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 19 of 163
Found at i:5354805 original size:86 final size:86
Alignment explanation
Indices: 5354667--5354861 Score: 302
Period size: 86 Copynumber: 2.3 Consensus size: 86
5354657 ATTTGGTATT
* * * * *
5354667 CTTCTCTATGTCTCATCAGGAAGATGACCGCCTCGCTTATTTTAATTTGCTTCTCTAGATCTCCT
1 CTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTATTTTAATTCGCTTCTCTAGATCTCCT
5354732 CAGGAAGACA-AATTTGGTCCA
66 CAGGAAGA-AGAATTTGGTCCA
* *
5354753 CTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTCGCTTCTCTGGATCTCCT
1 CTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTATTTTAATTCGCTTCTCTAGATCTCCT
*
5354818 CAGGAAGAAGAATTTGGTTCA
66 CAGGAAGAAGAATTTGGTCCA
5354839 CTTCTCTGTATCTCATCAGGAAG
1 CTTCTCTGTATCTCATCAGGAAG
5354862 CTAACCATTT
Statistics
Matches: 100, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
85 1 0.01
86 99 0.99
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (86 bp):
CTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTATTTTAATTCGCTTCTCTAGATCTCCT
CAGGAAGAAGAATTTGGTCCA
Found at i:5354998 original size:286 final size:286
Alignment explanation
Indices: 5354467--5355061 Score: 962
Period size: 286 Copynumber: 2.1 Consensus size: 286
5354457 AGTTGGTATT
* * *
5354467 CTTCTCTGTATCTCATCAGGAAGATGACCGCCTTGATTGTTTTAATTTGCTTCTCTGGATCTCCT
1 CTTCTCTGTATCTCATCAGGAAGATGACCGCCATCATTGTTTTAATTCGCTTCTCTGGATCTCCT
5354532 CAGGAAGACAAATTTGGTCCACTTCTCTATATCTCATCAAGAAACTAACCATGTTATTGTTTCGA
66 CAGGAAGACAAATTTGGTCCACTTCTCTATATCTCATCAAGAAACTAACCATGTTATTGTTTCGA
* *
5354597 CCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGCTTTGAGCGTTGATTTG
131 CCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTGGCTCGCTTTGAGCGTTGAATTG
* * * * * *
5354662 GTATTCTTCTCTATGTCTCATCAGGAAGATGACCGCCTCGCTTATTTTAATTTGCTTCTCTAGAT
196 GTATTCTTCTCTATATCTCATCAGGAAGATAACCACATCACTTATTTTAATTCGCTTCTCTAGAT
5354727 CTCCTCAGGAAGACAAATTTGGTCCA
261 CTCCTCAGGAAGACAAATTTGGTCCA
5354753 CTTCTCTGTATCTCATCAGGAAGATGACCG-CATCACTTGTTTTAATTCGCTTCTCTGGATCTCC
1 CTTCTCTGTATCTCATCAGGAAGATGACCGCCATCA-TTGTTTTAATTCGCTTCTCTGGATCTCC
* * * * *
5354817 TCAGGAAGA-AGAATTTGGTTCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTC
65 TCAGGAAGACA-AATTTGGTCCACTTCTCTATATCTCATCAAGAAACTAACCATGTTATTGTTTC
*
5354881 GACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTATGAAGATTGGCTCG-TGTTGAGCGTTGAA
129 GACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTGGCTCGCT-TTGAGCGTTGAA
* * *
5354945 TTGGTATTCTTCTCTGTATCTCATCAGGAAGATAACCACATCACTTGTTTTAATTCGCTTCTCTG
193 TTGGTATTCTTCTCTATATCTCATCAGGAAGATAACCACATCACTTATTTTAATTCGCTTCTCTA
5355010 GATCTCCTCAGGAAGACAAATTTGGTCCA
258 GATCTCCTCAGGAAGACAAATTTGGTCCA
5355039 CTTCTCTGTATCTCATCAGGAAG
1 CTTCTCTGTATCTCATCAGGAAG
5355062 CTAACCATTT
Statistics
Matches: 286, Mismatches: 20, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
285 5 0.02
286 281 0.98
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.36
Consensus pattern (286 bp):
CTTCTCTGTATCTCATCAGGAAGATGACCGCCATCATTGTTTTAATTCGCTTCTCTGGATCTCCT
CAGGAAGACAAATTTGGTCCACTTCTCTATATCTCATCAAGAAACTAACCATGTTATTGTTTCGA
CCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTGGCTCGCTTTGAGCGTTGAATTG
GTATTCTTCTCTATATCTCATCAGGAAGATAACCACATCACTTATTTTAATTCGCTTCTCTAGAT
CTCCTCAGGAAGACAAATTTGGTCCA
Found at i:5355000 original size:200 final size:200
Alignment explanation
Indices: 5354753--5355383 Score: 1102
Period size: 200 Copynumber: 3.2 Consensus size: 200
5354743 ATTTGGTCCA
* *
5354753 CTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATTCGCTTCTCTGGATCTCCT
1 CTTCTCTATATCTCATCAGGAAGATAACCGCATCACTTGTTTTAATTCGCTTCTCTGGATCTCCT
*
5354818 CAGGAAGAAGAATTTGGTTCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTCGA
66 CAGGAAGAAGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTCGA
*
5354883 CCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTATGAAGATTGGCTCGTGTTGAGCGTTGAATTG
131 CCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTGGCTCGTGTTGAGCGTTGAATTG
5354948 GTATT
196 GTATT
* *
5354953 CTTCTCTGTATCTCATCAGGAAGATAACCACATCACTTGTTTTAATTCGCTTCTCTGGATCTCCT
1 CTTCTCTATATCTCATCAGGAAGATAACCGCATCACTTGTTTTAATTCGCTTCTCTGGATCTCCT
5355018 CAGGAAGACA-AATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTCG
66 CAGGAAGA-AGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTCG
* *
5355082 ACTTGCTTCTCAGTGTCTCATCAGGAAGCTAGGTACGAAGATTGGCTCGTGTTGAGCGTTGAATT
130 ACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTGGCTCGTGTTGAGCGTTGAATT
5355147 GGTATT
195 GGTATT
* * *
5355153 CTTCTCTATATCTCATTAGGAAGATAACTGCATCACTTGTTTTAATTCGCTTCTCTGGATCTCCC
1 CTTCTCTATATCTCATCAGGAAGATAACCGCATCACTTGTTTTAATTCGCTTCTCTGGATCTCCT
* *
5355218 CAAGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTCGA
66 CAGGAAGAAGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTCGA
* *
5355283 CCTGCTTCTCAGTGTCTTATTAGGAAGCTGGGTACGAAGATTGGCTCGTGTTGAGCGTTGAATTG
131 CCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTGGCTCGTGTTGAGCGTTGAATTG
5355348 GTATT
196 GTATT
*
5355353 CTTCTCTATATCTCATCAGGAAGATGACCGC
1 CTTCTCTATATCTCATCAGGAAGATAACCGC
5355384 CTCGCTGTCT
Statistics
Matches: 409, Mismatches: 20, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
200 408 1.00
201 1 0.00
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.36
Consensus pattern (200 bp):
CTTCTCTATATCTCATCAGGAAGATAACCGCATCACTTGTTTTAATTCGCTTCTCTGGATCTCCT
CAGGAAGAAGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTCGA
CCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTGGCTCGTGTTGAGCGTTGAATTG
GTATT
Found at i:5355216 original size:486 final size:487
Alignment explanation
Indices: 5354278--5355261 Score: 1510
Period size: 486 Copynumber: 2.0 Consensus size: 487
5354268 TCCTTGTGTA
* *
5354278 TCATCAGGAAGATGACCGCAATCATCTGTTTTAATTCGCTTCTTTGGATCTCCTCAGGAAGACGA
1 TCATCAGGAAGATGACCGCAATCATCTGTTTTAATTCGCTTCTCTGGATCTCCTCAGGAAGAAGA
* * * *
5354343 ATTTGGTCCACTTCTCTGTGTCTTATCAGGAAGCTAACCTTTTTATTGCTTCAACCTGCTTCTTA
66 ATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCAACCTGCTTCTCA
* * * *
5354408 GTATCTCATCAAGAAGCTGGGTTCGAAGGTTTGCTCACATTGAGTGTTGAGTTGGTATTCTTCTC
131 GTATCTCATCAAGAAGCTGGGTTCGAAGATTGGCTCACATTGAGCGTTGAATTGGTATTCTTCTC
* * * * *
5354473 TGTATCTCATCAGGAAGATGACCGCCTTGATTGTTTTAATTTGCTTCTCTGGATCTCCTCAGGAA
196 TGTATCTCATCAGGAAGATAACCGACATCATTGTTTTAATTCGCTTCTCTGGATCTCCTCAGGAA
5354538 GACAAATTTGGTCCACTTCTCTATATCTCATCAAGAAACTAACCATGTTATTGTTTCGACCTGCT
261 GACAAATTTGGTCCACTTCTCTATATCTCATCAAGAAACTAACCATGTTATTGTTTCGACCTGCT
* * *
5354603 TCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGCTTTGAGCGTTGATTTGGTATTC
326 TCTCAGTGTCTCATCAGGAAGCTAGGTACGAAGATTGGCTCGCTTTGAGCGTTGAATTGGTATTC
* * * * * *
5354668 TTCTCTATGTCTCATCAGGAAGATGACCGCCTCGCTTATTTTAATTTGCTTCTCTAGATCTCCTC
391 TTCTCTATATCTCATCAGGAAGATAACCGCATCACTTATTTTAATTCGCTTCTCTAGATCTCCCC
*
5354733 AGGAAGACAAATTTGGTCCACTTCTCTGTATC
456 AAGAAGACAAATTTGGTCCACTTCTCTGTATC
5354765 TCATCAGGAAGATGACCGC-ATCA-CTTGTTTTAATTCGCTTCTCTGGATCTCCTCAGGAAGAAG
1 TCATCAGGAAGATGACCGCAATCATC-TGTTTTAATTCGCTTCTCTGGATCTCCTCAGGAAGAAG
* * *
5354828 AATTTGGTTCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTCGACCTGCTTCTC
65 AATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCAACCTGCTTCTC
* * ***
5354893 AGTGTCTCATCAGGAAGCTGGGTAT-GAAGATTGGCTCGTGTTGAGCGTTGAATTGGTATTCTTC
130 AGTATCTCATCAAGAAGCTGGGT-TCGAAGATTGGCTCACATTGAGCGTTGAATTGGTATTCTTC
5354957 TCTGTATCTCATCAGGAAGATAACC-ACATCACTTGTTTTAATTCGCTTCTCTGGATCTCCTCAG
194 TCTGTATCTCATCAGGAAGATAACCGACATCA-TTGTTTTAATTCGCTTCTCTGGATCTCCTCAG
* * * * *
5355021 GAAGACAAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTCGACTT
258 GAAGACAAATTTGGTCCACTTCTCTATATCTCATCAAGAAACTAACCATGTTATTGTTTCGACCT
5355086 GCTTCTCAGTGTCTCATCAGGAAGCTAGGTACGAAGATTGGCTCG-TGTTGAGCGTTGAATTGGT
323 GCTTCTCAGTGTCTCATCAGGAAGCTAGGTACGAAGATTGGCTCGCT-TTGAGCGTTGAATTGGT
* * * *
5355150 ATTCTTCTCTATATCTCATTAGGAAGATAACTGCATCACTTGTTTTAATTCGCTTCTCTGGATCT
387 ATTCTTCTCTATATCTCATCAGGAAGATAACCGCATCACTTATTTTAATTCGCTTCTCTAGATCT
*
5355215 CCCCAAGAAGACGAATTTGGTCCACTTCTCTGTATC
452 CCCCAAGAAGACAAATTTGGTCCACTTCTCTGTATC
5355251 TCATCAGGAAG
1 TCATCAGGAAG
5355262 CTAACCATTT
Statistics
Matches: 450, Mismatches: 43, Indels: 9
0.90 0.09 0.02
Matches are distributed among these distances:
485 5 0.01
486 425 0.94
487 20 0.04
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (487 bp):
TCATCAGGAAGATGACCGCAATCATCTGTTTTAATTCGCTTCTCTGGATCTCCTCAGGAAGAAGA
ATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCAACCTGCTTCTCA
GTATCTCATCAAGAAGCTGGGTTCGAAGATTGGCTCACATTGAGCGTTGAATTGGTATTCTTCTC
TGTATCTCATCAGGAAGATAACCGACATCATTGTTTTAATTCGCTTCTCTGGATCTCCTCAGGAA
GACAAATTTGGTCCACTTCTCTATATCTCATCAAGAAACTAACCATGTTATTGTTTCGACCTGCT
TCTCAGTGTCTCATCAGGAAGCTAGGTACGAAGATTGGCTCGCTTTGAGCGTTGAATTGGTATTC
TTCTCTATATCTCATCAGGAAGATAACCGCATCACTTATTTTAATTCGCTTCTCTAGATCTCCCC
AAGAAGACAAATTTGGTCCACTTCTCTGTATC
Found at i:5366374 original size:96 final size:96
Alignment explanation
Indices: 5366256--5366448 Score: 359
Period size: 96 Copynumber: 2.0 Consensus size: 96
5366246 GTGGAGTCGC
*
5366256 TAGCCGTCGAAATCACCTCGAAAATGGGGCTTCAAAAAATGATTTTAAAATTTGGAAAAAAGGGA
1 TAGCCGTCGAAATCACCTCGAAAACGGGGCTTCAAAAAATGATTTTAAAATTTGGAAAAAAGGGA
5366321 AAAAATGGGGGAGTCGCCACCAATCTTTTAT
66 AAAAATGGGGGAGTCGCCACCAATCTTTTAT
* *
5366352 TAGCTGTCGAAATCACCTCGAAAACGGGGCTTCGAAAAATGATTTTAAAATTTGGAAAAAAGGGA
1 TAGCCGTCGAAATCACCTCGAAAACGGGGCTTCAAAAAATGATTTTAAAATTTGGAAAAAAGGGA
5366417 AAAAATGGGGGAGTCGCCACCAATCTTTTAT
66 AAAAATGGGGGAGTCGCCACCAATCTTTTAT
5366448 T
1 T
5366449 TGGGTGTGAT
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
96 94 1.00
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (96 bp):
TAGCCGTCGAAATCACCTCGAAAACGGGGCTTCAAAAAATGATTTTAAAATTTGGAAAAAAGGGA
AAAAATGGGGGAGTCGCCACCAATCTTTTAT
Found at i:5367703 original size:30 final size:30
Alignment explanation
Indices: 5367670--5367772 Score: 115
Period size: 30 Copynumber: 3.4 Consensus size: 30
5367660 GTTTAAGGGT
5367670 AAAATGGTAATTTTTGGTGAAATCGGGGTTA
1 AAAATGG-AATTTTTGGTGAAATCGGGGTTA
* *
5367701 AAAATGGAA-TTTT-G-GAAAGTTTGGGGGT-
1 AAAATGGAATTTTTGGTGAAA--TCGGGGTTA
*
5367729 AAAATGGTAATTTTAGGTGAAATCGGGGTTA
1 AAAATGG-AATTTTTGGTGAAATCGGGGTTA
5367760 AAAATGGAATTTT
1 AAAATGGAATTTT
5367773 GGAAAGTTTG
Statistics
Matches: 60, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
27 4 0.07
28 8 0.13
29 12 0.20
30 17 0.28
31 15 0.25
32 4 0.07
ACGTcount: A:0.35, C:0.02, G:0.29, T:0.34
Consensus pattern (30 bp):
AAAATGGAATTTTTGGTGAAATCGGGGTTA
Found at i:5367782 original size:59 final size:58
Alignment explanation
Indices: 5367606--5367785 Score: 274
Period size: 59 Copynumber: 3.1 Consensus size: 58
5367596 TTTGGCTCTC
* *
5367606 GGGGGTGAAAAT-GTAATTTTGG-GAAATTCGAGGTTAAAAATAGAATTTTGGAAAGTTT
1 GGGGGT-AAAATGGTAATTTTGGTGAAA-TCGGGGTTAAAAATGGAATTTTGGAAAGTTT
**
5367664 AAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTT
1 GGGGGTAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTT
5367723 GGGGGTAAAATGGTAATTTTAGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTT
1 GGGGGTAAAATGGTAATTTT-GGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTT
5367782 GGGG
1 GGGG
5367786 ACTAGAGAGC
Statistics
Matches: 112, Mismatches: 6, Indels: 7
0.90 0.05 0.06
Matches are distributed among these distances:
57 5 0.04
58 12 0.11
59 91 0.81
60 4 0.04
ACGTcount: A:0.34, C:0.02, G:0.32, T:0.32
Consensus pattern (58 bp):
GGGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTT
Found at i:5367785 original size:29 final size:29
Alignment explanation
Indices: 5367604--5367774 Score: 131
Period size: 29 Copynumber: 5.8 Consensus size: 29
5367594 ATTTTGGCTC
* * *
5367604 TCGGGGGTGAAAATGTAATTTTGGGAAAT
1 TCGGGGTTAAAAATGGAATTTTGGGAAAT
* *
5367633 TCGAGGTTAAAAATAGAATTTT-GGAAAGTT
1 TCGGGGTTAAAAATGGAATTTTGGGAAA--T
**
5367663 TAAGGG-T-AAAATGGTAATTTTTGGTGAAA-
1 TCGGGGTTAAAAATGG-AA-TTTTGG-GAAAT
5367692 TCGGGGTTAAAAATGGAATTTT-GGAAAGT
1 TCGGGGTTAAAAATGGAATTTTGGGAAA-T
* *
5367721 TTGGGGGT-AAAATGGTAATTTTAGGTGAAA-
1 TCGGGGTTAAAAATGG-AATTTT-GG-GAAAT
5367751 TCGGGGTTAAAAATGGAATTTTGG
1 TCGGGGTTAAAAATGGAATTTTGG
5367775 AAAGTTTGGG
Statistics
Matches: 112, Mismatches: 15, Indels: 30
0.71 0.10 0.19
Matches are distributed among these distances:
27 4 0.04
28 19 0.17
29 42 0.38
30 23 0.21
31 16 0.14
32 8 0.07
ACGTcount: A:0.35, C:0.02, G:0.30, T:0.33
Consensus pattern (29 bp):
TCGGGGTTAAAAATGGAATTTTGGGAAAT
Found at i:5369611 original size:14 final size:13
Alignment explanation
Indices: 5369592--5369658 Score: 50
Period size: 13 Copynumber: 5.0 Consensus size: 13
5369582 TTGGGCCTAT
5369592 TTGGGCCATTGTAA
1 TTGGGCC-TTGTAA
*
5369606 TTGGGCCTT-CAA
1 TTGGGCCTTGTAA
5369618 TTTGGGCCTTTGT-A
1 -TTGGGCC-TTGTAA
*
5369632 TTGGGCCCT-TAA
1 TTGGGCCTTGTAA
5369644 TTTGGGCCTTTGTAA
1 -TTGGGCC-TTGTAA
5369659 ATAGACTTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
11 1 0.02
12 4 0.10
13 23 0.55
14 11 0.26
15 3 0.07
ACGTcount: A:0.15, C:0.18, G:0.27, T:0.40
Consensus pattern (13 bp):
TTGGGCCTTGTAA
Found at i:5369624 original size:13 final size:12
Alignment explanation
Indices: 5369606--5369653 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
5369596 GCCATTGTAA
5369606 TTGGGCCTTCAAT
1 TTGGGCCTT-AAT
**
5369619 TTGGGCCTTTGT
1 TTGGGCCTTAAT
5369631 ATTGGGCCCTTAAT
1 -TTGGG-CCTTAAT
5369645 TTGGGCCTT
1 TTGGGCCTT
5369654 TGTAAATAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
12 5 0.17
13 19 0.66
14 5 0.17
ACGTcount: A:0.10, C:0.21, G:0.27, T:0.42
Consensus pattern (12 bp):
TTGGGCCTTAAT
Found at i:5369625 original size:27 final size:27
Alignment explanation
Indices: 5369590--5369658 Score: 106
Period size: 26 Copynumber: 2.6 Consensus size: 27
5369580 CATTGGGCCT
*
5369590 ATTTGGGCCATTGTAATTGGG-CCTTCA
1 ATTTGGGCCTTTGTAATTGGGCCCTT-A
5369617 ATTTGGGCCTTTGT-ATTGGGCCCTTA
1 ATTTGGGCCTTTGTAATTGGGCCCTTA
5369643 ATTTGGGCCTTTGTAA
1 ATTTGGGCCTTTGTAA
5369659 ATAGACTTTG
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
26 21 0.54
27 18 0.46
ACGTcount: A:0.16, C:0.17, G:0.26, T:0.41
Consensus pattern (27 bp):
ATTTGGGCCTTTGTAATTGGGCCCTTA
Found at i:5369745 original size:17 final size:18
Alignment explanation
Indices: 5369723--5369763 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
5369713 TTTCAAATAT
*
5369723 TTTAAATTTAA-AATGAA
1 TTTAAATTTAATAATAAA
5369740 TTTAAATTTAATAATAAA
1 TTTAAATTTAATAATAAA
5369758 TTTAAA
1 TTTAAA
5369764 CCTAAAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
TTTAAATTTAATAATAAA
Found at i:5370577 original size:39 final size:39
Alignment explanation
Indices: 5370523--5370602 Score: 124
Period size: 39 Copynumber: 2.1 Consensus size: 39
5370513 GTGCGCTCAC
* * *
5370523 ATGTTGGGTTGATATATGTGGATCTTTATTATAATTGGT
1 ATGTTGGGTTCATATATGCGGATATTTATTATAATTGGT
*
5370562 ATGTTGGGTTCATATATGCGGATATTTATTATGATTGGT
1 ATGTTGGGTTCATATATGCGGATATTTATTATAATTGGT
5370601 AT
1 AT
5370603 ATATTTAGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.24, C:0.04, G:0.25, T:0.47
Consensus pattern (39 bp):
ATGTTGGGTTCATATATGCGGATATTTATTATAATTGGT
Found at i:5374673 original size:27 final size:28
Alignment explanation
Indices: 5374632--5374685 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
5374622 CAATTCGACC
5374632 CAAAACCTGAGCCCAAATACACCCAAACA
1 CAAAACCTGAGCCCAAAT-CACCCAAACA
*
5374661 CAAAA-CT-AGCCCAAATGACCCAAAC
1 CAAAACCTGAGCCCAAATCACCCAAAC
5374686 TAGCCTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 8 0.33
27 9 0.38
28 2 0.08
29 5 0.21
ACGTcount: A:0.48, C:0.37, G:0.07, T:0.07
Consensus pattern (28 bp):
CAAAACCTGAGCCCAAATCACCCAAACA
Found at i:5374825 original size:25 final size:25
Alignment explanation
Indices: 5374791--5374845 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
5374781 GCACCAGCAG
*
5374791 TGCCACCACCAGCTTCAACTTGCTC
1 TGCCACCACCAGCTTCAACCTGCTC
5374816 TGCCACCACCAGCTTCAACCTGCTC
1 TGCCACCACCAGCTTCAACCTGCTC
5374841 TGCCA
1 TGCCA
5374846 TCACTGCCAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.20, C:0.45, G:0.13, T:0.22
Consensus pattern (25 bp):
TGCCACCACCAGCTTCAACCTGCTC
Found at i:5376458 original size:29 final size:28
Alignment explanation
Indices: 5376424--5376880 Score: 153
Period size: 29 Copynumber: 15.5 Consensus size: 28
5376414 CTAAACTGCC
*
5376424 CAAAAATTA-TTTTTTGACCCCAAACTTT
1 CAAAAATTACATTTTT-ACCCCAAACTTT
**
5376452 ACAAAAATTACATTTTTACCTTTAAACTTT
1 -CAAAAATTACATTTTTACC-CCAAACTTT
* * *
5376482 CTAAAATTCCATTTTTTGACCTCAAACTTT
1 CAAAAATTACA-TTTTT-ACCCCAAACTTT
*
5376512 CCAAAAATTACATTTTTACCCCTAAACTCT
1 -CAAAAATTACATTTTTACCCC-AAACTTT
* * * * **
5376542 CCAAAATT-C-TATTTGACCTCGATTTTT
1 CAAAAATTACAT-TTTTACCCCAAACTTT
* * * *
5376569 CCAAAAATTCCATTTTTACTCTCGAACTTC
1 -CAAAAATTACATTTTTAC-CCCAAACTTT
* * *
5376599 CAAAAATTCCATTTTTAATCCTAAACTTT
1 CAAAAATTACATTTTT-ACCCCAAACTTT
* *
5376628 CTAAAAATTACCA-TTTTACCCCCGAA-TGTC
1 C-AAAAATTA-CATTTTTA-CCCCAAACT-TT
*
5376658 CAAAAATTTCATTTTTGACCCCAAACTTTT
1 CAAAAATTACATTTTT-ACCCCAAAC-TTT
** *
5376688 TGAAAATTACCA-TTTTACCCCCAAA-TGT
1 CAAAAATTA-CATTTTTA-CCCCAAACTTT
* * **
5376716 CTAAAATTCCATTTTTAACCCTGAACTTT
1 CAAAAATTACATTTTT-ACCCCAAACTTT
* ** *
5376745 CCAAATATTACCA-TTTTACCCCTGGA-TGT
1 -CAAAAATTA-CATTTTTACCCC-AAACTTT
* *** *
5376774 CTAAAAATTCCATTTTTGACCTTGAACATTC
1 C-AAAAATTACATTTTT-ACCCCAAAC-TTT
* *
5376805 CAAAAATTAC-TATTTTACCCTCGAA-TGT
1 CAAAAATTACAT-TTTTACCC-CAAACTTT
* *
5376833 CTAAAAATTCCATTTTTGACCCCCGAACCTTT
1 C-AAAAATTACATTTTT-A-CCCC-AAACTTT
5376865 CAAAAATTACCATTTT
1 CAAAAATTA-CATTTT
5376881 GCCCCTCGAG
Statistics
Matches: 318, Mismatches: 68, Indels: 81
0.68 0.15 0.17
Matches are distributed among these distances:
27 6 0.02
28 39 0.12
29 118 0.37
30 114 0.36
31 32 0.10
32 9 0.03
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.38
Consensus pattern (28 bp):
CAAAAATTACATTTTTACCCCAAACTTT
Found at i:5376508 original size:60 final size:59
Alignment explanation
Indices: 5376434--5376880 Score: 229
Period size: 59 Copynumber: 7.6 Consensus size: 59
5376424 CAAAAATTAT
* * *
5376434 TTTTTGACCCCAAACTTTACAAAAATTACATTTTTACCTTTAAACTTTCTAAAATTCCA
1 TTTTTGACCTCAAACTTTCCAAAAATTACATTTTTACCTTTAAACTTTCAAAAATTCCA
** * *
5376493 TTTTTTGACCTCAAACTTTCCAAAAATTACATTTTTACCCCTAAACTCTCCAAAATT-C-
1 -TTTTTGACCTCAAACTTTCCAAAAATTACATTTTTACCTTTAAACTTTCAAAAATTCCA
* * ** * ** *
5376551 TATTTGACCTCGATTTTTCCAAAAATTCCATTTTTA-CTCTCGAACTTCCAAAAATTCCA
1 TTTTTGACCTCAAACTTTCCAAAAATTACATTTTTACCT-TTAAACTTTCAAAAATTCCA
* * **** * *
5376610 TTTTTAATCCT-AAACTTTCTAAAAATTACCA-TTTTACCCCCGAA-TGTCCAAAAATTTCA
1 TTTTTGA-CCTCAAACTTTCCAAAAATTA-CATTTTTACCTTTAAACT-TTCAAAAATTCCA
* *** *** * *
5376669 TTTTTGACCCCAAACTTTTTGAAAATTACCA-TTTTACCCCCAAA-TGTCTAAAATTCCA
1 TTTTTGACCTCAAACTTTCCAAAAATTA-CATTTTTACCTTTAAACTTTCAAAAATTCCA
* * * ** ** *
5376727 TTTTTAACC-CTGAACTTTCCAAATATTACCA-TTTTACCCCTGGA-TGTCTAAAAATTCCA
1 TTTTTGACCTC-AAACTTTCCAAAAATTA-CATTTTTACCTTTAAACTTTC-AAAAATTCCA
** * * ** *
5376786 TTTTTGACCTTGAACATTCCAAAAATTAC-TATTTTACCCTCGAA-TGTCTAAAAATTCCA
1 TTTTTGACCTCAAACTTTCCAAAAATTACAT-TTTTACCTTTAAACTTTC-AAAAATTCCA
* *
5376845 TTTTTGACCCCCGAACCTTT-CAAAAATTACCATTTT
1 TTTTTGA-CCTC-AAACTTTCCAAAAATTA-CATTTT
5376881 GCCCCTCGAG
Statistics
Matches: 311, Mismatches: 59, Indels: 33
0.77 0.15 0.08
Matches are distributed among these distances:
56 1 0.00
57 43 0.14
58 51 0.16
59 140 0.45
60 67 0.22
61 8 0.03
62 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.38
Consensus pattern (59 bp):
TTTTTGACCTCAAACTTTCCAAAAATTACATTTTTACCTTTAAACTTTCAAAAATTCCA
Found at i:5376645 original size:59 final size:58
Alignment explanation
Indices: 5376566--5376885 Score: 306
Period size: 59 Copynumber: 5.4 Consensus size: 58
5376556 GACCTCGATT
* *
5376566 TTTCCAAAAATT-CCATTTTTACTCTCGAACT-TCCAAAAATTCCATTTTTAATCCTAAAC
1 TTTCCAAAAATTACCA-TTTTAC-CCCGAA-TGTCCAAAAATTCCATTTTTAACCCTAAAC
* * * *
5376625 TTTCTAAAAATTACCATTTTACCCCCGAATGTCCAAAAATTTCATTTTTGACCCCAAAC
1 TTTCCAAAAATTACCATTTTA-CCCCGAATGTCCAAAAATTCCATTTTTAACCCTAAAC
*** * * *
5376684 TTTTTGAAAATTACCATTTTACCCCCAAATGT-CTAAAATTCCATTTTTAACCCTGAAC
1 TTTCCAAAAATTACCATTTTA-CCCCGAATGTCCAAAAATTCCATTTTTAACCCTAAAC
* * * * * *
5376742 TTTCCAAATATTACCATTTTACCCCTGGATGTCTAAAAATTCCATTTTTGACCTTGAAC
1 TTTCCAAAAATTACCATTTTACCCC-GAATGTCCAAAAATTCCATTTTTAACCCTAAAC
* * * * * *
5376801 ATTCCAAAAATTACTATTTTACCCTCGAATGTCTAAAAATTCCATTTTTGACCCCCGAACC
1 TTTCCAAAAATTACCATTTTACCC-CGAATGTCCAAAAATTCCATTTTT-A-ACCCTAAAC
*
5376862 TTT-CAAAAATTACCATTTTGCCCC
1 TTTCCAAAAATTACCATTTTACCCC
5376886 TCGAGTATCC
Statistics
Matches: 216, Mismatches: 37, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
57 4 0.02
58 43 0.20
59 140 0.65
60 23 0.11
61 6 0.03
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.37
Consensus pattern (58 bp):
TTTCCAAAAATTACCATTTTACCCCGAATGTCCAAAAATTCCATTTTTAACCCTAAAC
Found at i:5376730 original size:117 final size:117
Alignment explanation
Indices: 5376434--5376909 Score: 353
Period size: 117 Copynumber: 4.0 Consensus size: 117
5376424 CAAAAATTAT
* * *** *
5376434 TTTTTGACCCCAAACTTTACAAAAATTA-CATTTTTACCTTTAAACTTTCT-AAAATTCCATTTT
1 TTTTTGACCCCAAACATTCCAAAAATTACCA-TTTTACCCCCAAA-TGTCTAAAAATTCCA-TTT
* ** *
5376497 TTGA-CCTCAAACTTTCCAAAAATTA-CATTTTTACCCCTAAACTCTCC-AAAATT-C-
63 TTAACCCT-AAACTTT-CAAAAATTACCA-TTTTACCCCCGAA-TGTCCAAAAATTCCA
* * * *** * * * *
5376551 TATTTGACCTCGATTTTTCCAAAAATT-CCATTTTTACTCTCGAACT-TCCAAAAATTCCATTTT
1 TTTTTGACCCCAAACATTCCAAAAATTACCA-TTTTAC-CCCCAAATGTCTAAAAATTCCATTTT
* *
5376614 TAATCCTAAACTTTCTAAAAATTACCATTTTACCCCCGAATGTCCAAAAATTTCA
64 TAACCCTAAACTTTC-AAAAATTACCATTTTACCCCCGAATGTCCAAAAATTCCA
* ***
5376669 TTTTTGACCCCAAACTTTTTGAAAATTACCATTTTACCCCCAAATGTCT-AAAATTCCATTTTTA
1 TTTTTGACCCCAAACATTCCAAAAATTACCATTTTACCCCCAAATGTCTAAAAATTCCATTTTTA
* * * * *
5376733 ACCCTGAACTTTCCAAATATTACCATTTTACCCCTGGATGTCTAAAAATTCCA
66 ACCCTAAACTTT-CAAAAATTACCATTTTACCCCCGAATGTCCAAAAATTCCA
*** * * *
5376786 TTTTTGACCTTGAACATTCCAAAAATTACTATTTTACCCTCGAATGTCTAAAAATTCCATTTTTG
1 TTTTTGACCCCAAACATTCCAAAAATTACCATTTTACCCCCAAATGTCTAAAAATTCCATTTTT-
* * * * * *
5376851 ACCCCCGAACCTTTCAAAAATTACCATTTTGCCCCTCGAGTATCC-AAAATTACCA
65 A-ACCCTAAACTTTCAAAAATTACCATTTTACCCC-CGAATGTCCAAAAATT-CCA
5376906 TTTT
1 TTTT
5376910 GCCCTCGAGT
Statistics
Matches: 288, Mismatches: 54, Indels: 31
0.77 0.14 0.08
Matches are distributed among these distances:
115 5 0.02
116 40 0.14
117 149 0.52
118 46 0.16
119 29 0.10
120 19 0.07
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (117 bp):
TTTTTGACCCCAAACATTCCAAAAATTACCATTTTACCCCCAAATGTCTAAAAATTCCATTTTTA
ACCCTAAACTTTCAAAAATTACCATTTTACCCCCGAATGTCCAAAAATTCCA
Found at i:5376923 original size:28 final size:29
Alignment explanation
Indices: 5376867--5376927 Score: 115
Period size: 28 Copynumber: 2.1 Consensus size: 29
5376857 GAACCTTTCA
5376867 AAAATTACCATTTTGCCCCTCGAGTATCC
1 AAAATTACCATTTTGCCCCTCGAGTATCC
5376896 AAAATTACCATTTTG-CCCTCGAGTATCC
1 AAAATTACCATTTTGCCCCTCGAGTATCC
5376924 AAAA
1 AAAA
5376928 ATCTCATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 17 0.53
29 15 0.47
ACGTcount: A:0.33, C:0.28, G:0.10, T:0.30
Consensus pattern (29 bp):
AAAATTACCATTTTGCCCCTCGAGTATCC
Found at i:5376928 original size:29 final size:30
Alignment explanation
Indices: 5376744--5376929 Score: 120
Period size: 29 Copynumber: 6.3 Consensus size: 30
5376734 CCCTGAACTT
* * *
5376744 TCCAAATATTACCATTTT-ACCCCTGGA-TG
1 TCCAAAAATTACCATTTTGA-CCCTCGAGTA
* * **
5376773 TCTAAAAATT-CCATTTTTGA-CCTTGAACA
1 TCCAAAAATTACCA-TTTTGACCCTCGAGTA
* * *
5376802 TTCCAAAAATTACTATTTT-ACCCTCGAATG
1 -TCCAAAAATTACCATTTTGACCCTCGAGTA
* * *
5376832 TCTAAAAATT-CCATTTTTGACCCCCGAACCT-
1 TCCAAAAATTACCA-TTTTGACCCTCG-A-GTA
* *
5376863 TTCAAAAATTACCATTTTGCCCCTCGAGTA
1 TCCAAAAATTACCATTTTGACCCTCGAGTA
5376893 TCC-AAAATTACCATTTTG-CCCTCGAGTA
1 TCCAAAAATTACCATTTTGACCCTCGAGTA
5376921 TCCAAAAAT
1 TCCAAAAAT
5376930 CTCATTTTCA
Statistics
Matches: 124, Mismatches: 20, Indels: 26
0.73 0.12 0.15
Matches are distributed among these distances:
28 23 0.19
29 47 0.38
30 29 0.23
31 21 0.17
32 4 0.03
ACGTcount: A:0.32, C:0.26, G:0.08, T:0.34
Consensus pattern (30 bp):
TCCAAAAATTACCATTTTGACCCTCGAGTA
Found at i:5376935 original size:28 final size:29
Alignment explanation
Indices: 5376865--5376937 Score: 105
Period size: 28 Copynumber: 2.5 Consensus size: 29
5376855 CCGAACCTTT
5376865 CAAAAATTACCATTTTGCCCCTCGAGTATC
1 CAAAAA-TACCATTTTGCCCCTCGAGTATC
*
5376895 CAAAATTACCATTTTG-CCCTCGAGTATC
1 CAAAAATACCATTTTGCCCCTCGAGTATC
5376923 CAAAAAT-CTCATTTT
1 CAAAAATAC-CATTTT
5376938 CAAACTCCGA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
27 1 0.03
28 24 0.60
29 10 0.25
30 5 0.12
ACGTcount: A:0.32, C:0.27, G:0.08, T:0.33
Consensus pattern (29 bp):
CAAAAATACCATTTTGCCCCTCGAGTATC
Found at i:5378309 original size:18 final size:18
Alignment explanation
Indices: 5378282--5378322 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
5378272 TTGTTTAAGT
* *
5378282 TACAAGCACAGTTGCAAA
1 TACAAGCACAATTACAAA
*
5378300 TACAATCACAATTACAAA
1 TACAAGCACAATTACAAA
5378318 TACAA
1 TACAA
5378323 ATAATATACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.51, C:0.22, G:0.07, T:0.20
Consensus pattern (18 bp):
TACAAGCACAATTACAAA
Found at i:5382153 original size:23 final size:23
Alignment explanation
Indices: 5382110--5382187 Score: 79
Period size: 23 Copynumber: 3.4 Consensus size: 23
5382100 ATAACATCCA
* *
5382110 AACAACAAAAATAACAGTAAAGC
1 AACAACAAAAATAATAATAAAGC
*
5382133 AACAACAAAAATAGTAATAAA--
1 AACAACAAAAATAATAATAAAGC
* *
5382154 AACAAAAAAAATAATAACAAAAGC
1 AACAACAAAAATAATAA-TAAAGC
*
5382178 AACACCAAAA
1 AACAACAAAA
5382188 TAGTAAAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
21 15 0.34
22 3 0.07
23 18 0.41
24 8 0.18
ACGTcount: A:0.71, C:0.15, G:0.05, T:0.09
Consensus pattern (23 bp):
AACAACAAAAATAATAATAAAGC
Found at i:5382163 original size:21 final size:20
Alignment explanation
Indices: 5382113--5382198 Score: 64
Period size: 21 Copynumber: 4.1 Consensus size: 20
5382103 ACATCCAAAC
* * **
5382113 AACAAAAATAACAGTAAAGC
1 AACAAAAAAAATAGTAAAAA
*
5382133 AACAACAAAAATAGTAATAAA
1 AACAAAAAAAATAGTAA-AAA
*
5382154 AACAAAAAAAATAATAACAAA
1 AACAAAAAAAATAGTAA-AAA
* *
5382175 AGCAACACCAAAATAGTAAAAA
1 AACAA-A-AAAAATAGTAAAAA
5382197 AA
1 AA
5382199 TAGCAATATA
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
20 14 0.27
21 23 0.45
22 5 0.10
23 9 0.18
ACGTcount: A:0.71, C:0.13, G:0.06, T:0.10
Consensus pattern (20 bp):
AACAAAAAAAATAGTAAAAA
Found at i:5382168 original size:18 final size:18
Alignment explanation
Indices: 5382136--5382170 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5382126 GTAAAGCAAC
* *
5382136 AACAAAAATAGTAATAAA
1 AACAAAAAAAATAATAAA
5382154 AACAAAAAAAATAATAA
1 AACAAAAAAAATAATAA
5382171 CAAAAGCAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.77, C:0.06, G:0.03, T:0.14
Consensus pattern (18 bp):
AACAAAAAAAATAATAAA
Found at i:5386837 original size:26 final size:26
Alignment explanation
Indices: 5386775--5386862 Score: 88
Period size: 31 Copynumber: 3.2 Consensus size: 26
5386765 TGGGATCAGC
* *
5386775 TATTAATTTAATTTAATTACATTATA
1 TATTAATTTAATTTAATCACATTACA
5386801 TAAAATTTTAATTTAATTTAATCACATTACA
1 T---A--TTAATTTAATTTAATCACATTACA
*
5386832 TATTAA-TTAATTTAATCTCATTACCA
1 TATTAATTTAATTTAATCACATTA-CA
5386858 TATTA
1 TATTA
5386863 TACACCTCAC
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
25 16 0.30
26 12 0.23
28 1 0.02
29 1 0.02
31 23 0.43
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (26 bp):
TATTAATTTAATTTAATCACATTACA
Found at i:5386844 original size:25 final size:27
Alignment explanation
Indices: 5386808--5386862 Score: 87
Period size: 25 Copynumber: 2.1 Consensus size: 27
5386798 ATATAAAATT
5386808 TTAATTTAATTTAATCACATTA-CATA
1 TTAATTTAATTTAATCACATTACCATA
*
5386834 TTAA-TTAATTTAATCTCATTACCATA
1 TTAATTTAATTTAATCACATTACCATA
5386860 TTA
1 TTA
5386863 TACACCTCAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 16 0.59
26 11 0.41
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (27 bp):
TTAATTTAATTTAATCACATTACCATA
Found at i:5396251 original size:25 final size:27
Alignment explanation
Indices: 5396205--5396255 Score: 88
Period size: 25 Copynumber: 2.0 Consensus size: 27
5396195 TGTTTTCTAG
5396205 TTTTTAAAGGGCCCAAAAAAATTTTAA
1 TTTTTAAAGGGCCCAAAAAAATTTTAA
5396232 TTTTTAAA-GG-CCAAAAAAATTTTA
1 TTTTTAAAGGGCCCAAAAAAATTTTA
5396256 CCAACTTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 14 0.58
26 2 0.08
27 8 0.33
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (27 bp):
TTTTTAAAGGGCCCAAAAAAATTTTAA
Found at i:5399373 original size:22 final size:22
Alignment explanation
Indices: 5399332--5399374 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5399322 TATCCAAACA
**
5399332 ATAATAATAAAATAGTAACAAC
1 ATAATAATAAAATAACAACAAC
*
5399354 ATAATAGTAAAATAACAACAA
1 ATAATAATAAAATAACAACAA
5399375 AACCGTGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.65, C:0.09, G:0.05, T:0.21
Consensus pattern (22 bp):
ATAATAATAAAATAACAACAAC
Found at i:5400763 original size:20 final size:20
Alignment explanation
Indices: 5400735--5400772 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5400725 ACTTTAAACA
*
5400735 TTAATAATTCAACTTCAAGT
1 TTAAAAATTCAACTTCAAGT
*
5400755 TTAAAAATTCAATTTCAA
1 TTAAAAATTCAACTTCAA
5400773 CCATTTTAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (20 bp):
TTAAAAATTCAACTTCAAGT
Found at i:5402960 original size:18 final size:18
Alignment explanation
Indices: 5402934--5402991 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
5402924 TTTGCTTCCA
* *
5402934 AGCAACAACAACAGCAGC
1 AGCAGCAACAACAGCAAC
5402952 AGCAGCAACAACAGCAAC
1 AGCAGCAACAACAGCAAC
5402970 AGCAGCAACAACAGCAATC
1 AGCAGCAACAACAGCAA-C
5402989 AGC
1 AGC
5402992 TCTTGTCTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
18 33 0.89
19 4 0.11
ACGTcount: A:0.48, C:0.33, G:0.17, T:0.02
Consensus pattern (18 bp):
AGCAGCAACAACAGCAAC
Found at i:5402966 original size:9 final size:9
Alignment explanation
Indices: 5402939--5402986 Score: 69
Period size: 9 Copynumber: 5.3 Consensus size: 9
5402929 TTCCAAGCAA
5402939 CAACAACAG
1 CAACAACAG
* *
5402948 CAGCAGCAG
1 CAACAACAG
5402957 CAACAACAG
1 CAACAACAG
*
5402966 CAACAGCAG
1 CAACAACAG
5402975 CAACAACAG
1 CAACAACAG
5402984 CAA
1 CAA
5402987 TCAGCTCTTG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.50, C:0.33, G:0.17, T:0.00
Consensus pattern (9 bp):
CAACAACAG
Found at i:5403340 original size:17 final size:16
Alignment explanation
Indices: 5403318--5403350 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
5403308 GGGTATTCTG
5403318 TTTTTTCTTCTCTTTTT
1 TTTTTTCTTCT-TTTTT
5403335 TTTTTTCTTCTTTTTT
1 TTTTTTCTTCTTTTTT
5403351 CAATTCTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTTTTCTTCTTTTTT
Found at i:5407132 original size:36 final size:36
Alignment explanation
Indices: 5407091--5407165 Score: 123
Period size: 36 Copynumber: 2.1 Consensus size: 36
5407081 TTCTATAATG
* *
5407091 TTAAATTAACTGTGGGAACAACTCAATAACTAACCC
1 TTAAATTAACTGTGGGAACAACCCAACAACTAACCC
*
5407127 TTAAATTAACTGTGGGAATAACCCAACAACTAACCC
1 TTAAATTAACTGTGGGAACAACCCAACAACTAACCC
5407163 TTA
1 TTA
5407166 TCAAGTGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.41, C:0.23, G:0.11, T:0.25
Consensus pattern (36 bp):
TTAAATTAACTGTGGGAACAACCCAACAACTAACCC
Found at i:5408678 original size:20 final size:20
Alignment explanation
Indices: 5408653--5408696 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
5408643 TTTAGAGTAG
5408653 AAAGATAAAGTGTACCCAAA
1 AAAGATAAAGTGTACCCAAA
5408673 AAAGATAAAGTGTACCCAAA
1 AAAGATAAAGTGTACCCAAA
5408693 AAAG
1 AAAG
5408697 TGGAATGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.57, C:0.14, G:0.16, T:0.14
Consensus pattern (20 bp):
AAAGATAAAGTGTACCCAAA
Found at i:5409151 original size:18 final size:18
Alignment explanation
Indices: 5409104--5409152 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
5409094 GGTTTAAGTT
5409104 AATTCTAAATTTATTTACA
1 AATT-TAAATTTATTTACA
**
5409123 AATTTGGATTTATCTTA-A
1 AATTTAAATTTAT-TTACA
5409141 AATTTAAATTTA
1 AATTTAAATTTA
5409153 AATCAATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (18 bp):
AATTTAAATTTATTTACA
Found at i:5409184 original size:17 final size:16
Alignment explanation
Indices: 5409162--5409201 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 16
5409152 AAATCAATTT
5409162 TTAAATTTAAATTTGTG
1 TTAAATTTAAATTTG-G
5409179 TTAAATTTAAATTTGG
1 TTAAATTTAAATTTGG
5409195 -TAAATTT
1 TTAAATTT
5409202 GGAATAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 7 0.30
16 1 0.04
17 15 0.65
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.53
Consensus pattern (16 bp):
TTAAATTTAAATTTGG
Found at i:5409293 original size:13 final size:13
Alignment explanation
Indices: 5409275--5409313 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
5409265 GCCAAATTAC
5409275 AAAGGCCCAAATT
1 AAAGGCCCAAATT
5409288 AAAGGCCC-AATT
1 AAAGGCCCAAATT
5409300 ACAATGGCCCAAAT
1 A-AA-GGCCCAAAT
5409314 AGGCCCAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 5 0.22
13 10 0.43
14 5 0.22
15 3 0.13
ACGTcount: A:0.44, C:0.26, G:0.15, T:0.15
Consensus pattern (13 bp):
AAAGGCCCAAATT
Found at i:5409310 original size:14 final size:14
Alignment explanation
Indices: 5409259--5409311 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
5409249 ACAAAAGGCC
*
5409259 CAATAGGCCAAATTA
1 CAAT-GGCCCAATTA
*
5409274 CAAAGGCCCAAATTA
1 CAATGGCCC-AATTA
5409289 -AA-GGCCCAATTA
1 CAATGGCCCAATTA
5409301 CAATGGCCCAA
1 CAATGGCCCAA
5409312 ATAGGCCCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
12 5 0.15
13 7 0.21
14 13 0.39
15 8 0.24
ACGTcount: A:0.43, C:0.26, G:0.15, T:0.15
Consensus pattern (14 bp):
CAATGGCCCAATTA
Found at i:5409322 original size:24 final size:24
Alignment explanation
Indices: 5409243--5409322 Score: 99
Period size: 27 Copynumber: 3.2 Consensus size: 24
5409233 AGTCCAGAGT
5409243 CCAATTACAAAAGGCCC-AATAGGC
1 CCAATTAC-AAAGGCCCAAATAGGC
*
5409267 CAAATTACAAAGGCCCAAATTAAAGGC
1 CCAATTACAAAGGCCCAAA-T--AGGC
*
5409294 CCAATTACAATGGCCCAAATAGGC
1 CCAATTACAAAGGCCCAAATAGGC
5409318 CCAAT
1 CCAAT
5409323 GCCTAGAACT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
23 8 0.16
24 18 0.37
25 1 0.02
26 1 0.02
27 21 0.43
ACGTcount: A:0.42, C:0.28, G:0.15, T:0.15
Consensus pattern (24 bp):
CCAATTACAAAGGCCCAAATAGGC
Found at i:5409844 original size:7 final size:7
Alignment explanation
Indices: 5409832--5409892 Score: 67
Period size: 7 Copynumber: 9.3 Consensus size: 7
5409822 TAAAAATATT
5409832 ATTAATA
1 ATTAATA
5409839 ATTAATA
1 ATTAATA
5409846 ATT-ATA
1 ATTAATA
5409852 ATTAAT-
1 ATTAATA
* *
5409858 ATTTATG
1 ATTAATA
5409865 ATT-ATA
1 ATTAATA
*
5409871 GTTAAT-
1 ATTAATA
5409877 ATTAATA
1 ATTAATA
5409884 ATTAATA
1 ATTAATA
5409891 AT
1 AT
5409893 ATTAAAATAA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
6 20 0.43
7 26 0.57
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (7 bp):
ATTAATA
Found at i:5409854 original size:13 final size:13
Alignment explanation
Indices: 5409836--5409892 Score: 55
Period size: 13 Copynumber: 4.4 Consensus size: 13
5409826 AATATTATTA
5409836 ATAATTAATAATT
1 ATAATTAATAATT
*
5409849 ATAATTAATATTT
1 ATAATTAATAATT
* *
5409862 ATGATT-ATAGTT
1 ATAATTAATAATT
5409874 A-ATATTAATAATT
1 ATA-ATTAATAATT
5409887 AATAAT
1 -ATAAT
5409893 ATTAAAATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
12 9 0.26
13 22 0.63
14 3 0.09
15 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (13 bp):
ATAATTAATAATT
Found at i:5409870 original size:19 final size:19
Alignment explanation
Indices: 5409832--5409892 Score: 77
Period size: 19 Copynumber: 3.1 Consensus size: 19
5409822 TAAAAATATT
5409832 ATTAATAATTAATAATTATA
1 ATTAAT-ATTAATAATTATA
* *
5409852 ATTAATATTTATGATTATA
1 ATTAATATTAATAATTATA
*
5409871 GTTAATATTAATAATTAATA
1 ATTAATATTAATAATT-ATA
5409891 AT
1 AT
5409893 ATTAAAATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 24 0.71
20 10 0.29
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (19 bp):
ATTAATATTAATAATTATA
Found at i:5410614 original size:34 final size:32
Alignment explanation
Indices: 5410551--5410615 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 32
5410541 TGTGTAAATG
* *
5410551 GTCCTTCCTCATTTTTTATTTGTTTCAATTTA
1 GTCCTTCCTCATTTTTTAATTATTTCAATTTA
*
5410583 GTCCTTTCTGCATTTTTTAATTATTTGCAATTT
1 GTCCTTCCT-CATTTTTTAATTATTT-CAATTT
5410616 TGCCTTGTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 8 0.29
33 14 0.50
34 6 0.21
ACGTcount: A:0.17, C:0.17, G:0.08, T:0.58
Consensus pattern (32 bp):
GTCCTTCCTCATTTTTTAATTATTTCAATTTA
Found at i:5410984 original size:29 final size:27
Alignment explanation
Indices: 5410947--5411144 Score: 102
Period size: 29 Copynumber: 6.9 Consensus size: 27
5410937 ACCCCGAAAC
5410947 TTCCAAAAATTACCATTTTACCCTCGAACT
1 TTCCAAAAATTACCATTTTACCC-CG-A-T
5410977 TTCC-AAAATT-CCATTTTTAACCCCGAT
1 TTCCAAAAATTACCA-TTTT-ACCCCGAT
5411004 TTCACCAAAAATTACCATTTTACCCCGTAT
1 TT--CCAAAAATTACCATTTTACCCCG-AT
** *
5411034 CTT-TTAAAATT-CCATTTTTAACCCTGAT
1 -TTCCAAAAATTACCA-TTTT-ACCCCGAT
* *
5411062 TTCATAGAAAATTACCATTTTATCCCCAAACT
1 TTC-CA-AAAATTACCATTTTA-CCCC-GA-T
* *
5411094 TTTC-GAAATT-CCATTTTAACCCCGAT
1 TTCCAAAAATTACCATTTT-ACCCCGAT
* * *
5411120 TTCACCAAAATCACCATTTTGCCCC
1 TTC-CAAAAATTACCATTTTACCCC
5411145 CAGGTATCCA
Statistics
Matches: 133, Mismatches: 14, Indels: 44
0.70 0.07 0.23
Matches are distributed among these distances:
26 3 0.02
27 10 0.08
28 35 0.26
29 40 0.30
30 33 0.25
31 9 0.07
32 3 0.02
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.36
Consensus pattern (27 bp):
TTCCAAAAATTACCATTTTACCCCGAT
Found at i:5411063 original size:58 final size:57
Alignment explanation
Indices: 5410949--5411144 Score: 245
Period size: 58 Copynumber: 3.4 Consensus size: 57
5410939 CCCGAAACTT
*
5410949 CCAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCC-CGAACTTT-TAAAATTCCATTTTTAACCCCGATTTCA
* *
5411008 CCAAAAATTACCATTTTACCCCGTATCTTTTAAAATTCCATTTTTAACCCTGATTTCA
1 CCAAAAATTACCATTTTACCCCG-AACTTTTAAAATTCCATTTTTAACCCCGATTTCA
* * *
5411066 -TAGAAAATTACCATTTTATCCCCAAACTTTTCGAAATTCCA-TTTTAACCCCGATTTCA
1 CCA-AAAATTACCATTTTA-CCCCGAACTTTT-AAAATTCCATTTTTAACCCCGATTTCA
* *
5411124 CC-AAAATCACCATTTTGCCCC
1 CCAAAAATTACCATTTTACCCC
5411145 CAGGTATCCA
Statistics
Matches: 121, Mismatches: 11, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
56 4 0.03
57 14 0.12
58 65 0.54
59 38 0.31
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.35
Consensus pattern (57 bp):
CCAAAAATTACCATTTTACCCCGAACTTTTAAAATTCCATTTTTAACCCCGATTTCA
Found at i:5411174 original size:116 final size:115
Alignment explanation
Indices: 5410952--5411182 Score: 281
Period size: 116 Copynumber: 2.0 Consensus size: 115
5410942 GAAACTTCCA
* *
5410952 AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATT
1 AAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATC
* *
5411017 ACCATTTTACCCCGTATCTTTTAAAATTCCATTTTTAACCCTGATTTCATAG
66 ACCATTTTACCCCGTATC--TCAAAATCCCATTTTTAACCCTGATTTCATAG
* *
5411069 AAAATTACCATTTTATCCC-CAAACTTTTCGAAATTCCA-TTTTAACCCCGATTTCACC-AAAAT
1 AAAATTACCATTTTA-CCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAAT
* * * *
5411131 CACCATTTTGCCCCCAGGTATC-CACAAGTCCCGTTTTTCACCCTGATTTCAT
65 CACCATTTT-ACCCC--GTATCTCA-AAATCCCATTTTTAACCCTGATTTCAT
5411183 CGTTTATCAA
Statistics
Matches: 99, Mismatches: 10, Indels: 11
0.82 0.08 0.09
Matches are distributed among these distances:
115 14 0.14
116 46 0.46
117 31 0.31
118 8 0.08
ACGTcount: A:0.30, C:0.29, G:0.06, T:0.35
Consensus pattern (115 bp):
AAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATC
ACCATTTTACCCCGTATCTCAAAATCCCATTTTTAACCCTGATTTCATAG
Found at i:5415181 original size:30 final size:30
Alignment explanation
Indices: 5415141--5415294 Score: 147
Period size: 30 Copynumber: 5.1 Consensus size: 30
5415131 AATATATAAA
5415141 AAAATTTATATTTTAACCCTCAAACTTTTCT
1 AAAA-TTATATTTTAACCCTCAAACTTTTCT
5415172 AAAATTATATTTTAACCC-CTAAACTTCTTC-
1 AAAATTATATTTTAACCCTC-AAACTT-TTCT
* ** *
5415202 AAAATTATATTTTAACCCTCTAACTTCCCC
1 AAAATTATATTTTAACCCTCAAACTTTTCT
* * *
5415232 AAAATTACATTTTAACCCTCTAAC-TTCCT
1 AAAATTATATTTTAACCCTCAAACTTTTCT
* *
5415261 CAAAATTACATTTTGACCC-CTAAAC-TTTCT
1 -AAAATTATATTTTAACCCTC-AAACTTTTCT
5415291 AAAA
1 AAAA
5415295 ACACATTTTC
Statistics
Matches: 108, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
29 10 0.09
30 90 0.83
31 8 0.07
ACGTcount: A:0.36, C:0.25, G:0.01, T:0.38
Consensus pattern (30 bp):
AAAATTATATTTTAACCCTCAAACTTTTCT
Found at i:5415210 original size:60 final size:60
Alignment explanation
Indices: 5415141--5415303 Score: 188
Period size: 60 Copynumber: 2.7 Consensus size: 60
5415131 AATATATAAA
* *
5415141 AAAATTTATATTTTAACCCTCAAACTTTTCTAAAATTATATTTTAACCC-CTAAACTTCTTC
1 AAAA-TTATATTTTAACCCTCAAACTTTTCTAAAATTACATTTTAACCCTCT-AACTTCCTC
* ** *
5415202 AAAATTATATTTTAACCCTCTAACTTCCCCAAAATTACATTTTAACCCTCTAACTTCCTC
1 AAAATTATATTTTAACCCTCAAACTTTTCTAAAATTACATTTTAACCCTCTAACTTCCTC
* * **
5415262 AAAATTACATTTTGACCC-CTAAAC-TTTCTAAAAACACATTTT
1 AAAATTATATTTTAACCCTC-AAACTTTTCTAAAATTACATTTT
5415304 CGACCTCAAA
Statistics
Matches: 86, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
59 14 0.16
60 66 0.77
61 6 0.07
ACGTcount: A:0.36, C:0.25, G:0.01, T:0.39
Consensus pattern (60 bp):
AAAATTATATTTTAACCCTCAAACTTTTCTAAAATTACATTTTAACCCTCTAACTTCCTC
Found at i:5415318 original size:29 final size:29
Alignment explanation
Indices: 5415180--5415323 Score: 69
Period size: 30 Copynumber: 4.9 Consensus size: 29
5415170 CTAAAATTAT
* * ** *
5415180 ATTTTAACCCCTAAACTTCTTCAAAATTAT
1 ATTTTGACCCCTAAACTT-TCCAAAAACAC
* * **
5415210 ATTTTAACCCTCT-AACTTCCCCAAAATTAC
1 ATTTTGACCC-CTAAACTT-TCCAAAAACAC
* * **
5415240 ATTTTAACCCTCT-AACTTCCTCAAAATTAC
1 ATTTTGACCC-CTAAACTTTC-CAAAAACAC
*
5415270 ATTTTGACCCCTAAACTTTCTAAAAACAC
1 ATTTTGACCCCTAAACTTTCCAAAAACAC
* *
5415299 ATTTTCGACCTC-AAATTTTCCAAAA
1 ATTTT-GACCCCTAAACTTTCCAAAA
5415324 GTTCGATTTT
Statistics
Matches: 99, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
29 26 0.26
30 71 0.72
31 2 0.02
ACGTcount: A:0.35, C:0.28, G:0.01, T:0.35
Consensus pattern (29 bp):
ATTTTGACCCCTAAACTTTCCAAAAACAC
Found at i:5417557 original size:19 final size:19
Alignment explanation
Indices: 5417533--5417570 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5417523 TTGAAACAAT
*
5417533 AATTGAATTGATTTCGAAC
1 AATTGAATCGATTTCGAAC
5417552 AATTGAATCGATTTCGAAC
1 AATTGAATCGATTTCGAAC
5417571 TACTCTGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (19 bp):
AATTGAATCGATTTCGAAC
Found at i:5417940 original size:27 final size:26
Alignment explanation
Indices: 5417886--5417942 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
5417876 TAATATTGTA
* **
5417886 TTTTTAAAAATATATATAATTTTTAT
1 TTTTTAAAAAAATATATAATTTAAAT
*
5417912 TTTTTAAAAAAATTGTATAATTTAAAT
1 TTTTTAAAAAAA-TATATAATTTAAAT
5417939 TTTT
1 TTTT
5417943 ATGTTTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 11 0.42
27 15 0.58
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (26 bp):
TTTTTAAAAAAATATATAATTTAAAT
Found at i:5417941 original size:26 final size:26
Alignment explanation
Indices: 5417885--5417943 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
5417875 ATAATATTGT
* *
5417885 ATTTTTAAAAATATATATAATTTTTA
1 ATTTTTAAAAAAATATATAATTTTAA
* *
5417911 TTTTTTAAAAAAATTGTATAA-TTTAA
1 ATTTTTAAAAAAA-TATATAATTTTAA
5417937 ATTTTTA
1 ATTTTTA
5417944 TGTTTTTTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 21 0.78
27 6 0.22
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (26 bp):
ATTTTTAAAAAAATATATAATTTTAA
Found at i:5420125 original size:197 final size:191
Alignment explanation
Indices: 5419790--5420332 Score: 659
Period size: 197 Copynumber: 2.8 Consensus size: 191
5419780 TGCGTGCAGG
* *
5419790 CAGAGCACGGCCTTAAACGGAGCTCC-GGAATGAAGAAG-AAC-ACCATCGTTTTGTAAATGAGT
1 CAGAGCAAGGCCTTAAACGGAG-TCCTGGAATGAAGAAGAAACGA-CACCG-TTTGTAAATGAGT
* *
5419852 TGAAAAAATT-AACATGTGGCCCATGCAGGTTTCGAACCTGCGACCTTCGCGTTATTAGCACGAC
63 TG-AAAAATTGAATATGTGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGAC
*
5419916 GCTCTAACCAACTGAGCTAATAGGCCAATACATTTGCTCCTAAAATATACAATTAGTTTAATACG
127 GCTCTAACCAACTGAGCTAATAGGCCAACACATTTGCTCCTAAAATATACAATTAG-TT--TA-G
5419981 TCAAA
188 T-AAA
*
5419986 CCAGAGCAAGGCCTTAAACGGAGTCCTGGAATAAAGAAGAAACGACACCGTTTGTAAATGAGTTG
1 -CAGAGCAAGGCCTTAAACGGAGTCCTGGAATGAAGAAGAAACGACACCGTTTGTAAATGAGTTG
5420051 AAAAATTGAATATGTGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACGCT
65 AAAAATTGAATATGTGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACGCT
* *** * * **
5420116 CTAACCAACTGAGCTAATAGGCCAACAC-TTT-CTGCTTTCATATATAATTTGTTTAGTTTA
130 CTAACCAACTGAGCTAATAGGCCAACACATTTGCTCCTAAAATATACAATTAGTTTAGTAAA
* * *
5420176 -ATA-C-A--CC-TAACCAGAGAG-CTCTGGAATGAAGAAAAAACGACACCG-TT-TAAATGAGT
1 CAGAGCAAGGCCTTAAAC-G-GAGTC-CTGGAATGAAGAAGAAACGACACCGTTTGTAAATGAGT
* *
5420232 TTAGAAAA-TGAATAAGTGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGAC
63 TGA-AAAATTGAATATGTGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGAC
*
5420296 GCTCTAACCAGCTGAGCTAATAGGCCAACACACTTTG
127 GCTCTAACCAACTGAGCTAATAGGCCAACACA-TTTG
5420333 TTTTCAAAAT
Statistics
Matches: 314, Mismatches: 21, Indels: 33
0.85 0.06 0.09
Matches are distributed among these distances:
183 100 0.32
184 10 0.03
185 29 0.09
186 1 0.00
187 1 0.00
188 2 0.01
190 1 0.00
191 2 0.01
192 2 0.01
194 2 0.01
195 14 0.04
196 13 0.04
197 129 0.41
198 7 0.02
199 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (191 bp):
CAGAGCAAGGCCTTAAACGGAGTCCTGGAATGAAGAAGAAACGACACCGTTTGTAAATGAGTTGA
AAAATTGAATATGTGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACGCTC
TAACCAACTGAGCTAATAGGCCAACACATTTGCTCCTAAAATATACAATTAGTTTAGTAAA
Found at i:5431477 original size:19 final size:19
Alignment explanation
Indices: 5431429--5431465 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
5431419 TATTTAAAAA
5431429 TATAAAT-TTTTAGAATTT
1 TATAAATATTTTAGAATTT
5431447 TATAAATATTTTA-AATTT
1 TATAAATATTTTAGAATTT
5431465 T
1 T
5431466 GAAAATCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
TATAAATATTTTAGAATTT
Found at i:5433817 original size:9 final size:10
Alignment explanation
Indices: 5433806--5433855 Score: 54
Period size: 9 Copynumber: 5.2 Consensus size: 10
5433796 TTGAATTAAT
5433806 AATCTAATT-
1 AATCTAATTC
5433815 AATTCTCAATTC
1 AA-TCT-AATTC
5433827 AAT-TAATTC
1 AATCTAATTC
5433836 AATC-AATT-
1 AATCTAATTC
5433844 AATCTAATTC
1 AATCTAATTC
5433854 AA
1 AA
5433856 ATAACATTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
8 4 0.11
9 18 0.51
10 6 0.17
11 5 0.14
12 2 0.06
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (10 bp):
AATCTAATTC
Found at i:5433843 original size:18 final size:17
Alignment explanation
Indices: 5433792--5433855 Score: 64
Period size: 16 Copynumber: 3.8 Consensus size: 17
5433782 TTTAACCCTT
5433792 TTAATTGAATT-AAT-AA
1 TTAATT-AATTCAATCAA
5433808 TCTAATTAATTC--TCAA
1 T-TAATTAATTCAATCAA
5433824 TTCAATTAATTCAATCAA
1 TT-AATTAATTCAATCAA
5433842 TTAATCTAATTCAA
1 TTAAT-TAATTCAA
5433856 ATAACATTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
15 2 0.05
16 17 0.41
17 8 0.20
18 14 0.34
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.42
Consensus pattern (17 bp):
TTAATTAATTCAATCAA
Found at i:5444372 original size:2 final size:2
Alignment explanation
Indices: 5444365--5444389 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5444355 TACACTGTAA
5444365 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5444390 CACACACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5452873 original size:16 final size:16
Alignment explanation
Indices: 5452852--5452885 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
5452842 ATTCAAACAG
5452852 TTTCACACATCAATCA
1 TTTCACACATCAATCA
*
5452868 TTTCACACATCACTCA
1 TTTCACACATCAATCA
5452884 TT
1 TT
5452886 ACATTAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (16 bp):
TTTCACACATCAATCA
Found at i:5457485 original size:22 final size:23
Alignment explanation
Indices: 5457460--5457520 Score: 81
Period size: 21 Copynumber: 2.7 Consensus size: 23
5457450 TAAAAATGAT
5457460 AAAATTTTAATTTAATTATT-TA
1 AAAATTTTAATTTAATTATTGTA
* *
5457482 AAAA-TTTATTTTTATTATTGTA
1 AAAATTTTAATTTAATTATTGTA
*
5457504 AAAATTATAATTTAATT
1 AAAATTTTAATTTAATT
5457521 TCGACCTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
21 13 0.41
22 10 0.31
23 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
AAAATTTTAATTTAATTATTGTA
Found at i:5492486 original size:22 final size:22
Alignment explanation
Indices: 5492458--5492507 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
5492448 TTTTTTTTTC
*
5492458 AAAAAAATGAAAAAA-AACCAGA
1 AAAAAAATCAAAAAATAACCA-A
*
5492480 AAAAAAATCAAAAAATAGCCAA
1 AAAAAAATCAAAAAATAACCAA
5492502 AAAAAA
1 AAAAAA
5492508 TAAGGAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.78, C:0.10, G:0.06, T:0.06
Consensus pattern (22 bp):
AAAAAAATCAAAAAATAACCAA
Found at i:5493156 original size:21 final size:22
Alignment explanation
Indices: 5493132--5493174 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
5493122 AAATAATTTT
*
5493132 AATAATTTT-ATATTTTTAAAA
1 AATAATTTTAATAATTTTAAAA
5493153 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
5493175 TCATTTGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AATAATTTTAATAATTTTAAAA
Found at i:5493169 original size:30 final size:30
Alignment explanation
Indices: 5493096--5493171 Score: 111
Period size: 30 Copynumber: 2.6 Consensus size: 30
5493086 AAAAAAAATC
*
5493096 ATAA-TTTAATAATTAT-TATTTCGAAAAA
1 ATAATTTTAATAATTTTATATTTCGAAAAA
**
5493124 ATAATTTTAATAATTTTATATTTTTAAAAA
1 ATAATTTTAATAATTTTATATTTCGAAAAA
5493154 ATAATTTTAATAATTTTA
1 ATAATTTTAATAATTTTA
5493172 AAATCATTTG
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
28 4 0.09
29 11 0.26
30 28 0.65
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (30 bp):
ATAATTTTAATAATTTTATATTTCGAAAAA
Found at i:5493829 original size:20 final size:20
Alignment explanation
Indices: 5493806--5493849 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
5493796 AAGCAAAAAG
*
5493806 AAAAATTACAAACATTATGA
1 AAAAATTACAAAAATTATGA
* *
5493826 AAAATTTCCAAAAATTATGA
1 AAAAATTACAAAAATTATGA
5493846 AAAA
1 AAAA
5493850 GAATATTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.61, C:0.09, G:0.05, T:0.25
Consensus pattern (20 bp):
AAAAATTACAAAAATTATGA
Found at i:5494136 original size:15 final size:15
Alignment explanation
Indices: 5494118--5494164 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
5494108 TCATTTTGAG
5494118 TTTAATTATTTTAAA
1 TTTAATTATTTTAAA
* *
5494133 TTTAAATACTTTCAAA
1 TTTAATTA-TTTTAAA
*
5494149 TTTAATTAATTTAAA
1 TTTAATTATTTTAAA
5494164 T
1 T
5494165 ATAAATAGAG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTAATTATTTTAAA
Found at i:5494151 original size:16 final size:15
Alignment explanation
Indices: 5494127--5494171 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
5494117 GTTTAATTAT
*
5494127 TTTAAATTTAAATAC
1 TTTAAATTTAAATAA
*
5494142 TTTCAAATTTAATTAA
1 TTT-AAATTTAAATAA
*
5494158 TTTAAATATAAATA
1 TTTAAATTTAAATA
5494172 GAGTGACGGG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTAAATTTAAATAA
Found at i:5500022 original size:13 final size:13
Alignment explanation
Indices: 5500004--5500031 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5499994 TCTCATTTGC
5500004 TTCTTAATTAGAT
1 TTCTTAATTAGAT
5500017 TTCTTAATTAGAT
1 TTCTTAATTAGAT
5500030 TT
1 TT
5500032 GTGGAGGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (13 bp):
TTCTTAATTAGAT
Found at i:5505194 original size:53 final size:53
Alignment explanation
Indices: 5505075--5505322 Score: 318
Period size: 53 Copynumber: 4.7 Consensus size: 53
5505065 TTCACATTTG
* * * *
5505075 ATAACTCACGATGACACAGAGTCATCAGACCTTTAATCCATGAT-GGATTCGT
1 ATAACTCACGATGACACATAGTCATCAGACCTTTAATCCATAATAAGATTCAT
* * * * * * * *
5505127 ATATCTCACGATGACATAAAGTCATCGGACCCTTAATCCGTAATAGGATTCGT
1 ATAACTCACGATGACACATAGTCATCAGACCTTTAATCCATAATAAGATTCAT
* * * *
5505180 ATAACTCATGATGACACATAGTAATCAAACCTTTAATCCATGATAAGATTCAT
1 ATAACTCACGATGACACATAGTCATCAGACCTTTAATCCATAATAAGATTCAT
* *
5505233 ATAACTCACGATGACACATAGTCATCAGACCCTTAATCCGTAATAAGATTCAT
1 ATAACTCACGATGACACATAGTCATCAGACCTTTAATCCATAATAAGATTCAT
*
5505286 ATAACTCACGATGACACATAGTCATCGGACCTTTAAT
1 ATAACTCACGATGACACATAGTCATCAGACCTTTAAT
5505323 ATTTGGCACA
Statistics
Matches: 168, Mismatches: 27, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
52 37 0.22
53 131 0.78
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.28
Consensus pattern (53 bp):
ATAACTCACGATGACACATAGTCATCAGACCTTTAATCCATAATAAGATTCAT
Found at i:5505268 original size:106 final size:105
Alignment explanation
Indices: 5505075--5505322 Score: 370
Period size: 106 Copynumber: 2.4 Consensus size: 105
5505065 TTCACATTTG
* * * *
5505075 ATAACTCACGATGACACAGAGTCATCAGACCTTTAATCCATGATGGATTCGTATATCTCACGATG
1 ATAACTCACGATGACACATAGTCATCAGACCTTTAATCCATGATAGATTCATATAACTCACGATG
* * * *
5505140 ACATAAAGTCATCGGACCCTTAATCCGTAATAGGATTCGT
66 ACACAAAGTCATCAGACCCTTAATCCGTAATAAGATTCAT
* * *
5505180 ATAACTCATGATGACACATAGTAATCAAACCTTTAATCCATGATAAGATTCATATAACTCACGAT
1 ATAACTCACGATGACACATAGTCATCAGACCTTTAATCCATGAT-AGATTCATATAACTCACGAT
*
5505245 GACACATAGTCATCAGACCCTTAATCCGTAATAAGATTCAT
65 GACACAAAGTCATCAGACCCTTAATCCGTAATAAGATTCAT
*
5505286 ATAACTCACGATGACACATAGTCATCGGACCTTTAAT
1 ATAACTCACGATGACACATAGTCATCAGACCTTTAAT
5505323 ATTTGGCACA
Statistics
Matches: 126, Mismatches: 16, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
105 40 0.32
106 86 0.68
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.28
Consensus pattern (105 bp):
ATAACTCACGATGACACATAGTCATCAGACCTTTAATCCATGATAGATTCATATAACTCACGATG
ACACAAAGTCATCAGACCCTTAATCCGTAATAAGATTCAT
Found at i:5505801 original size:16 final size:16
Alignment explanation
Indices: 5505780--5505811 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5505770 TTTAGCCTTC
5505780 CTTGAAATTGACATCT
1 CTTGAAATTGACATCT
5505796 CTTGAAATTGACATCT
1 CTTGAAATTGACATCT
5505812 AACTCCCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (16 bp):
CTTGAAATTGACATCT
Found at i:5506602 original size:57 final size:58
Alignment explanation
Indices: 5506541--5506652 Score: 138
Period size: 58 Copynumber: 1.9 Consensus size: 58
5506531 CATTTCCTTT
* * *
5506541 TAGAGATCTGCCACGAAGGCA-TCCTTTA-AGAGGTTCACCATAAAGGCTTACCTTTAA
1 TAGAGATCTGCCACAAAGGCAGTCATTTAGA-AGGTTCACCACAAAGGCTTACCTTTAA
* * * *
5506598 TAGAGTTTTGCTACAAAGGCAGTCATTTAGAAGGTTCACCACAAAGGCTTTCCTT
1 TAGAGATCTGCCACAAAGGCAGTCATTTAGAAGGTTCACCACAAAGGCTTACCTT
5506653 GACTTGTGTT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
57 17 0.37
58 28 0.61
59 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (58 bp):
TAGAGATCTGCCACAAAGGCAGTCATTTAGAAGGTTCACCACAAAGGCTTACCTTTAA
Found at i:5508972 original size:13 final size:13
Alignment explanation
Indices: 5508914--5508972 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
5508904 TAAAAAAAAT
5508914 TAAAATATTAATAA
1 TAAAAT-TTAATAA
*
5508928 TAAATATTTAAATAC
1 TAAA-ATTT-AATAA
*
5508943 TAATA-TT-ATAA
1 TAAAATTTAATAA
*
5508954 TAAAATTTAATAC
1 TAAAATTTAATAA
5508967 TAAAAT
1 TAAAAT
5508973 GTTATATGGA
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
11 7 0.19
12 2 0.06
13 11 0.31
14 7 0.19
15 9 0.25
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (13 bp):
TAAAATTTAATAA
Found at i:5509106 original size:18 final size:19
Alignment explanation
Indices: 5509083--5509128 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
5509073 ATGAAATTTT
* *
5509083 TATTATTAAATTCT-TATA
1 TATTATTAAACTATATATA
*
5509101 TATTA-TAAACTATATATT
1 TATTATTAAACTATATATA
5509119 TATTATTAAA
1 TATTATTAAA
5509129 ATAGTAGCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 6 0.26
18 13 0.57
19 4 0.17
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (19 bp):
TATTATTAAACTATATATA
Found at i:5509893 original size:23 final size:22
Alignment explanation
Indices: 5509867--5509917 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 22
5509857 GTTTAACAAG
5509867 TGTCAATATAAAAAAATGATAGA
1 TGTCAATATAAAAAAATGAT-GA
* *
5509890 TGTCAATATAAAAGAATGATGG
1 TGTCAATATAAAAAAATGATGA
5509912 TGTCAA
1 TGTCAA
5509918 CCCTTGAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 7 0.27
23 19 0.73
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.27
Consensus pattern (22 bp):
TGTCAATATAAAAAAATGATGA
Found at i:5512000 original size:31 final size:31
Alignment explanation
Indices: 5511962--5512020 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
5511952 ATAATTTTTT
5511962 ATAATTGAGTAACAA-AAGTGTAAATTTACTA
1 ATAATTGAGTAACAATAAGTGT-AATTTACTA
* *
5511993 ATAATTGAGTGATAATAAGTGTAATTTA
1 ATAATTGAGTAACAATAAGTGTAATTTA
5512021 TCCTTAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 19 0.76
32 6 0.24
ACGTcount: A:0.46, C:0.03, G:0.15, T:0.36
Consensus pattern (31 bp):
ATAATTGAGTAACAATAAGTGTAATTTACTA
Found at i:5513509 original size:59 final size:59
Alignment explanation
Indices: 5513358--5513815 Score: 532
Period size: 59 Copynumber: 7.8 Consensus size: 59
5513348 GAAAATTTGG
* * **
5513358 GGTT-AAAATGGGATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGT-AATTTTA
1 GGTTAAAAATGGGATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGATGAAATCGA
* * *
5513415 GGGTT-AAAATGGGATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTTGATGGAATCGT
1 -GGTTAAAAATGGGATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGATGAAATCGA
* * * *
5513474 GGTTAAAAATGGGATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGATAAAATTGG
1 GGTTAAAAATGGGATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGATGAAATCGA
* * * * *
5513533 GGTTAAAAATGGAATTTTGGAAGGTTTGGGGGTAAAATGGTAATTTTGGGTGAAATCGA
1 GGTTAAAAATGGGATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGATGAAATCGA
* *
5513592 GGTTAAAAATGGGATTTTGGAAAG-TTCGAGGGTAAAATGGTAATTTTTAAT-AGAATCGA
1 GGTTAAAAATGGGATTTTGGAAAGTTTAG-GGGTAAAATGGTAATTTTTGATGA-AATCGA
* * * ** * *
5513651 GGTTAAAAATAGAATTTTGGAAGGTTCGGGGGTAAAATAGTAATTTTGGATGAAATCGA
1 GGTTAAAAATGGGATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGATGAAATCGA
* * * * * *
5513710 GGTCAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAATGGTAATTTTGGGTGAAATAG-
1 GGTTAAAAATGGGATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGATGAAATCGA
* * * *
5513768 GGTTAAAAACGGGATTTTAGAAAGTTTAAGGGTAAAATGGAAATTTTT
1 GGTTAAAAATGGGATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTT
5513816 AGAAGTTTCG
Statistics
Matches: 343, Mismatches: 51, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
58 98 0.29
59 242 0.71
60 3 0.01
ACGTcount: A:0.35, C:0.02, G:0.29, T:0.34
Consensus pattern (59 bp):
GGTTAAAAATGGGATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGATGAAATCGA
Found at i:5513657 original size:177 final size:176
Alignment explanation
Indices: 5513333--5513816 Score: 647
Period size: 177 Copynumber: 2.8 Consensus size: 176
5513323 CTCGATGACA
* *
5513333 AAAATGTAATTTTAGGA-AAATTTGGGGTT-AAAATGGGATTTTGGAAAGTTTAGGGGTAAAATG
1 AAAATGTAATTTT-GGATAAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATG
* * *
5513396 GTAATTTTTGGT-AATTTTAG-GGTT-AAAATGGGATTTTGGAAAGTTTGGGGGTAAAATGGTAA
65 GTAATTTTGGGTGAA--ATAGAGGTTAAAAATGGGATTTTGGAAAGTTTGAGGGTAAAATGGTAA
* * * * *
5513458 TTTTTGATGGAATCGTGGTTAAAAATGGGATTTTGGAAAGTTCAGGGGT
128 TTTTTAATAGAATCGAGGTTAAAAATAGAATTTTGGAAAGTTCAGGGGT
* * *
5513507 AAAATGGTAATTTTTGATAAAATTGGGGTTAAAAATGGAATTTTGGAAGGTTTGGGGGTAAAATG
1 AAAAT-GTAATTTTGGATAAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATG
* *
5513572 GTAATTTTGGGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAGTTCGAGGGTAAAATGGTAATT
65 GTAATTTTGGGTGAAATAGAGGTTAAAAATGGGATTTTGGAAAGTTTGAGGGTAAAATGGTAATT
* *
5513637 TTTAATAGAATCGAGGTTAAAAATAGAATTTTGGAAGGTTCGGGGGT
130 TTTAATAGAATCGAGGTTAAAAATAGAATTTTGGAAAGTTCAGGGGT
* * * * *
5513684 AAAATAGTAATTTTGGATGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAATG
1 AAAAT-GTAATTTTGGATAAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATG
* * * *
5513749 GTAATTTTGGGTGAAATAG-GGTTAAAAACGGGATTTTAGAAAGTTTAAGGGTAAAATGGAAATT
65 GTAATTTTGGGTGAAATAGAGGTTAAAAATGGGATTTTGGAAAGTTTGAGGGTAAAATGGTAATT
5513813 TTTA
130 TTTA
5513817 GAAGTTTCGA
Statistics
Matches: 272, Mismatches: 32, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
174 7 0.03
175 21 0.08
176 90 0.33
177 154 0.57
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.34
Consensus pattern (176 bp):
AAAATGTAATTTTGGATAAAATTGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGG
TAATTTTGGGTGAAATAGAGGTTAAAAATGGGATTTTGGAAAGTTTGAGGGTAAAATGGTAATTT
TTAATAGAATCGAGGTTAAAAATAGAATTTTGGAAAGTTCAGGGGT
Found at i:5513667 original size:30 final size:30
Alignment explanation
Indices: 5513448--5513733 Score: 130
Period size: 30 Copynumber: 9.6 Consensus size: 30
5513438 GTTTGGGGGT
* ** *
5513448 AAAATGGTAATTTTTGATGGAATCGTGGTTA
1 AAAATGG-AATTTTGGAAAGAATCGAGGTTA
* * *
5513479 AAAATGGGATTTTGGAAAG-TTC-AGGGGT-
1 AAAATGGAATTTTGGAAAGAATCGA-GGTTA
* * *
5513507 AAAATGGTAATTTTTGATAA-AATTGGGGTTA
1 AAAATGG-AATTTTGGA-AAGAATCGAGGTTA
** * * *
5513538 AAAATGGAATTTTGG-AAGGTTTGGGGGT-
1 AAAATGGAATTTTGGAAAGAATCGAGGTTA
**
5513566 AAAATGGTAATTTTGG-GTGAAATCGAGGTTA
1 AAAATGG-AATTTTGGAAAG-AATCGAGGTTA
* * *
5513597 AAAATGGGATTTTGGAAAG-TTCGAGGGT-
1 AAAATGGAATTTTGGAAAGAATCGAGGTTA
*
5513625 AAAATGGTAATTTT-TAATAGAATCGAGGTTA
1 AAAATGG-AATTTTGGAA-AGAATCGAGGTTA
* ** * *
5513656 AAAATAGAATTTTGG-AAGGTTCGGGGGT-
1 AAAATGGAATTTTGGAAAGAATCGAGGTTA
* * *
5513684 AAAATAGTAATTTTGG-ATGAAATCGAGGTCA
1 AAAAT-GGAATTTTGGAAAG-AATCGAGGTTA
5513715 AAAATGGAATTTTGGAAAG
1 AAAATGGAATTTTGGAAAG
5513734 TTTAAGGGTA
Statistics
Matches: 186, Mismatches: 49, Indels: 40
0.68 0.18 0.15
Matches are distributed among these distances:
28 30 0.16
29 60 0.32
30 61 0.33
31 35 0.19
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.32
Consensus pattern (30 bp):
AAAATGGAATTTTGGAAAGAATCGAGGTTA
Found at i:5513813 original size:29 final size:28
Alignment explanation
Indices: 5513715--5513823 Score: 75
Period size: 29 Copynumber: 3.8 Consensus size: 28
5513705 ATCGAGGTCA
*
5513715 AAAATGGAATTTTGGAAAGTTTAAGGGT
1 AAAATGGAATTTTAGAAAGTTTAAGGGT
*
5513743 AAAATGGTAATTTTGGGTGAAA---T-AGGGTT
1 AAAATGG-AATTTT---AGAAAGTTTAAGGG-T
* *
5513772 AAAAACGGGATTTTAGAAAGTTTAAGGGT
1 -AAAATGGAATTTTAGAAAGTTTAAGGGT
5513801 AAAATGGAAATTTTTAG-AAGTTT
1 AAAATGG-AA-TTTTAGAAAGTTT
5513824 CGAGGTCAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 23
0.68 0.07 0.25
Matches are distributed among these distances:
26 4 0.06
28 17 0.27
29 22 0.35
30 16 0.25
32 4 0.06
ACGTcount: A:0.39, C:0.01, G:0.27, T:0.33
Consensus pattern (28 bp):
AAAATGGAATTTTAGAAAGTTTAAGGGT
Found at i:5515796 original size:18 final size:18
Alignment explanation
Indices: 5515773--5515807 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
5515763 TGGGCCTATA
5515773 TTTTGTAATTGGACTTTC
1 TTTTGTAATTGGACTTTC
5515791 TTTTGTAATTGGACTTT
1 TTTTGTAATTGGACTTT
5515808 TAATTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.09, G:0.17, T:0.57
Consensus pattern (18 bp):
TTTTGTAATTGGACTTTC
Found at i:5516856 original size:201 final size:200
Alignment explanation
Indices: 5516281--5516861 Score: 881
Period size: 200 Copynumber: 2.9 Consensus size: 200
5516271 CAATTATCTA
*
5516281 TTTTAATTCGCTTTCTCTGGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTATGTCTCATC
1 TTTTAATTCGC-TTCTCTGGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTCATC
* * *
5516346 AGGAAGCTAACCTTTTTATTGCTTCAACCTGCTTCTCAGTATCTCATCAA-GAAACTGGGTTCGA
65 AGGAAGCTAACCTTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCAT-AAGGAAGCTGGGTTCGA
5516410 AGATTTGCTC-------GCGTTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCC
129 AGATTTGCTCGTGTTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCC
5516468 TCGCTTG
194 TCGCTTG
* * * *
5516475 TTTTGATTCGCTTCTCTTGATCTCCTCAGGAAGACGAATCTGGTCCACTTCTCTGTATCTCATCA
1 TTTTAATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTCATCA
* * * *
5516540 GGAAGCTAACCATTTTATTGCTTCGACCCGCTTCTCAGTGTCTTATCAGGAAGCTGGGTTCGAAG
66 GGAAGCTAACCTTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATAAGGAAGCTGGGTTCGAAG
* * *
5516605 ATTTGTTCGTGTTGAGCTTTGAGTTGGTATTCTTCTCTATATCTCATCAGGAAGATGACCGCCTC
131 ATTTGCTCGTGTTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTC
5516670 GCTTG
196 GCTTG
* *
5516675 TTTTAATTCGCTTCTCTGGATCTCTTCAGGAAGACGAATTTGGTCTACTTCTCTGTGTCTCATCA
1 TTTTAATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTCATCA
* * *
5516740 GGAAGCTAACCTTTTTTATTGCTTCGAGCTTCTTCTCAGTGTCTCATAAGGAAGCTGGGTTTGAA
66 GGAAGCTAACC-TTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATAAGGAAGCTGGGTTCGAA
* *
5516805 GATTTGCTCGTGTTGAGCGCTGAGTTGGTGTTCTTCTCTGTATCTCATCAGGAAGAT
130 GATTTGCTCGTGTTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGAT
5516862 TACCTTCTTA
Statistics
Matches: 345, Mismatches: 33, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
192 1 0.00
193 113 0.33
194 10 0.03
200 123 0.36
201 98 0.28
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (200 bp):
TTTTAATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTCATCA
GGAAGCTAACCTTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATAAGGAAGCTGGGTTCGAAG
ATTTGCTCGTGTTGAGCGTTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTC
GCTTG
Found at i:5528666 original size:28 final size:28
Alignment explanation
Indices: 5528634--5528704 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
5528624 TCTCGATGGC
* *
5528634 AAAAATGTAATTTTGGGAATTTTGAGGTT
1 AAAAATGTAATTTT-GGAAGTTTGAGGGT
* *
5528663 AAAAATGGAATTTTGGAAGTTTGGGGGT
1 AAAAATGTAATTTTGGAAGTTTGAGGGT
5528691 -AAAATGGTAATTTT
1 AAAAAT-GTAATTTT
5528705 TGGTGAAATC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 5 0.14
28 18 0.50
29 13 0.36
ACGTcount: A:0.35, C:0.00, G:0.27, T:0.38
Consensus pattern (28 bp):
AAAAATGTAATTTTGGAAGTTTGAGGGT
Found at i:5528666 original size:29 final size:29
Alignment explanation
Indices: 5528634--5528802 Score: 110
Period size: 29 Copynumber: 5.8 Consensus size: 29
5528624 TCTCGATGGC
* *
5528634 AAAAATGTAATTTTGGGAATTTTGAGGTT
1 AAAAATGGAATTTTGGGAAGTTTGAGGTT
* *
5528663 AAAAATGGAATTTT-GGAAGTTTGGGGGT
1 AAAAATGGAATTTTGGGAAGTTTGAGGTT
* **
5528691 -AAAATGGTAATTTTTGGTGAAATCGGA-GTT
1 AAAAATGG-AA-TTTTGG-GAAGTTTGAGGTT
* * ** *
5528721 AAAAATGGGATTTTGGAAAGTTCAAGGGT
1 AAAAATGGAATTTTGGGAAGTTTGAGGTT
* ** *
5528750 AAAAATGGTACTTTTTGCTAATTTTGAGGTT
1 AAAAATGG-A-ATTTTGGGAAGTTTGAGGTT
* *
5528781 AAAAATGGGATTTTGGAAAGTT
1 AAAAATGGAATTTTGGGAAGTT
5528803 CAGGGGTAAA
Statistics
Matches: 103, Mismatches: 29, Indels: 16
0.70 0.20 0.11
Matches are distributed among these distances:
27 7 0.07
28 17 0.17
29 42 0.41
30 4 0.04
31 33 0.32
ACGTcount: A:0.34, C:0.02, G:0.27, T:0.36
Consensus pattern (29 bp):
AAAAATGGAATTTTGGGAAGTTTGAGGTT
Found at i:5528843 original size:30 final size:29
Alignment explanation
Indices: 5528805--5529088 Score: 93
Period size: 29 Copynumber: 9.7 Consensus size: 29
5528795 GGAAAGTTCA
5528805 GGGG-TAAAATGGTAATTTTTGATAGAATC
1 GGGGTTAAAATGG-AATTTTTGATAGAATC
5528834 GGGGTTAAAAAT-GAGA-TTTTGA-A-AAGTTC
1 GGGGTT-AAAATGGA-ATTTTTGATAGAA--TC
5528863 GAGGG-TAAAATGGTAATTTTTGAT-GAAATC
1 G-GGGTTAAAATGG-AATTTTTGATAG-AATC
*
5528893 GAGGTTAAAAAT-GAGA-TTTTGA-A-AAGTTC
1 GGGGTT-AAAATGGA-ATTTTTGATAGAA--TC
*
5528922 AAGGG-TAAAATGGTAATTTTTGAT-GAAATC
1 -GGGGTTAAAATGG-AATTTTTGATAG-AATC
* * **
5528952 AGGGTTAAAAATGGAATTTTGGA-AGGTTC
1 GGGGTT-AAAATGGAATTTTTGATAGAATC
* * * *
5528981 GAAGG-TAAAATTGTAATTTTGGGT-GAAATC
1 G-GGGTTAAAA-TGGAATTTTTGATAG-AATC
* * * *
5529011 AGGGTTAAAAAT-GAGATTTTGGAAAG-TTC
1 GGGGTT-AAAATGGA-ATTTTTGATAGAATC
*
5529040 GGGGCTAAAATGGTAATTTTTGAT-GTAATC
1 GGGGTTAAAATGG-AATTTTTGATAG-AATC
5529070 GGGGTTAAAATGGAATTTT
1 GGGGTTAAAATGGAATTTT
5529089 GGAAGGTTCA
Statistics
Matches: 191, Mismatches: 24, Indels: 80
0.65 0.08 0.27
Matches are distributed among these distances:
27 4 0.02
28 21 0.11
29 72 0.38
30 68 0.36
31 22 0.12
32 4 0.02
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (29 bp):
GGGGTTAAAATGGAATTTTTGATAGAATC
Found at i:5528843 original size:59 final size:59
Alignment explanation
Indices: 5528659--5529223 Score: 599
Period size: 59 Copynumber: 9.6 Consensus size: 59
5528649 GGAATTTTGA
* ** *
5528659 GGTTAAAAATGGAATTTTGG-AAGTTTGGGGGTAAAATGGTAATTTTTGGTGAAATCGG
1 GGTTAAAAATGGGATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGATGAAATCGG
* * * * * * *
5528717 AGTTAAAAATGGGATTTTGGAAAGTTCAAGGGTAAAAATGGTACTTTTTGCT-AATTTTGA
1 GGTTAAAAATGGGATTTTGGAAAGTTCAGGGGT-AAAATGGTAATTTTTGATGAA-ATCGG
5528777 GGTTAAAAATGGGATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGAT-AGAATCGG
1 GGTTAAAAATGGGATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGATGA-AATCGG
* * *
5528836 GGTTAAAAATGAGATTTTGAAAAGTTC-GAGGGTAAAATGGTAATTTTTGATGAAATCGA
1 GGTTAAAAATGGGATTTTGGAAAGTTCAG-GGGTAAAATGGTAATTTTTGATGAAATCGG
* * * *
5528895 GGTTAAAAATGAGATTTTGAAAAGTTCAAGGGTAAAATGGTAATTTTTGATGAAATCAG
1 GGTTAAAAATGGGATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGATGAAATCGG
* * * * * * *
5528954 GGTTAAAAATGGAATTTTGGAAGGTTC-GAAGGTAAAATTGTAATTTTGGGTGAAATCAG
1 GGTTAAAAATGGGATTTTGGAAAGTTCAG-GGGTAAAATGGTAATTTTTGATGAAATCGG
* *
5529013 GGTTAAAAATGAGATTTTGGAAAGTTC-GGGGCTAAAATGGTAATTTTTGATGTAATCGG
1 GGTTAAAAATGGGATTTTGGAAAGTTCAGGGG-TAAAATGGTAATTTTTGATGAAATCGG
* * * ** * * **
5529072 GGTT-AAAATGGAATTTTGGAAGGTTCAAGGGTAAAATGGTAATTTCAGGTAAAATCAA
1 GGTTAAAAATGGGATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGATGAAATCGG
* * ** * * *
5529130 GG-TCAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATAGTAATTTTGGGTGAAATCGG
1 GGTTAAAAATGGGATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGATGAAATCGG
* * *
5529188 GGTTAAAAATGAGATTTTAGAAAGTT-TGGGGTAAAA
1 GGTTAAAAATGGGATTTTGGAAAGTTCAGGGGTAAAA
5529224 CGAAAATATT
Statistics
Matches: 428, Mismatches: 67, Indels: 24
0.82 0.13 0.05
Matches are distributed among these distances:
57 1 0.00
58 117 0.27
59 259 0.61
60 51 0.12
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.33
Consensus pattern (59 bp):
GGTTAAAAATGGGATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGATGAAATCGG
Found at i:5531215 original size:18 final size:18
Alignment explanation
Indices: 5531194--5531228 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5531184 TGGGCCTATA
5531194 TTTTGTAATGGGACTTTC
1 TTTTGTAATGGGACTTTC
* *
5531212 TTTTGTTATTGGACTTT
1 TTTTGTAATGGGACTTT
5531229 TTAATTTATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.09, G:0.20, T:0.57
Consensus pattern (18 bp):
TTTTGTAATGGGACTTTC
Found at i:5535602 original size:23 final size:23
Alignment explanation
Indices: 5535576--5535626 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
5535566 TTTAACAAGG
*
5535576 GTCAATATAAAATAATGATAGAT
1 GTCAATATAAAAGAATGATAGAT
* * *
5535599 GTCAATATAAGAGGATGATAGGT
1 GTCAATATAAAAGAATGATAGAT
5535622 GTCAA
1 GTCAA
5535627 AGTTAAGTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.45, C:0.06, G:0.22, T:0.27
Consensus pattern (23 bp):
GTCAATATAAAAGAATGATAGAT
Found at i:5542832 original size:24 final size:23
Alignment explanation
Indices: 5542791--5542835 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
5542781 AATTTATTTC
5542791 TTTAAATTTTTTGAATTTTTATT
1 TTTAAATTTTTTGAATTTTTATT
5542814 TTTAATATTTTTT-ATATTTTTA
1 TTTAA-ATTTTTTGA-ATTTTTA
5542836 AAATTTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (23 bp):
TTTAAATTTTTTGAATTTTTATT
Found at i:5542833 original size:18 final size:17
Alignment explanation
Indices: 5542806--5542841 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
5542796 ATTTTTTGAA
*
5542806 TTTTTATTTTTAATATT
1 TTTTTATTTTTAAAATT
5542823 TTTTATATTTTTAAAATT
1 TTTT-TATTTTTAAAATT
5542841 T
1 T
5542842 ATATGGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTTATTTTTAAAATT
Found at i:5543086 original size:18 final size:17
Alignment explanation
Indices: 5543059--5543094 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
5543049 AGTTTTTGAA
*
5543059 TTTTTATTTTTAATATT
1 TTTTTATTTTTAAAATT
5543076 TTTTATATTTTTAAAATT
1 TTTT-TATTTTTAAAATT
5543094 T
1 T
5543095 ATATGGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTTATTTTTAAAATT
Found at i:5543100 original size:253 final size:254
Alignment explanation
Indices: 5542644--5543139 Score: 933
Period size: 253 Copynumber: 2.0 Consensus size: 254
5542634 TACTATCATG
5542644 TATTCACACTAGTATATTTAAAAAAATTATATGGTTAAACATGTATATAAAAAATACATAAAAAT
1 TATTCACACTAGTATATTTAAAAAAATTATATGGTTAAACATGTATATAAAAAATACATAAAAAT
5542709 AAATTTATTTAGCACATATATAATTTTTTTTGAACCCATACATCTTTTATTTTGAATTTGAAATT
66 AAATTTATTTAGCACATATATAATTTTTTTTGAACCCATACATCTTTTATTTTGAATTTGAAATT
*
5542774 TTAAATAAATTTATTTCTTTAAATTTTTTGAATTTTTATTTTTAATATTTTTTATATTTTTAAAA
131 TTAAATAAATTTATTTCTTTAAAGTTTTTGAATTTTTATTTTTAATATTTTTTATATTTTTAAAA
5542839 TTTATATGGTTTAAAATAAGGGTGAACTATTTGACGAGTTTTATTTTAAAAAACTAGTA
196 TTTATATGGTTTAAAATAAGGGTGAACTATTTGACGAGTTTTATTTTAAAAAACTAGTA
* *
5542898 TATTCATACTAGTATATTT-AAAAAATTATATGGTTAAATATGTATATAAAAAAATACATAAAAA
1 TATTCACACTAGTATATTTAAAAAAATTATATGGTTAAACATGTATAT-AAAAAATACATAAAAA
*
5542962 TAAATTTATTTAGCACATATATAA-TTTTTTTGAACCTATACATCTTTTATTTTGAATTTGAAAT
65 TAAATTTATTTAGCACATATATAATTTTTTTTGAACCCATACATCTTTTATTTTGAATTTGAAAT
5543026 TTTAAATAAATTTATTTCTTTAAAGTTTTTGAATTTTTATTTTTAATATTTTTTATATTTTTAAA
130 TTTAAATAAATTTATTTCTTTAAAGTTTTTGAATTTTTATTTTTAATATTTTTTATATTTTTAAA
5543091 ATTTATATGGTTTAAAATAAGGGTGAACTATTTGACGAGTTTTATTTTA
195 ATTTATATGGTTTAAAATAAGGGTGAACTATTTGACGAGTTTTATTTTA
5543140 TTATCTTAAC
Statistics
Matches: 237, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
253 179 0.76
254 58 0.24
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.48
Consensus pattern (254 bp):
TATTCACACTAGTATATTTAAAAAAATTATATGGTTAAACATGTATATAAAAAATACATAAAAAT
AAATTTATTTAGCACATATATAATTTTTTTTGAACCCATACATCTTTTATTTTGAATTTGAAATT
TTAAATAAATTTATTTCTTTAAAGTTTTTGAATTTTTATTTTTAATATTTTTTATATTTTTAAAA
TTTATATGGTTTAAAATAAGGGTGAACTATTTGACGAGTTTTATTTTAAAAAACTAGTA
Found at i:5543296 original size:304 final size:306
Alignment explanation
Indices: 5542927--5543515 Score: 1042
Period size: 305 Copynumber: 1.9 Consensus size: 306
5542917 AAAAAATTAT
* *
5542927 ATGGTTAAATATGTATATAAAAAAATACATAAAAATAAATTTATTTAGCACATATATAA-TTTTT
1 ATGGTTAAACATGTATATAAAAAAATACATAAAAATAAATTTATTCAGCACATATATAATTTTTT
*
5542991 TTGAACCTATACATCTTTTATTTTGAATTTGAAATTTTAAATAAATTTATTTCTTTAAAG-TTTT
66 TTGAACCTATACATCTGTTATTTTGAATTTGAAATTTTAAATAAATTTATTTCTTT-AAGCTTTT
*
5543055 TGAATTTTTATTTTTAATATTTTTTATATTTTTAAAATTTATATGGTTTAAAATAAGGGTGAACT
130 TGAATTTTTATTTTTAATATTTTTTATATTTTTAAAATTTATATGGTTTAAAATAAGGGTGAACG
* * *
5543120 ATTTGACGAGTTTTATTTTATTATCTTAACTCGATTTGAATTTTTTTTT-AATTGAGTCAAGTGA
195 AGTTGACGAGTTTTATTTTATCATCTTAACTCGATTTG-ATTTTTTTTTGAATCGAGTCAAGTGA
5543184 AATTGTTCGAGTTAAATTAAAAAAAATCAATTATATCGAGAAATTTAC
259 AATTGTTCGAGTTAAATTAAAAAAAATCAATTATATCGAGAAATTTAC
5543232 ATGGTTAAACATGTATAT-AAAAAATACATAAAAATAAATTTATTCAGCACATATATAATTTTTT
1 ATGGTTAAACATGTATATAAAAAAATACATAAAAATAAATTTATTCAGCACATATATAATTTTTT
*
5543296 TTGAACCTATACATCTGTTATTTTGAATTTGAATTTTTAAATAAATTTATTTCTTTAAGCTTTTT
66 TTGAACCTATACATCTGTTATTTTGAATTTGAAATTTTAAATAAATTTATTTCTTTAAGCTTTTT
*
5543361 GAATTTTTATTTTTAATATTTTTTATATTTTTAAAATTTATATGGTTTAAAATAAGGGTGAGCGA
131 GAATTTTTATTTTTAATATTTTTTATATTTTTAAAATTTATATGGTTTAAAATAAGGGTGAACGA
*
5543426 GTTGACGAGTTTTATTTTATCATCTTAACTCGATTTGATTTTTTTTTGAATCGGGTCAAGTGAAA
196 GTTGACGAGTTTTATTTTATCATCTTAACTCGATTTGATTTTTTTTTGAATCGAGTCAAGTGAAA
5543491 TTGTTCGAGTTAAATTAAAAAAAAT
261 TTGTTCGAGTTAAATTAAAAAAAAT
5543516 TAAACATGTC
Statistics
Matches: 271, Mismatches: 10, Indels: 6
0.94 0.03 0.02
Matches are distributed among these distances:
304 52 0.19
305 219 0.81
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.47
Consensus pattern (306 bp):
ATGGTTAAACATGTATATAAAAAAATACATAAAAATAAATTTATTCAGCACATATATAATTTTTT
TTGAACCTATACATCTGTTATTTTGAATTTGAAATTTTAAATAAATTTATTTCTTTAAGCTTTTT
GAATTTTTATTTTTAATATTTTTTATATTTTTAAAATTTATATGGTTTAAAATAAGGGTGAACGA
GTTGACGAGTTTTATTTTATCATCTTAACTCGATTTGATTTTTTTTTGAATCGAGTCAAGTGAAA
TTGTTCGAGTTAAATTAAAAAAAATCAATTATATCGAGAAATTTAC
Found at i:5543391 original size:18 final size:17
Alignment explanation
Indices: 5543364--5543399 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
5543354 GCTTTTTGAA
*
5543364 TTTTTATTTTTAATATT
1 TTTTTATTTTTAAAATT
5543381 TTTTATATTTTTAAAATT
1 TTTT-TATTTTTAAAATT
5543399 T
1 T
5543400 ATATGGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTTATTTTTAAAATT
Found at i:5560049 original size:14 final size:13
Alignment explanation
Indices: 5560008--5560050 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
5559998 TATTTTATTT
*
5560008 AAATTAAAAATTA
1 AAATTAAAAAGTA
5560021 AAATT-AAAAGATA
1 AAATTAAAAAG-TA
5560034 AAATTTAAAAAGTA
1 AAA-TTAAAAAGTA
5560048 AAA
1 AAA
5560051 ATAGGGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 4 0.15
13 10 0.38
14 7 0.27
15 5 0.19
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (13 bp):
AAATTAAAAAGTA
Found at i:5565033 original size:6 final size:6
Alignment explanation
Indices: 5565024--5565083 Score: 77
Period size: 6 Copynumber: 10.0 Consensus size: 6
5565014 TCCACCATCG
* *
5565024 GCTCCA GCTCCA GCTCCA GCTCCA GCTCCA GCTCC- GACTCCG GCTCCG
1 GCTCCA GCTCCA GCTCCA GCTCCA GCTCCA GCTCCA G-CTCCA GCTCCA
*
5565072 GCTCCG GCTCCA
1 GCTCCA GCTCCA
5565084 CCACCTCCAC
Statistics
Matches: 51, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
5 1 0.02
6 49 0.96
7 1 0.02
ACGTcount: A:0.12, C:0.50, G:0.22, T:0.17
Consensus pattern (6 bp):
GCTCCA
Found at i:5579048 original size:18 final size:18
Alignment explanation
Indices: 5579008--5579050 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
5578998 GTTCAATGTA
5579008 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
5579026 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
5579044 TAATTAA
1 TAATTAA
5579051 AAACCTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:5582178 original size:22 final size:22
Alignment explanation
Indices: 5582147--5582188 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
5582137 ACCCATTGAC
*
5582147 GAAGTTGATATCGTGATACCCA
1 GAAGTGGATATCGTGATACCCA
5582169 GAAGTGGATATCGTGATACC
1 GAAGTGGATATCGTGATACC
5582189 TCGAGCAGTG
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:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (22 bp):
GAAGTGGATATCGTGATACCCA
Found at i:5584549 original size:41 final size:42
Alignment explanation
Indices: 5584504--5584607 Score: 140
Period size: 41 Copynumber: 2.5 Consensus size: 42
5584494 AGTACATCGG
* * **
5584504 CATAAAGCCTGCTAGACACTAA-GCTCGATACAATCCACCAA
1 CATAAAGCCTGCTAGGCACTAAGGCCCGATACAATAAACCAA
*
5584545 CATAAAGCCTGCTAGGC-CTAAGGCCCGATACAATAAACCGA
1 CATAAAGCCTGCTAGGCACTAAGGCCCGATACAATAAACCAA
*
5584586 CATAAAGCTTGCTAGGCACTAA
1 CATAAAGCCTGCTAGGCACTAA
5584608 AAAACCATAA
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
40 4 0.07
41 47 0.85
42 4 0.07
ACGTcount: A:0.38, C:0.29, G:0.16, T:0.17
Consensus pattern (42 bp):
CATAAAGCCTGCTAGGCACTAAGGCCCGATACAATAAACCAA
Found at i:5593339 original size:25 final size:24
Alignment explanation
Indices: 5593290--5593341 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
5593280 GTTAAAAAAC
* *
5593290 AAAAAATAAATTATAAATTTGTAA
1 AAAAAACAAATTATAAATATGTAA
5593314 AAAAAACAAATTTATAAAATAT-TAA
1 AAAAAACAAA-TTAT-AAATATGTAA
5593339 AAA
1 AAA
5593342 TTAATAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 9 0.38
25 10 0.42
26 5 0.21
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (24 bp):
AAAAAACAAATTATAAATATGTAA
Found at i:5599583 original size:33 final size:33
Alignment explanation
Indices: 5599532--5599603 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
5599522 TTGGCTTGTA
*
5599532 TTTGATGGTGTTTCGAATGCCATGATAGGGGAG
1 TTTGTTGGTGTTTCGAATGCCATGATAGGGGAG
* * *
5599565 TTTGTTGGTGTTTTGAATGCCGTGATAGGTGAG
1 TTTGTTGGTGTTTCGAATGCCATGATAGGGGAG
5599598 TTTGTT
1 TTTGTT
5599604 TCACTTTGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.17, C:0.07, G:0.35, T:0.42
Consensus pattern (33 bp):
TTTGTTGGTGTTTCGAATGCCATGATAGGGGAG
Found at i:5608346 original size:96 final size:96
Alignment explanation
Indices: 5608172--5608363 Score: 289
Period size: 96 Copynumber: 2.0 Consensus size: 96
5608162 ACTTTTGGAA
* *
5608172 AAGGATATTCGATTATCTCGATTTGAAGAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGATATTCGATTATCTCGACTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCA
*
5608237 AAACCAGAGATAAA-GAAGCATTGCCTCGATT
66 AAACCAGAAATAAAGGAA-CATTGCCTCGATT
* * *
5608268 AAGGGTATTCGATTATTTCGACTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGATATTCGATTATCTCGACTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCA
*
5608333 AAACTC-GAAATAAAGGAATATTGCCTCGATT
66 AAAC-CAGAAATAAAGGAACATTGCCTCGATT
5608364 TTAAAGGTTT
Statistics
Matches: 87, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
96 83 0.95
97 4 0.05
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGACTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCA
AAACCAGAAATAAAGGAACATTGCCTCGATT
Found at i:5608620 original size:29 final size:29
Alignment explanation
Indices: 5608582--5609027 Score: 307
Period size: 29 Copynumber: 15.2 Consensus size: 29
5608572 TCGAAAATGC
* *
5608582 AATTTTTGGATGCTCGAGGGTAAAATGGT
1 AATTTTTGGAAGTTCGAGGGTAAAATGGT
5608611 AATTTTTGGATA-TTCGAGGGTAAAATGGT
1 AATTTTTGGA-AGTTCGAGGGTAAAATGGT
*
5608640 AATTTTTGGAAAGTTC-AAGGTCAAAAATGG-
1 AATTTTTGG-AAGTTCGAGGGT--AAAATGGT
* * *
5608670 ATTTTTTAGATA-TTCGGGGGTAAAATGGT
1 AATTTTTGGA-AGTTCGAGGGTAAAATGGT
* *
5608699 AA-TTTTGGAATGTTTG-GGGTCCAAACT-GT
1 AATTTTTGGAA-GTTCGAGGGT--AAAATGGT
** *
5608728 AATTTTTGGAAGTTTAAGGGTAAAATGGA
1 AATTTTTGGAAGTTCGAGGGTAAAATGGT
*
5608757 AATTTTTGAAAGTAT-GAGGGTAAAATGGT
1 AATTTTTGGAAGT-TCGAGGGTAAAATGGT
* *
5608786 AATTTTTGGAAAATTTG-GGGTAAAAATGG-
1 AATTTTTGG-AAGTTCGAGGGT-AAAATGGT
* *
5608815 AACTTTTGGAGGTTCGA-GGTCAAAAATGG-
1 AATTTTTGGAAGTTCGAGGGT--AAAATGGT
* *
5608844 AATTTTTGTAAGTTTGAGGGTAAAATGGT
1 AATTTTTGGAAGTTCGAGGGTAAAATGGT
* *
5608873 AATTTTTGGAAAATTTG-GGGTCAAATATGG-
1 AATTTTTGG-AAGTTCGAGGGT-AAA-ATGGT
*
5608903 AATTTTTGGAAGTTCGGGGGTTAAAAT-GT
1 AATTTTTGGAAGTTCGAGGG-TAAAATGGT
*
5608932 AATTTTTGGAAGCTCGAGGGTCAAAAT-GT
1 AATTTTTGGAAGTTCGAGGGT-AAAATGGT
* ** *
5608961 AATTTTTGAAAAACTCGAGGGTCAAAAT-AT
1 AATTTTTG-GAAGTTCGAGGGT-AAAATGGT
* * *
5608991 AATTTTTGAAAAGTTTGAGGGTCAAGAT-GT
1 AATTTTTG-GAAGTTCGAGGGT-AAAATGGT
5609021 AATTTTT
1 AATTTTT
5609028 AAAAAGTTTG
Statistics
Matches: 345, Mismatches: 41, Indels: 61
0.77 0.09 0.14
Matches are distributed among these distances:
27 1 0.00
28 37 0.11
29 175 0.51
30 120 0.35
31 12 0.03
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.36
Consensus pattern (29 bp):
AATTTTTGGAAGTTCGAGGGTAAAATGGT
Found at i:5608691 original size:59 final size:60
Alignment explanation
Indices: 5608603--5609027 Score: 309
Period size: 59 Copynumber: 7.2 Consensus size: 60
5608593 GCTCGAGGGT
**
5608603 AAAATGGTAATTTTTGGATATTCGAGGGTAAAATGGTAATTTTTGGAAAGTTCAAGGTCA
1 AAAATGGTAATTTTTGGATATTCGAGGGTAAAATGGTAATTTTTGGAAAGTTCGGGGTCA
* * * * * *
5608663 AAAATGG-ATTTTTTAGATATTCGGGGGTAAAATGGTAA-TTTTGGAATGTTTGGGGTCC
1 AAAATGGTAATTTTTGGATATTCGAGGGTAAAATGGTAATTTTTGGAAAGTTCGGGGTCA
* ** *
5608721 AAACT-GTAATTTTTGGA-AGTTTAAGGGTAAAATGGAAATTTTT-GAAAGTAT-GAGGGT--
1 AAAATGGTAATTTTTGGATA-TTCGAGGGTAAAATGGTAATTTTTGGAAAGT-TCG-GGGTCA
* * * * *
5608778 AAAATGGTAATTTTTGGAAAATTTG-GGGTAAAAATGG-AACTTTTGG-AGGTTCGAGGTCA
1 AAAATGGTAATTTTTGG-ATATTCGAGGGT-AAAATGGTAATTTTTGGAAAGTTCGGGGTCA
* * * *
5608837 AAAATGG-AATTTTTGTA-AGTTTGAGGGTAAAATGGTAATTTTTGGAAAATTTGGGGTCA
1 AAAATGGTAATTTTTGGATA-TTCGAGGGTAAAATGGTAATTTTTGGAAAGTTCGGGGTCA
* * *
5608896 AATATGG-AATTTTTGGA-AGTTCGGGGGTTAAAAT-GTAATTTTTGG-AAGCTCGAGGGTC-
1 AAAATGGTAATTTTTGGATA-TTCGAGGG-TAAAATGGTAATTTTTGGAAAGTTCG-GGGTCA
* * * * * *
5608954 AAAAT-GTAATTTTTGAAAAACTCGAGGGTCAAAAT-ATAATTTTTGAAAAGTTTGAGGGTC-
1 AAAATGGTAATTTTTG-GATATTCGAGGGT-AAAATGGTAATTTTTGGAAAGTTCG-GGGTCA
*
5609014 AAGAT-GTAATTTTT
1 AAAATGGTAATTTTT
5609028 AAAAAGTTTG
Statistics
Matches: 298, Mismatches: 43, Indels: 48
0.77 0.11 0.12
Matches are distributed among these distances:
56 1 0.00
57 23 0.08
58 110 0.37
59 125 0.42
60 39 0.13
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (60 bp):
AAAATGGTAATTTTTGGATATTCGAGGGTAAAATGGTAATTTTTGGAAAGTTCGGGGTCA
Found at i:5608788 original size:87 final size:86
Alignment explanation
Indices: 5608597--5608998 Score: 370
Period size: 88 Copynumber: 4.6 Consensus size: 86
5608587 TTGGATGCTC
* *
5608597 GAGGGTAAAATGGTAATTTTTGG-ATATTCGAGGGT-AAAATGGTAATTTTTGGAAAGTTCAAGG
1 GAGGGTAAAATGGTAATTTTTGGAAAATTTG-GGGTCAAAATGG-AATTTTTGG-AAGTTCAAGG
* *
5608660 TCAAAAATGG-ATTTTTTAGA-TATT
63 T-AAAAATGGAATTTTTGAAAGTA-T
* ** * * *
5608684 CGGGGGTAAAATGGTAA-TTTTGGAATGTTTGGGGTCCAAACTGTAATTTTTGGAAGTTTAAGGG
1 -GAGGGTAAAATGGTAATTTTTGGAAAATTTGGGGT-CAAAATGGAATTTTTGGAAGTTCAA-GG
5608748 T-AAAATGGAAATTTTTGAAAGTAT
63 TAAAAATGG-AATTTTTGAAAGTAT
* * * *
5608772 GAGGGTAAAATGGTAATTTTTGGAAAATTTGGGGTAAAAATGGAACTTTTGGAGGTTCGAGGTCA
1 GAGGGTAAAATGGTAATTTTTGGAAAATTTGGGGTCAAAATGGAATTTTTGGAAGTTCAAGGT-A
* *
5608837 AAAATGGAATTTTTGTAAGTTT
65 AAAATGGAATTTTTGAAAGTAT
**
5608859 GAGGGTAAAATGGTAATTTTTGGAAAATTTGGGGTCAAATATGGAATTTTTGGAAGTTCGGGGGT
1 GAGGGTAAAATGGTAATTTTTGGAAAATTTGGGGTCAAA-ATGGAATTTTTGGAAGTTC-AAGGT
* * * *
5608924 TAAAATGTAATTTTTGGAAGCT-C
64 AAAAATGGAATTTTTGAAAG-TAT
* * * **
5608947 GAGGGTCAAAAT-GTAATTTTTGAAAAACTCGAGGGTCAAAATATAATTTTTG
1 GAGGGT-AAAATGGTAATTTTTGGAAAATTTG-GGGTCAAAATGGAATTTTTG
5608999 AAAAGTTTGA
Statistics
Matches: 266, Mismatches: 33, Indels: 30
0.81 0.10 0.09
Matches are distributed among these distances:
86 10 0.04
87 101 0.38
88 130 0.49
89 25 0.09
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.35
Consensus pattern (86 bp):
GAGGGTAAAATGGTAATTTTTGGAAAATTTGGGGTCAAAATGGAATTTTTGGAAGTTCAAGGTAA
AAATGGAATTTTTGAAAGTAT
Found at i:5609021 original size:60 final size:60
Alignment explanation
Indices: 5608597--5609071 Score: 222
Period size: 59 Copynumber: 8.1 Consensus size: 60
5608587 TTGGATGCTC
* * * *
5608597 GAGGGT-AAAATGGTAATTTTTG-GATATTCGAGGGT-AAAATGGTAATTTTTGGAAAG-TT
1 GAGGGTCAAAAT-GTAATTTTTGAAAAATTCGAGGGTCAAAAT-ATAATTTTTGAAAAGTTT
* * * * * * * * * *
5608655 CAAGGTCAAAAATG-GATTTTTTAGATATTCGGGGGT-AAAATGGTAA-TTTTGGAATGTTT
1 GAGGGTC-AAAATGTAATTTTTGAAAAATTCGAGGGTCAAAAT-ATAATTTTTGAAAAGTTT
* * * ** *
5608714 G-GGGTCCAAACTGTAATTTTTG-GAAGTTTAAGGGT-AAAATGGA-AATTTTTG-AAAGTAT
1 GAGGGT-CAAAATGTAATTTTTGAAAAATTCGAGGGTCAAAAT--ATAATTTTTGAAAAGTTT
* * * ** * * * *
5608772 GAGGGT-AAAATGGTAATTTTTGGAAAATTTG-GGGTAAAAATGGAACTTTTG-GAGGTTC
1 GAGGGTCAAAAT-GTAATTTTTGAAAAATTCGAGGGTCAAAATATAATTTTTGAAAAGTTT
* * * * *
5608830 GA-GGTCAAAAATGGAATTTTTG-TAAGTTTGAGGGT-AAAATGGTAATTTTTGGAAAA-TTT
1 GAGGGTC-AAAATGTAATTTTTGAAAAATTCGAGGGTCAAAAT-ATAATTTTT-GAAAAGTTT
* * * * * * * * *
5608889 G-GGGTCAAATATGGAATTTTTG-GAAGTTCGGGGGTTAAAATGTAATTTTTG-GAAGCTC
1 GAGGGTCAAA-ATGTAATTTTTGAAAAATTCGAGGGTCAAAATATAATTTTTGAAAAGTTT
*
5608947 GAGGGTCAAAATGTAATTTTTGAAAAACTCGAGGGTCAAAATATAATTTTTGAAAAGTTT
1 GAGGGTCAAAATGTAATTTTTGAAAAATTCGAGGGTCAAAATATAATTTTTGAAAAGTTT
* * * * *
5609007 GAGGGTCAAGATGTAATTTTT-AAAAAGTTTGAGGGTCAAAATATGATTTCTAAAAAGTTT
1 GAGGGTCAAAATGTAATTTTTGAAAAA-TTCGAGGGTCAAAATATAATTTTTGAAAAGTTT
5609067 AGAGG
1 -GAGG
5609072 CCTTTTGAGT
Statistics
Matches: 330, Mismatches: 59, Indels: 53
0.75 0.13 0.12
Matches are distributed among these distances:
57 20 0.06
58 111 0.34
59 132 0.40
60 63 0.19
61 4 0.01
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.35
Consensus pattern (60 bp):
GAGGGTCAAAATGTAATTTTTGAAAAATTCGAGGGTCAAAATATAATTTTTGAAAAGTTT
Found at i:5609061 original size:30 final size:30
Alignment explanation
Indices: 5608853--5609071 Score: 155
Period size: 30 Copynumber: 7.3 Consensus size: 30
5608843 GAATTTTTGT
* *
5608853 AAGTTTGAGGGT-AAAATGGTAATTTTTGGAA
1 AAGTTTGAGGGTCAAAAT-ATAATTTTT-AAA
**
5608884 AA-TTTG-GGGTC-AAATATGGAATTTTT-GG
1 AAGTTTGAGGGTCAAAATAT--AATTTTTAAA
* * * * **
5608912 AAGTTCGGGGGTTAAAATGTAATTTTT-GG
1 AAGTTTGAGGGTCAAAATATAATTTTTAAA
* * *
5608941 AAGCTCGAGGGTCAAAATGTAATTTTTGAAA
1 AAGTTTGAGGGTCAAAATATAATTTTT-AAA
* * *
5608972 AA-CTCGAGGGTCAAAATATAATTTTTGAA
1 AAGTTTGAGGGTCAAAATATAATTTTTAAA
* *
5609001 AAGTTTGAGGGTCAAGATGTAATTTTTAAA
1 AAGTTTGAGGGTCAAAATATAATTTTTAAA
* *
5609031 AAGTTTGAGGGTCAAAATATGATTTCTAAA
1 AAGTTTGAGGGTCAAAATATAATTTTTAAA
5609061 AAGTTTAGAGG
1 AAGTTT-GAGG
5609072 CCTTTTGAGT
Statistics
Matches: 156, Mismatches: 22, Indels: 20
0.79 0.11 0.10
Matches are distributed among these distances:
28 3 0.02
29 48 0.31
30 92 0.59
31 13 0.08
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.34
Consensus pattern (30 bp):
AAGTTTGAGGGTCAAAATATAATTTTTAAA
Found at i:5609965 original size:16 final size:17
Alignment explanation
Indices: 5609944--5609976 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5609934 GTTGTACTTT
5609944 TTCA-TTTAAAAATCTG
1 TTCATTTTAAAAATCTG
*
5609960 TTCATTTTAGAAATCTG
1 TTCATTTTAAAAATCTG
5609977 AAATGGGTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.45
Consensus pattern (17 bp):
TTCATTTTAAAAATCTG
Found at i:5610200 original size:30 final size:29
Alignment explanation
Indices: 5610164--5610221 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
5610154 TCCTTTTTTG
* *
5610164 TTATTATTAATTAATATTTAAAAAATATTA
1 TTATTATTAATTAAGA-CTAAAAAATATTA
*
5610194 TTATTATTTATTAAGACTAAAAAATATT
1 TTATTATTAATTAAGACTAAAAAATATT
5610222 TAATATGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (29 bp):
TTATTATTAATTAAGACTAAAAAATATTA
Found at i:5612188 original size:201 final size:201
Alignment explanation
Indices: 5611836--5612677 Score: 1296
Period size: 201 Copynumber: 4.2 Consensus size: 201
5611826 ATTCAGTCTT
* * * * *
5611836 CTTCTCAGTATCTCATCAGGAAGATGA-CTGCATCGCTTATTTCAATCCGCTTCTCTGTATCTCA
1 CTTCTCTGTATCTCATCAGGAAGATGATC-GCCTCACTTATTTCAATCTGCTCCTCTGTATCTCA
5611900 TCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCG
65 TCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCG
* * * ** *
5611965 ACCTGCTTCTCAATACCTCATCAGGATGCCAAGGTTCGAAGATTTGCTCGCATTGAGCTTTGAGT
130 ACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCGCATTGAGCCTTGAGT
5612030 TGGTATA
195 TGGTATA
*
5612037 CTTCTCTGTATCTCATCAAGAAGATGA-CTGCCTCACTTATTTCAA-CTTGCTCCTCTGTATCTC
1 CTTCTCTGTATCTCATCAGGAAGATGATC-GCCTCACTTATTTCAATC-TGCTCCTCTGTATCTC
* * * * *
5612100 ATTAGGAAGATGAATTTGGTCCACTTCTCAATATCTCATCAGGAAGCTAAACATTTTATTGCTTC
64 ATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTC
* * *
5612165 GACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTTGAAGATTTGCTCGCTTTGAGCCTTGAG
129 GACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCGCATTGAGCCTTGAG
5612230 TTGGTATA
194 TTGGTATA
* *
5612238 CTTCTCTCTATCTCATCAGGAAGATGATCGCCTCACTTTTTTCAATCTGCTCCTCTGTATCTCAT
1 CTTCTCTGTATCTCATCAGGAAGATGATCGCCTCACTTATTTCAATCTGCTCCTCTGTATCTCAT
* * *
5612303 CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTTATCAGGAAGCTAACCATTTTATTTCTTCGA
66 CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGA
*
5612368 CCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCGCATTAAGCCTTGAGTT
131 CCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCGCATTGAGCCTTGAGTT
5612433 GGTATA
196 GGTATA
* * *
5612439 CTTCTCTGTATCTCATCAAGAAGATGATCGCCTCACTTGTTTCAAT-TCGCTTCTCTGTATCTCA
1 CTTCTCTGTATCTCATCAGGAAGATGATCGCCTCACTTATTTCAATCT-GCTCCTCTGTATCTCA
* *
5612503 TCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTACTTCG
65 TCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCG
* * *
5612568 ACCTGCTTCTCATTATCTCATCAGGAAGCTGGGGTTCGAAGAGTTGCTCGCATTGAGCCTTGAGT
130 ACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCGCATTGAGCCTTGAGT
5612633 TGGTATA
195 TGGTATA
* *
5612640 CTTCTCTATATCTCATTAGGAAGATGATCGCCTCACTT
1 CTTCTCTGTATCTCATCAGGAAGATGATCGCCTCACTT
5612678 TTTGTGGACA
Statistics
Matches: 589, Mismatches: 48, Indels: 8
0.91 0.07 0.01
Matches are distributed among these distances:
200 2 0.00
201 585 0.99
202 2 0.00
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.35
Consensus pattern (201 bp):
CTTCTCTGTATCTCATCAGGAAGATGATCGCCTCACTTATTTCAATCTGCTCCTCTGTATCTCAT
CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCGA
CCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCGCATTGAGCCTTGAGTT
GGTATA
Found at i:5618004 original size:13 final size:13
Alignment explanation
Indices: 5617986--5618016 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
5617976 ATTAAACGTC
5617986 CTTCATTTATTAA
1 CTTCATTTATTAA
5617999 CTTCATTTATTAA
1 CTTCATTTATTAA
5618012 CTTCA
1 CTTCA
5618017 CTTTCTGGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.29, C:0.19, G:0.00, T:0.52
Consensus pattern (13 bp):
CTTCATTTATTAA
Found at i:5623476 original size:421 final size:421
Alignment explanation
Indices: 5622692--5623529 Score: 1604
Period size: 421 Copynumber: 2.0 Consensus size: 421
5622682 GTCGGTGTCA
5622692 TGTCCACATTCTCAAAAGTGAAGCAACTGTAGGCTGGGTTCCAATGCTGCGCTAAGGCTCGAAAG
1 TGTCCACATTCTCAAAAGTGAAGCAACTGTAGGCTGGGTTCCAATGCTGCGCTAAGGCTCGAAAG
5622757 AGGAACTTATCTACCTTAACCTCGAACAAGTGTGGTAAATCTCCGTATTCTCGATAAAAAGTCTG
66 AGGAACTTATCTACCTTAACCTCGAACAAGTGTGGTAAATCTCCGTATTCTCGATAAAAAGTCTG
5622822 CTTCATGTCATTATCCTAACTGTCCCATATCTCTTTCAATTCTTGCACACTGTTTTGAGCCGTAC
131 CTTCATGTCATTATCCTAACTGTCCCATATCTCTTTCAATTCTTGCACACTGTTTTGAGCCGTAC
* *
5622887 TAATCCTGGTATAATCCCAAAGGTCTGACTCATATCCTTTTACTAAGCTATCCCCTTTTTGGCGT
196 TAATCCTGGTATAAACCCAAAGGTCTGACTCATATCCTTCTACTAAGCTATCCCCTTTTTGGCGT
*
5622952 TGAGTCTCCTTTGACCACATACGCACAACCATATTGCCTTCCACCTTATCAAGGTACTTGTTTTC
261 TGAGTCTCCTCTGACCACATACGCACAACCATATTGCCTTCCACCTTATCAAGGTACTTGTTTTC
5623017 CATGATCGATTCTCTTATCGGTAATTGAACTTTTGAATCTATACCCTTCCTTTTATGATGATGAA
326 CATGATCGATTCTCTTATCGGTAATTGAACTTTTGAATCTATACCCTTCCTTTTATGATGATGAA
5623082 ATGCAATGCAAAAGAGACAAGATAAAAGTCT
391 ATGCAATGCAAAAGAGACAAGATAAAAGTCT
*
5623113 TGTCCACATTCTCAAAAGTGAAGCAACTGTAGGTTGGGTTCCAATGCTGCGCTAAGGCTCGAAAG
1 TGTCCACATTCTCAAAAGTGAAGCAACTGTAGGCTGGGTTCCAATGCTGCGCTAAGGCTCGAAAG
5623178 AGGAACTTATCTACCTTAACCTCGAACAAGTGTGGTAAATCTCCGTATTCTCGATAAAAAGTCTG
66 AGGAACTTATCTACCTTAACCTCGAACAAGTGTGGTAAATCTCCGTATTCTCGATAAAAAGTCTG
* *
5623243 TTTCATGTCATTATCCTAACTGTCCCATATCTCTTTCAATTCTTGCACACTGTTTTGAGCCGTAT
131 CTTCATGTCATTATCCTAACTGTCCCATATCTCTTTCAATTCTTGCACACTGTTTTGAGCCGTAC
5623308 TAATCCTGGTATAAACCCAAAGGTCTGACTCATATCCTTCTACTAAGCTATCCCCTTTTTGGCGT
196 TAATCCTGGTATAAACCCAAAGGTCTGACTCATATCCTTCTACTAAGCTATCCCCTTTTTGGCGT
* *
5623373 TGAGTCTCCTCTGACCACATATGCACAACCATATTGCCTTCCACCTTATTAAGGTACTTGTTTTC
261 TGAGTCTCCTCTGACCACATACGCACAACCATATTGCCTTCCACCTTATCAAGGTACTTGTTTTC
5623438 CATGATCGATTCTCTTATCGGTAATTGAACTTTTGAATCTATACCCTTCCTTTTATGATGATGAA
326 CATGATCGATTCTCTTATCGGTAATTGAACTTTTGAATCTATACCCTTCCTTTTATGATGATGAA
5623503 ATGCAATGCAAAAGAGACAAGATAAAA
391 ATGCAATGCAAAAGAGACAAGATAAAA
5623530 CAAGTTAGCA
Statistics
Matches: 409, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
421 409 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.33
Consensus pattern (421 bp):
TGTCCACATTCTCAAAAGTGAAGCAACTGTAGGCTGGGTTCCAATGCTGCGCTAAGGCTCGAAAG
AGGAACTTATCTACCTTAACCTCGAACAAGTGTGGTAAATCTCCGTATTCTCGATAAAAAGTCTG
CTTCATGTCATTATCCTAACTGTCCCATATCTCTTTCAATTCTTGCACACTGTTTTGAGCCGTAC
TAATCCTGGTATAAACCCAAAGGTCTGACTCATATCCTTCTACTAAGCTATCCCCTTTTTGGCGT
TGAGTCTCCTCTGACCACATACGCACAACCATATTGCCTTCCACCTTATCAAGGTACTTGTTTTC
CATGATCGATTCTCTTATCGGTAATTGAACTTTTGAATCTATACCCTTCCTTTTATGATGATGAA
ATGCAATGCAAAAGAGACAAGATAAAAGTCT
Found at i:5627487 original size:55 final size:55
Alignment explanation
Indices: 5627415--5627550 Score: 211
Period size: 55 Copynumber: 2.5 Consensus size: 55
5627405 TGCTCGCACA
5627415 TGGTCTGTCCGCATGACAGCTCGCACCATTGCCTGCTCCCAAGTCTGC-ACGTTTT
1 TGGTCTGTCCGCATGACAGCTCGCACCATTGCCTGCTCCCAAGTCTGCTA-GTTTT
* *
5627470 TGGTCTGTCCGCATGACAGCTCGCGCCATTGCCTGCTCCTAAGTCTGCTAGTTTT
1 TGGTCTGTCCGCATGACAGCTCGCACCATTGCCTGCTCCCAAGTCTGCTAGTTTT
* * *
5627525 TGGTCTGTTCACGTGACAGCTCGCAC
1 TGGTCTGTCCGCATGACAGCTCGCAC
5627551 TTTACCTATT
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
55 73 0.99
56 1 0.01
ACGTcount: A:0.14, C:0.32, G:0.24, T:0.30
Consensus pattern (55 bp):
TGGTCTGTCCGCATGACAGCTCGCACCATTGCCTGCTCCCAAGTCTGCTAGTTTT
Found at i:5631495 original size:15 final size:13
Alignment explanation
Indices: 5631463--5631487 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5631453 TATTCAAGTT
5631463 TTTTTAATTAATC
1 TTTTTAATTAATC
5631476 TTTTTAATTAAT
1 TTTTTAATTAAT
5631488 AACTTTTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATC
Found at i:5631640 original size:33 final size:32
Alignment explanation
Indices: 5631505--5631640 Score: 91
Period size: 33 Copynumber: 4.2 Consensus size: 32
5631495 TTATTTATAT
*
5631505 AAATAAATTAATAAATATGTAATCATATAATA
1 AAATAAATTAATAAATATGTAATTATATAATA
* * * * * *
5631537 AAA-AATATATTATATATATATCATTATGT-TTA
1 AAATAA-AT-TAATAAATATGTAATTATATAATA
** *
5631569 AAATATTTTTAATTAATAAT-TAATTA-ATTAATA
1 AAATA-AATTAATAAAT-ATGTAATTATA-TAATA
5631602 TAAATAAATTAATAAATATGTAATTATATAATGA
1 -AAATAAATTAATAAATATGTAATTATATAAT-A
5631636 AAATA
1 AAATA
5631641 TATAATTTTT
Statistics
Matches: 75, Mismatches: 18, Indels: 21
0.66 0.16 0.18
Matches are distributed among these distances:
31 2 0.03
32 23 0.31
33 43 0.57
34 7 0.09
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (32 bp):
AAATAAATTAATAAATATGTAATTATATAATA
Found at i:5631936 original size:19 final size:19
Alignment explanation
Indices: 5631914--5631957 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
5631904 TAATCATTTC
*
5631914 AAATATCATTATTT-TAAGT
1 AAATATAATT-TTTATAAGT
*
5631933 AAATATAATTTTTATATGT
1 AAATATAATTTTTATAAGT
5631952 AAATAT
1 AAATAT
5631958 TTATTTTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (19 bp):
AAATATAATTTTTATAAGT
Found at i:5632093 original size:22 final size:23
Alignment explanation
Indices: 5632031--5632093 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 23
5632021 AAATATCTAT
5632031 TTGAAATATTTCACAT-ATAAAC
1 TTGAAATATTTCACATAATAAAC
* * * * *
5632053 ATAATAATATTTAAAATAATTAA-
1 TTGA-AATATTTCACATAATAAAC
5632076 TTGAAATATTTCACATAA
1 TTGAAATATTTCACATAA
5632094 AAAAATAAGG
Statistics
Matches: 30, Mismatches: 9, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
22 14 0.47
23 12 0.40
24 4 0.13
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (23 bp):
TTGAAATATTTCACATAATAAAC
Found at i:5632298 original size:80 final size:80
Alignment explanation
Indices: 5632138--5632526 Score: 425
Period size: 80 Copynumber: 4.9 Consensus size: 80
5632128 TTATATCATT
* * * *
5632138 TTTTTTTTGCTTTACTTG--C-ATAAAGATTCATTGAGTTAATACAATAATAA--TAT--TAGTA
1 TTTTTTTTGCCTTACTTGCACAATAAAGATTCATTGAATTAGTACAATAATAACCAATGATAGTA
* *
5632196 ATATTATTTTTTACA
66 ATATTGTCTTTTACA
* ** *
5632211 TTTTTTTTGCCTTACTTGCACAATAAAAATTCATTGAATTAGTACAATAATAAAAAATAATAGTA
1 TTTTTTTTGCCTTACTTGCACAATAAAGATTCATTGAATTAGTACAATAATAACCAATGATAGTA
5632276 ATATTGTCTTTTACA
66 ATATTGTCTTTTACA
* * * * *
5632291 TTTTTTTTTGGCCTTACTTGCACAAAAAAAATTCATTGAATTAGTACAACAATAACTAATGATGG
1 -TTTTTTTT-GCCTTACTTGCACAATAAAGATTCATTGAATTAGTACAATAATAACCAATGATAG
* *
5632356 TAATATTGTCTTCTGCA
64 TAATATTGTCTTTTACA
* * * * * *
5632373 -TTTTTTGGTCTTACTTGCACAATAGAGATTCATTAAATTAGTATAATAATAACCAATGATAATA
1 TTTTTTTTGCCTTACTTGCACAATAAAGATTCATTGAATTAGTACAATAATAACCAATGATAGTA
** * *
5632437 ACGTTCTCTTTTATA
66 ATATTGTCTTTTACA
* * * *
5632452 TTTTTTTGGACTTACTTGCACAATAGAGATTCATTGAATTAGTACAACAATAACCAATGATAGTA
1 TTTTTTTTGCCTTACTTGCACAATAAAGATTCATTGAATTAGTACAATAATAACCAATGATAGTA
5632517 ATATTGTCTT
66 ATATTGTCTT
5632527 CTGCATTGAA
Statistics
Matches: 266, Mismatches: 40, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
73 17 0.06
75 1 0.00
76 28 0.11
78 2 0.01
79 56 0.21
80 90 0.34
81 8 0.03
82 64 0.24
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (80 bp):
TTTTTTTTGCCTTACTTGCACAATAAAGATTCATTGAATTAGTACAATAATAACCAATGATAGTA
ATATTGTCTTTTACA
Found at i:5632511 original size:159 final size:160
Alignment explanation
Indices: 5632212--5632533 Score: 448
Period size: 159 Copynumber: 2.0 Consensus size: 160
5632202 TTTTTTACAT
* * *
5632212 TTTTTTTGCCTTACTTGCACAATAAAAATTCATTGAATTAGTACAATAATAAAAAATAATAGTAA
1 TTTTTTGGCCTTACTTGCACAATAAAAATTCATTAAATTAGTACAATAATAAAAAATAATAATAA
* * * *
5632277 TATTGTCTTTTACATTTTTTTTTGGCCTTACTTGCACAAAAAAAATTCATTGAATTAGTACAACA
66 CATTCTCTTTTA-ATATTTTTTTGGACTTACTTGCACAAAAAAAATTCATTGAATTAGTACAACA
* *
5632342 ATAACTAATGATGGTAATATTGTCTTCTGCA
130 ATAACCAATGATAGTAATATTGTCTTCTGCA
* * * * ** *
5632373 TTTTTTGGTCTTACTTGCACAATAGAGATTCATTAAATTAGTATAATAATAACCAATGATAATAA
1 TTTTTTGGCCTTACTTGCACAATAAAAATTCATTAAATTAGTACAATAATAAAAAATAATAATAA
* * * *
5632438 CGTTCTCTTTT-ATATTTTTTTGGACTTACTTGCACAATAGAGATTCATTGAATTAGTACAACAA
66 CATTCTCTTTTAATATTTTTTTGGACTTACTTGCACAAAAAAAATTCATTGAATTAGTACAACAA
5632502 TAACCAATGATAGTAATATTGTCTTCTGCA
131 TAACCAATGATAGTAATATTGTCTTCTGCA
5632532 TT
1 TT
5632534 GAATTAGTAT
Statistics
Matches: 141, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
159 78 0.55
161 63 0.45
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (160 bp):
TTTTTTGGCCTTACTTGCACAATAAAAATTCATTAAATTAGTACAATAATAAAAAATAATAATAA
CATTCTCTTTTAATATTTTTTTGGACTTACTTGCACAAAAAAAATTCATTGAATTAGTACAACAA
TAACCAATGATAGTAATATTGTCTTCTGCA
Found at i:5632989 original size:30 final size:30
Alignment explanation
Indices: 5632955--5633015 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
5632945 TGACATTTAT
* *
5632955 TCAGTCTTAACATATCAGAAATATGATAGA
1 TCAGTCTTAACAGATCAGAAAGATGATAGA
*
5632985 TCAGTCTTAACAGATCAGATAGATGATAGA
1 TCAGTCTTAACAGATCAGAAAGATGATAGA
5633015 T
1 T
5633016 TATTTCAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (30 bp):
TCAGTCTTAACAGATCAGAAAGATGATAGA
Done.