Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold26
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: 1656043
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.27
Warning! 334368 characters in sequence are not A, C, G, or T
File 3 of 8
Found at i:663489 original size:86 final size:86
Alignment explanation
Indices: 663343--663507 Score: 210
Period size: 86 Copynumber: 1.9 Consensus size: 86
663333 CGGGGCTTAC
* * *
663343 ACCATGCCAGGCACATGGTGCAAGCCACTTTCCACCTCCTGAGGGGAAGAGTGGGTAGGGCACGC
1 ACCATGCCAGGCACATGGGGCAAGCCACTTTCCACCTCCTGAGGGAAAGAGTGGGCAGGGCACGC
663408 ACCATGCCAAGCACGGCGCGT
66 ACCATGCCAAGCACGGCGCGT
* * *
663429 ACCATGCTAGGCATATGGGGCAAGCC-CTTTCCCACC-CCTTGGAGGGAAAG-GTGGGCAGGGCG
1 ACCATGCCAGGCACATGGGGCAAGCCACTTT-CCACCTCC-T-GAGGGAAAGAGTGGGCAGGGCA
* *
663491 TGCACCATGCTAAGCAC
63 CGCACCATGCCAAGCAC
663508 ACAGAGCATG
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
85 6 0.09
86 54 0.79
87 8 0.12
ACGTcount: A:0.23, C:0.30, G:0.32, T:0.15
Consensus pattern (86 bp):
ACCATGCCAGGCACATGGGGCAAGCCACTTTCCACCTCCTGAGGGAAAGAGTGGGCAGGGCACGC
ACCATGCCAAGCACGGCGCGT
Found at i:667513 original size:2 final size:2
Alignment explanation
Indices: 667508--667556 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
667498 CATCATAGCC
667508 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
667550 TA TA TA T
1 TA TA TA T
667557 TGCTAAATCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:668649 original size:13 final size:13
Alignment explanation
Indices: 668631--668692 Score: 55
Period size: 13 Copynumber: 5.2 Consensus size: 13
668621 ATTACTCAAA
668631 TGTATCGATACAT
1 TGTATCGATACAT
*
668644 TGTATCAATACA-
1 TGTATCGATACAT
668656 T-TACTC-A-A-A-
1 TGTA-TCGATACAT
668665 TGTATCGATACAT
1 TGTATCGATACAT
*
668678 TGTATCGATATAT
1 TGTATCGATACAT
668691 TG
1 TG
668693 ATCTTTGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
9 4 0.10
10 4 0.10
11 4 0.10
12 4 0.10
13 25 0.61
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:668655 original size:34 final size:34
Alignment explanation
Indices: 668610--668683 Score: 139
Period size: 34 Copynumber: 2.2 Consensus size: 34
668600 GCCAAGGAAA
*
668610 TGTATCGATACATTACTCAAATGTATCGATACAT
1 TGTATCAATACATTACTCAAATGTATCGATACAT
668644 TGTATCAATACATTACTCAAATGTATCGATACAT
1 TGTATCAATACATTACTCAAATGTATCGATACAT
668678 TGTATC
1 TGTATC
668684 GATATATTGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (34 bp):
TGTATCAATACATTACTCAAATGTATCGATACAT
Found at i:672127 original size:50 final size:50
Alignment explanation
Indices: 672052--672233 Score: 258
Period size: 50 Copynumber: 3.6 Consensus size: 50
672042 CTACAGTTTA
* *
672052 TATCGATACATTCTTCATTGTATCGATACATTCTGGGTTTTACCCAGATG
1 TATCGATACATTCTTCATTGTATCGATACATTATGGGTTTTACTCAGATG
* * * *
672102 TATCGATACATTTTTCATTGTATCGATATATTTTGAGTTTTACTCAGATG
1 TATCGATACATTCTTCATTGTATCGATACATTATGGGTTTTACTCAGATG
* *
672152 TATCAATACATTCTTCATTGTATCGATACATTATGGGTTTTACTCATATG
1 TATCGATACATTCTTCATTGTATCGATACATTATGGGTTTTACTCAGATG
* *
672202 TATAGATACATT-TCTCAATGTATCGATACATT
1 TATCGATACATTCT-TCATTGTATCGATACATT
672234 TAGAAATTTT
Statistics
Matches: 117, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
49 1 0.01
50 116 0.99
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.43
Consensus pattern (50 bp):
TATCGATACATTCTTCATTGTATCGATACATTATGGGTTTTACTCAGATG
Found at i:672189 original size:100 final size:100
Alignment explanation
Indices: 672052--672234 Score: 294
Period size: 100 Copynumber: 1.8 Consensus size: 100
672042 CTACAGTTTA
* * * *
672052 TATCGATACATTCTTCATTGTATCGATACATTCTGGGTTTTACCCAGATGTATCGATACATTTTT
1 TATCAATACATTCTTCATTGTATCGATACATTATGGGTTTTACCCAGATGTATAGATACATTTCT
* *
672117 CATTGTATCGATATATTTTGAGTTTTACTCAGATG
66 CAATGTATCGATACATTTTGAGTTTTACTCAGATG
* *
672152 TATCAATACATTCTTCATTGTATCGATACATTATGGGTTTTACTCATATGTATAGATACATTTCT
1 TATCAATACATTCTTCATTGTATCGATACATTATGGGTTTTACCCAGATGTATAGATACATTTCT
672217 CAATGTATCGATACATTT
66 CAATGTATCGATACATTT
672235 AGAAATTTTT
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
100 75 1.00
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (100 bp):
TATCAATACATTCTTCATTGTATCGATACATTATGGGTTTTACCCAGATGTATAGATACATTTCT
CAATGTATCGATACATTTTGAGTTTTACTCAGATG
Found at i:672224 original size:20 final size:21
Alignment explanation
Indices: 672194--672234 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
672184 ATGGGTTTTA
672194 CTCATATGTATAGATACATTT
1 CTCATATGTATAGATACATTT
*
672215 CTCA-ATGTATCGATACATTT
1 CTCATATGTATAGATACATTT
672235 AGAAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (21 bp):
CTCATATGTATAGATACATTT
Found at i:673362 original size:21 final size:19
Alignment explanation
Indices: 673337--673390 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 19
673327 TTTCAACAAT
673337 TTGTATCGATACAAACAGT-
1 TTGTATCGATACAAA-AGTG
*
673356 TAATGTATCGATACATAAGTG
1 T--TGTATCGATACAAAAGTG
673377 TTGTATCGATACAA
1 TTGTATCGATACAA
673391 TGTATCGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 13 0.43
20 3 0.10
21 14 0.47
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (19 bp):
TTGTATCGATACAAAAGTG
Found at i:673383 original size:19 final size:19
Alignment explanation
Indices: 673331--673390 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
673321 TTTGAATTTC
*
673331 AACAATTTGTATCGATACA
1 AACAGTTTGTATCGATACA
673350 AACAGTTAATGTATCGATACA
1 AACAGTT--TGTATCGATACA
*
673371 TA-AGTGTTGTATCGATACA
1 AACAGT-TTGTATCGATACA
673390 A
1 A
673391 TGTATCGATA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
19 18 0.51
20 3 0.09
21 14 0.40
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (19 bp):
AACAGTTTGTATCGATACA
Found at i:673396 original size:13 final size:13
Alignment explanation
Indices: 673378--673403 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
673368 ACATAAGTGT
673378 TGTATCGATACAA
1 TGTATCGATACAA
673391 TGTATCGATACAA
1 TGTATCGATACAA
673404 AGTTGCCCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:673453 original size:20 final size:21
Alignment explanation
Indices: 673428--673482 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
673418 CTGCCAAGGA
673428 AATGTATCGATACATT-ATTC
1 AATGTATCGATACATTGATTC
*
673448 AATGTATCAATACATTGA-TC
1 AATGTATCGATACATTGATTC
**
673468 TTTGTATCGATACAT
1 AATGTATCGATACAT
673483 CTGGGAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.40
Consensus pattern (21 bp):
AATGTATCGATACATTGATTC
Found at i:677967 original size:51 final size:51
Alignment explanation
Indices: 677859--677973 Score: 139
Period size: 51 Copynumber: 2.3 Consensus size: 51
677849 TATTTTTGAG
*
677859 AGGG-TACT-TAACCCCAGTTTTATTTCTAAAACACCGAGTTTTCACCATC
1 AGGGATACTCTAACCCCAGTTTTATTTCTAAAACACCGAATTTTCACCATC
* * *
677908 -GGGAATACTCTAACCCCAGTTTTATTTTTAAAACATC-AATTTTCCACTATC
1 AGGG-ATACTCTAACCCCAGTTTTATTTCTAAAACACCGAATTTT-CACCATC
*
677959 AGGGATACTCCAACC
1 AGGGATACTCTAACC
677974 TCGTTATTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
48 3 0.05
50 9 0.16
51 41 0.73
52 3 0.05
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.32
Consensus pattern (51 bp):
AGGGATACTCTAACCCCAGTTTTATTTCTAAAACACCGAATTTTCACCATC
Found at i:683374 original size:23 final size:23
Alignment explanation
Indices: 683329--683374 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
683319 AATTTTAATA
*
683329 GAATTTAATATTGAAGTTTTTAT
1 GAATTTAATATTCAAGTTTTTAT
*
683352 GAATTTAA-ATTCATGTTTATTAT
1 GAATTTAATATTCAAGTTT-TTAT
683375 CTTAGTACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.35, C:0.02, G:0.11, T:0.52
Consensus pattern (23 bp):
GAATTTAATATTCAAGTTTTTAT
Found at i:692554 original size:19 final size:20
Alignment explanation
Indices: 692530--692589 Score: 54
Period size: 19 Copynumber: 3.0 Consensus size: 20
692520 TTTGAATTTT
692530 AACAAT-TTGTATCGATACA
1 AACAATATTGTATCGATACA
*
692549 AACAATAACTGTATCGATA-A
1 AACAAT-ATTGTATCGATACA
* *
692569 ATA-ACTGTTGTATCGATACA
1 A-ACAATATTGTATCGATACA
692589 A
1 A
692590 TGTATCGCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
19 16 0.48
20 6 0.18
21 11 0.33
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.30
Consensus pattern (20 bp):
AACAATATTGTATCGATACA
Found at i:695799 original size:13 final size:13
Alignment explanation
Indices: 695781--695806 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
695771 CAATTTTTTG
695781 TGTATCGATACAT
1 TGTATCGATACAT
695794 TGTATCGATACAT
1 TGTATCGATACAT
695807 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:695821 original size:32 final size:33
Alignment explanation
Indices: 695761--695824 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
695751 TACAAGCCAA
** *
695761 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
695794 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
695825 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:695890 original size:20 final size:20
Alignment explanation
Indices: 695845--695917 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
695835 CTACCAAGAA
***
695845 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGAATC
695866 ATGTATCGATACATTGCAA-C
1 ATGTATCGATACATTG-AATC
* *
695886 ATGTATCGATACTTTGAATT
1 ATGTATCGATACATTGAATC
695906 ATGTATCGATAC
1 ATGTATCGATAC
695918 TTTTAAGGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.04
20 29 0.64
21 14 0.31
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTGAATC
Found at i:695918 original size:20 final size:20
Alignment explanation
Indices: 695865--695920 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
695855 ACATCTTTTT
*
695865 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGCAA
695885 CATGTATCGATACTTTG-AA
1 CATGTATCGATACTTTGCAA
*
695904 TTATGTATCGATACTTT
1 -CATGTATCGATACTTT
695921 TAAGGGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (20 bp):
CATGTATCGATACTTTGCAA
Found at i:696514 original size:21 final size:21
Alignment explanation
Indices: 696488--696550 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
696478 ATAATTTACA
696488 CACATATCAAAAATTTATTTG
1 CACATATCAAAAATTTATTTG
* *
696509 CACATAT---ACATCTA-TT-
1 CACATATCAAAAATTTATTTG
696525 --CATATCAAAAATTTATTTG
1 CACATATCAAAAATTTATTTG
696544 CACATAT
1 CACATAT
696551 ACATCTATTC
Statistics
Matches: 31, Mismatches: 4, Indels: 14
0.63 0.08 0.29
Matches are distributed among these distances:
14 5 0.16
17 7 0.23
18 7 0.23
21 12 0.39
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.38
Consensus pattern (21 bp):
CACATATCAAAAATTTATTTG
Found at i:696536 original size:35 final size:35
Alignment explanation
Indices: 696490--696560 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
696480 AATTTACACA
696490 CATATCAAAAATTTATTTGCACATATACATCTATT
1 CATATCAAAAATTTATTTGCACATATACATCTATT
696525 CATATCAAAAATTTATTTGCACATATACATCTATT
1 CATATCAAAAATTTATTTGCACATATACATCTATT
696560 C
1 C
696561 TCTCCTCCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.39, C:0.18, G:0.03, T:0.39
Consensus pattern (35 bp):
CATATCAAAAATTTATTTGCACATATACATCTATT
Found at i:699057 original size:84 final size:84
Alignment explanation
Indices: 698967--699131 Score: 210
Period size: 84 Copynumber: 2.0 Consensus size: 84
698957 CATTTTCCAC
* * *
698967 TTGCAACTCATTTC-TTTTCTCCTCTAATTCATTTATTTTCTTTTTAAAAGAAT-T-ATTTTCTA
1 TTGCAACTC-TTTCATATTCTCCTCTAATTCACTTAATTTC-TTTT-AAAGAATATCATTTTCTA
699029 AACTCATTGATTTACTTTCATT
63 AACTCATTGATTTACTTTCATT
* * *
699051 TTGCAACTCTTTCATATTCTTCTCTAATTCACTTAATTTCTTTTCAAGAATATCATTTTCTACAC
1 TTGCAACTCTTTCATATTCTCCTCTAATTCACTTAATTTCTTTTAAAGAATATCATTTTCTAAAC
* *
699116 TTATTGATTTATTTTC
66 TCATTGATTTACTTTC
699132 TTCTTTGAGT
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
82 6 0.09
83 9 0.13
84 55 0.79
ACGTcount: A:0.25, C:0.19, G:0.04, T:0.53
Consensus pattern (84 bp):
TTGCAACTCTTTCATATTCTCCTCTAATTCACTTAATTTCTTTTAAAGAATATCATTTTCTAAAC
TCATTGATTTACTTTCATT
Found at i:701193 original size:13 final size:13
Alignment explanation
Indices: 701175--701200 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
701165 CAATTTTTTG
701175 TGTATCGATACAT
1 TGTATCGATACAT
701188 TGTATCGATACAT
1 TGTATCGATACAT
701201 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:701215 original size:32 final size:33
Alignment explanation
Indices: 701155--701218 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
701145 TACAAGCCAA
** *
701155 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
701188 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
701219 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:703615 original size:24 final size:24
Alignment explanation
Indices: 703583--703631 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
703573 TAACCTCATT
*
703583 GCATCACTTGTTTTACCCATCAGG
1 GCATCACTTGTCTTACCCATCAGG
703607 GCATCACTTGTCTTACCCATCAGG
1 GCATCACTTGTCTTACCCATCAGG
703631 G
1 G
703632 TAATAATTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.20, C:0.31, G:0.18, T:0.31
Consensus pattern (24 bp):
GCATCACTTGTCTTACCCATCAGG
Found at i:706285 original size:39 final size:39
Alignment explanation
Indices: 706249--706327 Score: 108
Period size: 39 Copynumber: 2.0 Consensus size: 39
706239 CCTCAAAAGT
* *
706249 ACAAACACAAAAAAAA-AA-AAACAAAAGCAACACAAAAAA
1 ACAAAAACAAAAAAAACAACAAA-AAAA-CAAAACAAAAAA
706288 ACAAAAACAAAAAAAACAACAAAAAAACAAAACAAAAAA
1 ACAAAAACAAAAAAAACAACAAAAAAACAAAACAAAAAA
706327 A
1 A
706328 GTGCAAAGGC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
39 27 0.75
40 6 0.17
41 3 0.08
ACGTcount: A:0.82, C:0.16, G:0.01, T:0.00
Consensus pattern (39 bp):
ACAAAAACAAAAAAAACAACAAAAAAACAAAACAAAAAA
Found at i:706287 original size:19 final size:17
Alignment explanation
Indices: 706251--706326 Score: 73
Period size: 19 Copynumber: 4.2 Consensus size: 17
706241 TCAAAAGTAC
*
706251 AAACACAAA-AAAAAAA
1 AAACAAAAACAAAAAAA
*
706267 AAACAAAAGCAACACAAAA
1 AAACAAAAACAA-A-AAAA
706286 AAACAAAAACAAAAAAA
1 AAACAAAAACAAAAAAA
706303 ACAACAAAAAAACAAAACAAA
1 A-AAC--AAAAACAAAA-AAA
706324 AAA
1 AAA
706327 AGTGCAAAGG
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
16 7 0.14
17 7 0.14
18 5 0.10
19 15 0.30
20 12 0.24
21 4 0.08
ACGTcount: A:0.83, C:0.16, G:0.01, T:0.00
Consensus pattern (17 bp):
AAACAAAAACAAAAAAA
Found at i:706327 original size:25 final size:25
Alignment explanation
Indices: 706255--706327 Score: 98
Period size: 25 Copynumber: 3.0 Consensus size: 25
706245 AAGTACAAAC
**
706255 ACAA-AAAAAAA-AAAACAAAAGCA
1 ACAACAAAAAAACAAAACAAAAAAA
706278 AC-ACAAAAAAACAAAAACAAAAAAA
1 ACAACAAAAAAAC-AAAACAAAAAAA
706303 ACAACAAAAAAACAAAACAAAAAAA
1 ACAACAAAAAAACAAAACAAAAAAA
706328 GTGCAAAGGC
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
22 1 0.02
23 9 0.20
25 24 0.55
26 10 0.23
ACGTcount: A:0.84, C:0.15, G:0.01, T:0.00
Consensus pattern (25 bp):
ACAACAAAAAAACAAAACAAAAAAA
Found at i:707654 original size:31 final size:31
Alignment explanation
Indices: 707619--707818 Score: 144
Period size: 31 Copynumber: 6.5 Consensus size: 31
707609 TTTTTCAAGT
707619 CCACGACTCAGTGGCAATCTTTTCTCAAAGC
1 CCACGACTCAGTGGCAATCTTTTCTCAAAGC
* *
707650 CCACGACTCCGTGGC-AT-TTTGTCCCAAA-C
1 CCACGACTCAGTGGCAATCTTT-TCTCAAAGC
* * *
707679 TCCACGACTCAGTGGCATTTTTTTCTCCAAAGT
1 -CCACGACTCAGTGGCAATCTTTTCT-CAAAGC
** ** * * *
707712 ATATAACTCAGTGGCAATCTCTTTTTTAAAGT
1 CCACGACTCAGTGGCAATCT-TTTCTCAAAGC
*
707744 CCACGACTCAGTGGC-ATCTTTTCTTCAAAGT
1 CCACGACTCAGTGGCAATCTTTTC-TCAAAGC
* * *
707775 CCACAACTCTGTGGCACTC-TTT-T-AAAGC
1 CCACGACTCAGTGGCAATCTTTTCTCAAAGC
* *
707803 CCACAACTCCGTGGCA
1 CCACGACTCAGTGGCA
707819 CCTTTTTAAA
Statistics
Matches: 135, Mismatches: 25, Indels: 21
0.75 0.14 0.12
Matches are distributed among these distances:
28 19 0.14
29 5 0.04
30 25 0.19
31 43 0.32
32 39 0.29
33 4 0.03
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.30
Consensus pattern (31 bp):
CCACGACTCAGTGGCAATCTTTTCTCAAAGC
Found at i:707686 original size:30 final size:30
Alignment explanation
Indices: 707618--707700 Score: 107
Period size: 30 Copynumber: 2.7 Consensus size: 30
707608 CTTTTTCAAG
*
707618 TCCACGACTCAGTGGCAATCTTTTCTCAAAGC
1 TCCACGACTCAGTGGC-AT-TTTTCCCAAAGC
*
707650 -CCACGACTCCGTGGCATTTTGTCCCAAA-C
1 TCCACGACTCAGTGGCATTTT-TCCCAAAGC
707679 TCCACGACTCAGTGGCATTTTT
1 TCCACGACTCAGTGGCATTTTT
707701 TTCTCCAAAG
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
29 5 0.11
30 27 0.59
31 14 0.30
ACGTcount: A:0.22, C:0.33, G:0.17, T:0.29
Consensus pattern (30 bp):
TCCACGACTCAGTGGCATTTTTCCCAAAGC
Found at i:707806 original size:28 final size:28
Alignment explanation
Indices: 707735--707916 Score: 163
Period size: 28 Copynumber: 6.2 Consensus size: 28
707725 GCAATCTCTT
* * *
707735 TTTTAAAGTCCACGACTCAGTGGCATCTT
1 TTTTAAAGTCCACAACTCCGTGGCA-CTC
*
707764 TTCTTCAAAGTCCACAACTCTGTGGCACTC
1 TT-TT-AAAGTCCACAACTCCGTGGCACTC
*
707794 TTTTAAAGCCCACAACTCCGTGGCAC-C
1 TTTTAAAGTCCACAACTCCGTGGCACTC
*
707821 TTTTTAAACTCCACAACTCCGTGGCACCTTGTTCC
1 -TTTTAAAGTCCACAACTCCGTGGCA-C----T-C
** *
707856 TTTT-AAGTCCACAACTTTGTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACTC
*
707883 TTTT-AAGTCCACAACTCCGTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACTC
707910 TTTTAAA
1 TTTTAAA
707917 CCTACACCTC
Statistics
Matches: 129, Mismatches: 13, Indels: 23
0.78 0.08 0.14
Matches are distributed among these distances:
27 31 0.24
28 45 0.35
29 5 0.04
30 6 0.05
31 19 0.15
32 1 0.01
33 17 0.13
34 4 0.03
35 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.14, T:0.31
Consensus pattern (28 bp):
TTTTAAAGTCCACAACTCCGTGGCACTC
Found at i:707879 original size:89 final size:86
Alignment explanation
Indices: 707734--707917 Score: 251
Period size: 88 Copynumber: 2.1 Consensus size: 86
707724 GGCAATCTCT
* * * *
707734 TTTTTAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCTGTGGCACTCTTTTA
1 TTTTTAAACTCCACAACTCAGTGGCACCTTTTCTTCAAAGTCCACAACTCTGTGGCACCCTTTT-
707799 AAGCCCACAACTCCGTGGCACC
65 AAGCCCACAACTCCGTGGCACC
* ** *
707821 TTTTTAAACTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTTTGTGGCACCCTTT
1 TTTTTAAACTCCACAACTCAGTGGCACCTT-TT-CTTCAAAGTCCACAACTCTGTGGCACCCTTT
*
707886 TAAGTCCACAACTCCGTGGCACC
64 TAAGCCCACAACTCCGTGGCACC
*
707909 CTTTTAAAC
1 TTTTTAAAC
707918 CTACACCTCC
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
87 26 0.31
88 31 0.36
89 28 0.33
ACGTcount: A:0.23, C:0.32, G:0.14, T:0.32
Consensus pattern (86 bp):
TTTTTAAACTCCACAACTCAGTGGCACCTTTTCTTCAAAGTCCACAACTCTGTGGCACCCTTTTA
AGCCCACAACTCCGTGGCACC
Found at i:707927 original size:27 final size:26
Alignment explanation
Indices: 707775--707927 Score: 117
Period size: 27 Copynumber: 5.4 Consensus size: 26
707765 TCTTCAAAGT
* *
707775 CCACAACTCTGTGGCACTCTTTTAAA
1 CCACAACTCCGTGGCACCCTTTTAAA
*
707801 GCCCACAACTCCGTGGCACCTTTTTAAA
1 --CCACAACTCCGTGGCACCCTTTTAAA
*
707829 CTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGT
1 --CCACAACTCCGTGGCA-C-----CCTTTTAA-A
** *
707864 CCACAACTTTGTGGCACCCTTTTAAGT
1 CCACAACTCCGTGGCACCCTTTTAA-A
707891 CCACAACTCCGTGGCACCCTTTTAAA
1 CCACAACTCCGTGGCACCCTTTTAAA
*
707917 CCTACACCTCC
1 CC-ACAACTCC
707928 CTAGCATCTC
Statistics
Matches: 104, Mismatches: 13, Indels: 17
0.78 0.10 0.13
Matches are distributed among these distances:
26 2 0.02
27 40 0.38
28 39 0.38
29 1 0.01
32 1 0.01
33 14 0.13
34 7 0.07
ACGTcount: A:0.23, C:0.36, G:0.12, T:0.29
Consensus pattern (26 bp):
CCACAACTCCGTGGCACCCTTTTAAA
Found at i:707958 original size:88 final size:88
Alignment explanation
Indices: 707775--707967 Score: 205
Period size: 88 Copynumber: 2.2 Consensus size: 88
707765 TCTTCAAAGT
* * *
707775 CCACAACTCTGTGGCACTCTTTTAAAGCCCACAACTCCGTGGCACCTTTTTAAACTCCACAACTC
1 CCACAACTTTGTGGCACCCTTTTAAAGCCCACAACTCCGTGGCACCCTTTTAAACTCCACAACTC
* * * *
707840 CGTGGCACCTTGTTCCTTTTAAGT
66 CCTAGCACCTTGTT-CTTTCAAGG
* * *
707864 CCACAACTTTGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAAC-CTACACCTC
1 CCACAACTTTGTGGCACCCTTTTAAAGCCCACAACTCCGTGGCACCCTTTTAAACTCCACAACTC
*
707927 CCTAGCATCTCTT-TT-TTCTCACTGG
66 CCTAGCA-C-CTTGTTCTT-TCA-AGG
*
707952 CCACAACTTCGTGGCA
1 CCACAACTTTGTGGCA
707968 TCTTTAAGCC
Statistics
Matches: 88, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
86 2 0.02
87 14 0.16
88 48 0.55
89 24 0.27
ACGTcount: A:0.22, C:0.35, G:0.13, T:0.30
Consensus pattern (88 bp):
CCACAACTTTGTGGCACCCTTTTAAAGCCCACAACTCCGTGGCACCCTTTTAAACTCCACAACTC
CCTAGCACCTTGTTCTTTCAAGG
Found at i:708084 original size:43 final size:43
Alignment explanation
Indices: 708021--708474 Score: 539
Period size: 43 Copynumber: 10.1 Consensus size: 43
708011 CCTTTGTCAT
*
708021 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
* * *
708064 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTC
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA---C
*
708110 ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
1 --CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
* * * *
708155 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGTACCTCAT
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGG-----CAC
*
708203 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
* * *
708246 CTTTAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCACCTC
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA---C
*
708292 ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
1 --CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
* * *
708337 CTTTAAGTCCAATATCGCTGGTCTTGAATCAGCATATTGGCACC
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCA-C
*
708381 TTGTCTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCAT
1 ----CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
* * *
708428 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGC
1 CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
708471 CTTT
1 CTTT
708475 GTCATCTTTA
Statistics
Matches: 353, Mismatches: 38, Indels: 40
0.82 0.09 0.09
Matches are distributed among these distances:
43 195 0.55
44 1 0.00
45 2 0.01
46 2 0.01
48 153 0.43
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (43 bp):
CTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:708149 original size:91 final size:91
Alignment explanation
Indices: 707963--708518 Score: 871
Period size: 91 Copynumber: 6.0 Consensus size: 91
707953 CACAACTTCG
* * * * *
707963 TGGCATCTTTAAGCCCAATATCGCTGGTCTTGAATCAACATATTGGCGCCTTTGTCATCTTTAAG
1 TGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC----TCATCTTTAAG
708028 ACCAATGTCGCTGGCCTTGAATCAGCACAT
62 ACCAATGTCGCTGGCCTTGAATCAGCACAT
*
708058 TGGCACCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTCATCTTTAAGACCA
1 TGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCATCTTTAAGACCA
708123 ATGTCGCTGGCCTTGAATCAGCACAT
66 ATGTCGCTGGCCTTGAATCAGCACAT
* *
708149 TGGCACCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGTACCTCATCTTTAAGACCA
1 TGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCATCTTTAAGACCA
708214 ATGTCGCTGGCCTTGAATCAGCACAT
66 ATGTCGCTGGCCTTGAATCAGCACAT
*
708240 TGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCACCTCATCTTTAAGACCA
1 TGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCATCTTTAAGACCA
708305 ATGTCGCTGGCCTTGAATCAGCACAT
66 ATGTCGCTGGCCTTGAATCAGCACAT
* **
708331 TGGCACCTTTAAGTCCAATATCGCTGGTCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCA
1 TGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCATCTTTAAGACCA
*
708396 ATATCGCTGGCCTTGAATCAGCACAT
66 ATGTCGCTGGCCTTGAATCAGCACAT
* *
708422 TGGCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAA-
1 TGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC----TCATCTTTAAG
* *
708486 ACCCAATGTCGTTGGCCTTGAATTAGCACAT
62 A-CCAATGTCGCTGGCCTTGAATCAGCACAT
708517 TG
1 TG
708519 CCATTCTTCT
Statistics
Matches: 433, Mismatches: 23, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
91 352 0.81
94 1 0.00
95 80 0.18
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (91 bp):
TGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCATCTTTAAGACCA
ATGTCGCTGGCCTTGAATCAGCACAT
Found at i:708532 original size:52 final size:54
Alignment explanation
Indices: 708476--708617 Score: 162
Period size: 52 Copynumber: 2.6 Consensus size: 54
708466 GGCGCCTTTG
* *
708476 TCATCTTTAAACCCAATGTCGTTGGCCTTGAATTAGCACATTG-C-CATTCTTC
1 TCATCTTTAAACCCAATGTCGTTGGCCATGAATCAGCACATTGACACATTCTTC
** * * * * * *
708528 TCATCTTTAAGTCTAATGTCGCTGACCGTGAATCAGCACATTGACATCCTTTTTC
1 TCATCTTTAAACCCAATGTCGTTGGCCATGAATCAGCACATTGACA-CATTCTTC
*
708583 TCATCTTTAAACCCAATATCGTTGGCCATGAATCA
1 TCATCTTTAAACCCAATGTCGTTGGCCATGAATCA
708618 ACGTATTGGT
Statistics
Matches: 71, Mismatches: 16, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
52 36 0.51
53 1 0.01
55 34 0.48
ACGTcount: A:0.25, C:0.26, G:0.13, T:0.35
Consensus pattern (54 bp):
TCATCTTTAAACCCAATGTCGTTGGCCATGAATCAGCACATTGACACATTCTTC
Found at i:708615 original size:107 final size:104
Alignment explanation
Indices: 708425--708615 Score: 265
Period size: 104 Copynumber: 1.8 Consensus size: 104
708415 AGCACATTGG
* * * * *
708425 CATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAACCC
1 CATCTTTAAGTCCAATATCGCTGACCGTGAATCAGCACATTGACGCCTTTCTCATCTTTAAACCC
* *
708490 AATGTCGTTGGCCTTGAATTAGCACATTGCCATTCTTCT
66 AATATCGTTGGCCATGAATTAGCACATTGCCATTCTTCT
* * *
708529 CATCTTTAAGTCTAATGTCGCTGACCGTGAATCAGCACATTGACATCCTTTTTCTCATCTTTAAA
1 CATCTTTAAGTCCAATATCGCTGACCGTGAATCAGCACATTGAC-GCC--TTTCTCATCTTTAAA
708594 CCCAATATCGTTGGCCATGAAT
63 CCCAATATCGTTGGCCATGAAT
708616 CAACGTATTG
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
104 38 0.51
105 2 0.03
107 34 0.46
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.35
Consensus pattern (104 bp):
CATCTTTAAGTCCAATATCGCTGACCGTGAATCAGCACATTGACGCCTTTCTCATCTTTAAACCC
AATATCGTTGGCCATGAATTAGCACATTGCCATTCTTCT
Found at i:709327 original size:19 final size:19
Alignment explanation
Indices: 709303--709359 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
709293 TAACTATATT
709303 GATACATAAGTGTTGTATC
1 GATACATAAGTGTTGTATC
709322 GATAC--AA----TGTATC
1 GATACATAAGTGTTGTATC
709335 GATACATAAGTGTTGTATC
1 GATACATAAGTGTTGTATC
709354 GATACA
1 GATACA
709360 ATGTATCGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.34
15 2 0.06
17 2 0.06
19 17 0.53
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (19 bp):
GATACATAAGTGTTGTATC
Found at i:709334 original size:13 final size:13
Alignment explanation
Indices: 709316--709373 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
709306 ACATAAGTGT
709316 TGTATCGATACAA
1 TGTATCGATACAA
709329 TGTATCGATACATAA
1 TGTATCGATAC--AA
709344 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
*
709361 TGTATCGCTACAA
1 TGTATCGATACAA
709374 AACTATTGCC
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:709339 original size:32 final size:32
Alignment explanation
Indices: 709303--709372 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
709293 TAACTATATT
709303 GATACATAAGTGTTGTATCGATACAATGTATC
1 GATACATAAGTGTTGTATCGATACAATGTATC
709335 GATACATAAGTGTTGTATCGATACAATGTATC
1 GATACATAAGTGTTGTATCGATACAATGTATC
*
709367 GCTACA
1 GATACA
709373 AAACTATTGC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (32 bp):
GATACATAAGTGTTGTATCGATACAATGTATC
Found at i:709434 original size:33 final size:33
Alignment explanation
Indices: 709391--709456 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
709381 GCCAAGGAAA
709391 TGTATCGATACATT-A-CTTAATGTATCGATACAT
1 TGTATCGATACATTGATCTT--TGTATCGATACAT
*
709424 TGTATTGATACATTGATCTTTGTATCGATACAT
1 TGTATCGATACATTGATCTTTGTATCGATACAT
709457 CTGGGAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 26 0.87
34 1 0.03
35 3 0.10
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATTGATCTTTGTATCGATACAT
Found at i:715224 original size:105 final size:105
Alignment explanation
Indices: 715038--715230 Score: 273
Period size: 105 Copynumber: 1.8 Consensus size: 105
715028 ATGACACTAA
* *
715038 GTGACACCAAGTCACTCCAAATTTGATCGCCACCAAGGCATCATCATGACATCAACTGACACCAA
1 GTGACACCAAGTCACTCCAAATCTGATCGCCACCAAGACATCATCATGACATCAACTGACACCAA
*
715103 GTCACTCCAAAACTAATTGCCACCATGGCACCATCACAAT
66 GTCACTCCAAAACTAATCGCCACCATGGCACCATCACAAT
* * * * *
715143 GTGACACCAAGTCA-TACCGAATCTGATCGCCACCAAGACATCTTCATGACTTTAAGTGACACCA
1 GTGACACCAAGTCACT-CCAAATCTGATCGCCACCAAGACATCATCATGACATCAACTGACACCA
*
715207 AGTCACT-CAAAGGCTAATCGCCAC
65 AGTCACTCCAAA-ACTAATCGCCAC
715231 AAAGGCATAA
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
104 5 0.06
105 72 0.94
ACGTcount: A:0.34, C:0.32, G:0.14, T:0.20
Consensus pattern (105 bp):
GTGACACCAAGTCACTCCAAATCTGATCGCCACCAAGACATCATCATGACATCAACTGACACCAA
GTCACTCCAAAACTAATCGCCACCATGGCACCATCACAAT
Found at i:715227 original size:55 final size:54
Alignment explanation
Indices: 714989--715238 Score: 206
Period size: 55 Copynumber: 4.6 Consensus size: 54
714979 CTAAGCGATG
* * * * * ** *
714989 CCAAGTCACTCCAAATTTGATCACCACTAAAGTGTCATCATGACACTAAGTGACA
1 CCAAGTCACTCCAAATCTAATCGCCACCAAGGCATC-TCATGACATTAAGTGACA
* * * *
715044 CCAAGTCACTCCAAATTTGATCGCCACCAAGGCATCATCATGACATCAACTGACA
1 CCAAGTCACTCCAAATCTAATCGCCACCAAGGCATC-TCATGACATTAAGTGACA
* * * * *
715099 CCAAGTCACTCCAAAACTAATTGCCACCATGGCA-C-CATCACA--ATGTGACA
1 CCAAGTCACTCCAAATCTAATCGCCACCAAGGCATCTCATGACATTAAGTGACA
* * * *
715149 CCAAGTCA-TACCGAATCTGATCGCCACCAAGACATCTTCATGACTTTAAGTGACA
1 CCAAGTCACT-CCAAATCTAATCGCCACCAAGGCATC-TCATGACATTAAGTGACA
* *
715204 CCAAGTCACT-CAAAGGCTAATCGCCACAAAGGCAT
1 CCAAGTCACTCCAAA-TCTAATCGCCACCAAGGCAT
715239 AATCACTATT
Statistics
Matches: 157, Mismatches: 30, Indels: 16
0.77 0.15 0.08
Matches are distributed among these distances:
49 1 0.01
50 32 0.20
51 1 0.01
52 6 0.04
53 5 0.03
54 4 0.03
55 107 0.68
56 1 0.01
ACGTcount: A:0.35, C:0.31, G:0.14, T:0.20
Consensus pattern (54 bp):
CCAAGTCACTCCAAATCTAATCGCCACCAAGGCATCTCATGACATTAAGTGACA
Found at i:719409 original size:28 final size:27
Alignment explanation
Indices: 719354--719424 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
719344 GCCACCCATT
719354 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
719381 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
* *
719409 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
719425 AGGCTTGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.23, C:0.07, G:0.24, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:721891 original size:21 final size:22
Alignment explanation
Indices: 721862--721907 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
721852 TGTTCAGACA
** *
721862 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
721884 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
721905 AGT
1 AGT
721908 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:723844 original size:28 final size:27
Alignment explanation
Indices: 723789--723859 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
723779 GCTACCCATT
723789 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
723816 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
* *
723844 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
723860 AGGCTTGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.23, C:0.07, G:0.24, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:727449 original size:2 final size:2
Alignment explanation
Indices: 727442--727466 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
727432 GAATGCCTAG
727442 CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA C
727467 CCCTTTCATC
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:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:729578 original size:13 final size:13
Alignment explanation
Indices: 729560--729585 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
729550 GTGACGACAG
729560 GTTGGTCACTTCC
1 GTTGGTCACTTCC
729573 GTTGGTCACTTCC
1 GTTGGTCACTTCC
729586 TTTGCCTGGA
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:0.08, C:0.31, G:0.23, T:0.38
Consensus pattern (13 bp):
GTTGGTCACTTCC
Found at i:733101 original size:16 final size:16
Alignment explanation
Indices: 733081--733120 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
733071 GGTCTTTTAA
733081 GGTTCGAGCCTTTTC-
1 GGTTCGAGCCTTTTCT
*
733096 GAGTTCGAGCTTTTTCT
1 G-GTTCGAGCCTTTTCT
733113 GGTTCGAG
1 GGTTCGAG
733121 TTCGAGTTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 20 0.91
17 1 0.05
ACGTcount: A:0.10, C:0.20, G:0.30, T:0.40
Consensus pattern (16 bp):
GGTTCGAGCCTTTTCT
Found at i:733291 original size:14 final size:16
Alignment explanation
Indices: 733272--733304 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
733262 AATTTTGTTA
733272 TAATATA-TTATTT-T
1 TAATATATTTATTTAT
733286 TAATATATTTATTTAT
1 TAATATATTTATTTAT
733302 TAA
1 TAA
733305 AATCTATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 6 0.35
16 4 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TAATATATTTATTTAT
Found at i:733627 original size:2 final size:2
Alignment explanation
Indices: 733620--733644 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
733610 TTTATCATTG
733620 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
733645 CACATTTTAA
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:734261 original size:17 final size:18
Alignment explanation
Indices: 734236--734269 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
734226 ATTTTTTTTT
734236 TAAAAAATTT-AAATATA
1 TAAAAAATTTGAAATATA
*
734253 TAAATAATTTGAAATAT
1 TAAAAAATTTGAAATAT
734270 GATTTTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
TAAAAAATTTGAAATATA
Found at i:734629 original size:40 final size:40
Alignment explanation
Indices: 734574--734666 Score: 163
Period size: 40 Copynumber: 2.4 Consensus size: 40
734564 TATGTGTATG
*
734574 TATATATATATATATATATGTGTGTGTGTGTGTGTTTATA
1 TATATATATATATATATATGTGTGTGTGTGTGTGTATATA
734614 TATATATATATATATATATGTGTGTGTGTGTGTGTATATA
1 TATATATATATATATATATGTGTGTGTGTGTGTGTATATA
734654 -ATATA-ATATATAT
1 TATATATATATATAT
734667 TATAAAGTTG
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
38 8 0.15
39 5 0.10
40 39 0.75
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (40 bp):
TATATATATATATATATATGTGTGTGTGTGTGTGTATATA
Found at i:739875 original size:147 final size:147
Alignment explanation
Indices: 739608--739887 Score: 438
Period size: 147 Copynumber: 1.9 Consensus size: 147
739598 GTGGCAGGCA
*
739608 CTAGCATTGATTTAGTTGAATTTAACTCATGGTAAATTGCCAATCATTTTTTCATATTTGAATAA
1 CTAGCATTGATTTAGTTGAATTTAACCCATGGTAAATTGCCAATCATTTTTTCATATTTGAATAA
* * * * *
739673 TATTCGATTCAGGTATTATAATTATTATCTACATCTACTTATACAAGTAATGGTTTTGAATGCTT
66 TATTCAATTAAGATATTATAATTACTATCTACATCTACCTATACAAGTAATGGTTTTGAATGCTT
739738 GAAAATGCTTGAATTAT
131 GAAAATGCTTGAATTAT
* * *
739755 CTAGCATTGATTTAGTTGAATTTCACCCATGGTAAGATTGTCAATTA-TTTTTCGA-ATTTGAAT
1 CTAGCATTGATTTAGTTGAATTTAACCCATGGTAA-ATTGCCAATCATTTTTTC-ATATTTGAAT
*
739818 AATATTCAATTAAGATATTATAATTACTATCTACATCTACCTATACAAGTAATGGTTTTGAATGT
64 AATATTCAATTAAGATATTATAATTACTATCTACATCTACCTATACAAGTAATGGTTTTGAATGC
739883 TTGAA
129 TTGAA
739888 TTCATTATTG
Statistics
Matches: 121, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
147 111 0.92
148 10 0.08
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (147 bp):
CTAGCATTGATTTAGTTGAATTTAACCCATGGTAAATTGCCAATCATTTTTTCATATTTGAATAA
TATTCAATTAAGATATTATAATTACTATCTACATCTACCTATACAAGTAATGGTTTTGAATGCTT
GAAAATGCTTGAATTAT
Found at i:740448 original size:26 final size:26
Alignment explanation
Indices: 740416--740466 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
740406 ATAATATTTA
* *
740416 TATAAATATTTTA-TTATAATATCATT
1 TATAAATAATATATTTAT-ATATCATT
740442 TATAAATAATATATTTATATATCAT
1 TATAAATAATATATTTATATATCAT
740467 ATATTACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (26 bp):
TATAAATAATATATTTATATATCATT
Found at i:740457 original size:15 final size:15
Alignment explanation
Indices: 740409--740471 Score: 78
Period size: 15 Copynumber: 4.3 Consensus size: 15
740399 AGAATACATA
740409 ATATTTATATA-AAT
1 ATATTTATATATAAT
740423 AT-TTTAT-TATAAT
1 ATATTTATATATAAT
*
740436 ATCATTTATAAATAAT
1 AT-ATTTATATATAAT
*
740452 ATATTTATATATCAT
1 ATATTTATATATAAT
740467 ATATT
1 ATATT
740472 ACTTAACATT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
12 2 0.05
13 10 0.24
14 2 0.05
15 21 0.50
16 7 0.17
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.52
Consensus pattern (15 bp):
ATATTTATATATAAT
Found at i:740752 original size:14 final size:15
Alignment explanation
Indices: 740728--740761 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
740718 GTTAGACATT
740728 CTAATTAACTTGAAA
1 CTAATTAACTTGAAA
*
740743 -TAATTTACTTGAAA
1 CTAATTAACTTGAAA
740757 CTAAT
1 CTAAT
740762 AGTTAAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (15 bp):
CTAATTAACTTGAAA
Found at i:747758 original size:2 final size:2
Alignment explanation
Indices: 747743--747774 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
747733 AACAGTTATC
747743 TA TA -A TA T- 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 TA TA TA TA
747775 CACACATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:747758 original size:12 final size:13
Alignment explanation
Indices: 747738--747774 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
747728 GGTTCAACAG
*
747738 TTATCTATA-ATA
1 TTATATATATATA
747750 TTATATATATATA
1 TTATATATATATA
747763 -TATATATATATA
1 TTATATATATATA
747775 CACACATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 20 0.87
13 3 0.13
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (13 bp):
TTATATATATATA
Found at i:749983 original size:22 final size:25
Alignment explanation
Indices: 749950--750002 Score: 78
Period size: 22 Copynumber: 2.3 Consensus size: 25
749940 TTCATCTCTA
749950 ATTT-ATCAAAAAAATATAT-TTT-
1 ATTTAATCAAAAAAATATATATTTC
749972 ATTTAATC-AAAAAATATATATTTC
1 ATTTAATCAAAAAAATATATATTTC
749996 ATTTAAT
1 ATTTAAT
750003 TGAGGTTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 15 0.54
23 6 0.21
24 7 0.25
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (25 bp):
ATTTAATCAAAAAAATATATATTTC
Found at i:749990 original size:24 final size:23
Alignment explanation
Indices: 749950--750002 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 23
749940 TTCATCTCTA
*
749950 ATTT-ATCAAAAAAATATATTTT
1 ATTTAATCAAAAAAATATATTTC
749972 ATTTAATCAAAAAATATATATTTC
1 ATTTAATCAAAAAA-ATATATTTC
749996 ATTTAAT
1 ATTTAAT
750003 TGAGGTTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 4 0.14
23 9 0.32
24 15 0.54
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (23 bp):
ATTTAATCAAAAAAATATATTTC
Found at i:751213 original size:2 final size:2
Alignment explanation
Indices: 751200--751234 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
751190 CTTATAGAAC
* *
751200 AT AT AT AC AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
751235 CATAAAGAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:752638 original size:23 final size:23
Alignment explanation
Indices: 752605--752668 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
752595 CACACTTATC
*
752605 AAAATTTTTTTTAAAAAAAAAGA
1 AAAATTATTTTTAAAAAAAAAGA
* ** *
752628 ATAATTATTTTTTTAAAAAAATA
1 AAAATTATTTTTAAAAAAAAAGA
*
752651 AAAATTTATCTTTAAAAA
1 AAAA-TTATTTTTAAAAA
752669 TTTTGAGATT
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
23 21 0.68
24 10 0.32
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
AAAATTATTTTTAAAAAAAAAGA
Found at i:754835 original size:39 final size:39
Alignment explanation
Indices: 754792--754873 Score: 155
Period size: 39 Copynumber: 2.1 Consensus size: 39
754782 TGGTGGGACG
754792 AAATTAATATTTATCAACTTTAGAGTGTGATAATGAAGA
1 AAATTAATATTTATCAACTTTAGAGTGTGATAATGAAGA
*
754831 AAATTAATATTTATCAATTTTAGAGTGTGATAATGAAGA
1 AAATTAATATTTATCAACTTTAGAGTGTGATAATGAAGA
754870 AAAT
1 AAAT
754874 GAAACGATAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.45, C:0.04, G:0.15, T:0.37
Consensus pattern (39 bp):
AAATTAATATTTATCAACTTTAGAGTGTGATAATGAAGA
Found at i:755133 original size:51 final size:50
Alignment explanation
Indices: 755067--755201 Score: 157
Period size: 51 Copynumber: 2.7 Consensus size: 50
755057 TAATTAGATT
* * *
755067 TATCGATACATTAAAAAATATATCGATACATTT-GAGTTAGAA-CTCAAAATG
1 TATCGATACAATAAAAAATGTATCGATACATTTGGA-TCA-AACCT-AAAATG
* * * *
755118 TATTGATACAATAAAAAATGTATTGATACAATTGGATCAAACCTAGAATG
1 TATCGATACAATAAAAAATGTATCGATACATTTGGATCAAACCTAAAATG
755168 TATCGATACAATAAAAAAATGTATCGATACATTT
1 TATCGATACAAT-AAAAAATGTATCGATACATTT
755202 TCTTTTCATA
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
50 18 0.25
51 51 0.72
52 2 0.03
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.31
Consensus pattern (50 bp):
TATCGATACAATAAAAAATGTATCGATACATTTGGATCAAACCTAAAATG
Found at i:755137 original size:20 final size:20
Alignment explanation
Indices: 755112--755149 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
755102 GTTAGAACTC
755112 AAAATGTATTGATACAATAA
1 AAAATGTATTGATACAATAA
755132 AAAATGTATTGATACAAT
1 AAAATGTATTGATACAAT
755150 TGGATCAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.53, C:0.05, G:0.11, T:0.32
Consensus pattern (20 bp):
AAAATGTATTGATACAATAA
Found at i:755290 original size:24 final size:24
Alignment explanation
Indices: 755245--755302 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
755235 TCCTATATTG
*
755245 ATGTATCGATACATTCACTTATGT
1 ATGTATCGATACATTCAATTATGT
* *
755269 ATGTATCGATGCATTTAATTAT-T
1 ATGTATCGATACATTCAATTATGT
755292 A--TATCGATACA
1 ATGTATCGATACA
755303 AATTATAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 9 0.30
23 2 0.07
24 19 0.63
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (24 bp):
ATGTATCGATACATTCAATTATGT
Found at i:759212 original size:13 final size:13
Alignment explanation
Indices: 759190--759245 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
759180 ATAAATTTTT
*
759190 ATAAAAATTAATG
1 ATAAAAATTAATA
*
759203 ATAAATATTAATA
1 ATAAAAATTAATA
*
759216 ATAAAAAAATTAAAA
1 AT--AAAAATTAATA
759231 ATATAAAA-TAATA
1 ATA-AAAATTAATA
759244 AT
1 AT
759246 TATAACATGT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 20 0.57
14 4 0.11
15 11 0.31
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (13 bp):
ATAAAAATTAATA
Found at i:759805 original size:2 final size:2
Alignment explanation
Indices: 759798--759824 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
759788 ACCATTCTAA
759798 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 A
759825 CATCTCAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:761081 original size:15 final size:15
Alignment explanation
Indices: 761063--761096 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
761053 AATATTAGTT
**
761063 TATATATCATTTATA
1 TATATATCAAATATA
761078 TATATATCAAATATA
1 TATATATCAAATATA
761093 TATA
1 TATA
761097 CTAAAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (15 bp):
TATATATCAAATATA
Found at i:762777 original size:2 final size:2
Alignment explanation
Indices: 762770--762802 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
762760 TGAGTCTAAA
762770 AT AT 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 AT AT A
762803 CAGGAAAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:764158 original size:20 final size:21
Alignment explanation
Indices: 764126--764172 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
764116 TTACACTATA
* *
764126 ATATTATATATATTTATTCTTT
1 ATATGATATATATATATT-TTT
764148 ATATGATATATATATATTTTT
1 ATATGATATATATATATTTTT
764169 ATAT
1 ATAT
764173 AATAAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (21 bp):
ATATGATATATATATATTTTT
Found at i:764220 original size:26 final size:24
Alignment explanation
Indices: 764158--764231 Score: 71
Period size: 26 Copynumber: 3.0 Consensus size: 24
764148 ATATGATATA
*
764158 TATATATTTTTATATAATAAAAA-T
1 TATATA-TATTATATAATAAAAACT
*
764182 TACATA-ATGTATATAAGTATAAAACT
1 TATATATAT-TATATAA-TA-AAAACT
764208 TATATATATTATATAATTAAAAAC
1 TATATATATTATATAA-TAAAAAC
764232 AAATTGAACC
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
22 1 0.02
23 7 0.17
24 7 0.17
25 9 0.22
26 15 0.37
27 2 0.05
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (24 bp):
TATATATATTATATAATAAAAACT
Found at i:766305 original size:47 final size:46
Alignment explanation
Indices: 766251--766349 Score: 171
Period size: 47 Copynumber: 2.1 Consensus size: 46
766241 AAAAGGGAAA
* *
766251 CATAGTTGCCTATATATTGCGGTAACCATTCATACTTATGAATTCAG
1 CATAGTTGCCTACATATTGCGGTAACCATCCATACTTA-GAATTCAG
766298 CATAGTTGCCTACATATTGCGGTAACCATCCATACTTAGAATTCAG
1 CATAGTTGCCTACATATTGCGGTAACCATCCATACTTAGAATTCAG
766344 CATAGT
1 CATAGT
766350 GAAGAAATCT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
46 14 0.28
47 36 0.72
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.33
Consensus pattern (46 bp):
CATAGTTGCCTACATATTGCGGTAACCATCCATACTTAGAATTCAG
Found at i:766960 original size:25 final size:26
Alignment explanation
Indices: 766891--766970 Score: 119
Period size: 26 Copynumber: 3.1 Consensus size: 26
766881 ATTCTATTAT
766891 GAGAAAGAATTGAAGAGGATACAAGA
1 GAGAAAGAATTGAAGAGGATACAAGA
766917 GAGAAAGAATTGAAGAGGATACAAGA
1 GAGAAAGAATTGAAGAGGATACAAGA
* *
766943 GAGAATG-CTTG-AGAAGGATACAAGA
1 GAGAAAGAATTGAAG-AGGATACAAGA
766968 GAG
1 GAG
766971 GGATGAGGGA
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
24 2 0.04
25 17 0.33
26 32 0.63
ACGTcount: A:0.50, C:0.05, G:0.33, T:0.12
Consensus pattern (26 bp):
GAGAAAGAATTGAAGAGGATACAAGA
Found at i:767138 original size:27 final size:28
Alignment explanation
Indices: 767077--767147 Score: 108
Period size: 27 Copynumber: 2.6 Consensus size: 28
767067 AAACAAGCCT
* *
767077 CCATATTTGACAAATACAAAGAAAACCA
1 CCATTTTTGACAAACACAAAGAAAACCA
*
767105 CCATTTTTGACAAACACAAA-ATAACCA
1 CCATTTTTGACAAACACAAAGAAAACCA
767132 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
767148 AATGGGTGGC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 22 0.55
28 18 0.45
ACGTcount: A:0.48, C:0.24, G:0.06, T:0.23
Consensus pattern (28 bp):
CCATTTTTGACAAACACAAAGAAAACCA
Found at i:771578 original size:20 final size:20
Alignment explanation
Indices: 771552--771598 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
771542 AGAATGCTTG
771552 AGAGGGATACAAGAGAGGGA
1 AGAGGGATACAAGAGAGGGA
* * **
771572 TGAGGGATGCTTGAGAGGGA
1 AGAGGGATACAAGAGAGGGA
771592 AGAGGGA
1 AGAGGGA
771599 GCCTCTATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.04, G:0.49, T:0.11
Consensus pattern (20 bp):
AGAGGGATACAAGAGAGGGA
Found at i:771748 original size:24 final size:27
Alignment explanation
Indices: 771680--771745 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 27
771670 AGCCTTCATA
*
771680 TTTGACAAATACAAAGGA-AACCACCATT
1 TTTGACAAACACAAA--ATAACCACCATT
771708 TTTGACAAACACAAAATAACCACCATT
1 TTTGACAAACACAAAATAACCACCATT
771735 TTTGACAAACA
1 TTTGACAAACA
771746 AATGGGTGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
26 1 0.03
27 21 0.58
28 14 0.39
ACGTcount: A:0.47, C:0.23, G:0.08, T:0.23
Consensus pattern (27 bp):
TTTGACAAACACAAAATAACCACCATT
Found at i:772899 original size:2 final size:2
Alignment explanation
Indices: 772894--772931 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
772884 TGAACACATA
*
772894 AT AT AT AT AT AT AT AT A- AC AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
772932 GCACATAAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:772911 original size:17 final size:17
Alignment explanation
Indices: 772891--772924 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
772881 ACATGAACAC
*
772891 ATAATATATATATATAT
1 ATAACATATATATATAT
772908 ATAACATATATATATAT
1 ATAACATATATATATAT
772925 TATATATGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAACATATATATATAT
Found at i:772929 original size:13 final size:12
Alignment explanation
Indices: 772894--772931 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
772884 TGAACACATA
772894 ATATATATATAT
1 ATATATATATAT
*
772906 ATATA-ACATAT
1 ATATATATATAT
772917 ATATATAT-TAT
1 ATATATATATAT
772928 ATAT
1 ATAT
772932 GCACATAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 17 0.74
12 6 0.26
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (12 bp):
ATATATATATAT
Found at i:774795 original size:6 final size:6
Alignment explanation
Indices: 774784--774808 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
774774 AAAGATTTTT
774784 TAATTA TAATTA TAATTA TAATTA T
1 TAATTA TAATTA TAATTA TAATTA T
774809 TATTTTTAAA
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:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAATTA
Found at i:775424 original size:23 final size:23
Alignment explanation
Indices: 775398--775442 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
775388 TAATAGAATA
775398 AAAAATCA-TTAATTATTTAAAT
1 AAAAATCAGTTAATTATTTAAAT
*
775420 AAAAATTAGTTAATTATTTAAAT
1 AAAAATCAGTTAATTATTTAAAT
775443 GTTTAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
AAAAATCAGTTAATTATTTAAAT
Found at i:775521 original size:17 final size:17
Alignment explanation
Indices: 775468--775524 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
775458 AATTCCTAAT
* *
775468 AAAAATAGTTAATATTA
1 AAAAAGAGTTTATATTA
* *
775485 ATAAAAGA-TATATCAATA
1 A-AAAAGAGTTTAT-ATTA
775503 AAAAAGAGTTTATATTA
1 AAAAAGAGTTTATATTA
775520 AAAAA
1 AAAAA
775525 ATTCTGAGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
17 18 0.58
18 13 0.42
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (17 bp):
AAAAAGAGTTTATATTA
Found at i:775916 original size:6 final size:6
Alignment explanation
Indices: 775905--775929 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
775895 AAATCAATTA
775905 AAATAT AAATAT AAATAT AAATAT A
1 AAATAT AAATAT AAATAT AAATAT A
775930 TTTTTTAAAT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATAT
Found at i:775938 original size:19 final size:19
Alignment explanation
Indices: 775916--775977 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
775906 AATATAAATA
775916 TAAATATAAATATATTTTT
1 TAAATATAAATATATTTTT
* * *
775935 TAAATTTTAATAT-TATTT
1 TAAATATAAATATATTTTT
*
775953 TAAATAATAAA-ATAAATTTT
1 TAAAT-ATAAATAT-ATTTTT
775973 TAAAT
1 TAAAT
775978 TAATCGAACT
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
18 11 0.33
19 14 0.42
20 8 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TAAATATAAATATATTTTT
Found at i:779319 original size:2 final size:2
Alignment explanation
Indices: 779312--779342 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
779302 TTCCAAAATC
779312 TA 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 TA T
779343 TAATAATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:779604 original size:19 final size:18
Alignment explanation
Indices: 779580--779620 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
779570 TTCTATTTTC
* *
779580 TAATATTTTATTTTTTAT
1 TAATATTTAATTATTTAT
779598 ATAATATTTAATTATTTAT
1 -TAATATTTAATTATTTAT
779617 TAAT
1 TAAT
779621 TTCACCCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TAATATTTAATTATTTAT
Found at i:780696 original size:2 final size:2
Alignment explanation
Indices: 780684--780724 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
780674 ATCGAATAGC
*
780684 AG AG AG CG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
780725 TGGGTTGGTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.02, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:781520 original size:16 final size:15
Alignment explanation
Indices: 781499--781557 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
781489 TTTTGAATAG
781499 TTTCAAATTTTAATTA
1 TTTCAAA-TTTAATTA
*
781515 TTTCAAATATAATT-
1 TTTCAAATTTAATTA
**
781529 TTT-TTATTTAAATTA
1 TTTCAAATTT-AATTA
781544 TTTCAAATTTAATT
1 TTTCAAATTTAATT
781558 CGTGTTCGAG
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
13 3 0.09
14 7 0.21
15 13 0.38
16 11 0.32
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTCAAATTTAATTA
Found at i:782257 original size:19 final size:18
Alignment explanation
Indices: 782229--782269 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
782219 GTTAATAATT
782229 TATATTATATAATTTTAA
1 TATATTATATAATTTTAA
* *
782247 TATATTTATATTATTTTTA
1 TATA-TTATATAATTTTAA
782266 TATA
1 TATA
782270 AATCATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TATATTATATAATTTTAA
Found at i:789001 original size:16 final size:16
Alignment explanation
Indices: 788960--789001 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
788950 ACATAATTTT
788960 TAAAATAAAAAATATA
1 TAAAATAAAAAATATA
* *
788976 TATAATAAAAATTATA
1 TAAAATAAAAAATATA
*
788992 -AAAATCAAAA
1 TAAAATAAAAA
789002 TACTTTAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAAATAAAAAATATA
Found at i:789267 original size:33 final size:33
Alignment explanation
Indices: 789229--789319 Score: 108
Period size: 25 Copynumber: 3.0 Consensus size: 33
789219 CAAAAAAGTA
*
789229 ATATATTAGTAGGTAATAATAGGTATAAGTGAT
1 ATATATAAGTAGGTAATAATAGGTATAAGTGAT
*
789262 ATATATAAGTAAGTAATAAT-GG-----GT-A-
1 ATATATAAGTAGGTAATAATAGGTATAAGTGAT
789287 ATATATAAGTAGGTAATAATAGGTATAAGTGAT
1 ATATATAAGTAGGTAATAATAGGTATAAGTGAT
789320 GTATCAATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 16
0.71 0.05 0.24
Matches are distributed among these distances:
25 19 0.40
26 3 0.06
27 2 0.04
31 2 0.04
32 3 0.06
33 18 0.38
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (33 bp):
ATATATAAGTAGGTAATAATAGGTATAAGTGAT
Found at i:792481 original size:16 final size:15
Alignment explanation
Indices: 792462--792501 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
792452 TTCGGATTCA
792462 AACTTTTATGGGTTTG
1 AACTTTT-TGGGTTTG
*
792478 AACTTTTTCGGGTTCG
1 AACTTTTT-GGGTTTG
792494 AACTTTTT
1 AACTTTTT
792502 TGAGTTTGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 1 0.05
16 21 0.95
ACGTcount: A:0.17, C:0.12, G:0.20, T:0.50
Consensus pattern (15 bp):
AACTTTTTGGGTTTG
Found at i:792520 original size:32 final size:32
Alignment explanation
Indices: 792441--792526 Score: 100
Period size: 32 Copynumber: 2.7 Consensus size: 32
792431 ACTCATTCGG
** * * *
792441 GTTTGAACTCGTTCGGATTCAAACTTTTATGG
1 GTTTGAACTTATTCGGGTTCGAACTTTTATGA
* *
792473 GTTTGAACTTTTTCGGGTTCGAACTTTTTTGA
1 GTTTGAACTTATTCGGGTTCGAACTTTTATGA
*
792505 GTTTGAGCTTATTCGGGTTCGA
1 GTTTGAACTTATTCGGGTTCGA
792527 GTTTAGGTCG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.17, C:0.14, G:0.24, T:0.44
Consensus pattern (32 bp):
GTTTGAACTTATTCGGGTTCGAACTTTTATGA
Found at i:792652 original size:27 final size:29
Alignment explanation
Indices: 792622--792686 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 29
792612 TTTTCTTAAA
*
792622 AAGTAAA-TTATTAAATTATTA-ATTTTT
1 AAGTAAATTTATTAAACTATTATATTTTT
*
792649 AAGTAAATTTTTATTATACTATTATATTTTT
1 AAGTAAA--TTTATTAAACTATTATATTTTT
792680 AAGTAAA
1 AAGTAAA
792687 ATTTTAAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 7 0.22
30 12 0.38
31 13 0.41
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.51
Consensus pattern (29 bp):
AAGTAAATTTATTAAACTATTATATTTTT
Found at i:792672 original size:30 final size:31
Alignment explanation
Indices: 792629--792692 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
792619 AAAAAGTAAA
* *
792629 TTATTAAATTATTA-ATTTTTAAGTAAATTT
1 TTATTAAACTATTATATTTTTAAGTAAAATT
*
792659 TTATTATACTATTATATTTTTAAGTAAAATT
1 TTATTAAACTATTATATTTTTAAGTAAAATT
792690 TTA
1 TTA
792693 AGTAAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 12 0.40
31 18 0.60
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (31 bp):
TTATTAAACTATTATATTTTTAAGTAAAATT
Found at i:793624 original size:16 final size:16
Alignment explanation
Indices: 793605--793647 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
793595 GTTTGGGTTC
*
793605 TTTCGAGTTCGAGTTT
1 TTTCGAGTTCGAGCTT
* *
793621 TTTCAAGTTCGGGCTT
1 TTTCGAGTTCGAGCTT
*
793637 TTTCGGGTTCG
1 TTTCGAGTTCG
793648 GACTATCTTG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.09, C:0.16, G:0.28, T:0.47
Consensus pattern (16 bp):
TTTCGAGTTCGAGCTT
Found at i:793972 original size:20 final size:20
Alignment explanation
Indices: 793949--793988 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
793939 ATTTATTTAT
793949 TTTTAAATGCTTTTAGACTA
1 TTTTAAATGCTTTTAGACTA
793969 TTTTAAATGCTTTTAGACTA
1 TTTTAAATGCTTTTAGACTA
793989 AGTAATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTTAAATGCTTTTAGACTA
Found at i:794914 original size:25 final size:26
Alignment explanation
Indices: 794886--794940 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
794876 TCATTTCCTA
*
794886 AATCA-TTTAATATAAAAGA-AGATTT
1 AATCATTTTAAGA-AAAAGATAGATTT
*
794911 AATCATTTTAAGAAAATGATAGATTT
1 AATCATTTTAAGAAAAAGATAGATTT
794937 AATC
1 AATC
794941 TATGTTTCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.36
Consensus pattern (26 bp):
AATCATTTTAAGAAAAAGATAGATTT
Found at i:797447 original size:20 final size:20
Alignment explanation
Indices: 797422--797496 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
797412 TTTTACTCAG
797422 ATGTATCGATATATTTTTCA
1 ATGTATCGATATATTTTTCA
* * * * *
797442 ATGTATAGATACATGTATGA
1 ATGTATCGATATATTTTTCA
*
797462 ATGTATTGATATATTTTTCA
1 ATGTATCGATATATTTTTCA
*
797482 ATGTATCAATATATT
1 ATGTATCGATATATT
797497 CTGTTTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.47
Consensus pattern (20 bp):
ATGTATCGATATATTTTTCA
Found at i:797544 original size:19 final size:19
Alignment explanation
Indices: 797516--797564 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
797506 TACCCAGATG
797516 TATCGATACATTTTCAATA
1 TATCGATACATTTTCAATA
* *
797535 TATTGATACATTTTCAATG
1 TATCGATACATTTTCAATA
797554 TATCGATACAT
1 TATCGATACAT
797565 CTAGTTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (19 bp):
TATCGATACATTTTCAATA
Found at i:801244 original size:26 final size:26
Alignment explanation
Indices: 801215--801267 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
801205 TTCTTTGTTA
801215 TGCTGGTAGAATTCCGAAAAGAAATT
1 TGCTGGTAGAATTCCGAAAAGAAATT
* * **
801241 TGCTGTTGGAATTTTGAAAAGAAATT
1 TGCTGGTAGAATTCCGAAAAGAAATT
801267 T
1 T
801268 TCTCACAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.36, C:0.08, G:0.23, T:0.34
Consensus pattern (26 bp):
TGCTGGTAGAATTCCGAAAAGAAATT
Found at i:802470 original size:21 final size:21
Alignment explanation
Indices: 802420--802470 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
802410 CGTTCTTTCA
*
802420 ATTCAAATACGCATATAAAAT
1 ATTCAAATACGCATAGAAAAT
*
802441 ATTCTAATAC-CATAGAGGAAAT
1 ATTCAAATACGCATAGA--AAAT
802463 -TTCAAATA
1 ATTCAAATA
802471 GGTTTGAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 5 0.20
21 16 0.64
22 4 0.16
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.29
Consensus pattern (21 bp):
ATTCAAATACGCATAGAAAAT
Found at i:802705 original size:26 final size:26
Alignment explanation
Indices: 802676--802734 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
802666 AACTTGGAAA
802676 CATCTTTAT-TATCTTTTCATTCAGCT
1 CATCTTTATAT-TCTTTTCATTCAGCT
***
802702 CATCGACATATTCTTTTCATTCAGCT
1 CATCTTTATATTCTTTTCATTCAGCT
802728 CATCTTT
1 CATCTTT
802735 TCATCATGTA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
26 25 0.96
27 1 0.04
ACGTcount: A:0.20, C:0.25, G:0.05, T:0.49
Consensus pattern (26 bp):
CATCTTTATATTCTTTTCATTCAGCT
Found at i:806228 original size:22 final size:23
Alignment explanation
Indices: 806186--806233 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
806176 GTTTTTACGT
*
806186 TTTATTTTATAAATTTATTATAA
1 TTTAATTTATAAATTTATTATAA
* *
806209 TTTAATTTA-AAATTTTTTATCA
1 TTTAATTTATAAATTTATTATAA
806231 TTT
1 TTT
806234 TCTCACTGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTAATTTATAAATTTATTATAA
Found at i:806431 original size:43 final size:43
Alignment explanation
Indices: 806345--806431 Score: 97
Period size: 43 Copynumber: 2.0 Consensus size: 43
806335 AATAATATAA
* * *
806345 ATTACATATATTTAATTTTTTTATTTTACAAGAATAACTACTT
1 ATTACATATATTTAATTTTTTTAATTTAAAAGAATAACCACTT
* *
806388 ATTACA-AT-TTTAATTTTTTTTAATTTAAATATAATAGCCACTT
1 ATTACATATATTTAA-TTTTTTTAATTTAAA-AGAATAACCACTT
806431 A
1 A
806432 CTAAAAACTC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
41 5 0.14
42 15 0.41
43 17 0.46
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (43 bp):
ATTACATATATTTAATTTTTTTAATTTAAAAGAATAACCACTT
Found at i:806941 original size:17 final size:18
Alignment explanation
Indices: 806913--806958 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
806903 AAAAATTATT
806913 TATTTATTATTTTA-AAAA
1 TATTT-TTATTTTATAAAA
* *
806931 TATTTTTATTTTATATAT
1 TATTTTTATTTTATAAAA
806949 TATTTTTATT
1 TATTTTTATT
806959 AAATTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TATTTTTATTTTATAAAA
Found at i:807695 original size:18 final size:18
Alignment explanation
Indices: 807672--807709 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
807662 CTTTCCAACG
807672 TTTTGG-TTTTCATTTCTT
1 TTTTGGCTTTTC-TTTCTT
807690 TTTTGGCCTTTTCTTTCTT
1 TTTTGG-CTTTTCTTTCTT
807709 T
1 T
807710 GGCTTTCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 7 0.39
20 5 0.28
ACGTcount: A:0.03, C:0.16, G:0.11, T:0.71
Consensus pattern (18 bp):
TTTTGGCTTTTCTTTCTT
Found at i:812768 original size:38 final size:38
Alignment explanation
Indices: 812716--812824 Score: 173
Period size: 38 Copynumber: 2.9 Consensus size: 38
812706 CACCAGCCAC
* * **
812716 CGGCTAATTCCAAATTGAATTCTCTAGTCGTCAGCCGT
1 CGGCCAATTTCAAATTGAATTCTCTAACCGTCAGCCGT
812754 CGGCCAATTTCAAATTGAATTCTCTAACCGTCAGCCGT
1 CGGCCAATTTCAAATTGAATTCTCTAACCGTCAGCCGT
*
812792 CAGCCAATTTCAAATTGAATTCTCTAACCGTCA
1 CGGCCAATTTCAAATTGAATTCTCTAACCGTCA
812825 ACTAATTCAA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 66 1.00
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (38 bp):
CGGCCAATTTCAAATTGAATTCTCTAACCGTCAGCCGT
Found at i:822297 original size:19 final size:20
Alignment explanation
Indices: 822270--822314 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
822260 TTTCTTTTAT
* *
822270 AAAACTTATAT-TTACAAGC
1 AAAAATTATATCTCACAAGC
*
822289 AAAAATTATATCTCATAAGC
1 AAAAATTATATCTCACAAGC
822309 AAAAAT
1 AAAAAT
822315 ATACATTGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.53, C:0.13, G:0.04, T:0.29
Consensus pattern (20 bp):
AAAAATTATATCTCACAAGC
Found at i:823724 original size:17 final size:18
Alignment explanation
Indices: 823693--823737 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
823683 AAATGATGAG
*
823693 TAGTCTTTTAGTGGAT-AT
1 TAGT-TTTTAATGGATAAT
823711 TAGTTTTTAATGGATAAT
1 TAGTTTTTAATGGATAAT
*
823729 TATTTTTTA
1 TAGTTTTTA
823738 CAAGTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.27, C:0.02, G:0.16, T:0.56
Consensus pattern (18 bp):
TAGTTTTTAATGGATAAT
Found at i:828265 original size:18 final size:18
Alignment explanation
Indices: 828244--828293 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
828234 CCAATTCATA
828244 AAAATTAAAAAATTTTAT
1 AAAATTAAAAAATTTTAT
* *
828262 AAAATTAGATAATTTTAT
1 AAAATTAAAAAATTTTAT
*
828280 AAATTTTAAAAAAT
1 AAA-ATTAAAAAAT
828294 AAAGTATGTG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 19 0.73
19 7 0.27
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
AAAATTAAAAAATTTTAT
Found at i:828790 original size:28 final size:27
Alignment explanation
Indices: 828759--828823 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 27
828749 ACATAAATAG
828759 ATAAATAATATGTCAAAATTTATATAAA
1 ATAAATAATATGTCAAAATTTATAT-AA
* * *
828787 ATAAATTATTATTTTAAAATTTATATAA
1 ATAAA-TAATATGTCAAAATTTATATAA
*
828815 ATATATAAT
1 ATAAATAAT
828824 GAAAATAACA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
27 3 0.10
28 11 0.35
29 17 0.55
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (27 bp):
ATAAATAATATGTCAAAATTTATATAA
Found at i:829100 original size:20 final size:18
Alignment explanation
Indices: 829075--829117 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
829065 AGTTAATATT
*
829075 TAATTAATATATATTTATAA
1 TAATTAA-AAATA-TTATAA
829095 TAATTAAAAATATTATAA
1 TAATTAAAAATATTATAA
829113 -AATTA
1 TAATTA
829118 TAATTAGTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 5 0.23
18 6 0.27
19 4 0.18
20 7 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAATTAAAAATATTATAA
Found at i:829258 original size:2 final size:2
Alignment explanation
Indices: 829251--829289 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
829241 ATCATTTCAG
829251 AT AT AT AT AT 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 AT AT AT AT AT A
829290 GAATTTACTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:829500 original size:82 final size:82
Alignment explanation
Indices: 829414--829565 Score: 250
Period size: 82 Copynumber: 1.9 Consensus size: 82
829404 ATTTTCTTTT
* *
829414 AATCTTGAACTTAACTTTAATTATCAAGTCATTAAAATTATTTTTGACTTGATTTTATTTATACG
1 AATCTTGAACTTAACTTTAATTATCAAGTAATTAAAATTATTTTTGACTTGATTTTATTTATACA
829479 AGAATTTATATGCCTTA
66 AGAATTTATATGCCTTA
* * * *
829496 AATCTTGAACTTAACTTTAGTTGTCAAGTAATTAAGATTATTTTTGGCTTGATTTTATTTATACA
1 AATCTTGAACTTAACTTTAATTATCAAGTAATTAAAATTATTTTTGACTTGATTTTATTTATACA
829561 AGAAT
66 AGAAT
829566 AGGTGCATAT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
82 64 1.00
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.46
Consensus pattern (82 bp):
AATCTTGAACTTAACTTTAATTATCAAGTAATTAAAATTATTTTTGACTTGATTTTATTTATACA
AGAATTTATATGCCTTA
Found at i:829993 original size:30 final size:30
Alignment explanation
Indices: 829959--830019 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
829949 TGTGATCTTA
* * *
829959 ATTAATATTTTATTTTTATTTATATTTTTT
1 ATTAATATTTTATTTTCATTCATAATTTTT
829989 ATTAATATTTTATTTTCATTCATAATTTTT
1 ATTAATATTTTATTTTCATTCATAATTTTT
830019 A
1 A
830020 AAAATTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (30 bp):
ATTAATATTTTATTTTCATTCATAATTTTT
Found at i:830404 original size:14 final size:15
Alignment explanation
Indices: 830378--830407 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
830368 TTATAATGTG
830378 ATTATAGCTTCTGTA
1 ATTATAGCTTCTGTA
830393 ATTATA-CTTCTGTA
1 ATTATAGCTTCTGTA
830407 A
1 A
830408 AACTCATTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.47
Consensus pattern (15 bp):
ATTATAGCTTCTGTA
Found at i:836790 original size:68 final size:68
Alignment explanation
Indices: 836681--836818 Score: 240
Period size: 68 Copynumber: 2.0 Consensus size: 68
836671 CAATAGTGTT
*
836681 TTATGTTACTCATGTAAATCCTAGAGACGTTCATTGGTAATATCTCTTTTATGAACGACCTCCTC
1 TTATGTTACTCATGTAAATCCCAGAGACGTTCATTGGTAATATCTCTTTTATGAACGACCTCCTC
*
836746 GAA
66 AAA
* *
836749 TTATGTTGCTCATGTAAATCCCAGAGACGTTCATTGGTAATATCTCTTTTATGAATGACCTCCTC
1 TTATGTTACTCATGTAAATCCCAGAGACGTTCATTGGTAATATCTCTTTTATGAACGACCTCCTC
836814 AAA
66 AAA
836817 TT
1 TT
836819 TTCTATTTTG
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (68 bp):
TTATGTTACTCATGTAAATCCCAGAGACGTTCATTGGTAATATCTCTTTTATGAACGACCTCCTC
AAA
Done.