Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 36 of 163
Found at i:9554388 original size:59 final size:59
Alignment explanation
Indices: 9554313--9554740 Score: 614
Period size: 59 Copynumber: 7.3 Consensus size: 59
9554303 GGACGCGTGG
* * * * *
9554313 GGGGCAAAATGGTAATTTTTGGTGAAACTGGGGTTAAAAATGGAATCTTGGGAAGTTT-
1 GGGGTAAAATGGTAATTTTTGATGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
* *
9554371 GAGGGTAAAATGGTAATTTTTGATGAAACCGGGGTTAATAATGGAATTTTGGAAAGTTCA
1 G-GGGTAAAATGGTAATTTTTGATGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
*
9554431 GGGGTAAAATGGTAATTTTTGATGAAACCGAGGTTAAAAATGGAATTTTGGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGATGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
* * * ** *
9554490 GGGGTAAAATGGTAATTTTTGGTGAAACTGGGGTAAAAAATATAATTTT-GAAAGTTCA
1 GGGGTAAAATGGTAATTTTTGATGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
* **
9554548 GGGGTAAAATGGTAATTTTTGATGAAACCGGGGTTAAAAATGGAATTTGGGAAAGTTCG
1 GGGGTAAAATGGTAATTTTTGATGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
* * **
9554607 GGGGTAAAATGGTAATTTTTGATGAAACTGAGGTT-AAAATTAAATTTTGGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGATGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
*
9554665 GGGGTAAAATGGTAATTTTTGATGAAACC-GGGTT-AAAATGGAATTTTGGAAAGTGTA
1 GGGGTAAAATGGTAATTTTTGATGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
9554722 GGGGTAAAATGGTAATTTT
1 GGGGTAAAATGGTAATTTT
9554741 CAGATAGTCC
Statistics
Matches: 331, Mismatches: 36, Indels: 7
0.89 0.10 0.02
Matches are distributed among these distances:
57 43 0.13
58 98 0.30
59 189 0.57
60 1 0.00
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.32
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGATGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
Found at i:9554594 original size:117 final size:117
Alignment explanation
Indices: 9554313--9554740 Score: 639
Period size: 117 Copynumber: 3.7 Consensus size: 117
9554303 GGACGCGTGG
* * * * *
9554313 GGGGCAAAATGGTAATTTTTGGTGAAACTGGGGTTAAAAATGGAATCTTGGGAAGTTT-GAGGGT
1 GGGGTAAAATGGTAATTTTTGATGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTTAG-GGGT
* * *
9554377 AAAATGGTAATTTTTGATGAAACCGGGGTTAATAATGGAATTTTGGAAAGTTCA
65 AAAATGGTAATTTTTGATGAAACTGGGGTTAAAAAT-AAATTTTGGAAAGTTCA
*
9554431 GGGGTAAAATGGTAATTTTTGATGAAACCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTA
1 GGGGTAAAATGGTAATTTTTGATGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTA
* *
9554496 AAATGGTAATTTTTGGTGAAACTGGGGTAAAAAATATAATTTT-GAAAGTTCA
66 AAATGGTAATTTTTGATGAAACTGGGGTTAAAAATA-AATTTTGGAAAGTTCA
* **
9554548 GGGGTAAAATGGTAATTTTTGATGAAACCGGGGTTAAAAATGGAATTTGGGAAAGTTCGGGGGTA
1 GGGGTAAAATGGTAATTTTTGATGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTA
* * *
9554613 AAATGGTAATTTTTGATGAAACTGAGGTTAAAATTAAATTTTGGAAAGTTTA
66 AAATGGTAATTTTTGATGAAACTGGGGTTAAAAATAAATTTTGGAAAGTTCA
*
9554665 GGGGTAAAATGGTAATTTTTGATGAAACC-GGGTT-AAAATGGAATTTTGGAAAGTGTAGGGGTA
1 GGGGTAAAATGGTAATTTTTGATGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTA
9554728 AAATGGTAATTTT
66 AAATGGTAATTTT
9554741 CAGATAGTCC
Statistics
Matches: 283, Mismatches: 24, Indels: 9
0.90 0.08 0.03
Matches are distributed among these distances:
115 38 0.13
116 11 0.04
117 139 0.49
118 94 0.33
119 1 0.00
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.32
Consensus pattern (117 bp):
GGGGTAAAATGGTAATTTTTGATGAAACCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTA
AAATGGTAATTTTTGATGAAACTGGGGTTAAAAATAAATTTTGGAAAGTTCA
Found at i:9556678 original size:31 final size:31
Alignment explanation
Indices: 9556630--9556691 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
9556620 CATTTTAAAT
* *
9556630 TTGATTAAACTTAAATTTAAAGTAAATTTAA
1 TTGAGTAAACTTAAATTTAAAATAAATTTAA
*
9556661 TTGAGTAAATTTAAATTTAAAATAAATTTAA
1 TTGAGTAAACTTAAATTTAAAATAAATTTAA
9556692 AACCCATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (31 bp):
TTGAGTAAACTTAAATTTAAAATAAATTTAA
Found at i:9564742 original size:15 final size:15
Alignment explanation
Indices: 9564724--9564767 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
9564714 AAATTTCAAT
9564724 AAATAAAAAATATTA
1 AAATAAAAAATATTA
**
9564739 AAATATTAAATATTA
1 AAATAAAAAATATTA
*
9564754 AATTAAAATAATAT
1 AAATAAAA-AATAT
9564768 AAATTTTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATAAAAAATATTA
Found at i:9564770 original size:22 final size:22
Alignment explanation
Indices: 9564735--9564795 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
9564725 AATAAAAAAT
9564735 ATTAAAAT-AT-TAAATATTAA
1 ATTAAAATAATATAAATATTAA
**
9564755 ATTAAAATAATATAAAT-TTTT
1 ATTAAAATAATATAAATATTAA
*
9564776 TTTAAAAATAATATAAATAT
1 ATT-AAAATAATATAAATAT
9564796 GAGCGAGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 8 0.24
21 6 0.18
22 19 0.56
23 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTAAAATAATATAAATATTAA
Found at i:9565118 original size:25 final size:27
Alignment explanation
Indices: 9565073--9565127 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
9565063 TTCGTATTTT
9565073 TTTTCTCAATTAAATATTA-TTTTTAG
1 TTTTCTCAATTAAATATTATTTTTTAG
*
9565099 TTTTC-CACTTAAAT-TCTATTTTTTAG
1 TTTTCTCAATTAAATAT-TATTTTTTAG
9565125 TTT
1 TTT
9565128 CACACTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 1 0.04
25 10 0.38
26 15 0.58
ACGTcount: A:0.25, C:0.11, G:0.04, T:0.60
Consensus pattern (27 bp):
TTTTCTCAATTAAATATTATTTTTTAG
Found at i:9565887 original size:17 final size:17
Alignment explanation
Indices: 9565860--9565941 Score: 85
Period size: 17 Copynumber: 4.8 Consensus size: 17
9565850 CGAGCCCAAC
9565860 AAAATTTAAATTTATTTT
1 AAAA-TTAAATTTATTTT
9565878 AAAATTAAATTTATTTT
1 AAAATTAAATTTATTTT
** *
9565895 AAGTTTAAATTTA-CTT
1 AAAATTAAATTTATTTT
*
9565911 AAAATTTAAATTTATTAT
1 AAAA-TTAAATTTATTTT
* *
9565929 AAATTTAAGTTTA
1 AAAATTAAATTTA
9565942 AATTTATTTA
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
16 4 0.08
17 41 0.77
18 8 0.15
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.51
Consensus pattern (17 bp):
AAAATTAAATTTATTTT
Found at i:9565907 original size:34 final size:34
Alignment explanation
Indices: 9565861--9565941 Score: 110
Period size: 34 Copynumber: 2.4 Consensus size: 34
9565851 GAGCCCAACA
* *
9565861 AAATTTAAATTTATTTTAAAA-TTAAATTTATTTT
1 AAATTTAAATTTA-CTTAAAATTTAAATTTATTAT
*
9565895 AAGTTTAAATTTACTTAAAATTTAAATTTATTAT
1 AAATTTAAATTTACTTAAAATTTAAATTTATTAT
*
9565929 AAATTTAAGTTTA
1 AAATTTAAATTTA
9565942 AATTTATTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
33 6 0.15
34 35 0.85
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (34 bp):
AAATTTAAATTTACTTAAAATTTAAATTTATTAT
Found at i:9566977 original size:21 final size:21
Alignment explanation
Indices: 9566943--9567000 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
9566933 TTTTCTTGAA
*
9566943 GATCTA-AGCTAGATCTGTTC
1 GATCTAGACCTAGATCTGTTC
9566963 GATCTAGACCTAGATCTGTTC
1 GATCTAGACCTAGATCTGTTC
9566984 GATCTAGACCTAGATCT
1 GATCTAGACCTAGATCT
9567001 ATCCTTTTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 6 0.17
21 30 0.83
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (21 bp):
GATCTAGACCTAGATCTGTTC
Found at i:9567904 original size:88 final size:89
Alignment explanation
Indices: 9567758--9568153 Score: 236
Period size: 88 Copynumber: 4.5 Consensus size: 89
9567748 TTTGACTCCC
* *
9567758 AAACTTCTCAAAAATTACA-TTTTGACCCTTAAATTTTCCAAAAATCATATTTTAACCCCTA-AA
1 AAACTTC-CAAAAATTACATTTTTGACCCCTAAATTTTCCAAAAATCATATTTTAACCCCGATAA
* * * *
9567821 CTTCCTAAAATT-CCATTTTGCCCTT
65 CTT-CAAAAATTACCATCTTACCCCT
* * * *
9567846 GAACTTCACAAAAATTACATTTTTG-CCCCTGAA-TTTCCATAAATTCCAT-TTTTGACCCCGAT
1 AAACTTC-CAAAAATTACATTTTTGACCCCTAAATTTTCCA-AAAAT-CATATTTTAACCCCGAT
*
9567908 ATCTTCAAAAATTACCATCTTACCCCT
63 AACTTCAAAAATTACCATCTTACCCCT
* * * * * * *
9567935 AAACTTCCAAAAATTCCA-TTTT-AACCTTAAACTTTCCAAAAAT-AGCATTTTCACCCCCA-AA
1 AAACTTCCAAAAATTACATTTTTGACCCCTAAATTTTCCAAAAATCA-TATTTTAACCCCGATAA
* * * * *
9567996 CTTCAAAAATTCCCTTTTTGACCTCG
65 CTTCAAAAATTACCATCTT-ACCCCT
* * * * *
9568022 AAATTTCCAAAAATTACCA-TTTT-A-CCCTCAGA-TGTCCAAAATTTTCAT-TTTTGA-CCCGA
1 AAACTTCCAAAAATTA-CATTTTTGACCCCT-AAATTTTCCAAAA--ATCATATTTTAACCCCGA
*
9568081 -AACTTTCCAAAAATTACCATTTTACCCC-
62 TAAC-TT-CAAAAATTACCATCTTACCCCT
* * * *
9568109 AAAATGTCTAAAAATTCCATTTTTGACCCCAAAATTTT-CAAAAAT
1 AAACT-TCCAAAAATTACATTTTTGACCCCTAAATTTTCCAAAAAT
9568154 TGTCATTTTG
Statistics
Matches: 240, Mismatches: 46, Indels: 45
0.73 0.14 0.14
Matches are distributed among these distances:
85 1 0.00
86 17 0.07
87 72 0.30
88 93 0.39
89 51 0.21
90 6 0.03
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (89 bp):
AAACTTCCAAAAATTACATTTTTGACCCCTAAATTTTCCAAAAATCATATTTTAACCCCGATAAC
TTCAAAAATTACCATCTTACCCCT
Found at i:9567934 original size:59 final size:59
Alignment explanation
Indices: 9567766--9568220 Score: 273
Period size: 59 Copynumber: 7.8 Consensus size: 59
9567756 CCAAACTTCT
* ** * * * *
9567766 CAAAAATTACA-TTTTGACCCTTAAATTTTCCAAAAATCA-TATTTTAACCCCTAAACTTC
1 CAAAAATTCCATTTTTGACCC-CGAATCTTCCAAAAATTACCATTTT-ACCCCTAAATTTC
* * * *
9567825 CTAAAATTCCA-TTTTG-CCCTTGAA-CTTCACAAAAATTA-CATTTTTGCCCCTGAATTTC
1 CAAAAATTCCATTTTTGACCC-CGAATCTTC-CAAAAATTACCA-TTTTACCCCTAAATTTC
* * *
9567883 CATAAATTCCATTTTTGACCCCGATATCTT-CAAAAATTACCATCTTACCCCTAAACTTC
1 CAAAAATTCCATTTTTGACCCCGA-ATCTTCCAAAAATTACCATTTTACCCCTAAATTTC
* ** * * * *
9567942 CAAAAATTCCA-TTTT-AACCTTAAACTTTCCAAAAA-TAGCATTTTCACCCCCAAACTT-
1 CAAAAATTCCATTTTTGACCCCGAATC-TTCCAAAAATTACCATTTT-ACCCCTAAATTTC
* * * *
9567999 CAAAAATTCCCTTTTTGACCTCGAAAT-TTCCAAAAATTACCATTTTA-CCCTCAGATGTC
1 CAAAAATTCCATTTTTGACCCCG-AATCTTCCAAAAATTACCATTTTACCCCT-AAATTTC
* * * * *
9568058 CAAAATTTTCATTTTTGA-CCCGAAACTTTCCAAAAATTACCATTTTACCCCAAAATGTC
1 CAAAAATTCCATTTTTGACCCCGAATC-TTCCAAAAATTACCATTTTACCCCTAAATTTC
* * * ** * * *
9568117 TAAAAATTCCATTTTTGACCCCAAAAT-TTTCAAAAATTGTCATTTTGCCCCT-AAGTAC
1 CAAAAATTCCATTTTTGACCCC-GAATCTTCCAAAAATTACCATTTTACCCCTAAATTTC
* * *
9568175 CTAAAAATTAC-TATTTT-ACCCTTGAA-CCTCCAAAAATTACCATTTT
1 C-AAAAATTCCAT-TTTTGACCC-CGAATCTTCCAAAAATTACCATTTT
9568221 GCCCTCGGGC
Statistics
Matches: 308, Mismatches: 63, Indels: 51
0.73 0.15 0.12
Matches are distributed among these distances:
56 2 0.01
57 31 0.10
58 101 0.33
59 155 0.50
60 14 0.05
61 5 0.02
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (59 bp):
CAAAAATTCCATTTTTGACCCCGAATCTTCCAAAAATTACCATTTTACCCCTAAATTTC
Found at i:9567934 original size:117 final size:116
Alignment explanation
Indices: 9567766--9568220 Score: 378
Period size: 117 Copynumber: 3.9 Consensus size: 116
9567756 CCAAACTTCT
* ** * *
9567766 CAAAAATTACA-TTTTGACCCTTAAATTTTCCAAAAATCA-TATTTTAACCCCTAAACTTCCTAA
1 CAAAAATTCCATTTTTGACCCCGAAA-TTT-CAAAAATTACCATTTT-ACCCCTAAACTTCCTAA
* * **
9567829 AATTCCATTTTGCCCTTGAAC-TTCACAAAAATTA-CATTTTTGCCCCTGAATTTC
63 AATTCCATTTTACCCTTGAACTTTC-CAAAAATTACCA-TTTTACCCCAAAATTTC
* * * *
9567883 CATAAATTCCATTTTTGACCCCGATATCTTCAAAAATTACCATCTTACCCCTAAACTTCCAAAAA
1 CAAAAATTCCATTTTTGACCCCGAAAT-TTCAAAAATTACCATTTTACCCCTAAACTTCCTAAAA
* * * * *
9567948 TTCCATTTTAACCTTAAACTTTCCAAAAA-TAGCATTTTCACCCCCAAACTT-
65 TTCCATTTTACCCTTGAACTTTCCAAAAATTACCATTTT-ACCCCAAAATTTC
* * *
9567999 CAAAAATTCCCTTTTTGACCTCGAAATTTCCAAAAATTACCATTTTA-CCCTCAGA-TGTCC-AA
1 CAAAAATTCCATTTTTGACCCCGAAATTT-CAAAAATTACCATTTTACCCCT-AAACT-TCCTAA
* *
9568061 AATTTTCATTTTTGACCC--GAAACTTTCCAAAAATTACCATTTTACCCCAAAATGTC
63 AA-TTCCA-TTTT-ACCCTTG-AACTTTCCAAAAATTACCATTTTACCCCAAAATTTC
* * ** * * *
9568117 TAAAAATTCCATTTTTGACCCCAAAATTTTCAAAAATTGTCATTTTGCCCCT-AAGTACCTAAAA
1 CAAAAATTCCATTTTTGACCCCGAAA-TTTCAAAAATTACCATTTTACCCCTAAACTTCCT-AAA
* *
9568181 ATTACTATTTTACCCTTGAAC-CTCCAAAAATTACCATTTT
64 ATT-CCATTTTACCCTTGAACTTTCCAAAAATTACCATTTT
9568221 GCCCTCGGGC
Statistics
Matches: 274, Mismatches: 41, Indels: 46
0.76 0.11 0.13
Matches are distributed among these distances:
115 11 0.04
116 54 0.20
117 119 0.43
118 77 0.28
119 13 0.05
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (116 bp):
CAAAAATTCCATTTTTGACCCCGAAATTTCAAAAATTACCATTTTACCCCTAAACTTCCTAAAAT
TCCATTTTACCCTTGAACTTTCCAAAAATTACCATTTTACCCCAAAATTTC
Found at i:9568013 original size:28 final size:28
Alignment explanation
Indices: 9567758--9568220 Score: 231
Period size: 29 Copynumber: 15.8 Consensus size: 28
9567748 TTTGACTCCC
* *
9567758 AAACTTCTCAAAAATTACATTTTGACCCTT
1 AAACTTC-CAAAAATTCCATTTT-ACCCCT
* *
9567788 AAATTTTCCAAAAA-TCATATTTTAACCCCT
1 AAA-CTTCCAAAAATTC-CATTTT-ACCCCT
* * *
9567818 AAACTTCCTAAAATTCCATTTTGCCCTT
1 AAACTTCCAAAAATTCCATTTTACCCCT
* * *
9567846 GAACTTCACAAAAATTACATTTTTGCCCCT
1 AAACTTC-CAAAAATTCCA-TTTTACCCCT
* * * *
9567876 GAATTTCCATAAATTCCATTTTTGACCCCG
1 AAACTTCCAAAAATTCCA-TTTT-ACCCCT
* *
9567906 ATATCTT-CAAAAATTACCATCTTACCCCT
1 A-AACTTCCAAAAATT-CCATTTTACCCCT
* *
9567935 AAACTTCCAAAAATTCCATTTTAACCTT
1 AAACTTCCAAAAATTCCATTTTACCCCT
** *
9567963 AAACTTTCCAAAAATAGCATTTTCACCCCC
1 AAAC-TTCCAAAAATTCCATTTT-ACCCCT
* * *
9567993 AAACTT-CAAAAATTCCCTTTTTGACCTCG
1 AAACTTCCAAAAATT-CCATTTT-ACCCCT
*
9568022 AAATTTCCAAAAATTACCATTTTA-CCCT
1 AAACTTCCAAAAATT-CCATTTTACCCCT
* * * *
9568050 CAGA-TGTCCAAAATTTTCATTTTTGA-CCCG
1 -AAACT-TCCAAAAATTCCA-TTTT-ACCCCT
9568080 AAACTTTCCAAAAATTACCATTTTACCCC-
1 AAAC-TTCCAAAAATT-CCATTTTACCCCT
* * *
9568109 AAAATGTCTAAAAATTCCATTTTTGACCCCA
1 AAACT-TCCAAAAATTCCA-TTTT-ACCCCT
* * * *
9568140 AAATTTTCAAAAATTGTCATTTTGCCCCT
1 AAACTTCCAAAAATT-CCATTTTACCCCT
* * * *
9568169 -AAGTACCTAAAAATTACTATTTTACCCTT
1 AAACTTCC-AAAAATT-CCATTTTACCCCT
* *
9568198 GAACCTCCAAAAATTACCATTTT
1 AAACTTCCAAAAATT-CCATTTT
9568221 GCCCTCGGGC
Statistics
Matches: 333, Mismatches: 72, Indels: 57
0.72 0.16 0.12
Matches are distributed among these distances:
28 48 0.14
29 152 0.46
30 115 0.35
31 18 0.05
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (28 bp):
AAACTTCCAAAAATTCCATTTTACCCCT
Found at i:9568075 original size:175 final size:175
Alignment explanation
Indices: 9567755--9568131 Score: 421
Period size: 175 Copynumber: 2.1 Consensus size: 175
9567745 TATTTTGACT
* * * * *
9567755 CCCAAACTTCTCAAAAATTACATTTTGACCCTTAAATTTTCCAAAAATCATATTTTAACCCCTAA
1 CCCAAACTTC-CAAAAATTCCATTTTGAACCTTAAACTTTCCAAAAATCACATTTTAACCCCCAA
* * * * * *
9567820 ACTTCCTAAAATTCCATTTTGCCCTTGAACTTCACAAAAATTACATTTTTGCCCCTGAATTTCCA
65 ACTTCCAAAAATTCCATTTTGACCTCGAACTTCACAAAAATTACATTTTTACCCCAGAATGTCCA
*
9567885 TAAATTCCATTTTTGACCCCGATA-TCTT-CAAAAATTACCATCTTAC
130 TAAATTCCATTTTTGA-CCCGAAACT-TTCCAAAAATTACCATCTTAC
*
9567931 CCCTAAACTTCCAAAAATTCCATTTT-AACCTTAAACTTTCCAAAAAT-AGCATTTTCACCCCCA
1 CCC-AAACTTCCAAAAATTCCATTTTGAACCTTAAACTTTCCAAAAATCA-CATTTTAACCCCCA
* *
9567994 AACTT-CAAAAATTCCCTTTTTGACCTCGAAATTTC-CAAAAATTACCA-TTTTACCCTCAG-AT
64 AACTTCCAAAAATT-CCATTTTGACCTCG-AACTTCACAAAAATTA-CATTTTTACCC-CAGAAT
* *
9568055 GTCCA-AAATTTTCATTTTTGACCCGAAACTTTCCAAAAATTACCATTTTAC
125 GTCCATAAA-TTCCATTTTTGACCCGAAACTTTCCAAAAATTACCATCTTAC
* *
9568106 CCCAAAATGTCTAAAAATTCCATTTT
1 CCCAAACT-TCCAAAAATTCCATTTT
9568132 TGACCCCAAA
Statistics
Matches: 172, Mismatches: 19, Indels: 21
0.81 0.09 0.10
Matches are distributed among these distances:
174 23 0.13
175 116 0.67
176 26 0.15
177 7 0.04
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (175 bp):
CCCAAACTTCCAAAAATTCCATTTTGAACCTTAAACTTTCCAAAAATCACATTTTAACCCCCAAA
CTTCCAAAAATTCCATTTTGACCTCGAACTTCACAAAAATTACATTTTTACCCCAGAATGTCCAT
AAATTCCATTTTTGACCCGAAACTTTCCAAAAATTACCATCTTAC
Found at i:9572654 original size:31 final size:31
Alignment explanation
Indices: 9572616--9572682 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
9572606 TTATCCTCCT
*
9572616 ATTTGATAC-CGAAGGTTAGCCTCAAGGTTCA
1 ATTTGATACACG-AGGTTAGCCTCAAAGTTCA
* * *
9572647 ATTTGATACATGAGTTTAGCTTCAAAGTTCA
1 ATTTGATACACGAGGTTAGCCTCAAAGTTCA
9572678 ATTTG
1 ATTTG
9572683 GTAATAATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (31 bp):
ATTTGATACACGAGGTTAGCCTCAAAGTTCA
Found at i:9573059 original size:15 final size:15
Alignment explanation
Indices: 9573041--9573072 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
9573031 CTTTTCCGTC
9573041 ATTCCCTTATTGAAA
1 ATTCCCTTATTGAAA
*
9573056 ATTCTCTTATTGAAA
1 ATTCCCTTATTGAAA
9573071 AT
1 AT
9573073 GGATAAGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.44
Consensus pattern (15 bp):
ATTCCCTTATTGAAA
Found at i:9573585 original size:30 final size:30
Alignment explanation
Indices: 9573550--9573612 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
9573540 ACGTGTTGTG
9573550 CATGGTTGAACTCGAATCTATACCTTATAA
1 CATGGTTGAACTCGAATCTATACCTTATAA
9573580 CATGGTTGAACTCGAATCTATACCTTATAA
1 CATGGTTGAACTCGAATCTATACCTTATAA
9573610 CAT
1 CAT
9573613 ATAGGGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (30 bp):
CATGGTTGAACTCGAATCTATACCTTATAA
Found at i:9597434 original size:2 final size:2
Alignment explanation
Indices: 9597429--9597461 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
9597419 TCTCTCTCTC
*
9597429 TA TA TA TA TA TG 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 T
9597462 GAAACAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9603173 original size:3 final size:3
Alignment explanation
Indices: 9603165--9603222 Score: 68
Period size: 3 Copynumber: 20.0 Consensus size: 3
9603155 ATATTTAACG
* *
9603165 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AT TAA -ACA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
9603209 TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA
9603223 CGTGAAATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
2 4 0.09
3 43 0.91
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:9603450 original size:3 final size:3
Alignment explanation
Indices: 9603442--9603471 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
9603432 ACCGACTGAG
9603442 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
9603472 GACCATTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:9605195 original size:28 final size:29
Alignment explanation
Indices: 9605137--9605198 Score: 74
Period size: 28 Copynumber: 2.1 Consensus size: 29
9605127 ATTGTATTTG
*
9605137 AATTTTTTAATATGAAAATTAGAGGCATTA
1 AATTTTTGAATATG-AAATTAGAGGCATTA
*
9605167 AATTTTTGAATATG-AATGTAG-GGGATTA
1 AATTTTTGAATATGAAAT-TAGAGGCATTA
9605195 AATT
1 AATT
9605199 CTAAATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 13 0.45
29 3 0.10
30 13 0.45
ACGTcount: A:0.40, C:0.02, G:0.18, T:0.40
Consensus pattern (29 bp):
AATTTTTGAATATGAAATTAGAGGCATTA
Found at i:9607176 original size:23 final size:24
Alignment explanation
Indices: 9607122--9607215 Score: 93
Period size: 25 Copynumber: 3.9 Consensus size: 24
9607112 AGTACTTAAT
* *
9607122 AGAGGGCAC-ATAAGTGCTGGATAAC
1 AGAGGGCACAAAAAGTGCT-AAT-AC
9607147 AGAGGGCACAAAAAGTGCTAAT-C
1 AGAGGGCACAAAAAGTGCTAATAC
** *
9607170 AGAGGGCACACGAAGTGCTAATAAT
1 AGAGGGCACAAAAAGTGCTAAT-AC
*
9607195 AGAGGGCACAAAACGTGCTAA
1 AGAGGGCACAAAAAGTGCTAA
9607216 ACAAAGGACA
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
23 21 0.36
25 29 0.50
26 8 0.14
ACGTcount: A:0.40, C:0.17, G:0.29, T:0.14
Consensus pattern (24 bp):
AGAGGGCACAAAAAGTGCTAATAC
Found at i:9607176 original size:48 final size:47
Alignment explanation
Indices: 9607118--9607215 Score: 135
Period size: 48 Copynumber: 2.1 Consensus size: 47
9607108 CCGAAGTACT
* *
9607118 TAATAGAGGGCACA-TAAGTGCTGGATAACAGAGGGCACAAAAAGTGC
1 TAATAGAGGGCACACGAAGTGCT-AATAACAGAGGGCACAAAAAGTGC
* *
9607165 TAATCAGAGGGCACACGAAGTGCTAATAATAGAGGGCACAAAACGTGC
1 TAAT-AGAGGGCACACGAAGTGCTAATAACAGAGGGCACAAAAAGTGC
9607213 TAA
1 TAA
9607216 ACAAAGGACA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
47 4 0.09
48 34 0.76
49 7 0.16
ACGTcount: A:0.41, C:0.16, G:0.28, T:0.15
Consensus pattern (47 bp):
TAATAGAGGGCACACGAAGTGCTAATAACAGAGGGCACAAAAAGTGC
Found at i:9610742 original size:118 final size:118
Alignment explanation
Indices: 9610590--9610845 Score: 291
Period size: 118 Copynumber: 2.2 Consensus size: 118
9610580 AAATTGAGGG
* * *
9610590 TCAAAAATGGAATCTTTAGACATCCGGGGGTAAAACGGTAATTTTTAGAAA-AATCAGGATCAAA
1 TCAAAAATGGAATTTTTAGACATCCGGGAGTAAAACAGTAATTTTT-GAAAGAATCAGGATCAAA
* **
9610654 AATAGAATTTTTGGACTTTTTAGGGTAAAATAGTAA-TTTTTGAAAGTTTCGAGA
65 AATAGAATTTTTGGACATTCGA-GGTAAAATAGTAATTTTTTGAAAGTTTCGAGA
* * * * ** ** * *
9610708 TCAAAAATGGAGTTTTTGGACATTCGGGAGTAAAATAGTAATTTTTGAAAGTTTTGGGGTTAAAA
1 TCAAAAATGGAATTTTTAGACATCCGGGAGTAAAACAGTAATTTTTGAAAGAATCAGGATCAAAA
* * * *
9610773 ATGGAATTTTTGGACATTCGAGGTAAAATGGTAATTTTTTGAAAGTTTTGAGG
66 ATAGAATTTTTGGACATTCGAGGTAAAATAGTAATTTTTTGAAAGTTTCGAGA
*
9610826 TTAAAAATGGAATTTTTAGA
1 TCAAAAATGGAATTTTTAGA
9610846 AGTTTAAGGG
Statistics
Matches: 113, Mismatches: 23, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
117 16 0.14
118 97 0.86
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.35
Consensus pattern (118 bp):
TCAAAAATGGAATTTTTAGACATCCGGGAGTAAAACAGTAATTTTTGAAAGAATCAGGATCAAAA
ATAGAATTTTTGGACATTCGAGGTAAAATAGTAATTTTTTGAAAGTTTCGAGA
Found at i:9610947 original size:119 final size:118
Alignment explanation
Indices: 9610649--9611010 Score: 382
Period size: 119 Copynumber: 3.1 Consensus size: 118
9610639 AAAATCAGGA
* ** ** * * *
9610649 TCAAAAATAGAATTTTTGGACTTTTTAGGGTAAAAT-AGTAA-TTTTTGAAAGTTTCGAGATCAA
1 TCAAAAATGGAATTTTTGGAAATTCGA-GGTAAAATGA-TAATTTTTTGAAAGTTTTGAGGTTAA
* * ** *
9610712 AAATGGAGTTTTTGGACA--TTCGGGAGTAAAATAGTAATTTTTGAAAGTTTTGGGG
64 AAATGGAATTTTT-GAAAGTTTAAGG-GTAAAATGGTAATTTTTGAAAGTTTTGGGG
* * *
9610767 TTAAAAATGGAATTTTTGGACATTCGAGGTAAAATGGTAATTTTTTGAAAGTTTTGAGGTTAAAA
1 TCAAAAATGGAATTTTTGGAAATTCGAGGTAAAATGATAATTTTTTGAAAGTTTTGAGGTTAAAA
9610832 ATGGAATTTTT-AGAAGTTTAAGGGTAAAATGGTAATTTTTGAAAGTTTTAGGGG
66 ATGGAATTTTTGA-AAGTTTAAGGGTAAAATGGTAATTTTTGAAAGTTTT-GGGG
*
9610886 TCAAAAATGGAATTTTT-GAAAGTTCGGGAGTAAAAAT-ATAA-TTTTTGAAAGTTTT-AGGGTT
1 TCAAAAATGGAATTTTTGGAAA-TTCGAG-GT-AAAATGATAATTTTTTGAAAGTTTTGA-GGTT
* * *
9610947 AAAAATGTAATTTTTGAAAGTTTGAGGGTAAAATGATAATTTTTGAAAGTTTTGGGGG
62 AAAAATGGAATTTTTGAAAGTTTAAGGGTAAAATGGTAATTTTTGAAAGTTTT-GGGG
9611005 TCAAAA
1 TCAAAA
9611011 TATAATTTCT
Statistics
Matches: 211, Mismatches: 22, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
116 1 0.00
117 12 0.06
118 82 0.39
119 105 0.50
120 6 0.03
121 5 0.02
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (118 bp):
TCAAAAATGGAATTTTTGGAAATTCGAGGTAAAATGATAATTTTTTGAAAGTTTTGAGGTTAAAA
ATGGAATTTTTGAAAGTTTAAGGGTAAAATGGTAATTTTTGAAAGTTTTGGGG
Found at i:9611011 original size:59 final size:59
Alignment explanation
Indices: 9610675--9611003 Score: 361
Period size: 59 Copynumber: 5.6 Consensus size: 59
9610665 TGGACTTTTT
* * * * * *
9610675 AGGGTAAAAT-AGTAATTTTTGAAAGTTTCGAGATCAAAAATGGAGTTTTTGGACA-TTCG
1 AGGGTAAAATGA-TAATTTTTGAAAGTTTTGGGGTTAAAAATGGAATTTTT-GAAAGTTCG
*
9610734 -GGAGTAAAAT-AGTAATTTTTGAAAGTTTTGGGGTTAAAAATGGAATTTTTGGACA-TTCG
1 AGG-GTAAAATGA-TAATTTTTGAAAGTTTTGGGGTTAAAAATGGAATTTTT-GAAAGTTCG
* * **
9610793 A-GGTAAAATGGTAATTTTTTGAAAGTTTTGAGGTTAAAAATGGAATTTTT-AGAAGTTTA
1 AGGGTAAAATGATAA-TTTTTGAAAGTTTTGGGGTTAAAAATGGAATTTTTGA-AAGTTCG
* *
9610852 AGGGTAAAATGGTAATTTTTGAAAGTTTTAGGGGTCAAAAATGGAATTTTTGAAAGTTCG
1 AGGGTAAAATGATAATTTTTGAAAGTTTT-GGGGTTAAAAATGGAATTTTTGAAAGTTCG
* * *
9610912 -GGAGTAAAAAT-ATAATTTTTGAAAGTTTTAGGGTTAAAAATGTAATTTTTGAAAGTTTG
1 AGG-GT-AAAATGATAATTTTTGAAAGTTTTGGGGTTAAAAATGGAATTTTTGAAAGTTCG
9610971 AGGGTAAAATGATAATTTTTGAAAGTTTTGGGG
1 AGGGTAAAATGATAATTTTTGAAAGTTTTGGGG
9611004 GTCAAAATAT
Statistics
Matches: 237, Mismatches: 20, Indels: 26
0.84 0.07 0.09
Matches are distributed among these distances:
57 1 0.00
58 18 0.08
59 154 0.65
60 58 0.24
61 6 0.03
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.37
Consensus pattern (59 bp):
AGGGTAAAATGATAATTTTTGAAAGTTTTGGGGTTAAAAATGGAATTTTTGAAAGTTCG
Found at i:9611016 original size:30 final size:30
Alignment explanation
Indices: 9610739--9611018 Score: 202
Period size: 30 Copynumber: 9.4 Consensus size: 30
9610729 ATTCGGGAGT
*
9610739 AAAATAGTAATTTTTGAAAGTTTTGGGGTTA
1 AAAATA-TAATTTTTGAAAGTTTTGGGGGTA
** * * *
9610770 AAAATGGAATTTTTGGACA---TTCGAGGT-
1 AAAATATAATTTTT-GAAAGTTTTGGGGGTA
* * *
9610797 AAAATGGTAATTTTTTGAAAGTTTTGAGGTTA
1 AAAAT-ATAA-TTTTTGAAAGTTTTGGGGGTA
** **
9610829 AAAATGGAATTTTT-AGAAG-TTTAAGGGT-
1 AAAATATAATTTTTGA-AAGTTTTGGGGGTA
* *
9610857 AAAATGGTAATTTTTGAAAGTTTTAGGGGTCA
1 AAAAT-ATAATTTTTGAAAGTTTTGGGGGT-A
** * *
9610889 AAAATGGAATTTTTGAAAG-TTCGGGAGTA
1 AAAATATAATTTTTGAAAGTTTTGGGGGTA
* *
9610918 AAAATATAATTTTTGAAAGTTTTAGGGTTA
1 AAAATATAATTTTTGAAAGTTTTGGGGGTA
* *
9610948 AAAATGTAATTTTTGAAAG-TTTGAGGGT-
1 AAAATATAATTTTTGAAAGTTTTGGGGGTA
*
9610976 AAAATGATAATTTTTGAAAGTTTTGGGGGTC
1 AAAAT-ATAATTTTTGAAAGTTTTGGGGGTA
9611007 AAAATATAATTT
1 AAAATATAATTT
9611019 CTAGACAGTA
Statistics
Matches: 199, Mismatches: 33, Indels: 35
0.75 0.12 0.13
Matches are distributed among these distances:
27 5 0.03
28 21 0.11
29 61 0.31
30 69 0.35
31 33 0.17
32 10 0.05
ACGTcount: A:0.37, C:0.02, G:0.23, T:0.39
Consensus pattern (30 bp):
AAAATATAATTTTTGAAAGTTTTGGGGGTA
Found at i:9613804 original size:201 final size:198
Alignment explanation
Indices: 9613342--9613969 Score: 741
Period size: 201 Copynumber: 3.1 Consensus size: 198
9613332 CTTGGCCTTT
** * * * *
9613342 TTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCAGTGTTTCATC
1 TTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCTACTTCTCTGTATCTCATC
* * * * *
9613407 AGGAAGACGGATTTGGTTAACTTCTTCGTATCTCATCAGGAAGCAAACCACTTTATTGTTTCGAC
66 AGGAAGACGAATTTGGTCAACTTCTTAGTATCTCATCAGGAAGCAAACCATTTTATTGCTTCGAC
* * * **
9613472 --C-TGT--T-TCTCATCAGGAAGTTAGGGTTTGAAGATTTGCTCATATCGAGCGT-GAGTTTGA
131 TGCTTCTCATATCTCATCAGGAAGTGA-GGTTCGAAGATTTGCTCGCATCGAGCGTCGA----G-
* *
9613530 TTTGGTCTTC
190 -TTGGTATAC
* **
9613540 TTCTCAGTATCTCATCAAGAAGATGACCGCATCGTTTGTTTCAATCTACTTCTCTGTATCTCATC
1 TTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCTACTTCTCTGTATCTCATC
* * *
9613605 AGGAAGATGAATTTGGTCCACTTCTTAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGAT
66 AGGAAGACGAATTTGGTCAACTTCTTAGTATCTCATCAGGAAGCAAACCATTTTATTGCTTCGA-
9613670 CTGCTTCTCAATATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCGCATCGAGCGTCGAGTTG
130 CTGCTTCTC-ATATCTCATCAGGAAG-TGAGGTTCGAAGATTTGCTCGCATCGAGCGTCGAGTTG
9613735 GTATAC
193 GTATAC
* * * *
9613741 TTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCTGCTTCTCTGCATCTCATC
1 TTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCTACTTCTCTGTATCTCATC
* * *
9613806 AGGAAGACGAATTTGGTCTACTTCTCAGTATCTCATCAAGAAGCAAACCATTTTATTGCTTCGAC
66 AGGAAGACGAATTTGGTCAACTTCTTAGTATCTCATCAGGAAGCAAACCATTTTATTGCTTCGA-
* * *
9613871 CTGCTTCTCAGTATCTCATAAGGAAGTTGAGGTTCGAAGATTTGCTTGCATCGAGTGTCGAGTTG
130 CTGCTTCTCA-TATCTCATCAGGAAG-TGAGGTTCGAAGATTTGCTCGCATCGAGCGTCGAGTTG
*
9613936 GTATGC
193 GTATAC
* *
9613942 TTCTTTA-TATCTCATCAGGAAAATGACC
1 TTC-TCAGTATCTCATCAGGAAGATGACC
9613970 ATCTCTCTGT
Statistics
Matches: 373, Mismatches: 45, Indels: 21
0.85 0.10 0.05
Matches are distributed among these distances:
198 112 0.30
199 1 0.00
200 1 0.00
201 212 0.57
202 3 0.01
203 1 0.00
205 1 0.00
206 38 0.10
207 4 0.01
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (198 bp):
TTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCTACTTCTCTGTATCTCATC
AGGAAGACGAATTTGGTCAACTTCTTAGTATCTCATCAGGAAGCAAACCATTTTATTGCTTCGAC
TGCTTCTCATATCTCATCAGGAAGTGAGGTTCGAAGATTTGCTCGCATCGAGCGTCGAGTTGGTA
TAC
Found at i:9627260 original size:23 final size:23
Alignment explanation
Indices: 9627230--9627331 Score: 100
Period size: 23 Copynumber: 4.3 Consensus size: 23
9627220 TGCTGGGTAA
9627230 CAGAGGGCACACAAAGTGCTAAT
1 CAGAGGGCACACAAAGTGCTAAT
*
9627253 CAGAGGGCACACGAAGTGCTAAT
1 CAGAGGGCACACAAAGTGCTAAT
* *
9627276 AACAGAGGGCACACATAGTTCTGAA-
1 --CAGAGGGCACACAAAGTGCT-AAT
* * *
9627301 CAAAGGGCACGA-AACGTGCTAAA
1 CAGAGGGCAC-ACAAAGTGCTAAT
9627324 CAGAGGGC
1 CAGAGGGC
9627332 GCGCTAGTGT
Statistics
Matches: 65, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
22 2 0.03
23 43 0.66
24 1 0.02
25 17 0.26
26 2 0.03
ACGTcount: A:0.38, C:0.22, G:0.28, T:0.12
Consensus pattern (23 bp):
CAGAGGGCACACAAAGTGCTAAT
Found at i:9627287 original size:25 final size:25
Alignment explanation
Indices: 9627227--9627290 Score: 105
Period size: 23 Copynumber: 2.6 Consensus size: 25
9627217 AAGTGCTGGG
9627227 TAACAGAGGGCACACAAAGTGCTAA
1 TAACAGAGGGCACACAAAGTGCTAA
*
9627252 T--CAGAGGGCACACGAAGTGCTAA
1 TAACAGAGGGCACACAAAGTGCTAA
9627275 TAACAGAGGGCACACA
1 TAACAGAGGGCACACA
9627291 TAGTTCTGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 22 0.63
25 13 0.37
ACGTcount: A:0.41, C:0.22, G:0.27, T:0.11
Consensus pattern (25 bp):
TAACAGAGGGCACACAAAGTGCTAA
Found at i:9627320 original size:48 final size:46
Alignment explanation
Indices: 9627227--9627331 Score: 117
Period size: 48 Copynumber: 2.2 Consensus size: 46
9627217 AAGTGCTGGG
*
9627227 TAACAGAGGGCACACAAAGTGCTAATCAGAGGGCACACGAAGTGCTAA
1 TAACAGAGGGCACACAAAGTGCTAATCAAAGGGCACAC-AAGTGCT-A
* *
9627275 TAACAGAGGGCACACATAGTTCTGAA-CAAAGGGCACGA-AACGTGCTA
1 TAACAGAGGGCACACAAAGTGCT-AATCAAAGGGCAC-ACAA-GTGCTA
9627322 -AACAGAGGGC
1 TAACAGAGGGC
9627332 GCGCTAGTGT
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
46 10 0.20
47 3 0.06
48 35 0.69
49 3 0.06
ACGTcount: A:0.39, C:0.21, G:0.28, T:0.12
Consensus pattern (46 bp):
TAACAGAGGGCACACAAAGTGCTAATCAAAGGGCACACAAGTGCTA
Found at i:9630599 original size:32 final size:31
Alignment explanation
Indices: 9630543--9630604 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 31
9630533 TTTAATTTTT
*
9630543 TTTGAAAATTTTAATTAAAATCATTTAAAATA
1 TTTGAAAAGTTTAATTAAAATCA-TTAAAATA
* **
9630575 TTTGAAAAGTTTCATTAATCTCATTAAAAT
1 TTTGAAAAGTTTAATTAAAATCATTAAAAT
9630605 TTTAATTAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 7 0.27
32 19 0.73
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (31 bp):
TTTGAAAAGTTTAATTAAAATCATTAAAATA
Found at i:9630982 original size:3 final size:3
Alignment explanation
Indices: 9630974--9631001 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
9630964 ATTTGAAACG
9630974 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
9631002 TAGGAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:9631421 original size:20 final size:21
Alignment explanation
Indices: 9631376--9631423 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
9631366 TTTAATGATT
*
9631376 ATTTTAAATATTTTAAATATA
1 ATTTTATATATTTTAAATATA
*
9631397 A-TTTATATATTTTAATTA-A
1 ATTTTATATATTTTAAATATA
9631416 ATTTTATA
1 ATTTTATA
9631424 AATAATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.88
21 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTTATATATTTTAAATATA
Found at i:9631466 original size:30 final size:30
Alignment explanation
Indices: 9631427--9631483 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
9631417 TTTTATAAAT
9631427 AATTAATATTT-AT-TGCTTAAAAATATTTAA
1 AATTAATATTTCATAT-CTT-AAAATATTTAA
*
9631457 AATTTATATTTCATATCTTAAAATATT
1 AATTAATATTTCATATCTTAAAATATT
9631484 AACAACAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 18 0.75
31 5 0.21
32 1 0.04
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (30 bp):
AATTAATATTTCATATCTTAAAATATTTAA
Found at i:9631987 original size:17 final size:18
Alignment explanation
Indices: 9631957--9631994 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
9631947 AGTTTTAATA
*
9631957 TTTACTCTCTTTTTCAGT
1 TTTACTCTCATTTTCAGT
*
9631975 TTTACTCT-ATTTTTAGT
1 TTTACTCTCATTTTCAGT
9631992 TTT
1 TTT
9631995 TACTTTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.13, C:0.16, G:0.05, T:0.66
Consensus pattern (18 bp):
TTTACTCTCATTTTCAGT
Found at i:9631998 original size:18 final size:18
Alignment explanation
Indices: 9631957--9631994 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
9631947 AGTTTTAATA
*
9631957 TTTACTCTCTTTTTCAGT
1 TTTACTCTATTTTTCAGT
9631975 TTTACTCTATTTTT-AGT
1 TTTACTCTATTTTTCAGT
9631992 TTT
1 TTT
9631995 TACTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.13, C:0.16, G:0.05, T:0.66
Consensus pattern (18 bp):
TTTACTCTATTTTTCAGT
Found at i:9633103 original size:14 final size:15
Alignment explanation
Indices: 9633086--9633122 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
9633076 TATAATTTTT
*
9633086 AAAATTAAAAATT-A
1 AAAATAAAAAATTGA
9633100 AAAATAAAAAATTGA
1 AAAATAAAAAATTGA
9633115 AAAA-AAAA
1 AAAATAAAA
9633123 GTAAATGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (15 bp):
AAAATAAAAAATTGA
Found at i:9633413 original size:17 final size:15
Alignment explanation
Indices: 9633391--9633424 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
9633381 AAATGAAAAA
9633391 TAATAAAATAATAATTT
1 TAATAAAA-AA-AATTT
9633408 TAATAAAAAAAATTT
1 TAATAAAAAAAATTT
9633423 TA
1 TA
9633425 TTACTATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 2 0.12
17 8 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TAATAAAAAAAATTT
Found at i:9635265 original size:20 final size:18
Alignment explanation
Indices: 9635242--9635282 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
9635232 TAACCATACG
*
9635242 TTTAGTTATTTTTTTTCTAA
1 TTTAGTT-TTTTTATT-TAA
9635262 TTTAGTTTTTTTATTTAA
1 TTTAGTTTTTTTATTTAA
9635280 TTT
1 TTT
9635283 GGAAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 7 0.35
20 7 0.35
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (18 bp):
TTTAGTTTTTTTATTTAA
Found at i:9639521 original size:24 final size:25
Alignment explanation
Indices: 9639492--9639540 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
9639482 TGCCTTCTTT
9639492 CAATCTTT-AT-TACCACTTTTTCAA
1 CAATCTTTCATCTACC-CTTTTTCAA
*
9639516 CAATCTTTCATCTACCTTTTTTCAA
1 CAATCTTTCATCTACCCTTTTTCAA
9639541 AATAATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 8 0.36
25 10 0.45
26 4 0.18
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.47
Consensus pattern (25 bp):
CAATCTTTCATCTACCCTTTTTCAA
Found at i:9652417 original size:6 final size:6
Alignment explanation
Indices: 9652406--9652433 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
9652396 ACTTATAATT
9652406 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
9652434 TAACAATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:9658352 original size:27 final size:28
Alignment explanation
Indices: 9658312--9658373 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 28
9658302 GAAAAAGCCT
*
9658312 AAGG-AGAAGAAGGA-AATTGAA-GAAGAG
1 AAGGAAGAAGAAGGAGAA--GAATGAAGAA
9658339 AAGGAAGAAG-AGGAGAAGAATGAAGAA
1 AAGGAAGAAGAAGGAGAAGAATGAAGAA
9658366 AAGGAAGA
1 AAGGAAGA
9658374 TGCCTCGACA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
26 3 0.10
27 21 0.68
28 7 0.23
ACGTcount: A:0.58, C:0.00, G:0.37, T:0.05
Consensus pattern (28 bp):
AAGGAAGAAGAAGGAGAAGAATGAAGAA
Found at i:9658363 original size:15 final size:16
Alignment explanation
Indices: 9658319--9658365 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
9658309 CCTAAGGAGA
9658319 AGAAGGAAATTGAAGAAG
1 AGAAGG-AA-TGAAGAAG
*
9658337 AGAAGGAA-GAAGAGG
1 AGAAGGAATGAAGAAG
9658352 AGAA-GAATGAAGAA
1 AGAAGGAATGAAGAA
9658366 AAGGAAGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 3 0.12
15 15 0.58
17 2 0.08
18 6 0.23
ACGTcount: A:0.57, C:0.00, G:0.36, T:0.06
Consensus pattern (16 bp):
AGAAGGAATGAAGAAG
Found at i:9658802 original size:17 final size:17
Alignment explanation
Indices: 9658775--9658817 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
9658765 ATGCATAACA
* *
9658775 TTTAGTTGTCATTGCAT
1 TTTATTTGTCACTGCAT
*
9658792 TTTTTTTGTCACTGCAT
1 TTTATTTGTCACTGCAT
9658809 TTTATTTGT
1 TTTATTTGT
9658818 TAGTACATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.14, C:0.12, G:0.14, T:0.60
Consensus pattern (17 bp):
TTTATTTGTCACTGCAT
Found at i:9666558 original size:19 final size:19
Alignment explanation
Indices: 9666508--9666600 Score: 98
Period size: 19 Copynumber: 4.9 Consensus size: 19
9666498 AGGAATAGCA
**
9666508 ATACTGGCTCGTTTGAGC-
1 ATACTGGCTCGTAAGAGCG
*
9666526 ATACTAGCTCGTAAGAGCG
1 ATACTGGCTCGTAAGAGCG
* *
9666545 ATACTGGCTTGTAAGAGCA
1 ATACTGGCTCGTAAGAGCG
* * *
9666564 ATATTGGCTTGTAAGCGCG
1 ATACTGGCTCGTAAGAGCG
*
9666583 ATACTAGCTCGTAAGAGC
1 ATACTGGCTCGTAAGAGC
9666601 AAGTTACTGA
Statistics
Matches: 61, Mismatches: 13, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
18 15 0.25
19 46 0.75
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (19 bp):
ATACTGGCTCGTAAGAGCG
Found at i:9666669 original size:35 final size:35
Alignment explanation
Indices: 9666630--9666712 Score: 123
Period size: 35 Copynumber: 2.4 Consensus size: 35
9666620 TAAGAGCTAA
* *
9666630 AAATTACTGGGAAT-TTGGAAGAGCTCGTATGAGTT
1 AAATTACTGGGAATCTT-GAAGAACTCATATGAGTT
*
9666665 AAATTACTGAGAATCTTGAAGAACTCATATGAGTT
1 AAATTACTGGGAATCTTGAAGAACTCATATGAGTT
9666700 AAATTACTGGGAA
1 AAATTACTGGGAA
9666713 ACCTGAAAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
35 41 0.95
36 2 0.05
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (35 bp):
AAATTACTGGGAATCTTGAAGAACTCATATGAGTT
Found at i:9672821 original size:20 final size:19
Alignment explanation
Indices: 9672789--9672832 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
9672779 AGTTATATAC
*
9672789 TAAAATTAATTTTAAAATA
1 TAAAATTAATTTTAAAAAA
*
9672808 TAAATATTATTTTTAAAAAA
1 TAAA-ATTAATTTTAAAAAA
9672828 TAAAA
1 TAAAA
9672833 CAATGGGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAAATTAATTTTAAAAAA
Found at i:9673506 original size:3 final size:3
Alignment explanation
Indices: 9673498--9673538 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
9673488 AGCAAAAATA
9673498 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
9673539 AGGGAGGGGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:9673943 original size:23 final size:23
Alignment explanation
Indices: 9673917--9673973 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
9673907 TTTTGATGCT
*
9673917 TTTTTTTATTGTTTTAGTTGTTG
1 TTTTTTTATTGTTTTAGTTGTTA
** *
9673940 TTTTCGTATTGTTTTTGTTGTTA
1 TTTTTTTATTGTTTTAGTTGTTA
9673963 TTTTTGTTATT
1 TTTTT-TTATT
9673974 TTTAATGTTG
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 23 0.85
24 4 0.15
ACGTcount: A:0.09, C:0.02, G:0.16, T:0.74
Consensus pattern (23 bp):
TTTTTTTATTGTTTTAGTTGTTA
Found at i:9673966 original size:12 final size:12
Alignment explanation
Indices: 9673951--9674027 Score: 81
Period size: 12 Copynumber: 6.8 Consensus size: 12
9673941 TTTCGTATTG
9673951 TTTTTGTTGTTA
1 TTTTTGTTGTTA
9673963 --TTT-TTGTTA
1 TTTTTGTTGTTA
**
9673972 TTTTTAATGTT-
1 TTTTTGTTGTTA
*
9673983 GTTTTGTTGTTA
1 TTTTTGTTGTTA
*
9673995 TTTTTGTTGCTA
1 TTTTTGTTGTTA
*
9674007 TTTTGGTTGTTA
1 TTTTTGTTGTTA
9674019 TTTTTGTTG
1 TTTTTGTTG
9674028 CTTGGATGTT
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
9 6 0.12
10 3 0.06
11 11 0.21
12 32 0.62
ACGTcount: A:0.09, C:0.01, G:0.18, T:0.71
Consensus pattern (12 bp):
TTTTTGTTGTTA
Found at i:9674027 original size:44 final size:42
Alignment explanation
Indices: 9673850--9674043 Score: 106
Period size: 44 Copynumber: 4.4 Consensus size: 42
9673840 AATTATATTA
* * *
9673850 TTGTTTTG-GTTCTTTTT-TTACTATTTTGGTTGCTATTTTTG
1 TTGTTTTGTGTTATTTTTGTTGCTATTTTGGTTG-TTTTTTTG
* * * * ** *
9673891 GTGTTATT-TTTTACTATTTTGATGCTTTTTTTTATTGTTTTAGTTG
1 TTGTT-TTGTGTTA-T-TTTTGTTGC-TATTTTGGTTGTTTT-TTTG
* * * * * *
9673937 TTGTTTTCGTATTGTTTTTGTTGTTATTTTTGTTATTTTTAATG
1 TTGTTTT-GTGTTATTTTTGTTGCTATTTTGGTTGTTTTT-TTG
9673981 TTGTTTTGTTGTTATTTTTGTTGCTATTTTGGTTGTTATTTTTG
1 TTGTTTTG-TGTTATTTTTGTTGCTATTTTGGTTGTT-TTTTTG
* *
9674025 TTGCTTGGATGTTATTTTT
1 TTGTTTTG-TGTTATTTTT
9674044 TATGCGTTTT
Statistics
Matches: 112, Mismatches: 29, Indels: 21
0.69 0.18 0.13
Matches are distributed among these distances:
41 4 0.04
42 4 0.04
43 2 0.02
44 66 0.59
45 17 0.15
46 16 0.14
47 3 0.03
ACGTcount: A:0.10, C:0.04, G:0.18, T:0.69
Consensus pattern (42 bp):
TTGTTTTGTGTTATTTTTGTTGCTATTTTGGTTGTTTTTTTG
Found at i:9674037 original size:20 final size:21
Alignment explanation
Indices: 9673990--9674043 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 21
9673980 GTTGTTTTGT
*
9673990 TGTTATTTTTGTTGCTATTTTGGT
1 TGTTATTTTTGTTGC---TTTGGA
9674014 TGTTATTTTTGTTGC-TTGGA
1 TGTTATTTTTGTTGCTTTGGA
9674034 TGTTATTTTT
1 TGTTATTTTT
9674044 TATGCGTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 14 0.48
24 15 0.52
ACGTcount: A:0.09, C:0.04, G:0.20, T:0.67
Consensus pattern (21 bp):
TGTTATTTTTGTTGCTTTGGA
Found at i:9677090 original size:27 final size:27
Alignment explanation
Indices: 9677052--9677105 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
9677042 TAATCAATAG
9677052 TGAAATAGGAACGTGAAGGAAGGGTAA
1 TGAAATAGGAACGTGAAGGAAGGGTAA
9677079 TGAAATAGGAACGTGAAGGAAGGGTAA
1 TGAAATAGGAACGTGAAGGAAGGGTAA
9677106 ATTGTAACTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.04, G:0.37, T:0.15
Consensus pattern (27 bp):
TGAAATAGGAACGTGAAGGAAGGGTAA
Found at i:9678463 original size:17 final size:18
Alignment explanation
Indices: 9678428--9678464 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
9678418 AGAAATAAAA
*
9678428 TTATGGGTTTCACAAATT
1 TTATGGGTTTCAAAAATT
9678446 TTATGGGTTT-AAAAATT
1 TTATGGGTTTCAAAAATT
9678463 TT
1 TT
9678465 GCTTCAAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.49
Consensus pattern (18 bp):
TTATGGGTTTCAAAAATT
Found at i:9679797 original size:67 final size:67
Alignment explanation
Indices: 9679689--9679823 Score: 252
Period size: 67 Copynumber: 2.0 Consensus size: 67
9679679 GACACCATAA
* *
9679689 AAAAATTACCAATTTTAGAGTCCAAACAGTATGTTAAGCATTAAATTTATAACCCAATCTGAAAT
1 AAAAATTACCAATTTCAGAGGCCAAACAGTATGTTAAGCATTAAATTTATAACCCAATCTGAAAT
9679754 GC
66 GC
9679756 AAAAATTACCAATTTCAGAGGCCAAACAGTATGTTAAGCATTAAATTTATAACCCAATCTGAAAT
1 AAAAATTACCAATTTCAGAGGCCAAACAGTATGTTAAGCATTAAATTTATAACCCAATCTGAAAT
9679821 GC
66 GC
9679823 A
1 A
9679824 TTTTCACATT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.28
Consensus pattern (67 bp):
AAAAATTACCAATTTCAGAGGCCAAACAGTATGTTAAGCATTAAATTTATAACCCAATCTGAAAT
GC
Found at i:9681684 original size:6 final size:6
Alignment explanation
Indices: 9681673--9681735 Score: 126
Period size: 6 Copynumber: 10.5 Consensus size: 6
9681663 CCCCTGGGTG
9681673 GGGTAA GGGTAA GGGTAA GGGTAA GGGTAA GGGTAA GGGTAA GGGTAA
1 GGGTAA GGGTAA GGGTAA GGGTAA GGGTAA GGGTAA GGGTAA GGGTAA
9681721 GGGTAA GGGTAA GGG
1 GGGTAA GGGTAA GGG
9681736 GAGACGACAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 57 1.00
ACGTcount: A:0.32, C:0.00, G:0.52, T:0.16
Consensus pattern (6 bp):
GGGTAA
Found at i:9682584 original size:25 final size:27
Alignment explanation
Indices: 9682556--9682629 Score: 71
Period size: 31 Copynumber: 2.6 Consensus size: 27
9682546 AAAAACTTTC
9682556 AATAAATAAAAAAATAAA-ATTATTAA
1 AATAAATAAAAAAATAAATATTATTAA
*
9682582 ATATTAAAATAATATAAAATAAATATTTTTAA
1 A-A-T-AAATAA-A-AAAATAAATATTATTAA
*
9682614 AA-AAATTAAAAAATAA
1 AATAAATAAAAAAATAA
9682630 TATGAACGGG
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
26 8 0.20
27 2 0.05
28 6 0.15
29 6 0.15
30 1 0.03
31 9 0.22
32 8 0.20
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (27 bp):
AATAAATAAAAAAATAAATATTATTAA
Found at i:9692649 original size:17 final size:17
Alignment explanation
Indices: 9692627--9692660 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
9692617 ATTTAATGAG
9692627 GGTTTAAAGGAGTTAGA
1 GGTTTAAAGGAGTTAGA
9692644 GGTTTAAAGGAGTTAGA
1 GGTTTAAAGGAGTTAGA
9692661 CATCCACTTA
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:0.35, C:0.00, G:0.35, T:0.29
Consensus pattern (17 bp):
GGTTTAAAGGAGTTAGA
Found at i:9710305 original size:20 final size:20
Alignment explanation
Indices: 9710282--9710319 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
9710272 AAATACAATT
9710282 AATT-TTAAAAAATATATTAC
1 AATTATTAAAAAAT-TATTAC
*
9710302 AATTATTGAAAAATTATT
1 AATTATTAAAAAATTATT
9710320 TATATACTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (20 bp):
AATTATTAAAAAATTATTAC
Found at i:9711499 original size:22 final size:23
Alignment explanation
Indices: 9711463--9711519 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
9711453 TATTTAAATC
9711463 TTAATAATTAT-TTTAAAT-TAAA
1 TTAA-AATTATATTTAAATGTAAA
*
9711485 TTAAAATTATATTTAAATGTTAA
1 TTAAAATTATATTTAAATGTAAA
*
9711508 TTTAAA-TATATT
1 TTAAAATTATATT
9711520 ATAGGTTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 6 0.19
22 17 0.55
23 8 0.26
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
TTAAAATTATATTTAAATGTAAA
Found at i:9719101 original size:19 final size:19
Alignment explanation
Indices: 9719077--9719114 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
9719067 GAGGTCCATA
9719077 TAAAATATTTATTTTTAAG
1 TAAAATATTTATTTTTAAG
9719096 TAAAATATTTATTTTTAAG
1 TAAAATATTTATTTTTAAG
9719115 ATTAAAATAA
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:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (19 bp):
TAAAATATTTATTTTTAAG
Found at i:9729578 original size:16 final size:17
Alignment explanation
Indices: 9729559--9729592 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
9729549 AAGTTTTTTT
9729559 TTTAAAA-ACTCAATTA
1 TTTAAAACACTCAATTA
*
9729575 TTTAAAACACTCATTTA
1 TTTAAAACACTCAATTA
9729592 T
1 T
9729593 CCTCATCCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (17 bp):
TTTAAAACACTCAATTA
Found at i:9733473 original size:59 final size:57
Alignment explanation
Indices: 9733405--9733834 Score: 278
Period size: 59 Copynumber: 7.3 Consensus size: 57
9733395 CTCGAGGGCA
* * *
9733405 AAAAT-GTAATTTTGGGAAAATTTAGGGTTAAAAATGGGATTTTAGAAGATTCGAGGGT
1 AAAATGGTAATTTTGGGAAAATTCA-GGTTAAAAATGGAATTTTGGAAGATTCG-GGGT
* * *
9733463 AAAGTGGTAATTTTTGGTG-AAA-TCGAGGTTAAAAATGGGATTTTGGAA-AGTTTGAGGGT
1 AAAATGGTAA-TTTTGG-GAAAATTC-AGGTTAAAAATGGAATTTTGGAAGA-TTCG-GGGT
* * * ** * *
9733522 AAAATGGCAATTTT-TGATGAAA-TCAGGGTTAAAAATAGAATTTTATAAGGTTGGGGGGT
1 AAAATGGTAATTTTGGGA--AAATTCA-GGTTAAAAATGGAATTTTGGAAGATT-CGGGGT
* *
9733581 AAAATGGTAATTTTTGGTG-AAA-TCGAGGTT-AAAATGGAATTTTGGAAAGTTTAGGGGT
1 AAAATGGTAA-TTTTGG-GAAAATTC-AGGTTAAAAATGGAATTTTGG-AAGATTCGGGGT
* * *
9733639 AAAATGGTAATTTT-GGATGAAA-TCGAGGTTAAAAATGAAATTTTAGAAAATTCTGGGGT
1 AAAATGGTAATTTTGGGA--AAATTC-AGGTTAAAAATGGAATTTTGGAAGATTC-GGGGT
* * * *
9733698 AAATTGGTAATTTTTGGTG-AAA-TCAAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGCT
1 AAAATGGTAA-TTTTGG-GAAAATTC-AGGTTAAAAATGGAATTTTGG-AAGATTCGGGGT
* * *
9733757 AAAATGGTAATTTT-GGATGAAA-TCGGGGTTAAAAATGGAATTTTGGAAAATTTTGGGGT
1 AAAATGGTAATTTTGGGA--AAATTC-AGGTTAAAAATGGAATTTTGGAAGA-TTCGGGGT
*
9733816 AAAATGGTAATTTTTGGAA
1 AAAATGGTAATTTTGGGAA
9733835 GTTTTAAGGT
Statistics
Matches: 302, Mismatches: 40, Indels: 60
0.75 0.10 0.15
Matches are distributed among these distances:
55 1 0.00
56 3 0.01
57 5 0.02
58 59 0.20
59 203 0.67
60 27 0.09
61 2 0.01
62 2 0.01
ACGTcount: A:0.37, C:0.02, G:0.27, T:0.34
Consensus pattern (57 bp):
AAAATGGTAATTTTGGGAAAATTCAGGTTAAAAATGGAATTTTGGAAGATTCGGGGT
Found at i:9733581 original size:118 final size:117
Alignment explanation
Indices: 9733428--9733832 Score: 580
Period size: 118 Copynumber: 3.4 Consensus size: 117
9733418 GGGAAAATTT
* * * *
9733428 AGGGTTAAAAATGGGATTTTAGAAGATTCGAGGGTAAAGTGGTAATTTTTGGTGAAATCGAGGTT
1 AGGGTTAAAAATGGAATTTTAGAAAATTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTT
* * *
9733493 AAAAATGGGATTTTGGAAAGTTTGAGGGTAAAATGGCAATTTTTGATGAAATC
66 AAAAATGGAATTTTGGAAAGTTT-AGGGTAAAATGGTAATTTTGGATGAAATC
* * ** *
9733546 AGGGTTAAAAATAGAATTTTATAAGGTTGGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTT
1 AGGGTTAAAAATGGAATTTTAGAAAATTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTT
9733611 -AAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTGGATGAAATC
66 AAAAATGGAATTTTGGAAAGTTTA-GGGTAAAATGGTAATTTTGGATGAAATC
* * * *
9733663 -GAGGTTAAAAATGAAATTTTAGAAAATTCTGGGGTAAATTGGTAATTTTTGGTGAAATCAAGGT
1 AG-GGTTAAAAATGGAATTTTAGAAAATTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGT
9733727 TAAAAATGGAATTTTGGAAAGTTTAGGGCTAAAATGGTAATTTTGGATGAAATC
65 TAAAAATGGAATTTTGGAAAGTTTAGGG-TAAAATGGTAATTTTGGATGAAATC
* * **
9733781 GGGGTTAAAAATGGAATTTTGGAAAATTTTGGGGTAAAATGGTAATTTTTGG
1 AGGGTTAAAAATGGAATTTTAGAAAATTCGGGGGTAAAATGGTAATTTTTGG
9733833 AAGTTTTAAG
Statistics
Matches: 259, Mismatches: 23, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
116 2 0.01
117 104 0.40
118 152 0.59
119 1 0.00
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.34
Consensus pattern (117 bp):
AGGGTTAAAAATGGAATTTTAGAAAATTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTT
AAAAATGGAATTTTGGAAAGTTTAGGGTAAAATGGTAATTTTGGATGAAATC
Found at i:9733671 original size:176 final size:176
Alignment explanation
Indices: 9733430--9733829 Score: 520
Period size: 176 Copynumber: 2.3 Consensus size: 176
9733420 GAAAATTTAG
* * * * *
9733430 GGTTAAAAATGGGATTTTAGAAGA-TTCGAGGGTAAAGTGGTAATTTTTGGTGAAATCGAGGTTA
1 GGTTAAAAATGGAATTTTGGAAAATTTAG-GGGTAAAATGGTAA-TTTTGGTGAAATCGAGGTTA
** * * *
9733494 AAAATGGGATTTTGGAAAGTT-TGAGGGTAAAATGGCAATTTTTGATGAAATCAGGGTTAAAAAT
64 AAAATGAAATTTTAGAAAATTCTG-GGGTAAAATGGCAATTTTTGATGAAATCAAGGTTAAAAAT
* * * *
9733558 AGAATTTTATAAGGTTGGGGGGTAAAATGGTAATTTTTGG-TGAAATCGA
128 AGAATTTTAGAAAGTTGAGGGCTAAAATGGTAA-TTTTGGATGAAATCGA
*
9733607 GGTT-AAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTGGATGAAATCGAGGTTAA
1 GGTTAAAAATGGAATTTTGGAAAATTTAGGGGTAAAATGGTAATTTTGG-TGAAATCGAGGTTAA
* * * *
9733671 AAATGAAATTTTAGAAAATTCTGGGGTAAATTGGTAATTTTTGGTGAAATCAAGGTTAAAAATGG
65 AAATGAAATTTTAGAAAATTCTGGGGTAAAATGGCAATTTTTGATGAAATCAAGGTTAAAAATAG
* * *
9733736 AATTTTGGAAAGTTTAGGGCTAAAATGGTAATTTTGGATGAAATCGG
130 AATTTTAGAAAGTTGAGGGCTAAAATGGTAATTTTGGATGAAATCGA
*
9733783 GGTTAAAAATGGAATTTTGGAAAATTTTGGGGTAAAATGGTAATTTT
1 GGTTAAAAATGGAATTTTGGAAAATTTAGGGGTAAAATGGTAATTTT
9733830 TGGAAGTTTT
Statistics
Matches: 194, Mismatches: 24, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
175 12 0.06
176 133 0.69
177 49 0.25
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.34
Consensus pattern (176 bp):
GGTTAAAAATGGAATTTTGGAAAATTTAGGGGTAAAATGGTAATTTTGGTGAAATCGAGGTTAAA
AATGAAATTTTAGAAAATTCTGGGGTAAAATGGCAATTTTTGATGAAATCAAGGTTAAAAATAGA
ATTTTAGAAAGTTGAGGGCTAAAATGGTAATTTTGGATGAAATCGA
Found at i:9733839 original size:29 final size:29
Alignment explanation
Indices: 9733727--9733898 Score: 95
Period size: 29 Copynumber: 5.8 Consensus size: 29
9733717 AAATCAAGGT
* *
9733727 TAAAAATGG-AATTTTGGAAAGTTTAGGGC
1 TAAAAATGGTAATTTTGG-AAGTTTTGGGG
* ** *
9733756 T-AAAATGGTAATTTTGGATGAAATCGGGG
1 TAAAAATGGTAATTTTGGAAG-TTTTGGGG
*
9733785 TTAAAAATGG-AATTTTGGAAAATTTTGGGG
1 -TAAAAATGGTAATTTTGG-AAGTTTTGGGG
**
9733815 T-AAAATGGTAATTTTTGGAAGTTTTAAGG
1 TAAAAATGGTAA-TTTTGGAAGTTTTGGGG
* ** *
9733844 TCAAAA-CATAATTTTTTGAAGTTTTGGGG
1 TAAAAATGGTAA-TTTTGGAAGTTTTGGGG
*
9733873 TCAAAAAT-ATAATTTTTGGATAGTTT
1 T-AAAAATGGTAA-TTTTGGA-AGTTT
9733899 AAGGACTTGT
Statistics
Matches: 112, Mismatches: 20, Indels: 20
0.74 0.13 0.13
Matches are distributed among these distances:
28 16 0.14
29 44 0.39
30 39 0.35
31 13 0.12
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (29 bp):
TAAAAATGGTAATTTTGGAAGTTTTGGGG
Found at i:9733860 original size:30 final size:30
Alignment explanation
Indices: 9733823--9733902 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 30
9733813 GGTAAAATGG
*
9733823 TAATTTTTGGAAGTTTTAAGGTC-AAAACA
1 TAATTTTTGGAAGTTTTAAGGTCAAAAATA
* **
9733852 TAATTTTTTGAAGTTTTGGGGTCAAAAATA
1 TAATTTTTGGAAGTTTTAAGGTCAAAAATA
9733882 TAATTTTTGGATAG-TTTAAGG
1 TAATTTTTGGA-AGTTTTAAGG
9733903 ACTTGTAAGC
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 20 0.48
30 20 0.48
31 2 0.05
ACGTcount: A:0.34, C:0.04, G:0.20, T:0.42
Consensus pattern (30 bp):
TAATTTTTGGAAGTTTTAAGGTCAAAAATA
Found at i:9734756 original size:22 final size:21
Alignment explanation
Indices: 9734731--9734773 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
9734721 TATTATTCTT
*
9734731 AAAATTAATTAATATCATTTAA
1 AAAATCAATTAATA-CATTTAA
9734753 AAAATCAATTAATACATTTAA
1 AAAATCAATTAATACATTTAA
9734774 TATATATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAATCAATTAATACATTTAA
Found at i:9735526 original size:18 final size:18
Alignment explanation
Indices: 9735503--9735537 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
9735493 TGAGCCTATA
9735503 TTTTGTAATTGAACTTTC
1 TTTTGTAATTGAACTTTC
*
9735521 TTTTGTAATTGGACTTT
1 TTTTGTAATTGAACTTT
9735538 TTAATTTATA
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:0.20, C:0.09, G:0.14, T:0.57
Consensus pattern (18 bp):
TTTTGTAATTGAACTTTC
Found at i:9743723 original size:4 final size:4
Alignment explanation
Indices: 9743707--9743786 Score: 65
Period size: 4 Copynumber: 19.2 Consensus size: 4
9743697 TAAATAAAAA
* *
9743707 AAAG -AAG AGAAG AAAG AAAG AAAAG AAAG AAAA AGAAT AAA- AAAG AAAG
1 AAAG AAAG A-AAG AAAG AAAG -AAAG AAAG AAAG A-AAG AAAG AAAG AAAG
* *
9743756 AAAAG AAAG AAAAG AAAA AAAG AAAA AAAG A
1 -AAAG AAAG -AAAG AAAG AAAG AAAG AAAG A
9743787 GGAAAAAAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
3 6 0.10
4 38 0.60
5 19 0.30
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (4 bp):
AAAG
Found at i:9743779 original size:13 final size:13
Alignment explanation
Indices: 9743703--9743781 Score: 74
Period size: 14 Copynumber: 5.9 Consensus size: 13
9743693 AAAATAAATA
*
9743703 AAAAAAAGAAGAG
1 AAAAAAAGAAAAG
*
9743716 -AAGAAAG-AAAG
1 AAAAAAAGAAAAG
9743727 AAAAGAAAGAAAAAG
1 AAAA-AAAG-AAAAG
9743742 AATAAAAA-AGAAAG
1 AA-AAAAAGA-AAAG
9743756 AAAAGAAAGAAAAG
1 AAAA-AAAGAAAAG
9743770 AAAAAAAGAAAA
1 AAAAAAAGAAAA
9743782 AAAGAGGAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
11 3 0.05
12 8 0.15
13 15 0.27
14 17 0.31
15 10 0.18
16 2 0.04
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (13 bp):
AAAAAAAGAAAAG
Found at i:9743785 original size:54 final size:52
Alignment explanation
Indices: 9743702--9743836 Score: 152
Period size: 54 Copynumber: 2.6 Consensus size: 52
9743692 AAAAATAAAT
* *
9743702 AAAAAAAAG-AAGAGAAGAAAGAAAGAAAAGAAA-GAAAAAGAATAAAAAA-G
1 AAAAAAAAGAAAGAAAAGAAAAAAAGAAAAGAAAGGAAAAA-AATAAAAAAGG
* *
9743752 AAAGAAAAGAAAGAAAAGAAAAAAAGAAAAAAAGAGGAAAAAAATAGAAAAAGG
1 AAAAAAAAGAAAGAAAAGAAAAAAAGAAAAGAA-AGGAAAAAAATA-AAAAAGG
* *
9743806 AAAAAAATAGAAA-AAAGGAGAAAAAGAAAAG
1 AAAAAAA-AGAAAGAAAAGAAAAAAAGAAAAG
9743837 GAGAGGTCAA
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
50 8 0.11
51 20 0.28
52 5 0.07
53 11 0.15
54 22 0.31
55 5 0.07
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (52 bp):
AAAAAAAAGAAAGAAAAGAAAAAAAGAAAAGAAAGGAAAAAAATAAAAAAGG
Found at i:9743819 original size:10 final size:9
Alignment explanation
Indices: 9743689--9743821 Score: 115
Period size: 9 Copynumber: 14.0 Consensus size: 9
9743679 GGATTCAATG
9743689 AAGAAAAATA
1 AAGAAAAA-A
*
9743699 AATAAAAAA
1 AAGAAAAAA
9743708 AAGAAGAGAAGA
1 AAGAA-A-AA-A
*
9743720 AAGAAAGAA
1 AAGAAAAAA
9743729 AAGAAAGAAA
1 AAGAAA-AAA
9743739 AAGAATAAAA
1 AAGAA-AAAA
*
9743749 AAGAAAGAA
1 AAGAAAAAA
*
9743758 AAGAAAGAA
1 AAGAAAAAA
9743767 AAG-AAAAA
1 AAGAAAAAA
9743775 AAGAAAAAA
1 AAGAAAAAA
*
9743784 AGAGGAAAAA
1 A-AGAAAAAA
* *
9743794 AATAGAAAA
1 AAGAAAAAA
*
9743803 AGGAAAAAA
1 AAGAAAAAA
9743812 ATAGAAAAAA
1 A-AGAAAAAA
9743822 GGAGAAAAAG
Statistics
Matches: 101, Mismatches: 14, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
8 7 0.07
9 45 0.45
10 39 0.39
11 4 0.04
12 6 0.06
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:9743842 original size:54 final size:52
Alignment explanation
Indices: 9743689--9743842 Score: 147
Period size: 54 Copynumber: 2.9 Consensus size: 52
9743679 GGATTCAATG
* * * *
9743689 AAGAA-AAATAAATAAAAAAAAG-AAGAGAAGAAAGAAAGAAAAGA-AAGAAA
1 AAGAATAAA-AAAGAAAAAAAAGAAAGAAAAGAAAAAAAGAAAAGAGAGGAAA
* *
9743739 AAGAATAAAAAAGAAAGAAAAGAAAGAAAAGAAAAAAAGAAAAAAAGAGGAAA
1 AAGAATAAAAAAGAAAAAAAAGAAAGAAAAGAAAAAAAG-AAAAGAGAGGAAA
* *
9743792 AA-AATAGAAAAAGGAAAAAAATAGAAA-AAAGGAGAAAAAGAAAAGGAGAGG
1 AAGAATA-AAAAA-GAAAAAAA-AGAAAGAAAAGAAAAAAAGAAAA-GAGAGG
9743843 TCAAGGTGAA
Statistics
Matches: 86, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
50 16 0.19
51 17 0.20
52 9 0.10
53 16 0.19
54 23 0.27
55 5 0.06
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (52 bp):
AAGAATAAAAAAGAAAAAAAAGAAAGAAAAGAAAAAAAGAAAAGAGAGGAAA
Found at i:9744972 original size:50 final size:50
Alignment explanation
Indices: 9744758--9744961 Score: 234
Period size: 50 Copynumber: 4.1 Consensus size: 50
9744748 GAAAAACATG
* * *
9744758 AAGATGTGAAGGGAAAGGTTGAGGCCGCAACGACGAACCCGGTACCATGA
1 AAGATGTGAAGGGAAAGGTTGAGGCCGCAACGACAAACCCGGTACCTTAA
* * * * * *
9744808 AA-ATTTGAAGGG-AAGGATTGAGGACGCGACGACAAATCTGGTACCTTAG
1 AAGATGTGAAGGGAAAGG-TTGAGGCCGCAACGACAAACCCGGTACCTTAA
* * *
9744857 AAGATGTGATGGGAAAGGTTGAGACCGCAACGGCAAACCCGGTACC-TAA
1 AAGATGTGAAGGGAAAGGTTGAGGCCGCAACGACAAACCCGGTACCTTAA
* * *
9744906 GAAGAGGTGAAGGGAAAAGTTGAGGCCGCAACGATAAACCCGGTACCTTAA
1 -AAGATGTGAAGGGAAAGGTTGAGGCCGCAACGACAAACCCGGTACCTTAA
9744957 AAGAT
1 AAGAT
9744962 ATTATGGGAA
Statistics
Matches: 124, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
48 4 0.03
49 37 0.30
50 76 0.61
51 7 0.06
ACGTcount: A:0.36, C:0.18, G:0.31, T:0.15
Consensus pattern (50 bp):
AAGATGTGAAGGGAAAGGTTGAGGCCGCAACGACAAACCCGGTACCTTAA
Found at i:9745348 original size:78 final size:78
Alignment explanation
Indices: 9745239--9745461 Score: 297
Period size: 78 Copynumber: 2.9 Consensus size: 78
9745229 GAAGATTTCG
* * * *
9745239 ATCTTTTACCCTGACCATGGGGCAGATCACAGTCAACCAATCTCTTACCCTAAGCCTAAGGCTGA
1 ATCTTTTACCCCGAGCATGGGGCAGATCACAGTCAACCAATCTCTTACCCTAAGCCTAGGGCAGA
9745304 TTGCAGCCATCCA
66 TTGCAGCCATCCA
* ** * * *
9745317 ATCTTTTGCCCCGAGTTTGGGGTAGATCACAGT-AAGCCAATCTCTTACCCCAAGCCTGGGGCAG
1 ATCTTTTACCCCGAGCATGGGGCAGATCACAGTCAA-CCAATCTCTTACCCTAAGCCTAGGGCAG
*
9745381 ATTGCAGCCATCCG
65 ATTGCAGCCATCCA
* *
9745395 ATCTTTTACCCCGAGCATGAGGCAGATCACCA-TCAACCAATCTCTTACCCTGAGCCTAGGGCAG
1 ATCTTTTACCCCGAGCATGGGGCAGATCA-CAGTCAACCAATCTCTTACCCTAAGCCTAGGGCAG
9745459 ATT
65 ATT
9745462 ACAGTTATCC
Statistics
Matches: 123, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
77 2 0.02
78 117 0.95
79 4 0.03
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (78 bp):
ATCTTTTACCCCGAGCATGGGGCAGATCACAGTCAACCAATCTCTTACCCTAAGCCTAGGGCAGA
TTGCAGCCATCCA
Found at i:9745404 original size:39 final size:39
Alignment explanation
Indices: 9745239--9745465 Score: 143
Period size: 39 Copynumber: 5.8 Consensus size: 39
9745229 GAAGATTTCG
* * *
9745239 ATCTTTTACCCTGA-CCATGGGGCAGATCACAGTCAACCA
1 ATCTTTTACCCCGAGCC-TGGGGCAGATCACAGCCATCCA
* ** ** * **
9745278 ATCTCTTACCCTAAGCCTAAGGCTGATTGCAGCCATCCA
1 ATCTTTTACCCCGAGCCTGGGGCAGATCACAGCCATCCA
* ** * ** *
9745317 ATCTTTTGCCCCGAGTTTGGGGTAGATCACAGTAAGCCA
1 ATCTTTTACCCCGAGCCTGGGGCAGATCACAGCCATCCA
* * ** *
9745356 ATCTCTTACCCCAAGCCTGGGGCAGATTGCAGCCATCCG
1 ATCTTTTACCCCGAGCCTGGGGCAGATCACAGCCATCCA
* * * *
9745395 ATCTTTTACCCCGAGCATGAGGCAGATCACCA-TCAACCA
1 ATCTTTTACCCCGAGCCTGGGGCAGATCA-CAGCCATCCA
* * * *
9745434 ATCTCTTACCCTGAGCCTAGGGCAGATTACAG
1 ATCTTTTACCCCGAGCCTGGGGCAGATCACAG
9745466 TTATCCAAAA
Statistics
Matches: 134, Mismatches: 51, Indels: 6
0.70 0.27 0.03
Matches are distributed among these distances:
38 2 0.01
39 128 0.96
40 4 0.03
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.24
Consensus pattern (39 bp):
ATCTTTTACCCCGAGCCTGGGGCAGATCACAGCCATCCA
Found at i:9745832 original size:209 final size:209
Alignment explanation
Indices: 9745483--9746989 Score: 2250
Period size: 209 Copynumber: 7.2 Consensus size: 209
9745473 AAACAACGAG
* * * *
9745483 GCGGTCATCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAAGCTCTATGTGA
1 GCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAGCC-AAGCTCAAAGTGA
* ** * *
9745548 GCAAATCTTCGAACCCCAGCTTTCTGACAAGATACTGAGAAGTAGGTCAAAGCAATAAAATGGTT
65 GCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTT
* *
9745613 AGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCATCTTCCTGATGAGATATAAAGAAGCGG
130 AGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCGG
9745678 ATTAAAACAAGTGAT
195 ATTAAAACAAGTGAT
* *
9745693 GCGGTCATCTTTCTGATGAGATACTGAGAAGAAGGCCAAATCAATGAAGCCAAGCTCAAAGTGAG
1 GCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAGCCAAGCTCAAAGTGAG
* *
9745758 CAAATCTTCGAACCCCAGCTTCCTGATGAGATATTGGGAAGCAGGTCGAAGCAATAAAATGGTTA
66 CAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTA
* * *
9745823 GCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTTCTGATGATATACAGAGAAGCGGA
131 GCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCGGA
*
9745888 TTAAAATAAGTGAT
196 TTAAAACAAGTGAT
* *
9745902 GCGGTCATCTTCTTGATGAGATACTGAGAAGAAG---AAATCAATGAAGCCAAGCTCAGAGTGAG
1 GCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAGCCAAGCTCAAAGTGAG
* * *
9745964 CAAATCATCGAACCCCAGCTTCCTGATGAGATACTGAGAATCAGGTTGAAGCAATAAAATGGTTA
66 CAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTA
* * *
9746029 GCTTTCTGATGAGATACTGAGAAGTGGACCAAATTCATCTTCCTGATGAGATATAAAGAAGCGGA
131 GCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCGGA
*
9746094 TTAGAACAAGTGAT
196 TTAAAACAAGTGAT
* * *
9746108 ACGGTCATCTTTCTGATGAGATACTGAGAAGAAGACCAAATCAACG-AGCCAAGCTCAAAGTGAG
1 GCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAGCCAAGCTCAAAGTGAG
* *
9746172 CAAATCTTCGAACCCCAACTTCCTGATGAGATATTGAGAAGCAGGTCGAAGCAATAAAATGGTTA
66 CAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTA
* * *
9746237 GCTTCCTGATGAGATACTGAGAAGTGGACCAAAATCGTCTTTCTGATGATATACAAAGAAGCGGA
131 GCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCGGA
*
9746302 TTAAAATAAGTGAT
196 TTAAAACAAGTGAT
* *
9746316 GCGGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAAATCAATGAAGCCAAGCTCAGAGTGAG
1 GCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAGCCAAGCTCAAAGTGAG
* * *
9746381 CAAATCATCGAACCCCAGCTTCCTGATGAGATACTAAGAAGCAGGTCAAAGCAATAAAATGGTTA
66 CAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTA
* * *
9746446 GCTTCCTGATGAGGTACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGA
131 GCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCGGA
9746511 TTAAAACAAGTGAT
196 TTAAAACAAGTGAT
* *
9746525 GCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAGGCAAGCTCAAAGTGTG
1 GCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAGCCAAGCTCAAAGTGAG
* * *
9746590 CAAATCTTCGAACCCTAGCTTCCTGATGAGATATTAAGAAGCAGGTCGAAGCAATAAAATGGTTA
66 CAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTA
** * *
9746655 GCTTCCTGATGAGATACTGAGAAGTAAACCAAATTCGTCTTCCTGGTGAGATACAGAGAAGCGGA
131 GCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCGGA
*
9746720 TTGAAACAAGTGAT
196 TTAAAACAAGTGAT
* * * * *
9746734 ACAGTCATCTTTCTGATGAGGTACTGAGAAGAAGACCAAATCAATGAAGCCAGGCTCAAAGTGAG
1 GCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAGCCAAGCTCAAAGTGAG
* * **
9746799 CGAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGTAGGTCGAAGCAATAAAGCGGTTA
66 CAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTA
* * * * * * * * * *
9746864 TCTTCCTGATGATATACAGAGAAGTGAACCAGATCCGTCTTCTTAATGAGACACAGAA-AAGTGG
131 GCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACA-AAGAAGCGG
*
9746928 ATCAAAACAAGTGAT
195 ATTAAAACAAGTGAT
* * * *
9746943 GCAGTTATCTTCCTGATGAGACACTGAGAAGTAGACCAAATCAATGA
1 GCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGA
9746990 CACCAAACCA
Statistics
Matches: 1174, Mismatches: 118, Indels: 11
0.90 0.09 0.01
Matches are distributed among these distances:
206 189 0.16
208 190 0.16
209 747 0.64
210 48 0.04
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (209 bp):
GCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAATGAAGCCAAGCTCAAAGTGAG
CAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTA
GCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAAAGAAGCGGA
TTAAAACAAGTGAT
Found at i:9747311 original size:17 final size:17
Alignment explanation
Indices: 9747288--9747412 Score: 160
Period size: 17 Copynumber: 7.3 Consensus size: 17
9747278 AACCCATTTT
*
9747288 TTTAAATTTATTTTAAG
1 TTTAAATTTATTTTAAA
*
9747305 GTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
9747322 TTTAAATTTATTTTAAT
1 TTTAAATTTATTTTAAA
*
9747339 TTTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
* *
9747356 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
*
9747373 TTTAAATTTATCTATAAA
1 TTTAAATTTAT-TTTAAA
* *
9747391 TTTAAAATTATTCTAAA
1 TTTAAATTTATTTTAAA
9747408 TTTAA
1 TTTAA
9747413 TTAATAATGT
Statistics
Matches: 93, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
17 79 0.85
18 14 0.15
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:9747325 original size:6 final size:6
Alignment explanation
Indices: 9747288--9747396 Score: 75
Period size: 6 Copynumber: 19.0 Consensus size: 6
9747278 AACCCATTTT
* * * * *
9747288 TTTAAA TTT-AT TTTAAG GTTAAA TTT-AT TTTAAA TTTAAA TTT-AT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* ** *
9747333 TTTAAT TTTAAA TTT-GT TTTAAA TTTAAA TTT-AA TTTAAG TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
** *
9747379 TTTATC TATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
9747397 ATTATTCTAA
Statistics
Matches: 77, Mismatches: 21, Indels: 10
0.71 0.19 0.09
Matches are distributed among these distances:
5 20 0.26
6 57 0.74
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:9747503 original size:26 final size:26
Alignment explanation
Indices: 9747471--9747522 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
9747461 AGCCCAATTA
* *
9747471 CAAACAGGCCTAAATAGCCCAAACAC
1 CAAACAGGCCCAAATAGCCAAAACAC
*
9747497 CAAACAGGCCCAAATGGCCAAAACAC
1 CAAACAGGCCCAAATAGCCAAAACAC
9747523 TATAATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.46, C:0.35, G:0.13, T:0.06
Consensus pattern (26 bp):
CAAACAGGCCCAAATAGCCAAAACAC
Found at i:9754088 original size:22 final size:22
Alignment explanation
Indices: 9754040--9754081 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
9754030 ACAGTGCCGT
*
9754040 GACACCCACTTCCCAATGTCGC
1 GACATCCACTTCCCAATGTCGC
*
9754062 GACATCCATTTCCCAATGTC
1 GACATCCACTTCCCAATGTC
9754082 AGGACATTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.40, G:0.12, T:0.24
Consensus pattern (22 bp):
GACATCCACTTCCCAATGTCGC
Found at i:9755218 original size:22 final size:22
Alignment explanation
Indices: 9755193--9755235 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
9755183 TTGGATTTAA
*
9755193 ATAAATA-TTTTAAAATAATTAG
1 ATAAATAGATTTAAAA-AATTAG
9755215 ATAAATAGATTTAAAAAATTA
1 ATAAATAGATTTAAAAAATTA
9755236 ATGTTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (22 bp):
ATAAATAGATTTAAAAAATTAG
Found at i:9763998 original size:97 final size:98
Alignment explanation
Indices: 9763780--9764342 Score: 640
Period size: 99 Copynumber: 5.8 Consensus size: 98
9763770 CTCAGTACAT
** ** *
9763780 CGAAGAA-ACAAGGGAAAGGTTTAAGTCGTAATGGAAAACCTAGTACCTCGGAGACATGAAGGGA
1 CGAAGAACACAAGGGAAAGGTTTAAGTCACAATGGCGAACCTAGTACCTCAGAGACATGAAGGGA
* * * *
9763844 AAGA-TTAAGCCGCAATGACGGATCCAGTACCA
66 AAGATTTAAGCCGCAACGGCGAATCCAGTACCG
*
9763876 CGAA-AACACAAGGGAAAGGTTTAAGTCACAATGGCGAACCTAGTACCTCAGAGACATGAA-GAA
1 CGAAGAACACAAGGGAAAGGTTTAAGTCACAATGGCGAACCTAGTACCTCAGAGACATGAAGGGA
* ** *
9763939 AAGGATTTAAGTCGCAACGGTAAATCCAGTACCA
66 AA-GATTTAAGCCGCAACGGCGAATCCAGTACCG
* * *
9763973 CGAAG-ACGCAAGGGAAAGGTTTAAGTCACAACGACGAACCTAGTACCTCAGAGACATGAAGGGA
1 CGAAGAACACAAGGGAAAGGTTTAAGTCACAATGGCGAACCTAGTACCTCAGAGACATGAAGGGA
* * * *
9764037 AAGATCTAAGCCACAATGGCGGATCCAGTACCG
66 AAGATTTAAGCCGCAACGGCGAATCCAGTACCG
* * ** * * * *
9764070 CAAAGATACAAAAGGGAAAGGTTTAAGTTGCAACGACGAACCTATTACCTCAGTGACATGAAGGG
1 CGAAGA-ACACAAGGGAAAGGTTTAAGTCACAATGGCGAACCTAGTACCTCAGAGACATGAAGGG
*
9764135 AAAGATTTAAGCCGCAACGGCGAATCCAATACCG
65 AAAGATTTAAGCCGCAACGGCGAATCCAGTACCG
* * * *
9764169 CAAAGATACAAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTCCCTCAGAGACATGAAGGG
1 CGAAGA-ACACAAGGGAAAGGTTTAAGTCACAATGGCGAACCTAGTACCTCAGAGACATGAAGGG
* *
9764234 AAAGATTTAGGCCGCAACGGCAAATCCAGTACCG
65 AAAGATTTAAGCCGCAACGGCGAATCCAGTACCG
* * * * *
9764268 CGAAGATAC-GAAGGGAAAAGTTTAAGTCACAATGGCAAACCTCA-TACCTCA-AAAGCATGAAA
1 CGAAGA-ACACAAGGGAAAGGTTTAAGTCACAATGGCGAACCT-AGTACCTCAGAGA-CATGAAG
9764330 GGAAA-ATTTAAGC
63 GGAAAGATTTAAGC
9764343 TACAATGGTG
Statistics
Matches: 404, Mismatches: 54, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
95 6 0.01
96 54 0.13
97 114 0.28
98 50 0.12
99 180 0.45
ACGTcount: A:0.40, C:0.20, G:0.25, T:0.16
Consensus pattern (98 bp):
CGAAGAACACAAGGGAAAGGTTTAAGTCACAATGGCGAACCTAGTACCTCAGAGACATGAAGGGA
AAGATTTAAGCCGCAACGGCGAATCCAGTACCG
Found at i:9764052 original size:49 final size:49
Alignment explanation
Indices: 9763789--9764341 Score: 325
Period size: 49 Copynumber: 11.3 Consensus size: 49
9763779 TCGAAGAAAC
* * * ** *
9763789 AAGGGAAAGGTTTAAGTCGTAATGGAAAACCTAGTACCTCGGAGACATG
1 AAGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACCTCAGAGACATG
* * * * * * *
9763838 AAGGGAAAGA-TTAAGCCGCAATGACGGATCC-AGTACCAC-GAAAACA-C
1 AAGGGAAAGATTTAAGTCGCAACGGC-GAACCTAGTACCTCAG-AGACATG
* * *
9763885 AAGGGAAAGGTTTAAGTCACAATGGCGAACCTAGTACCTCAGAGACATG
1 AAGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACCTCAGAGACATG
* ** *
9763934 AA-GAAAAGGATTTAAGTCGCAACGGTAAATCC-AGTACCAC-GAAGAC--G
1 AAGGGAAA-GATTTAAGTCGCAACGGCGAA-CCTAGTACCTCAG-AGACATG
* * *
9763981 CAAGGGAAAGGTTTAAGTCACAACGACGAACCTAGTACCTCAGAGACATG
1 -AAGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACCTCAGAGACATG
* * * * * * * *
9764031 AAGGGAAAGATCTAAGCCACAATGGCGGATCC-AGTACCGCAAAGATACA-A
1 AAGGGAAAGATTTAAGTCGCAACGGC-GAACCTAGTACCTC--AGAGACATG
* * * * *
9764081 AAGGGAAAGGTTTAAGTTGCAACGACGAACCTATTACCTCAGTGACATG
1 AAGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACCTCAGAGACATG
* * * * *
9764130 AAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AATACCGCAAAGATACA-A
1 AAGGGAAAGATTTAAGTCGCAACGGCGAA-CCTAGTACCTC--AGAGACATG
* * *
9764180 AAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTCCCTCAGAGACATG
1 AAGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACCTCAGAGACATG
* * * * * *
9764229 AAGGGAAAGATTTAGGCCGCAACGGCAAATCC-AGTACCGC-GAAGATACG
1 AAGGGAAAGATTTAAGTCGCAACGGCGAA-CCTAGTACCTCAG-AGACATG
* * * *
9764278 AAGGGAAA-AGTTTAAGTCACAATGGCAAACCTCA-TACCTCA-AAAGCATG
1 AAGGGAAAGA-TTTAAGTCGCAACGGCGAACCT-AGTACCTCAGAGA-CATG
*
9764327 AAAGGAAA-ATTTAAG
1 AAGGGAAAGATTTAAG
9764342 CTACAATGGT
Statistics
Matches: 383, Mismatches: 89, Indels: 65
0.71 0.17 0.12
Matches are distributed among these distances:
47 17 0.04
48 102 0.27
49 185 0.48
50 68 0.18
51 11 0.03
ACGTcount: A:0.40, C:0.20, G:0.25, T:0.16
Consensus pattern (49 bp):
AAGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACCTCAGAGACATG
Found at i:9765780 original size:29 final size:28
Alignment explanation
Indices: 9765702--9765781 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 28
9765692 TTTTCGAAGG
*
9765702 TTCGAGGGTAAAATGGTAATTTTGGTAA
1 TTCGAGGGTAAAATGGTAATTTTAGTAA
* * * *
9765730 ATCAAGGTTTAAAAAGG-AATTTTAAAG-AA
1 TTCGAGG-GTAAAATGGTAATTTT--AGTAA
9765759 TTCGAGGGTAAAATGGTAATTTT
1 TTCGAGGGTAAAATGGTAATTTT
9765782 TGGTGAAATT
Statistics
Matches: 39, Mismatches: 9, Indels: 7
0.71 0.16 0.13
Matches are distributed among these distances:
28 18 0.46
29 20 0.51
30 1 0.03
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.34
Consensus pattern (28 bp):
TTCGAGGGTAAAATGGTAATTTTAGTAA
Found at i:9765811 original size:30 final size:30
Alignment explanation
Indices: 9765777--9765870 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
9765767 TAAAATGGTA
9765777 ATTTTTGGTGAAATTAGGGTTAAAAATGAG
1 ATTTTTGGTGAAATTAGGGTTAAAAATGAG
*
9765807 A-TTTT-G-GAAAGTTTAGGGGT-AAAATG-G
1 ATTTTTGGTGAAA--TTAGGGTTAAAAATGAG
*
9765834 TAATTTTTGATGAAATTAGGGTTAAAAATGAG
1 --ATTTTTGGTGAAATTAGGGTTAAAAATGAG
9765866 ATTTT
1 ATTTT
9765871 AGAAAGTTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 18
0.71 0.04 0.25
Matches are distributed among these distances:
27 5 0.10
28 7 0.13
29 12 0.23
30 17 0.33
31 6 0.12
32 5 0.10
ACGTcount: A:0.36, C:0.00, G:0.26, T:0.38
Consensus pattern (30 bp):
ATTTTTGGTGAAATTAGGGTTAAAAATGAG
Found at i:9765838 original size:59 final size:59
Alignment explanation
Indices: 9765679--9766192 Score: 578
Period size: 59 Copynumber: 8.8 Consensus size: 59
9765669 GAAAATTCAA
* * *
9765679 GGTT-AAAATGGGATTTTCG-AAGGTTCGAGGGTAAAATGGTAA-TTTTGGT-AAATCAAG
1 GGTTAAAAATGAGATTTTGGAAAGTTTCG-GGGTAAAATGGTAATTTTTGGTGAAATC-AG
* * * *
9765736 GTTTAAAAAGGA-ATTTT--AAAGAATTCGAGGGTAAAATGGTAATTTTTGGTGAAATTAG
1 GGTTAAAAATGAGATTTTGGAAAG-TTTCG-GGGTAAAATGGTAATTTTTGGTGAAATCAG
* * *
9765794 GGTTAAAAATGAGATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGATGAAATTAG
1 GGTTAAAAATGAGATTTTGGAAAGTTTCGGGGTAAAATGGTAATTTTTGGTGAAATCAG
* * *
9765853 GGTTAAAAATGAGATTTTAGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATCGG
1 GGTTAAAAATGAGATTTTGGAAAGTTTCGGGGTAAAATGGTAATTTTTGGTGAAATCAG
* * ** *
9765912 GGTT-AAAATGGGATTTTAGAAAGTTTAAGGGTAAAAATGGTAATTTTTGGTGAAATCGG
1 GGTTAAAAATGAGATTTTGGAAAGTTTCGGGGT-AAAATGGTAATTTTTGGTGAAATCAG
*
9765971 GGTTAAAAATGGGATTTTGGAAAG-TTCGAGGGTAAAATGGTAATTTTTGGTGAAATC-G
1 GGTTAAAAATGAGATTTTGGAAAGTTTCG-GGGTAAAATGGTAATTTTTGGTGAAATCAG
* * * *
9766029 GAGTT-AAAATG-GAATTTTGGAAAGTTTGGGGGTAAAATGGCAATTTTTGGTAAAATCGG
1 G-GTTAAAAATGAG-ATTTTGGAAAGTTTCGGGGTAAAATGGTAATTTTTGGTGAAATCAG
*
9766088 GGTTAAAAAT-AGGATTTTGGAAAG-TTCGGGGATAAAATGGTAA-TTTTGGTGAAATCAA
1 GGTTAAAAATGA-GATTTTGGAAAGTTTCGGGG-TAAAATGGTAATTTTTGGTGAAATCAG
9766146 GGTTAAAAATG-GAATTTTGG-AAG-TTCGAGGGTAAAATGGTAATTTTT
1 GGTTAAAAATGAG-ATTTTGGAAAGTTTCG-GGGTAAAATGGTAATTTTT
9766193 AGAAGTTTCA
Statistics
Matches: 407, Mismatches: 27, Indels: 45
0.85 0.06 0.09
Matches are distributed among these distances:
56 3 0.01
57 47 0.12
58 140 0.34
59 187 0.46
60 26 0.06
61 4 0.01
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (59 bp):
GGTTAAAAATGAGATTTTGGAAAGTTTCGGGGTAAAATGGTAATTTTTGGTGAAATCAG
Found at i:9766216 original size:29 final size:29
Alignment explanation
Indices: 9766142--9766250 Score: 116
Period size: 29 Copynumber: 3.8 Consensus size: 29
9766132 TTTGGTGAAA
* *
9766142 TCAAGGTTAAAAATGGAA-TTTTGGAAG-T
1 TCAAGGTT-AAAATGTAATTTTTAGAAGTT
* *
9766170 TCGAGGGTAAAATGGTAATTTTTAGAAGTT
1 TCAAGGTTAAAAT-GTAATTTTTAGAAGTT
9766200 TCAAGGTTAAAATGTAATTTTCTA-AAGTT
1 TCAAGGTTAAAATGTAATTTT-TAGAAGTT
* *
9766229 TTAGGGTTAAAATGTAATTTTT
1 TCAAGGTTAAAATGTAATTTTT
9766251 GAATAGTTTA
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
27 5 0.07
28 10 0.14
29 40 0.58
30 14 0.20
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.39
Consensus pattern (29 bp):
TCAAGGTTAAAATGTAATTTTTAGAAGTT
Found at i:9766260 original size:29 final size:27
Alignment explanation
Indices: 9766146--9766263 Score: 103
Period size: 29 Copynumber: 4.1 Consensus size: 27
9766136 GTGAAATCAA
* ** *
9766146 GGTTAAAAATGGAATTTTGGAAGTTCGAG
1 GGTT-AAAATGTAATTTTTAAAGTT-TAG
*
9766175 GG-TAAAATGGTAATTTTTAGAAGTTTCAA
1 GGTTAAAAT-GTAATTTTTA-AAGTTT-AG
9766204 GGTTAAAATGTAATTTTCTAAAGTTTTAG
1 GGTTAAAATGTAATTTT-TAAAG-TTTAG
9766233 GGTTAAAATGTAATTTTTGAATAGTTTAG
1 GGTTAAAATGTAATTTTT-AA-AGTTTAG
9766262 GG
1 GG
9766264 ACCTATAAGT
Statistics
Matches: 75, Mismatches: 6, Indels: 16
0.77 0.06 0.16
Matches are distributed among these distances:
27 5 0.07
28 9 0.12
29 48 0.64
30 13 0.17
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.39
Consensus pattern (27 bp):
GGTTAAAATGTAATTTTTAAAGTTTAG
Found at i:9767474 original size:3 final size:3
Alignment explanation
Indices: 9767427--9767456 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
9767417 AAAATAATGT
9767427 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
9767457 AAACCACACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:9767867 original size:26 final size:26
Alignment explanation
Indices: 9767838--9767930 Score: 89
Period size: 26 Copynumber: 3.4 Consensus size: 26
9767828 TTTCTCGGAA
9767838 AGGGTTTGTATATTGATTTCAAGAGC
1 AGGGTTTGTATATTGATTTCAAGAGC
** *
9767864 AGGGTTTGTAACTTGAATTGATTTCTCG-GAA
1 AGGGTTTGT-A--T--ATTGATTTCAAGAG-C
*
9767895 AGGGTTTGTATATTGATTTCAAGAAC
1 AGGGTTTGTATATTGATTTCAAGAGC
9767921 AGGGTTTGTA
1 AGGGTTTGTA
9767931 ACCCTTTACA
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
26 29 0.55
27 1 0.02
28 1 0.02
29 1 0.02
30 2 0.04
31 19 0.36
ACGTcount: A:0.27, C:0.08, G:0.27, T:0.39
Consensus pattern (26 bp):
AGGGTTTGTATATTGATTTCAAGAGC
Found at i:9767897 original size:57 final size:57
Alignment explanation
Indices: 9767810--9767932 Score: 230
Period size: 57 Copynumber: 2.2 Consensus size: 57
9767800 TACTTCCAGA
*
9767810 GGTTTGTAA-TTGAATTGATTTCTCGGAAAGGGTTTGTATATTGATTTCAAGAGCAG
1 GGTTTGTAACTTGAATTGATTTCTCGGAAAGGGTTTGTATATTGATTTCAAGAACAG
9767866 GGTTTGTAACTTGAATTGATTTCTCGGAAAGGGTTTGTATATTGATTTCAAGAACAG
1 GGTTTGTAACTTGAATTGATTTCTCGGAAAGGGTTTGTATATTGATTTCAAGAACAG
9767923 GGTTTGTAAC
1 GGTTTGTAAC
9767933 CCTTTACAAT
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
56 9 0.14
57 56 0.86
ACGTcount: A:0.27, C:0.08, G:0.26, T:0.39
Consensus pattern (57 bp):
GGTTTGTAACTTGAATTGATTTCTCGGAAAGGGTTTGTATATTGATTTCAAGAACAG
Found at i:9768297 original size:6 final size:6
Alignment explanation
Indices: 9768275--9768307 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
9768265 TCTTTTGGAC
9768275 TTTTAA -TTTAA -TTTAA TTTTAA TTTTAA TTTTA
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTA
9768308 TAATAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.38
6 16 0.62
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTTAA
Found at i:9768318 original size:17 final size:17
Alignment explanation
Indices: 9768279--9768326 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
9768269 TTGGACTTTT
* **
9768279 AATTTAATTTAATTTTA
1 AATTTAATTTTATAATA
*
9768296 ATTTTAATTTTATAATA
1 AATTTAATTTTATAATA
9768313 AATTTAAATTTTAT
1 AATTT-AATTTTAT
9768327 GCAAATTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 17 0.68
18 8 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
AATTTAATTTTATAATA
Found at i:9768349 original size:17 final size:18
Alignment explanation
Indices: 9768329--9768369 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
9768319 AATTTTATGC
9768329 AAATTTAAATTCAAAA-T
1 AAATTTAAATTCAAAACT
* *
9768346 AAATCT-AATTTAAAACT
1 AAATTTAAATTCAAAACT
9768363 AAATTTA
1 AAATTTA
9768370 TATCCCATTG
Statistics
Matches: 19, Mismatches: 3, Indels: 3
0.76 0.12 0.12
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (18 bp):
AAATTTAAATTCAAAACT
Found at i:9768795 original size:18 final size:17
Alignment explanation
Indices: 9768754--9768882 Score: 163
Period size: 17 Copynumber: 7.4 Consensus size: 17
9768744 CTAAACCCGT
9768754 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
9768772 -TTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
9768788 TTTTAAA-TTATTTTTAAA
1 -TTTAAATTTA-TTTTAAA
9768806 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
* *
9768824 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
*
9768841 TTTAAATTTAAATTTAAA
1 TTTAAATTT-ATTTTAAA
*
9768859 TTTAAATTTATTGTAAA
1 TTTAAATTTATTTTAAA
9768876 TTTAAAT
1 TTTAAAT
9768883 GAATAAAAGC
Statistics
Matches: 101, Mismatches: 5, Indels: 11
0.86 0.04 0.09
Matches are distributed among these distances:
16 1 0.01
17 51 0.50
18 49 0.49
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:9768811 original size:6 final size:6
Alignment explanation
Indices: 9768754--9768882 Score: 119
Period size: 6 Copynumber: 22.2 Consensus size: 6
9768744 CTAAACCCGT
* * **
9768754 TTTAAA TTT-AT TTTAAGA -TTAAA TTT-AT TTTAAA TTTTAAA -TTATT
1 TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA -TTTAAA TTTAAA
** *
9768800 TTTAAA TTTAAA TTTATT TTTAAA TTTAAA TTT-AA TTTAAG TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
9768847 TTTAAA TTTAAA TTTAAA TTT--A TTGTAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA T
9768883 GAATAAAAGC
Statistics
Matches: 99, Mismatches: 14, Indels: 20
0.74 0.11 0.15
Matches are distributed among these distances:
4 3 0.03
5 18 0.18
6 69 0.70
7 9 0.09
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:9768880 original size:35 final size:35
Alignment explanation
Indices: 9768754--9768882 Score: 165
Period size: 35 Copynumber: 3.7 Consensus size: 35
9768744 CTAAACCCGT
9768754 TTTAAATTTATTTTAAGA-TTAAATTT-ATTTTAAA
1 TTTAAATTTATTTTAA-ATTTAAATTTAATTTTAAA
*
9768788 TTTTAAA-TTATTTTTAAATTTAAATTTATTTTTAAA
1 -TTTAAATTTA-TTTTAAATTTAAATTTAATTTTAAA
* * *
9768824 TTTAAATTTAATTTAAGTTTAAATTTAAATTTAAA
1 TTTAAATTTATTTTAAATTTAAATTTAATTTTAAA
*
9768859 TTTAAATTTATTGTAAATTTAAAT
1 TTTAAATTTATTTTAAATTTAAAT
9768883 GAATAAAAGC
Statistics
Matches: 82, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
34 4 0.05
35 68 0.83
36 10 0.12
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (35 bp):
TTTAAATTTATTTTAAATTTAAATTTAATTTTAAA
Found at i:9769582 original size:3 final size:3
Alignment explanation
Indices: 9769574--9769632 Score: 64
Period size: 3 Copynumber: 19.0 Consensus size: 3
9769564 AATAGGGCAC
* * **
9769574 TAA TAA TAA TAAA TAA TAT TAA TAA CAA TAA TAA TAA TAA TTT TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
9769620 TAA TAAA TAA TAA
1 TAA T-AA TAA TAA
9769633 AGAAATCTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
3 40 0.87
4 6 0.13
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:9770688 original size:29 final size:29
Alignment explanation
Indices: 9770656--9771079 Score: 156
Period size: 29 Copynumber: 14.6 Consensus size: 29
9770646 AAACTATCCA
9770656 AAAATTACATTTTTACCCTCGAATTTTCC
1 AAAATTACATTTTTACCCTCGAATTTTCC
** * *
9770685 AAAATT-CTATTTTTAATCTTGATTTTTTTCC
1 AAAATTAC-ATTTTTACCCTCGA--ATTTTCC
* * *
9770716 AAAAATTATA-TTTTACCCCCGAACTTTCC
1 -AAAATTACATTTTTACCCTCGAATTTTCC
* * * **
9770745 AAAATTCCATTTATGA-CCTCGATTTTTGG
1 AAAATTACATTT-TTACCCTCGAATTTTCC
* *
9770774 AAAATTACCA-TTTTACCC-CAAACTTTCC
1 AAAATTA-CATTTTTACCCTCGAATTTTCC
* * *
9770802 AAAATTCCAGTTTTGA-CCTC-AATTTTTTCA
1 AAAATTACA-TTTTTACCCTCGAA--TTTTCC
* * * * *
9770832 AAAATTATATTTTTACCCCCAAACTTTCT
1 AAAATTACATTTTTACCCTCGAATTTTCC
*
9770861 AAAATTTCATTTTTGA-CCTCG-ATTTTCC
1 AAAATTACATTTTT-ACCCTCGAATTTTCC
**
9770889 AAAAATTACATTTTTACCCT--AAACTTCC
1 -AAAATTACATTTTTACCCTCGAATTTTCC
* *
9770917 AAAATTCCATTTTGACCCT--AATTTTTCC
1 AAAATTACATTTTTACCCTCGAA-TTTTCC
* **
9770945 AAAAATTACCA-TTTTACCC-CTAAACTTCC
1 -AAAATTA-CATTTTTACCCTCGAATTTTCC
*
9770974 AAAAATTCCATTTTTGACCC-CG-ATTCTTCC
1 -AAAATTACATTTTT-ACCCTCGAATT-TTCC
* * *
9771004 AAAAAGTACCA-TTTTACCGC-CGAA-TGTCTA
1 -AAAATTA-CATTTTTACC-CTCGAATTTTC-C
* *
9771034 AAAATTCCATTTTGACCCT--AATTTTCC
1 AAAATTACATTTTTACCCTCGAATTTTCC
9771061 TAAAATTACCA-TTTTACCC
1 -AAAATTA-CATTTTTACCC
9771080 CCAAGTGACC
Statistics
Matches: 290, Mismatches: 68, Indels: 75
0.67 0.16 0.17
Matches are distributed among these distances:
27 23 0.08
28 61 0.21
29 134 0.46
30 46 0.16
31 19 0.07
32 7 0.02
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.39
Consensus pattern (29 bp):
AAAATTACATTTTTACCCTCGAATTTTCC
Found at i:9770805 original size:57 final size:56
Alignment explanation
Indices: 9770710--9771103 Score: 363
Period size: 57 Copynumber: 6.9 Consensus size: 56
9770700 ATCTTGATTT
* * *
9770710 TTTTCCAAAAATTA-TATTTTACCCCCGAACTTTCCAAAATTCCATTTATGACCTCGA
1 TTTTCCAAAAATTACCATTTTA-CCCCAAACTTTCCAAAATTCCATTT-TGACCTCAA
***
9770767 TTTTTGGAAAATTACCATTTTACCCCAAACTTTCCAAAATTCCAGTTTTGACCTCAA
1 TTTTCCAAAAATTACCATTTTACCCCAAACTTTCCAAAATTCCA-TTTTGACCTCAA
* * * * *
9770824 TTTTTTCAAAAATTA-TATTTTTACCCCCAAACTTTCTAAAATTTCATTTTTGACCTCGA
1 -TTTTCCAAAAATTACCA-TTTTA-CCCCAAACTTTCCAAAATTCCA-TTTTGACCTCAA
*
9770883 TTTTCCAAAAATTA-CATTTTTACCCTAAAC-TTCCAAAATTCCATTTTGACC-CTAA
1 TTTTCCAAAAATTACCA-TTTTACCCCAAACTTTCCAAAATTCCATTTTGACCTC-AA
* *
9770938 TTTTTCCAAAAATTACCATTTTACCCCTAAAC-TTCCAAAAATTCCATTTTTGACCCCGA
1 -TTTTCCAAAAATTACCATTTTACCCC-AAACTTTCC-AAAATTCCA-TTTTGACCTCAA
* * * *
9770997 TTCTTCCAAAAAGTACCATTTTACCGCCGAA-TGTCTAAAAATTCCATTTTGACC-CTAA
1 TT-TTCCAAAAATTACCATTTTACC-CCAAACTTTC-CAAAATTCCATTTTGACCTC-AA
* * * **
9771055 TTTTCCTAAAATTACCATTTTACCCCCAAGTGACCAAAATTACCATTTT
1 TTTTCCAAAAATTACCATTTTACCCCAAACTTTCCAAAATT-CCATTTT
9771104 ACCCCCGGGT
Statistics
Matches: 287, Mismatches: 31, Indels: 38
0.81 0.09 0.11
Matches are distributed among these distances:
54 1 0.00
55 9 0.03
56 43 0.15
57 89 0.31
58 68 0.24
59 74 0.26
60 3 0.01
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (56 bp):
TTTTCCAAAAATTACCATTTTACCCCAAACTTTCCAAAATTCCATTTTGACCTCAA
Found at i:9771078 original size:116 final size:112
Alignment explanation
Indices: 9770709--9771083 Score: 443
Period size: 116 Copynumber: 3.3 Consensus size: 112
9770699 AATCTTGATT
* * * ***
9770709 TTTTTCCAAAAATTATATTTTACCCCCGAACTTTCCAAAATTCCATTTATGACCTCGATTTTTGG
1 TTTTTCCAAAAATTACATTTTACCCCCAAAC-TTCCAAAATTCCATTTTTGACCTCGATTTTCCA
9770774 AAAATTACCATTTTACCCCAAACTTTCCAAAATTCCAGTTTTGA-CCTCAA
65 AAAATTACCATTTTACCCCAAAC-TTCCAAAATTCCA-TTTTGACCCT-AA
* * * *
9770824 TTTTTTCAAAAATTATATTTTTACCCCCAAACTTTCTAAAATTTCATTTTTGACCTCGATTTTCC
1 TTTTTCCAAAAATTACA-TTTTACCCCCAAAC-TTCCAAAATTCCATTTTTGACCTCGATTTTCC
*
9770889 AAAAATTA-CATTTTTACCCTAAACTTCCAAAATTCCATTTTGACCCTAA
64 AAAAATTACCA-TTTTACCCCAAACTTCCAAAATTCCATTTTGACCCTAA
* *
9770938 TTTTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATTCCATTTTTGACCCCGATTCTTC
1 TTTTTCCAAAAATTA-CATTTTACCCCCAAACTTCC-AAAATTCCATTTTTGACCTCGATT-TTC
* * *
9771003 CAAAAAGTACCATTTTACCGCCGAA-TGTCTAAAAATTCCATTTTGACCCTAA
63 CAAAAATTACCATTTTACC-CCAAACT-TC-CAAAATTCCATTTTGACCCTAA
*
9771055 -TTTTCCTAAAATTACCATTTTACCCCCAA
1 TTTTTCCAAAAATTA-CATTTTACCCCCAA
9771084 GTGACCAAAA
Statistics
Matches: 229, Mismatches: 21, Indels: 19
0.85 0.08 0.07
Matches are distributed among these distances:
113 3 0.01
114 57 0.25
115 54 0.24
116 94 0.41
117 21 0.09
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.38
Consensus pattern (112 bp):
TTTTTCCAAAAATTACATTTTACCCCCAAACTTCCAAAATTCCATTTTTGACCTCGATTTTCCAA
AAATTACCATTTTACCCCAAACTTCCAAAATTCCATTTTGACCCTAA
Found at i:9772315 original size:31 final size:31
Alignment explanation
Indices: 9772279--9772337 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
9772269 TCTAAAATTA
*
9772279 AAAATTAAAAAATCTCTTAAACTTTATTTTT
1 AAAATTAAAAAATATCTTAAACTTTATTTTT
*
9772310 AAAATTAAAAAATATTTTAAACTTTATT
1 AAAATTAAAAAATATCTTAAACTTTATT
9772338 ATAATAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (31 bp):
AAAATTAAAAAATATCTTAAACTTTATTTTT
Found at i:9773385 original size:25 final size:25
Alignment explanation
Indices: 9773337--9773385 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
9773327 GCCCTGATTC
**
9773337 GAATAAAATTATAATTTTACTATAA
1 GAATAAAATTATAATTAAACTATAA
* *
9773362 GAATAAAATTATAGTTAAATTATA
1 GAATAAAATTATAATTAAACTATA
9773386 GGTTTTCTGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (25 bp):
GAATAAAATTATAATTAAACTATAA
Found at i:9780897 original size:22 final size:22
Alignment explanation
Indices: 9780870--9780911 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
9780860 GAAAAACTAT
9780870 TGAAATTAGAGATGAATAATGA
1 TGAAATTAGAGATGAATAATGA
*
9780892 TGAAATTATAGATGAATAAT
1 TGAAATTAGAGATGAATAAT
9780912 CTAATGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (22 bp):
TGAAATTAGAGATGAATAATGA
Found at i:9781163 original size:68 final size:68
Alignment explanation
Indices: 9781054--9781191 Score: 231
Period size: 68 Copynumber: 2.0 Consensus size: 68
9781044 TCTCTAAAGA
*
9781054 TACTATTTAATGCTATCAAAGATTCTCAGCACTCCCCCTCAAGTTGATACATAGATGTCTCGCAT
1 TACTATTTAATGCTATCAAAGATTCTCAACACTCCCCCTCAAGTTGATACATAGATGTCTCGCAT
9781119 GCC
66 GCC
* * * *
9781122 TACTATTTAATGTTATCAAAGATTGTCAACACTTCCCCTCAAGTTGATGCATAGATGTCTCGCAT
1 TACTATTTAATGCTATCAAAGATTCTCAACACTCCCCCTCAAGTTGATACATAGATGTCTCGCAT
9781187 GCC
66 GCC
9781190 TA
1 TA
9781192 ACTTGCAAAG
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 65 1.00
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (68 bp):
TACTATTTAATGCTATCAAAGATTCTCAACACTCCCCCTCAAGTTGATACATAGATGTCTCGCAT
GCC
Found at i:9782807 original size:22 final size:22
Alignment explanation
Indices: 9782782--9782823 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
9782772 GAAAAACTAT
9782782 TGAAATTAGAGATGAATAATGA
1 TGAAATTAGAGATGAATAATGA
*
9782804 TGAAATTATAGATGAATAAT
1 TGAAATTAGAGATGAATAAT
9782824 TTAATGCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (22 bp):
TGAAATTAGAGATGAATAATGA
Found at i:9783858 original size:14 final size:14
Alignment explanation
Indices: 9783839--9783865 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9783829 CACAATTAGA
9783839 ACAAAAAAACATCC
1 ACAAAAAAACATCC
9783853 ACAAAAAAACATC
1 ACAAAAAAACATC
9783866 AAATAGATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.26, G:0.00, T:0.07
Consensus pattern (14 bp):
ACAAAAAAACATCC
Found at i:9784250 original size:22 final size:22
Alignment explanation
Indices: 9784220--9784263 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
9784210 GCTTTGATAC
* *
9784220 CATGTTGAAATTAGAGATGAAT
1 CATGATGAAATTACAGATGAAT
9784242 CATGATGAAATTACAGATGAAT
1 CATGATGAAATTACAGATGAAT
9784264 ACTCTAATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (22 bp):
CATGATGAAATTACAGATGAAT
Found at i:9784842 original size:14 final size:14
Alignment explanation
Indices: 9784823--9784850 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
9784813 ATTTAGGTGC
9784823 AAATCCTTTGAAGA
1 AAATCCTTTGAAGA
9784837 AAATCCTTTGAAGA
1 AAATCCTTTGAAGA
9784851 TGTTTAGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (14 bp):
AAATCCTTTGAAGA
Found at i:9785510 original size:20 final size:23
Alignment explanation
Indices: 9785485--9785537 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 23
9785475 TTAAAAAGTT
*
9785485 AAAAATTAAA-ATT-AGTTAA-A
1 AAAAATTAAAGATTAAATTAACA
9785505 AAAAA-TAAAGATTAAATTAACA
1 AAAAATTAAAGATTAAATTAACA
9785527 AAAAATATAAA
1 AAAAAT-TAAA
9785538 TACTAAAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 4 0.15
20 8 0.30
21 5 0.19
22 6 0.22
24 4 0.15
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.25
Consensus pattern (23 bp):
AAAAATTAAAGATTAAATTAACA
Found at i:9787839 original size:27 final size:27
Alignment explanation
Indices: 9787809--9787868 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
9787799 CTATTAATTC
*
9787809 TCATAAATATTAAAAAAAAACCTAAAA
1 TCATAAATATTAAAAAAAAACATAAAA
* *
9787836 TCATAAATATTAAAAAAATACATATAA
1 TCATAAATATTAAAAAAAAACATAAAA
9787863 TCATAA
1 TCATAA
9787869 TTTAACCTCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (27 bp):
TCATAAATATTAAAAAAAAACATAAAA
Found at i:9788378 original size:44 final size:46
Alignment explanation
Indices: 9788288--9788381 Score: 133
Period size: 44 Copynumber: 2.1 Consensus size: 46
9788278 ATAGAGCTGT
9788288 AATGGAATATGACTATAATCAGTAATTTAGTTGTTTGGTTGAATGG
1 AATGGAATATGACTATAATCAGTAATTTAGTTGTTTGGTTGAATGG
*
9788334 AATGGAATA-GAGCTATAAT-AGT-ATTCTTG-TGTTTGGTTGAATGG
1 AATGGAATATGA-CTATAATCAGTAATT-TAGTTGTTTGGTTGAATGG
9788378 AATG
1 AATG
9788382 ATGTTGTAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
44 22 0.49
45 7 0.16
46 16 0.36
ACGTcount: A:0.32, C:0.04, G:0.26, T:0.38
Consensus pattern (46 bp):
AATGGAATATGACTATAATCAGTAATTTAGTTGTTTGGTTGAATGG
Found at i:9788540 original size:58 final size:59
Alignment explanation
Indices: 9788478--9788628 Score: 198
Period size: 58 Copynumber: 2.6 Consensus size: 59
9788468 TTTTAATAAG
*
9788478 ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATTAT-ATTTTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAATGATTTTAACATA
* * * *
9788536 ATTATTATTAAATATAATTAAAT-AAAATAATATATAATTTAATAATGTTTTTAATATA
1 ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAATGATTTTAACATA
* * * *
9788594 TTTATTATTAAAATATAAATTAGTAAAAATTATAA
1 ATTATTATT-AAATATAATTTAATAAAAATAATAA
9788629 TATATAGTAT
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
57 21 0.27
58 39 0.49
59 11 0.14
60 8 0.10
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (59 bp):
ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAATGATTTTAACATA
Found at i:9788625 original size:25 final size:24
Alignment explanation
Indices: 9788597--9788647 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
9788587 TAATATATTT
9788597 ATTATTAAAATATA-AATTAGTAAAA
1 ATTA-TAAAATATAGAATTAG-AAAA
* *
9788622 ATTATAATATATAGTATTAGAAAA
1 ATTATAAAATATAGAATTAGAAAA
9788646 AT
1 AT
9788648 AATATATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (24 bp):
ATTATAAAATATAGAATTAGAAAA
Found at i:9798432 original size:2 final size:2
Alignment explanation
Indices: 9798427--9798452 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9798417 TTAAGAAATA
9798427 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
9798453 GACTCAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9800589 original size:21 final size:21
Alignment explanation
Indices: 9800565--9800618 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
9800555 AAATAACTGT
*
9800565 TTTAATAAAAAAAAATTTAAA
1 TTTAATAAAAAAAAATATAAA
* * *
9800586 TTTAATTATAAAATATATAAA
1 TTTAATAAAAAAAAATATAAA
9800607 TATTAAATAAAA
1 T-TT-AATAAAA
9800619 TAGTAAACTA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 18 0.72
22 2 0.08
23 5 0.20
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TTTAATAAAAAAAAATATAAA
Found at i:9801040 original size:18 final size:17
Alignment explanation
Indices: 9801009--9801120 Score: 134
Period size: 18 Copynumber: 6.4 Consensus size: 17
9800999 CTAAATCGAT
9801009 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
9801026 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
* *
9801044 TTAAAATTTGTTTTAAAA
1 TTTAAATTTATTTT-AAA
* *
9801062 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
*
9801079 TTCAAATTTATTTTTAAA
1 TTTAAATTTA-TTTTAAA
* *
9801097 TTTAAAGTTATTGTAAA
1 TTTAAATTTATTTTAAA
9801114 TTTAAAT
1 TTTAAAT
9801121 GAATAAAAGC
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
17 37 0.47
18 42 0.53
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Done.