Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 17 of 206
Found at i:5091045 original size:9 final size:9
Alignment explanation
Indices: 5091028--5091082 Score: 92
Period size: 9 Copynumber: 6.1 Consensus size: 9
5091018 TGAGTTTTCG
5091028 AATTCGAAT
1 AATTCGAAT
*
5091037 AAATCGAAT
1 AATTCGAAT
5091046 AATTCGAAT
1 AATTCGAAT
*
5091055 AACTCGAAT
1 AATTCGAAT
5091064 AATTCGAAT
1 AATTCGAAT
5091073 AATTCGAAT
1 AATTCGAAT
5091082 A
1 A
5091083 TCAAACTATA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 42 1.00
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (9 bp):
AATTCGAAT
Found at i:5091530 original size:5 final size:5
Alignment explanation
Indices: 5091520--5091545 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
5091510 CTCGAAAATT
5091520 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
5091546 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:5094243 original size:37 final size:37
Alignment explanation
Indices: 5094193--5094271 Score: 149
Period size: 37 Copynumber: 2.1 Consensus size: 37
5094183 CCTGGAATTG
5094193 CCATGGCATTTCTGTTGGCAATATATCCCACCATTTA
1 CCATGGCATTTCTGTTGGCAATATATCCCACCATTTA
*
5094230 CCATGGCATTTCTGTTGGCAATATATCCCACCATTTT
1 CCATGGCATTTCTGTTGGCAATATATCCCACCATTTA
5094267 CCATG
1 CCATG
5094272 ACAATGTTTC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.23, C:0.28, G:0.14, T:0.35
Consensus pattern (37 bp):
CCATGGCATTTCTGTTGGCAATATATCCCACCATTTA
Found at i:5109521 original size:20 final size:20
Alignment explanation
Indices: 5109496--5109536 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
5109486 GACATATGGT
* *
5109496 CGTGTCTGTGCTCGTGTGGA
1 CGTGTCTATGCCCGTGTGGA
5109516 CGTGTCTATGCCCGTGTGGA
1 CGTGTCTATGCCCGTGTGGA
5109536 C
1 C
5109537 AAAAAATAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.07, C:0.24, G:0.37, T:0.32
Consensus pattern (20 bp):
CGTGTCTATGCCCGTGTGGA
Found at i:5110688 original size:25 final size:25
Alignment explanation
Indices: 5110629--5110693 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
5110619 TTGTACATGT
** * *
5110629 ATGCTCACACAAGCTGTAAATCAAA
1 ATGCTCACATGAGCTATAAAGCAAA
*
5110654 ATGCTCACATGAGCTATAAAGCAGA
1 ATGCTCACATGAGCTATAAAGCAAA
5110679 ATGCTCACATGAGCT
1 ATGCTCACATGAGCT
5110694 GTGGAGTACC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (25 bp):
ATGCTCACATGAGCTATAAAGCAAA
Found at i:5124603 original size:39 final size:39
Alignment explanation
Indices: 5124559--5124758 Score: 276
Period size: 39 Copynumber: 5.2 Consensus size: 39
5124549 TGGGATAATT
5124559 ATTCTACTGAAAGTATGCTCAATCGAGCCATACCTACTG
1 ATTCTACTGAAAGTATGCTCAATCGAGCCATACCTACTG
* ** *
5124598 ATTCTATTGAAAGTATATTCAATCGAGCCATACCCACT-
1 ATTCTACTGAAAGTATGCTCAATCGAGCCATACCTACTG
* * * * *
5124636 ATTCTATTGAATGTATGATCAATCGAGTCATACTTACTG
1 ATTCTACTGAAAGTATGCTCAATCGAGCCATACCTACTG
* *
5124675 ATTCTACTAAAAGTATGCTCAATTGAGCCATACCTACTG
1 ATTCTACTGAAAGTATGCTCAATCGAGCCATACCTACTG
* *
5124714 ATTCTACTGAAAGTATGCTCAATCAAGCCATACCCACTG
1 ATTCTACTGAAAGTATGCTCAATCGAGCCATACCTACTG
5124753 ATTCTA
1 ATTCTA
5124759 TAGAAATTTG
Statistics
Matches: 139, Mismatches: 21, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
38 32 0.23
39 107 0.77
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.32
Consensus pattern (39 bp):
ATTCTACTGAAAGTATGCTCAATCGAGCCATACCTACTG
Found at i:5124688 original size:77 final size:77
Alignment explanation
Indices: 5124558--5124758 Score: 276
Period size: 77 Copynumber: 2.6 Consensus size: 77
5124548 ATGGGATAAT
* * *
5124558 TATTCTACTGAAAGTATGCTCAATCGAGCCATACCTACTGATTCTATTGAAAGTATATTCAATCG
1 TATTCTACTGAAAGTATGCTCAATCGAGCCATACCTACTGATTCTACTAAAAGTATACTCAATCG
5124623 AGCCATACCCAC
66 AGCCATACCCAC
* * * * * * *
5124635 TATTCTATTGAATGTATGATCAATCGAGTCATACTTACTGATTCTACTAAAAGTATGCTCAATTG
1 TATTCTACTGAAAGTATGCTCAATCGAGCCATACCTACTGATTCTACTAAAAGTATACTCAATCG
*
5124700 AGCCATACCTAC
66 AGCCATACCCAC
* *
5124712 TGATTCTACTGAAAGTATGCTCAATCAAGCCATACCCACTGATTCTA
1 T-ATTCTACTGAAAGTATGCTCAATCGAGCCATACCTACTGATTCTA
5124759 TAGAAATTTG
Statistics
Matches: 105, Mismatches: 18, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
77 67 0.64
78 38 0.36
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (77 bp):
TATTCTACTGAAAGTATGCTCAATCGAGCCATACCTACTGATTCTACTAAAAGTATACTCAATCG
AGCCATACCCAC
Found at i:5130161 original size:17 final size:17
Alignment explanation
Indices: 5130139--5130175 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
5130129 GGCTATGTTG
5130139 GACTGAGTTGGGTGAGC
1 GACTGAGTTGGGTGAGC
5130156 GACTGAGTTGGGTGAGC
1 GACTGAGTTGGGTGAGC
5130173 GAC
1 GAC
5130176 GGATTTTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.19, C:0.14, G:0.46, T:0.22
Consensus pattern (17 bp):
GACTGAGTTGGGTGAGC
Found at i:5133250 original size:44 final size:44
Alignment explanation
Indices: 5133187--5133274 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
5133177 GAGTTCTCTG
5133187 AGTCGACCCAACTCCACTTCATGATTCATATGTGGAATCCTACT
1 AGTCGACCCAACTCCACTTCATGATTCATATGTGGAATCCTACT
5133231 AGTCGACCCAACTCCACTTCATGATTCATATGTGGAATCCTACT
1 AGTCGACCCAACTCCACTTCATGATTCATATGTGGAATCCTACT
5133275 CTTCAGTTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.27, C:0.30, G:0.14, T:0.30
Consensus pattern (44 bp):
AGTCGACCCAACTCCACTTCATGATTCATATGTGGAATCCTACT
Found at i:5134414 original size:57 final size:57
Alignment explanation
Indices: 5134304--5134425 Score: 133
Period size: 57 Copynumber: 2.1 Consensus size: 57
5134294 CTGATATACA
* * *
5134304 AAAAAGAAGGAAAAAAAATTTGGGTGCTGGCTTATCAATGGCTAGCACCCAGTAC-G-
1 AAAAA-AAGGAAAAAAAATTTAGGTGCTAGCCTATCAATGGCTAGCACCCAGTACAGT
* * *
5134360 AAAAAAAGGAAAAAAAAATTTTAGGTGCTAGCCTGTCAATGG-TCGGCACTCAGTACAGT
1 AAAAAAAGG-AAAAAAAA-TTTAGGTGCTAGCCTATCAATGGCT-AGCACCCAGTACAGT
5134419 AAAAAAA
1 AAAAAAA
5134426 ATTCGAGTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
55 4 0.07
56 14 0.25
57 29 0.53
58 1 0.02
59 7 0.13
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.20
Consensus pattern (57 bp):
AAAAAAAGGAAAAAAAATTTAGGTGCTAGCCTATCAATGGCTAGCACCCAGTACAGT
Found at i:5134515 original size:108 final size:105
Alignment explanation
Indices: 5134336--5134536 Score: 285
Period size: 108 Copynumber: 1.9 Consensus size: 105
5134326 GGTGCTGGCT
* *
5134336 TATCAATGGCTAGCACCCAGTACGAAAAAAAGGAAAAAAAAATTTTAGGTGCTAGCCTGTCAATG
1 TATCAATGGCCAGCACCCAGTACAAAAAAAAGGAAAAAAAAATTTTAGGTGCTAGCCTGTCAATG
* *
5134401 GTCGGCACTCAGTACAGTAAAAAAAATTCGAGTTTTGGTC
66 GCCGGCACCCAGTACAGTAAAAAAAATTCGAGTTTTGGTC
* * * * *
5134441 TATCAATGGCCGGCACCAGAGTACAAAAAAAAGTTAAAAAAAAATTTTTGGGTGCTGGCCTGTCA
1 TATCAATGGCCAGCACC-CAGTACAAAAAAAAG-GAAAAAAAAA-TTTTAGGTGCTAGCCTGTCA
*
5134506 ATGGCCGGCACCCAGTATAGTAAAAAAAATT
63 ATGGCCGGCACCCAGTACAGTAAAAAAAATT
5134537 ACTTTTTTTC
Statistics
Matches: 83, Mismatches: 10, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
105 15 0.18
106 13 0.16
107 9 0.11
108 46 0.55
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (105 bp):
TATCAATGGCCAGCACCCAGTACAAAAAAAAGGAAAAAAAAATTTTAGGTGCTAGCCTGTCAATG
GCCGGCACCCAGTACAGTAAAAAAAATTCGAGTTTTGGTC
Found at i:5135272 original size:49 final size:49
Alignment explanation
Indices: 5135130--5135280 Score: 126
Period size: 49 Copynumber: 3.1 Consensus size: 49
5135120 AAAGAATTTT
* * *
5135130 TTTTGGGTGCTGGCCTATCAATGGTCGGCACCTAGTACAGT-AAAAAAA
1 TTTTGGGTGCTGGCCTATCAATGGACGGCACCCAGTACAATAAAAAAAA
* * * ** * * * * ** * *
5135178 TATCGAGTTTTGGTCTGTCAATGGCCGACACTAGAGTTCGA-AAAAAAAA
1 TTTTGGGTGCTGGCCTATCAATGGACGGCAC-CCAGTACAATAAAAAAAA
5135227 TTTTGGGTGCTGGCCTATCAATGGACGGCACCCAGTACAATAAAAAAAAA
1 TTTTGGGTGCTGGCCTATCAATGGACGGCACCCAGTACAAT-AAAAAAAA
5135277 TTTT
1 TTTT
5135281 ATTGCACTGG
Statistics
Matches: 72, Mismatches: 27, Indels: 6
0.69 0.26 0.06
Matches are distributed among these distances:
48 27 0.38
49 33 0.46
50 12 0.17
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (49 bp):
TTTTGGGTGCTGGCCTATCAATGGACGGCACCCAGTACAATAAAAAAAA
Found at i:5136950 original size:18 final size:18
Alignment explanation
Indices: 5136927--5136961 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5136917 TTTTGAGCTA
5136927 AATAAAGTGAGTTATTCG
1 AATAAAGTGAGTTATTCG
*
5136945 AATAAATTGAGTTATTC
1 AATAAAGTGAGTTATTC
5136962 TAGGCAACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.37
Consensus pattern (18 bp):
AATAAAGTGAGTTATTCG
Found at i:5138491 original size:22 final size:23
Alignment explanation
Indices: 5138452--5138496 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
5138442 CCCGGCCCAT
**
5138452 TTTTAATAAATACCAAAAATTTA
1 TTTTAATAAATAAAAAAAATTTA
5138475 TTTTAA-AAATAAAAAAAATTTA
1 TTTTAATAAATAAAAAAAATTTA
5138497 AAAATATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (23 bp):
TTTTAATAAATAAAAAAAATTTA
Found at i:5140270 original size:555 final size:555
Alignment explanation
Indices: 5139191--5140393 Score: 2365
Period size: 555 Copynumber: 2.2 Consensus size: 555
5139181 ATAATGGTGT
*
5139191 TTCCTAATTCTTGAAGCTCAATATTTGAG-AATTTTTTAGAAAGCTTTGGAAGCTCCTATATTAA
1 TTCCTAATTCTTGAAGCTCAATATTTGAGAAAATTTTTAGAAAGCTTTGGAAGCTCCTATATTAA
*
5139255 TTTTTGGTTAATTTCATGAAT-TAGGAAACACCAAAACTTTCCTTGGTGTTTTTGGTGTTTCCTG
66 TTTTTGGTTAATTTCATGAATATAGAAAACACCAAAACTTTCCTTGGTGTTTTTGGTGTTTCCTG
5139319 CCACCCCTCTCTTTCCATGGTTTTTCCCTTTCTTTTTCTTCATCTTCCATGTCTTTTTTTTAACA
131 CCACCCCTCTCTTTCCATGGTTTTTCCCTTTCTTTTTCTTCATCTTCCATGTCTTTTTTTTAACA
5139384 AAGATTTTCATGAGTTTTAATGTGAGAAATTGAAGTTATAGAAAGAAAACTTCAACAAAGCAAAT
196 AAGATTTTCATGAGTTTTAATGTGAGAAATTGAAGTTATAGAAAGAAAACTTCAACAAAGCAAAT
5139449 GATGGTGTTTCCTAATTAGAGGCTCGGCCCGACGGCCTGCCCAAAATATGGGAGGGTTTGGGTAA
261 GATGGTGTTTCCTAATTAGAGGCTCGGCCCGACGGCCTGCCCAAAATATGGGAGGGTTTGGGTAA
5139514 AAATATAGGCTCGAAATATAGATTTTGGTAAAAAATGAGGTCCGTTTAGAAAACGGGCCGGCCTC
326 AAATATAGGCTCGAAATATAGATTTTGGTAAAAAATGAGGTCCGTTTAGAAAACGGGCCGGCCTC
5139579 GGGCACCACTTTTTTGTCTCGGGCCGGGCCGAACTTGGGCTTAGGAATTTTTCCCGGGTCGAGCC
391 GGGCACCACTTTTTTGTCTCGGGCCGGGCCGAACTTGGGCTTAGGAATTTTTCCCGGGTCGAGCC
5139644 TGAACAAAATTTTAGGCCCATATTTCGGGCCGAGCCGAGCCCGAGCCTAGGACGTGGGCTGAATT
456 TGAACAAAATTTTAGGCCCATATTTCGGGCCGAGCCGAGCCCGAGCCTAGGACGTGGGCTGAATT
5139709 TTTTTTTGGGCCTGGCCCAGCCATGATCACCTCTA
521 TTTTTTTGGGCCTGGCCCAGCCATGATCACCTCTA
5139744 TTCCTAATTCTTGAAGCTCAATATTTGAGAAAATTTTTAGAAAGCTTTGGAAGCTCCTATATTAA
1 TTCCTAATTCTTGAAGCTCAATATTTGAGAAAATTTTTAGAAAGCTTTGGAAGCTCCTATATTAA
*
5139809 TTTTTGGTTAATTTCATGAATATAGAAAACCCCAAAACTTTCCTTGGTGTTTTTGGTGTTTCCTG
66 TTTTTGGTTAATTTCATGAATATAGAAAACACCAAAACTTTCCTTGGTGTTTTTGGTGTTTCCTG
5139874 CCACCCCTCTCTTTCCATGGTTTTTCCCTTTCTTTTTCTTCATCTTCCATGTCTTTTTTTTAACA
131 CCACCCCTCTCTTTCCATGGTTTTTCCCTTTCTTTTTCTTCATCTTCCATGTCTTTTTTTTAACA
5139939 AAGATTTTCATGAGTTTTAATGTGAGAAATTGAAGTTATAGAAAGAAAACTTCAACAAAGCAAAT
196 AAGATTTTCATGAGTTTTAATGTGAGAAATTGAAGTTATAGAAAGAAAACTTCAACAAAGCAAAT
5140004 GATGGTGTTTCCTAATTAGAGGCTCGGCCCGACGGCCTGCCCAAAATATGGGAGGGTTTGGGTAA
261 GATGGTGTTTCCTAATTAGAGGCTCGGCCCGACGGCCTGCCCAAAATATGGGAGGGTTTGGGTAA
5140069 AAATATAGGCTCGAAATATAGATTTTGGTAAAAAATGAGGTCCGTTTAGAAAACGGGCCGGCCTC
326 AAATATAGGCTCGAAATATAGATTTTGGTAAAAAATGAGGTCCGTTTAGAAAACGGGCCGGCCTC
5140134 GGGCACCACTTTTTTGTCTCGGGCCGGGCCGAACTTGGGCTTAGGAATTTTTCCCGGGTCGAGCC
391 GGGCACCACTTTTTTGTCTCGGGCCGGGCCGAACTTGGGCTTAGGAATTTTTCCCGGGTCGAGCC
5140199 TGAACAAAATTTTAGGCCCATATTTCGGGCCGAGCCGAGCCCGAGCCTAGGACGTGGGCTGAATT
456 TGAACAAAATTTTAGGCCCATATTTCGGGCCGAGCCGAGCCCGAGCCTAGGACGTGGGCTGAATT
5140264 TTTTTTTGGGCCTGGCCCAGCCATGATCACCTCTA
521 TTTTTTTGGGCCTGGCCCAGCCATGATCACCTCTA
5140299 TTCCTAATTCTTGAAGCTCAATATTTGAGAAAATTTTTAGAAAGCTTTGGAAGCTCCTATATTAA
1 TTCCTAATTCTTGAAGCTCAATATTTGAGAAAATTTTTAGAAAGCTTTGGAAGCTCCTATATTAA
5140364 TTTTTGGTTAATTTCATGAATATAGAAAAC
66 TTTTTGGTTAATTTCATGAATATAGAAAAC
5140394 TGTGATAGTA
Statistics
Matches: 645, Mismatches: 3, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
553 29 0.04
554 55 0.09
555 561 0.87
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.34
Consensus pattern (555 bp):
TTCCTAATTCTTGAAGCTCAATATTTGAGAAAATTTTTAGAAAGCTTTGGAAGCTCCTATATTAA
TTTTTGGTTAATTTCATGAATATAGAAAACACCAAAACTTTCCTTGGTGTTTTTGGTGTTTCCTG
CCACCCCTCTCTTTCCATGGTTTTTCCCTTTCTTTTTCTTCATCTTCCATGTCTTTTTTTTAACA
AAGATTTTCATGAGTTTTAATGTGAGAAATTGAAGTTATAGAAAGAAAACTTCAACAAAGCAAAT
GATGGTGTTTCCTAATTAGAGGCTCGGCCCGACGGCCTGCCCAAAATATGGGAGGGTTTGGGTAA
AAATATAGGCTCGAAATATAGATTTTGGTAAAAAATGAGGTCCGTTTAGAAAACGGGCCGGCCTC
GGGCACCACTTTTTTGTCTCGGGCCGGGCCGAACTTGGGCTTAGGAATTTTTCCCGGGTCGAGCC
TGAACAAAATTTTAGGCCCATATTTCGGGCCGAGCCGAGCCCGAGCCTAGGACGTGGGCTGAATT
TTTTTTTGGGCCTGGCCCAGCCATGATCACCTCTA
Found at i:5142141 original size:5 final size:5
Alignment explanation
Indices: 5142131--5142166 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
5142121 TGAGCATTCG
5142131 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
5142167 AATTTTCGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:5142761 original size:31 final size:30
Alignment explanation
Indices: 5142726--5142785 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
5142716 GGAGGTGGGA
*
5142726 TGGGAAGAGAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AGAGAATAAAAATTTTAGGGGAAAAG
* * *
5142757 TGGGAGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAGAGAATAAAAATTTTAGGGGAAAA
5142786 TAAAAAGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (30 bp):
TGGGAGAGAATAAAAATTTTAGGGGAAAAG
Found at i:5143014 original size:9 final size:9
Alignment explanation
Indices: 5143000--5143036 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
5142990 TATAGTTTGA
5143000 TATTCGAAT
1 TATTCGAAT
5143009 TATTCGAAT
1 TATTCGAAT
*
5143018 TATTCGAGT
1 TATTCGAAT
5143027 TATTCGAAT
1 TATTCGAAT
5143036 T
1 T
5143037 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:5147379 original size:21 final size:21
Alignment explanation
Indices: 5147350--5147399 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
5147340 TTGTCCTTGG
5147350 TGTCACGACACCACTAGAGGA
1 TGTCACGACACCACTAGAGGA
* *
5147371 TGTCGCGACACCACTGGAGGA
1 TGTCACGACACCACTAGAGGA
*
5147392 TGTTACGA
1 TGTCACGA
5147400 TACCCCTATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.18
Consensus pattern (21 bp):
TGTCACGACACCACTAGAGGA
Found at i:5156121 original size:36 final size:37
Alignment explanation
Indices: 5156060--5156191 Score: 132
Period size: 36 Copynumber: 3.6 Consensus size: 37
5156050 ACTCCTTGTT
*
5156060 TTGGCGTGTTTAT-GGTTGGACTAGCTCTT-CGGACAA
1 TTGGCGTG-TTATCGGTTGGAATAGCTCTTACGGACAA
* * *
5156096 TTGGCGTGTTATCGGATGGATTAGCTTTTAC-GAGC-A
1 TTGGCGTGTTATCGGTTGGAATAGCTCTTACGGA-CAA
* *
5156132 TCTGGCATGTTATCGGGTGGAATAGCTCTTACGAGA-AA
1 T-TGGCGTGTTATCGGTTGGAATAGCTCTTACG-GACAA
5156170 TTGGCGTGTT-TCGGTTGGAATA
1 TTGGCGTGTTATCGGTTGGAATA
5156192 ACTATGTACT
Statistics
Matches: 80, Mismatches: 9, Indels: 14
0.78 0.09 0.14
Matches are distributed among these distances:
35 4 0.05
36 36 0.45
37 36 0.45
38 2 0.03
39 2 0.03
ACGTcount: A:0.20, C:0.14, G:0.31, T:0.35
Consensus pattern (37 bp):
TTGGCGTGTTATCGGTTGGAATAGCTCTTACGGACAA
Found at i:5157385 original size:21 final size:21
Alignment explanation
Indices: 5157361--5157406 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
5157351 TTTGCATCTT
5157361 TTTCCTAAACT-TCCCAAACTG
1 TTTCC-AAACTGTCCCAAACTG
*
5157382 TTT-CAAACTGGTCCCAAATTG
1 TTTCCAAACT-GTCCCAAACTG
5157403 TTTC
1 TTTC
5157407 TAGGTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
19 5 0.24
20 1 0.05
21 15 0.71
ACGTcount: A:0.26, C:0.28, G:0.09, T:0.37
Consensus pattern (21 bp):
TTTCCAAACTGTCCCAAACTG
Found at i:5169031 original size:257 final size:257
Alignment explanation
Indices: 5168571--5169081 Score: 668
Period size: 257 Copynumber: 2.0 Consensus size: 257
5168561 AGGAGCTTGG
* *
5168571 GTGCATGCCTTAGATGCGGATCTTTGAACCATAAGATAAATGATTGTCCACTTCAAAATAAGTAG
1 GTGCATGCCTTAGATGCGGATCCTTGAACCATAAGATAAATGATTGTCCACTTCAAAATAAGCAG
* * * *
5168636 ATACAAGCCCCAGAACAGAATTGAGCTTAGAACTAAAAAGTTGAAAAGTAGGCTTAGAAAGGTCA
66 ATACAAGCCCCAAAACAGAATCGAGCTTAGAACCAAAAAGCTGAAAAGTAGGCTTAGAAAGGTCA
*
5168701 AGGTCCAAATAGGGGTGGTAATGTAGGTCAGAGACAGAGAACACTGGGTCAGGGTGCTAACCGAG
131 AGGTCCAAATAGGGGTGGTAATGTAGGTCAGAGACAGAGAACACTGGGTCAGGGTGCTAACCGAC
* * *
5168766 TCGATGTAAGACAACCTGCACTGGTCTGTGCAACTAGACGCAGAGAGGATCATGACACAGCC
196 TCGATGTAAGACAACCTGCACTGGTCTATGCAACTAGACACAGAGAGGACCATGACACAGCC
* * * * *
5168828 GTGCATGCCTTAGATGTGGATCCTTGAACCATAAGATCAATTACTT-TCCAGTTCGAAATGAA-C
1 GTGCATGCCTTAGATGCGGATCCTTGAACCATAAGATAAATGA-TTGTCCACTTCAAAAT-AAGC
* * * * * * * *
5168891 ATATTCAATCCCCAAAACATAATCGAGCTTAGAACCAAAGAGCTGGACAGTAGGCTTAGAGAGGT
64 AGATACAAGCCCCAAAACAGAATCGAGCTTAGAACCAAAAAGCTGAAAAGTAGGCTTAGAAAGGT
* * * * * *
5168956 CAAGGTCCGAATAGGGGTGGTAATGTTGGTCAGAGACAGAGAGCATTGGGTTAGGGTGCTAACTG
129 CAAGGTCCAAATAGGGGTGGTAATGTAGGTCAGAGACAGAGAACACTGGGTCAGGGTGCTAACCG
* * * * *
5169021 AACT-GATGTAAGACAACTTGCACTGGTCTATGTAGCTAGACATAGAGAGGACCGTGACACA
194 -ACTCGATGTAAGACAACCTGCACTGGTCTATGCAACTAGACACAGAGAGGACCATGACACA
5169082 ACCAACATCA
Statistics
Matches: 217, Mismatches: 34, Indels: 6
0.84 0.13 0.02
Matches are distributed among these distances:
257 211 0.97
258 6 0.03
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.22
Consensus pattern (257 bp):
GTGCATGCCTTAGATGCGGATCCTTGAACCATAAGATAAATGATTGTCCACTTCAAAATAAGCAG
ATACAAGCCCCAAAACAGAATCGAGCTTAGAACCAAAAAGCTGAAAAGTAGGCTTAGAAAGGTCA
AGGTCCAAATAGGGGTGGTAATGTAGGTCAGAGACAGAGAACACTGGGTCAGGGTGCTAACCGAC
TCGATGTAAGACAACCTGCACTGGTCTATGCAACTAGACACAGAGAGGACCATGACACAGCC
Found at i:5175152 original size:16 final size:17
Alignment explanation
Indices: 5175121--5175154 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5175111 CAATTCAGTC
*
5175121 CAAAATTCATACTTTTG
1 CAAAATTCACACTTTTG
5175138 CAAAATT-ACACTTTTG
1 CAAAATTCACACTTTTG
5175154 C
1 C
5175155 CCTTAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.38
Consensus pattern (17 bp):
CAAAATTCACACTTTTG
Found at i:5177444 original size:26 final size:26
Alignment explanation
Indices: 5177406--5177473 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
5177396 TATACATCAT
*
5177406 TGCTCACATGAGCTGTGAAATGGACC
1 TGCTCACACGAGCTGTGAAATGGACC
*
5177432 TGCTCACACGAGCTGTGAAATGGGCC
1 TGCTCACACGAGCTGTGAAATGGACC
*
5177458 TGCTCACACAAGCTGT
1 TGCTCACACGAGCTGT
5177474 AGGTCGAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.25, C:0.26, G:0.26, T:0.22
Consensus pattern (26 bp):
TGCTCACACGAGCTGTGAAATGGACC
Found at i:5194712 original size:19 final size:19
Alignment explanation
Indices: 5194678--5194715 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5194668 CTTACATGCC
**
5194678 AAAGTGAAAATTTGATTTT
1 AAAGTGAAAAAGTGATTTT
5194697 AAAGTGAAAAAGTGATTTT
1 AAAGTGAAAAAGTGATTTT
5194716 TTTTGGCCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.18, T:0.37
Consensus pattern (19 bp):
AAAGTGAAAAAGTGATTTT
Found at i:5197197 original size:12 final size:12
Alignment explanation
Indices: 5197180--5197204 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5197170 TGTGACACAG
5197180 CCGTGTGTGACA
1 CCGTGTGTGACA
5197192 CCGTGTGTGACA
1 CCGTGTGTGACA
5197204 C
1 C
5197205 ACGGCCTGGC
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:0.28, G:0.32, T:0.24
Consensus pattern (12 bp):
CCGTGTGTGACA
Found at i:5210764 original size:51 final size:50
Alignment explanation
Indices: 5210643--5210837 Score: 212
Period size: 51 Copynumber: 3.9 Consensus size: 50
5210633 TGACCATTGT
* * * * *
5210643 CATCTGATACACGTAGTAGCCTACACATAGTACTATACACATGATCAAGC
1 CATCTGATACACATAGTAGCCTGCACATAGTACTACACACGTGACCAAGC
** * *
5210693 TTTCTGGTTCACATAGTAGCCTGCACATAGTACTACACACGTGACCAAGGC
1 CATCTGATACACATAGTAGCCTGCACATAGTACTACACACGTGACCAA-GC
* * *
5210744 CATCTGGTACACATAGTAGCCTGCACATAGTACTACACATGTGACCATTATC
1 CATCTGATACACATAGTAGCCTGCACATAGTACTACACACGTGACCA--AGC
* * * *
5210796 TATC-GATACACGTAGTAGCTTGCACTTAGTACTACACACGTG
1 CATCTGATACACATAGTAGCCTGCACATAGTACTACACACGTG
5210838 TTCATAGGTA
Statistics
Matches: 122, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
50 39 0.32
51 78 0.64
52 4 0.03
53 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (50 bp):
CATCTGATACACATAGTAGCCTGCACATAGTACTACACACGTGACCAAGC
Found at i:5222402 original size:25 final size:25
Alignment explanation
Indices: 5222328--5222403 Score: 82
Period size: 25 Copynumber: 3.0 Consensus size: 25
5222318 ACGAATTTTC
* *
5222328 TCAAAATTTTACAAAGGT-AAATTCG
1 TCAAAATTTTACTAGGGTAAAATT-G
* *
5222353 TTAAAATTTTACTCAGAGTAAAATTG
1 TCAAAATTTTACT-AGGGTAAAATTG
*
5222379 TCAAAATTTTGCTAGGGTAAAATTG
1 TCAAAATTTTACTAGGGTAAAATTG
5222404 GATGAGAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
25 22 0.52
26 15 0.36
27 5 0.12
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (25 bp):
TCAAAATTTTACTAGGGTAAAATTG
Found at i:5242976 original size:20 final size:20
Alignment explanation
Indices: 5242951--5242989 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
5242941 TTACTTCTTT
5242951 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
5242971 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
5242990 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:5243314 original size:50 final size:50
Alignment explanation
Indices: 5243197--5243374 Score: 173
Period size: 50 Copynumber: 3.6 Consensus size: 50
5243187 ACATGCTAAA
* * * *
5243197 GCCATGTCCCAGACATGTTCTTACGTGGGATGTT-TCCTAAAC--TACCAAT
1 GCCATGTCCCAGACATGGTCTTACGTGGGA-GTTCTCAT-ATCGGTGCCAAT
* * * * *
5243246 GCCATATCTCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACGTGGGAGTTCTCATATCGGTGCCAAT
* ** * *
5243296 GCCATGTCCCAGACATGGTCTTACGGGGGAACTCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACGTGGGAGTTCTCATATCGGTGCCAAT
* *
5243346 GCCATGTCCCAGACATGGTATTATGTGGG
1 GCCATGTCCCAGACATGGTCTTACGTGGG
5243375 GCCTCTAATA
Statistics
Matches: 104, Mismatches: 22, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
48 5 0.05
49 28 0.27
50 71 0.68
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACGTGGGAGTTCTCATATCGGTGCCAAT
Found at i:5245675 original size:25 final size:25
Alignment explanation
Indices: 5245641--5245690 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
5245631 AGAGGAATGT
5245641 ATGTGAATGAATGCAATATTATATA
1 ATGTGAATGAATGCAATATTATATA
5245666 ATGTGAATGAATGCAATATTATATA
1 ATGTGAATGAATGCAATATTATATA
5245691 CATTTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.36
Consensus pattern (25 bp):
ATGTGAATGAATGCAATATTATATA
Found at i:5247663 original size:20 final size:20
Alignment explanation
Indices: 5247638--5247678 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
5247628 AAAAAGAAAC
*
5247638 TTAATTTTTTGTTTCATGCT
1 TTAATTTTTTGCTTCATGCT
5247658 TTAATTTTTTGCTTCATGCT
1 TTAATTTTTTGCTTCATGCT
5247678 T
1 T
5247679 ATATAATAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.12, G:0.10, T:0.63
Consensus pattern (20 bp):
TTAATTTTTTGCTTCATGCT
Found at i:5251986 original size:6 final size:6
Alignment explanation
Indices: 5251977--5252001 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5251967 CTTGTGCTTG
5251977 TTCTTA TTCTTA TTCTTA TTCTTA T
1 TTCTTA TTCTTA TTCTTA TTCTTA T
5252002 ACTTGTACTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (6 bp):
TTCTTA
Found at i:5252638 original size:253 final size:253
Alignment explanation
Indices: 5252190--5252698 Score: 1018
Period size: 253 Copynumber: 2.0 Consensus size: 253
5252180 TGAAGCATAC
5252190 CTCGACATTCCCTTATCCCTCCACAATCCTATGGCATGTAACTGTATCCAACATATAAGATCTCG
1 CTCGACATTCCCTTATCCCTCCACAATCCTATGGCATGTAACTGTATCCAACATATAAGATCTCG
5252255 CATAAGGAGCTCTCATAAAAGCACTTGTTTATATAGAGATCACACAAAAATCTCATAAAAACATT
66 CATAAGGAGCTCTCATAAAAGCACTTGTTTATATAGAGATCACACAAAAATCTCATAAAAACATT
5252320 GTACTTTAAAAACATATCTTAACACATTAGCTGACATAAGAACACACATAAAACATAACTTTAAA
131 GTACTTTAAAAACATATCTTAACACATTAGCTGACATAAGAACACACATAAAACATAACTTTAAA
5252385 AGCATAACTTAAAATTAGAGTCTCAAAACTTGAAAACAAATTTTATTAGAAAATCCTA
196 AGCATAACTTAAAATTAGAGTCTCAAAACTTGAAAACAAATTTTATTAGAAAATCCTA
5252443 CTCGACATTCCCTTATCCCTCCACAATCCTATGGCATGTAACTGTATCCAACATATAAGATCTCG
1 CTCGACATTCCCTTATCCCTCCACAATCCTATGGCATGTAACTGTATCCAACATATAAGATCTCG
5252508 CATAAGGAGCTCTCATAAAAGCACTTGTTTATATAGAGATCACACAAAAATCTCATAAAAACATT
66 CATAAGGAGCTCTCATAAAAGCACTTGTTTATATAGAGATCACACAAAAATCTCATAAAAACATT
5252573 GTACTTTAAAAACATATCTTAACACATTAGCTGACATAAGAACACACATAAAACATAACTTTAAA
131 GTACTTTAAAAACATATCTTAACACATTAGCTGACATAAGAACACACATAAAACATAACTTTAAA
5252638 AGCATAACTTAAAATTAGAGTCTCAAAACTTGAAAACAAATTTTATTAGAAAATCCTA
196 AGCATAACTTAAAATTAGAGTCTCAAAACTTGAAAACAAATTTTATTAGAAAATCCTA
5252696 CTC
1 CTC
5252699 TTGGAACTTA
Statistics
Matches: 256, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
253 256 1.00
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (253 bp):
CTCGACATTCCCTTATCCCTCCACAATCCTATGGCATGTAACTGTATCCAACATATAAGATCTCG
CATAAGGAGCTCTCATAAAAGCACTTGTTTATATAGAGATCACACAAAAATCTCATAAAAACATT
GTACTTTAAAAACATATCTTAACACATTAGCTGACATAAGAACACACATAAAACATAACTTTAAA
AGCATAACTTAAAATTAGAGTCTCAAAACTTGAAAACAAATTTTATTAGAAAATCCTA
Found at i:5261485 original size:24 final size:24
Alignment explanation
Indices: 5261458--5261505 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
5261448 GCATGAAATG
5261458 GTTGATCTATTTCCCTATGTTGAT
1 GTTGATCTATTTCCCTATGTTGAT
*
5261482 GTTGATCTATTTGCCTATGTTGAT
1 GTTGATCTATTTCCCTATGTTGAT
5261506 TTTCTCTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.17, C:0.15, G:0.19, T:0.50
Consensus pattern (24 bp):
GTTGATCTATTTCCCTATGTTGAT
Found at i:5262633 original size:159 final size:163
Alignment explanation
Indices: 5262335--5262638 Score: 449
Period size: 159 Copynumber: 1.9 Consensus size: 163
5262325 GGATTTTTTC
5262335 AAATTAAAAATTAATTCCATCTTGGATATTACCTACCATGTCGTCATTTAATGGCGAATTCTTAA
1 AAATTAAAAATTAATTCCATCTTGGATATTACCTACCATGTCG--ATTTAATGGCGAATTCTTAA
* *
5262400 CAAAATGAAATAATTTACACTTTTTGTCTAATGTACAAAGATTAATTTACTCATTTTTAAAAGAG
64 CAAAATGAAATAATTTA-ACTTTTTGTCTAATGTACAAAGATTAATTTACTCACTTTTAAAAGAA
5262465 AGAAAAAAATACAATCCTATTTCTACTAAATGGGCA
128 AGAAAAAAATACAATCCTATTTCTACTAAATGGGCA
* * *
5262501 AAATTAAACATTAATTCCATCTTGGATATTACCTACCATGATCG-TTTAATGGTGAATTTTTAAC
1 AAATTAAAAATTAATTCCATCTTGGATATTACCTACCATG-TCGATTTAATGGCGAATTCTTAAC
* *
5262565 AAAATGAAATAATTT-A-TTTTT-T-TAATGTATAAAGATTAATTTA-TCCACTTTTAATAGAAA
65 AAAATGAAATAATTTAACTTTTTGTCTAATGTACAAAGATTAATTTACT-CACTTTTAAAAGAAA
*
5262625 GAATAAAATACAAT
129 GAAAAAAATACAAT
5262639 TCAACTATTA
Statistics
Matches: 128, Mismatches: 8, Indels: 11
0.87 0.05 0.07
Matches are distributed among these distances:
158 1 0.01
159 45 0.35
160 1 0.01
161 5 0.04
162 1 0.01
164 33 0.26
166 39 0.30
167 3 0.02
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (163 bp):
AAATTAAAAATTAATTCCATCTTGGATATTACCTACCATGTCGATTTAATGGCGAATTCTTAACA
AAATGAAATAATTTAACTTTTTGTCTAATGTACAAAGATTAATTTACTCACTTTTAAAAGAAAGA
AAAAAATACAATCCTATTTCTACTAAATGGGCA
Found at i:5263436 original size:125 final size:125
Alignment explanation
Indices: 5263196--5263849 Score: 985
Period size: 125 Copynumber: 5.3 Consensus size: 125
5263186 AACAAATAAG
* * * * * * * *
5263196 TCGCACCCACGTGTACGCACTTTTGCTATAGTAGGT-CTTGAAAAAATAATTTCGAGTTGACGTT
1 TCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAAAAATAATTTTGACTTGACGTT
* * * *
5263260 TCTGAGCAAATAGTATAAAATCGCTTCTAACAGGATGCTGTTTGATAAGAATTTGTGAAA
66 TCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTATGAAA
* * * *
5263320 TCGCGCCCTCGTCGATGCGCTTTTGCTACAGTAGGTCCTGGAAGAAATAATTTTGACTTGACGTG
1 TCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAAAAATAATTTTGACTTGACGTT
* *
5263385 TCTGAGCCAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAA
66 TCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTATGAAA
* * *
5263445 TCGCGCCCTCCTGGACGCGCTTTTGCTACAATAGGTCCTGGAAGAAATAATTTTGACTTGACGTT
1 TCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAAAAATAATTTTGACTTGACGTT
*
5263510 TCTAAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTATGAAA
66 TCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTATGAAA
* * *
5263570 TCGCACCCTCGTGGACGTGCTTTTGCTACAGTAGGTCCT-GAAAAAATAATTTCGACTTGACGTT
1 TCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAAAAATAATTTTGACTTGACGTT
5263634 TCTGAGCAAATAGTAT-AAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTATGAAA
66 TCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTATGAAA
**
5263693 TCGAACCCTCGTGGACGCGCTTTTGCTACAGTAGGTCCTGG-AAAAATAATTTTGACTTGACGTT
1 TCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAAAAATAATTTTGACTTGACGTT
* *
5263757 TCTGAGCAAATAGTAT-AAATCGCTTCTAGCTGGATGTTATTTGAGAAGAATTTATGAAA
66 TCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTATGAAA
* * *
5263816 TCGTGCCCTCGTGGATGCACTTTTGCTACAGTAG
1 TCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
5263850 CATGTTTGAG
Statistics
Matches: 488, Mismatches: 40, Indels: 5
0.92 0.08 0.01
Matches are distributed among these distances:
123 189 0.39
124 68 0.14
125 231 0.47
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (125 bp):
TCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAAAAATAATTTTGACTTGACGTT
TCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTATGAAA
Found at i:5265252 original size:44 final size:44
Alignment explanation
Indices: 5265189--5265273 Score: 170
Period size: 44 Copynumber: 1.9 Consensus size: 44
5265179 AGGTGTTTCA
5265189 CAAGATCATCCCAAGATGGATTCAGCTATGTTAGCTAGCTTGAT
1 CAAGATCATCCCAAGATGGATTCAGCTATGTTAGCTAGCTTGAT
5265233 CAAGATCATCCCAAGATGGATTCAGCTATGTTAGCTAGCTT
1 CAAGATCATCCCAAGATGGATTCAGCTATGTTAGCTAGCTT
5265274 CATACTACCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.29
Consensus pattern (44 bp):
CAAGATCATCCCAAGATGGATTCAGCTATGTTAGCTAGCTTGAT
Found at i:5267102 original size:114 final size:114
Alignment explanation
Indices: 5266901--5267283 Score: 712
Period size: 114 Copynumber: 3.4 Consensus size: 114
5266891 ATTATATTTT
* *
5266901 TAAAATTATTAATTGATAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATCAACTTATTA
1 TAAAATTATTAACTGAT-AATTGTATTAATGGTTAGTAAAATTATCAAATTATATCAAATTATTA
5266966 ATTGTTAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATG
65 ATTGTTAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATG
*
5267016 TAAAATTATTAAATGATAATTGTATTAATGGTTAGTAAAATTATCAAATTATATCAAATTATTAA
1 TAAAATTATTAACTGATAATTGTATTAATGGTTAGTAAAATTATCAAATTATATCAAATTATTAA
*
5267081 TTGTTAGTACCAGTCAAAACATTTTTCCAAATCTAACATCATGTGAATG
66 TTGTTAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATG
5267130 TAAAATTATTAACTGATAATTGTATTAATGGTTAGTAAAATTATCAAATTATATCAAATTATTAA
1 TAAAATTATTAACTGATAATTGTATTAATGGTTAGTAAAATTATCAAATTATATCAAATTATTAA
*
5267195 TTGTTAGTACCAGTGAAAACATTTTTCCAAATCTAACATTATGTGAATG
66 TTGTTAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATG
5267244 TAAAATTATTAACTGATAATTGTATTAATGGTTAGTAAAA
1 TAAAATTATTAACTGATAATTGTATTAATGGTTAGTAAAA
5267284 ACCTTAAGGT
Statistics
Matches: 262, Mismatches: 6, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
114 246 0.94
115 16 0.06
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.39
Consensus pattern (114 bp):
TAAAATTATTAACTGATAATTGTATTAATGGTTAGTAAAATTATCAAATTATATCAAATTATTAA
TTGTTAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATG
Found at i:5267355 original size:21 final size:21
Alignment explanation
Indices: 5267291--5267655 Score: 475
Period size: 21 Copynumber: 17.2 Consensus size: 21
5267281 AAAACCTTAA
*
5267291 GGTTTTTAAGTTAAGAATTTAG
1 GGTTTTTAAGTTAAG-GTTTAG
5267313 GGTTTTTAAGTTAAGGGTTTAG
1 GGTTTTTAAGTTAA-GGTTTAG
*
5267335 GGTTTTTAAGTTAAGGGTTAG
1 GGTTTTTAAGTTAAGGTTTAG
* *
5267356 GGTTATTAAGTTAAGATTTAG
1 GGTTTTTAAGTTAAGGTTTAG
*
5267377 GGTTTTTTAATTTAAGGTTTAG
1 GG-TTTTTAAGTTAAGGTTTAG
* *
5267399 GGTTTTTAATTTAAGGGTTAG
1 GGTTTTTAAGTTAAGGTTTAG
*
5267420 GGTTTTTAAGTTAAGATTTAG
1 GGTTTTTAAGTTAAGGTTTAG
*
5267441 GGTTTTTAAGTAAAGGTTTAG
1 GGTTTTTAAGTTAAGGTTTAG
* * *
5267462 GGTTATTAATTTAAGATTTAG
1 GGTTTTTAAGTTAAGGTTTAG
*
5267483 GGTTTTTAAGTTAAGGGTTAG
1 GGTTTTTAAGTTAAGGTTTAG
*
5267504 GGTTTTTAATTTAAAGG-TTAG
1 GGTTTTTAAGTT-AAGGTTTAG
*
5267525 TGTTTTTAAGTTAAGGTTTAG
1 GGTTTTTAAGTTAAGGTTTAG
5267546 GGTTTTTAAGTTAAGGGTTTAG
1 GGTTTTTAAGTTAA-GGTTTAG
*
5267568 TGTTTTTAAGTTAAGGTTTAG
1 GGTTTTTAAGTTAAGGTTTAG
* *
5267589 GGTTATTAATTTAAAGG-TTAG
1 GGTTTTTAAGTT-AAGGTTTAG
5267610 GGTTTTTAAGTTAAAGG-TTAG
1 GGTTTTTAAGTT-AAGGTTTAG
*
5267631 GGTTTTTAAGTTAATGTTTAG
1 GGTTTTTAAGTTAAGGTTTAG
5267652 GGTT
1 GGTT
5267656 AGGGTTTTTT
Statistics
Matches: 303, Mismatches: 33, Indels: 15
0.86 0.09 0.04
Matches are distributed among these distances:
20 7 0.02
21 216 0.71
22 79 0.26
23 1 0.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.47
Consensus pattern (21 bp):
GGTTTTTAAGTTAAGGTTTAG
Found at i:5267462 original size:106 final size:105
Alignment explanation
Indices: 5267291--5267655 Score: 502
Period size: 106 Copynumber: 3.4 Consensus size: 105
5267281 AAAACCTTAA
** * *
5267291 GGTTTTTAAGTTAAGAATTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTAG
1 GGTTTTTAAGTTAA-AGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTAAAGGTTTAG
5267356 GGTTATTAAGTTAAGATTTAGGGTTTTTTAATTTAAGGTTTAG
65 GGTTATTAAGTTAAGATTTAGGG-TTTTTAATTTAAGG-TTAG
* * *
5267399 GGTTTTTAATTTAAGGGTTAGGGTTTTTAAGTTAA-GATTTAGGGTTTTTAAGTAAAGGTTTAGG
1 GGTTTTTAAGTTAAAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTAAAGGTTTAGG
* *
5267463 GTTATTAATTTAAGATTTAGGGTTTTTAAGTTAAGGGTTAG
66 GTTATTAAGTTAAGATTTAGGGTTTTTAATTTAA-GGTTAG
* * *
5267504 GGTTTTTAATTTAAAGGTTAGTGTTTTTAAGTTAA-GGTTTAGGGTTTTTAAGTTAAGGGTTTAG
1 GGTTTTTAAGTTAAAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAG-TAAAGGTTTAG
* * * *
5267568 TGTTTTTAAGTTAAGGTTTAGGGTTATTAATTTAAAGGTTAG
65 GGTTATTAAGTTAAGATTTAGGGTTTTTAATTT-AAGGTTAG
*
5267610 GGTTTTTAAGTTAAAGGTTAGGGTTTTTAAGTTAA-TGTTTAGGGTT
1 GGTTTTTAAGTTAAAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
5267656 AGGGTTTTTT
Statistics
Matches: 232, Mismatches: 22, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
105 64 0.28
106 135 0.58
107 20 0.09
108 13 0.06
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.47
Consensus pattern (105 bp):
GGTTTTTAAGTTAAAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTAAAGGTTTAGG
GTTATTAAGTTAAGATTTAGGGTTTTTAATTTAAGGTTAG
Found at i:5267676 original size:27 final size:27
Alignment explanation
Indices: 5267615--5267682 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 27
5267605 GTTAGGGTTT
*
5267615 TTAA-GTTAAAGGTTAGGGTTTTTAAG
1 TTAAGGTTTAAGGTTAGGGTTTTTAAG
* * *
5267641 TTAATGTTTAGGGTTAGGGTTTTT-TG
1 TTAAGGTTTAAGGTTAGGGTTTTTAAG
5267667 TTAAGGGTTTAAGGTT
1 TTAA-GGTTTAAGGTT
5267683 TGTCAATTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 9 0.26
27 26 0.74
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (27 bp):
TTAAGGTTTAAGGTTAGGGTTTTTAAG
Found at i:5267975 original size:21 final size:21
Alignment explanation
Indices: 5267938--5267984 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
5267928 GCGGCTGTTG
*
5267938 TGGTTCTTCCGGCAGGG-ATTC
1 TGGTTCTTCCAGCAGGGCA-TC
*
5267959 TGGTTCTTCCAGTAGGGCATC
1 TGGTTCTTCCAGCAGGGCATC
5267980 TGGTT
1 TGGTT
5267985 GTCGGAGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.11, C:0.21, G:0.32, T:0.36
Consensus pattern (21 bp):
TGGTTCTTCCAGCAGGGCATC
Found at i:5268246 original size:18 final size:18
Alignment explanation
Indices: 5268219--5268262 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
5268209 GCCATAGGAC
*
5268219 TAGGAAACATATAAGGGT
1 TAGGAAACATAAAAGGGT
*
5268237 TAGGATACATAAAAGGGT
1 TAGGAAACATAAAAGGGT
5268255 TAGGAAAC
1 TAGGAAAC
5268263 GCACCTGGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.45, C:0.07, G:0.27, T:0.20
Consensus pattern (18 bp):
TAGGAAACATAAAAGGGT
Found at i:5269134 original size:20 final size:20
Alignment explanation
Indices: 5269097--5269134 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5269087 TTTATTTTTA
*
5269097 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
5269117 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
5269135 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:5270162 original size:12 final size:12
Alignment explanation
Indices: 5270122--5270164 Score: 56
Period size: 11 Copynumber: 3.8 Consensus size: 12
5270112 ATTAAATATG
5270122 AATTTGAGA-GA
1 AATTTGAGAGGA
5270133 AATTTG-GAAGGA
1 AATTTGAG-AGGA
5270145 AA-TTGAGAGGA
1 AATTTGAGAGGA
5270156 AATTTGAGA
1 AATTTGAGA
5270165 TAGGATTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
10 1 0.04
11 16 0.57
12 11 0.39
ACGTcount: A:0.44, C:0.00, G:0.30, T:0.26
Consensus pattern (12 bp):
AATTTGAGAGGA
Found at i:5276704 original size:38 final size:38
Alignment explanation
Indices: 5276653--5276728 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
5276643 GGTATGTGGG
* **
5276653 TGTTACAGGGAACAGAGCCTTATTGGTTTGGAAACTAT
1 TGTTACAAGGAACAGAGCCTTATCAGTTTGGAAACTAT
5276691 TGTTACAAGGAACAGAGCCTTATCAGTTTGGAAACTAT
1 TGTTACAAGGAACAGAGCCTTATCAGTTTGGAAACTAT
5276729 CTTACGAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (38 bp):
TGTTACAAGGAACAGAGCCTTATCAGTTTGGAAACTAT
Found at i:5280933 original size:19 final size:19
Alignment explanation
Indices: 5280911--5280958 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
5280901 GAAATCATAT
5280911 ATAATAAATAT-CAAATGAA
1 ATAATAAATATCCAAAT-AA
*
5280930 ATAAT-AGTATCCAAATAA
1 ATAATAAATATCCAAATAA
*
5280948 AAAATAAATAT
1 ATAATAAATAT
5280959 TATAATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.27
Consensus pattern (19 bp):
ATAATAAATATCCAAATAA
Found at i:5281946 original size:17 final size:18
Alignment explanation
Indices: 5281912--5281948 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
5281902 TCAGTTTTTC
5281912 AAAATGAAAATAAAAAAG
1 AAAATGAAAATAAAAAAG
5281930 AAAAT-AAAA-AAATAAAG
1 AAAATGAAAATAAA-AAAG
5281947 AA
1 AA
5281949 TAAAAAGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.17
17 10 0.56
18 5 0.28
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.11
Consensus pattern (18 bp):
AAAATGAAAATAAAAAAG
Found at i:5283177 original size:44 final size:44
Alignment explanation
Indices: 5283116--5283714 Score: 303
Period size: 44 Copynumber: 13.8 Consensus size: 44
5283106 ACCTGATGCG
* * * *
5283116 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCTAATACTTTA
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTAATACTTCA
* * * * *
5283160 ATCCGCTCCACTGTAACTTCAGGGAGATAGGA--TAGTGTCTTCG
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTAAT-ACTTCA
* * *
5283203 ATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGATCT-CTGGCTTCA
1 ATCTGCTCCACTGTAACT-TCAGGGAGATAAGATCTAAT-ACTTCA
* * *
5283247 ATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCG
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCT--AATACTTCA
* ** * * * * * *
5283293 GTCAACTCCACTGTAACCTCAGAGAGATAAGACCT--GA-TGCG
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTAATACTTCA
* * * * *
5283334 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCTATTACTTTA
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTAATACTTCA
** ** * *
5283378 ATCCACTCCACTACAACTTCAGGGAGATAGGAT-TATTGACTTCA
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTAAT-ACTTCA
* * * *
5283422 ATCTGCTCCACTGCAACCTCAGGGAGATAAGATCTATTACTTTA
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTAATACTTCA
* ** * *
5283466 ATCCGCTCCACTACAACTTCAGGGAGATAGGAT-T-ATCGAATTCA
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTAAT--ACTTCA
* * * * ** *
5283510 ATCTACTCCACTGCAACCTCAGGGAGATAAGATTTGCTTCTTCA
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTAATACTTCA
* * * * * ** **
5283554 GTCAGCCCCACTGTGACTTCAGGGGGATAAGA-CTTGTTTTCTCA
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTAATACT-TCA
* * ** *** * *
5283598 GTCTGCTCCGCTACAACTTCAGGGAGATAAGA-C-CCGA-TGCG
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTAATACTTCA
* * * * *
5283639 ATCTGCTCCACTACT-GCTT-AGGGAGATAAGATCTATTATTTTA
1 ATCTGCTCCACT-GTAACTTCAGGGAGATAAGATCTAATACTTCA
* * *
5283682 ATCCGCTCCACTGCAACTTTAGGGAGATAAGAT
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGAT
5283715 TGATTTCTTC
Statistics
Matches: 426, Mismatches: 105, Indels: 48
0.74 0.18 0.08
Matches are distributed among these distances:
40 12 0.03
41 48 0.11
42 7 0.02
43 55 0.13
44 262 0.62
45 6 0.01
46 35 0.08
47 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (44 bp):
ATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTAATACTTCA
Found at i:5283463 original size:88 final size:88
Alignment explanation
Indices: 5283334--5283542 Score: 346
Period size: 88 Copynumber: 2.4 Consensus size: 88
5283324 ACCTGATGCG
* * * *
5283334 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCTATTACTTTAATCCACTCCACTACAACTTCA
1 ATCTACTCCACTGCAACCTCAGGGAGATAAGATCTATTACTTTAATCCACTCCACTACAACTTCA
5283399 GGGAGATAGGATTATTGACTTCA
66 GGGAGATAGGATTATTGACTTCA
* *
5283422 ATCTGCTCCACTGCAACCTCAGGGAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCA
1 ATCTACTCCACTGCAACCTCAGGGAGATAAGATCTATTACTTTAATCCACTCCACTACAACTTCA
* *
5283487 GGGAGATAGGATTATCGAATTCA
66 GGGAGATAGGATTATTGACTTCA
5283510 ATCTACTCCACTGCAACCTCAGGGAGATAAGAT
1 ATCTACTCCACTGCAACCTCAGGGAGATAAGAT
5283543 TTGCTTCTTC
Statistics
Matches: 112, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 112 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (88 bp):
ATCTACTCCACTGCAACCTCAGGGAGATAAGATCTATTACTTTAATCCACTCCACTACAACTTCA
GGGAGATAGGATTATTGACTTCA
Found at i:5284081 original size:132 final size:132
Alignment explanation
Indices: 5283762--5284069 Score: 519
Period size: 132 Copynumber: 2.3 Consensus size: 132
5283752 TAAGACTTGT
* *
5283762 AATTTCCAACTTATTCCATTGCTGGTCAGGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTAC
1 AATTTCCAACCTATTCCACTGCTGGTCAGGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTAC
* * *
5283827 TCCTGGGGAAGATAAGATTCGTCATCTTCGATCTACTGCACTGCTGCTTAGGGAGACAAAGGTCT
66 TCCTGGGAAAGATAAGATTCGTCATCTTCGATCTACTCCACTGCTGCTCAGGGAGACAAAGGTCT
5283892 GC
131 GC
* *
5283894 AATTTCCAACCTATTCCACTGCTGGTTAGGGACATATGACTTGTGGCTTAAATCTGTTTCCCTAC
1 AATTTCCAACCTATTCCACTGCTGGTCAGGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTAC
* * *
5283959 TTCTGGGAAAGATAAGATTCGTCGTCTTCGATCTACTCCGCTGCTGCTCAGGGAGAC-AAGGTCT
66 TCCTGGGAAAGATAAGATTCGTCATCTTCGATCTACTCCACTGCTGCTCAGGGAGACAAAGGTCT
5284023 GC
131 GC
5284025 AATTTCCAACCTATTCCACTGCTGGTCAGGGACATAGGACTTGTG
1 AATTTCCAACCTATTCCACTGCTGGTCAGGGACATAGGACTTGTG
5284070 CTCTTTGATC
Statistics
Matches: 164, Mismatches: 12, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
131 52 0.32
132 112 0.68
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (132 bp):
AATTTCCAACCTATTCCACTGCTGGTCAGGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTAC
TCCTGGGAAAGATAAGATTCGTCATCTTCGATCTACTCCACTGCTGCTCAGGGAGACAAAGGTCT
GC
Found at i:5284207 original size:87 final size:87
Alignment explanation
Indices: 5284102--5284602 Score: 822
Period size: 87 Copynumber: 5.8 Consensus size: 87
5284092 GACACGGGAG
* * * * *
5284102 GGCAAGATTTACTATCTTTAACCAGCTCCACTGCAACCGATGAAGACAAGGCTTTGTTTTTGATC
1 GGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATC
*
5284167 TACTTCGCTATTAACGCAGGAA
66 TACTTCGCTGTTAACGCAGGAA
* * *
5284189 GGCAAGATCTGCTATCTTTAACCAGCTCCACTGGAACCGATGGAGGCAAGACTTTGTTTCCGATC
1 GGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATC
*
5284254 TGCTTCGCTGTTAACGCAGGAA
66 TACTTCGCTGTTAACGCAGGAA
*
5284276 GGCAAGATCTGCGATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATC
1 GGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATC
*
5284341 TACTTCGTTGTTAACGCAGGAA
66 TACTTCGCTGTTAACGCAGGAA
5284363 GGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATC
1 GGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATC
*
5284428 TACTTCGCTATTAACGCAGGAA
66 TACTTCGCTGTTAACGCAGGAA
*
5284450 GGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTCGTTTTCGATC
1 GGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATC
* *
5284515 TGCTTCGCTGTTAACGCAAGAA
66 TACTTCGCTGTTAACGCAGGAA
* * * *
5284537 GGCAAGATCTGCTATTTTTAACTAGCTCAACTACAACCGATGGAGGCAAGGCTTTGTTTTCGATC
1 GGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATC
5284602 T
66 T
5284603 TCATTGATCT
Statistics
Matches: 386, Mismatches: 28, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 386 1.00
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.28
Consensus pattern (87 bp):
GGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATC
TACTTCGCTGTTAACGCAGGAA
Found at i:5285761 original size:13 final size:14
Alignment explanation
Indices: 5285736--5285764 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5285726 TGACAAAATC
5285736 AAAATGTATTTAAA
1 AAAATGTATTTAAA
5285750 AAAATGTA-TTAAA
1 AAAATGTATTTAAA
5285763 AA
1 AA
5285765 TGTCAATGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (14 bp):
AAAATGTATTTAAA
Found at i:5286064 original size:17 final size:18
Alignment explanation
Indices: 5286042--5286085 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
5286032 TTAAAACACG
5286042 AAAATATAAATAT-TATA
1 AAAATATAAATATATATA
* *
5286059 AAAATATGAATGTATATA
1 AAAATATAAATATATATA
5286077 AAATATATA
1 AAA-ATATA
5286086 TAAACTATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 11 0.50
18 7 0.32
19 4 0.18
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (18 bp):
AAAATATAAATATATATA
Found at i:5287987 original size:7 final size:7
Alignment explanation
Indices: 5287968--5288014 Score: 71
Period size: 7 Copynumber: 6.9 Consensus size: 7
5287958 TTAGCCTCTC
5287968 CATTTTT
1 CATTTTT
5287975 -ACTTTTT
1 CA-TTTTT
5287982 CATTTTT
1 CATTTTT
5287989 CATTTTT
1 CATTTTT
5287996 CA-TTTT
1 CATTTTT
5288002 CATTTTT
1 CATTTTT
5288009 CATTTT
1 CATTTT
5288015 CTCCCCCTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
6 7 0.19
7 29 0.78
8 1 0.03
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (7 bp):
CATTTTT
Found at i:5287994 original size:13 final size:13
Alignment explanation
Indices: 5287977--5288015 Score: 69
Period size: 13 Copynumber: 2.9 Consensus size: 13
5287967 CCATTTTTAC
5287977 TTTTTCATTTTTCA
1 TTTTTCA-TTTTCA
5287991 TTTTTCATTTTCA
1 TTTTTCATTTTCA
5288004 TTTTTCATTTTC
1 TTTTTCATTTTC
5288016 TCCCCCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 18 0.72
14 7 0.28
ACGTcount: A:0.13, C:0.15, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTCATTTTCA
Found at i:5288945 original size:45 final size:46
Alignment explanation
Indices: 5288895--5288990 Score: 110
Period size: 45 Copynumber: 2.1 Consensus size: 46
5288885 CCTTTTTTCT
5288895 TTTTTTCTTCTCTCTTT-T-TCATTTTCATTTTGA-CTTTGATT-TTGA
1 TTTTTTCTT-T-TCTTTCTCTCATTTT-ATTTTGATCTTTGATTCTTGA
* * *
5288940 TTTTTTCTTTTTTTTCTCTCATTTTATTTTGATTTTTTATTCTTGA
1 TTTTTTCTTTTCTTTCTCTCATTTTATTTTGATCTTTGATTCTTGA
5288986 TTTTT
1 TTTTT
5288991 CATTTTTTTG
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
43 4 0.09
44 9 0.20
45 22 0.50
46 9 0.20
ACGTcount: A:0.10, C:0.12, G:0.05, T:0.72
Consensus pattern (46 bp):
TTTTTTCTTTTCTTTCTCTCATTTTATTTTGATCTTTGATTCTTGA
Found at i:5288987 original size:14 final size:13
Alignment explanation
Indices: 5288961--5288996 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
5288951 TTTTCTCTCA
5288961 TTTTATTTTGATT
1 TTTTATTTTGATT
5288974 TTTTATTCTTGATT
1 TTTTATT-TTGATT
*
5288988 TTTCATTTT
1 TTTTATTTT
5288997 TTTGAATTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.14, C:0.06, G:0.06, T:0.75
Consensus pattern (13 bp):
TTTTATTTTGATT
Found at i:5288994 original size:32 final size:32
Alignment explanation
Indices: 5288933--5288996 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
5288923 TTTGACTTTG
* *
5288933 ATTTTGATTTTTTCTTTTTTTTCTCTCATTTT
1 ATTTTGATTTTTTATTTTATTTCTCTCATTTT
5288965 ATTTTGATTTTTTATTCTTGATTT-T-TCATTTT
1 ATTTTGATTTTTTATT-TT-ATTTCTCTCATTTT
5288997 TTTGAATTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 22 0.79
33 3 0.11
34 3 0.11
ACGTcount: A:0.12, C:0.09, G:0.05, T:0.73
Consensus pattern (32 bp):
ATTTTGATTTTTTATTTTATTTCTCTCATTTT
Found at i:5288996 original size:53 final size:54
Alignment explanation
Indices: 5288880--5288998 Score: 138
Period size: 53 Copynumber: 2.2 Consensus size: 54
5288870 TGGCCTCTCC
* *
5288880 TTTTTCCTTTTTTCTTTTTTTCTTCTCTCTTTTTCATTTTCATTTTGACTTTGA
1 TTTTTCATTTTTTCTTTTTTTCTTCTCTCATTTTCATTTTCATTTTGACTTTGA
* * * *
5288934 -TTTTGATTTTTTC-TTTTTT-TTCTCTCATTTT-ATTTTGATTTTTTATTCTTGA
1 TTTTTCATTTTTTCTTTTTTTCTTCTCTCATTTTCATTTTCA-TTTTGACT-TTGA
5288986 TTTTTCATTTTTT
1 TTTTTCATTTTTT
5288999 TGAATTGGAT
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
50 6 0.11
51 17 0.31
52 10 0.18
53 22 0.40
ACGTcount: A:0.09, C:0.13, G:0.04, T:0.73
Consensus pattern (54 bp):
TTTTTCATTTTTTCTTTTTTTCTTCTCTCATTTTCATTTTCATTTTGACTTTGA
Found at i:5295041 original size:318 final size:317
Alignment explanation
Indices: 5294444--5295076 Score: 1176
Period size: 318 Copynumber: 2.0 Consensus size: 317
5294434 AGTCGCCAAA
*
5294444 CTGTCGAAACCATTTTTTCAAGTTTGAAAAATGGGGGATCGACTTTTAGAATGAAAACAGGAGTC
1 CTGTCGAAACCATTTTTTCAAGTTTGAAAAATGGGGGATCGACTTTTAAAATGAAAACAGGAGTC
5294509 GCCACCAACCTTTTATTATGGTGCGATCGGATCACCCTGAAAATAATTTTAGGTCTGCGAGTTTT
66 GCCACCAACCTTTTATTATGGTGCGATCGGATCACCCTGAAAATAATTTTAGGTCTGCGAGTTTT
* * *
5294574 GAGAAAACATGTTCGGGAGTCGGTTACGTACGAGGAAGGGTTAGCACCCTCGTGACGCCCAAAAT
131 GAGAAAAAAGGTTCGGGAGTCGGTTACGCACGAGGAAGGGTTAGCACCCTCGTGACGCCCAAAAT
5294639 TGGTACCGAATTGATTGTCTAATGTCTTAATGCCGAAAATTTGAAAAGATTTTAAAATACAATCC
196 TGGTACCGAATTGATTGTCTAATGTCTTAATGCCGAAAATTTGAAAAGATTTTAAAATACAATCC
5294704 TTTGAAATCCAAACTTAAATAATGGCATTGGTTGAATAGACGGACCTATTTCAAAAG
261 TTTGAAATCCAAACTTAAATAATGGCATTGGTTGAATAGACGGACCTATTTCAAAAG
**
5294761 CTGTCGAAACCATTTTTTCAAGTTTGAAAAATGGGGGATCGACTTTTAAAATGAAAATGGGAGTC
1 CTGTCGAAACCATTTTTTCAAGTTTGAAAAATGGGGGATCGACTTTTAAAATGAAAACAGGAGTC
*
5294826 GCCACCGACCTTTTATTATGGTGCGATCGGATCACCCTGAAAATAATTTTAGGTCTGCGAGTTTT
66 GCCACCAACCTTTTATTATGGTGCGATCGGATCACCCTGAAAATAATTTTAGGTCTGCGAGTTTT
5294891 GAGAAAAAAAGGTTCGGGAGTCGGTTACGCACGAGGAAGGGTTAGCACCCTCGTGACGCCCAAAA
131 GAG-AAAAAAGGTTCGGGAGTCGGTTACGCACGAGGAAGGGTTAGCACCCTCGTGACGCCCAAAA
5294956 TTGGTACCGAATTGATTGTCTAATGTCTTAATGCCGAAAATTTGAAAAGATTTTAAAATACAATC
195 TTGGTACCGAATTGATTGTCTAATGTCTTAATGCCGAAAATTTGAAAAGATTTTAAAATACAATC
* *
5295021 CTTTGAAATGCAAGCTTAAATAATGGCATTGGTTGAATAGACGGACCTATTTCAAA
260 CTTTGAAATCCAAACTTAAATAATGGCATTGGTTGAATAGACGGACCTATTTCAAA
5295077 GAAATAAACC
Statistics
Matches: 306, Mismatches: 9, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
317 129 0.42
318 177 0.58
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (317 bp):
CTGTCGAAACCATTTTTTCAAGTTTGAAAAATGGGGGATCGACTTTTAAAATGAAAACAGGAGTC
GCCACCAACCTTTTATTATGGTGCGATCGGATCACCCTGAAAATAATTTTAGGTCTGCGAGTTTT
GAGAAAAAAGGTTCGGGAGTCGGTTACGCACGAGGAAGGGTTAGCACCCTCGTGACGCCCAAAAT
TGGTACCGAATTGATTGTCTAATGTCTTAATGCCGAAAATTTGAAAAGATTTTAAAATACAATCC
TTTGAAATCCAAACTTAAATAATGGCATTGGTTGAATAGACGGACCTATTTCAAAAG
Found at i:5304048 original size:9 final size:9
Alignment explanation
Indices: 5304034--5304079 Score: 83
Period size: 9 Copynumber: 5.1 Consensus size: 9
5304024 TGAGTTTTCG
5304034 AATTCGAAT
1 AATTCGAAT
5304043 AATTCGAAT
1 AATTCGAAT
5304052 AATTCGAAT
1 AATTCGAAT
5304061 AATTCGAAT
1 AATTCGAAT
*
5304070 AATTCAAAT
1 AATTCGAAT
5304079 A
1 A
5304080 TCAAACTACA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.33
Consensus pattern (9 bp):
AATTCGAAT
Found at i:5308620 original size:19 final size:19
Alignment explanation
Indices: 5308569--5308621 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
5308559 TCTAGAAAGA
* *
5308569 AGTTGTCAATTGTATCCACC
1 AGTTG-CAATCGTATCAACC
5308589 AGTTGCTAATCGTATCAACC
1 AGTTGC-AATCGTATCAACC
5308609 AGTTGCAATCGTA
1 AGTTGCAATCGTA
5308622 ATTGCTAGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 8 0.27
20 22 0.73
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (19 bp):
AGTTGCAATCGTATCAACC
Found at i:5313364 original size:56 final size:56
Alignment explanation
Indices: 5313278--5313387 Score: 211
Period size: 56 Copynumber: 2.0 Consensus size: 56
5313268 TCAGCGTATA
5313278 GAGTGGGTGTGTACAGTTATATGGTTATGTTAATAAATGTTCCAGGTCAAGTGGTT
1 GAGTGGGTGTGTACAGTTATATGGTTATGTTAATAAATGTTCCAGGTCAAGTGGTT
*
5313334 GAGTGGGTGTGTACAGTTATATGGTTATGTTAATAAATGTTCCTGGTCAAGTGG
1 GAGTGGGTGTGTACAGTTATATGGTTATGTTAATAAATGTTCCAGGTCAAGTGG
5313388 CAATGTTAGT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.25, C:0.07, G:0.31, T:0.37
Consensus pattern (56 bp):
GAGTGGGTGTGTACAGTTATATGGTTATGTTAATAAATGTTCCAGGTCAAGTGGTT
Found at i:5316430 original size:27 final size:26
Alignment explanation
Indices: 5316392--5316508 Score: 85
Period size: 27 Copynumber: 4.4 Consensus size: 26
5316382 AAGCACGTCA
* *
5316392 GAAATGAAAGCTTTTGTGGTAAATCAT
1 GAAAAGAAAGCCTTTGTGGTAAA-CAT
* **
5316419 GAAAAGAAAGCTTTTGTGACATAACAT
1 GAAAAGAAAGCCTTTGTGGTA-AACAT
* * *
5316446 G-AAAGCAAAGCCTCTATGGTGAATCAT
1 GAAAAG-AAAGCCTTTGTGGT-AAACAT
* *
5316473 GAAAAGAAAACCTTTGTGGTGTAACAT
1 GAAAAGAAAGCCTTTGTGGT-AAACAT
5316500 G-AAAGAAAG
1 GAAAAGAAAG
5316509 TCTTCATGGC
Statistics
Matches: 71, Mismatches: 15, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
26 11 0.15
27 53 0.75
28 7 0.10
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.25
Consensus pattern (26 bp):
GAAAAGAAAGCCTTTGTGGTAAACAT
Found at i:5318031 original size:26 final size:26
Alignment explanation
Indices: 5318001--5318063 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
5317991 TTTGCACCAG
5318001 TAAAATTTTGATGATTTTACCCCCAA
1 TAAAATTTTGATGATTTTACCCCCAA
* * *
5318027 TAAAATATTGATGATTTTACCCTCTA
1 TAAAATTTTGATGATTTTACCCCCAA
*
5318053 TAAAAATTTGA
1 TAAAATTTTGA
5318064 GAAAATTCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (26 bp):
TAAAATTTTGATGATTTTACCCCCAA
Found at i:5337352 original size:43 final size:43
Alignment explanation
Indices: 5337209--5337361 Score: 123
Period size: 49 Copynumber: 3.4 Consensus size: 43
5337199 TCAATCCAAC
* **
5337209 CCACTGCAACTTTAGGGGTATAGGATTTGTAGCTTCAATCTTTT
1 CCACTGCAACTTTA-GGGTATAGGATTTGTAACTTCAATCTACT
* * * *
5337253 CTACTGCAACTTTAGGATATAAGATTCACTATAGTAGA-TTCAATTTGAC-
1 CCACTGCAACTTTAGGGTATAGGA-T---T-T-GTA-ACTTCAATCT-ACT
5337302 CCACTGCAACTTTAGGGTATAGGATTTGTAACTTCAATCTACT
1 CCACTGCAACTTTAGGGTATAGGATTTGTAACTTCAATCTACT
*
5337345 GCACTGCAA-TTTCAGGG
1 CCACTGCAACTTT-AGGG
5337362 AGAGAAGATT
Statistics
Matches: 86, Mismatches: 12, Indels: 23
0.71 0.10 0.19
Matches are distributed among these distances:
42 6 0.07
43 30 0.35
44 15 0.17
45 1 0.01
47 1 0.01
48 2 0.02
49 31 0.36
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (43 bp):
CCACTGCAACTTTAGGGTATAGGATTTGTAACTTCAATCTACT
Found at i:5337465 original size:94 final size:95
Alignment explanation
Indices: 5337207--5337623 Score: 418
Period size: 94 Copynumber: 4.5 Consensus size: 95
5337197 TTTCAATCCA
* * *
5337207 ACCCACTGCAACTTTAGGGGTATAGGATTTGTAGCTTCAATCTT-TTCTACTGCAACTTTA-GGA
1 ACCCACTGCAACTTTAGGGGTATAGGATTTGTAGCTTCAATCTTGCTCCACTGCAACTTCAGGGA
* *
5337270 TATAAGATTCACTATAGTAGATTCAATTTG
66 GATAAGATTCGCTATAGTAGATTCAATTTG
* * * *
5337300 ACCCACTGCAACTTTA-GGGTATAGGATTTGTAACTTCAATC-TACTGCACTGCAATTTCAGGGA
1 ACCCACTGCAACTTTAGGGGTATAGGATTTGTAGCTTCAATCTTGCTCCACTGCAACTTCAGGGA
* * *
5337363 GAGAAGATTCGCCATGGTAGATTCAATTTG
66 GATAAGATTCGCTATAGTAGATTCAATTTG
** * * *
5337393 ACCTTCTGCAACTTTATGGGTATAGGATTTGTAGCTTC-ATCTTGCTCCACTACAACTTCAGGAA
1 ACCCACTGCAACTTTAGGGGTATAGGATTTGTAGCTTCAATCTTGCTCCACTGCAACTTCAGGGA
** * ** *
5337457 GATAAGATTCGAAATTGTAG-TTTTATTTCT
66 GATAAGATTCGCTATAGTAGATTCAATTT-G
* * * * * ** *
5337487 ACCCACTACTACTTCAAGGGTATAGGAATTGTAG-TTTTATCTTGCTCCACTGCAACTTGAGGGA
1 ACCCACTGCAACTTTAGGGGTATAGGATTTGTAGCTTCAATCTTGCTCCACTGCAACTTCAGGGA
**
5337551 GATAAGATTCGCTATAGTA-ACTTCAATCCG
66 GATAAGATTCGCTATAGTAGA-TTCAATTTG
* * * * *
5337581 ACACACTACAACTTCAGGGGTATAGGATTTGTAGATTTAATCT
1 ACCCACTGCAACTTTAGGGGTATAGGATTTGTAGCTTCAATCT
5337624 GATCTACTGT
Statistics
Matches: 265, Mismatches: 50, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
91 1 0.00
92 35 0.13
93 69 0.26
94 149 0.56
95 11 0.04
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (95 bp):
ACCCACTGCAACTTTAGGGGTATAGGATTTGTAGCTTCAATCTTGCTCCACTGCAACTTCAGGGA
GATAAGATTCGCTATAGTAGATTCAATTTG
Found at i:5337653 original size:44 final size:44
Alignment explanation
Indices: 5337589--5337699 Score: 134
Period size: 44 Copynumber: 2.5 Consensus size: 44
5337579 CGACACACTA
* *
5337589 CAACTTCAGGGGTATAGGATTTGTAGATTTAATCTGA-TCTACTG
1 CAACTTCAGGGATATAGGATTTGTAG-CTTAATCTGACTCTACTG
* * * *
5337633 TAACTTTAGGGATATAGGATTTGTAGCTTCATCTTACTCTACTG
1 CAACTTCAGGGATATAGGATTTGTAGCTTAATCTGACTCTACTG
* *
5337677 CAACTTCAGGGAGATAAGATTTG
1 CAACTTCAGGGATATAGGATTTG
5337700 CCATTGTAGT
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 7 0.12
44 49 0.88
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (44 bp):
CAACTTCAGGGATATAGGATTTGTAGCTTAATCTGACTCTACTG
Found at i:5337751 original size:138 final size:137
Alignment explanation
Indices: 5337503--5337761 Score: 313
Period size: 138 Copynumber: 1.9 Consensus size: 137
5337493 TACTACTTCA
* * * * *
5337503 AGGGTATAGGAATTGTAGTTTTATCTTGCTCCACTGCAACTTGAGGGAGATAAGATTCGCTATAG
1 AGGGTATAGGAATTGTAGCTTCATCTTACTCCACTGCAACTTCAGGGAGATAAGATTCGCCATAG
* * * *
5337568 TAACTTCAATCCGACACACTACAACTTCAGGGGTATAGGATTTGTAGATTTAATCTGATCTACTG
66 TAACTTCAATCCAACACACTACAACTTCAGGGGTATAGAAATTGTAGATTCAATCTGATCTACTG
5337633 TAACTTT
131 TAACTTT
* * * *
5337640 AGGGATATAGGATTTGTAGCTTCATCTTACTCTACTGCAACTTCAGGGAGATAAGATTTGCCATT
1 AGGG-TATAGGAATTGTAGCTTCATCTTACTCCACTGCAACTTCAGGGAGATAAGATTCGCCATA
** * * * * *
5337705 GTAGTTTCATTCCAACCCACTGCAACTTTAGGGGTATCA-AAATTGTAGCTTCAATCT
65 GTAACTTCAATCCAACACACTACAACTTCAGGGGTAT-AGAAATTGTAGATTCAATCT
5337762 ATTCCACTGC
Statistics
Matches: 100, Mismatches: 20, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
137 4 0.04
138 95 0.95
139 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.34
Consensus pattern (137 bp):
AGGGTATAGGAATTGTAGCTTCATCTTACTCCACTGCAACTTCAGGGAGATAAGATTCGCCATAG
TAACTTCAATCCAACACACTACAACTTCAGGGGTATAGAAATTGTAGATTCAATCTGATCTACTG
TAACTTT
Found at i:5337886 original size:44 final size:44
Alignment explanation
Indices: 5337815--5338062 Score: 130
Period size: 44 Copynumber: 5.5 Consensus size: 44
5337805 TCAATCCGAC
* *
5337815 CAACTTCAAGGG-TATAGGAATT-GTAGCTTTAATCCGATCCACTG
1 CAACTTC-AGGGATATAGG-ATTCATAGCTTTAATCTGATCCACTG
* *
5337859 CAACTTCAGGGATATAGGATTCATAGC-TTCATCTTACTCCACTG
1 CAACTTCAGGGATATAGGATTCATAGCTTTAATCTGA-TCCACTG
* * * * ** * *
5337903 CAACTTCAGGGAGAGAAGATTTGCCATTGTAG-TTTCATTCCAACCCACTT
1 CAACTTCAGGGATATAGGA-TT--CA---TAGCTTT-AATCTGATCCACTG
* * * * * *
5337953 CAACTTCAGGGGTATAGAAATT-GTAGCTTCAATTTGATCCATTG
1 CAACTTCAGGGATATAG-GATTCATAGCTTTAATCTGATCCACTG
* * * *
5337997 CAACTTCAGGGATATAGGATTTATAGC-TTCATCTTGCTCCACTA
1 CAACTTCAGGGATATAGGATTCATAGCTTTAATC-TGATCCACTG
* *
5338041 CAACTTCAGGGAGATAAGATTC
1 CAACTTCAGGGATATAGGATTC
5338063 GATATGGTGA
Statistics
Matches: 150, Mismatches: 39, Indels: 30
0.68 0.18 0.14
Matches are distributed among these distances:
43 19 0.13
44 96 0.64
45 4 0.03
47 2 0.01
50 25 0.17
51 4 0.03
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (44 bp):
CAACTTCAGGGATATAGGATTCATAGCTTTAATCTGATCCACTG
Found at i:5338084 original size:138 final size:138
Alignment explanation
Indices: 5337815--5338107 Score: 381
Period size: 138 Copynumber: 2.1 Consensus size: 138
5337805 TCAATCCGAC
* *
5337815 CAACTTCAAGGGTATAGGAATTGTAGCTTTAATCCGATCCACTGCAACTTCAGGGATATAGGATT
1 CAACTTCAAGGGTATAGAAATTGTAGCTTCAATCCGATCCACTGCAACTTCAGGGATATAGGATT
* * * * * **
5337880 CATAGCTTCATCTTACTCCACTGCAACTTCAGGGAGAGAAGATTTGCCATTGTAGTTTCATTCCA
66 CATAGCTTCATCTTACTCCACTACAACTTCAGGGAGAGAAGATTCGACATGGTAGCTTCAACCCA
5337945 ACCCACTT
131 ACCCACTT
* ** *
5337953 CAACTTCAGGGGTATAGAAATTGTAGCTTCAATTTGATCCATTGCAACTTCAGGGATATAGGATT
1 CAACTTCAAGGGTATAGAAATTGTAGCTTCAATCCGATCCACTGCAACTTCAGGGATATAGGATT
* * * *
5338018 TATAGCTTCATCTTGCTCCACTACAACTTCAGGGAGATAAGATTCGATATGGT-GACTTCAACCC
66 CATAGCTTCATCTTACTCCACTACAACTTCAGGGAGAGAAGATTCGACATGGTAG-CTTCAACCC
* *
5338082 AACCTACTG
130 AACCCACTT
* *
5338091 CAATTTTAAGGGTATAG
1 CAACTTCAAGGGTATAG
5338108 GATTTGTGGT
Statistics
Matches: 132, Mismatches: 22, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
137 1 0.01
138 131 0.99
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (138 bp):
CAACTTCAAGGGTATAGAAATTGTAGCTTCAATCCGATCCACTGCAACTTCAGGGATATAGGATT
CATAGCTTCATCTTACTCCACTACAACTTCAGGGAGAGAAGATTCGACATGGTAGCTTCAACCCA
ACCCACTT
Found at i:5347445 original size:7 final size:7
Alignment explanation
Indices: 5347418--5347458 Score: 57
Period size: 7 Copynumber: 5.7 Consensus size: 7
5347408 TTAGAATAAT
5347418 AAAAATA
1 AAAAATA
5347425 ATAATAAT-
1 A-AA-AATA
5347433 AAAAATA
1 AAAAATA
5347440 AAAAATA
1 AAAAATA
5347447 AAAAATA
1 AAAAATA
5347454 AAAAA
1 AAAAA
5347459 AGTACCATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
6 3 0.10
7 22 0.71
8 3 0.10
9 3 0.10
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (7 bp):
AAAAATA
Found at i:5347459 original size:15 final size:16
Alignment explanation
Indices: 5347412--5347458 Score: 64
Period size: 15 Copynumber: 3.1 Consensus size: 16
5347402 ATGATATTAG
*
5347412 AATAATAAAAAT-AAT
1 AATAATAAAAATAAAA
5347427 AATAATAAAAATAAAA
1 AATAATAAAAATAAAA
5347443 AAT-A-AAAAATAAAA
1 AATAATAAAAATAAAA
5347457 AA
1 AA
5347459 AGTACCATGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 12 0.40
15 13 0.43
16 5 0.17
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (16 bp):
AATAATAAAAATAAAA
Found at i:5357537 original size:65 final size:65
Alignment explanation
Indices: 5357433--5357563 Score: 262
Period size: 65 Copynumber: 2.0 Consensus size: 65
5357423 CATATGACTC
5357433 AATGGAATTATTCATGGTTTTTTAATTTAATGCATTTGATAAATTTAAGTTGTTTATACAAACTT
1 AATGGAATTATTCATGGTTTTTTAATTTAATGCATTTGATAAATTTAAGTTGTTTATACAAACTT
5357498 AATGGAATTATTCATGGTTTTTTAATTTAATGCATTTGATAAATTTAAGTTGTTTATACAAACTT
1 AATGGAATTATTCATGGTTTTTTAATTTAATGCATTTGATAAATTTAAGTTGTTTATACAAACTT
5357563 A
1 A
5357564 CTAAGCCTTA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.47
Consensus pattern (65 bp):
AATGGAATTATTCATGGTTTTTTAATTTAATGCATTTGATAAATTTAAGTTGTTTATACAAACTT
Found at i:5360084 original size:31 final size:31
Alignment explanation
Indices: 5360008--5360197 Score: 186
Period size: 31 Copynumber: 6.1 Consensus size: 31
5359998 TCCCACTAGA
* *
5360008 CTCTATCTATGTTTAC-AGTCCCAACGGGCTAT
1 CTCT-TCTATGTTTACTA-TCCCAACAGACTAT
5360040 CT-TTCTATGTTTACTATCCCAACAGACTAT
1 CTCTTCTATGTTTACTATCCCAACAGACTAT
* * ***
5360070 CTCTTCTATCTTTACTATCCTAGTGGACTAT
1 CTCTTCTATGTTTACTATCCCAACAGACTAT
* * * **
5360101 CTCTTCTGTGTTTACAATCCCAGCAGGTTAT
1 CTCTTCTATGTTTACTATCCCAACAGACTAT
* * * * *
5360132 CTCTTATGTGTTTACTGTCCCGATAGACTAT
1 CTCTTCTATGTTTACTATCCCAACAGACTAT
*
5360163 CTCTTCTATGTTTACTGTCCCAACAGACTAT
1 CTCTTCTATGTTTACTATCCCAACAGACTAT
5360194 CTCT
1 CTCT
5360198 GGGGATGCTA
Statistics
Matches: 129, Mismatches: 27, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
30 25 0.19
31 102 0.79
32 2 0.02
ACGTcount: A:0.21, C:0.27, G:0.12, T:0.40
Consensus pattern (31 bp):
CTCTTCTATGTTTACTATCCCAACAGACTAT
Found at i:5367682 original size:16 final size:16
Alignment explanation
Indices: 5367640--5367670 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5367630 AGAGAACAAA
*
5367640 AAAATAAAAATTAAAG
1 AAAATTAAAATTAAAG
5367656 AAAATTAAAATTAAA
1 AAAATTAAAATTAAA
5367671 ACAATTTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (16 bp):
AAAATTAAAATTAAAG
Found at i:5371512 original size:49 final size:47
Alignment explanation
Indices: 5371449--5371547 Score: 117
Period size: 47 Copynumber: 2.1 Consensus size: 47
5371439 TCCATTGATA
* * *
5371449 AATGGATGCCCATAACCCCCTCAAATTTATTCTATTGTAACTCATAAAG
1 AATGAATGCCCATAA-CCCCT-AAATTCATTATATTGTAACTCATAAAG
* * * *
5371498 AATGAATGTCCATAACCCCTGAATTCATTATCTTGTAACTCCTAAAG
1 AATGAATGCCCATAACCCCTAAATTCATTATATTGTAACTCATAAAG
5371545 AAT
1 AAT
5371548 TTATAGGGTA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
47 25 0.58
48 5 0.12
49 13 0.30
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.31
Consensus pattern (47 bp):
AATGAATGCCCATAACCCCTAAATTCATTATATTGTAACTCATAAAG
Found at i:5375180 original size:20 final size:21
Alignment explanation
Indices: 5375144--5375187 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
5375134 CATTAGATTT
*
5375144 TTTAAAACTTTACATA-TTAA
1 TTTAAAACTTTAAATATTTAA
5375164 TTTAAAA-TTTAAAATATTTAA
1 TTTAAAACTTT-AAATATTTAA
5375185 TTT
1 TTT
5375188 TAGGAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 11 0.52
21 7 0.33
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTAAAACTTTAAATATTTAA
Found at i:5376920 original size:2 final size:2
Alignment explanation
Indices: 5376865--5376901 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5376855 TTTTCTCTTT
5376865 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5376902 TCTTTTTTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5376925 original size:16 final size:17
Alignment explanation
Indices: 5376897--5376949 Score: 60
Period size: 16 Copynumber: 3.3 Consensus size: 17
5376887 TATATATATA
*
5376897 TATATTCTTTTTTACTT
1 TATATACTTTTTTACTT
5376914 TATATA-TTTTTTA---
1 TATATACTTTTTTACTT
5376927 TATATACTCTTTTTACTT
1 TATATACT-TTTTTACTT
5376945 TATAT
1 TATAT
5376950 TTCTTTCTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
13 6 0.20
14 1 0.03
15 6 0.20
16 7 0.23
17 5 0.17
18 5 0.17
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (17 bp):
TATATACTTTTTTACTT
Found at i:5379075 original size:241 final size:241
Alignment explanation
Indices: 5378652--5379134 Score: 822
Period size: 241 Copynumber: 2.0 Consensus size: 241
5378642 AAGTTATTTG
*
5378652 AGTCATTTCTAAGCTTCTTTTAAAATTTGGTTGCATTTGGGGGCCATTCAGGACATTTTTGGAGC
1 AGTCATTTCTAAGCTTCCTTTAAAATTTGGTTGCATTTGGGGGCCATTCAGGACATTTTTGGAGC
* * *
5378717 AAATCTGGGTAAAGAGGATCAATATTGTGCCATTGGTAAGTGAATGTCAAAACATTGGTGGTAGA
66 AAATCTAGGTAAAGAGGATCAATATTGTGACATTGGTAAGTGAATGTCAAAACATTGGCGGTAGA
* * *
5378782 ATACCCCAAGGCCACAGCAATCGCTAGTGGTATTGTGACATTGATACCAGAATTAACCAATGTTG
131 ATACCCCAAGGCCACAACAATCGCTAGTGGTATCGCGACATTGATACCAGAATTAACCAATGTTG
* *
5378847 TAACCTTGGCTAGTGAATATCGTAACATAAGGGACAATTTGCCCAA
196 TAACCTTGGCTAGTGAAAATCATAACATAAGGGACAATTTGCCCAA
* * *
5378893 AGTCATTTCTAAGCTTCCTTTAAATTTTGGTTGCATTTGGTGGCCATTCGGGACATTTTTGGAGC
1 AGTCATTTCTAAGCTTCCTTTAAAATTTGGTTGCATTTGGGGGCCATTCAGGACATTTTTGGAGC
*
5378958 AAATCTAGGTAAAGATGATCAATATTGTGACATTGGTAAGTGAATGTCAAAACATTGGCGGTAGA
66 AAATCTAGGTAAAGAGGATCAATATTGTGACATTGGTAAGTGAATGTCAAAACATTGGCGGTAGA
* **
5379023 ATACCCCAAGGTCACAACAATCGCTAGTGGTATCGCGACATTGATACCAGAATTGCCCAATGTTG
131 ATACCCCAAGGCCACAACAATCGCTAGTGGTATCGCGACATTGATACCAGAATTAACCAATGTTG
5379088 TAACCTTGGCTAGTGAAAATCATAACATAAGGGACAATTTGCCCAA
196 TAACCTTGGCTAGTGAAAATCATAACATAAGGGACAATTTGCCCAA
5379134 A
1 A
5379135 ATATGACTGA
Statistics
Matches: 226, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
241 226 1.00
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (241 bp):
AGTCATTTCTAAGCTTCCTTTAAAATTTGGTTGCATTTGGGGGCCATTCAGGACATTTTTGGAGC
AAATCTAGGTAAAGAGGATCAATATTGTGACATTGGTAAGTGAATGTCAAAACATTGGCGGTAGA
ATACCCCAAGGCCACAACAATCGCTAGTGGTATCGCGACATTGATACCAGAATTAACCAATGTTG
TAACCTTGGCTAGTGAAAATCATAACATAAGGGACAATTTGCCCAA
Found at i:5387108 original size:12 final size:12
Alignment explanation
Indices: 5387039--5387099 Score: 54
Period size: 12 Copynumber: 5.1 Consensus size: 12
5387029 AATCATCGAG
*
5387039 ATCAACATCAAC
1 ATCAACATCATC
5387051 ATCAACATCAGT-
1 ATCAACATCA-TC
5387063 ATCGAA-ATCATC
1 ATC-AACATCATC
*
5387075 ATCATCATCATC
1 ATCAACATCATC
* *
5387087 ATTAAGATCATC
1 ATCAACATCATC
5387099 A
1 A
5387100 AAATCATCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
11 2 0.05
12 36 0.90
13 2 0.05
ACGTcount: A:0.43, C:0.26, G:0.05, T:0.26
Consensus pattern (12 bp):
ATCAACATCATC
Found at i:5388398 original size:7 final size:7
Alignment explanation
Indices: 5388388--5388414 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
5388378 TTTTTTCTAT
5388388 TTTTAAA
1 TTTTAAA
5388395 TTTTAAA
1 TTTTAAA
5388402 TTTTAAA
1 TTTTAAA
5388409 TTTTAA
1 TTTTAA
5388415 TAAACCTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTTAAA
Found at i:5395434 original size:105 final size:105
Alignment explanation
Indices: 5395259--5395456 Score: 351
Period size: 105 Copynumber: 1.9 Consensus size: 105
5395249 TTAAATATTA
*
5395259 GTGAGCTTCTGAATCAACATTCTTTTAAGAGCCTCGATGTGACCATATACCTTCTTATTCCAATC
1 GTGAGCTTCTGAATCAACATTCTTTTAAGAGCCTCGACGTGACCATATACCTTCTTATTCCAATC
5395324 CTTGAGTTAACTCGTAAAATGAGAAAGCTTCTGAATATGT
66 CTTGAGTTAACTCGTAAAATGAGAAAGCTTCTGAATATGT
** *
5395364 GTGAGCTTCTGAATCAGTATTCTTTTAAGAGCCTCGACGTGACCATATACCTTTTTATTCCAATC
1 GTGAGCTTCTGAATCAACATTCTTTTAAGAGCCTCGACGTGACCATATACCTTCTTATTCCAATC
*
5395429 CTTGAGTTGACTCGTAAAATGAGAAAGC
66 CTTGAGTTAACTCGTAAAATGAGAAAGC
5395457 ACAGTGGACA
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 88 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (105 bp):
GTGAGCTTCTGAATCAACATTCTTTTAAGAGCCTCGACGTGACCATATACCTTCTTATTCCAATC
CTTGAGTTAACTCGTAAAATGAGAAAGCTTCTGAATATGT
Found at i:5399070 original size:9 final size:9
Alignment explanation
Indices: 5399056--5399101 Score: 67
Period size: 9 Copynumber: 5.2 Consensus size: 9
5399046 ATTTTGTTGG
5399056 GGAAGAAGA
1 GGAAGAAGA
5399065 GGAAGAAGA
1 GGAAGAAGA
*
5399074 AGAAGAAGA
1 GGAAGAAGA
*
5399083 AGAAGAAGA
1 GGAAGAAGA
5399092 GGAAG-AGA
1 GGAAGAAGA
5399100 GG
1 GG
5399102 GAAATTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
8 5 0.14
9 30 0.86
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (9 bp):
GGAAGAAGA
Found at i:5399072 original size:3 final size:3
Alignment explanation
Indices: 5399057--5399097 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
5399047 TTTTGTTGGG
* *
5399057 GAA GAA GAG GAA GAA GAA GAA GAA GAA GAA GAA GAG GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
5399098 GAGGGAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:5407418 original size:27 final size:27
Alignment explanation
Indices: 5407363--5407461 Score: 67
Period size: 27 Copynumber: 3.7 Consensus size: 27
5407353 ACCTAGGCAA
* * * *
5407363 TAAACATGGGGTAGTTCATCGGGACAG
1 TAAACACGAGGTAGTCCATCGAGACAG
*
5407390 TAAACACGAGGTAGTCCATCGAGATAG
1 TAAACACGAGGTAGTCCATCGAGACAG
* * ** *
5407417 TAGAA-A-TAGGGTAGCCCGCCAAGACAG
1 TA-AACACGA-GGTAGTCCATCGAGACAG
*
5407444 TAAACACAAGGTAGTCCA
1 TAAACACGAGGTAGTCCA
5407462 CCGCGACTGC
Statistics
Matches: 54, Mismatches: 14, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
26 3 0.06
27 48 0.89
28 3 0.06
ACGTcount: A:0.36, C:0.19, G:0.27, T:0.17
Consensus pattern (27 bp):
TAAACACGAGGTAGTCCATCGAGACAG
Found at i:5412313 original size:20 final size:19
Alignment explanation
Indices: 5412268--5412305 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
5412258 TCGATCCAAT
5412268 ATCGATACTTTTTGTCAAG
1 ATCGATACTTTTTGTCAAG
5412287 ATCGATACTTTTTGTCAAG
1 ATCGATACTTTTTGTCAAG
5412306 TACTGATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (19 bp):
ATCGATACTTTTTGTCAAG
Found at i:5413956 original size:17 final size:17
Alignment explanation
Indices: 5413934--5413967 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5413924 TGCAAAAGAA
5413934 GGTTAAATTCTATTACT
1 GGTTAAATTCTATTACT
5413951 GGTTAAATTCTATTACT
1 GGTTAAATTCTATTACT
5413968 AGGCTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (17 bp):
GGTTAAATTCTATTACT
Found at i:5417486 original size:15 final size:15
Alignment explanation
Indices: 5417465--5417495 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
5417455 TTATGTTCAT
5417465 CTTTTTTTT-CTTTC
1 CTTTTTTTTACTTTC
5417479 CTTTTTTTTACTTTC
1 CTTTTTTTTACTTTC
5417494 CT
1 CT
5417496 CAAAATCCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (15 bp):
CTTTTTTTTACTTTC
Found at i:5420015 original size:19 final size:19
Alignment explanation
Indices: 5419993--5420030 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
5419983 TCAATCATCC
5419993 CTCATCCCATCA-TCTCTCA
1 CTCAT-CCATCATTCTCTCA
*
5420012 CTCATTCATCATTCTCTCA
1 CTCATCCATCATTCTCTCA
5420031 ACTCTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (19 bp):
CTCATCCATCATTCTCTCA
Found at i:5430651 original size:22 final size:22
Alignment explanation
Indices: 5430586--5430651 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
5430576 TTTATTGTTC
*
5430586 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
5430608 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
5430630 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
5430652 CAAGTCCAGC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:5433792 original size:60 final size:61
Alignment explanation
Indices: 5433708--5433866 Score: 178
Period size: 61 Copynumber: 2.6 Consensus size: 61
5433698 TTCAAGAAGT
* * * *
5433708 TCGCCACGAAGGCTTACATTTCCAGAGTTTTGCCACAAAGAC-AT-CTCTTACATCCAATAC
1 TCGCCACAAAGGATTTCATGTCCAGAGTTTTGCCACAAAGACTATCCT-TTACATCCAATAC
* * * * * *
5433768 TCGCCATAAAGGATTTCATGTCCAGAGTTGTGCCAGAAAGGCTATCCTTTACATTCAGTAC
1 TCGCCACAAAGGATTTCATGTCCAGAGTTTTGCCACAAAGACTATCCTTTACATCCAATAC
* * *
5433829 TCGCCACAAAGGATTTCTTGTCTAGAGATTTGCCACAA
1 TCGCCACAAAGGATTTCATGTCCAGAGTTTTGCCACAA
5433867 GGTTTATCAT
Statistics
Matches: 81, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
60 34 0.42
61 45 0.56
62 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (61 bp):
TCGCCACAAAGGATTTCATGTCCAGAGTTTTGCCACAAAGACTATCCTTTACATCCAATAC
Found at i:5433833 original size:61 final size:59
Alignment explanation
Indices: 5433728--5433906 Score: 182
Period size: 61 Copynumber: 2.9 Consensus size: 59
5433718 GGCTTACATT
* * *
5433728 TCCAGAGTTTTGCCACAAAGAC-AT-CTCTTACATCCAATACTCGCCATAAAGGATTTCATG
1 TCCAGAG-TTTGCCA-AAAGGCTATCCT-TTACATTCAGTACTCGCCATAAAGGATTTCATG
* *
5433788 TCCAGAGTTGTGCCAGAAAGGCTATCCTTTACATTCAGTACTCGCCACAAAGGATTTCTTG
1 TCCAGAGTT-TGCCA-AAAGGCTATCCTTTACATTCAGTACTCGCCATAAAGGATTTCATG
* * * * * *
5433849 TCTAGAGATTTGCCACAAGGTTTATCATTTACATTCAGTACTTGCCATAAAGGCTTTC
1 TCCAGAG-TTTGCCAAAAGG-CTATCCTTTACATTCAGTACTCGCCATAAAGGATTTC
5433907 CTTTGACCAA
Statistics
Matches: 101, Mismatches: 13, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
59 2 0.02
60 21 0.21
61 74 0.73
62 4 0.04
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.31
Consensus pattern (59 bp):
TCCAGAGTTTGCCAAAAGGCTATCCTTTACATTCAGTACTCGCCATAAAGGATTTCATG
Found at i:5440941 original size:41 final size:41
Alignment explanation
Indices: 5440838--5440991 Score: 168
Period size: 41 Copynumber: 3.7 Consensus size: 41
5440828 TGTATTTTCG
* *
5440838 TGTAAGACCACGTCTGGGACGTTGGCATCG-ACTTGTGTATACA
1 TGTAAGACCACGTCTGGGACATTGGCATCGTA-TT-TG-ATTCA
* * **
5440881 TGTAAGACCATGTCCGGGACATTGGCATCGTATTTGATTTG
1 TGTAAGACCACGTCTGGGACATTGGCATCGTATTTGATTCA
* * *
5440922 TGTAAGACC-CTGTCTGGGACAGTGGCATCATATGTGATTACA
1 TGTAAGACCAC-GTCTGGGACATTGGCATCGTATTTGATT-CA
5440964 TGTAAGACCACGTCTGGGACATTGGCAT
1 TGTAAGACCACGTCTGGGACATTGGCAT
5440992 TGTACGAGCC
Statistics
Matches: 93, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
41 35 0.38
42 27 0.29
43 30 0.32
44 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.29
Consensus pattern (41 bp):
TGTAAGACCACGTCTGGGACATTGGCATCGTATTTGATTCA
Found at i:5440990 original size:83 final size:84
Alignment explanation
Indices: 5440837--5440991 Score: 221
Period size: 83 Copynumber: 1.9 Consensus size: 84
5440827 ATGTATTTTC
*
5440837 GTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTATACATGTAAGACCATGTCCGGGACA
1 GTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTATACATGTAAGACCACGTCCGGGACA
5440902 TTGGCATCGTATTTGATTT
66 TTGGCATCGTATTTGATTT
*
5440921 GTGTAAGACC-CTGTCTGGGACAG-TGGCATC-A-TATGTG-ATTACATGTAAGACCACGTCTGG
1 GTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGACT-TGTGTA-TACATGTAAGACCACGTCCGG
5440981 GACATTGGCAT
62 GACATTGGCAT
5440992 TGTACGAGCC
Statistics
Matches: 65, Mismatches: 2, Indels: 9
0.86 0.03 0.12
Matches are distributed among these distances:
82 2 0.03
83 36 0.55
84 26 0.40
85 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (84 bp):
GTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTATACATGTAAGACCACGTCCGGGACA
TTGGCATCGTATTTGATTT
Found at i:5441182 original size:16 final size:17
Alignment explanation
Indices: 5441153--5441184 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5441143 TGAATTGATG
5441153 ATATGAAGTTATGTGAA
1 ATATGAAGTTATGTGAA
5441170 ATATGAA-TTATGTGA
1 ATATGAAGTTATGTGA
5441185 TTGCATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (17 bp):
ATATGAAGTTATGTGAA
Found at i:5443837 original size:3 final size:3
Alignment explanation
Indices: 5443829--5443884 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
5443819 AAAGAGAGTT
5443829 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5443877 TTA TTA TT
1 TTA TTA TT
5443885 GATGAATGAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5462062 original size:50 final size:50
Alignment explanation
Indices: 5461945--5462133 Score: 202
Period size: 49 Copynumber: 3.7 Consensus size: 50
5461935 GATAATAACA
* ** * *
5461945 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* * **
5461994 TGCCAATGCCATATCCCAGATATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
5462044 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG
5462099 ATGCCAATGCCATGTCCCAGACATGGTCTTACATG
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATG
5462134 AGATCTCTTT
Statistics
Matches: 116, Mismatches: 16, Indels: 9
0.82 0.11 0.06
Matches are distributed among these distances:
48 1 0.01
49 38 0.33
50 37 0.32
53 5 0.04
55 2 0.02
56 33 0.28
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:5462120 original size:56 final size:50
Alignment explanation
Indices: 5461945--5462141 Score: 200
Period size: 56 Copynumber: 3.8 Consensus size: 50
5461935 GATAATAACA
* * ** * *
5461945 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCT-CGG
* * ** *
5461994 TGCCAATGCCATATCCCAGATATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGG
*
5462044 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTC---ATCTC--GG
*
5462099 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGAGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCT
5462142 TTACCCAAAT
Statistics
Matches: 123, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
48 1 0.01
49 38 0.31
50 37 0.30
53 5 0.04
55 2 0.02
56 40 0.33
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGG
Found at i:5472385 original size:50 final size:50
Alignment explanation
Indices: 5472261--5472549 Score: 296
Period size: 50 Copynumber: 5.7 Consensus size: 50
5472251 GATAATAACA
* ** * *
5472261 TGCCAAAT-CCATGTCCCATACATGGTCTTACATGGGATGTTTCATGTAC--
1 TGCC-AATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * **
5472310 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * ** *
5472360 TGCCCATGCCATGTCCCAAACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * *
5472410 TGCCAACGCCATGTCCCAGAGATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *
5472460 TGCCAATTCCATGCCCCAGACATGGTCTTACATGGCACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-ATC----GG
5472515 ATGCCAATGCCATGTCCCAGACATGGTCTTACATG
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATG
5472550 AGATCTCTTT
Statistics
Matches: 199, Mismatches: 32, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
48 4 0.02
49 36 0.18
50 123 0.62
51 2 0.01
55 2 0.01
56 32 0.16
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:5475002 original size:18 final size:20
Alignment explanation
Indices: 5474973--5475022 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
5474963 AAAGCAAAAA
5474973 CCAAAAACCAAAACACAGC-
1 CCAAAAACCAAAACACAGCT
*
5474992 CCAAAAA-CAAAATACAGCT
1 CCAAAAACCAAAACACAGCT
5475011 CCAAAAATCCAA
1 CCAAAAA-CCAA
5475023 GAATAAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 10 0.37
19 14 0.52
21 3 0.11
ACGTcount: A:0.58, C:0.32, G:0.04, T:0.06
Consensus pattern (20 bp):
CCAAAAACCAAAACACAGCT
Found at i:5475327 original size:5 final size:5
Alignment explanation
Indices: 5475283--5475375 Score: 102
Period size: 5 Copynumber: 18.8 Consensus size: 5
5475273 TATATTAGAA
* * * * *
5475283 CATAT CTTAT CATAC CAGAG CATGT CATAT CGAT-T CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT C-ATAT CATAT CATAT CATAT
5475333 CGAT-T CATAT CATAT CATAT CATA- CATAT CATAT CATAT CATA
1 C-ATAT CATAT CATAT CATAT CATAT CATAT CATAT CATAT CATA
5475376 CAAAGTCCTA
Statistics
Matches: 74, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
4 8 0.11
5 62 0.84
6 4 0.05
ACGTcount: A:0.37, C:0.22, G:0.05, T:0.37
Consensus pattern (5 bp):
CATAT
Found at i:5475330 original size:20 final size:20
Alignment explanation
Indices: 5475307--5475372 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
5475297 CCAGAGCATG
5475307 TCATATCGATTCATATCATA
1 TCATATCGATTCATATCATA
5475327 TCATATCGATTCATATCATA
1 TCATATCGATTCATATCATA
*
5475347 TCATATC-ATACATATCATA
1 TCATATCGATTCATATCATA
5475366 TCATATC
1 TCATATC
5475373 ATACAAAGTC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
19 18 0.40
20 27 0.60
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.39
Consensus pattern (20 bp):
TCATATCGATTCATATCATA
Found at i:5480103 original size:22 final size:23
Alignment explanation
Indices: 5480062--5480110 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
5480052 CCGGCCCGGT
*
5480062 TTTTAATAAAT-ACAAAAAAATA
1 TTTTAATAAATAAAAAAAAAATA
5480084 TTTTAA-AAATAAAAATAAAAATA
1 TTTTAATAAATAAAAA-AAAAATA
5480107 TTTT
1 TTTT
5480111 TAAAGTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 4 0.17
22 9 0.38
23 11 0.46
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (23 bp):
TTTTAATAAATAAAAAAAAAATA
Found at i:5494420 original size:24 final size:23
Alignment explanation
Indices: 5494384--5494429 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
5494374 ACAACTGGAC
5494384 AAAAGATGCCATCCTTATTCAAAG
1 AAAAGATGCCATCCTTA-TCAAAG
* * *
5494408 AAAATATGTCATCTTTATCAAA
1 AAAAGATGCCATCCTTATCAAA
5494430 AAACTGTGCG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.30
Consensus pattern (23 bp):
AAAAGATGCCATCCTTATCAAAG
Found at i:5495318 original size:34 final size:34
Alignment explanation
Indices: 5495275--5495344 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
5495265 TTCAGTAGTC
*
5495275 ACTTCCCAAGCCTGATACGAGAGAACTAATTGCT
1 ACTTCCCAAGCCAGATACGAGAGAACTAATTGCT
5495309 ACTTCCCAAGCCAGATACGAGAGAACTAATTGCT
1 ACTTCCCAAGCCAGATACGAGAGAACTAATTGCT
5495343 AC
1 AC
5495345 GTACCGCATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.21
Consensus pattern (34 bp):
ACTTCCCAAGCCAGATACGAGAGAACTAATTGCT
Found at i:5501187 original size:17 final size:18
Alignment explanation
Indices: 5501158--5501211 Score: 64
Period size: 17 Copynumber: 3.2 Consensus size: 18
5501148 AAATCTACGC
5501158 AAATT-TTTT-TAAAAAT
1 AAATTATTTTATAAAAAT
5501174 -AATTATTTTAT-AAAAT
1 AAATTATTTTATAAAAAT
5501190 AAATTATTTTATATAAAA-
1 AAATTATTTTATA-AAAAT
5501208 AAAT
1 AAAT
5501212 AAATTTCTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
15 4 0.12
16 9 0.27
17 12 0.36
18 4 0.12
19 4 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATTATTTTATAAAAAT
Found at i:5501188 original size:16 final size:17
Alignment explanation
Indices: 5501158--5501202 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
5501148 AAATCTACGC
*
5501158 AAATTTTTTTA-AAAAT
1 AAATTATTTTATAAAAT
5501174 -AATTATTTTATAAAAT
1 AAATTATTTTATAAAAT
5501190 AAATTATTTTATA
1 AAATTATTTTATA
5501203 TAAAAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 9 0.35
16 5 0.19
17 12 0.46
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AAATTATTTTATAAAAT
Found at i:5504943 original size:16 final size:16
Alignment explanation
Indices: 5504922--5504953 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5504912 TCAATTAATC
*
5504922 TAATTAACCTAAAAAT
1 TAATTAAACTAAAAAT
5504938 TAATTAAACTAAAAAT
1 TAATTAAACTAAAAAT
5504954 CAACCAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.31
Consensus pattern (16 bp):
TAATTAAACTAAAAAT
Found at i:5510818 original size:22 final size:23
Alignment explanation
Indices: 5510772--5510853 Score: 73
Period size: 22 Copynumber: 3.7 Consensus size: 23
5510762 ACCACACCAA
*
5510772 TAGGCACTGAAGTGCTTTAATAG
1 TAGGCACTGAAGTGCTTGAATAG
5510795 TAGGCA-TCGAAGTG-TTGAATAG
1 TAGGCACT-GAAGTGCTTGAATAG
* * * *
5510817 TAGGCACCGAGGTGC--AAATTTG
1 TAGGCACTGAAGTGCTTGAA-TAG
5510839 TAGGCACTGAAGTGC
1 TAGGCACTGAAGTGC
5510854 AAAGCAGTAA
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
21 2 0.04
22 34 0.71
23 12 0.25
ACGTcount: A:0.29, C:0.15, G:0.30, T:0.26
Consensus pattern (23 bp):
TAGGCACTGAAGTGCTTGAATAG
Found at i:5510908 original size:22 final size:21
Alignment explanation
Indices: 5510814--5510910 Score: 86
Period size: 22 Copynumber: 4.4 Consensus size: 21
5510804 AAGTGTTGAA
* *
5510814 TAGTAGGCACCGAGGTGCAAAT
1 TAGTAGGCACC-AAGTGCAAAG
* *
5510836 TTGTAGGCACTGAAGTGCAAAG
1 TAGTAGGCAC-CAAGTGCAAAG
* * *
5510858 CAGTAAGCACCATAGTGCAAAT
1 TAGTAGGCACCA-AGTGCAAAG
*
5510880 TATTAGGCACCATAGTGCAAAG
1 TAGTAGGCACCA-AGTGCAAAG
5510902 TAGTAGGCA
1 TAGTAGGCA
5510911 TAGAAGTGCA
Statistics
Matches: 59, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
21 1 0.02
22 58 0.98
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.21
Consensus pattern (21 bp):
TAGTAGGCACCAAGTGCAAAG
Found at i:5512988 original size:13 final size:13
Alignment explanation
Indices: 5512970--5512994 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5512960 GGGCTCACAC
5512970 GCCCATGTGGTCT
1 GCCCATGTGGTCT
5512983 GCCCATGTGGTC
1 GCCCATGTGGTC
5512995 CTACACACCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.32, G:0.32, T:0.28
Consensus pattern (13 bp):
GCCCATGTGGTCT
Found at i:5520792 original size:19 final size:19
Alignment explanation
Indices: 5520758--5520810 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 19
5520748 GAATTTTGGG
5520758 AAAATTAAATTTAATCAAAT
1 AAAATTAAA-TTAATCAAAT
5520778 AAAATTAAATTAATCAAAT
1 AAAATTAAATTAATCAAAT
*
5520797 -TAATTAAAATTAAT
1 AAAATT-AAATTAAT
5520811 ATGATATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
18 4 0.13
19 18 0.58
20 9 0.29
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAATTAAATTAATCAAAT
Found at i:5521280 original size:62 final size:58
Alignment explanation
Indices: 5521174--5521307 Score: 178
Period size: 62 Copynumber: 2.2 Consensus size: 58
5521164 TCCAAAAATA
* * * *
5521174 ATATTATTTTAATAAATTTAATATTTAATTTAATTTAATGTTTATCTTGTAAATAAATATT
1 ATATTAATTTAATAAATTTAATATTAAATTTAATCTAATATTTATCTTG---ATAAATATT
* *
5521235 CTATTAATTTAATAAATTTTAATATTAAATTTTATCTAATATTTATCTTGATAAATATT
1 ATATTAATTTAATAAA-TTTAATATTAAATTTAATCTAATATTTATCTTGATAAATATT
5521294 ATATTAATTTAATA
1 ATATTAATTTAATA
5521308 TTAAAGTGAT
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
59 22 0.34
61 14 0.22
62 29 0.45
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (58 bp):
ATATTAATTTAATAAATTTAATATTAAATTTAATCTAATATTTATCTTGATAAATATT
Found at i:5522739 original size:31 final size:31
Alignment explanation
Indices: 5522704--5522771 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
5522694 AACTTTCAGC
5522704 TCAGTCACTTAAC-TT-TCAAAAAAATAGCAAA
1 TCAGTCAC-TAACATTATC-AAAAAATAGCAAA
* *
5522735 TCAGTCACTAACATTATCAAAAAGTGGCAAA
1 TCAGTCACTAACATTATCAAAAAATAGCAAA
5522766 TCAGTC
1 TCAGTC
5522772 GTCTATTAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 4 0.12
31 27 0.82
32 2 0.06
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.25
Consensus pattern (31 bp):
TCAGTCACTAACATTATCAAAAAATAGCAAA
Found at i:5524883 original size:19 final size:20
Alignment explanation
Indices: 5524859--5524909 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
5524849 ATATTAATAA
*
5524859 TATTATTAAAATTCAAA-TT
1 TATTATTAAAATTAAAATTT
5524878 TATTATTAAAA-TAAAATTT
1 TATTATTAAAATTAAAATTT
*
5524897 TAATATTAAAATT
1 TATTATTAAAATT
5524910 TTAAAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 4 0.14
19 23 0.82
20 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
TATTATTAAAATTAAAATTT
Found at i:5526266 original size:25 final size:25
Alignment explanation
Indices: 5526214--5526266 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
5526204 CATGCTTACA
**
5526214 TTTTTTTCTCAATGCTTTCCCATTT
1 TTTTTTTCTCAATGCTTTCCCAGAT
*
5526239 TTTTTTTCTCGATGCTTTCCCAGAT
1 TTTTTTTCTCAATGCTTTCCCAGAT
5526264 TTT
1 TTT
5526267 CTTAATCCTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.11, C:0.23, G:0.08, T:0.58
Consensus pattern (25 bp):
TTTTTTTCTCAATGCTTTCCCAGAT
Done.