Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009317.1 Hibiscus syriacus cultivar Beakdansim tig00113073_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 334282
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
File 2 of 2
Found at i:194292 original size:122 final size:121
Alignment explanation
Indices: 194009--194300 Score: 303
Period size: 122 Copynumber: 2.4 Consensus size: 121
193999 TACCTCCCCA
* *
194009 CCACATGATGTTAG-TTTTTTC-CC--CTCAAACCCTAGAGCATTAAGCCTTCGCAACGCCCCCC
1 CCACACGATGTTAGTTTTTTTCTCCAGCTCAAACCCCA-AGCATTAAGCCTTCGCAACGCCCCCC
* * *
194070 ACGTGATGTTAGTTTTTTTAGCTCAAACCCCAGAGCATTAAGCCTTCGAAACGCTCT
65 ACGTGATGTTAGTTCTTTTAGCTCAAACCCCAAAGCATTAAGCCTTCGAAACGCTCC
** * * *** *
194127 CCACGTGATGTTAGTTTTTTTTTTCAGCTCAAACCCCAAAGCATTAAGCCTTCGCAACTTTCTCC
1 CCACACGATGTTAGTTTTTTTCTCCAGCTCAAACCCC-AAGCATTAAGCCTTCGCAACGCCCCCC
* *
194192 ATGTGATGTTAGTTCTTTTAGCTCAAACCCCAAAGCATTAAGTCTTC-ATAACG-TGCC
65 ACGTGATGTTAGTTCTTTTAGCTCAAACCCCAAAGCATTAAGCCTTCGA-AACGCT-CC
* * *
194249 CCGCACGATGTT-GTTGTTTTCTCTCCTAGCTTAAATCCC-AGCATTAAGCCTT
1 CCACACGATGTTAGTT-TTTT-TCTCC-AGCTCAAACCCCAAGCATTAAGCCTT
194301 TTGCAATATG
Statistics
Matches: 144, Mismatches: 20, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
118 13 0.09
119 6 0.04
120 1 0.01
121 5 0.03
122 105 0.73
123 4 0.03
124 10 0.07
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.33
Consensus pattern (121 bp):
CCACACGATGTTAGTTTTTTTCTCCAGCTCAAACCCCAAGCATTAAGCCTTCGCAACGCCCCCCA
CGTGATGTTAGTTCTTTTAGCTCAAACCCCAAAGCATTAAGCCTTCGAAACGCTCC
Found at i:198632 original size:17 final size:17
Alignment explanation
Indices: 198598--198649 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
198588 ACCGGACAAA
* *
198598 TTTATTATTTTAGAGAG
1 TTTATTAATTTACAGAG
*
198615 TTTATTAATTTACCGAG
1 TTTATTAATTTACAGAG
*
198632 --TATTAATTTAAAGAG
1 TTTATTAATTTACAGAG
198647 TTT
1 TTT
198650 CTACTGTACG
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (17 bp):
TTTATTAATTTACAGAG
Found at i:202365 original size:31 final size:33
Alignment explanation
Indices: 202330--202403 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
202320 GATGGAGAAG
*
202330 GTGGAGGAGGGGAC-T-TGTAGTA-AGTGAACCA
1 GTGGAGGAGGGGACGTGTGT-GAAGAGTGAACCA
* *
202361 GTGGAGGAGGTGACGTGTGTGAAGAGTGAACTA
1 GTGGAGGAGGGGACGTGTGTGAAGAGTGAACCA
202394 GTGGAGGAGG
1 GTGGAGGAGG
202404 TGATTTATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 13 0.35
32 3 0.08
33 21 0.57
ACGTcount: A:0.27, C:0.07, G:0.47, T:0.19
Consensus pattern (33 bp):
GTGGAGGAGGGGACGTGTGTGAAGAGTGAACCA
Found at i:202641 original size:24 final size:24
Alignment explanation
Indices: 202613--202696 Score: 82
Period size: 24 Copynumber: 3.5 Consensus size: 24
202603 GATGAAGAAG
202613 GTGGTGGTGGAGACTTGTAGTAAT
1 GTGGTGGTGGAGACTTGTAGTAAT
* ** *
202637 ATGGTGGTGGTAGA-GAGTAG-ACT
1 GTGGTGGTGG-AGACTTGTAGTAAT
*
202660 GGTGGTGGTGGAGACTTGTAGTAGT
1 -GTGGTGGTGGAGACTTGTAGTAAT
*
202685 GTGGTGGAGGAG
1 GTGGTGGTGGAG
202697 GAGGTGACTT
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
23 5 0.11
24 37 0.79
25 5 0.11
ACGTcount: A:0.20, C:0.04, G:0.48, T:0.29
Consensus pattern (24 bp):
GTGGTGGTGGAGACTTGTAGTAAT
Found at i:202642 original size:27 final size:27
Alignment explanation
Indices: 202563--202691 Score: 84
Period size: 27 Copynumber: 5.2 Consensus size: 27
202553 CTACATGCTT
*
202563 TGGTGGTGGTGGAGACTTGTAGTAGTA
1 TGGTGGTGGTGGAGACTTGTAGTAATA
* ** * *
202590 CGGTGAAGGTGGTGA--TGAAG--A-A
1 TGGTGGTGGTGGAGACTTGTAGTAATA
202612 -GGTGGTGGTGGAGACTTGTAGTAATA
1 TGGTGGTGGTGGAGACTTGTAGTAATA
* *
202638 TGGTGGTGGTAGAGA---GTAG--A-C
1 TGGTGGTGGTGGAGACTTGTAGTAATA
* *
202659 TGGTGGTGGTGGAGACTTGTAGTAGTG
1 TGGTGGTGGTGGAGACTTGTAGTAATA
202686 TGGTGG
1 TGGTGG
202692 AGGAGGAGGT
Statistics
Matches: 75, Mismatches: 15, Indels: 24
0.66 0.13 0.21
Matches are distributed among these distances:
21 25 0.33
22 2 0.03
23 4 0.05
24 8 0.11
25 5 0.07
26 1 0.01
27 30 0.40
ACGTcount: A:0.21, C:0.04, G:0.47, T:0.29
Consensus pattern (27 bp):
TGGTGGTGGTGGAGACTTGTAGTAATA
Found at i:202690 original size:48 final size:48
Alignment explanation
Indices: 202563--202694 Score: 167
Period size: 48 Copynumber: 2.8 Consensus size: 48
202553 CTACATGCTT
* * * *
202563 TGGTGGTGGTGGAGACTTGTAGTAGTACGGTGAAGGTGGTGATGAAGA
1 TGGTGGTGGTGGAGACTTGTAGTAGTATGGTGGAGGTAGAGATGAAGA
* * * *
202611 AGGTGGTGGTGGAGACTTGTAGTAATATGGTGGTGGTAGAGA-GTAGA
1 TGGTGGTGGTGGAGACTTGTAGTAGTATGGTGGAGGTAGAGATGAAGA
*
202658 CTGGTGGTGGTGGAGACTTGTAGTAGTGTGGTGGAGG
1 -TGGTGGTGGTGGAGACTTGTAGTAGTATGGTGGAGG
202695 AGGAGGTGAC
Statistics
Matches: 71, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
47 4 0.06
48 67 0.94
ACGTcount: A:0.21, C:0.04, G:0.47, T:0.28
Consensus pattern (48 bp):
TGGTGGTGGTGGAGACTTGTAGTAGTATGGTGGAGGTAGAGATGAAGA
Found at i:202743 original size:36 final size:36
Alignment explanation
Indices: 202699--202846 Score: 114
Period size: 36 Copynumber: 4.3 Consensus size: 36
202689 TGGAGGAGGA
202699 GGTGACTTGTAAACATAGGTGGGGGATGGTGGTGGT
1 GGTGACTTGTAAACATAGGTGGGGGATGGTGGTGGT
* * *
202735 GGAGACTTGTAGTA-ATA--T-GGGGA----GGAGGT
1 GGTGACTTGTA-AACATAGGTGGGGGATGGTGGTGGT
* * *
202764 GGTGACTTGTAGACATAGGTGGGAGTTGGTGGTGGT
1 GGTGACTTGTAAACATAGGTGGGGGATGGTGGTGGT
* * * * * * *
202800 GGTGACTTATAAACAAAGGTAGGTGACGGTGGAGGA
1 GGTGACTTGTAAACATAGGTGGGGGATGGTGGTGGT
202836 GGTGACTTGTA
1 GGTGACTTGTA
202847 GTATTATGGA
Statistics
Matches: 85, Mismatches: 18, Indels: 18
0.70 0.15 0.15
Matches are distributed among these distances:
28 1 0.01
29 18 0.21
31 1 0.01
32 3 0.04
33 5 0.06
34 1 0.01
36 55 0.65
37 1 0.01
ACGTcount: A:0.24, C:0.06, G:0.44, T:0.26
Consensus pattern (36 bp):
GGTGACTTGTAAACATAGGTGGGGGATGGTGGTGGT
Found at i:202780 original size:65 final size:66
Alignment explanation
Indices: 202659--202807 Score: 228
Period size: 65 Copynumber: 2.3 Consensus size: 66
202649 GAGAGTAGAC
* * *
202659 TGGTGGTGGTGGAGACTTGTAGTAGTGTGGTGGAGGAGGAGGTGACTTGTAAACATAGGTGGGGG
1 TGGTGGTGGTGGAGACTTGTAGTAATATGGTGGAGGAGGAGGTGACTTGTAAACATAGGTGGGAG
202724 A
66 A
* *
202725 TGGTGGTGGTGGAGACTTGTAGTAATATGG-GGAGGAGGTGGTGACTTGTAGACATAGGTGGGAG
1 TGGTGGTGGTGGAGACTTGTAGTAATATGGTGGAGGAGGAGGTGACTTGTAAACATAGGTGGGAG
*
202789 T
66 A
*
202790 TGGTGGTGGTGGTGACTT
1 TGGTGGTGGTGGAGACTT
202808 ATAAACAAAG
Statistics
Matches: 76, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
65 48 0.63
66 28 0.37
ACGTcount: A:0.19, C:0.05, G:0.48, T:0.28
Consensus pattern (66 bp):
TGGTGGTGGTGGAGACTTGTAGTAATATGGTGGAGGAGGAGGTGACTTGTAAACATAGGTGGGAG
A
Found at i:202845 original size:72 final size:71
Alignment explanation
Indices: 202693--203032 Score: 198
Period size: 72 Copynumber: 4.7 Consensus size: 71
202683 GTGTGGTGGA
* * * * * **
202693 GGAGGAGGTGACTTGTAAACATAGGTGGGGGATGGTGGTGGTGGAGACTTGT--AGTAA-TA--T
1 GGAGGAGGTGACTTGTAGACATAGGTGGGAGTTGGTGGTGGTGGTGACTTATAAACAAAGTAGGT
* *
202753 G-GGGA
66 GACGGT
*
202758 GGAGGTGGTGACTTGTAGACATAGGTGGGAGTTGGTGGTGGTGGTGACTTATAAACAAAGGTAGG
1 GGAGGAGGTGACTTGTAGACATAGGTGGGAGTTGGTGGTGGTGGTGACTTATAAACAAA-GTAGG
202823 TGACGGT
65 TGACGGT
* ** * * *
202830 GGAGGAGGTGACTTGTAGTATTATGGAGGATTCTCAACGTGTTTCGGTGGTGTTGGAGACTT-T-
1 GGAGGAGGTGACTTGTAG-A-CAT--AGG----T--GGGAG-TT-GGTGGTGGTGGTGACTTATA
* * ** * *
202893 TA-ATAGTA--TTTCAGA
54 AACAAAGTAGGTGACGGT
* * * *
202908 GGAGGTGGTGATTTGTAGACATATGTGGGAGTTGGTGGTGGTGGTGACTTATAGACATAAGTAGG
1 GGAGGAGGTGACTTGTAGACATAGGTGGGAGTTGGTGGTGGTGGTGACTTATAAACA-AAGTAGG
* * *
202973 AGATGAT
65 TGACGGT
* *
202980 GGAGGAGGTGACTTGTAGACATAAGTGGGAGTTGGTGGGGGTGGTGACTTATA
1 GGAGGAGGTGACTTGTAGACATAGGTGGGAGTTGGTGGTGGTGGTGACTTATA
203033 GACGTAAGCT
Statistics
Matches: 205, Mismatches: 45, Indels: 43
0.70 0.15 0.15
Matches are distributed among these distances:
65 46 0.22
66 15 0.07
67 6 0.03
68 3 0.01
69 3 0.01
70 5 0.02
71 2 0.01
72 68 0.33
73 1 0.00
74 4 0.02
76 5 0.02
77 1 0.00
78 19 0.09
80 4 0.02
81 2 0.01
82 3 0.01
83 3 0.01
84 15 0.07
ACGTcount: A:0.24, C:0.06, G:0.41, T:0.29
Consensus pattern (71 bp):
GGAGGAGGTGACTTGTAGACATAGGTGGGAGTTGGTGGTGGTGGTGACTTATAAACAAAGTAGGT
GACGGT
Found at i:202951 original size:36 final size:36
Alignment explanation
Indices: 202908--203040 Score: 167
Period size: 36 Copynumber: 3.7 Consensus size: 36
202898 GTATTTCAGA
* * *
202908 GGAGGTGGTGATTTGTAGACATATGTGGGAGTTGGT
1 GGAGGTGGTGACTTATAGACATAAGTGGGAGTTGGT
* * * *
202944 GGTGGTGGTGACTTATAGACATAAGTAGGAGATGAT
1 GGAGGTGGTGACTTATAGACATAAGTGGGAGTTGGT
* *
202980 GGAGGAGGTGACTTGTAGACATAAGTGGGAGTTGGT
1 GGAGGTGGTGACTTATAGACATAAGTGGGAGTTGGT
* *
203016 GGGGGTGGTGACTTATAGACGTAAG
1 GGAGGTGGTGACTTATAGACATAAG
203041 CTGGTGAAGG
Statistics
Matches: 80, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 80 1.00
ACGTcount: A:0.25, C:0.05, G:0.42, T:0.28
Consensus pattern (36 bp):
GGAGGTGGTGACTTATAGACATAAGTGGGAGTTGGT
Found at i:203053 original size:36 final size:34
Alignment explanation
Indices: 202908--203065 Score: 136
Period size: 36 Copynumber: 4.4 Consensus size: 34
202898 GTATTTCAGA
* * *
202908 GGAGGTGGTGATTTGTAGACATATGTGGGAGTTGGT
1 GGAGGTGGTGACTTATAGACATAAGTGGGA--TGGT
* *
202944 GGTGGTGGTGACTTATAGACATAAGTAGGAGATGAT
1 GGAGGTGGTGACTTATAGACATAAGT-GG-GATGGT
* *
202980 GGAGGAGGTGACTTGTAGACATAAGTGGGAGTTGGT
1 GGAGGTGGTGACTTATAGACATAAGTGGGA--TGGT
* * *
203016 GGGGGTGGTGACTTATAGACGTAAGCTGGTGAAGGT
1 GGAGGTGGTGACTTATAGACATAAG-TGG-GATGGT
* *
203052 GGCGGTGGAGACTT
1 GGAGGTGGTGACTT
203066 GTAATAATAC
Statistics
Matches: 100, Mismatches: 16, Indels: 12
0.78 0.12 0.09
Matches are distributed among these distances:
34 2 0.02
35 2 0.02
36 87 0.87
37 5 0.05
38 4 0.04
ACGTcount: A:0.23, C:0.06, G:0.43, T:0.27
Consensus pattern (34 bp):
GGAGGTGGTGACTTATAGACATAAGTGGGATGGT
Found at i:203065 original size:72 final size:72
Alignment explanation
Indices: 202908--203068 Score: 216
Period size: 72 Copynumber: 2.2 Consensus size: 72
202898 GTATTTCAGA
* * *
202908 GGAGGTGGTGATTTGTAGACATATGTGGGAGTTGGTGGTGGTGGTGACTTATAGACATAAGTAGG
1 GGAGGTGGTGACTTGTAGACATAAGTGGGAGTTGGTGGGGGTGGTGACTTATAGACATAAGTAGG
*
202973 AGATGAT
66 AGAAGAT
* *
202980 GGAGGAGGTGACTTGTAGACATAAGTGGGAGTTGGTGGGGGTGGTGACTTATAGACGTAAGCT-G
1 GGAGGTGGTGACTTGTAGACATAAGTGGGAGTTGGTGGGGGTGGTGACTTATAGACATAAG-TAG
* *
203044 GTGAAGGT
65 GAGAAGAT
* *
203052 GGCGGTGGAGACTTGTA
1 GGAGGTGGTGACTTGTA
203069 ATAATACGGT
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
72 76 0.99
73 1 0.01
ACGTcount: A:0.24, C:0.06, G:0.43, T:0.27
Consensus pattern (72 bp):
GGAGGTGGTGACTTGTAGACATAAGTGGGAGTTGGTGGGGGTGGTGACTTATAGACATAAGTAGG
AGAAGAT
Found at i:206797 original size:15 final size:15
Alignment explanation
Indices: 206768--206805 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
206758 GGTGGCAATT
*
206768 GGATCA-TTTGGATC
1 GGATCATTTTGAATC
*
206782 GGGTCATTTTGAATC
1 GGATCATTTTGAATC
206797 GGATCATTT
1 GGATCATTT
206806 CAAGTCATAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.21, C:0.13, G:0.26, T:0.39
Consensus pattern (15 bp):
GGATCATTTTGAATC
Found at i:206986 original size:26 final size:27
Alignment explanation
Indices: 206957--207010 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
206947 AGATTGGTTG
*
206957 GTTTTGGGTCGGGTCAA-TTTAGATTT
1 GTTTCGGGTCGGGTCAACTTTAGATTT
* *
206983 GTTTCGGTTCGTGTCAACTTTTAGATTT
1 GTTTCGGGTCGGGTCAAC-TTTAGATTT
207011 TCGGGTCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 14 0.61
28 9 0.39
ACGTcount: A:0.15, C:0.11, G:0.26, T:0.48
Consensus pattern (27 bp):
GTTTCGGGTCGGGTCAACTTTAGATTT
Found at i:207039 original size:26 final size:25
Alignment explanation
Indices: 206965--207045 Score: 73
Period size: 26 Copynumber: 3.4 Consensus size: 25
206955 TGGTTTTGGG
*
206965 TCGGGTCAATTTAGATTTGTTTCGGT
1 TCGGGTCAATTTAG-TTAGTTTCGGT
* * *
206991 TCGTGTCAACTT--TTAGATT---T
1 TCGGGTCAATTTAGTTAGTTTCGGT
207011 TCGGGTCAATTTAGGTTAGTTTCGGT
1 TCGGGTCAATTTA-GTTAGTTTCGGT
207037 TCGGGTCAA
1 TCGGGTCAA
207046 CCATCGTCGT
Statistics
Matches: 42, Mismatches: 7, Indels: 12
0.69 0.11 0.20
Matches are distributed among these distances:
20 11 0.26
23 11 0.26
26 20 0.48
ACGTcount: A:0.17, C:0.14, G:0.26, T:0.43
Consensus pattern (25 bp):
TCGGGTCAATTTAGTTAGTTTCGGT
Found at i:208640 original size:21 final size:23
Alignment explanation
Indices: 208600--208647 Score: 73
Period size: 21 Copynumber: 2.2 Consensus size: 23
208590 TTTTTGTTTC
208600 ATTTTAGTATATCCTCGTTCAAA
1 ATTTTAGTATATCCTCGTTCAAA
*
208623 ATTTTAGTATCT-CT-GTTCAAA
1 ATTTTAGTATATCCTCGTTCAAA
208644 ATTT
1 ATTT
208648 AACGTTAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 11 0.46
22 2 0.08
23 11 0.46
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.48
Consensus pattern (23 bp):
ATTTTAGTATATCCTCGTTCAAA
Found at i:210387 original size:110 final size:110
Alignment explanation
Indices: 210184--210404 Score: 307
Period size: 110 Copynumber: 2.0 Consensus size: 110
210174 TAAGTATCCA
* * * * * *
210184 AGCAAGGATTTTATATATACACAAAGGCTCGAATTCGAAACTTGCTTAGGTCATATTAAATTGTT
1 AGCAAGGATTTTATATATACACAAAGACTCGAACTCGAAACTTACTTAAGTCATATTAAACTGTA
* *
210249 TATCACTTGAACCAACCCCGTTCGTAACCTTTCTTTTTCTCATGT
66 TATCACTTAAACCAACCCCGTTCATAACCTTTCTTTTTCTCATGT
* * * * *
210294 AGCAGGGATTTTCTATTTACACAAAGACTCGAACTCGAAACTTACTTAATTCTTATTAAACTGTA
1 AGCAAGGATTTTATATATACACAAAGACTCGAACTCGAAACTTACTTAAGTCATATTAAACTGTA
* *
210359 TATCATTTAAACCAATCCCGTTCATAACCTTTCTTTTTCTCATGT
66 TATCACTTAAACCAACCCCGTTCATAACCTTTCTTTTTCTCATGT
210404 A
1 A
210405 ATGCACAGTG
Statistics
Matches: 96, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
110 96 1.00
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.37
Consensus pattern (110 bp):
AGCAAGGATTTTATATATACACAAAGACTCGAACTCGAAACTTACTTAAGTCATATTAAACTGTA
TATCACTTAAACCAACCCCGTTCATAACCTTTCTTTTTCTCATGT
Found at i:211288 original size:26 final size:30
Alignment explanation
Indices: 211232--211290 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
211222 TTAGTTTTTC
*
211232 ACCCGACCCGACCCGATAGATAGTTTAAAAA
1 ACCCGACCCGACCCGATAGATAG-ATAAAAA
211263 ACCCGACCCGACCCGA-A-ATA-ATAAAAA
1 ACCCGACCCGACCCGATAGATAGATAAAAA
211290 A
1 A
211291 ATTATTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 7 0.26
29 3 0.11
30 1 0.04
31 16 0.59
ACGTcount: A:0.44, C:0.31, G:0.14, T:0.12
Consensus pattern (30 bp):
ACCCGACCCGACCCGATAGATAGATAAAAA
Found at i:212342 original size:31 final size:31
Alignment explanation
Indices: 212307--212367 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
212297 TAATATAGGG
212307 TCACTTTCATTTTTATTTAATTAAGATATGA
1 TCACTTTCATTTTTATTTAATTAAGATATGA
*
212338 TCACTTTCGTTTTTATTTAATTAAGATATG
1 TCACTTTCATTTTTATTTAATTAAGATATG
212368 GTTAATTGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.52
Consensus pattern (31 bp):
TCACTTTCATTTTTATTTAATTAAGATATGA
Found at i:214488 original size:29 final size:30
Alignment explanation
Indices: 214455--214555 Score: 87
Period size: 30 Copynumber: 3.4 Consensus size: 30
214445 ATAAACATTT
*
214455 TGATCACTAAACTTTT-AAAAGTTATAAAA
1 TGATCACTAAACTTTTAAAAAGTTACAAAA
* **
214484 TGATCATTAATTTTTTAAAAAGTTACAAAA
1 TGATCACTAAACTTTTAAAAAGTTACAAAA
* * * * **
214514 TGAACATTAAATTTATTGAACTGTTACAAAA
1 TGATCACTAAACTT-TTAAAAAGTTACAAAA
*
214545 TGATCATTAAA
1 TGATCACTAAA
214556 TTTAGGTAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
29 13 0.22
30 24 0.40
31 23 0.38
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.37
Consensus pattern (30 bp):
TGATCACTAAACTTTTAAAAAGTTACAAAA
Found at i:214507 original size:30 final size:29
Alignment explanation
Indices: 214467--214554 Score: 104
Period size: 31 Copynumber: 2.9 Consensus size: 29
214457 ATCACTAAAC
*
214467 TTTTAAAAGTTATAAAATGATCATTAATT
1 TTTTAAAAGTTACAAAATGATCATTAATT
*
214496 TTTTAAAAAGTTACAAAATGAACATTAAATT
1 TTTT-AAAAGTTACAAAATGATCATT-AATT
* **
214527 TATTGAACTGTTACAAAATGATCATTAA
1 T-TTTAAAAGTTACAAAATGATCATTAA
214555 ATTTAGGTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 4 0.08
30 21 0.42
31 23 0.46
32 2 0.04
ACGTcount: A:0.47, C:0.07, G:0.08, T:0.39
Consensus pattern (29 bp):
TTTTAAAAGTTACAAAATGATCATTAATT
Found at i:214763 original size:21 final size:21
Alignment explanation
Indices: 214702--214765 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
214692 TGACCATTAC
* *
214702 GTGTTGATGTGGTAGTTCAAA
1 GTGTTGATGTGGTAGTCCACA
*
214723 GTGTTGATGTGGTTGTCCACA
1 GTGTTGATGTGGTAGTCCACA
214744 GTGTTGATGTGGTAGTCCACA
1 GTGTTGATGTGGTAGTCCACA
214765 G
1 G
214766 AGGTTGACAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.19, C:0.11, G:0.34, T:0.36
Consensus pattern (21 bp):
GTGTTGATGTGGTAGTCCACA
Found at i:217118 original size:35 final size:37
Alignment explanation
Indices: 217047--217119 Score: 105
Period size: 36 Copynumber: 2.0 Consensus size: 37
217037 GTTGAAAAAT
* *
217047 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
*
217084 ATTTATATATTTT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
217119 A
1 A
217120 ATGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 6 0.18
36 14 0.42
37 13 0.39
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:222331 original size:77 final size:77
Alignment explanation
Indices: 222204--222346 Score: 207
Period size: 77 Copynumber: 1.9 Consensus size: 77
222194 CTTATTGATT
* * *
222204 AATGAAGATGAAGACTAAATGTTACTATTAGAGAGGATCAAACTTAGAACCTTTGTAAAAGAGGT
1 AATGAAAATGAAGACTAAATGTTACTATTAGAGAAGATCAAACTTAGAACCCTTGTAAAAGAGGT
222269 ACTTTGTTTGTG
66 ACTTTGTTTGTG
* * **
222281 AATGAAAATGAAGA-TAAAATGTTATTATTAGGGAAGATTGAACTTAGAACCCTTGTAAAAGAGG
1 AATGAAAATGAAGACT-AAATGTTACTATTAGAGAAGATCAAACTTAGAACCCTTGTAAAAGAGG
222345 TA
65 TA
222347 AAACATTCAT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
76 1 0.02
77 57 0.98
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.29
Consensus pattern (77 bp):
AATGAAAATGAAGACTAAATGTTACTATTAGAGAAGATCAAACTTAGAACCCTTGTAAAAGAGGT
ACTTTGTTTGTG
Found at i:225554 original size:33 final size:33
Alignment explanation
Indices: 225517--225608 Score: 80
Period size: 33 Copynumber: 2.8 Consensus size: 33
225507 GAAATAGAAA
*
225517 TTAACCCAAACCGAAAGAAACCTGAACCGAATT
1 TTAACCCAAACCGAAAGAAACCCGAACCGAATT
* * * * *
225550 TTAACTCGATCTGAAAGCAACCCGAACCGAA-T
1 TTAACCCAAACCGAAAGAAACCCGAACCGAATT
* * *
225582 TTAACTC-GACCTGAAAGCAACCCGAAC
1 TTAACCCAAACC-GAAAGAAACCCGAAC
225609 ATAAACTAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
31 1 0.02
32 23 0.47
33 25 0.51
ACGTcount: A:0.40, C:0.29, G:0.14, T:0.16
Consensus pattern (33 bp):
TTAACCCAAACCGAAAGAAACCCGAACCGAATT
Found at i:225590 original size:32 final size:33
Alignment explanation
Indices: 225529--225608 Score: 126
Period size: 32 Copynumber: 2.5 Consensus size: 33
225519 AACCCAAACC
* * *
225529 GAAAGAAACCTGAACCGAATTTTAACTCGATCT
1 GAAAGCAACCCGAACCGAATTTTAACTCGACCT
225562 GAAAGCAACCCGAACCGAA-TTTAACTCGACCT
1 GAAAGCAACCCGAACCGAATTTTAACTCGACCT
225594 GAAAGCAACCCGAAC
1 GAAAGCAACCCGAAC
225609 ATAAACTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
32 27 0.61
33 17 0.39
ACGTcount: A:0.40, C:0.28, G:0.16, T:0.16
Consensus pattern (33 bp):
GAAAGCAACCCGAACCGAATTTTAACTCGACCT
Found at i:230696 original size:31 final size:31
Alignment explanation
Indices: 230658--230785 Score: 118
Period size: 31 Copynumber: 4.1 Consensus size: 31
230648 GAACCTCGAC
* *
230658 AACTGTCCATAGGTCCCGAAGAACTTAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* **
230689 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* *
230720 TACTGTCCATATGTCCC-AAAAGACATAGGTA
1 AACTGTCCATATGTCCCGAAGA-ACATAGGTA
* *
230751 ATTA-TGTCAATATGTTCCGTAA-AACATAGGTA
1 A--ACTGTCCATATGTCCCG-AAGAACATAGGTA
230783 AAC
1 AAC
230786 CCTCGACTCT
Statistics
Matches: 79, Mismatches: 12, Indels: 12
0.77 0.12 0.12
Matches are distributed among these distances:
30 3 0.04
31 50 0.63
32 22 0.28
33 2 0.03
34 2 0.03
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGAAGAACATAGGTA
Found at i:233535 original size:20 final size:21
Alignment explanation
Indices: 233510--233550 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
233500 TTGTTTGGCT
233510 CTGAATG-GAACCATTCAGCG
1 CTGAATGTGAACCATTCAGCG
*
233530 CTGAATGTTGAACCGTTCAGC
1 CTGAATG-TGAACCATTCAGC
233551 ATTCAGACTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (21 bp):
CTGAATGTGAACCATTCAGCG
Found at i:243767 original size:14 final size:15
Alignment explanation
Indices: 243740--243776 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
243730 ATAAATTAAT
243740 TAAAA-ATTTAAAAA
1 TAAAATATTTAAAAA
*
243754 TAAATTATTT-AAAA
1 TAAAATATTTAAAAA
243768 TAAAATATT
1 TAAAATATT
243777 GATTATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAAATATTTAAAAA
Found at i:244652 original size:7 final size:7
Alignment explanation
Indices: 244642--244668 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
244632 ATTTAATATT
244642 TATTTTA
1 TATTTTA
244649 TATTTTA
1 TATTTTA
244656 TATTTTA
1 TATTTTA
244663 TATTTT
1 TATTTT
244669 TAAAATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TATTTTA
Found at i:245102 original size:14 final size:14
Alignment explanation
Indices: 245083--245110 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
245073 TTATTGATAA
245083 AAATAATAATTAAT
1 AAATAATAATTAAT
245097 AAATAATAATTAAT
1 AAATAATAATTAAT
245111 TTGATCCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AAATAATAATTAAT
Found at i:267545 original size:51 final size:51
Alignment explanation
Indices: 267469--267576 Score: 198
Period size: 51 Copynumber: 2.1 Consensus size: 51
267459 AGTGGTAGAA
*
267469 CATCAACAAATGCAACAAGATAAAGCTCACGGGTTCAAGCATCAATGATTG
1 CATCAACAAATGCAACAAGATAAAGCTCACGGGTTCAAGCACCAATGATTG
*
267520 CATCAACAAATGCAACAAGATAAAGCTCACGGGTTCAAGCACCAATTATTG
1 CATCAACAAATGCAACAAGATAAAGCTCACGGGTTCAAGCACCAATGATTG
267571 CATCAA
1 CATCAA
267577 GACGATGGAG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.19
Consensus pattern (51 bp):
CATCAACAAATGCAACAAGATAAAGCTCACGGGTTCAAGCACCAATGATTG
Found at i:267784 original size:38 final size:38
Alignment explanation
Indices: 267742--267818 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
267732 TCAACTAAAC
267742 ACCGAAAAAGGAGGAAAATATGTTTCGAAAAACCAATT
1 ACCGAAAAAGGAGGAAAATATGTTTCGAAAAACCAATT
* *
267780 ACCGAAAAATGAGGAAAATATGTTTCGAAAATCCAATT
1 ACCGAAAAAGGAGGAAAATATGTTTCGAAAAACCAATT
267818 A
1 A
267819 GAGTGAAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.49, C:0.13, G:0.17, T:0.21
Consensus pattern (38 bp):
ACCGAAAAAGGAGGAAAATATGTTTCGAAAAACCAATT
Found at i:272311 original size:15 final size:15
Alignment explanation
Indices: 272268--272335 Score: 70
Period size: 14 Copynumber: 4.7 Consensus size: 15
272258 TATGTTATAT
272268 AACTATTAAAATACA
1 AACTATTAAAATACA
272283 AACTA--AATAATACA
1 AACTATTAA-AATACA
272297 AACTATTAAAATACA
1 AACTATTAAAATACA
* * *
272312 AA-TGTTACAATTCA
1 AACTATTAAAATACA
*
272326 AACAATTAAA
1 AACTATTAAA
272336 TAATAAAAAC
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
13 2 0.05
14 22 0.51
15 17 0.40
16 2 0.05
ACGTcount: A:0.59, C:0.13, G:0.01, T:0.26
Consensus pattern (15 bp):
AACTATTAAAATACA
Found at i:273796 original size:20 final size:21
Alignment explanation
Indices: 273757--273798 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
273747 TTACTTCAGG
*
273757 GGTATCGATACCCCTGCTACA
1 GGTACCGATACCCCTGCTACA
*
273778 GGTACCGATA-CCTTGCTACA
1 GGTACCGATACCCCTGCTACA
273798 G
1 G
273799 TAACTTTCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.24
Consensus pattern (21 bp):
GGTACCGATACCCCTGCTACA
Found at i:276084 original size:75 final size:75
Alignment explanation
Indices: 275957--276104 Score: 251
Period size: 75 Copynumber: 2.0 Consensus size: 75
275947 GACCATTTTA
*
275957 CCCTTTAATTCCTTTGATAATTACTAACAACTTTCAGGAAACATTTCCAAATAAATCATTGAACT
1 CCCTTTAATTCCTTTGATAATTACTAACAACTTTCAGGAAACATTTCCAAATAAATCATTAAACT
276022 ATTCAACTTG
66 ATTCAACTTG
* * **
276032 CCCTTTAATTCCTTTGATAATTACTAACAACTTTCATGAAATATTTTTAAATAAATCATTAAACT
1 CCCTTTAATTCCTTTGATAATTACTAACAACTTTCAGGAAACATTTCCAAATAAATCATTAAACT
276097 ATTCAACT
66 ATTCAACT
276105 ATTTTACTTT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 68 1.00
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.39
Consensus pattern (75 bp):
CCCTTTAATTCCTTTGATAATTACTAACAACTTTCAGGAAACATTTCCAAATAAATCATTAAACT
ATTCAACTTG
Found at i:278683 original size:103 final size:103
Alignment explanation
Indices: 278557--278877 Score: 570
Period size: 103 Copynumber: 3.1 Consensus size: 103
278547 GTCGAGGGTC
278557 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACACATAC
278622 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
278660 TATGTGGTCCTTCGGGATATATATGTATTATTTGGAATATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACACATAC
*
278725 TTGATCATTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* *
278763 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACACATAC
* * *
278828 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
278866 TATGTTGTCCTT
1 TATGTGGTCCTT
278878 ATGGACATTA
Statistics
Matches: 208, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 208 1.00
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:278927 original size:23 final size:23
Alignment explanation
Indices: 278893--278956 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
278883 CATTATTATA
*
278893 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGTAATTCTACG
*
278916 TGGCACTCCGGTGTAATTCTACG
1 TGGCACTACGGTGTAATTCTACG
*
278939 TGGCACTTCGGTGTAATT
1 TGGCACTACGGTGTAATT
278957 ATATGAGTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.19, C:0.23, G:0.27, T:0.31
Consensus pattern (23 bp):
TGGCACTACGGTGTAATTCTACG
Found at i:285743 original size:12 final size:12
Alignment explanation
Indices: 285726--285750 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
285716 GAACACTGCA
285726 GAAGCTGATGAT
1 GAAGCTGATGAT
285738 GAAGCTGATGAT
1 GAAGCTGATGAT
285750 G
1 G
285751 CCGGTGCTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.36, T:0.24
Consensus pattern (12 bp):
GAAGCTGATGAT
Found at i:290879 original size:25 final size:26
Alignment explanation
Indices: 290827--290888 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 26
290817 AATTCTTATT
* *
290827 TAATATTATAATTTTTAATAGTTTAA
1 TAATATTATTATTTTTAATAGTTAAA
290853 TAATATTATTA-TTTTAATAAG-TAAA
1 TAATATTATTATTTTTAAT-AGTTAAA
*
290878 TAATATAATTA
1 TAATATTATTA
290889 ATAATATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 20 0.62
26 12 0.38
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (26 bp):
TAATATTATTATTTTTAATAGTTAAA
Found at i:290947 original size:42 final size:42
Alignment explanation
Indices: 290856--290936 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
290846 AGTTTAATAA
* *
290856 TATTATTATTTTAATAAGTAAATAATATAATTAATAATATAT
1 TATTTTTATTTTAATAAATAAATAATATAATTAATAATATAT
* * *
290898 TATTTTTATTTTAATAAATAATTAGTATAATTTATAATA
1 TATTTTTATTTTAATAAATAAATAATATAATTAATAATA
290937 ATTTTGTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (42 bp):
TATTTTTATTTTAATAAATAAATAATATAATTAATAATATAT
Found at i:291032 original size:20 final size:21
Alignment explanation
Indices: 291009--291091 Score: 70
Period size: 21 Copynumber: 4.0 Consensus size: 21
290999 ATTATTCTAA
291009 TATTTTAA-AAATAATATTAT
1 TATTTTAATAAATAATATTAT
*
291029 TATTTAGTTAATAAAT-ATACTA-
1 TA-TT--TTAATAAATAATATTAT
291051 TATTTT-A-AAATAATA-TAT
1 TATTTTAATAAATAATATTAT
*
291069 TATAGTTAATAAATAATATTAT
1 TAT-TTTAATAAATAATATTAT
291091 T
1 T
291092 TATTGTATTT
Statistics
Matches: 51, Mismatches: 2, Indels: 18
0.72 0.03 0.25
Matches are distributed among these distances:
17 6 0.12
18 7 0.14
19 4 0.08
20 3 0.06
21 12 0.24
22 6 0.12
23 9 0.18
24 4 0.08
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (21 bp):
TATTTTAATAAATAATATTAT
Found at i:291087 original size:41 final size:41
Alignment explanation
Indices: 291008--291083 Score: 122
Period size: 38 Copynumber: 1.9 Consensus size: 41
290998 AATTATTCTA
291008 ATATTTTAAAAATAATATTATTATTTAGTTAATAAATATACT
1 ATATTTTAAAAATAATATTATTA-TTAGTTAATAAATATACT
291050 ATATTTT-AAAATAATA-TATTA-TAGTTAATAAATA
1 ATATTTTAAAAATAATATTATTATTAGTTAATAAATA
291084 ATATTATTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
38 13 0.38
40 5 0.15
41 9 0.26
42 7 0.21
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (41 bp):
ATATTTTAAAAATAATATTATTATTAGTTAATAAATATACT
Found at i:294746 original size:50 final size:50
Alignment explanation
Indices: 294684--294782 Score: 171
Period size: 50 Copynumber: 2.0 Consensus size: 50
294674 TATAAATACG
* *
294684 AGATGTTTTATTTTATCATACGAGTGCATGTTATCATACACTTCTTCAAT
1 AGATGTTCTATTTTATCATACGAATGCATGTTATCATACACTTCTTCAAT
*
294734 AGATGTTCTATTTTGTCATACGAATGCATGTTATCATACACTTCTTCAA
1 AGATGTTCTATTTTATCATACGAATGCATGTTATCATACACTTCTTCAA
294783 GAGTAAGTGC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.42
Consensus pattern (50 bp):
AGATGTTCTATTTTATCATACGAATGCATGTTATCATACACTTCTTCAAT
Found at i:296932 original size:2 final size:2
Alignment explanation
Indices: 296925--296949 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
296915 ATTTGGTCTA
296925 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
296950 GCTTCCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:299800 original size:24 final size:24
Alignment explanation
Indices: 299769--299814 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
299759 ATAATTTTAA
*
299769 AAATTTATTTAAAATTTAAAAAGT
1 AAATTTATATAAAATTTAAAAAGT
* *
299793 AAATTTATATATATTTTAAAAA
1 AAATTTATATAAAATTTAAAAA
299815 ATAGAAAACG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
AAATTTATATAAAATTTAAAAAGT
Found at i:299846 original size:18 final size:19
Alignment explanation
Indices: 299820--299855 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
299810 AAAAAATAGA
*
299820 AAACGCAAAA-TTTGAAAT
1 AAACCCAAAACTTTGAAAT
299838 AAACCCAAAACTTTGAAA
1 AAACCCAAAACTTTGAAA
299856 ATATTCATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.56, C:0.17, G:0.08, T:0.19
Consensus pattern (19 bp):
AAACCCAAAACTTTGAAAT
Found at i:302006 original size:37 final size:36
Alignment explanation
Indices: 301931--302007 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 36
301921 TTTTTATATT
*
301931 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
301967 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
302004 TTTA
1 TTTA
302008 TAATATTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 26 0.72
37 10 0.28
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:302027 original size:18 final size:18
Alignment explanation
Indices: 301983--302030 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
301973 TTTTTAAAGA
*
301983 AAATATATAAATATTTTAC
1 AAATATAT-AATATTATAC
*
302002 -AATTTATAATATTATAC
1 AAATATATAATATTATAC
302019 AAATATATAATA
1 AAATATATAATA
302031 AGGACAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATATATAATATTATAC
Found at i:308839 original size:44 final size:44
Alignment explanation
Indices: 308770--308885 Score: 142
Period size: 44 Copynumber: 2.6 Consensus size: 44
308760 ACGTCTACCT
* * * *
308770 TACTGTTCTTGGATCTTGTAATATTTAATAGCAAAAACTCCAGC
1 TACTGCTCTTGCAACTTGTAATATTTAATAGCAAAAACTCCACC
* * **
308814 TATTGCTCTTGCAACTTGTAATATTTAATAGCCAAAACTTTACC
1 TACTGCTCTTGCAACTTGTAATATTTAATAGCAAAAACTCCACC
* *
308858 TACTGCTCTTGGAACTTGTAATACTTAA
1 TACTGCTCTTGCAACTTGTAATATTTAA
308886 AAGTTGAGAT
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 61 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (44 bp):
TACTGCTCTTGCAACTTGTAATATTTAATAGCAAAAACTCCACC
Found at i:319200 original size:27 final size:26
Alignment explanation
Indices: 319152--319202 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
319142 GTCTGACGTG
*
319152 GCAGTTTCTAGAAGGTACAGTCAGTA
1 GCAGTTTCTAGAAGATACAGTCAGTA
319178 GCAGTTTTCTAGAAGAT-CTAGTCAG
1 GCAG-TTTCTAGAAGATAC-AGTCAG
319203 CACCTTCTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (26 bp):
GCAGTTTCTAGAAGATACAGTCAGTA
Found at i:319463 original size:24 final size:24
Alignment explanation
Indices: 319431--319477 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
319421 TCTTCTTTTC
319431 TTTATTTTTAAGCTTTCATTTTTAT
1 TTTATTTTTAAG-TTTCATTTTTAT
*
319456 TTTA-TTTTAAGTTTTATTTTTA
1 TTTATTTTTAAGTTTCATTTTTA
319478 AACATAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.48
24 7 0.33
25 4 0.19
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.70
Consensus pattern (24 bp):
TTTATTTTTAAGTTTCATTTTTAT
Found at i:320201 original size:33 final size:33
Alignment explanation
Indices: 320159--320227 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
320149 TTTTTACTAC
320159 TTATTGTCTGGTTTAAACAATTCAAACAGAAAT
1 TTATTGTCTGGTTTAAACAATTCAAACAGAAAT
320192 TTATTGTCTGGTTTAAACAATTCAAACAGAAAT
1 TTATTGTCTGGTTTAAACAATTCAAACAGAAAT
320225 TTA
1 TTA
320228 GGAATTTTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.38
Consensus pattern (33 bp):
TTATTGTCTGGTTTAAACAATTCAAACAGAAAT
Found at i:324849 original size:17 final size:17
Alignment explanation
Indices: 324824--324862 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
324814 TTTTGAGTTA
*
324824 TATTGAATACAACTACG
1 TATTCAATACAACTACG
* *
324841 TATTCAATACGACTATG
1 TATTCAATACAACTACG
324858 TATTC
1 TATTC
324863 GGTACAAGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (17 bp):
TATTCAATACAACTACG
Found at i:328700 original size:145 final size:141
Alignment explanation
Indices: 328194--328838 Score: 584
Period size: 145 Copynumber: 4.4 Consensus size: 141
328184 AATTCAATGT
* *
328194 TCAATTAACAAAA-CAAAAAAG-AAGCA-TGAAAGAAACAACACTGTAACATTCATAAAACCTCA
1 TCAATTAACAAAACCAAAAAAGTAAGCACT-AAAGAAACACCATTGTAACATTCATAAAACCTCA
* *** * * * * * ** **
328256 AGTAACTTCAACCGATTATCGTCTGGGACGAAC-A-CAAGATTTTATGTCACAGAAAAACTTATA
65 AGTAACTTCAACCAAGGCT-TTCTAGAAGGAACGATCAAGATTTTATATCAGGGACGAACTTATA
*
328319 AAATTATAGAGGAC
129 AAATTTTAG-GGAC
* * * * **
328333 TCAGTTAACAAAACCAAAAAAAAAATTGAAGCACCAAATAAACATTATTGTAACATTCATAAAAC
1 TCAATTAACAAAACC----AAAAAAGT-AAGCACTAAAGAAACACCATTGTAACATTCATAAAAC
* *
328398 CTCAAGTAACTTCAACCAAGGCTTTCTGGCATA-G-ACGAACTCAAGGTTTTATATCAGGGACGA
61 CTCAAGTAACTTCAACCAAGGCTTTCTAG-A-AGGAACG-A-TCAAGATTTTATATCAGGGACGA
*
328461 ACTTATAAAATCTTAGGGGAC
122 ACTTATAAAATTTTA-GGGAC
* * * * * *
328482 TCAGTTAACAAAACCACACAAAAAAAATGAAGAACCAAAGTAACACCATTGTAATATTCATAAAA
1 TCAATTAAC-AAA--AC-C-AAAAAAGT-AAGCACTAAAGAAACACCATTGTAACATTCATAAAA
* *
328547 CCTCAAGTAACTTCAACCAAGGCTTTCTAGAAGGAACAGATGCAAGATTTCATATTAGGGGACGA
60 CCTCAAGTAACTTCAACCAAGGCTTTCTAGAAGGAAC-GAT-CAAGATTTTATATCA-GGGACGA
*
328612 ACTTATAAAATTTTAAGGGGC
122 ACTTATAAAATTTT-AGGGAC
328633 TCAATTAACAAAACCAAAAAAGTAAGCACTAAAGAAACACCATTGTAACATTCATAAAACCTCAA
1 TCAATTAACAAAACCAAAAAAGTAAGCACTAAAGAAACACCATTGTAACATTCATAAAACCTCAA
* * * * * * *
328698 GTAACTTCAACTAGGGCTTTCCAGAAGGAAGAGACGCAAGATTTTATATTAGGGGATGAACTTAT
66 GTAACTTCAACCAAGGCTTTCTAGAAGGAA-CGA-TCAAGATTTTATATCA-GGGACGAACTTAT
*
328763 AAAATTTTAAGGGAT
128 AAAATTTT-AGGGAC
* * * *
328778 TCAATTAATAAAACCAAAAAAGTAAACACTAAAGAAGCACCATTGTAACATTCATGAAACC
1 TCAATTAACAAAACCAAAAAAGTAAGCACTAAAGAAACACCATTGTAACATTCATAAAACC
328839 AAACGGATGC
Statistics
Matches: 426, Mismatches: 53, Indels: 48
0.81 0.10 0.09
Matches are distributed among these distances:
139 12 0.03
140 1 0.00
144 6 0.01
145 171 0.40
146 58 0.14
147 3 0.01
148 3 0.01
149 45 0.11
150 90 0.21
151 33 0.08
152 3 0.01
153 1 0.00
ACGTcount: A:0.45, C:0.18, G:0.14, T:0.23
Consensus pattern (141 bp):
TCAATTAACAAAACCAAAAAAGTAAGCACTAAAGAAACACCATTGTAACATTCATAAAACCTCAA
GTAACTTCAACCAAGGCTTTCTAGAAGGAACGATCAAGATTTTATATCAGGGACGAACTTATAAA
ATTTTAGGGAC
Found at i:329799 original size:13 final size:13
Alignment explanation
Indices: 329781--329806 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
329771 ATTCCTTGAC
329781 CATTAAAGAAAAT
1 CATTAAAGAAAAT
329794 CATTAAAGAAAAT
1 CATTAAAGAAAAT
329807 TTGAGTTAAA
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:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (13 bp):
CATTAAAGAAAAT
Found at i:331610 original size:22 final size:24
Alignment explanation
Indices: 331568--331612 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
331558 ACGATTAAAA
331568 ATTTAATAGTATAAAAGATATATC
1 ATTTAATAGTATAAAAGATATATC
331592 ATTTAA-AGT-TAAATA-ATATAT
1 ATTTAATAGTATAAA-AGATATAT
331613 GGTGTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 10 0.50
23 4 0.20
24 6 0.30
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.40
Consensus pattern (24 bp):
ATTTAATAGTATAAAAGATATATC
Done.