Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 103 of 135
Found at i:35275133 original size:46 final size:46
Alignment explanation
Indices: 35275077--35275286 Score: 195
Period size: 46 Copynumber: 4.3 Consensus size: 46
35275067 TCACATTTAG
* * **
35275077 TCACATTTAATATTTAAGCATAAATCATATTAGCATTTAAGCATAAA
1 TCACA-TTAATATTTAAGCACAAATCACATTAATATTTAAGCATAAA
* * * *
35275124 TTACATTAATGTTTAAGCACAAATCACATTAATATTTAAACACAAA
1 TCACATTAATATTTAAGCACAAATCACATTAATATTTAAGCATAAA
* * ** *
35275170 TCATATAAATCATATTAGCATTTAAGCATAAATTGCATTAATATTTAAGCACAAA
1 TCACAT---T-A-A-T---ATTTAAGCACAAATCACATTAATATTTAAGCATAAA
* *
35275225 TCACATTAATATTTAAACACAAATCACATTAATATTTAAGTATAAA
1 TCACATTAATATTTAAGCACAAATCACATTAATATTTAAGCATAAA
35275271 TCACATTAATATTTAA
1 TCACATTAATATTTAA
35275287 CCATTTTACT
Statistics
Matches: 132, Mismatches: 22, Indels: 19
0.76 0.13 0.11
Matches are distributed among these distances:
46 84 0.64
47 4 0.03
49 2 0.02
50 2 0.02
51 2 0.02
52 2 0.02
55 36 0.27
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.35
Consensus pattern (46 bp):
TCACATTAATATTTAAGCACAAATCACATTAATATTTAAGCATAAA
Found at i:35275178 original size:55 final size:55
Alignment explanation
Indices: 35275119--35275227 Score: 137
Period size: 55 Copynumber: 2.0 Consensus size: 55
35275109 GCATTTAAGC
* **
35275119 ATAAATTACATTAATGTTTAAGCACAAATCACATTAATATTTAAACACAAATCAT
1 ATAAATCACATTAACATTTAAGCACAAATCACATTAATATTTAAACACAAATCAT
* * * ** *
35275174 ATAAATCATATTAGCATTTAAGCATAAATTGCATTAATATTTAAGCACAAATCA
1 ATAAATCACATTAACATTTAAGCACAAATCACATTAATATTTAAACACAAATCA
35275228 CATTAATATT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
55 45 1.00
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.33
Consensus pattern (55 bp):
ATAAATCACATTAACATTTAAGCACAAATCACATTAATATTTAAACACAAATCAT
Found at i:35275184 original size:78 final size:78
Alignment explanation
Indices: 35275096--35275250 Score: 292
Period size: 78 Copynumber: 2.0 Consensus size: 78
35275086 ATATTTAAGC
*
35275096 ATAAATCATATTAGCATTTAAGCATAAATTACATTAATGTTTAAGCACAAATCACATTAATATTT
1 ATAAATCATATTAGCATTTAAGCATAAATTACATTAATATTTAAGCACAAATCACATTAATATTT
35275161 AAACACAAATCAT
66 AAACACAAATCAT
*
35275174 ATAAATCATATTAGCATTTAAGCATAAATTGCATTAATATTTAAGCACAAATCACATTAATATTT
1 ATAAATCATATTAGCATTTAAGCATAAATTACATTAATATTTAAGCACAAATCACATTAATATTT
35275239 AAACACAAATCA
66 AAACACAAATCA
35275251 CATTAATATT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 75 1.00
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.33
Consensus pattern (78 bp):
ATAAATCATATTAGCATTTAAGCATAAATTACATTAATATTTAAGCACAAATCACATTAATATTT
AAACACAAATCAT
Found at i:35275201 original size:23 final size:23
Alignment explanation
Indices: 35275174--35275286 Score: 145
Period size: 23 Copynumber: 4.9 Consensus size: 23
35275164 CACAAATCAT
* **
35275174 ATAAATCATATTAGCATTTAAGC
1 ATAAATCACATTAATATTTAAGC
**
35275197 ATAAATTGCATTAATATTTAAGC
1 ATAAATCACATTAATATTTAAGC
* *
35275220 ACAAATCACATTAATATTTAAAC
1 ATAAATCACATTAATATTTAAGC
* *
35275243 ACAAATCACATTAATATTTAAGT
1 ATAAATCACATTAATATTTAAGC
35275266 ATAAATCACATTAATATTTAA
1 ATAAATCACATTAATATTTAA
35275287 CCATTTTACT
Statistics
Matches: 78, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 78 1.00
ACGTcount: A:0.48, C:0.12, G:0.04, T:0.35
Consensus pattern (23 bp):
ATAAATCACATTAATATTTAAGC
Found at i:35275384 original size:10 final size:10
Alignment explanation
Indices: 35275365--35275401 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
35275355 ACATCATATA
35275365 TTAATCACAT
1 TTAATCACAT
* *
35275375 CTAGTCACAT
1 TTAATCACAT
35275385 TTAATCACAT
1 TTAATCACAT
35275395 TTAATCA
1 TTAATCA
35275402 TATTAGTCAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.38
Consensus pattern (10 bp):
TTAATCACAT
Found at i:35275441 original size:47 final size:47
Alignment explanation
Indices: 35275388--35275608 Score: 196
Period size: 47 Copynumber: 4.6 Consensus size: 47
35275378 GTCACATTTA
*
35275388 ATCACATTTAATCATATTAGTCACATGAATATTTCAACATTTATCAC
1 ATCACATTTAATCACATTAGTCACATGAATATTTCAACATTTATCAC
* *
35275435 ATCACATTTAATCACATTAATCACAAT-AATATTTCAACATTAATCAC
1 ATCACATTTAATCACATTAGTCAC-ATGAATATTTCAACATTTATCAC
* * * * ** *
35275482 ATCACATATTAATTATATTTA-TCACATGAGTACTTAAGCACAACACATATTA-
1 ATCACAT-TTAATCACA-TTAGTCACATGAATA-TT----TCAACATTTATCAC
* * *
35275534 ATCGCATTTAACCACATTAGCCACATGAATATTTCAACATTTATCAC
1 ATCACATTTAATCACATTAGTCACATGAATATTTCAACATTTATCAC
* *
35275581 AACACATATTAAGCACATTTAGTCACAT
1 ATCACAT-TTAATCACA-TTAGTCACAT
35275609 TTAATCACAT
Statistics
Matches: 136, Mismatches: 25, Indels: 24
0.74 0.14 0.13
Matches are distributed among these distances:
46 9 0.07
47 55 0.40
48 24 0.18
49 14 0.10
50 5 0.04
51 15 0.11
52 6 0.04
53 8 0.06
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.34
Consensus pattern (47 bp):
ATCACATTTAATCACATTAGTCACATGAATATTTCAACATTTATCAC
Found at i:35275584 original size:58 final size:59
Alignment explanation
Indices: 35275520--35275631 Score: 163
Period size: 58 Copynumber: 1.9 Consensus size: 59
35275510 AGTACTTAAG
* * *
35275520 CACAACACATATTAATCGCATTTAACCACA-TTAGCCACATGAATATTTCAACATTTAT
1 CACAACACATATTAAGCACATTTAACCACATTTAACCACATGAATATTTCAACATTTAT
** *
35275578 CACAACACATATTAAGCACATTTAGTCACATTTAATCACATGAATATTTCAACA
1 CACAACACATATTAAGCACATTTAACCACATTTAACCACATGAATATTTCAACA
35275632 CAAATCACAT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
58 26 0.55
59 21 0.45
ACGTcount: A:0.41, C:0.23, G:0.05, T:0.30
Consensus pattern (59 bp):
CACAACACATATTAAGCACATTTAACCACATTTAACCACATGAATATTTCAACATTTAT
Found at i:35276195 original size:36 final size:36
Alignment explanation
Indices: 35276147--35276283 Score: 156
Period size: 36 Copynumber: 3.9 Consensus size: 36
35276137 ATATTCACCT
* * * *
35276147 TCACATGACATGAATAATATACCCACATATTTTTTG
1 TCACATGGCATGAATAACATACCCACATATTTATTA
* * *
35276183 TCTCAAGGCATGAATAACAT----ACTTATTTATTA
1 TCACATGGCATGAATAACATACCCACATATTTATTA
* *
35276215 TCACATGGCATGAATAACATACCCATATATTTACTA
1 TCACATGGCATGAATAACATACCCACATATTTATTA
*
35276251 TCACATGGCATGAATAACATACCCACACATTTA
1 TCACATGGCATGAATAACATACCCACATATTTA
35276284 CTGTCAGAAC
Statistics
Matches: 83, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
32 27 0.33
36 56 0.67
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (36 bp):
TCACATGGCATGAATAACATACCCACATATTTATTA
Found at i:35279632 original size:79 final size:80
Alignment explanation
Indices: 35279523--35279681 Score: 207
Period size: 79 Copynumber: 2.0 Consensus size: 80
35279513 ACTTGTATCC
* * * *
35279523 AAATCCGTCAATTCATGGCACCCGATGCCTAGCATATAAACCGCAATAAGTGAGCCCA-ACTCTT
1 AAATCAGTCAATTCATGGCACCCGATGCCTAGCAGATAAACCACAATAAGTGAGCCCAGA-TCTA
35279587 GTTGGATTAACCAACA
65 GTTGGATTAACCAACA
* * * *
35279603 AAATCAGT-AATTCATGGTACCC-AGTGCCTAGCGGATAAACCACGATAAGTGAGCCTAGATCTA
1 AAATCAGTCAATTCATGGCACCCGA-TGCCTAGCAGATAAACCACAATAAGTGAGCCCAGATCTA
35279666 GTTGGATTAACCAACA
65 GTTGGATTAACCAACA
35279682 GTTTTGCGCC
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
78 1 0.01
79 60 0.87
80 8 0.12
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.23
Consensus pattern (80 bp):
AAATCAGTCAATTCATGGCACCCGATGCCTAGCAGATAAACCACAATAAGTGAGCCCAGATCTAG
TTGGATTAACCAACA
Found at i:35279855 original size:81 final size:81
Alignment explanation
Indices: 35279720--35279868 Score: 205
Period size: 81 Copynumber: 1.8 Consensus size: 81
35279710 CCGATGATCT
35279720 TGGCACCCAGTACCTAGCGGATAATCCGCAGAAGTGAGCCGAACTCTAGTTGGTTTAACCAACAA
1 TGGCACCCAGTACCTAGCGGATAATCCGCAGAAGTGAGCCGAACTCTAGTTGGTTTAACCAACAA
35279785 ATAATCCGTCAAATCC
66 ATAATCCGTCAAATCC
* * * *
35279801 TGGCACCTAGTTCCTAGCGGTTAAAT-CGC-GATAGTGAGGCC-AACTCTGGTTGGTTTAACCAA
1 TGGCACCCAGTACCTAGCGGAT-AATCCGCAGA-AGTGA-GCCGAACTCTAGTTGGTTTAACCAA
*
35279863 CGAATA
63 CAAATA
35279869 TTGTACAGTT
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
80 2 0.03
81 52 0.87
82 6 0.10
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (81 bp):
TGGCACCCAGTACCTAGCGGATAATCCGCAGAAGTGAGCCGAACTCTAGTTGGTTTAACCAACAA
ATAATCCGTCAAATCC
Found at i:35286508 original size:21 final size:21
Alignment explanation
Indices: 35286484--35286537 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
35286474 GTTGGGATGG
*
35286484 TTCTACCGATACAAGT-GTAAC
1 TTCTACCGATACAAGTCAT-AC
* * *
35286505 TTCTGCCGAAACAAGTCATGC
1 TTCTACCGATACAAGTCATAC
35286526 TTCTACCGATAC
1 TTCTACCGATAC
35286538 TAAAAACTCC
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (21 bp):
TTCTACCGATACAAGTCATAC
Found at i:35288953 original size:28 final size:28
Alignment explanation
Indices: 35288922--35289081 Score: 146
Period size: 28 Copynumber: 5.7 Consensus size: 28
35288912 CCAAACCCAG
35288922 AATAATGCTCTTTCGAGCCAGAATACAA
1 AATAATGCTCTTTCGAGCCAGAATACAA
* * * *
35288950 AAT-ATCGCTTTTTTGGGCCAGAATACAT
1 AATAAT-GCTCTTTCGAGCCAGAATACAA
* *
35288978 AATATTGCTCTCTT-GAGCTAGAATACAA
1 AATAATGCTCT-TTCGAGCCAGAATACAA
** * *
35289006 AATAACACTCTTTCGAGCCAAAATACAG
1 AATAATGCTCTTTCGAGCCAGAATACAA
* * *
35289034 AATATTGTTCTCTT-GAGCCAGAATACAG
1 AATAATGCTCT-TTCGAGCCAGAATACAA
*
35289062 AATAACGCTCTTTCGAGCCA
1 AATAATGCTCTTTCGAGCCA
35289082 AAGTTCAGAG
Statistics
Matches: 103, Mismatches: 23, Indels: 12
0.75 0.17 0.09
Matches are distributed among these distances:
27 6 0.06
28 92 0.89
29 5 0.05
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (28 bp):
AATAATGCTCTTTCGAGCCAGAATACAA
Found at i:35289001 original size:56 final size:56
Alignment explanation
Indices: 35288919--35289083 Score: 215
Period size: 56 Copynumber: 2.9 Consensus size: 56
35288909 TCGCCAAACC
* * * * * *
35288919 CAGAATAATGCTCT-TTCGAGCCAGAATACAAAATATCGCTTTTTTGGGCCAGAATA
1 CAGAATATTGCTCTCTT-GAGCCAGAATACAAAATAACGCTCTTTCGAGCCAAAATA
* * *
35288975 CATAATATTGCTCTCTTGAGCTAGAATACAAAATAACACTCTTTCGAGCCAAAATA
1 CAGAATATTGCTCTCTTGAGCCAGAATACAAAATAACGCTCTTTCGAGCCAAAATA
* *
35289031 CAGAATATTGTTCTCTTGAGCCAGAATACAGAATAACGCTCTTTCGAGCCAAA
1 CAGAATATTGCTCTCTTGAGCCAGAATACAAAATAACGCTCTTTCGAGCCAAA
35289084 GTTCAGAGTA
Statistics
Matches: 94, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
56 92 0.98
57 2 0.02
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (56 bp):
CAGAATATTGCTCTCTTGAGCCAGAATACAAAATAACGCTCTTTCGAGCCAAAATA
Found at i:35291850 original size:17 final size:17
Alignment explanation
Indices: 35291830--35291863 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
35291820 AGCAGAGGGA
*
35291830 AATGAAGGGAGAATGTG
1 AATGAAGAGAGAATGTG
35291847 AATGAAGAGAGAATGTG
1 AATGAAGAGAGAATGTG
35291864 TTGTGGATGA
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:0.44, C:0.00, G:0.38, T:0.18
Consensus pattern (17 bp):
AATGAAGAGAGAATGTG
Found at i:35293528 original size:38 final size:38
Alignment explanation
Indices: 35293443--35293529 Score: 95
Period size: 38 Copynumber: 2.3 Consensus size: 38
35293433 AGGGAGAGGG
** * *
35293443 AGAGGGAGAGGGTCGGAGTAGAGGGGAGGGACGGTGGG
1 AGAGGGAGAGAATCGGAGTAGAGGGAAGGGACGGTGGA
* *
35293481 GGAGAGGAGAGAATCGGAGTAG-GGGAAGGGATGGTAGGA
1 AGAG-GGAGAGAATCGGAGTAGAGGGAAGGGACGGT-GGA
35293520 AGAGGGAGAG
1 AGAGGGAGAG
35293530 GGAGAGGGAG
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
38 20 0.50
39 20 0.50
ACGTcount: A:0.30, C:0.03, G:0.59, T:0.08
Consensus pattern (38 bp):
AGAGGGAGAGAATCGGAGTAGAGGGAAGGGACGGTGGA
Found at i:35293529 original size:6 final size:6
Alignment explanation
Indices: 35293520--35293562 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
35293510 GATGGTAGGA
35293520 AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG A
1 AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG AGAGGG A
35293563 TGGGAGAACG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (6 bp):
AGAGGG
Found at i:35294000 original size:34 final size:34
Alignment explanation
Indices: 35293962--35294030 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
35293952 ATAATGATTT
35293962 GATTTTGATCAATGTCGAAAAATACAATTTTGAA
1 GATTTTGATCAATGTCGAAAAATACAATTTTGAA
35293996 GATTTTGATCAATGTCGAAAAATACAATTTTGAA
1 GATTTTGATCAATGTCGAAAAATACAATTTTGAA
35294030 G
1 G
35294031 GTGAATTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.35
Consensus pattern (34 bp):
GATTTTGATCAATGTCGAAAAATACAATTTTGAA
Found at i:35303258 original size:90 final size:89
Alignment explanation
Indices: 35303066--35303323 Score: 302
Period size: 91 Copynumber: 2.8 Consensus size: 89
35303056 TTAAATGTGT
** ** *
35303066 AAAAAGCCCTCAAACTTTTTTTAAAAAGCAATTAAGCCCCTTCTTTTTTTTTACACTCAATTGGG
1 AAAAAGCCCTCAAACTTTTTAAAAAAAAAAATTAAGCCCCTACTTTTTTTTTACACTCAATTGGG
35303131 TACTTGAACTACCAAAATGCATAA
66 TACTTGAACTACCAAAATGCATAA
* * *
35303155 AAAAAGGTCCTCAAACTTTTTCAAAAAAAAAAATCAAGCCCCTACTTTTTCTTTACACTCAATTG
1 AAAAA-GCCCTCAAACTTTTT-AAAAAAAAAAATTAAGCCCCTACTTTTTTTTTACACTCAATTG
* **
35303220 AGTACTTGAACTTTCAAAATGCAT-A
64 GGTACTTGAACTACCAAAATGCATAA
* * * * *
35303245 CAAAAGACCCTCAAACTTTTTAAAAAAAAGCAATTTAAGCCCTTGATTTTTTTTTTTGCACTCAA
1 AAAAAG-CCCTCAAACTTTTTAAAAAAAA--AAATTAAGCCCCT-A-CTTTTTTTTTACACTCAA
35303310 TTGGGTACTTGAAC
61 TTGGGTACTTGAAC
35303324 CACCCACAAT
Statistics
Matches: 142, Mismatches: 20, Indels: 10
0.83 0.12 0.06
Matches are distributed among these distances:
89 14 0.10
90 32 0.23
91 67 0.47
92 1 0.01
93 28 0.20
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.33
Consensus pattern (89 bp):
AAAAAGCCCTCAAACTTTTTAAAAAAAAAAATTAAGCCCCTACTTTTTTTTTACACTCAATTGGG
TACTTGAACTACCAAAATGCATAA
Found at i:35303455 original size:30 final size:31
Alignment explanation
Indices: 35303419--35303476 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
35303409 AATAAAAGTT
*
35303419 ATAAAAATTA-TTAAAGTTTAATAAAAAACA
1 ATAAAAAATATTTAAAGTTTAATAAAAAACA
* *
35303449 ATAAAAAATATTTAAATTTTATTAAAAA
1 ATAAAAAATATTTAAAGTTTAATAAAAA
35303477 TTAGAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 9 0.38
31 15 0.62
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (31 bp):
ATAAAAAATATTTAAAGTTTAATAAAAAACA
Found at i:35303900 original size:20 final size:20
Alignment explanation
Indices: 35303796--35303891 Score: 183
Period size: 20 Copynumber: 4.8 Consensus size: 20
35303786 TTTGATGCAT
*
35303796 TTTATAATTTTTTATAAAAA
1 TTTACAATTTTTTATAAAAA
35303816 TTTACAATTTTTTATAAAAA
1 TTTACAATTTTTTATAAAAA
35303836 TTTACAATTTTTTATAAAAA
1 TTTACAATTTTTTATAAAAA
35303856 TTTACAATTTTTTATAAAAA
1 TTTACAATTTTTTATAAAAA
35303876 TTTACAATTTTTTATA
1 TTTACAATTTTTTATA
35303892 GTTTTTTACG
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
20 75 1.00
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTACAATTTTTTATAAAAA
Found at i:35303900 original size:60 final size:59
Alignment explanation
Indices: 35303796--35303914 Score: 175
Period size: 60 Copynumber: 2.0 Consensus size: 59
35303786 TTTGATGCAT
*
35303796 TTTATAATTTTTTATAAAAATTTACAATTTTTTATAAAAATTTACAATTTTTTATAAAAA
1 TTTACAATTTTTTATAAAAATTTACAATTTTTTATAAAAATTTACAA-TTTTTATAAAAA
**** *
35303856 TTTACAATTTTTTATAAAAATTTACAATTTTTTATAGTTTTTTACGATTTTTATAAAAA
1 TTTACAATTTTTTATAAAAATTTACAATTTTTTATAAAAATTTACAATTTTTATAAAAA
35303915 AAATTCTAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
59 12 0.23
60 41 0.77
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (59 bp):
TTTACAATTTTTTATAAAAATTTACAATTTTTTATAAAAATTTACAATTTTTATAAAAA
Found at i:35303915 original size:40 final size:40
Alignment explanation
Indices: 35303796--35303915 Score: 154
Period size: 40 Copynumber: 3.0 Consensus size: 40
35303786 TTTGATGCAT
*
35303796 TTTATAATTTTTTATAAAAATTTACAATTTTT-TATAAAAA
1 TTTACAATTTTTTATAAAAATTTACAATTTTTATA-AAAAA
35303836 TTTACAATTTTTTATAAAAATTTACAATTTTT-TATAAAAA
1 TTTACAATTTTTTATAAAAATTTACAATTTTTATA-AAAAA
**** *
35303876 TTTACAATTTTTTATAGTTTTTTACGATTTTTATAAAAAA
1 TTTACAATTTTTTATAAAAATTTACAATTTTTATAAAAAA
35303916 AATTCTAATT
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
40 71 0.97
41 2 0.03
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (40 bp):
TTTACAATTTTTTATAAAAATTTACAATTTTTATAAAAAA
Found at i:35303931 original size:60 final size:60
Alignment explanation
Indices: 35303801--35303928 Score: 168
Period size: 60 Copynumber: 2.1 Consensus size: 60
35303791 TGCATTTTAT
* *
35303801 AATTTTTTATAAAAATTTACAATTTTTTATAAAAATTTACAATTTTTTATAAAAATTTAC
1 AATTTTTTATAAAAATTTACAATTTTTTATAAAAATTTACAATTTTTTAAAAAAAATTAC
**** *
35303861 AATTTTTTATAAAAATTTACAATTTTTTATAGTTTTTTACGATTTTTATAAAAAAAATT-C
1 AATTTTTTATAAAAATTTACAATTTTTTATAAAAATTTACAATTTTT-TAAAAAAAATTAC
35303921 TAATTTTT
1 -AATTTTT
35303929 ATATTTTTTA
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
60 43 0.73
61 16 0.27
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (60 bp):
AATTTTTTATAAAAATTTACAATTTTTTATAAAAATTTACAATTTTTTAAAAAAAATTAC
Found at i:35303934 original size:29 final size:30
Alignment explanation
Indices: 35303902--35303967 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 30
35303892 GTTTTTTACG
*
35303902 ATTTTTATAAAAAAAATT-CTAATTTTTAT
1 ATTTTTATAAAAAAAATTAATAATTTTTAT
** *
35303931 ATTTTT-TATTAAAATTTAATAATTTTTAT
1 ATTTTTATAAAAAAAATTAATAATTTTTAT
*
35303960 AATTTTAT
1 ATTTTTAT
35303968 TTATTTTTAC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 8 0.27
29 21 0.70
30 1 0.03
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (30 bp):
ATTTTTATAAAAAAAATTAATAATTTTTAT
Found at i:35310368 original size:17 final size:17
Alignment explanation
Indices: 35310348--35310389 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
35310338 CTCCCTTGAC
*
35310348 CTTTAACCTTCCATCTT
1 CTTTAACCTTCCATATT
*
35310365 CTTTAACCTTTCATATT
1 CTTTAACCTTCCATATT
35310382 CTTGTAAC
1 CTT-TAAC
35310390 TACTTTTTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.21, C:0.29, G:0.02, T:0.48
Consensus pattern (17 bp):
CTTTAACCTTCCATATT
Found at i:35310373 original size:24 final size:24
Alignment explanation
Indices: 35310328--35310375 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
35310318 ATGGATGTTC
* *
35310328 AACCTTTCATCTCCCTTGACCTTT
1 AACCTTCCATCTCCCTTAACCTTT
* *
35310352 AACCTTCCATCTTCTTTAACCTTT
1 AACCTTCCATCTCCCTTAACCTTT
35310376 CATATTCTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.19, C:0.35, G:0.02, T:0.44
Consensus pattern (24 bp):
AACCTTCCATCTCCCTTAACCTTT
Found at i:35312552 original size:20 final size:19
Alignment explanation
Indices: 35312503--35312541 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
35312493 CAAGCTTGAA
35312503 TACTCACGAAAAATAAAAT
1 TACTCACGAAAAATAAAAT
35312522 TACTCACGAAAAATAAAAT
1 TACTCACGAAAAATAAAAT
35312541 T
1 T
35312542 TACTTTGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.56, C:0.15, G:0.05, T:0.23
Consensus pattern (19 bp):
TACTCACGAAAAATAAAAT
Found at i:35316150 original size:24 final size:24
Alignment explanation
Indices: 35316114--35316159 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
35316104 ACATTCATCC
* *
35316114 AATTCATGCATTA-GCATTCAAAAG
1 AATTCAAGAATTATGCA-TCAAAAG
35316138 AATTCAAGAATTATGCATCAAA
1 AATTCAAGAATTATGCATCAAA
35316160 TGAAAAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.28
Consensus pattern (24 bp):
AATTCAAGAATTATGCATCAAAAG
Found at i:35330846 original size:30 final size:30
Alignment explanation
Indices: 35330806--35330875 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 30
35330796 AAGGGTCTAA
*
35330806 TTTT-TTTTTTAATTTTTAAGGGACCC-AAT
1 TTTTGTTTTTTAATTTTTAAGAG-CCCAAAT
*
35330835 TTTTGTTTTTTAGTTTTTAAGAGCCCAAAT
1 TTTTGTTTTTTAATTTTTAAGAGCCCAAAT
35330865 TTATTGTTTTT
1 TT-TTGTTTTT
35330876 ACCAACTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
29 7 0.19
30 21 0.58
31 8 0.22
ACGTcount: A:0.21, C:0.09, G:0.11, T:0.59
Consensus pattern (30 bp):
TTTTGTTTTTTAATTTTTAAGAGCCCAAAT
Found at i:35340156 original size:52 final size:52
Alignment explanation
Indices: 35340033--35340265 Score: 317
Period size: 52 Copynumber: 4.5 Consensus size: 52
35340023 GGGTCTGATC
35340033 ACTATGTGTCATCGTGAGTATATAAATCCTTTACGGATTATGAGG-CCAATG
1 ACTATGTGTCATCGTGAGTATATAAATCCTTTACGGATTATGAGGTCCAATG
35340084 ACTATGTGTCATCGTGAGTATATAAATCCTTTACGGATTATGAGGTCCAATG
1 ACTATGTGTCATCGTGAGTATATAAATCCTTTACGGATTATGAGGTCCAATG
* * * **
35340136 ACTATGCGTCATCGTGAGTATATAAATCCTGTAGGGATTATGAGGTCTGATG
1 ACTATGTGTCATCGTGAGTATATAAATCCTTTACGGATTATGAGGTCCAATG
* * * ** * * * * *
35340188 ACTACGTATCATCGTGAGTATATGAATCCTTTGTGGGTTATAAGGTTCGATA
1 ACTATGTGTCATCGTGAGTATATAAATCCTTTACGGATTATGAGGTCCAATG
35340240 ACTATGTGTCATCGTGAGTAT-TAAAT
1 ACTATGTGTCATCGTGAGTATATAAAT
35340266 GAAAATGAAT
Statistics
Matches: 161, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
51 49 0.30
52 112 0.70
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (52 bp):
ACTATGTGTCATCGTGAGTATATAAATCCTTTACGGATTATGAGGTCCAATG
Found at i:35341032 original size:21 final size:21
Alignment explanation
Indices: 35341008--35341059 Score: 76
Period size: 17 Copynumber: 2.7 Consensus size: 21
35340998 TAGAAGTAAG
35341008 ACTTGTATCGGTAGTAGAGTC
1 ACTTGTATCGGTAGTAGAGTC
35341029 ACTTGTA----TAGTAGAGTC
1 ACTTGTATCGGTAGTAGAGTC
35341046 ACTTGTATCGGTAG
1 ACTTGTATCGGTAG
35341060 AATTGTCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 17 0.63
21 10 0.37
ACGTcount: A:0.25, C:0.13, G:0.27, T:0.35
Consensus pattern (21 bp):
ACTTGTATCGGTAGTAGAGTC
Found at i:35345206 original size:23 final size:26
Alignment explanation
Indices: 35345182--35345229 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
35345172 GTTGTAAATA
35345182 AAAAT-ATCTC-T-AGAG-ATTTTCT
1 AAAATAATCTCTTCAGAGAATTTTCT
35345204 AAAATAATCTCTTCAGAGAATTTTCT
1 AAAATAATCTCTTCAGAGAATTTTCT
35345230 CTCTACAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.23
23 5 0.23
24 1 0.05
25 4 0.18
26 7 0.32
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.40
Consensus pattern (26 bp):
AAAATAATCTCTTCAGAGAATTTTCT
Found at i:35345493 original size:20 final size:18
Alignment explanation
Indices: 35345446--35345552 Score: 62
Period size: 20 Copynumber: 5.8 Consensus size: 18
35345436 GAAGATAAAC
35345446 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
35345463 ATTAAGA-TAATCATTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
** *
35345483 ATTAAATTAATAAAATACT
1 ATTAAATTAAT-ATTTAAT
35345502 ATTAGAA-TAAGTA-TTAA-
1 ATTA-AATTAA-TATTTAAT
*
35345519 ATTAAATTTAATATTAAATT
1 ATTAAA-TTAATATTTAA-T
*
35345539 ATTAAAATAATATT
1 ATTAAATTAATATT
35345553 ATTTTTGGAA
Statistics
Matches: 70, Mismatches: 8, Indels: 22
0.70 0.08 0.22
Matches are distributed among these distances:
16 2 0.03
17 14 0.20
18 9 0.13
19 20 0.29
20 25 0.36
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:35345656 original size:9 final size:9
Alignment explanation
Indices: 35345636--35345666 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
35345626 AAAATATCAT
35345636 ATTAATTTTA
1 ATTAA-TTTA
35345646 ATTAATTTA
1 ATTAATTTA
35345655 ATTAATTTA
1 ATTAATTTA
35345664 ATT
1 ATT
35345667 TTACTTGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.76
10 5 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
ATTAATTTA
Found at i:35356523 original size:90 final size:90
Alignment explanation
Indices: 35356370--35356553 Score: 350
Period size: 90 Copynumber: 2.0 Consensus size: 90
35356360 TGCTTTTGGA
35356370 ATTTTGCTAGCCTATTCGAGGACGATTCTTCTACCAACCTAGGGGTTAATATGGTTACGAAGGAG
1 ATTTTGCTAGCCTATTCGAGGACGATTCTTCTACCAACCTAGGGGTTAATATGGTTACGAAGGAG
35356435 GCTAATTTTGAGGGAGGAAACACAC
66 GCTAATTTTGAGGGAGGAAACACAC
* *
35356460 ATTTTGCTAGCCTATTCGAGGACTATTCTTCTACCAACCTAGGGGTTAATATGGTTATGAAGGAG
1 ATTTTGCTAGCCTATTCGAGGACGATTCTTCTACCAACCTAGGGGTTAATATGGTTACGAAGGAG
35356525 GCTAATTTTGAGGGAGGAAACACAC
66 GCTAATTTTGAGGGAGGAAACACAC
35356550 ATTT
1 ATTT
35356554 GGAGGTTGTG
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
90 92 1.00
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (90 bp):
ATTTTGCTAGCCTATTCGAGGACGATTCTTCTACCAACCTAGGGGTTAATATGGTTACGAAGGAG
GCTAATTTTGAGGGAGGAAACACAC
Found at i:35356596 original size:12 final size:13
Alignment explanation
Indices: 35356574--35356638 Score: 57
Period size: 12 Copynumber: 5.1 Consensus size: 13
35356564 GATACAGATG
35356574 AGGAGAAAGAAGA
1 AGGAGAAAGAAGA
35356587 AGGA-AAAGAAGA
1 AGGAGAAAGAAGA
* *
35356599 AGAACGAGAAGAGGA
1 AGGA-GA-AAGAAGA
35356614 A-GAGAAAGAAGA
1 AGGAGAAAGAAGA
35356626 A--AGAAAGGAAGA
1 AGGAGAAA-GAAGA
35356638 A
1 A
35356639 CATACTGTCG
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
11 5 0.11
12 24 0.55
13 6 0.14
14 2 0.05
15 7 0.16
ACGTcount: A:0.63, C:0.02, G:0.35, T:0.00
Consensus pattern (13 bp):
AGGAGAAAGAAGA
Found at i:35363069 original size:37 final size:36
Alignment explanation
Indices: 35363006--35363122 Score: 107
Period size: 37 Copynumber: 3.2 Consensus size: 36
35362996 ATTCCAAAAA
*
35363006 TAATATTATTTTAATTGTTTAATATTAAATTTAAT-T
1 TAATATTATTTTAATAGTTTAATATT-AATTTAATAT
*
35363042 TAATACTTATTTTAATAGTATT-TTATTAATTTAATAT
1 TAATA-TTATTTTAATAGT-TTAATATTAATTTAATAT
* *
35363079 TAAAGTGATTATCTTAATA-TTAAAT-TTAATTTAATAT
1 T-AA-T-ATTATTTTAATAGTTTAATATTAATTTAATAT
*
35363116 TTATATT
1 TAATATT
35363123 TTAGATAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
34 3 0.04
35 1 0.01
36 14 0.21
37 32 0.47
38 6 0.09
39 11 0.16
40 1 0.01
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (36 bp):
TAATATTATTTTAATAGTTTAATATTAATTTAATAT
Found at i:35363089 original size:20 final size:18
Alignment explanation
Indices: 35363007--35363116 Score: 66
Period size: 19 Copynumber: 5.9 Consensus size: 18
35362997 TTCCAAAAAT
* * *
35363007 AATATTATTTTAATTGTTT
1 AATATTAATTTAA-TATTA
35363026 AATATTAAATTTAAT-TT-
1 AATATT-AATTTAATATTA
* *
35363043 AATACTTATTTTAATAGTA
1 AATA-TTAATTTAATATTA
**
35363062 TTTTATTAATTTAATATTA
1 -AATATTAATTTAATATTA
35363081 AAGTGATT-ATCTTAATATTA
1 AA-T-ATTAAT-TTAATATTA
35363101 AAT-TTAATTTAATATT
1 AATATTAATTTAATATT
35363117 TATATTTTAG
Statistics
Matches: 73, Mismatches: 9, Indels: 20
0.72 0.09 0.20
Matches are distributed among these distances:
17 21 0.29
18 7 0.10
19 23 0.32
20 22 0.30
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (18 bp):
AATATTAATTTAATATTA
Found at i:35363150 original size:20 final size:20
Alignment explanation
Indices: 35363115--35363161 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
35363105 TAATTTAATA
35363115 TTTATATTTTAGATAAAAAT
1 TTTATATTTTAGATAAAAAT
35363135 TTTATTATTTTA-AT-AAAAT
1 TTTA-TATTTTAGATAAAAAT
*
35363154 TTAATATT
1 TTTATATT
35363162 AAATTTAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 4 0.16
19 8 0.32
20 6 0.24
21 7 0.28
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TTTATATTTTAGATAAAAAT
Found at i:35363156 original size:18 final size:19
Alignment explanation
Indices: 35363114--35363161 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
35363104 TTAATTTAAT
35363114 ATTTATATTTTAGATAAAA
1 ATTTATATTTTAGATAAAA
35363133 ATTTTATTATTTTA-AT-AAA
1 A-TTTA-TATTTTAGATAAAA
35363152 ATTTAATATT
1 ATTT-ATATT
35363162 AAATTTAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 7 0.27
19 6 0.23
20 6 0.23
21 7 0.27
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
ATTTATATTTTAGATAAAA
Found at i:35363162 original size:21 final size:21
Alignment explanation
Indices: 35363115--35363152 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
35363105 TAATTTAATA
35363115 TTTA-TATTTTAGATAAAAAT
1 TTTATTATTTTAGATAAAAAT
35363135 TTTATTATTTTA-ATAAAA
1 TTTATTATTTTAGATAAAA
35363153 TTTAATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (21 bp):
TTTATTATTTTAGATAAAAAT
Found at i:35373000 original size:14 final size:14
Alignment explanation
Indices: 35372981--35373012 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
35372971 ATTGAAGCTT
35372981 ACTATCTCTAGACC
1 ACTATCTCTAGACC
35372995 ACTATCTCTAGACC
1 ACTATCTCTAGACC
35373009 ACTA
1 ACTA
35373013 GGACTATTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.34, G:0.06, T:0.28
Consensus pattern (14 bp):
ACTATCTCTAGACC
Found at i:35374584 original size:44 final size:44
Alignment explanation
Indices: 35374521--35374648 Score: 220
Period size: 44 Copynumber: 2.9 Consensus size: 44
35374511 TTCGATGATG
35374521 AAATTACTATGTTTGTTCCAAGTTTGTTTCAATACATCTCCTTT
1 AAATTACTATGTTTGTTCCAAGTTTGTTTCAATACATCTCCTTT
35374565 AAATTACTATGTTTGTTCCAAGTTTGTTTCAATACATCTCCTTT
1 AAATTACTATGTTTGTTCCAAGTTTGTTTCAATACATCTCCTTT
* * * *
35374609 AAATTACTATATTTGTTTCAAGTTTGTTCCAACACATCTC
1 AAATTACTATGTTTGTTCCAAGTTTGTTTCAATACATCTC
35374649 ATTTGAACAA
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 80 1.00
ACGTcount: A:0.27, C:0.19, G:0.09, T:0.46
Consensus pattern (44 bp):
AAATTACTATGTTTGTTCCAAGTTTGTTTCAATACATCTCCTTT
Found at i:35374848 original size:33 final size:33
Alignment explanation
Indices: 35374806--35374886 Score: 117
Period size: 33 Copynumber: 2.5 Consensus size: 33
35374796 TCTGTCCGTG
* *
35374806 AGGAGTGGTGTACTGCATTGGTAATGGGCTAGA
1 AGGAGTGGTGTACTGCAGTGATAATGGGCTAGA
* *
35374839 AGGAGTGGTGTACTACGGTGATAATGGGCTAGA
1 AGGAGTGGTGTACTGCAGTGATAATGGGCTAGA
*
35374872 AGGAGTGGAGTACTG
1 AGGAGTGGTGTACTG
35374887 TGGTGGCTCG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.26, C:0.09, G:0.41, T:0.25
Consensus pattern (33 bp):
AGGAGTGGTGTACTGCAGTGATAATGGGCTAGA
Found at i:35382977 original size:136 final size:138
Alignment explanation
Indices: 35382718--35383012 Score: 386
Period size: 136 Copynumber: 2.1 Consensus size: 138
35382708 TAACTTTAAA
* * * * *
35382718 TTAAATTAAAAATAGCAAAATAATTTACCTTTGTTTTAGCTTTCTTCCCTTTAATCTACTTTACT
1 TTAAATTAAAATTA--AAAATAATTTACCTCTCTTTTAACTTTCTTCCCTTTAATCTACTCTACT
* **
35382783 AAACAAAAAAATTTATAGCAAAGCACATAAACATTAAACTAAACAGATAATTTATAATAATTACT
64 AAACAAAAAAATTTATAACAAA-CACATAAACATTAAACTAAACAGATAATTTATAATAATTAAA
35382848 AACAAAATAACT
128 AACAAAATAA-T
35382860 TTAAATTAAAATTAAAAA-AA-TTACCTCTCTTTTAACTTTCTTTCCCTTTAATCTACTCTACTA
1 TTAAATTAAAATTAAAAATAATTTACCTCTCTTTTAACTTTC-TTCCCTTTAATCTACTCTACTA
* *
35382923 AATAAAAAAA-TTATAACAAA-TCATAAACATTAAACTAAACTA-ATAATTTATAATAATTAAAA
65 AACAAAAAAATTTATAACAAACACATAAACATTAAACTAAAC-AGATAATTTATAATAATTAAAA
35382985 ACAAAATAAT
129 ACAAAATAAT
*
35382995 TGTAAAAT-AAATTAAAAA
1 T-TAAATTAAAATTAAAAA
35383013 CAAGAAAAAT
Statistics
Matches: 139, Mismatches: 11, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
135 12 0.09
136 51 0.37
137 1 0.01
138 26 0.19
139 32 0.23
140 4 0.03
142 13 0.09
ACGTcount: A:0.49, C:0.14, G:0.02, T:0.35
Consensus pattern (138 bp):
TTAAATTAAAATTAAAAATAATTTACCTCTCTTTTAACTTTCTTCCCTTTAATCTACTCTACTAA
ACAAAAAAATTTATAACAAACACATAAACATTAAACTAAACAGATAATTTATAATAATTAAAAAC
AAAATAAT
Found at i:35383007 original size:27 final size:25
Alignment explanation
Indices: 35382964--35383015 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 25
35382954 AAACTAAACT
*
35382964 AATAATTTATAATAATTAAAAACAA
1 AATAATTTAAAATAATTAAAAACAA
35382989 AATAATTGTAAAATAAATTAAAAACAA
1 AATAATT-TAAAAT-AATTAAAAACAA
35383016 GAAAAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 7 0.29
26 5 0.21
27 12 0.50
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (25 bp):
AATAATTTAAAATAATTAAAAACAA
Found at i:35383038 original size:136 final size:138
Alignment explanation
Indices: 35382762--35383044 Score: 326
Period size: 136 Copynumber: 2.1 Consensus size: 138
35382752 TTTAGCTTTC
* *
35382762 TTCCCTTTAATCTACTTTACTAAACAAAAAAATTTATAGCAAAGCACATAAACATTAAACTAAAC
1 TTCCCTTTAATCTACTCTACTAAACAAAAAAATTTATAACAAA-CACATAAACATTAAACTAAAC
** * ** ** ****
35382827 AGATAATTTATAATAATTACTAACAAAATAACTTTAAATTAAAATTAAAAAAATTACCTCTCTTT
65 AGATAATTTATAATAATTAAAAACAAAATAACTTTAAAATAAAATTAAAAAAAAAAAATCAAAAT
*
35382892 TAACTTTCT
130 TAACTCTCT
* *
35382901 TTCCCTTTAATCTACTCTACTAAATAAAAAAA-TTATAACAAA-TCATAAACATTAAACTAAACT
1 TTCCCTTTAATCTACTCTACTAAACAAAAAAATTTATAACAAACACATAAACATTAAACTAAAC-
35382964 A-ATAATTTATAATAATTAAAAACAAAATAA-TTGTAAAAT-AAATTAAAAACAAGAAAAAT-AA
65 AGATAATTTATAATAATTAAAAACAAAATAACTT-TAAAATAAAATTAAAAA-AA-AAAAATCAA
*
35383025 AATTACCTCTCT
127 AATTAACTCTCT
35383037 TTCCCTTT
1 TTCCCTTT
35383045 CTTCTCCTTC
Statistics
Matches: 123, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
135 12 0.10
136 69 0.56
137 3 0.02
138 9 0.07
139 30 0.24
ACGTcount: A:0.50, C:0.15, G:0.02, T:0.33
Consensus pattern (138 bp):
TTCCCTTTAATCTACTCTACTAAACAAAAAAATTTATAACAAACACATAAACATTAAACTAAACA
GATAATTTATAATAATTAAAAACAAAATAACTTTAAAATAAAATTAAAAAAAAAAAATCAAAATT
AACTCTCT
Found at i:35383549 original size:10 final size:10
Alignment explanation
Indices: 35383536--35383560 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
35383526 TTGGTAATTT
35383536 TTTTATATTA
1 TTTTATATTA
35383546 TTTTATATTA
1 TTTTATATTA
35383556 TTTTA
1 TTTTA
35383561 GTAAAAAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTTATATTA
Found at i:35384884 original size:107 final size:107
Alignment explanation
Indices: 35384698--35384912 Score: 430
Period size: 107 Copynumber: 2.0 Consensus size: 107
35384688 ATTTTTAATA
35384698 GCCATTTGAACACCAAATTTGATCCAACTTTAATCGTTAATGTACAACTTGTTTCCTATCCCTTA
1 GCCATTTGAACACCAAATTTGATCCAACTTTAATCGTTAATGTACAACTTGTTTCCTATCCCTTA
35384763 CTTGAATACAATTCTAACGCGACTTTAATTGAGTCCAGCTCG
66 CTTGAATACAATTCTAACGCGACTTTAATTGAGTCCAGCTCG
35384805 GCCATTTGAACACCAAATTTGATCCAACTTTAATCGTTAATGTACAACTTGTTTCCTATCCCTTA
1 GCCATTTGAACACCAAATTTGATCCAACTTTAATCGTTAATGTACAACTTGTTTCCTATCCCTTA
35384870 CTTGAATACAATTCTAACGCGACTTTAATTGAGTCCAGCTCG
66 CTTGAATACAATTCTAACGCGACTTTAATTGAGTCCAGCTCG
35384912 G
1 G
35384913 TTAAGTCAGC
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
107 108 1.00
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (107 bp):
GCCATTTGAACACCAAATTTGATCCAACTTTAATCGTTAATGTACAACTTGTTTCCTATCCCTTA
CTTGAATACAATTCTAACGCGACTTTAATTGAGTCCAGCTCG
Found at i:35392205 original size:27 final size:27
Alignment explanation
Indices: 35392175--35392228 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
35392165 TGGAAATAAT
*
35392175 AATGAT-TTACCACCATTGCTGCCACAA
1 AATGATATT-CCACCAGTGCTGCCACAA
*
35392202 AATGATATTCCTCCAGTGCTGCCACAA
1 AATGATATTCCACCAGTGCTGCCACAA
35392229 GTAGTTAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 22 0.92
28 2 0.08
ACGTcount: A:0.31, C:0.30, G:0.13, T:0.26
Consensus pattern (27 bp):
AATGATATTCCACCAGTGCTGCCACAA
Found at i:35412655 original size:23 final size:25
Alignment explanation
Indices: 35412629--35412674 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
35412619 CCAATTAGGG
35412629 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
35412652 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
35412675 TGGATCCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:35419089 original size:118 final size:118
Alignment explanation
Indices: 35418872--35419176 Score: 377
Period size: 118 Copynumber: 2.6 Consensus size: 118
35418862 CACGTCTTAT
* * *
35418872 ACACACGGAG-GTGTTTCAAGACCTTGT-AACCACTGGAG-TTTATTTTTTGAAATATCCAAAA-
1 ACACAC-GAGCGTGTTTCAAGACCGTGTGAA-CACTAGAGCTTTATTTTCTGAAATAT-CAAAAT
* *
35418933 AGCACACGGTTTACAGACACGAGCGTGAGAGAAGCGAAGACAGGCCCACGGCCACC
63 AGCACACGGTTTACAGACACAAACGTGAGAGAAGCGAAGACAGGCCCACGGCCACC
* * * * *
35418989 ACATACGGGTGTGTTTCAAGACCGTGTGAACACTAGAGCCTTATTTTCTGAAATGTCAAAATAGC
1 ACACACGAGCGTGTTTCAAGACCGTGTGAACACTAGAGCTTTATTTTCTGAAATATCAAAATAGC
* * * *
35419054 ACACGGTTTATAGACACAAACGTGGGAGAAGCGAAGACAGGCCCACGGTCACG
66 ACACGGTTTACAGACACAAACGTGAGAGAAGCGAAGACAGGCCCACGGCCACC
* * * * *
35419107 ACACACGAGCATGTTCCAAGACCGTGTGACCACTAGAGCTTTA-TTTCTGAAATTTCAAAATAGT
1 ACACACGAGCGTGTTTCAAGACCGTGTGAACACTAGAGCTTTATTTTCTGAAATATCAAAATAGC
35419171 ACACGG
66 ACACGG
35419177 CCTGAAGACA
Statistics
Matches: 162, Mismatches: 22, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
116 2 0.01
117 58 0.36
118 102 0.63
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.22
Consensus pattern (118 bp):
ACACACGAGCGTGTTTCAAGACCGTGTGAACACTAGAGCTTTATTTTCTGAAATATCAAAATAGC
ACACGGTTTACAGACACAAACGTGAGAGAAGCGAAGACAGGCCCACGGCCACC
Found at i:35419751 original size:3 final size:3
Alignment explanation
Indices: 35419726--35419815 Score: 59
Period size: 3 Copynumber: 30.7 Consensus size: 3
35419716 TTACTTTTTG
* * *
35419726 TTA TT- TTA ATA TTA TT- TTC TTA TTA TTTG TTA TTTA GTT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA -TTA -TTA TTA TTA
35419771 TTA TTA TTTA TT- TTA TT- TTA TT- TTA TTTA TTA TTA TTA TT- TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
35419814 TT
1 TT
35419816 TGTCATTTGT
Statistics
Matches: 70, Mismatches: 6, Indels: 22
0.71 0.06 0.22
Matches are distributed among these distances:
2 14 0.20
3 43 0.61
4 13 0.19
ACGTcount: A:0.24, C:0.01, G:0.02, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:35419771 original size:23 final size:21
Alignment explanation
Indices: 35419726--35419815 Score: 83
Period size: 23 Copynumber: 4.0 Consensus size: 21
35419716 TTACTTTTTG
* *
35419726 TTATTTTAATATTATTTTCTTA
1 TTATTTTTAT-TTATTTTATTA
35419748 TTATTTGTTATTTAGTTTTATTA
1 TTATTT-TTATTTA-TTTTATTA
35419771 TTATTATTTATTTTATTTTATT-
1 TTATT-TTTA-TTTATTTTATTA
35419793 TTATTTATTATTATTATTTTATT
1 TTATTT-TTA-T-TTATTTTATT
35419816 TGTCATTTGT
Statistics
Matches: 60, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
21 1 0.02
22 19 0.32
23 35 0.58
24 5 0.08
ACGTcount: A:0.24, C:0.01, G:0.02, T:0.72
Consensus pattern (21 bp):
TTATTTTTATTTATTTTATTA
Found at i:35419777 original size:29 final size:29
Alignment explanation
Indices: 35419722--35419811 Score: 98
Period size: 29 Copynumber: 3.1 Consensus size: 29
35419712 TTCTTTACTT
* *
35419722 TTTGTTATTTTAATATTATT-TTCTTATTA
1 TTTGTTATTTT-ATTTTATTATTATTATTA
35419751 TTTGTTA-TTTAGTTTTATTATTATTATT-
1 TTTGTTATTTTA-TTTTATTATTATTATTA
35419779 TATT-TTATTTTATTTTATTTATTATTATTA
1 T-TTGTTATTTTATTTTA-TTATTATTATTA
35419809 TTT
1 TTT
35419812 TATTTGTCAT
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
27 1 0.02
28 18 0.34
29 33 0.62
30 1 0.02
ACGTcount: A:0.23, C:0.01, G:0.03, T:0.72
Consensus pattern (29 bp):
TTTGTTATTTTATTTTATTATTATTATTA
Found at i:35419783 original size:4 final size:5
Alignment explanation
Indices: 35419726--35419816 Score: 58
Period size: 5 Copynumber: 16.2 Consensus size: 5
35419716 TTACTTTTTG
* *
35419726 TTATT TTAATA TTATT TTCTT ATTATT TGT-TAT TTAGTT TTATT ATTATTAT
1 TTATT TT-ATT TTATT TTATT -TTATT T-TAT-T TTA-TT TTATT -TTA-T-T
35419778 TTATT TTATT TTATT TTATTT ATTATT ATTATT TTATT T
1 TTATT TTATT TTATT TTA-TT -TTATT -TTATT TTATT T
35419817 GTCATTTGTC
Statistics
Matches: 71, Mismatches: 4, Indels: 22
0.73 0.04 0.23
Matches are distributed among these distances:
5 33 0.46
6 29 0.41
7 8 0.11
8 1 0.01
ACGTcount: A:0.24, C:0.01, G:0.02, T:0.73
Consensus pattern (5 bp):
TTATT
Found at i:35419786 original size:28 final size:27
Alignment explanation
Indices: 35419745--35419816 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 27
35419735 TATTATTTTC
*
35419745 TTATTATT-TGTTATTTAGTTTTA-TTA
1 TTATTATTATTTTATTTA-TTTTATTTA
35419771 TTATTATTTATTTTATTTTATTTTATTTA
1 TTATTA-TTATTTTA-TTTATTTTATTTA
35419800 TTATTATTATTTTATTT
1 TTATTATTATTTTATTT
35419817 GTCATTTGTC
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
26 6 0.15
27 5 0.12
28 17 0.41
29 13 0.32
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (27 bp):
TTATTATTATTTTATTTATTTTATTTA
Found at i:35419816 original size:23 final size:23
Alignment explanation
Indices: 35419737--35419815 Score: 92
Period size: 23 Copynumber: 3.4 Consensus size: 23
35419727 TATTTTAATA
* *
35419737 TTATTTTCTTATTATTTGTTA-T
1 TTATTTTATTATTATTTATTATT
35419759 TTAGTTTTATTATTA-TTATTTATT
1 TTA-TTTTATTATTATTTA-TTATT
35419783 TTATTTTATT-TTATTTATTATT
1 TTATTTTATTATTATTTATTATT
35419805 ATTATTTTATT
1 -TTATTTTATT
35419816 TGTCATTTGT
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
22 13 0.26
23 33 0.66
24 4 0.08
ACGTcount: A:0.23, C:0.01, G:0.03, T:0.73
Consensus pattern (23 bp):
TTATTTTATTATTATTTATTATT
Found at i:35422206 original size:8 final size:8
Alignment explanation
Indices: 35422207--35422236 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
35422197 AAAAGTAAAA
35422207 AAAAAAGT
1 AAAAAAGT
35422215 AAAAAAGT
1 AAAAAAGT
*
35422223 AAAAAAAT
1 AAAAAAGT
35422231 AAAAAA
1 AAAAAA
35422237 AAATTGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (8 bp):
AAAAAAGT
Found at i:35422211 original size:12 final size:12
Alignment explanation
Indices: 35422194--35422252 Score: 55
Period size: 12 Copynumber: 4.7 Consensus size: 12
35422184 TTTATTATTT
35422194 AAAAAAAGTAAA
1 AAAAAAAGTAAA
35422206 AAAAAAAGTAAA
1 AAAAAAAGTAAA
**
35422218 AAAGTAAAAAAATAA
1 AAA--AAAAGTA-AA
* *
35422233 AAAAAAATTGAA
1 AAAAAAAGTAAA
35422245 AAAAAAAG
1 AAAAAAAG
35422253 AGAAAAAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
12 24 0.63
13 4 0.11
14 5 0.13
15 5 0.13
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.10
Consensus pattern (12 bp):
AAAAAAAGTAAA
Found at i:35422220 original size:20 final size:19
Alignment explanation
Indices: 35422195--35422260 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 19
35422185 TTATTATTTA
35422195 AAAAAAGTAAAAAAAAAAG
1 AAAAAAGTAAAAAAAAAAG
35422214 TAAAAAAGTAAAAAAATAAA-
1 -AAAAAAGTAAAAAAA-AAAG
*
35422234 AAAAAATTGAAAAAAAAAGAG
1 AAAAAAGT-AAAAAAAAA-AG
35422255 AAAAAA
1 AAAAAA
35422261 TTGGGAAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
19 9 0.22
20 23 0.56
21 9 0.22
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (19 bp):
AAAAAAGTAAAAAAAAAAG
Found at i:35422269 original size:21 final size:21
Alignment explanation
Indices: 35422195--35422277 Score: 66
Period size: 21 Copynumber: 4.1 Consensus size: 21
35422185 TTATTATTTA
* * *
35422195 AAAAAAGTAAAAAAAAAAG-T
1 AAAAAATTGAAAAAAAAAGAG
*
35422215 AAAAAAGT-AAAAAAATAA-A-
1 AAAAAATTGAAAAAAA-AAGAG
35422234 AAAAAATTGAAAAAAAAAGAG
1 AAAAAATTGAAAAAAAAAGAG
** *
35422255 AAAAAATTGGGAAAATAAGAG
1 AAAAAATTGAAAAAAAAAGAG
35422276 AA
1 AA
35422278 GATAAAGACA
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
19 16 0.30
20 18 0.33
21 20 0.37
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (21 bp):
AAAAAATTGAAAAAAAAAGAG
Found at i:35423349 original size:23 final size:25
Alignment explanation
Indices: 35423323--35423368 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
35423313 CCAATTAGGG
35423323 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
35423346 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
35423369 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:35430538 original size:31 final size:28
Alignment explanation
Indices: 35430458--35430551 Score: 104
Period size: 31 Copynumber: 3.3 Consensus size: 28
35430448 TTAATATAAT
35430458 ATTTGGTATTTAAACTTGATTTTTTTTA
1 ATTTGGTATTTAAACTTGATTTTTTTTA
* **
35430486 ATTTAGTACCTAAA-TT--TTTTTTTATA
1 ATTTGGTATTTAAACTTGATTTTTTT-TA
35430512 ATTTGGTATTTAAACTTGATACTTTTTTCTA
1 ATTTGGTATTTAAACTTGAT--TTTTTT-TA
35430543 ATTTGGTAT
1 ATTTGGTAT
35430552 CTAAGTTTGA
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
25 7 0.13
26 13 0.25
27 4 0.08
28 11 0.21
29 1 0.02
31 17 0.32
ACGTcount: A:0.27, C:0.06, G:0.10, T:0.57
Consensus pattern (28 bp):
ATTTGGTATTTAAACTTGATTTTTTTTA
Found at i:35430538 original size:32 final size:31
Alignment explanation
Indices: 35430502--35430591 Score: 90
Period size: 32 Copynumber: 2.8 Consensus size: 31
35430492 TACCTAAATT
*
35430502 TTTTTTTATAATTTGGTATTTAAACTTGATAC
1 TTTTTTT-TAATTTGGTATTTAAACTTGACAC
* * **
35430534 TTTTTTCTAATTTGGTATCTAAGTTTGACAC
1 TTTTTTTTAATTTGGTATTTAAACTTGACAC
* * *
35430565 TCTTTTTTTAAATTGATACTTAAACTT
1 T-TTTTTTTAATTTGGTATTTAAACTT
35430592 TTTGGGATCC
Statistics
Matches: 45, Mismatches: 12, Indels: 2
0.76 0.20 0.03
Matches are distributed among these distances:
31 21 0.47
32 24 0.53
ACGTcount: A:0.27, C:0.10, G:0.09, T:0.54
Consensus pattern (31 bp):
TTTTTTTTAATTTGGTATTTAAACTTGACAC
Found at i:35430894 original size:34 final size:35
Alignment explanation
Indices: 35430827--35430910 Score: 93
Period size: 34 Copynumber: 2.4 Consensus size: 35
35430817 TAAATACCAA
35430827 ATTAAAAAATATATTCAAATTTAAATACTAAATTG
1 ATTAAAAAATATATTCAAATTTAAATACTAAATTG
**
35430862 ACTTAAAAAA-ATA-TCAAATTTATTTA-TCAAATTG
1 A-TTAAAAAATATATTCAAATTTAAATACT-AAATTG
*
35430896 AATAAAAAATTATAT
1 ATTAAAAAA-TATAT
35430911 ACTAAAATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
33 8 0.20
34 18 0.44
35 7 0.17
36 8 0.20
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (35 bp):
ATTAAAAAATATATTCAAATTTAAATACTAAATTG
Found at i:35431488 original size:9 final size:9
Alignment explanation
Indices: 35431475--35431528 Score: 54
Period size: 9 Copynumber: 5.8 Consensus size: 9
35431465 AATATATAAA
*
35431475 AAATTAACT
1 AAATTAACC
*
35431484 GAATTAACC
1 AAATTAACC
*
35431493 AAATGAACC
1 AAATTAACC
*
35431502 GAAATTAACT
1 -AAATTAACC
35431512 AAATTAACC
1 AAATTAACC
35431521 GAAATTAA
1 -AAATTAA
35431529 AGTATTGAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
9 22 0.61
10 14 0.39
ACGTcount: A:0.54, C:0.15, G:0.07, T:0.24
Consensus pattern (9 bp):
AAATTAACC
Found at i:35431509 original size:19 final size:19
Alignment explanation
Indices: 35431485--35431528 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
35431475 AAATTAACTG
35431485 AATTAACCAAATGAACCGA
1 AATTAACCAAATGAACCGA
* *
35431504 AATTAACTAAATTAACCGA
1 AATTAACCAAATGAACCGA
35431523 AATTAA
1 AATTAA
35431529 AGTATTGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.55, C:0.16, G:0.07, T:0.23
Consensus pattern (19 bp):
AATTAACCAAATGAACCGA
Found at i:35454272 original size:66 final size:66
Alignment explanation
Indices: 35454188--35454318 Score: 208
Period size: 66 Copynumber: 2.0 Consensus size: 66
35454178 CATTTAAACA
* * * *
35454188 ATAATTTGGCACAGTAATCATATTATCATTAAAGCACATATCAGATTACACAAAATCATATTAAT
1 ATAATCTGGCACAATAATCATATTATCATTAAAGCACATATCACATTACACAAAATCACATTAAT
35454253 G
66 G
* *
35454254 ATAATCTGGCACAATAATCATATTCTCATTTAAGCACATATCACATTACACAAAATCACATTAAT
1 ATAATCTGGCACAATAATCATATTATCATTAAAGCACATATCACATTACACAAAATCACATTAAT
35454319 ATTCAAGCAT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.31
Consensus pattern (66 bp):
ATAATCTGGCACAATAATCATATTATCATTAAAGCACATATCACATTACACAAAATCACATTAAT
G
Found at i:35455410 original size:41 final size:42
Alignment explanation
Indices: 35455315--35455413 Score: 139
Period size: 42 Copynumber: 2.4 Consensus size: 42
35455305 AAAGATAGAG
*
35455315 GAAGCTACATGGAAAAAGCCACATTCAAGAAATGACAAAGGAA
1 GAAGCTACGTGGAAAAAGCCACATTCAAGAAATGACAAA-GAA
* *
35455358 GAAGCTACGTGGAAAAA-CCACTTTCATGAAATGACAAA-AA
1 GAAGCTACGTGGAAAAAGCCACATTCAAGAAATGACAAAGAA
35455398 GAAAGCTACGTGGAAA
1 G-AAGCTACGTGGAAA
35455414 GCATCTACTA
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
40 3 0.06
41 14 0.27
42 19 0.37
43 16 0.31
ACGTcount: A:0.48, C:0.16, G:0.21, T:0.14
Consensus pattern (42 bp):
GAAGCTACGTGGAAAAAGCCACATTCAAGAAATGACAAAGAA
Found at i:35457413 original size:50 final size:50
Alignment explanation
Indices: 35457320--35457414 Score: 136
Period size: 50 Copynumber: 1.9 Consensus size: 50
35457310 GCAAATGTAT
** * *
35457320 TAATGCAAAACATTAAACAAAGATGCATTTTTCAAATATAAAACACATAA
1 TAATGCAAAACATTAAACAAAGATGCATTTAACAAACACAAAACACATAA
* *
35457370 TAATGCAAAATATTAAATAAAGATGCATTTAACAAACACAAAACA
1 TAATGCAAAACATTAAACAAAGATGCATTTAACAAACACAAAACA
35457415 TAATTAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 39 1.00
ACGTcount: A:0.56, C:0.14, G:0.06, T:0.24
Consensus pattern (50 bp):
TAATGCAAAACATTAAACAAAGATGCATTTAACAAACACAAAACACATAA
Found at i:35458027 original size:12 final size:13
Alignment explanation
Indices: 35458010--35458038 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
35458000 ATTTCAGATG
35458010 AAAATTGATCCA-
1 AAAATTGATCCAC
35458022 AAAATTGATCCAC
1 AAAATTGATCCAC
35458035 AAAA
1 AAAA
35458039 CTCCAAGATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.55, C:0.17, G:0.07, T:0.21
Consensus pattern (13 bp):
AAAATTGATCCAC
Found at i:35461437 original size:51 final size:50
Alignment explanation
Indices: 35461375--35461624 Score: 272
Period size: 52 Copynumber: 4.9 Consensus size: 50
35461365 AAATGCATGG
* * *
35461375 TTTAA-GATGCAAACTAAATGAACA-AATGAGTTACTTAATGCATGACTTAA
1 TTTAATGATGCAAACTAACT-AACATGA-GAGTTACTTAATGCATGACATAA
*
35461425 TTTAATGATGCAAACTTTAACTAACATGAGAGTTACTTAATGCACGACATAA
1 TTTAATGATGCAAAC--TAACTAACATGAGAGTTACTTAATGCATGACATAA
* * *
35461477 TTTAATGTTGCAAGCTTTAACTAACATGAGAGTTACTTAATGCATGACACAA
1 TTTAATGATGCAAAC--TAACTAACATGAGAGTTACTTAATGCATGACATAA
* * * * *
35461529 TTTAATGATTCAAATTTAACTAACACGAGAGTTACTTAATGCATGCCATTA
1 TTTAATGATGCAAA-CTAACTAACATGAGAGTTACTTAATGCATGACATAA
* * *
35461580 TTT-ATGATGCAAACTTAACTATCATGAGAGTTTCATAATGCATGA
1 TTTAATGATGCAAAC-TAACTAACATGAGAGTTACTTAATGCATGA
35461625 GTTTATTAAA
Statistics
Matches: 171, Mismatches: 23, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
50 39 0.23
51 43 0.25
52 84 0.49
53 5 0.03
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (50 bp):
TTTAATGATGCAAACTAACTAACATGAGAGTTACTTAATGCATGACATAA
Found at i:35461463 original size:52 final size:52
Alignment explanation
Indices: 35461402--35461624 Score: 317
Period size: 52 Copynumber: 4.3 Consensus size: 52
35461392 ATGAACAAAT
*
35461402 GAGTTACTTAATGCATGACTTAATTTAATGATGCAAACTTTAACTAACATGA
1 GAGTTACTTAATGCATGACATAATTTAATGATGCAAACTTTAACTAACATGA
* * *
35461454 GAGTTACTTAATGCACGACATAATTTAATGTTGCAAGCTTTAACTAACATGA
1 GAGTTACTTAATGCATGACATAATTTAATGATGCAAACTTTAACTAACATGA
* * *
35461506 GAGTTACTTAATGCATGACACAATTTAATGATTCAAA-TTTAACTAACACGA
1 GAGTTACTTAATGCATGACATAATTTAATGATGCAAACTTTAACTAACATGA
* * *
35461557 GAGTTACTTAATGCATGCCATTATTT-ATGATGCAAAC-TTAACTATCATGA
1 GAGTTACTTAATGCATGACATAATTTAATGATGCAAACTTTAACTAACATGA
* *
35461607 GAGTTTCATAATGCATGA
1 GAGTTACTTAATGCATGA
35461625 GTTTATTAAA
Statistics
Matches: 151, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
50 35 0.23
51 36 0.24
52 80 0.53
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (52 bp):
GAGTTACTTAATGCATGACATAATTTAATGATGCAAACTTTAACTAACATGA
Found at i:35461568 original size:103 final size:102
Alignment explanation
Indices: 35461402--35461624 Score: 313
Period size: 103 Copynumber: 2.2 Consensus size: 102
35461392 ATGAACAAAT
** *
35461402 GAGTTACTTAATGCATGACTTAATTTAATGATGCAAACTTTAACTAACATGAGAGTTACTTAATG
1 GAGTTACTTAATGCATGACACAATTTAATGATGCAAACTTTAACTAACACGAGAGTTACTTAATG
* *
35461467 CACGACATAATTTAATGTTGCAAGCTTTAACTAACATGA
66 CACGACATAATTT-ATGATGCAAAC-TTAACTAACATGA
*
35461506 GAGTTACTTAATGCATGACACAATTTAATGATTCAAA-TTTAACTAACACGAGAGTTACTTAATG
1 GAGTTACTTAATGCATGACACAATTTAATGATGCAAACTTTAACTAACACGAGAGTTACTTAATG
* * * *
35461570 CATGCCATTATTTATGATGCAAACTTAACTATCATGA
66 CACGACATAATTTATGATGCAAACTTAACTAACATGA
* *
35461607 GAGTTTCATAATGCATGA
1 GAGTTACTTAATGCATGA
35461625 GTTTATTAAA
Statistics
Matches: 107, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
101 28 0.26
102 9 0.08
103 36 0.34
104 34 0.32
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (102 bp):
GAGTTACTTAATGCATGACACAATTTAATGATGCAAACTTTAACTAACACGAGAGTTACTTAATG
CACGACATAATTTATGATGCAAACTTAACTAACATGA
Found at i:35465374 original size:52 final size:51
Alignment explanation
Indices: 35465312--35465495 Score: 201
Period size: 50 Copynumber: 3.6 Consensus size: 51
35465302 ATGAACAAAT
* * *
35465312 GAGTTTCTTAATGCATGACTTAATTTAATGATGCAAACTTTAACTACCATGG
1 GAGTTACTTAATGCATGACTTAATTTAATGATGCAAAC-TTAACTAACATGA
* * * * *
35465364 GAGTTACTTAATACATTACATAATTTAATGATGCAAACTTAACTAACTTAA
1 GAGTTACTTAATGCATGACTTAATTTAATGATGCAAACTTAACTAACATGA
* * *
35465415 GAGTTACTTAATGCATGTCATT-ATTT-ATGATGAAAACTTAACTATCATGA
1 GAGTTACTTAATGCATGAC-TTAATTTAATGATGCAAACTTAACTAACATGA
* * * *
35465465 GAGTTACATAATGAATGACTTTATTAAATGA
1 GAGTTACTTAATGCATGACTTAATTTAATGA
35465496 AGAACACATA
Statistics
Matches: 109, Mismatches: 20, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
49 2 0.02
50 39 0.36
51 33 0.30
52 35 0.32
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.36
Consensus pattern (51 bp):
GAGTTACTTAATGCATGACTTAATTTAATGATGCAAACTTAACTAACATGA
Found at i:35478723 original size:3 final size:3
Alignment explanation
Indices: 35478715--35478771 Score: 55
Period size: 3 Copynumber: 19.0 Consensus size: 3
35478705 GTATTGAGGC
* *
35478715 AGA AGA AGA AGAA AGA A-A AGA AGA AGA AAA AGG AG- AGAA AGA AGA
1 AGA AGA AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA
*
35478760 AAA AGA AGA AGA
1 AGA AGA AGA AGA
35478772 CGTTGCCCCG
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
2 4 0.09
3 36 0.80
4 5 0.11
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:35478738 original size:18 final size:17
Alignment explanation
Indices: 35478715--35478771 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 17
35478705 GTATTGAGGC
35478715 AGAAGAAGAAGAAAGAAA
1 AGAAGAAGAA-AAAGAAA
* *
35478733 AGAAGAAGAAAAAGGAG
1 AGAAGAAGAAAAAGAAA
35478750 AGAAAGAAGAAAAAGAAGA
1 AG-AAGAAGAAAAAGAA-A
35478769 AGA
1 AGA
35478772 CGTTGCCCCG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 7 0.21
18 24 0.73
19 2 0.06
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (17 bp):
AGAAGAAGAAAAAGAAA
Found at i:35479150 original size:17 final size:17
Alignment explanation
Indices: 35479125--35479168 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
35479115 CATGCATTTC
35479125 TTTTAATTGTCATTGCA
1 TTTTAATTGTCATTGCA
* *
35479142 TTTTTATTGTCTTTGCA
1 TTTTAATTGTCATTGCA
*
35479159 TTTTATTTGT
1 TTTTAATTGT
35479169 TCTAGCATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.16, C:0.09, G:0.11, T:0.64
Consensus pattern (17 bp):
TTTTAATTGTCATTGCA
Found at i:35491350 original size:32 final size:32
Alignment explanation
Indices: 35491307--35491588 Score: 269
Period size: 32 Copynumber: 8.8 Consensus size: 32
35491297 CATGAACTAA
* *
35491307 TGTTCACAGATTGATAGCTCTTATGAGCTTAT
1 TGTTCATAGATTGATAGCTCTTACGAGCTTAT
* *
35491339 TGTTCATAGATTGACAGCTCTTACAAGCTTAT
1 TGTTCATAGATTGATAGCTCTTACGAGCTTAT
* *
35491371 TGTTCATAGATCGACAGCTCTTACGAGCTTAT
1 TGTTCATAGATTGATAGCTCTTACGAGCTTAT
* ** * *
35491403 TATTCATAGATCAACAACTCTTACGAGCTTAT
1 TGTTCATAGATTGATAGCTCTTACGAGCTTAT
* *
35491435 TGTTCATAGATTGACAGCTCTTACAAGCTTAT
1 TGTTCATAGATTGATAGCTCTTACGAGCTTAT
* * *
35491467 TATTCATAGATTGATAGCT-TCTACAAGCTTAC
1 TGTTCATAGATTGATAGCTCT-TACGAGCTTAT
* * * * * ** *
35491499 TATTCACATATTGATTGCTCTTATGAGCACAC
1 TGTTCATAGATTGATAGCTCTTACGAGCTTAT
* * * *
35491531 TGTTCACAGATTGATATCTCTTATGAGCATAT
1 TGTTCATAGATTGATAGCTCTTACGAGCTTAT
* * *
35491563 TATTCATAGATTAATAGCTCATACGA
1 TGTTCATAGATTGATAGCTCTTACGA
35491589 ATATACTGGG
Statistics
Matches: 212, Mismatches: 36, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
31 1 0.00
32 210 0.99
33 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (32 bp):
TGTTCATAGATTGATAGCTCTTACGAGCTTAT
Found at i:35491520 original size:96 final size:97
Alignment explanation
Indices: 35491309--35491581 Score: 325
Period size: 96 Copynumber: 2.8 Consensus size: 97
35491299 TGAACTAATG
*
35491309 TTCACAGATTGATAGCTCTTATGAGCTTATTGTTCATAGATTGACAGCTCTTACAAGCTTATTGT
1 TTCACAGATTGATAGCTCTTATGAGCTTATTGTTCATAGATTGACAGCTCTTACAAGCTTATTAT
* * * *
35491374 TCATAGATCGACAGC-TCTTACGAGCTTATTA
66 TCATAGATTGATAGCTTCTTACAAGCTTACTA
* ** * * *
35491405 TTCATAGATCAACAACTCTTACGAGCTTATTGTTCATAGATTGACAGCTCTTACAAGCTTATTAT
1 TTCACAGATTGATAGCTCTTATGAGCTTATTGTTCATAGATTGACAGCTCTTACAAGCTTATTAT
35491470 TCATAGATTGATAGCTTC-TACAAGCTTACTA
66 TCATAGATTGATAGCTTCTTACAAGCTTACTA
* * ** * * * * ** *
35491501 TTCACATATTGATTGCTCTTATGAGCACACTGTTCACAGATTGATATCTCTTATGAGCATATTAT
1 TTCACAGATTGATAGCTCTTATGAGCTTATTGTTCATAGATTGACAGCTCTTACAAGCTTATTAT
*
35491566 TCATAGATTAATAGCT
66 TCATAGATTGATAGCT
35491582 CATACGAATA
Statistics
Matches: 147, Mismatches: 29, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
96 145 0.99
97 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (97 bp):
TTCACAGATTGATAGCTCTTATGAGCTTATTGTTCATAGATTGACAGCTCTTACAAGCTTATTAT
TCATAGATTGATAGCTTCTTACAAGCTTACTA
Found at i:35492365 original size:18 final size:19
Alignment explanation
Indices: 35492342--35492378 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
35492332 CCCTATAAGG
35492342 CAAAATT-TTCAGTTTTGT
1 CAAAATTGTTCAGTTTTGT
*
35492360 CAAAATTGTTCTGTTTTGT
1 CAAAATTGTTCAGTTTTGT
35492379 TCTGGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.24, C:0.11, G:0.14, T:0.51
Consensus pattern (19 bp):
CAAAATTGTTCAGTTTTGT
Found at i:35505939 original size:18 final size:17
Alignment explanation
Indices: 35505908--35505954 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
35505898 AGATTGCATA
*
35505908 CATTTTTATTGTCATCG
1 CATTTTTTTTGTCATCG
*
35505925 CATTTTATTTTGTCATTG
1 CATTTT-TTTTGTCATCG
35505943 CATTTTTTTTGT
1 CATTTTTTTTGT
35505955 TAATTTAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.15, C:0.13, G:0.11, T:0.62
Consensus pattern (17 bp):
CATTTTTTTTGTCATCG
Found at i:35506544 original size:6 final size:6
Alignment explanation
Indices: 35506533--35506575 Score: 52
Period size: 6 Copynumber: 6.8 Consensus size: 6
35506523 ATTGTGGATG
35506533 AGAAAA AG-AAA AGAAAAA GAGAAAA AGAGAAA AGAAAA AGAAA
1 AGAAAA AGAAAA AG-AAAA -AGAAAA AGA-AAA AGAAAA AGAAA
35506576 TATTGCTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.15
6 13 0.39
7 13 0.39
8 2 0.06
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:35506557 original size:13 final size:13
Alignment explanation
Indices: 35506535--35506575 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
35506525 TGTGGATGAG
35506535 AAAAAG-AAAAGA
1 AAAAAGAAAAAGA
35506547 AAAAGAGAAAAAGA
1 AAAA-AGAAAAAGA
*
35506561 GAAAAGAAAAAGA
1 AAAAAGAAAAAGA
35506574 AA
1 AA
35506576 TATTGCTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 4 0.16
13 12 0.48
14 9 0.36
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAGA
Found at i:35506563 original size:21 final size:20
Alignment explanation
Indices: 35506535--35506573 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
35506525 TGTGGATGAG
35506535 AAAAAGAAAAGAAAAAGAGA
1 AAAAAGAAAAGAAAAAGAGA
35506555 AAAAGAGAAAAGAAAAAGA
1 AAAA-AGAAAAGAAAAAGA
35506574 AATATTGCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAAAGAAAAGAAAAAGAGA
Found at i:35518493 original size:15 final size:14
Alignment explanation
Indices: 35518473--35518503 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
35518463 TCCTCACAGT
35518473 AAGGGAGTTATAGAC
1 AAGGGAGTTATA-AC
35518488 AAGGGAGTTATAAC
1 AAGGGAGTTATAAC
35518502 AA
1 AA
35518504 CAATTAGCAA
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:0.45, C:0.06, G:0.29, T:0.19
Consensus pattern (14 bp):
AAGGGAGTTATAAC
Found at i:35525292 original size:17 final size:17
Alignment explanation
Indices: 35525246--35525288 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
35525236 TTCTTTGTCA
35525246 TTGCATTTCATTTGTTAG
1 TTGCATTTCA-TTGTTAG
35525264 -TGCATTTGCATTG-TAG
1 TTGCATTT-CATTGTTAG
35525280 TTGCATTTC
1 TTGCATTTC
35525289 CATTCTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 4 0.17
17 17 0.74
18 2 0.09
ACGTcount: A:0.16, C:0.14, G:0.19, T:0.51
Consensus pattern (17 bp):
TTGCATTTCATTGTTAG
Found at i:35525866 original size:10 final size:10
Alignment explanation
Indices: 35525853--35525893 Score: 55
Period size: 10 Copynumber: 3.9 Consensus size: 10
35525843 AAAAAATCAC
35525853 AAAAAGAAAG
1 AAAAAGAAAG
35525863 AAAAAGAAAG
1 AAAAAGAAAG
*
35525873 AAGAAGAAAAG
1 AAAAAG-AAAG
35525884 AGAAAAGAAA
1 A-AAAAGAAA
35525894 AGTAATACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 15 0.56
11 8 0.30
12 4 0.15
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:35546463 original size:23 final size:22
Alignment explanation
Indices: 35546433--35546476 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
35546423 TAAAGAATAA
*
35546433 AATTAACCCAATTTAATTAATT
1 AATTAACCCAAATTAATTAATT
*
35546455 AATTCAACCCAAATTATTTAAT
1 AATT-AACCCAAATTAATTAAT
35546477 GAAATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTAACCCAAATTAATTAATT
Found at i:35549998 original size:21 final size:22
Alignment explanation
Indices: 35549968--35550022 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
35549958 TTAATCACTT
*
35549968 AAAAAAAGAAAAAG-AAAAGA-
1 AAAAGAAGAAAAAGTAAAAGAG
*
35549988 AAAAGGAAG-AAGAGTAAAAGAG
1 AAAA-GAAGAAAAAGTAAAAGAG
35550010 AAAAGAAGAAAAA
1 AAAAGAAGAAAAA
35550023 ATATATATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 8 0.29
21 13 0.46
22 7 0.25
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (22 bp):
AAAAGAAGAAAAAGTAAAAGAG
Found at i:35556251 original size:22 final size:22
Alignment explanation
Indices: 35556226--35556268 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
35556216 TTGTTGGTTG
* *
35556226 GTCTCGAGACAATATGCTTTTT
1 GTCTCAAGACAAGATGCTTTTT
*
35556248 GTCTCAAGACAAGATTCTTTT
1 GTCTCAAGACAAGATGCTTTT
35556269 GAAACATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.40
Consensus pattern (22 bp):
GTCTCAAGACAAGATGCTTTTT
Found at i:35562246 original size:24 final size:24
Alignment explanation
Indices: 35562218--35562267 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
35562208 CTCACCCTCT
* * *
35562218 TCTTTGTGCTTCTTCTTCTTCTTA
1 TCTTTGCGCCTCTTCCTCTTCTTA
*
35562242 TCTTTGCGCCTCTTCCTCTTTTTA
1 TCTTTGCGCCTCTTCCTCTTCTTA
35562266 TC
1 TC
35562268 CGTCGCACCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.04, C:0.30, G:0.08, T:0.58
Consensus pattern (24 bp):
TCTTTGCGCCTCTTCCTCTTCTTA
Found at i:35564456 original size:20 final size:21
Alignment explanation
Indices: 35564431--35564469 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
35564421 AAAAGGAATT
35564431 TGAAAC-AACAAAAGTAAAAG
1 TGAAACAAACAAAAGTAAAAG
*
35564451 TGAAACAAATAAAAGTAAA
1 TGAAACAAACAAAAGTAAA
35564470 TAGAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.67, C:0.08, G:0.13, T:0.13
Consensus pattern (21 bp):
TGAAACAAACAAAAGTAAAAG
Found at i:35576588 original size:235 final size:235
Alignment explanation
Indices: 35576177--35576882 Score: 1403
Period size: 235 Copynumber: 3.0 Consensus size: 235
35576167 TAAAACACCT
35576177 AAAAGAAAATGTAAAATTAGAAACAAAAGAAAAAAAGTTAGTAACAAATAAAGATTAGGTAAGAA
1 AAAAGAAAATGTAAAATTAGAAACAAAAGAAAAAAAGTTAGTAACAAATAAAGATTAGGTAAGAA
35576242 AGAATAAATGCAGAGATAAAAATAATCATTAAACAAACGTCATCCCCGACAACAGTGCCAAAACT
66 AGAATAAATGCAGAGATAAAAATAATCATTAAACAAACGTCATCCCCGACAACAGTGCCAAAACT
35576307 TGATCGCGCTATGAACGTCACAGCAAATATGTGCAAACGTACATTGTCGATGCAAGTATAGTAGA
131 TGATCGCGCTATGAACGTCACAGCAAATATGTGCAAACGTACATTGTCGATGCAAGTATAGTAGA
35576372 CAAATGTATAACCTGTCAAATATCGATCCCACGAGGATGG
196 CAAATGTATAACCTGTCAAATATCGATCCCACGAGGATGG
35576412 AAAAGAAAATGTAAAATTAGAAACAAAAGAAAAAAAGTTAGTAACAAATAAAGATTAGGTAAGAA
1 AAAAGAAAATGTAAAATTAGAAACAAAAGAAAAAAAGTTAGTAACAAATAAAGATTAGGTAAGAA
35576477 AGAATAAATGCAGAGATAAAAATAATCATTAAACAAACGTCATCCCCGACAACAGTGCCAAAACT
66 AGAATAAATGCAGAGATAAAAATAATCATTAAACAAACGTCATCCCCGACAACAGTGCCAAAACT
35576542 TGATCGCGCTATGAACGTCACAGCAAATATGTGCAAACGTACATTGTCGATGCAAGTATAGTAGA
131 TGATCGCGCTATGAACGTCACAGCAAATATGTGCAAACGTACATTGTCGATGCAAGTATAGTAGA
35576607 CAAATGTATAACCTGTCAAATATCGATCCCACGAGGATGG
196 CAAATGTATAACCTGTCAAATATCGATCCCACGAGGATGG
35576647 AAAAGAAAATGTAAAATTAGAAACAAAAGAAAAAAAGTTAGTAACAAATAAAGATTAGGTAAGAA
1 AAAAGAAAATGTAAAATTAGAAACAAAAGAAAAAAAGTTAGTAACAAATAAAGATTAGGTAAGAA
*
35576712 AGAATAAATGCAGAGATAAAAATAATCATTAAACAAACGCCATCCCCGACAACAGTGCCAAAACT
66 AGAATAAATGCAGAGATAAAAATAATCATTAAACAAACGTCATCCCCGACAACAGTGCCAAAACT
35576777 TGATCGCGCTATGAACGTCACAGCAAATATGTGCAAACGTACATTGTCGATGCAAGTATAGTAGA
131 TGATCGCGCTATGAACGTCACAGCAAATATGTGCAAACGTACATTGTCGATGCAAGTATAGTAGA
35576842 CAAATGTATAACCTGTCAAATATCGATCCCACGAGGATGG
196 CAAATGTATAACCTGTCAAATATCGATCCCACGAGGATGG
35576882 A
1 A
35576883 TGTTTGTTGT
Statistics
Matches: 470, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
235 470 1.00
ACGTcount: A:0.47, C:0.16, G:0.17, T:0.20
Consensus pattern (235 bp):
AAAAGAAAATGTAAAATTAGAAACAAAAGAAAAAAAGTTAGTAACAAATAAAGATTAGGTAAGAA
AGAATAAATGCAGAGATAAAAATAATCATTAAACAAACGTCATCCCCGACAACAGTGCCAAAACT
TGATCGCGCTATGAACGTCACAGCAAATATGTGCAAACGTACATTGTCGATGCAAGTATAGTAGA
CAAATGTATAACCTGTCAAATATCGATCCCACGAGGATGG
Found at i:35577859 original size:26 final size:26
Alignment explanation
Indices: 35577830--35577888 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 26
35577820 CAACGACAAC
*
35577830 TCTGGACATATTCATGCAGCAATAAT
1 TCTGGACAGATTCATGCAGCAATAAT
* * * * *
35577856 TCTGAACAGGTTCTTGTAGCGATAAT
1 TCTGGACAGATTCATGCAGCAATAAT
35577882 TCTGGAC
1 TCTGGAC
35577889 GCAATGTTAA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (26 bp):
TCTGGACAGATTCATGCAGCAATAAT
Found at i:35588042 original size:25 final size:25
Alignment explanation
Indices: 35588013--35588083 Score: 92
Period size: 24 Copynumber: 2.9 Consensus size: 25
35588003 ATTCCAAATT
**
35588013 TTAGCTCACACGAGCCCAGACAAA-A
1 TTAGCTCTTACGAGCCCAGA-AAAGA
*
35588038 TTAGCTCTTACGAGCCCA-AAAAGG
1 TTAGCTCTTACGAGCCCAGAAAAGA
35588062 TTAGCTCTTACGAGCCCAGAAA
1 TTAGCTCTTACGAGCCCAGAAA
35588084 GGTTAACCAG
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
23 3 0.07
24 19 0.46
25 19 0.46
ACGTcount: A:0.35, C:0.28, G:0.18, T:0.18
Consensus pattern (25 bp):
TTAGCTCTTACGAGCCCAGAAAAGA
Found at i:35588070 original size:24 final size:24
Alignment explanation
Indices: 35588038--35588088 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
35588028 CCAGACAAAA
35588038 TTAGCTCTTACGAGCCCAAAAAGG
1 TTAGCTCTTACGAGCCCAAAAAGG
*
35588062 TTAGCTCTTACGAGCCCAGAAAGG
1 TTAGCTCTTACGAGCCCAAAAAGG
35588086 TTA
1 TTA
35588089 ACCAGTATAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.24
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCCAAAAAGG
Found at i:35592713 original size:24 final size:24
Alignment explanation
Indices: 35592668--35592731 Score: 83
Period size: 24 Copynumber: 2.6 Consensus size: 24
35592658 TAGCTCACAT
** *
35592668 GAGCCCAGACAAAATTAGCTCTTAC
1 GAGCCCAGA-AAGGTTAGCTCTTAA
*
35592693 GAGCCTAGAAAGGTTAGCTCTTAA
1 GAGCCCAGAAAGGTTAGCTCTTAA
35592717 GAGCCCAGAAAGGTT
1 GAGCCCAGAAAGGTT
35592732 GACCAGTATA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 26 0.76
25 8 0.24
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.20
Consensus pattern (24 bp):
GAGCCCAGAAAGGTTAGCTCTTAA
Found at i:35594521 original size:37 final size:37
Alignment explanation
Indices: 35594480--35594729 Score: 401
Period size: 37 Copynumber: 6.8 Consensus size: 37
35594470 TGCATCTAAA
* * *
35594480 TATTCAGGCTATGTGCCTAGGAAGCTTTGTGTCGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
*
35594517 TATTCAGGCTATGTGCCTAGTTGGCTTTGTGCCGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
*
35594554 TATTCAGGCTATGTTCCTAGTAGGCTTTGTGCCGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
* *
35594591 TATTTAGGCTATGTGCCTAGTAGGCTTTGTGCTGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
* *
35594628 TATTCAGGCTATGTACCTAGTAGGCTTTGTGCCAGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
*
35594665 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGTCGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
*
35594702 TATTCAGGCTGTGTGCCTAGTAGGCTTT
1 TATTCAGGCTATGTGCCTAGTAGGCTTT
35594730 AGGCTGGTGA
Statistics
Matches: 196, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 196 1.00
ACGTcount: A:0.14, C:0.17, G:0.31, T:0.38
Consensus pattern (37 bp):
TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
Found at i:35613394 original size:37 final size:37
Alignment explanation
Indices: 35613342--35613517 Score: 235
Period size: 37 Copynumber: 4.8 Consensus size: 37
35613332 TGCATCTAAA
*
35613342 TATTCAGGCTATGTGCCTAGTAAGCTTTGTGCCGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
* *
35613379 TATTCAGGCTGTGTGCCTAGTAGGCTTTGTGTCGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
* *
35613416 TATTTAGGCTATGTGCATAGTAGGCTTTGTGCCGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
* * *
35613453 TATTCAGGCTATGTGCCTAGTAGGGTTTTTACCGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
* * * * *
35613490 TATTCGGGTTGTATGCCTAGTAAGCTTT
1 TATTCAGGCTATGTGCCTAGTAGGCTTT
35613518 AAGCTGGTGA
Statistics
Matches: 121, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 121 1.00
ACGTcount: A:0.15, C:0.16, G:0.31, T:0.38
Consensus pattern (37 bp):
TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
Found at i:35613467 original size:21 final size:20
Alignment explanation
Indices: 35613369--35613469 Score: 56
Period size: 21 Copynumber: 5.3 Consensus size: 20
35613359 TAGTAAGCTT
*
35613369 TGTGCCGGTGTATTCAGGCTG
1 TGTGCCGGTGTATT-AGGCTA
* *
35613390 TGTGCC----TAGTAGGCTT
1 TGTGCCGGTGTATTAGGCTA
*
35613406 TGTGTCGGTGTATTTAGGCTA
1 TGTGCCGGTGTA-TTAGGCTA
* * *
35613427 TGTG-C---ATAGTAGGCTT
1 TGTGCCGGTGTATTAGGCTA
35613443 TGTGCCGGTGTATTCAGGCTA
1 TGTGCCGGTGTATT-AGGCTA
35613464 TGTGCC
1 TGTGCC
35613470 TAGTAGGGTT
Statistics
Matches: 59, Mismatches: 11, Indels: 20
0.66 0.12 0.22
Matches are distributed among these distances:
16 20 0.34
17 6 0.10
20 6 0.10
21 27 0.46
ACGTcount: A:0.13, C:0.17, G:0.34, T:0.37
Consensus pattern (20 bp):
TGTGCCGGTGTATTAGGCTA
Found at i:35617243 original size:21 final size:21
Alignment explanation
Indices: 35617184--35617250 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
35617174 TGCCTAGTAA
*
35617184 GCTTTGTGCAGGTGTATTCAG
1 GCTTTGTGCCGGTGTATTCAG
* *
35617205 GCTGTGTGCC----TAGT-AG
1 GCTTTGTGCCGGTGTATTCAG
35617221 GCTTTGTGCCGGTGTATTCAG
1 GCTTTGTGCCGGTGTATTCAG
*
35617242 GCTATGTGC
1 GCTTTGTGC
35617251 ATAGTAGGCC
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
16 11 0.31
17 3 0.09
20 3 0.09
21 18 0.51
ACGTcount: A:0.12, C:0.18, G:0.34, T:0.36
Consensus pattern (21 bp):
GCTTTGTGCCGGTGTATTCAG
Found at i:35617257 original size:37 final size:37
Alignment explanation
Indices: 35617161--35617288 Score: 162
Period size: 37 Copynumber: 3.6 Consensus size: 37
35617151 TGCATCTAAA
*
35617161 TATTCAGGCTATGTGCCTAGTAAGCTTTGTGCAGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCAGGTG
* *
35617198 TATTCAGGCTGTGTGCCTAGTAGGCTTTGTGCCGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCAGGTG
*
35617235 TATTCAGGCTATGTGCATAGTAGGC------C-GGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCAGGTG
*
35617265 TATTCAGGCTATGTGCCTTGTAGG
1 TATTCAGGCTATGTGCCTAGTAGG
35617289 GTTTTTTCCC
Statistics
Matches: 84, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
30 26 0.31
31 1 0.01
37 57 0.68
ACGTcount: A:0.16, C:0.17, G:0.32, T:0.34
Consensus pattern (37 bp):
TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCAGGTG
Found at i:35620984 original size:37 final size:37
Alignment explanation
Indices: 35620943--35621118 Score: 244
Period size: 37 Copynumber: 4.8 Consensus size: 37
35620933 TGTATCTAAA
* *
35620943 TATTCAGGCTATGTGCCTAGTAAGCTTTGTGCAGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
*
35620980 TATTCAGGCTGTGTGCCTAGTAGGCTTTGTGCCGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
* *
35621017 TATTCAGGCTATGTGCATAGTAGGCTTTGTGCTGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
* *
35621054 TATTCAGGCTATGTGCCTAGTTGGGTTTGTGCCGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
* * * * *
35621091 TATTCGGGTTGTATGCCTAGTAAGCTTT
1 TATTCAGGCTATGTGCCTAGTAGGCTTT
35621119 AAGCTGGTGA
Statistics
Matches: 122, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 122 1.00
ACGTcount: A:0.15, C:0.16, G:0.32, T:0.38
Consensus pattern (37 bp):
TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
Found at i:35621025 original size:21 final size:21
Alignment explanation
Indices: 35620966--35621070 Score: 68
Period size: 21 Copynumber: 5.5 Consensus size: 21
35620956 TGCCTAGTAA
*
35620966 GCTTTGTGCAGGTGTATTCAG
1 GCTTTGTGCCGGTGTATTCAG
* *
35620987 GCTGTGTGCC----TAGT-AG
1 GCTTTGTGCCGGTGTATTCAG
35621003 GCTTTGTGCCGGTGTATTCAG
1 GCTTTGTGCCGGTGTATTCAG
* * *
35621024 GCTATGTG-C---ATAGT-AG
1 GCTTTGTGCCGGTGTATTCAG
*
35621040 GCTTTGTGCTGGTGTATTCAG
1 GCTTTGTGCCGGTGTATTCAG
*
35621061 GCTATGTGCC
1 GCTTTGTGCC
35621071 TAGTTGGGTT
Statistics
Matches: 60, Mismatches: 14, Indels: 20
0.64 0.15 0.21
Matches are distributed among these distances:
16 20 0.33
17 6 0.10
20 7 0.12
21 27 0.45
ACGTcount: A:0.13, C:0.17, G:0.33, T:0.36
Consensus pattern (21 bp):
GCTTTGTGCCGGTGTATTCAG
Found at i:35624824 original size:37 final size:37
Alignment explanation
Indices: 35624769--35624935 Score: 212
Period size: 37 Copynumber: 4.6 Consensus size: 37
35624759 TGCATCTAAA
* **
35624769 TATTCAGGCTTTGTGCCTAGTAGGCTTTGTTTCGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
*
35624806 TATTTAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
* * **
35624843 TATTCAGGATATGTGCCTAGTAGGCATTGTGTTGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
* * *
35624880 TTTTCAAGTTATGTGCCTAGTAGGCTTTGTGCCGGTG
1 TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
*
35624917 TATTCGGGC--TGTGCCTAGT
1 TATTCAGGCTATGTGCCTAGT
35624936 CGTCTTTAGG
Statistics
Matches: 111, Mismatches: 19, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
35 10 0.09
37 101 0.91
ACGTcount: A:0.14, C:0.16, G:0.31, T:0.40
Consensus pattern (37 bp):
TATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTG
Found at i:35627660 original size:22 final size:22
Alignment explanation
Indices: 35627635--35627678 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
35627625 TTAATTTAAC
35627635 TTGTCACTGCACCTTCCAGTGA
1 TTGTCACTGCACCTTCCAGTGA
* *
35627657 TTGTGACTGCACCTTCTAGTGA
1 TTGTCACTGCACCTTCCAGTGA
35627679 CTATGACTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.34
Consensus pattern (22 bp):
TTGTCACTGCACCTTCCAGTGA
Found at i:35627685 original size:22 final size:22
Alignment explanation
Indices: 35627640--35627689 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
35627630 TTAACTTGTC
* *
35627640 ACTGCACCTTCCAGTGATTGTG
1 ACTGCACCTTCCAGTGACTATG
*
35627662 ACTGCACCTTCTAGTGACTATG
1 ACTGCACCTTCCAGTGACTATG
35627684 ACTGCA
1 ACTGCA
35627690 ATAGCACTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTGCACCTTCCAGTGACTATG
Found at i:35629975 original size:27 final size:28
Alignment explanation
Indices: 35629932--35629985 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
35629922 AAAGTCTTCC
* *
35629932 TCTTTCTTGTCTTCCTT-TCCTTCTTAT
1 TCTTTCTTGTCTGCCTTCTCCTCCTTAT
35629959 TCTTTCTCT-TCTGCCTTCTCCTCCTTA
1 TCTTTCT-TGTCTGCCTTCTCCTCCTTA
35629986 ATACCCATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.04, C:0.35, G:0.04, T:0.57
Consensus pattern (28 bp):
TCTTTCTTGTCTGCCTTCTCCTCCTTAT
Found at i:35639514 original size:15 final size:15
Alignment explanation
Indices: 35639494--35639523 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35639484 TGTGACCCCT
*
35639494 TTTCGCAGACACACA
1 TTTCGCAAACACACA
35639509 TTTCGCAAACACACA
1 TTTCGCAAACACACA
35639524 CGGGCTAGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.33, G:0.10, T:0.20
Consensus pattern (15 bp):
TTTCGCAAACACACA
Found at i:35644490 original size:17 final size:17
Alignment explanation
Indices: 35644479--35644517 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
35644469 CAAATGCGTT
35644479 GACAAATAAAATGCAGA
1 GACAAATAAAATGCAGA
*
35644496 GACAAATAAAATGCAGT
1 GACAAATAAAATGCAGA
35644513 GACAA
1 GACAA
35644518 CTATATGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.56, C:0.13, G:0.18, T:0.13
Consensus pattern (17 bp):
GACAAATAAAATGCAGA
Found at i:35644943 original size:15 final size:15
Alignment explanation
Indices: 35644910--35644954 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
35644900 CACGACAAAG
* *
35644910 TCTTCCTCTTTCTCA
1 TCTTCTTCTTTCTCT
35644925 TCTTC--CTTTCT-T
1 TCTTCTTCTTTCTCT
35644937 TCTTCTTCTTTCTCT
1 TCTTCTTCTTTCTCT
35644952 TCT
1 TCT
35644955 GCCTTCTCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 5 0.19
13 6 0.23
14 6 0.23
15 9 0.35
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (15 bp):
TCTTCTTCTTTCTCT
Found at i:35666651 original size:15 final size:16
Alignment explanation
Indices: 35666625--35666654 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
35666615 GAAAATGAGA
35666625 AAAAGAAAGAAAAAAG
1 AAAAGAAAGAAAAAAG
35666641 AAAAG-AAGAAAAAA
1 AAAAGAAAGAAAAAA
35666655 TGTTTAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAGAAAGAAAAAAG
Found at i:35671007 original size:22 final size:22
Alignment explanation
Indices: 35670982--35671024 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
35670972 AAAATATTTC
*
35670982 ATTA-ATAATTTGGGTTTAATTA
1 ATTATATAAATTGGG-TTAATTA
*
35671004 ATTATTTAAATTGGGTTAATT
1 ATTATATAAATTGGGTTAATT
35671025 TTATTCTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
ATTATATAAATTGGGTTAATTA
Found at i:35688362 original size:12 final size:12
Alignment explanation
Indices: 35688345--35688379 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
35688335 AAACTTTTGC
*
35688345 TTTTATTTTCTA
1 TTTTATTTTATA
*
35688357 TTTTATTTTATC
1 TTTTATTTTATA
35688369 TTTTATTTTAT
1 TTTTATTTTAT
35688380 GCTCTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTATTTTATA
Found at i:35688367 original size:17 final size:17
Alignment explanation
Indices: 35688345--35688379 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
35688335 AAACTTTTGC
35688345 TTTTAT-TTTCTATTTTA
1 TTTTATCTTT-TATTTTA
35688362 TTTTATCTTTTATTTTA
1 TTTTATCTTTTATTTTA
35688379 T
1 T
35688380 GCTCTCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTATCTTTTATTTTA
Found at i:35693578 original size:21 final size:21
Alignment explanation
Indices: 35693554--35693612 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
35693544 TAGAAGTAAG
* *
35693554 ACTTGTTTCGGTAGAAGAGTC
1 ACTTGTATCAGTAGAAGAGTC
* * **
35693575 ACTTGTATCTGTAAAACTGTC
1 ACTTGTATCAGTAGAAGAGTC
35693596 ACTTGTATCAGTAGAAG
1 ACTTGTATCAGTAGAAG
35693613 TCTACACTAT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (21 bp):
ACTTGTATCAGTAGAAGAGTC
Found at i:35702802 original size:21 final size:21
Alignment explanation
Indices: 35702778--35702817 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
35702768 CGGTAAAAGA
35702778 GTCACTTGTATCGATAGAACT
1 GTCACTTGTATCGATAGAACT
35702799 GTCACTTGTATCGATAGAA
1 GTCACTTGTATCGATAGAA
35702818 GTCTACACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (21 bp):
GTCACTTGTATCGATAGAACT
Found at i:35706529 original size:22 final size:23
Alignment explanation
Indices: 35706499--35706541 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
35706489 TAACAAAAAG
35706499 AAATGAAATAACTAAACCTAAGA
1 AAATGAAATAACTAAACCTAAGA
*
35706522 AAAT-AAATGACTAAACCTAA
1 AAATGAAATAACTAAACCTAA
35706542 TTTACAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.60, C:0.14, G:0.07, T:0.19
Consensus pattern (23 bp):
AAATGAAATAACTAAACCTAAGA
Done.