Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005234.1 Hibiscus syriacus cultivar Beakdansim tig00011848_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: 296100
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 1 of 2
Found at i:4850 original size:23 final size:23
Alignment explanation
Indices: 4768--4842 Score: 123
Period size: 23 Copynumber: 3.3 Consensus size: 23
4758 ATTATTATAT
*
4768 GGCACTACGATGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
4791 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
4814 GGCACTACGGTGCAATTCTATGT
1 GGCACTACGGTGCAATTCTACGC
4837 GGCACT
1 GGCACT
4843 TCAGTGCATT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:4858 original size:23 final size:23
Alignment explanation
Indices: 4758--4858 Score: 69
Period size: 23 Copynumber: 4.3 Consensus size: 23
4748 CCTTATGAAC
*
4758 ATTATTATATGGCACTAC-GATGCA
1 ATTA-TATGTGGCACTACAG-TGCA
* * * *
4782 ATTCTACGCGGCACTACGGTGCA
1 ATTATATGTGGCACTACAGTGCA
* * * *
4805 ATTCTACGCGGCACTACGGTGCA
1 ATTATATGTGGCACTACAGTGCA
* *
4828 ATTCTATGTGGCACTTCAGTGCA
1 ATTATATGTGGCACTACAGTGCA
*
4851 TTTATATG
1 ATTATATG
4859 AGCTGTGGTG
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
23 62 0.94
24 4 0.06
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.31
Consensus pattern (23 bp):
ATTATATGTGGCACTACAGTGCA
Found at i:6307 original size:24 final size:25
Alignment explanation
Indices: 6275--6335 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 25
6265 AGGGAATTCG
6275 GCGGTGGCTT-AC-AGGACCATGAGA
1 GCGGTGGCTTAACGAGGACC-TGAGA
*
6299 GCGGTGGCTTGCAACGGGGACCTGAGA
1 GCGGTGGCTT--AACGAGGACCTGAGA
6326 GCGGTGGCTT
1 GCGGTGGCTT
6336 GCAACGGGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
24 10 0.31
27 17 0.53
28 5 0.16
ACGTcount: A:0.18, C:0.21, G:0.43, T:0.18
Consensus pattern (25 bp):
GCGGTGGCTTAACGAGGACCTGAGA
Found at i:6330 original size:27 final size:28
Alignment explanation
Indices: 6288--6345 Score: 109
Period size: 27 Copynumber: 2.1 Consensus size: 28
6278 GTGGCTTACA
6288 GGACCATGAGAGCGGTGGCTTGCAACGG
1 GGACCATGAGAGCGGTGGCTTGCAACGG
6316 GGACC-TGAGAGCGGTGGCTTGCAACGG
1 GGACCATGAGAGCGGTGGCTTGCAACGG
6343 GGA
1 GGA
6346 AAGGAAGCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 25 0.83
28 5 0.17
ACGTcount: A:0.21, C:0.21, G:0.45, T:0.14
Consensus pattern (28 bp):
GGACCATGAGAGCGGTGGCTTGCAACGG
Found at i:15891 original size:26 final size:26
Alignment explanation
Indices: 15862--15920 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
15852 TACAATTATT
*
15862 TTATATGTATTAAACTA-TTTTTAATA
1 TTATAT-TATTAAAATATTTTTTAATA
15888 TTAT-TTATTAAAATATTTTTTTAATA
1 TTATATTATTAAAATA-TTTTTTAATA
15914 TTATATT
1 TTATATT
15921 CAAAAAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 9 0.31
25 1 0.03
26 17 0.59
27 2 0.07
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (26 bp):
TTATATTATTAAAATATTTTTTAATA
Found at i:15892 original size:20 final size:22
Alignment explanation
Indices: 15843--15892 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
15833 AACTTTTATT
*
15843 TATTATTAATACAATTATTTTA
1 TATTATTAATACAATTATTTAA
*
15865 TATGTATTAA-ACTATT-TTTAA
1 TAT-TATTAATACAATTATTTAA
15886 TATTATT
1 TATTATT
15893 TATTAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 4 0.16
21 7 0.28
22 8 0.32
23 6 0.24
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (22 bp):
TATTATTAATACAATTATTTAA
Found at i:16653 original size:17 final size:18
Alignment explanation
Indices: 16631--16672 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
16621 TCTTAATCTC
*
16631 TTATTTTTATGA-CTTAA
1 TTATTTTTAGGACCTTAA
*
16648 TTATTTTTAGGACCTTAT
1 TTATTTTTAGGACCTTAA
16666 TTATTTT
1 TTATTTT
16673 AAATAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (18 bp):
TTATTTTTAGGACCTTAA
Found at i:20921 original size:144 final size:144
Alignment explanation
Indices: 20656--20934 Score: 450
Period size: 144 Copynumber: 1.9 Consensus size: 144
20646 ACGGTCGTAT
20656 TTATCACGATTGTGGATATAACAAAATGTTATTACGGTTACCTCGATCTTGTAATAGCAATTTCA
1 TTATCACGATTGTGGATATAACAAAATGTTATTACGGTTACCTCGATCTTGTAATAGCAATTTCA
* ** * * * *
20721 TACGACGGTATCATCACTATATACCAGTCATTATTCTGATAACAGACCGCTATTTAAATCTATGG
66 GACGACACTATCATCACTATATAACAATCATTATTATGATAACAGACCGCTATTTAAATCTATGA
20786 TAAACAAAATGTTA
131 TAAACAAAATGTTA
* * *
20800 TTATTACGATTGTGGATATAACAAAATGTTATTATGGTTACCTCGATCTTTTAATAGCAATTTCA
1 TTATCACGATTGTGGATATAACAAAATGTTATTACGGTTACCTCGATCTTGTAATAGCAATTTCA
* *
20865 GATGGCACTATCATCACTATATAACAATCATTATTATGATAACAGACCGCTATTTAAATCTATGA
66 GACGACACTATCATCACTATATAACAATCATTATTATGATAACAGACCGCTATTTAAATCTATGA
20930 TAAAC
131 TAAAC
20935 GAAACAGAGA
Statistics
Matches: 123, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
144 123 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (144 bp):
TTATCACGATTGTGGATATAACAAAATGTTATTACGGTTACCTCGATCTTGTAATAGCAATTTCA
GACGACACTATCATCACTATATAACAATCATTATTATGATAACAGACCGCTATTTAAATCTATGA
TAAACAAAATGTTA
Found at i:25039 original size:38 final size:38
Alignment explanation
Indices: 24988--25064 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
24978 TAAGCTTTAA
*
24988 TATAGAAGCAATGGAGTAGACTAGGGTTTTAATAAGAT
1 TATAGAAACAATGGAGTAGACTAGGGTTTTAATAAGAT
* *
25026 TATAGAAATAATGGAGTAGACTAGGGTTTTGATAAGAT
1 TATAGAAACAATGGAGTAGACTAGGGTTTTAATAAGAT
25064 T
1 T
25065 CAATTCAGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.39, C:0.04, G:0.26, T:0.31
Consensus pattern (38 bp):
TATAGAAACAATGGAGTAGACTAGGGTTTTAATAAGAT
Found at i:26014 original size:2 final size:2
Alignment explanation
Indices: 26003--26032 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
25993 ACTTTAAATT
26003 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
26033 TTAATCTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27158 original size:3 final size:3
Alignment explanation
Indices: 27150--27197 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
27140 TTCGAACATC
27150 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
27198 ACCTAAACAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:27942 original size:121 final size:120
Alignment explanation
Indices: 27698--27982 Score: 351
Period size: 121 Copynumber: 2.3 Consensus size: 120
27688 AGTTTTGGGG
* * ** *
27698 AAAAATAAAAGTTTATGTATTAAAACGAAACAAATTTGATAGTTTATATACTAAACACGTTAAGC
1 AAAAATAAAAGTTTATATACTAAAACGAAACAAAACTGATAGTTTATATACTAAACACGTTAAGA
*
27763 TTTTAACGACGGTACTAAAATGAAACAAAAACTAAACTGTAGGTATAATTTTGAAA
66 TTTTAACGACGGTACTAAAATGAAACAAAAACTAAACTGTAGGCATAATTTT-AAA
* * *
27819 AAAAATAAAAGTTTATATACTAAAACG-GACTAAAACTGTTAGTTTATATACTAAACGCGTTAAG
1 AAAAATAAAAGTTTATATACTAAAACGAAAC-AAAACTGATAGTTTATATACTAAACACGTTAAG
*
27883 ATTTTAACCGTGGA-GGTACTAAAATGAAACAAAAACTAAACTGTAGGCATAATTTAAAA
65 ATTTTAA-C---GACGGTACTAAAATGAAACAAAAACTAAACTGTAGGCATAATTTTAAA
* * * * *
27942 AAAAATAAAAATTCATGTAGTAAAAC-ATATCAAAACTGATA
1 AAAAATAAAAGTTTATATACTAAAACGA-AACAAAACTGATA
27983 ATATATGTAT
Statistics
Matches: 140, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
120 2 0.01
121 60 0.43
122 1 0.01
123 34 0.24
124 41 0.29
125 2 0.01
ACGTcount: A:0.49, C:0.11, G:0.12, T:0.28
Consensus pattern (120 bp):
AAAAATAAAAGTTTATATACTAAAACGAAACAAAACTGATAGTTTATATACTAAACACGTTAAGA
TTTTAACGACGGTACTAAAATGAAACAAAAACTAAACTGTAGGCATAATTTTAAA
Found at i:29001 original size:2 final size:2
Alignment explanation
Indices: 28996--29021 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28986 TACAAGTACT
28996 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
29022 ATCGGCCAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30056 original size:23 final size:23
Alignment explanation
Indices: 30026--30113 Score: 81
Period size: 23 Copynumber: 3.9 Consensus size: 23
30016 GAACACAAAC
*
30026 AAACGAACATAATAAATGAACAT
1 AAACGAACACAATAAATGAACAT
30049 AAACGAACACAATAAATGAACA-
1 AAACGAACACAATAAATGAACAT
* * * *
30071 ACAA-AAACACAAAAAATAAACTT
1 A-AACGAACACAATAAATGAACAT
** *
30094 ATTCGAACACAACAAATGAA
1 AAACGAACACAATAAATGAA
30114 TGTAAAAAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
22 15 0.29
23 37 0.71
ACGTcount: A:0.62, C:0.17, G:0.07, T:0.14
Consensus pattern (23 bp):
AAACGAACACAATAAATGAACAT
Found at i:31802 original size:20 final size:20
Alignment explanation
Indices: 31767--31804 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31757 TTTCATTATT
31767 TTATTTATTTTATTATTTGC
1 TTATTTATTTTATTATTTGC
31787 TTATTATATTTT-TTATTT
1 TTATT-TATTTTATTATTT
31805 TTAAATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (20 bp):
TTATTTATTTTATTATTTGC
Found at i:37874 original size:24 final size:24
Alignment explanation
Indices: 37843--37890 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
37833 CAGATGAGAG
37843 AAAAAAGAGGATTTTTAGGTCTTA
1 AAAAAAGAGGATTTTTAGGTCTTA
37867 AAAAAAGAGGATTTTTAGGTCTTA
1 AAAAAAGAGGATTTTTAGGTCTTA
37891 GAACCCTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.04, G:0.21, T:0.33
Consensus pattern (24 bp):
AAAAAAGAGGATTTTTAGGTCTTA
Found at i:50090 original size:198 final size:198
Alignment explanation
Indices: 49657--50326 Score: 884
Period size: 198 Copynumber: 3.4 Consensus size: 198
49647 AAGTATCGGC
* **
49657 CCCAAAAACATCGAAACCTATAATTATAATGTAATAGGTAATTTTACAATGAAACCGGTATAAAT
1 CCCAAAAACATCGAAACCTATAATTATAATGTAATAGGTAAATTTACAATGTTACCGGTATAAAT
* * ** ** *
49722 ATACCGGTTTTATGATAGAATATATCAACATAATGTATCGACAAAAATTTTAAA--AATATCGAT
66 ATACCGGTTTTATGAGAGAATATGTCAACATAATGTATCGAC--ACTTTTTAAATTTGTGTCGAT
* * * * * * *
49785 ACATTTTGTACAGAATGAATGTCAAACGAGGTGCACGCATAAAGTGTAGATACATTTATTAAA--
129 AC-TTTTTTCCAAAATGAATGCCCAACGAGATGCACGCATAAAGTGTCGATACATTTA--AAATT
*
49848 ATATCGAT
191 GTATCGAT
* * * * * *
49856 CCCAAAAATATTGAAA-CTGATAATTACAATGTAATAGGTAAATTTATAATG-TACCTGTTAGAA
1 CCCAAAAACATCGAAACCT-ATAATTATAATGTAATAGGTAAATTTACAATGTTACC-GGTATAA
49919 ATATACCGGTTTTATGAGAGAATATGTCAACATAATGTATCGACACTTTTTAAATTTGTGTCGAT
64 ATATACCGGTTTTATGAGAGAATATGTCAACATAATGTATCGACACTTTTTAAATTTGTGTCGAT
49984 ACTTTTTTCCAAAATGAATGCCCAACGAGATGCACGCATAAAGTGTCGATACATTTAAAATTGTA
129 ACTTTTTTCCAAAATGAATGCCCAACGAGATGCACGCATAAAGTGTCGATACATTTAAAATTGTA
50049 TCGAT
194 TCGAT
* * *
50054 CCCAAAAACATCGAAACCAATAATTATAATGTAATAGGTAAATTTACAATGTTACTGATATAAAT
1 CCCAAAAACATCGAAACCTATAATTATAATGTAATAGGTAAATTTACAATGTTACCGGTATAAAT
** * * *
50119 ATACCAATTTTATGAGAGAATATGTCAACATAATGTATCAACACTTTTTAAATTTGTGTCGTTAT
66 ATACCGGTTTTATGAGAGAATATGTCAACATAATGTATCGACACTTTTTAAATTTGTGTCGATAC
**
50184 TTTTTTCCAAAATGAATGCCCAACGAGATGCAAACATAAAGTGTCGATACATTTAAAATTGTATC
131 TTTTTTCCAAAATGAATGCCCAACGAGATGCACGCATAAAGTGTCGATACATTTAAAATTGTATC
50249 GAT
196 GAT
* * * * *
50252 CCAAAAAATATCAAAACCTATAATTATAATATAATAGGTAAATTTATAATGTTACCGGTATAAAT
1 CCCAAAAACATCGAAACCTATAATTATAATGTAATAGGTAAATTTACAATGTTACCGGTATAAAT
50317 ATACCGGTTT
66 ATACCGGTTT
50327 AGTTAGAAAA
Statistics
Matches: 415, Mismatches: 48, Indels: 17
0.86 0.10 0.04
Matches are distributed among these distances:
196 3 0.01
197 8 0.02
198 302 0.73
199 102 0.25
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (198 bp):
CCCAAAAACATCGAAACCTATAATTATAATGTAATAGGTAAATTTACAATGTTACCGGTATAAAT
ATACCGGTTTTATGAGAGAATATGTCAACATAATGTATCGACACTTTTTAAATTTGTGTCGATAC
TTTTTTCCAAAATGAATGCCCAACGAGATGCACGCATAAAGTGTCGATACATTTAAAATTGTATC
GAT
Found at i:50391 original size:23 final size:23
Alignment explanation
Indices: 50335--50391 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
50325 TTAGTTAGAA
50335 AATATGTTAATATAAACGTTACCT
1 AATATGTT-ATATAAACGTTACCT
* ** * *
50359 ATTACATTATATAAATGTTATCT
1 AATATGTTATATAAACGTTACCT
50382 AATATGTTAT
1 AATATGTTAT
50392 TGTACTTGAT
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (23 bp):
AATATGTTATATAAACGTTACCT
Found at i:50435 original size:87 final size:87
Alignment explanation
Indices: 50344--50505 Score: 193
Period size: 87 Copynumber: 1.9 Consensus size: 87
50334 AAATATGTTA
** * * * * * *
50344 ATATAAACGTTACCTATTACATTATATAAATGTTATC-TAATATGTTATTGTACTTGATATTATT
1 ATATAAACACTACCTATTACATTATATAAACGCTA-CATAATATATTATTATACTTAATAATATT
50408 T-TCGGTTAAATGCCTATTTTATT
65 TCT-GGTTAAATGCCTATTTTATT
* * *
50431 ATATAAGCACTACTTATTATATTATATAAACGCTACATAATATATTATTATACTTAATAATATTT
1 ATATAAACACTACCTATTACATTATATAAACGCTACATAATATATTATTATACTTAATAATATTT
50496 CTGGTTAAAT
66 CTGGTTAAAT
50506 TATATAACAT
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
86 1 0.02
87 60 0.97
88 1 0.02
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.46
Consensus pattern (87 bp):
ATATAAACACTACCTATTACATTATATAAACGCTACATAATATATTATTATACTTAATAATATTT
CTGGTTAAATGCCTATTTTATT
Found at i:50466 original size:23 final size:23
Alignment explanation
Indices: 50422--50478 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
50412 GTTAAATGCC
* * *
50422 TATTTTATTATATAAGCACTACT
1 TATTATATTATATAAACACTACA
*
50445 TATTATATTATATAAACGCTACA
1 TATTATATTATATAAACACTACA
*
50468 TAATATATTAT
1 TATTATATTAT
50479 TATACTTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.46
Consensus pattern (23 bp):
TATTATATTATATAAACACTACA
Found at i:54789 original size:193 final size:193
Alignment explanation
Indices: 54460--54845 Score: 745
Period size: 193 Copynumber: 2.0 Consensus size: 193
54450 GTCGGGGTCG
54460 TGGGAGGGGACGTGGATCCCGAGGGCGTGGTAGAGGGTATGGTGGTGAAAATATGCAGTGGGATT
1 TGGGAGGGGACGTGGATCCCGAGGGCGTGGTAGAGGGTATGGTGGTGAAAATATGCAGTGGGATT
* *
54525 CGGGATATTATAATGATAATGGTCCATCAGGACCATTTCCTGGACAGGGTCGTGGTAAATCTATG
66 CGGGATATTATAATGATAATAGTCCATCAGGACCATTTCCTGGACAGGGTCGTGGTAAATATATG
54590 CCTCATTTGCTTTCCTTGTTCTTTTGTTCTGCCTAACTGTTAGTTTAGTGGTCCGACATATCC
131 CCTCATTTGCTTTCCTTGTTCTTTTGTTCTGCCTAACTGTTAGTTTAGTGGTCCGACATATCC
54653 TGGGAGGGGACGTGGATCCCGAGGGCGTGGTAGAGGGTATGGTGGTGAAAATATGCAGTGGGATT
1 TGGGAGGGGACGTGGATCCCGAGGGCGTGGTAGAGGGTATGGTGGTGAAAATATGCAGTGGGATT
*
54718 CGGGATATTATACTGATAATAGTCCATCAGGACCATTTCCTGGACAGGGTCGTGGTAAATATATG
66 CGGGATATTATAATGATAATAGTCCATCAGGACCATTTCCTGGACAGGGTCGTGGTAAATATATG
54783 CCTCATTTGCTTTCCTTGTTCTTTTGTTCTGCCTAACTGTTAGTTTAGTGGTCCGACATATCC
131 CCTCATTTGCTTTCCTTGTTCTTTTGTTCTGCCTAACTGTTAGTTTAGTGGTCCGACATATCC
54846 AAAAACAAAT
Statistics
Matches: 190, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
193 190 1.00
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.32
Consensus pattern (193 bp):
TGGGAGGGGACGTGGATCCCGAGGGCGTGGTAGAGGGTATGGTGGTGAAAATATGCAGTGGGATT
CGGGATATTATAATGATAATAGTCCATCAGGACCATTTCCTGGACAGGGTCGTGGTAAATATATG
CCTCATTTGCTTTCCTTGTTCTTTTGTTCTGCCTAACTGTTAGTTTAGTGGTCCGACATATCC
Found at i:55732 original size:87 final size:87
Alignment explanation
Indices: 55586--55835 Score: 410
Period size: 87 Copynumber: 2.9 Consensus size: 87
55576 TATGTTATAT
* * *
55586 TATTTAACCGGAAATATTATCAAATACAATAATATATTAGGTAACGCTTATATAATGTAATAGAT
1 TATTTAACAGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
* *
55651 ATCGTTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
*
55673 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1 TATTTAACAGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
55738 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
* * *
55760 TATTTAACAGAAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 TATTTAACAGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
*
55825 AACGCTTATAT
66 AGCGCTTATAT
55836 TGACCTATTT
Statistics
Matches: 153, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 153 1.00
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.34
Consensus pattern (87 bp):
TATTTAACAGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
AGCGCTTATATAATAAAATAGG
Found at i:56299 original size:260 final size:246
Alignment explanation
Indices: 55948--56465 Score: 761
Period size: 260 Copynumber: 2.0 Consensus size: 246
55938 CTTTTTATAA
55948 AAGTATCGACACTTTATGCTTGCACCTCGTTAGGCATTAATATTTCATTCTGGACAAAAATATCG
1 AAGTATCGACACTTTATGCTTGCACCTCGTTAGGCATTAATATTTCATTCTGGACAAAAATATCG
*
56013 ACACAAACTAAAAAAGTGTCGATACATGATTTAGACATATTCTCTCATAAAATCGGTATAATTAT
66 ACACAAACTAAAAAAGTGTCGATACATGATTTAGACATATTCTCTCATAAAACCGGTATAATTAT
*
56078 ACCGGTTTCATTGATCATTTACCTATTACATTATACTTATGGGTTTCGATGTTTTAGGGATCAAT
131 ACCAGTTTCATTG-----------A--ACATTATACTTATGGGTTTCGATGTTTTAGGGATCAAT
*
56143 ATTTTTTTAATAAATGTATCGACACTTTTTAAGGGTACA-TCTCTTTTGGCATTCATTCTAGACC
183 ACTTTTTTAATAAATGTATCGACAC--TTTAAGGGTACACT-TCTTTTGGCATTCATTCTAGACC
56207 GT
245 GT
**
56209 AAGTATCGACACTTTATGCTTGCACCTCGTT-GGTTTTAATATTTCATTCTGGACAAAAATATCG
1 AAGTATCGACACTTTATGCTTGCACCTCGTTAGGCATTAATATTTCATTCTGGACAAAAATATCG
* * *
56273 ACATAAACTAAAAAAGTGTTGATACATGATTTAGACCTATTCTCTCATAAAACCGGTATAATTAT
66 ACACAAACTAAAAAAGTGTCGATACATGATTTAGACATATTCTCTCATAAAACCGGTATAATTAT
*
56338 ACCAGTTTCATTGAACATTATACTTATGGGTTTCGATGTTTTAGGGATCGATACTTTTTTAATAA
131 ACCAGTTTCATTGAACATTATACTTATGGGTTTCGATGTTTTAGGGATCAATACTTTTTTAATAA
* * * *
56403 ATGTATCGACACTTTAAGGGTATACTTTTTTTTGCATTCATTTTAGACCGT
196 ATGTATCGACACTTTAAGGGTACACTTCTTTTGGCATTCATTCTAGACCGT
56454 AAGTATCGACAC
1 AAGTATCGACAC
56466 AACTTTAACA
Statistics
Matches: 243, Mismatches: 13, Indels: 18
0.89 0.05 0.07
Matches are distributed among these distances:
245 45 0.19
246 1 0.00
247 61 0.25
249 1 0.00
260 104 0.43
261 31 0.13
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.38
Consensus pattern (246 bp):
AAGTATCGACACTTTATGCTTGCACCTCGTTAGGCATTAATATTTCATTCTGGACAAAAATATCG
ACACAAACTAAAAAAGTGTCGATACATGATTTAGACATATTCTCTCATAAAACCGGTATAATTAT
ACCAGTTTCATTGAACATTATACTTATGGGTTTCGATGTTTTAGGGATCAATACTTTTTTAATAA
ATGTATCGACACTTTAAGGGTACACTTCTTTTGGCATTCATTCTAGACCGT
Found at i:60892 original size:200 final size:200
Alignment explanation
Indices: 60542--60901 Score: 621
Period size: 200 Copynumber: 1.8 Consensus size: 200
60532 ATATATACCA
* *
60542 ATTCTCCCATAAAATCGGTATACTTATACCGGTTAGATTGAAAAATTACCTAATACATTATAGTT
1 ATTCTCCCATAAAACCGGTATACTTATACCGGTTAGATTGAAAAATTACCTAATACATTATACTT
* ** *
60607 TTGGGTTTCGATGTTTATTGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACAC
66 ATGGGTTTCGATGTTTACGGGATCGACACTTTTTATATATGAATCGACACTTTATGGTTGCACAC
60672 TGTTTGCCATTCATTCTGGACCAAAAATATCGTCACAAACTACAAAAATGTCGACACATTATTTA
131 TGTTTGCCATTCATTCTGGACCAAAAATATCGTCACAAACTACAAAAATGTCGACACATTATTTA
60737 GATCT
196 GATCT
* * *
60742 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
1 ATTCTCCCATAAAACCGGTATACTTATACCGGTTAGATTGAAAAATTACCTAATACATTATACTT
* *
60807 ATGGGTTTCGATGTTTACGGGATCGACACTTTTTATATATGAATCGACACTTTATTGTTGCACCC
66 ATGGGTTTCGATGTTTACGGGATCGACACTTTTTATATATGAATCGACACTTTATGGTTGCACAC
60872 TGTTTGCCATTCATTCTGGACCAAAAATAT
131 TGTTTGCCATTCATTCTGGACCAAAAATAT
60902 GGGTTAGACT
Statistics
Matches: 149, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
200 149 1.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (200 bp):
ATTCTCCCATAAAACCGGTATACTTATACCGGTTAGATTGAAAAATTACCTAATACATTATACTT
ATGGGTTTCGATGTTTACGGGATCGACACTTTTTATATATGAATCGACACTTTATGGTTGCACAC
TGTTTGCCATTCATTCTGGACCAAAAATATCGTCACAAACTACAAAAATGTCGACACATTATTTA
GATCT
Found at i:60942 original size:171 final size:171
Alignment explanation
Indices: 60741--61072 Score: 594
Period size: 171 Copynumber: 1.9 Consensus size: 171
60731 TATTTAGATC
60741 TATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACT
1 TATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACT
60806 TATGGGTTTCGATGTTTA-CGGGATCGACACTTTTTATATATGAATCGACACTTTATTGTTGCAC
66 TATGGGTTTCGATGTTTATC-GGATCGACACTTTTTATATATGAATCGACACTTTATTGTTGCAC
60870 CCTGTTTGCCATTCATTCTGGACCAAAAATATGGGTTAGACT
130 CCTGTTTGCCATTCATTCTGGACCAAAAATATGGGTTAGACT
* * *
60912 TATTCTCTCATAAAATCGGTATATTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATATT
1 TATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACT
* *
60977 TATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGTACC
66 TATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATGAATCGACACTTTATTGTTGCACC
*
61042 CTGTTTGCCATTCATTCTGGATCAAAAATAT
131 CTGTTTGCCATTCATTCTGGACCAAAAATAT
61073 CGACACAAAC
Statistics
Matches: 154, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
171 153 0.99
172 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (171 bp):
TATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACT
TATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATGAATCGACACTTTATTGTTGCACC
CTGTTTGCCATTCATTCTGGACCAAAAATATGGGTTAGACT
Found at i:61232 original size:371 final size:371
Alignment explanation
Indices: 60542--61252 Score: 1210
Period size: 371 Copynumber: 1.9 Consensus size: 371
60532 ATATATACCA
60542 ATTCTCCCATAAAATCGGTATACTTATACCGGTTAGATTGAAAAATTACCTAATACATTATAGTT
1 ATTCTCCCATAAAATCGGTATACTTATACCGGTTAGATTGAAAAATTACCTAATACATTATAGTT
*
60607 TTGGGTTTCGATGTTTATTGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACAC
66 TTGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACAC
*
60672 TGTTTGCCATTCATTCTGGACCAAAAATATCGTCACAAACTACAAAAATGTCGACACATTATTTA
131 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAATGTCGACACATTATTTA
*
60737 GATCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTA
196 GATCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGAAAAATTACCTATTACATTA
* * *
60802 TACTTATGGGTTTCGATGTTTACGGGATCGACACTTTTTATATATGAATCGACACTTTATTGTTG
261 TACTTATGAGTTTCGATGTTTACGGGATCAACACTTTTTATATATGAATCGACACTTTATGGTTG
60867 CACCCTGTTTGCCATTCATTCTGGACCAAAAATATGGGTTAGACTT
326 CACCCTGTTTGCCATTCATTCTGGACCAAAAATATGGGTTAGACTT
* * * *
60913 ATTCTCTCATAAAATCGGTATATTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATA-TT
1 ATTCTCCCATAAAATCGGTATACTTATACCGGTTAGATTGAAAAATTACCTAATACATTATAGTT
* * *
60977 TATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGTACC
66 T-TGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACA
* * * *
61042 CTGTTTGCCATTCATTCTGGATCAAAAATATCGACACAAACTACAAAAGTGTCTATACATTATTT
130 CTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAATGTCGACACATTATTT
61107 AGA-CATATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGAAAAATTACCTATTACAT
195 AGATC-TATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGAAAAATTACCTATTACAT
* * *
61171 TATACTTTTGAGTTTCGATGTTTATGGGATCAACACTTTTTATATATGGATCGACACTTTATGGT
259 TATACTTATGAGTTTCGATGTTTACGGGATCAACACTTTTTATATATGAATCGACACTTTATGGT
61236 TGCACCCTGTTTGCCAT
324 TGCACCCTGTTTGCCAT
61253 ATTGTAAATT
Statistics
Matches: 318, Mismatches: 20, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
370 4 0.01
371 314 0.99
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.38
Consensus pattern (371 bp):
ATTCTCCCATAAAATCGGTATACTTATACCGGTTAGATTGAAAAATTACCTAATACATTATAGTT
TTGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACAC
TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAATGTCGACACATTATTTA
GATCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGAAAAATTACCTATTACATTA
TACTTATGAGTTTCGATGTTTACGGGATCAACACTTTTTATATATGAATCGACACTTTATGGTTG
CACCCTGTTTGCCATTCATTCTGGACCAAAAATATGGGTTAGACTT
Found at i:61497 original size:18 final size:18
Alignment explanation
Indices: 61474--61534 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
61464 TCTTATTCAT
*
61474 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
61492 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
61511 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
61530 AATTA
1 AATTA
61535 ACCTTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:61510 original size:19 final size:19
Alignment explanation
Indices: 61486--61534 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
61476 TTATATTCAC
61486 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
61505 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
61524 ATACAAAATTA
1 ATACAAAATTA
61535 ACCTTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:63125 original size:21 final size:21
Alignment explanation
Indices: 63099--63139 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
63089 TATCCTCATT
63099 TCTTCCATCTCTTCTTCTTCC
1 TCTTCCATCTCTTCTTCTTCC
* *
63120 TCTTCCCTCTTTTCTTCTTC
1 TCTTCCATCTCTTCTTCTTC
63140 ATATTTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.02, C:0.41, G:0.00, T:0.56
Consensus pattern (21 bp):
TCTTCCATCTCTTCTTCTTCC
Found at i:63448 original size:21 final size:21
Alignment explanation
Indices: 63423--63485 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
63413 CCACTTATGC
* *
63423 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
63444 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
63465 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
63486 ATTGATTGTC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.17, C:0.30, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:64473 original size:24 final size:24
Alignment explanation
Indices: 64446--64495 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
64436 CAACGATCCA
64446 AAACCTATTTCTCCCGGCACATTC
1 AAACCTATTTCTCCCGGCACATTC
* *
64470 AAACCTATTTCTCTCGGCGCATTC
1 AAACCTATTTCTCCCGGCACATTC
64494 AA
1 AA
64496 CTGACCCTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.26, C:0.34, G:0.10, T:0.30
Consensus pattern (24 bp):
AAACCTATTTCTCCCGGCACATTC
Found at i:66448 original size:21 final size:21
Alignment explanation
Indices: 66424--66486 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
66414 GACAATCAAT
*
66424 AGTCGAAGAGAAACTTGATAG
1 AGTCGAAGAGAAACTTGAGAG
66445 AGTCGAAGAGAAACTTGAGAG
1 AGTCGAAGAGAAACTTGAGAG
* * *
66466 AGTTGAAGATACACTTGAGAG
1 AGTCGAAGAGAAACTTGAGAG
66487 GCATAAAGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.41, C:0.10, G:0.30, T:0.19
Consensus pattern (21 bp):
AGTCGAAGAGAAACTTGAGAG
Found at i:67443 original size:285 final size:280
Alignment explanation
Indices: 66912--67459 Score: 1010
Period size: 285 Copynumber: 1.9 Consensus size: 280
66902 ATTTTTATTA
66912 TGTTGTTGTGACAAATTTGTATGCAAATTGTAGGTTGAAAAAAGCGGTATTCCAAGCGAAATTGA
1 TGTTGTTGTGACAAATTTGTATGCAAATTGTAGGTTGAAAAAAGCGGTATTCCAAGCGAAATTGA
66977 TGACATCGAAGTTGCAATTTGTGATTATTTATGGAATAGTGAGTTAGAATCGGAGTAAGAAATAT
66 TGACATCGAAGTTGCAATTTGTGATTATTTATGGAATAGTGAGTTAGAATCGGAGTAAGAAATAT
67042 ATTGCTTGTGAGTTATATTTAAATATTTCATGACAACATATTAATCCAAATGATTCATACAAATA
131 ATTGCTTGTGAGTTATATTTAAATATTTCATGACAACATATTAATCCAAATGATTCATACAAATA
67107 TTCTGTAATCTCAATGGGAAATCAATTCGCTAGTGTATATGAAGTTGCAACG-TGAAGCCTACGG
196 TTCTGTAATCTCAATGGGAAATCAATTCGCTAGTGTATATGAAGTTGCAACGTTGAAGCCTACGG
67171 AATTTGAATTTTATTATTGT
261 AATTTGAATTTTATTATTGT
67191 TGTTGTTGTGACAAAAATTTGTATGCAAAATTGTAGGTTG-AAAAAGCGGGTATTCCAAGCGAAA
1 TGTTGTTGTGAC--AAATTTGTATGC-AAATTGTAGGTTGAAAAAAGC-GGTATTCCAAGCGAAA
67255 TTGATGACATCGAAGTTGCAATTTGTGATTATTTATGGAATAGTGAGTTAGAATCGGAGTAAGTG
62 TTGATGACATCGAAGTTGCAATTTGTGATTATTTATGGAATAGTGAGTTAGAATCGGAGTAA--G
67320 AAATATATTGCTTTGTGAGTTATATTTAAATATTTCATGACAACATATTAATCCAAATGATTCAT
125 AAATATATTGC-TTGTGAGTTATATTTAAATATTTCATGACAACATATTAATCCAAATGATTCAT
*
67385 ACAAATATTCTGTAATCTCAATGGGAAATCAATTCGCTAGTGTATATGACGTTGCAACGTTGAAG
189 ACAAATATTCTGTAATCTCAATGGGAAATCAATTCGCTAGTGTATATGAAGTTGCAACGTTGAAG
67450 CCTACGGAAT
254 CCTACGGAAT
67460 GGGTTGGCGG
Statistics
Matches: 260, Mismatches: 1, Indels: 9
0.96 0.00 0.03
Matches are distributed among these distances:
279 12 0.05
281 19 0.07
282 91 0.35
284 12 0.05
285 111 0.43
286 15 0.06
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.35
Consensus pattern (280 bp):
TGTTGTTGTGACAAATTTGTATGCAAATTGTAGGTTGAAAAAAGCGGTATTCCAAGCGAAATTGA
TGACATCGAAGTTGCAATTTGTGATTATTTATGGAATAGTGAGTTAGAATCGGAGTAAGAAATAT
ATTGCTTGTGAGTTATATTTAAATATTTCATGACAACATATTAATCCAAATGATTCATACAAATA
TTCTGTAATCTCAATGGGAAATCAATTCGCTAGTGTATATGAAGTTGCAACGTTGAAGCCTACGG
AATTTGAATTTTATTATTGT
Found at i:68636 original size:19 final size:19
Alignment explanation
Indices: 68612--68657 Score: 62
Period size: 17 Copynumber: 2.6 Consensus size: 19
68602 AATGTAGGGT
68612 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
68631 TAATTTTG--TACGATTTA
1 TAATTTTGTATAAGATTTA
68648 TAA-TTTGTAT
1 TAATTTTGTAT
68658 GTGAATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 4 0.17
17 11 0.46
18 1 0.04
19 8 0.33
ACGTcount: A:0.33, C:0.02, G:0.11, T:0.54
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:70642 original size:183 final size:182
Alignment explanation
Indices: 70302--70700 Score: 622
Period size: 183 Copynumber: 2.2 Consensus size: 182
70292 CAAAGTTTTC
*
70302 ACACTTTTTAATATTGTGTTGGTACTTTATGTCCAGAATAGAAGAAAAATGTGTCAATACCTTTT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATAGAAGAAAAATGTGTCAATACCTTTT
* * *
70367 CAAATAGTATCGATTGAAAAAACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATA
66 CAAAAAGTATCGATT--AAAAACATCGGAACCCAGAATTATAATGTAATAAATAATTTTGTAATA
* *
70432 TAATCGGTATAAATATATCGATTTTATGAGCGAATAGGTCTACAACCTATATCG
129 TAACCGGTATAAATATACCGATTTTATGAGCGAATAGGTCTACAACCTATATCG
*
70486 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATAGAAGAAAAATGTGTCGATA-CTTTG
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATAGAAGAAAAATGTGTCAATACCTTT-
* * * *
70550 TCAAAAAGTGTCGACATT-TACACATTGGAACCCAGAATTATAATGTAATAAATAATTTTGTAAT
65 TCAAAAAGTATCG--ATTAAAAACATCGGAACCCAGAATTATAATGTAATAAATAATTTTGTAAT
*
70614 ATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
128 ATAACCGGTATAAATATACCGATTTTATGAGCGAATAGGTCTACAACCTATATCG
*
70669 ACACTTTTTAATTTTGTGTCGGTACTTTATGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGT
70701 TCATAATTAT
Statistics
Matches: 199, Mismatches: 13, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
183 128 0.64
184 68 0.34
186 3 0.02
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.36
Consensus pattern (182 bp):
ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATAGAAGAAAAATGTGTCAATACCTTTT
CAAAAAGTATCGATTAAAAACATCGGAACCCAGAATTATAATGTAATAAATAATTTTGTAATATA
ACCGGTATAAATATACCGATTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:70798 original size:120 final size:120
Alignment explanation
Indices: 70585--70820 Score: 400
Period size: 120 Copynumber: 2.0 Consensus size: 120
70575 TGGAACCCAG
* *
70585 AATTATAATGTAATAAATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAAT
1 AATTATAATGTAATAAATAATTTTGTAATATAACCGGTATAAATATACCGATTTTATAAGCGAAT
*
70650 AGGTCTACAACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGTTCAT
66 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTTCAT
* * *
70705 AATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGATTTTATAAGCGAAT
1 AATTATAATGTAATAAATAATTTTGTAATATAACCGGTATAAATATACCGATTTTATAAGCGAAT
* *
70770 AGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCTGTACTTTATGT
66 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
70821 CCAGAATGGA
Statistics
Matches: 108, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
120 108 1.00
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (120 bp):
AATTATAATGTAATAAATAATTTTGTAATATAACCGGTATAAATATACCGATTTTATAAGCGAAT
AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTTCAT
Found at i:71115 original size:119 final size:120
Alignment explanation
Indices: 70888--71129 Score: 405
Period size: 119 Copynumber: 2.0 Consensus size: 120
70878 TGGAACCCAT
*
70888 AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAAT
1 AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGATTTATGAGCGAAT
*
70953 AGGTCTACAACCTATATCCACACTTTTTAATTTTGTGTCGGTACTTTATGTCCAG
66 AGGTCTACAACCTATATCCACACTTTTTAATATTGTGTCGGTACTTTATGTCCAG
* * * *
71008 AATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACC-GATTTATTAGTGAAT
1 AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGATTTATGAGCGAAT
* *
71072 AGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAG
66 AGGTCTACAACCTATATCCACACTTTTTAATATTGTGTCGGTACTTTATGTCCAG
71127 AAT
1 AAT
71130 GGAAGAAAAA
Statistics
Matches: 114, Mismatches: 8, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
119 67 0.59
120 47 0.41
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (120 bp):
AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGATTTATGAGCGAAT
AGGTCTACAACCTATATCCACACTTTTTAATATTGTGTCGGTACTTTATGTCCAG
Found at i:71232 original size:302 final size:303
Alignment explanation
Indices: 70402--71294 Score: 1572
Period size: 303 Copynumber: 3.0 Consensus size: 303
70392 CGGAACCCAT
* * * * *
70402 AATTATAATGTAATAGATAATTTTGTAATATAATCGGTATAAATATATCGATTTTATGAGCGAAT
1 AATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGATTTTATAAGCGAAT
* *
70467 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATAGAAGAA
66 AGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAA
*
70532 AAATGTGTCGATACTTTGTCAAAAAGTGTCGACATTTACACATTGGAACCCAGAATTATAATGTA
131 AAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATTGGAACCCAGAATTATAATGTA
*
70597 ATAAATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACC
196 ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACC
* *
70662 TATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGTTCAT
261 TATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGTCCAG
70705 AATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGATTTTATAAGCGAAT
1 AATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGATTTTATAAGCGAAT
*
70770 AGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCTGTACTTTATGTCCAGAATGGAAGAA
66 AGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAA
* *
70835 AAATGTGTCGATATCTTGTCAAAAAGTGTCGACATTTACACATTGGAACCCATAATTATAATGTA
131 AAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATTGGAACCCAGAATTATAATGTA
70900 ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACC
196 ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACC
*
70965 TATATCCACACTTTTTAATTTTGTGTCGGTACTTTATGTCCAG
261 TATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGTCCAG
* *
71008 AATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGA-TTTATTAGTGAAT
1 AATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGATTTTATAAGCGAAT
71072 AGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAA
66 AGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAA
* * *
71137 AAATGTGTAGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGAA
131 AAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATTGGAACCCAGAATTATAATGTA
* *
71202 ATAGATAATTTTATAATATAACTGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACC
196 ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACC
*
71267 TATATCGACACTTTTTAATATTGTGTCG
261 TATATCGACACTTTTTAATTTTGTGTCG
71295 CTAATTTTAA
Statistics
Matches: 563, Mismatches: 27, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
302 224 0.40
303 339 0.60
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.36
Consensus pattern (303 bp):
AATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGATTTTATAAGCGAAT
AGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAA
AAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATTGGAACCCAGAATTATAATGTA
ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACC
TATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGTCCAG
Found at i:74745 original size:87 final size:87
Alignment explanation
Indices: 74641--74890 Score: 455
Period size: 87 Copynumber: 2.9 Consensus size: 87
74631 AAATAGGTCA
* * *
74641 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTATTTGATAATATTT
1 ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
74706 CCCGTTAAATACCTATTTTATT
66 CCCGTTAAATACCTATTTTATT
74728 ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
74793 CCCGTTAAATACCTATTTTATT
66 CCCGTTAAATACCTATTTTATT
*
74815 ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTATACTTGATAATATTT
1 ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
*
74880 CCGGTTAAATA
66 CCCGTTAAATA
74891 ATATAACATA
Statistics
Matches: 158, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 158 1.00
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (87 bp):
ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
CCCGTTAAATACCTATTTTATT
Found at i:74775 original size:23 final size:23
Alignment explanation
Indices: 74725--74769 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
74715 TACCTATTTT
* *
74725 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
74748 ATTATATAAGCGTTACCTAATA
1 ATTATATAAGCGCTACCTAATA
74770 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:74862 original size:23 final size:23
Alignment explanation
Indices: 74812--74856 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
74802 TACCTATTTT
* *
74812 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
74835 ATTATATAAGCGTTACCTAATA
1 ATTATATAAGCGCTACCTAATA
74857 TGTTATTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:81858 original size:30 final size:29
Alignment explanation
Indices: 81808--81873 Score: 123
Period size: 29 Copynumber: 2.3 Consensus size: 29
81798 TAATGAATTC
*
81808 TTTTTTATAATGATCCTTTTTTGTTTTTG
1 TTTTTTATAATGATCCTTTTTTGTTTTTA
81837 TTTTTTATAATGATCCTTTTTTGTTTTTA
1 TTTTTTATAATGATCCTTTTTTGTTTTTA
81866 TTTTTTAT
1 TTTTTTAT
81874 TTTATATTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.15, C:0.06, G:0.08, T:0.71
Consensus pattern (29 bp):
TTTTTTATAATGATCCTTTTTTGTTTTTA
Found at i:82676 original size:19 final size:19
Alignment explanation
Indices: 82630--82677 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
82620 AATGTAATTG
*
82630 TAGTATTTTTTTATATAAA
1 TAGTATATTTTTATATAAA
*
82649 TAGTCTATTTTTAGTATAAA
1 TAGTATATTTTTA-TATAAA
82669 TA-TATATTT
1 TAGTATATTT
82678 AATTTCTCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.56
Consensus pattern (19 bp):
TAGTATATTTTTATATAAA
Found at i:82962 original size:28 final size:28
Alignment explanation
Indices: 82874--82966 Score: 93
Period size: 27 Copynumber: 3.4 Consensus size: 28
82864 ATTACATCAT
**
82874 TTAAAAAAATAGATA-CTAATTGGACCA
1 TTAAAAAAATAGATACCTAATTATACCA
* * *
82901 TTAAAAAGATATG-TGCCTAATTATACTA
1 TTAAAAAAATA-GATACCTAATTATACCA
* *
82929 TTAAAAAATTA-ATACCTAATTTTACCA
1 TTAAAAAAATAGATACCTAATTATACCA
82956 TTAAAAAAATA
1 TTAAAAAAATA
82967 AATTATACTA
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
27 33 0.63
28 19 0.37
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.32
Consensus pattern (28 bp):
TTAAAAAAATAGATACCTAATTATACCA
Found at i:83921 original size:31 final size:31
Alignment explanation
Indices: 83886--83996 Score: 177
Period size: 31 Copynumber: 3.6 Consensus size: 31
83876 TTTAACGTCC
* *
83886 AAGTGACCAAAACTTAATAAAACGATAACTT
1 AAGTGACCAAAACTTAATAAAACAATAACAT
* *
83917 AAGTGACCACAACTTAATAAAACAATGACAT
1 AAGTGACCAAAACTTAATAAAACAATAACAT
*
83948 AAGTGACCAAAATTTAATAAAACAATAACAT
1 AAGTGACCAAAACTTAATAAAACAATAACAT
83979 AAGTGACCAAAACTTAAT
1 AAGTGACCAAAACTTAAT
83997 CAAAGTATAA
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 72 1.00
ACGTcount: A:0.53, C:0.16, G:0.09, T:0.22
Consensus pattern (31 bp):
AAGTGACCAAAACTTAATAAAACAATAACAT
Found at i:84540 original size:21 final size:21
Alignment explanation
Indices: 84498--84541 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
84488 AATTCTTAAA
* *
84498 TATTTTAATTAAAATAATATT
1 TATTTAAATAAAAATAATATT
84519 TATTTAAATAAAACATAA-ATT
1 TATTTAAATAAAA-ATAATATT
84540 TA
1 TA
84542 ATAGATAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
TATTTAAATAAAAATAATATT
Found at i:86751 original size:183 final size:184
Alignment explanation
Indices: 86435--86820 Score: 645
Period size: 183 Copynumber: 2.1 Consensus size: 184
86425 ATTAAATTTT
* *
86435 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAATCATTAAAAACTCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTAAAAACCCAATTAATAA
* *
86500 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAAATTATATAAATTTT
66 TTTAAGATCAAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
*
86565 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTTTTTTT-AATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
*
86618 AAATATTAAATATATTATATATAACATATGGGCT-AAGCCCAAACCATTTAAAACCCAATTAATA
1 AAATATTAAATATATTATATATAACATATGGGCTCAA-CCCAAACCATTAAAAACCCAATTAATA
* *
86682 ATTTAAGATCAAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTTATCTAAAATT
65 ATTTAAGATCAAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAAATTATATAAAATT
*
86747 TTTATTTTATAATTATTTATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
130 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
*
86802 AAATATTTAAT-T-TTATATA
1 AAATATTAAATATATTATATA
86821 AATTAGAAAA
Statistics
Matches: 191, Mismatches: 10, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
182 9 0.05
183 165 0.86
184 17 0.09
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (184 bp):
AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTAAAAACCCAATTAATAA
TTTAAGATCAAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
Found at i:88534 original size:24 final size:23
Alignment explanation
Indices: 88502--88558 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
88492 ACAAGCCCAA
* *
88502 AAAAGAAAATTTGGGCCCCTTTAC
1 AAAATAAAATTCGGG-CCCTTTAC
*
88526 AAAATAAAACTCGGGCCCTTTAC
1 AAAATAAAATTCGGGCCCTTTAC
88549 AAAATAAAAT
1 AAAATAAAAT
88559 CTAGATCCGA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 17 0.59
24 12 0.41
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.23
Consensus pattern (23 bp):
AAAATAAAATTCGGGCCCTTTAC
Found at i:89329 original size:11 final size:12
Alignment explanation
Indices: 89308--89332 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
89298 TTTTTGGTGT
89308 AAAATGAAAAAA
1 AAAATGAAAAAA
89320 AAAATGAAAAAA
1 AAAATGAAAAAA
89332 A
1 A
89333 TGTATATATA
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:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (12 bp):
AAAATGAAAAAA
Found at i:93640 original size:21 final size:22
Alignment explanation
Indices: 93602--93644 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
93592 TATAAGAAAT
93602 TATTTCTAAAATACAAAAATGA
1 TATTTCTAAAATACAAAAATGA
**
93624 TATTTC-AAAATTGAAAAATGA
1 TATTTCTAAAATACAAAAATGA
93645 AAATAATCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (22 bp):
TATTTCTAAAATACAAAAATGA
Found at i:99787 original size:13 final size:13
Alignment explanation
Indices: 99765--99799 Score: 61
Period size: 14 Copynumber: 2.6 Consensus size: 13
99755 GTGGGGAGTA
99765 ATTTCAAAAATTG
1 ATTTCAAAAATTG
99778 ATTTTCAAAAATTG
1 A-TTTCAAAAATTG
99792 ATTTCAAA
1 ATTTCAAA
99800 TGATTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.40
Consensus pattern (13 bp):
ATTTCAAAAATTG
Found at i:100230 original size:65 final size:64
Alignment explanation
Indices: 100147--100301 Score: 172
Period size: 65 Copynumber: 2.4 Consensus size: 64
100137 CACACCAATT
* * *
100147 TCAAATGC-ATTTTGTGTACCGATGCACA-AGCTATGCATCGATACACT-CTGGAATATTTTGAA
1 TCAAATGCAATTTT-TGTACCGATGCACATA-CCATGCATCGATACACTACTAG-AT-CTTTGAA
100209 ACA
62 ACA
* * *
100212 TCGAATGCAATTTTTGTACCGATGCACATACCATGCATCGATGCACTACTAGCTCTTTGAAACA
1 TCAAATGCAATTTTTGTACCGATGCACATACCATGCATCGATACACTACTAGATCTTTGAAACA
* **
100276 TCAAATGTAATTAGTGTACCGATGCA
1 TCAAATGCAATTTTTGTACCGATGCA
100302 TCCCTAGTGT
Statistics
Matches: 77, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
64 31 0.40
65 37 0.48
66 9 0.12
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (64 bp):
TCAAATGCAATTTTTGTACCGATGCACATACCATGCATCGATACACTACTAGATCTTTGAAACA
Found at i:102938 original size:29 final size:29
Alignment explanation
Indices: 102896--102955 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
102886 CAATTAAACA
*
102896 ACCGAATAATTGTCAAGATGGGTGAATTG
1 ACCGAATAATTGTCAAGAGGGGTGAATTG
102925 ACCGAATAATTGTCAAGAGGGGTGAATTG
1 ACCGAATAATTGTCAAGAGGGGTGAATTG
102954 AC
1 AC
102956 TTTTTGAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.35, C:0.12, G:0.28, T:0.25
Consensus pattern (29 bp):
ACCGAATAATTGTCAAGAGGGGTGAATTG
Found at i:102978 original size:7 final size:7
Alignment explanation
Indices: 102966--102995 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
102956 TTTTTGAGAT
102966 TAAGGAG
1 TAAGGAG
102973 TAAGGAG
1 TAAGGAG
*
102980 TAAGAAG
1 TAAGGAG
102987 TAAGGAG
1 TAAGGAG
102994 TA
1 TA
102996 TAAATATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.37, T:0.17
Consensus pattern (7 bp):
TAAGGAG
Found at i:107160 original size:21 final size:23
Alignment explanation
Indices: 107125--107166 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
107115 AAAAGGACGA
107125 GTAATAAATATATGTCTTGAAGC
1 GTAATAAATATATGTCTTGAAGC
107148 GTAA-AAA-ATATGTCTTGAA
1 GTAATAAATATATGTCTTGAA
107167 TCAAACACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.63
22 3 0.16
23 4 0.21
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (23 bp):
GTAATAAATATATGTCTTGAAGC
Found at i:112032 original size:15 final size:15
Alignment explanation
Indices: 112014--112047 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
112004 CCCCTCTCTC
112014 CCTTCCCCCCTTCCT
1 CCTTCCCCCCTTCCT
112029 CCTT-CCCCCTTCCT
1 CCTTCCCCCCTTCCT
112043 -CTTCC
1 CCTTCC
112048 ATGGTCATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 3 0.17
14 11 0.61
15 4 0.22
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (15 bp):
CCTTCCCCCCTTCCT
Found at i:113992 original size:20 final size:21
Alignment explanation
Indices: 113959--113997 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
113949 TCGACTCATA
*
113959 TTAACATATCTAAATATATCT
1 TTAACATATATAAATATATCT
113980 TTAA-ATATATAAATATAT
1 TTAACATATATAAATATAT
113998 TTAAAAATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.44
Consensus pattern (21 bp):
TTAACATATATAAATATATCT
Found at i:114005 original size:20 final size:20
Alignment explanation
Indices: 113959--114003 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
113949 TCGACTCATA
* *
113959 TTAACATATCTAAATATATC
1 TTAAAATATATAAATATATC
*
113979 TTTAAATATATAAATATAT-
1 TTAAAATATATAAATATATC
113998 TTAAAA
1 TTAAAA
114004 ATGGATTTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAAAATATATAAATATATC
Found at i:118593 original size:16 final size:16
Alignment explanation
Indices: 118572--118605 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
118562 CAATTATTAA
118572 AAAAATTA-AAATGAAT
1 AAAAATTATAAAT-AAT
118588 AAAAATTATAAATAAT
1 AAAAATTATAAATAAT
118604 AA
1 AA
118606 CATTAAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
AAAAATTATAAATAAT
Found at i:127334 original size:24 final size:26
Alignment explanation
Indices: 127285--127336 Score: 90
Period size: 24 Copynumber: 2.1 Consensus size: 26
127275 TAACAATAGG
127285 GATTGAAAATTGTATATTTTTTTATA
1 GATTGAAAATTGTATATTTTTTTATA
127311 GATTG-AAATTGTATA-TTTTTTATA
1 GATTGAAAATTGTATATTTTTTTATA
127335 GA
1 GA
127337 CAAAAAGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 11 0.42
25 10 0.38
26 5 0.19
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (26 bp):
GATTGAAAATTGTATATTTTTTTATA
Found at i:135477 original size:35 final size:35
Alignment explanation
Indices: 135433--135507 Score: 150
Period size: 35 Copynumber: 2.1 Consensus size: 35
135423 TGCCCTTACA
135433 AAATTTACTTCTAAGACGTTGCATCATTAAAAGAC
1 AAATTTACTTCTAAGACGTTGCATCATTAAAAGAC
135468 AAATTTACTTCTAAGACGTTGCATCATTAAAAGAC
1 AAATTTACTTCTAAGACGTTGCATCATTAAAAGAC
135503 AAATT
1 AAATT
135508 AGATTTATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (35 bp):
AAATTTACTTCTAAGACGTTGCATCATTAAAAGAC
Found at i:138152 original size:17 final size:18
Alignment explanation
Indices: 138113--138159 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
138103 CGTTTCAGAG
*
138113 GGAATTGAAATCTGTGAA
1 GGAATTGGAATCTGTGAA
*
138131 GGAATTGGAATCTGT-CA
1 GGAATTGGAATCTGTGAA
*
138148 GGAATTTGAATC
1 GGAATTGGAATC
138160 CAATTTCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.30
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Found at i:139558 original size:25 final size:26
Alignment explanation
Indices: 139524--139579 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
139514 ATATTTTTAA
* * *
139524 TAAATTAAAAT-AAATTATATAATTT
1 TAAATAAAAATGAAAATAAATAATTT
*
139549 TAAATAAAAATGAAAATAAATATTTT
1 TAAATAAAAATGAAAATAAATAATTT
139575 TAAAT
1 TAAAT
139580 TCAGTTAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (26 bp):
TAAATAAAAATGAAAATAAATAATTT
Found at i:139636 original size:24 final size:24
Alignment explanation
Indices: 139514--139662 Score: 92
Period size: 27 Copynumber: 5.8 Consensus size: 24
139504 CAAATTAGTC
139514 ATATTTTTAATAAATTAA-AATAAA
1 ATATTTTTAAT-AATTAATAATAAA
* *
139538 TTATATAATTTTAAATAA-AAATGAAAATAA
1 --ATAT--TTTT-AATAATTAAT-AATA-AA
*
139568 ATATTTTTAAATTCAGTTAATAATAAA
1 ATATTTTT-AA-T-AATTAATAATAAA
139595 ATATTTTTAAATTCAATTAATAATAAA
1 ATATTTTT-AA-T-AATTAATAATAAA
*
139622 CTATTTTTAATAATTAAT-ATAAAA
1 ATATTTTTAATAATTAATAAT-AAA
139646 ATATTTTT-A-AATTAATA
1 ATATTTTTAATAATTAATA
139663 TATATAATTA
Statistics
Matches: 104, Mismatches: 8, Indels: 25
0.76 0.06 0.18
Matches are distributed among these distances:
22 7 0.07
23 3 0.03
24 17 0.16
25 1 0.01
26 13 0.12
27 38 0.37
28 14 0.13
29 9 0.09
30 2 0.02
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (24 bp):
ATATTTTTAATAATTAATAATAAA
Found at i:139661 original size:26 final size:27
Alignment explanation
Indices: 139566--139658 Score: 131
Period size: 27 Copynumber: 3.6 Consensus size: 27
139556 AAATGAAAAT
*
139566 AAATATTTTTAAATTCAGTTAATAATA
1 AAATATTTTTAAATTCAATTAATAATA
139593 AAATATTTTTAAATTCAATTAATAATA
1 AAATATTTTTAAATTCAATTAATAATA
*
139620 AACTATTTTT-AA-T-AATTAAT-ATAA
1 AAATATTTTTAAATTCAATTAATAAT-A
139644 AAATATTTTTAAATT
1 AAATATTTTTAAATT
139659 AATATATATA
Statistics
Matches: 60, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
23 2 0.03
24 17 0.28
25 3 0.05
26 3 0.05
27 35 0.58
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.46
Consensus pattern (27 bp):
AAATATTTTTAAATTCAATTAATAATA
Found at i:139665 original size:24 final size:24
Alignment explanation
Indices: 139584--139666 Score: 77
Period size: 24 Copynumber: 3.4 Consensus size: 24
139574 TTAAATTCAG
139584 TTAATA-AT-AAAATATTTTTAAA
1 TTAATATATAAAAATATTTTTAAA
139606 TTCAAT-TAATAATAAACTATTTTT-AA
1 TT-AATAT-ATAA-AAA-TATTTTTAAA
139632 -TAATTAATATAAAAATATTTTTAAA
1 TTAA-T-ATATAAAAATATTTTTAAA
139657 TTAATATATA
1 TTAATATATA
139667 TAATTATATT
Statistics
Matches: 50, Mismatches: 0, Indels: 20
0.71 0.00 0.29
Matches are distributed among these distances:
22 2 0.04
23 3 0.06
24 16 0.32
25 9 0.18
26 12 0.24
27 8 0.16
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
TTAATATATAAAAATATTTTTAAA
Found at i:139675 original size:26 final size:24
Alignment explanation
Indices: 139563--139676 Score: 83
Period size: 27 Copynumber: 4.5 Consensus size: 24
139553 TAAAAATGAA
*
139563 AATAA-ATATTTTTAAATTCAGTTAAT
1 AATAATATATTTTTAAATT-A-AT-AT
*
139589 AATAAAATATTTTTAAATTCAAT-T
1 AATAATATATTTTTAAATT-AATAT
139613 AATAATAAACTATTTTTAATAATTAATAT
1 AATAAT--A-TATTTTT-A-AATTAATAT
139642 AA-AA-ATATTTTTAAATTAATAT
1 AATAATATATTTTTAAATTAATAT
139664 ATATAATTATATT
1 A-ATAA-TATATT
139677 ATATATAATC
Statistics
Matches: 75, Mismatches: 2, Indels: 22
0.76 0.02 0.22
Matches are distributed among these distances:
22 10 0.13
23 2 0.03
24 15 0.20
25 1 0.01
26 12 0.16
27 22 0.29
28 6 0.08
29 7 0.09
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (24 bp):
AATAATATATTTTTAAATTAATAT
Found at i:139956 original size:39 final size:39
Alignment explanation
Indices: 139901--140024 Score: 112
Period size: 39 Copynumber: 3.2 Consensus size: 39
139891 AAATAAATAT
*
139901 TTAAAAAATTAAAACGTTAATGTGAAATAATTTAAGAAA
1 TTAAAAATTTAAAACGTTAATGTGAAATAATTTAAGAAA
* *
139940 TTAAAAATTTAGAACG-TAATGGTGTCAA-AATTTAAGAAA
1 TTAAAAATTTAAAACGTTAAT-GTG-AAATAATTTAAGAAA
** * * *
139979 TTAGGATTTTAAAATC-TTATTGTGAAATAATTTGAG-AA
1 TTAAAAATTTAAAA-CGTTAATGTGAAATAATTTAAGAAA
*
140017 TTATAAAT
1 TTAAAAAT
140025 AAAATTTTTA
Statistics
Matches: 67, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
38 13 0.19
39 48 0.72
40 6 0.09
ACGTcount: A:0.48, C:0.03, G:0.13, T:0.35
Consensus pattern (39 bp):
TTAAAAATTTAAAACGTTAATGTGAAATAATTTAAGAAA
Found at i:141407 original size:16 final size:16
Alignment explanation
Indices: 141386--141425 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
141376 TTTGTAGTTC
141386 CAAAACCTGTATTAGA
1 CAAAACCTGTATTAGA
141402 CAAAACCTGTATTAGA
1 CAAAACCTGTATTAGA
141418 CAAAACCT
1 CAAAACCT
141426 TACTCCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.45, C:0.23, G:0.10, T:0.23
Consensus pattern (16 bp):
CAAAACCTGTATTAGA
Found at i:142504 original size:2 final size:2
Alignment explanation
Indices: 142497--142525 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
142487 AAATAAGAAT
142497 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
142526 GTATCAGGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:144971 original size:23 final size:23
Alignment explanation
Indices: 144911--144987 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
144901 ATCAAAAGAT
* *
144911 AGAGAAAAACGTGCCACAAAAAC
1 AGAGAAAAACGTGCTATAAAAAC
*
144934 AGAGAAAAATGTGCTATAAAAAC
1 AGAGAAAAACGTGCTATAAAAAC
**
144957 AGAGAAAAACGTGCTATAAAGGC
1 AGAGAAAAACGTGCTATAAAAAC
144980 AGAGAAAA
1 AGAGAAAA
144988 TGTCACAAAG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.56, C:0.13, G:0.21, T:0.10
Consensus pattern (23 bp):
AGAGAAAAACGTGCTATAAAAAC
Found at i:145237 original size:2 final size:2
Alignment explanation
Indices: 145232--145260 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
145222 TGATTGTTAC
145232 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
145261 CGTACAAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:146059 original size:60 final size:60
Alignment explanation
Indices: 145946--146073 Score: 161
Period size: 60 Copynumber: 2.1 Consensus size: 60
145936 ATAATTGGGT
*
145946 GACCATTTTGTAACTTTTAATAGTAGAGGGACTCAACAAAGCAACACTCTATAGTTGA-AG
1 GACCATTTTGTAACTTTCAATAGTAGAGGGACTCAACAAAGCAACACTCTATAG-TGAGAG
* * * * * *
146006 GACCATTTTGTAACTTTCAATAGTCGAGGGACTTAATAAAGTAATAC-CTTATAGTGAGGG
1 GACCATTTTGTAACTTTCAATAGTAGAGGGACTCAACAAAGCAACACTC-TATAGTGAGAG
146066 GACCATTT
1 GACCATTT
146074 GTGTTCTTTG
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
59 4 0.07
60 55 0.93
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (60 bp):
GACCATTTTGTAACTTTCAATAGTAGAGGGACTCAACAAAGCAACACTCTATAGTGAGAG
Found at i:154213 original size:26 final size:24
Alignment explanation
Indices: 154165--154215 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
154155 GCATATAAAT
*
154165 GAACATAAATAGATATAAACGAAC
1 GAACATAAATACATATAAACGAAC
*
154189 GAACATAAATAAACATATTAACGAAC
1 GAACATAAAT--ACATATAAACGAAC
154215 G
1 G
154216 TTCATGAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 10 0.43
26 13 0.57
ACGTcount: A:0.57, C:0.14, G:0.12, T:0.18
Consensus pattern (24 bp):
GAACATAAATACATATAAACGAAC
Found at i:154798 original size:6 final size:6
Alignment explanation
Indices: 154787--154811 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
154777 ACCAGAGGCG
154787 GCAACA GCAACA GCAACA GCAACA G
1 GCAACA GCAACA GCAACA GCAACA G
154812 AAACCGGAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.32, G:0.20, T:0.00
Consensus pattern (6 bp):
GCAACA
Found at i:191779 original size:57 final size:57
Alignment explanation
Indices: 191691--191816 Score: 173
Period size: 57 Copynumber: 2.2 Consensus size: 57
191681 ACCATTTAAT
* * * *
191691 TATTTCACATAGTATTAATCAAATTGTCATTTGTTCATATAAAAC-ATATACTCATAG
1 TATTTCACATAGCATTAATCAAATTATCATTTATTCACATAAAACAAT-TACTCATAG
* *
191748 TATTTCACATAGCATTACTCAAATTATCATTTATTCACATAAAACAATTACTCATTG
1 TATTTCACATAGCATTAATCAAATTATCATTTATTCACATAAAACAATTACTCATAG
*
191805 CATTTCACATAG
1 TATTTCACATAG
191817 TATGTATACT
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
57 59 0.97
58 2 0.03
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.39
Consensus pattern (57 bp):
TATTTCACATAGCATTAATCAAATTATCATTTATTCACATAAAACAATTACTCATAG
Found at i:193221 original size:62 final size:62
Alignment explanation
Indices: 193149--193268 Score: 231
Period size: 62 Copynumber: 1.9 Consensus size: 62
193139 ATTTATTAAT
*
193149 TTAAAGATTTATATTTAATTGGTAGTGTACAAATTCATACACAATTAATAAATTATATCAAG
1 TTAAAGATTTATATTTAATTGGTAGTGTACAAATTCATACACAATTAATAAACTATATCAAG
193211 TTAAAGATTTATATTTAATTGGTAGTGTACAAATTCATACACAATTAATAAACTATAT
1 TTAAAGATTTATATTTAATTGGTAGTGTACAAATTCATACACAATTAATAAACTATAT
193269 AAAGGGTATA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.43, C:0.08, G:0.09, T:0.39
Consensus pattern (62 bp):
TTAAAGATTTATATTTAATTGGTAGTGTACAAATTCATACACAATTAATAAACTATATCAAG
Found at i:196322 original size:20 final size:20
Alignment explanation
Indices: 196297--196389 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
196287 TTTTCCCAAT
196297 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
196317 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
196337 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
196358 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
196379 TCGCAATGCGA
1 TCGCAATGCGA
196390 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:196343 original size:21 final size:20
Alignment explanation
Indices: 196297--196389 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
196287 TTTTCCCAAT
*
196297 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
196317 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
196337 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
196358 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
196379 TCGCAATGCGA
1 TCGCAATGCGA
196390 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:196351 original size:41 final size:41
Alignment explanation
Indices: 196294--196389 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
196284 CGATTTTCCC
196294 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
196335 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
196376 AAATCGCAATGCGA
1 AATTCGCAATGCGA
196390 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:196403 original size:20 final size:20
Alignment explanation
Indices: 196378--196471 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
196368 AATTGGGAAA
*
196378 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
196398 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
196419 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
196439 TTCGCAACACGATACTGACT
1 ATCGCAACGCGATACTGACT
*
196459 TTCGCAACGCGAT
1 ATCGCAACGCGAT
196472 TTACTTAGCG
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 44 0.76
21 14 0.24
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:196452 original size:41 final size:41
Alignment explanation
Indices: 196375--196452 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
196365 GCGAATTGGG
* * **
196375 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
* *
196416 AAAATCGCAACGAGATACTTACTTTCGCAACACGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATA
196453 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
Found at i:197034 original size:18 final size:18
Alignment explanation
Indices: 196990--197053 Score: 74
Period size: 18 Copynumber: 3.4 Consensus size: 18
196980 CGAGAATGAG
*
196990 AATCGCAACGCGGAAATGAC
1 AATCGCAACGC-GAAAT-AA
*
197010 TATCGCAACGCGAAATAA
1 AATCGCAACGCGAAATAA
*
197028 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-TAA
197047 AATCGCA
1 AATCGCA
197054 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
18 15 0.38
19 14 0.36
20 10 0.26
ACGTcount: A:0.44, C:0.27, G:0.19, T:0.11
Consensus pattern (18 bp):
AATCGCAACGCGAAATAA
Found at i:197071 original size:19 final size:19
Alignment explanation
Indices: 197049--197119 Score: 90
Period size: 19 Copynumber: 3.7 Consensus size: 19
197039 GAAACCAAAA
197049 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
197068 TCGCGTTGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
197087 TCG-AGGTTGCGATTTTCATT
1 TCGCA--TTGCGATTTTCATT
*
197107 TCGCGTTGCGATT
1 TCGCATTGCGATT
197120 GTCTGGTCGC
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
19 28 0.64
20 16 0.36
ACGTcount: A:0.14, C:0.18, G:0.23, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:197097 original size:20 final size:19
Alignment explanation
Indices: 197049--197214 Score: 127
Period size: 20 Copynumber: 9.1 Consensus size: 19
197039 GAAACCAAAA
*
197049 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
197068 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
*
197087 TCGAGGTTGCGATTTTCATT
1 TCG-CGTTGCGATTTTCATT
*
197107 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
197123 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
197140 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
197154 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
197173 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
197193 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
197213 TC
1 TC
197215 AACCAAAAGA
Statistics
Matches: 117, Mismatches: 17, Indels: 26
0.73 0.11 0.16
Matches are distributed among these distances:
14 20 0.17
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 40 0.34
20 48 0.41
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:197139 original size:33 final size:33
Alignment explanation
Indices: 197102--197189 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
197092 GTTGCGATTT
* *
197102 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
197135 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
197168 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
197190 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:199177 original size:42 final size:42
Alignment explanation
Indices: 199117--199239 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
199107 GCCCGACTCG
* * *
199117 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
199159 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
199201 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
199240 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:199197 original size:21 final size:21
Alignment explanation
Indices: 199173--199239 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
199163 TCATTCCTCG
199173 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
199194 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
199215 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
199236 AGAG
1 AGAG
199240 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:200614 original size:14 final size:14
Alignment explanation
Indices: 200595--200630 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
200585 ATTGTTTAAT
200595 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
200609 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
200623 TGATTTGT
1 TGATTTGT
200631 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:200799 original size:19 final size:19
Alignment explanation
Indices: 200737--200790 Score: 81
Period size: 20 Copynumber: 2.8 Consensus size: 19
200727 AAAAAGTACT
*
200737 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
200756 ATCGCAACGCGAAAATGAAA
1 ATCGCAACGCG-AAATGAAA
*
200776 ATCGCAACGTGAAAT
1 ATCGCAACGCGAAAT
200791 TAAATTCGCG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 14 0.44
20 18 0.56
ACGTcount: A:0.46, C:0.19, G:0.20, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:200817 original size:19 final size:19
Alignment explanation
Indices: 200795--200912 Score: 85
Period size: 19 Copynumber: 6.7 Consensus size: 19
200785 TGAAATTAAA
200795 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
200814 TTCGCATTGCGA-TTTC--
1 TTCGCGTTGCGATTTTCAT
*
200830 --CTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
200847 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
200862 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
200880 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
200899 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
200913 GGACATTAAG
Statistics
Matches: 75, Mismatches: 13, Indels: 21
0.69 0.12 0.19
Matches are distributed among these distances:
14 17 0.23
15 4 0.05
16 3 0.04
17 3 0.04
18 4 0.05
19 34 0.45
20 10 0.13
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.43
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:200841 original size:33 final size:34
Alignment explanation
Indices: 200799--200892 Score: 174
Period size: 33 Copynumber: 2.8 Consensus size: 34
200789 ATTAAATTCG
200799 CGTTGCGATTTTCATTTCGCATTGCGATTTC-CT
1 CGTTGCGATTTTCATTTCGCATTGCGATTTCTCT
200832 CGTTGCGATTTTCATTTCGCATTGCGA-TTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTTCTCT
200865 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
200893 AGTAATTTCC
Statistics
Matches: 59, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
32 3 0.05
33 56 0.95
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTTCTCT
Found at i:203203 original size:12 final size:12
Alignment explanation
Indices: 203186--203210 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
203176 TCTTCGGGGA
203186 CTTTTTCTTCTT
1 CTTTTTCTTCTT
203198 CTTTTTCTTCTT
1 CTTTTTCTTCTT
203210 C
1 C
203211 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:204667 original size:14 final size:14
Alignment explanation
Indices: 204648--204684 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
204638 CATCAATTAA
204648 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
204662 ACAAATCATCTTTT
1 ACAAATCAACATTT
204676 ACAAATCAA
1 ACAAATCAA
204685 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:205074 original size:20 final size:20
Alignment explanation
Indices: 205049--205099 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
205039 ATTCATTTGA
*
205049 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGCGAAAATGG
205069 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
205089 TTATCGCAACG
1 CTATCGCAACG
205100 AGAATATCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.20
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:205149 original size:14 final size:15
Alignment explanation
Indices: 205129--205201 Score: 60
Period size: 14 Copynumber: 4.5 Consensus size: 15
205119 TGAAAATCGC
205129 ATTGCGATTTTCTCG
1 ATTGCGATTTTCTCG
205144 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC---TCG
*
205161 CATTGCGATTTCATTTCG
1 -ATTGCGATTT--TCTCG
205179 CATTGCGATTTTCTCG
1 -ATTGCGATTTTCTCG
205195 -TTGCGAT
1 ATTGCGAT
205202 AGCCATTTCG
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.37
16 4 0.08
17 3 0.06
18 14 0.29
19 9 0.18
21 1 0.02
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (15 bp):
ATTGCGATTTTCTCG
Found at i:205166 original size:19 final size:19
Alignment explanation
Indices: 205125--205191 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
205115 GAAATGAAAA
205125 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
205141 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
205158 TCGCATTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
205176 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
205192 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
18 18 0.40
19 10 0.22
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:205327 original size:14 final size:14
Alignment explanation
Indices: 205308--205344 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
205298 CATCAATTAA
205308 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
205322 ACAAATCATCTTTT
1 ACAAATCAACATTT
205336 ACAAATCAA
1 ACAAATCAA
205345 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:207244 original size:20 final size:19
Alignment explanation
Indices: 207209--207275 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
207199 GAAACATAAA
207209 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
207228 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
207248 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
207267 ATCGCAACG
1 ATCGCAACG
207276 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:207283 original size:14 final size:14
Alignment explanation
Indices: 207264--207321 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
207254 ATGCGAAATG
207264 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
207278 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
207294 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
207310 AAAATCGCAACG
1 AAAATCGCAACG
207322 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:207306 original size:32 final size:33
Alignment explanation
Indices: 207248--207326 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
207238 GGAAATGGCT
*
207248 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
207281 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
207313 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
207327 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:207374 original size:14 final size:14
Alignment explanation
Indices: 207355--207412 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
207345 TTTCATTTCG
207355 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
207369 CGTTGCGATTTCATTTT
1 CGTTGCGA-TT--TTGT
*
207386 GCGTTGCAATTTTGT
1 -CGTTGCGATTTTGT
207401 CGTTGCGATTTT
1 CGTTGCGATTTT
207413 AATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.53
15 5 0.14
17 5 0.14
18 7 0.19
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:207390 original size:32 final size:32
Alignment explanation
Indices: 207338--207425 Score: 122
Period size: 32 Copynumber: 2.7 Consensus size: 32
207328 ACAAATCGCA
*
207338 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGA-TTTCATTTCGCGTTGCAATTTTGTCG
*
207371 TTGCGATTTCATTTTGCGTTGCAATTTTGTCG
1 TTGCGATTTCATTTCGCGTTGCAATTTTGTCG
* *
207403 TTGCGATTTTAATTTCGCATTGC
1 TTGCGA-TTTCATTTCGCGTTGC
207426 GATAGCCATT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
32 30 0.61
33 19 0.39
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.49
Consensus pattern (32 bp):
TTGCGATTTCATTTCGCGTTGCAATTTTGTCG
Found at i:207467 original size:20 final size:20
Alignment explanation
Indices: 207414--207459 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
207404 TGCGATTTTA
207414 ATTT-CGCATTGCGATAGCC
1 ATTTCCGCATTGCGATAGCC
*
207433 ATTTCCGCATTGCGATAGTC
1 ATTTCCGCATTGCGATAGCC
207453 ATTTCCG
1 ATTTCCG
207460 TGTTGCGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.35
Consensus pattern (20 bp):
ATTTCCGCATTGCGATAGCC
Found at i:207972 original size:18 final size:18
Alignment explanation
Indices: 207946--207990 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
207936 GTCGATCAGA
*
207946 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
207964 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
207982 TGATGGCTC
1 TGATGGCTC
207991 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:209631 original size:22 final size:22
Alignment explanation
Indices: 209606--209649 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
209596 GATTTAGATA
209606 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
209628 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
209650 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:209862 original size:20 final size:20
Alignment explanation
Indices: 209837--209889 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
209827 GATTATGTAT
*
209837 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
209857 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
209877 TATCTCGTTGCGA
1 TATCGCGTTGCGA
209890 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:209923 original size:20 final size:20
Alignment explanation
Indices: 209817--209928 Score: 82
Period size: 20 Copynumber: 5.5 Consensus size: 20
209807 CGCTTTGAAA
*
209817 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
209838 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
209858 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
209878 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
209899 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
209919 ATCGCATTGC
1 ATCGCATTGC
209929 AATTTTCCCA
Statistics
Matches: 73, Mismatches: 16, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
19 2 0.03
20 47 0.64
21 24 0.33
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:209934 original size:41 final size:41
Alignment explanation
Indices: 209857--209934 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
209847 CGAAAGTCAG
* * * *
209857 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCAATTTTTTAT
* *
209898 TATCGCATTGCGATAGTCAGTATCGCATTGCAATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCAATTTT
209935 CCCAATTCGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCAATTTTTTAT
Found at i:209949 original size:21 final size:21
Alignment explanation
Indices: 209920--209996 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
209910 ATAGTCAGTA
209920 TCGCATTGCAATTTTCCCAAT
1 TCGCATTGCAATTTTCCCAAT
* * * **
209941 TCGCGTTGCGATTTTACTTAT
1 TCGCATTGCAATTTTCCCAAT
209962 TCGCATTGCGAA-TTTCCCAAT
1 TCGCATTGC-AATTTTCCCAAT
* *
209983 TCGCGTTGCGATTT
1 TCGCATTGCAATTT
209997 ACTTATTCGC
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
20 1 0.02
21 40 0.95
22 1 0.02
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.40
Consensus pattern (21 bp):
TCGCATTGCAATTTTCCCAAT
Found at i:210010 original size:41 final size:42
Alignment explanation
Indices: 209920--210016 Score: 171
Period size: 42 Copynumber: 2.3 Consensus size: 42
209910 ATAGTCAGTA
209920 TCGCATTGC-AATTTTCCCAATTCGCGTTGCGATTTTACTTAT
1 TCGCATTGCGAA-TTTCCCAATTCGCGTTGCGATTTTACTTAT
209962 TCGCATTGCGAATTTCCCAATTCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTTACTTAT
210003 TCGCATTGCGAATT
1 TCGCATTGCGAATT
210017 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
41 23 0.43
42 29 0.54
43 2 0.04
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.40
Consensus pattern (42 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTTACTTAT
Found at i:210461 original size:15 final size:16
Alignment explanation
Indices: 210441--210492 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 16
210431 AAAATACAAC
210441 ATTCCCAG-TAATCTT
1 ATTCCCAGATAATCTT
*
210456 ATTCCCCGATAATCTTTT
1 ATTCCCAGATAATC--TT
210474 ATTCCCACTGATAATCTT
1 ATTCCCA--GATAATCTT
210492 A
1 A
210493 CATTCCGTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
15 7 0.23
16 5 0.17
18 11 0.37
20 7 0.23
ACGTcount: A:0.27, C:0.27, G:0.06, T:0.40
Consensus pattern (16 bp):
ATTCCCAGATAATCTT
Found at i:210477 original size:18 final size:20
Alignment explanation
Indices: 210454--210491 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
210444 CCCAGTAATC
210454 TTATTCCC-C-GATAATCTT
1 TTATTCCCACTGATAATCTT
210472 TTATTCCCACTGATAATCTT
1 TTATTCCCACTGATAATCTT
210492 ACATTCCGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 1 0.06
20 9 0.50
ACGTcount: A:0.24, C:0.26, G:0.05, T:0.45
Consensus pattern (20 bp):
TTATTCCCACTGATAATCTT
Found at i:210578 original size:2 final size:2
Alignment explanation
Indices: 210571--210595 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
210561 TTCAACCTTT
210571 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
210596 GTGTGTGTGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:214399 original size:31 final size:31
Alignment explanation
Indices: 214345--214431 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
214335 TTTACTTTCA
* * * *
214345 TTTTAATACCTAAATTATTAATTTTGATC-CG
1 TTTTAGTACTTAAACTATTAATTTT-AACACG
*
214376 TTTTAGTACTTAAACTATCAATTTTAACACG
1 TTTTAGTACTTAAACTATTAATTTTAACACG
*
214407 TTTTAGTA-TCTAAACTTTTAATTTT
1 TTTTAGTACT-TAAACTATTAATTTT
214432 TTTCAAAGAT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
30 3 0.06
31 44 0.94
ACGTcount: A:0.32, C:0.13, G:0.06, T:0.49
Consensus pattern (31 bp):
TTTTAGTACTTAAACTATTAATTTTAACACG
Found at i:217288 original size:96 final size:96
Alignment explanation
Indices: 217122--217309 Score: 295
Period size: 96 Copynumber: 2.0 Consensus size: 96
217112 ACAAGATTAT
* * *
217122 TCAAGCCAGGAGATGAAACTCTTCCTAATTCAGACCCAAACTGTCTTTCTTCAGCACCAAGTGAA
1 TCAAGCCAGGAGATGAAACCCTTCCTAATTCAGACCCAAACAGTCTTTCTTCAGCACCAAGCGAA
*
217187 GGAAAATCACGTTCAAAAGCAGATTTACTAA
66 GGAAAATCACGCTCAAAAGCAGATTTACTAA
* * *
217218 TCAAGCCAGGAGATGAAACCCTTCCTATTTCAGACCCTACCAGTCTTTCTTCAGCACCAAGCGAA
1 TCAAGCCAGGAGATGAAACCCTTCCTAATTCAGACCCAAACAGTCTTTCTTCAGCACCAAGCGAA
* *
217283 TGAAAATCACGCTCAAATGCAGATTTA
66 GGAAAATCACGCTCAAAAGCAGATTTA
217310 TCACGGACAA
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
96 83 1.00
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (96 bp):
TCAAGCCAGGAGATGAAACCCTTCCTAATTCAGACCCAAACAGTCTTTCTTCAGCACCAAGCGAA
GGAAAATCACGCTCAAAAGCAGATTTACTAA
Found at i:228726 original size:19 final size:20
Alignment explanation
Indices: 228687--228726 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
228677 GGTTTGCGTA
228687 TATGAAAAATACTGATTAAT
1 TATGAAAAATACTGATTAAT
* *
228707 TATGTAAAATA-TGTTTAAT
1 TATGAAAAATACTGATTAAT
228726 T
1 T
228727 TAAGGAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (20 bp):
TATGAAAAATACTGATTAAT
Found at i:234435 original size:21 final size:20
Alignment explanation
Indices: 234403--234448 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 20
234393 AAATATAAAA
234403 ATTTTAGTAAAAAT-TATTATT
1 ATTTTAGT-AAAATGTATT-TT
234424 ATTTTAAG-AAAATGTATTTT
1 ATTTT-AGTAAAATGTATTTT
234444 ATTTT
1 ATTTT
234449 TTTAAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
20 12 0.52
21 9 0.39
22 2 0.09
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (20 bp):
ATTTTAGTAAAATGTATTTT
Found at i:237992 original size:30 final size:31
Alignment explanation
Indices: 237912--237995 Score: 100
Period size: 31 Copynumber: 2.8 Consensus size: 31
237902 TTTATAAAAT
* *
237912 GTGTATAACTGAAT-TAAATCAAAATTTTAA
1 GTGTACAACTGAATCAAAATCAAAATTTTAA
* * *
237942 GTGTTCAATTGAATCAAAATCAAAATTTTAT
1 GTGTACAACTGAATCAAAATCAAAATTTTAA
*
237973 GTGTACAACTGCA-CAAAATCAAA
1 GTGTACAACTGAATCAAAATCAAA
237996 CTTATGTATC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
30 21 0.47
31 24 0.53
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (31 bp):
GTGTACAACTGAATCAAAATCAAAATTTTAA
Found at i:243698 original size:57 final size:57
Alignment explanation
Indices: 243629--243739 Score: 168
Period size: 57 Copynumber: 1.9 Consensus size: 57
243619 ACTGCTTTCT
* * * *
243629 CCATGCAAAACCTTGTGAGAACCAATCAGATCACCGCCTTCTTCATGCAAAAACTCG
1 CCATGCAAAACCTCGTGAGAACAAATCAGACCACCACCTTCTTCATGCAAAAACTCG
* *
243686 CCATGCAAAACCTCGTGAGAACAAATCAGACCATCACCTTCTTCATGTAAAAAC
1 CCATGCAAAACCTCGTGAGAACAAATCAGACCACCACCTTCTTCATGCAAAAAC
243740 ACGTACGAAC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.36, C:0.31, G:0.13, T:0.21
Consensus pattern (57 bp):
CCATGCAAAACCTCGTGAGAACAAATCAGACCACCACCTTCTTCATGCAAAAACTCG
Done.