Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 47 of 230
Found at i:12603057 original size:9 final size:9
Alignment explanation
Indices: 12603043--12603073 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
12603033 GTTAAACGAA
12603043 TCGAGTTAT
1 TCGAGTTAT
*
12603052 TCGAGTTAA
1 TCGAGTTAT
12603061 TCGAGTTAT
1 TCGAGTTAT
12603070 TCGA
1 TCGA
12603074 ATCAACTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:12603236 original size:30 final size:31
Alignment explanation
Indices: 12603202--12603262 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
12603192 AAACTTTTTT
* *
12603202 ACTTTTCCCTAAAAACTTTTACCCCT-TCCC
1 ACTTTCCCCCAAAAACTTTTACCCCTCTCCC
* *
12603232 ACTTTCCCCCCAAAACTTTTACTCCTCTCCC
1 ACTTTCCCCCAAAAACTTTTACCCCTCTCCC
12603263 CTCCCAACCC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.21, C:0.44, G:0.00, T:0.34
Consensus pattern (31 bp):
ACTTTCCCCCAAAAACTTTTACCCCTCTCCC
Found at i:12603549 original size:21 final size:21
Alignment explanation
Indices: 12603520--12603559 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
12603510 TCCCTCAAAC
12603520 TTTTATTCCCCAAAACTTTTTA
1 TTTTATT-CCCAAAACTTTTTA
*
12603542 TTTT-TTCCCTAAACTTTT
1 TTTTATTCCCAAAACTTTT
12603560 ACTTCCCACC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTATTCCCAAAACTTTTTA
Found at i:12611729 original size:10 final size:10
Alignment explanation
Indices: 12611714--12611744 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
12611704 CACATATTTT
12611714 AATAATTTAA
1 AATAATTTAA
12611724 AATAATTT-A
1 AATAATTTAA
12611733 AATAATTTAA
1 AATAATTTAA
12611743 AA
1 AA
12611745 AACTTCTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
AATAATTTAA
Found at i:12611735 original size:9 final size:9
Alignment explanation
Indices: 12611709--12611743 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
12611699 AAATTCACAT
*
12611709 ATTTTAATA
1 ATTTAAATA
12611718 ATTTAAAATA
1 ATTT-AAATA
12611728 ATTTAAATA
1 ATTTAAATA
12611737 ATTTAAA
1 ATTTAAA
12611744 AAACTTCTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
ATTTAAATA
Found at i:12611880 original size:21 final size:21
Alignment explanation
Indices: 12611856--12611908 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
12611846 CATTGTTTCT
* *
12611856 AATCTCACTGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
12611877 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
12611898 AATCTCACCGC
1 AATCTCACCGC
12611909 CACCGCTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.36, G:0.09, T:0.25
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:12612608 original size:14 final size:15
Alignment explanation
Indices: 12612578--12612611 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
12612568 TTAACATGGC
*
12612578 AATTTGGAACCTTTG
1 AATTTGGAACATTTG
12612593 AATTTGGAA-ATTTG
1 AATTTGGAACATTTG
12612607 AATTT
1 AATTT
12612612 TAAAAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (15 bp):
AATTTGGAACATTTG
Found at i:12613120 original size:21 final size:22
Alignment explanation
Indices: 12613080--12613121 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
12613070 TTTTGAATTA
*
12613080 ATTCAAATTTAATGTTTGGATG
1 ATTCAAATTTAATATTTGGATG
12613102 ATTCAAATTTAA-ATTTGGAT
1 ATTCAAATTTAATATTTGGAT
12613122 TTTATCTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (22 bp):
ATTCAAATTTAATATTTGGATG
Found at i:12614625 original size:21 final size:21
Alignment explanation
Indices: 12614599--12614639 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
12614589 GACAAGTAAC
12614599 AGATCAGACAAATCGTATCAT
1 AGATCAGACAAATCGTATCAT
* *
12614620 AGATCATACATATCGTATCA
1 AGATCAGACAAATCGTATCA
12614640 CGCTACATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (21 bp):
AGATCAGACAAATCGTATCAT
Found at i:12616063 original size:22 final size:22
Alignment explanation
Indices: 12616038--12616107 Score: 88
Period size: 22 Copynumber: 3.2 Consensus size: 22
12616028 AAATTCAATA
12616038 TCAATTTCTTTCAAAAATTCTC
1 TCAATTTCTTTCAAAAATTCTC
* *
12616060 TCAATTCCTTTCAAAATTTC-C
1 TCAATTTCTTTCAAAAATTCTC
* *
12616081 ATCAATTTCCTTCCAAAATTCTC
1 -TCAATTTCTTTCAAAAATTCTC
12616104 TCAA
1 TCAA
12616108 ACTCTCAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
21 1 0.03
22 38 0.95
23 1 0.03
ACGTcount: A:0.31, C:0.27, G:0.00, T:0.41
Consensus pattern (22 bp):
TCAATTTCTTTCAAAAATTCTC
Found at i:12616140 original size:52 final size:50
Alignment explanation
Indices: 12616057--12616159 Score: 127
Period size: 52 Copynumber: 2.0 Consensus size: 50
12616047 TTCAAAAATT
* * *
12616057 CTCTCAATTCCTTTCAAAATTTCCATCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAATTCCTTCCAAAA-TTCCATCAATTTCCTTCAAAAAATCTC-CAAA
*
12616109 CTCTCAAATTCCTTCCAAAA-TCCTCTCAATTTCCTTCAAAAAATCTCCAAA
1 CTCTC-AATTCCTTCCAAAATTCC-ATCAATTTCCTTCAAAAAATCTCCAAA
12616160 TCCATATTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
51 7 0.16
52 25 0.56
53 13 0.29
ACGTcount: A:0.33, C:0.32, G:0.00, T:0.35
Consensus pattern (50 bp):
CTCTCAATTCCTTCCAAAATTCCATCAATTTCCTTCAAAAAATCTCCAAA
Found at i:12616148 original size:21 final size:22
Alignment explanation
Indices: 12616109--12616150 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
12616099 TTCTCTCAAA
12616109 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
12616131 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
12616151 ATCTCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:12616255 original size:29 final size:30
Alignment explanation
Indices: 12616192--12616255 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 30
12616182 ATTAAATTTC
*
12616192 ATTTTTTAAGAAAATTTTAAAATTTTTTAT
1 ATTTTTTAAGAAAATTTTAAAATTTTTAAT
* *
12616222 TTTTTTTAA-ATAATTTTAAAATTTTTAAT
1 ATTTTTTAAGAAAATTTTAAAATTTTTAAT
12616251 ATTTT
1 ATTTT
12616256 CAACAATGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 22 0.73
30 8 0.27
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (30 bp):
ATTTTTTAAGAAAATTTTAAAATTTTTAAT
Found at i:12620161 original size:125 final size:124
Alignment explanation
Indices: 12619932--12620163 Score: 333
Period size: 125 Copynumber: 1.9 Consensus size: 124
12619922 GTTTGCTCAG
* *
12619932 AAACGTCAAAAAAATTATTTCCTACATGACCAACTGTAGCGAAATCGAGTCCACGAGGGCGCTAT
1 AAACGTCAAAAAAATTATTTCCTACATGACCAACTGTAGCGAAATCGAGTCCACGAGGCCACTAT
* * **
12619997 TTCACAATTTCTTCTCATATAGCATCCTGGTATCAGCGATTTTATACTATTTCCTCATA
66 TTCACAATTTCTTCTCAAATAGCATCCTAGTAGAAGCGATTTTATACTATTTCCTCATA
* *
12620056 AAACGTCAAAAAAAAATTATTT-CTCACATTACC-ACTGTAGCGAAATCGCGTCCACGAGGCCAC
1 AAACGTC--AAAAAAATTATTTCCT-ACATGACCAACTGTAGCGAAATCGAGTCCACGAGGCCAC
* *
12620119 TATTTTACAATTTCTTCTTAAATAGCATCCTAGTAGAAGCGATTT
63 TATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAAGCGATTT
12620164 CCCACTATTT
Statistics
Matches: 95, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
124 7 0.07
125 68 0.72
126 20 0.21
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (124 bp):
AAACGTCAAAAAAATTATTTCCTACATGACCAACTGTAGCGAAATCGAGTCCACGAGGCCACTAT
TTCACAATTTCTTCTCAAATAGCATCCTAGTAGAAGCGATTTTATACTATTTCCTCATA
Found at i:12620196 original size:125 final size:123
Alignment explanation
Indices: 12619909--12620188 Score: 332
Period size: 125 Copynumber: 2.3 Consensus size: 123
12619899 CCACGAGGGC
* * *
12619909 GCGATTTGACACTGTTTGCTCAGAAACGTCAAAAAAATTATTTCCTACATGACCAACTGTAGCGA
1 GCGATTTCACACTATTTACTCAGAAACGTCAAAAAAATTATTTCCTACATGACCAACTGTAGCGA
* * * * **
12619974 AATCGAGTCCACGAGGGCGCTATTTCACAATTTCTTCTCATATAGCATCCTGGTATCA
66 AATCGAGTCCACGAGGCCACTATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
* * * * *
12620032 GCGATTTTATACTATTTCCTCATAAAACGTCAAAAAAAAATTATTT-CTCACATTACC-ACTGTA
1 GCGATTTCACACTATTTACTCA-GAAACGTC--AAAAAAATTATTTCCT-ACATGACCAACTGTA
* * *
12620095 GCGAAATCGCGTCCACGAGGCCACTATTTTACAATTTCTTCTTAAATAGCATCCTAGTAGAA
62 GCGAAATCGAGTCCACGAGGCCACTATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
*
12620157 GCGATTTCCCACTATTTAAC-CAGAAACGTCAA
1 GCGATTTCACACTATTT-ACTCAGAAACGTCAA
12620189 CTCAAAAAAA
Statistics
Matches: 132, Mismatches: 20, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
122 2 0.02
123 18 0.14
124 14 0.11
125 77 0.58
126 21 0.16
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.30
Consensus pattern (123 bp):
GCGATTTCACACTATTTACTCAGAAACGTCAAAAAAATTATTTCCTACATGACCAACTGTAGCGA
AATCGAGTCCACGAGGCCACTATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
Found at i:12622238 original size:21 final size:22
Alignment explanation
Indices: 12622205--12622246 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
12622195 GAAACCAACA
*
12622205 AGTTTGTACGCAA-AAATTAGC
1 AGTTTATACGCAATAAATTAGC
*
12622226 AGTTTATATGCAATAAATTAG
1 AGTTTATACGCAATAAATTAG
12622247 TAAAAATCAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (22 bp):
AGTTTATACGCAATAAATTAGC
Found at i:12634431 original size:22 final size:22
Alignment explanation
Indices: 12634406--12634497 Score: 89
Period size: 22 Copynumber: 4.1 Consensus size: 22
12634396 TGCAAAAAGA
* *
12634406 TTTGCTGCTATTTTTTTATTAT
1 TTTGCTACTATTTTATTATTAT
* *
12634428 TTTGCCACTATTCTT-TTCATTGT
1 TTTGCTACTATT-TTATT-ATTAT
*
12634451 TTTGCTA-TCATTTTACTATTAT
1 TTTGCTACT-ATTTTATTATTAT
*
12634473 ATTGCTACTATTTTATTATTAT
1 TTTGCTACTATTTTATTATTAT
12634495 TTT
1 TTT
12634498 TTGAATATTC
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
22 39 0.70
23 17 0.30
ACGTcount: A:0.18, C:0.13, G:0.07, T:0.62
Consensus pattern (22 bp):
TTTGCTACTATTTTATTATTAT
Found at i:12635897 original size:19 final size:19
Alignment explanation
Indices: 12635837--12635898 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
12635827 ACGGATTGAC
12635837 AATTTGAGCTACAATATTAT
1 AATTTGAGCTAC-ATATTAT
* *
12635857 GAATATT-AACTACA-ATACAT
1 -AAT-TTGAGCTACATAT-TAT
12635877 AATTTGAGCTACATATTAT
1 AATTTGAGCTACATATTAT
12635896 AAT
1 AAT
12635899 AATACATTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
18 2 0.06
19 16 0.48
20 5 0.15
21 8 0.24
22 2 0.06
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.37
Consensus pattern (19 bp):
AATTTGAGCTACATATTAT
Found at i:12635948 original size:20 final size:20
Alignment explanation
Indices: 12635920--12635961 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
12635910 ATGTATTATT
* *
12635920 AGGGGCAAAATACCAAAAAA
1 AGGGACAAAATACAAAAAAA
*
12635940 AGGGACAAATTACAAAAAAA
1 AGGGACAAAATACAAAAAAA
12635960 AG
1 AG
12635962 CCCTATTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.62, C:0.12, G:0.19, T:0.07
Consensus pattern (20 bp):
AGGGACAAAATACAAAAAAA
Found at i:12649769 original size:22 final size:22
Alignment explanation
Indices: 12649737--12649790 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
12649727 TCCAAAAACA
*
12649737 TAAAATTACTAAAAACAGAAGC
1 TAAAATCACTAAAAACAGAAGC
12649759 TAAAATCACTAAAAACAGAAGC
1 TAAAATCACTAAAAACAGAAGC
12649781 TAAAATCACT
1 TAAAATCACT
12649791 TACATGCATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.57, C:0.17, G:0.07, T:0.19
Consensus pattern (22 bp):
TAAAATCACTAAAAACAGAAGC
Found at i:12654998 original size:62 final size:57
Alignment explanation
Indices: 12654922--12655069 Score: 190
Period size: 57 Copynumber: 2.5 Consensus size: 57
12654912 AATTGACGGT
12654922 AAAAAGGATCTAGCCCGGACGGGTGATCCTATCCTGATATAGCCCTCCCGAAGAATATGTGTG
1 AAAAA-GATCTAGCCCGGACGGGTGATCC--T--TGATATAGCCCTCCCGAAGAATATGTG-G
*
12654985 AAAAAGATCTAGCCCGGACGAGTGAT-CTTGATATAGCCCTCCCGAAGAATATGTGG
1 AAAAAGATCTAGCCCGGACGGGTGATCCTTGATATAGCCCTCCCGAAGAATATGTGG
* * *
12655041 AAAATGGATTTAGCCCGGACGGGTAATCC
1 AAAA-AGATCTAGCCCGGACGGGTGATCC
12655070 GAATTAGGGT
Statistics
Matches: 78, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
56 5 0.06
57 45 0.58
58 1 0.01
59 1 0.01
61 1 0.01
62 20 0.26
63 5 0.06
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (57 bp):
AAAAAGATCTAGCCCGGACGGGTGATCCTTGATATAGCCCTCCCGAAGAATATGTGG
Found at i:12663365 original size:13 final size:13
Alignment explanation
Indices: 12663347--12663376 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
12663337 AGCCCAAACT
12663347 CAATTACCCAACC
1 CAATTACCCAACC
12663360 CAATTACCCAACC
1 CAATTACCCAACC
12663373 CAAT
1 CAAT
12663377 AAAACTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (13 bp):
CAATTACCCAACC
Found at i:12663532 original size:9 final size:9
Alignment explanation
Indices: 12663520--12663576 Score: 71
Period size: 9 Copynumber: 6.2 Consensus size: 9
12663510 ATAAAAAAAT
12663520 TTCGGGTAA
1 TTCGGGTAA
*
12663529 TTCGGGTATTT
1 TTCGGGTA--A
12663540 TTC-GGTAA
1 TTCGGGTAA
*
12663548 TTCGGTTAA
1 TTCGGGTAA
12663557 TTCGGGTAA
1 TTCGGGTAA
12663566 TTCGGGTAA
1 TTCGGGTAA
12663575 TT
1 TT
12663577 TTTAACCAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
8 3 0.07
9 31 0.76
10 4 0.10
11 3 0.07
ACGTcount: A:0.19, C:0.11, G:0.28, T:0.42
Consensus pattern (9 bp):
TTCGGGTAA
Found at i:12666314 original size:42 final size:43
Alignment explanation
Indices: 12666211--12666370 Score: 134
Period size: 43 Copynumber: 3.7 Consensus size: 43
12666201 ATATGAGTTA
* * * *
12666211 TCGTGTAAGACCATATCTGGGAC-GTTGGCGTCGATTTGA-GATT
1 TCGTGTAAGACCCTGTCTGGGACAG-TGGCATCGATAT-ACGATT
* *
12666254 TACGTATAAGACCATGTCTGGGACA-TCGGCATCG-TATACGATT
1 T-CGTGTAAGACCCTGTCTGGGACAGT-GGCATCGATATACGATT
**
12666297 TCGTGTAAGACCCTGTCTGGGACAGTGGCATCGATATTTGATT
1 TCGTGTAAGACCCTGTCTGGGACAGTGGCATCGATATACGATT
* *
12666340 ACATGTAAGACCAC-GTCTGGGAC-GTTGGCAT
1 TCGTGTAAGACC-CTGTCTGGGACAG-TGGCAT
12666371 TGTAAGAGCT
Statistics
Matches: 99, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
42 30 0.30
43 42 0.42
44 27 0.27
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (43 bp):
TCGTGTAAGACCCTGTCTGGGACAGTGGCATCGATATACGATT
Found at i:12669365 original size:26 final size:26
Alignment explanation
Indices: 12669335--12669402 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
12669325 CACCATCAAT
*
12669335 TCATA-AACATATATAGATATCAAATA
1 TCATATAACATA-ATACATATCAAATA
* *
12669361 TCATATAACATAATTCATATCACATA
1 TCATATAACATAATACATATCAAATA
*
12669387 TCATATATCAATAATA
1 TCATATAAC-ATAATA
12669403 TCACACTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 24 0.69
27 11 0.31
ACGTcount: A:0.50, C:0.15, G:0.01, T:0.34
Consensus pattern (26 bp):
TCATATAACATAATACATATCAAATA
Found at i:12671348 original size:4 final size:4
Alignment explanation
Indices: 12671334--12671383 Score: 50
Period size: 4 Copynumber: 12.8 Consensus size: 4
12671324 GATGGAATAA
* * *
12671334 AAAT AAAAT AAAT AAAT AAAT -AA- AAAT AAAC AAAG AAAT AAAT CAAT
1 AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
12671381 AAA
1 AAA
12671384 CCAATCAGGA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
3 4 0.11
4 30 0.79
5 4 0.11
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (4 bp):
AAAT
Found at i:12671361 original size:18 final size:18
Alignment explanation
Indices: 12671334--12671375 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
12671324 GATGGAATAA
* *
12671334 AAAT-AAAATAAATAAAT
1 AAATAAAAATAAACAAAG
12671351 AAATAAAAATAAACAAAG
1 AAATAAAAATAAACAAAG
12671369 AAATAAA
1 AAATAAA
12671376 TCAATAAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (18 bp):
AAATAAAAATAAACAAAG
Found at i:12689586 original size:14 final size:14
Alignment explanation
Indices: 12689554--12689587 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
12689544 CCATTAGTAA
12689554 AATA-TCATATTTT
1 AATATTCATATTTT
12689567 ATATATTCATATTTT
1 A-ATATTCATATTTT
12689582 AATATT
1 AATATT
12689588 TTGAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.05
14 8 0.42
15 10 0.53
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (14 bp):
AATATTCATATTTT
Found at i:12692905 original size:2 final size:2
Alignment explanation
Indices: 12692898--12692922 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12692888 CTAAAAACTA
12692898 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
12692923 AATAAGTAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12693247 original size:42 final size:41
Alignment explanation
Indices: 12693167--12693268 Score: 93
Period size: 42 Copynumber: 2.4 Consensus size: 41
12693157 CATTAAACTT
12693167 TTTTATTTTTAATTTTT-TTTGAAATTTTAACTAAATTTGTTAA
1 TTTTATTTTT-ATTTTTATTTGAAATTTTAACTAAATTTG--AA
** *
12693210 TTTTATTTTTATTTTTATTTTCAA-TTTATA-TATATTTGAA
1 TTTTATTTTTATTTTTATTTGAAATTTTA-ACTAAATTTGAA
*
12693250 TTTTTTTCTTATATTTTTA
1 TTTTATT-TT-TATTTTTA
12693269 ACAAATTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
40 8 0.16
41 2 0.04
42 25 0.49
43 16 0.31
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (41 bp):
TTTTATTTTTATTTTTATTTGAAATTTTAACTAAATTTGAA
Found at i:12696486 original size:24 final size:24
Alignment explanation
Indices: 12696459--12696505 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
12696449 TATCACAATT
* *
12696459 ATAATATAA-TATAATATAAATATC
1 ATAA-ATAATTATAAAACAAATATC
12696483 ATAAATAATTATAAAACAAATAT
1 ATAAATAATTATAAAACAAATAT
12696506 AAAAAGATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (24 bp):
ATAAATAATTATAAAACAAATATC
Found at i:12697474 original size:31 final size:30
Alignment explanation
Indices: 12697439--12697541 Score: 93
Period size: 31 Copynumber: 3.4 Consensus size: 30
12697429 TAATCATATT
12697439 AATATTAAATTAATAAAATAATATCTAGATA
1 AATATTAAATT-ATAAAATAATATCTAGATA
** * *
12697470 AATATTAAATTA-AATTTCATATCTCATG-TT
1 AATATTAAATTATAAAATAATATCT-A-GATA
* * *
12697500 AATATTCAATTGATAAAATACTATTTAGATA
1 AATATTAAATT-ATAAAATAATATCTAGATA
12697531 AATATTAAATT
1 AATATTAAATT
12697542 TAATTTAATT
Statistics
Matches: 55, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
29 9 0.16
30 14 0.25
31 25 0.45
32 7 0.13
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.41
Consensus pattern (30 bp):
AATATTAAATTATAAAATAATATCTAGATA
Found at i:12697518 original size:61 final size:61
Alignment explanation
Indices: 12697432--12697547 Score: 178
Period size: 61 Copynumber: 1.9 Consensus size: 61
12697422 TTAGAATTAA
12697432 TCATATTAATATTAAATTAATAAAATAATATCTAGATAAATATTAAATTAAATTTCATATC
1 TCATATTAATATTAAATTAATAAAATAATATCTAGATAAATATTAAATTAAATTTCATATC
* * * * * *
12697493 TCATGTTAATATTCAATTGATAAAATACTATTTAGATAAATATTAAATTTAATTT
1 TCATATTAATATTAAATTAATAAAATAATATCTAGATAAATATTAAATTAAATTT
12697548 AATTTTAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.43
Consensus pattern (61 bp):
TCATATTAATATTAAATTAATAAAATAATATCTAGATAAATATTAAATTAAATTTCATATC
Found at i:12698802 original size:3 final size:3
Alignment explanation
Indices: 12698794--12698831 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
12698784 GAGTATTAAA
12698794 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
12698832 CATCATCATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:12699276 original size:23 final size:23
Alignment explanation
Indices: 12699250--12699293 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
12699240 TAAATATTAT
*
12699250 TTTATTAATGTTTTACTTAGATA
1 TTTATTAATATTTTACTTAGATA
* *
12699273 TTTATTATTATTTTATTTAGA
1 TTTATTAATATTTTACTTAGA
12699294 AAATGGTAGT
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:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (23 bp):
TTTATTAATATTTTACTTAGATA
Found at i:12707055 original size:21 final size:22
Alignment explanation
Indices: 12707031--12707075 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
12707021 AGAAAAAGAG
12707031 AAATACAAAAAAG-AATAG-ATC
1 AAAT-CAAAAAAGAAATAGAATC
*
12707052 AAATCAAAAAGGAAATAGAATC
1 AAATCAAAAAAGAAATAGAATC
12707074 AA
1 AA
12707076 CAATTTGCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 9 0.43
22 5 0.24
ACGTcount: A:0.67, C:0.09, G:0.11, T:0.13
Consensus pattern (22 bp):
AAATCAAAAAAGAAATAGAATC
Found at i:12709961 original size:35 final size:32
Alignment explanation
Indices: 12709884--12710104 Score: 271
Period size: 35 Copynumber: 6.6 Consensus size: 32
12709874 AAATAATACA
* *
12709884 TGAACAGGAGAGATTCCCTGCAAGAAATGATG
1 TGAACAGGAGAGATTCCCTGCAAAAAATAATG
12709916 TGAACAGGAGAGATTCCCTGCAACAAAATAATCCG
1 TGAACAGGAGAGATTCCCTGCAA-AAAATAAT--G
* *
12709951 TGAACAGGAGAGATTCCCTGCAAGAAATGATG
1 TGAACAGGAGAGATTCCCTGCAAAAAATAATG
* *
12709983 TTAACAGGAAAGATTCCCTGCAACAAAATAATGTG
1 TGAACAGGAGAGATTCCCTGCAA-AAAATAA--TG
12710018 TGAACAGGAGAGATTCCCTGCAACAAAATAATGCG
1 TGAACAGGAGAGATTCCCTGCAA-AAAATAAT--G
* *
12710053 TGAACAGGAGAGATTCCCTGCAAGAAATGATG
1 TGAACAGGAGAGATTCCCTGCAAAAAATAATG
* *
12710085 TGAACAGGAAATATTCCCTG
1 TGAACAGGAGAGATTCCCTG
12710105 TAAGAAAAGA
Statistics
Matches: 167, Mismatches: 14, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
32 64 0.38
33 12 0.07
34 12 0.07
35 79 0.47
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.19
Consensus pattern (32 bp):
TGAACAGGAGAGATTCCCTGCAAAAAATAATG
Found at i:12709982 original size:67 final size:66
Alignment explanation
Indices: 12709874--12710111 Score: 309
Period size: 67 Copynumber: 3.5 Consensus size: 66
12709864 GTCCAAAAAG
*
12709874 AAATAATACATGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAGAGATTCCCTGCAA
1 AAATAAT-CGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAGAGATTCCCTGCAA
12709939 CA
65 CA
* *
12709941 AAATAATCCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTTAACAGGAAAGATTCCCTGCAA
1 AAATAAT-CGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAGAGATTCCCTGCAA
12710006 CA
65 CA
* * *
12710008 AAATAATGTGTGAACAGGAGAGATTCCCTGCAACAAAATAATGCGTGAACAGGAGAGATTCCCTG
1 AAATAAT-CGTGAACAGGAGAGATTCCCTGCAA-GAAATGAT--GTGAACAGGAGAGATTCCCTG
*
12710073 CAA-G
62 CAACA
* * * *
12710077 AAATGAT-GTGAACAGGAAATATTCCCTGTAAGAAA
1 AAATAATCGTGAACAGGAGAGATTCCCTGCAAGAAA
12710112 AGACAAGTGA
Statistics
Matches: 152, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
66 3 0.02
67 115 0.76
68 6 0.04
69 6 0.04
70 22 0.14
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.19
Consensus pattern (66 bp):
AAATAATCGTGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAGAGATTCCCTGCAAC
A
Found at i:12710059 original size:102 final size:99
Alignment explanation
Indices: 12709884--12710104 Score: 361
Period size: 102 Copynumber: 2.2 Consensus size: 99
12709874 AAATAATACA
* * *
12709884 TGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAGAGATTCCCTGCAACAAAATAATC
1 TGAACAGGAAAGATTCCCTGCAAAAAATAATGTGAACAGGAGAGATTCCCTGCAACAAAATAATC
12709949 CGTGAACAGGAGAGATTCCCTGCAAGAAATGATG
66 CGTGAACAGGAGAGATTCCCTGCAAGAAATGATG
*
12709983 TTAACAGGAAAGATTCCCTGCAACAAAATAATGTGTGAACAGGAGAGATTCCCTGCAACAAAATA
1 TGAACAGGAAAGATTCCCTGCAA-AAAATAA--TGTGAACAGGAGAGATTCCCTGCAACAAAATA
*
12710048 ATGCGTGAACAGGAGAGATTCCCTGCAAGAAATGATG
63 ATCCGTGAACAGGAGAGATTCCCTGCAAGAAATGATG
*
12710085 TGAACAGGAAATATTCCCTG
1 TGAACAGGAAAGATTCCCTG
12710105 TAAGAAAAGA
Statistics
Matches: 112, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
99 21 0.19
100 5 0.04
102 86 0.77
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.19
Consensus pattern (99 bp):
TGAACAGGAAAGATTCCCTGCAAAAAATAATGTGAACAGGAGAGATTCCCTGCAACAAAATAATC
CGTGAACAGGAGAGATTCCCTGCAAGAAATGATG
Found at i:12723193 original size:17 final size:18
Alignment explanation
Indices: 12723130--12723194 Score: 60
Period size: 19 Copynumber: 3.6 Consensus size: 18
12723120 AAAAAATTTC
*
12723130 AATAAAAATATATAAAATT
1 AATAAAAATATTTAAAA-T
* * *
12723149 ATTAAATATTAATTAAAAT
1 AATAAA-AATATTTAAAAT
*
12723168 AATATAAATATTTAAAA-
1 AATAAAAATATTTAAAAT
12723185 AATAAAAATA
1 AATAAAAATA
12723195 GTATGGGTTA
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
17 9 0.25
18 9 0.25
19 10 0.28
20 8 0.22
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AATAAAAATATTTAAAAT
Found at i:12725118 original size:41 final size:41
Alignment explanation
Indices: 12725061--12725145 Score: 143
Period size: 41 Copynumber: 2.1 Consensus size: 41
12725051 GGAAGTGATT
* *
12725061 GTAGCAAATCAACATTGTAGACACTAAAACACTGCCTAGTG
1 GTAGCAAATCAACATTGCAGACACTAAAACACTGCCTAGCG
*
12725102 GTAGCAAATCAACATTGCAGACACTGAAACACTGCCTAGCG
1 GTAGCAAATCAACATTGCAGACACTAAAACACTGCCTAGCG
12725143 GTA
1 GTA
12725146 AAGGATGTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.20
Consensus pattern (41 bp):
GTAGCAAATCAACATTGCAGACACTAAAACACTGCCTAGCG
Found at i:12728046 original size:24 final size:24
Alignment explanation
Indices: 12727993--12728047 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
12727983 TGTATAACAA
* *
12727993 GAAGCTCATGCGAGCCATAATTGG
1 GAAGCTCATGCGAGCAATAATAGG
12728017 GAAGCTCATGCGAGGCAATAA-AGG
1 GAAGCTCATGCGA-GCAATAATAGG
*
12728041 GTAGCTC
1 GAAGCTC
12728048 TGAAGAGCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 21 0.78
25 6 0.22
ACGTcount: A:0.31, C:0.20, G:0.31, T:0.18
Consensus pattern (24 bp):
GAAGCTCATGCGAGCAATAATAGG
Found at i:12728070 original size:24 final size:22
Alignment explanation
Indices: 12727993--12728073 Score: 63
Period size: 24 Copynumber: 3.4 Consensus size: 22
12727983 TGTATAACAA
*
12727993 GAAGCTCATGCGAGCCATAATTGG
1 GAAGCTC-TGAGAGCCATAA-TGG
* * *
12728017 GAAGCTCATGCGAGGCAATAAAGG
1 GAAGCTC-TGAGA-GCCATAATGG
*
12728041 GTAGCTCTGAAGAGCCATTAATGG
1 GAAGCTCTG-AGAGCCA-TAATGG
12728065 GAAGCTCTG
1 GAAGCTCTG
12728074 GATAGCTATA
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
23 5 0.11
24 36 0.77
25 6 0.13
ACGTcount: A:0.31, C:0.19, G:0.31, T:0.20
Consensus pattern (22 bp):
GAAGCTCTGAGAGCCATAATGG
Found at i:12728140 original size:26 final size:26
Alignment explanation
Indices: 12728106--12728172 Score: 100
Period size: 26 Copynumber: 2.6 Consensus size: 26
12728096 CAAGTGAGCC
12728106 ATAACGGGAAGCTCACAAAGAGCC-T
1 ATAACGGGAAGCTCACAAAGAGCCAT
*
12728131 TTAATCGGGAAGCTCACAAAGAGCCAT
1 ATAA-CGGGAAGCTCACAAAGAGCCAT
*
12728158 ATAACGGGACGCTCA
1 ATAACGGGAAGCTCA
12728173 TAAGAGCTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
25 3 0.08
26 30 0.81
27 4 0.11
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (26 bp):
ATAACGGGAAGCTCACAAAGAGCCAT
Found at i:12728456 original size:24 final size:24
Alignment explanation
Indices: 12728421--12728471 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
12728411 GTCGGATATG
* *
12728421 TTATCAATTTCATATATATAACAT
1 TTATCAATTTCACATATATAAAAT
*
12728445 TTATACAA-TTCACATATTTAAAAT
1 TTAT-CAATTTCACATATATAAAAT
12728469 TTA
1 TTA
12728472 ATTCAAACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 20 0.87
25 3 0.13
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (24 bp):
TTATCAATTTCACATATATAAAAT
Found at i:12728648 original size:5 final size:5
Alignment explanation
Indices: 12728619--12728662 Score: 61
Period size: 5 Copynumber: 8.6 Consensus size: 5
12728609 TAAATTTAAC
* *
12728619 TCAAT TTAAT ACAAT TCATAT TCAAT TCAAT TCAAT TCAAT TCA
1 TCAAT TCAAT TCAAT TCA-AT TCAAT TCAAT TCAAT TCAAT TCA
12728663 CATATTAGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 29 0.85
6 5 0.15
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (5 bp):
TCAAT
Found at i:12733520 original size:71 final size:74
Alignment explanation
Indices: 12733396--12733588 Score: 304
Period size: 71 Copynumber: 2.6 Consensus size: 74
12733386 TAAAATTGGA
*
12733396 AAAGCCCTTCCTTGTCAATTGGAATGTTTTATGTCCTCAACTGAAAATCTTTTTTATGCTCAAAA
1 AAAGTCCTTCCTTGTCAATTGGAATGTTTTATGTCCTCAACTGAAAA-CTTTTTTATGCTCAAAA
*
12733461 T-A-AG-GAG
65 TCAGAGAAAG
* *
12733468 -AAGTCCTTCCTTGTCAATTGGAGTGTTTTATGTCCTCAATTGAAAACTTTTTTATGCTCAAAAT
1 AAAGTCCTTCCTTGTCAATTGGAATGTTTTATGTCCTCAACTGAAAACTTTTTTATGCTCAAAAT
12733532 CAGAGAAAAG
66 CAGAG-AAAG
12733542 AAAGTCCTTCCTTGTCAATTGGAATGTTTTATGTCCTCAACTGAAAA
1 AAAGTCCTTCCTTGTCAATTGGAATGTTTTATGTCCTCAACTGAAAA
12733589 AATAAATCTC
Statistics
Matches: 110, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
70 18 0.16
71 44 0.40
72 2 0.02
74 2 0.02
75 44 0.40
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.36
Consensus pattern (74 bp):
AAAGTCCTTCCTTGTCAATTGGAATGTTTTATGTCCTCAACTGAAAACTTTTTTATGCTCAAAAT
CAGAGAAAG
Found at i:12739623 original size:24 final size:23
Alignment explanation
Indices: 12739579--12739623 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
12739569 TATAAAAAAT
**
12739579 AATTATATTAAGAATTGTTATGA
1 AATTATATTAAGAATAATTATGA
*
12739602 AATTATATTTAATAATAATTAT
1 AATTATA-TTAAGAATAATTAT
12739624 ATTAAAATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 7 0.39
24 11 0.61
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (23 bp):
AATTATATTAAGAATAATTATGA
Found at i:12739871 original size:16 final size:16
Alignment explanation
Indices: 12739850--12739900 Score: 84
Period size: 16 Copynumber: 3.2 Consensus size: 16
12739840 TGAATTACTT
*
12739850 ATTACAACCCTATTCC
1 ATTACAGCCCTATTCC
*
12739866 ATTACAGCTCTATTCC
1 ATTACAGCCCTATTCC
12739882 ATTACAGCCCTATTCC
1 ATTACAGCCCTATTCC
12739898 ATT
1 ATT
12739901 CCAGTGAACC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.27, C:0.33, G:0.04, T:0.35
Consensus pattern (16 bp):
ATTACAGCCCTATTCC
Found at i:12741203 original size:21 final size:21
Alignment explanation
Indices: 12741170--12741212 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12741160 TTTGATTTTT
*
12741170 TTTAAGATAAAAATACTAAAG
1 TTTAAAATAAAAATACTAAAG
* *
12741191 TTTAAAATGAAAATACTGAAG
1 TTTAAAATAAAAATACTAAAG
12741212 T
1 T
12741213 GACATTAAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.53, C:0.05, G:0.12, T:0.30
Consensus pattern (21 bp):
TTTAAAATAAAAATACTAAAG
Found at i:12744795 original size:24 final size:24
Alignment explanation
Indices: 12744763--12744823 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
12744753 CAGCTCGCAA
*
12744763 GAGCGTCCCGATAATAACTCTCAT
1 GAGCATCCCGATAATAACTCTCAT
* * *
12744787 GAGCATCCCGATATTAGCTCTCTT
1 GAGCATCCCGATAATAACTCTCAT
* *
12744811 GAGCTTCCTGATA
1 GAGCATCCCGATA
12744824 TATGGCTCCC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.30
Consensus pattern (24 bp):
GAGCATCCCGATAATAACTCTCAT
Found at i:12752813 original size:9 final size:9
Alignment explanation
Indices: 12752797--12752848 Score: 95
Period size: 9 Copynumber: 5.8 Consensus size: 9
12752787 GGTATTTTTC
12752797 GGTAATTCG
1 GGTAATTCG
*
12752806 GTTAATTCG
1 GGTAATTCG
12752815 GGTAATTCG
1 GGTAATTCG
12752824 GGTAATTCG
1 GGTAATTCG
12752833 GGTAATTCG
1 GGTAATTCG
12752842 GGTAATT
1 GGTAATT
12752849 TTTAACCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.23, C:0.10, G:0.31, T:0.37
Consensus pattern (9 bp):
GGTAATTCG
Found at i:12753026 original size:12 final size:12
Alignment explanation
Indices: 12753009--12753033 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12752999 AGTAATTTCG
12753009 GGTCGGTTAACC
1 GGTCGGTTAACC
12753021 GGTCGGTTAACC
1 GGTCGGTTAACC
12753033 G
1 G
12753034 AATGAACACC
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:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:12753668 original size:53 final size:53
Alignment explanation
Indices: 12753568--12753697 Score: 165
Period size: 53 Copynumber: 2.4 Consensus size: 53
12753558 TCACCCCAAA
* * * *
12753568 AAAACTTTTACTTCCCCCTAAACCCCCAATTTTTTTTCTTTTTTACTTTCTCCCC
1 AAAACTTTTACTTCCACC-AAACCCCAAAATATTTTTCTTTTTTACTTT-TCCCC
*
12753623 AAAACTTTTACTT-CTCCAAACCCCAAAAATATTTTTC-TTTTTACTTTTCCCC
1 AAAACTTTTACTTCCACCAAACCCC-AAAATATTTTTCTTTTTTACTTTTCCCC
*
12753675 AAAATTTTTACTTCCACCAAACC
1 AAAACTTTTACTTCCACCAAACC
12753698 TCAATAACTT
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
52 17 0.25
53 25 0.37
54 12 0.18
55 13 0.19
ACGTcount: A:0.27, C:0.32, G:0.00, T:0.42
Consensus pattern (53 bp):
AAAACTTTTACTTCCACCAAACCCCAAAATATTTTTCTTTTTTACTTTTCCCC
Found at i:12760218 original size:21 final size:22
Alignment explanation
Indices: 12760189--12760235 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
12760179 CAGAAGGAGT
*
12760189 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
12760211 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
12760232 GAGT
1 GAGT
12760236 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:12769849 original size:19 final size:20
Alignment explanation
Indices: 12769825--12769863 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
12769815 CACTGTTCAT
12769825 TTGG-TCAAGTATCGATACC
1 TTGGCTCAAGTATCGATACC
*
12769844 TTGGTCTCTAGTATCGATAC
1 TTGG-CTCAAGTATCGATAC
12769864 TTTTATCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
21 13 0.76
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.36
Consensus pattern (20 bp):
TTGGCTCAAGTATCGATACC
Found at i:12773338 original size:41 final size:44
Alignment explanation
Indices: 12773275--12773388 Score: 110
Period size: 46 Copynumber: 2.6 Consensus size: 44
12773265 ATACACACTT
* * *
12773275 TTTTATAA-CGTAAATACTTATATTTTAAATA-TT-T-TTTTGTA
1 TTTTATAATC-TATATACATATATTTTAAATATTTATCTTTTATA
* *
12773316 TTTTATAATCTATATACCTATATATGTAAATATTTATGCTTTTATA
1 TTTTATAATCTATATACATATAT-TTTAAATATTTAT-CTTTTATA
* *
12773362 TTTTATAATCCATATACATATCTTTTA
1 TTTTATAATCTATATACATATATTTTA
12773389 TTTATTTTCT
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
41 19 0.32
42 8 0.14
43 2 0.03
44 1 0.02
45 3 0.05
46 26 0.44
ACGTcount: A:0.34, C:0.09, G:0.04, T:0.54
Consensus pattern (44 bp):
TTTTATAATCTATATACATATATTTTAAATATTTATCTTTTATA
Found at i:12780838 original size:23 final size:23
Alignment explanation
Indices: 12780794--12780838 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
12780784 TCGTCCACCT
* *
12780794 ATTTATAACATAAAAATATTTAG
1 ATTTATAAAAAAAAAATATTTAG
12780817 ATTTATAAAAAAATAAAT-TTTA
1 ATTTATAAAAAAA-AAATATTTA
12780839 ACATAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
ATTTATAAAAAAAAAATATTTAG
Found at i:12780952 original size:19 final size:18
Alignment explanation
Indices: 12780924--12780959 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
12780914 AAAGCAGATT
12780924 AGAGAGGCATCCATTTTG
1 AGAGAGGCATCCATTTTG
12780942 AGAGAAGGCATCCATTTT
1 AGAG-AGGCATCCATTTT
12780960 TAATTAAGCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.28
Consensus pattern (18 bp):
AGAGAGGCATCCATTTTG
Found at i:12783691 original size:12 final size:12
Alignment explanation
Indices: 12783658--12783693 Score: 56
Period size: 11 Copynumber: 3.1 Consensus size: 12
12783648 TTCTCTATAA
*
12783658 AAATTACAAAAT
1 AAATTTCAAAAT
12783670 AAATTT-AAAAT
1 AAATTTCAAAAT
12783681 AAATTTCAAAAT
1 AAATTTCAAAAT
12783693 A
1 A
12783694 TTTATTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.31
Consensus pattern (12 bp):
AAATTTCAAAAT
Found at i:12783768 original size:21 final size:20
Alignment explanation
Indices: 12783722--12783769 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
12783712 TTTATCTTTA
*
12783722 TTAAAAAAATTATAAAAAAT
1 TTAAAAAAATTATAAAAAAG
12783742 TCTAAAAAAGA-TATAAAGAAAG
1 T-TAAAAAA-ATTATAAA-AAAG
12783764 TTAAAA
1 TTAAAA
12783770 TTTTAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 18 0.75
22 5 0.21
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (20 bp):
TTAAAAAAATTATAAAAAAG
Found at i:12795937 original size:19 final size:20
Alignment explanation
Indices: 12795915--12795952 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12795905 AAATGATTGC
12795915 AAAAT-GAAAAAATTTTAAA
1 AAAATAGAAAAAATTTTAAA
* *
12795934 AAAATAGTAAAAGTTTTAA
1 AAAATAGAAAAAATTTTAA
12795953 TATATATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (20 bp):
AAAATAGAAAAAATTTTAAA
Found at i:12802698 original size:42 final size:42
Alignment explanation
Indices: 12802605--12802701 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
12802595 ACGACCAAAC
* *
12802605 CACACACCCGTGTGCATCGTCGTGTCTCACACACGACTGAGA
1 CACACGCCCGTGTGCATCGCCGTGTCTCACACACGACTGAGA
* * * * *
12802647 CACACGCCCGTGTGCATGGCCGTGTGTGACACACGGCTGAGG
1 CACACGCCCGTGTGCATCGCCGTGTCTCACACACGACTGAGA
* *
12802689 GACATGCCCGTGT
1 CACACGCCCGTGT
12802702 CTCTGCCCGT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.20, C:0.33, G:0.29, T:0.19
Consensus pattern (42 bp):
CACACGCCCGTGTGCATCGCCGTGTCTCACACACGACTGAGA
Found at i:12808390 original size:23 final size:22
Alignment explanation
Indices: 12808364--12808417 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
12808354 TAATTAAAAT
* *
12808364 TAAAATTAAAATTATTTTTTTAA
1 TAAAATTAAAATTA-ATTGTTAA
*
12808387 TAAAATTAAAATTAATTGTTAT
1 TAAAATTAAAATTAATTGTTAA
12808409 TAAAATTAA
1 TAAAATTAA
12808418 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
TAAAATTAAAATTAATTGTTAA
Found at i:12808412 original size:16 final size:16
Alignment explanation
Indices: 12808391--12808432 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
12808381 TTTTAATAAA
12808391 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGTT
12808407 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGTT
*
12808423 AGTAAAATTA
1 ATTAAAATTA
12808433 TCAAATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (16 bp):
ATTAAAATTAATTGTT
Found at i:12808415 original size:22 final size:23
Alignment explanation
Indices: 12808362--12808417 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
12808352 TTTAATTAAA
* *
12808362 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAATTATATTGTT
*
12808385 AATAAAATTAAAATTA-ATTGTT
1 ATTAAAATTAAAATTATATTGTT
12808407 ATTAAAATTAA
1 ATTAAAATTAA
12808418 TTGTTAGTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 14 0.48
23 15 0.52
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
ATTAAAATTAAAATTATATTGTT
Found at i:12808502 original size:66 final size:59
Alignment explanation
Indices: 12808435--12808554 Score: 197
Period size: 59 Copynumber: 2.1 Consensus size: 59
12808425 TAAAATTATC
* * *
12808435 AAATTAT-TAATTATTAATTGTATTAATTTTTGTAATAAAATCTAACATTTGATTAGTA
1 AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
*
12808493 AATTTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
1 AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
12808552 AAA
1 AAA
12808555 CAAACTTGAT
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
58 6 0.11
59 50 0.89
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (59 bp):
AAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTA
Found at i:12815849 original size:20 final size:20
Alignment explanation
Indices: 12815821--12815873 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
12815811 GGTAGTACAA
12815821 CAGAATAGAACAAAACAAAG
1 CAGAATAGAACAAAACAAAG
* * *
12815841 CAGAGTAGAATAGAACAAAG
1 CAGAATAGAACAAAACAAAG
*
12815861 CAGAACAGAACAA
1 CAGAATAGAACAA
12815874 CAAATGTATG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.60, C:0.15, G:0.19, T:0.06
Consensus pattern (20 bp):
CAGAATAGAACAAAACAAAG
Found at i:12821633 original size:23 final size:22
Alignment explanation
Indices: 12821582--12821633 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
12821572 CCTCGTCTTT
12821582 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTGTTTCTTTTTCTAAC
*
12821604 -TCATTTTATTTTCTTTCTTC-AAC
1 TTC-TTTT-GTTTCTTT-TTCTAAC
12821627 TTCTTTT
1 TTCTTTT
12821634 TCAAATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 4 0.16
23 14 0.56
24 5 0.20
ACGTcount: A:0.12, C:0.19, G:0.02, T:0.67
Consensus pattern (22 bp):
TTCTTTTGTTTCTTTTTCTAAC
Found at i:12821648 original size:18 final size:18
Alignment explanation
Indices: 12821627--12821665 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
12821617 TTTCTTCAAC
* *
12821627 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTCCTT
*
12821645 TTCTGTTTCACATTCCTT
1 TTCTGTTTCAAATTCCTT
12821663 TTC
1 TTC
12821666 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.62
Consensus pattern (18 bp):
TTCTGTTTCAAATTCCTT
Found at i:12826404 original size:32 final size:32
Alignment explanation
Indices: 12826359--12826420 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
12826349 ACTTTTAAAC
12826359 TGAAATTGCTAATTATATTGCATCATCACAAT
1 TGAAATTGCTAATTATATTGCATCATCACAAT
*
12826391 TGAAATTGTTAATTATATTGCATCATCACA
1 TGAAATTGCTAATTATATTGCATCATCACA
12826421 CATTAACATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.39
Consensus pattern (32 bp):
TGAAATTGCTAATTATATTGCATCATCACAAT
Found at i:12829503 original size:50 final size:50
Alignment explanation
Indices: 12829393--12829677 Score: 261
Period size: 50 Copynumber: 5.6 Consensus size: 50
12829383 TTGGGTAAAG
* *
12829393 AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAG
1 AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAA
* * *
12829449 AGGTCCCATGTAAGACCACGTCTGGAACTTGGCATTGGCACCGAGATGAA
1 AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAA
* * *
12829499 AGGTCCCATGTAAGACCATGTCTGGGATATGGCGTTGGCACCGAGATGAG
1 AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAA
*** * * * *
12829549 AGGTCCCCCATAAGACCATGTCTGGGACATGACATGGGCACCTATATGAGA
1 AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGA-A
* * * * * *
12829600 A-CTCCCATGTAAGACCATATCTGGGATATGACATTGGCA--GTACAAGAA
1 AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAA
** *
12829648 ACATCCCATGTAAGACTATGTCTGGGACAT
1 AGGTCCCATGTAAGACCATGTCTGGGACAT
12829678 AGCTTTGGTA
Statistics
Matches: 191, Mismatches: 35, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
48 2 0.01
49 28 0.15
50 119 0.62
51 1 0.01
53 3 0.02
55 1 0.01
56 37 0.19
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.23
Consensus pattern (50 bp):
AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAA
Found at i:12834763 original size:46 final size:44
Alignment explanation
Indices: 12834694--12834781 Score: 106
Period size: 46 Copynumber: 2.0 Consensus size: 44
12834684 AACAGATACA
*
12834694 CGGTGGATTCAGCACACAACAACCACACTTTGTAATCAATGATATC
1 CGGTGGATTCAGCACACAACAACCAC-C-TTATAATCAATGATATC
* * *
12834740 CGGTGGGA-TCAGCACATAGCAACCACCTTATAATTAATGATA
1 CGGT-GGATTCAGCACACAACAACCACCTTATAATCAATGATA
12834782 CCGATTCACA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
44 13 0.35
45 1 0.03
46 20 0.54
47 3 0.08
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (44 bp):
CGGTGGATTCAGCACACAACAACCACCTTATAATCAATGATATC
Found at i:12834847 original size:51 final size:51
Alignment explanation
Indices: 12834782--12834982 Score: 248
Period size: 51 Copynumber: 4.0 Consensus size: 51
12834772 ATTAATGATA
* *
12834782 CCGATTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTAT
1 CCGATACACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACTAT
* *
12834833 CCGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGA--AGCTAT
1 CCGATACACATAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTAT
* * * *
12834884 TCGGTACACATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-T
1 CCGATACACATAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTAT
* * *
12834934 CTGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
1 CCGATACACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
12834983 TTCACTTTCA
Statistics
Matches: 129, Mismatches: 15, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
49 4 0.03
50 42 0.33
51 80 0.62
52 2 0.02
53 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (51 bp):
CCGATACACATAGTAGCCTGCACATAGTACTACACACGTGACCATCACTAT
Found at i:12834969 original size:101 final size:102
Alignment explanation
Indices: 12834788--12834974 Score: 324
Period size: 101 Copynumber: 1.8 Consensus size: 102
12834778 GATACCGATT
*
12834788 CACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATACACGTAGTAGCCTG
1 CACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTG
12834853 CACATAGTACTACACACGTGATCGAAGCTATTCGGTA
66 CACATAGTACTACACACGTGATCGAAGCTATTCGGTA
* *
12834890 CACATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACGTAGTAGCCT
1 CACATAGTAGCCTGCACATAGTACTACACATGCGACC-ATCACTATCCGATACACGTAGTAGCCT
12834953 GCACATAGTACTACACACGTGA
65 GCACATAGTACTACACACGTGA
12834975 CCATCACTTT
Statistics
Matches: 81, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
101 40 0.49
102 37 0.46
103 4 0.05
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.24
Consensus pattern (102 bp):
CACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTG
CACATAGTACTACACACGTGATCGAAGCTATTCGGTA
Found at i:12837243 original size:27 final size:27
Alignment explanation
Indices: 12837175--12837248 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
12837165 AACATGTCAG
* * *
12837175 AAAAGAGTAGCCTTCATGGCGAAGCCT
1 AAAAGAATAGCCTTTATGGCAAAGCCT
* * *
12837202 AAAAGAATAACCTTTTTGGCAAAGTCT
1 AAAAGAATAGCCTTTATGGCAAAGCCT
*
12837229 AAAAGAATAGCCTTTGTGGC
1 AAAAGAATAGCCTTTATGGC
12837249 GTATTACGAA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (27 bp):
AAAAGAATAGCCTTTATGGCAAAGCCT
Found at i:12840259 original size:23 final size:21
Alignment explanation
Indices: 12840233--12840295 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
12840223 TTAAAAACCC
* *
12840233 TAAATTTTAAGCCTTAATTATAT
1 TAAATTCTAAACCTTAA--ATAT
*
12840256 TAAACTCTAAACCTTAAATAT
1 TAAATTCTAAACCTTAAATAT
* *
12840277 TAAATACTAAATCTTAAAT
1 TAAATTCTAAACCTTAAAT
12840296 GTATCTAACC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 20 0.59
23 14 0.41
ACGTcount: A:0.46, C:0.13, G:0.02, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAACCTTAAATAT
Found at i:12842309 original size:43 final size:44
Alignment explanation
Indices: 12842207--12842309 Score: 104
Period size: 42 Copynumber: 2.3 Consensus size: 44
12842197 TTTAGATCAT
** **
12842207 ATTATTTTAAAATTTTTTAAAACATAACTTCTTTTAGAATTTTTTT
1 ATTATTTT-AAATTTTTTAAAACATAAC-AATTTTAGAATTTTTAA
* *
12842253 ATT-TTTTATATTTTTTAAAA-ATATA-AATTTTCGAATTTTTAA
1 ATTATTTTAAATTTTTTAAAACATA-ACAATTTTAGAATTTTTAA
12842295 ATTATTTTAAATTTT
1 ATTATTTTAAATTTT
12842310 AATTTTTTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
42 15 0.31
43 13 0.27
44 13 0.27
45 4 0.08
46 3 0.06
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (44 bp):
ATTATTTTAAATTTTTTAAAACATAACAATTTTAGAATTTTTAA
Found at i:12842354 original size:22 final size:22
Alignment explanation
Indices: 12842299--12842354 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
12842289 TTTTAAATTA
* * *
12842299 TTTTAAATTTTAATTTTTTTAT
1 TTTTAAAATTTAATTTATCTAT
* * *
12842321 TGTGAAAGTTTAATTTATCTAT
1 TTTTAAAATTTAATTTATCTAT
12842343 TTTTAAAATTTA
1 TTTTAAAATTTA
12842355 CTGAAACTAA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (22 bp):
TTTTAAAATTTAATTTATCTAT
Found at i:12842714 original size:16 final size:16
Alignment explanation
Indices: 12842695--12842741 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
12842685 AAATTTTAAA
12842695 TTTTTTTTAAAATACT
1 TTTTTTTTAAAATACT
* *
12842711 TTTTTTTTTAAAT-TT
1 TTTTTTTTAAAATACT
12842726 TTTCATTTTTAAAATA
1 TTT--TTTTTAAAATA
12842742 AATTTTTAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 4 0.16
16 12 0.48
17 9 0.36
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTTTTTAAAATACT
Found at i:12847637 original size:13 final size:12
Alignment explanation
Indices: 12847611--12847649 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 12
12847601 AAAATAAGGG
12847611 AGAAGGAGAAAGA
1 AGAA-GAGAAAGA
12847624 AGAAGAGAAGAGA
1 AGAAGAGAA-AGA
12847637 AGAAGATGAAAGA
1 AGAAGA-GAAAGA
12847650 TAGAGAAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.21
13 16 0.67
14 3 0.12
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.03
Consensus pattern (12 bp):
AGAAGAGAAAGA
Found at i:12852583 original size:26 final size:26
Alignment explanation
Indices: 12852536--12852585 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
12852526 GGAGAATGAG
* *
12852536 AAAGAAAAAGAGAACTTTTAGAGAGA
1 AAAGAAAAAGAGAACATATAGAGAGA
12852562 AAAGAAAAAGATGAA-ATATAGAGA
1 AAAGAAAAAGA-GAACATATAGAGA
12852586 AGCTAGAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 18 0.86
27 3 0.14
ACGTcount: A:0.62, C:0.02, G:0.22, T:0.14
Consensus pattern (26 bp):
AAAGAAAAAGAGAACATATAGAGAGA
Found at i:12858990 original size:23 final size:24
Alignment explanation
Indices: 12858940--12858990 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
12858930 GGCTTGGCTC
* * *
12858940 ATTTTTTAATTTTTTTAATGTATT
1 ATTTTTTAATTTTTATAATATATA
*
12858964 ATTTTTTAA-TTTTATATTATATA
1 ATTTTTTAATTTTTATAATATATA
12858987 ATTT
1 ATTT
12858991 ATATCATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (24 bp):
ATTTTTTAATTTTTATAATATATA
Found at i:12861471 original size:16 final size:16
Alignment explanation
Indices: 12861424--12861472 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
12861414 AGTAACTGGA
12861424 AAAAAAATAAGATTGTTG
1 AAAAAAATAA-ATT-TTG
* * *
12861442 AAAATATTACATTTTG
1 AAAAAAATAAATTTTG
12861458 AAAAAAATAAATTTT
1 AAAAAAATAAATTTT
12861473 TTTATCCAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
16 15 0.60
17 3 0.12
18 7 0.28
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (16 bp):
AAAAAAATAAATTTTG
Found at i:12869579 original size:44 final size:44
Alignment explanation
Indices: 12869478--12870243 Score: 313
Period size: 44 Copynumber: 17.8 Consensus size: 44
12869468 ACTCCATTAG
* * * ***
12869478 TCTGCTCCACTGCAACTTCAAGGAGATAAGA-CT-A-GATGCGA
1 TCTGCTTCACTGCAACTTCAGGGAGATAAGATCTAAGGTTTTAA
* *
12869519 TCTGC-TCTCTGCAACTTCAGAGAGATAAGATCTAAGGTTTTAA
1 TCTGCTTCACTGCAACTTCAGGGAGATAAGATCTAAGGTTTTAA
* * * *
12869562 TCCGCTTCACTGCAACTTCAGGAAGATAGGAT-TATCGGTTTTAA
1 TCTGCTTCACTGCAACTTCAGGGAGATAAGATCTA-AGGTTTTAA
* * * *
12869606 TCTGCTCCACTGCAACTTCAGGGAGATAAGAT-T-TGCTATCTTCAG
1 TCTGCTTCACTGCAACTTCAGGGAGATAAGATCTAAGGT-T-TT-AA
* * * *
12869651 TCTACTTCACTGCAACTTCAGGGAGATAAGAT-T-TGCTTACTTAG
1 TCTGCTTCACTGCAACTTCAGGGAGATAAGATCTAAGGTT--TTAA
** * **
12869695 TCTGC-TCTACTGC-ACTTCAATGAGATAAGA-CT-A-GATTCGA
1 TCTGCTTC-ACTGCAACTTCAGGGAGATAAGATCTAAGGTTTTAA
* * * * *
12869735 TTTGC-TCTCTACAACTTCAGAGAGATAATATCTAAGGTTTTAA
1 TCTGCTTCACTGCAACTTCAGGGAGATAAGATCTAAGGTTTTAA
* * * * *
12869778 TTTGCTTCACTGCAACTTCAGGGTGATAGGAT-TATCGATTTTAA
1 TCTGCTTCACTGCAACTTCAGGGAGATAAGATCTA-AGGTTTTAA
* * **** * *
12869822 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAG
1 TCTGCTTCACTGCAACTTCAGGGAGATAAGATCTAAGGT-TTTAA
* * *
12869867 TCTGCCTCACTGCAACTTCA-GGAGGATAAGA-CT-TGCTTGCTTAA
1 TCTGCTTCACTGCAACTTCAGGGA-GATAAGATCTAAGGTT--TTAA
* * * ***
12869911 TATGCTCCACTGCAACTTCAGGGAGATAAGA-CT-A-GATGCGA
1 TCTGCTTCACTGCAACTTCAGGGAGATAAGATCTAAGGTTTTAA
* * *
12869952 TCTGC-TCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAA
1 TCTGCTTCACTGCAACTTCAGGGAGATAAGATCTAAGGTTTTAA
* * * * *
12869995 TCTGC-TCTATTACAACTTCAGGGAGATAGGAT-TATCGGCTTTAA
1 TCTGCTTC-ACTGCAACTTCAGGGAGATAAGATCTA-AGGTTTTAA
* * * * * **** * *
12870039 CCTGCTCCACTTCAACTTCAGGGAAATAAGATTTGCCATCTTCAG
1 TCTGCTTCACTGCAACTTCAGGGAGATAAGATCTAAGGT-TTTAA
* * * * *
12870084 TCTGCCTCACTGTAACTTCA-GGAGGATAAGA-CT-TGCTTGCTTAG
1 TCTGCTTCACTGCAACTTCAGGGA-GATAAGATCTAAGGTT--TTAA
* * * ***
12870128 TCTACTCCACTGCAACTTCAGGGAGATAAGA-CT-A-GATGCGA
1 TCTGCTTCACTGCAACTTCAGGGAGATAAGATCTAAGGTTTTAA
* * * *
12870169 TCTGC-TCTCTGTAACTTCAGAGAGATAAGATCT--GTGATTTAA
1 TCTGCTTCACTGCAACTTCAGGGAGATAAGATCTAAG-GTTTTAA
** * *
12870211 TCCACTCCACTGCAACTTCAGGGAGATAGGATC
1 TCTGCTTCACTGCAACTTCAGGGAGATAAGATC
12870244 ATTGGCTTTC
Statistics
Matches: 546, Mismatches: 140, Indels: 76
0.72 0.18 0.10
Matches are distributed among these distances:
39 3 0.01
40 85 0.16
41 21 0.04
42 15 0.03
43 76 0.14
44 246 0.45
45 100 0.18
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (44 bp):
TCTGCTTCACTGCAACTTCAGGGAGATAAGATCTAAGGTTTTAA
Found at i:12869678 original size:89 final size:88
Alignment explanation
Indices: 12869478--12870238 Score: 377
Period size: 89 Copynumber: 8.8 Consensus size: 88
12869468 ACTCCATTAG
* * * * *** * *
12869478 TCTGCTCCACTGCAACTTCAAGGAGATAAGACTA--GATGCGATCTGCT-CTCTGCAACTTCAGA
1 TCTGCTTCACTGCAACTTCAGGGAGATAAGATTATGGTTTTAATCTGCTCCACTGCAACTTCAGG
* *
12869540 GAGATAAGATCTAAGGT-T-TT-AA
66 GAGATAAGAT-T-TGCTATCTTCAA
* * *
12869562 TCCGCTTCACTGCAACTTCAGGAAGATAGGATTATCGGTTTTAATCTGCTCCACTGCAACTTCAG
1 TCTGCTTCACTGCAACTTCAGGGAGATAAGATTAT-GGTTTTAATCTGCTCCACTGCAACTTCAG
*
12869627 GGAGATAAGATTTGCTATCTTCAG
65 GGAGATAAGATTTGCTATCTTCAA
* * * *
12869651 TCTACTTCACTGCAACTTCAGGGAGATAAGATT-TGCTTACTTAGTCTGCTCTACTGC-ACTTCA
1 TCTGCTTCACTGCAACTTCAGGGAGATAAGATTATGGTT--TTAATCTGCTCCACTGCAACTTCA
** ** *
12869714 ATGAGATAAGA----CTAGATTCGA
64 GGGAGATAAGATTTGCTATCTTCAA
* * * * * * * *
12869735 TTTGC-TCTCTACAACTTCAGAGAGATAATATCTAAGGTTTTAATTTGCTTCACTGCAACTTCAG
1 TCTGCTTCACTGCAACTTCAGGGAGATAAGAT-TATGGTTTTAATCTGCTCCACTGCAACTTCAG
* * * *
12869799 GGTGATAGGATTAT-CGAT-TTTAA
65 GGAGATAAGATT-TGCTATCTTCAA
* * * *
12869822 TCTGCTCCACTGCAACTTCAGGGAGATAAGATT-TGCCATCTTCAGTCTGC-CTCACTGCAACTT
1 TCTGCTTCACTGCAACTTCAGGGAGATAAGATTATG--GT-TTTAATCTGCTC-CACTGCAACTT
*
12869885 CA-GGAGGATAAGACTTGCT-TGCTT-AA
62 CAGGGA-GATAAGATTTGCTAT-CTTCAA
* * * * *** * *
12869911 TATGCTCCACTGCAACTTCAGGGAGATAAGACTA--GATGCGATCTGCT-CTCTGCAACTTCAGA
1 TCTGCTTCACTGCAACTTCAGGGAGATAAGATTATGGTTTTAATCTGCTCCACTGCAACTTCAGG
* * *
12869973 GAGATAAGA--TCCAAGGT-TTTAA
66 GAGATAAGATTTGCTA--TCTTCAA
* * * * * *
12869995 TCTGC-TCTATTACAACTTCAGGGAGATAGGATTATCGGCTTTAACCTGCTCCACTTCAACTTCA
1 TCTGCTTC-ACTGCAACTTCAGGGAGATAAGATTAT-GGTTTTAATCTGCTCCACTGCAACTTCA
* * *
12870059 GGGAAATAAGATTTGCCATCTTCAG
64 GGGAGATAAGATTTGCTATCTTCAA
* * * * * *
12870084 TCTGCCTCACTGTAACTTCA-GGAGGATAAGACT-TGCTTGCTTAGTCTACTCCACTGCAACTTC
1 TCTGCTTCACTGCAACTTCAGGGA-GATAAGATTATGGTT--TTAATCTGCTCCACTGCAACTTC
** * *
12870147 AGGGAGATAAGA----CTAGATGCGA
63 AGGGAGATAAGATTTGCTATCTTCAA
* * * * * **
12870169 TCTGC-TCTCTGTAACTTCAGAGAGATAAGA-TCTGTGATTTAATCCACTCCACTGCAACTTCAG
1 TCTGCTTCACTGCAACTTCAGGGAGATAAGATTATG-GTTTTAATCTGCTCCACTGCAACTTCAG
12870232 GGAGATA
65 GGAGATA
12870239 GGATCATTGG
Statistics
Matches: 512, Mismatches: 118, Indels: 95
0.71 0.16 0.13
Matches are distributed among these distances:
82 2 0.00
83 69 0.13
84 120 0.23
85 25 0.05
86 3 0.01
87 32 0.06
88 94 0.18
89 160 0.31
90 7 0.01
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (88 bp):
TCTGCTTCACTGCAACTTCAGGGAGATAAGATTATGGTTTTAATCTGCTCCACTGCAACTTCAGG
GAGATAAGATTTGCTATCTTCAA
Found at i:12869866 original size:216 final size:217
Alignment explanation
Indices: 12869474--12870242 Score: 1170
Period size: 217 Copynumber: 3.6 Consensus size: 217
12869464 AACTACTCCA
12869474 TTAGTCTGCTCCACTGCAACTTCAAGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAG
1 TTAGTCTGCTCCACTGCAACTTCAAGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAG
*
12869539 AGAGATAAGATCTAAGGTTTTAATCCGCTTCACTGCAACTTCAGGAAGATAGGATTATCGGTTTT
66 AGAGATAAGATCTAAGGTTTTAATCCGCTTCACTGCAACTTCAGGGAGATAGGATTATCGGTTTT
* * *
12869604 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAGTCTACTTCACTGCAACTT
131 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTT
* *
12869669 CAGG-GAGATAAGATTTGCTTAC
196 CAGGAG-GATAAGACTTGCTTGC
* * * * *
12869691 TTAGTCTGCTCTACTGC-ACTTCAATGAGATAAGACTAGATTCGATTTGCTCTCTACAACTTCAG
1 TTAGTCTGCTCCACTGCAACTTCAAGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAG
* ** * *
12869755 AGAGATAATATCTAAGGTTTTAATTTGCTTCACTGCAACTTCAGGGTGATAGGATTATCGATTTT
66 AGAGATAAGATCTAAGGTTTTAATCCGCTTCACTGCAACTTCAGGGAGATAGGATTATCGGTTTT
12869820 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTT
131 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTT
12869885 CAGGAGGATAAGACTTGCTTGC
196 CAGGAGGATAAGACTTGCTTGC
* * *
12869907 TTAATATGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAG
1 TTAGTCTGCTCCACTGCAACTTCAAGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAG
* * * * *
12869972 AGAGATAAGATCCAAGGTTTTAATCTGC-TCTATTACAACTTCAGGGAGATAGGATTATCGGCTT
66 AGAGATAAGATCTAAGGTTTTAATCCGCTTC-ACTGCAACTTCAGGGAGATAGGATTATCGGTTT
* * * *
12870036 TAACCTGCTCCACTTCAACTTCAGGGAAATAAGATTTGCCATCTTCAGTCTGCCTCACTGTAACT
130 TAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACT
12870101 TCAGGAGGATAAGACTTGCTTGC
195 TCAGGAGGATAAGACTTGCTTGC
* * *
12870124 TTAGTCTACTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGTAACTTCAG
1 TTAGTCTGCTCCACTGCAACTTCAAGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAG
* * *
12870189 AGAGATAAGATCT--GTGATTTAATCCACTCCACTGCAACTTCAGGGAGATAGGAT
66 AGAGATAAGATCTAAG-GTTTTAATCCGCTTCACTGCAACTTCAGGGAGATAGGAT
12870243 CATTGGCTTT
Statistics
Matches: 500, Mismatches: 47, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
215 1 0.00
216 229 0.46
217 270 0.54
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (217 bp):
TTAGTCTGCTCCACTGCAACTTCAAGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAG
AGAGATAAGATCTAAGGTTTTAATCCGCTTCACTGCAACTTCAGGGAGATAGGATTATCGGTTTT
AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTT
CAGGAGGATAAGACTTGCTTGC
Found at i:12890561 original size:54 final size:56
Alignment explanation
Indices: 12890476--12890580 Score: 169
Period size: 54 Copynumber: 1.9 Consensus size: 56
12890466 ATTTGGCTTC
*
12890476 TGAGCATGAAAGGTATGCAAGTCTTTTTTATTATTT-TT-GACCTGCTTTAAATGT
1 TGAGCATGAAAGGTATGCAAGTCTTTCTTATTATTTCTTCGACCTGCTTTAAATGT
* *
12890530 TGAGCATGAAAGGTATGCAAGTCTTTCTTATTGTTTCTTCTACCTGCTTTA
1 TGAGCATGAAAGGTATGCAAGTCTTTCTTATTATTTCTTCGACCTGCTTTA
12890581 TGTGGATGCT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
54 34 0.74
55 2 0.04
56 10 0.22
ACGTcount: A:0.24, C:0.14, G:0.18, T:0.44
Consensus pattern (56 bp):
TGAGCATGAAAGGTATGCAAGTCTTTCTTATTATTTCTTCGACCTGCTTTAAATGT
Found at i:12890610 original size:26 final size:26
Alignment explanation
Indices: 12890574--12890626 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
12890564 TTCTTCTACC
12890574 TGCTTTATGTGGATGCTTAAATCCTA
1 TGCTTTATGTGGATGCTTAAATCCTA
12890600 TGCTTTATGTGGATGCTTAAATCCTA
1 TGCTTTATGTGGATGCTTAAATCCTA
12890626 T
1 T
12890627 TTTGCGTTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (26 bp):
TGCTTTATGTGGATGCTTAAATCCTA
Found at i:12896242 original size:16 final size:16
Alignment explanation
Indices: 12896221--12896291 Score: 54
Period size: 16 Copynumber: 4.4 Consensus size: 16
12896211 ATTTGGTTCA
*
12896221 CTGTAATAGAATAGGG
1 CTGTAATAGAATAGAG
* *
12896237 CTGTAATTGGATAGAG
1 CTGTAATAGAATAGAG
*
12896253 CTGTAAT-GAAATAAAG
1 CTGTAATAG-AATAGAG
* * *
12896269 TTATAATGGAATAGAG
1 CTGTAATAGAATAGAG
*
12896285 TTGTAAT
1 CTGTAAT
12896292 CAGTAATTCA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
15 1 0.02
16 42 0.95
17 1 0.02
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.31
Consensus pattern (16 bp):
CTGTAATAGAATAGAG
Found at i:12896525 original size:62 final size:57
Alignment explanation
Indices: 12896428--12896566 Score: 161
Period size: 62 Copynumber: 2.3 Consensus size: 57
12896418 TTATTATTAA
* * * * *
12896428 ATTTTAAGAAAATTATTATTAAATATATTTTAATAAAAATAATAAAAAAATAATTTAATCAT
1 ATTTTAACATAATTATTATTAAATAAAATTTAAT-AAAATAAT----AAATAATTTAATAAT
*
12896490 ATTTTAACATAATTATTATTAAATAAAATTTAATAAAATAATATATAATTTAATAAT
1 ATTTTAACATAATTATTATTAAATAAAATTTAATAAAATAATAAATAATTTAATAAT
*
12896547 ATTTTTAATATAATTATTAT
1 A-TTTTAACATAATTATTAT
12896567 AATATGAATT
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
57 14 0.20
58 17 0.25
61 8 0.12
62 30 0.43
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (57 bp):
ATTTTAACATAATTATTATTAAATAAAATTTAATAAAATAATAAATAATTTAATAAT
Found at i:12896614 original size:16 final size:15
Alignment explanation
Indices: 12896583--12896616 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
12896573 AATTAAAAAT
12896583 TTATAAAATATAATA
1 TTATAAAATATAATA
12896598 TTATAAAA-ATAATA
1 TTATAAAATATAATA
12896612 -TATAA
1 TTATAA
12896617 TCTACTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.26
14 6 0.32
15 8 0.42
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TTATAAAATATAATA
Found at i:12900315 original size:19 final size:19
Alignment explanation
Indices: 12900279--12900315 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12900269 GGAGTTAGTA
*
12900279 ATATATATATATGCGTGTT
1 ATATATATATATACGTGTT
*
12900298 ATATATATATATATGTGT
1 ATATATATATATACGTGT
12900316 GGTTGTATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.14, T:0.49
Consensus pattern (19 bp):
ATATATATATATACGTGTT
Found at i:12900335 original size:21 final size:22
Alignment explanation
Indices: 12900279--12900357 Score: 90
Period size: 21 Copynumber: 3.5 Consensus size: 22
12900269 GGAGTTAGTA
*
12900279 ATATATATATATGCGT-GTTAT
1 ATATATATATATGTGTGGTTAT
*
12900300 ATATATATATATGTGTGGTTGT
1 ATATATATATATGTGTGGTTAT
*
12900322 ATATATAT-TATGTGTGAGTTTT
1 ATATATATATATGTGTG-GTTAT
12900344 ATTATATAATATAT
1 A-TATAT-ATATAT
12900358 ATATGTTTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
21 23 0.46
22 17 0.34
23 5 0.10
24 2 0.04
25 3 0.06
ACGTcount: A:0.33, C:0.01, G:0.15, T:0.51
Consensus pattern (22 bp):
ATATATATATATGTGTGGTTAT
Found at i:12900731 original size:21 final size:21
Alignment explanation
Indices: 12900680--12900731 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
12900670 TGAAGTTTTC
* *
12900680 TCGAATC-AAATCGAGTCGAG
1 TCGAATCGAATTCGAGTCGAA
*
12900700 T-GAGATGGAATTCGAGTCGAA
1 TCGA-ATCGAATTCGAGTCGAA
12900721 TCGAATCGAAT
1 TCGAATCGAAT
12900732 ATATTTGTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
19 2 0.08
20 3 0.12
21 18 0.72
22 2 0.08
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (21 bp):
TCGAATCGAATTCGAGTCGAA
Found at i:12901106 original size:17 final size:17
Alignment explanation
Indices: 12901064--12901110 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
12901054 AATTCAATTT
12901064 TAATATAAAT-ATTCAA
1 TAATATAAATAATTCAA
12901080 T-ATGACTAAATAATTCAA
1 TAAT-A-TAAATAATTCAA
12901098 TAATATAAATAAT
1 TAATATAAATAAT
12901111 ATAAAATGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 2 0.07
16 2 0.07
17 13 0.48
18 8 0.30
19 2 0.07
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.36
Consensus pattern (17 bp):
TAATATAAATAATTCAA
Found at i:12901709 original size:9 final size:9
Alignment explanation
Indices: 12901692--12901722 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
12901682 TCGAGTTGAT
12901692 TCGAATAAC
1 TCGAATAAC
*
12901701 TCGATTAAC
1 TCGAATAAC
12901710 TCGAATAAC
1 TCGAATAAC
12901719 TCGA
1 TCGA
12901723 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:12906357 original size:23 final size:22
Alignment explanation
Indices: 12906322--12906364 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
12906312 CAAAGAATTC
12906322 TATTTTTACGTTTTGAGGGTTCT
1 TATTTTTACGTTTTG-GGGTTCT
**
12906345 TATTTTTGGGTTTTGGGGTT
1 TATTTTTACGTTTTGGGGTT
12906365 TAGTTTTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.09, C:0.05, G:0.28, T:0.58
Consensus pattern (22 bp):
TATTTTTACGTTTTGGGGTTCT
Found at i:12910267 original size:15 final size:16
Alignment explanation
Indices: 12910242--12910271 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12910232 TTTATTTTGT
12910242 AGTTAAAATAAAAATA
1 AGTTAAAATAAAAATA
12910258 AGTT-AAATAAAAAT
1 AGTTAAAATAAAAAT
12910272 TAAATAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.27
Consensus pattern (16 bp):
AGTTAAAATAAAAATA
Found at i:12912019 original size:17 final size:17
Alignment explanation
Indices: 12911994--12912027 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12911984 ACACAGTTAT
12911994 CCTACTCATAAGGCCTA
1 CCTACTCATAAGGCCTA
*
12912011 CCTATTCATAAGGCCTA
1 CCTACTCATAAGGCCTA
12912028 TGAGAAAGGA
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:0.29, C:0.32, G:0.12, T:0.26
Consensus pattern (17 bp):
CCTACTCATAAGGCCTA
Found at i:12915629 original size:20 final size:20
Alignment explanation
Indices: 12915604--12915641 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12915594 TGATTCTTTG
12915604 TTTTTTAA-TAATTATTTAAT
1 TTTTTTAATTAATT-TTTAAT
12915624 TTTTTTAATTAATTTTTA
1 TTTTTTAATTAATTTTTA
12915642 CCGACATTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTTTAATTAATTTTTAAT
Found at i:12915758 original size:22 final size:23
Alignment explanation
Indices: 12915694--12915775 Score: 74
Period size: 23 Copynumber: 3.9 Consensus size: 23
12915684 AACATTTAAT
12915694 TAATTTTTATA-A-TTTTAAAAA
1 TAATTTTTATATATTTTTAAAAA
* *
12915715 T-A-TTTT-TGTACTTTT--AAA
1 TAATTTTTATATATTTTTAAAAA
12915733 TAA-TTTTA-ATGATTTTTAAAAA
1 TAATTTTTATAT-ATTTTTAAAAA
12915755 TAATTTTTATATATTTTTAAA
1 TAATTTTTATATATTTTTAAA
12915776 TTTTTAAATT
Statistics
Matches: 49, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
18 5 0.10
19 11 0.22
20 10 0.20
21 1 0.02
22 6 0.12
23 14 0.29
24 2 0.04
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.56
Consensus pattern (23 bp):
TAATTTTTATATATTTTTAAAAA
Found at i:12915798 original size:39 final size:37
Alignment explanation
Indices: 12915695--12915798 Score: 104
Period size: 38 Copynumber: 2.6 Consensus size: 37
12915685 ACATTTAATT
*
12915695 AATTTTTATAATTTTAAAAAT-A-TTTTTGTACTTTTA
1 AATTTTTA-AATTTTAAAAATAATTTTTTATACTTTTA
*
12915731 AATAATTTTAATGATTTTTAAAAATAATTTTTATATATTTTTA
1 AAT--TTTTAA--A-TTTTAAAAATAATTTTT-TATACTTTTA
12915774 AATTTTTAAATTTTAAAAATTAATT
1 AATTTTTAAATTTTAAAAA-TAATT
12915799 AAATGTTGAC
Statistics
Matches: 57, Mismatches: 2, Indels: 15
0.77 0.03 0.20
Matches are distributed among these distances:
36 3 0.05
37 1 0.02
38 14 0.25
39 7 0.12
40 10 0.18
41 7 0.12
42 4 0.07
43 11 0.19
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (37 bp):
AATTTTTAAATTTTAAAAATAATTTTTTATACTTTTA
Found at i:12923613 original size:106 final size:106
Alignment explanation
Indices: 12923423--12923634 Score: 406
Period size: 106 Copynumber: 2.0 Consensus size: 106
12923413 CTCGCTTTGG
12923423 GTGCAAGAGGTCCCGAGTTCGATTCTCGGAACGCCCCGAATTTATGAATGCTTTACACATTTTCT
1 GTGCAAGAGGTCCCGAGTTCGATTCTCGGAACGCCCCGAATTTATGAATGCTTTACACATTTTCT
12923488 ATGTGATAAGTGGTCTTGATTTCGGCAGTTCTGTTTTCCAT
66 ATGTGATAAGTGGTCTTGATTTCGGCAGTTCTGTTTTCCAT
* *
12923529 GTGCGAGAGGTCCCGAGTTCGATTCTCGGAATGCCCCGAATTTATGAATGCTTTACACATTTTCT
1 GTGCAAGAGGTCCCGAGTTCGATTCTCGGAACGCCCCGAATTTATGAATGCTTTACACATTTTCT
12923594 ATGTGATAAGTGGTCTTGATTTCGGCAGTTCTGTTTTCCAT
66 ATGTGATAAGTGGTCTTGATTTCGGCAGTTCTGTTTTCCAT
12923635 CTAGATCGTA
Statistics
Matches: 104, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 104 1.00
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.36
Consensus pattern (106 bp):
GTGCAAGAGGTCCCGAGTTCGATTCTCGGAACGCCCCGAATTTATGAATGCTTTACACATTTTCT
ATGTGATAAGTGGTCTTGATTTCGGCAGTTCTGTTTTCCAT
Found at i:12935106 original size:26 final size:26
Alignment explanation
Indices: 12935076--12935129 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
12935066 TAACTCGAAC
*
12935076 AATTTCA-TTCATTTCAACTCAACTTG
1 AATTTCATTTCA-CTCAACTCAACTTG
*
12935102 AATTTCATTTCACTCAACTCAATTTG
1 AATTTCATTTCACTCAACTCAACTTG
12935128 AA
1 AA
12935130 AAAATTTCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.41
Consensus pattern (26 bp):
AATTTCATTTCACTCAACTCAACTTG
Found at i:12936931 original size:16 final size:16
Alignment explanation
Indices: 12936910--12936955 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
12936900 GCTGTATTGG
*
12936910 AATAGAGGCGTAATGA
1 AATAGAAGCGTAATGA
* *
12936926 AATAGATGCGTAATGG
1 AATAGAAGCGTAATGA
12936942 AATAGAAGCGTAAT
1 AATAGAAGCGTAAT
12936956 AGCAAATCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.43, C:0.07, G:0.28, T:0.22
Consensus pattern (16 bp):
AATAGAAGCGTAATGA
Found at i:12937397 original size:145 final size:145
Alignment explanation
Indices: 12937106--12937398 Score: 432
Period size: 145 Copynumber: 2.0 Consensus size: 145
12937096 TAAATGATTA
* * *
12937106 TTATTATTGTTTTTAAATTTTAATAAGATTATTAATATCAGTAATAAATAATTTAATCATATTTT
1 TTATTATTGTTATTAAATTTTAATAAGATTATTAATATAAATAATAAATAATTTAATCATATTTT
* *
12937171 AACATAATTATTATTAAATATATTTTAATTAAAATATACAATTTAATAAAATTCTTAATAATCAA
66 AACATAATTATTATTAAATATAATTTAATTAAAATATACAATTTAATAAAATTCATAATAATCAA
**
12937236 TATTATTATATGAAT
131 TATTAAAATATGAAT
12937251 TTATTATTGTTATTAAATTTTAATAAGATTATTAATATAAATAATAAATAATTTAATCATATTTT
1 TTATTATTGTTATTAAATTTTAATAAGATTATTAATATAAATAATAAATAATTTAATCATATTTT
* * *
12937316 AACATAATTATTATTAAATTTAATTTAA-TAAAATATATGAATTTACTAAAA-TCATAATATAT-
66 AACATAATTATTATTAAATATAATTTAATTAAAATATA-CAATTTAATAAAATTCATAATA-ATC
12937378 AATACTATAAAATAT-AAT
129 AATA-T-TAAAATATGAAT
12937396 TTA
1 TTA
12937399 AAATAATTAT
Statistics
Matches: 134, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
144 20 0.15
145 108 0.81
146 6 0.04
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.46
Consensus pattern (145 bp):
TTATTATTGTTATTAAATTTTAATAAGATTATTAATATAAATAATAAATAATTTAATCATATTTT
AACATAATTATTATTAAATATAATTTAATTAAAATATACAATTTAATAAAATTCATAATAATCAA
TATTAAAATATGAAT
Found at i:12937417 original size:26 final size:26
Alignment explanation
Indices: 12937387--12937526 Score: 82
Period size: 26 Copynumber: 5.5 Consensus size: 26
12937377 TAATACTATA
12937387 AAATATAATTTAAAATAATTATTATT
1 AAATATAATTTAAAATAATTATTATT
** *
12937413 AAATATAATTTGATAAAATTCTTAGTATT
1 AAATATAA-TT--TAAAATAATTATTATT
* *
12937442 AAATAT--TCTT-ATATGAA-T-TTACTA
1 AAATATAAT-TTAAAAT-AATTATTA-TT
* * *
12937466 AAATCATAA--T-ATATAA-TACTATA
1 AAAT-ATAATTTAAAATAATTATTATT
12937489 AAATATAATTTAAAATAATTATTATT
1 AAATATAATTTAAAATAATTATTATT
12937515 AAATATAATTTA
1 AAATATAATTTA
12937527 TAATCTACTT
Statistics
Matches: 88, Mismatches: 12, Indels: 28
0.69 0.09 0.22
Matches are distributed among these distances:
22 4 0.05
23 11 0.12
24 17 0.19
25 8 0.09
26 26 0.30
27 3 0.03
29 19 0.22
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (26 bp):
AAATATAATTTAAAATAATTATTATT
Found at i:12937775 original size:42 final size:42
Alignment explanation
Indices: 12937716--12937799 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
12937706 CCAAATATAA
12937716 GCCTACAGATATTTTTAACCTCACATTGTGTCTTCTACTGCT
1 GCCTACAGATATTTTTAACCTCACATTGTGTCTTCTACTGCT
12937758 GCCTACAGATATTTTTAACCTCACATTGTGTCTTCTACTGCT
1 GCCTACAGATATTTTTAACCTCACATTGTGTCTTCTACTGCT
12937800 TGCATGGAGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.21, C:0.26, G:0.12, T:0.40
Consensus pattern (42 bp):
GCCTACAGATATTTTTAACCTCACATTGTGTCTTCTACTGCT
Found at i:12941487 original size:174 final size:173
Alignment explanation
Indices: 12941203--12941879 Score: 870
Period size: 174 Copynumber: 3.9 Consensus size: 173
12941193 GCTGGCTCAA
* * *
12941203 AGGACACTGTAGTTTTAAGAGTGGAACCTCTTCGTGAATTTGAAGGAGAGTCCA-TTGTCTTATG
1 AGGAAACTGTAGTTTTAAGAGTGGAACCTCTTCGTGAATTT---GGAGAG-GCAGTTGTCCTATG
* * ** * *
12941267 AGAAAAACCAGTGCTTGAATGAGTCTTTGAACTTGTTTCCGGAAGATCTTCATCAGAACCACTGT
62 AGAAAAACCA-TGCTTGAACGAGCCTTTGAACTTGTTTTAGGAAGATCTTCATCAGAATCACTAT
* * * *
12941332 TTCCTGGACCTAAATATGGCATTGGGTCAGAAACTACCTTTGATTCAG
126 TTCCTGGACCAAAATATGGCATGGGGTCAGAAACTAGCTTCGATTCAG
* * *
12941380 AGGAAACTGTAGTTTTAAGAGTGGAAACTCTTCTTGCATTTGGAGAGGCAGTTGTCCTATGAGAA
1 AGGAAACTGTAGTTTTAAGAGTGGAACCTCTTCGTGAATTTGGAGAGGCAGTTGTCCTATGAG-A
* *
12941445 AAAATCATGCTTGAACGAGCCTTTGAACTTATTTTAGGAAGATCTTCATCAGAATCACTATTTCC
65 AAAACCATGCTTGAACGAGCCTTTGAACTTGTTTTAGGAAGATCTTCATCAGAATCACTATTTCC
** *
12941510 TGGACCAAAATGCGGCATGGGGTCAAAAACTAGCTTCGATTCAG
130 TGGACCAAAATATGGCATGGGGTCAGAAACTAGCTTCGATTCAG
*
12941554 AGGAAACTGTAGTTTTAAGAGTGGAACCTCTTCGTGCATTTGGAGAGGCAGTTGTCCTATGAGAA
1 AGGAAACTGTAGTTTTAAGAGTGGAACCTCTTCGTGAATTTGGAGAGGCAGTTGTCCTATGAG-A
***
12941619 AAAATTGTGCTTGAACGAGCCTTTGAACTTGTTTTAGGAAGATCTTCATCAGAATCACTATTTCC
65 AAAACCATGCTTGAACGAGCCTTTGAACTTGTTTTAGGAAGATCTTCATCAGAATCACTATTTCC
* * * *
12941684 TGGACCAAAATATGGTATGGGGTTAGAAACTAGCGTCGATTCGG
130 TGGACCAAAATATGGCATGGGGTCAGAAACTAGCTTCGATTCAG
* * * * * * * * *
12941728 AGGAAACTGCAGCTTTAACAGTGGAACCTTTTCCTGAATTCGGGGAGGCAGTTGTCTTGTGAGAA
1 AGGAAACTGTAGTTTTAAGAGTGGAACCTCTTCGTGAATTTGGAGAGGCAGTTGTCCTATGAGAA
* * * *
12941793 AAACCAATGCTTGAATGAACCTTTGAACCTGTTTTAGGAAGATCTTCATCGGAATCACTATTTCC
66 AAACC-ATGCTTGAACGAGCCTTTGAACTTGTTTTAGGAAGATCTTCATCAGAATCACTATTTCC
* * *
12941858 TGAATCAAAATATGCCATGGGG
130 TGGACCAAAATATGGCATGGGG
12941880 ACCCTTGAGG
Statistics
Matches: 443, Mismatches: 54, Indels: 9
0.88 0.11 0.02
Matches are distributed among these distances:
173 7 0.02
174 392 0.88
175 7 0.02
177 37 0.08
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.30
Consensus pattern (173 bp):
AGGAAACTGTAGTTTTAAGAGTGGAACCTCTTCGTGAATTTGGAGAGGCAGTTGTCCTATGAGAA
AAACCATGCTTGAACGAGCCTTTGAACTTGTTTTAGGAAGATCTTCATCAGAATCACTATTTCCT
GGACCAAAATATGGCATGGGGTCAGAAACTAGCTTCGATTCAG
Found at i:12947207 original size:23 final size:23
Alignment explanation
Indices: 12947168--12947215 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
12947158 ACATTTAATT
*
12947168 ATATTATACATTGATTTAT-TGA
1 ATATTATACATTAATTTATATGA
*
12947190 ATATTAATGCATTAATTTATATGA
1 ATATT-ATACATTAATTTATATGA
12947214 AT
1 AT
12947216 TTTTCAGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 5 0.23
23 12 0.55
24 5 0.23
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (23 bp):
ATATTATACATTAATTTATATGA
Found at i:12950480 original size:17 final size:17
Alignment explanation
Indices: 12950458--12950492 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
12950448 ATGTAAATAT
*
12950458 AATATATTATTTATAAA
1 AATATAGTATTTATAAA
12950475 AATATAGTATTTATAAA
1 AATATAGTATTTATAAA
12950492 A
1 A
12950493 TCTTAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AATATAGTATTTATAAA
Found at i:12952849 original size:27 final size:29
Alignment explanation
Indices: 12952818--12952874 Score: 82
Period size: 27 Copynumber: 2.0 Consensus size: 29
12952808 CTCCTGCTAG
*
12952818 GGTTAGGGTTTT-TGG-TTTAAGGTTTAA
1 GGTTAGGGTTTTGGGGTTTTAAGGTTTAA
*
12952845 GGTTAGGGTTTTGGGGTTTTTAGGTTTAA
1 GGTTAGGGTTTTGGGGTTTTAAGGTTTAA
12952874 G
1 G
12952875 TTTTTAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 12 0.46
28 2 0.08
29 12 0.46
ACGTcount: A:0.16, C:0.00, G:0.37, T:0.47
Consensus pattern (29 bp):
GGTTAGGGTTTTGGGGTTTTAAGGTTTAA
Found at i:12953197 original size:99 final size:98
Alignment explanation
Indices: 12952905--12953223 Score: 382
Period size: 95 Copynumber: 3.3 Consensus size: 98
12952895 TAAATAAGGG
* * * * * * *
12952905 ATTAGGGTTTATGATTTCTTAATTAAATTAATTAT-AATTTTTT-CAAAATTAGAGTAGGGTTTC
1 ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTTTAAAAAATTAGATTAGGG-TTC
* * * *
12952968 -GTGTTTATAGTTTTTAAAGAAAAAAT-AATTAA
65 AGTGTTTAAAGTTTTTTAAGGAAAAATCAAATAA
* * *
12953000 ATTAGGGTTTAGAGTTACTTGAGTAAATTAATTA-AAA-ATTTTAAAAAATTAGATTAGGGTTTA
1 ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTTTAAAAAATTAGATTAGGGTTCA
* *
12953063 GTG-TTAAGGGTTTTTAAGGAAAAATCAAATAA
66 GTGTTTAAAGTTTTTTAAGGAAAAATCAAATAA
*
12953095 ATTAGGGTCTAGGGTTACTTGAGTAAATTAATTATAAATTTTTTAAAAAAATTAGATTAGGGTTC
1 ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTTT-AAAAAATTAGATTAGGGTTC
* *
12953160 AGTGTTTAAATTTTTTTAAGGAAAACTCAAATAA
65 AGTGTTTAAAGTTTTTTAAGGAAAAATCAAATAA
* *
12953194 ATTAGGGTTTAGGGTTACTTAATTAAATTA
1 ATTAGGGTTTAGGGTTACTTGAGTAAATTA
12953224 TTTGTTAATT
Statistics
Matches: 189, Mismatches: 27, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
94 23 0.12
95 84 0.44
96 3 0.02
97 4 0.02
98 23 0.12
99 52 0.28
ACGTcount: A:0.39, C:0.03, G:0.17, T:0.41
Consensus pattern (98 bp):
ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTTTAAAAAATTAGATTAGGGTTCA
GTGTTTAAAGTTTTTTAAGGAAAAATCAAATAA
Found at i:12953410 original size:126 final size:126
Alignment explanation
Indices: 12953258--12953528 Score: 425
Period size: 126 Copynumber: 2.2 Consensus size: 126
12953248 CGTGGACTTT
* * *
12953258 TTTTGCTATAGTATCTCCTGAAAAAATAATTTCGAGAAGACGTTTCTGAGCAAATAGTGTCAAAA
1 TTTTGCTACAGTAGCTCCTGAAAAAATAATTTCAAGAAGACGTTTCTGAGCAAATAGTGTCAAAA
*
12953323 ACGCTTTAAGCAGGATGCATTGTCAACAAAAGTACTAAAAGAAGATCCCACATGGATGCGC
66 ACGCTTTAAGCAGGATGCATTGTCAACAAAAGTACTAAAAGAAGATCCCACATGGACGCGC
* *
12953384 TTTTGCTACAGTAGCTCTTGAAAAAATAATTTCAAGTAGACGTTTCTGAGCAAATAGTGTCAAAA
1 TTTTGCTACAGTAGCTCCTGAAAAAATAATTTCAAGAAGACGTTTCTGAGCAAATAGTGTCAAAA
* * * * * * *
12953449 ACGTTTTAAGCAGGATGCTTTGTCAGCAAAAGTATTGAAAGAAGCTCCCACGTGGACGCGC
66 ACGCTTTAAGCAGGATGCATTGTCAACAAAAGTACTAAAAGAAGATCCCACATGGACGCGC
12953510 TTTTGCTACAGTAGCTCCT
1 TTTTGCTACAGTAGCTCCT
12953529 ATTTTGCCTG
Statistics
Matches: 131, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
126 131 1.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (126 bp):
TTTTGCTACAGTAGCTCCTGAAAAAATAATTTCAAGAAGACGTTTCTGAGCAAATAGTGTCAAAA
ACGCTTTAAGCAGGATGCATTGTCAACAAAAGTACTAAAAGAAGATCCCACATGGACGCGC
Found at i:12957254 original size:18 final size:18
Alignment explanation
Indices: 12957228--12957271 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
12957218 GACTAGAAAA
* * *
12957228 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
*
12957246 AGGATACATAAAATGGCT
1 AGGATACATAAAAGGGCT
12957264 AGGATACA
1 AGGATACA
12957272 CACCTGGCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.45, C:0.09, G:0.25, T:0.20
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:12957905 original size:7 final size:7
Alignment explanation
Indices: 12957895--12957930 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
12957885 CATAATACAT
12957895 AATACTA
1 AATACTA
12957902 AATACTA
1 AATACTA
12957909 AATACTA
1 AATACTA
12957916 AATACTA
1 AATACTA
12957923 AATACTA
1 AATACTA
12957930 A
1 A
12957931 TCGACTATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:12958721 original size:16 final size:16
Alignment explanation
Indices: 12958697--12958729 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
12958687 CACCTCTCAA
12958697 TCAACGCATTGATGAG
1 TCAACGCATTGATGAG
*
12958713 TCAATGCATTGATGAG
1 TCAACGCATTGATGAG
12958729 T
1 T
12958730 TTTGGGTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (16 bp):
TCAACGCATTGATGAG
Found at i:12959158 original size:12 final size:10
Alignment explanation
Indices: 12959112--12959170 Score: 73
Period size: 11 Copynumber: 5.5 Consensus size: 10
12959102 TTTTTTAAGA
*
12959112 AGAATTTGAG
1 AGAAATTGAG
12959122 AGGAAATTGAG
1 A-GAAATTGAG
12959133 AGAAATTTGAG
1 AGAAA-TTGAG
12959144 AGAATATTGGAG
1 AGAA-ATT-GAG
12959156 AGAAATTGAG
1 AGAAATTGAG
12959166 AGAAA
1 AGAAA
12959171 GGATTTAGAT
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
10 13 0.30
11 23 0.52
12 8 0.18
ACGTcount: A:0.47, C:0.00, G:0.31, T:0.22
Consensus pattern (10 bp):
AGAAATTGAG
Found at i:12963659 original size:15 final size:14
Alignment explanation
Indices: 12963635--12963665 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
12963625 CCATGATTAA
12963635 TTTTATCATTTTAT
1 TTTTATCATTTTAT
12963649 TTTTCATCATTTTAT
1 TTTT-ATCATTTTAT
12963664 TT
1 TT
12963666 GTTTATTCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTATCATTTTAT
Done.