Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 139 of 161
Found at i:43272260 original size:726 final size:726
Alignment explanation
Indices: 43270868--43272274 Score: 2796
Period size: 726 Copynumber: 1.9 Consensus size: 726
43270858 CGGACGAACC
43270868 GAACATAATAGAAGCGAACCTATATCTTATGCTATAATTGAAGGTAACATCGATAACTAAATGAC
1 GAACATAATAGAAGCGAACCTATATCTTATGCTATAATTGAAGGTAACATCGATAACTAAATGAC
43270933 TGAAAGAAATTGATAGTGAATAGATTGTAATCAAGAAGTAAAATTTAGAAATACCAAAAGACGTA
66 TGAAAGAAATTGATAGTGAATAGATTGTAATCAAGAAGTAAAATTTAGAAATACCAAAAGACGTA
43270998 AGACGAAATTCTAACCAATCAAGAAACATGGTACTAAAAATAATGAGAGGCTTGTAGAAATCAAA
131 AGACGAAATTCTAACCAATCAAGAAACATGGTACTAAAAATAATGAGAGGCTTGTAGAAATCAAA
43271063 CTAAATAAAAACAAAGAATCACTAAATCAAAATTTTCTAAACTAAAAACAATATTCATAAACAAA
196 CTAAATAAAAACAAAGAATCACTAAATCAAAATTTTCTAAACTAAAAACAATATTCATAAACAAA
*
43271128 ATGGAACCAATTGATAAAAGACAAATGGGAGAAACATAATATTAAATAAAATATAACTAAATAAG
261 ATGAAACCAATTGATAAAAGACAAATGGGAGAAACATAATATTAAATAAAATATAACTAAATAAG
43271193 AAGCAAAACTGAAAAAAATACTAACTGCAAAGCAAAAAAACACCAATATATAATAAGAACAAGAG
326 AAGCAAAACTGAAAAAAATACTAACTGCAAAGCAAAAAAACACCAATATATAATAAGAACAAGAG
43271258 AAGAAATGAACTAGAATAAAAATAAATGAGAATTAATTAAGAATAATAATAAAAAACTAATAAAC
391 AAGAAATGAACTAGAATAAAAATAAATGAGAATTAATTAAGAATAATAATAAAAAACTAATAAAC
43271323 AAAACAAAGAAATAATAAAATAAAATAAAGACTAAAAGGAGCAAATAGGGGTTGACTGATGGTGG
456 AAAACAAAGAAATAATAAAATAAAATAAAGACTAAAAGGAGCAAATAGGGGTTGACTGATGGTGG
43271388 GATGACTGGAGCTCGGAGGGTCGCATGGTATGGTGCGGGCAACAGTGGAGCGTTTCTGATCGTGG
521 GATGACTGGAGCTCGGAGGGTCGCATGGTATGGTGCGGGCAACAGTGGAGCGTTTCTGATCGTGG
43271453 TCGGCGCGGGGGTGGTGAGGAGGAGATGAAAAGTGAAGGAGAAAAGAGGAAGAAGGAAAGGAAGG
586 TCGGCGCGGGGGTGGTGAGGAGGAGATGAAAAGTGAAGGAGAAAAGAGGAAGAAGGAAAGGAAGG
43271518 GTGTGGCTTGGTGAGGGAAGGACGGTGGAGCAAGGGAGAGGAGAGGAGGGGTTGTGGGATGGTGC
651 GTGTGGCTTGGTGAGGGAAGGACGGTGGAGCAAGGGAGAGGAGAGGAGGGGTTGTGGGATGGTGC
43271583 GACGGTGGCCA
716 GACGGTGGCCA
43271594 GAACATAATAGAAGCGAACCTATATCTTATGCTATAATTGAAGGTAACATCGATAACTAAATGAC
1 GAACATAATAGAAGCGAACCTATATCTTATGCTATAATTGAAGGTAACATCGATAACTAAATGAC
43271659 TGAAAGAAATTGATAGTGAATAGATTGTAATCAAGAAGTAAAATTTAGAAATACCAAAAGACGTA
66 TGAAAGAAATTGATAGTGAATAGATTGTAATCAAGAAGTAAAATTTAGAAATACCAAAAGACGTA
43271724 AGACGAAATTCTAACCAATCAAGAAACATGGTACTAAAAATAATGAGAGGCTTGTAGAAATCAAA
131 AGACGAAATTCTAACCAATCAAGAAACATGGTACTAAAAATAATGAGAGGCTTGTAGAAATCAAA
*
43271789 CTAAATAAAAACAAAGAATCACTAAATCAAATTTTTCTAAACTAAAAACAATATTCATAAACAAA
196 CTAAATAAAAACAAAGAATCACTAAATCAAAATTTTCTAAACTAAAAACAATATTCATAAACAAA
43271854 ATGAAACCAATTGATAAAAGACAAATGGGAGAAACATAATATTAAATAAAATATAACTAAATAAG
261 ATGAAACCAATTGATAAAAGACAAATGGGAGAAACATAATATTAAATAAAATATAACTAAATAAG
43271919 AAGCAAAACTGAAAAAAATACTAACTGCAAAGCAAAAAAACACCAATATATAATAAGAACAAGAG
326 AAGCAAAACTGAAAAAAATACTAACTGCAAAGCAAAAAAACACCAATATATAATAAGAACAAGAG
43271984 AAGAAATGAACTAGAATAAAAATAAATGAGAATTAATTAAGAATAATAATAAAAAACTAATAAAC
391 AAGAAATGAACTAGAATAAAAATAAATGAGAATTAATTAAGAATAATAATAAAAAACTAATAAAC
43272049 AAAACAAAGAAATAATAAAATAAAATAAAGACTAAAAGGAGCAAATAGGGGTTGACTGATGGTGG
456 AAAACAAAGAAATAATAAAATAAAATAAAGACTAAAAGGAGCAAATAGGGGTTGACTGATGGTGG
43272114 GATGACTGGAGCTCGGAGGGTCGCATGGTATGGTGCGGGCAACAGTGGAGCGTTTCTGATCGTGG
521 GATGACTGGAGCTCGGAGGGTCGCATGGTATGGTGCGGGCAACAGTGGAGCGTTTCTGATCGTGG
43272179 TCGGCGCGGGGGTGGTGAGGAGGAGATGAAAAGTGAAGGAGAAAAGAGGAAGAAGGAAAGGAAGG
586 TCGGCGCGGGGGTGGTGAGGAGGAGATGAAAAGTGAAGGAGAAAAGAGGAAGAAGGAAAGGAAGG
43272244 GTGTGGCTTGGTGAGGGAAGGACGGTGGAGC
651 GTGTGGCTTGGTGAGGGAAGGACGGTGGAGC
43272275 TAGCTCCTTC
Statistics
Matches: 679, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
726 679 1.00
ACGTcount: A:0.47, C:0.11, G:0.23, T:0.20
Consensus pattern (726 bp):
GAACATAATAGAAGCGAACCTATATCTTATGCTATAATTGAAGGTAACATCGATAACTAAATGAC
TGAAAGAAATTGATAGTGAATAGATTGTAATCAAGAAGTAAAATTTAGAAATACCAAAAGACGTA
AGACGAAATTCTAACCAATCAAGAAACATGGTACTAAAAATAATGAGAGGCTTGTAGAAATCAAA
CTAAATAAAAACAAAGAATCACTAAATCAAAATTTTCTAAACTAAAAACAATATTCATAAACAAA
ATGAAACCAATTGATAAAAGACAAATGGGAGAAACATAATATTAAATAAAATATAACTAAATAAG
AAGCAAAACTGAAAAAAATACTAACTGCAAAGCAAAAAAACACCAATATATAATAAGAACAAGAG
AAGAAATGAACTAGAATAAAAATAAATGAGAATTAATTAAGAATAATAATAAAAAACTAATAAAC
AAAACAAAGAAATAATAAAATAAAATAAAGACTAAAAGGAGCAAATAGGGGTTGACTGATGGTGG
GATGACTGGAGCTCGGAGGGTCGCATGGTATGGTGCGGGCAACAGTGGAGCGTTTCTGATCGTGG
TCGGCGCGGGGGTGGTGAGGAGGAGATGAAAAGTGAAGGAGAAAAGAGGAAGAAGGAAAGGAAGG
GTGTGGCTTGGTGAGGGAAGGACGGTGGAGCAAGGGAGAGGAGAGGAGGGGTTGTGGGATGGTGC
GACGGTGGCCA
Found at i:43278925 original size:6 final size:6
Alignment explanation
Indices: 43278914--43278940 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
43278904 TTACCATCTC
43278914 TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTT
43278941 TCCACAAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:43280196 original size:5 final size:5
Alignment explanation
Indices: 43280186--43280210 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
43280176 TGCATATGCA
43280186 TTGGG TTGGG TTGGG TTGGG TTGGG
1 TTGGG TTGGG TTGGG TTGGG TTGGG
43280211 ATTTTGTGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.60, T:0.40
Consensus pattern (5 bp):
TTGGG
Found at i:43287153 original size:13 final size:13
Alignment explanation
Indices: 43287137--43287162 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43287127 ACTTTACGCA
43287137 AACAAATGGTTTT
1 AACAAATGGTTTT
43287150 AACAAATGGTTTT
1 AACAAATGGTTTT
43287163 TGGAAACACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
AACAAATGGTTTT
Found at i:43292647 original size:91 final size:91
Alignment explanation
Indices: 43292498--43292746 Score: 315
Period size: 91 Copynumber: 2.8 Consensus size: 91
43292488 TTATCAATGG
* * * *
43292498 GAAAGCTCTTATGAGCAATCTACCGTGTTATTGGGGGAGAATATTTAGCCTACGGGCTTTGCACT
1 GAAAGCTCTTATGAGCAATCTAACATGTTATCGGGGGAGAATATTTAGCCTACAGGCTTTGCACT
*
43292563 ATGTACACTTGGCATGATATCAGCGA
66 ATGTACACTTAGCATGATATCAGCGA
*
43292589 GAAAGCTCTAATGAGCAATCTAACATGTTATCGGGGGAGAATATTTAGCCTACAGGCTTTGCACT
1 GAAAGCTCTTATGAGCAATCTAACATGTTATCGGGGGAGAATATTTAGCCTACAGGCTTTGCACT
* * * * * *
43292654 ATGTGCATTTAGCATTATATCGGTGG
66 ATGTACACTTAGCATGATATCAGCGA
* ** * *
43292680 GAAAGCTCTTATGAGCAATATGGCATGTTATC-GGGGAAAACATTTAGCCTACAGG-TTTAG-AC
1 GAAAGCTCTTATGAGCAATCTAACATGTTATCGGGGGAGAATATTTAGCCTACAGGCTTT-GCAC
43292742 TATGT
65 TATGT
43292747 GCATCTAGTG
Statistics
Matches: 139, Mismatches: 18, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
89 10 0.07
90 22 0.16
91 107 0.77
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (91 bp):
GAAAGCTCTTATGAGCAATCTAACATGTTATCGGGGGAGAATATTTAGCCTACAGGCTTTGCACT
ATGTACACTTAGCATGATATCAGCGA
Found at i:43292779 original size:89 final size:90
Alignment explanation
Indices: 43292495--43292787 Score: 290
Period size: 91 Copynumber: 3.2 Consensus size: 90
43292485 GTGTTATCAA
* * * * * * *
43292495 TGGGAAAGCTCTTATGAGCAATCTACCGTGTTATTGGGGGAGAATATTTAGCCTACGGGCTTTGC
1 TGGGAAAGCTCTTATGAGCAATATAACATGTTATCGGGGGAAAACATTTAGCCTACAGGCTTTGC
* * * *
43292560 ACTATGTACA-CTTGGCATGATATCAG
66 ACTATGTGCATC-TAG-ATTATATCGG
* * * * * *
43292586 CGAGAAAGCTCTAATGAGCAATCTAACATGTTATCGGGGGAGAATATTTAGCCTACAGGCTTTGC
1 TGGGAAAGCTCTTATGAGCAATATAACATGTTATCGGGGGAAAACATTTAGCCTACAGGCTTTGC
*
43292651 ACTATGTGCATTTAGCATTATATCGG
66 ACTATGTGCATCTAG-ATTATATCGG
**
43292677 TGGGAAAGCTCTTATGAGCAATATGGCATGTTATC-GGGGAAAACATTTAGCCTACAGG-TTTAG
1 TGGGAAAGCTCTTATGAGCAATATAACATGTTATCGGGGGAAAACATTTAGCCTACAGGCTTT-G
* *
43292740 -ACTATGTGCATCTAG-TGTGTCATTGG
65 CACTATGTGCATCTAGAT-TAT-ATCGG
*
43292766 TGGGAAAGCTCTTAAGAGCAAT
1 TGGGAAAGCTCTTATGAGCAAT
43292788 CTGTCATATT
Statistics
Matches: 174, Mismatches: 24, Indels: 10
0.84 0.12 0.05
Matches are distributed among these distances:
87 1 0.01
88 2 0.01
89 42 0.24
90 22 0.13
91 107 0.61
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (90 bp):
TGGGAAAGCTCTTATGAGCAATATAACATGTTATCGGGGGAAAACATTTAGCCTACAGGCTTTGC
ACTATGTGCATCTAGATTATATCGG
Found at i:43299765 original size:22 final size:22
Alignment explanation
Indices: 43299722--43299766 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
43299712 TCGTGGACCA
* *
43299722 AAATCGTTGTTTTAATAAAATC
1 AAATCGTTGTGTTAAAAAAATC
43299744 AAATCGTT-TGTTAAAAACAATC
1 AAATCGTTGTGTTAAAAA-AATC
43299766 A
1 A
43299767 CTTTTTGAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (22 bp):
AAATCGTTGTGTTAAAAAAATC
Found at i:43308640 original size:27 final size:27
Alignment explanation
Indices: 43308610--43308664 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
43308600 CCTTCACCTC
43308610 TTCACGTTATGACTTCTCCATGGCCTT
1 TTCACGTTATGACTTCTCCATGGCCTT
43308637 TTCACGTTATGACTTCTCCATGGCCTT
1 TTCACGTTATGACTTCTCCATGGCCTT
43308664 T
1 T
43308665 CTCCATGTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.42
Consensus pattern (27 bp):
TTCACGTTATGACTTCTCCATGGCCTT
Found at i:43311218 original size:45 final size:44
Alignment explanation
Indices: 43311169--43311297 Score: 131
Period size: 41 Copynumber: 3.0 Consensus size: 44
43311159 TCTTACTGAG
* *
43311169 GTTGCAGTAGAGTAGACTGAAGATAGCAGATCTTATCTCTCTAAA
1 GTTGCAGTAGAGCAGA-TGAAGATAGCAGATCTTATCTCCCTAAA
* * * *
43311214 GTTGCAGTAAAGCAGATCACG--ACCA-ATCTTATCTCCCTAAA
1 GTTGCAGTAGAGCAGATGAAGATAGCAGATCTTATCTCCCTAAA
* *
43311255 GTTGCAGTGGAGCAGATTGAAGATAGC-GAATCTTATTTCCCTA
1 GTTGCAGTAGAGCAGA-TGAAGATAGCAG-ATCTTATCTCCCTA
43311298 TAAATTATCG
Statistics
Matches: 67, Mismatches: 12, Indels: 10
0.75 0.13 0.11
Matches are distributed among these distances:
41 29 0.43
42 6 0.09
44 5 0.07
45 27 0.40
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (44 bp):
GTTGCAGTAGAGCAGATGAAGATAGCAGATCTTATCTCCCTAAA
Found at i:43311475 original size:45 final size:44
Alignment explanation
Indices: 43311386--43311475 Score: 99
Period size: 45 Copynumber: 2.0 Consensus size: 44
43311376 ATAGGTTGAT
* * * * * *
43311386 GATACAAGTCTTATCTCCTTGGAGTTGCAGTGGAGCAGACTAAA
1 GATACAAATCTTATCTCCCTGAAGTTACAGTGAAACAGACTAAA
* *
43311430 GATAGCAAATCTTATTTCCCTGAAGTTACAGTGAAACAGATTAAA
1 GATA-CAAATCTTATCTCCCTGAAGTTACAGTGAAACAGACTAAA
43311475 G
1 G
43311476 CTATAAATTA
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
44 4 0.11
45 33 0.89
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (44 bp):
GATACAAATCTTATCTCCCTGAAGTTACAGTGAAACAGACTAAA
Found at i:43312296 original size:15 final size:16
Alignment explanation
Indices: 43312271--43312305 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
43312261 GTTCTTGAGT
43312271 TTTTCATTTATTTTAC
1 TTTTCATTTATTTTAC
*
43312287 TTTT-ATTTATTTTTC
1 TTTTCATTTATTTTAC
43312302 TTTT
1 TTTT
43312306 TTTTTCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTCATTTATTTTAC
Found at i:43315960 original size:33 final size:30
Alignment explanation
Indices: 43315881--43315960 Score: 72
Period size: 33 Copynumber: 2.5 Consensus size: 30
43315871 GGTATCTTAA
* *
43315881 AAATTAATAATGTTTACATTGTATTATTAT
1 AAATTAATAATATTTAAATTGTATTATTAT
* *
43315911 ATATTATTATAA-ATTTAAATTTTTATGTATTAT
1 AAATTA--ATAATATTTAAA-TTGTAT-TATTAT
43315944 AAATTACATAATATTTA
1 AAATTA-ATAATATTTA
43315961 TAAATAACAT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
30 5 0.13
31 5 0.13
32 13 0.33
33 16 0.41
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (30 bp):
AAATTAATAATATTTAAATTGTATTATTAT
Found at i:43315963 original size:18 final size:18
Alignment explanation
Indices: 43315940--43315975 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
43315930 TTTTTATGTA
*
43315940 TTATAAATTACATAATAT
1 TTATAAATAACATAATAT
43315958 TTATAAATAACATAATAT
1 TTATAAATAACATAATAT
43315976 AACATATTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (18 bp):
TTATAAATAACATAATAT
Found at i:43316881 original size:13 final size:13
Alignment explanation
Indices: 43316863--43316887 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43316853 GCTTTTTTTA
43316863 TTTATAATTAATG
1 TTTATAATTAATG
43316876 TTTATAATTAAT
1 TTTATAATTAAT
43316888 AAATATATTA
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:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
TTTATAATTAATG
Found at i:43316944 original size:16 final size:16
Alignment explanation
Indices: 43316913--43316942 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43316903 AAGTTTTTTA
43316913 TTTTTATTTAATAAAT
1 TTTTTATTTAATAAAT
43316929 TTTTTATTT-ATAAA
1 TTTTTATTTAATAAA
43316943 ATGAAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTTTATTTAATAAAT
Found at i:43320878 original size:23 final size:23
Alignment explanation
Indices: 43320852--43320901 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
43320842 ACAAATATGT
*
43320852 TAAATTT-AAATAATGATACATA
1 TAAATTTCAAATAATAATACATA
43320874 GTAAATTTCAAATAATAATACATA
1 -TAAATTTCAAATAATAATACATA
43320898 TAAA
1 TAAA
43320902 AACTTAAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.34
Consensus pattern (23 bp):
TAAATTTCAAATAATAATACATA
Found at i:43327840 original size:19 final size:19
Alignment explanation
Indices: 43327791--43327842 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
43327781 TGTGCTTTCA
43327791 GCTTACTTTTATGGGTTTT
1 GCTTACTTTTATGGGTTTT
* **
43327810 TCTTTTTATTTATGGGTTTT
1 GCTTACT-TTTATGGGTTTT
43327830 GCTTACTTTTATG
1 GCTTACTTTTATG
43327843 TTAGTAATAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.62
Consensus pattern (19 bp):
GCTTACTTTTATGGGTTTT
Found at i:43328115 original size:27 final size:27
Alignment explanation
Indices: 43328077--43328129 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
43328067 AATCATGTCG
43328077 TTGTATACTATTGTCTTAATTTTTTCA
1 TTGTATACTATTGTCTTAATTTTTTCA
43328104 TTGTATACTATTGTCTTAATTTTTTC
1 TTGTATACTATTGTCTTAATTTTTTC
43328130 TTTCATCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.21, C:0.11, G:0.08, T:0.60
Consensus pattern (27 bp):
TTGTATACTATTGTCTTAATTTTTTCA
Found at i:43328247 original size:8 final size:8
Alignment explanation
Indices: 43328234--43328258 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
43328224 CCTATATTGT
43328234 TAATTAAA
1 TAATTAAA
43328242 TAATTAAA
1 TAATTAAA
43328250 TAATTAAA
1 TAATTAAA
43328258 T
1 T
43328259 GCGAACATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TAATTAAA
Found at i:43331238 original size:24 final size:24
Alignment explanation
Indices: 43331183--43331241 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
43331173 GGTTTAATGC
* *
43331183 AAATGGAGATATTTTGGAGAGATG
1 AAATGGATATATTTTGGAAAGATG
43331207 AAATGGATATATTTTGGAAAGATG
1 AAATGGATATATTTTGGAAAGATG
43331231 AAATGGATATA
1 AAATGGATATA
43331242 AATGGAGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.31
Consensus pattern (24 bp):
AAATGGATATATTTTGGAAAGATG
Found at i:43331313 original size:17 final size:17
Alignment explanation
Indices: 43331291--43331351 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
43331281 AATTCAAGAC
43331291 TTATGTAATATTTTTAA
1 TTATGTAATATTTTTAA
* ** *
43331308 TTATGTAGTGATTCAAATAT
1 TTATGTAAT-ATT--TTTAA
*
43331328 TTATGTAATGTTTTTAA
1 TTATGTAATATTTTTAA
43331345 TTATGTA
1 TTATGTA
43331352 GTGATTCAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
17 17 0.53
18 3 0.09
19 2 0.06
20 10 0.31
ACGTcount: A:0.33, C:0.02, G:0.11, T:0.54
Consensus pattern (17 bp):
TTATGTAATATTTTTAA
Found at i:43331373 original size:9 final size:9
Alignment explanation
Indices: 43331359--43331429 Score: 97
Period size: 9 Copynumber: 7.4 Consensus size: 9
43331349 GTAGTGATTC
43331359 AATTCGGGT
1 AATTCGGGT
43331368 AATTCGGGT
1 AATTCGGGT
*
43331377 AATTTGGGT
1 AATTCGGGT
43331386 AATTTTCGGGT
1 AA--TTCGGGT
43331397 AATTCGGGT
1 AATTCGGGT
43331406 AATTCGGGT
1 AATTCGGGT
43331415 AATTTTCGGGT
1 AA--TTCGGGT
43331426 AATT
1 AATT
43331430 TATTTATGTA
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
9 39 0.70
11 17 0.30
ACGTcount: A:0.23, C:0.08, G:0.30, T:0.39
Consensus pattern (9 bp):
AATTCGGGT
Found at i:43331399 original size:29 final size:29
Alignment explanation
Indices: 43331361--43331572 Score: 150
Period size: 29 Copynumber: 7.1 Consensus size: 29
43331351 AGTGATTCAA
*
43331361 TTCGGGTAATTCGGGTAATTTGGGTAATT
1 TTCGGGTAATTCGGGTAATTCGGGTAATT
43331390 TTCGGGTAATTCGGGTAATTCGGGTAATT
1 TTCGGGTAATTCGGGTAATTCGGGTAATT
*** ***
43331419 TTCGGGTAATTTATTTATGTAATGT-TTTTAATT
1 TTCGGGT-A---ATTCGGGTAAT-TCGGGTAATT
* *
43331452 ATGTAGTGATTCAATTCGGGTAATTCGGGTAA-T
1 -T-TCG-G-GT-AATTCGGGTAATTCGGGTAATT
43331485 TT-GGGTAATTTTCGGGTAATTCGGGTAA--
1 TTCGGGTAA--TTCGGGTAATTCGGGTAATT
43331513 TTCGGGTAATTTTCGGGTAATTCGGGTAA--
1 TTCGGGTAA--TTCGGGTAATTCGGGTAATT
* *
43331542 GTCGGGTAATTCGGGTAAGTCGGGTAATT
1 TTCGGGTAATTCGGGTAATTCGGGTAATT
43331571 TT
1 TT
43331573 TAACCAAAAA
Statistics
Matches: 148, Mismatches: 20, Indels: 30
0.75 0.10 0.15
Matches are distributed among these distances:
27 19 0.13
28 3 0.02
29 89 0.60
30 2 0.01
31 1 0.01
32 1 0.01
33 15 0.10
34 13 0.09
35 2 0.01
36 1 0.01
37 2 0.01
ACGTcount: A:0.22, C:0.08, G:0.29, T:0.41
Consensus pattern (29 bp):
TTCGGGTAATTCGGGTAATTCGGGTAATT
Found at i:43331462 original size:105 final size:105
Alignment explanation
Indices: 43331325--43331534 Score: 420
Period size: 105 Copynumber: 2.0 Consensus size: 105
43331315 GTGATTCAAA
43331325 TATTTATGTAATGTTTTTAATTATGTAGTGATTCAATTCGGGTAATTCGGGTAATTTGGGTAATT
1 TATTTATGTAATGTTTTTAATTATGTAGTGATTCAATTCGGGTAATTCGGGTAATTTGGGTAATT
43331390 TTCGGGTAATTCGGGTAATTCGGGTAATTTTCGGGTAATT
66 TTCGGGTAATTCGGGTAATTCGGGTAATTTTCGGGTAATT
43331430 TATTTATGTAATGTTTTTAATTATGTAGTGATTCAATTCGGGTAATTCGGGTAATTTGGGTAATT
1 TATTTATGTAATGTTTTTAATTATGTAGTGATTCAATTCGGGTAATTCGGGTAATTTGGGTAATT
43331495 TTCGGGTAATTCGGGTAATTCGGGTAATTTTCGGGTAATT
66 TTCGGGTAATTCGGGTAATTCGGGTAATTTTCGGGTAATT
43331535 CGGGTAAGTC
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 105 1.00
ACGTcount: A:0.24, C:0.07, G:0.25, T:0.45
Consensus pattern (105 bp):
TATTTATGTAATGTTTTTAATTATGTAGTGATTCAATTCGGGTAATTCGGGTAATTTGGGTAATT
TTCGGGTAATTCGGGTAATTCGGGTAATTTTCGGGTAATT
Found at i:43331478 original size:9 final size:9
Alignment explanation
Indices: 43331464--43331570 Score: 151
Period size: 9 Copynumber: 11.4 Consensus size: 9
43331454 GTAGTGATTC
43331464 AATTCGGGT
1 AATTCGGGT
43331473 AATTCGGGT
1 AATTCGGGT
*
43331482 AATTTGGGT
1 AATTCGGGT
43331491 AATTTTCGGGT
1 AA--TTCGGGT
43331502 AATTCGGGT
1 AATTCGGGT
43331511 AATTCGGGT
1 AATTCGGGT
43331520 AATTTTCGGGT
1 AA--TTCGGGT
43331531 AATTCGGGT
1 AATTCGGGT
*
43331540 AAGTCGGGT
1 AATTCGGGT
43331549 AATTCGGGT
1 AATTCGGGT
*
43331558 AAGTCGGGT
1 AATTCGGGT
43331567 AATT
1 AATT
43331571 TTTAACCAAA
Statistics
Matches: 88, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
9 71 0.81
11 17 0.19
ACGTcount: A:0.22, C:0.09, G:0.33, T:0.36
Consensus pattern (9 bp):
AATTCGGGT
Found at i:43331748 original size:12 final size:12
Alignment explanation
Indices: 43331731--43331755 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43331721 AAGAATTTCG
43331731 GGTCGGTTAACC
1 GGTCGGTTAACC
43331743 GGTCGGTTAACC
1 GGTCGGTTAACC
43331755 G
1 G
43331756 ACTGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:43333053 original size:3 final size:3
Alignment explanation
Indices: 43333045--43333120 Score: 134
Period size: 3 Copynumber: 25.3 Consensus size: 3
43333035 CAGTTGAGGA
*
43333045 CTT CTT CTT CTT CTT CTT CTT CTT ATT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
43333093 CTT CTT CTT CTT CTT CTT ATT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
43333121 AGTGTATTGG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:43338482 original size:9 final size:9
Alignment explanation
Indices: 43338468--43338497 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
43338458 TTAACTTTTG
43338468 AAATTTTAA
1 AAATTTTAA
43338477 AAATTTTAA
1 AAATTTTAA
*
43338486 AAATTATAA
1 AAATTTTAA
43338495 AAA
1 AAA
43338498 ATACTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
AAATTTTAA
Found at i:43339223 original size:20 final size:20
Alignment explanation
Indices: 43339198--43339235 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
43339188 TAGGGATCAA
*
43339198 GGTAAAACAGCATTGTTTAG
1 GGTAAAACAACATTGTTTAG
43339218 GGTAAAACAACATTGTTT
1 GGTAAAACAACATTGTTT
43339236 TGCATGGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (20 bp):
GGTAAAACAACATTGTTTAG
Found at i:43345568 original size:18 final size:19
Alignment explanation
Indices: 43345541--43345583 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
43345531 AATAATAAAA
*
43345541 ATTTTATATTATTT-TAAT
1 ATTTTTTATTATTTATAAT
*
43345559 ATTTTTTATTTTTTATAAT
1 ATTTTTTATTATTTATAAT
43345578 ATTTTT
1 ATTTTT
43345584 GTAAAAAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
ATTTTTTATTATTTATAAT
Found at i:43349757 original size:5 final size:5
Alignment explanation
Indices: 43349747--43349772 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
43349737 TGAGCATTCG
43349747 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
43349773 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:43350557 original size:97 final size:100
Alignment explanation
Indices: 43350421--43350617 Score: 346
Period size: 98 Copynumber: 2.0 Consensus size: 100
43350411 AATAAAAGTT
*
43350421 TGAGGGAAAGTAAATAGGGTGGAGTAAAATTTTGGAGGGAAAATATTAAAAA-AAAAATGGAGGG
1 TGAGGGAAAGTAAATAGGGTGGAGTAAAATTTTAGAGGGAAAATATTAAAAAGAAAAATGGAGGG
43350485 GGGAAGGTTTGGGATAGATGGGAGGTGAGATGGGA
66 GGGAAGGTTTGGGATAGATGGGAGGTGAGATGGGA
*
43350520 TGAGGGAAAGTAAATA-GG-GGAGTAAAATTTTAGAGGGAAAATATTAAAAAGAAAATTGGAGGG
1 TGAGGGAAAGTAAATAGGGTGGAGTAAAATTTTAGAGGGAAAATATTAAAAAGAAAAATGGAGGG
*
43350583 GGGAGGGTTTGGGATAGATGGGAGGTGAGATGGGA
66 GGGAAGGTTTGGGATAGATGGGAGGTGAGATGGGA
43350618 AGGGAATAAA
Statistics
Matches: 94, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
97 31 0.33
98 47 0.50
99 16 0.17
ACGTcount: A:0.39, C:0.00, G:0.41, T:0.20
Consensus pattern (100 bp):
TGAGGGAAAGTAAATAGGGTGGAGTAAAATTTTAGAGGGAAAATATTAAAAAGAAAAATGGAGGG
GGGAAGGTTTGGGATAGATGGGAGGTGAGATGGGA
Found at i:43350658 original size:30 final size:31
Alignment explanation
Indices: 43350612--43350672 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
43350602 GGGAGGTGAG
*
43350612 ATGGGAAGGGAATAAAAGTTTTAGGGGAAAA
1 ATGGGAAGGGAATAAAAATTTTAGGGGAAAA
* *
43350643 ATGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 ATGGGAAGGGAATAAAAATTTTAGGGGAAAA
43350673 TAAAAGGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
ATGGGAAGGGAATAAAAATTTTAGGGGAAAA
Found at i:43350901 original size:9 final size:9
Alignment explanation
Indices: 43350887--43350923 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
43350877 TATAGTTTGA
43350887 TATTCGAAT
1 TATTCGAAT
43350896 TATTCGAAT
1 TATTCGAAT
*
43350905 TATTCGAGT
1 TATTCGAAT
43350914 TATTCGAAT
1 TATTCGAAT
43350923 T
1 T
43350924 TGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:43352039 original size:108 final size:108
Alignment explanation
Indices: 43351914--43352330 Score: 762
Period size: 108 Copynumber: 3.9 Consensus size: 108
43351904 TAAGAGGATA
* *
43351914 TTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTCGATTTTCC
1 TTTGGCTATTTGGTCGAACGAGAAACCGAAACCCAGCACGTTAGGGCACGTTTTCTCGATTTTCC
43351979 AAATGTAAAATATTGCCTTGTTTTGAAAGTTTAAAAAGGATTT
66 AAATGTAAAATATTGCCTTGTTTTGAAAGTTTAAAAAGGATTT
43352022 TTTGGCTATTTGGTCGAACGAGAAACCGAAACCCAGCACGTTAGGGCACGTTTTCTCGATTTTCC
1 TTTGGCTATTTGGTCGAACGAGAAACCGAAACCCAGCACGTTAGGGCACGTTTTCTCGATTTTCC
43352087 AAATGTAAAATATTGCCTTGTTTTGAAAGTTTAAAAAGGATTT
66 AAATGTAAAATATTGCCTTGTTTTGAAAGTTTAAAAAGGATTT
43352130 TTTGGCTATTTGGTCGAACGAGAAACCGAAACCCAGCACGTTAGGGCACGTTTTCTCGATTTTCC
1 TTTGGCTATTTGGTCGAACGAGAAACCGAAACCCAGCACGTTAGGGCACGTTTTCTCGATTTTCC
43352195 AAATGTAAAATATTGCCTTGTTTTGAAAGTTTAAAAAGGATTT
66 AAATGTAAAATATTGCCTTGTTTTGAAAGTTTAAAAAGGATTT
43352238 TTTGGCTATTTGGTCGAACGAGAAACCGAAACCCAGCACGTTAGGGCACGTTTTCTCGATTTTCC
1 TTTGGCTATTTGGTCGAACGAGAAACCGAAACCCAGCACGTTAGGGCACGTTTTCTCGATTTTCC
* * * * * *
43352303 AGACGCAAAACATTGCCTTATTTAGAAA
66 AAATGTAAAATATTGCCTTGTTTTGAAA
43352331 AAAATTTTCT
Statistics
Matches: 301, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 301 1.00
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (108 bp):
TTTGGCTATTTGGTCGAACGAGAAACCGAAACCCAGCACGTTAGGGCACGTTTTCTCGATTTTCC
AAATGTAAAATATTGCCTTGTTTTGAAAGTTTAAAAAGGATTT
Found at i:43352654 original size:21 final size:21
Alignment explanation
Indices: 43352632--43352669 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
43352622 AAATGCATAT
43352632 ATATTAT--AAATATATGTCA
1 ATATTATAAAAATATATGTCA
43352651 ATATTATAAAAATATATGT
1 ATATTATAAAAATATATGT
43352670 ATGCATGTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
21 10 0.59
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (21 bp):
ATATTATAAAAATATATGTCA
Found at i:43352886 original size:21 final size:18
Alignment explanation
Indices: 43352860--43352903 Score: 52
Period size: 21 Copynumber: 2.3 Consensus size: 18
43352850 ACATGTATAA
43352860 GTATGTATATTAATTAAGAAT
1 GTATGTATATT-A-TAA-AAT
*
43352881 GTATGTGTATTATAAAAT
1 GTATGTATATTATAAAAT
43352899 GTATG
1 GTATG
43352904 CATGTATATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 8 0.36
19 3 0.14
20 1 0.05
21 10 0.45
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.43
Consensus pattern (18 bp):
GTATGTATATTATAAAAT
Found at i:43353043 original size:40 final size:40
Alignment explanation
Indices: 43352998--43353132 Score: 121
Period size: 40 Copynumber: 3.4 Consensus size: 40
43352988 GTTTGGAACA
* *
43352998 AAAGCGCCACAAAAAATCGAGCATTAGCGGCGATTTAGCC
1 AAAGCGCCACAAAAAATAGAGCATTAGCGGCGATTTATCC
* * ** *
43353038 AAAGCGCCGCTAAAGGTAGAGCATCAGCGGCGA-TTATCC
1 AAAGCGCCACAAAAAATAGAGCATTAGCGGCGATTTATCC
* * * * * **
43353077 GGAAGCGCCGCTAAAAATAG-GAATTAGCGGCGTTTTATAT
1 -AAAGCGCCACAAAAAATAGAGCATTAGCGGCGATTTATCC
43353117 AAAGCGCCACAAAAAA
1 AAAGCGCCACAAAAAA
43353133 CCTAAGACCA
Statistics
Matches: 75, Mismatches: 18, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
39 28 0.37
40 47 0.63
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.16
Consensus pattern (40 bp):
AAAGCGCCACAAAAAATAGAGCATTAGCGGCGATTTATCC
Found at i:43353228 original size:41 final size:41
Alignment explanation
Indices: 43353171--43353485 Score: 290
Period size: 41 Copynumber: 7.8 Consensus size: 41
43353161 TTTTTTAAAC
*
43353171 CTTTAGCGGCGTTTTTGTGTAAGCGCCGCTAATGCTCCGAT
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCCGAT
43353212 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCT-CGAGT
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCCGA-T
* * *
43353253 CTTTAGCGGC------CTCTAAGCACCGCTAATGCTCAGAT
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCCGAT
* * *
43353288 CTTTAGCGGCGTTTTTGTCTATGTGCCGCTAATGCTCGGAT
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCCGAT
* * * * *
43353329 CTTTAGCGGCGTTTTTGTCTACGCACCACTAATGCTCGGGT
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCCGAT
* * *
43353370 CTTTAGCGGCGTTTTTATAC-AAGCGTCGCTAATGCT-TGAAT
1 CTTTAGCGGCGTTTTTGT-CTAAGCGCCGCTAATGCTCCG-AT
** * * * * *
43353411 CTTTAGCGGCGTTTTTAACTGAGAGCCACTAATTCTCTTG-T
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTC-CGAT
* * * *
43353452 CTTCAGCGGCGTTTGTATCTAAGCGTCGCTAATG
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATG
43353486 TATTTACTTT
Statistics
Matches: 226, Mismatches: 35, Indels: 26
0.79 0.12 0.09
Matches are distributed among these distances:
35 29 0.13
36 2 0.01
40 5 0.02
41 187 0.83
42 1 0.00
43 2 0.01
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCCGAT
Found at i:43353276 original size:35 final size:35
Alignment explanation
Indices: 43353229--43353297 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
43353219 GGCGTTTTTG
*
43353229 TCTAAGCGCCGCTAATGCTC-GAGTCTTTAGCGGCC
1 TCTAAGCACCGCTAATGCTCAGA-TCTTTAGCGGCC
43353264 TCTAAGCACCGCTAATGCTCAGATCTTTAGCGGC
1 TCTAAGCACCGCTAATGCTCAGATCTTTAGCGGC
43353298 GTTTTTGTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 30 0.94
36 2 0.06
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.26
Consensus pattern (35 bp):
TCTAAGCACCGCTAATGCTCAGATCTTTAGCGGCC
Found at i:43353279 original size:76 final size:77
Alignment explanation
Indices: 43353190--43353420 Score: 261
Period size: 76 Copynumber: 2.9 Consensus size: 77
43353180 CGTTTTTGTG
* *
43353190 TAAGCGCCGCTAATGCTCCGATCTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGAGTCT
1 TAAGCACCGCTAATGCTCAGATCTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGAGTCT
43353255 TTAGCGGC-CTC
66 TTAGCGGCTCTC
* *
43353266 TAAGCACCGCTAATGCTCAGATCTTTAGCGGCGTTTTTGTCTATGTGCCGCTAATGCTCG-GATC
1 TAAGCACCGCTAATGCTCAGATCTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGAG-TC
*
43353330 TTTAGCGGCGTTTTTGTC
65 TTTAGCGGC-----TCTC
* * * * * * * *
43353348 TACGCACCACTAATGCTCGGGTCTTTAGCGGCGTTTTTATAC-AAGCGTCGCTAATGCTTGAATC
1 TAAGCACCGCTAATGCTCAGATCTTTAGCGGCGTTTTTGT-CTAAGCGCCGCTAATGCTCGAGTC
43353412 TTTAGCGGC
65 TTTAGCGGC
43353421 GTTTTTAACT
Statistics
Matches: 131, Mismatches: 15, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
75 1 0.01
76 67 0.51
82 62 0.47
83 1 0.01
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.33
Consensus pattern (77 bp):
TAAGCACCGCTAATGCTCAGATCTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGAGTCT
TTAGCGGCTCTC
Found at i:43353498 original size:82 final size:82
Alignment explanation
Indices: 43353354--43353508 Score: 197
Period size: 82 Copynumber: 1.9 Consensus size: 82
43353344 TGTCTACGCA
* * *
43353354 CCACTAATGCTCGGGTCTTTAGCGGCGTTTTTATACAAGCGTCGCTAATGCTTGAATCTTTAGCG
1 CCACTAATGCTCGGGTCTTCAGCGGCGTTTGTATACAAGCGTCGCTAATGATTGAATCTTTAGCG
*
43353419 GCGTTTTTAACTGAGAG
66 GCATTTTTAACTGAGAG
* ** * *
43353436 CCACTAATTCTCTTGTCTTCAGCGGCGTTTGTAT-CTAAGCGTCGCTAATGTATTTACT-TTTAG
1 CCACTAATGCTCGGGTCTTCAGCGGCGTTTGTATAC-AAGCGTCGCTAATG-ATTGAATCTTTAG
43353499 CGGCATTTTT
64 CGGCATTTTT
43353509 GCCGAAGCGC
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
81 1 0.02
82 57 0.92
83 4 0.06
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (82 bp):
CCACTAATGCTCGGGTCTTCAGCGGCGTTTGTATACAAGCGTCGCTAATGATTGAATCTTTAGCG
GCATTTTTAACTGAGAG
Found at i:43353966 original size:15 final size:15
Alignment explanation
Indices: 43353945--43353982 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
43353935 TTTAAGGTTA
43353945 ATTTAGGGGTTAGAG
1 ATTTAGGGGTTAGAG
* *
43353960 GTTTAGGGGTTTGAG
1 ATTTAGGGGTTAGAG
43353975 ATTTAGGG
1 ATTTAGGG
43353983 TTAATTTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.42, T:0.37
Consensus pattern (15 bp):
ATTTAGGGGTTAGAG
Found at i:43358177 original size:22 final size:22
Alignment explanation
Indices: 43358149--43358247 Score: 86
Period size: 22 Copynumber: 4.7 Consensus size: 22
43358139 TATACATAAA
*
43358149 ATACATAACTTACATTAATATT
1 ATACATAAATTACATTAATATT
*
43358171 ATACATAAATTACA-TAACT-TA
1 ATACATAAATTACATTAA-TATT
*
43358192 ATTA-ATTAATATACA-TAA-A-T
1 A-TACATAAAT-TACATTAATATT
*
43358212 -TACATAACTTACATTAATATT
1 ATACATAAATTACATTAATATT
43358233 ATACATAAATTACAT
1 ATACATAAATTACAT
43358248 AACTTAGTTA
Statistics
Matches: 61, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
18 6 0.10
19 7 0.11
20 1 0.02
21 11 0.18
22 36 0.59
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.38
Consensus pattern (22 bp):
ATACATAAATTACATTAATATT
Found at i:43358224 original size:62 final size:62
Alignment explanation
Indices: 43358127--43359253 Score: 1917
Period size: 62 Copynumber: 18.0 Consensus size: 62
43358117 TACATATCAT
* * *
43358127 TTAATTAATTAATATACATAAAATACATAACTTACATTAATATTATACATAAATTACATAAC
1 TTAATTAGTTAATATACATAAATTACATAACATACATTAATATTATACATAAATTACATAAC
* *
43358189 TTAATTAATTAATATACATAAATTACATAACTTACATTAATATTATACATAAATTACATAAC
1 TTAATTAGTTAATATACATAAATTACATAACATACATTAATATTATACATAAATTACATAAC
* * *
43358251 TTAGTTAATTAATAT---T--A-TACATAACTTACATTAATATTATACATAAATTACATAAC
1 TTAATTAGTTAATATACATAAATTACATAACATACATTAATATTATACATAAATTACATAAC
43358307 TTAATTAGTTAATATACATAAATTACATAACATACATTAATATTATACATAAATTACATAAC
1 TTAATTAGTTAATATACATAAATTACATAACATACATTAATATTATACATAAATTACATAAC
43358369 TTAATTAGTTAATATACATAAATTACATAACATACATTAATATTATACATAAATTACATAAC
1 TTAATTAGTTAATATACATAAATTACATAACATACATTAATATTATACATAAATTACATAAC
43358431 TTAATTAGTTAATATACATAAATTACATAACATACATTAATATTATACATAAATTACATAAC
1 TTAATTAGTTAATATACATAAATTACATAACATACATTAATATTATACATAAATTACATAAC
43358493 TTAATTAGTTAATATACATAAATTACATAACATACATTAATATTATACATAAATTACATAAC
1 TTAATTAGTTAATATACATAAATTACATAACATACATTAATATTATACATAAATTACATAAC
43358555 TTAATTAGTTAATATACATAAATTACATAACATACATTAATATTATACATAAATTACATAAC
1 TTAATTAGTTAATATACATAAATTACATAACATACATTAATATTATACATAAATTACATAAC
43358617 TTAATTAGTTAATATACATAAATTACATAACATACATTAATATTATACATAAATTACATAAC
1 TTAATTAGTTAATATACATAAATTACATAACATACATTAATATTATACATAAATTACATAAC
43358679 TTAATTAGTTAATATACATAAATTACATAACATACATTAATATTATACATAAATTACATAAC
1 TTAATTAGTTAATATACATAAATTACATAACATACATTAATATTATACATAAATTACATAAC
43358741 TTAATTAGTTAATATACATAAATTACATAACATACATTAATATTATACATAAATTACATAAC
1 TTAATTAGTTAATATACATAAATTACATAACATACATTAATATTATACATAAATTACATAAC
43358803 TTAATTAGTTAATATACATAAATTACATAACATACATTAATATTATACATAAATTACATAAC
1 TTAATTAGTTAATATACATAAATTACATAACATACATTAATATTATACATAAATTACATAAC
43358865 TTAATTAGTTAATATACATAAATTACATAACATACATTAATATTATACATAAATTACATAAC
1 TTAATTAGTTAATATACATAAATTACATAACATACATTAATATTATACATAAATTACATAAC
43358927 TTAATTAGTTAATATACATAAATTACATAACATACATTAATATTATACATAAATTACATAAC
1 TTAATTAGTTAATATACATAAATTACATAACATACATTAATATTATACATAAATTACATAAC
43358989 TTAATTAGTTAATATACATAAATTACATAACATACATTAATATTATACATAAATTACATAAC
1 TTAATTAGTTAATATACATAAATTACATAACATACATTAATATTATACATAAATTACATAAC
43359051 TTAATTAGTTAATATACATAAATTACATAACATACATTAATATTATACATAAATTACATAAC
1 TTAATTAGTTAATATACATAAATTACATAACATACATTAATATTATACATAAATTACATAAC
* * * ** * *
43359113 TTAGTTAATTAATATTATACATAACTTACAACTTACATAACTTACATTTTTTTTAATTA-TTCAT
1 TTAATTAGTT-A-A-TATAC---A--TA-AA-TTACATAACATACATTAATATT-A-TACAT-A-
43359177 AAATTACATAAC
52 A-ATTACATAAC
* *
43359189 TTAATTAGTTAATATACATAACTTACATAACTTACATTAATATTATACATAAATTACATAAC
1 TTAATTAGTTAATATACATAAATTACATAACATACATTAATATTATACATAAATTACATAAC
43359251 TTA
1 TTA
43359254 GTTAACTTAC
Statistics
Matches: 1024, Mismatches: 19, Indels: 44
0.94 0.02 0.04
Matches are distributed among these distances:
56 52 0.05
57 1 0.00
59 2 0.00
61 1 0.00
62 878 0.86
63 2 0.00
64 4 0.00
65 7 0.01
66 19 0.02
67 1 0.00
68 3 0.00
70 3 0.00
71 2 0.00
72 18 0.02
73 7 0.01
74 4 0.00
75 2 0.00
76 18 0.02
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.38
Consensus pattern (62 bp):
TTAATTAGTTAATATACATAAATTACATAACATACATTAATATTATACATAAATTACATAAC
Found at i:43358271 original size:25 final size:22
Alignment explanation
Indices: 43358243--43358296 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 22
43358233 ATACATAAAT
43358243 TACATAACTTAGTTAATTAATATTA
1 TACATAACTTA---AATTAATATTA
*
43358268 TACATAACTTACATTAATATTA
1 TACATAACTTAAATTAATATTA
43358290 TACATAA
1 TACATAA
43358297 ATTACATAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 17 0.61
25 11 0.39
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.41
Consensus pattern (22 bp):
TACATAACTTAAATTAATATTA
Found at i:43359215 original size:138 final size:138
Alignment explanation
Indices: 43359030--43359297 Score: 468
Period size: 138 Copynumber: 1.9 Consensus size: 138
43359020 ATACATTAAT
43359030 ATTATACATAAATTACATAACTTAATTAGTTAATATACATAAATTACATAACATACATTAATATT
1 ATTATACATAAATTACATAACTTAATTAGTTAATATACATAAATTACATAACATACATTAATATT
*
43359095 ATACATAAATTACATAACTTAGTTAA-TTA-ATATTATACATAACTTACAACTTACATAACTTAC
66 ATACATAAATTACATAACTTAGTTAACTTACA-ACT-TACATAACTTACAACTTACATAACTTAC
43359158 ATTTTTTTTA
129 ATTTTTTTTA
* * *
43359168 ATTATTCATAAATTACATAACTTAATTAGTTAATATACATAACTTACATAACTTACATTAATATT
1 ATTATACATAAATTACATAACTTAATTAGTTAATATACATAAATTACATAACATACATTAATATT
43359233 ATACATAAATTACATAACTTAGTTAACTTACAACTTACATAACTTACAACTTACATAACTTACAT
66 ATACATAAATTACATAACTTAGTTAACTTACAACTTACATAACTTACAACTTACATAACTTACAT
43359298 ATTTCATAAT
Statistics
Matches: 124, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
138 118 0.95
139 5 0.04
140 1 0.01
ACGTcount: A:0.45, C:0.14, G:0.01, T:0.39
Consensus pattern (138 bp):
ATTATACATAAATTACATAACTTAATTAGTTAATATACATAAATTACATAACATACATTAATATT
ATACATAAATTACATAACTTAGTTAACTTACAACTTACATAACTTACAACTTACATAACTTACAT
TTTTTTTA
Found at i:43359217 original size:9 final size:9
Alignment explanation
Indices: 43359203--43359359 Score: 113
Period size: 9 Copynumber: 18.3 Consensus size: 9
43359193 TTAGTTAATA
43359203 TACATAACT
1 TACATAACT
43359212 TACATAACT
1 TACATAACT
*
43359221 TACATTAATATT
1 TACA-T-A-ACT
*
43359233 ATACATAAAT
1 -TACATAACT
43359243 TACATAACT
1 TACATAACT
**
43359252 TAGTTAACT
1 TACATAACT
43359261 TAC--AACT
1 TACATAACT
43359268 TACATAACT
1 TACATAACT
43359277 TAC--AACT
1 TACATAACT
43359284 TACATAACT
1 TACATAACT
43359293 TACAT-A-T
1 TACATAACT
*
43359300 TTCATAA--
1 TACATAACT
*
43359307 TACACAACT
1 TACATAACT
*
43359316 TACATAATT
1 TACATAACT
*
43359325 TTCATAA--
1 TACATAACT
*
43359332 TAAATAACT
1 TACATAACT
43359341 TACATAA--
1 TACATAACT
43359348 TACATAACT
1 TACATAACT
43359357 TAC
1 TAC
43359360 GTAGCTTAAT
Statistics
Matches: 118, Mismatches: 15, Indels: 30
0.72 0.09 0.18
Matches are distributed among these distances:
7 36 0.31
8 2 0.02
9 68 0.58
10 3 0.03
11 2 0.02
12 3 0.03
13 4 0.03
ACGTcount: A:0.45, C:0.18, G:0.01, T:0.36
Consensus pattern (9 bp):
TACATAACT
Found at i:43359269 original size:16 final size:16
Alignment explanation
Indices: 43359256--43359322 Score: 84
Period size: 16 Copynumber: 4.2 Consensus size: 16
43359246 ATAACTTAGT
43359256 TAACTTACAACTTACA
1 TAACTTACAACTTACA
43359272 TAACTTACAACTTACA
1 TAACTTACAACTTACA
*
43359288 TAACTTACATA-TTTCA
1 TAACTTACA-ACTTACA
*
43359304 TAA-TACACAACTTACA
1 TAACT-TACAACTTACA
43359320 TAA
1 TAA
43359323 TTTTCATAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
15 2 0.04
16 42 0.93
17 1 0.02
ACGTcount: A:0.45, C:0.22, G:0.00, T:0.33
Consensus pattern (16 bp):
TAACTTACAACTTACA
Found at i:43359306 original size:32 final size:32
Alignment explanation
Indices: 43359132--43359359 Score: 92
Period size: 32 Copynumber: 6.8 Consensus size: 32
43359122 TAATATTATA
*
43359132 CATAACTTACAACTTACATAACTTACATTTTT
1 CATAACTTACAACTTACATAACTTACATATTT
** * *
43359164 TTTAA-TTATTCATAAATTACATAACTTA-ATTAGTT
1 CATAACTTA--C--AACTTACATAACTTACA-TATTT
* *
43359199 AATATAC--ATAACTTACATAACTTACATTAATATTAT
1 CATA-ACTTACAACTTACATAACTTAC----ATATT-T
* ** *
43359235 ACATAAATTACATAACTTAGTTAACTTACA-ACTTA
1 -CATAACTTAC--AACTTACATAACTTACATA-TTT
43359270 CATAACTTACAACTTACATAACTTACATATTT
1 CATAACTTACAACTTACATAACTTACATATTT
* * * * *
43359302 CATAA-TACACAACTTACATAATTTTCATAATA
1 CATAACT-TACAACTTACATAACTTACATATTT
* *
43359334 AATAACTTACATA-ATACATAACTTAC
1 CATAACTTACA-ACTTACATAACTTAC
43359360 GTAGCTTAAT
Statistics
Matches: 143, Mismatches: 30, Indels: 46
0.65 0.14 0.21
Matches are distributed among these distances:
31 18 0.13
32 62 0.43
33 4 0.03
34 10 0.07
35 24 0.17
36 7 0.05
37 3 0.02
38 1 0.01
40 14 0.10
ACGTcount: A:0.44, C:0.17, G:0.01, T:0.38
Consensus pattern (32 bp):
CATAACTTACAACTTACATAACTTACATATTT
Found at i:43359338 original size:16 final size:16
Alignment explanation
Indices: 43359327--43359359 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
43359317 ACATAATTTT
43359327 CATAATAAATAACTTA
1 CATAATAAATAACTTA
*
43359343 CATAATACATAACTTA
1 CATAATAAATAACTTA
43359359 C
1 C
43359360 GTAGCTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.18, G:0.00, T:0.30
Consensus pattern (16 bp):
CATAATAAATAACTTA
Found at i:43368056 original size:132 final size:132
Alignment explanation
Indices: 43367767--43368207 Score: 561
Period size: 132 Copynumber: 3.3 Consensus size: 132
43367757 ATTCACCGTA
** * * *
43367767 TTCGATCCACTCCGCTAATGCTTAGGGAGATAAGATCTG-TAAT-TTCCAACCTATTCCACTGCT
1 TTCGATCTGCTCCACTAGTGCTTAGGGAGATAAGATCTGCT-ATCTT-CAACCTACTCCACTGCT
* * * * * * *
43367830 GGTCA-GG-GACATAGGACTTGTGGCTTAAATTTG-TTTCC-CTACTCCTGGGGAAGATATGATT
64 GCTCAGGGAGACA-AGGCCTGGTGGCTTAAATCTGCTTTCCACTA-T-CTTGGAAAGATAAGATT
* * *
43367891 CGTCATT
126 TGTCGTC
* *
43367898 TTCGATCTGCTCCACTAGTGCTTAGGGAGATAATATCTGCTATCTTCAACCTCCTCCACTGCTGC
1 TTCGATCTGCTCCACTAGTGCTTAGGGAGATAAGATCTGCTATCTTCAACCTACTCCACTGCTGC
*
43367963 TCAGGGAGACGAGGCCTGGTGGCTTAAATCTGCTTTCCACTATCTTGGAAAGATAAGATTTGTCG
66 TCAGGGAGACAAGGCCTGGTGGCTTAAATCTGCTTTCCACTATCTTGGAAAGATAAGATTTGTCG
43368028 TC
131 TC
*
43368030 TTCGATCTTCTCCACTAGTGCTTAGGGAGATAAGATCTGCTATCTTCAACCTACTCCACTGCTGC
1 TTCGATCTGCTCCACTAGTGCTTAGGGAGATAAGATCTGCTATCTTCAACCTACTCCACTGCTGC
* * * * *
43368095 TCAGGGAGACAATGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGTTTTTTCG
66 TCAGGGAGACAAGGCCTGGTGGCTTAAATCTGCTTTCCACTATCTTGGAAAGATAAGATTTGTCG
43368160 TC
131 TC
* *
43368162 TTCGATCTGCTCCACGAGTGCTTAGGGAGATAAGATCTGTTATCTT
1 TTCGATCTGCTCCACTAGTGCTTAGGGAGATAAGATCTGCTATCTT
43368208 TAATGATCTG
Statistics
Matches: 274, Mismatches: 30, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
131 55 0.20
132 207 0.76
133 9 0.03
134 3 0.01
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (132 bp):
TTCGATCTGCTCCACTAGTGCTTAGGGAGATAAGATCTGCTATCTTCAACCTACTCCACTGCTGC
TCAGGGAGACAAGGCCTGGTGGCTTAAATCTGCTTTCCACTATCTTGGAAAGATAAGATTTGTCG
TC
Found at i:43368063 original size:44 final size:44
Alignment explanation
Indices: 43367902--43368197 Score: 121
Period size: 44 Copynumber: 6.7 Consensus size: 44
43367892 GTCATTTTCG
* * *
43367902 ATCTGCTCCACTAGTGCTTAGGGAGATAATATCTG-CTATCTTCA
1 ATCTGCTCCACTAGTGCTTAGGGAGATAAGATTTGTC-GTCTTCA
* * * * * ** * * *
43367946 ACCTCCTCCACT-GCTGCTCAGGGAGACGAGGCCTGGT-GGCTTAA
1 ATCTGCTCCACTAG-TGCTTAGGGAGA-TAAGATTTGTCGTCTTCA
* *
43367990 ATCTGCTTTCCACTA-T-CTT-GGAAAGATAAGATTTGTCGTCTTCG
1 ATCTGC--TCCACTAGTGCTTAGG-GAGATAAGATTTGTCGTCTTCA
* * *
43368034 ATCTTCTCCACTAGTGCTTAGGGAGATAAGATCTG-CTATCTTCA
1 ATCTGCTCCACTAGTGCTTAGGGAGATAAGATTTGTC-GTCTTCA
* * * * * * * *
43368078 ACCTACTCCACT-GCTGCTCAGGGAGACAATGCTTGGT-GGCTTAA
1 ATCTGCTCCACTAG-TGCTTAGGGAGATAA-GATTTGTCGTCTTCA
* * * *
43368122 ATCTGCTTCCCACTA-T-CTT-GGAAAGATAAGTTTTTTCGTCTTCG
1 ATCTGC-T-CCACTAGTGCTTAGG-GAGATAAGATTTGTCGTCTTCA
*
43368166 ATCTGCTCCACGAGTGCTTAGGGAGATAAGAT
1 ATCTGCTCCACTAGTGCTTAGGGAGATAAGAT
43368198 CTGTTATCTT
Statistics
Matches: 175, Mismatches: 54, Indels: 46
0.64 0.20 0.17
Matches are distributed among these distances:
42 12 0.07
43 19 0.11
44 121 0.69
45 12 0.07
46 11 0.06
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (44 bp):
ATCTGCTCCACTAGTGCTTAGGGAGATAAGATTTGTCGTCTTCA
Found at i:43382084 original size:21 final size:18
Alignment explanation
Indices: 43382058--43382101 Score: 52
Period size: 21 Copynumber: 2.3 Consensus size: 18
43382048 ACATGTATAA
43382058 GTATGTATATTAATTAAGAAT
1 GTATGTATATT-A-TAA-AAT
*
43382079 GTATGTGTATTATAAAAT
1 GTATGTATATTATAAAAT
43382097 GTATG
1 GTATG
43382102 CATGTATATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 8 0.36
19 3 0.14
20 1 0.05
21 10 0.45
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.43
Consensus pattern (18 bp):
GTATGTATATTATAAAAT
Found at i:43383156 original size:19 final size:20
Alignment explanation
Indices: 43383112--43383156 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
43383102 AAAGGGTGAG
43383112 AAGT-AAAAGTTTAGGAGAA
1 AAGTAAAAAGTTTAGGAGAA
*
43383131 AAATAAAAAGTTTGAGG-G-A
1 AAGTAAAAAGTTT-AGGAGAA
43383150 AAGTAAA
1 AAGTAAA
43383157 TAGGGGAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 10 0.45
20 9 0.41
21 3 0.14
ACGTcount: A:0.56, C:0.00, G:0.24, T:0.20
Consensus pattern (20 bp):
AAGTAAAAAGTTTAGGAGAA
Found at i:43383275 original size:30 final size:31
Alignment explanation
Indices: 43383236--43383295 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
43383226 GGAGGTGGGA
*
43383236 TGGGAAGGGAATAAAAGTTTTAGAGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGAGGAAAAG
* * *
43383267 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGAGGAAAA
43383296 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGAGGAAAAG
Found at i:43385082 original size:15 final size:15
Alignment explanation
Indices: 43385062--43385091 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
43385052 GACCCAAAAG
43385062 GCCCAACAGCCCAAA
1 GCCCAACAGCCCAAA
*
43385077 GCCCAATAGCCCAAA
1 GCCCAACAGCCCAAA
43385092 ACTTAAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.43, G:0.13, T:0.03
Consensus pattern (15 bp):
GCCCAACAGCCCAAA
Found at i:43386351 original size:13 final size:13
Alignment explanation
Indices: 43386333--43386359 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
43386323 TTTTATTTGG
43386333 TCATTAATTATTA
1 TCATTAATTATTA
43386346 TCATTAATTATTA
1 TCATTAATTATTA
43386359 T
1 T
43386360 AAGTACTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (13 bp):
TCATTAATTATTA
Found at i:43389241 original size:20 final size:20
Alignment explanation
Indices: 43389218--43389255 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
43389208 CTAGAAAAAA
43389218 GATAGAGAAGTTAGAAGAAG
1 GATAGAGAAGTTAGAAGAAG
*
43389238 GATAGAGAAGTTGGAAGA
1 GATAGAGAAGTTAGAAGA
43389256 GGAGAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.37, T:0.16
Consensus pattern (20 bp):
GATAGAGAAGTTAGAAGAAG
Found at i:43398349 original size:94 final size:95
Alignment explanation
Indices: 43398186--43398452 Score: 335
Period size: 94 Copynumber: 2.8 Consensus size: 95
43398176 AACTCCAGTC
* * ** *
43398186 CCCCTGAAGTTGTAGTGGGTTTGAATGAAGCTACAATAGTGAATCTTATC-TCCTTGAAGTTACA
1 CCCCTGAAGTTGCAGTGGGTTGGAATGAAGCTACAATAGAAAATCTTATCTTCCTTAAAGTTACA
*
43398250 ATGGAGCAAGATGAAGCTACAAATCCTATG
66 ATGGAGCAAGATGAAGCTACAAATCCTATA
* * *
43398280 CCCCTGAAGTGGCAGTGGGTTGGAGTGAAGCTACCATAGAAAATCTTATCTTCC-TAAAGTTACA
1 CCCCTGAAGTTGCAGTGGGTTGGAATGAAGCTACAATAGAAAATCTTATCTTCCTTAAAGTTACA
*
43398344 GTGGAGCAAGATGAAGCTACAAATCCTATA
66 ATGGAGCAAGATGAAGCTACAAATCCTATA
* * * * * **
43398374 CCTCTGAAGTTGCAGTGGGTTGGAATGAAACTACAACA-ACAAATCTTATC-TCCTTGAAGCTGT
1 CCCCTGAAGTTGCAGTGGGTTGGAATGAAGCTACAATAGA-AAATCTTATCTTCCTTAAAGTTAC
*
43398437 AATGGAGCAATATGAA
65 AATGGAGCAAGATGAA
43398453 ACTGTGACAC
Statistics
Matches: 148, Mismatches: 22, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
93 4 0.03
94 141 0.95
95 3 0.02
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (95 bp):
CCCCTGAAGTTGCAGTGGGTTGGAATGAAGCTACAATAGAAAATCTTATCTTCCTTAAAGTTACA
ATGGAGCAAGATGAAGCTACAAATCCTATA
Found at i:43398384 original size:44 final size:43
Alignment explanation
Indices: 43398236--43398391 Score: 109
Period size: 44 Copynumber: 3.4 Consensus size: 43
43398226 GAATCTTATC
*
43398236 TCCT-TGAAGTTACAATGGAGCAAGATGAAGCTACAAATCCTA
1 TCCTCTGAAGTTACAGTGGAGCAAGATGAAGCTACAAATCCTA
* ** *** *
43398278 TGCCCCTGAAGTGGCAGTGG-GTTGGAGTGAAGCTACCATAGAAAATCTTA
1 T-CCTCTGAAGTTACAGTGGAGCAAGA-TGAAGCTA-C-----AAATCCTA
* *
43398328 TCTTCCTAAAGTTACAGTGGAGCAAGATGAAGCTACAAATCCTA
1 TCCT-CTGAAGTTACAGTGGAGCAAGATGAAGCTACAAATCCTA
*
43398372 TACCTCTGAAGTTGCAGTGG
1 T-CCTCTGAAGTTACAGTGG
43398392 GTTGGAATGA
Statistics
Matches: 82, Mismatches: 20, Indels: 22
0.66 0.16 0.18
Matches are distributed among these distances:
42 1 0.01
43 5 0.06
44 40 0.49
45 3 0.04
49 2 0.02
50 28 0.34
51 3 0.04
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (43 bp):
TCCTCTGAAGTTACAGTGGAGCAAGATGAAGCTACAAATCCTA
Found at i:43398402 original size:44 final size:43
Alignment explanation
Indices: 43398260--43398409 Score: 104
Period size: 44 Copynumber: 3.3 Consensus size: 43
43398250 ATGGAGCAAG
* *
43398260 ATGAAGCTACAAATCCTATGCCCCTGAAGTGGCAGTGGGTTGGA
1 ATGAAGCTACAAATCCTAT-CCTCTGAAGTTGCAGTGGGTTGGA
* * * * * ***
43398304 GTGAAGCTACCATAGAAAATCTTATCTTCCTAAAGTTACAGTGGAGCAAG-
1 ATGAAGCTA-C-----AAATCCTATCCT-CTGAAGTTGCAGTGG-GTTGGA
43398354 ATGAAGCTACAAATCCTATACCTCTGAAGTTGCAGTGGGTTGGA
1 ATGAAGCTACAAATCCTAT-CCTCTGAAGTTGCAGTGGGTTGGA
*
43398398 ATGAAACTACAA
1 ATGAAGCTACAA
43398410 CAACAAATCT
Statistics
Matches: 77, Mismatches: 19, Indels: 20
0.66 0.16 0.17
Matches are distributed among these distances:
43 2 0.03
44 40 0.52
45 3 0.04
49 2 0.03
50 28 0.36
51 2 0.03
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (43 bp):
ATGAAGCTACAAATCCTATCCTCTGAAGTTGCAGTGGGTTGGA
Found at i:43402684 original size:15 final size:15
Alignment explanation
Indices: 43402637--43402687 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
43402627 TTTGAAATTA
*
43402637 AATTTATGTTTTTAT
1 AATTTATATTTTTAT
* * *
43402652 AAGTTATTACTTTAAT
1 AATTTA-TATTTTTAT
43402668 AATTTATATTTTTAT
1 AATTTATATTTTTAT
43402683 AATTT
1 AATTT
43402688 TAAAAAATTT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (15 bp):
AATTTATATTTTTAT
Found at i:43415042 original size:40 final size:39
Alignment explanation
Indices: 43414964--43415044 Score: 108
Period size: 40 Copynumber: 2.1 Consensus size: 39
43414954 GTAAGGGAAT
*
43414964 AGGGAAAGGAAATGAAGAAAAATGGAAGGGAATGAAGAG
1 AGGGAAAGAAAATGAAGAAAAATGGAAGGGAATGAAGAG
* * * *
43415003 NAGGGAAAGAAAATGAAGAACAATGGACGGGGATTAAGAG
1 -AGGGAAAGAAAATGAAGAAAAATGGAAGGGAATGAAGAG
43415043 AG
1 AG
43415045 AAAAATAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 2 0.06
40 34 0.94
ACGTcount: A:0.51, C:0.02, G:0.37, T:0.09
Consensus pattern (39 bp):
AGGGAAAGAAAATGAAGAAAAATGGAAGGGAATGAAGAG
Found at i:43423959 original size:22 final size:22
Alignment explanation
Indices: 43423884--43424120 Score: 131
Period size: 25 Copynumber: 10.1 Consensus size: 22
43423874 CAACCCTGTT
*
43423884 TTGGACAGCAATTATTCATCAAA
1 TTGGACAGC-ATTATACATCAAA
*
43423907 TTGGACAGCAATAATATGC-TCAAA
1 TTGGACAGC-AT--TATACATCAAA
*
43423931 ATGGACAGCATTATACATCAAA
1 TTGGACAGCATTATACATCAAA
* *
43423953 TTAGACAGC-TTAAATATACTCAAAA
1 TTGGACAGCATT--ATACA-TC-AAA
* * *
43423978 TTTGATAGCATTATACATTAAA
1 TTGGACAGCATTATACATCAAA
* * *
43424000 ATGGACAGCATCAATATACTTAAAA
1 TTGGACAGCAT---TATACATCAAA
*
43424025 TTGGACAGCATTATACATTAAA
1 TTGGACAGCATTATACATCAAA
*
43424047 ATGGACAGCATCAATATAC-TCAAAA
1 TTGGACAGCAT---TATACATC-AAA
*
43424072 TTGGACAGCAATAATATGC-TCAAAA
1 TTGGACAGC-AT--TATACATC-AAA
* *
43424097 TTGGACAACATTATACATTAAA
1 TTGGACAGCATTATACATCAAA
43424119 TT
1 TT
43424121 ATAACAAAAA
Statistics
Matches: 172, Mismatches: 25, Indels: 35
0.74 0.11 0.15
Matches are distributed among these distances:
21 6 0.03
22 51 0.30
23 20 0.12
24 22 0.13
25 69 0.40
26 4 0.02
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (22 bp):
TTGGACAGCATTATACATCAAA
Found at i:43424007 original size:47 final size:47
Alignment explanation
Indices: 43423884--43424081 Score: 256
Period size: 47 Copynumber: 4.2 Consensus size: 47
43423874 CAACCCTGTT
* * * *
43423884 TTGGACAGCAATTATTCATCAAATTGGACAGCAAT-AATATGCTCAAAA
1 TTGGACAGC-ATTATACATTAAAATGGACAGC-ATCAATATACTCAAAA
* * * * *
43423932 -TGGACAGCATTATACATCAAATTAGACAGCTTAAATATACTCAAAA
1 TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTCAAAA
* * *
43423978 TTTGATAGCATTATACATTAAAATGGACAGCATCAATATACTTAAAA
1 TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTCAAAA
43424025 TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTCAAAA
1 TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTCAAAA
43424072 TTGGACAGCA
1 TTGGACAGCA
43424082 ATAATATGCT
Statistics
Matches: 133, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
45 1 0.01
46 32 0.24
47 100 0.75
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.27
Consensus pattern (47 bp):
TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTCAAAA
Found at i:43424018 original size:25 final size:25
Alignment explanation
Indices: 43423904--43424103 Score: 149
Period size: 25 Copynumber: 8.4 Consensus size: 25
43423894 ATTATTCATC
* *
43423904 AAATTGGACAGCAAT-AATATGCTCA
1 AAATTGGACAGC-ATCAATATACTTA
* *
43423929 AAA-TGGACAGCAT---TATACATC
1 AAATTGGACAGCATCAATATACTTA
* * * *
43423950 AAATTAGACAGCTTAAATATACTCA
1 AAATTGGACAGCATCAATATACTTA
* *
43423975 AAATTTGATAGCAT---TATACATTA
1 AAATTGGACAGCATCAATATAC-TTA
43423998 AAA-TGGACAGCATCAATATACTTA
1 AAATTGGACAGCATCAATATACTTA
43424022 AAATTGGACAGCAT---TATACATTA
1 AAATTGGACAGCATCAATATAC-TTA
*
43424045 AAA-TGGACAGCATCAATATACTCA
1 AAATTGGACAGCATCAATATACTTA
* *
43424069 AAATTGGACAGCAAT-AATATGCTCA
1 AAATTGGACAGC-ATCAATATACTTA
43424094 AAATTGGACA
1 AAATTGGACA
43424104 ACATTATACA
Statistics
Matches: 143, Mismatches: 17, Indels: 30
0.75 0.09 0.16
Matches are distributed among these distances:
21 7 0.05
22 36 0.25
23 13 0.09
24 19 0.13
25 66 0.46
26 2 0.01
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.27
Consensus pattern (25 bp):
AAATTGGACAGCATCAATATACTTA
Found at i:43425084 original size:28 final size:27
Alignment explanation
Indices: 43425052--43425150 Score: 112
Period size: 28 Copynumber: 3.6 Consensus size: 27
43425042 TTAATAAGTA
*
43425052 CGCACACTTAGTGCTTAATAATCAAACT
1 CGCACACTTAGTGCTT-ATAATTAAACT
* *
43425080 CGCACACTTAGTGCTT-TACCCTTATACT
1 CGCACACTTAGTGCTTATA--ATTAAACT
43425108 CGCACACTTAGTGCATT-TCAATTAAACT
1 CGCACACTTAGTGC-TTAT-AATTAAACT
43425136 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
43425151 AATCTCATTA
Statistics
Matches: 62, Mismatches: 5, Indels: 9
0.82 0.07 0.12
Matches are distributed among these distances:
26 2 0.03
27 1 0.02
28 55 0.89
29 3 0.05
30 1 0.02
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.31
Consensus pattern (27 bp):
CGCACACTTAGTGCTTATAATTAAACT
Found at i:43431277 original size:26 final size:28
Alignment explanation
Indices: 43431224--43431277 Score: 67
Period size: 30 Copynumber: 1.9 Consensus size: 28
43431214 TTTCTACTTA
43431224 AAAATTAATCATTCATAATTAACCTTAATT
1 AAAATTAATCATT-ATAATTAA-CTTAATT
*
43431254 AAAATTATTCATT-TAATTAA-TTAA
1 AAAATTAATCATTATAATTAACTTAA
43431278 CCATGTTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 4 0.17
28 7 0.30
30 12 0.52
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (28 bp):
AAAATTAATCATTATAATTAACTTAATT
Found at i:43432662 original size:43 final size:43
Alignment explanation
Indices: 43432586--43432812 Score: 235
Period size: 43 Copynumber: 5.3 Consensus size: 43
43432576 AATCAAAGTG
* * *
43432586 AATATATTGGCACACATA-TCGCATCATCGGACGAACTGAAGCA
1 AATATACTGGCACACACAGT-GCATCATCGGACGAACCGAAGCA
* * * **
43432629 AATATACTGGCACACATAGTGCATTATCAGACGAATTGAAGCA
1 AATATACTGGCACACACAGTGCATCATCGGACGAACCGAAGCA
* * * *
43432672 AATATACTGACAGACACAGTGCATCACCGGATGAACCGAAGCA
1 AATATACTGGCACACACAGTGCATCATCGGACGAACCGAAGCA
* * * * * *
43432715 AATATATTGGCACACACAGTACATTATCGAACGAACCAAAACA
1 AATATACTGGCACACACAGTGCATCATCGGACGAACCGAAGCA
* * *
43432758 AATATGCTGG--CACACAGTGCATCATCGGACGAACCAAAGTA
1 AATATACTGGCACACACAGTGCATCATCGGACGAACCGAAGCA
43432799 AATATACTGGCACA
1 AATATACTGGCACA
43432813 TGAAGTGCAT
Statistics
Matches: 150, Mismatches: 31, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
41 35 0.23
43 114 0.76
44 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.18, T:0.19
Consensus pattern (43 bp):
AATATACTGGCACACACAGTGCATCATCGGACGAACCGAAGCA
Found at i:43435667 original size:22 final size:23
Alignment explanation
Indices: 43435642--43435692 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 23
43435632 TACATGAAAC
43435642 TTAAAATAAT-TATATGATAAAT
1 TTAAAATAATATATATGATAAAT
*
43435664 TTAAAATAATAATATGTGATAAAT
1 TTAAAATAAT-ATATATGATAAAT
43435688 TTAAA
1 TTAAA
43435693 CAACATTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 10 0.38
24 16 0.62
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (23 bp):
TTAAAATAATATATATGATAAAT
Found at i:43437284 original size:50 final size:51
Alignment explanation
Indices: 43437202--43437472 Score: 214
Period size: 50 Copynumber: 5.4 Consensus size: 51
43437192 TAACTCGTAA
* * * *
43437202 CTTTAATCTGTTTAACTGCAATG-TCGGGGAAGTAAGATTCGCCGTTGTGG
1 CTTTAATCTGTTTCACTGCACTGCTCTGAGAAGTAAGATTCGCCGTTGTGG
* * * *
43437252 CTTTAATCTGTTCCATTGCACCGCT-TGAGAAGTAAGACTT-GCTGTTGTGG
1 CTTTAATCTGTTTCACTGCACTGCTCTGAGAAGTAAGA-TTCGCCGTTGTGG
* * * * * * **
43437302 CTTTAATCTTTTTAAATGCGA-TG-TCGGGGAAGCAAGATTCATCGTTGTGG
1 CTTTAATCTGTTTCACTGC-ACTGCTCTGAGAAGTAAGATTCGCCGTTGTGG
* * * *
43437352 CTTTAATCTATTTCACTGCACTGCT-TAAGAAGTAAGATTCGCTGTTGTAG
1 CTTTAATCTGTTTCACTGCACTGCTCTGAGAAGTAAGATTCGCCGTTGTGG
* * * * * *
43437402 CTTTAATCTTTTTAACTGCAATG-TCTGGGAAGCAAGATTCGTCGTTGTGG
1 CTTTAATCTGTTTCACTGCACTGCTCTGAGAAGTAAGATTCGCCGTTGTGG
* * *
43437452 CGTTAATCTGTTCCATTGCAC
1 CTTTAATCTGTTTCACTGCAC
43437473 CGCCAGGGAA
Statistics
Matches: 168, Mismatches: 45, Indels: 16
0.73 0.20 0.07
Matches are distributed among these distances:
49 5 0.03
50 158 0.94
51 5 0.03
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.37
Consensus pattern (51 bp):
CTTTAATCTGTTTCACTGCACTGCTCTGAGAAGTAAGATTCGCCGTTGTGG
Found at i:43437492 original size:100 final size:100
Alignment explanation
Indices: 43437202--43437494 Score: 392
Period size: 100 Copynumber: 2.9 Consensus size: 100
43437192 TAACTCGTAA
* * *
43437202 CTTTAATCTGTTTAACTGCAATGTCGGGGAAGTAAGATTCGCCGTTGTGGCTTTAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGTCGTTGTGGCTTTAATCTGTTCCA
* *
43437267 TTGCACCGCTTGAGAAGTAAGACTT-GCTGTTGTGG
66 TTGCACCGCTAGAGAAGTAAGA-TTCGCTGTTGTAG
* * * * *
43437302 CTTTAATCTTTTTAAATGCGATGTCGGGGAAGCAAGATTCATCGTTGTGGCTTTAATCTATTTCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGTCGTTGTGGCTTTAATCTGTTCCA
* *
43437367 CTGCACTGCTTA-AGAAGTAAGATTCGCTGTTGTAG
66 TTGCACCGC-TAGAGAAGTAAGATTCGCTGTTGTAG
* *
43437402 CTTTAATCTTTTTAACTGCAATGTCTGGGAAGCAAGATTCGTCGTTGTGGCGTTAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGTCGTTGTGGCTTTAATCTGTTCCA
* * * *
43437467 TTGCACCGCCAGGGAAATAACATTCGCT
66 TTGCACCGCTAGAGAAGTAAGATTCGCT
43437495 ATTCTCAGTC
Statistics
Matches: 165, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
99 3 0.02
100 161 0.98
101 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (100 bp):
CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGTCGTTGTGGCTTTAATCTGTTCCA
TTGCACCGCTAGAGAAGTAAGATTCGCTGTTGTAG
Found at i:43437901 original size:132 final size:132
Alignment explanation
Indices: 43437652--43438553 Score: 1653
Period size: 132 Copynumber: 6.8 Consensus size: 132
43437642 ACTGTAATTT
* * * * * * * * * *
43437652 CAGGGAGATAGGATTAGTGGCTTCAATATACTCCACTGTAACCTCAAGAAGGTAAAATCTGCCAT
1 CAGGGATATAGAATTACTGGCTTCTATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGTCAT
* *
43437717 CCTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCAATTCCACTGCTG
66 CTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCAATTCCACTGCTG
43437782 CC
131 CC
43437784 CAGGGATATAGAATTACTGGCTTCTATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGTCAT
1 CAGGGATATAGAATTACTGGCTTCTATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGTCAT
* *
43437849 CTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGAAATC-CCAAATCAATTCCACTGCT
66 CTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTC-AATCAATTCCACTGCT
43437913 GCC
130 GCC
43437916 CAGGGATATAGAATTACTGGCTTCTATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGTCAT
1 CAGGGATATAGAATTACTGGCTTCTATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGTCAT
43437981 CTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCAATTCCACTGCTG
66 CTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCAATTCCACTGCTG
43438046 CC
131 CC
43438048 CAGGGATATAGAATTACTGGCTTCTATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGTCAT
1 CAGGGATATAGAATTACTGGCTTCTATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGTCAT
43438113 CTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCAATTCCACTGCTG
66 CTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCAATTCCACTGCTG
43438178 CC
131 CC
43438180 CAGGGATATAGAATTACTGGCTTCTATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGTCAT
1 CAGGGATATAGAATTACTGGCTTCTATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGTCAT
43438245 CTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCAATTCCACTGCTG
66 CTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCAATTCCACTGCTG
43438310 CC
131 CC
43438312 CAGGGATATAGAATTACTGGCTTCTATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGTCAT
1 CAGGGATATAGAATTACTGGCTTCTATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGTCAT
43438377 CTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCAATTCCACTGCTG
66 CTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCAATTCCACTGCTG
43438442 CC
131 CC
43438444 CAGGGATATAGAATTACTGGCTTCTATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGTCAT
1 CAGGGATATAGAATTACTGGCTTCTATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGTCAT
*
43438509 CTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGAAATC
66 CTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATC
43438554 CCAACCTATT
Statistics
Matches: 751, Mismatches: 17, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
131 1 0.00
132 749 1.00
133 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.28
Consensus pattern (132 bp):
CAGGGATATAGAATTACTGGCTTCTATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGTCAT
CTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCAATTCCACTGCTG
CC
Found at i:43438980 original size:131 final size:131
Alignment explanation
Indices: 43438826--43439132 Score: 515
Period size: 131 Copynumber: 2.3 Consensus size: 131
43438816 TGAAATCCCA
*
43438826 ATCTGCTCCACTATTTCTTAGGGAGATAAGATCTGTAGTTTCCAACCTATTCCACTGCTGCTCAG
1 ATCTGCTCCACTATTTCTTAGGGAGATAAGATCTGTAGTTTCCAACATATTCCACTGCTGCTCAG
* * * *
43438891 GGAAATAGGACTTGTAGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCTGTCTTC
66 AGAAATAGGACTTGTAGCTTAAATCTATTTCCCTACTCCTAGGGAAGATAAGATTCGCCGTCTTC
43438956 G
131 G
* *
43438957 ATCTGCTCCACTATTTCTTAGGGAGATAAGATCTGTAGTTTACAACATATTCCACTGTTGCTCAG
1 ATCTGCTCCACTATTTCTTAGGGAGATAAGATCTGTAGTTTCCAACATATTCCACTGCTGCTCAG
*
43439022 AGAAATAGGACTTGTGGCTTAAATCTATTTCCCTACTCCTAGGGAAGATAAGATTCGCCGTCTTC
66 AGAAATAGGACTTGTAGCTTAAATCTATTTCCCTACTCCTAGGGAAGATAAGATTCGCCGTCTTC
43439087 G
131 G
* * *
43439088 ATCTGCTCCACTATTGCTTAAGGAGATAAGATCTGTAATTTCCAA
1 ATCTGCTCCACTATTTCTTAGGGAGATAAGATCTGTAGTTTCCAA
43439133 TATTCAACCT
Statistics
Matches: 164, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
131 164 1.00
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (131 bp):
ATCTGCTCCACTATTTCTTAGGGAGATAAGATCTGTAGTTTCCAACATATTCCACTGCTGCTCAG
AGAAATAGGACTTGTAGCTTAAATCTATTTCCCTACTCCTAGGGAAGATAAGATTCGCCGTCTTC
G
Found at i:43439151 original size:313 final size:308
Alignment explanation
Indices: 43438519--43439122 Score: 701
Period size: 313 Copynumber: 2.0 Consensus size: 308
43438509 CTTCGATCTA
* *
43438519 CTCCACTACTGCTTAGGGAGATAAGATCTGAAATCCCAACCTATTTCACTACTGACTAGGGAGAT
1 CTCCACTACTGCTTAGGGAGATAAGATCTGAAATCCCAACCTATTCCACTACTGACTAGGGAAAT
*
43438584 AGGACTTGTGGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTG
66 AGGACTTGTAGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTG
* *
43438649 CTCCACTATTGCTTAGGGAGATAAGATCTGTAATTTCCAATCTTCAACCTGCTCCACTACAACCG
131 CTCCACTATTGCTTAGGGAGATAAGATCTGTAATTTCAAATATTCAACCTGCTCCACTACAA-CG
** * * * * * *
43438714 AGGGAGGCAACGCTTGTGCCTTAGATCTGCTTCGCCGTCGACGCAGGAAGGCGAGATCTGCTATC
195 AAAGAGG-AAC-CTTGTGCCTTAAATCTACTTCGCCGTC-ACCCAGGAAGACAAGATCTGCCATC
* *
43438779 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCCCAATCTG
257 TTCGATCTGCTCCACTACTGCTTAAGGAGATAAGATCTGAAATCCCAACCTG
* * ** * *
43438831 CTCCACTATTTCTTAGGGAGATAAGATCTGTAGTTTCCAACCTATTCCACTGCTG-CTCAGGGAA
1 CTCCACTACTGCTTAGGGAGATAAGATCTG-AAATCCCAACCTATTCCACTACTGACT-AGGGAA
* *
43438895 ATAGGACTTGTAGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCTGTCTTCGATC
64 ATAGGACTTGTAGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATC
* * * **
43438960 TGCTCCACTATTTCTTAGGGAGATAAGATCTGTAGTTTACAACATATTCCA-CTG-T-TGCT-CA
129 TGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATTT-CAA-ATATTCAACCTGCTCCACTACA
* * * *
43439021 GA-GAAATAGG-A-CTTGTGGCTTAAATCTATTTC-CC-T-ACTCCTAGGGAAGATAAGAT-TCG
192 -ACGAAAGAGGAACCTTGTGCCTTAAATCTACTTCGCCGTCAC-CC-A-GGAAGACAAGATCT-G
* *
43439079 CCGTCTTCGATCTGCTCCACTATTGCTTAAGGAGATAAGATCTG
252 CCATCTTCGATCTGCTCCACTACTGCTTAAGGAGATAAGATCTG
43439123 TAATTTCCAA
Statistics
Matches: 250, Mismatches: 33, Indels: 25
0.81 0.11 0.08
Matches are distributed among these distances:
302 2 0.01
303 1 0.00
304 3 0.01
305 52 0.21
306 17 0.07
308 1 0.00
310 5 0.02
311 2 0.01
312 33 0.13
313 123 0.49
314 5 0.02
315 6 0.02
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (308 bp):
CTCCACTACTGCTTAGGGAGATAAGATCTGAAATCCCAACCTATTCCACTACTGACTAGGGAAAT
AGGACTTGTAGCTTAAATCTGCTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTG
CTCCACTATTGCTTAGGGAGATAAGATCTGTAATTTCAAATATTCAACCTGCTCCACTACAACGA
AAGAGGAACCTTGTGCCTTAAATCTACTTCGCCGTCACCCAGGAAGACAAGATCTGCCATCTTCG
ATCTGCTCCACTACTGCTTAAGGAGATAAGATCTGAAATCCCAACCTG
Found at i:43439254 original size:44 final size:44
Alignment explanation
Indices: 43439206--43439343 Score: 136
Period size: 44 Copynumber: 3.2 Consensus size: 44
43439196 CGACGCAGGA
*
43439206 AGGCAAGATCTGCTATCTTCAACCTACTCCACTGCAACCGAGGG
1 AGGCAAGATCTGCTATCTTCAACCTGCTCCACTGCAACCGAGGG
* * * **** **
43439250 AGGCAAGGT-TAG-TATCTTCGATCTGCTCCACTATTGCTTAGGG
1 AGGCAAGATCT-GCTATCTTCAACCTGCTCCACTGCAACCGAGGG
* * *
43439293 AGGCAAGATCCGCTATCTTTAACCTGCTCCACTGCAACCGAAGG
1 AGGCAAGATCTGCTATCTTCAACCTGCTCCACTGCAACCGAGGG
43439337 AGGCAAG
1 AGGCAAG
43439344 GCTTTGTTTT
Statistics
Matches: 69, Mismatches: 22, Indels: 6
0.71 0.23 0.06
Matches are distributed among these distances:
43 32 0.46
44 37 0.54
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (44 bp):
AGGCAAGATCTGCTATCTTCAACCTGCTCCACTGCAACCGAGGG
Found at i:43439326 original size:87 final size:88
Alignment explanation
Indices: 43439135--43439347 Score: 259
Period size: 87 Copynumber: 2.4 Consensus size: 88
43439125 ATTTCCAATA
* * * * *
43439135 TTCAACCTGCTCCACTACAACCGAGGGAGGCAAGGCTTGTGCCTTCCATCTGCTTCGCCGTCGAC
1 TTCAACCTGCTCCACTGCAACCGAGGGAGGCAAGGCTTGTACCTTCCATCTGCTCCACCATCGAC
*
43439200 GCAGGAAGGCAAGATCTGCTATC
66 GCAGGAAGGCAAGATCCGCTATC
* * * * *
43439223 TTCAACCTACTCCACTGCAACCGAGGGAGGCAAGG-TTAGTATCTTCGATCTGCTCCACTATTG-
1 TTCAACCTGCTCCACTGCAACCGAGGGAGGCAAGGCTT-GTACCTTCCATCTGCTCCACCATCGA
** *
43439286 CTTAGGGAGGCAAGATCCGCTATC
65 CGCAGGAAGGCAAGATCCGCTATC
* *
43439310 TTTAACCTGCTCCACTGCAACCGAAGGAGGCAAGGCTT
1 TTCAACCTGCTCCACTGCAACCGAGGGAGGCAAGGCTT
43439348 TGTTTTCGAT
Statistics
Matches: 106, Mismatches: 17, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
87 54 0.51
88 52 0.49
ACGTcount: A:0.23, C:0.30, G:0.24, T:0.23
Consensus pattern (88 bp):
TTCAACCTGCTCCACTGCAACCGAGGGAGGCAAGGCTTGTACCTTCCATCTGCTCCACCATCGAC
GCAGGAAGGCAAGATCCGCTATC
Found at i:43440600 original size:16 final size:17
Alignment explanation
Indices: 43440579--43440611 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
43440569 TTAGCCTCTC
43440579 CATTTTAC-TTTTTCAT
1 CATTTTACATTTTTCAT
*
43440595 CATTTTTCATTTTTCAT
1 CATTTTACATTTTTCAT
43440612 TCACTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (17 bp):
CATTTTACATTTTTCAT
Found at i:43441585 original size:29 final size:29
Alignment explanation
Indices: 43441547--43441630 Score: 99
Period size: 29 Copynumber: 3.1 Consensus size: 29
43441537 CATTTTCATA
43441547 TTTTTA-TTTTGACTTTGATTGATTTTTT
1 TTTTTACTTTTGACTTTGATTGATTTTTT
*
43441575 TTTTTACTTTTGACTTTGATT-TTTCTTTT
1 TTTTTACTTTTGACTTTGATTGATT-TTTT
*
43441604 TTTTTTCTTTTG--TTT--TTGATTTTTT
1 TTTTTACTTTTGACTTTGATTGATTTTTT
43441629 TT
1 TT
43441631 GAATCTAAAC
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
25 8 0.16
26 2 0.04
27 3 0.06
28 8 0.16
29 29 0.58
ACGTcount: A:0.10, C:0.06, G:0.08, T:0.76
Consensus pattern (29 bp):
TTTTTACTTTTGACTTTGATTGATTTTTT
Found at i:43446899 original size:22 final size:23
Alignment explanation
Indices: 43446874--43446924 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 23
43446864 TACATGAAAC
43446874 TTAAAATAAT-TATATGATAAAT
1 TTAAAATAATATATATGATAAAT
*
43446896 TTAAAATAATAATATGTGATAAAT
1 TTAAAATAAT-ATATATGATAAAT
43446920 TTAAA
1 TTAAA
43446925 CAACATTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 10 0.38
24 16 0.62
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (23 bp):
TTAAAATAATATATATGATAAAT
Found at i:43447163 original size:43 final size:44
Alignment explanation
Indices: 43447087--43447176 Score: 137
Period size: 43 Copynumber: 2.1 Consensus size: 44
43447077 TTTTAAAACA
* *
43447087 AAATCAGAACGAAAAAAAGCAAAAATAAGATAAAATTGAAGGAC
1 AAATCAGAAAGAAAAAAAGCAAAAATAAAATAAAATTGAAGGAC
**
43447131 AAATCAGAAAG-AAAAAAGTGAAAATAAAATAAAATTGAAGGAC
1 AAATCAGAAAGAAAAAAAGCAAAAATAAAATAAAATTGAAGGAC
43447174 AAA
1 AAA
43447177 AATGCAGTGC
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 32 0.76
44 10 0.24
ACGTcount: A:0.66, C:0.07, G:0.16, T:0.12
Consensus pattern (44 bp):
AAATCAGAAAGAAAAAAAGCAAAAATAAAATAAAATTGAAGGAC
Found at i:43461062 original size:34 final size:35
Alignment explanation
Indices: 43461018--43461084 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
43461008 CAGTAAAATA
*
43461018 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
43461052 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
43461085 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:43469241 original size:10 final size:10
Alignment explanation
Indices: 43469216--43469246 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
43469206 CAATAAGAGT
43469216 AATAATAAATA
1 AATAATAAA-A
43469227 AATAATAAAA
1 AATAATAAAA
43469237 AATAATAAAA
1 AATAATAAAA
43469247 TTAATTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.55
11 9 0.45
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (10 bp):
AATAATAAAA
Found at i:43470079 original size:3 final size:3
Alignment explanation
Indices: 43470071--43470132 Score: 54
Period size: 3 Copynumber: 20.3 Consensus size: 3
43470061 ATAACCAAAC
* * *
43470071 ATA ATA ATA AT- ATCA ACA ATA ATA AGA GTA ATA ATA ATAA ATA ATA
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA
* *
43470117 AAA ATA AAA ATA ATA A
1 ATA ATA ATA ATA ATA A
43470133 AATTAATTAA
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
2 2 0.04
3 40 0.87
4 4 0.09
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (3 bp):
ATA
Found at i:43470116 original size:22 final size:22
Alignment explanation
Indices: 43470088--43470133 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
43470078 TAATATCAAC
* * *
43470088 AATAATAAGAGTAATAATAATA
1 AATAATAAAAATAAAAATAATA
43470110 AATAATAAAAATAAAAATAATA
1 AATAATAAAAATAAAAATAATA
43470132 AA
1 AA
43470134 ATTAATTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (22 bp):
AATAATAAAAATAAAAATAATA
Found at i:43470127 original size:15 final size:16
Alignment explanation
Indices: 43470103--43470154 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
43470093 TAAGAGTAAT
43470103 AATAATAAATAATAAA
1 AATAATAAATAATAAA
43470119 AATAA-AAATAATAAA
1 AATAATAAATAATAAA
* * **
43470134 ATTAATTAATAGCAAA
1 AATAATAAATAATAAA
43470150 AATAA
1 AATAA
43470155 CAAACAGGAC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
15 14 0.47
16 16 0.53
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (16 bp):
AATAATAAATAATAAA
Found at i:43471083 original size:890 final size:881
Alignment explanation
Indices: 43469134--43470896 Score: 2433
Period size: 890 Copynumber: 2.0 Consensus size: 881
43469124 AAAAATAATA
* *
43469134 GTACATAGTAAGATAATATATAT-ATAAATAGGTAAATGAAAATATAACCAAACATAATAATAAT
1 GTACATAGT-AGATAATATATATAAAAAATAGGTAAATGAAAATATAACCAAACACAATAATAAT
* * * * * * * * * *
43469198 ATCAATAACAATAAGAGT--AATAATAAATAAATAATAAAAAATAATAAAATTAATTAATAGAAA
65 AGCAACAATAATAAGAGTAGAAGAATAAA-GAAGAA-AAATAATAATAAAATTAAGT-AGAGCAA
* * * * *
43469261 AAATAACAAACAAGACTAAATTGAAACTAAAACAGAAATTTAGGGGCAAATCTAAAATAAATAAA
127 AAAGAACAAACAGGACGAAACTGAAACT-AAATAGAAATTTAGGGGCAAATCTAAAATAAATAAA
*
43469326 AGGAGAAGGACCATTCTGAACACGCGAATAATAAGGAGGGATTGAAGGGTAATTCCCCCTGTCCT
191 AGGAGAAGGACCATTCTGAACACGCGAATAACAAGGAGGGATTGAAGGGTAATTCCCCCTGTCCT
* * *
43469391 CCAAAATAACGTCGTTCGAATATTGACGTAATTGAAATCGAAACAAATCATGGGGTACAAAATTA
256 CCAAAACAACGTCGTTCGAATATGGACCTAATTGAAATCGAAACAAATCATGGGGTACAAAATTA
*
43469456 AAATAAAAAACTGAATTAAAATAATAAAGAATGCAGAAAGACCTAATGCGCAAATAGACCATTGA
321 AAAAAAAAAACTGAATTAAAATAATAAAGAATGCAGAAAGACCTAATGCGCAAATAGACCATTGA
* * *
43469521 GACAAAACGCGCAGATCCTTCCCTCGAGTCAGGTTACCGCGCGGATCTCGGCTCTATACGACGCC
386 GACAAAACGCACAGATCCTTCCCTCGAGTCAGGTCACCGCGCGGATCTCAGCTCTATACGACGCC
* * * *
43469586 ATTTTGAAACTACTGAAATGTCATCAAACAATGTCAATTCTTATGTCGTATATAGGTCAAAACAA
451 ATTTTGAAACTACTGAAATGGCATCAAACAACGTCAATTCTTACGCCGTATATAGGTCAAAACAA
* *
43469651 ACCCTAAATGCTAACAGACACTTCATTTAAAAATCTAACCAAAAAACCTAAAATCTACTCTCTGT
516 ACCCTAAATACTAACAGACACTTCATTTAAAAATCTAACAAAAAAACCTAAAATCTACTCTCTGT
* ** * *
43469716 GCACCGCTTTCAGATTTGAAATCCCCCATCCCCTTCAATATACTCAGATCAACAGGGACGACGGC
581 GCACCACTTTCAGATTCAAAATCCCCCATCCCCTTCAATATACGCAGATCAACAGGGACAACGGC
* *
43469781 GTAATGGCGCAGGTAAGGTATTTTTTTTCTTTTTCTCTTTCTTTTCACACAAAAAAAAAATCATG
646 ATAATGGCGCAGGTAAGGTATTTTTTTTCCTTTTCTCTTTCTTTTCACACAAAAAAAAAATCATG
*
43469846 AATCTTAAGAAAAAAACATGAAAAACTGGAAAATCACCTTCAAATCTACTCGATTCTCGGTATTT
711 AATCTTAAGAAAAAAACATGAAAAACTAGAAAATCACCTTCAAATCTACTCGATTCTCGGTATTT
* *
43469911 TTTTTTATCTTTTTCCCCCTTTTTTACAACTTTTAATCGGCTTTTATAGCCAAAAATAATATGAA
776 TTTTTTATCTTTTTCCCCCTTTTTTACAACTTTGAATCAGCTTTTATAGCCAAAAATAATATGAA
* *
43469976 ATTATAACAAATAAAAATTCTATATAAAAGGAGTAATAATT
841 ATTACAACAAATAAAAATTCTATATAAAAGGAGTAACAATT
*
43470017 GTACATAGTAAGATAATATATATAAAAAATAGGTAAATGAAAATATAACCAAACATAATAATAAT
1 GTACATAGT-AGATAATATATATAAAAAATAGGTAAATGAAAATATAACCAAACACAATAATAAT
* * * * * * *
43470082 ATCAACAATAATAAGAGTAATAATAATAAATAATAAAAATAAAAATAATAAAATTAATTAATAGC
65 AGCAACAATAATAAGAGT-AGAAGAATAAAGAAGAAAAAT---AATAATAAAATTAAGT-AGAGC
* * *
43470147 AAAAATAACAAACAGGACTAAATTGAAACTAAAATAGAAATTTAGGGGCAAATCTAAAATAAATA
125 AAAAAGAACAAACAGGACGAAACTGAAACT-AAATAGAAATTTAGGGGCAAATCTAAAATAAATA
* * * *
43470212 AAAGGATAAGGACCATTCTGAACATGCGAATAACAAGGAGGGATTGAAAGGGTAATTTCCCTTGT
189 AAAGGAGAAGGACCATTCTGAACACGCGAATAACAAGGAGGGATTG-AAGGGTAATTCCCCCTGT
* * *
43470277 CCTCCAAAGCGACGTCGTTCGAATATGGACCTAATTGAAATCGAAACAAATCATGGGGTACAAAT
253 CCTCCAAAACAACGTCGTTCGAATATGGACCTAATTGAAATCGAAACAAATCATGGGGTACAAAA
* * *
43470342 TTAAAAGAAAAAAACTGAATTAAAATAATAAAGAATGCGGAAGGACCTAATGCGTAAATAGACCA
318 TTAAAA-AAAAAAACTGAATTAAAATAATAAAGAATGCAGAAAGACCTAATGCGCAAATAGACCA
* *
43470407 TTGAGACAAAACGCACAGATCTTTCCCTCG-GATCAGGTCACTGCGCGGATCTCAGCTCTATACG
382 TTGAGACAAAACGCACAGATCCTTCCCTCGAG-TCAGGTCACCGCGCGGATCTCAGCTCTATACG
* * * **
43470471 ACGCCGTTTTGAAACTTCTGAAATGGCATCAAACGACGTCGTTTCTTACGCCGTATATAGGTCAA
446 ACGCCATTTTGAAACTACTGAAATGGCATCAAACAACGTCAATTCTTACGCCGTATATAGGTCAA
* *
43470536 AACAAACCCTAAATATTAGCAGACACTTCATTTAAAAAATCTAACAAAAAAAAACCTAAAAATCT
511 AACAAACCCTAAATACTAACAGACACTTCATTT-AAAAATCTAAC--AAAAAAACCT-AAAATCT
* * * * * * * **
43470601 ACTCTTTGTGCGCCATTTTCAGATTCAAAATCTCCCATCCCTTTCGATATGCGCAGATCAATGGG
572 ACTCTCTGTGCACCACTTTCAGATTCAAAATCCCCCATCCCCTTCAATATACGCAGATCAACAGG
* *
43470666 GACAACGGCATAATGGCGCAGGTAAGGTA-TTTTTTTCCTTTTCTTTTTCTTTTCACACATGAAA
637 GACAACGGCATAATGGCGCAGGTAAGGTATTTTTTTTCCTTTTCTCTTTCTTTTCACACA-AAAA
* *
43470730 AACAATCATGAATCTTAAGAAAAAAACATGAGAAACTAGAAAATCACCTTCAAATCTACTCGATT
701 AAAAATCATGAATCTTAAGAAAAAAACATGAAAAACTAGAAAATCACCTTCAAATCTACTCGATT
* * *
43470795 CTCTGTATTATTATTATTATTAT-TATTTTTCCCCTTTTTTACAGCTTTGAATCAGCTTTTATAG
766 CTCGGTA-T-TT-TT-TT-TTATCT-TTTTCCCCCTTTTTTACAACTTTGAATCAGCTTTTATAG
*
43470859 CC-AAAATGATATGAAATTACAACAAATAAAAATTCTAT
825 CCAAAAATAATATGAAATTACAACAAATAAAAATTCTAT
43470897 TCTGTCATTC
Statistics
Matches: 790, Mismatches: 69, Indels: 27
0.89 0.08 0.03
Matches are distributed among these distances:
883 23 0.03
884 56 0.07
885 3 0.00
886 5 0.01
887 9 0.01
888 127 0.16
889 82 0.10
890 197 0.25
891 11 0.01
893 37 0.05
894 157 0.20
895 1 0.00
896 2 0.00
897 2 0.00
898 37 0.05
899 41 0.05
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.27
Consensus pattern (881 bp):
GTACATAGTAGATAATATATATAAAAAATAGGTAAATGAAAATATAACCAAACACAATAATAATA
GCAACAATAATAAGAGTAGAAGAATAAAGAAGAAAAATAATAATAAAATTAAGTAGAGCAAAAAG
AACAAACAGGACGAAACTGAAACTAAATAGAAATTTAGGGGCAAATCTAAAATAAATAAAAGGAG
AAGGACCATTCTGAACACGCGAATAACAAGGAGGGATTGAAGGGTAATTCCCCCTGTCCTCCAAA
ACAACGTCGTTCGAATATGGACCTAATTGAAATCGAAACAAATCATGGGGTACAAAATTAAAAAA
AAAAACTGAATTAAAATAATAAAGAATGCAGAAAGACCTAATGCGCAAATAGACCATTGAGACAA
AACGCACAGATCCTTCCCTCGAGTCAGGTCACCGCGCGGATCTCAGCTCTATACGACGCCATTTT
GAAACTACTGAAATGGCATCAAACAACGTCAATTCTTACGCCGTATATAGGTCAAAACAAACCCT
AAATACTAACAGACACTTCATTTAAAAATCTAACAAAAAAACCTAAAATCTACTCTCTGTGCACC
ACTTTCAGATTCAAAATCCCCCATCCCCTTCAATATACGCAGATCAACAGGGACAACGGCATAAT
GGCGCAGGTAAGGTATTTTTTTTCCTTTTCTCTTTCTTTTCACACAAAAAAAAAATCATGAATCT
TAAGAAAAAAACATGAAAAACTAGAAAATCACCTTCAAATCTACTCGATTCTCGGTATTTTTTTT
TATCTTTTTCCCCCTTTTTTACAACTTTGAATCAGCTTTTATAGCCAAAAATAATATGAAATTAC
AACAAATAAAAATTCTATATAAAAGGAGTAACAATT
Found at i:43475242 original size:21 final size:20
Alignment explanation
Indices: 43475199--43475247 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
43475189 TTTAGCTCTC
* *
43475199 ATGAGCTTTAGTTAACTCAT
1 ATGAGTTTTAGTTAACCCAT
*
43475219 ATGAGTTTTAGATTAACCCTT
1 ATGAGTTTTAG-TTAACCCAT
*
43475240 ATGGGTTT
1 ATGAGTTT
43475248 CAATTCAGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (20 bp):
ATGAGTTTTAGTTAACCCAT
Found at i:43475308 original size:42 final size:42
Alignment explanation
Indices: 43475228--43475342 Score: 142
Period size: 42 Copynumber: 2.7 Consensus size: 42
43475218 TATGAGTTTT
43475228 AGATTAACCCTTATGGGTTTCAATTCAGCTCTTTTGAGCTTC
1 AGATTAACCCTTATGGGTTTCAATTCAGCTCTTTTGAGCTTC
* * * * * *
43475270 AGTTTAACCCTAATGGGTTTTAGTTTATCT-TTTCTGAGCTTC
1 AGATTAACCCTTATGGGTTTCAATTCAGCTCTTT-TGAGCTTC
**
43475312 AGATTAACCCTTATGGGTTTCTGTTCAGCTC
1 AGATTAACCCTTATGGGTTTCAATTCAGCTC
43475343 CTTATGGTTG
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
41 3 0.05
42 56 0.95
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.43
Consensus pattern (42 bp):
AGATTAACCCTTATGGGTTTCAATTCAGCTCTTTTGAGCTTC
Found at i:43488230 original size:17 final size:16
Alignment explanation
Indices: 43488180--43488231 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
43488170 CAATCGATTA
43488180 AAAAAAGTAATATTTC
1 AAAAAAGTAATATTTC
* * * *
43488196 AACATAGCAATCTATTC
1 AAAAAAGTAATAT-TTC
43488213 AAAAGAAGTAATATTTC
1 AAAA-AAGTAATATTTC
43488230 AA
1 AA
43488232 TATTATAATC
Statistics
Matches: 26, Mismatches: 8, Indels: 3
0.70 0.22 0.08
Matches are distributed among these distances:
16 9 0.35
17 11 0.42
18 6 0.23
ACGTcount: A:0.52, C:0.12, G:0.08, T:0.29
Consensus pattern (16 bp):
AAAAAAGTAATATTTC
Found at i:43498726 original size:41 final size:43
Alignment explanation
Indices: 43498618--43498730 Score: 142
Period size: 43 Copynumber: 2.7 Consensus size: 43
43498608 AATTCTAACA
**
43498618 ATAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTAATT
1 ATAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATAATTAATT
* * *
43498661 GTGAAAGG-GGTTGCTATGTGCTGATTCC-CCGTATAATTGATT
1 AT-AAAGGTGGTTGCTAAGTGCTGATTCCACCGTATAATTAATT
*
43498703 AT-AAGGTGGTTGCTAAGTACTGATTCCA
1 ATAAAGGTGGTTGCTAAGTGCTGATTCCA
43498731 TCGGGATCCT
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
40 4 0.07
41 18 0.31
42 12 0.20
43 20 0.34
44 5 0.08
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.35
Consensus pattern (43 bp):
ATAAAGGTGGTTGCTAAGTGCTGATTCCACCGTATAATTAATT
Found at i:43498758 original size:44 final size:44
Alignment explanation
Indices: 43498622--43498821 Score: 198
Period size: 44 Copynumber: 4.6 Consensus size: 44
43498612 CTAACAATAA
* **
43498622 AGGTGGTTGCTAAGTGCTGATTCCACC-GTATCC-TT-AATTGTG
1 AGGTGGTTGCTAAGTGCTGATTCCACCGGGATCCTTTGAA-CATG
* * ** ** *
43498664 AAAGG-GGTTGCTATGTGCTGATTCC-CC-GTAT-AATTGATTATA
1 --AGGTGGTTGCTAAGTGCTGATTCCACCGGGATCCTTTGAACATG
* *
43498706 AGGTGGTTGCTAAGTACTGATTCCATCGGGATCCTTTGAACATG
1 AGGTGGTTGCTAAGTGCTGATTCCACCGGGATCCTTTGAACATG
*
43498750 AGGTGGTTGCTAAGTGCTAATTCCACCGGGATCCTTTGAACATG
1 AGGTGGTTGCTAAGTGCTGATTCCACCGGGATCCTTTGAACATG
*
43498794 AGGTGGTTACTAAGTGCTGATTCCACCG
1 AGGTGGTTGCTAAGTGCTGATTCCACCG
43498822 TGTAACGATT
Statistics
Matches: 131, Mismatches: 19, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
40 3 0.02
41 18 0.14
42 11 0.08
43 23 0.18
44 76 0.58
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.33
Consensus pattern (44 bp):
AGGTGGTTGCTAAGTGCTGATTCCACCGGGATCCTTTGAACATG
Found at i:43511494 original size:17 final size:17
Alignment explanation
Indices: 43511472--43511524 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
43511462 ATTACAGAAT
*
43511472 CATATCTTTTAAGATTG
1 CATATCTTTTAAGATTA
*
43511489 CATATCATATCTAAGATTA
1 CATATC-T-TTTAAGATTA
* *
43511508 CATATCCTTGAAGATTA
1 CATATCTTTTAAGATTA
43511525 TGTTTCCATA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
17 14 0.48
18 1 0.03
19 14 0.48
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (17 bp):
CATATCTTTTAAGATTA
Found at i:43512517 original size:17 final size:18
Alignment explanation
Indices: 43512489--43512524 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
43512479 GCATGCATGC
43512489 AAAAAGACAAAAAAAAAG
1 AAAAAGACAAAAAAAAAG
43512507 AAAAAGA-AAAAAAAAAG
1 AAAAAGACAAAAAAAAAG
43512524 A
1 A
43512525 CGTGGTTGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.86, C:0.03, G:0.11, T:0.00
Consensus pattern (18 bp):
AAAAAGACAAAAAAAAAG
Found at i:43525103 original size:17 final size:19
Alignment explanation
Indices: 43525081--43525118 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
43525071 AAAATTGAAA
43525081 AAAATAA-TTGA-AAAAAT
1 AAAATAATTTGATAAAAAT
43525098 AAAATAATTTGATAAAAAT
1 AAAATAATTTGATAAAAAT
43525117 AA
1 AA
43525119 GAAAAGTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.37
18 4 0.21
19 8 0.42
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.26
Consensus pattern (19 bp):
AAAATAATTTGATAAAAAT
Found at i:43533061 original size:16 final size:15
Alignment explanation
Indices: 43533034--43533063 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
43533024 GTCTAAAGTA
43533034 TAAATAATATATATC
1 TAAATAATATATATC
43533049 TAAATATATATATAT
1 TAAATA-ATATATAT
43533064 GAATAAACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (15 bp):
TAAATAATATATATC
Found at i:43533319 original size:13 final size:13
Alignment explanation
Indices: 43533301--43533336 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
43533291 TAATAGTAAT
43533301 AATAAAACTAAA-A
1 AATAAAA-TAAATA
43533314 AATAAAATAAATA
1 AATAAAATAAATA
43533327 AATAAAATAA
1 AATAAAATAA
43533337 TGGGACTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 4 0.18
13 18 0.82
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (13 bp):
AATAAAATAAATA
Found at i:43533721 original size:14 final size:14
Alignment explanation
Indices: 43533698--43533728 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
43533688 GGTAGCCTGT
*
43533698 ATAAATAGAAAAAA
1 ATAAAGAGAAAAAA
43533712 ATAAAGAGAAAAAA
1 ATAAAGAGAAAAAA
43533726 ATA
1 ATA
43533729 TTTTCATTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (14 bp):
ATAAAGAGAAAAAA
Found at i:43541538 original size:25 final size:25
Alignment explanation
Indices: 43541510--43541589 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
43541500 AATTCATGGT
43541510 TAACATTTTTATTCCACTATACAAG
1 TAACATTTTTATTCCACTATACAAG
* ** * *
43541535 TAACTTATTTTAAGCC-TTAT-CATGG
1 TAACAT-TTTTATTCCACTATACA-AG
*
43541560 TTAACATTTTTATTCCACTACACAAG
1 -TAACATTTTTATTCCACTATACAAG
43541586 TAAC
1 TAAC
43541590 TTATTTTAAA
Statistics
Matches: 39, Mismatches: 11, Indels: 10
0.65 0.18 0.17
Matches are distributed among these distances:
24 2 0.05
25 20 0.51
26 15 0.38
27 2 0.05
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (25 bp):
TAACATTTTTATTCCACTATACAAG
Found at i:43541579 original size:51 final size:51
Alignment explanation
Indices: 43541503--43541607 Score: 183
Period size: 51 Copynumber: 2.1 Consensus size: 51
43541493 AAATTCAAAT
* * *
43541503 TCATGGTTAACATTTTTATTCCACTATACAAGTAACTTATTTTAAGCCTTA
1 TCATGGTTAACATTTTTATTCCACTACACAAGTAACTTATTTTAAACCTCA
43541554 TCATGGTTAACATTTTTATTCCACTACACAAGTAACTTATTTTAAACCTCA
1 TCATGGTTAACATTTTTATTCCACTACACAAGTAACTTATTTTAAACCTCA
43541605 TCA
1 TCA
43541608 ACTAACTTTA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (51 bp):
TCATGGTTAACATTTTTATTCCACTACACAAGTAACTTATTTTAAACCTCA
Found at i:43542752 original size:35 final size:35
Alignment explanation
Indices: 43542713--43542780 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
43542703 AACTGGATCA
*
43542713 GAAGACAACTTTCCTTCAGAACTGGTGCAGTGTCG
1 GAAGACAACTTTCCTTCAGAACTAGTGCAGTGTCG
*
43542748 GAAGACAACTTTCCTTCAGAACTAGTGTAGTGT
1 GAAGACAACTTTCCTTCAGAACTAGTGCAGTGT
43542781 TTTTCATATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (35 bp):
GAAGACAACTTTCCTTCAGAACTAGTGCAGTGTCG
Found at i:43545132 original size:18 final size:17
Alignment explanation
Indices: 43545111--43545251 Score: 72
Period size: 17 Copynumber: 8.2 Consensus size: 17
43545101 CAAAGATGTA
*
43545111 AGCTCACCTAAAGTTGCG
1 AGCTCACC-AAAATTGCG
*
43545129 AGCTCACCAAAATTGTG
1 AGCTCACCAAAATTGCG
*
43545146 AGCTC-CTC-AAATGTACG
1 AGCTCAC-CAAAAT-TGCG
* *
43545163 AGCTCACCAAGACTGCG
1 AGCTCACCAAAATTGCG
* * * *
43545180 ATCTCATCAATATTGTG
1 AGCTCACCAAAATTGCG
***
43545197 AGCTCACCAAGGCTGCG
1 AGCTCACCAAAATTGCG
* **
43545214 AGCTCATCAAAGCTGCG
1 AGCTCACCAAAATTGCG
**
43545231 AAG-TCACCAAAGGTGCG
1 -AGCTCACCAAAATTGCG
43545248 AGCT
1 AGCT
43545252 ATGTTAGGCG
Statistics
Matches: 95, Mismatches: 22, Indels: 13
0.73 0.17 0.10
Matches are distributed among these distances:
16 7 0.07
17 75 0.79
18 13 0.14
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.21
Consensus pattern (17 bp):
AGCTCACCAAAATTGCG
Found at i:43545150 original size:17 final size:17
Alignment explanation
Indices: 43545093--43545206 Score: 65
Period size: 17 Copynumber: 6.6 Consensus size: 17
43545083 CCAAAGGTAC
*
43545093 GAGCTTACCAAAGA-TGT
1 GAGCTCACCAAA-ATTGT
* * *
43545110 AAGCTCACCTAAAGTTGC
1 GAGCTCACC-AAAATTGT
43545128 GAGCTCACCAAAATTGT
1 GAGCTCACCAAAATTGT
43545145 GAGCTC-CTC-AAA-TGT
1 GAGCTCAC-CAAAATTGT
* * *
43545160 ACGAGCTCACCAAGACTGC
1 --GAGCTCACCAAAATTGT
* * *
43545179 GATCTCATCAATATTGT
1 GAGCTCACCAAAATTGT
43545196 GAGCTCACCAA
1 GAGCTCACCAA
43545207 GGCTGCGAGC
Statistics
Matches: 73, Mismatches: 16, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
15 3 0.04
16 4 0.05
17 48 0.66
18 16 0.22
19 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.23
Consensus pattern (17 bp):
GAGCTCACCAAAATTGT
Found at i:43545238 original size:34 final size:34
Alignment explanation
Indices: 43545161--43545251 Score: 98
Period size: 34 Copynumber: 2.7 Consensus size: 34
43545151 CTCAAATGTA
* * *
43545161 CGAGCTCACCAAGACTGCGATCTCATCAATATTG
1 CGAGCTCACCAAGGCTGCGAGCTCATCAATACTG
*
43545195 TGAGCTCACCAAGGCTGCGAGCTCATCAA-AGCTG
1 CGAGCTCACCAAGGCTGCGAGCTCATCAATA-CTG
43545229 CGAAG-TCACCAAAGG-TGCGAGCT
1 CG-AGCTCACC-AAGGCTGCGAGCT
43545252 ATGTTAGGCG
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
33 1 0.02
34 42 0.86
35 6 0.12
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.19
Consensus pattern (34 bp):
CGAGCTCACCAAGGCTGCGAGCTCATCAATACTG
Found at i:43546608 original size:36 final size:36
Alignment explanation
Indices: 43546568--43546646 Score: 95
Period size: 36 Copynumber: 2.2 Consensus size: 36
43546558 GCATTATGCA
* * * *
43546568 AACCCTTTTGTGAAGCCTAGTTCGCTGCACCATGTG
1 AACCCTCTTGTAAAGCCCAATTCGCTGCACCATGTG
* *
43546604 AACCCTCTTGTAAAGCCCAATTTGTTGCACCATGTG
1 AACCCTCTTGTAAAGCCCAATTCGCTGCACCATGTG
*
43546640 AATCCTC
1 AACCCTC
43546647 CAGCAAAGAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.23, C:0.29, G:0.18, T:0.30
Consensus pattern (36 bp):
AACCCTCTTGTAAAGCCCAATTCGCTGCACCATGTG
Found at i:43552682 original size:6 final size:7
Alignment explanation
Indices: 43552651--43552681 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
43552641 AAAATTTGGG
*
43552651 TTTTAAT
1 TTTTGAT
43552658 TTTTGAT
1 TTTTGAT
43552665 TTTTGAT
1 TTTTGAT
43552672 TTTTGAT
1 TTTTGAT
43552679 TTT
1 TTT
43552682 GGGTACGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.16, C:0.00, G:0.10, T:0.74
Consensus pattern (7 bp):
TTTTGAT
Found at i:43552864 original size:20 final size:20
Alignment explanation
Indices: 43552819--43552864 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
43552809 GTCTACCTGC
43552819 AAAAATAAAAAAATATAAAT
1 AAAAATAAAAAAATATAAAT
* * *
43552839 ATAAATAAATAAATATATAT
1 AAAAATAAAAAAATATAAAT
43552859 AAAAAT
1 AAAAAT
43552865 TAAAGTTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAAATAAAAAAATATAAAT
Found at i:43552887 original size:23 final size:22
Alignment explanation
Indices: 43552861--43552906 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
43552851 ATATATATAA
* *
43552861 AAATTAAAGTTAAAAATACAAAT
1 AAATAAAAATTAAAAATA-AAAT
*
43552884 AAATAAAAATTAAAATTAAAAT
1 AAATAAAAATTAAAAATAAAAT
43552906 A
1 A
43552907 TGTATTTCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (22 bp):
AAATAAAAATTAAAAATAAAAT
Found at i:43552899 original size:16 final size:15
Alignment explanation
Indices: 43552821--43552899 Score: 54
Period size: 14 Copynumber: 5.0 Consensus size: 15
43552811 CTACCTGCAA
*
43552821 AAATAAAAA-AATAT
1 AAATAAAAATAAAAT
*
43552835 AAATATAAAT-AAAT
1 AAATAAAAATAAAAT
* *
43552849 AAATATATATAAAAATT
1 AAATAAAAAT-AAAA-T
43552866 AAAGTTAAAAATACAAAT
1 AAA--TAAAAATA-AAAT
43552884 AAATAAAAATTAAAAT
1 AAATAAAAA-TAAAAT
43552900 TAAAATATGT
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
14 20 0.38
16 13 0.25
17 6 0.12
18 5 0.10
19 8 0.15
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.27
Consensus pattern (15 bp):
AAATAAAAATAAAAT
Found at i:43561336 original size:18 final size:18
Alignment explanation
Indices: 43561286--43561336 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 18
43561276 ATGCAAACTT
43561286 CCCAAAGGTGCGAGCTCA
1 CCCAAAGGTGCGAGCTCA
** *
43561304 -TGAAAGGTGCAAGCTCA
1 CCCAAAGGTGCGAGCTCA
*
43561321 CCCAAAGTTGCGAGCT
1 CCCAAAGGTGCGAGCT
43561337 GTGTTAGGTG
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.16
Consensus pattern (18 bp):
CCCAAAGGTGCGAGCTCA
Found at i:43562343 original size:15 final size:15
Alignment explanation
Indices: 43562323--43562400 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
43562313 TTTATGGAAA
43562323 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
43562338 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
43562352 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
43562368 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
43562382 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
43562398 ATC
1 ATC
43562401 GAGATATTGG
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
14 8 0.18
15 29 0.64
16 8 0.18
ACGTcount: A:0.45, C:0.08, G:0.22, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:43562360 original size:30 final size:30
Alignment explanation
Indices: 43562319--43562400 Score: 137
Period size: 30 Copynumber: 2.7 Consensus size: 30
43562309 CATATTTATG
*
43562319 GAAAATCAAAGATATGGGTATCAAATAATA
1 GAAAGTCAAAGATATGGGTATCAAATAATA
* *
43562349 GAAAGTCAAAGATATGGGTATCAAATATTG
1 GAAAGTCAAAGATATGGGTATCAAATAATA
43562379 GAAAGTCAAAGATATGGGTATC
1 GAAAGTCAAAGATATGGGTATC
43562401 GAGATATTGG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.46, C:0.07, G:0.22, T:0.24
Consensus pattern (30 bp):
GAAAGTCAAAGATATGGGTATCAAATAATA
Found at i:43567002 original size:15 final size:15
Alignment explanation
Indices: 43566982--43567089 Score: 71
Period size: 15 Copynumber: 7.2 Consensus size: 15
43566972 TTTATGGAAA
43566982 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
43566997 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
43567011 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
**
43567027 AT-AAA-ATATTGGAA
1 ATCAAAGATA-TGGGT
43567041 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
43567057 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
43567071 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
43567087 ATC
1 ATC
43567090 GAGATATTGG
Statistics
Matches: 67, Mismatches: 18, Indels: 16
0.66 0.18 0.16
Matches are distributed among these distances:
13 3 0.04
14 15 0.22
15 31 0.46
16 15 0.22
17 3 0.04
ACGTcount: A:0.45, C:0.06, G:0.22, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:43567019 original size:30 final size:30
Alignment explanation
Indices: 43566976--43567099 Score: 194
Period size: 30 Copynumber: 4.1 Consensus size: 30
43566966 TCCATATTTA
* *
43566976 TGGAAAATCAAAGATATGGGTATCAAATAA
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
* *
43567006 TAGAAAGTCAAAGATATGGGTATAAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
43567036 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
43567066 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
43567097 TGG
1 TGG
43567100 CATAATAAAA
Statistics
Matches: 86, Mismatches: 7, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
30 78 0.91
31 8 0.09
ACGTcount: A:0.44, C:0.06, G:0.24, T:0.26
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:43569358 original size:6 final size:6
Alignment explanation
Indices: 43569347--43569379 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
43569337 TATGTGTGCA
43569347 TTTTTG TTTTTG TTTTTG TTTTT- TTTTT- TTTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
43569380 ACTTCACTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 10 0.37
6 17 0.63
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (6 bp):
TTTTTG
Found at i:43575644 original size:23 final size:23
Alignment explanation
Indices: 43575599--43575654 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
43575589 AATAACAAAG
*
43575599 ATATTTATACTAATAAATGCTAA
1 ATATTTATACTAATAAATACTAA
43575622 ATATATTATACTAATAAA-ACTAA
1 ATAT-TTATACTAATAAATACTAA
43575645 ATATTCTATA
1 ATATT-TATA
43575655 AAGTAAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 1 0.03
23 16 0.53
24 13 0.43
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (23 bp):
ATATTTATACTAATAAATACTAA
Found at i:43580016 original size:24 final size:23
Alignment explanation
Indices: 43579970--43580018 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
43579960 AATAACAAAG
**
43579970 ATATTTATACTAATAAATGCTAA
1 ATATTTATACTAATAAAAACTAA
43579993 ATATATTATACTAATAAAAACTAA
1 ATAT-TTATACTAATAAAAACTAA
43580017 AT
1 AT
43580019 CTTCTAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.37
Consensus pattern (23 bp):
ATATTTATACTAATAAAAACTAA
Found at i:43586599 original size:17 final size:17
Alignment explanation
Indices: 43586556--43586600 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
43586546 TACCTGTGTC
*
43586556 TGTATATATATAATATG
1 TGTATATATATAATAAG
* *
43586573 TGTGTATATATAGTAAG
1 TGTATATATATAATAAG
*
43586590 TGTATTTATAT
1 TGTATATATAT
43586601 GTAGTGGATG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (17 bp):
TGTATATATATAATAAG
Found at i:43591659 original size:42 final size:42
Alignment explanation
Indices: 43591601--43591685 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
43591591 CTAAAATTAA
*
43591601 TTTTTTTTACAAATAATTTGCTTTCACAAAAATAAAAAATAT
1 TTTTTTTTACAAATAATTTGCTTCCACAAAAATAAAAAATAT
*
43591643 TTTTTTTTACATATAATTTGCTTCCACAAAAATAAAAAATAT
1 TTTTTTTTACAAATAATTTGCTTCCACAAAAATAAAAAATAT
43591685 T
1 T
43591686 AACTCCTGGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.44
Consensus pattern (42 bp):
TTTTTTTTACAAATAATTTGCTTCCACAAAAATAAAAAATAT
Done.