Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008926.1 Hibiscus syriacus cultivar Beakdansim tig00112231_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: 4069050
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 20
Found at i:3452743 original size:21 final size:21
Alignment explanation
Indices: 3452719--3452761 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
3452709 TTTAACAAAT
*
3452719 CTCTTCATT-AAATGGTTTTAA
1 CTCTTCATTGAAA-GGTCTTAA
*
3452740 CTCTTGATTGAAAGGTCTTAA
1 CTCTTCATTGAAAGGTCTTAA
3452761 C
1 C
3452762 CTTTCAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (21 bp):
CTCTTCATTGAAAGGTCTTAA
Found at i:3452901 original size:17 final size:17
Alignment explanation
Indices: 3452879--3452912 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3452869 CATTCTGTCG
3452879 GGTGATAGAGAAAGGCA
1 GGTGATAGAGAAAGGCA
3452896 GGTGATAGAGAAAGGCA
1 GGTGATAGAGAAAGGCA
3452913 AGATTGTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.41, T:0.12
Consensus pattern (17 bp):
GGTGATAGAGAAAGGCA
Found at i:3453501 original size:186 final size:189
Alignment explanation
Indices: 3453167--3453553 Score: 656
Period size: 186 Copynumber: 2.0 Consensus size: 189
3453157 GCTTCATTCA
3453167 GTTATATAATAATATTTGTTTATCATTATTATTTTATGTATTGGATTAACCATTCTGTCCAACAG
1 GTTATATAATAATATTTGTTTATCATTATTATTTTATGTATTGGATTAACCATTCTGTCCAACAG
3453232 TTACTACCATTTGACGTCTTCGCCTCCACCGCATATTCATAAAAGTTTGTTTCTCAATCCAAATC
66 TTACTACCATTTGACGTCTTCGCCTCCACCGCATATTCATAAAAGTTTGTTTCTCAATCCAAATC
**
3453297 TATTTTCTTTTTATTC-TTTTAAGAATTTTGGAGTGTACGAACGAATC-AAATTTTCCT
131 TATTTTCTTTGAATTCTTTTTAAGAATTTTGGAGTGTACGAACGAATCAAAATTTTCCT
3453354 GTTATATAATAATA-TTGTTTATCATTATTATTTTATGTATTGGATTAACCATTCTGTCCAACAG
1 GTTATATAATAATATTTGTTTATCATTATTATTTTATGTATTGGATTAACCATTCTGTCCAACAG
3453418 TTACTACCATTTGACGTCTTCGCCTCCACCGCATATTCATAAAAGTTTGTTTCTCAATCCAAATC
66 TTACTACCATTTGACGTCTTCGCCTCCACCGCATATTCATAAAAGTTTGTTTCTCAATCCAAATC
3453483 TATTTTCTTTGAATTCTTTTTTATGTTTTAAGAATTTTGGAGTGTACGAACGAATCAAAATTTTC
131 TATTTTCTTTGAATTC-------T-TTTTAAGAATTTTGGAGTGTACGAACGAATCAAAATTTTC
3453548 CT
188 CT
3453550 -TTAT
1 GTTAT
3453554 GTGCATCGTT
Statistics
Matches: 188, Mismatches: 2, Indels: 12
0.93 0.01 0.06
Matches are distributed among these distances:
186 129 0.69
187 14 0.07
195 35 0.19
196 10 0.05
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (189 bp):
GTTATATAATAATATTTGTTTATCATTATTATTTTATGTATTGGATTAACCATTCTGTCCAACAG
TTACTACCATTTGACGTCTTCGCCTCCACCGCATATTCATAAAAGTTTGTTTCTCAATCCAAATC
TATTTTCTTTGAATTCTTTTTAAGAATTTTGGAGTGTACGAACGAATCAAAATTTTCCT
Found at i:3459587 original size:13 final size:13
Alignment explanation
Indices: 3459569--3459593 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3459559 CGAATAATAG
3459569 TATATATATATAA
1 TATATATATATAA
3459582 TATATATATATA
1 TATATATATATA
3459594 TTCTCAGTTT
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:0.00, T:0.48
Consensus pattern (13 bp):
TATATATATATAA
Found at i:3460449 original size:13 final size:12
Alignment explanation
Indices: 3460421--3460469 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
3460411 TATATTTAGG
3460421 TTTATT-TTATTT
1 TTTATTGTTA-TT
3460433 TTTATTTGTTATT
1 TTTA-TTGTTATT
*
3460446 TTTACT-TT-TT
1 TTTATTGTTATT
3460456 TTTATTGTTATT
1 TTTATTGTTATT
3460468 TT
1 TT
3460470 AATTATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
10 7 0.23
11 4 0.13
12 9 0.29
13 8 0.26
14 3 0.10
ACGTcount: A:0.14, C:0.02, G:0.04, T:0.80
Consensus pattern (12 bp):
TTTATTGTTATT
Found at i:3460478 original size:22 final size:24
Alignment explanation
Indices: 3460427--3460478 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 24
3460417 TAGGTTTATT
*
3460427 TTATTTTTTATTTGTTATTTTTAC
1 TTATTTTTTATTTGTTATTTTTAA
3460451 TT-TTTTTTA-TTGTTA-TTTTAA
1 TTATTTTTTATTTGTTATTTTTAA
3460472 TTATTTT
1 TTATTTT
3460479 AATTAGGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 7 0.27
22 10 0.38
23 7 0.27
24 2 0.08
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.77
Consensus pattern (24 bp):
TTATTTTTTATTTGTTATTTTTAA
Found at i:3462385 original size:31 final size:29
Alignment explanation
Indices: 3462328--3462385 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 29
3462318 TGAATAATCA
*
3462328 TTTCAACTAACTTGATTCTTTTTGTCTCG
1 TTTCAACTAACTTGATTCCTTTTGTCTCG
3462357 TTTCAACTAACGTTGATTTCCTTTTGTCT
1 TTTCAACTAAC-TTGA-TTCCTTTTGTCT
3462386 GGACTTATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 11 0.42
30 4 0.15
31 11 0.42
ACGTcount: A:0.17, C:0.21, G:0.10, T:0.52
Consensus pattern (29 bp):
TTTCAACTAACTTGATTCCTTTTGTCTCG
Found at i:3465902 original size:56 final size:56
Alignment explanation
Indices: 3465816--3465927 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
3465806 AAAATAAAAA
3465816 TAAAGAAAACATTTTCAAACAGAATAATCTCTCTGGAGAGTTTAGTTTGGAAATTG
1 TAAAGAAAACATTTTCAAACAGAATAATCTCTCTGGAGAGTTTAGTTTGGAAATTG
3465872 TAAAGAAAACATTTTCAAACAGAATAATCTCTCTGGAGAGTTTAGTTTGGAAATTG
1 TAAAGAAAACATTTTCAAACAGAATAATCTCTCTGGAGAGTTTAGTTTGGAAATTG
3465928 ACAAAGGTCT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (56 bp):
TAAAGAAAACATTTTCAAACAGAATAATCTCTCTGGAGAGTTTAGTTTGGAAATTG
Found at i:3466650 original size:109 final size:109
Alignment explanation
Indices: 3466520--3466841 Score: 454
Period size: 109 Copynumber: 3.0 Consensus size: 109
3466510 TGATAGGATG
*
3466520 TTCAAATGAACTTTT-AAAAGAAGATAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGA
1 TTCAAATGAA-TTTTGAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGA
*
3466584 GTTTTTAGAAACTAAGCCTGA-TTTAAGGGGTTTCTTGATGACGAT
65 GTTTTTAGAAACTAAGCCTGATTTTAAGGGGTTTTTTGATGA-GAT
* *
3466629 TTCAAATGAATTTTGAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTTTTTATGTTTTCAAATGAG
1 TTCAAATGAATTTTGAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAG
* * * *
3466694 TTTTTAGACACTAAGACTGATTTTCAGGGGTTTTTTGATTAGAT
66 TTTTTAGAAACTAAGCCTGATTTTAAGGGGTTTTTTGATGAGAT
* * * * *
3466738 TTCCAATGAATTTTGAAAATAAGCTAAGCCTAATTTTTAGGGGTTTCTAGAT-TTTTTAAATGAA
1 TTCAAATGAATTTTGAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAG
* * *
3466802 TTTTTAGAAACTAA-CCTAATTTTTAGGAGTTTTTTGATGA
66 TTTTTAGAAACTAAGCCTGATTTTAAGGGGTTTTTTGATGA
3466842 TAACTGAAAA
Statistics
Matches: 190, Mismatches: 21, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
107 21 0.11
108 27 0.14
109 125 0.66
110 17 0.09
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (109 bp):
TTCAAATGAATTTTGAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAG
TTTTTAGAAACTAAGCCTGATTTTAAGGGGTTTTTTGATGAGAT
Found at i:3466717 original size:52 final size:51
Alignment explanation
Indices: 3466544--3466840 Score: 222
Period size: 54 Copynumber: 5.6 Consensus size: 51
3466534 TAAAAGAAGA
* *
3466544 TAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAGTTTTTAGAAAC
1 TAAGCCTGATTTTTAGGGGTTTTTTGATGTTTTCAAATGAGTTTTTAG-AAC
* * * * *
3466596 TAAGCCTGA-TTTAAGGGGTTTCTTGATGACGATTTCAAATGAATTTTGAAAAGAAGC
1 TAAGCCTGATTTTTAGGGGTTT-TT--TGATGTTTTCAAATGAGTTTT---TAGAA-C
* *
3466653 TAAGCCTAATTTTTAGGGGTTTTTTTATGTTTTCAAATGAGTTTTTAGACAC
1 TAAGCCTGATTTTTAGGGGTTTTTTGATGTTTTCAAATGAGTTTTTAGA-AC
* * * * * * *
3466705 TAAGACTGATTTTCAGGGGTTTTTTGATTAGATTTCCAATGAATTTTGAAAATAAGC
1 TAAGCCTGATTTTTAGGGGTTTTTTGA-T-GTTTTCAAATGAGTTTT---TAGAA-C
* * * * *
3466762 TAAGCCTAATTTTTAGGGGTTTCTAGAT-TTTTTAAATGAATTTTTAGAAAC
1 TAAGCCTGATTTTTAGGGGTTTTTTGATGTTTTCAAATGAGTTTTTAG-AAC
* *
3466813 TAA-CCTAATTTTTAGGAGTTTTTTGATG
1 TAAGCCTGATTTTTAGGGGTTTTTTGATG
3466841 ATAACTGAAA
Statistics
Matches: 192, Mismatches: 36, Indels: 35
0.73 0.14 0.13
Matches are distributed among these distances:
50 21 0.11
51 16 0.08
52 38 0.20
53 2 0.01
54 45 0.23
55 17 0.09
56 4 0.02
57 38 0.20
58 11 0.06
ACGTcount: A:0.29, C:0.09, G:0.19, T:0.43
Consensus pattern (51 bp):
TAAGCCTGATTTTTAGGGGTTTTTTGATGTTTTCAAATGAGTTTTTAGAAC
Found at i:3466873 original size:108 final size:111
Alignment explanation
Indices: 3466531--3466898 Score: 348
Period size: 109 Copynumber: 3.4 Consensus size: 111
3466521 TCAAATGAAC
*
3466531 TTTT-AAAAGAAGATAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAGTTTTTAGAAA
1 TTTTGAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAGTTTTTAGAAA
* * ***
3466595 CTAAGCCTGA-TTTAAGGGGTTTCTTGATG--ACGATTTC-AAATGAA
66 CTAAGCCTGATTTTAAGGGGTTTTTTGATGATATGAAAACGAAA-G-A
* * *
3466639 TTTTGAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTTTTTATGTTTTCAAATGAGTTTTTAGACA
1 TTTTGAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAGTTTTTAGAAA
* * *** * *
3466704 CTAAGACTGATTTTCAGGGGTTTTTTGAT--TA-GATTTCCAATGAA
66 CTAAGCCTGATTTTAAGGGGTTTTTTGATGATATGAAAACGAAAG-A
* * * *
3466748 TTTTGAAAATAAGCTAAGCCTAATTTTTAGGGGTTTCTAGAT-TTTTTAAATGAATTTTTAGAAA
1 TTTTGAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAGTTTTTAGAAA
* * *
3466812 CTAA-CCTAATTTTTAGGAGTTTTTTGATGATAACTGAAAACGAAAGA
66 CTAAGCCTGATTTTAAGGGGTTTTTTGATGAT-A-TGAAAACGAAAGA
** * * *
3466859 TTTT-AAAA-AA-CTAAGTTTAATTTTCAAGGGTTTCCTGATG
1 TTTTGAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATG
3466899 AGTAAGTCCT
Statistics
Matches: 220, Mismatches: 30, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
107 20 0.09
108 50 0.23
109 115 0.52
110 24 0.11
111 5 0.02
112 6 0.03
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (111 bp):
TTTTGAAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAGTTTTTAGAAA
CTAAGCCTGATTTTAAGGGGTTTTTTGATGATATGAAAACGAAAGA
Found at i:3467206 original size:78 final size:77
Alignment explanation
Indices: 3467049--3467223 Score: 253
Period size: 78 Copynumber: 2.2 Consensus size: 77
3467039 AGGAATAAAC
* * * *
3467049 ATCTCGCTTCAGATAGTTTCACTTGAAGCAGAAGATTTATCTCGCTTGAGATAGTTTCACTTAAA
1 ATCTCGCTTGAGATAGTTTCACTAGAAACAGAAGATTTATCTCGCTTGAGATAGTTTCACTCAAA
3467114 ACAGAAGATTTTT
66 ACAGAAGA-TTTT
*
3467127 ATCTCGCTTGAGATAGTTTCACTAGAAACAGAAGATTTTTATCTCGCTTGAGATAGTTTCACTCG
1 ATCTCGCTTGAGATAGTTTCACTAGAAACAGAAGA--TTTATCTCGCTTGAGATAGTTTCACTCA
3467192 AAACAGAAGA-TTT
64 AAACAGAAGATTTT
* *
3467205 ATCTCACTTGAGATTGTTT
1 ATCTCGCTTGAGATAGTTT
3467224 TTCATAAAAA
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
78 52 0.59
80 36 0.41
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (77 bp):
ATCTCGCTTGAGATAGTTTCACTAGAAACAGAAGATTTATCTCGCTTGAGATAGTTTCACTCAAA
ACAGAAGATTTT
Found at i:3467227 original size:40 final size:39
Alignment explanation
Indices: 3467049--3467223 Score: 255
Period size: 40 Copynumber: 4.5 Consensus size: 39
3467039 AGGAATAAAC
* *
3467049 ATCTCGCTTCAGATAGTTTCACTTGAAGCAGAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTTGAAACAGAAGATTTT
*
3467087 ATCTCGCTTGAGATAGTTTCACTTAAAACAGAAGATTTTT
1 ATCTCGCTTGAGATAGTTTCACTTGAAACAGAAGA-TTTT
*
3467127 ATCTCGCTTGAGATAGTTTCACTAGAAACAGAAGATTTTT
1 ATCTCGCTTGAGATAGTTTCACTTGAAACAGAAGA-TTTT
*
3467167 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTTGAAACAGAAGATTTT
* *
3467205 ATCTCACTTGAGATTGTTT
1 ATCTCGCTTGAGATAGTTT
3467224 TTCATAAAAA
Statistics
Matches: 127, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
38 52 0.41
40 75 0.59
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (39 bp):
ATCTCGCTTGAGATAGTTTCACTTGAAACAGAAGATTTT
Found at i:3471483 original size:21 final size:21
Alignment explanation
Indices: 3471459--3471501 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
3471449 TTTAACAAAT
*
3471459 CTCTTCATT-AAATGGTTTTAA
1 CTCTTCATTGAAA-GGTCTTAA
*
3471480 CTCTTGATTGAAAGGTCTTAA
1 CTCTTCATTGAAAGGTCTTAA
3471501 C
1 C
3471502 CTTTCAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (21 bp):
CTCTTCATTGAAAGGTCTTAA
Found at i:3471641 original size:17 final size:17
Alignment explanation
Indices: 3471619--3471652 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3471609 CATTCTGTCG
3471619 GGTGATAGAGAAAGGCA
1 GGTGATAGAGAAAGGCA
3471636 GGTGATAGAGAAAGGCA
1 GGTGATAGAGAAAGGCA
3471653 AGATTGTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.41, T:0.12
Consensus pattern (17 bp):
GGTGATAGAGAAAGGCA
Found at i:3479231 original size:17 final size:17
Alignment explanation
Indices: 3479191--3479231 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
3479181 CGATCCGAAA
*
3479191 TTTCGGATATCCTAATT
1 TTTCGGATATCCGAATT
*
3479208 TTT-GGATATCCGATTT
1 TTTCGGATATCCGAATT
3479224 TTTCGGAT
1 TTTCGGAT
3479232 TAGATACGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.49
Consensus pattern (17 bp):
TTTCGGATATCCGAATT
Found at i:3479287 original size:16 final size:17
Alignment explanation
Indices: 3479255--3479288 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3479245 TTACTTTAGG
*
3479255 TATCCGAAATTTTCGGA
1 TATCCGAAATATTCGGA
3479272 TATCCGAAA-ATTCGGA
1 TATCCGAAATATTCGGA
3479288 T
1 T
3479289 CGGATAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (17 bp):
TATCCGAAATATTCGGA
Found at i:3481887 original size:31 final size:31
Alignment explanation
Indices: 3481851--3481911 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
3481841 CAGAAAATAT
3481851 AAGATATGGTCACTTTCGTTTTTATTTAATC
1 AAGATATGGTCACTTTCGTTTTTATTTAATC
3481882 AAGATATGGTCACTTTCGTTTTTATTTAAT
1 AAGATATGGTCACTTTCGTTTTTATTTAAT
3481912 TAATACGTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.49
Consensus pattern (31 bp):
AAGATATGGTCACTTTCGTTTTTATTTAATC
Found at i:3481923 original size:31 final size:31
Alignment explanation
Indices: 3481851--3481925 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
3481841 CAGAAAATAT
*
3481851 AAGATATGGTCACTTTCGTTTTTATTTAATC
1 AAGACATGGTCACTTTCGTTTTTATTTAATC
* *
3481882 AAGATATGGTCACTTTCGTTTTTATTTAATT
1 AAGACATGGTCACTTTCGTTTTTATTTAATC
* *
3481913 AATACGTGGTCAC
1 AAGACATGGTCAC
3481926 CCCGAGTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.45
Consensus pattern (31 bp):
AAGACATGGTCACTTTCGTTTTTATTTAATC
Found at i:3482095 original size:27 final size:27
Alignment explanation
Indices: 3482043--3482134 Score: 95
Period size: 27 Copynumber: 3.6 Consensus size: 27
3482033 AATAAATTAT
* **
3482043 ATATTTTTAAATGAAAATAA-AGATAAA
1 ATATTTTTAAATTAAGTTAATA-ATAAA
3482070 ATATTTTTAAATTAAGTTAATAATAAA
1 ATATTTTTAAATTAAGTTAATAATAAA
*
3482097 ATATATTT-AA-TAAGTTAAT-A-AAA
1 ATATTTTTAAATTAAGTTAATAATAAA
*
3482120 ATATTTTTAAGTTAA
1 ATATTTTTAAATTAA
3482135 TATATATAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
23 10 0.18
24 2 0.04
25 12 0.21
26 2 0.04
27 29 0.52
28 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.41
Consensus pattern (27 bp):
ATATTTTTAAATTAAGTTAATAATAAA
Found at i:3482132 original size:20 final size:22
Alignment explanation
Indices: 3482090--3482136 Score: 71
Period size: 20 Copynumber: 2.2 Consensus size: 22
3482080 ATTAAGTTAA
3482090 TAATAAAATATATTTAATAAGT
1 TAATAAAATATATTTAATAAGT
*
3482112 TAATAAAA-ATATTT-TTAAGT
1 TAATAAAATATATTTAATAAGT
3482132 TAATA
1 TAATA
3482137 TATATAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 10 0.42
21 6 0.25
22 8 0.33
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (22 bp):
TAATAAAATATATTTAATAAGT
Found at i:3483482 original size:27 final size:23
Alignment explanation
Indices: 3483427--3483479 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
3483417 TGTATGTATT
*
3483427 CATGTATATGTATGATATTGATG
1 CATGTATATATATGATATTGATG
**
3483450 CATGTATATATATGATATAAATG
1 CATGTATATATATGATATTGATG
3483473 CATGTAT
1 CATGTAT
3483480 GTACGTATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.42
Consensus pattern (23 bp):
CATGTATATATATGATATTGATG
Found at i:3483501 original size:4 final size:4
Alignment explanation
Indices: 3483494--3484491 Score: 1450
Period size: 4 Copynumber: 253.0 Consensus size: 4
3483484 GTATGATATG
* *
3483494 CATA CATA CATGT CA-A CATG CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CAT-A CATA CATA CATA CATA CATA CATA CATA CATA CATA
3483542 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
3483590 CATA CATA CATA CATA CATA CATA CATA CATA CATA C--A CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
3483636 CATA CATA CATA C-TA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
3483683 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
3483731 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
3483779 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * *
3483827 CATA CATG CATG CAT- CATA C--A CATG CATA CAT- TATA TATA CTTA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * *
3483871 CATG GAT- CATA CATA CATA CATGTT C-TA CATA CATA C--A CATA CATA
1 CATA CATA CATA CATA CATA CA--TA CATA CATA CATA CATA CATA CATA
3483917 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
3483965 CATA CATA CATA CATA CATA C-TA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
3484012 CATA CATA C-TA CATA CATA CATA CATA C-TA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
3484058 CATA CATA CATA CATA CATA CATA CATA TATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
3484106 CATA CATA CATA CATA CATCA CATA CATA CATTA CATA CATA CATA CATA
1 CATA CATA CATA CATA CAT-A CATA CATA CA-TA CATA CATA CATA CATA
3484156 CATA CATA CATA CATA CATA CATA CCATA CATA CATA CAT- -ATA CATA
1 CATA CATA CATA CATA CATA CATA -CATA CATA CATA CATA CATA CATA
*
3484203 CATA CATA CATA CATA CATA CATA TATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * *
3484251 TATA CATA CATG CATG CATG CATG CATA CATA CATA CATG CATG CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
3484299 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
3484347 CATA CATA CATA CATA TATA TATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * *
3484395 CATG CAT- CATA C--A CATG CATA CAT- TATA TATA CTTA CATG GAT-
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * *
3484438 CATA CATA CATA CATGTT C-TA CATG CAT- CATA CATA CATA TGTATA
1 CATA CATA CATA CA--TA CATA CATA CATA CATA CATA CATA --CATA
3484484 CATA CATA
1 CATA CATA
3484492 ACATGCATCC
Statistics
Matches: 917, Mismatches: 43, Indels: 68
0.89 0.04 0.07
Matches are distributed among these distances:
2 10 0.01
3 35 0.04
4 851 0.93
5 14 0.02
6 7 0.01
ACGTcount: A:0.47, C:0.24, G:0.02, T:0.27
Consensus pattern (4 bp):
CATA
Found at i:3488756 original size:134 final size:135
Alignment explanation
Indices: 3488503--3488865 Score: 507
Period size: 134 Copynumber: 2.7 Consensus size: 135
3488493 TCTCTACTAG
* * ** *
3488503 AAATGTTGATCCCTCCAGTGAGGTGTCGCTGATTCGAAATAATGTGAATCGAGCAAAGGTTTAAC
1 AAATGTTAATCCCTCAAGTGAGGTGTCGCTGATTCGAAATGTTGTGAATCGAGCAAAGGTTGAAC
* *
3488568 AAGTTCTTCACATTACAAACTTCTTCTCCCTCTATCAGATGAGTTCTTCTTATTATGAACTCTCC
66 AAGTTCTTCTCATTACAAACTTCTTCTCCCTCTAACAGATGAGTTCTTCTTATTATGAACTCTCC
3488633 ATTGA
131 ATTGA
* * * * **
3488638 AAATGTTAATCCCTCAAATGAGGTGTCACTGATTTGAAATGTTGTGAATCGA-AAAATATTGAAC
1 AAATGTTAATCCCTCAAGTGAGGTGTCGCTGATTCGAAATGTTGTGAATCGAGCAAAGGTTGAAC
* *
3488702 AAGTTCTTCTCATTACAAACTT-TGTCTCCCTCTAACGGATGAGTTCTTTTTATTATGAACTCTC
66 AAGTTCTTCTCATTACAAACTTCT-TCTCCCTCTAACAGATGAGTTCTTCTTATTATGAACTCTC
*
3488766 CATTGG
130 CATTGA
* * *
3488772 AAATGTTAATCCCTCAAGTGAGATGTCGCTGATTCAAAATGTCT-TGAATTGAGCAAAGGTTGAA
1 AAATGTTAATCCCTCAAGTGAGGTGTCGCTGATTCGAAATGT-TGTGAATCGAGCAAAGGTTGAA
*
3488836 CAAGTTCTTCTCATTACTAACTTCTTCTCC
65 CAAGTTCTTCTCATTACAAACTTCTTCTCC
3488866 ATTGGAAATG
Statistics
Matches: 198, Mismatches: 26, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
133 1 0.01
134 115 0.58
135 81 0.41
136 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (135 bp):
AAATGTTAATCCCTCAAGTGAGGTGTCGCTGATTCGAAATGTTGTGAATCGAGCAAAGGTTGAAC
AAGTTCTTCTCATTACAAACTTCTTCTCCCTCTAACAGATGAGTTCTTCTTATTATGAACTCTCC
ATTGA
Found at i:3489429 original size:75 final size:75
Alignment explanation
Indices: 3489307--3489704 Score: 514
Period size: 75 Copynumber: 5.3 Consensus size: 75
3489297 AGACTTTCTT
* * * * * * *
3489307 AAGCGAGATGAAATTTGTTTTAAGAAAAACAATCTCGATTGAAATAAAATTTCATGTTTCAAGTA
1 AAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTT-ATGTTTCGAGTG
*
3489372 AAAATTATCTC
65 AAAACTATCTC
** * * *
3489383 TGGCGAGACAAAGTTTGTTTTAAGAAAAA-AATCTCAAGTGAGATAAAATTTTTGTTTCTAGTGA
1 AAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTATGTTTCGAGTGA
*
3489447 AAACTATCGC
66 AAACTATCTC
* *
3489457 AAGCAAGATGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTATGTTTCGAGTGA
1 AAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTATGTTTCGAGTGA
* *
3489522 AAATTGTCTC
66 AAACTATCTC
* * *
3489532 AAGCGAGACGAAGTTTGTTTTAAGAAAAACTATATCAAGTGAGATAAAATTTCTGTTTCGAGTGA
1 AAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTATGTTTCGAGTGA
*
3489597 AAACTGTCTC
66 AAACTATCTC
* *
3489607 AAGCGAGATGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTATG-TTC-AGGTT
1 AAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTATGTTTCGA-GTG
**
3489670 AAAACTGCCTC
65 AAAACTATCTC
*
3489681 AAGTGAGACGAAGTTTGTTTTAAG
1 AAGCGAGACGAAGTTTGTTTTAAG
3489705 TCGAGTGAAA
Statistics
Matches: 283, Mismatches: 37, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
73 1 0.00
74 79 0.28
75 179 0.63
76 24 0.08
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.32
Consensus pattern (75 bp):
AAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTATGTTTCGAGTGA
AAACTATCTC
Found at i:3489532 original size:39 final size:38
Alignment explanation
Indices: 3489311--3489849 Score: 194
Period size: 36 Copynumber: 14.3 Consensus size: 38
3489301 TTTCTTAAGC
* * ** * *
3489311 GAGATGAAA-TTTGTTTTAAG-AAAAACAATCTCGATT
1 GAGATAAAATTTTGTTTCAAGTAAAAACTGTCTCAAGT
* * * ** *
3489347 GAAATAAAATTTCATGTTTCAAGTAAAAATTATCTCTGGC
1 GAGATAAAATTT--TGTTTCAAGTAAAAACTGTCTCAAGT
* * * **
3489387 GAGA-CAAAGTTTGTTTTAAG-AAAAA-AATCTCAAGT
1 GAGATAAAATTTTGTTTCAAGTAAAAACTGTCTCAAGT
* * * * *
3489422 GAGATAAAATTTTTGTTTCTAGTGAAAACTATCGCAAGC
1 GAGATAAAA-TTTTGTTTCAAGTAAAAACTGTCTCAAGT
* * * * **
3489461 AAGAT-GAAGTTTGTTTTAAG-AAAAACAATCTCAAGT
1 GAGATAAAATTTTGTTTCAAGTAAAAACTGTCTCAAGT
* * * *
3489497 GAGATAAAATTTATGTTTCGAGTGAAAATTGTCTCAAGC
1 GAGATAAAATTT-TGTTTCAAGTAAAAACTGTCTCAAGT
** * * * *
3489536 GAGA-CGAAGTTTGTTTTAAG-AAAAACTATATCAAGT
1 GAGATAAAATTTTGTTTCAAGTAAAAACTGTCTCAAGT
* * *
3489572 GAGATAAAATTTCTGTTTCGAGTGAAAACTGTCTCAAGC
1 GAGATAAAATTT-TGTTTCAAGTAAAAACTGTCTCAAGT
* * * **
3489611 GAGAT-GAAGTTTGTTTTAAG-AAAAACAATCTCAAGT
1 GAGATAAAATTTTGTTTCAAGTAAAAACTGTCTCAAGT
* * *
3489647 GAGATAAAATTTATG-TTCAGGTTAAAACTGCCTCAAGT
1 GAGATAAAATTT-TGTTTCAAGTAAAAACTGTCTCAAGT
** * * *
3489685 GAGA-CGAAGTTTGTTTTAAGTCGAGTGAAAACTGTCTCAAGC
1 GAGATAAAATTTTGTTTCAAGT--A---AAAACTGTCTCAAGT
** * * * *
3489727 GAGA-CGAAGTTTGTTTTAAG-AAAAACTATCTCAAGG
1 GAGATAAAATTTTGTTTCAAGTAAAAACTGTCTCAAGT
* * ** * * *
3489763 GAAATAAAATTTCTTTTTTGAGTGAAAACGGTCTCAAGA
1 GAGATAAAATTT-TGTTTCAAGTAAAAACTGTCTCAAGT
** * * *
3489802 GAGA-CGAAGTTTGTTTTAAG-AAAAACTATCTCAAGT
1 GAGATAAAATTTTGTTTCAAGTAAAAACTGTCTCAAGT
*
3489838 GAGACAAAATTT
1 GAGATAAAATTT
3489850 CTATTAAATG
Statistics
Matches: 364, Mismatches: 112, Indels: 53
0.69 0.21 0.10
Matches are distributed among these distances:
35 10 0.03
36 97 0.27
37 82 0.23
38 57 0.16
39 72 0.20
40 13 0.04
42 33 0.09
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (38 bp):
GAGATAAAATTTTGTTTCAAGTAAAAACTGTCTCAAGT
Found at i:3489720 original size:116 final size:117
Alignment explanation
Indices: 3489589--3489821 Score: 351
Period size: 116 Copynumber: 2.0 Consensus size: 117
3489579 AATTTCTGTT
* * *
3489589 TCGAGTGAAAACTGTCTCAAGCGAGATGAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAA
1 TCGAGTGAAAACTGTCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGGGAAATAA
* * *
3489654 AATTTATGTTCAG-GTTAAAACTGCCTCAAGTGAGACGAAGTTTGTTTTAAG
66 AATTTATGTTCAGAGTGAAAACGGCCTCAAGAGAGACGAAGTTTGTTTTAAG
*
3489705 TCGAGTGAAAACTGTCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACTATCTCAAGGGAAATAA
1 TCGAGTGAAAACTGTCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGGGAAATAA
* * ** *
3489770 AATTTCTTTTTTGAGTGAAAACGGTCTCAAGAGAGACGAAGTTTGTTTTAAG
66 AATTTATGTTCAGAGTGAAAACGGCCTCAAGAGAGACGAAGTTTGTTTTAAG
3489822 AAAAACTATC
Statistics
Matches: 104, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
116 70 0.67
117 34 0.33
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (117 bp):
TCGAGTGAAAACTGTCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACAATCTCAAGGGAAATAA
AATTTATGTTCAGAGTGAAAACGGCCTCAAGAGAGACGAAGTTTGTTTTAAG
Found at i:3489797 original size:75 final size:75
Alignment explanation
Indices: 3489707--3489851 Score: 245
Period size: 75 Copynumber: 1.9 Consensus size: 75
3489697 GTTTTAAGTC
* * *
3489707 GAGTGAAAACTGTCTCAAGCGAGACGAAGTTTGTTTTAAGAAAAACTATCTCAAGGGAAATAAAA
1 GAGTGAAAACGGTCTCAAGAGAGACGAAGTTTGTTTTAAGAAAAACTATCTCAAGGGAAACAAAA
3489772 TTTCTTTTTT
66 TTTCTTTTTT
* *
3489782 GAGTGAAAACGGTCTCAAGAGAGACGAAGTTTGTTTTAAGAAAAACTATCTCAAGTGAGACAAAA
1 GAGTGAAAACGGTCTCAAGAGAGACGAAGTTTGTTTTAAGAAAAACTATCTCAAGGGAAACAAAA
3489847 TTTCT
66 TTTCT
3489852 ATTAAATGAG
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 65 1.00
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (75 bp):
GAGTGAAAACGGTCTCAAGAGAGACGAAGTTTGTTTTAAGAAAAACTATCTCAAGGGAAACAAAA
TTTCTTTTTT
Found at i:3491710 original size:19 final size:19
Alignment explanation
Indices: 3491677--3491727 Score: 84
Period size: 19 Copynumber: 2.6 Consensus size: 19
3491667 TCTCAGTTTG
*
3491677 CATCAGAATGCCCCATCATT
1 CATC-GAATGTCCCATCATT
3491697 CATCGAATGTCCCATCATT
1 CATCGAATGTCCCATCATT
3491716 CATCGAATGTCC
1 CATCGAATGTCC
3491728 ATGCCCTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 26 0.87
20 4 0.13
ACGTcount: A:0.27, C:0.33, G:0.12, T:0.27
Consensus pattern (19 bp):
CATCGAATGTCCCATCATT
Found at i:3493176 original size:15 final size:15
Alignment explanation
Indices: 3493158--3493188 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3493148 AAATTTTTTA
3493158 TTTTAATGAATGATT
1 TTTTAATGAATGATT
*
3493173 TTTTAATGCATGATT
1 TTTTAATGAATGATT
3493188 T
1 T
3493189 GGAAATGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.03, G:0.13, T:0.55
Consensus pattern (15 bp):
TTTTAATGAATGATT
Found at i:3493678 original size:18 final size:19
Alignment explanation
Indices: 3493655--3493698 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
3493645 CCAGTAATCC
* *
3493655 TATTCC-CTGGTAATCTTT
1 TATTCCACTGATAATCTTA
3493673 TATTCCGACTGATAATCTTA
1 TATTCC-ACTGATAATCTTA
3493693 TATTCC
1 TATTCC
3493699 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
20 16 0.73
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (19 bp):
TATTCCACTGATAATCTTA
Found at i:3504492 original size:30 final size:30
Alignment explanation
Indices: 3504456--3504522 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
3504446 GTCGTAGATT
* *
3504456 GCCAATTAAATATTCAGCCTGGCCTAATGG
1 GCCAATTAAATATACAGCCTGGCCTAATGA
*
3504486 GCCAATTAAATATACGGCCTGGCCTAATGA
1 GCCAATTAAATATACAGCCTGGCCTAATGA
3504516 GCCAATT
1 GCCAATT
3504523 TCGCCTAGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (30 bp):
GCCAATTAAATATACAGCCTGGCCTAATGA
Found at i:3504914 original size:15 final size:16
Alignment explanation
Indices: 3504894--3504923 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3504884 AGGTCTAATT
3504894 ACTTGTTTT-ATTTAG
1 ACTTGTTTTAATTTAG
3504909 ACTTGTTTTAATTTA
1 ACTTGTTTTAATTTA
3504924 CTTAAGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.23, C:0.07, G:0.10, T:0.60
Consensus pattern (16 bp):
ACTTGTTTTAATTTAG
Found at i:3521248 original size:30 final size:30
Alignment explanation
Indices: 3521188--3521318 Score: 149
Period size: 30 Copynumber: 4.4 Consensus size: 30
3521178 TTATTTTGTG
3521188 TTTTAGTCCTTTAAATTTATG-TTTTACTA
1 TTTTAGTCCTTTAAATTTATGTTTTTACTA
* *
3521217 TTTTAGTCCTTTAACTTTATGTTTCTACTA
1 TTTTAGTCCTTTAAATTTATGTTTTTACTA
* * * * * *
3521247 TTTTAATCCTTTAAGTTTCTATTTTTATTG
1 TTTTAGTCCTTTAAATTTATGTTTTTACTA
* *
3521277 TTTTAGTCCTGTAAATTTATGTTTTTGCTA
1 TTTTAGTCCTTTAAATTTATGTTTTTACTA
*
3521307 -TTTATTCCTTTA
1 TTTTAGTCCTTTA
3521319 TTTTACTAAG
Statistics
Matches: 82, Mismatches: 19, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
29 30 0.37
30 52 0.63
ACGTcount: A:0.21, C:0.12, G:0.08, T:0.60
Consensus pattern (30 bp):
TTTTAGTCCTTTAAATTTATGTTTTTACTA
Found at i:3521607 original size:5 final size:5
Alignment explanation
Indices: 3521597--3521642 Score: 76
Period size: 5 Copynumber: 9.4 Consensus size: 5
3521587 TCGCTTTTCA
*
3521597 ATTTT ATTTT ATTTT A-TTT ATTTT ATTTT ATTGT ATTTT ATTTT AT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT AT
3521643 CTTGGTGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
4 4 0.11
5 34 0.89
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (5 bp):
ATTTT
Found at i:3521618 original size:14 final size:14
Alignment explanation
Indices: 3521599--3521642 Score: 79
Period size: 14 Copynumber: 3.1 Consensus size: 14
3521589 GCTTTTCAAT
3521599 TTTATTTTATTTTA
1 TTTATTTTATTTTA
3521613 TTTATTTTATTTTA
1 TTTATTTTATTTTA
3521627 TTGTATTTTATTTTA
1 TT-TATTTTATTTTA
3521642 T
1 T
3521643 CTTGGTGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
14 16 0.55
15 13 0.45
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.77
Consensus pattern (14 bp):
TTTATTTTATTTTA
Found at i:3521621 original size:19 final size:20
Alignment explanation
Indices: 3521597--3521642 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
3521587 TCGCTTTTCA
*
3521597 ATTTTATTTTATTTTA-TTT
1 ATTTTATTTTATTGTATTTT
3521616 ATTTTATTTTATTGTATTTT
1 ATTTTATTTTATTGTATTTT
3521636 ATTTTAT
1 ATTTTAT
3521643 CTTGGTGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (20 bp):
ATTTTATTTTATTGTATTTT
Found at i:3524836 original size:26 final size:27
Alignment explanation
Indices: 3524805--3524877 Score: 123
Period size: 26 Copynumber: 2.8 Consensus size: 27
3524795 ATTAAAGATG
3524805 AATTTATAAAATTTTAGAAAGAAAAT-
1 AATTTATAAAATTTTAGAAAGAAAATA
3524831 AATTTATAAAATTTTAGAAA-AAAATA
1 AATTTATAAAATTTTAGAAAGAAAATA
*
3524857 AATTTATAAAATTTTAAAAAG
1 AATTTATAAAATTTTAGAAAG
3524878 GTAAAAGTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
25 5 0.11
26 39 0.89
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (27 bp):
AATTTATAAAATTTTAGAAAGAAAATA
Found at i:3528644 original size:24 final size:23
Alignment explanation
Indices: 3528609--3528654 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
3528599 AAACAGCTGC
* *
3528609 GTAGAATTTGCACCGAAGTGCCAT
1 GTAGAATATGCACCAAAG-GCCAT
3528633 GTAGAATATGCACCAAAGGCCA
1 GTAGAATATGCACCAAAGGCCA
3528655 CATAGATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.20
Consensus pattern (23 bp):
GTAGAATATGCACCAAAGGCCAT
Found at i:3528660 original size:23 final size:24
Alignment explanation
Indices: 3528610--3528660 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
3528600 AACAGCTGCG
* * **
3528610 TAGAATTTGCACCGAAGTGCCATG
1 TAGAATATGCACCAAAGTGCCACA
3528634 TAGAATATGCACCAAAG-GCCACA
1 TAGAATATGCACCAAAGTGCCACA
3528657 TAGA
1 TAGA
3528661 TTTGTCCTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.20
Consensus pattern (24 bp):
TAGAATATGCACCAAAGTGCCACA
Found at i:3528685 original size:46 final size:46
Alignment explanation
Indices: 3528632--3528730 Score: 112
Period size: 46 Copynumber: 2.2 Consensus size: 46
3528622 CGAAGTGCCA
* * **
3528632 TGTAGAATATG-CACCAAAGG-CCACATAGATTTGTCCTGAAGGACCG
1 TGTAGAAT-TGTC-CCAAAGGACCACATAGAATTATCCCAAAGGACCG
*
3528678 TGTAGAATTGTCCCGAAGGACCACATAGAATTATCCCAAAGGACCG
1 TGTAGAATTGTCCCAAAGGACCACATAGAATTATCCCAAAGGACCG
*
3528724 CGTAGAA
1 TGTAGAA
3528731 ACCCTCAACT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
45 8 0.18
46 37 0.82
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.20
Consensus pattern (46 bp):
TGTAGAATTGTCCCAAAGGACCACATAGAATTATCCCAAAGGACCG
Found at i:3528706 original size:23 final size:23
Alignment explanation
Indices: 3528648--3528722 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 23
3528638 ATATGCACCA
* *
3528648 AAGG-CCACATAGATTTGTCCTG
1 AAGGACCACATAGAATTGTCCCG
***
3528670 AAGGACCGTGTAGAATTGTCCCG
1 AAGGACCACATAGAATTGTCCCG
* *
3528693 AAGGACCACATAGAATTATCCCA
1 AAGGACCACATAGAATTGTCCCG
3528716 AAGGACC
1 AAGGACC
3528723 GCGTAGAAAC
Statistics
Matches: 42, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
22 4 0.10
23 38 0.90
ACGTcount: A:0.33, C:0.24, G:0.23, T:0.20
Consensus pattern (23 bp):
AAGGACCACATAGAATTGTCCCG
Found at i:3528729 original size:23 final size:23
Alignment explanation
Indices: 3528670--3528730 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
3528660 ATTTGTCCTG
* * *
3528670 AAGGACCGTGTAGAATTGTCCCG
1 AAGGACCGCGTAGAATTATCCCA
* *
3528693 AAGGACCACATAGAATTATCCCA
1 AAGGACCGCGTAGAATTATCCCA
3528716 AAGGACCGCGTAGAA
1 AAGGACCGCGTAGAA
3528731 ACCCTCAACT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.16
Consensus pattern (23 bp):
AAGGACCGCGTAGAATTATCCCA
Found at i:3536034 original size:3 final size:3
Alignment explanation
Indices: 3536022--3536095 Score: 130
Period size: 3 Copynumber: 24.3 Consensus size: 3
3536012 CTACTACTAC
*
3536022 TAA TAC TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3536068 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3536096 TTTTTAAGAT
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
3 65 0.96
4 3 0.04
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3536501 original size:135 final size:131
Alignment explanation
Indices: 3536307--3536641 Score: 348
Period size: 131 Copynumber: 2.5 Consensus size: 131
3536297 GGTCATTTTT
* * * * * *
3536307 AGGGAGACACGACTCCTGCGTGATGAGGAGATCTGGTCGGTGGATTACACTGTTCCTACGTGATG
1 AGGGTGACACAACTCCTACGCGATGAGGAGATCTGGTCGGTGGATGACACAGTTCCTACGTGATG
* * * **
3536372 AGGACGTCTTG-GACATTTTTAGGGATGATGATAACACAGTTCCTACGCGATGAGGACGACTGGT
66 AGGACGGC-TGAAAC-TCTTTA-GG--GATGATAACACAGTTCCTACGCGATGAGGACGAAGGGT
3536436 TATCTA
126 TATCTA
* * * * *
3536442 GGGGTGACATAACTCTTACGCGATGAGGAGATCTGGTCGGGGGATGACACGGTTCCTACGTGATG
1 AGGGTGACACAACTCCTACGCGATGAGGAGATCTGGTCGGTGGATGACACAGTTCCTACGTGATG
* * * * *
3536507 AGGATGGCTGAAACTCTTTAGGGATGATAACACGGTTCTTACGTGATGAGGATGAAGGGTTATCT
66 AGGACGGCTGAAACTCTTTAGGGATGATAACACAGTTCCTACGCGATGAGGACGAAGGGTTATCT
3536572 A
131 A
* * * * * * * * *
3536573 AGGTTGACGCGACTCCTATGTGACGAGAAGGTCTGGTCGGTGGATGACACAGTTCCTACGCGATG
1 AGGGTGACACAACTCCTACGCGATGAGGAGATCTGGTCGGTGGATGACACAGTTCCTACGTGATG
3536638 AGGA
66 AGGA
3536642 TAACTGTCAA
Statistics
Matches: 165, Mismatches: 34, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
131 93 0.56
133 2 0.01
134 7 0.04
135 63 0.38
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.25
Consensus pattern (131 bp):
AGGGTGACACAACTCCTACGCGATGAGGAGATCTGGTCGGTGGATGACACAGTTCCTACGTGATG
AGGACGGCTGAAACTCTTTAGGGATGATAACACAGTTCCTACGCGATGAGGACGAAGGGTTATCT
A
Found at i:3536715 original size:36 final size:36
Alignment explanation
Indices: 3536665--3536789 Score: 111
Period size: 36 Copynumber: 3.6 Consensus size: 36
3536655 TTAGGGATAA
*
3536665 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTAAAGAGAAACTATCTCAAGAGAGACAAAATT
* * * *
3536701 TGTTTCAAGCGAAACGATCTTAA-AGATG------TT
1 TGTTTAAAGAGAAACTATCTCAAGAGA-GACAAAATT
* *
3536731 TGTTTAAAGAGAAACTGTCTCGAGAGAGACAAAATT
1 TGTTTAAAGAGAAACTATCTCAAGAGAGACAAAATT
* *
3536767 CGTTTAAAGGGAAACTATCTCAA
1 TGTTTAAAGAGAAACTATCTCAA
3536790 AGATGATTGT
Statistics
Matches: 68, Mismatches: 13, Indels: 16
0.70 0.13 0.16
Matches are distributed among these distances:
30 20 0.29
31 3 0.04
35 3 0.04
36 42 0.62
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (36 bp):
TGTTTAAAGAGAAACTATCTCAAGAGAGACAAAATT
Found at i:3536757 original size:66 final size:66
Alignment explanation
Indices: 3536665--3536811 Score: 213
Period size: 66 Copynumber: 2.2 Consensus size: 66
3536655 TTAGGGATAA
* * * *
3536665 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGCGAAACGATCTTAAAGATGT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCGTTTAAAGCGAAACGATCTCAAAGATGA
3536730 T
66 T
* * * * *
3536731 TGTTTAAAGAGAAACTGTCTCGAGAGAGACAAAATTCGTTTAAAGGGAAACTATCTCAAAGATGA
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCGTTTAAAGCGAAACGATCTCAAAGATGA
3536796 T
66 T
3536797 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
3536812 AAAATTCGTT
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 71 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (66 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCGTTTAAAGCGAAACGATCTCAAAGATGA
T
Found at i:3536811 original size:30 final size:31
Alignment explanation
Indices: 3536665--3536811 Score: 84
Period size: 36 Copynumber: 4.5 Consensus size: 31
3536655 TTAGGGATAA
3536665 TGTTTCAAGAGAAACTATCTCAAGAGA-GACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAGATG-----A-T
* * * *
3536701 TGTTTCAAGCGAAACGATCTTAA-AGATGTT
1 TGTTTCAAGAGAAACTATCTCAAGAGATGAT
* * **
3536731 TGTTTAAAGAGAAACTGTCTCGAGAGAGACAAAAT
1 TGTTTCAAGAGAAACTATCTC-A-AGAG--ATGAT
* *
3536766 TCGTTTAAAGGGAAACTATCTCAA-AGATGAT
1 T-GTTTCAAGAGAAACTATCTCAAGAGATGAT
3536797 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
3536812 AAAATTCGTT
Statistics
Matches: 86, Mismatches: 18, Indels: 20
0.69 0.15 0.16
Matches are distributed among these distances:
30 29 0.34
31 5 0.06
32 1 0.01
33 4 0.05
34 1 0.01
35 7 0.08
36 39 0.45
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (31 bp):
TGTTTCAAGAGAAACTATCTCAAGAGATGAT
Found at i:3536814 original size:51 final size:51
Alignment explanation
Indices: 3536753--3536862 Score: 193
Period size: 51 Copynumber: 2.2 Consensus size: 51
3536743 AACTGTCTCG
* *
3536753 AGAGAGACAAAATTCGTTTAAAGGGAAACTATCTCAAAGATGATTGTTTCA
1 AGAGAAACAAAATTCGTTTAAAGGGAAACGATCTCAAAGATGATTGTTTCA
*
3536804 AGAGAAACAAAATTCGTTTAAAGGGAAACGATCTCAAAGATGATTGTTTTA
1 AGAGAAACAAAATTCGTTTAAAGGGAAACGATCTCAAAGATGATTGTTTCA
3536855 AGAGAAAC
1 AGAGAAAC
3536863 TGTCTCAAGA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.25
Consensus pattern (51 bp):
AGAGAAACAAAATTCGTTTAAAGGGAAACGATCTCAAAGATGATTGTTTCA
Found at i:3536863 original size:117 final size:116
Alignment explanation
Indices: 3536684--3536927 Score: 344
Period size: 117 Copynumber: 2.1 Consensus size: 116
3536674 AGAAACTATC
* * * * *
3536684 TCAAGAGAGACAAAATTTGTTTCAAGCGAAACGATCTTAAAGATGTTTGTTTAAAGAGAAACTGT
1 TCAAGAGAAACAAAATTCGTTTAAAGCGAAACGATCTCAAAGATGATTGTTTAAAGAGAAACTGT
* * * * * *
3536749 CTCGAGAGAGACAAAATTCGTTTAAAGGGAAACTATCTCAAAGATGATTGTT
66 CTCAAGAAAGACAAAATTCATTTAAAGGGAAACGATCTCAAAGATGA-CGCT
* *
3536801 TCAAGAGAAACAAAATTCGTTTAAAGGGAAACGATCTCAAAGATGATTGTTTTAAGAGAAACTGT
1 TCAAGAGAAACAAAATTCGTTTAAAGCGAAACGATCTCAAAGATGATTGTTTAAAGAGAAACTGT
* *
3536866 CTCAAGAAAGATAAAATTCATTTAAAGGGAAACGATCTCAAAGGTGACGCT
66 CTCAAGAAAGACAAAATTCATTTAAAGGGAAACGATCTCAAAGATGACGCT
3536917 TCAAGAGAAAC
1 TCAAGAGAAAC
3536928 TGTCTCAAGA
Statistics
Matches: 112, Mismatches: 15, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
116 13 0.12
117 99 0.88
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.25
Consensus pattern (116 bp):
TCAAGAGAAACAAAATTCGTTTAAAGCGAAACGATCTCAAAGATGATTGTTTAAAGAGAAACTGT
CTCAAGAAAGACAAAATTCATTTAAAGGGAAACGATCTCAAAGATGACGCT
Found at i:3536905 original size:36 final size:35
Alignment explanation
Indices: 3536812--3536907 Score: 96
Period size: 36 Copynumber: 2.9 Consensus size: 35
3536802 CAAGAGAAAC
3536812 AAAATTCGTTTAAAGGGAAACGATCTC--AAAGAT
1 AAAATTCGTTTAAAGGGAAACGATCTCAAAAAGAT
* * *
3536845 --GATT-GTTTTAAGAGAAACTG-TCTCAAGAAAGAT
1 AAAATTCGTTTAAAGGGAAAC-GATCTCAA-AAAGAT
*
3536878 AAAATTCATTTAAAGGGAAACGATCTCAAA
1 AAAATTCGTTTAAAGGGAAACGATCTCAAA
3536908 GGTGACGCTT
Statistics
Matches: 48, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
30 16 0.33
31 4 0.08
33 6 0.12
35 5 0.10
36 17 0.35
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.26
Consensus pattern (35 bp):
AAAATTCGTTTAAAGGGAAACGATCTCAAAAAGAT
Found at i:3537015 original size:130 final size:131
Alignment explanation
Indices: 3536801--3537038 Score: 352
Period size: 130 Copynumber: 1.8 Consensus size: 131
3536791 GATGATTGTT
* * *
3536801 TCAAGAGAAACAAAATTCGTTTAAAGGGAAACGATCTCAAAGATGATTGTTTTAAGAGAAACTGT
1 TCAAGAGAAACAAAATTCGTTTAAAGGGAAACGATCTCAAAGAGGATTATTTCAAGAGAAACTGT
* *
3536866 CTCAAGAAAGATAAAATTCATTTAAAGGGAAACGATCTCAAAGGTGACGCTTCAAGAGAAACTGT
66 CTCAAGAAAGACAAAATTCATTTAAAGGGAAACAATCTCAAAGGTGACGCTTCAAGAGAAACTGT
3536931 C
131 C
* * * * * *
3536932 TCAAGAGAGATAAACTTTGTTTCAAGGGTAACGATCTCAAAGAGGA-TATTTCAAGAGAAACTGT
1 TCAAGAGAAACAAAATTCGTTTAAAGGGAAACGATCTCAAAGAGGATTATTTCAAGAGAAACTGT
* *
3536996 CTCAAGAGAGACAAAATTCATTTCAAGGGAAACAATCTCAAAG
66 CTCAAGAAAGACAAAATTCATTTAAAGGGAAACAATCTCAAAG
3537039 ATTTATCAAT
Statistics
Matches: 94, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
130 55 0.59
131 39 0.41
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (131 bp):
TCAAGAGAAACAAAATTCGTTTAAAGGGAAACGATCTCAAAGAGGATTATTTCAAGAGAAACTGT
CTCAAGAAAGACAAAATTCATTTAAAGGGAAACAATCTCAAAGGTGACGCTTCAAGAGAAACTGT
C
Found at i:3537039 original size:65 final size:65
Alignment explanation
Indices: 3536801--3537039 Score: 300
Period size: 65 Copynumber: 3.7 Consensus size: 65
3536791 GATGATTGTT
* * * *
3536801 TCAAGAGAAACAAAATTCGTTTAAAGGGAAACGATCTCAAAGATGATTGTTTTAAGAGAAACTGT
1 TCAAGAGAGACAAAATTCATTTAAAGGGAAACGATCTCAAAGAGGA-TGTTTCAAGAGAAACTGT
3536866 C
65 C
* * * *
3536867 TCAAGAAAGATAAAATTCATTTAAAGGGAAACGATCTCAAAG-GTGACGCTTCAAGAGAAACTGT
1 TCAAGAGAGACAAAATTCATTTAAAGGGAAACGATCTCAAAGAG-GATGTTTCAAGAGAAACTGT
3536931 C
65 C
* * ** * * *
3536932 TCAAGAGAGATAAACTTTGTTTCAAGGGTAACGATCTCAAAGAGGATATTTCAAGAGAAACTGTC
1 TCAAGAGAGACAAAATTCATTTAAAGGGAAACGATCTCAAAGAGGATGTTTCAAGAGAAACTGTC
* *
3536997 TCAAGAGAGACAAAATTCATTTCAAGGGAAACAATCTCAAAGA
1 TCAAGAGAGACAAAATTCATTTAAAGGGAAACGATCTCAAAGA
3537040 TTTATCAATT
Statistics
Matches: 148, Mismatches: 23, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
65 107 0.72
66 41 0.28
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.23
Consensus pattern (65 bp):
TCAAGAGAGACAAAATTCATTTAAAGGGAAACGATCTCAAAGAGGATGTTTCAAGAGAAACTGTC
Found at i:3537220 original size:37 final size:36
Alignment explanation
Indices: 3537091--3537220 Score: 111
Period size: 35 Copynumber: 3.6 Consensus size: 36
3537081 CGTTTTGAGG
* * **
3537091 AAAAATGCCTCAAGCGAGATGAAATTTGTTTTTAAGAA
1 AAAAATGTCTCTAGCGAGACAAAATTT-TTTTTAAG-A
* **
3537129 AAAAATGTCTATAGCGAGACAACACCTTTTTTT-AG-
1 AAAAATGTCTCTAGCGAGACAA-AATTTTTTTTAAGA
* *
3537164 AAAACTGTCTCAAGCGAGACAAAATTTTCTTTTAAGA
1 AAAAATGTCTCTAGCGAGACAAAATTTT-TTTTAAGA
* *
3537201 AAAATTTTCTCTAGCGAGAC
1 AAAAATGTCTCTAGCGAGAC
3537221 GACACTTTGT
Statistics
Matches: 73, Mismatches: 15, Indels: 9
0.75 0.15 0.09
Matches are distributed among these distances:
34 4 0.05
35 23 0.32
36 2 0.03
37 19 0.26
38 22 0.30
39 3 0.04
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (36 bp):
AAAAATGTCTCTAGCGAGACAAAATTTTTTTTAAGA
Found at i:3537239 original size:73 final size:73
Alignment explanation
Indices: 3537083--3537241 Score: 180
Period size: 73 Copynumber: 2.2 Consensus size: 73
3537073 AAGTTTTACG
**
3537083 TTTTGAGGAAAAATGCCTCAAGCGAGATGAAATTTGTTTTTAAGAAAAAAATGTCTATAGCGAGA
1 TTTTGA-GAAAAATGCCTCAAGCGAGACAAAATTTGTTTTTAAGAAAAAAATGTCTATAGCGAGA
3537148 CAACACCTT
65 CAACACCTT
* * * * * *
3537157 TTTTTAGAAAACTGTCTCAAGCGAGACAAAATTT-TCTTTTAAG-AAAAATTTTCTCTAGCGAGA
1 TTTTGAGAAAAATGCCTCAAGCGAGACAAAATTTGT-TTTTAAGAAAAAAATGTCTATAGCGAGA
*
3537220 CGACA-CTT
65 CAACACCTT
3537228 TGTTTCGAGAAAAA
1 T-TTT-GAGAAAAA
3537242 CACCCTCAAA
Statistics
Matches: 71, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
71 4 0.06
72 25 0.35
73 37 0.52
74 5 0.07
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (73 bp):
TTTTGAGAAAAATGCCTCAAGCGAGACAAAATTTGTTTTTAAGAAAAAAATGTCTATAGCGAGAC
AACACCTT
Found at i:3538281 original size:15 final size:15
Alignment explanation
Indices: 3538254--3538317 Score: 60
Period size: 17 Copynumber: 4.1 Consensus size: 15
3538244 CATGTGCTTC
3538254 TTGTCTTTGTTTTTT
1 TTGTCTTTGTTTTTT
3538269 TTGT-TTTGTTTTTTTTT
1 TTGTCTTTG---TTTTTT
*
3538286 TTCTCTTTGCTTTTTCT
1 TTGTCTTTG-TTTTT-T
3538303 TT-TCTTTGTTTTTT
1 TTGTCTTTGTTTTTT
3538317 T
1 T
3538318 CTTTTCTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
14 6 0.14
15 9 0.21
16 11 0.26
17 12 0.29
18 4 0.10
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.81
Consensus pattern (15 bp):
TTGTCTTTGTTTTTT
Found at i:3538285 original size:17 final size:17
Alignment explanation
Indices: 3538263--3538327 Score: 78
Period size: 18 Copynumber: 3.8 Consensus size: 17
3538253 CTTGTCTTTG
*
3538263 TTTTTTTTGTTTTGTTT
1 TTTTTTTTCTTTTGTTT
*
3538280 TTTTTTTTCTCTTTGCTT
1 TTTTTTTTCT-TTTGTTT
*
3538298 TTTCTTTTC-TTTGTTT
1 TTTTTTTTCTTTTGTTT
3538314 TTTTCTTTTCTTTT
1 TTTT-TTTTCTTTT
3538328 TTTACTTGCT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
16 9 0.22
17 14 0.35
18 17 0.43
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (17 bp):
TTTTTTTTCTTTTGTTT
Found at i:3538315 original size:30 final size:28
Alignment explanation
Indices: 3538266--3538328 Score: 81
Period size: 30 Copynumber: 2.2 Consensus size: 28
3538256 GTCTTTGTTT
* * *
3538266 TTTTTGTTTTGTTTTTTTTTTTCTCTTTGC
1 TTTTTCTTTTCTTTGTTTTTTTCT-TTT-C
3538296 TTTTTCTTTTCTTTGTTTTTTTCTTTTC
1 TTTTTCTTTTCTTTGTTTTTTTCTTTTC
3538324 TTTTT
1 TTTTT
3538329 TTACTTGCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 6 0.20
29 3 0.10
30 21 0.70
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (28 bp):
TTTTTCTTTTCTTTGTTTTTTTCTTTTC
Found at i:3542189 original size:6 final size:6
Alignment explanation
Indices: 3542180--3542448 Score: 502
Period size: 6 Copynumber: 44.8 Consensus size: 6
3542170 AATGTAAATT
* * *
3542180 TACTAG TACTAA TTCTAG TACTAA TACTAA TACTAA TACTAA TACTAA
1 TACTAA TACTAA TACTAA TACTAA TACTAA TACTAA TACTAA TACTAA
3542228 TACTAA TACTAA TACTAA TACTAA TACTAA TACTAA TACTAA TACTAA
1 TACTAA TACTAA TACTAA TACTAA TACTAA TACTAA TACTAA TACTAA
*
3542276 TACTAA TACTAA TACTAA TACTAA TACTAG TACTAA TACTAA TACTAA
1 TACTAA TACTAA TACTAA TACTAA TACTAA TACTAA TACTAA TACTAA
3542324 TACTAA TACTAA TACTAA TACTAA TACTAA TACTAA TACTAA TACTAA
1 TACTAA TACTAA TACTAA TACTAA TACTAA TACTAA TACTAA TACTAA
3542372 TACTAA TACTAA TACTAA TACTAA TACTAA TACTAA TACTAA TACTAA
1 TACTAA TACTAA TACTAA TACTAA TACTAA TACTAA TACTAA TACTAA
3542420 TACTAA TACTAA TACTAA TACTAA TACTA
1 TACTAA TACTAA TACTAA TACTAA TACTA
3542449 GTTACACTAT
Statistics
Matches: 256, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 256 1.00
ACGTcount: A:0.48, C:0.17, G:0.01, T:0.34
Consensus pattern (6 bp):
TACTAA
Found at i:3544100 original size:3 final size:3
Alignment explanation
Indices: 3544092--3544268 Score: 176
Period size: 3 Copynumber: 59.0 Consensus size: 3
3544082 ATGTAAACTT
3544092 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
* * * * * * * *
3544140 TAC TAC TAC GAC GAC GAC GAC GAC GAC GAC TAC TAC TAC TAC TAC CAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
* * * * * *
3544188 CAC CAC TAC TAC TAC CAC GAC GA- TGAC TAC TAC TAC TAC TAC TGC
1 TAC TAC TAC TAC TAC TAC TAC TAC T-AC TAC TAC TAC TAC TAC TAC
* * * *
3544233 TGC TGC TGC TGC TAC TAC TAC TAC TAC TAC TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
3544269 GACAACCACC
Statistics
Matches: 163, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
3 162 0.99
4 1 0.01
ACGTcount: A:0.31, C:0.35, G:0.08, T:0.26
Consensus pattern (3 bp):
TAC
Found at i:3544296 original size:3 final size:3
Alignment explanation
Indices: 3544290--3544322 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
3544280 CCACCACTAC
*
3544290 CAA CAA CAA CAA CAA CAA CAA CAA AAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
3544323 TAATAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.70, C:0.30, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:3544809 original size:131 final size:130
Alignment explanation
Indices: 3544526--3544884 Score: 339
Period size: 131 Copynumber: 2.7 Consensus size: 130
3544516 GGTCGTTTAT
* * * * ** *
3544526 AGGGTGACACGACTCCTACATGA-AGAGGAGATATGGTCTGTTGATTACACTGTTCCTACGTGAT
1 AGGGTGACGCGACTCCTACGTGATA-AGGAGATCTGGTCGGGGGATGACAC-GTTCCTACGTGAT
* * * *
3544590 GAGGA-CGTCTTGGCCATCTTTAGGGATGATGATAACATGGTTACTTCGTGATGAGGACAATTGA
64 GAGGATAG-C-TGGCCATCTTTAGGGAT-A--ATAACACGATTACTTCGTGATGAGAACAATTGA
3544654 TTATCTA
124 TTATCTA
* * * *
3544661 GGGGTGACGCGATTCCTATGTGATAAGGAGATCTGGTCGGGGGATGACTCAGTTCCTACGTGATG
1 AGGGTGACGCGACTCCTACGTGATAAGGAGATCTGGTCGGGGGATGACAC-GTTCCTACGTGATG
*
3544726 AGGATAGCTGGCCATCTTTAGGGATAATAACACGATTCCTAT-GTGATGAGAACTAA-TGATTAT
65 AGGATAGCTGGCCATCTTTAGGGATAATAACACGATTACT-TCGTGATGAGAAC-AATTGATTAT
3544789 CTA
128 CTA
* * * * * * * * *
3544792 AGGTTGACGCGGCTCCTACGTGATGAGGAGGTTTGGTCGGTGGATGACACGATTCTTAAGCGATG
1 AGGGTGACGCGACTCCTACGTGATAAGGAGATCTGGTCGGGGGATGACACG-TTCCTACGTGATG
* **
3544857 AGGATGGCTGTACATCTTTAGGGATAAT
65 AGGATAGCTGGCCATCTTTAGGGATAAT
3544885 GTTTCAAGAG
Statistics
Matches: 186, Mismatches: 33, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
130 1 0.01
131 106 0.57
132 3 0.02
133 1 0.01
134 17 0.09
135 56 0.30
136 2 0.01
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.29
Consensus pattern (130 bp):
AGGGTGACGCGACTCCTACGTGATAAGGAGATCTGGTCGGGGGATGACACGTTCCTACGTGATGA
GGATAGCTGGCCATCTTTAGGGATAATAACACGATTACTTCGTGATGAGAACAATTGATTATCTA
Found at i:3544959 original size:30 final size:29
Alignment explanation
Indices: 3544923--3545039 Score: 101
Period size: 30 Copynumber: 3.7 Consensus size: 29
3544913 AAAAAATTCA
*
3544923 TTTCAAGGGAAACGATCTCAAAGATGTTTG
1 TTTCAAGAGAAACGATCTCAAAGAT-TTTG
* *
3544953 TTTCAAGAGAAACTATCTCAAGAAAGACAAAATTTG
1 TTTCAAGAGAAACGATCTC---AAAG----ATTTTG
*
3544989 TTTCAAGGGAAACGATCTCAAAGATTATTG
1 TTTCAAGAGAAACGATCTCAAAGATT-TTG
3545019 TTTCAAGAGAAACTG-TCTCAA
1 TTTCAAGAGAAAC-GATCTCAA
3545040 GAGAGACAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
29 2 0.03
30 38 0.54
31 1 0.01
33 8 0.11
36 21 0.30
37 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (29 bp):
TTTCAAGAGAAACGATCTCAAAGATTTTG
Found at i:3544989 original size:36 final size:35
Alignment explanation
Indices: 3544884--3545271 Score: 141
Period size: 36 Copynumber: 11.7 Consensus size: 35
3544874 TTAGGGATAA
* *
3544884 TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGA-A-AGAAAAATT
** * * **
3544921 CATTTCAAGGGAAACGATCTC---AAAG--ATGTT
1 TGTTTCAAGAGAAACTATCTCAAGAAAGAAAAATT
3544951 TGTTTCAAGAGAAACTATCTCAAGAAAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAAAGA-AAAATT
* * **
3544987 TGTTTCAAGGGAAACGATCTC---AAAG-ATTA-T
1 TGTTTCAAGAGAAACTATCTCAAGAAAGAAAAATT
* *
3545017 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAAAGA-AAAATT
* **
3545053 CT-TTTCAATG-GAAACAATCTC---AAAG-ATTA-T
1 -TGTTTCAA-GAGAAACTATCTCAAGAAAGAAAAATT
* * *
3545083 TGTTTCAAGAGAAACTGTCTTAAGATAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAAAGA-AAAATT
* * ***
3545119 TGTTTCAAGGGAAACAATCTC---AAAG-GTGA--
1 TGTTTCAAGAGAAACTATCTCAAGAAAGAAAAATT
* * *
3545148 TGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAAAGA-AAAATT
* * * **
3545184 CGTTTCAAGGGAAACGATCTC---AAAG-ATGA--
1 TGTTTCAAGAGAAACTATCTCAAGAAAGAAAAATT
* * *
3545213 TGTTTCAAGAGAAATTGTCTCAAGAGAGAAAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAAAG-AAAAATT
* * *
3545249 CGTTTCAAGGGAAACAATCTCAA
1 TGTTTCAAGAGAAACTATCTCAA
3545272 TGATTTATCA
Statistics
Matches: 243, Mismatches: 72, Indels: 73
0.63 0.19 0.19
Matches are distributed among these distances:
29 35 0.14
30 54 0.22
31 7 0.03
32 7 0.03
33 24 0.10
34 4 0.02
35 4 0.02
36 90 0.37
37 18 0.07
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.27
Consensus pattern (35 bp):
TGTTTCAAGAGAAACTATCTCAAGAAAGAAAAATT
Found at i:3545089 original size:30 final size:29
Alignment explanation
Indices: 3544923--3545097 Score: 82
Period size: 30 Copynumber: 5.4 Consensus size: 29
3544913 AAAAAATTCA
*
3544923 TTTCAAGGGAAACGATCTCAAAGATGT-TTG
1 TTTCAA-GGAAACAATCTCAAAGAT-TATTG
* **
3544953 TTTCAAGAGAAACTATCTCAAGAAAGACAAAATTTG
1 TTTCAAG-GAAACAATCTC---AAAG--ATTA-TTG
*
3544989 TTTCAAGGGAAACGATCTCAAAGATTATTG
1 TTTCAA-GGAAACAATCTCAAAGATTATTG
** ** *
3545019 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCT
1 TTTCAAG-GAAACAATCTC-A-A-AG--ATTATT-G
3545055 TTTCAATGGAAACAATCTCAAAGATTATTG
1 TTTCAA-GGAAACAATCTCAAAGATTATTG
3545085 TTTCAAGAGAAAC
1 TTTCAAG-GAAAC
3545098 TGTCTTAAGA
Statistics
Matches: 111, Mismatches: 16, Indels: 36
0.68 0.10 0.22
Matches are distributed among these distances:
29 3 0.03
30 45 0.41
31 7 0.06
32 1 0.01
33 12 0.11
34 1 0.01
35 6 0.05
36 34 0.31
37 2 0.02
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (29 bp):
TTTCAAGGAAACAATCTCAAAGATTATTG
Found at i:3545152 original size:29 final size:29
Alignment explanation
Indices: 3545119--3545226 Score: 72
Period size: 29 Copynumber: 3.5 Consensus size: 29
3545109 AGACAAAATT
*
3545119 TGTTTCAAGGGAAACAATCTCAAAGGTGA
1 TGTTTCAAGAGAAACAATCTCAAAGGTGA
* ** **
3545148 TGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TGTTTCAAGAGAAACAATCTCAA-AG-G---TGA
* * *
3545182 TTCGTTTCAAGGGAAACGATCTCAAAGATGA
1 -T-GTTTCAAGAGAAACAATCTCAAAGGTGA
3545213 TGTTTCAAGAGAAA
1 TGTTTCAAGAGAAA
3545227 TTGTCTCAAG
Statistics
Matches: 58, Mismatches: 14, Indels: 14
0.67 0.16 0.16
Matches are distributed among these distances:
29 31 0.53
30 3 0.05
31 2 0.03
34 1 0.02
35 3 0.05
36 18 0.31
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.25
Consensus pattern (29 bp):
TGTTTCAAGAGAAACAATCTCAAAGGTGA
Found at i:3545189 original size:65 final size:65
Alignment explanation
Indices: 3544883--3545271 Score: 562
Period size: 66 Copynumber: 5.9 Consensus size: 65
3544873 TTTAGGGATA
* * *
3544883 ATGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAAATTCATTTCAAGGGAAACGATCTCAAAGAT
1 ATGTTTCAAGAGAAACTGTCTCAAGAGAG-ACAAAATTCGTTTCAAGGGAAACAATCTCAAAGAT
3544948 G
65 G
* * * * *
3544949 TTTGTTTCAAGAGAAACTATCTCAAGAAAGACAAAATTTGTTTCAAGGGAAACGATCTCAAAGAT
1 -ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACAATCTCAAAGAT
*
3545014 T
65 G
* *
3545015 ATTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCTTTTCAATGGAAACAATCTCAAAGAT
1 A-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACAATCTCAAAGAT
*
3545080 T
65 G
* * * *
3545081 ATTGTTTCAAGAGAAACTGTCTTAAGATAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGT
1 A-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACAATCTCAAAGAT
3545146 G
65 G
* *
3545147 ATGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGATG
1 ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACAATCTCAAAGATG
* *
3545212 ATGTTTCAAGAGAAATTGTCTCAAGAGAGAAAAAATTCGTTTCAAGGGAAACAATCTCAA
1 ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACAATCTCAA
3545272 TGATTTATCA
Statistics
Matches: 290, Mismatches: 31, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
65 114 0.39
66 150 0.52
67 26 0.09
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (65 bp):
ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACAATCTCAAAGATG
Found at i:3545465 original size:37 final size:36
Alignment explanation
Indices: 3545354--3545475 Score: 111
Period size: 37 Copynumber: 3.3 Consensus size: 36
3545344 ATGAAATTTT
* * *
3545354 TTTTAAGAAAAATTGTCTCTAGCTAGACAACTCTTTT
1 TTTTAAGAAAAATTGTCTCTAGCGAGAC-ACACTTTA
** * * * *
3545391 TTTTTTGAGAAAACTGTCTCAAGCGAGA-AAAATTTA
1 TTTTAAGA-AAAATTGTCTCTAGCGAGACACACTTTA
*
3545427 TTTTAAGAAAAATTATCTCTAGCGAGACGACACTTTA
1 TTTTAAGAAAAATTGTCTCTAGCGAGAC-ACACTTTA
*
3545464 TTTCAAGAAAAA
1 TTTTAAGAAAAA
3545476 CACCCTCTGC
Statistics
Matches: 65, Mismatches: 17, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
35 16 0.25
36 10 0.15
37 23 0.35
38 16 0.25
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (36 bp):
TTTTAAGAAAAATTGTCTCTAGCGAGACACACTTTA
Found at i:3546566 original size:5 final size:5
Alignment explanation
Indices: 3546486--3546628 Score: 68
Period size: 5 Copynumber: 29.0 Consensus size: 5
3546476 TTACATGTGC
* * * * *
3546486 TTCTT GTCTT ATTTTT TTCTT CTCTT TGCTT TT-TT GTT-TT TTGTT TTCTT
1 TTCTT TTCTT -TTCTT TTCTT TTCTT TTCTT TTCTT -TTCTT TTCTT TTCTT
* * * * *
3546536 TT-TT CT-TT TTGTT TTATT TTGTTT TTCTT TTCTT TTCTT TGCTTTT
1 TTCTT TTCTT TTCTT TTCTT TT-CTT TTCTT TTCTT TTCTT T--TCTT
* *
3546582 TTCTT TT-TC TTCCT TTCTT TGT-TT TTCTT TTC-- TTCTT TTCTT TTCTT
1 TTCTT TTCTT TTCTT TTCTT T-TCTT TTCTT TTCTT TTCTT TTCTT TTCTT
3546629 CTTTGATCTT
Statistics
Matches: 106, Mismatches: 20, Indels: 24
0.71 0.13 0.16
Matches are distributed among these distances:
3 3 0.03
4 14 0.13
5 77 0.73
6 8 0.08
7 4 0.04
ACGTcount: A:0.01, C:0.15, G:0.06, T:0.78
Consensus pattern (5 bp):
TTCTT
Found at i:3546581 original size:44 final size:45
Alignment explanation
Indices: 3546497--3546632 Score: 142
Period size: 44 Copynumber: 3.1 Consensus size: 45
3546487 TCTTGTCTTA
* *
3546497 TTTTT-TTCTTCTCTTTGCTTTTT-TGTT-TTTTGTTTTCTTTTTTC
1 TTTTTCTTCTT-TCTTTG-TTTTTCTTTTCTTTTCTTTTCTTTTTTC
* *
3546541 TTTTTGTT-TTAT-TTTGTTTTTCTTTTCTTTTCTTTGCTTTTTTC
1 TTTTTCTTCTT-TCTTTGTTTTTCTTTTCTTTTCTTTTCTTTTTTC
3546585 TTTTTCTTCCTTTCTTTGTTTTTCTTTTC--TTCTTTTCTTTTCTTC
1 TTTTTCTT-CTTTCTTTGTTTTTCTTTTCTTTTCTTTTCTTTT-TTC
3546630 TTT
1 TTT
3546633 GATCTTTGTA
Statistics
Matches: 79, Mismatches: 6, Indels: 13
0.81 0.06 0.13
Matches are distributed among these distances:
42 5 0.06
43 7 0.09
44 41 0.52
45 9 0.11
46 17 0.22
ACGTcount: A:0.01, C:0.15, G:0.05, T:0.79
Consensus pattern (45 bp):
TTTTTCTTCTTTCTTTGTTTTTCTTTTCTTTTCTTTTCTTTTTTC
Found at i:3546598 original size:8 final size:8
Alignment explanation
Indices: 3546565--3546623 Score: 52
Period size: 8 Copynumber: 7.2 Consensus size: 8
3546555 TGTTTTTCTT
3546565 TTCTTTTC
1 TTCTTTTC
3546573 TTTGCTTTT-
1 -TT-CTTTTC
3546582 TTCTTTTTC
1 TTC-TTTTC
*
3546591 TTCCTTTC
1 TTCTTTTC
3546599 TT-TGTTT-
1 TTCT-TTTC
3546606 TTCTTTTC
1 TTCTTTTC
3546614 TTCTTTTC
1 TTCTTTTC
3546622 TT
1 TT
3546624 TTCTTCTTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
7 6 0.14
8 26 0.62
9 5 0.12
10 5 0.12
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:3546608 original size:36 final size:36
Alignment explanation
Indices: 3546559--3546629 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
3546549 TTATTTTGTT
3546559 TTTCTTTTCTTTTCTTTGCTT-TTTTCTTTTTCTTCC
1 TTTCTTTTCTTTTCTTTGCTTCTTTTC-TTTTCTTCC
*
3546595 TTTCTTTGT-TTTTCTTTTCTTCTTTTCTTTTCTTC
1 TTTCTTT-TCTTTTCTTTGCTTCTTTTCTTTTCTTC
3546630 TTTGATCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 26 0.81
37 6 0.19
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (36 bp):
TTTCTTTTCTTTTCTTTGCTTCTTTTCTTTTCTTCC
Found at i:3546626 original size:18 final size:17
Alignment explanation
Indices: 3546497--3546632 Score: 77
Period size: 18 Copynumber: 7.8 Consensus size: 17
3546487 TCTTGTCTTA
3546497 TTTTTTTCTTCTCTTTGCTT
1 TTTTTTTCTTCT-TTT-C-T
* *
3546517 TTTTGTTTTTTGTTTTCT
1 TTTT-TTTCTTCTTTTCT
* * *
3546535 TTTTTCTTTTTGTTTTAT
1 TTTTT-TTCTTCTTTTCT
*
3546553 TTTGTTT-TTCTTTTCT
1 TTTTTTTCTTCTTTTCT
*
3546569 TTTCTTTGCTT-TTTTC-
1 TTT-TTTTCTTCTTTTCT
*
3546585 --TTTTTCTTCCTTTCT
1 TTTTTTTCTTCTTTTCT
3546600 TTGTTTTTCTT-TTCTTCT
1 TT-TTTTTCTTCTT-TTCT
3546618 TTTCTTTTCTTCTTT
1 TTT-TTTTCTTCTTT
3546633 GATCTTTGTA
Statistics
Matches: 93, Mismatches: 11, Indels: 26
0.72 0.08 0.20
Matches are distributed among these distances:
13 6 0.06
14 5 0.05
16 10 0.11
17 12 0.13
18 44 0.47
19 3 0.03
20 7 0.08
21 6 0.06
ACGTcount: A:0.01, C:0.15, G:0.05, T:0.79
Consensus pattern (17 bp):
TTTTTTTCTTCTTTTCT
Found at i:3550086 original size:11 final size:12
Alignment explanation
Indices: 3550074--3550119 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
3550064 ATATGATGAT
3550074 AATAAAATAATAA
1 AATAAAATAAT-A
3550087 AATAAAATAA-A
1 AATAAAATAATA
* *
3550098 AATAAAATCATG
1 AATAAAATAATA
3550110 AA-AAAATAAT
1 AATAAAATAAT
3550120 CTTGTTTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 17 0.59
12 2 0.07
13 10 0.34
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (12 bp):
AATAAAATAATA
Found at i:3551037 original size:12 final size:12
Alignment explanation
Indices: 3551020--3551049 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
3551010 ATTCCCTCTC
3551020 TCTCCACCCCTT
1 TCTCCACCCCTT
3551032 TCTCCACCCCTT
1 TCTCCACCCCTT
3551044 TCTCCA
1 TCTCCA
3551050 TTGTGGAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.57, G:0.00, T:0.33
Consensus pattern (12 bp):
TCTCCACCCCTT
Found at i:3557258 original size:82 final size:83
Alignment explanation
Indices: 3557080--3557368 Score: 343
Period size: 82 Copynumber: 3.5 Consensus size: 83
3557070 CAAAATGGTA
* ** * * **
3557080 ACTTTAGCGGCATTTTTATACAAACACCGCAATAGGGTTAATCTATAGTGATATTTTTTCAACAA
1 ACTTTAGCGGCGTTTTTATACAAATGCTGCAATAGGGTTCATCTATAGTGGCATTTTTTCAACAA
* *
3557145 ACGCCACAAC-AGAGTAAT
66 ACGCCGC-ACTAGAGTAGT
** *
3557163 ACTTTAGTAGCGTTTTCATACAAATGCTGCAAT-GAGGTTCATCTATAGTGGCA-TTTTTCAACA
1 ACTTTAGCGGCGTTTTTATACAAATGCTGCAATAG-GGTTCATCTATAGTGGCATTTTTTCAACA
*
3557226 AACGCCGCACTAAAGTAGT
65 AACGCCGCACTAGAGTAGT
* *
3557245 ACTTTAGTGGCGTTTTTATACAAATGCTGTAATAGGGTTCATCTATAGTGGCATTGTTTTCAACA
1 ACTTTAGCGGCGTTTTTATACAAATGCTGCAATAGGGTTCATCTATAGTGGCATT-TTTTCAACA
*
3557310 AACGCCGCAATAGAGTAGT
65 AACGCCGCACTAGAGTAGT
* * * *
3557329 AATTTAGCGG-TTTTTTATACAAATGCCGAAATAGGGTTCA
1 ACTTTAGCGGCGTTTTTATACAAATGCTGCAATAGGGTTCA
3557369 ATGAAACAAT
Statistics
Matches: 178, Mismatches: 23, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
81 2 0.01
82 72 0.40
83 70 0.39
84 34 0.19
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (83 bp):
ACTTTAGCGGCGTTTTTATACAAATGCTGCAATAGGGTTCATCTATAGTGGCATTTTTTCAACAA
ACGCCGCACTAGAGTAGT
Found at i:3557294 original size:41 final size:41
Alignment explanation
Indices: 3557167--3557296 Score: 106
Period size: 41 Copynumber: 3.2 Consensus size: 41
3557157 AGTAATACTT
* *
3557167 TAGTAGCGTTTTCATACAAATGCTGCAAT-GAGGTTCATCTA
1 TAGTGGCGTTTTTATACAAATGCTGCAATAG-GGTTCATCTA
* * * * ** *
3557208 TAGTGGCATTTTTCA-ACAAACGCCGCACTAAAG-T-AGTACTT
1 TAGTGGCGTTTTT-ATACAAATGCTGCAATAGGGTTCA-T-CTA
*
3557249 TAGTGGCGTTTTTATACAAATGCTGTAATAGGGTTCATCTA
1 TAGTGGCGTTTTTATACAAATGCTGCAATAGGGTTCATCTA
3557290 TAGTGGC
1 TAGTGGC
3557297 ATTGTTTTCA
Statistics
Matches: 65, Mismatches: 17, Indels: 14
0.68 0.18 0.15
Matches are distributed among these distances:
39 1 0.02
40 3 0.05
41 57 0.88
42 3 0.05
43 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (41 bp):
TAGTGGCGTTTTTATACAAATGCTGCAATAGGGTTCATCTA
Found at i:3557884 original size:41 final size:41
Alignment explanation
Indices: 3557839--3557964 Score: 162
Period size: 41 Copynumber: 3.1 Consensus size: 41
3557829 TCTGGATAGA
* * *
3557839 AAATACCACTAAAGACTTATACTTTAGTGGCGTTTTTATAC
1 AAATACCGCTAAAGACTCATACTTTAGTGGCATTTTTATAC
* * * * *
3557880 AAATATCGCTATAGACTCGTACTTTAGAGGCATTTTTATAA
1 AAATACCGCTAAAGACTCATACTTTAGTGGCATTTTTATAC
**
3557921 AAACGCCGCTAAAGACTCATACTTTAGTGGCATTTTTATAC
1 AAATACCGCTAAAGACTCATACTTTAGTGGCATTTTTATAC
3557962 AAA
1 AAA
3557965 CGCTGTAATA
Statistics
Matches: 70, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 70 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.34
Consensus pattern (41 bp):
AAATACCGCTAAAGACTCATACTTTAGTGGCATTTTTATAC
Found at i:3583416 original size:37 final size:37
Alignment explanation
Indices: 3583363--3583467 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
3583353 CCTTTTCGTC
3583363 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
3583400 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** * *
3583437 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
3583468 CCACAAGCAT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:3583505 original size:13 final size:13
Alignment explanation
Indices: 3583489--3583522 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
3583479 ATAAATAGTC
3583489 ATTGTAACTCACT
1 ATTGTAACTCACT
3583502 ATTGTAACTCACT
1 ATTGTAACTCACT
3583515 ATTGTAAC
1 ATTGTAAC
3583523 ACATTCGGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.38
Consensus pattern (13 bp):
ATTGTAACTCACT
Found at i:3584091 original size:24 final size:22
Alignment explanation
Indices: 3584064--3584117 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 22
3584054 GTTATATATA
*
3584064 TATATTTACTTATTTATTTTATTT
1 TATATTTAC-TATTT-TTTTAGTT
3584088 TATATGATTACTATTTTTTTAGTT
1 TATAT--TTACTATTTTTTTAGTT
*
3584112 AATATT
1 TATATT
3584118 ATAAGTATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
22 1 0.04
24 16 0.62
25 5 0.19
26 4 0.15
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.65
Consensus pattern (22 bp):
TATATTTACTATTTTTTTAGTT
Found at i:3584175 original size:18 final size:19
Alignment explanation
Indices: 3584140--3584179 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
3584130 ATTTTTCATT
*
3584140 TATTTATTATTATTATTAC
1 TATTTAGTATTATTATTAC
3584159 TATTTAGTATT-TTATTAC
1 TATTTAGTATTATTATTAC
3584177 TAT
1 TAT
3584180 ACATACATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (19 bp):
TATTTAGTATTATTATTAC
Found at i:3584202 original size:22 final size:22
Alignment explanation
Indices: 3584177--3584220 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3584167 ATTTTATTAC
3584177 TATACATACATTTT-TATATTTT
1 TATACATACATTTTAT-TATTTT
* *
3584199 TATATATATATTTTATTATTTT
1 TATACATACATTTTATTATTTT
3584221 ATTTATACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (22 bp):
TATACATACATTTTATTATTTT
Found at i:3584232 original size:22 final size:21
Alignment explanation
Indices: 3584146--3584255 Score: 68
Period size: 21 Copynumber: 5.1 Consensus size: 21
3584136 CATTTATTTA
*
3584146 TTATTATTATTACTATTTAGTATT
1 TTATTATT-TTA-TATATA-TATT
* * * *
3584170 TTATTACTATACATACAT-TT
1 TTATTATTTTATATATATATT
3584190 TTA-TATTTTTATATATATATT
1 TTATTA-TTTTATATATATATT
*
3584211 TTATTATTTTATTTATACTA-T
1 TTATTATTTTATATATA-TATT
3584232 TTATTTATTTTCAT-TATAT-TT
1 TTA-TTATTTT-ATATATATATT
3584253 TTA
1 TTA
3584256 GTTTCTTTTC
Statistics
Matches: 69, Mismatches: 10, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
19 2 0.03
20 13 0.19
21 25 0.36
22 18 0.26
23 4 0.06
24 7 0.10
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.64
Consensus pattern (21 bp):
TTATTATTTTATATATATATT
Found at i:3584368 original size:20 final size:19
Alignment explanation
Indices: 3584341--3584397 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
3584331 TTTTATCTTC
3584341 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATTCA
* *
3584360 ATTTCATTTTTTTTTCATCCA
1 ATTT-ATTTTATTTT-ATTCA
3584381 A-TTATTTTATGTTTATT
1 ATTTATTTTAT-TTTATT
3584398 ATTATTGGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 12 0.39
20 14 0.45
21 5 0.16
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.67
Consensus pattern (19 bp):
ATTTATTTTATTTTATTCA
Found at i:3586558 original size:18 final size:17
Alignment explanation
Indices: 3586531--3586564 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3586521 TCAATACTCC
3586531 TGGATGAGTATCGATAT
1 TGGATGAGTATCGATAT
*
3586548 TGGACTGAGTATGGATA
1 TGGA-TGAGTATCGATA
3586565 CCCTTTCTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.29, C:0.06, G:0.32, T:0.32
Consensus pattern (17 bp):
TGGATGAGTATCGATAT
Found at i:3590669 original size:20 final size:20
Alignment explanation
Indices: 3590644--3590734 Score: 72
Period size: 20 Copynumber: 5.0 Consensus size: 20
3590634 TAAATTAAAT
*
3590644 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
*
3590664 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTA
* *
3590684 ATT--CT---ATTAG--TT-
1 ATTAGATAGAATCAGTTTTA
* *
3590696 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCAGTTTTA
3590716 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
3590735 TTATTCTATT
Statistics
Matches: 54, Mismatches: 9, Indels: 16
0.68 0.11 0.20
Matches are distributed among these distances:
12 3 0.06
13 2 0.04
14 1 0.02
15 4 0.07
17 3 0.06
18 1 0.02
19 2 0.04
20 38 0.70
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:3590759 original size:53 final size:52
Alignment explanation
Indices: 3590643--3590791 Score: 273
Period size: 53 Copynumber: 2.9 Consensus size: 52
3590633 CTAAATTAAA
*
3590643 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
3590695 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAG-TTTTTATTCTATTAGT
3590748 TATTAGATAGGATCATTTTTAATTAGATAGAATCA-TTTTTATTC
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTC
3590792 AGTTGCTAAT
Statistics
Matches: 95, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
51 9 0.09
52 35 0.37
53 51 0.54
ACGTcount: A:0.33, C:0.06, G:0.13, T:0.48
Consensus pattern (52 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
Found at i:3590774 original size:20 final size:20
Alignment explanation
Indices: 3590749--3590788 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3590739 TCTATTAGTT
*
3590749 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
3590769 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
3590789 TTCAGTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:3593180 original size:20 final size:20
Alignment explanation
Indices: 3593155--3593193 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3593145 TAAATTAAAT
*
3593155 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
3593175 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
3593194 TTATTCTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:3593233 original size:20 final size:20
Alignment explanation
Indices: 3593208--3593247 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3593198 TCTATTAGTT
*
3593208 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
3593228 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
3593248 TTCTGTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:3597846 original size:20 final size:20
Alignment explanation
Indices: 3597813--3597903 Score: 63
Period size: 20 Copynumber: 5.0 Consensus size: 20
3597803 TAAATTAAAT
*
3597813 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
* *
3597833 ATTAGTTAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTA
* *
3597853 ATT--CT---ATTAG--TT-
1 ATTAGATAGAATCAGTTTTA
* *
3597865 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCAGTTTTA
3597885 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
3597904 TTATTCTATT
Statistics
Matches: 53, Mismatches: 10, Indels: 16
0.67 0.13 0.20
Matches are distributed among these distances:
12 3 0.06
13 2 0.04
14 1 0.02
15 4 0.08
17 3 0.06
18 1 0.02
19 2 0.04
20 37 0.70
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.46
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:3597931 original size:53 final size:52
Alignment explanation
Indices: 3597812--3597961 Score: 257
Period size: 53 Copynumber: 2.9 Consensus size: 52
3597802 CTAAATTAAA
* *
3597812 TATTAGATAGGATCAGTTTTAATTAGTTAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
3597864 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAG-TTTTTATTCTATTAGT
*
3597917 TATTAGATATGATCATTTTTAATTAGATAGAATCA-TTTTTATTCT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCT
3597962 GTTGCTAATT
Statistics
Matches: 94, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
51 10 0.11
52 34 0.36
53 50 0.53
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.49
Consensus pattern (52 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
Found at i:3597943 original size:20 final size:20
Alignment explanation
Indices: 3597918--3597957 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3597908 TCTATTAGTT
3597918 ATTAGATATG-ATCATTTTTA
1 ATTAGATA-GAATCATTTTTA
3597938 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
3597958 TTCTGTTGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:3605097 original size:31 final size:31
Alignment explanation
Indices: 3605054--3605173 Score: 159
Period size: 31 Copynumber: 3.9 Consensus size: 31
3605044 AGGGTCTATA
*
3605054 GGCCTACCCAAGAAAGTTCTCAGGGCCACGG
1 GGCCTACCCAAGAAAGATCTCAGGGCCACGG
* * ***
3605085 GGCCTACGCAAGAAAGATATCAGGGCCGTAG
1 GGCCTACCCAAGAAAGATCTCAGGGCCACGG
* *
3605116 GGCCTACCCAAGAATGATCTCAGGGCTACGG
1 GGCCTACCCAAGAAAGATCTCAGGGCCACGG
*
3605147 GGCCTACCCAAGAAAAATCTCAGGGCC
1 GGCCTACCCAAGAAAGATCTCAGGGCC
3605174 GCAGAATCTA
Statistics
Matches: 73, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 73 1.00
ACGTcount: A:0.29, C:0.29, G:0.28, T:0.13
Consensus pattern (31 bp):
GGCCTACCCAAGAAAGATCTCAGGGCCACGG
Found at i:3605151 original size:62 final size:62
Alignment explanation
Indices: 3605054--3605200 Score: 195
Period size: 62 Copynumber: 2.4 Consensus size: 62
3605044 AGGGTCTATA
* * * * *
3605054 GGCCTACCCAAGAAAGTTCTCAGGGCCACGGGGCCTACGCAAGAAAGATATCAGGGCCGTAG
1 GGCCTACCCAAGAATGATCTCAGGGCCACGGGGCCTACCCAAGAAAAATATCAGGGCCGCAG
* *
3605116 GGCCTACCCAAGAATGATCTCAGGGCTACGGGGCCTACCCAAGAAAAATCTCAGGGCCGCAG
1 GGCCTACCCAAGAATGATCTCAGGGCCACGGGGCCTACCCAAGAAAAATATCAGGGCCGCAG
*** *
3605178 AATCTACCCAATAATGATCTCAG
1 GGCCTACCCAAGAATGATCTCAG
3605201 CCTGCTGAGC
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
62 74 1.00
ACGTcount: A:0.31, C:0.29, G:0.26, T:0.15
Consensus pattern (62 bp):
GGCCTACCCAAGAATGATCTCAGGGCCACGGGGCCTACCCAAGAAAAATATCAGGGCCGCAG
Found at i:3606445 original size:25 final size:27
Alignment explanation
Indices: 3606416--3606466 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
3606406 GATATTCTTG
* *
3606416 GGTCA-TTTCCAT-TCCAGTGTATTTT
1 GGTCATTTTACATATCCAGGGTATTTT
3606441 GGTCATTTTACATATCCAGGGTATTT
1 GGTCATTTTACATATCCAGGGTATTT
3606467 CAATTTCCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 5 0.23
26 6 0.27
27 11 0.50
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.45
Consensus pattern (27 bp):
GGTCATTTTACATATCCAGGGTATTTT
Found at i:3610345 original size:30 final size:30
Alignment explanation
Indices: 3610311--3610383 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
3610301 TTGATGTTTC
* * *
3610311 AAAATCGATCATTGATGTTATCGTTTGTTA
1 AAAATCGATCACTAATGTTATCGTTTATTA
*
3610341 AAAATTGATCACTAATGTTATCGTTTATTA
1 AAAATCGATCACTAATGTTATCGTTTATTA
* *
3610371 CAAATCGGTCACT
1 AAAATCGATCACT
3610384 CCACGTTAAC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (30 bp):
AAAATCGATCACTAATGTTATCGTTTATTA
Found at i:3612204 original size:13 final size:12
Alignment explanation
Indices: 3612182--3612212 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
3612172 TTAAATATTG
3612182 TTAAATAGATAA
1 TTAAATAGATAA
3612194 TTAAGATAGATAA
1 TTAA-ATAGATAA
3612207 TTAAAT
1 TTAAAT
3612213 TAATAAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (12 bp):
TTAAATAGATAA
Found at i:3615405 original size:41 final size:42
Alignment explanation
Indices: 3615351--3615539 Score: 151
Period size: 41 Copynumber: 4.6 Consensus size: 42
3615341 ATCTTATGAG
* *
3615351 TCTATAGCGGCGTTTGTATAAAAATGCCACTAAAGTACT-AC
1 TCTATTGCGGCGTTTGTATAAAAATGCCACTAAAGTACTGAA
* * *
3615392 TCTGTTGCGGCGTTTGTTTAAAAAATGCCACTATAG-A-TGAA
1 TCTATTGCGGCGTTTGTAT-AAAAATGCCACTAAAGTACTGAA
* ** *
3615433 TTTATTGCGGCGTTTGTATAAAAACACCGCTAAAGTACTTG--
1 TCTATTGCGGCGTTTGTATAAAAATGCCACTAAAGTAC-TGAA
* * *
3615474 TCACATTACGGCGTTTGT-TGAAAAAATGCCACTATAG-A-TGAA
1 TC-TATTGCGGCGTTTGTAT--AAAAATGCCACTAAAGTACTGAA
* *
3615516 CCTATTGCGGCGTTTATATAAAAA
1 TCTATTGCGGCGTTTGTATAAAAA
3615540 CATCGCTAAA
Statistics
Matches: 114, Mismatches: 23, Indels: 23
0.71 0.14 0.14
Matches are distributed among these distances:
40 20 0.18
41 49 0.43
42 31 0.27
43 14 0.12
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (42 bp):
TCTATTGCGGCGTTTGTATAAAAATGCCACTAAAGTACTGAA
Found at i:3615515 original size:83 final size:82
Alignment explanation
Indices: 3615352--3615549 Score: 261
Period size: 83 Copynumber: 2.4 Consensus size: 82
3615342 TCTTATGAGT
* ** * ** * *
3615352 CTATAGCGGCGTTTGTATAAAAATGCCACTAAAGTACTACTCTGTTGCGGCGTTTGTTTAAAAAA
1 CTATTGCGGCGTTTGTATAAAAACACCGCTAAAGTACTACTCCATTACGGCGTTTGTTGAAAAAA
*
3615417 TGCCACTATAGATGAAT
66 TGCCACTATAGATGAAC
* **
3615434 TTATTGCGGCGTTTGTATAAAAACACCGCTAAAGTACTTGTCACATTACGGCGTTTGTTGAAAAA
1 CTATTGCGGCGTTTGTATAAAAACACCGCTAAAGTACTACTC-CATTACGGCGTTTGTTGAAAAA
3615499 ATGCCACTATAGATGAAC
65 ATGCCACTATAGATGAAC
* *
3615517 CTATTGCGGCGTTTATATAAAAACATCGCTAAA
1 CTATTGCGGCGTTTGTATAAAAACACCGCTAAA
3615550 CTTACCATTT
Statistics
Matches: 100, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
82 35 0.35
83 65 0.65
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Consensus pattern (82 bp):
CTATTGCGGCGTTTGTATAAAAACACCGCTAAAGTACTACTCCATTACGGCGTTTGTTGAAAAAA
TGCCACTATAGATGAAC
Found at i:3621712 original size:14 final size:15
Alignment explanation
Indices: 3621677--3621718 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3621667 TCAACATGTT
* *
3621677 TGAGTCAACTCGGTC
1 TGAGTTAACTCGTTC
3621692 TGAGTTAACTCGTTC
1 TGAGTTAACTCGTTC
3621707 -GAGTTAAC-CGTT
1 TGAGTTAACTCGTT
3621719 GACTTTGACC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.33
Consensus pattern (15 bp):
TGAGTTAACTCGTTC
Found at i:3626328 original size:29 final size:30
Alignment explanation
Indices: 3626295--3626361 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
3626285 TCCAGTCACC
*
3626295 GAGTCAACAT-GTCCAAGTCAACTCGGTCT
1 GAGTCAACATGGTCCAAGTCAACTAGGTCT
*
3626324 GAGTCAACATGGTCTAAGTCAACTAGGTCT
1 GAGTCAACATGGTCCAAGTCAACTAGGTCT
3626354 GAGTCAAC
1 GAGTCAAC
3626362 TCGTCCGAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 10 0.29
30 25 0.71
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (30 bp):
GAGTCAACATGGTCCAAGTCAACTAGGTCT
Found at i:3626330 original size:15 final size:15
Alignment explanation
Indices: 3626310--3626364 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
3626300 AACATGTCCA
3626310 AGTCAACTCGGTCTG
1 AGTCAACTCGGTCTG
*
3626325 AGTCAACAT-GGTCTA
1 AGTCAAC-TCGGTCTG
*
3626340 AGTCAACTAGGTCTG
1 AGTCAACTCGGTCTG
3626355 AGTCAACTCG
1 AGTCAACTCG
3626365 TCCGAGTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
14 1 0.03
15 33 0.94
16 1 0.03
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (15 bp):
AGTCAACTCGGTCTG
Found at i:3628175 original size:20 final size:20
Alignment explanation
Indices: 3628150--3628192 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
3628140 TAGTATTGGA
3628150 TCCCTTCAATTGGACTTTGT
1 TCCCTTCAATTGGACTTTGT
3628170 TCCCTTCAATTGGACTTTGT
1 TCCCTTCAATTGGACTTTGT
3628190 TCC
1 TCC
3628193 TAGAATTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.28, G:0.14, T:0.44
Consensus pattern (20 bp):
TCCCTTCAATTGGACTTTGT
Found at i:3633882 original size:17 final size:18
Alignment explanation
Indices: 3633843--3633889 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
3633833 TGTTTCTGAG
3633843 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTGAA
*
3633861 GGAATTGGAATCTGT-CA
1 GGAATTGGAATCTGTGAA
3633878 GGAATTGGAATC
1 GGAATTGGAATC
3633890 CAATTCCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.32, C:0.09, G:0.32, T:0.28
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Found at i:3634137 original size:22 final size:22
Alignment explanation
Indices: 3634109--3634156 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
3634099 GATTGATTAT
3634109 TCATTTCAATAAATTATAAAAA
1 TCATTTCAATAAATTATAAAAA
*
3634131 TCATTTCAATAAATTATAAATA
1 TCATTTCAATAAATTATAAAAA
3634153 TCAT
1 TCAT
3634157 GCTAATAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (22 bp):
TCATTTCAATAAATTATAAAAA
Found at i:3634163 original size:22 final size:22
Alignment explanation
Indices: 3634109--3634165 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
3634099 GATTGATTAT
*
3634109 TCATTTCAATAAATTATAAAAA
1 TCATCTCAATAAATTATAAAAA
* *
3634131 TCATTTCAATAAATTATAAATA
1 TCATCTCAATAAATTATAAAAA
3634153 TCATGCT-AATAAA
1 TCAT-CTCAATAAA
3634166 CATCATAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 31 0.97
23 1 0.03
ACGTcount: A:0.51, C:0.11, G:0.02, T:0.37
Consensus pattern (22 bp):
TCATCTCAATAAATTATAAAAA
Found at i:3634775 original size:256 final size:251
Alignment explanation
Indices: 3634270--3634877 Score: 888
Period size: 256 Copynumber: 2.4 Consensus size: 251
3634260 CTCCATCCGA
* * * *
3634270 GACCCGACCCGACCAAAATAAAGTTTCATCTGACCCGACCCAAATATATGAATTAG-AA---ACC
1 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGAACCGAATATATGAATTAGAAACCGACC
* * * * *
3634331 CGACTCGAAATAATAAAAAAATTATTTTTATTCAATAAAAATAGTGATTTAATTGGAATATATAT
66 CGACCCGAAATAATAAAAAAA-TATTTTTATTCAATAAAAACAATGACTTAATTGAAATATATAT
*
3634396 AGGGGTATTATTGTAATTATTCCTAAATATATAAGCTAAAATTATATATTTTTTGGGTCGGGTCG
130 AGGGGTATTATTGTAATTATTCCTAAATATATAAGCTAAAATTATATATATTTT--GTCGGGTCG
3634461 GGTATTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCACACTTAAAAAAACC
193 GGTATTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCACACTTAAAAAAACC
*
3634520 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGAATCGAATATATGAATTAGAAATCCGAC
1 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGAACCGAATATATGAATTAGAAA-CCGAC
3634585 CCGACCCGAAATAAT-AAAAAATATTTTTATTCAATAAAAACAATGACTTAATTGAAAAAATTAT
65 CCGACCCGAAATAATAAAAAAATATTTTTATTCAATAAAAACAATGACTTAATTG---AAA-TAT
* *
3634649 ATATAGAGGGGTATTATTGTTATTATTCCTAAATATATAAGGTAAAATTATATATATTTT-TCGG
126 ATAT--AGGGGTATTATTGTAATTATTCCTAAATATATAAGCTAAAATTATATATATTTTGTCGG
* * *
3634713 GTTGGGTATTTTTCACCCTAAACCCGAACTCGACCTGACCTGAATATCACACTTAAAAAAACC
189 GTCGGGTATTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCACACTTAAAAAAACC
* * *
3634776 GATCCGGCCCGACCAAAATAAAGTTTCACCCGACCCG-ACCTGAATATATAAATTAGAAACCCGA
1 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGAACC-GAATATATGAATTAGAAA-CCGA
3634840 CCCGACCCGAAATAATAAAAAAATATTTTTATTCAATA
64 CCCGACCCGAAATAATAAAAAAATATTTTTATTCAATA
3634878 TATGAATAAG
Statistics
Matches: 324, Mismatches: 21, Indels: 19
0.89 0.06 0.05
Matches are distributed among these distances:
250 51 0.16
251 2 0.01
253 30 0.09
254 6 0.02
255 18 0.06
256 138 0.43
257 28 0.09
259 51 0.16
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (251 bp):
GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGAACCGAATATATGAATTAGAAACCGACC
CGACCCGAAATAATAAAAAAATATTTTTATTCAATAAAAACAATGACTTAATTGAAATATATATA
GGGGTATTATTGTAATTATTCCTAAATATATAAGCTAAAATTATATATATTTTGTCGGGTCGGGT
ATTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCACACTTAAAAAAACC
Found at i:3644410 original size:3 final size:3
Alignment explanation
Indices: 3644402--3644433 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3644392 CTTTATTTAT
3644402 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3644434 TAACTTTCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3651810 original size:30 final size:32
Alignment explanation
Indices: 3651771--3651849 Score: 99
Period size: 33 Copynumber: 2.5 Consensus size: 32
3651761 TTTAAGACAA
*
3651771 TTTCTCTTAAAACAAA-C-ATCTTTGGGATTG
1 TTTCTCTTAAAACAAACCTATCTTTGAGATTG
* *
3651801 TTTCCCTTAAAACAAAACCTATCTTTGAGTTTG
1 TTTCTCTTAAAAC-AAACCTATCTTTGAGATTG
*
3651834 TTTCTCTTGAAACAAA
1 TTTCTCTTAAAACAAA
3651850 AGTCTGTGAG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 12 0.29
31 3 0.07
32 4 0.10
33 22 0.54
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (32 bp):
TTTCTCTTAAAACAAACCTATCTTTGAGATTG
Found at i:3651835 original size:33 final size:31
Alignment explanation
Indices: 3651771--3651896 Score: 109
Period size: 29 Copynumber: 4.2 Consensus size: 31
3651761 TTTAAGACAA
*
3651771 TTTCTCTTAAAAC-AAACATCTTTGGGATTG
1 TTTCTCTTAAAACAAAACATCTTTGAGATTG
* *
3651801 TTTCCCTTAAAACAAAACCTATCTTTGAGTTTG
1 TTTCTCTTAAAACAAAA-C-ATCTTTGAGATTG
* * *
3651834 TTTCTCTTGAAACAAAA-GTCTGTGAG-TTG
1 TTTCTCTTAAAACAAAACATCTTTGAGATTG
* * * *
3651863 TTTCTTTTGAAATAAAA-ATCATTGAG-TTG
1 TTTCTCTTAAAACAAAACATCTTTGAGATTG
3651892 TTTCT
1 TTTCT
3651897 TTTGAAAATA
Statistics
Matches: 81, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
29 32 0.40
30 19 0.23
31 3 0.04
32 1 0.01
33 26 0.32
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.42
Consensus pattern (31 bp):
TTTCTCTTAAAACAAAACATCTTTGAGATTG
Found at i:3651984 original size:88 final size:89
Alignment explanation
Indices: 3651867--3652096 Score: 223
Period size: 92 Copynumber: 2.5 Consensus size: 89
3651857 GAGTTGTTTC
* * * * *
3651867 TTTTGAAATAAAAATCATTGAGTTGTTTCTTTTGAAAATAT-TCTGAGTCTGTTTCTTTTGAACC
1 TTTTG-AA-AAAAATCTTTGAG-TATTTCTTTTGAAAAAATCTCTGAGTCTATTTCTTTTGAAAC
** *
3651931 AAAGTTTTGTTTCTCTTAAGACA-ATT
63 AAAACTTTGTCTCTCTTAAGACAGATT
*
3651957 TTTTGAAAAAAATCTTTGAGTCATTTCTTTTGAAACCAAAATCTTTGAGTCTATTTCTTTTGAAA
1 TTTTGAAAAAAATCTTTGAGT-ATTTCTTTTG-AA--AAAATCTCTGAGTCTATTTCTTTTGAAA
* *
3652022 CAAAACTTTGTCTCTCTTGAGACAGTTT
62 CAAAACTTTGTCTCTCTTAAGACAGATT
* * *
3652050 TTCTTGAGAAAAATATTTGAGTATGTTCCTTTTG-AAAAATCTTTGAG
1 TT-TTGAAAAAAATCTTTGAGTAT-TT-CTTTTGAAAAAATCTCTGAG
3652097 ATTGTGTCTC
Statistics
Matches: 118, Mismatches: 13, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
87 1 0.01
88 21 0.18
89 4 0.03
90 5 0.04
91 16 0.14
92 39 0.33
93 7 0.06
94 19 0.16
95 6 0.05
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.44
Consensus pattern (89 bp):
TTTTGAAAAAAATCTTTGAGTATTTCTTTTGAAAAAATCTCTGAGTCTATTTCTTTTGAAACAAA
ACTTTGTCTCTCTTAAGACAGATT
Found at i:3651997 original size:29 final size:29
Alignment explanation
Indices: 3651957--3652031 Score: 120
Period size: 29 Copynumber: 2.7 Consensus size: 29
3651947 TAAGACAATT
3651957 TTTTGAAA-AAAATCTTTGAGTC-ATTTC
1 TTTTGAAACAAAATCTTTGAGTCTATTTC
3651984 TTTTGAAACCAAAATCTTTGAGTCTATTTC
1 TTTTGAAA-CAAAATCTTTGAGTCTATTTC
3652014 TTTTGAAACAAAA-CTTTG
1 TTTTGAAACAAAATCTTTG
3652032 TCTCTCTTGA
Statistics
Matches: 45, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
27 8 0.18
28 5 0.11
29 19 0.42
30 13 0.29
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (29 bp):
TTTTGAAACAAAATCTTTGAGTCTATTTC
Found at i:3652038 original size:92 final size:96
Alignment explanation
Indices: 3651901--3652086 Score: 238
Period size: 92 Copynumber: 2.0 Consensus size: 96
3651891 GTTTCTTTTG
* * ** *
3651901 AAAATATTCTGAGTCTGTTTCTTTTGAACCAAAGTTTTGTTTCTCTTAAGACA-ATTTT-TTGAA
1 AAAATATTCTGAGTCTATTTCTTTTGAAACAAAACTTTGTCTCTCTTAAGACAGATTTTCTTGAA
*
3651964 AAAAATCTTTGAGTCAT-TT-CTTTTGAAACC
66 AAAAATATTTGAGT-ATGTTCCTTTTGAAACC
* * * *
3651994 AAAATCTT-TGAGTCTATTTCTTTTGAAACAAAACTTTGTCTCTCTTGAGACAGTTTTTCTTGAG
1 AAAATATTCTGAGTCTATTTCTTTTGAAACAAAACTTTGTCTCTCTTAAGACAGATTTTCTTGAA
3652058 AAAAATATTTGAGTATGTTCCTTTTGAAA
66 AAAAATATTTGAGTATGTTCCTTTTGAAA
3652087 AATCTTTGAG
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
92 38 0.48
93 13 0.16
94 19 0.24
95 9 0.11
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (96 bp):
AAAATATTCTGAGTCTATTTCTTTTGAAACAAAACTTTGTCTCTCTTAAGACAGATTTTCTTGAA
AAAAATATTTGAGTATGTTCCTTTTGAAACC
Found at i:3652526 original size:91 final size:92
Alignment explanation
Indices: 3652410--3652610 Score: 257
Period size: 92 Copynumber: 2.2 Consensus size: 92
3652400 TAACCATACG
* * *
3652410 TCCTCATCACGTAGGAAC-CATGTTATCA-CCTTAAC-TAAAGATGGCC-ATAACTCTTCATCAG
1 TCCTCATCACATAGGAACGGA-GTTATCACCCTT--CTTAAAGATGGCCAATAACTCTTCATCAC
* *
3652471 GTATGACCCGTGTCATCCCCCGACTAGATC
63 GTATGACCAGTGTCATCCCCCGACCAGATC
*
3652501 TCCTCATCGCATAGGAACGGAGTTATCACCCTTCTTAAAGATGGCCAATAACTCTTCATCACGTA
1 TCCTCATCACATAGGAACGGAGTTATCACCCTTCTTAAAGATGGCCAATAACTCTTCATCACGTA
* * *
3652566 TGAGCAGTGTCATCCCTCGACCAGATT
66 TGACCAGTGTCATCCCCCGACCAGATC
*
3652593 TCCTCATCACGTAGGAAC
1 TCCTCATCACATAGGAAC
3652611 CGTGTCACCC
Statistics
Matches: 95, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
90 1 0.01
91 34 0.36
92 60 0.63
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.26
Consensus pattern (92 bp):
TCCTCATCACATAGGAACGGAGTTATCACCCTTCTTAAAGATGGCCAATAACTCTTCATCACGTA
TGACCAGTGTCATCCCCCGACCAGATC
Found at i:3652812 original size:3 final size:3
Alignment explanation
Indices: 3652804--3652844 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
3652794 CCGGGTCTTT
3652804 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3652845 TAACTTACAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3656594 original size:32 final size:32
Alignment explanation
Indices: 3656558--3656619 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
3656548 ATTTATCAGT
*
3656558 ACTAA-TTAATTTATTTTCTTTTGTTTGTGTAC
1 ACTAACTT-ATTTATTTTCATTTGTTTGTGTAC
* *
3656590 ACTAACTTGTTTCTTTTCATTTGTTTGTGT
1 ACTAACTTATTTATTTTCATTTGTTTGTGT
3656620 CATTTTGTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 24 0.92
33 2 0.08
ACGTcount: A:0.18, C:0.11, G:0.11, T:0.60
Consensus pattern (32 bp):
ACTAACTTATTTATTTTCATTTGTTTGTGTAC
Found at i:3657160 original size:21 final size:21
Alignment explanation
Indices: 3657134--3657176 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
3657124 AAGTTTCATA
3657134 TGCATTTGCATCATTGCATTC
1 TGCATTTGCATCATTGCATTC
3657155 TGCATTTGCATCATTGCATTC
1 TGCATTTGCATCATTGCATTC
3657176 T
1 T
3657177 ACAAAACATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.23, G:0.14, T:0.44
Consensus pattern (21 bp):
TGCATTTGCATCATTGCATTC
Found at i:3660753 original size:35 final size:35
Alignment explanation
Indices: 3660673--3660813 Score: 162
Period size: 36 Copynumber: 3.9 Consensus size: 35
3660663 TGAGAATTTT
* *
3660673 AAAACAAATTTTTGTCTCGCTTGAGATAATTTTTCTC
1 AAAACAAA-TTTTGACTCGCTTGAGA-CATTTTTCTC
3660710 AAAACAAATTTTGACTCGCTTGAGACATTTTTCT-
1 AAAACAAATTTTGACTCGCTTGAGACATTTTTCTC
3660744 AAAAGCAAATTTT-ATCTCGCTTGAGACAATTTCTT-TC
1 AAAA-CAAATTTTGA-CTCGCTTGAGAC-ATTT-TTCTC
* * *
3660781 AAAACAAATTTCGTCTCACTTGAGACATTTTTC
1 AAAACAAATTTTGACTCGCTTGAGACATTTTTC
3660814 CTTTGAGACA
Statistics
Matches: 92, Mismatches: 5, Indels: 16
0.81 0.04 0.14
Matches are distributed among these distances:
34 7 0.08
35 32 0.35
36 39 0.42
37 14 0.15
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (35 bp):
AAAACAAATTTTGACTCGCTTGAGACATTTTTCTC
Done.