Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000851.1 Hibiscus syriacus cultivar Beakdansim tig00001644_pilon, whole genome shotgun sequence
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: 7304151
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 31
Found at i:3010115 original size:13 final size:13
Alignment explanation
Indices: 3010097--3010121 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3010087 TTTCTTGCAC
3010097 TTGAAAAAATGTA
1 TTGAAAAAATGTA
3010110 TTGAAAAAATGT
1 TTGAAAAAATGT
3010122 CATCCAATAC
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:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (13 bp):
TTGAAAAAATGTA
Found at i:3014692 original size:2 final size:2
Alignment explanation
Indices: 3014685--3014725 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3014675 TAAGTGTTGA
3014685 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT A
3014726 AAGATTTTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3020729 original size:180 final size:181
Alignment explanation
Indices: 3020424--3020786 Score: 701
Period size: 180 Copynumber: 2.0 Consensus size: 181
3020414 CTTGGAACAA
3020424 TGGTGTTTGCCAAGGAGAATGAGAGCCAAGTTCAAAGAAGGTTGCCGATATTCGAGAAGGCTACT
1 TGGTGTTTGCCAAGGAGAATGAGAGCCAAGTTCAAAGAAGGTTGCCGATATTCGAGAAGG--ACT
3020489 AGAGATCTTGCCGAGCATGTTCGTGGGGAGAAAATGGCTTCAGAGATCATCATTGGAGAAGGGTC
64 AGAGATCTTGCCGAGCATGTTCGTGGGGAGAAAATGGCTTCAGAGATCATCATTGGAGAAGGGTC
3020554 AAAGGAGCAGCTTCTCGAGGGTGTTCAAGTGCAGAAGAACATCCCTTAAAAGG
129 AAAGGAGCAGCTTCTCGAGGGTGTTCAAGTGCAGAAGAACATCCCTTAAAAGG
3020607 TGGTGTTTGCCAAGGAGAATGAGAGCCAAGTTCAAAGAAGGTTGCCGATATTCGAGAAGG-CTAG
1 TGGTGTTTGCCAAGGAGAATGAGAGCCAAGTTCAAAGAAGGTTGCCGATATTCGAGAAGGACTAG
3020671 AGATCTTGCCGAGCATGTTCGTGGGGAGAAAATGGCTTCAGAGATCATCATTGGAGAAGGGTCAA
66 AGATCTTGCCGAGCATGTTCGTGGGGAGAAAATGGCTTCAGAGATCATCATTGGAGAAGGGTCAA
3020736 AGGAGCAGCTTCTCGAGGGTGTTCAAGTGCAGAAGAACATCCCTTAAAAGG
131 AGGAGCAGCTTCTCGAGGGTGTTCAAGTGCAGAAGAACATCCCTTAAAAGG
3020787 CCATGAATAA
Statistics
Matches: 180, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
180 120 0.67
183 60 0.33
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.22
Consensus pattern (181 bp):
TGGTGTTTGCCAAGGAGAATGAGAGCCAAGTTCAAAGAAGGTTGCCGATATTCGAGAAGGACTAG
AGATCTTGCCGAGCATGTTCGTGGGGAGAAAATGGCTTCAGAGATCATCATTGGAGAAGGGTCAA
AGGAGCAGCTTCTCGAGGGTGTTCAAGTGCAGAAGAACATCCCTTAAAAGG
Found at i:3026240 original size:20 final size:19
Alignment explanation
Indices: 3026211--3026265 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
3026201 TGATTGATTC
* *
3026211 AGTATTGATACCAATGAGG
1 AGTATCGATACCAATAAGG
3026230 TAGTATCGATACCATGATAAGG
1 -AGTATCGATACCA--ATAAGG
*
3026252 GGTATCGATACCAA
1 AGTATCGATACCAA
3026266 ACAACATCGA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.03
20 12 0.40
21 12 0.40
22 5 0.17
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (19 bp):
AGTATCGATACCAATAAGG
Found at i:3026420 original size:92 final size:92
Alignment explanation
Indices: 3026231--3026446 Score: 224
Period size: 92 Copynumber: 2.3 Consensus size: 92
3026221 CCAATGAGGT
* *
3026231 AGTATCGATACCATGATAAGGGGTATCGATACCAAACAACATCGAATCTAATTTGGTAATGATAC
1 AGTATCGATACCATGGTAA-GGGTATCGATACCAAACAACATCGAATCTAATTTGGTAATGAAAC
* *
3026296 CAGAAGGGTATCAGTACCATAATATGGT
65 CAGAAGGGTATCAGTACCATAATATAGA
* *
3026324 AGTATCGATACCATGGTAAGGGTATCGATACCAGGA-AACATTGAAT-TAATTTTGGT-ATCGAA
1 AGTATCGATACCATGGTAAGGGTATCGATACCA-AACAACATCGAATCTAA-TTTGGTAAT-GAA
*** * * *
3026386 ATTGGAGGGGTATCGGTACCATAGTATAGA
63 ACCAGAAGGGTATCAGTACCATAATATAGA
* * *
3026416 AGTATCGGTACCAGGGT-AGTAGTATCGATAC
1 AGTATCGATACCATGGTAAG-GGTATCGATAC
3026447 TATGTAGATA
Statistics
Matches: 104, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
91 7 0.07
92 78 0.75
93 19 0.18
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (92 bp):
AGTATCGATACCATGGTAAGGGTATCGATACCAAACAACATCGAATCTAATTTGGTAATGAAACC
AGAAGGGTATCAGTACCATAATATAGA
Found at i:3026840 original size:55 final size:55
Alignment explanation
Indices: 3026773--3027150 Score: 478
Period size: 55 Copynumber: 6.9 Consensus size: 55
3026763 CTAAGTGTAC
* * *
3026773 TACAGGCACTTCGTGTGCATATTTACAGAATTCATCATGAGTTGATGAATCACCA
1 TACAGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
* *
3026828 TACAGGAACTTCGTGTGCATAATCACGGAATTCATCATGAGTTGATGAATCACCG
1 TACAGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
* *
3026883 TACATGCACTTCGTGTGCATATTCAAGGAATTCATCATGAGTTGATGAATCACCG
1 TACAGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
* * *
3026938 TACAGGCACTTTGTGTGCATATTCACGGAATTCATCATGAGTTTATGAATCACCA
1 TACAGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
* * * * *
3026993 TACAAGCACTTCGTGTGCATATTCATGGAATTCATCATGAATT-TTGAATCACTG
1 TACAGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
* * * *
3027047 TACATGCACCTT-GTGTGTAAATCCAC-GAAGTTCATCATGAGTTGATGAATCACCG
1 TACAGGCA-CTTCGTGTGCATATTCACGGAA-TTCATCATGAGTTGATGAATCACCG
* ** **
3027102 TACATGCACTAT-GTGTGCA-ACCCATTGAATTCATCATGAGTTGATGAAT
1 TACAGGCACT-TCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAAT
3027151 TTTCGTATAG
Statistics
Matches: 286, Mismatches: 32, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
53 3 0.01
54 63 0.22
55 220 0.77
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (55 bp):
TACAGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
Found at i:3028575 original size:56 final size:56
Alignment explanation
Indices: 3028405--3028776 Score: 506
Period size: 56 Copynumber: 6.8 Consensus size: 56
3028395 ACCAAAACGT
* ** * *
3028405 AAATTCATATACTTATTATGTTTTTCTTAG-TTTTGCACACAAAGTGCCTATACGG
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCCATACGA
* * *
3028460 AAATTCTTAAACTTATTATGAATTTCTTAG-CTTTGCACACAAAGTGCCCATACGG
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCCATACGA
* * * *
3028515 AAATTCATAAAATAATTATGAATTTCATAGTTTTTGCATACAAAGTGCCCATACGA
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCCATACGA
* *
3028571 AAATTCATAAACTTATTATGAATTTCTTAG----CGCACACAAAGTGCCCATACAA
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCCATACGA
** *
3028623 AAATTCATAAACTCCTTATGAATTTCCTAGTTTTTGCACACAAAGTGCCCATACGA
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCCATACGA
* *
3028679 AAATTCATAAACTTATTATGAATTTCTTAGCTTTTT-CACACAAAGTGCCCATATGG
1 AAATTCATAAACTTATTATGAATTTCTTAG-TTTTTGCACACAAAGTGCCCATACGA
*
3028735 AAATTCATAAACTTACTATGAATTTCTTAGTTTTTGCACACA
1 AAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACA
3028777 CATTGCCATT
Statistics
Matches: 280, Mismatches: 30, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
52 46 0.16
55 80 0.29
56 149 0.53
57 5 0.02
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (56 bp):
AAATTCATAAACTTATTATGAATTTCTTAGTTTTTGCACACAAAGTGCCCATACGA
Found at i:3028660 original size:108 final size:109
Alignment explanation
Indices: 3028405--3028776 Score: 509
Period size: 108 Copynumber: 3.4 Consensus size: 109
3028395 ACCAAAACGT
* ** * * *
3028405 AAATTCATATACTTA-TTATGTTTTTCTTAG-TTTTGCACACAAAGTGCCTATACGGAAATTCTT
1 AAATTCATAAAC-TACTTATGAATTTCTTAGTTTTTGCACACAAAGTGCCCATACGAAAATTCAT
3028468 AAACTTATTATGAATTTCTTAGCTTTGCACACAAAGTGCCCATACGG
65 AAACTTATTATGAATTTCTTAGC--TGCACACAAAGTGCCCATACGG
* * * *
3028515 AAATTCATAAAATAATTATGAATTTCATAGTTTTTGCATACAAAGTGCCCATACGAAAATTCATA
1 AAATTCATAAACTACTTATGAATTTCTTAGTTTTTGCACACAAAGTGCCCATACGAAAATTCATA
**
3028580 AACTTATTATGAATTTCTTAGC-GCACACAAAGTGCCCATACAA
66 AACTTATTATGAATTTCTTAGCTGCACACAAAGTGCCCATACGG
* *
3028623 AAATTCATAAACTCCTTATGAATTTCCTAGTTTTTGCACACAAAGTGCCCATACGAAAATTCATA
1 AAATTCATAAACTACTTATGAATTTCTTAGTTTTTGCACACAAAGTGCCCATACGAAAATTCATA
* *
3028688 AACTTATTATGAATTTCTTAGCTTTTTCACACAAAGTGCCCATATGG
66 AACTTATTATGAATTTCTTAGC---TGCACACAAAGTGCCCATACGG
3028735 AAATTCATAAACTTAC-TATGAATTTCTTAGTTTTTGCACACA
1 AAATTCATAAAC-TACTTATGAATTTCTTAGTTTTTGCACACA
3028777 CATTGCCATT
Statistics
Matches: 233, Mismatches: 22, Indels: 12
0.87 0.08 0.04
Matches are distributed among these distances:
108 101 0.43
109 2 0.01
110 22 0.09
111 52 0.22
112 54 0.23
113 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (109 bp):
AAATTCATAAACTACTTATGAATTTCTTAGTTTTTGCACACAAAGTGCCCATACGAAAATTCATA
AACTTATTATGAATTTCTTAGCTGCACACAAAGTGCCCATACGG
Found at i:3028685 original size:164 final size:164
Alignment explanation
Indices: 3028405--3028765 Score: 492
Period size: 164 Copynumber: 2.2 Consensus size: 164
3028395 ACCAAAACGT
* ** * * ** *
3028405 AAATTCATATACTTATTATGTTTTTCTTAGTTTTGCACACAAAGTGCCTATACGGAAATTCTTAA
1 AAATTCATAAACTTATTATGAATTTCTTAG--TCGCACACAAAGTGCCCATACAAAAATTCATAA
* * *
3028470 ACTTATTATGAATTTCTTAGCTTTGCACACAAAGTGCCCATACGGAAATTCATAAAATAATTATG
64 ACTCATTATGAATTTCCTAGCTTTGCACACAAAGTGCCCATACGAAAATTCATAAAATAATTATG
*
3028535 AATTTCATAG-TTTTTGCATACAAAGTGCCCATACGA
129 AATTTCATAGCTTTTT-CACACAAAGTGCCCATACGA
3028571 AAATTCATAAACTTATTATGAATTTCTTAG-CGCACACAAAGTGCCCATACAAAAATTCATAAAC
1 AAATTCATAAACTTATTATGAATTTCTTAGTCGCACACAAAGTGCCCATACAAAAATTCATAAAC
* * * *
3028635 TCCTTATGAATTTCCTAGTTTTTGCACACAAAGTGCCCATACGAAAATTCATAAACTTATTATGA
66 TCATTATGAATTTCCTAG-CTTTGCACACAAAGTGCCCATACGAAAATTCATAAAATAATTATGA
* * *
3028700 ATTTCTTAGCTTTTTCACACAAAGTGCCCATATGG
130 ATTTCATAGCTTTTTCACACAAAGTGCCCATACGA
*
3028735 AAATTCATAAACTTACTATGAATTTCTTAGT
1 AAATTCATAAACTTATTATGAATTTCTTAGT
3028766 TTTTGCACAC
Statistics
Matches: 172, Mismatches: 20, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
163 44 0.26
164 96 0.56
165 5 0.03
166 27 0.16
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.35
Consensus pattern (164 bp):
AAATTCATAAACTTATTATGAATTTCTTAGTCGCACACAAAGTGCCCATACAAAAATTCATAAAC
TCATTATGAATTTCCTAGCTTTGCACACAAAGTGCCCATACGAAAATTCATAAAATAATTATGAA
TTTCATAGCTTTTTCACACAAAGTGCCCATACGA
Found at i:3029785 original size:64 final size:65
Alignment explanation
Indices: 3029717--3029852 Score: 193
Period size: 64 Copynumber: 2.1 Consensus size: 65
3029707 ACACTATTTA
* * *
3029717 CATTCGATGTTTCAAAAGAGTCAGGAGTGCATTGATGCA-GGGTTGTGCATCAGTACACAAAATG
1 CATTCGATGTTTCAAAAGAGTCAAGAGTGCATCGATGCATGGCTTGTGCATCAGTACACAAAATG
* * * * *
3029781 CATTCGATGTTTCAAAATATTCAAGAGTGTATCGATGCATGGCTTGTGCATCGGTACATAAAATG
1 CATTCGATGTTTCAAAAGAGTCAAGAGTGCATCGATGCATGGCTTGTGCATCAGTACACAAAATG
3029846 CATTCGA
1 CATTCGA
3029853 AATGGGTGTG
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
64 34 0.54
65 29 0.46
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (65 bp):
CATTCGATGTTTCAAAAGAGTCAAGAGTGCATCGATGCATGGCTTGTGCATCAGTACACAAAATG
Found at i:3034890 original size:45 final size:44
Alignment explanation
Indices: 3034815--3034934 Score: 179
Period size: 45 Copynumber: 2.7 Consensus size: 44
3034805 ATAAGTTTAT
3034815 GAGCTTATGGAAT-AATGGTAAGTATATTGGTAAAATAAGCTAAC
1 GAGCTTAT-GAATAAATGGTAAGTATATTGGTAAAATAAGCTAAC
* *
3034859 GAGCTTATGAATTAAATGGTAAGTGTATTGGTAAAATAAGCTTAC
1 GAGCTTATGAA-TAAATGGTAAGTATATTGGTAAAATAAGCTAAC
*
3034904 GAGCTCATGAGATAAATGGTAAGTATATTGG
1 GAGCTTATGA-ATAAATGGTAAGTATATTGG
3034935 ATATGCTAGT
Statistics
Matches: 69, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
43 3 0.04
44 9 0.13
45 56 0.81
46 1 0.01
ACGTcount: A:0.38, C:0.07, G:0.24, T:0.31
Consensus pattern (44 bp):
GAGCTTATGAATAAATGGTAAGTATATTGGTAAAATAAGCTAAC
Found at i:3040808 original size:20 final size:21
Alignment explanation
Indices: 3040769--3040808 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
3040759 GAGGCTTTAA
* *
3040769 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTTACTCTTGAT
3040790 GATCAT-AATTTACTCTTGA
1 GATCATCAATTTACTCTTGA
3040809 AAGTAGGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.47
Consensus pattern (21 bp):
GATCATCAATTTACTCTTGAT
Found at i:3042849 original size:21 final size:21
Alignment explanation
Indices: 3042825--3042938 Score: 221
Period size: 21 Copynumber: 5.5 Consensus size: 21
3042815 GGGAGCATAT
3042825 GTGCATCGATGCATGGTCAAG
1 GTGCATCGATGCATGGTCAAG
3042846 GTGCATCGAT-CATGGTCAAG
1 GTGCATCGATGCATGGTCAAG
3042866 GTGCATCGATGCATGGTCAAG
1 GTGCATCGATGCATGGTCAAG
3042887 GTGCATCGATGCATGGTCAAG
1 GTGCATCGATGCATGGTCAAG
3042908 GTGCATCGATGCATGGTCAAG
1 GTGCATCGATGCATGGTCAAG
3042929 GTGCATCGAT
1 GTGCATCGAT
3042939 AGACTATGTG
Statistics
Matches: 92, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
20 20 0.22
21 72 0.78
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (21 bp):
GTGCATCGATGCATGGTCAAG
Found at i:3043075 original size:65 final size:65
Alignment explanation
Indices: 3043003--3043222 Score: 377
Period size: 65 Copynumber: 3.4 Consensus size: 65
3042993 ACACTAGGGA
* * * * *
3043003 TGCATCGGTACACTAATTACATTCGATGTTTCAAAAGATTCAGGAGTGCATCGATGCATGGTTTG
1 TGCATCGGTACACAAAATACATTCGATGTTTCATAATATTCAAGAGTGCATCGATGCATGGTTTG
*
3043068 TGCATCGGTACACAAAATATATTCGATGTTTCATAATATTCAAGAGTGCATCGATGCATGGTTTG
1 TGCATCGGTACACAAAATACATTCGATGTTTCATAATATTCAAGAGTGCATCGATGCATGGTTTG
3043133 TGCATCGGTACACAAAATACATTCGATGTTTCATAATATTCAAGAGTGCATCGATGCATGGTTTG
1 TGCATCGGTACACAAAATACATTCGATGTTTCATAATATTCAAGAGTGCATCGATGCATGGTTTG
*
3043198 TGCATCGGTACACAAAATGCATTCG
1 TGCATCGGTACACAAAATACATTCG
3043223 GAATGGGTGT
Statistics
Matches: 147, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 147 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (65 bp):
TGCATCGGTACACAAAATACATTCGATGTTTCATAATATTCAAGAGTGCATCGATGCATGGTTTG
Found at i:3043793 original size:19 final size:22
Alignment explanation
Indices: 3043743--3043793 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 22
3043733 TTGTCTCTTA
3043743 GTAC-CGATACTTCTATACTATG
1 GTACTCGATACTTCTATA-TATG
3043765 GTACTC-ATAC-TCTAT-TATG
1 GTACTCGATACTTCTATATATG
3043784 GTA-TCGATAC
1 GTACTCGATAC
3043794 CATTTCTGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 2 0.07
19 11 0.41
21 5 0.19
22 8 0.30
23 1 0.04
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (22 bp):
GTACTCGATACTTCTATATATG
Found at i:3049726 original size:17 final size:17
Alignment explanation
Indices: 3049704--3049737 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3049694 TTTCCTCTTG
3049704 AGCTCT-TTTATTAACTT
1 AGCTCTGTTT-TTAACTT
3049721 AGCTCTGTTTTTAACTT
1 AGCTCTGTTTTTAACTT
3049738 CTTGCAGGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.21, C:0.18, G:0.09, T:0.53
Consensus pattern (17 bp):
AGCTCTGTTTTTAACTT
Found at i:3050136 original size:168 final size:170
Alignment explanation
Indices: 3049858--3050198 Score: 659
Period size: 168 Copynumber: 2.0 Consensus size: 170
3049848 TAACGACTAA
3049858 GCTTATTGTATTCAGCCTCATACTCATACACTGTTCGATCGCCTTGTTTCAAGTTAAGAAATTTT
1 GCTTATTGTATTCAGCCTCATACTCATACACTGTTCGATCGCCTTGTTTCAAGTTAAGAAATTTT
3049923 AATAGCATTTTCCTCATAAACTGCTCCCCGATATACTTTTTCTTAAACTC-ATTGGAAGAATTGT
66 AATAGCATTTTCCTCATAAACTGCTCCCCGATATACTTTTTCTTAAACTCAATTGGAAGAATTGT
3049987 CA-TTTACTTGTTCAGGTGATACATACATCGTCGTATTTG
131 CATTTTACTTGTTCAGGTGATACATACATCGTCGTATTTG
3050026 GCTTATTGTATTCAGCCTCATACTCATACACTGTTCGATCGCCTTGTTTCAAGTTAAGAAATTTT
1 GCTTATTGTATTCAGCCTCATACTCATACACTGTTCGATCGCCTTGTTTCAAGTTAAGAAATTTT
3050091 AATAGCATTTTCCTCATAAACTGCTCCCCGATATACTTTTTCTTAAACTCATATTGGAAGAATTG
66 AATAGCATTTTCCTCATAAACTGCTCCCCGATATACTTTTTCTTAAACTCA-ATTGGAAGAATTG
3050156 TCATTTTACTTGTTCAGGTGATACATACATCGTCGTATTTG
130 TCATTTTACTTGTTCAGGTGATACATACATCGTCGTATTTG
3050197 GC
1 GC
3050199 CACTAAACCA
Statistics
Matches: 170, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
168 115 0.68
170 16 0.09
171 39 0.23
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (170 bp):
GCTTATTGTATTCAGCCTCATACTCATACACTGTTCGATCGCCTTGTTTCAAGTTAAGAAATTTT
AATAGCATTTTCCTCATAAACTGCTCCCCGATATACTTTTTCTTAAACTCAATTGGAAGAATTGT
CATTTTACTTGTTCAGGTGATACATACATCGTCGTATTTG
Found at i:3051536 original size:56 final size:55
Alignment explanation
Indices: 3051346--3051728 Score: 450
Period size: 55 Copynumber: 6.9 Consensus size: 55
3051336 CCCACTACCA
* * *
3051346 ATACGAAAATTCATATACTTATTATGAATTTCTTAGTTTTACACATAAAGTGCCC
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
* * *
3051401 ATATGTAAATTCATAAACTTATTATGAATTTCTTAGCTTTGCACACAAA--GCCC
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
* * * * * *
3051454 AATAAG-GAATTCATAAACTCAATATGAATTTCATAGTTTTTGCACACAAAGTGTCC
1 -ATACGAAAATTCATAAACTTATTATGAATTTCTTAG-TTTTGCACACAAAGTGCCC
* * *
3051510 ATACGAAAATTCATAAACTTATTATGAATTTATTAGCTTTGCACACAAAGTACCC
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
* ** * * * **
3051565 ATACTG-AAATTCATAAAATCGTTATGAATTTCTTAGTTTTTGCGCACAAAATACTT
1 ATAC-GAAAATTCATAAACTTATTATGAATTTCTTAG-TTTTGCACACAAAGTGCCC
* * *
3051621 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGCTTTGCATACAAAGTGCCC
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
*
3051676 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACACAGTG
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAG-TTTTGCACACAAAGTG
3051729 TCATTTGGTA
Statistics
Matches: 274, Mismatches: 45, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
53 30 0.11
54 16 0.06
55 141 0.51
56 87 0.32
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.36
Consensus pattern (55 bp):
ATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
Found at i:3051631 original size:111 final size:109
Alignment explanation
Indices: 3051346--3051723 Score: 458
Period size: 111 Copynumber: 3.4 Consensus size: 109
3051336 CCCACTACCA
* * * * * * *
3051346 ATACGAAAATTCATATACTTATTATGAATTTCTTAG-TTTTACACATAAAGTGC-CCATATGTAA
1 ATACG-AAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCACACAAAAT-CTCCATACGAAA
3051409 ATTCATAAACTTATTATGAATTTCTTAGCTTTGCACACAAAG-CCC
64 ATTCATAAACTTATTATGAATTTCTTAGCTTTGCACACAAAGTCCC
* * * * * *
3051454 AATAAGGAATTCATAAACTCAATATGAATTTCATAGTTTTTGCACACAAAGTGTCCATACGAAAA
1 -ATACGAAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCACACAAAATCTCCATACGAAAA
*
3051519 TTCATAAACTTATTATGAATTTATTAGCTTTGCACACAAAGTACCC
65 TTCATAAACTTATTATGAATTTCTTAGCTTTGCACACAAAGT-CCC
* * * * *
3051565 ATACTGAAATTCATAAAATCGTTATGAATTTCTTAGTTTTTGCGCACAAAATACT-TATACGGAA
1 ATAC-GAAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCACACAAAAT-CTCCATACGAAA
*
3051629 ATTCATAAACTTATTATGAATTTCTTAGCTTTGCATACAAAGTGCCC
64 ATTCATAAACTTATTATGAATTTCTTAGCTTTGCACACAAAGT-CCC
* *
3051676 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGCTTTTGCACACA
1 ATACG-AAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCACACA
3051724 CAGTGTCATT
Statistics
Matches: 231, Mismatches: 31, Indels: 12
0.84 0.11 0.04
Matches are distributed among these distances:
108 25 0.11
109 66 0.29
110 4 0.02
111 135 0.58
112 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (109 bp):
ATACGAAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCACACAAAATCTCCATACGAAAAT
TCATAAACTTATTATGAATTTCTTAGCTTTGCACACAAAGTCCC
Found at i:3057417 original size:13 final size:12
Alignment explanation
Indices: 3057380--3057419 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
3057370 GAGTAATAGT
*
3057380 AAATGAAGAACAT
1 AAATGAAGAA-AA
3057393 AAATGAAGAAAA
1 AAATGAAGAAAA
3057405 AAATGAACGAAAA
1 AAATGAA-GAAAA
3057418 AA
1 AA
3057420 GAATAAGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 8 0.32
13 17 0.68
ACGTcount: A:0.70, C:0.05, G:0.15, T:0.10
Consensus pattern (12 bp):
AAATGAAGAAAA
Found at i:3058513 original size:14 final size:15
Alignment explanation
Indices: 3058483--3058515 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
3058473 ATGATAATAG
3058483 TGAGGCATTTAGGGT
1 TGAGGCATTTAGGGT
*
3058498 TGAGGCA-TTAGTGT
1 TGAGGCATTTAGGGT
3058512 TGAG
1 TGAG
3058516 TGGTGTAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.21, C:0.06, G:0.39, T:0.33
Consensus pattern (15 bp):
TGAGGCATTTAGGGT
Found at i:3060726 original size:9 final size:9
Alignment explanation
Indices: 3060712--3060740 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
3060702 ACTTAAAAGT
3060712 AAAAAATGA
1 AAAAAATGA
3060721 AAAAAA-GA
1 AAAAAATGA
3060729 AAAAAATGA
1 AAAAAATGA
3060738 AAA
1 AAA
3060741 CTTTATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (9 bp):
AAAAAATGA
Found at i:3060726 original size:17 final size:17
Alignment explanation
Indices: 3060706--3060740 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3060696 ATAAGAACTT
*
3060706 AAAAGTAAAAAATGAAA
1 AAAAGAAAAAAATGAAA
3060723 AAAAGAAAAAAATGAAA
1 AAAAGAAAAAAATGAAA
3060740 A
1 A
3060741 CTTTATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (17 bp):
AAAAGAAAAAAATGAAA
Found at i:3060927 original size:65 final size:69
Alignment explanation
Indices: 3060856--3060990 Score: 242
Period size: 65 Copynumber: 2.0 Consensus size: 69
3060846 ATAGCTAAAG
3060856 ATAAATCCTAAAAATATTCAAATAAAATTCT-AAAACAA-GGATAATTTCTAATTC-AATTT-AA
1 ATAAATCCTAAAAATATTCAAATAAAATTCTAAAAACAAGGGATAATTTCTAATTCAAATTTAAA
3060917 CTAA
66 CTAA
3060921 ATAAATCCTAAAAATATTCAAATAAAATTCTAAAAACAAGGGATAATTTCTAATTCAAATTTAAA
1 ATAAATCCTAAAAATATTCAAATAAAATTCTAAAAACAAGGGATAATTTCTAATTCAAATTTAAA
3060986 CTAA
66 CTAA
3060990 A
1 A
3060991 GTCGAGTCAT
Statistics
Matches: 66, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
65 31 0.47
66 7 0.11
67 16 0.24
68 5 0.08
69 7 0.11
ACGTcount: A:0.53, C:0.12, G:0.04, T:0.31
Consensus pattern (69 bp):
ATAAATCCTAAAAATATTCAAATAAAATTCTAAAAACAAGGGATAATTTCTAATTCAAATTTAAA
CTAA
Found at i:3061214 original size:16 final size:18
Alignment explanation
Indices: 3061193--3061229 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
3061183 AAAGTACCCA
3061193 AATCAACAAT-A-TAATT
1 AATCAACAATGAGTAATT
3061209 AATCAACAATGAGTAATT
1 AATCAACAATGAGTAATT
3061227 AAT
1 AAT
3061230 GGAAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.53
17 1 0.05
18 8 0.42
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.30
Consensus pattern (18 bp):
AATCAACAATGAGTAATT
Found at i:3061685 original size:23 final size:23
Alignment explanation
Indices: 3061659--3061703 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3061649 TAACCAAATG
*
3061659 TTTTT-AAATATTTATTTGTTTTA
1 TTTTTGAAATATTT-TTTCTTTTA
*
3061682 TTTTTGGAATATTTTTTCTTTT
1 TTTTTGAAATATTTTTTCTTTT
3061704 TTATGTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.20, C:0.02, G:0.07, T:0.71
Consensus pattern (23 bp):
TTTTTGAAATATTTTTTCTTTTA
Found at i:3061771 original size:19 final size:18
Alignment explanation
Indices: 3061740--3061775 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3061730 TTTGAACTAG
*
3061740 TTTTTTTTGTTTCTTCTC
1 TTTTTTATGTTTCTTCTC
3061758 TTTTTTATGTTTTCTTCT
1 TTTTTTATG-TTTCTTCT
3061776 TCTTCTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.03, C:0.14, G:0.06, T:0.78
Consensus pattern (18 bp):
TTTTTTATGTTTCTTCTC
Found at i:3064473 original size:25 final size:25
Alignment explanation
Indices: 3064445--3064502 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
3064435 AATAAACCTA
3064445 AAAAATCAATATCTCATGATTTTAT
1 AAAAATCAATATCTCATGATTTTAT
3064470 AAAAATCAATATCTCATGATTTTAT
1 AAAAATCAATATCTCATGATTTTAT
3064495 AAAAATCA
1 AAAAATCA
3064503 TGACAGTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.48, C:0.12, G:0.03, T:0.36
Consensus pattern (25 bp):
AAAAATCAATATCTCATGATTTTAT
Found at i:3064855 original size:36 final size:36
Alignment explanation
Indices: 3064813--3064888 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
3064803 TTATAGCTAA
*
3064813 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
3064849 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
3064885 AAAA
1 AAAA
3064889 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:3069311 original size:36 final size:36
Alignment explanation
Indices: 3069269--3069344 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
3069259 GTTATAGCTA
*
3069269 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
3069305 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
3069341 AAAA
1 AAAA
3069345 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:3074154 original size:45 final size:45
Alignment explanation
Indices: 3074094--3074287 Score: 284
Period size: 45 Copynumber: 4.3 Consensus size: 45
3074084 CGATATATGG
*
3074094 TTATGGAA-AAATGGTAAGTATGTTGATAAAATAAGCTTACGAGC
1 TTATGGAATAAATGGTAAGTATATTGATAAAATAAGCTTACGAGC
*
3074138 TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
1 TTATGGAATAAATGGTAAGTATATTGATAAAATAAGCTTACGAGC
* * * *
3074183 TTATGGAATAAATGGTAAGTACATTGGTAAAATAAGCTAATGAGC
1 TTATGGAATAAATGGTAAGTATATTGATAAAATAAGCTTACGAGC
* *
3074228 TTATGGATTAAATTGTAAGTATATT-AGTAAAATAAGCTTACGAGC
1 TTATGGAATAAATGGTAAGTATATTGA-TAAAATAAGCTTACGAGC
*
3074273 TTATGGGATAAATGG
1 TTATGGAATAAATGG
3074288 AAAATAAATG
Statistics
Matches: 134, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
44 8 0.06
45 126 0.94
ACGTcount: A:0.40, C:0.06, G:0.22, T:0.31
Consensus pattern (45 bp):
TTATGGAATAAATGGTAAGTATATTGATAAAATAAGCTTACGAGC
Found at i:3075442 original size:31 final size:31
Alignment explanation
Indices: 3075404--3075466 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
3075394 GACTGCAAAA
3075404 AGAAGATAGGATTTTAGATTTTAAGTGAAAC
1 AGAAGATAGGATTTTAGATTTTAAGTGAAAC
3075435 AGAAGATAGGATTTTAGATTTTAAGTGAAAC
1 AGAAGATAGGATTTTAGATTTTAAGTGAAAC
3075466 A
1 A
3075467 TGTGTGAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.43, C:0.03, G:0.22, T:0.32
Consensus pattern (31 bp):
AGAAGATAGGATTTTAGATTTTAAGTGAAAC
Found at i:3078755 original size:54 final size:54
Alignment explanation
Indices: 3078682--3078784 Score: 143
Period size: 54 Copynumber: 1.9 Consensus size: 54
3078672 ATTGCACCGA
* * **
3078682 AGTGCCGAAATGGAAATTCACAAACTCATTATGAATTCCATGGGTTGCACACAT
1 AGTGCCGAAAAGGAAATTCACAAACGCATTATGAAAACCATGGGTTGCACACAT
** *
3078736 AGTGCCGAAAAGGTCATTCATAAACGCATTATGAAAACCATGGGTTGCA
1 AGTGCCGAAAAGGAAATTCACAAACGCATTATGAAAACCATGGGTTGCA
3078785 TATTTAATGT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 42 1.00
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.24
Consensus pattern (54 bp):
AGTGCCGAAAAGGAAATTCACAAACGCATTATGAAAACCATGGGTTGCACACAT
Found at i:3081115 original size:881 final size:885
Alignment explanation
Indices: 3078835--3081482 Score: 5232
Period size: 885 Copynumber: 3.0 Consensus size: 885
3078825 TCGATCGATA
3078835 ACTTATATACATAATTTCATATCGAAATGGTAATTCACAAACTCATTATGACTACCATGATTGCA
1 ACTTATATACATAATTTCATATCGAAATGGTAATTCACAAACTCATTATGACTACCATGATTGCA
3078900 CATAAATTCCCAAAAGTACACATAGTATTGATACGAAAATACACCGTTATGCATTAAACAAAATC
66 CATAAATTCCCAAAAGTACACATAGTATTGATACGAAAATACACCGTTATGCATTAAACAAAATC
3078965 GAACGATACAATCATACACGAAGTATGTCGAAATGCACCTATGACTCCCAATTATATACAATGGG
131 GAACGATACAATCATACACGAAGTATGTCGAAATGCACCTATGACTCCCAATTATATACAATGGG
3079030 TTTTTAGTCAAATTCACAGATTTAAACATTTATTGCTGCAATATCGATAGTAATTGAACAATATC
196 TTTTTAGTCAAATTCACAGATTTAAACATTTATTGCTGCAATATCGATAGTAATTGAACAATATC
3079095 AACGTTCATCTATTCATTTTAGAGCAATTCATACTCTAAAATTTATTCGTAATATTATTTTCATA
261 AACGTTCATCTATTCATTTTAGAGCAATTCATACTCTAAAATTTATTCGTAATATTATTTTCATA
3079160 AACATTATGAAAACATGTCAAAGTGCAGTAAAACATGCTTTATCAAAATATTTGAGGTTGACTCG
326 AACATTATGAAAACATGTCAAAGTGCAGTAAAACATGCTTTATCAAAATATTTGAGGTTGACTCG
3079225 TCGCAAGTCTCCCTCATTTAATAGAACTACAATAAATACACTCACCTAATATGCCTTACTAGTAT
391 TCGCAAGTCTCCCTCATTTAATAGAACTACAATAAATACACTCACCTAATATGCCTTACTAGTAT
*
3079290 GCTGCAATGATGTCAGACTATTCGGTAATTTTATCCTTGCCCTTTTTCTTACCTGAATCTGGAGC
456 GCTGCAATGATGTCAGACTATTCGGTAATTTTATCCTTGCCCTTTTTCTTACCTGACTCTGGAGC
3079355 TTCGTTACGATCTATACAAGTATCCATTAATTACACGTACCATATAAATGTTAGTATACTTCTAA
521 TTCGTTACGATCTATACAAGTATCCATTAATTACACGTACCATATAAATGTTAGTATACTTCTAA
3079420 CATTACTCAAAAGTACCATTATTTCAATTTCTATTAAAATTCATCATATCTAAAAATTCAAGGCT
586 CATTACTCAAAAGTACCATTATTTCAATTTCTATTAAAATTCATCATATCTAAAAATTCAAGGCT
3079485 TAATAGTATCGGTACCTCTATTATGGTATCGATAGTTACATACTATGGTACCGATACTCCCTTAA
651 TAATAGTATCGGTACCTCTATTATGGTATCGATAGTTACATACTATGGTACCGATACTCCCTTAA
3079550 GTTTCGATACCATTTTTGCATTTTGGAATCCATAGTATCGATACCTTCCTCTTAGTACCGATACC
716 GTTTCGATACCATTTTTGCATTTTGGAATCCATAGTATCGATACCTTCCTCTTAGTACCGATACC
3079615 CACAGTAGTATCGATACTAATTGCATCAGTATCGATATTGTTCATCCTATTTCCTCAAATTTAAA
781 CACAGTAGTATCGATACTAATTGCATCAGTATCGATATTGTTCATCCTATTTCCTCAAATTTAAA
3079680 GCTATAGTATCGATATTGTTCTTCCAATACCAATACCAAT
846 GCTATAGTATCGATATTGTTCTTCCAATACCAATACCAAT
3079720 ACTTATATACATAATTTCATATCGAAATGGTAATTCACAAACTCATTATGACTACCATGATTGCA
1 ACTTATATACATAATTTCATATCGAAATGGTAATTCACAAACTCATTATGACTACCATGATTGCA
3079785 CATAAATTCCCAAAAGTACACATAGTATTGATACGAAAATACACCGTTATGCATTAAACAAAATC
66 CATAAATTCCCAAAAGTACACATAGTATTGATACGAAAATACACCGTTATGCATTAAACAAAATC
3079850 GAACGATACAATCATACACGAAGTATGTCGAAATGCACCTATGACTCCCAATTATATACAATGGG
131 GAACGATACAATCATACACGAAGTATGTCGAAATGCACCTATGACTCCCAATTATATACAATGGG
3079915 TTTTTAGTCAAATTCACAGATTTAAACATTTATTGCTGCAATATCGATAGTAATTGAACAATATC
196 TTTTTAGTCAAATTCACAGATTTAAACATTTATTGCTGCAATATCGATAGTAATTGAACAATATC
3079980 AACGTTCATCTATTCATTTTAGAGCAATTCATACTCTAAAATTTATTCGTAATATTATTTTCATA
261 AACGTTCATCTATTCATTTTAGAGCAATTCATACTCTAAAATTTATTCGTAATATTATTTTCATA
3080045 AACATTATGAAAACATGTCAAAGTGCAGTAAAACATGCTTTATCAAAATATTTGAGGTTGACTCG
326 AACATTATGAAAACATGTCAAAGTGCAGTAAAACATGCTTTATCAAAATATTTGAGGTTGACTCG
3080110 TCGCAAGTCTCCCTCATTTAATAGAACTACAATAAATACACTCACCTAATATGCCTTACTAGTAT
391 TCGCAAGTCTCCCTCATTTAATAGAACTACAATAAATACACTCACCTAATATGCCTTACTAGTAT
3080175 GCTGCAATGATGTCAGACTATTCGGTAATTTTATCCTTGCCCTTTTTCTTACCTGACTCTGGAGC
456 GCTGCAATGATGTCAGACTATTCGGTAATTTTATCCTTGCCCTTTTTCTTACCTGACTCTGGAGC
3080240 TTCGTTACGATCTATACAAGTATCCATTAATTACACGTACCATATAAATGTTAGTATACTTCTAA
521 TTCGTTACGATCTATACAAGTATCCATTAATTACACGTACCATATAAATGTTAGTATACTTCTAA
3080305 CATTACTCAAAAGTACCATTATTTCAATTTCTATTAAAATTCATCATATCTAAAAATTCAAGGCT
586 CATTACTCAAAAGTACCATTATTTCAATTTCTATTAAAATTCATCATATCTAAAAATTCAAGGCT
3080370 TAATAGTATCGGTACCTCTATTATGGTATCGATAGTTACATACTATGGTACCGATACTCCCTTAA
651 TAATAGTATCGGTACCTCTATTATGGTATCGATAGTTACATACTATGGTACCGATACTCCCTTAA
3080435 GTTTCGATACCATTTTTGCATTTTGGAATCCATAGTATCGATACCTTCCTC-TAGTACCGATACC
716 GTTTCGATACCATTTTTGCATTTTGGAATCCATAGTATCGATACCTTCCTCTTAGTACCGATACC
3080499 CACAGTAGTATCGATACTAA-TGCATCAGTATCGATATTGTTCATCCTATTTCCTCAAATTTAAA
781 CACAGTAGTATCGATACTAATTGCATCAGTATCGATATTGTTCATCCTATTTCCTCAAATTTAAA
3080563 GCTATAGTATCGATATTGTTCTTCCAATACCAATACCAAT
846 GCTATAGTATCGATATTGTTCTTCCAATACCAATACCAAT
3080603 AC-T-TATACATAATTTCATATCGAAATGGTAATTCACAAACTCATTATGACTACCATGATTGCA
1 ACTTATATACATAATTTCATATCGAAATGGTAATTCACAAACTCATTATGACTACCATGATTGCA
3080666 CATAAATTCCCAAAAGTACACATAGTATTGATACGAAAATACACCGTTATGCATTAAACAAAATC
66 CATAAATTCCCAAAAGTACACATAGTATTGATACGAAAATACACCGTTATGCATTAAACAAAATC
3080731 GAACGATACAATCATACACGAAGTATGTCGAAATGCACCTATGACTCCCAATTATATACAATGGG
131 GAACGATACAATCATACACGAAGTATGTCGAAATGCACCTATGACTCCCAATTATATACAATGGG
3080796 TTTTTAGTCAAATTCACAGATTTAAACATTTATTGCTGCAATATCGATAGTAATTGAACAATATC
196 TTTTTAGTCAAATTCACAGATTTAAACATTTATTGCTGCAATATCGATAGTAATTGAACAATATC
3080861 AACGTTCATCTATTCATTTTAGAGCAATTCATACTCTAAAATTTATTCGTAATATTATTTTCATA
261 AACGTTCATCTATTCATTTTAGAGCAATTCATACTCTAAAATTTATTCGTAATATTATTTTCATA
3080926 AACATTATGAAAACATGTCAAAGTGCAGTAAAACATGCTTTATCAAAATATTTGAGGTTGACTCG
326 AACATTATGAAAACATGTCAAAGTGCAGTAAAACATGCTTTATCAAAATATTTGAGGTTGACTCG
*
3080991 TCACAAGTCTCCCTCATTTAATAGAACTACAATAAATACACTCACCTAATATGCCTTACTAGTAT
391 TCGCAAGTCTCCCTCATTTAATAGAACTACAATAAATACACTCACCTAATATGCCTTACTAGTAT
3081056 GCTGCAATGATGTCAGACTATTCGGTAATTTTATCCTTGCCCTTTTTCTTACCTGACTCTGGAGC
456 GCTGCAATGATGTCAGACTATTCGGTAATTTTATCCTTGCCCTTTTTCTTACCTGACTCTGGAGC
3081121 TTCGTTACGATCTATACAAGTATCCATTAATTACACGTACCATATAAATGTTAGTATACTTCTAA
521 TTCGTTACGATCTATACAAGTATCCATTAATTACACGTACCATATAAATGTTAGTATACTTCTAA
3081186 CATTACTCAAAAGTACCATTATTTCAATTTCTATTAAAATTCATCATATCTAAAAATTCAAGGCT
586 CATTACTCAAAAGTACCATTATTTCAATTTCTATTAAAATTCATCATATCTAAAAATTCAAGGCT
* *
3081251 TAATAGTATCGGTACCTGTACTATGGTATCGATAGTTACATACTATGGTACCGATACTCCCTTAA
651 TAATAGTATCGGTACCTCTATTATGGTATCGATAGTTACATACTATGGTACCGATACTCCCTTAA
3081316 GTTTCGATACCATTTTTGCATTTTGGAATCCATAGTATCGATACCTTCCTCTTAGTACCGATACC
716 GTTTCGATACCATTTTTGCATTTTGGAATCCATAGTATCGATACCTTCCTCTTAGTACCGATACC
3081381 CACAGTAGTATCGATACTAATTGCATCAGTATCGATATTGTTCATCCTATTTCCTCAAATTTAAA
781 CACAGTAGTATCGATACTAATTGCATCAGTATCGATATTGTTCATCCTATTTCCTCAAATTTAAA
3081446 GCTATAGTATCGATATTGTTCTTCCAATACCAATACC
846 GCTATAGTATCGATATTGTTCTTCCAATACCAATACC
3081483 TTTACCCAGA
Statistics
Matches: 1757, Mismatches: 4, Indels: 6
0.99 0.00 0.00
Matches are distributed among these distances:
881 758 0.43
882 34 0.02
883 167 0.10
884 33 0.02
885 765 0.44
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (885 bp):
ACTTATATACATAATTTCATATCGAAATGGTAATTCACAAACTCATTATGACTACCATGATTGCA
CATAAATTCCCAAAAGTACACATAGTATTGATACGAAAATACACCGTTATGCATTAAACAAAATC
GAACGATACAATCATACACGAAGTATGTCGAAATGCACCTATGACTCCCAATTATATACAATGGG
TTTTTAGTCAAATTCACAGATTTAAACATTTATTGCTGCAATATCGATAGTAATTGAACAATATC
AACGTTCATCTATTCATTTTAGAGCAATTCATACTCTAAAATTTATTCGTAATATTATTTTCATA
AACATTATGAAAACATGTCAAAGTGCAGTAAAACATGCTTTATCAAAATATTTGAGGTTGACTCG
TCGCAAGTCTCCCTCATTTAATAGAACTACAATAAATACACTCACCTAATATGCCTTACTAGTAT
GCTGCAATGATGTCAGACTATTCGGTAATTTTATCCTTGCCCTTTTTCTTACCTGACTCTGGAGC
TTCGTTACGATCTATACAAGTATCCATTAATTACACGTACCATATAAATGTTAGTATACTTCTAA
CATTACTCAAAAGTACCATTATTTCAATTTCTATTAAAATTCATCATATCTAAAAATTCAAGGCT
TAATAGTATCGGTACCTCTATTATGGTATCGATAGTTACATACTATGGTACCGATACTCCCTTAA
GTTTCGATACCATTTTTGCATTTTGGAATCCATAGTATCGATACCTTCCTCTTAGTACCGATACC
CACAGTAGTATCGATACTAATTGCATCAGTATCGATATTGTTCATCCTATTTCCTCAAATTTAAA
GCTATAGTATCGATATTGTTCTTCCAATACCAATACCAAT
Found at i:3085153 original size:74 final size:76
Alignment explanation
Indices: 3085075--3085245 Score: 278
Period size: 74 Copynumber: 2.3 Consensus size: 76
3085065 TTATCTTTGC
3085075 ATTTTAGTTTAAATAGATTTTAGTATTTTAATTAAGTTTTAGGATATTA-TTTT-TATTTTATCT
1 ATTTTAGTTTAAATAGATTTTAGTATTTTAATTAAGTTTTAGGATATTATTTTTATATTTTATCT
3085138 TTGTTTTAGGT
66 TTGTTTTAGGT
* *
3085149 ATTTTAGTTTAAATA-ATTTTTAGTATTTTAATTAATTTTTAGGATATTATTTTTATATTTTATT
1 ATTTTAGTTTAAATAGA-TTTTAGTATTTTAATTAAGTTTTAGGATATTATTTTTATATTTTATC
3085213 TTTGTTTTAGGT
65 TTTGTTTTAGGT
*
3085225 ATTTTATTTTAAATAG-TTTTA
1 ATTTTAGTTTAAATAGATTTTA
3085246 AGTGTTTTTA
Statistics
Matches: 90, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
73 1 0.01
74 46 0.51
75 9 0.10
76 34 0.38
ACGTcount: A:0.28, C:0.01, G:0.10, T:0.61
Consensus pattern (76 bp):
ATTTTAGTTTAAATAGATTTTAGTATTTTAATTAAGTTTTAGGATATTATTTTTATATTTTATCT
TTGTTTTAGGT
Found at i:3085286 original size:76 final size:76
Alignment explanation
Indices: 3085075--3085269 Score: 243
Period size: 76 Copynumber: 2.6 Consensus size: 76
3085065 TTATCTTTGC
* *
3085075 ATTTTAGTTTAAATAGATTTT-AGTATTTTAATTAAGTTTTAGGATATTATT-TT-TATTTTATC
1 ATTTTAGTTTAAATA-ATTTTAAGTATTTTAATTAAGATTTAAGATATTATTCTTATATTTTATC
3085137 TTTGTTTTAGGT
65 TTTGTTTTAGGT
* ** * * *
3085149 ATTTTAGTTTAAATAATTTTTAGTATTTTAATTAATTTTTAGGATATTATTTTTATATTTTATTT
1 ATTTTAGTTTAAATAATTTTAAGTATTTTAATTAAGATTTAAGATATTATTCTTATATTTTATCT
3085214 TTGTTTTAGGT
66 TTGTTTTAGGT
* * * * *
3085225 ATTTTATTTTAAATAGTTTTAAGTGTTTTTATTAGGATTTAAGAT
1 ATTTTAGTTTAAATAATTTTAAGTATTTTAATTAAGATTTAAGAT
3085270 GTTTTAGCTT
Statistics
Matches: 107, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
73 5 0.05
74 44 0.41
75 2 0.02
76 56 0.52
ACGTcount: A:0.28, C:0.01, G:0.11, T:0.60
Consensus pattern (76 bp):
ATTTTAGTTTAAATAATTTTAAGTATTTTAATTAAGATTTAAGATATTATTCTTATATTTTATCT
TTGTTTTAGGT
Found at i:3094141 original size:54 final size:54
Alignment explanation
Indices: 3094038--3094156 Score: 141
Period size: 55 Copynumber: 2.2 Consensus size: 54
3094028 ATTGCACCGA
* *
3094038 AGTGCTGAAATGGAAATTCACAAACTCATTATGAATTTAAATGGGTTGCACATAT
1 AGTGCCGAAATGGAAATTCACAAACACATTATGAA-TTAAATGGGTTGCACATAT
** * * *
3094093 AGTGCCGAAATGGTCATTCATAAACACATTATGAA-TACCATGGGTTGCACATTT
1 AGTGCCGAAATGGAAATTCACAAACACATTATGAATTA-AATGGGTTGCACATAT
*
3094147 AGTGTCGAAA
1 AGTGCCGAAA
3094157 ATACATCATT
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
53 2 0.04
54 23 0.42
55 30 0.55
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.29
Consensus pattern (54 bp):
AGTGCCGAAATGGAAATTCACAAACACATTATGAATTAAATGGGTTGCACATAT
Found at i:3096557 original size:21 final size:21
Alignment explanation
Indices: 3096533--3096596 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
3096523 ACTATGCTAG
*
3096533 AAATTAATGTTAGAATGTTGA
1 AAATTGATGTTAGAATGTTGA
3096554 AAATTGATGTTAGAATGTTGA
1 AAATTGATGTTAGAATGTTGA
3096575 AAATTGATGTTAGAATG-TGA
1 AAATTGATGTTAGAATGTTGA
3096595 AA
1 AA
3096597 TTGGGCCATT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
20 5 0.12
21 37 0.88
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (21 bp):
AAATTGATGTTAGAATGTTGA
Found at i:3101357 original size:22 final size:19
Alignment explanation
Indices: 3101305--3101376 Score: 81
Period size: 19 Copynumber: 3.6 Consensus size: 19
3101295 CCGAAGGGAA
*
3101305 GGTATCGATACCATAATAG
1 GGTATCGATACCATAGTAG
*
3101324 GGTATCGGTACCATAGTAGG
1 GGTATCGATACCATAGTA-G
*
3101344 GTAGTATCGATACCATGGTAAG
1 G--GTATCGATACCATAGT-AG
3101366 GGTATCGATAC
1 GGTATCGATAC
3101377 TAGATAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
19 16 0.36
20 12 0.27
22 16 0.36
23 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (19 bp):
GGTATCGATACCATAGTAG
Found at i:3101896 original size:20 final size:20
Alignment explanation
Indices: 3101871--3101944 Score: 67
Period size: 20 Copynumber: 3.4 Consensus size: 20
3101861 TAATTAAAAT
3101871 GCATGAAAAGATGCATTAAG
1 GCATGAAAAGATGCATTAAG
* *
3101891 GCATGAAATGATGCCATAATTAAAAT
1 GCATGAAAAGATG-C---ATT--AAG
*
3101917 GCATGAAAGGATGCATTAAG
1 GCATGAAAAGATGCATTAAG
3101937 GCATGAAA
1 GCATGAAA
3101945 GGATACCATA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
20 22 0.50
21 1 0.02
22 3 0.07
24 3 0.07
25 1 0.02
26 14 0.32
ACGTcount: A:0.45, C:0.11, G:0.23, T:0.22
Consensus pattern (20 bp):
GCATGAAAAGATGCATTAAG
Found at i:3101930 original size:46 final size:46
Alignment explanation
Indices: 3101858--3102112 Score: 402
Period size: 46 Copynumber: 5.5 Consensus size: 46
3101848 TAAATCGAAT
* *
3101858 CCATAATTAAAATGCATGAAAAGATGCATTAAGGCATGAAATGATG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
*
3101904 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATA
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
3101950 CCATAATTAAAATGCATGAAATGATACATTAAGGCATGAAAGGATG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * * *
3101996 CCATAATTAAAATGCTTGAAAGGTTGCATTAAGGCATGAAATGATT
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
3102042 CCATAATTAAAATGCATGAAAGGATGCATTAAGGAATAAAAGGATG
1 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
*
3102088 CCATAATTAAAATGAATGAAAGGAT
1 CCATAATTAAAATGCATGAAAGGAT
3102113 ACCATAATTA
Statistics
Matches: 190, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 190 1.00
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.24
Consensus pattern (46 bp):
CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
Found at i:3102107 original size:138 final size:141
Alignment explanation
Indices: 3101858--3102152 Score: 443
Period size: 138 Copynumber: 2.1 Consensus size: 141
3101848 TAAATCGAAT
3101858 CCATAATTAAAATGCATGAAAAGATGCATTAAGGCATGAAATGATGCCATAATTAAAATGCATGA
1 CCATAATTAAAATGCATGAAAAGATGCATTAAGGCATGAAATGATGCCATAATTAAAATGCATGA
* * * *
3101923 AAGGATGCATTAAGGCATGAAAGGATACCATAATTAAAATGCATGAAATGATA-C-ATT-AAGGC
66 AAGGATGCATTAAGGAATAAAAGGATACCATAATTAAAATGAATGAAAGGATACCAATTAAAGGC
3101985 ATGAAAGGATG
131 ATGAAAGGATG
* * * *
3101996 CCATAATTAAAATGCTTGAAAGGTTGCATTAAGGCATGAAATGATTCCATAATTAAAATGCATGA
1 CCATAATTAAAATGCATGAAAAGATGCATTAAGGCATGAAATGATGCCATAATTAAAATGCATGA
*
3102061 AAGGATGCATTAAGGAATAAAAGGATGCCATAATTAAAATGAATGAAAGGATACCATAATTAAAA
66 AAGGATGCATTAAGGAATAAAAGGATACCATAATTAAAATGAATGAAAGGATACC--AATT-AAA
*
3102126 TGCATGAAAGGATG
128 GGCATGAAAGGATG
*
3102140 CCATAATTTAAAT
1 CCATAATTAAAAT
3102153 ATATCATGGA
Statistics
Matches: 140, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
138 109 0.78
139 1 0.01
142 3 0.02
144 27 0.19
ACGTcount: A:0.46, C:0.11, G:0.19, T:0.25
Consensus pattern (141 bp):
CCATAATTAAAATGCATGAAAAGATGCATTAAGGCATGAAATGATGCCATAATTAAAATGCATGA
AAGGATGCATTAAGGAATAAAAGGATACCATAATTAAAATGAATGAAAGGATACCAATTAAAGGC
ATGAAAGGATG
Found at i:3102274 original size:27 final size:28
Alignment explanation
Indices: 3102233--3102298 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
3102223 TATATTAGAA
* *
3102233 TGGTTATGATGAT-AAATGACCAAAGTT
1 TGGTTATGATAATAAAACGACCAAAGTT
* *
3102260 TGGTTATGATAATAAAACGAGCAGAGTT
1 TGGTTATGATAATAAAACGACCAAAGTT
3102288 TGGTTATGATA
1 TGGTTATGATA
3102299 CGAAGGATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 12 0.35
28 22 0.65
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.33
Consensus pattern (28 bp):
TGGTTATGATAATAAAACGACCAAAGTT
Found at i:3108252 original size:20 final size:20
Alignment explanation
Indices: 3108226--3108276 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
3108216 GATTTAATCA
3108226 ATATCGATACCAAAGGGGAAG
1 ATATCGATACCAAA-GGGAAG
*
3108247 -TATCGATACCGAAGGGAAG
1 ATATCGATACCAAAGGGAAG
*
3108266 ATATTGATACC
1 ATATCGATACC
3108277 TTTTTAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 6 0.22
20 21 0.78
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.20
Consensus pattern (20 bp):
ATATCGATACCAAAGGGAAG
Found at i:3110029 original size:16 final size:16
Alignment explanation
Indices: 3110008--3110045 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3109998 AATTAGTTAA
3110008 TTTGATACAATGTT-TG
1 TTTGATA-AATGTTATG
*
3110024 TTTGATAAATTTTATG
1 TTTGATAAATGTTATG
3110040 TTTGAT
1 TTTGAT
3110046 TCTATGCTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.26, C:0.03, G:0.16, T:0.55
Consensus pattern (16 bp):
TTTGATAAATGTTATG
Found at i:3110923 original size:33 final size:33
Alignment explanation
Indices: 3110881--3111094 Score: 135
Period size: 33 Copynumber: 6.2 Consensus size: 33
3110871 TAGCTAGGTA
*
3110881 TATGATATAAGTGCTTGCCATGAAAGTTCATGT
1 TATGATATAAGTTCTTGCCATGAAAGTTCATGT
* * * * **
3110914 TATGATATAAGTTATAGTCATGAAAATTCAACT
1 TATGATATAAGTTCTTGCCATGAAAGTTCATGT
* ** *
3110947 TATGATATAAGTTATTATCATGAAAG-TCATAT
1 TATGATATAAGTTCTTGCCATGAAAGTTCATGT
* * *
3110979 ATGATGAATTATGATATTTGTGCTTGCGATGAAAATTTACATGT
1 -T-ATG-A-TAT-A-A---GTTCTTGCCATG-AAAGTT-CATGT
* * *
3111023 TACT-ATATAAGTTCTTGGCAAGAAAGATCATGT
1 TA-TGATATAAGTTCTTGCCATGAAAGTTCATGT
* *
3111056 TTTGATATAAGTTCTTTCCATGAAAGTTCATGT
1 TATGATATAAGTTCTTGCCATGAAAGTTCATGT
3111089 TATGAT
1 TATGAT
3111095 GAGTTTATTA
Statistics
Matches: 136, Mismatches: 31, Indels: 28
0.70 0.16 0.14
Matches are distributed among these distances:
32 5 0.04
33 86 0.63
34 7 0.05
35 9 0.07
36 3 0.02
37 1 0.01
38 2 0.01
39 1 0.01
40 3 0.02
41 8 0.06
42 4 0.03
43 3 0.02
44 4 0.03
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.39
Consensus pattern (33 bp):
TATGATATAAGTTCTTGCCATGAAAGTTCATGT
Found at i:3115932 original size:19 final size:19
Alignment explanation
Indices: 3115905--3115949 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
3115895 AAGCGGTCGG
*
3115905 CATAGCCCTAGGGTTTCAT
1 CATAACCCTAGGGTTTCAT
3115924 CATAACCCTAGGGTTTCAT
1 CATAACCCTAGGGTTTCAT
3115943 CATAACC
1 CATAACC
3115950 ATCATTTGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.29
Consensus pattern (19 bp):
CATAACCCTAGGGTTTCAT
Found at i:3116199 original size:6 final size:6
Alignment explanation
Indices: 3116176--3116228 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
3116166 ATTTATTTGT
* * * * * *
3116176 AATAAT AATAAT AATAAC AATAAC AACAAC AATAAC AACAAC ATTAAT
1 AATAAC AATAAC AATAAC AATAAC AATAAC AATAAC AATAAC AATAAC
3116224 AATAA
1 AATAA
3116229 AAAAAATACG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.66, C:0.13, G:0.00, T:0.21
Consensus pattern (6 bp):
AATAAC
Found at i:3116483 original size:31 final size:30
Alignment explanation
Indices: 3116413--3116491 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 30
3116403 TATCTTGCTT
* * *
3116413 CACTACTCTTCTGTGAAGGCTGAATCTTTT
1 CACTACTCTTCTGTGGAGGCTGAATCTCTC
* *
3116443 CTCTACTCTTTTGTGGAGGCTGAATCTACTC
1 CACTACTCTTCTGTGGAGGCTGAATCT-CTC
3116474 CACTACTCTTCTGTGGAG
1 CACTACTCTTCTGTGGAG
3116492 ATCAGACATG
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 24 0.59
31 17 0.41
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.38
Consensus pattern (30 bp):
CACTACTCTTCTGTGGAGGCTGAATCTCTC
Found at i:3116595 original size:36 final size:36
Alignment explanation
Indices: 3116504--3117048 Score: 640
Period size: 36 Copynumber: 15.2 Consensus size: 36
3116494 CAGACATGAA
* ** *
3116504 ATTGATATT-CTTCACTACTCTTTTTGTGAAAACTAAA
1 ATTGAT-TTGCTTCACTACTC-TTCTGTGAAGGCTAAG
* *
3116541 ATTGA-TTGTTTCACTACTCTTATGTGAAGGCTAAG
1 ATTGATTTGCTTCACTACTCTTCTGTGAAGGCTAAG
* *
3116576 ATTGATTTGC-TCTATTACTCTTCTATGAAGGCTAAG
1 ATTGATTTGCTTC-ACTACTCTTCTGTGAAGGCTAAG
* *
3116612 ATTGATTTGC-TCTACTACTCTTTTCTGAAGGCTAAG
1 ATTGATTTGCTTC-ACTACTCTTCTGTGAAGGCTAAG
* *
3116648 ATTGATTTGCTTCACTACTCTTATCTGAAGGCTAAG
1 ATTGATTTGCTTCACTACTCTTCTGTGAAGGCTAAG
*
3116684 ATTGATTTGCTTCACTA--CTT-T-TGAATGCTAAG
1 ATTGATTTGCTTCACTACTCTTCTGTGAAGGCTAAG
*
3116716 ATTGATTTGCTTCACTACTCTTCTGTGAAGGGTAAG
1 ATTGATTTGCTTCACTACTCTTCTGTGAAGGCTAAG
* * * *
3116752 ATGGATTTTCTTCACTACACTTATGTGAAGGCTAAG
1 ATTGATTTGCTTCACTACTCTTCTGTGAAGGCTAAG
* * *
3116788 ATT-AGTTTGCTTCACCACTCTTCAGTGAAGGTTAAG
1 ATTGA-TTTGCTTCACTACTCTTCTGTGAAGGCTAAG
* **
3116824 ATTGTTTTGCTTCACTACTCTTCTGTGAAGGCGCAG
1 ATTGATTTGCTTCACTACTCTTCTGTGAAGGCTAAG
* * * * *
3116860 ATTGGTTTGATTTACTACTCTTTTGTGATGGCTAAG
1 ATTGATTTGCTTCACTACTCTTCTGTGAAGGCTAAG
* * *
3116896 ATTGATTTGCTTAACTACTATTATGTGAAGGCTAAG
1 ATTGATTTGCTTCACTACTCTTCTGTGAAGGCTAAG
* ** *
3116932 ATAGATTTGCTTCAAGACTCTTCTGTGAAAGCTAAG
1 ATTGATTTGCTTCACTACTCTTCTGTGAAGGCTAAG
*
3116968 ATTGATTTGTTTCACTACTCTTCTGTGAAGGCTAAG
1 ATTGATTTGCTTCACTACTCTTCTGTGAAGGCTAAG
*
3117004 ATTTATTTGCTTCACTACTCTTCTGTGAAGGCTAAG
1 ATTGATTTGCTTCACTACTCTTCTGTGAAGGCTAAG
3117040 ATTGATTTG
1 ATTGATTTG
3117049 AGAAGAATAT
Statistics
Matches: 436, Mismatches: 62, Indels: 21
0.84 0.12 0.04
Matches are distributed among these distances:
32 27 0.06
33 1 0.00
34 6 0.01
35 23 0.05
36 372 0.85
37 7 0.02
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.40
Consensus pattern (36 bp):
ATTGATTTGCTTCACTACTCTTCTGTGAAGGCTAAG
Found at i:3117184 original size:89 final size:89
Alignment explanation
Indices: 3117047--3117250 Score: 252
Period size: 89 Copynumber: 2.3 Consensus size: 89
3117037 AAGATTGATT
* * * *
3117047 TGAGAAGAATATGTTCCACTACTATTCCTTGGAGATCAAACTCGAGGTTGATTTGATTCGCTTCT
1 TGAGAAGAATCTGTTCCACTACTATTCCTTGAAGATCAAACTCAAGGTTGATTTGATTCGCTACT
* * *
3117112 TTTCCAGGAAGCCCAAATTTG-GAA
66 TTGCCAGGAAGACCAAATCTGTG-A
* * * *
3117136 TGAGAAGAATCTATTCCACTACTCTTTCC-TGAAGATTAGACTCAAGGTTGATTTGATTCGCTAC
1 TGAGAAGAATCTGTTCCACTACT-ATTCCTTGAAGATCAAACTCAAGGTTGATTTGATTCGCTAC
*
3117200 TTTGCTAGGAAGACCAAATCTGTGA
65 TTTGCCAGGAAGACCAAATCTGTGA
3117225 TG-GAAAGAATCTGTTCCACTACTATT
1 TGAG-AAGAATCTGTTCCACTACTATT
3117251 ACGGGGATAT
Statistics
Matches: 98, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
88 3 0.03
89 90 0.92
90 5 0.05
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (89 bp):
TGAGAAGAATCTGTTCCACTACTATTCCTTGAAGATCAAACTCAAGGTTGATTTGATTCGCTACT
TTGCCAGGAAGACCAAATCTGTGA
Found at i:3129478 original size:3 final size:3
Alignment explanation
Indices: 3129470--3129495 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3129460 TATTTATTTG
3129470 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
3129496 TTATTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3129500 original size:3 final size:3
Alignment explanation
Indices: 3129494--3129542 Score: 89
Period size: 3 Copynumber: 16.0 Consensus size: 3
3129484 ATAATAATAA
3129494 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
3129540 TAT
1 TAT
3129543 AAATACGTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3135823 original size:22 final size:22
Alignment explanation
Indices: 3135780--3135823 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
3135770 GAGCTGAGGG
* * *
3135780 TTCTATACGGTCCTTTGGGATA
1 TTCTATACGATCCTTCGAGATA
*
3135802 TTCTATATGATCCTTCGAGATA
1 TTCTATACGATCCTTCGAGATA
3135824 CTTTTAAGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (22 bp):
TTCTATACGATCCTTCGAGATA
Found at i:3144438 original size:18 final size:17
Alignment explanation
Indices: 3144416--3144456 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
3144406 TTTTGTGTGG
*
3144416 TTATTTTTTTGTTTTTA
1 TTATTTTTTTGTTTTAA
3144433 -TATATTTTTTGTTTTAA
1 TTAT-TTTTTTGTTTTAA
3144450 TTATTTT
1 TTATTTT
3144457 AGTTAAGTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 3 0.14
17 15 0.71
18 3 0.14
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (17 bp):
TTATTTTTTTGTTTTAA
Found at i:3146516 original size:31 final size:29
Alignment explanation
Indices: 3146459--3146521 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 29
3146449 TGACTAATCA
* *
3146459 TTTCAACTAACTTGATTCTTTTTGTCTTG
1 TTTCAACTAACTTGATTCCTTTTGTCTAG
*
3146488 TTTCTACTAACATTGATTTCCTTTTGTCTAG
1 TTTCAACTAAC-TTGA-TTCCTTTTGTCTAG
3146519 TTT
1 TTT
3146522 TGTTGCATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 10 0.34
30 4 0.14
31 15 0.52
ACGTcount: A:0.17, C:0.17, G:0.10, T:0.56
Consensus pattern (29 bp):
TTTCAACTAACTTGATTCCTTTTGTCTAG
Found at i:3147417 original size:19 final size:19
Alignment explanation
Indices: 3147393--3147471 Score: 63
Period size: 19 Copynumber: 3.9 Consensus size: 19
3147383 TAGGGAAGAA
3147393 AAGAGAAAAAAAGAAAAAG
1 AAGAGAAAAAAAGAAAAAG
*
3147412 AAGAGAGAAAGAAAAACCAAACAG
1 AAGAGA-AAA-AAAGA--AAA-AG
* *
3147436 AAG-GGAAAAAAGGAAAA-
1 AAGAGAAAAAAAGAAAAAG
3147453 AAGAAGAAAAAAAGAAAAA
1 AAG-AGAAAAAAAGAAAAA
3147472 ATAAGAAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
17 3 0.06
18 1 0.02
19 21 0.45
20 3 0.06
21 7 0.15
22 3 0.06
23 4 0.09
24 5 0.11
ACGTcount: A:0.75, C:0.04, G:0.22, T:0.00
Consensus pattern (19 bp):
AAGAGAAAAAAAGAAAAAG
Found at i:3147424 original size:11 final size:11
Alignment explanation
Indices: 3147388--3147426 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
3147378 AAAGATAGGG
3147388 AAGAAAAGAGA
1 AAGAAAAGAGA
*
3147399 AA-AAAAGAAA
1 AAGAAAAGAGA
*
3147409 AAGAAGAGAGA
1 AAGAAAAGAGA
3147420 AAGAAAA
1 AAGAAAA
3147427 ACCAAACAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (11 bp):
AAGAAAAGAGA
Found at i:3147461 original size:18 final size:18
Alignment explanation
Indices: 3147391--3147479 Score: 65
Period size: 18 Copynumber: 4.6 Consensus size: 18
3147381 GATAGGGAAG
3147391 AAAAG-AGAAAAAAAGAAA
1 AAAAGAAGAAAAAAAG-AA
3147409 AAGAAGAGAGAAAGAAAA-ACCA
1 AA-AAGA-AGAAA-AAAAGA--A
* *
3147431 AACAGAAGGGAAAAAAGGAA
1 AAAAGAA--GAAAAAAAGAA
3147451 AAAAGAAGAAAAAAAGAA
1 AAAAGAAGAAAAAAAGAA
*
3147469 AAAATAAGAAA
1 AAAAGAAGAAA
3147480 TAAGAAAATA
Statistics
Matches: 57, Mismatches: 5, Indels: 18
0.71 0.06 0.22
Matches are distributed among these distances:
18 22 0.39
19 3 0.05
20 9 0.16
21 11 0.19
22 12 0.21
ACGTcount: A:0.75, C:0.03, G:0.20, T:0.01
Consensus pattern (18 bp):
AAAAGAAGAAAAAAAGAA
Found at i:3149121 original size:44 final size:44
Alignment explanation
Indices: 3149031--3149561 Score: 192
Period size: 44 Copynumber: 12.1 Consensus size: 44
3149021 TCTATCAACC
* * * **
3149031 TTTTGCTCGATTCTATCACAGAATGAGGTAGATCAACACAAACA
1 TTTTGCTCGATTCCATCACAGAAGGAGGTGGATCAACATTAACA
* *
3149075 TTTTGTTCGATTCCATCACAGAAGGAGGTGGATCAACATTATCA
1 TTTTGCTCGATTCCATCACAGAAGGAGGTGGATCAACATTAACA
* * * * * * * *
3149119 TTTCT-CTCAAATCCATCACATAAGGAGTTGGATTAGCATCAACC
1 TTT-TGCTCGATTCCATCACAGAAGGAGGTGGATCAACATTAACA
* * * *
3149163 TTTTGCTCGATTCTATCACAGAAGGAGGTAG-TCAACACCT-ATA
1 TTTTGCTCGATTCCATCACAGAAGGAGGTGGATCAACA-TTAACA
*** * * * ***
3149206 TTTCATTCTATTCCATCACAAAAGGAGATGGATCAACATTTTTA
1 TTTTGCTCGATTCCATCACAGAAGGAGGTGGATCAACATTAACA
** * * * * ** * * *
3149250 TTTCACTCAAATCTAGCGGATAAGG-GGTTGGATCAACATCAACT
1 TTTTGCTCGATTCCATCACAGAAGGAGG-TGGATCAACATTAACA
* * * * * * ***
3149294 TTTTGCTCGATTCTATCGCATAAGGAGGTAGAACAGCACCGACA
1 TTTTGCTCGATTCCATCACAGAAGGAGGTGGATCAACATTAACA
* * * * **
3149338 TTTCGTTCGATTCCATCACAAAATGAGGTGGATCAACATTTTCA
1 TTTTGCTCGATTCCATCACAGAAGGAGGTGGATCAACATTAACA
** * ** * ** * * *
3149382 TTTCACTCAAACCCA-AATCATTAGGAGTTGGATCAACATCAACT
1 TTTTGCTCGATTCCATCA-CAGAAGGAGGTGGATCAACATTAACA
* * * * * * **
3149426 TTTTGCTTGATTCTATTACATAAGGAGGTAGATCAGCACCAACA
1 TTTTGCTCGATTCCATCACAGAAGGAGGTGGATCAACATTAACA
* * * * * ***
3149470 TTTCGTTCGATTCCATCACAAAAGGAGATGGATCCACATTTTTA
1 TTTTGCTCGATTCCATCACAGAAGGAGGTGGATCAACATTAACA
* * * * * * *
3149514 TTTTGCTCAAATCCATCGCATAAGGAGTTGGATCAGCATCAAC-
1 TTTTGCTCGATTCCATCACAGAAGGAGGTGGATCAACATTAACA
3149557 TTTTG
1 TTTTG
3149562 ACCGGTTCTA
Statistics
Matches: 344, Mismatches: 134, Indels: 19
0.69 0.27 0.04
Matches are distributed among these distances:
43 37 0.11
44 303 0.88
45 4 0.01
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (44 bp):
TTTTGCTCGATTCCATCACAGAAGGAGGTGGATCAACATTAACA
Found at i:3149238 original size:87 final size:88
Alignment explanation
Indices: 3149075--3149238 Score: 217
Period size: 87 Copynumber: 1.9 Consensus size: 88
3149065 AACACAAACA
* * * *
3149075 TTTTGTTCGATTCCATCACAGAAGGAGGTGGATCAACATTATCATTTCTCTCAAATCCATCACAT
1 TTTTGCTCGATTCCATCACAGAAGGAGGTAGATCAACACTATCATTTCTCTCAAATCCATCACAA
*
3149140 AAGGAGTTGGATTAGCATCAACC
66 AAGGAGATGGATTAGCATCAACC
* * *
3149163 TTTTGCTCGATTCTATCACAGAAGGAGGTAG-TCAACACCTAT-ATTTCAT-TCTATTCCATCAC
1 TTTTGCTCGATTCCATCACAGAAGGAGGTAGATCAACA-CTATCATTTC-TCTCAAATCCATCAC
3149225 AAAAGGAGATGGAT
64 AAAAGGAGATGGAT
3149239 CAACATTTTT
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
87 34 0.52
88 32 0.48
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (88 bp):
TTTTGCTCGATTCCATCACAGAAGGAGGTAGATCAACACTATCATTTCTCTCAAATCCATCACAA
AAGGAGATGGATTAGCATCAACC
Found at i:3149412 original size:132 final size:132
Alignment explanation
Indices: 3149024--3149560 Score: 664
Period size: 132 Copynumber: 4.1 Consensus size: 132
3149014 GCTCGATTCT
* * * *
3149024 ATCAACCTTTTGCTCGATTCTATCACAGAATGAGGTAGATCAACACAAACATTTTGTTCGATTCC
1 ATCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACACCAACATTTCGTTCGATTCC
* * * * * *
3149089 ATCACAGAAGGAGGTGGATCAACATTATCATTTCTCTCAAATCCATCA-CATAAGGAGTTGGATT
66 ATCACAAAAGGAGATGGATCAACATTTTCATTTCACTCAAATCCA-AAGCATAAGGAGTTGGATC
*
3149153 AGC
130 AAC
* * * * *
3149156 ATCAACCTTTTGCTCGATTCTATCACAGAAGGAGGTAG-TCAACACCTATATTTCATTCTATTCC
1 ATCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACACCAACATTTCGTTCGATTCC
* * ** * *
3149220 ATCACAAAAGGAGATGGATCAACATTTTTATTTCACTCAAATCTAGCGGATAAGGGGTTGGATCA
66 ATCACAAAAGGAGATGGATCAACATTTTCATTTCACTCAAATCCAAAGCATAAGGAGTTGGATCA
3149285 AC
131 AC
* * * * *
3149287 ATCAACTTTTTGCTCGATTCTATCGCATAAGGAGGTAGAACAGCACCGACATTTCGTTCGATTCC
1 ATCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACACCAACATTTCGTTCGATTCC
* * * * *
3149352 ATCACAAAATGAGGTGGATCAACATTTTCATTTCACTCAAACCCAAATCATTAGGAGTTGGATCA
66 ATCACAAAAGGAGATGGATCAACATTTTCATTTCACTCAAATCCAAAGCATAAGGAGTTGGATCA
3149417 AC
131 AC
* * * *
3149419 ATCAACTTTTTGCTTGATTCTATTACATAAGGAGGTAGATCAGCACCAACATTTCGTTCGATTCC
1 ATCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACACCAACATTTCGTTCGATTCC
* * ** **
3149484 ATCACAAAAGGAGATGGATCCACATTTTTATTTTGCTCAAATCCATCGCATAAGGAGTTGGATCA
66 ATCACAAAAGGAGATGGATCAACATTTTCATTTCACTCAAATCCAAAGCATAAGGAGTTGGATCA
*
3149549 GC
131 AC
3149551 ATCAACTTTT
1 ATCAACTTTT
3149561 GACCGGTTCT
Statistics
Matches: 347, Mismatches: 56, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
131 109 0.31
132 238 0.69
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.31
Consensus pattern (132 bp):
ATCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAACACCAACATTTCGTTCGATTCC
ATCACAAAAGGAGATGGATCAACATTTTCATTTCACTCAAATCCAAAGCATAAGGAGTTGGATCA
AC
Found at i:3154905 original size:14 final size:14
Alignment explanation
Indices: 3154886--3154943 Score: 70
Period size: 14 Copynumber: 4.4 Consensus size: 14
3154876 CGTTCGGTAA
3154886 TATGTTCGTTCATT
1 TATGTTCGTTCATT
*
3154900 TATGTTCGTTCGTT
1 TATGTTCGTTCATT
3154914 TATGTTCG----TT
1 TATGTTCGTTCATT
*
3154924 TATGTGCGTTCATT
1 TATGTTCGTTCATT
3154938 TATGTT
1 TATGTT
3154944 TAGCCTAATC
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 9 0.24
14 28 0.76
ACGTcount: A:0.12, C:0.12, G:0.19, T:0.57
Consensus pattern (14 bp):
TATGTTCGTTCATT
Found at i:3154925 original size:24 final size:24
Alignment explanation
Indices: 3154893--3154943 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
3154883 TAATATGTTC
* *
3154893 GTTCATTTATGTTCGTTCGTTTAT
1 GTTCATTTATGTGCGTTCATTTAT
*
3154917 GTTCGTTTATGTGCGTTCATTTAT
1 GTTCATTTATGTGCGTTCATTTAT
3154941 GTT
1 GTT
3154944 TAGCCTAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.12, C:0.12, G:0.20, T:0.57
Consensus pattern (24 bp):
GTTCATTTATGTGCGTTCATTTAT
Found at i:3156150 original size:3 final size:3
Alignment explanation
Indices: 3156142--3156237 Score: 192
Period size: 3 Copynumber: 32.0 Consensus size: 3
3156132 GTCCTATTGC
3156142 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3156190 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3156238 AATTTTGTTT
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 93 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3160061 original size:6 final size:6
Alignment explanation
Indices: 3160050--3160079 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
3160040 TTGTAGGCCA
3160050 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
3160080 GCATGTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:3160303 original size:33 final size:33
Alignment explanation
Indices: 3160265--3160331 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
3160255 TGAAAGTTTT
* *
3160265 TCCCATTTAGTGACAGGAATTAAATTGAATTCA
1 TCCCATTTAGTGACACGAATTAAATCGAATTCA
3160298 TCCCATTTAGTGACACGAATTAAATCGAATTCA
1 TCCCATTTAGTGACACGAATTAAATCGAATTCA
3160331 T
1 T
3160332 TTTAAAATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (33 bp):
TCCCATTTAGTGACACGAATTAAATCGAATTCA
Found at i:3161781 original size:18 final size:18
Alignment explanation
Indices: 3161758--3161793 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3161748 ACAACACACA
3161758 AAAGGAGAAAGGTATGAT
1 AAAGGAGAAAGGTATGAT
3161776 AAAGGAGAAAGGTATGAT
1 AAAGGAGAAAGGTATGAT
3161794 CTTATATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17
Consensus pattern (18 bp):
AAAGGAGAAAGGTATGAT
Found at i:3164842 original size:19 final size:19
Alignment explanation
Indices: 3164818--3164859 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
3164808 AAGAGCAATT
3164818 GGGAAAAACGATGGAACTA
1 GGGAAAAACGATGGAACTA
*
3164837 GGGAAAAATGATGGAACTA
1 GGGAAAAACGATGGAACTA
3164856 GGGA
1 GGGA
3164860 TTTCAATTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.45, C:0.07, G:0.36, T:0.12
Consensus pattern (19 bp):
GGGAAAAACGATGGAACTA
Found at i:3170563 original size:26 final size:26
Alignment explanation
Indices: 3170527--3170593 Score: 116
Period size: 26 Copynumber: 2.5 Consensus size: 26
3170517 TTCTTGATTT
*
3170527 AGAAGAAGATAGAATTTTAGATAAAAA
1 AGAA-AAGATAGAATTTCAGATAAAAA
3170554 AGAAAAGATAGAATTTCAGATAAAAA
1 AGAAAAGATAGAATTTCAGATAAAAA
3170580 AGAAAAGATAGAAT
1 AGAAAAGATAGAAT
3170594 AAAATAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
26 35 0.90
27 4 0.10
ACGTcount: A:0.61, C:0.01, G:0.18, T:0.19
Consensus pattern (26 bp):
AGAAAAGATAGAATTTCAGATAAAAA
Found at i:3171394 original size:31 final size:31
Alignment explanation
Indices: 3171341--3171406 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
3171331 AATTTAAAAT
* *
3171341 AAAATAGAAAAATATGTGTAAAGCTTGAAAG
1 AAAATAGAAAAATATGTATAAAGCTAGAAAG
* *
3171372 AAAATAGAGAAAAT-TTTATAAAGCTAGAGAG
1 AAAATAGA-AAAATATGTATAAAGCTAGAAAG
3171403 AAAA
1 AAAA
3171407 ACAAGATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 25 0.83
32 5 0.17
ACGTcount: A:0.58, C:0.03, G:0.18, T:0.21
Consensus pattern (31 bp):
AAAATAGAAAAATATGTATAAAGCTAGAAAG
Found at i:3171626 original size:33 final size:33
Alignment explanation
Indices: 3171522--3171628 Score: 94
Period size: 33 Copynumber: 3.2 Consensus size: 33
3171512 AAATCCTAAT
3171522 TAAAACACTTAAA-ACTATTTAAACTAAACTACC
1 TAAAACACTTAAAGA-TATTTAAACTAAACTACC
* *** * * *
3171555 TAAAGCAAAGATAAGATA-ATAACCTAAATCCTA-A
1 TAAAACACTTA-AAGATATTTAAACTAAA--CTACC
3171589 TAAAACACTTAAAGATATTTAAACTAAACTACC
1 TAAAACACTTAAAGATATTTAAACTAAACTACC
3171622 TAAAACA
1 TAAAACA
3171629 AAGATAAAAT
Statistics
Matches: 54, Mismatches: 14, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
32 3 0.06
33 28 0.52
34 19 0.35
35 4 0.07
ACGTcount: A:0.54, C:0.18, G:0.04, T:0.24
Consensus pattern (33 bp):
TAAAACACTTAAAGATATTTAAACTAAACTACC
Found at i:3172559 original size:39 final size:40
Alignment explanation
Indices: 3172508--3172588 Score: 103
Period size: 39 Copynumber: 2.0 Consensus size: 40
3172498 TCGATTTTCC
*
3172508 TTCTTCTTCTTTTTCTGATGTTCAAAACAATGAA-ATATTT
1 TTCTTCTTCTTTTTCTGATGCTCAAAACAATGAACA-ATTT
* * *
3172548 TTCTT-TTCTTTTTTTGTTGCTCGAAACAATGAACAATTT
1 TTCTTCTTCTTTTTCTGATGCTCAAAACAATGAACAATTT
3172587 TT
1 TT
3172589 TTGACTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
39 30 0.83
40 6 0.17
ACGTcount: A:0.25, C:0.15, G:0.09, T:0.52
Consensus pattern (40 bp):
TTCTTCTTCTTTTTCTGATGCTCAAAACAATGAACAATTT
Found at i:3175524 original size:5 final size:5
Alignment explanation
Indices: 3175516--3175541 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3175506 TTAAGCATCT
3175516 AATAA AATAA AATAA AATAA AATAA A
1 AATAA AATAA AATAA AATAA AATAA A
3175542 TGGAAAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:3175589 original size:23 final size:23
Alignment explanation
Indices: 3175563--3175606 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
3175553 TGATAAAAAT
3175563 AAAAC-AAAATGAAAATGAAATTA
1 AAAACGAAAAT-AAAATGAAATTA
3175586 AAAACGAAAATAAAATGAAAT
1 AAAACGAAAATAAAATGAAAT
3175607 GGGTTATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.70, C:0.05, G:0.09, T:0.16
Consensus pattern (23 bp):
AAAACGAAAATAAAATGAAATTA
Found at i:3182201 original size:68 final size:69
Alignment explanation
Indices: 3182121--3182253 Score: 232
Period size: 68 Copynumber: 1.9 Consensus size: 69
3182111 AAATAAAGAA
3182121 ATAAATCCTAATTAAAACACTTAAAACTATTTAAACAAAACTACCTAAAACAAAG-AAAATATAA
1 ATAAATCCTAATTAAAACACTTAAAACTATTTAAACAAAACTACCTAAAACAAAGAAAAATATAA
3182185 TATC
66 TATC
* *
3182189 ATAAATCCTAATTAAAACACTTAAAGCTATTTAAACTAAACTACCTAAAACAAAGATAAAATATA
1 ATAAATCCTAATTAAAACACTTAAAACTATTTAAACAAAACTACCTAAAACAAAGA-AAAATATA
3182254 TATTTAAAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
68 53 0.87
70 8 0.13
ACGTcount: A:0.56, C:0.16, G:0.02, T:0.26
Consensus pattern (69 bp):
ATAAATCCTAATTAAAACACTTAAAACTATTTAAACAAAACTACCTAAAACAAAGAAAAATATAA
TATC
Found at i:3194067 original size:32 final size:32
Alignment explanation
Indices: 3194029--3194133 Score: 192
Period size: 32 Copynumber: 3.3 Consensus size: 32
3194019 GTGGGTTGAA
* *
3194029 GAGGATGAGGATTGTAGCATCAATGGAGTGAG
1 GAGGATGACGATTGCAGCATCAATGGAGTGAG
3194061 GAGGATGACGATTGCAGCATCAATGGAGTGAG
1 GAGGATGACGATTGCAGCATCAATGGAGTGAG
3194093 GAGGATGACGATTGCAGCATCAATGGAGTGAG
1 GAGGATGACGATTGCAGCATCAATGGAGTGAG
3194125 GAGGATGAC
1 GAGGATGAC
3194134 CCAAATCCTG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 71 1.00
ACGTcount: A:0.31, C:0.10, G:0.39, T:0.19
Consensus pattern (32 bp):
GAGGATGACGATTGCAGCATCAATGGAGTGAG
Found at i:3194774 original size:139 final size:140
Alignment explanation
Indices: 3194603--3194881 Score: 508
Period size: 139 Copynumber: 2.0 Consensus size: 140
3194593 AAATAAAATG
3194603 TTAATTAATTAAAAAATAAACATCATCACAATGCTAGGGGAAAAACGTTAGAGTAACAAAAAAAA
1 TTAATTAATTAAAAAATAAACATCATCACAATGCTAGGGGAAAAACGTTAGAGTAACAAAAAAAA
3194668 ATTCAATGTCTAAAGTTCACTGAGCAAATTG-AAAAAAAAA-TGAAAGTACGGTGAGTGAAATAA
66 ATTCAATGTCTAAAGTTCACTGAGCAAATTGAAAAAAAAAATTGAAAGTACGGTGAGTGAAATAA
3194731 GAGAGAGAAT
131 GAGAGAGAAT
3194741 TTAATTAATTAAAAAATAACACATCATCACAATGCTAGGGGAAAAACGTTAGAGTAACAAAAAAA
1 TTAATTAATTAAAAAATAA-ACATCATCACAATGCTAGGGGAAAAACGTTAGAGTAACAAAAAAA
* * *
3194806 AGTTCAATGTCTAAAGTTCATTGAGCAAATTGAAAAAAAAAATTGAAATTACGGTGAGTGAAATA
65 AATTCAATGTCTAAAGTTCACTGAGCAAATTGAAAAAAAAAATTGAAAGTACGGTGAGTGAAATA
3194871 AGAGAGAGAAT
130 AGAGAGAGAAT
3194882 AAAATTCAGT
Statistics
Matches: 135, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
138 19 0.14
139 75 0.56
140 9 0.07
141 32 0.24
ACGTcount: A:0.51, C:0.09, G:0.17, T:0.23
Consensus pattern (140 bp):
TTAATTAATTAAAAAATAAACATCATCACAATGCTAGGGGAAAAACGTTAGAGTAACAAAAAAAA
ATTCAATGTCTAAAGTTCACTGAGCAAATTGAAAAAAAAAATTGAAAGTACGGTGAGTGAAATAA
GAGAGAGAAT
Found at i:3209658 original size:57 final size:57
Alignment explanation
Indices: 3209566--3210194 Score: 895
Period size: 57 Copynumber: 10.9 Consensus size: 57
3209556 CAAATTGCAT
* * *
3209566 TTTGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTACGAATTTTCGTATGGGTAC
1 TTTGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCAC
* * * * * *
3209623 TTTATGTGCTAAAAGTTAAGAAATTCATAATAAGTTAATAAATTTTCGTATGGACAC
1 TTTGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCAC
* * *
3209680 TTTGTGTGCATAAAGATAAGAAATTCTTAATAAGTTTATGAATTTCCGTATGGGCAC
1 TTTGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCAC
* *
3209737 TTTATGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCATATGGGCAC
1 TTTGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCAC
* * *
3209794 TTTATGTGCAAAAAGATAAGAAATTCATAATAAGTTTATGAATTTCCATATGGGCAC
1 TTTGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCAC
* *
3209851 TTTGTGTGCAAAAAGATAAGAAATTCATAATAAGTTTATGAATTTTCGTGTGCTCCTATATGGGC
1 TTTGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAA------T-T--TCC-GTATGGGC
3209916 AC
56 AC
* * *
3209918 TTTGTGTGCAAAAAGATAAGAAATTCATAATAAGTTTATGAATTTCCGTATGAGCAA
1 TTTGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCAC
3209975 TTTGT-TGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCAC
1 TTTGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCAC
3210031 TTTGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCAC
1 TTTGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCAC
* *
3210088 TTTGTGTGCAAAAAGTTAAGAAATCCATAATAAGTTTATGAATTTTCGTATGAGG-AC
1 TTTGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG-GGCAC
* * *
3210145 TTTATGTGCAAAAAG-TAAGAAATTCATAATAAGTATATGACTTTCCGTAT
1 TTTGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
3210195 TGGTAGTGGG
Statistics
Matches: 524, Mismatches: 36, Indels: 25
0.90 0.06 0.04
Matches are distributed among these distances:
56 84 0.16
57 376 0.72
58 5 0.01
60 1 0.00
61 1 0.00
63 1 0.00
64 1 0.00
66 3 0.01
67 52 0.10
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.35
Consensus pattern (57 bp):
TTTGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCAC
Found at i:3210086 original size:294 final size:284
Alignment explanation
Indices: 3209566--3210194 Score: 904
Period size: 294 Copynumber: 2.2 Consensus size: 284
3209556 CAAATTGCAT
* *
3209566 TTTGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTACGAATTTTCGTATGGGTACTTTATGTG
1 TTTGTGTGCAAAAAG-TAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTTTATGTG
* * * * *
3209631 CTAAAAGTTAAGAAATTCATAATAAGTTAATAAATTTTCGTATGGACACTTTGTGTGCATAAAGA
65 CAAAAAGATAAGAAATTCATAATAAGTTAATAAATTTCCGTATGGACAATTTGTGTGCAAAAAGA
*
3209696 TAAGAAATTCTTAATAAGTTTATGAATTTCCGTATGGGCACTTTATGTGCAAAAAGTTAAGAAAT
130 TAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTATGTGCAAAAAGTTAAGAAAT
*
3209761 TCATAATAAGTTTATGAATTTCCATATGGGCACTTTATGTGCAAAAAGATAAGAAATTCATAATA
195 TCATAATAAGTTTATGAATTTCCATATGGGCACTTTATGTGCAAAAAGATAAGAAATCCATAATA
3209826 AGTTTATGAATTTCCATATG-GGCAC
260 AGTTTATGAATTTCCATATGAGG-AC
3209851 TTTGTGTGCAAAAAGATAAGAAATTCATAATAAGTTTATGAATTTTCGTGTGCTCCTATATGGGC
1 TTTGTGTGCAAAAAG-TAAGAAATTCATAATAAGTTTATGAATTTTC----G------TATGGGC
* * *
3209916 ACTTTGTGTGCAAAAAGATAAGAAATTCATAATAAGTTTATGAATTTCCGTAT-GAGCAATTTGT
55 ACTTTATGTGCAAAAAGATAAGAAATTCATAATAAGTTAATAAATTTCCGTATGGA-CAATTTGT
* *
3209980 -TGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAA
119 GTGCAAAAAGATAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTATGTGCAAAA
* * *
3210044 AGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAAGTTAAGA
184 AGTTAAGAAATTCATAATAAGTTTATGAATTTCCATATGGGCACTTTATGTGCAAAAAGATAAGA
* *
3210109 AATCCATAATAAGTTTATGAATTTTCGTATGAGGAC
249 AATCCATAATAAGTTTATGAATTTCCATATGAGGAC
* * * *
3210145 TTTATGTGCAAAAAGTAAGAAATTCATAATAAGTATATGACTTTCCGTAT
1 TTTGTGTGCAAAAAGTAAGAAATTCATAATAAGTTTATGAATTTTCGTAT
3210195 TGGTAGTGGG
Statistics
Matches: 308, Mismatches: 24, Indels: 26
0.86 0.07 0.07
Matches are distributed among these distances:
283 3 0.01
285 45 0.15
289 2 0.01
293 28 0.09
294 168 0.55
295 62 0.20
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.35
Consensus pattern (284 bp):
TTTGTGTGCAAAAAGTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTTTATGTGC
AAAAAGATAAGAAATTCATAATAAGTTAATAAATTTCCGTATGGACAATTTGTGTGCAAAAAGAT
AAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTATGTGCAAAAAGTTAAGAAATT
CATAATAAGTTTATGAATTTCCATATGGGCACTTTATGTGCAAAAAGATAAGAAATCCATAATAA
GTTTATGAATTTCCATATGAGGAC
Found at i:3210164 original size:113 final size:113
Alignment explanation
Indices: 3209909--3210194 Score: 468
Period size: 113 Copynumber: 2.5 Consensus size: 113
3209899 TGTGCTCCTA
3209909 TATGGGCACTTTGTGTGCAAAAAGATAAGAAATTCATAATAAGTTTATGAATTTCCGTATGAGCA
1 TATGGGCACTTTGTGTGCAAAAAGATAAGAAATTCATAATAAGTTTATGAATTTCCGTATGAGCA
*
3209974 ATTTGTTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCG
66 ATTTGTTGCAAAAAGTTAAGAAATCCATAATAAGTTTATGAATTTCCG
* *
3210022 TATGGGCACTTTGTGTGCAAAAAGTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCA
1 TATGGGCACTTTGTGTGCAAAAAGATAAGAAATTCATAATAAGTTTATGAATTTCCGTATGAGCA
* *
3210087 CTTTGTGTGCAAAAAGTTAAGAAATCCATAATAAGTTTATGAATTTTCG
66 ATTTGT-TGCAAAAAGTTAAGAAATCCATAATAAGTTTATGAATTTCCG
* * *
3210136 TATGAGG-ACTTTATGTGCAAAAAG-TAAGAAATTCATAATAAGTATATGACTTTCCGTAT
1 TATG-GGCACTTTGTGTGCAAAAAGATAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
3210195 TGGTAGTGGG
Statistics
Matches: 163, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
113 101 0.62
114 60 0.37
115 2 0.01
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (113 bp):
TATGGGCACTTTGTGTGCAAAAAGATAAGAAATTCATAATAAGTTTATGAATTTCCGTATGAGCA
ATTTGTTGCAAAAAGTTAAGAAATCCATAATAAGTTTATGAATTTCCG
Found at i:3216347 original size:20 final size:19
Alignment explanation
Indices: 3216322--3216374 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
3216312 TGATGTAAGC
*
3216322 AGTATCGATACCAAAAGGGG
1 AGTATCGATACCAAAA-GGA
* *
3216342 AGTATCGATACTATAAGGA
1 AGTATCGATACCAAAAGGA
3216361 AGGTATCGATACCA
1 A-GTATCGATACCA
3216375 TTGATAACAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 3 0.11
20 25 0.89
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.21
Consensus pattern (19 bp):
AGTATCGATACCAAAAGGA
Found at i:3216824 original size:30 final size:31
Alignment explanation
Indices: 3216788--3216849 Score: 117
Period size: 30 Copynumber: 2.0 Consensus size: 31
3216778 TTCATACTAA
3216788 GTTTATGAATTTCCGAAT-GGCACTTTGTGT
1 GTTTATGAATTTCCGAATGGGCACTTTGTGT
3216818 GTTTATGAATTTCCGAATGGGCACTTTGTGT
1 GTTTATGAATTTCCGAATGGGCACTTTGTGT
3216849 G
1 G
3216850 CAAAAAGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 18 0.58
31 13 0.42
ACGTcount: A:0.19, C:0.13, G:0.26, T:0.42
Consensus pattern (31 bp):
GTTTATGAATTTCCGAATGGGCACTTTGTGT
Found at i:3216906 original size:57 final size:56
Alignment explanation
Indices: 3216818--3217226 Score: 484
Period size: 57 Copynumber: 7.2 Consensus size: 56
3216808 CACTTTGTGT
* *
3216818 GTTTATGAATTTCCGAATGGGCACTTTGTGTGCAAAAAGTTAATAAATTCATAATAA
1 GTTTATGAATTTCC-TATGGGCACTTTGTGTGCAAAAAGTTAAGAAATTCATAATAA
* *
3216875 GTTTATGAATTTTCCTATGGGTACTTTGTGTGCAAAAAGATAAGAAATTCATAATAA
1 GTTTATGAA-TTTCCTATGGGCACTTTGTGTGCAAAAAGTTAAGAAATTCATAATAA
* * *
3216932 GTTTATGTATTTCCGTATAGGCACATTGTGTGCAAAAAGTTAAGAAATTCATAATAA
1 GTTTATGAATTTCC-TATGGGCACTTTGTGTGCAAAAAGTTAAGAAATTCATAATAA
* **
3216989 GTTTATGAATTTTCGTATGGGCACTTTGTGTGCAAAAA-TATAAGTTATTCATAATAA
1 GTTTATGAA-TTTCCTATGGGCACTTTGTGTGCAAAAAGT-TAAGAAATTCATAATAA
* * * *
3217046 GTTTATGAATTTCGTAT-AGCCCTTTGTGTG-AAAAACGTTAAGAAATTCATAAAAA
1 GTTTATGAATTTCCTATGGGCACTTTGTGTGCAAAAA-GTTAAGAAATTCATAATAA
*** * *
3217101 GTTTATGAATTTCCATATTTACACTTTGTGTGCAAATAGTTAAGAAATTCATATTAA
1 GTTTATGAATTTCC-TATGGGCACTTTGTGTGCAAAAAGTTAAGAAATTCATAATAA
* * ** **
3217158 GTTTTTGAATTTTCGTATGACCACTTTGTGTGCAATTAG-TAAGAAATTCATAATAA
1 GTTTATGAA-TTTCCTATGGGCACTTTGTGTGCAAAAAGTTAAGAAATTCATAATAA
*
3217214 GTATATGAATTTC
1 GTTTATGAATTTC
3217227 TATTTTAGTT
Statistics
Matches: 306, Mismatches: 36, Indels: 22
0.84 0.10 0.06
Matches are distributed among these distances:
54 5 0.02
55 42 0.14
56 41 0.13
57 201 0.66
58 17 0.06
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.38
Consensus pattern (56 bp):
GTTTATGAATTTCCTATGGGCACTTTGTGTGCAAAAAGTTAAGAAATTCATAATAA
Found at i:3217151 original size:169 final size:170
Alignment explanation
Indices: 3216818--3217226 Score: 524
Period size: 169 Copynumber: 2.4 Consensus size: 170
3216808 CACTTTGTGT
* *
3216818 GTTTATGAATTTCCGAATGGGCACTTTGTGTGCAAAAAGT-TAA-TAAATTCATAATAAGTTTAT
1 GTTTATGAATTTTCGTATGGGCACTTTGTGTGCAAAAA-TATAAGT-AATTCATAATAAGTTTAT
* * * *
3216881 GAATTTTCCTATGGGTACTTTGTGTGCAAAAAGATAAGAAATTCATAATAAGTTTATGTATTTCC
64 GAA-TTTCCTATGAGCACTTTGTGTGCAAAAAGATAAGAAATTCATAAAAAGTTTATGAATTTCC
* *
3216946 GTATAGGCACATTGTGTGCAAAAAGTTAAGAAATTCATAATAA
128 ATATAGACACATTGTGTGCAAAAAGTTAAGAAATTCATAATAA
*
3216989 GTTTATGAATTTTCGTATGGGCACTTTGTGTGCAAAAATATAAGTTATTCATAATAAGTTTATGA
1 GTTTATGAATTTTCGTATGGGCACTTTGTGTGCAAAAATATAAGTAATTCATAATAAGTTTATGA
* * *
3217054 ATTTCGTAT-AGCCCTTTGTGTG-AAAAACGTTAAGAAATTCATAAAAAGTTTATGAATTTCCAT
66 ATTTCCTATGAGCACTTTGTGTGCAAAAA-GATAAGAAATTCATAAAAAGTTTATGAATTTCCAT
** * * *
3217117 ATTTACACTTTGTGTGCAAATAGTTAAGAAATTCATATTAA
130 ATAGACACATTGTGTGCAAAAAGTTAAGAAATTCATAATAA
* ** * * *
3217158 GTTTTTGAATTTTCGTATGACCACTTTGTGTGC--AATTAGTAAGAAATTCATAATAAGTATATG
1 GTTTATGAATTTTCGTATGGGCACTTTGTGTGCAAAAATA-TAAGTAATTCATAATAAGTTTATG
3217221 AATTTC
65 AATTTC
3217227 TATTTTAGTT
Statistics
Matches: 210, Mismatches: 24, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
167 4 0.02
168 32 0.15
169 106 0.50
170 8 0.04
171 59 0.28
172 1 0.00
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.38
Consensus pattern (170 bp):
GTTTATGAATTTTCGTATGGGCACTTTGTGTGCAAAAATATAAGTAATTCATAATAAGTTTATGA
ATTTCCTATGAGCACTTTGTGTGCAAAAAGATAAGAAATTCATAAAAAGTTTATGAATTTCCATA
TAGACACATTGTGTGCAAAAAGTTAAGAAATTCATAATAA
Found at i:3223975 original size:20 final size:21
Alignment explanation
Indices: 3223950--3223988 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3223940 AACTAGGGTA
3223950 TTTAA-TTGTTTAAAAATATT
1 TTTAATTTGTTTAAAAATATT
*
3223970 TTTAATTTTTTTAAAAATA
1 TTTAATTTGTTTAAAAATA
3223989 AAATTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (21 bp):
TTTAATTTGTTTAAAAATATT
Found at i:3234024 original size:24 final size:24
Alignment explanation
Indices: 3233992--3234048 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
3233982 AACTTCAAGG
3233992 TGAGGTATTCTTATTTGATTTGAT
1 TGAGGTATTCTTATTTGATTTGAT
*
3234016 TGAGGTATTCTTATTTTATTTGAT
1 TGAGGTATTCTTATTTGATTTGAT
* *
3234040 GGAGCTATT
1 TGAGGTATT
3234049 ATTTCATGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.21, C:0.05, G:0.21, T:0.53
Consensus pattern (24 bp):
TGAGGTATTCTTATTTGATTTGAT
Found at i:3238464 original size:50 final size:51
Alignment explanation
Indices: 3238389--3238491 Score: 181
Period size: 50 Copynumber: 2.0 Consensus size: 51
3238379 CTAGTAGTAT
3238389 TGTAATAGAAGATAACAATCTTCAATC-ATAATCAAAAAATGAACTTGAAA
1 TGTAATAGAAGATAACAATCTTCAATCTATAATCAAAAAATGAACTTGAAA
3238439 TGTAATAGAAGATAACAATCTTCAATCATTATAATCAAAAAATGAACTTGAAA
1 TGTAATAGAAGATAACAATCTTCAATC--TATAATCAAAAAATGAACTTGAAA
3238492 GTCATAAGAT
Statistics
Matches: 50, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
50 27 0.54
53 23 0.46
ACGTcount: A:0.51, C:0.12, G:0.10, T:0.27
Consensus pattern (51 bp):
TGTAATAGAAGATAACAATCTTCAATCTATAATCAAAAAATGAACTTGAAA
Found at i:3238570 original size:15 final size:15
Alignment explanation
Indices: 3238550--3238579 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3238540 AAGACACTGA
3238550 AAAAGAGGCACAAAC
1 AAAAGAGGCACAAAC
*
3238565 AAAAGAGGTACAAAC
1 AAAAGAGGCACAAAC
3238580 CTAAGCCAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.17, G:0.20, T:0.03
Consensus pattern (15 bp):
AAAAGAGGCACAAAC
Found at i:3241102 original size:2 final size:2
Alignment explanation
Indices: 3241089--3241152 Score: 119
Period size: 2 Copynumber: 31.5 Consensus size: 2
3241079 GTATGATAAC
3241089 AT AT AT ACT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3241132 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
3241153 AAATATGCTC
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 59 0.97
3 2 0.03
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3246085 original size:143 final size:143
Alignment explanation
Indices: 3245903--3246188 Score: 483
Period size: 141 Copynumber: 2.0 Consensus size: 143
3245893 TGGGACCCCC
3245903 ATGCTTCATAAACTTGTTATATTTCCATATTATGATAAATTAAATAAAGTTATAAATTTTAAACA
1 ATGCTTCATAAACTTGTTATATTTCCATATTATGATAAATTAAAT-AAGTT-TAAATTTTAAACA
3245968 AAATTTTGGGTTGACCATTCGGTAGTTCCGTGTAGC-TCTAA-TTCATGGATCTTTGTGGCATCC
64 AAATTTTGGGTTGACCATTCGGTAGTTCCGTGTAGCATCTAATTTCATGGATCTTTGTGGCATCC
3246031 T-AAG-TTCACACGA
129 TAAAGTTTCACACGA
*
3246044 ATGCTTCATAAACTTGTCTTCTATTTCCAGT-TTATGATAAATTAAATAAGTTTAAATTTTAAAC
1 ATGCTTCATAAACTTG--TTATATTTCCA-TATTATGATAAATTAAATAAGTTTAAATTTTAAAC
3246108 AAAATTTTGGGTTGACCATTCGGTAGTTCCGTGTAGCATCTAATTTCATGGATCTTTGTGGCATC
63 AAAATTTTGGGTTGACCATTCGGTAGTTCCGTGTAGCATCTAATTTCATGGATCTTTGTGGCATC
3246173 CTAAAGTTTCACACGA
128 CTAAAGTTTCACACGA
3246189 GGCTATCGAG
Statistics
Matches: 137, Mismatches: 1, Indels: 10
0.93 0.01 0.07
Matches are distributed among these distances:
141 65 0.47
142 10 0.07
143 49 0.36
144 4 0.03
145 9 0.07
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (143 bp):
ATGCTTCATAAACTTGTTATATTTCCATATTATGATAAATTAAATAAGTTTAAATTTTAAACAAA
ATTTTGGGTTGACCATTCGGTAGTTCCGTGTAGCATCTAATTTCATGGATCTTTGTGGCATCCTA
AAGTTTCACACGA
Found at i:3251286 original size:23 final size:23
Alignment explanation
Indices: 3251260--3251315 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
3251250 CAGCTAGTAT
*
3251260 AATTGCACCGAAGTTCCACGTAG
1 AATTGCACCGAAGTACCACGTAG
* *
3251283 AATTGCACCGGAGTACCGCGTAG
1 AATTGCACCGAAGTACCACGTAG
*
3251306 AATTACACCG
1 AATTGCACCG
3251316 TAGTGCCATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (23 bp):
AATTGCACCGAAGTACCACGTAG
Found at i:3261300 original size:31 final size:30
Alignment explanation
Indices: 3261265--3261343 Score: 95
Period size: 31 Copynumber: 2.6 Consensus size: 30
3261255 GTACTGATAC
* *
3261265 GCATTACCTAAATGCAACCTGAACATATTGT
1 GCATTATCTGAATGCAACCT-AACATATTGT
* * *
3261296 GCATTATTTGAATGCACCCCTAGCATATTGT
1 GCATTATCTGAATGCA-ACCTAACATATTGT
3261327 GCATTATCTGAATGCAA
1 GCATTATCTGAATGCAA
3261344 ACATGACTAG
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
31 37 0.93
32 3 0.08
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.32
Consensus pattern (30 bp):
GCATTATCTGAATGCAACCTAACATATTGT
Found at i:3267033 original size:20 final size:20
Alignment explanation
Indices: 3267004--3267046 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3266994 ATTTCACCAC
*
3267004 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
* *
3267024 ATGCATCTATATTATCCTAA
1 ATGCAACTATATGATCCTAA
3267044 ATG
1 ATG
3267047 GGCTTTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:3275601 original size:20 final size:20
Alignment explanation
Indices: 3275572--3275614 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3275562 ATTTCACCAT
* *
3275572 ATGCAACTATATGCTCTTAA
1 ATGCAACTATATGATCCTAA
*
3275592 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
3275612 ATG
1 ATG
3275615 GGCTTTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:3281497 original size:21 final size:21
Alignment explanation
Indices: 3281467--3281506 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3281457 TGGCCTGTAA
*
3281467 TTTGTTGAGGCCATGAAATCT
1 TTTGTCGAGGCCATGAAATCT
3281488 TTTGTCGAGGCCATGAAAT
1 TTTGTCGAGGCCATGAAAT
3281507 TTGATAGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (21 bp):
TTTGTCGAGGCCATGAAATCT
Found at i:3287049 original size:20 final size:20
Alignment explanation
Indices: 3287024--3287066 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
3287014 TCAAAATCAT
*
3287024 TTTTCAAAATTTC-ATTTTGC
1 TTTTCAAAA-TCCAATTTTGC
3287044 TTTTCAAAATCCAATTTTGC
1 TTTTCAAAATCCAATTTTGC
3287064 TTT
1 TTT
3287067 CAGAAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.53
Consensus pattern (20 bp):
TTTTCAAAATCCAATTTTGC
Found at i:3290743 original size:101 final size:100
Alignment explanation
Indices: 3290568--3290768 Score: 303
Period size: 101 Copynumber: 2.0 Consensus size: 100
3290558 TAACTTCAAC
* * * * *
3290568 TTTTTTTTACATACTTCAAGGAGATTCAGCTCATCACACTGCCATCCCACACTCTAAGTTAAAGG
1 TTTTTTTAACATACTTCAAGGAGAGTCAGCTCATCACACTACCATCCCACACTCTAAGTGAAAAG
*
3290633 GAGCATACCTTCCACCCTCGAGCTAGTCAAGTAGA
66 GAGCATACCTTCCACCCCCGAGCTAGTCAAGTAGA
* * *
3290668 TTTTTTTAAGCATACTTTAAGGGGAGTCAGCTCATCACACTACCATTCCACACTCTAAGTGAAAA
1 TTTTTTTAA-CATACTTCAAGGAGAGTCAGCTCATCACACTACCATCCCACACTCTAAGTGAAAA
*
3290733 GGAGCATACCTTCCACCCCCGAGCTAGTCAGGTAGA
65 GGAGCATACCTTCCACCCCCGAGCTAGTCAAGTAGA
3290769 GTCATCATGT
Statistics
Matches: 90, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
100 8 0.09
101 82 0.91
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.27
Consensus pattern (100 bp):
TTTTTTTAACATACTTCAAGGAGAGTCAGCTCATCACACTACCATCCCACACTCTAAGTGAAAAG
GAGCATACCTTCCACCCCCGAGCTAGTCAAGTAGA
Found at i:3305086 original size:21 final size:21
Alignment explanation
Indices: 3305062--3305108 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
3305052 TGTTTTGGCA
3305062 AAGCCCACACAATATCGATCG
1 AAGCCCACACAATATCGATCG
*
3305083 AAGCCCACACAATTTCGATCG
1 AAGCCCACACAATATCGATCG
3305104 AAGCC
1 AAGCC
3305109 TTAACGGGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.34, G:0.15, T:0.15
Consensus pattern (21 bp):
AAGCCCACACAATATCGATCG
Found at i:3317545 original size:15 final size:16
Alignment explanation
Indices: 3317522--3317553 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3317512 CCCGACCACG
3317522 GTGCTCCCGGAATCCT
1 GTGCTCCCGGAATCCT
3317538 GTGC-CCCGGAATCCT
1 GTGCTCCCGGAATCCT
3317553 G
1 G
3317554 CGCGATTGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.12, C:0.38, G:0.28, T:0.22
Consensus pattern (16 bp):
GTGCTCCCGGAATCCT
Found at i:3319128 original size:17 final size:17
Alignment explanation
Indices: 3319106--3319140 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3319096 CCATTTTTGG
3319106 ACGAATTTAAATAGTGC
1 ACGAATTTAAATAGTGC
3319123 ACGAATTTAAATAGTGC
1 ACGAATTTAAATAGTGC
3319140 A
1 A
3319141 GTAATGCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.29
Consensus pattern (17 bp):
ACGAATTTAAATAGTGC
Found at i:3322020 original size:94 final size:94
Alignment explanation
Indices: 3321827--3322025 Score: 235
Period size: 94 Copynumber: 2.1 Consensus size: 94
3321817 AACAAGGGGA
* * *
3321827 AGTATCGATACCATGGATCCAGAATGTCAAAATGGTATCGATACTGAAACGGAGTATCAGTATCA
1 AGTATCGATACCATGGAACCAGAATATCAAAATGGTATCGATACTGAAACGGAGTATCAGTACCA
* * *
3321892 TAGTATAGTAGTATCGATACTGAGAGAAG
66 TAGTATAGAAGTATCAATACTCAGAGAAG
* * *
3321921 GGTATCGATACCA-GGCAACACAGAATAT-AGAAATGGTTTCGATACTGAAA-GGGGTATCAGTA
1 AGTATCGATACCATGG-AAC-CAGAATATCA-AAATGGTATCGATACTGAAACGGAGTATCAGTA
* *
3321983 CCATAGTATAGAAGTATCAATA-TCAGGGTAG
63 CCATAGTATAGAAGTATCAATACTCAGAGAAG
3322014 TAGTATCGATAC
1 -AGTATCGATAC
3322026 TATTGAGCTT
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
93 8 0.09
94 55 0.62
95 26 0.29
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (94 bp):
AGTATCGATACCATGGAACCAGAATATCAAAATGGTATCGATACTGAAACGGAGTATCAGTACCA
TAGTATAGAAGTATCAATACTCAGAGAAG
Found at i:3322218 original size:19 final size:19
Alignment explanation
Indices: 3322183--3322219 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3322173 ATGACCAACA
* *
3322183 AAATCGCAATGCTATCTCT
1 AAATCGCAACGCAATCTCT
3322202 AAATCGCAACGCAATCTC
1 AAATCGCAACGCAATCTC
3322220 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.30, G:0.11, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCAATCTCT
Found at i:3323126 original size:24 final size:24
Alignment explanation
Indices: 3323075--3323128 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
3323065 GTATTCGAAA
* *
3323075 TTTGGTCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCAGGAC
* *
3323099 TTTGATCTTGGTCAATACTAGGAT
1 TTTGATCTTGGTCAATACCAGGAC
3323123 TTTGAT
1 TTTGAT
3323129 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCAGGAC
Found at i:3323632 original size:19 final size:19
Alignment explanation
Indices: 3323588--3323634 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
3323578 CGTGGCGTAT
*
3323588 GATTGCAAAGAGGATAAAA
1 GATTGCGAAGAGGATAAAA
3323607 GATTGCGAAGAGGATAAAA
1 GATTGCGAAGAGGATAAAA
3323626 GATTGCGAA
1 GATTGCGAA
3323635 ATCTTTCAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.47, C:0.06, G:0.30, T:0.17
Consensus pattern (19 bp):
GATTGCGAAGAGGATAAAA
Found at i:3325709 original size:140 final size:140
Alignment explanation
Indices: 3325457--3325879 Score: 783
Period size: 140 Copynumber: 3.0 Consensus size: 140
3325447 GCAAACATTG
*
3325457 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGCATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
* *
3325522 TTGAACATTGCTATGGTTTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
3325587 CGAATTTGAC
131 CGAATTTGAC
*
3325597 TATTATGTATATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
3325662 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
3325727 CGAATTTGAC
131 CGAATTTGAC
3325737 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
* * *
3325802 TTGAACATTGCTATGATCTGTTCAGTTTTTATCACTTATTACATATTCATTTGAATATCACAACG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
3325867 CGAATTTGAC
131 CGAATTTGAC
3325877 TAT
1 TAT
3325880 CGCAATGCGA
Statistics
Matches: 275, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 275 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.43
Consensus pattern (140 bp):
TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
CGAATTTGAC
Found at i:3325875 original size:20 final size:20
Alignment explanation
Indices: 3325850--3326000 Score: 161
Period size: 20 Copynumber: 7.8 Consensus size: 20
3325840 TTACATATTC
* *
3325850 ATTTGAATATCACAACGCGA
1 ATTTGACTATCGCAACGCGA
*
3325870 ATTTGACTATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
* *
3325890 ATATGACTACCGCAACGC-A
1 ATTTGACTATCGCAACGCGA
* *
3325909 A----A-AAGCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
3325924 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
*
3325944 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* *
3325964 ATTTGATTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
3325984 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
3326001 AGAAAATCGC
Statistics
Matches: 111, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
14 9 0.08
15 3 0.03
19 3 0.03
20 96 0.86
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.25
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:3326026 original size:94 final size:94
Alignment explanation
Indices: 3325850--3326034 Score: 228
Period size: 94 Copynumber: 2.0 Consensus size: 94
3325840 TTACATATTC
*
3325850 ATTTGAATATCACAACGCGAATTTGACTATCGCAATGCGAATATGACTACCGCAACGCAAAAAGC
1 ATTTGAATATCACAACGCGAATTTGACTATCGCAACGCGAATATGACTACCGCAACGCAAAAAGC
* * *
3325915 GCAACGCGAATTTGACTATCGCAACGTGA
66 GCAAAGCGAATTAGACTATCACAACGTGA
* * * * * * * *
3325944 ATTTGACTATCGCAACGTGAATTTGATTATCGCAACGGGAATTTGACTATCGCAACG-AGAAAAT
1 ATTTGAATATCACAACGCGAATTTGACTATCGCAACGCGAATATGACTACCGCAACGCA-AAAAG
* *
3326008 CGCAAATCGTATTAGACTATCACAACG
65 CGCAAAGCGAATTAGACTATCACAACG
3326035 CGAAATGACT
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
93 1 0.01
94 75 0.99
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.24
Consensus pattern (94 bp):
ATTTGAATATCACAACGCGAATTTGACTATCGCAACGCGAATATGACTACCGCAACGCAAAAAGC
GCAAAGCGAATTAGACTATCACAACGTGA
Found at i:3326068 original size:20 final size:20
Alignment explanation
Indices: 3326040--3326102 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
3326030 CAACGCGAAA
*
3326040 TGACTTTCG-AGTTGCGATTT
1 TGACTTTCGCA-TTGCAATTT
*
3326060 TGGCTTTCGCATTGCAATTT
1 TGACTTTCGCATTGCAATTT
3326080 TGACTTTCGCATTGCAATTT
1 TGACTTTCGCATTGCAATTT
3326100 TGA
1 TGA
3326103 GTTTAGCGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
20 38 0.97
21 1 0.03
ACGTcount: A:0.17, C:0.17, G:0.21, T:0.44
Consensus pattern (20 bp):
TGACTTTCGCATTGCAATTT
Found at i:3326114 original size:20 final size:20
Alignment explanation
Indices: 3326051--3326114 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
3326041 GACTTTCGAG
* * *
3326051 TTGCGATTTTGGCTTTCGCA
1 TTGCAATTTTGACTTTAGCA
*
3326071 TTGCAATTTTGACTTTCGCA
1 TTGCAATTTTGACTTTAGCA
* *
3326091 TTGCAATTTTGAGTTTAGCG
1 TTGCAATTTTGACTTTAGCA
3326111 TTGC
1 TTGC
3326115 GAAAGTGTAC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.16, C:0.17, G:0.22, T:0.45
Consensus pattern (20 bp):
TTGCAATTTTGACTTTAGCA
Found at i:3326257 original size:14 final size:14
Alignment explanation
Indices: 3326236--3326272 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3326226 CATCAATTAA
3326236 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3326250 ATAAATCAACTTTT
1 ACAAATCAACTTTT
3326264 ACAAATCAA
1 ACAAATCAA
3326273 TTAAACAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3328202 original size:90 final size:90
Alignment explanation
Indices: 3328088--3328263 Score: 291
Period size: 90 Copynumber: 2.0 Consensus size: 90
3328078 TCTCGAATAT
* * * *
3328088 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAAT-AAAATCCCTGATATGATTA
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAAACCCTAATATGACTA
3328152 GGGTAACTTGGATATAAAAGGATTA
66 GGGTAACTTGGATATAAAAGGATTA
3328177 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAAACCCTAATATGACT
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAAACCCTAATATGACT
*
3328242 AGGGTAACTTGGCTATAAAAGG
65 AGGGTAACTTGGATATAAAAGG
3328264 GTGTGTTAGG
Statistics
Matches: 80, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
89 7 0.09
90 37 0.46
91 36 0.45
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (90 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAAACCCTAATATGACTA
GGGTAACTTGGATATAAAAGGATTA
Found at i:3335931 original size:21 final size:21
Alignment explanation
Indices: 3335907--3336009 Score: 82
Period size: 21 Copynumber: 4.9 Consensus size: 21
3335897 GTGGGAGTGA
*
3335907 CCTCTTCAACGATGACAGGGG
1 CCTCTTGAACGATGACAGGGG
* **
3335928 CCTCATGAACGATGGGAGGGG
1 CCTCTTGAACGATGACAGGGG
* ** *
3335949 ACTCTTGAGGGATGATAGGGG
1 CCTCTTGAACGATGACAGGGG
* * *
3335970 CCTCTTGAATGAT-ATGAGAGG
1 CCTCTTGAACGATGA-CAGGGG
*
3335991 CCGCTTGAACGATGACAGG
1 CCTCTTGAACGATGACAGG
3336010 TGAGTCGGGC
Statistics
Matches: 61, Mismatches: 19, Indels: 4
0.73 0.23 0.05
Matches are distributed among these distances:
20 1 0.02
21 59 0.97
22 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.35, T:0.20
Consensus pattern (21 bp):
CCTCTTGAACGATGACAGGGG
Found at i:3336005 original size:42 final size:42
Alignment explanation
Indices: 3335914--3336009 Score: 102
Period size: 42 Copynumber: 2.3 Consensus size: 42
3335904 TGACCTCTTC
* * *
3335914 AACGATGACAGGGGCCTCATGAACGATGGGAGGGGACTCTTG
1 AACGATGACAGGGGCCTCATGAACGATAGGAGAGGACGCTTG
** * * * * *
3335956 AGGGATGATAGGGGCCTCTTGAATGATATGAGAGGCCGCTTG
1 AACGATGACAGGGGCCTCATGAACGATAGGAGAGGACGCTTG
3335998 AACGATGACAGG
1 AACGATGACAGG
3336010 TGAGTCGGGC
Statistics
Matches: 41, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.27, C:0.17, G:0.38, T:0.19
Consensus pattern (42 bp):
AACGATGACAGGGGCCTCATGAACGATAGGAGAGGACGCTTG
Found at i:3336505 original size:20 final size:20
Alignment explanation
Indices: 3336480--3336523 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
3336470 AATAGTTTCT
3336480 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
* *
3336500 GAAACTTAAAATTGCAACGC
1 GAAACTTAAAATCGCAACAC
3336520 GAAA
1 GAAA
3336524 ATGACTATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.50, C:0.20, G:0.14, T:0.16
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACAC
Found at i:3336536 original size:20 final size:20
Alignment explanation
Indices: 3336513--3336573 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
3336503 ACTTAAAATT
3336513 GCAACGCGAAAATGACTATC
1 GCAACGCGAAAATGACTATC
*
3336533 GCAATGCGGAAAA-GACTATC
1 GCAACGC-GAAAATGACTATC
* **
3336553 ACAACGCGAATTTGACTATC
1 GCAACGCGAAAATGACTATC
3336573 G
1 G
3336574 TAACAAGATA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 3 0.09
20 25 0.76
21 5 0.15
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.18
Consensus pattern (20 bp):
GCAACGCGAAAATGACTATC
Found at i:3336607 original size:19 final size:19
Alignment explanation
Indices: 3336583--3336636 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
3336573 GTAACAAGAT
** *
3336583 AATCGCAATTCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
3336602 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
*
3336621 AATCGCAACGTGAAAC
1 AATCGCAACGCGAAAC
3336637 TAAATTCGCG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.48, C:0.24, G:0.15, T:0.13
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:3336645 original size:19 final size:19
Alignment explanation
Indices: 3336600--3336636 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3336590 ATTCGAAATA
3336600 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
*
3336619 AAAATCGCAACGTGAAAC
1 AAAATCGCAACGCGAAAC
3336637 TAAATTCGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.08
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACC
Found at i:3336677 original size:14 final size:14
Alignment explanation
Indices: 3336658--3336690 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
3336648 TGCGATTTTC
3336658 ATTTTCACATTGCG
1 ATTTTCACATTGCG
*
3336672 ATTTTCACGTTGCG
1 ATTTTCACATTGCG
3336686 ATTTT
1 ATTTT
3336691 TATTTCACGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.48
Consensus pattern (14 bp):
ATTTTCACATTGCG
Found at i:3336688 original size:34 final size:33
Alignment explanation
Indices: 3336645--3336709 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
3336635 ACTAAATTCG
*
3336645 CGTTGCGATTTTCATTTTCACATTGCGATTTTCA
1 CGTTGCGATTTTCA-TTTCACATTGCAATTTTCA
* *
3336679 CGTTGCGATTTTTATTTCACGTTGCAATTTT
1 CGTTGCGATTTTCATTTCACATTGCAATTTT
3336710 TATTTCGCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 15 0.54
34 13 0.46
ACGTcount: A:0.17, C:0.18, G:0.15, T:0.49
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCACATTGCAATTTTCA
Done.