCTCGA
1 TATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCATCGA
* * * *
30794964 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCTTTGGCATTGA
1 TATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCATCGA
* * * * *
30795012 TATGAGAGCTAGTGTAAGACTATGTTTGGGACATGGCATCAGCCTCGA
1 TATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCATCGA
* * * *
30795060 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCTTTGGCATTGA
1 TATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCATCGA
* * *
30795108 TATGAGAGCTAGTGTAAGACTATGTTTGGGACATGGCATCGGCATC
1 TATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCATC
30795154 TTACCCTTTT
Statistics
Matches: 318, Mismatches: 64, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 318 1.00
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.27
Consensus pattern (48 bp):
TATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCATCGA
Found at i:30794893 original size:96 final size:96
Alignment explanation
Indices: 30794724--30795147 Score: 659
Period size: 96 Copynumber: 4.4 Consensus size: 96
30794714 ATACTAGGGT
* *
30794724 TATGTGAGCCAGTGTAAGACCATGTTCGGGACATGGCATCAGCCTCGATATGTGAGCCAGTGTAA
1 TATGAGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCAGCCTCGATATGTGAGCCAGTGTAA
30794789 GACCATATTTGGAACATGACATCGACATTGA
66 GACCATATTTGGAACATGACATCGACATTGA
**
30794820 TATGAGAGCCAGTGTAAGACCATGTTTGGGACATGGCATTGGCCTCGATATGTGAGCCAGTGTAA
1 TATGAGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCAGCCTCGATATGTGAGCCAGTGTAA
*
30794885 GACCATATTTGGAACATGACATCGACATTGT
66 GACCATATTTGGAACATGACATCGACATTGA
**
30794916 TATGAGAGCCAGTGTAAGACCATGTTTGGGACATGGCATTGGCCTCGATATGTGAGCCAGTGTAA
1 TATGAGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCAGCCTCGATATGTGAGCCAGTGTAA
* * * * *
30794981 GACCATGTTTGGAACATGGCTTTGGCATTGA
66 GACCATATTTGGAACATGACATCGACATTGA
* *
30795012 TATGAGAGCTAGTGTAAGACTATGTTTGGGACATGGCATCAGCCTCGATATGTGAGCCAGTGTAA
1 TATGAGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCAGCCTCGATATGTGAGCCAGTGTAA
* * * * *
30795077 GACCATGTTTGGAACATGGCTTTGGCATTGA
66 GACCATATTTGGAACATGACATCGACATTGA
* *
30795108 TATGAGAGCTAGTGTAAGACTATGTTTGGGACATGGCATC
1 TATGAGAGCCAGTGTAAGACCATGTTTGGGACATGGCATC
30795148 GGCATCTTAC
Statistics
Matches: 313, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
96 313 1.00
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (96 bp):
TATGAGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCAGCCTCGATATGTGAGCCAGTGTAA
GACCATATTTGGAACATGACATCGACATTGA
Found at i:30794984 original size:144 final size:144
Alignment explanation
Indices: 30794724--30795153 Score: 601
Period size: 144 Copynumber: 3.0 Consensus size: 144
30794714 ATACTAGGGT
*
30794724 TATGTGAGCCAGTGTAAGACCATGTTCGGGACATGGCATCAGCCTCGATATGTGAGCCAGTGTAA
1 TATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCAGCCTCGATATGTGAGCCAGTGTAA
* * * *
30794789 GACCATATTTGGAACATGACATCGACATTGATATGAGAGCCAGTGTAAGACCATGTTTGGGACAT
66 GACCATGTTTGGAACATGGCATTGGCATTGATATGAGAGCCAGTGTAAGACCATGTTTGGGACAT
*
30794854 GGCATTGGCCTCGA
131 GGCATTGGCATCGA
* * * * * * *
30794868 TATGTGAGCCAGTGTAAGACCATATTTGGAACATGACATC-GACATTGTTATGAGAGCCAGTGTA
1 TATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCAG-CCTCGATATGTGAGCCAGTGTA
* * * * *
30794932 AGACCATGTTTGGGACATGGCATTGGCCTCGATATGTGAGCCAGTGTAAGACCATGTTTGGAACA
65 AGACCATGTTTGGAACATGGCATTGGCATTGATATGAGAGCCAGTGTAAGACCATGTTTGGGACA
* *
30794997 TGGCTTTGGCATTGA
130 TGGCATTGGCATCGA
* * *
30795012 TATGAGAGCTAGTGTAAGACTATGTTTGGGACATGGCATCAGCCTCGATATGTGAGCCAGTGTAA
1 TATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCAGCCTCGATATGTGAGCCAGTGTAA
* * *
30795077 GACCATGTTTGGAACATGGCTTTGGCATTGATATGAGAGCTAGTGTAAGACTATGTTTGGGACAT
66 GACCATGTTTGGAACATGGCATTGGCATTGATATGAGAGCCAGTGTAAGACCATGTTTGGGACAT
*
30795142 GGCATCGGCATC
131 GGCATTGGCATC
30795154 TTACCCTTTT
Statistics
Matches: 243, Mismatches: 41, Indels: 4
0.84 0.14 0.01
Matches are distributed among these distances:
143 1 0.00
144 241 0.99
145 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.27
Consensus pattern (144 bp):
TATGTGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCAGCCTCGATATGTGAGCCAGTGTAA
GACCATGTTTGGAACATGGCATTGGCATTGATATGAGAGCCAGTGTAAGACCATGTTTGGGACAT
GGCATTGGCATCGA
Found at i:30802662 original size:43 final size:43
Alignment explanation
Indices: 30802505--30802663 Score: 146
Period size: 43 Copynumber: 3.7 Consensus size: 43
30802495 TATGTGTTTG
* *
30802505 CATGTAAGACCACGTCTAGGACGTTGACATTGAC-TTATGATTT
1 CATGTAAGACCACGTCTAGGACGTTGGCATCGACATT-TGATTT
* * * * *
30802548 ACGTGTAAGACCATGTCTAGGACATCGGCATCG-TATTTGATTT
1 -CATGTAAGACCACGTCTAGGACGTTGGCATCGACATTTGATTT
** *
30802591 TGTGTATGACC-CTGTCTAGGACAG-TGGCATCGACATTTGATTT
1 CATGTAAGACCAC-GTCTAGGAC-GTTGGCATCGACATTTGATTT
* *
30802634 CATGTAAGACCACGTCTGGGATGTTGGCAT
1 CATGTAAGACCACGTCTAGGACGTTGGCAT
30802664 TGTACGAGCT
Statistics
Matches: 91, Mismatches: 18, Indels: 13
0.75 0.15 0.11
Matches are distributed among these distances:
42 26 0.29
43 36 0.40
44 29 0.32
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (43 bp):
CATGTAAGACCACGTCTAGGACGTTGGCATCGACATTTGATTT
Found at i:30802871 original size:21 final size:20
Alignment explanation
Indices: 30802847--30802902 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 20
30802837 AGTATAAGAA
*
30802847 AATATGCTATATGTGCAAATG
1 AATATGCAATATGTG-AAATG
* *
30802868 AATAGGGAATATGTGAAATG
1 AATATGCAATATGTGAAATG
*
30802888 CATATG-AACTATGTG
1 AATATGCAA-TATGTG
30802903 GTTTGTGATA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 2 0.07
20 15 0.52
21 12 0.41
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.30
Consensus pattern (20 bp):
AATATGCAATATGTGAAATG
Found at i:30804472 original size:44 final size:44
Alignment explanation
Indices: 30804406--30804492 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 44
30804396 TTCACAGAAT
* *
30804406 AATTTCTTTTAAGCATTTTTTAGAATAGATGACCTTATAACGTC
1 AATTTCTTCTAAGCATTATTTAGAATAGATGACCTTATAACGTC
30804450 AATTTCTTCTAAGCATTATTTAGAATAGATGACCTTATAACGT
1 AATTTCTTCTAAGCATTATTTAGAATAGATGACCTTATAACGT
30804493 TCCAACATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.41
Consensus pattern (44 bp):
AATTTCTTCTAAGCATTATTTAGAATAGATGACCTTATAACGTC
Found at i:30806477 original size:5 final size:6
Alignment explanation
Indices: 30806463--30806498 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
30806453 GATACTTGGG
30806463 AAAATA AAAATA AAAATA AAAAT- AAAAT- AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AA
30806499 GTACAAGAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 10 0.34
6 19 0.66
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:30811685 original size:17 final size:17
Alignment explanation
Indices: 30811660--30811693 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
30811650 TACTTATAGG
*
30811660 ATCAGCGTTGGAAACTA
1 ATCACCGTTGGAAACTA
30811677 ATCACCGTTGGAAACTA
1 ATCACCGTTGGAAACTA
30811694 CGTGTACCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.24
Consensus pattern (17 bp):
ATCACCGTTGGAAACTA
Found at i:30812889 original size:17 final size:18
Alignment explanation
Indices: 30812867--30812904 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
30812857 ATGTGGCTTA
30812867 CCCATGT-GGCCCACACG
1 CCCATGTGGGCCCACACG
30812884 CCCATGTGGGCCCACACG
1 CCCATGTGGGCCCACACG
30812902 CCC
1 CCC
30812905 GTGTAACTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.16, C:0.50, G:0.24, T:0.11
Consensus pattern (18 bp):
CCCATGTGGGCCCACACG
Found at i:30814783 original size:7 final size:7
Alignment explanation
Indices: 30814771--30814805 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
30814761 CCAGCAATCA
30814771 CCCTTCC
1 CCCTTCC
30814778 CCCTTCC
1 CCCTTCC
30814785 CCCTTCC
1 CCCTTCC
30814792 CCCTTCC
1 CCCTTCC
30814799 CCCTTCC
1 CCCTTCC
30814806 TTTCGCTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.00, C:0.71, G:0.00, T:0.29
Consensus pattern (7 bp):
CCCTTCC
Found at i:30815253 original size:22 final size:22
Alignment explanation
Indices: 30815228--30815272 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
30815218 TTTAATAAAG
30815228 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* *
30815250 AAAATATTTACAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
30815272 A
1 A
30815273 CACTCCCCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:30819031 original size:22 final size:22
Alignment explanation
Indices: 30819006--30819050 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
30818996 TTTAATAAAG
30819006 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* *
30819028 AAAATATTTACAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
30819050 A
1 A
30819051 CATGTTCAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:30824530 original size:29 final size:30
Alignment explanation
Indices: 30824476--30824536 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
30824466 TAAATCAAAC
30824476 ATTTTAATTTAATGTGGAATATTATACATAA
1 ATTTTAATTT-ATGTGGAATATTATACATAA
* * *
30824507 ATTTTAATTT-TGTGTAATTTTATATATAA
1 ATTTTAATTTATGTGGAATATTATACATAA
30824536 A
1 A
30824537 AATTTGATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 17 0.63
31 10 0.37
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.51
Consensus pattern (30 bp):
ATTTTAATTTATGTGGAATATTATACATAA
Found at i:30830743 original size:3 final size:3
Alignment explanation
Indices: 30830735--30830775 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
30830725 ATACATCAAC
* *
30830735 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATT GTA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
30830776 GAGAGCTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:30831815 original size:6 final size:6
Alignment explanation
Indices: 30831804--30831828 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
30831794 ATTTTTGTTC
30831804 TAATTG TAATTG TAATTG TAATTG T
1 TAATTG TAATTG TAATTG TAATTG T
30831829 GACTTTTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (6 bp):
TAATTG
Found at i:30832713 original size:47 final size:47
Alignment explanation
Indices: 30832644--30832738 Score: 172
Period size: 47 Copynumber: 2.0 Consensus size: 47
30832634 GGTTGTTAAC
* *
30832644 ATCGCTATTGTATGATCACCTCTGGTACCACCACCTGCATCAAATGA
1 ATCGCTATTGTATGACCACCTCTGGTACCACCACCTCCATCAAATGA
30832691 ATCGCTATTGTATGACCACCTCTGGTACCACCACCTCCATCAAATGA
1 ATCGCTATTGTATGACCACCTCTGGTACCACCACCTCCATCAAATGA
30832738 A
1 A
30832739 AGCTTTTTCT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.28, C:0.32, G:0.14, T:0.26
Consensus pattern (47 bp):
ATCGCTATTGTATGACCACCTCTGGTACCACCACCTCCATCAAATGA
Found at i:30849977 original size:3 final size:3
Alignment explanation
Indices: 30849969--30849999 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
30849959 AATCATGCCA
30849969 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
30850000 TATTGAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:30851553 original size:25 final size:26
Alignment explanation
Indices: 30851513--30851574 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
30851503 ATTCCACACT
30851513 ATTTTT-T-TTTTGAATTTTT-ATGA
1 ATTTTTATATTTTGAATTTTTGATGA
* *
30851536 ACTTTTTATATTTT-AATTTTTGGTGT
1 A-TTTTTATATTTTGAATTTTTGATGA
30851562 ATTTTTATATTTT
1 ATTTTTATATTTT
30851575 TTGAATTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 1 0.03
24 5 0.15
25 20 0.61
26 7 0.21
ACGTcount: A:0.21, C:0.02, G:0.08, T:0.69
Consensus pattern (26 bp):
ATTTTTATATTTTGAATTTTTGATGA
Found at i:30853482 original size:13 final size:13
Alignment explanation
Indices: 30853464--30853490 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
30853454 TGTGTTTGTT
30853464 TATCACATAGGAA
1 TATCACATAGGAA
30853477 TATCACATAGGAA
1 TATCACATAGGAA
30853490 T
1 T
30853491 TGGAGGAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (13 bp):
TATCACATAGGAA
Found at i:30855858 original size:161 final size:161
Alignment explanation
Indices: 30855677--30856001 Score: 605
Period size: 161 Copynumber: 2.0 Consensus size: 161
30855667 TGATTTCAAC
*
30855677 AATCAGTATAGAATCTATTTATCAGGGATTGATTTGATATTGAGAGAAAAGATAATTTCAGCAAT
1 AATCAGTAGAGAATCTATTTATCAGGGATTGATTTGATATTGAGAGAAAAGATAATTTCAGCAAT
30855742 GGAGCAAAAATTTGATGCAAAGAAGATGATGAAAAATAAATAGGAAGAGAAAAGAGAAATTCTAA
66 GGAGCAAAAATTTGATGCAAAGAAGATGATGAAAAATAAATAGGAAGAGAAAAGAGAAATTCTAA
30855807 TTGGGATGGGAAAGAAACATAATCCTAGTGT
131 TTGGGATGGGAAAGAAACATAATCCTAGTGT
* *
30855838 AATCAGTAGATAATCTATTTATCAGGGATTGATTTGATATTGAGAGCAAAGATAATTTCAGCAAT
1 AATCAGTAGAGAATCTATTTATCAGGGATTGATTTGATATTGAGAGAAAAGATAATTTCAGCAAT
* *
30855903 GGAGCGAAAATTTGATGCAAAGAAGATGATGAAAAATAAATAGGAAGAGAGAAGAGAAATTCTAA
66 GGAGCAAAAATTTGATGCAAAGAAGATGATGAAAAATAAATAGGAAGAGAAAAGAGAAATTCTAA
30855968 TTGGGATGGGAAAGAAACATAATCCTAGTGT
131 TTGGGATGGGAAAGAAACATAATCCTAGTGT
30855999 AAT
1 AAT
30856002 TAGGGGAAAA
Statistics
Matches: 159, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
161 159 1.00
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.26
Consensus pattern (161 bp):
AATCAGTAGAGAATCTATTTATCAGGGATTGATTTGATATTGAGAGAAAAGATAATTTCAGCAAT
GGAGCAAAAATTTGATGCAAAGAAGATGATGAAAAATAAATAGGAAGAGAAAAGAGAAATTCTAA
TTGGGATGGGAAAGAAACATAATCCTAGTGT
Found at i:30859273 original size:34 final size:34
Alignment explanation
Indices: 30859228--30859294 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
30859218 AATAACAATC
* *
30859228 ATTATGGTTATAATAGT-TCGATTCAGTGGAAAAT
1 ATTATGCTTATAATA-TATCGATTCAGTAGAAAAT
*
30859262 ATTATGCTTATAATATATTGATTCAGTAGAAAA
1 ATTATGCTTATAATATATCGATTCAGTAGAAAA
30859295 AAACATGCTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 1 0.03
34 28 0.97
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (34 bp):
ATTATGCTTATAATATATCGATTCAGTAGAAAAT
Found at i:30859723 original size:13 final size:13
Alignment explanation
Indices: 30859707--30859731 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30859697 TGAGGGGGCT
30859707 GTGTGGTCCACAC
1 GTGTGGTCCACAC
30859720 GTGTGGTCCACA
1 GTGTGGTCCACA
30859732 TGCCCGTGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.28, G:0.32, T:0.24
Consensus pattern (13 bp):
GTGTGGTCCACAC
Found at i:30862164 original size:5 final size:6
Alignment explanation
Indices: 30862150--30862183 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
30862140 TAATTTTCCC
30862150 TTTTCT TTTTCT TTTTCT TTTTCCT TCTTTCT TT
1 TTTTCT TTTTCT TTTTCT TTTT-CT T-TTTCT TT
30862184 CCCTCAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 17 0.65
7 6 0.23
8 3 0.12
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTCT
Found at i:30862165 original size:12 final size:13
Alignment explanation
Indices: 30862143--30862183 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
30862133 AAAGTCCTAA
*
30862143 TTTTCCCTTTTCT
1 TTTTCCTTTTTCT
30862156 TTTT-CTTTTTCT
1 TTTTCCTTTTTCT
30862168 TTTTCCTTCTTTCT
1 TTTTCCTT-TTTCT
30862182 TT
1 TT
30862184 CCCTCAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 11 0.44
13 7 0.28
14 7 0.28
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTCCTTTTTCT
Found at i:30862290 original size:28 final size:29
Alignment explanation
Indices: 30862236--30862306 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 29
30862226 TTTCTTTCTT
* * *
30862236 CTTTTTATTATT-TCTTTTATTTGTTTTA
1 CTTTATATTATTATATTATATTTGTTTTA
30862264 CTTTATATTATTATATTATATTT-TTTTA
1 CTTTATATTATTATATTATATTTGTTTTA
**
30862292 AATTATAATTATTAT
1 CTTTAT-ATTATTAT
30862307 TTCTTAAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 20 0.56
29 16 0.44
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (29 bp):
CTTTATATTATTATATTATATTTGTTTTA
Found at i:30862313 original size:21 final size:21
Alignment explanation
Indices: 30862273--30862320 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
30862263 ACTTTATATT
*
30862273 ATTAT-ATTATATTTTTTTAA
1 ATTATAATTATATTTTCTTAA
30862293 ATTATAATTAT-TATTTCTTAA
1 ATTATAATTATAT-TTTCTTAA
*
30862314 ATAATAA
1 ATTATAA
30862321 GCAAATACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTATAATTATATTTTCTTAA
Found at i:30868052 original size:17 final size:17
Alignment explanation
Indices: 30868019--30868052 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
30868009 ATCACACGCC
*
30868019 CATGTGCCAGGCCGTGT
1 CATGTGCCAAGCCGTGT
*
30868036 CATGTGCCAAGCTGTGT
1 CATGTGCCAAGCCGTGT
30868053 GGACTCAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.26, G:0.32, T:0.26
Consensus pattern (17 bp):
CATGTGCCAAGCCGTGT
Found at i:30870053 original size:46 final size:46
Alignment explanation
Indices: 30869952--30870039 Score: 113
Period size: 46 Copynumber: 1.9 Consensus size: 46
30869942 TGTAACCCGC
* * * *
30869952 CCATAAGCGAACTCGAACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGAACTCAACTCAACGAGCTCGGACGCTCCCAT
* * *
30869998 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC
1 CCATAAGTGAACTCGAACTCAACTCAACGAGCTCGGACGCTC
30870040 AACCATCCTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 36 1.00
ACGTcount: A:0.28, C:0.31, G:0.22, T:0.19
Consensus pattern (46 bp):
CCATAAGTGAACTCGAACTCAACTCAACGAGCTCGGACGCTCCCAT
Found at i:30870491 original size:30 final size:30
Alignment explanation
Indices: 30870457--30870516 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
30870447 ATTTAATACG
30870457 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
30870487 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
30870517 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:30877563 original size:93 final size:93
Alignment explanation
Indices: 30877456--30877626 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
30877446 GCCCCTAAGT
* *
30877456 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
30877521 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
30877549 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
30877614 CGAGTTCGGATGC
66 CGAGTTCGGATGC
30877627 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:30877623 original size:46 final size:46
Alignment explanation
Indices: 30877451--30877623 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
30877441 AACCCGCCCC
* * *
30877451 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
*
30877497 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
30877545 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
30877590 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
30877624 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 61 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:30878080 original size:30 final size:30
Alignment explanation
Indices: 30878046--30878105 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
30878036 ATTTAATACG
30878046 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
30878076 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
30878106 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:30880004 original size:16 final size:17
Alignment explanation
Indices: 30879970--30880006 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
30879960 AAGCCCTAAT
30879970 TTTCCCATTTCTTTTTC
1 TTTCCCATTTCTTTTTC
30879987 TTTCCC-TTT-TTCTTTC
1 TTTCCCATTTCTT-TTTC
30880003 TTTC
1 TTTC
30880007 TTTCCCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 2 0.11
16 11 0.58
17 6 0.32
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTCCCATTTCTTTTTC
Found at i:30880098 original size:25 final size:26
Alignment explanation
Indices: 30880065--30880113 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
30880055 CTTTATTCTT
*
30880065 TTTATTATTTCTTTTATT-TATTTTAC
1 TTTATTA-TTCTTATATTATATTTTAC
30880091 TTTA-TATTCTTATATTATATTTT
1 TTTATTATTCTTATATTATATTTT
30880114 TAAAAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 9 0.43
25 8 0.38
26 4 0.19
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.71
Consensus pattern (26 bp):
TTTATTATTCTTATATTATATTTTAC
Found at i:30887447 original size:16 final size:18
Alignment explanation
Indices: 30887428--30887461 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
30887418 TAATTAATGT
30887428 AAAATAA-TATT-ATTAA
1 AAAATAATTATTAATTAA
30887444 AAAATAATTATTAATTAA
1 AAAATAATTATTAATTAA
30887462 CATAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATAATTATTAATTAA
Found at i:30887753 original size:7 final size:7
Alignment explanation
Indices: 30887741--30887773 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
30887731 AAAGAAATTA
30887741 TTTTTCT
1 TTTTTCT
30887748 TTTTTCT
1 TTTTTCT
30887755 TTTTTCT
1 TTTTTCT
30887762 TTTCTT-T
1 TTT-TTCT
30887769 TTTTT
1 TTTTT
30887774 AATAGAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 2 0.08
7 21 0.84
8 2 0.08
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:30887818 original size:21 final size:22
Alignment explanation
Indices: 30887774--30887818 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
30887764 TCTTTTTTTT
* *
30887774 AATAGAAAGATAATTTAATTTA
1 AATAGAAAGATAATTAAATATA
*
30887796 AATATAAA-ATAATTAAATATA
1 AATAGAAAGATAATTAAATATA
30887817 AA
1 AA
30887819 ATTTGAGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (22 bp):
AATAGAAAGATAATTAAATATA
Found at i:30888333 original size:22 final size:22
Alignment explanation
Indices: 30888301--30888343 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
30888291 ATGTTTGTTT
30888301 CAATTAATGTTTTGTTATTTTC
1 CAATTAATGTTTTGTTATTTTC
* *
30888323 CAATTACTGTTTTTTTATTTT
1 CAATTAATGTTTTGTTATTTT
30888344 TACACCAAGC
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:0.21, C:0.09, G:0.07, T:0.63
Consensus pattern (22 bp):
CAATTAATGTTTTGTTATTTTC
Found at i:30891060 original size:10 final size:11
Alignment explanation
Indices: 30891030--30891059 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
30891020 CTATTTTTAT
30891030 TTAAATAAATTC
1 TTAAA-AAATTC
30891042 TTAAAAAATTC
1 TTAAAAAATTC
30891053 TTAAAAA
1 TTAAAAA
30891060 TAAAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (11 bp):
TTAAAAAATTC
Found at i:30896417 original size:55 final size:55
Alignment explanation
Indices: 30896356--30896468 Score: 190
Period size: 55 Copynumber: 2.1 Consensus size: 55
30896346 TTATATATCT
*
30896356 ATTCTCATGGGCAAATGAATCGGCTCAAATTGAAAATTAGTGGCCAAGACCACAA
1 ATTCTCATGGGCAAATGAATCGGCTCAAATGGAAAATTAGTGGCCAAGACCACAA
* * *
30896411 ATTCTCATGGGCAAATGAGTCGGCTCAAATGGAAAATTGGTGGCCAATACCACAA
1 ATTCTCATGGGCAAATGAATCGGCTCAAATGGAAAATTAGTGGCCAAGACCACAA
30896466 ATT
1 ATT
30896469 TTACAAAATT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.23
Consensus pattern (55 bp):
ATTCTCATGGGCAAATGAATCGGCTCAAATGGAAAATTAGTGGCCAAGACCACAA
Found at i:30897214 original size:6 final size:6
Alignment explanation
Indices: 30897205--30897232 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
30897195 AAAAAAAAAT
30897205 AGCAAA AGCAAA AGCAAA AGCAAA AGCA
1 AGCAAA AGCAAA AGCAAA AGCAAA AGCA
30897233 CCACTTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.64, C:0.18, G:0.18, T:0.00
Consensus pattern (6 bp):
AGCAAA
Found at i:30897426 original size:16 final size:16
Alignment explanation
Indices: 30897405--30897436 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
30897395 TTCATTACAA
30897405 CCGGGTTTAGTTTAGT
1 CCGGGTTTAGTTTAGT
30897421 CCGGGTTTAGTTTAGT
1 CCGGGTTTAGTTTAGT
30897437 TGGTTCATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.31, T:0.44
Consensus pattern (16 bp):
CCGGGTTTAGTTTAGT
Found at i:30904666 original size:27 final size:27
Alignment explanation
Indices: 30904647--30904746 Score: 112
Period size: 27 Copynumber: 3.6 Consensus size: 27
30904637 ATATATTAAG
*
30904647 TCCGCACACTCAGTGCTATATAATCAA
1 TCCGCACACTTAGTGCTATATAATCAA
30904674 -CTCGCACACTTAGTGCTATATAATCAA
1 TC-CGCACACTTAGTGCTATATAATCAA
* * *
30904701 ACTCGCACACTTAGTGCTATACAATTTGAA
1 TC-CGCACACTTAGTGCTATATAA--TCAA
*
30904731 CCCGCACACTTAGTGC
1 TCCGCACACTTAGTGC
30904747 CAATCTCATG
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
26 1 0.02
27 24 0.37
28 22 0.34
29 14 0.22
30 4 0.06
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
TCCGCACACTTAGTGCTATATAATCAA
Found at i:30904712 original size:28 final size:27
Alignment explanation
Indices: 30904649--30904746 Score: 133
Period size: 28 Copynumber: 3.5 Consensus size: 27
30904639 ATATTAAGTC
*
30904649 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
30904676 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
* * *
30904704 CGCACACTTAGTGCTATACAATTTGAACC
1 CGCACACTTAGTGCTATATAA--TCAACT
30904733 CGCACACTTAGTGC
1 CGCACACTTAGTGC
30904747 CAATCTCATG
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
27 22 0.34
28 24 0.38
29 17 0.27
30 1 0.02
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:30913371 original size:47 final size:47
Alignment explanation
Indices: 30913303--30913520 Score: 218
Period size: 47 Copynumber: 4.6 Consensus size: 47
30913293 TTTGTGTGCT
30913303 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG-CACATTATGAGAGCC
* * * *
30913349 AGTGTAAGACCATGTCTGGGACAT-GCATCGACTACATGAT--GTGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-ACATTATGAGAGCC
* * * * *
30913394 AGTGTAAGACCATTTTTGGGACATGGCATCAGCACGGATACATGAGAGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAC--AT-TATGAGAGCC
*
30913444 AGTGTAAGACCATGTCTGAGACATGGCATC-G-AC-TTAACGTGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACATT-A--TGAGAGCC
30913491 AGTGTAAGACCATGTCTGGGACATGGCATC
1 AGTGTAAGACCATGTCTGGGACATGGCATC
30913521 AGCATTATAC
Statistics
Matches: 145, Mismatches: 16, Indels: 21
0.80 0.09 0.12
Matches are distributed among these distances:
45 29 0.20
46 16 0.11
47 64 0.44
48 4 0.03
49 1 0.01
50 31 0.21
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.23
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCACATTATGAGAGCC
Found at i:30913524 original size:97 final size:92
Alignment explanation
Indices: 30913303--30913524 Score: 279
Period size: 97 Copynumber: 2.4 Consensus size: 92
30913293 TTTGTGTGCT
* *
30913303 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACATTATGAGAGCCAGTGTAAGACCATGTCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAG-CACATCATGAGAGCCAGTGTAAGACCATGTCT
* * *
30913366 GGGACATGCATCGACTACATGATGTGTC
65 GAGACATGCATCGACTACATGATGAGCC
* * *
30913394 AGTGTAAGACCATTTTTGGGACATGGCATCAGCACGGATACATGAGAGTCAGTGTAAGACCATGT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCAC--AT-CATGAGAGCCAGTGTAAGACCATGT
*
30913459 CTGAGACATGGCATCGACTTAACGTGA-GAGCC
63 CTGAGACAT-GCATCGAC-T-ACATGATGAGCC
30913491 AGTGTAAGACCATGTCTGGGACATGGCATCAGCA
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCA
30913525 TTATACCCTA
Statistics
Matches: 112, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
91 9 0.08
92 15 0.13
93 6 0.05
94 2 0.02
95 31 0.28
96 8 0.07
97 36 0.32
98 5 0.04
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (92 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCAGCACATCATGAGAGCCAGTGTAAGACCATGTCTG
AGACATGCATCGACTACATGATGAGCC
Found at i:30916131 original size:2 final size:2
Alignment explanation
Indices: 30916124--30916148 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30916114 CACAAACGTG
30916124 CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA C
30916149 TCTATCTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:30918044 original size:47 final size:47
Alignment explanation
Indices: 30917979--30918196 Score: 218
Period size: 47 Copynumber: 4.6 Consensus size: 47
30917969 TTTGTGTGCT
30917979 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG-CACATTATGAGAGCC
* * * *
30918025 AGTGTAAGACCATGTCTGGGACAT-GCATCGACTACATGAT--GTGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-ACATTATGAGAGCC
* * * * *
30918070 AGTGTAAGACCATTTTTGGGACATGGCATCAGCACGGATACATGAGAGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAC--AT-TATGAGAGCC
*
30918120 AGTGTAAGACCATGTCTGAGACATGGCATC-G-AC-TTAACGTGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACATT-A--TGAGAGCC
30918167 AGTGTAAGACCATGTCTGGGACATGGCATC
1 AGTGTAAGACCATGTCTGGGACATGGCATC
30918197 AGCATTATAC
Statistics
Matches: 145, Mismatches: 16, Indels: 21
0.80 0.09 0.12
Matches are distributed among these distances:
45 29 0.20
46 16 0.11
47 64 0.44
48 4 0.03
49 1 0.01
50 31 0.21
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.23
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCACATTATGAGAGCC
Found at i:30918200 original size:97 final size:92
Alignment explanation
Indices: 30917979--30918200 Score: 279
Period size: 97 Copynumber: 2.4 Consensus size: 92
30917969 TTTGTGTGCT
* *
30917979 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACATTATGAGAGCCAGTGTAAGACCATGTCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAG-CACATCATGAGAGCCAGTGTAAGACCATGTCT
* * *
30918042 GGGACATGCATCGACTACATGATGTGTC
65 GAGACATGCATCGACTACATGATGAGCC
* * *
30918070 AGTGTAAGACCATTTTTGGGACATGGCATCAGCACGGATACATGAGAGTCAGTGTAAGACCATGT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCAC--AT-CATGAGAGCCAGTGTAAGACCATGT
*
30918135 CTGAGACATGGCATCGACTTAACGTGA-GAGCC
63 CTGAGACAT-GCATCGAC-T-ACATGATGAGCC
30918167 AGTGTAAGACCATGTCTGGGACATGGCATCAGCA
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCA
30918201 TTATACCCTA
Statistics
Matches: 112, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
91 9 0.08
92 15 0.13
93 6 0.05
94 2 0.02
95 31 0.28
96 8 0.07
97 36 0.32
98 5 0.04
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (92 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCAGCACATCATGAGAGCCAGTGTAAGACCATGTCTG
AGACATGCATCGACTACATGATGAGCC
Found at i:30920828 original size:2 final size:2
Alignment explanation
Indices: 30920823--30920894 Score: 63
Period size: 2 Copynumber: 36.0 Consensus size: 2
30920813 CACACACACA
* * * * * * *
30920823 CT CT CT CT CT CT CT CT CT CT CT CA CT CA CT CA CT CA CA CA CA
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* *
30920865 CA CT CT CT CT CT CT CT CT CC CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
30920895 TCTTGACGAC
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.11, C:0.51, G:0.00, T:0.38
Consensus pattern (2 bp):
CT
Found at i:30923129 original size:70 final size:70
Alignment explanation
Indices: 30923016--30923155 Score: 244
Period size: 70 Copynumber: 2.0 Consensus size: 70
30923006 GGAATTGGAA
* *
30923016 AGTTTTTTAGGCATTTCTTTTTCAATTTCGGCCTAAAATGCCATAGGAGAGAGAGCTTAAGCTGG
1 AGTTTTTTAGGCATTTCTTCTTCAATTTCGGCCTAAAACGCCATAGGAGAGAGAGCTTAAGCTGG
30923081 TTTTT
66 TTTTT
* *
30923086 AGTTTTTTAGGTATTTGTTCTTCAATTTCGGCCTAAAACGCCATAGGAGAGAGAGCTTAAGCTGG
1 AGTTTTTTAGGCATTTCTTCTTCAATTTCGGCCTAAAACGCCATAGGAGAGAGAGCTTAAGCTGG
30923151 TTTTT
66 TTTTT
30923156 CATATTTTTG
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 66 1.00
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.39
Consensus pattern (70 bp):
AGTTTTTTAGGCATTTCTTCTTCAATTTCGGCCTAAAACGCCATAGGAGAGAGAGCTTAAGCTGG
TTTTT
Found at i:30924017 original size:21 final size:21
Alignment explanation
Indices: 30923991--30924057 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 21
30923981 ATTAGGTGAA
* *
30923991 TTAGCTCTTAGAAGCTTTTAT
1 TTAGCTCTTACAAGCTTCTAT
30924012 TTAGCTCTTACAAGCTTCTAT
1 TTAGCTCTTACAAGCTTCTAT
* * *
30924033 TTTGCT-TT-CGAGCTTCTGT
1 TTAGCTCTTACAAGCTTCTAT
30924052 TTAGCT
1 TTAGCT
30924058 TTCGAGCTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
19 14 0.35
20 2 0.05
21 24 0.60
ACGTcount: A:0.18, C:0.19, G:0.15, T:0.48
Consensus pattern (21 bp):
TTAGCTCTTACAAGCTTCTAT
Found at i:30924048 original size:19 final size:19
Alignment explanation
Indices: 30924003--30924068 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
30923993 AGCTCTTAGA
* *
30924003 AGCTTTTATTTAGCTCTTACA
1 AGCTTCTATTTAGCT-TT-CG
*
30924024 AGCTTCTATTTTGCTTTCG
1 AGCTTCTATTTAGCTTTCG
*
30924043 AGCTTCTGTTTAGCTTTCG
1 AGCTTCTATTTAGCTTTCG
30924062 AGCTTCT
1 AGCTTCT
30924069 GTTGATGTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
19 25 0.62
20 2 0.05
21 13 0.32
ACGTcount: A:0.15, C:0.21, G:0.15, T:0.48
Consensus pattern (19 bp):
AGCTTCTATTTAGCTTTCG
Found at i:30927437 original size:25 final size:25
Alignment explanation
Indices: 30927409--30927465 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
30927399 CAACTCATAT
*
30927409 GAGCTTACCT-TTATTCA-TTTCGAAA
1 GAGCTTA-CTGTTATTCAGATT-GAAA
*
30927434 GAGCTTATTGTTATTCAGATTGAAA
1 GAGCTTACTGTTATTCAGATTGAAA
30927459 GAGCTTA
1 GAGCTTA
30927466 TCGTTTAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 1 0.04
25 25 0.89
26 2 0.07
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (25 bp):
GAGCTTACTGTTATTCAGATTGAAA
Found at i:30932657 original size:40 final size:41
Alignment explanation
Indices: 30932597--30932690 Score: 122
Period size: 40 Copynumber: 2.3 Consensus size: 41
30932587 GTCGATATCA
* *
30932597 CACACTTAGTGCC-TTATATAGCCGGAGCTAT-CCCAACTCG
1 CACACTTAGTGCCATTATATAGCCGAAGCTATACCAAAC-CG
**
30932637 CACACTTAGTGCCATT-TATAGCCGAAGCTATATTAAACCG
1 CACACTTAGTGCCATTATATAGCCGAAGCTATACCAAACCG
30932677 CACACTTAGTGCCA
1 CACACTTAGTGCCA
30932691 AGCATAATCA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
40 43 0.90
41 5 0.10
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.26
Consensus pattern (41 bp):
CACACTTAGTGCCATTATATAGCCGAAGCTATACCAAACCG
Found at i:30936442 original size:25 final size:25
Alignment explanation
Indices: 30936384--30936444 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
30936374 AGCTTGTATA
* *
30936384 AGCTTGCCATTATTCAACTCAGAGG
1 AGCTTACCGTTATTCAACTCAGAGG
*
30936409 AGCTTACCGTTATTCAGCTCAGAGG
1 AGCTTACCGTTATTCAACTCAGAGG
30936434 AGCTTACCGTT
1 AGCTTACCGTT
30936445 TACAGCTTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (25 bp):
AGCTTACCGTTATTCAACTCAGAGG
Found at i:30940141 original size:46 final size:46
Alignment explanation
Indices: 30940004--30940142 Score: 224
Period size: 46 Copynumber: 3.0 Consensus size: 46
30939994 GTTTGGGCAT
* * * * *
30940004 CCGAACTCGCTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGC
30940050 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGC
*
30940096 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGC
30940142 C
1 C
30940143 GGTAGCTTGG
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 87 1.00
ACGTcount: A:0.21, C:0.24, G:0.29, T:0.26
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGC
Found at i:30956653 original size:126 final size:126
Alignment explanation
Indices: 30956428--30956683 Score: 458
Period size: 126 Copynumber: 2.0 Consensus size: 126
30956418 ATCATTATAC
30956428 ATCTTTGTACTACCTGGATGAATAGACAAAGAACTACTATGTGCTTCCGGTAAGATCTTTCGAAT
1 ATCTTTGTACTACCTGGATGAATAGACAAAGAACTACTATGTGCTTCCGGTAAGATCTTTCGAAT
30956493 AAGCTCATCATTCTTCGGTACGCATACCCTATCTCTAAACATCAAACAACCGTCAGAACTG
66 AAGCTCATCATTCTTCGGTACGCATACCCTATCTCTAAACATCAAACAACCGTCAGAACTG
* * *
30956554 ATCTTTGTACTACCTTGATGAATAGACAAAGTACTACTATGTGCTTCCTGTAAGATCTTTCGAAT
1 ATCTTTGTACTACCTGGATGAATAGACAAAGAACTACTATGTGCTTCCGGTAAGATCTTTCGAAT
* * *
30956619 AAGCTTATCATTCTTCGGTACGCATACCCTATCTCTGAACATCAAACAACCGTCAGGACTG
66 AAGCTCATCATTCTTCGGTACGCATACCCTATCTCTAAACATCAAACAACCGTCAGAACTG
30956680 ATCT
1 ATCT
30956684 GAAACTCTGA
Statistics
Matches: 124, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
126 124 1.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (126 bp):
ATCTTTGTACTACCTGGATGAATAGACAAAGAACTACTATGTGCTTCCGGTAAGATCTTTCGAAT
AAGCTCATCATTCTTCGGTACGCATACCCTATCTCTAAACATCAAACAACCGTCAGAACTG
Found at i:30961232 original size:16 final size:16
Alignment explanation
Indices: 30961213--30961243 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30961203 CTTCTTCACT
30961213 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
30961229 TACTTACTTACTTAA
1 TACTCACTTACTTAA
30961244 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:30961249 original size:20 final size:20
Alignment explanation
Indices: 30961210--30961249 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
30961200 AAACTTCTTC
* *
30961210 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
30961230 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
30961250 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Done.