Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold56
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: 1793205
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 19648 characters in sequence are not A, C, G, or T
File 4 of 11
Found at i:509612 original size:79 final size:79
Alignment explanation
Indices: 509469--509771 Score: 304
Period size: 79 Copynumber: 3.8 Consensus size: 79
509459 TCCATAAACA
* * * * ** * ** *
509469 GGGATACTCCAACCCCGGTTGTA-TTCCAAAAAACTAATTTTTCACAATCGAAGATACTTCAACC
1 GGGATACTCCAACCCCGATTTTATTTTCAAAACACCGATTTTCCACAATCGGGGATACTCCAACC
*
509533 CCGTTATCTATGAG
66 CCGTTATTTATGAG
* * * *
509547 GGGATACTCCAACCCCGATTTTATTTTCAAAACATCGATTTTCTACCATTGGGGATACTCCAACC
1 GGGATACTCCAACCCCGATTTTATTTTCAAAACACCGATTTTCCACAATCGGGGATACTCCAACC
*** *
509612 CCGTTATTTCCAAA
66 CCGTTATTTATGAG
* * * * *
509626 GGGATACTCCAACTCCGGTTTTATTTCCAAAAAACCTATTTTCCACAATCGGGGATACTCCAACC
1 GGGATACTCCAACCCCGATTTTATTTTCAAAACACCGATTTTCCACAATCGGGGATACTCCAACC
*
509691 CCGTTATTTTTGAG
66 CCGTTATTTATGAG
* * * * *
509705 GGGATACTCCAACCCCTATTTTA-TTTCTAAAACACCAATTTTTTCATAATCGGTGATACTCCAA
1 GGGATACTCCAACCCCGATTTTATTTTC-AAAACACCGA-TTTTCCACAATCGGGGATACTCCAA
509769 CCC
64 CCC
509772 TGGTTTTAAT
Statistics
Matches: 181, Mismatches: 41, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
78 24 0.13
79 132 0.73
80 25 0.14
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (79 bp):
GGGATACTCCAACCCCGATTTTATTTTCAAAACACCGATTTTCCACAATCGGGGATACTCCAACC
CCGTTATTTATGAG
Found at i:509638 original size:28 final size:30
Alignment explanation
Indices: 509598--509656 Score: 86
Period size: 28 Copynumber: 2.0 Consensus size: 30
509588 TCTACCATTG
509598 GGGATACTCCAAC-CCCG-TTATTTCCAAA
1 GGGATACTCCAACTCCCGTTTATTTCCAAA
*
509626 GGGATACTCCAACTCCGGTTTTATTTCCAAA
1 GGGATACTCCAACTCCCG-TTTATTTCCAAA
509657 AAACCTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 13 0.48
29 3 0.11
31 11 0.41
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (30 bp):
GGGATACTCCAACTCCCGTTTATTTCCAAA
Found at i:509788 original size:131 final size:129
Alignment explanation
Indices: 509626--509901 Score: 331
Period size: 130 Copynumber: 2.1 Consensus size: 129
509616 TATTTCCAAA
* *
509626 GGGATACTCCAACTCCGGTTTTATTTCCAAAAAACCTATTTTCCACAATCGGGGATACTCCAACC
1 GGGATACTCCAAC-CCGGTTTTATTTCCAAAAAACCGATTTTCCACAATCAGGGATACTCCAACC
* * * * * * *
509691 CCGTTATTTTTGAGGGGATACTCCAACCCCTATTTTATTTCTAAAACACCA-ATTTTTTCATAAT
65 CCGTTA-TTTCGAGGGAATACTCCAACCCCAATTTTATTTCCAAAAAAACATA-TTTTTCACAAT
*
509755 CG
128 AG
* * * * * *
509757 GTGATACTCCAACCCTGGTTTTAATTT-CAAAACATCGATTTTCTACCATTAGGGATACTCCAAC
1 GGGATACTCCAACCC-GGTTTT-ATTTCCAAAAAACCGATTTTCCACAATCAGGGATACTCCAAC
* *
509821 CCCGTTATTTCGAGGGAATACTTCAACCCCAATTTTATTTCCAAAAAAACTTATTTTTCACAATA
64 CCCGTTATTTCGAGGGAATACTCCAACCCCAATTTTATTTCCAAAAAAACATATTTTTCACAATA
509886 G
129 G
509887 GGGATACTCCAACCC
1 GGGATACTCCAACCC
509902 CGTTATTTTT
Statistics
Matches: 123, Mismatches: 19, Indels: 7
0.83 0.13 0.05
Matches are distributed among these distances:
130 63 0.51
131 56 0.46
132 4 0.03
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.33
Consensus pattern (129 bp):
GGGATACTCCAACCCGGTTTTATTTCCAAAAAACCGATTTTCCACAATCAGGGATACTCCAACCC
CGTTATTTCGAGGGAATACTCCAACCCCAATTTTATTTCCAAAAAAACATATTTTTCACAATAG
Found at i:509822 original size:210 final size:210
Alignment explanation
Indices: 509549--509940 Score: 635
Period size: 210 Copynumber: 1.9 Consensus size: 210
509539 TCTATGAGGG
* *
509549 GATACTCCAACCCCGATTTTATTTTCAAAACATCGATTTTCTACCATTGGGGATACTCCAACCCC
1 GATACTCCAACCCCGATTTTAATTTCAAAACATCGATTTTCTACCATTAGGGATACTCCAACCCC
* ** *
509614 GTTATTTCCAAAGGG-ATACTCCAACTCCGGTTTTATTTCC-AAAAAACCTATTTTCCACAATCG
66 GTTATTT-C-AAGGGAATACTCCAACCCCAATTTTATTTCCAAAAAAACCTATTTTCCACAATAG
*
509677 GGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCTATTTTATTTCTAAAACACCA
129 GGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCA
509742 ATTTTTTCATAATCGGT
194 ATTTTTTCATAATCGGT
* *
509759 GATACTCCAACCCTGGTTTTAATTTCAAAACATCGATTTTCTACCATTAGGGATACTCCAACCCC
1 GATACTCCAACCCCGATTTTAATTTCAAAACATCGATTTTCTACCATTAGGGATACTCCAACCCC
* * * *
509824 GTTATTTCGAGGGAATACTTCAACCCCAATTTTATTTCCAAAAAAACTTATTTTTCACAATAGGG
66 GTTATTTCAAGGGAATACTCCAACCCCAATTTTATTTCCAAAAAAACCTATTTTCCACAATAGGG
509889 GATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCGATTTTATTT
131 GATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCGATTTTATTT
509941 TCAAAATATC
Statistics
Matches: 167, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
208 4 0.02
209 22 0.13
210 141 0.84
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (210 bp):
GATACTCCAACCCCGATTTTAATTTCAAAACATCGATTTTCTACCATTAGGGATACTCCAACCCC
GTTATTTCAAGGGAATACTCCAACCCCAATTTTATTTCCAAAAAAACCTATTTTCCACAATAGGG
GATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAAT
TTTTTCATAATCGGT
Found at i:509901 original size:130 final size:130
Alignment explanation
Indices: 509626--509901 Score: 333
Period size: 131 Copynumber: 2.1 Consensus size: 130
509616 TATTTCCAAA
* *
509626 GGGATACTCCAACTCCGGTTTTATTTCCAAAAAACCTATTTTCCACAATCGGGGATACTCCAACC
1 GGGATACTCCAAC-CCGGTTTTATTTCCAAAAAACCGATTTTCCACAATCAGGGATACTCCAACC
* * * * * * *
509691 CCGTTATTTTTGAGGGGATACTCCAACCCCTATTTTATTTCTAAAACACCAATTTTTTCATAATC
65 CCGTTATTTTCGAGGGAATACTCCAACCCCAATTTTATTTCAAAAAAACCAATTTTTTCACAATA
509756 G
130 G
* * * * * *
509757 GTGATACTCCAACCCTGGTTTTAATTT-CAAAACATCGATTTTCTACCATTAGGGATACTCCAAC
1 GGGATACTCCAACCC-GGTTTT-ATTTCCAAAAAACCGATTTTCCACAATCAGGGATACTCCAAC
* **
509821 CCCGTTA-TTTCGAGGGAATACTTCAACCCCAATTTTATTTCCAAAAAAACTTA-TTTTTCACAA
64 CCCGTTATTTTCGAGGGAATACTCCAACCCCAATTTTATTT-CAAAAAAACCAATTTTTTCACAA
509884 TAG
128 TAG
509887 GGGATACTCCAACCC
1 GGGATACTCCAACCC
509902 CGTTATTTTT
Statistics
Matches: 123, Mismatches: 19, Indels: 7
0.83 0.13 0.05
Matches are distributed among these distances:
130 56 0.46
131 63 0.51
132 4 0.03
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.33
Consensus pattern (130 bp):
GGGATACTCCAACCCGGTTTTATTTCCAAAAAACCGATTTTCCACAATCAGGGATACTCCAACCC
CGTTATTTTCGAGGGAATACTCCAACCCCAATTTTATTTCAAAAAAACCAATTTTTTCACAATAG
Found at i:509937 original size:80 final size:78
Alignment explanation
Indices: 509759--510082 Score: 391
Period size: 79 Copynumber: 4.1 Consensus size: 78
509749 CATAATCGGT
* * * * *
509759 GATACTCCAACCCTGGTTTTAATTTCAAAACATCGATTTTCTACCATTAGGGATACTCCAACCCC
1 GATACTCCAACCCCGATTTTATTTTCAAAAAATCGATTTTCTA-CATTGGGGATACTCCAACCCC
509824 GTTA-TTTCGAGGG
65 GTTATTTTCGAGGG
* * * * * * *
509837 AATACTTCAACCCCAATTTTATTTCCAAAAAAACTTATTTT-TCACAATAGGGGATACTCCAACC
1 GATACTCCAACCCCGATTTTATTTTCAAAAAATC-GATTTTCT-AC-ATTGGGGATACTCCAACC
*
509901 CCGTTATTTTTGAGGG
63 CCGTTATTTTCGAGGG
*
509917 GATACTCCAACCCCGATTTTATTTTCAAAATATCGATTTTCTACTATTGGGGATACTCCAACCCC
1 GATACTCCAACCCCGATTTTATTTTCAAAAAATCGATTTTCTAC-ATTGGGGATACTCCAACCCC
*
509982 ATTATTTTCGAGGG
65 GTTATTTTCGAGGG
* * *
509996 GATACTCCAACCCCGATTTTGTTTTCAAAACATCGATTTTCTATCATTGGGGATACTCCAACCTC
1 GATACTCCAACCCCGATTTTATTTTCAAAAAATCGATTTTCTA-CATTGGGGATACTCCAACCCC
**
510061 GTTATTTTTTAGGG
65 GTTATTTTCGAGGG
*
510075 GGTACTCC
1 GATACTCC
510083 GAGCTTGTTT
Statistics
Matches: 209, Mismatches: 31, Indels: 11
0.83 0.12 0.04
Matches are distributed among these distances:
78 27 0.13
79 144 0.69
80 38 0.18
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (78 bp):
GATACTCCAACCCCGATTTTATTTTCAAAAAATCGATTTTCTACATTGGGGATACTCCAACCCCG
TTATTTTCGAGGG
Found at i:511740 original size:89 final size:88
Alignment explanation
Indices: 511647--511867 Score: 219
Period size: 88 Copynumber: 2.5 Consensus size: 88
511637 TAAAGAAGCC
* * * * *
511647 AATGCACT-CGAAATAAGGCAAATGCCAATGTCATCCAATGGTGTAGATGCACCTAAAATAATGT
1 AATGCA-TACGAAATAAGGCAAATACCAATGTCATCCAA-AGTGCAGATGCACCGAAAATAATGC
* *
511711 AAATGCAAGCATTAATAAAATGGCA
64 AAATGCAAACATCAATAAAATGGCA
* * * * * ** * *
511736 AATGCATATGAAATGATGCAAATACCAATGTCATCTAAAGTGCAGATGTATGGGAAATGATGCAA
1 AATGCATACGAAATAAGGCAAATACCAATGTCATCCAAAGTGCAGATGCACCGAAAATAATGCAA
511801 ATGCAAACATCAATAAAATGGCA
66 ATGCAAACATCAATAAAATGGCA
** * * * *
511824 AATGCATATAAAATGACGCAAATACCAATATCATCTAAAGTGCA
1 AATGCATACGAAATAAGGCAAATACCAATGTCATCCAAAGTGCA
511868 AACATATGTG
Statistics
Matches: 112, Mismatches: 19, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
88 81 0.72
89 31 0.28
ACGTcount: A:0.44, C:0.16, G:0.17, T:0.23
Consensus pattern (88 bp):
AATGCATACGAAATAAGGCAAATACCAATGTCATCCAAAGTGCAGATGCACCGAAAATAATGCAA
ATGCAAACATCAATAAAATGGCA
Found at i:511826 original size:88 final size:88
Alignment explanation
Indices: 511702--511934 Score: 331
Period size: 88 Copynumber: 2.6 Consensus size: 88
511692 GATGCACCTA
* * * * *
511702 AAATAATGTAAATGCAAGCATTAATAAAATGGCAAATGCATATGAAATGATGCAAATACCAATGT
1 AAATGATGCAAATGCAAGCATCAATAAAATGGCAAATGCATATAAAATGATGCAAATACCAATAT
* **
511767 CATCTAAAGTGCAGATGTATGGG
66 CATCTAAAGTGCAAACATATGGG
* *
511790 AAATGATGCAAATGCAAACATCAATAAAATGGCAAATGCATATAAAATGACGCAAATACCAATAT
1 AAATGATGCAAATGCAAGCATCAATAAAATGGCAAATGCATATAAAATGATGCAAATACCAATAT
*
511855 CATCTAAAGTGCAAACATATGTG
66 CATCTAAAGTGCAAACATATGGG
* ** *
511878 AAATGATGCAAATGGAAGCATCAATAAAATGAAAAATGCATATAAAATGATGTAAAT
1 AAATGATGCAAATGCAAGCATCAATAAAATGGCAAATGCATATAAAATGATGCAAAT
511935 GCGAATGAAG
Statistics
Matches: 128, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
88 128 1.00
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.23
Consensus pattern (88 bp):
AAATGATGCAAATGCAAGCATCAATAAAATGGCAAATGCATATAAAATGATGCAAATACCAATAT
CATCTAAAGTGCAAACATATGGG
Found at i:511838 original size:44 final size:44
Alignment explanation
Indices: 511700--511936 Score: 158
Period size: 44 Copynumber: 5.4 Consensus size: 44
511690 TAGATGCACC
* * * *
511700 TAAAATAATGTAAATGCAAGCATTAATAAAATGGCAAATGCATA
1 TAAAATGATGCAAATGCAAACATCAATAAAATGGCAAATGCATA
* * * ** * * * * *
511744 TGAAATGATGCAAATACCAATGTCATCTAAAGT-GCAGATGTATG
1 TAAAATGATGCAAATGCAAACATCA-ATAAAATGGCAAATGCATA
**
511788 GGAAATGATGCAAATGCAAACATCAATAAAATGGCAAATGCATA
1 TAAAATGATGCAAATGCAAACATCAATAAAATGGCAAATGCATA
* * * * * *
511832 TAAAATGACGCAAATACCAATATCATCTAAAGT-GCAAA--CATA
1 TAAAATGATGCAAATGCAAACATCA-ATAAAATGGCAAATGCATA
* * * **
511874 TGTGAAATGATGCAAATGGAAGCATCAATAAAATGAAAAATGCATA
1 --TAAAATGATGCAAATGCAAACATCAATAAAATGGCAAATGCATA
*
511920 TAAAATGATGTAAATGC
1 TAAAATGATGCAAATGC
511937 GAATGAAGTC
Statistics
Matches: 139, Mismatches: 46, Indels: 16
0.69 0.23 0.08
Matches are distributed among these distances:
42 4 0.03
43 10 0.07
44 111 0.80
45 10 0.07
46 4 0.03
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.23
Consensus pattern (44 bp):
TAAAATGATGCAAATGCAAACATCAATAAAATGGCAAATGCATA
Found at i:512493 original size:112 final size:109
Alignment explanation
Indices: 512192--512520 Score: 344
Period size: 112 Copynumber: 3.0 Consensus size: 109
512182 AAAACCTTGG
*
512192 TTGGCTCAAAAATTTCAAAATTGATAGAATACATGCCTTATTTTCCTA-T-GAATGGATT-AGGT
1 TTGGCTC-AAAATTTCAAAA-TGATAGAATACATGCCCTATTTTCCTAGTAGAATGGATTGAGGT
** * *** * * *
512254 CATATAAAATAGGAATTTCTTTGAAAATTTGATAACTTTGATGTTG
64 TGTATAAAATACGAATTTCTTTGAAAATCAAACAAATTTGATGTTA
* * * * * *
512300 TTGGCTCAAAATTTCAAACTGATAGGATGCATGCCCTATTTTCCTAGACATGAATGGA-TGATGA
1 TTGGCTCAAAATTTCAAAATGATAGAATACATGCCCTATTTTCCTAG-TA-GAATGGATTGAGGT
*
512364 TGTATAAAACACGAATTTCTTTGAAAATCAAACAAATTTGATGTTA
64 TGTATAAAATACGAATTTCTTTGAAAATCAAACAAATTTGATGTTA
* *
512410 TTGGCTCAACAATTTCAAAATCGATAGCATACATGCCCAATTTTCCTAGGTACGAATGGATTGA-
1 TTGGCTCAA-AATTTCAAAAT-GATAGAATACATGCCCTATTTTCCTA-GTA-GAATGGATTGAG
* ** *
512474 GTTGTATGAAATATAAATTTCTTTGAAAACCAAACAAATTTGATGTT
62 GTTGTATAAAATACGAATTTCTTTGAAAATCAAACAAATTTGATGTT
512521 CTTCCAAGTC
Statistics
Matches: 183, Mismatches: 29, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
106 24 0.13
107 11 0.06
108 7 0.04
109 1 0.01
110 54 0.30
111 10 0.05
112 72 0.39
113 4 0.02
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (109 bp):
TTGGCTCAAAATTTCAAAATGATAGAATACATGCCCTATTTTCCTAGTAGAATGGATTGAGGTTG
TATAAAATACGAATTTCTTTGAAAATCAAACAAATTTGATGTTA
Found at i:516790 original size:155 final size:153
Alignment explanation
Indices: 516401--516928 Score: 591
Period size: 153 Copynumber: 3.4 Consensus size: 153
516391 GGTTATGAAG
* * * * *
516401 AAATTACCAAAATGCCCTTGGGTATACCTTCGACATGAAAGTATCTCAATAACCTTAAAGGACAA
1 AAATTACCAAAATG-CCTTGGGTATACCTTCGACATGAAAGTATCCCAGTAACCCTAAAAGACAC
* * * * *
516466 TAAAAGATCGTAAAACGGTGAACCTATCCTAAATGTAAACCCTTAGCATAAAAGCAACCTGGTGA
65 GAAAAGATCGTAAAAAGGTGAACCTATCCTAAATGTAAACCCTTGGCATAAAAGCGACCTAGTGA
* *
516531 CTACCTAAGACT-TAGTTC-TAAAA
130 CTACCTAGGACTCGA-TTCTTAAAA
* * * *
516554 AAATTACCAAAATGCCTTGGGGTATACCTTCGACATAAAAGTATCCCGGTAATCCTAAAAGTCAC
1 AAATTACCAAAATGCCTT-GGGTATACCTTCGACATGAAAGTATCCCAGTAACCCTAAAAGACAC
* * * * *
516619 GAAATGATTGTGAAAAGGTGAACCTATCCTAAATGTAAACCCTTGGCATAAAAGTGACTTAGTGA
65 GAAAAGATCGTAAAAAGGTGAACCTATCCTAAATGTAAACCCTTGGCATAAAAGCGACCTAGTGA
**
516684 CTATTTAGGACTCGATTCTTAAAA
130 CTACCTAGGACTCGATTCTTAAAA
* * *
516708 AAATTACCAAAATGCCTATGAGGTATACCTTTGACATTAAAGTATCCCAGTAACCCTAAAAGATA
1 AAATTACCAAAATGCCT-TG-GGTATACCTTCGACATGAAAGTATCCCAGTAACCCTAAAAGACA
*** * * * * * *
516773 CGAAAAGATCGTAAAAAGACAAAACTATCCGAAATGTAGACCCTTGGCATAACAGGGACCCAGTG
64 CGAAAAGATCGTAAAAAGGTGAACCTATCCTAAATGTAAACCCTTGGCATAAAAGCGACCTAGTG
516838 ACTACCTAGGACTCGATT-TT-AAA
129 ACTACCTAGGACTCGATTCTTAAAA
* * * * *
516861 AAATTACCAAAATACCCCTAGGGTATACCTTCAACGTGAAAGTATCCTAGTAA--CTAAAAGACA
1 AAATTACCAAAAT--GCCTTGGGTATACCTTCGACATGAAAGTATCCCAGTAACCCTAAAAGACA
516924 CGAAA
64 CGAAA
516929 CCATTATGAA
Statistics
Matches: 316, Mismatches: 52, Indels: 16
0.82 0.14 0.04
Matches are distributed among these distances:
151 14 0.04
152 4 0.01
153 161 0.51
154 27 0.09
155 110 0.35
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (153 bp):
AAATTACCAAAATGCCTTGGGTATACCTTCGACATGAAAGTATCCCAGTAACCCTAAAAGACACG
AAAAGATCGTAAAAAGGTGAACCTATCCTAAATGTAAACCCTTGGCATAAAAGCGACCTAGTGAC
TACCTAGGACTCGATTCTTAAAA
Found at i:517192 original size:56 final size:58
Alignment explanation
Indices: 517065--517209 Score: 168
Period size: 56 Copynumber: 2.4 Consensus size: 58
517055 ATTAAACATC
* * * *
517065 GACCCTTATAAATTTTCAAAATTACACTTTGATCCCCAAATTTACTTTCCAAAATTACATTTT
1 GACCCTTA-AACTTTTCAAAATTACA--TTAATCCACAAATTTA--TTCCAAAATTACATGTT
** *
517128 GAGTCTTAAACTTTTCAAAATTACATTAATCCACAAATTTA-T-CAAAATTTCATGTT
1 GACCCTTAAACTTTTCAAAATTACATTAATCCACAAATTTATTCCAAAATTACATGTT
517184 GACCCTTAAACTTTTCAAAATTACAT
1 GACCCTTAAACTTTTCAAAATTACAT
517210 GCTGACCTCA
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
56 36 0.49
57 1 0.01
60 14 0.19
62 16 0.22
63 6 0.08
ACGTcount: A:0.37, C:0.20, G:0.04, T:0.39
Consensus pattern (58 bp):
GACCCTTAAACTTTTCAAAATTACATTAATCCACAAATTTATTCCAAAATTACATGTT
Found at i:517216 original size:29 final size:28
Alignment explanation
Indices: 517017--517209 Score: 106
Period size: 29 Copynumber: 6.6 Consensus size: 28
517007 AAGTTTCTAG
* ** *
517017 ACTTTCCAAAATTATGTATTGA-CCTTGA
1 ACTTTTCAAAATTACAT-TTGACCCTTAA
*
517045 ACTTTTCAAAATTAAACA-TCGACCCTTATA
1 ACTTTTCAAAATT--ACATTTGACCCTTA-A
* **
517075 AATTTTCAAAATTACACTTTGATCCCCAAA
1 ACTTTTCAAAATTACA-TTTGA-CCCTTAA
* **
517105 TTTACTTTCCAAAATTACATTTTGAGTCTTAA
1 ---ACTTTTCAAAATTACA-TTTGACCCTTAA
* * **
517137 ACTTTTCAAAATTACA-TTAATCCACAA
1 ACTTTTCAAAATTACATTTGACCCTTAA
*
517164 A-TTTATCAAAATTTCATGTTGACCCTTAA
1 ACTTT-TCAAAATTACAT-TTGACCCTTAA
517193 ACTTTTCAAAATTACAT
1 ACTTTTCAAAATTACAT
517210 GCTGACCTCA
Statistics
Matches: 123, Mismatches: 28, Indels: 27
0.69 0.16 0.15
Matches are distributed among these distances:
26 3 0.02
27 17 0.14
28 18 0.15
29 38 0.31
30 21 0.17
31 4 0.03
32 3 0.02
33 19 0.15
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.38
Consensus pattern (28 bp):
ACTTTTCAAAATTACATTTGACCCTTAA
Found at i:522904 original size:20 final size:20
Alignment explanation
Indices: 522879--522995 Score: 117
Period size: 20 Copynumber: 5.7 Consensus size: 20
522869 TTTTACCTAG
*
522879 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTGTTCA
* * * *
522899 ATGTATTGATACATGGATGA
1 ATGTATCGATACATTGTTCA
*
522919 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTGTTCA
* * *
522939 ATGTATCGATAGATTCTACCCA
1 ATGTATCGATACATTGT--TCA
*
522961 GATGCATCGATACATTGTTCA
1 -ATGTATCGATACATTGTTCA
522982 ATGTATCGATACAT
1 ATGTATCGATACAT
522996 CTAGTTAAAA
Statistics
Matches: 77, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
20 59 0.77
21 2 0.03
22 2 0.03
23 14 0.18
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGTTCA
Found at i:523442 original size:12 final size:13
Alignment explanation
Indices: 523411--523446 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
523401 TACCATCCAT
523411 ATCAACACAAAAC
1 ATCAACACAAAAC
523424 ATCAACACAAAAC
1 ATCAACACAAAAC
523437 -TCAACA-AAAA
1 ATCAACACAAAA
523447 GTCCATTCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 4 0.17
12 6 0.26
13 13 0.57
ACGTcount: A:0.64, C:0.28, G:0.00, T:0.08
Consensus pattern (13 bp):
ATCAACACAAAAC
Found at i:536922 original size:11 final size:11
Alignment explanation
Indices: 536906--536992 Score: 54
Period size: 11 Copynumber: 7.6 Consensus size: 11
536896 TCCTTCATAC
536906 AAAAAAAAACA
1 AAAAAAAAACA
**
536917 AAAAAAACCCA
1 AAAAAAAAACA
**
536928 AAAAAAACCCA
1 AAAAAAAAACA
536939 AAAAAACAAA-A
1 AAAAAA-AAACA
536950 AAAAATAGAAA-A
1 AAAAA-A-AAACA
536962 AACCAAGAAAAA-A
1 AA--AA-AAAAACA
*
536975 AACAAAAAACA
1 AAAAAAAAACA
536986 AAAAAAA
1 AAAAAAA
536993 TAGAAAGGGG
Statistics
Matches: 63, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
10 5 0.08
11 40 0.63
12 8 0.13
13 6 0.10
14 3 0.05
15 1 0.02
ACGTcount: A:0.83, C:0.14, G:0.02, T:0.01
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:536932 original size:20 final size:20
Alignment explanation
Indices: 536905--536992 Score: 92
Period size: 21 Copynumber: 4.5 Consensus size: 20
536895 GTCCTTCATA
536905 CAAAAAAAAACAAAAAAAACC
1 CAAAAAAAAACAAAAAAAA-C
* *
536926 CAAAAAAAACCCAAAAAAA-
1 CAAAAAAAAACAAAAAAAAC
* *
536945 CAAAAAAAAATAGAAAAAAC
1 CAAAAAAAAACAAAAAAAAC
*
536965 CAAGAAAAAAA-ACAAAAAA-
1 CAA-AAAAAAACAAAAAAAAC
536984 CAAAAAAAA
1 CAAAAAAAA
536993 TAGAAAGGGG
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
18 6 0.10
19 18 0.31
20 10 0.17
21 24 0.41
ACGTcount: A:0.82, C:0.15, G:0.02, T:0.01
Consensus pattern (20 bp):
CAAAAAAAAACAAAAAAAAC
Found at i:536948 original size:40 final size:39
Alignment explanation
Indices: 536904--536992 Score: 117
Period size: 40 Copynumber: 2.3 Consensus size: 39
536894 CGTCCTTCAT
**
536904 ACAAAAAAAAACAAAAAAAACCCAA-AAAAAACCCAAAAAA
1 ACAAAAAAAAACAAAAAAAA-CCAAGAAAAAAAAC-AAAAA
* *
536944 ACAAAAAAAAATAGAAAAAACCAAGAAAAAAAACAAAAA
1 ACAAAAAAAAACAAAAAAAACCAAGAAAAAAAACAAAAA
536983 ACAAAAAAAA
1 ACAAAAAAAA
536993 TAGAAAGGGG
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
39 19 0.43
40 25 0.57
ACGTcount: A:0.82, C:0.15, G:0.02, T:0.01
Consensus pattern (39 bp):
ACAAAAAAAAACAAAAAAAACCAAGAAAAAAAACAAAAA
Found at i:541038 original size:52 final size:52
Alignment explanation
Indices: 540963--541088 Score: 207
Period size: 52 Copynumber: 2.4 Consensus size: 52
540953 AATATGAAAT
*
540963 TTTGCCTGCATATATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
1 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
* * *
541015 TTTGCCTGTATGTATCAATACATTTCATAGTGTATCGATACATCTGGGTAAA
1 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
*
541067 TTTGCCTGCGTGTATCGATACA
1 TTTGCCTGCATGTATCGATACA
541089 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (52 bp):
TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
Found at i:541099 original size:52 final size:52
Alignment explanation
Indices: 540963--541108 Score: 177
Period size: 52 Copynumber: 2.8 Consensus size: 52
540953 AATATGAAAT
* * **
540963 TTTGCCTGCATATATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
1 TTTGCCTGCATGTATCAATACATAACATAGTGTATCGATACATCTGGGCAAA
* ** *
541015 TTTGCCTGTATGTATCAATACATTTCATAGTGTATCGATACATCTGGGTAAA
1 TTTGCCTGCATGTATCAATACATAACATAGTGTATCGATACATCTGGGCAAA
* * *
541067 TTTGCCTGCGTGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTTGCCTGCATGTATCAATACATAACAT-AGTGTATCGATACA
541109 ATGTATCGAT
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
51 2 0.02
52 81 0.98
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
TTTGCCTGCATGTATCAATACATAACATAGTGTATCGATACATCTGGGCAAA
Found at i:541115 original size:13 final size:13
Alignment explanation
Indices: 541097--541121 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
541087 CAAAGATCAG
541097 TGTATCGATACAA
1 TGTATCGATACAA
541110 TGTATCGATACA
1 TGTATCGATACA
541122 TTTAAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:541224 original size:19 final size:18
Alignment explanation
Indices: 541163--541225 Score: 55
Period size: 19 Copynumber: 3.7 Consensus size: 18
541153 AGTAACTTCA
*
541163 TATGTATCAATACAACACT
1 TATGTATCGATA-AACACT
541182 TATGTATCGAT--ACA--
1 TATGTATCGATAAACACT
*
541196 T-TGTACCGATAAAACACT
1 TATGTATCGAT-AAACACT
541214 TATGTATCGATA
1 TATGTATCGATA
541226 CAAATCATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 13
0.69 0.06 0.25
Matches are distributed among these distances:
13 8 0.23
14 1 0.03
16 6 0.17
18 2 0.06
19 18 0.51
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.33
Consensus pattern (18 bp):
TATGTATCGATAAACACT
Found at i:542129 original size:154 final size:155
Alignment explanation
Indices: 541848--542208 Score: 526
Period size: 154 Copynumber: 2.3 Consensus size: 155
541838 AGAAAAGTGA
* * *
541848 GAAAGATACCAATATGCTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTC
1 GAAAGATGCCAATATGCTGATTCAAGGCCAACGATATTGGGCTTAAAGATAAGAAAAAGGATGTC
* **
541913 AATGTGCTTATTCACGGTCAGCGGCATTAGACTTGGAGAAGAATGTCAATGTGCTAAGACAAGGC
66 AATGTGCTGATTCACGGTCAGCGAAATTAGACTTGGAGAAGAATGTCAATGTGCTAAGACAAGGC
* *
541978 CAACGACATTGGGCTTAGGGATGTT
131 CAACGACATCGGGCTTAGGAATGTT
* *
542003 -AAAGATGCCAATACGCTGATTCAAGGCCAACGATATTGGGCTTAAAGATAAGAAAAAGGATGTT
1 GAAAGATGCCAATATGCTGATTCAAGGCCAACGATATTGGGCTTAAAGATAAGAAAAAGGATGTC
*
542067 AATGTGCTGATTCACGGTCAGCGAAATTAGACTTGGAGAAGAATGTCAATGTGCTGAGACAAGGC
66 AATGTGCTGATTCACGGTCAGCGAAATTAGACTTGGAGAAGAATGTCAATGTGCTAAGACAAGGC
*
542132 CAGCGACATCGGGCTTAGGAATGTT
131 CAACGACATCGGGCTTAGGAATGTT
* * * *
542157 GAAGATGAAGGTGCCACTGTGCTGATTCAAGGCCAGCGATATTGGACTTAAA
1 GAA-A-G-A--TGCCAATATGCTGATTCAAGGCCAACGATATTGGGCTTAAA
542209 AGATGACAAA
Statistics
Matches: 183, Mismatches: 17, Indels: 7
0.88 0.08 0.03
Matches are distributed among these distances:
154 142 0.78
155 2 0.01
156 1 0.01
157 1 0.01
158 1 0.01
160 36 0.20
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.23
Consensus pattern (155 bp):
GAAAGATGCCAATATGCTGATTCAAGGCCAACGATATTGGGCTTAAAGATAAGAAAAAGGATGTC
AATGTGCTGATTCACGGTCAGCGAAATTAGACTTGGAGAAGAATGTCAATGTGCTAAGACAAGGC
CAACGACATCGGGCTTAGGAATGTT
Found at i:542347 original size:49 final size:49
Alignment explanation
Indices: 542158--542873 Score: 853
Period size: 49 Copynumber: 15.1 Consensus size: 49
542148 AGGAATGTTG
* * *
542158 AAGATGAAGGTGCCACTGTGCTGATTCAAGGCCAGCGATATTGGACTTAA
1 AAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-A
* *
542208 AAGATGACAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAA
1 AAGATG---AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-A
* *
542261 AAGATGACAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA
1 AAGATG---AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
* *
542313 AAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
1 AAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
* * *
542362 AAGATAAAGGTGCCAATATGCTGATTTAAGGCCAACTATATTGGACTT-
1 AAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
* *
542410 ---A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
1 AAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
*
542454 AAGATGAAGGTGCCAATATGCTGATTCAAGGCCATCTATATTGGACTT-
1 AAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
* * * *
542502 ---A--AAGGTGCCAATGTGCTAATTCAAGGCCAACTACATTGGACTTA
1 AAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
*
542546 AAGATGAAGGTGCCAATATGCTAATTCAAGGCCAGCTATATTGGACTT-
1 AAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
* * * *
542594 ---A--AAGGTGCCAATGTGTTGATTCAAGGCCAGCTACATTAGACTTA
1 AAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
*
542638 AAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-
1 AAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
* *
542686 ---A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
1 AAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
* *
542730 AAGATGAAGGTGCCAATATGTTGATTCAAGGCCAGCGATATTGGACTT-
1 AAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
* *
542778 AA-A-G-A--TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
1 AAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
**
542822 AAGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
1 AAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
542871 AAG
1 AAG
542874 GAAGATGCCA
Statistics
Matches: 583, Mismatches: 50, Indels: 67
0.83 0.07 0.10
Matches are distributed among these distances:
43 186 0.32
44 2 0.00
45 6 0.01
46 1 0.00
47 6 0.01
48 2 0.00
49 275 0.47
50 6 0.01
52 7 0.01
53 92 0.16
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (49 bp):
AAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
Found at i:542452 original size:92 final size:92
Alignment explanation
Indices: 542216--542874 Score: 1039
Period size: 92 Copynumber: 7.1 Consensus size: 92
542206 AAAAGATGAC
* * * * *
542216 AAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAGATGACAAAGGCGCCAAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT-AAAGATG---AAGGTGCCAAT
*
542281 ATGCTGATTCAAGGCCAGCGATATTGGACTT
62 ATGCTGATTCAAGGCCAGCTATATTGGACTT
*
542312 AAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCA
1 ----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCA
* *
542377 ATATGCTGATTTAAGGCCAACTATATTGGACTT
60 ATATGCTGATTCAAGGCCAGCTATATTGGACTT
542410 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
542475 TGATTCAAGGCCATCTATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
* *
542502 AAAGGTGCCAATGTGCTAATTCAAGGCCAACTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
542567 TAATTCAAGGCCAGCTATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
* *
542594 AAAGGTGCCAATGTGTTGATTCAAGGCCAGCTACATTAGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
542659 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
*
542686 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
542751 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
* **
542778 AAAGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGACAAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
542843 TGATTCAAGGCCAGCTATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
542870 AAAGG
1 AAAGG
542875 AAGATGCCAC
Statistics
Matches: 526, Mismatches: 31, Indels: 12
0.92 0.05 0.02
Matches are distributed among these distances:
92 442 0.84
94 1 0.00
98 38 0.07
100 1 0.00
101 6 0.01
102 38 0.07
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.25
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
TGATTCAAGGCCAGCTATATTGGACTT
Found at i:542950 original size:33 final size:32
Alignment explanation
Indices: 542879--543006 Score: 184
Period size: 32 Copynumber: 4.0 Consensus size: 32
542869 TAAAGGAAGA
*
542879 TGCCACCAACTTGTGTGGGCTTTGAAGAAGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAAAAGGT
*
542911 TGCCACCGACTTGTGTGGGCTTTAGAAAAAGGT
1 TGCCACCAACTTGTGTGGGCTTT-GAAAAAGGT
* * *
542944 TACCACCAACTTGTGTGGGCTTTGAGAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAAAAGGT
* *
542976 TGCCACCGACTTGTGTGGGCTTTGGAAAAGG
1 TGCCACCAACTTGTGTGGGCTTTGAAAAAGG
543007 AGAAAGATGC
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
32 55 0.65
33 29 0.35
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.27
Consensus pattern (32 bp):
TGCCACCAACTTGTGTGGGCTTTGAAAAAGGT
Found at i:542985 original size:65 final size:65
Alignment explanation
Indices: 542881--543004 Score: 223
Period size: 65 Copynumber: 1.9 Consensus size: 65
542871 AAGGAAGATG
542881 CCACCAACTTGTGTGGGCTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGAAAAAGGTTA
1 CCACCAACTTGTGTGGGCTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGAAAAAGGTTA
*
542946 CCACCAACTTGTGTGGGCTTTG-AGAAGGGTTGCCACCGACTTGTGTGGGCTTTGGAAAA
1 CCACCAACTTGTGTGGGCTTTGAAGAA-GGTTGCCACCGACTTGTGTGGGCTTTAGAAAA
543005 GGAGAAAGAT
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
64 4 0.07
65 53 0.93
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (65 bp):
CCACCAACTTGTGTGGGCTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGAAAAAGGTTA
Found at i:543060 original size:35 final size:34
Alignment explanation
Indices: 543001--543099 Score: 100
Period size: 31 Copynumber: 3.0 Consensus size: 34
542991 TGGGCTTTGG
* *
543001 AAAAGGAGAAAGA-TGCCACGGAGTTGTGGACTT
1 AAAAGGAAAAAGAGTGCCACAGAGTTGTGGACTT
543034 AAAAGGGAAAAAGAGTGCCACAGAGTTGT-GAGCTT
1 AAAA-GGAAAAAGAGTGCCACAGAGTTGTGGA-CTT
** *
543069 TGAA--AAGAAG-GTGCCACAGAGTTGTGGACTT
1 AAAAGGAAAAAGAGTGCCACAGAGTTGTGGACTT
543100 TAAGAAGGTA
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
31 18 0.32
32 7 0.12
33 4 0.07
34 10 0.18
35 18 0.32
ACGTcount: A:0.36, C:0.12, G:0.32, T:0.19
Consensus pattern (34 bp):
AAAAGGAAAAAGAGTGCCACAGAGTTGTGGACTT
Found at i:547824 original size:33 final size:32
Alignment explanation
Indices: 547782--547846 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
547772 CACACCCAGA
* *
547782 TGTATCGATACATGCTGCTTTTTATCGATACAT
1 TGTATCGATACATG-TGCATTGTATCGATACAT
*
547815 TGTATCGATACATGTTCATTGTATCGATACAT
1 TGTATCGATACATGTGCATTGTATCGATACAT
547847 GGACAAATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (32 bp):
TGTATCGATACATGTGCATTGTATCGATACAT
Found at i:547858 original size:21 final size:19
Alignment explanation
Indices: 547811--547867 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
547801 TTTTATCGAT
*
547811 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
547830 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
547849 ACAAATTGTATCGATACAT
1 AC--ATTGTATCGATACAT
547868 CAAACTAGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 18 0.55
21 15 0.45
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:547934 original size:13 final size:13
Alignment explanation
Indices: 547913--547976 Score: 68
Period size: 13 Copynumber: 5.4 Consensus size: 13
547903 TGATACATGG
*
547913 TACAATGTATCGA
1 TACATTGTATCGA
547926 TACATTGTATCGA
1 TACATTGTATCGA
*
547939 TACA-TG-A-AGA
1 TACATTGTATCGA
547949 -A-A-TGTATCGA
1 TACATTGTATCGA
547959 TACATTGTATCGA
1 TACATTGTATCGA
547972 TACAT
1 TACAT
547977 GAAGAAATGT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
8 3 0.07
9 2 0.05
10 4 0.09
11 2 0.05
12 3 0.07
13 29 0.67
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:547941 original size:33 final size:32
Alignment explanation
Indices: 547897--547996 Score: 148
Period size: 33 Copynumber: 3.0 Consensus size: 32
547887 CTATCACTAT
*
547897 TTGTATTGATACATG-GTACAATGTATCGATACA
1 TTGTATCGATACATGAG-A-AATGTATCGATACA
547930 TTGTATCGATACATGAAGAAATGTATCGATACA
1 TTGTATCGATACATG-AGAAATGTATCGATACA
547963 TTGTATCGATACATGAAGAAATGTATCGATACA
1 TTGTATCGATACATG-AGAAATGTATCGATACA
547996 T
1 T
547997 AGCTTGTAAC
Statistics
Matches: 64, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
33 62 0.97
34 1 0.02
35 1 0.02
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (32 bp):
TTGTATCGATACATGAGAAATGTATCGATACA
Found at i:547956 original size:20 final size:20
Alignment explanation
Indices: 547931--547996 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
547921 ATCGATACAT
547931 TGTATCGATACATGAAGAAA
1 TGTATCGATACATGAAGAAA
547951 TGTATCGATACAT-------
1 TGTATCGATACATGAAGAAA
547964 TGTATCGATACATGAAGAAA
1 TGTATCGATACATGAAGAAA
547984 TGTATCGATACAT
1 TGTATCGATACAT
547997 AGCTTGTAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 13 0.33
20 26 0.67
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (20 bp):
TGTATCGATACATGAAGAAA
Found at i:548656 original size:17 final size:19
Alignment explanation
Indices: 548624--548661 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
548614 TCGATTATTT
*
548624 TTTCGTTTTGTCTTTCGAA
1 TTTCGTTTTGTCTTTCAAA
548643 TTTC-TTTT-TCTTTCAAA
1 TTTCGTTTTGTCTTTCAAA
548660 TT
1 TT
548662 CAAAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 10 0.56
18 4 0.22
19 4 0.22
ACGTcount: A:0.13, C:0.16, G:0.08, T:0.63
Consensus pattern (19 bp):
TTTCGTTTTGTCTTTCAAA
Found at i:554167 original size:13 final size:13
Alignment explanation
Indices: 554149--554176 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
554139 ACAACACTCC
554149 TTGTATCGATACA
1 TTGTATCGATACA
554162 TTGTATCGATACA
1 TTGTATCGATACA
554175 TT
1 TT
554177 AGGTACTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:556048 original size:18 final size:19
Alignment explanation
Indices: 556015--556050 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
556005 AAATTTTTAT
*
556015 ATATAAAAAGGTGGAGAAG
1 ATATAAAAAGGAGGAGAAG
556034 ATATAAAAA-GAGGAGAA
1 ATATAAAAAGGAGGAGAA
556051 TTTTTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.58, C:0.00, G:0.28, T:0.14
Consensus pattern (19 bp):
ATATAAAAAGGAGGAGAAG
Found at i:556088 original size:17 final size:16
Alignment explanation
Indices: 556056--556102 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
556046 GAGAATTTTT
*
556056 TTTAAGAGGAGAGAATCG
1 TTTAAG-GGGGAGAAT-G
*
556074 TTTAAGGGGGAGAATT
1 TTTAAGGGGGAGAATG
556090 TTTAA-GGGGAGAA
1 TTTAAGGGGGAGAA
556103 AAACGAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 8 0.30
16 5 0.19
17 8 0.30
18 6 0.22
ACGTcount: A:0.36, C:0.02, G:0.36, T:0.26
Consensus pattern (16 bp):
TTTAAGGGGGAGAATG
Found at i:556641 original size:20 final size:19
Alignment explanation
Indices: 556618--556691 Score: 87
Period size: 19 Copynumber: 3.7 Consensus size: 19
556608 CACACCCAGA
*
556618 TGTATCGATACATGCTGCTT
1 TGTATCGATACATG-TGCAT
*
556638 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTGCAT
556657 TGTATCGATACATG-GACAAAT
1 TGTATCGATACATGTG-C--AT
556678 TGTATCGATACATG
1 TGTATCGATACATG
556692 AAACTGCCAG
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.38
20 14 0.29
21 16 0.33
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.36
Consensus pattern (19 bp):
TGTATCGATACATGTGCAT
Found at i:557412 original size:17 final size:19
Alignment explanation
Indices: 557380--557417 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
557370 TCGATTATCT
*
557380 TTTCGTTTTGTCTTTCGAA
1 TTTCGTTTTGTCTTTCAAA
557399 TTTC-TTTT-TCTTTCAAA
1 TTTCGTTTTGTCTTTCAAA
557416 TT
1 TT
557418 CAAAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 10 0.56
18 4 0.22
19 4 0.22
ACGTcount: A:0.13, C:0.16, G:0.08, T:0.63
Consensus pattern (19 bp):
TTTCGTTTTGTCTTTCAAA
Found at i:561437 original size:29 final size:29
Alignment explanation
Indices: 561405--561606 Score: 230
Period size: 29 Copynumber: 7.0 Consensus size: 29
561395 CTATTAAGTT
** *
561405 CCTAAACTTGGCAAAATTACGCTTTGACC
1 CCTAAACTTTTCAAAATTACACTTTGACC
*
561434 CCTAAACTTTTCAAAATTACA-TGTTGATC
1 CCTAAACTTTTCAAAATTACACT-TTGACC
* * *
561463 CCTAAGCTTTTCAAAATCACATTTTGA--
1 CCTAAACTTTTCAAAATTACACTTTGACC
561490 CCTAAAACTTTTCAAAATTACACTTTGACC
1 CCT-AAACTTTTCAAAATTACACTTTGACC
* *
561520 CCTAAACTTTTCAAAATTGCACATTGACC
1 CCTAAACTTTTCAAAATTACACTTTGACC
* * * *
561549 CTTAAACTTTTTAGAATCACACTTTGACC
1 CCTAAACTTTTCAAAATTACACTTTGACC
* *
561578 TCTAAACTTTTCAAAATTATACTTTGACC
1 CCTAAACTTTTCAAAATTACACTTTGACC
561607 TAATAATAGT
Statistics
Matches: 145, Mismatches: 23, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
27 3 0.02
28 22 0.15
29 116 0.80
30 4 0.03
ACGTcount: A:0.34, C:0.24, G:0.07, T:0.35
Consensus pattern (29 bp):
CCTAAACTTTTCAAAATTACACTTTGACC
Found at i:561507 original size:86 final size:87
Alignment explanation
Indices: 561416--561606 Score: 269
Period size: 86 Copynumber: 2.2 Consensus size: 87
561406 CTAAACTTGG
* ** *
561416 CAAAATTACGCTTTGACCCCTAAACTTTTCAAAATTACATGTTGATCCC-TAAGCTTTTCAAAAT
1 CAAAATTACACTTTGACCCCTAAACTTTTCAAAATTACACATTGA-CCCTTAAACTTTTCAAAAT
*
561480 CACATTTTGACCT-AAAACTTTT
65 CACACTTTGACCTCAAAACTTTT
* * *
561502 CAAAATTACACTTTGACCCCTAAACTTTTCAAAATTGCACATTGACCCTTAAACTTTTTAGAATC
1 CAAAATTACACTTTGACCCCTAAACTTTTCAAAATTACACATTGACCCTTAAACTTTTCAAAATC
*
561567 ACACTTTGACCTCTAAACTTTT
66 ACACTTTGACCTCAAAACTTTT
*
561589 CAAAATTATACTTTGACC
1 CAAAATTACACTTTGACC
561607 TAATAATAGT
Statistics
Matches: 93, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
85 3 0.03
86 65 0.70
87 25 0.27
ACGTcount: A:0.34, C:0.24, G:0.06, T:0.36
Consensus pattern (87 bp):
CAAAATTACACTTTGACCCCTAAACTTTTCAAAATTACACATTGACCCTTAAACTTTTCAAAATC
ACACTTTGACCTCAAAACTTTT
Found at i:561511 original size:57 final size:55
Alignment explanation
Indices: 561437--561609 Score: 188
Period size: 57 Copynumber: 3.0 Consensus size: 55
561427 TTTGACCCCT
*
561437 AAACTTTTCAAAATTACA-TGTTGATCCCTAAGCTTTTCAAAATCACATTTTGACCTA
1 AAACTTTTCAAAATTACACT-TTGA-CCCTAAACTTTTCAAAATCACA-TTTGACCTA
*
561494 AAACTTTTCAAAATTACACTTTGACCCCTAAACTTTTCAAAATTGCACA-TTGACCCTT
1 AAACTTTTCAAAATTACACTTTGA-CCCTAAACTTTTCAAAA-T-CACATTTGA-CCTA
* * * * *
561552 AAACTTTTTAGAATCACACTTTGACCTCTAAACTTTTCAAAATTATACTTTGACCTA
1 AAACTTTTCAAAATTACACTTTGACC-CTAAACTTTTCAAAATCACA-TTTGACCTA
561609 A
1 A
561610 TAATAGTCTA
Statistics
Matches: 100, Mismatches: 9, Indels: 14
0.81 0.07 0.11
Matches are distributed among these distances:
56 2 0.02
57 49 0.49
58 45 0.45
59 4 0.04
ACGTcount: A:0.35, C:0.23, G:0.06, T:0.36
Consensus pattern (55 bp):
AAACTTTTCAAAATTACACTTTGACCCTAAACTTTTCAAAATCACATTTGACCTA
Found at i:562729 original size:145 final size:144
Alignment explanation
Indices: 562531--562987 Score: 503
Period size: 144 Copynumber: 3.2 Consensus size: 144
562521 ATAACCTAAG
* * * ** * *
562531 AAAGGTAAAAATTACATTTTAGACCCTATA-AGTTTCAGTCAACCTAAGA-ACACTCCTATATGA
1 AAAGG-AAAAATTGCATTTTAGACCCCATAGACTTT-AACCAACC-AAAATACACTCCTAAATGA
*
562594 GCTTAAAAAATCTAAAAAAATTATTAAACAGTTCCTACAAGTGCTACCATGAAACAAAATAGTCC
63 GCTTAAAAAATTTAAAAAAATTATTAAACA-TTCCTACAAGTGCTACCATGAAACAAAATAGTCC
562659 CTAAATGGCCTAAAAATT
127 CTAAATGGCCTAAAAATT
* * *** * *
562677 AAAGGAAAAATTGCATTTGAGACCCCATAGGCTTTAACCAACTTTAGTACACTCCTAAAAGAGCT
1 AAAGGAAAAATTGCATTTTAGACCCCATAGACTTTAACCAACCAAAATACACTCCTAAATGAGCT
* * * * *
562742 TAAAAGATTTAAAAAAATTATTAAATAATCCCTACAAGTG-TGCCATGAAACAAAATAGGCCCTA
66 TAAAAAATTTAAAAAAATTATTAAA-CATTCCTACAAGTGCTACCATGAAACAAAATAGTCCCTA
562806 AATGGCCTAAAAATT
130 AATGGCCTAAAAATT
* * * * *
562821 AAAGGACAAATTGCATTTTAGACCCCATATATTTTAACTAACCAAAATACACTCTTAAAT-AGGC
1 AAAGGAAAAATTGCATTTTAGACCCCATAGACTTTAACCAACCAAAATACACTCCTAAATGA-GC
* ** * * *
562885 TTAAAAATTTTGGAAAAATTATTAAACATTCCCTATAAATGCTACCATG-AACTAAAATAATCCC
65 TTAAAAAATTTAAAAAAATTATTAAACATT-CCTACAAGTGCTACCATGAAAC-AAAATAGTCCC
562949 TAAATGGCCTAAAAATT
128 TAAATGGCCTAAAAATT
* *
562966 -AAGGAAAATTTGTATTTTAGAC
1 AAAGGAAAAATTGCATTTTAGAC
562988 ACACCTTTTT
Statistics
Matches: 258, Mismatches: 46, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
143 3 0.01
144 139 0.54
145 107 0.41
146 9 0.03
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.28
Consensus pattern (144 bp):
AAAGGAAAAATTGCATTTTAGACCCCATAGACTTTAACCAACCAAAATACACTCCTAAATGAGCT
TAAAAAATTTAAAAAAATTATTAAACATTCCTACAAGTGCTACCATGAAACAAAATAGTCCCTAA
ATGGCCTAAAAATT
Found at i:563533 original size:11 final size:11
Alignment explanation
Indices: 563495--563533 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
563485 ATAAATGAAA
563495 TTTTCT-TTTT
1 TTTTCTCTTTT
*
563505 TTTTCTATTTT
1 TTTTCTCTTTT
*
563516 TTCTCTCTTTT
1 TTTTCTCTTTT
563527 TTTTCTC
1 TTTTCTC
563534 CCAAAACCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
10 6 0.24
11 19 0.76
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTCTCTTTT
Found at i:566143 original size:66 final size:66
Alignment explanation
Indices: 566032--566163 Score: 183
Period size: 66 Copynumber: 2.0 Consensus size: 66
566022 TTAGAAAGTA
* * * *
566032 CATAGTTTGTACTAGATATGGGTTCCTACTAAACCTGTCATGACTTTCGCTAATAGCATTCACCT
1 CATAATTTGTACCAGATATGGGTTCCTACTAAACCTGGCATGACTTTCACTAATAGCATTCACCT
566097 C
66 C
* * * **
566098 CATAATTTGTACCGGATGTGGGTTTCTACTAAACCTGGCATGACTTTCACTAATAGTGTTCACCT
1 CATAATTTGTACCAGATATGGGTTCCTACTAAACCTGGCATGACTTTCACTAATAGCATTCACCT
566163 C
66 C
566164 TTTCTCCTTC
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (66 bp):
CATAATTTGTACCAGATATGGGTTCCTACTAAACCTGGCATGACTTTCACTAATAGCATTCACCT
C
Found at i:569602 original size:34 final size:34
Alignment explanation
Indices: 569533--569603 Score: 81
Period size: 34 Copynumber: 2.1 Consensus size: 34
569523 GTGTTGCTGC
* *
569533 TTGCTTGCTTCAGCTGCTGTCATTACTGGTGTTG
1 TTGCTTGCTTCAGCTGATGTCATTACTGCTGTTG
* * *
569567 TTGCTTGCTTCAGCT-ATTTCGTTGCTGCTGTTTG
1 TTGCTTGCTTCAGCTGATGTCATTACTGCTG-TTG
569601 TTG
1 TTG
569604 ATGTCTTGCA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 10 0.32
34 21 0.68
ACGTcount: A:0.07, C:0.20, G:0.25, T:0.48
Consensus pattern (34 bp):
TTGCTTGCTTCAGCTGATGTCATTACTGCTGTTG
Found at i:569702 original size:25 final size:24
Alignment explanation
Indices: 569670--569719 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
569660 TCTTTTTGTG
*
569670 TTTTTTTTCT-GTTTCATTTCTTTC
1 TTTTTTTTCTCGTTTC-TTGCTTTC
*
569694 TTTTCTTTTTTCGTTTCTTGCTTTC
1 TTTT-TTTTCTCGTTTCTTGCTTTC
569719 T
1 T
569720 CTCTGTTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 4 0.18
25 13 0.59
26 5 0.23
ACGTcount: A:0.02, C:0.18, G:0.06, T:0.74
Consensus pattern (24 bp):
TTTTTTTTCTCGTTTCTTGCTTTC
Found at i:569728 original size:25 final size:27
Alignment explanation
Indices: 569672--569729 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 27
569662 TTTTTGTGTT
* *
569672 TTTTTTCTGTTTCATTTCTTTCTTTTC
1 TTTTTTCTGTTTCATTGCTTTCTTCTC
569699 TTTTTTC-GTTTC-TTGCTTTC-TCTC
1 TTTTTTCTGTTTCATTGCTTTCTTCTC
*
569723 TGTTTTC
1 TTTTTTC
569730 CTATTGCTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 9 0.32
25 7 0.25
26 5 0.18
27 7 0.25
ACGTcount: A:0.02, C:0.21, G:0.07, T:0.71
Consensus pattern (27 bp):
TTTTTTCTGTTTCATTGCTTTCTTCTC
Found at i:570178 original size:3 final size:3
Alignment explanation
Indices: 570170--570222 Score: 88
Period size: 3 Copynumber: 17.7 Consensus size: 3
570160 TTCCTTTTTC
* *
570170 ATT ATT ATT ATT ATT ATA ATT ATT AAT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
570218 ATT AT
1 ATT AT
570223 ATTTTTTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:570238 original size:9 final size:10
Alignment explanation
Indices: 570170--570236 Score: 58
Period size: 9 Copynumber: 7.3 Consensus size: 10
570160 TTCCTTTTTC
570170 ATTATTA-TT
1 ATTATTATTT
*
570179 ATTATTA-TA
1 ATTATTATTT
*
570188 ATTATTA-AT
1 ATTATTATTT
570197 ATTATTA-TT
1 ATTATTATTT
570206 ATTATTA-TT
1 ATTATTATTT
570215 ATTATTATATT
1 ATTATTAT-TT
570226 -TT-TTATTT
1 ATTATTATTT
570234 ATT
1 ATT
570237 TTTTTAAATA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
8 2 0.04
9 45 0.88
10 2 0.04
11 2 0.04
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
ATTATTATTT
Found at i:575329 original size:79 final size:79
Alignment explanation
Indices: 575187--575805 Score: 597
Period size: 80 Copynumber: 7.8 Consensus size: 79
575177 TGAAAATCGA
* * * *
575187 GGTTGGAGTATCCCCAAAGATGAAAAATTTAGTTTTTTAGAAGT-AAAATGGGGTTGGAATATTC
1 GGTTAGAGTATCCCCAAAGATGAAAAATTTAGTGTTTTAGAAGTAAAAATGGGGTTAGAGTA-TC
*
575251 CTTTGGAGATGGTGG
65 CTTCGGAGATGGTGG
* * *
575266 GGTTAGAGTAT-CCCAAAGATGAAAATTTTGGTGTTTTAGAAGTAAAAATGGGGTTGGAGTATTC
1 GGTTAGAGTATCCCCAAAGATGAAAAATTTAGTGTTTTAGAAGTAAAAATGGGGTTAGAGTA-TC
*
575330 TTTCGGAGATGGTGG
65 CTTCGGAGATGGTGG
* * * * * * * *
575345 GGTTAGGGTATCCCTAGAGTTGAAAAATTTGGTATCTTAGAAGTAAAAA-GAGGTTAGAGTATCC
1 GGTTAGAGTATCCCCAAAGATGAAAAATTTAGTGTTTTAGAAGTAAAAATGGGGTTAGAGTATCC
* **
575409 CTCAAAGATGGTGG
66 TTCGGAGATGGTGG
* * * *
575423 GATTAGAGTATCCCTAGAGATG-AAAATTTTGATGTTTTAGAAGTAAAAATGGGGTTAGAGTATC
1 GGTTAGAGTATCCCCAAAGATGAAAAATTTAG-TGTTTTAGAAGTAAAAATGGGGTTAGAGTATC
*
575487 CTCTCGGAGATGGTAG
65 CT-TCGGAGATGGTGG
* * * * *
575503 GGTTGGCGTAT-CCCAATAGATGAAAAATTTAGTATTTTAGAAG-AAAAATGAGGTTGGAGTATC
1 GGTTAGAGTATCCCCAA-AGATGAAAAATTTAGTGTTTTAGAAGTAAAAATGGGGTTAGAGTATC
*
575566 CCTCGGATG-TGGTGG
65 CTTCGGA-GATGGTGG
* * *
575581 GGTTAGAGTATCCCCAAAGATGAAAATTTTGGTGTTTTAAAAGTAAAAATGGGGTTAGAGTATCC
1 GGTTAGAGTATCCCCAAAGATGAAAAATTTAGTGTTTTAGAAGTAAAAATGGGGTTAGAGTAT-C
*
575646 CTTCGAAGATGGTGG
65 CTTCGGAGATGGTGG
* * * ** * ** * ** * *
575661 GATTGGACTATCCCCAGGGATGAAAATTTTAGCATTTTGGAAGTAAAAACAGAGTTGGAGTATCC
1 GGTTAGAGTATCCCCAAAGATGAAAAATTTAGTGTTTTAGAAGTAAAAATGGGGTTAGAGTATCC
*
575726 TCTTGGATG-TGGTGG
66 T-TCGGA-GATGGTGG
* * * * * **
575741 AGTTGGAGTATCCCCAAAAATGAAAAATTCAATGTTTTAGAAGTAAAAACAGGGTTAGAGTATCC
1 GGTTAGAGTATCCCCAAAGATGAAAAATTTAGTGTTTTAGAAGTAAAAATGGGGTTAGAGTATCC
575806 CCCCAAGATG
Statistics
Matches: 444, Mismatches: 82, Indels: 27
0.80 0.15 0.05
Matches are distributed among these distances:
77 8 0.02
78 117 0.26
79 125 0.28
80 185 0.42
81 9 0.02
ACGTcount: A:0.32, C:0.10, G:0.28, T:0.30
Consensus pattern (79 bp):
GGTTAGAGTATCCCCAAAGATGAAAAATTTAGTGTTTTAGAAGTAAAAATGGGGTTAGAGTATCC
TTCGGAGATGGTGG
Found at i:575444 original size:158 final size:158
Alignment explanation
Indices: 575187--575805 Score: 635
Period size: 158 Copynumber: 3.9 Consensus size: 158
575177 TGAAAATCGA
* * * * * * *
575187 GGTTGGAGTATCCCCAA-AGATGAAAAATTTAGTTTTTTAGAAGTAAAATGGGGTTGGAATATTC
1 GGTTGGCGTAT-CCCAAGAGATGAAAAATTTAGTATCTTAGAAGAAAAATGAGGTTAGAGTA-TC
* * *
575251 CTTTG-GAGATGGTGGGGTTAGAGTATCCCAAAGATGAAAATTTTGGTGTTTTAGAAGTAAAAAT
64 CCTCGAAAGATGGTGGGGTTAGAGTATCCCAAAGATGAAAATTTTGGTGTTTTAGAAGTAAAAAT
* *
575315 GGGGTTGGAGTATTCTTTCGGAGATGGTGG
129 GGGGTTAGAGTATCCTTTCGGAGATGGTGG
* * *
575345 GGTTAGG-GTATCCCTAGAGTTGAAAAATTTGGTATCTTAGAAGTAAAAA-GAGGTTAGAGTATC
1 GGTT-GGCGTATCCCAAGAGATGAAAAATTTAGTATCTTAGAAG-AAAAATGAGGTTAGAGTATC
* * *
575408 CCTC-AAAGATGGTGGGATTAGAGTATCCCTAGAGATGAAAATTTTGATGTTTTAGAAGTAAAAA
64 CCTCGAAAGATGGTGGGGTTAGAGTATCCC-AAAGATGAAAATTTTGGTGTTTTAGAAGTAAAAA
* *
575472 TGGGGTTAGAGTATCCTCTCGGAGATGGTAG
128 TGGGGTTAGAGTATCCTTTCGGAGATGGTGG
* * *
575503 GGTTGGCGTATCCCAATAGATGAAAAATTTAGTATTTTAGAAGAAAAATGAGGTTGGAGTATCCC
1 GGTTGGCGTATCCCAAGAGATGAAAAATTTAGTATCTTAGAAGAAAAATGAGGTTAGAGTATCCC
* * *
575568 TCGGATG-TGGTGGGGTTAGAGTATCCCCAAAGATGAAAATTTTGGTGTTTTAAAAGTAAAAATG
66 TCGAAAGATGGTGGGGTTAGAGTAT-CCCAAAGATGAAAATTTTGGTGTTTTAGAAGTAAAAATG
* *
575632 GGGTTAGAGTATCCCTTCGAAGATGGTGG
130 GGGTTAGAGTATCCTTTCGGAGATGGTGG
* * * * * * * * *
575661 GATTGGAC-TATCCCCAGGGATGAAAATTTTAGCATTTTGGAAGTAAAAA-CAGAGTTGGAGTAT
1 GGTTGG-CGTATCCCAAGAGATGAAAAATTTAGTATCTTAGAAG-AAAAATGAG-GTTAGAGTAT
* * * * * * * ***
575724 CCTCTTGGATG-TGGTGGAGTTGGAGTATCCCCAAAAATGAAAAATTCAATGTTTTAGAAGTAAA
63 CC-CTCGAAAGATGGTGGGGTTAGAGTAT-CCCAAAGATGAAAATTTTGGTGTTTTAGAAGTAAA
**
575788 AACAGGGTTAGAGTATCC
126 AATGGGGTTAGAGTATCC
575806 CCCCAAGATG
Statistics
Matches: 394, Mismatches: 54, Indels: 24
0.83 0.11 0.05
Matches are distributed among these distances:
157 37 0.09
158 260 0.66
159 29 0.07
160 68 0.17
ACGTcount: A:0.32, C:0.10, G:0.28, T:0.30
Consensus pattern (158 bp):
GGTTGGCGTATCCCAAGAGATGAAAAATTTAGTATCTTAGAAGAAAAATGAGGTTAGAGTATCCC
TCGAAAGATGGTGGGGTTAGAGTATCCCAAAGATGAAAATTTTGGTGTTTTAGAAGTAAAAATGG
GGTTAGAGTATCCTTTCGGAGATGGTGG
Found at i:576838 original size:13 final size:13
Alignment explanation
Indices: 576820--576845 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
576810 CAATATTTTG
576820 TGTATCGATACAT
1 TGTATCGATACAT
576833 TGTATCGATACAT
1 TGTATCGATACAT
576846 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:576861 original size:32 final size:33
Alignment explanation
Indices: 576800--576863 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
576790 TACAAGCCAA
*
576800 TGTATCGATACAATATTTTGTGTATCGATACAT
1 TGTATCGATACAATATCTTGTGTATCGATACAT
576833 TGTATCGATAC-ATA-CTTGCTGTATCGATACA
1 TGTATCGATACAATATCTTG-TGTATCGATACA
576864 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 3 0.10
32 15 0.52
33 11 0.38
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATATCTTGTGTATCGATACAT
Found at i:576910 original size:21 final size:21
Alignment explanation
Indices: 576884--576959 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
576874 CTGCCAAGAA
*
576884 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
576905 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
576925 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
576946 ATGTATCGATACAT
1 ATGTATCGATACAT
576960 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:576930 original size:20 final size:20
Alignment explanation
Indices: 576905--576977 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
576895 CATCTTTTTT
576905 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
576925 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
576946 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
576966 ATGTATCGATAC
1 ATGTATCGATAC
576978 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:576941 original size:41 final size:41
Alignment explanation
Indices: 576884--576977 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
576874 CTGCCAAGAA
*
576884 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
576925 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
576966 ATGTATCGATAC
1 ATGTATCGATAC
576978 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:579438 original size:13 final size:13
Alignment explanation
Indices: 579420--579458 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
579410 ATAATCACCC
*
579420 TGTATCGATACAG
1 TGTATCGATACAA
579433 TGTATCGATACAA
1 TGTATCGATACAA
579446 TGTATCGATACAA
1 TGTATCGATACAA
579459 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:579469 original size:20 final size:20
Alignment explanation
Indices: 579444--579522 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
579434 GTATCGATAC
579444 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
579464 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
579489 GATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
579509 CATGTATCGATACA
1 AATGTATCGATACA
579523 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
20 32 0.65
25 16 0.33
26 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:585648 original size:13 final size:13
Alignment explanation
Indices: 585630--585655 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
585620 CAATATTTTG
585630 TGTATCGATACAT
1 TGTATCGATACAT
585643 TGTATCGATACAT
1 TGTATCGATACAT
585656 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:585671 original size:32 final size:33
Alignment explanation
Indices: 585610--585673 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
585600 TACAAGCCAA
*
585610 TGTATCGATACAATATTTTGTGTATCGATACAT
1 TGTATCGATACAATATCTTGTGTATCGATACAT
585643 TGTATCGATAC-ATA-CTTGCTGTATCGATACA
1 TGTATCGATACAATATCTTG-TGTATCGATACA
585674 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 3 0.10
32 15 0.52
33 11 0.38
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATATCTTGTGTATCGATACAT
Found at i:585720 original size:21 final size:21
Alignment explanation
Indices: 585694--585769 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
585684 CTGCCAAGAA
*
585694 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
585715 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
585735 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
585756 ATGTATCGATACAT
1 ATGTATCGATACAT
585770 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:585740 original size:20 final size:20
Alignment explanation
Indices: 585715--585787 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
585705 CATCTTTTTT
585715 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
585735 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
585756 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
585776 ATGTATCGATAC
1 ATGTATCGATAC
585788 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:585751 original size:41 final size:41
Alignment explanation
Indices: 585694--585787 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
585684 CTGCCAAGAA
*
585694 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
585735 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
585776 ATGTATCGATAC
1 ATGTATCGATAC
585788 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:588190 original size:20 final size:20
Alignment explanation
Indices: 588163--588211 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
588153 TTATATTGAA
*
588163 GAATGTATCGATACAGTGAGT
1 GAATGTATCGATACA-TAAGT
588184 G-ATGTATCGATACATAAGT
1 GAATGTATCGATACATAAGT
588203 GAATGTATC
1 GAATGTATC
588212 AATATAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 5 0.19
20 20 0.77
21 1 0.04
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (20 bp):
GAATGTATCGATACATAAGT
Found at i:588300 original size:20 final size:20
Alignment explanation
Indices: 588275--588328 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
588265 AATTTTAAGC
*
588275 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTAACTT
*
588295 ATGTATTGATACATTAACTT
1 ATGTATCGATACATTAACTT
588315 ATTGTATCGATACA
1 A-TGTATCGATACA
588329 AATTGTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTAACTT
Found at i:589305 original size:67 final size:66
Alignment explanation
Indices: 589162--589318 Score: 190
Period size: 66 Copynumber: 2.3 Consensus size: 66
589152 GAAACCAAAA
* * * * * *
589162 AAAATCAACTAAGAGTGACGAAGGTGGAACCTAAGTCGAAAAGAGATTGACCAGGGCGAAATCGA
1 AAAATCAACTAAGGGTGACTAAGGTGAAACCTAAGTCAAAAAAAGATTGACCAGAGCGAAATCGA
589227 T
66 T
* * * *
589228 AAAGTCAACTAAGGGTGACTAGGGTGAAACCTAAGTCAAAATAAAGGTTGACTAGAGCGAAA-CT
1 AAAATCAACTAAGGGTGACTAAGGTGAAACCTAAGTCAAAA-AAAGATTGACCAGAGCGAAATC-
589292 GAT
64 GAT
589295 AAAATCAACTAAGGGATGACTAAG
1 AAAATCAACTAAGGG-TGACTAAG
589319 ATGCATCCTA
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
66 36 0.47
67 33 0.43
68 7 0.09
ACGTcount: A:0.43, C:0.14, G:0.25, T:0.17
Consensus pattern (66 bp):
AAAATCAACTAAGGGTGACTAAGGTGAAACCTAAGTCAAAAAAAGATTGACCAGAGCGAAATCGA
T
Found at i:589449 original size:16 final size:16
Alignment explanation
Indices: 589428--589459 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
589418 AAACCAAAAT
589428 AGTCAACTAAGATGGA
1 AGTCAACTAAGATGGA
589444 AGTCAACTAAGATGGA
1 AGTCAACTAAGATGGA
589460 TTAGGATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.25, T:0.19
Consensus pattern (16 bp):
AGTCAACTAAGATGGA
Found at i:589707 original size:41 final size:40
Alignment explanation
Indices: 589632--589872 Score: 149
Period size: 40 Copynumber: 6.0 Consensus size: 40
589622 AACAAGCCAA
*
589632 TAAATAGT-AAAGTTTGATCGAAATAAAA-CTGATAAGTCAAC
1 TAAATAGTAAAAG-TTGA-CGAGATAAAATC-GATAAGTCAAC
589673 TAAA-AGTAAAAGATTGACCGAGATAAAATCGATAAGTCAAC
1 TAAATAGTAAAAG-TTGA-CGAGATAAAATCGATAAGTCAAC
* * * * * * * *
589714 -AATTGAG-AAAGGTTGACCGAAATGAAACCAACAAGTTAAC
1 TAAAT-AGTAAAAGTTGA-CGAGATAAAATCGATAAGTCAAC
* * * * *
589754 -AAAGAGTAAATGTTGATCGAGACAAAATCGACAAGCCAA-
1 TAAATAGTAAAAGTTGA-CGAGATAAAATCGATAAGTCAAC
* *
589793 TAAATAGT-AAAGTTGACTAGGATAAAATCAATAAGTCAAC
1 TAAATAGTAAAAGTTGACGA-GATAAAATCGATAAGTCAAC
* * *
589833 T-AAGAGTAAAAGGTTGACTAGGACAAAATCGATAAGTCAA
1 TAAATAGTAAAA-GTTGACGA-GATAAAATCGATAAGTCAA
589873 TAATTGGAAA
Statistics
Matches: 158, Mismatches: 32, Indels: 20
0.75 0.15 0.10
Matches are distributed among these distances:
38 2 0.01
39 29 0.18
40 62 0.39
41 62 0.39
42 3 0.02
ACGTcount: A:0.49, C:0.12, G:0.18, T:0.21
Consensus pattern (40 bp):
TAAATAGTAAAAGTTGACGAGATAAAATCGATAAGTCAAC
Found at i:589763 original size:121 final size:119
Alignment explanation
Indices: 589614--589832 Score: 257
Period size: 121 Copynumber: 1.8 Consensus size: 119
589604 GTTTATCGGG
* * * * * *
589614 ATGAAACTAACAAGCCAATAAATAGTAAA-GTTTGATCGAAATAAAA-CTGATAAGTCAACTAAA
1 ATGAAACCAACAAGCCAACAAAGAGTAAATG-TTGATCGAAACAAAATC-GACAAGCCAA-TAAA
*
589677 -AGTAAAAGATTGACCGA-GATAAAATCGATAAGTCAACAATTGAGAAAGGTTGACCGAA
63 TAGT-AAAG-TTGA-CGAGGATAAAATCAATAAGTCAACAATTGAGAAAGGTTGACCGAA
** *
589735 ATGAAACCAACAAGTTAACAAAGAGTAAATGTTGATCGAGACAAAATCGACAAGCCAATAAATAG
1 ATGAAACCAACAAGCCAACAAAGAGTAAATGTTGATCGAAACAAAATCGACAAGCCAATAAATAG
*
589800 TAAAGTTGACTAGGATAAAATCAATAAGTCAAC
66 TAAAGTTGACGAGGATAAAATCAATAAGTCAAC
589833 TAAGAGTAAA
Statistics
Matches: 83, Mismatches: 11, Indels: 10
0.80 0.11 0.10
Matches are distributed among these distances:
118 2 0.02
119 23 0.28
120 8 0.10
121 48 0.58
122 2 0.02
ACGTcount: A:0.50, C:0.13, G:0.17, T:0.20
Consensus pattern (119 bp):
ATGAAACCAACAAGCCAACAAAGAGTAAATGTTGATCGAAACAAAATCGACAAGCCAATAAATAG
TAAAGTTGACGAGGATAAAATCAATAAGTCAACAATTGAGAAAGGTTGACCGAA
Found at i:589820 original size:39 final size:41
Alignment explanation
Indices: 589774--589875 Score: 129
Period size: 41 Copynumber: 2.5 Consensus size: 41
589764 TGTTGATCGA
* * *
589774 GACAAAATCGACAAGCCAATAAATAGT-AAA-GTTGACTAG
1 GACAAAATCGATAAGTCAATAAAGAGTAAAAGGTTGACTAG
* *
589813 GATAAAATCAATAAGTCAACT-AAGAGTAAAAGGTTGACTAG
1 GACAAAATCGATAAGTCAA-TAAAGAGTAAAAGGTTGACTAG
589854 GACAAAATCGATAAGTCAATAA
1 GACAAAATCGATAAGTCAATAA
589876 TTGGAAAGGT
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
39 20 0.38
40 5 0.10
41 27 0.52
ACGTcount: A:0.50, C:0.13, G:0.18, T:0.20
Consensus pattern (41 bp):
GACAAAATCGATAAGTCAATAAAGAGTAAAAGGTTGACTAG
Found at i:589906 original size:80 final size:79
Alignment explanation
Indices: 589657--589912 Score: 225
Period size: 80 Copynumber: 3.2 Consensus size: 79
589647 GATCGAAATA
* * * * *
589657 AAACTGATAAGTCAACTAAAAGTAAAAGATTGAC-CGAGATAAAATCGATAAGTCAACAATTGAG
1 AAACTAATAAGTCAACTAAGAGTAAAAGGTTGACTCGAGACAAAATCGATAAGTCAATAATTG-G
* *
589721 AAAGGTTGACCGAAAT
65 AAAGGTTGACAG-GAT
* * * * * * * *
589737 GAAACCAACAAGTTAACAAAGAGT-AAATGTTGA-TCGAGACAAAATCGACAAGCCAATAAATAG
1 -AAACTAATAAGTCAACTAAGAGTAAAAGGTTGACTCGAGACAAAATCGATAAGTCAAT-AATTG
*
589800 TAAA-GTTGACTAGGAT
64 GAAAGGTTGAC-AGGAT
* *
589816 AAAATCAATAAGTCAACTAAGAGTAAAAGGTTGACTAG-GACAAAATCGATAAGTCAATAATTGG
1 AAACT-AATAAGTCAACTAAGAGTAAAAGGTTGACTCGAGACAAAATCGATAAGTCAATAATTGG
* *
589880 AAAGGTTAATCGGGACT
65 AAAGGTTGA-CAGGA-T
589897 AAACTAATAAGTCAAC
1 AAACTAATAAGTCAAC
589913 AATTGAGAAA
Statistics
Matches: 136, Mismatches: 30, Indels: 19
0.74 0.16 0.10
Matches are distributed among these distances:
78 3 0.02
79 30 0.22
80 74 0.54
81 29 0.21
ACGTcount: A:0.48, C:0.13, G:0.19, T:0.20
Consensus pattern (79 bp):
AAACTAATAAGTCAACTAAGAGTAAAAGGTTGACTCGAGACAAAATCGATAAGTCAATAATTGGA
AAGGTTGACAGGAT
Found at i:589950 original size:40 final size:39
Alignment explanation
Indices: 589852--589950 Score: 108
Period size: 40 Copynumber: 2.5 Consensus size: 39
589842 AAGGTTGACT
* * * *
589852 AGGACAAAATCGATAAGTCAATAATTGGAAAGGTTAATC
1 AGGACAAAATTGATAAGTCAACAATTGGAAAGGTAAACC
* * * *
589891 GGGACTAAACTAATAAGTCAACAATTGAGAAAGGTAAACC
1 AGGACAAAATTGATAAGTCAACAATTG-GAAAGGTAAACC
*
589931 AGGACAAAATTGATGAGTCA
1 AGGACAAAATTGATAAGTCA
589951 CCAACTAAAA
Statistics
Matches: 46, Mismatches: 13, Indels: 1
0.77 0.22 0.02
Matches are distributed among these distances:
39 21 0.46
40 25 0.54
ACGTcount: A:0.46, C:0.12, G:0.21, T:0.20
Consensus pattern (39 bp):
AGGACAAAATTGATAAGTCAACAATTGGAAAGGTAAACC
Found at i:590767 original size:30 final size:30
Alignment explanation
Indices: 590733--590889 Score: 83
Period size: 30 Copynumber: 5.2 Consensus size: 30
590723 CTAGAAGTCT
590733 ACAAAATGACTTAGGCAAAACCAAGACTCA
1 ACAAAATGACTTAGGCAAAACCAAGACTCA
* * * *
590763 ACAAAATTG-CCTAGACGAAACCAAAATCCTCA
1 ACAAAA-TGACTTAGGCAAAACCAAGA--CTCA
*** *
590795 AC--AATGACTTAGATGAAACTAAGACTCAA
1 ACAAAATGACTTAGGCAAAACCAAGACTC-A
* * * *
590824 ACAAAATGGCTT-GGATAAAACTGAAAAC-CTA
1 ACAAAATGACTTAGG-CAAAAC-CAAGACTC-A
*
590855 A-AAAATGACTTGGGCAAAACCAAGACTCA
1 ACAAAATGACTTAGGCAAAACCAAGACTCA
590884 ATCAAA
1 A-CAAA
590890 TAGCCTAGAT
Statistics
Matches: 96, Mismatches: 18, Indels: 25
0.69 0.13 0.18
Matches are distributed among these distances:
28 3 0.03
29 11 0.11
30 50 0.52
31 22 0.23
32 10 0.10
ACGTcount: A:0.49, C:0.21, G:0.13, T:0.17
Consensus pattern (30 bp):
ACAAAATGACTTAGGCAAAACCAAGACTCA
Found at i:590915 original size:60 final size:61
Alignment explanation
Indices: 590737--591047 Score: 242
Period size: 60 Copynumber: 5.2 Consensus size: 61
590727 AAGTCTACAA
* ** * *
590737 AATGACTTAGGCAAAACCAAGACTCAA-CAAAATTGCCTAGACGAAACCA-AAATCCTCAAC
1 AATGACTTAGGCAAAACCAAGACTCAATCAAAATGGCCTAGATAAAACTAGAAA-CCTAAAC
*** * * * * *
590797 AATGACTTAGATGAAACTAAGACTCAAACAAAATGGCTTGGATAAAACT-GAAAACCTAAAA
1 AATGACTTAGGCAAAACCAAGACTCAATCAAAATGGCCTAGATAAAACTAG-AAACCTAAAC
* *
590858 AATGACTTGGGCAAAACCAAGACTCAATC-AAATAGCCTAGATAAAACTAGAAACCTAAAC
1 AATGACTTAGGCAAAACCAAGACTCAATCAAAATGGCCTAGATAAAACTAGAAACCTAAAC
* * * * * * *
590918 AATGACGTATGCAAAA-CAAGACTCAAT-AAAATGGTCTGGATAAAA-TCAAAAACTTGAAC
1 AATGACTTAGGCAAAACCAAGACTCAATCAAAATGGCCTAGATAAAACT-AGAAACCTAAAC
* * * * * * * * * *
590977 AATGACTTAGGTAAAACTAAGACTCAA-CTACATGACTTCGATGAAACAAAAAACCTAAAC
1 AATGACTTAGGCAAAACCAAGACTCAATCAAAATGGCCTAGATAAAACTAGAAACCTAAAC
*
591037 AATGACATAGG
1 AATGACTTAGG
591048 TGAAATCAGA
Statistics
Matches: 196, Mismatches: 46, Indels: 18
0.75 0.18 0.07
Matches are distributed among these distances:
58 1 0.01
59 47 0.24
60 101 0.52
61 44 0.22
62 3 0.02
ACGTcount: A:0.49, C:0.19, G:0.14, T:0.18
Consensus pattern (61 bp):
AATGACTTAGGCAAAACCAAGACTCAATCAAAATGGCCTAGATAAAACTAGAAACCTAAAC
Found at i:592315 original size:112 final size:112
Alignment explanation
Indices: 592065--592622 Score: 644
Period size: 112 Copynumber: 5.0 Consensus size: 112
592055 AAAAGTTTGG
* * * * ** *
592065 TTGGCTCAGAAA-TTTCAAAACTGATATGATACATGCCCCACTTTCCTAGGAAAAAATGGATC-G
1 TTGGCTCA-AAATTTTCAAAACTGATAGGATACATGCCCTATTTTCCTAGGCATGAATGGATCAA
* * * ** *
592128 GCTCATATAAAAT-TGGAATTTTTTTTGAAAATCTGACAAATTTGATGTTG
65 GAT-GTATAAAATAT-GAA-TTTCTTTGAAAATCAAACAAATTTGATGTTA
* * *
592178 TTGGCTCAAAAATTTT-AAAACTGATAGGATAGATGTCGTATTTTCCTAGGCATGAATGGATCAA
1 TTGGCTC-AAAATTTTCAAAACTGATAGGATACATGCCCTATTTTCCTAGGCATGAATGGATCAA
**
592242 GATGTATAAAATACAAATTTCTTTGAAAATCAAACAAATTTGATGTTA
65 GATGTATAAAATATGAATTTCTTTGAAAATCAAACAAATTTGATGTTA
*
592290 TTGGCTCAAAATTTTCAAAATTGATAGGATACATGCCCTATTTTCCTAGGCATGAATGGATCAAG
1 TTGGCTCAAAATTTTCAAAACTGATAGGATACATGCCCTATTTTCCTAGGCATGAATGGATCAAG
* * * * * *
592355 -TAATATAGAATAGGAATTTCTTTG--AATCTAACAAATTTAATGTTG
66 AT-GTATAAAATATGAATTTCTTTGAAAATCAAACAAATTTGATGTTA
* * ** *
592400 TTGGCTCAAAATTTTCAAAATTGATAGAATACATGCGTTATTTTCCTAGGCATGAATGGATCAGG
1 TTGGCTCAAAATTTTCAAAACTGATAGGATACATGCCCTATTTTCCTAGGCATGAATGGATCAAG
* * * *
592465 ATGTATAAAACATTAATTTCTTTGAAAATTAGACAAATTTGATGTTA
66 ATGTATAAAATATGAATTTCTTTGAAAATCAAACAAATTTGATGTTA
* * * * *
592512 TTGGCTCAAAAATTTCAAAACTGATAGGACACATGCCCCATTTTCTTAGGCATGAATGGATCAGG
1 TTGGCTCAAAATTTTCAAAACTGATAGGATACATGCCCTATTTTCCTAGGCATGAATGGATCAAG
* *
592577 TTGTATAAAATATGAATTTCTTTGAAAACCAAACAAATTTGATGTT
66 ATGTATAAAATATGAATTTCTTTGAAAATCAAACAAATTTGATGTT
592623 CTTCCAAGTC
Statistics
Matches: 379, Mismatches: 57, Indels: 19
0.83 0.13 0.04
Matches are distributed among these distances:
110 96 0.25
111 10 0.03
112 210 0.55
113 57 0.15
114 6 0.02
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.34
Consensus pattern (112 bp):
TTGGCTCAAAATTTTCAAAACTGATAGGATACATGCCCTATTTTCCTAGGCATGAATGGATCAAG
ATGTATAAAATATGAATTTCTTTGAAAATCAAACAAATTTGATGTTA
Found at i:592470 original size:222 final size:221
Alignment explanation
Indices: 592065--592602 Score: 722
Period size: 222 Copynumber: 2.4 Consensus size: 221
592055 AAAAGTTTGG
* * * **
592065 TTGGCTCAGAAATTTCAAAACTGATATGATACATGCCCCACTTTCCTAGGAAAAAATGGATC-GG
1 TTGGCTCA-AAATTTCAAAACTGATAGGATACATGCCCCATTTTCCTAGGCATGAATGGATCAGG
* * * * *
592129 CTCATATAAAATTGGAATTTTTTTTGAAAATCTGACAAATTTGATGTTGTTGGCTCAAAAATTTT
65 -TAATATAAAATAGGAA-TTTCTTTG--AATCTAACAAATTTAATGTTGTTGGCTCAAAAATTTT
* * *
592194 AAAACTGATAGGATAGATGTCGTATTTTCCTAGGCATGAATGGATCAAGATGTATAAAATACAAA
126 AAAACTGATAGAATACATGTCGTATTTTCCTAGGCATGAATGGATCAAGATGTATAAAACACAAA
592259 TTTCTTTGAAAATCAAACAAATTTGATGTTA
191 TTTCTTTGAAAATCAAACAAATTTGATGTTA
* * *
592290 TTGGCTCAAAATTTTCAAAATTGATAGGATACATGCCCTATTTTCCTAGGCATGAATGGATCAAG
1 TTGGCTCAAAA-TTTCAAAACTGATAGGATACATGCCCCATTTTCCTAGGCATGAATGGATCAGG
*
592355 TAATATAGAATAGGAATTTCTTTGAATCTAACAAATTTAATGTTGTTGGCTC-AAAATTTTCAAA
65 TAATATAAAATAGGAATTTCTTTGAATCTAACAAATTTAATGTTGTTGGCTCAAAAATTTT-AAA
* * **
592419 ATTGATAGAATACATG-CGTTATTTTCCTAGGCATGAATGGATCAGGATGTATAAAACATTAATT
129 ACTGATAGAATACATGTCG-TATTTTCCTAGGCATGAATGGATCAAGATGTATAAAACACAAATT
* *
592483 TCTTTGAAAATTAGACAAATTTGATGTTA
193 TCTTTGAAAATCAAACAAATTTGATGTTA
* *
592512 TTGGCTCAAAAATTTCAAAACTGATAGGACACATGCCCCATTTTCTTAGGCATGAATGGATCAGG
1 TTGGCTC-AAAATTTCAAAACTGATAGGATACATGCCCCATTTTCCTAGGCATGAATGGATCAGG
** *
592577 TTGTATAAAATATGAATTTCTTTGAA
65 TAATATAAAATAGGAATTTCTTTGAA
592603 AACCAAACAA
Statistics
Matches: 276, Mismatches: 32, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
221 10 0.04
222 187 0.68
223 4 0.01
224 10 0.04
225 64 0.23
226 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.35
Consensus pattern (221 bp):
TTGGCTCAAAATTTCAAAACTGATAGGATACATGCCCCATTTTCCTAGGCATGAATGGATCAGGT
AATATAAAATAGGAATTTCTTTGAATCTAACAAATTTAATGTTGTTGGCTCAAAAATTTTAAAAC
TGATAGAATACATGTCGTATTTTCCTAGGCATGAATGGATCAAGATGTATAAAACACAAATTTCT
TTGAAAATCAAACAAATTTGATGTTA
Found at i:593241 original size:13 final size:13
Alignment explanation
Indices: 593223--593247 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
593213 TACATAATGT
593223 ATGTATCGATACA
1 ATGTATCGATACA
593236 ATGTATCGATAC
1 ATGTATCGATAC
593248 TTGAGAAAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:598695 original size:157 final size:159
Alignment explanation
Indices: 598405--598775 Score: 410
Period size: 157 Copynumber: 2.4 Consensus size: 159
598395 TTATTCATGT
* * * * *
598405 TTTTATTTTTAAAATACTGATTTTCCACCATCGGGGACACTCCAATCCCGTTA-CTTCTAAGGAG
1 TTTTATTTTCAAAACACTGATTTTCCACCATCGGGGATACTCCAACCCCGTTATTTTCTAAGGAG
* * * * * *
598469 ATGCTCTAACCTCGATTTTATTTTCAAAACATCAATTTTCCACCATTAGGGATACTCCAACCTCA
66 ATGCTCCAACCTAGATTTTATTTCCAAAACACCAATTTTCCACAATTAGGGATACTCCAACCCCA
* * *
598534 TTA-TTTCGAGGGGATACTCAAACCTAGA
131 TTATTTTCGAAGAGATACTCAAACCCAGA
* * * * * * *
598562 TTTTATTTTCAAAACACTAATTTTCCACAATCAGGGATACTTCAACCCCATTATTTTC-GAGGGG
1 TTTTATTTTCAAAACACTGATTTTCCACCATCGGGGATACTCCAACCCCGTTATTTTCTAAGGAG
* * *
598626 ATGCTCCAACTCTAG-TTTTATTTCCAAAACACCGATTTTTCACAATTGGGGATACTCCAACCCC
66 ATGCTCCAAC-CTAGATTTTATTTCCAAAACACCAATTTTCCACAATTAGGGATACTCCAACCCC
* * * *
598690 TTTATTTTCGAAGAGATGCTCGAACCCAGG
130 ATTATTTTCGAAGAGATACTCAAACCCAGA
* * *
598720 TTTTATTTCCAAAACA-TCGATTTTTCACCATCGGGGATACTCCAACCTCGTTATTT
1 TTTTATTTTCAAAACACT-GATTTTCCACCATCGGGGATACTCCAACCCCGTTATTT
598776 CTGAAGGCAT
Statistics
Matches: 174, Mismatches: 36, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
157 103 0.59
158 71 0.41
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (159 bp):
TTTTATTTTCAAAACACTGATTTTCCACCATCGGGGATACTCCAACCCCGTTATTTTCTAAGGAG
ATGCTCCAACCTAGATTTTATTTCCAAAACACCAATTTTCCACAATTAGGGATACTCCAACCCCA
TTATTTTCGAAGAGATACTCAAACCCAGA
Found at i:598795 original size:79 final size:79
Alignment explanation
Indices: 598423--598802 Score: 342
Period size: 79 Copynumber: 4.8 Consensus size: 79
598413 TTAAAATACT
* * * * *
598423 GATTTTCCACCATCGGGGACACTCCAATCCCGTTACTTCT-AAGGAGATGCTCTAACCTC-GATT
1 GATTTTCCACCATCGGGGATACTCCAACCCCATTATTTCTGAAGG-GATGCTCCAACC-CAGATT
*
598486 TTATTTTCAAAACATC
64 TTATTTCCAAAACATC
* ** * * * * *
598502 AATTTTCCACCATTAGGGATACTCCAACCTCATTATTTC-GAGGGGATACTCAAACCTAGATTTT
1 GATTTTCCACCATCGGGGATACTCCAACCCCATTATTTCTGAAGGGATGCTCCAACCCAGATTTT
*
598566 ATTTTCAAAACA-C
66 ATTTCCAAAACATC
* * * * * *
598579 TAATTTTCCACAATCAGGGATACTTCAACCCCATTATTT-TCGAGGGGATGCTCCAACTCTAG-T
1 -GATTTTCCACCATCGGGGATACTCCAACCCCATTATTTCT-GAAGGGATGCTCCAAC-CCAGAT
*
598642 TTTATTTCCAAAACACC
63 TTTATTTCCAAAACATC
* * * * * * *
598659 GATTTTTCACAATTGGGGATACTCCAACCCCTTTATTT-TCGAAGAGATGCTCGAACCCAGGTTT
1 GATTTTCCACCATCGGGGATACTCCAACCCCATTATTTCT-GAAGGGATGCTCCAACCCAGATTT
598723 TATTTCCAAAACATC
65 TATTTCCAAAACATC
* * * * * *
598738 GATTTTTCACCATCGGGGATACTCCAACCTCGTTATTTCTGAAGGCATACTCCAACCCCGATTTT
1 GATTTTCCACCATCGGGGATACTCCAACCCCATTATTTCTGAAGGGATGCTCCAACCCAGATTTT
598803 CCACAATCGG
Statistics
Matches: 252, Mismatches: 40, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
77 1 0.00
78 65 0.26
79 180 0.71
80 6 0.02
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (79 bp):
GATTTTCCACCATCGGGGATACTCCAACCCCATTATTTCTGAAGGGATGCTCCAACCCAGATTTT
ATTTCCAAAACATC
Found at i:598832 original size:59 final size:59
Alignment explanation
Indices: 598737--598855 Score: 152
Period size: 59 Copynumber: 2.0 Consensus size: 59
598727 TCCAAAACAT
* * * *
598737 CGATTTTTCACCATCGGGGATACTCCAACCTCGTTA-TTTCTGAAGGCATACTCCAACCC
1 CGATTTTCCACAATCGGGGATACTACAACCTCGTTATTTTC-GAAGGAATACTCCAACCC
* *
598796 CGATTTTCCACAATCGGGGATACTATAACC-CTGTTATTTTCGAGGGAATACTCCAACCC
1 CGATTTTCCACAATCGGGGATACTACAACCTC-GTTATTTTCGAAGGAATACTCCAACCC
598855 C
1 C
598856 AGTTTTATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
58 1 0.02
59 47 0.90
60 4 0.08
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.29
Consensus pattern (59 bp):
CGATTTTCCACAATCGGGGATACTACAACCTCGTTATTTTCGAAGGAATACTCCAACCC
Found at i:599022 original size:79 final size:78
Alignment explanation
Indices: 598796--599209 Score: 392
Period size: 79 Copynumber: 5.3 Consensus size: 78
598786 ACTCCAACCC
* * * * *
598796 CGATTTTCCACAATCGGGGATACTATAACCCTGTTATTTTCGAGGGAATACTCCAACCCCAGTTT
1 CGATTTTTCACAATCGGGGATACTCTAACCCTATTATTTTCGAGGG-ATACTTCAACCCCGGTTT
* *
598861 TATTTTCAAAACAC
65 TATTTCCAAAACAT
* * * * *
598875 CGATTTTTCACAATCGGGGATA-TCTAACCTTGTTATTTTTGAAAGGATAC-TCTAACCCCGATT
1 CGATTTTTCACAATCGGGGATACTCTAACCCTATTATTTTCG-AGGGATACTTC-AACCCCGGTT
598938 TTATTTCCAAAACA-
64 TTATTTCCAAAACAT
* * * *
598952 CTGATTTTTCACCATCGGGGATACTCCAACCCAAATATTTTCGAAGGGATACTTCAACCCCGGTT
1 C-GATTTTTCACAATCGGGGATACTCTAACCCTATTATTTTCG-AGGGATACTTCAACCCCGGTT
*
599017 TTATTTCTAAAACAT
64 TTATTTCCAAAACAT
* * * * * * *
599032 CGATTTTTCATAATTGAGGATACTCTAACCCCATTATTTTCGAGGAGATGCTTCAACCCTGGCTT
1 CGATTTTTCACAATCGGGGATACTCTAACCCTATTATTTTCGAGG-GATACTTCAACCCCGGTTT
*
599097 TATTTCTAAAACAT
65 TATTTCCAAAACAT
* *
599111 CGA-TTTTCTACAATCGGGGATACTTTTAA-CCTATTA-TTTCTGAGGGGATAC-TCTAACCCCA
1 CGATTTTTC-ACAATCGGGGATAC-TCTAACCCTATTATTTTC-GA-GGGATACTTC-AACCCCG
* *
599172 ATTTTTTTTCCAAAACAT
61 GTTTTATTTCCAAAACAT
* * *
599190 CGCTTTTCCACCATCGGGGA
1 CGATTTTTCACAATCGGGGA
599210 ATGTACTCTA
Statistics
Matches: 278, Mismatches: 44, Indels: 26
0.80 0.13 0.07
Matches are distributed among these distances:
77 2 0.01
78 75 0.27
79 188 0.68
80 13 0.05
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (78 bp):
CGATTTTTCACAATCGGGGATACTCTAACCCTATTATTTTCGAGGGATACTTCAACCCCGGTTTT
ATTTCCAAAACAT
Found at i:599118 original size:157 final size:155
Alignment explanation
Indices: 598796--599134 Score: 362
Period size: 157 Copynumber: 2.1 Consensus size: 155
598786 ACTCCAACCC
* ***
598796 CGATTTTCCACAATCGGGGATACTATAACCCTGTTATTTTCGAGGGAATACTCCAACCCCAGTTT
1 CGATTTT-CACAATCGGGGATACTACAACCCAAATATTTTCGAGGGAATACTCCAACCCCAGTTT
* *** *
598861 TATTTTCAAAACACCGATTTTTCACAATCGGGGATATCTAACCTTGTTATTTTTGAAAGGATACT
65 TATTTTCAAAACACCGATTTTTCACAATCGAGGATATCTAACCCCATTATTTTCGAAAGGATACT
*
598926 CTAACCCCGATTTTATTTCCAAAACA
130 CTAACCCCGACTTTATTTCCAAAACA
* * * *
598952 CTGATTTTTCACCATCGGGGATACTCCAACCCAAATATTTTCGAAGGG-ATACTTCAACCCCGGT
1 C-GA-TTTTCACAATCGGGGATACTACAACCCAAATATTTTCG-AGGGAATACTCCAACCCCAGT
* * * *
599016 TTTA-TTTCTAAAACATCGATTTTTCATAATTGAGGATACTCTAACCCCATTATTTTCG-AGGAG
63 TTTATTTTC-AAAACACCGATTTTTCACAATCGAGGATA-TCTAACCCCATTATTTTCGAAAG-G
* * * *
599079 ATGCT-TCAACCCTGGCTTTATTTCTAAAACA
125 ATACTCT-AACCCCGACTTTATTTCCAAAACA
599110 TCGATTTTCTACAATCGGGGATACT
1 -CGATTTTC-ACAATCGGGGATACT
599135 TTTAACCTAT
Statistics
Matches: 151, Mismatches: 23, Indels: 16
0.79 0.12 0.08
Matches are distributed among these distances:
156 5 0.03
157 81 0.54
158 64 0.42
159 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (155 bp):
CGATTTTCACAATCGGGGATACTACAACCCAAATATTTTCGAGGGAATACTCCAACCCCAGTTTT
ATTTTCAAAACACCGATTTTTCACAATCGAGGATATCTAACCCCATTATTTTCGAAAGGATACTC
TAACCCCGACTTTATTTCCAAAACA
Found at i:601918 original size:32 final size:33
Alignment explanation
Indices: 601879--601946 Score: 104
Period size: 32 Copynumber: 2.1 Consensus size: 33
601869 TCGTTACAAG
*
601879 CAATGTATCGATACATT-TCATCATGTATC-ATA
1 CAATGTATCGATACATTGT-ACCATGTATCGATA
601911 CAATGTATCGATACATTGTACCATGTATCGATA
1 CAATGTATCGATACATTGTACCATGTATCGATA
601944 CAA
1 CAA
601947 ATAGTGATAG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 26 0.79
33 7 0.21
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (33 bp):
CAATGTATCGATACATTGTACCATGTATCGATA
Found at i:602019 original size:19 final size:19
Alignment explanation
Indices: 601975--602027 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
601965 CTGCCAGTTT
* **
601975 CATGTATCGATACCATTGTC
1 CATGTATCGATA-CAGTGAA
601995 CATGTATCGATACAGTGAA
1 CATGTATCGATACAGTGAA
*
602014 CATGTATCAATACA
1 CATGTATCGATACA
602028 ATATATCGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAGTGAA
Found at i:607277 original size:20 final size:20
Alignment explanation
Indices: 607252--607306 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
607242 CTGCCAGTTT
**
607252 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
*
607272 CATGTATCGATAC-AGTGAA
1 CATGTATCGATACAATTGAA
607291 CATGTATCGATACAAT
1 CATGTATCGATACAAT
607307 GTATCGATAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:607310 original size:13 final size:13
Alignment explanation
Indices: 607292--607323 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
607282 TACAGTGAAC
607292 ATGTATCGATACA
1 ATGTATCGATACA
607305 ATGTATCGATACA
1 ATGTATCGATACA
*
607318 AAGTAT
1 ATGTAT
607324 AATGTATCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:607966 original size:20 final size:19
Alignment explanation
Indices: 607922--607970 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
607912 GTAGCCAAAC
* **
607922 TTGTATCGATACACCAAGT
1 TTGTATCGATACACAAAAA
607941 TTGTATCGATACACAAAAAA
1 TTGTATCGATACAC-AAAAA
607961 TTGTATCGAT
1 TTGTATCGAT
607971 GCATTGGCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (19 bp):
TTGTATCGATACACAAAAA
Found at i:612043 original size:15 final size:15
Alignment explanation
Indices: 612023--612053 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
612013 TAAAAATGTC
*
612023 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
612038 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
612053 C
1 C
612054 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:614153 original size:13 final size:13
Alignment explanation
Indices: 614135--614173 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
614125 CATTTTTCTT
614135 TGTATCGATACAA
1 TGTATCGATACAA
*
614148 TGTATCGATACAC
1 TGTATCGATACAA
614161 TGTATCGATACAA
1 TGTATCGATACAA
614174 AGGGATTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:614327 original size:20 final size:20
Alignment explanation
Indices: 614284--614329 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
614274 AAATCTTTTG
614284 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
614305 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
614325 CAAAA
1 CAAAA
614330 CTAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:616764 original size:13 final size:13
Alignment explanation
Indices: 616746--616771 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
616736 TACACCAAGT
616746 ATGTATCGATACA
1 ATGTATCGATACA
616759 ATGTATCGATACA
1 ATGTATCGATACA
616772 CAAAAAATTG
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:616769 original size:32 final size:33
Alignment explanation
Indices: 616728--616791 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
616718 TAGCCAAACT
* **
616728 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
616760 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
616792 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:619164 original size:157 final size:155
Alignment explanation
Indices: 618628--619197 Score: 472
Period size: 156 Copynumber: 3.7 Consensus size: 155
618618 ACCTACTTCT
* * * * * * *
618628 AATGCACACTTTTGGCATAAAAGCGACCT-AGTGATTACAT-GAGACTCGATT-TTAATAAAATT
1 AATGCACACCTTTGGCATAAAAGTGACCTGA-TGATGACCTAG-GACTCGGTTATAAAAAAAATT
* ** * ** * *
618690 ACCAAAATGCCCTTACATATATCTTCGATATGAAAGTATCTCGATAACCCTAAAAGATATG-AAA
64 ATCAAAATGCCC-TAGGTATACCTTCGACGTAAAAGTATCTCGGTAACCCTAAAAGATATGAAAA
*
618754 AGATAA-TAAAAGGATGAACCTATCCATA
128 AGATAAGTAAAAGGATTAACCTATCC-TA
** * * * * *
618782 AACACACACCTTTGGCATAAAAGTGACCTGATGATGACCTAGGACTCAGATAT-AGAGAAATTAC
1 AATGCACACCTTTGGCATAAAAGTGACCTGATGATGACCTAGGACTCGGTTATAAAAAAAATTAT
* * * * * * * * *
618846 CAAAATACCCCTAGGTATATCTTCGACATCAAAGTATCCCGGTAACCCTAAAGGTTACGAAAAAA
66 CAAAAT-GCCCTAGGTATACCTTCGACGTAAAAGTATCTCGGTAACCCTAAAAGATATGAAAAAG
* ** *
618911 ATAAGAAAAACAACTAACCTATCCTAA
130 ATAAGTAAAAGGATTAACCTATCCT-A
* * * * *
618938 AATGCACACCTTTAGCATAAAAGTAACTTGGTGATGACCTAGGACTCGGTTCTAAAGAAAAA--A
1 AATGCACACCTTTGGCATAAAAGTGACCTGATGATGACCTAGGACTCGGTTATAAA-AAAAATTA
* * *
619001 TCAAAATGCACCTAAGGTATACCTTCAACGTAAAAGTATCTCGGTAAACCTAAAAGACATGAAAA
65 TCAAAATGC-CCT-AGGTATACCTTCGACGTAAAAGTATCTCGGTAACCCTAAAAGATATGAAAA
619066 AGATAAGTAAAAGGATTAACCTATCCTA
128 AGATAAGTAAAAGGATTAACCTATCCTA
* * * ** * ** * *
619094 AATGCACACCTTCGGCATAAAAGCGACCTGCTGACCACTTAAAACTTGGTTTTAAAAAAAATTAT
1 AATGCACACCTTTGGCATAAAAGTGACCTGATGATGACCTAGGACTCGGTTATAAAAAAAATTAT
* * *
619159 GAAAATGCCTTTAGGATATACCTTCGACGTAAAGGTATC
66 CAAAATGCC-CTAGG-TATACCTTCGACGTAAAAGTATC
619198 CTGATAACCT
Statistics
Matches: 328, Mismatches: 73, Indels: 27
0.77 0.17 0.06
Matches are distributed among these distances:
154 91 0.28
155 21 0.06
156 117 0.36
157 95 0.29
158 4 0.01
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.24
Consensus pattern (155 bp):
AATGCACACCTTTGGCATAAAAGTGACCTGATGATGACCTAGGACTCGGTTATAAAAAAAATTAT
CAAAATGCCCTAGGTATACCTTCGACGTAAAAGTATCTCGGTAACCCTAAAAGATATGAAAAAGA
TAAGTAAAAGGATTAACCTATCCTA
Found at i:619370 original size:55 final size:58
Alignment explanation
Indices: 619306--619418 Score: 151
Period size: 55 Copynumber: 2.0 Consensus size: 58
619296 CTACTAAGTT
* * **
619306 CCTAGACTTTTTAAAATTATGCTTTGA-CCTTAAA-TTCT-AAAATTACACTTTGACC
1 CCTAAACTTTTTAAAATCACACTTTGACCCTTAAACTTCTCAAAATTACACTTTGACC
* *
619361 CCTAAACTTTTTCAAATCACACTTTGACCCTTAAACTTTTCAAAATTACACTTTGACC
1 CCTAAACTTTTTAAAATCACACTTTGACCCTTAAACTTCTCAAAATTACACTTTGACC
619419 TCAAAATGAC
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
55 22 0.45
56 7 0.14
57 3 0.06
58 17 0.35
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (58 bp):
CCTAAACTTTTTAAAATCACACTTTGACCCTTAAACTTCTCAAAATTACACTTTGACC
Found at i:619382 original size:29 final size:29
Alignment explanation
Indices: 619306--619418 Score: 117
Period size: 29 Copynumber: 4.0 Consensus size: 29
619296 CTACTAAGTT
* * **
619306 CCTAGACTTTTTAAAATTATGCTTTGA-C
1 CCTAAACTTTTCAAAATTACACTTTGACC
* *
619334 CTTAAA-TTCT-AAAATTACACTTTGACC
1 CCTAAACTTTTCAAAATTACACTTTGACC
*
619361 CCTAAACTTTTTC-AAATCACACTTTGACC
1 CCTAAAC-TTTTCAAAATTACACTTTGACC
*
619390 CTTAAACTTTTCAAAATTACACTTTGACC
1 CCTAAACTTTTCAAAATTACACTTTGACC
619419 TCAAAATGAC
Statistics
Matches: 70, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
26 13 0.19
27 9 0.13
28 9 0.13
29 39 0.56
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (29 bp):
CCTAAACTTTTCAAAATTACACTTTGACC
Found at i:623481 original size:15 final size:15
Alignment explanation
Indices: 623439--623474 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
623429 TAAAGTATTT
* *
623439 AAATAAAAAAAGTAA
1 AAATAAAAGAATTAA
623454 AAATAAAAGAATTAA
1 AAATAAAAGAATTAA
623469 AAATAA
1 AAATAA
623475 TATAATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.17
Consensus pattern (15 bp):
AAATAAAAGAATTAA
Found at i:624465 original size:6 final size:6
Alignment explanation
Indices: 624454--624545 Score: 52
Period size: 6 Copynumber: 16.2 Consensus size: 6
624444 TTGAGTTTTT
* ** * *
624454 AATTTA AATTTA TATAGA TATTT- AATTTA AATTTA AA--TG AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* * * *
624499 AATTTA AATTTA TATTT- TA-TTA AATAT- ATTTTA AATATTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AAT-TTA AATTTA
624545 A
1 A
624546 TTATTTTGAT
Statistics
Matches: 65, Mismatches: 14, Indels: 14
0.70 0.15 0.15
Matches are distributed among these distances:
4 5 0.08
5 10 0.15
6 44 0.68
7 6 0.09
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (6 bp):
AATTTA
Found at i:624477 original size:23 final size:21
Alignment explanation
Indices: 624451--624513 Score: 90
Period size: 23 Copynumber: 2.9 Consensus size: 21
624441 TAATTGAGTT
624451 TTTAATTTAAATTTATATAGATA
1 TTTAATTTAAATTTATAT-GA-A
*
624474 TTTAATTTAAATTTAAATGAA
1 TTTAATTTAAATTTATATGAA
624495 TTTAAATTTAAATTTATAT
1 TTT-AATTTAAATTTATAT
624514 TTTATTAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 4 0.11
22 16 0.43
23 17 0.46
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (21 bp):
TTTAATTTAAATTTATATGAA
Found at i:624498 original size:16 final size:16
Alignment explanation
Indices: 624477--624507 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
624467 ATAGATATTT
624477 AATTTAAATTTAAATG
1 AATTTAAATTTAAATG
624493 AATTTAAATTTAAAT
1 AATTTAAATTTAAAT
624508 TTATATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
AATTTAAATTTAAATG
Found at i:624521 original size:22 final size:22
Alignment explanation
Indices: 624454--624523 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 22
624444 TTGAGTTTTT
* *
624454 AATTTAAATTTATATAGATATTT
1 AATTTAAATTTATAT-TATATTA
* *
624477 AATTTAAATTTAAATGA-ATTTA
1 AATTTAAATTTATATTATA-TTA
*
624499 AATTTAAATTTATATTTTATTA
1 AATTTAAATTTATATTATATTA
624521 AAT
1 AAT
624524 ATATTTTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
21 1 0.03
22 24 0.60
23 15 0.38
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (22 bp):
AATTTAAATTTATATTATATTA
Found at i:624898 original size:2 final size:2
Alignment explanation
Indices: 624893--624924 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
624883 ATATATATAT
*
624893 AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
624925 GAAAGAGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:627159 original size:2 final size:2
Alignment explanation
Indices: 627152--627189 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
627142 TTTTATTAGG
* *
627152 AT AT AT AT -T AG AT AT AT AT CT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
627190 AAAGTAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:628715 original size:8 final size:8
Alignment explanation
Indices: 628696--628728 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
628686 ATCATAAAAA
628696 TAAATT-T
1 TAAATTAT
628703 TAAATTAT
1 TAAATTAT
*
628711 TAAATTAA
1 TAAATTAT
628719 TAAATTAT
1 TAAATTAT
628727 TA
1 TA
628729 TATTTAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
TAAATTAT
Found at i:628812 original size:3 final size:3
Alignment explanation
Indices: 628806--628918 Score: 121
Period size: 3 Copynumber: 38.7 Consensus size: 3
628796 GTAGTAGTAG
628806 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
628854 TAA T-A TGA GAA TAA T-A TAA TAA TAGA T-A GAA TTA TAA -AA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA T-AA
628897 TAA T-A TAA TAA -AA TAAA TAA TA
1 TAA TAA TAA TAA TAA T-AA TAA TA
628919 TTATTTAGAA
Statistics
Matches: 94, Mismatches: 7, Indels: 18
0.79 0.06 0.15
Matches are distributed among these distances:
2 11 0.12
3 75 0.80
4 8 0.09
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:635118 original size:59 final size:59
Alignment explanation
Indices: 635030--635188 Score: 169
Period size: 60 Copynumber: 2.7 Consensus size: 59
635020 GTCACTTAAT
* * * **
635030 TGACTCTAAAATGCATGGAAATGGATAAATGATCCCTAAAATATATAGTAT-ATCTTAAA
1 TGACTCTAAAATGCATGTAAATTGCTAAATGATCCCTAAAATATATAAAATAATC-TAAA
* * * ** *
635089 TGGCTTTAAAATGCATGTAAATTGCTAAATGACCCCTTAAGTTATGTAAAATAATCTAAA
1 TGACTCTAAAATGCATGTAAATTGCTAAATGATCCC-TAAAATATATAAAATAATCTAAA
*
635149 TGACTCTAATATGCATGTAAATTGCTAAAT-ATTCCCTAAA
1 TGACTCTAAAATGCATGTAAATTGCTAAATGA-TCCCTAAA
635189 TCATGTATAA
Statistics
Matches: 81, Mismatches: 16, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
59 34 0.42
60 44 0.54
61 3 0.04
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.33
Consensus pattern (59 bp):
TGACTCTAAAATGCATGTAAATTGCTAAATGATCCCTAAAATATATAAAATAATCTAAA
Found at i:635831 original size:13 final size:12
Alignment explanation
Indices: 635813--635846 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
635803 ATTTCTCTTT
635813 TTTTTCTTTTGCC
1 TTTTTCTTTTG-C
635826 TTTTTCTTTTGC
1 TTTTTCTTTTGC
635838 -TTTTCTTTT
1 TTTTTCTTTT
635847 TCAACTACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.43
12 1 0.05
13 11 0.52
ACGTcount: A:0.00, C:0.18, G:0.06, T:0.76
Consensus pattern (12 bp):
TTTTTCTTTTGC
Found at i:637175 original size:15 final size:15
Alignment explanation
Indices: 637143--637176 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
637133 TAAAAATATT
*
637143 ATATTTTTATTATCA
1 ATATTTTTATTATAA
*
637158 ATATTTTTATTTTAA
1 ATATTTTTATTATAA
637173 ATAT
1 ATAT
637177 AAAAATGTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
ATATTTTTATTATAA
Found at i:637770 original size:35 final size:34
Alignment explanation
Indices: 637714--637829 Score: 85
Period size: 35 Copynumber: 3.3 Consensus size: 34
637704 TCATATAAAG
* *
637714 AAAATATA-TATGTAATATTATAATATAAATATTAA
1 AAAATATATTAAGTTAT-TTATAAT-TAAATATTAA
*
637749 AAAATATATTAAGTTATTTATATTTTAAA-ACTTAA
1 AAAATATATTAAGTTATTTATA-ATTAAATA-TTAA
* * * *
637784 TAAAAAATTATTAAATTA-TTAAAATTAAATGTTAA
1 -AAAATA-TATTAAGTTATTTATAATTAAATATTAA
*
637819 AAAATAGATTA
1 AAAATATATTA
637830 GAAAAAAAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
33 4 0.06
34 6 0.09
35 30 0.46
36 16 0.25
37 9 0.14
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (34 bp):
AAAATATATTAAGTTATTTATAATTAAATATTAA
Found at i:638424 original size:17 final size:17
Alignment explanation
Indices: 638402--638434 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
638392 CCTATTGTAT
638402 TTTTATTATATTTATTA
1 TTTTATTATATTTATTA
*
638419 TTTTATTATTTTTATT
1 TTTTATTATATTTATT
638435 TTTATTTATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTATTATATTTATTA
Found at i:638425 original size:23 final size:23
Alignment explanation
Indices: 638394--638440 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
638384 TTCAATCCCC
638394 TATTGTATT-TTTATTATATTTAT
1 TATTGTATTATTT-TTATATTTAT
* *
638417 TATTTTATTATTTTTATTTTTAT
1 TATTGTATTATTTTTATATTTAT
638440 T
1 T
638441 TATCTTACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (23 bp):
TATTGTATTATTTTTATATTTAT
Found at i:638431 original size:9 final size:9
Alignment explanation
Indices: 638399--638434 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
638389 TCCCCTATTG
638399 TATTTTTAT
1 TATTTTTAT
*
638408 TATATTTAT
1 TATTTTTAT
638417 TA-TTTTAT
1 TATTTTTAT
638425 TATTTTTAT
1 TATTTTTAT
638434 T
1 T
638435 TTTATTTATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (9 bp):
TATTTTTAT
Found at i:644375 original size:91 final size:91
Alignment explanation
Indices: 644195--644362 Score: 282
Period size: 91 Copynumber: 1.8 Consensus size: 91
644185 ACATTATCAA
* * **
644195 TTTTTTATCCAATAATTATTAACCATTTAAATAATTAAATTTCAAATTTCAAAATAAAAAGCATG
1 TTTTTTATCCAACAATTATTAACCATTTAAATAATTAAATTACAAATTTCAAAATAAAAAGCACA
*
644260 TCTAATCTTTCTCTATATAAATAACT
66 TCTAATATTTCTCTATATAAATAACT
*
644286 TTTTTTATCCAACAATTATTAACCATTTAAATAATTAAATTACAAATTTCAAAATCAAAAGCACA
1 TTTTTTATCCAACAATTATTAACCATTTAAATAATTAAATTACAAATTTCAAAATAAAAAGCACA
644351 TCTAATATTTCT
66 TCTAATATTTCT
644363 TTTTGTAAAT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 71 1.00
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.40
Consensus pattern (91 bp):
TTTTTTATCCAACAATTATTAACCATTTAAATAATTAAATTACAAATTTCAAAATAAAAAGCACA
TCTAATATTTCTCTATATAAATAACT
Found at i:645007 original size:19 final size:19
Alignment explanation
Indices: 644971--645008 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
644961 TAATTATAAT
*
644971 AGATAAAAAAACATTATTA
1 AGATAAAAAAACACTATTA
644990 AGATAATAAAAA-ACTATTA
1 AGATAA-AAAAACACTATTA
645009 TTTTCAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.26
Consensus pattern (19 bp):
AGATAAAAAAACACTATTA
Found at i:646789 original size:43 final size:43
Alignment explanation
Indices: 646723--646804 Score: 137
Period size: 43 Copynumber: 1.9 Consensus size: 43
646713 GAGATATTCT
* *
646723 AACCTCATTTTTATTTTTAAAATATTAAAATTTTCATCTATCC
1 AACCCCATTTTTATTTTCAAAATATTAAAATTTTCATCTATCC
*
646766 AACCCCATTTTTATTTTCAAAATATTAAATTTTTCATCT
1 AACCCCATTTTTATTTTCAAAATATTAAAATTTTCATCT
646805 CGGGAATACT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49
Consensus pattern (43 bp):
AACCCCATTTTTATTTTCAAAATATTAAAATTTTCATCTATCC
Found at i:646903 original size:79 final size:77
Alignment explanation
Indices: 646767--647222 Score: 522
Period size: 79 Copynumber: 5.8 Consensus size: 77
646757 CATCTATCCA
*
646767 ACCCCATTTTTATTTTCAAAATATTAAATTTTTCATCTCGGGAATACTCTAACCCCGTTATTTTC
1 ACCCCATTTTTATTTCCAAAATATTAAATTTTTCATCTCGGG-ATACTCTAACCCCGTTATTTTC
*
646832 GAGGGGATACTTC
65 GAGGGGATACTCC
* ** * *
646845 AGTCCCATTTTTATTTTTAAAATATTAAATTTTACATCTCGAGGATACTCTAATCCCGTTATTTT
1 A-CCCCATTTTTATTTCCAAAATATTAAATTTTTCATCTCG-GGATACTCTAACCCCGTTATTTT
**
646910 -GAGGAAATACTCC
64 CGAGGGGATACTCC
* * * *
646923 AACCTCA-TTTTATTTCTAAAATATTAAATTTTTCATCTCGGGGATACTCTAATCCCGTTATTTC
1 -ACCCCATTTTTATTTCCAAAATATTAAATTTTTCATCTC-GGGATACTCTAACCCCGTTATTTT
*
646987 CGAGAGGATACTCC
64 CGAGGGGATACTCC
* * *
647001 AACCCCATCTTTATTTCCAAAATATTAAATTTTTCATCTCTGAGATACTCTAACCTCGTTATTTT
1 -ACCCCATTTTTATTTCCAAAATATTAAATTTTTCATCTC-GGGATACTCTAACCCCGTTATTTT
* *
647066 CGAGAGTATACTCC
64 CGAGGGGATACTCC
* * *
647080 AACCCCATTTTTATTTCCAAAATATTAAATTTTTAATCGTGGGGATACTCCAACCCCGTTATTTT
1 -ACCCCATTTTTATTTCCAAAATATTAAATTTTTCATC-TCGGGATACTCTAACCCCGTTATTTT
* *
647145 TGAGGGGATACTTC
64 CGAGGGGATACTCC
* * * **
647159 A-ACTATTTTTTTATTTCCAAAATATTAAATTTTTCATCTCGGAGATACTCCAACCTTGTTATTT
1 ACCCCA--TTTTTATTTCCAAAATATTAAATTTTTCATCTCGG-GATACTCTAACCCCGTTATTT
647223 CTGAGATGAT
Statistics
Matches: 328, Mismatches: 40, Indels: 19
0.85 0.10 0.05
Matches are distributed among these distances:
77 54 0.16
78 35 0.11
79 236 0.72
80 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (77 bp):
ACCCCATTTTTATTTCCAAAATATTAAATTTTTCATCTCGGGATACTCTAACCCCGTTATTTTCG
AGGGGATACTCC
Found at i:647156 original size:158 final size:157
Alignment explanation
Indices: 646763--647255 Score: 622
Period size: 158 Copynumber: 3.1 Consensus size: 157
646753 TTTTCATCTA
* *
646763 TCCAACCCCATTTTTATTTTCAAAATATTAAATTTTTCATCTCGGGAATACTCTAACCCCGTTAT
1 TCCAACCCCATTTTTATTTCCAAAATATTAAATTTTTCATCTCGGGGATACTCTAACCCCGTTAT
** ** *
646828 TTTCGAGGGGATACTTCAGTCCCATTTTTATTTTTAAAATATTAAATTTTACATCTCGAGGATAC
66 TTTCGAGGGGATACTTCAACCCCATTTTTATTTCCAAAATATTAAATTTTTCATCTCGA-GATAC
*
646893 TCTAATCC-CGTTATTTT-GAG-GAAATAC
130 TCTAA-CCTCGTTATTTTCGAGAG-TATAC
* * *
646920 TCCAACCTCA-TTTTATTTCTAAAATATTAAATTTTTCATCTCGGGGATACTCTAATCCCGTTAT
1 TCCAACCCCATTTTTATTTCCAAAATATTAAATTTTTCATCTCGGGGATACTCTAACCCCGTTAT
* * * *
646984 TTCCGAGAGGATACTCCAACCCCATCTTTATTTCCAAAATATTAAATTTTTCATCTCTGAGATAC
66 TTTCGAGGGGATACTTCAACCCCATTTTTATTTCCAAAATATTAAATTTTTCATCTC-GAGATAC
647049 TCTAACCTCGTTATTTTCGAGAGTATAC
130 TCTAACCTCGTTATTTTCGAGAGTATAC
* *
647077 TCCAACCCCATTTTTATTTCCAAAATATTAAATTTTTAATCGT-GGGGATACTCCAACCCCGTTA
1 TCCAACCCCATTTTTATTTCCAAAATATTAAATTTTTCATC-TCGGGGATACTCTAACCCCGTTA
* ****
647141 TTTTTGAGGGGATACTTCAACTATTTTTTTATTTCCAAAATATTAAATTTTTCATCTCGGAGATA
65 TTTTCGAGGGGATACTTCAACCCCATTTTTATTTCCAAAATATTAAATTTTTCATCTC-GAGATA
* *
647206 CTCCAACCTTGTTA-TTTCTGAGA-TGATAC
129 CTCTAACCTCGTTATTTTC-GAGAGT-ATAC
** *
647235 TTTAACCCCGTTTTTATTTCC
1 TCCAACCCCATTTTTATTTCC
647256 TATCGGGGAT
Statistics
Matches: 293, Mismatches: 35, Indels: 15
0.85 0.10 0.04
Matches are distributed among these distances:
155 2 0.01
156 117 0.40
157 32 0.11
158 141 0.48
159 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.40
Consensus pattern (157 bp):
TCCAACCCCATTTTTATTTCCAAAATATTAAATTTTTCATCTCGGGGATACTCTAACCCCGTTAT
TTTCGAGGGGATACTTCAACCCCATTTTTATTTCCAAAATATTAAATTTTTCATCTCGAGATACT
CTAACCTCGTTATTTTCGAGAGTATAC
Found at i:649724 original size:35 final size:36
Alignment explanation
Indices: 649681--649753 Score: 94
Period size: 36 Copynumber: 1.9 Consensus size: 36
649671 TTAAGTTAAA
649681 TTAATTAATTATATATAAATTATAAAG-TAAATTATTTTC
1 TTAATTAA-T-TA-ATAAATTA-AAAGTTAAATTATTTTC
*
649720 TTAATTAATTAATAATTTAAAAGTTAAATTATTT
1 TTAATTAATTAATAAATTAAAAGTTAAATTATTT
649754 AATTAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
35 4 0.12
36 17 0.53
37 2 0.06
38 1 0.03
39 8 0.25
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (36 bp):
TTAATTAATTAATAAATTAAAAGTTAAATTATTTTC
Found at i:649768 original size:31 final size:32
Alignment explanation
Indices: 649666--649770 Score: 92
Period size: 31 Copynumber: 3.2 Consensus size: 32
649656 ATAAATTAAT
* * *
649666 TAATTT-T-AAGTTAAATTAATTAATTATATA
1 TAATTTATAAAGTTAAATTATTTAATTAAAAA
* *
649696 TAAATTATAAAG-TAAATTATTTTCTTAATTAATTAA
1 TAATTTATAAAGTTAAATTA---T-TTAATTAA-AAA
649732 TAATTTA-AAAGTTAAATTATTTAATTAAAAA
1 TAATTTATAAAGTTAAATTATTTAATTAAAAA
649763 TAATTTAT
1 TAATTTAT
649771 TTAATTTTAT
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
30 5 0.08
31 17 0.29
32 11 0.19
33 1 0.02
35 11 0.19
36 14 0.24
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.48
Consensus pattern (32 bp):
TAATTTATAAAGTTAAATTATTTAATTAAAAA
Found at i:650209 original size:18 final size:18
Alignment explanation
Indices: 650172--650213 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
650162 CACAAAACAG
**
650172 AAGATAATTACAAATTTA
1 AAGATAATTACAAAAGTA
*
650190 AAGATAATTATAAAAGTA
1 AAGATAATTACAAAAGTA
650208 AA-ATAA
1 AAGATAA
650214 CAAATAAGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (18 bp):
AAGATAATTACAAAAGTA
Done.