Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold90
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: 1707176
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.31
Warning! 87245 characters in sequence are not A, C, G, or T
File 3 of 5
Found at i:750483 original size:18 final size:18
Alignment explanation
Indices: 750457--750497 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
750447 ATAGAGGCGA
*
750457 AGCCAAAGCCCAAGCCTG
1 AGCCCAAGCCCAAGCCTG
**
750475 AGCCCAAGCCTGAGCCTG
1 AGCCCAAGCCCAAGCCTG
750493 AGCCC
1 AGCCC
750498 GTCAGCCAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.27, C:0.41, G:0.24, T:0.07
Consensus pattern (18 bp):
AGCCCAAGCCCAAGCCTG
Found at i:750496 original size:12 final size:12
Alignment explanation
Indices: 750463--750490 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
750453 GCGAAGCCAA
750463 AGCCCAAGCCTG
1 AGCCCAAGCCTG
750475 AGCCCAAGCCTG
1 AGCCCAAGCCTG
750487 AGCC
1 AGCC
750491 TGAGCCCGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.43, G:0.25, T:0.07
Consensus pattern (12 bp):
AGCCCAAGCCTG
Found at i:750669 original size:33 final size:33
Alignment explanation
Indices: 750618--750706 Score: 108
Period size: 33 Copynumber: 2.7 Consensus size: 33
750608 TAGTACAGTA
* *
750618 CCACCGCAGTACAACACTCCTCCT-AGCCTGTAT
1 CCACCGCAGTACAGCACTCCTCCTAAGCC-ATAT
* * *
750651 CCACCGCATTACTGCACTCCTCCTAAGTCATAT
1 CCACCGCAGTACAGCACTCCTCCTAAGCCATAT
*
750684 CCACCACAGTACAGCACTCCTCC
1 CCACCGCAGTACAGCACTCCTCC
750707 CGGCTCAAGT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
33 44 0.94
34 3 0.06
ACGTcount: A:0.25, C:0.44, G:0.10, T:0.21
Consensus pattern (33 bp):
CCACCGCAGTACAGCACTCCTCCTAAGCCATAT
Found at i:751047 original size:47 final size:47
Alignment explanation
Indices: 750986--751082 Score: 151
Period size: 47 Copynumber: 2.1 Consensus size: 47
750976 TAATTGCAAC
750986 ATTAAAACATTACAACATTAAAACATGGAACAAACTTTGTAAT-TAA
1 ATTAAAACATTACAACATTAAAACATGGAACAAACTTTGTAATATAA
* * *
751032 ATTAAATACATTACAATATTAAAACTTGGAACTAACTTTGTAATATAA
1 ATTAAA-ACATTACAACATTAAAACATGGAACAAACTTTGTAATATAA
751080 ATT
1 ATT
751083 TTGTTATATA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
46 6 0.13
47 34 0.74
48 6 0.13
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.33
Consensus pattern (47 bp):
ATTAAAACATTACAACATTAAAACATGGAACAAACTTTGTAATATAA
Found at i:751098 original size:62 final size:62
Alignment explanation
Indices: 751021--751161 Score: 239
Period size: 62 Copynumber: 2.3 Consensus size: 62
751011 TGGAACAAAC
* * * *
751021 TTTGTAAT-TAAATTAAATACATTACAATATTAAAACTTGGAACTAACTTTGTAATATAAAT
1 TTTGTTATATAAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAAT
751082 TTTGTTATATAAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAAT
1 TTTGTTATATAAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAAT
751144 TTTGTTATATAAATTAAA
1 TTTGTTATATAAATTAAA
751162 AGCTCGAAAG
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
61 7 0.09
62 68 0.91
ACGTcount: A:0.47, C:0.07, G:0.06, T:0.40
Consensus pattern (62 bp):
TTTGTTATATAAATTAAATACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAAT
Found at i:754517 original size:211 final size:209
Alignment explanation
Indices: 754163--754573 Score: 630
Period size: 211 Copynumber: 1.9 Consensus size: 209
754153 TGAGTTGGAT
754163 GGGGGAGGGAATAACTTTAAAACAAAACATAAAAAAAACACAAAACAAACCATATAATACTAACA
1 GGGGGAGGGAATAACTTTAAAACAAAACATAAAAAAAACACAAAACAAACCATATAATACT----
*
754228 AAATAAATTTTTCTTACAATAATATATTCTATTTGAAAATAACAATAAAAATAATAATACCTTTT
62 AAATAAATTTTTCTTACAATAATATATTCTATTTGAAAATAACAATAAAAATAATAATA-C--AT
* * * *
754293 CTTTCTTTCTTCTCTTCTCTTCTCCCTCTCTTGTTCTGCTATTTTTT-TAACTGATACTTTAAAA
124 -ATTCTTTCTT-TCTTCTCTTCACCCTCTCTTGTTATGCTATTTTTTAAAACTGATACTTTAAAA
754357 TTGAGCCGGATGGGGGAGCGGCC
187 TTGAGCCGGATGGGGGAGCGGCC
* *
754380 GGGGG-GGGAATAACTTTAAAACAAAACATAAAAATAACACAAAACAAACTATATAATACT-AAT
1 GGGGGAGGGAATAACTTTAAAACAAAACATAAAAAAAACACAAAACAAACCATATAATACTAAAT
* *
754443 AAATTTTTCTTATAATAATCTATTCTATTTGAAAATAACAATAAAAATAATAATACATATTCTTT
66 AAATTTTTCTTACAATAATATATTCTATTTGAAAATAACAATAAAAATAATAATACATATTCTTT
*
754508 CTTTCTTCTCTTCACCCTCTCTTGTTATGCTATTTTTTAAAACTGATATTTTAAAATTGAGCCGG
131 CTTTCTTCTCTTCACCCTCTCTTGTTATGCTATTTTTTAAAACTGATACTTTAAAATTGAGCCGG
754573 A
196 A
754574 AAGGGGAGTG
Statistics
Matches: 183, Mismatches: 10, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
206 33 0.18
207 34 0.19
208 1 0.01
210 1 0.01
211 56 0.31
216 53 0.29
217 5 0.03
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (209 bp):
GGGGGAGGGAATAACTTTAAAACAAAACATAAAAAAAACACAAAACAAACCATATAATACTAAAT
AAATTTTTCTTACAATAATATATTCTATTTGAAAATAACAATAAAAATAATAATACATATTCTTT
CTTTCTTCTCTTCACCCTCTCTTGTTATGCTATTTTTTAAAACTGATACTTTAAAATTGAGCCGG
ATGGGGGAGCGGCC
Found at i:767369 original size:60 final size:60
Alignment explanation
Indices: 767261--767384 Score: 178
Period size: 60 Copynumber: 2.1 Consensus size: 60
767251 CTGGAATATT
* * *
767261 TTCTTCCTCATTTGTTGAAGTTTTATCTTCATCTGAATTATAATTAGTGACTTTTAAGTC
1 TTCTTCCTCATCTGTTGAAGTTTTATCTTCATCAGAATTATAACTAGTGACTTTTAAGTC
* * *
767321 TTCTTCCTGATCTGTTGAAGTTTTTTCTTCATCAG-ATTGATAACTAGTGACTTTTAAGTT
1 TTCTTCCTCATCTGTTGAAGTTTTATCTTCATCAGAATT-ATAACTAGTGACTTTTAAGTC
767381 TTCT
1 TTCT
767385 GTATTTTCAG
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
59 3 0.05
60 54 0.95
ACGTcount: A:0.22, C:0.15, G:0.13, T:0.50
Consensus pattern (60 bp):
TTCTTCCTCATCTGTTGAAGTTTTATCTTCATCAGAATTATAACTAGTGACTTTTAAGTC
Found at i:767625 original size:9 final size:9
Alignment explanation
Indices: 767589--767644 Score: 60
Period size: 9 Copynumber: 6.0 Consensus size: 9
767579 CTGGAAATCT
767589 TTTTTTCATA
1 TTTTTT-ATA
767599 TTTTTT-TA
1 TTTTTTATA
*
767607 CGTTTTTTATG
1 --TTTTTTATA
767618 TTTTTTATA
1 TTTTTTATA
*
767627 ATTTTTATA
1 TTTTTTATA
767636 TTTTTTATA
1 TTTTTTATA
767645 CTAAAGGATT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
8 2 0.05
9 24 0.62
10 12 0.31
11 1 0.03
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.73
Consensus pattern (9 bp):
TTTTTTATA
Found at i:769509 original size:17 final size:18
Alignment explanation
Indices: 769487--769528 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
769477 TATATTTGTG
769487 TATATATAATGTATG-AA
1 TATATATAATGTATGTAA
*
769504 TATATAT-ATGTGTGTAA
1 TATATATAATGTATGTAA
769521 TATATATA
1 TATATATA
769529 TAAATTCTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (18 bp):
TATATATAATGTATGTAA
Found at i:769529 original size:17 final size:17
Alignment explanation
Indices: 769477--769529 Score: 67
Period size: 15 Copynumber: 3.3 Consensus size: 17
769467 GTTTGGATGT
*
769477 TATATTTGTGT-ATATA
1 TATATGTGTGTAATATA
*
769493 TA-ATGTATG-AATATA
1 TATATGTGTGTAATATA
769508 TATATGTGTGTAATATA
1 TATATGTGTGTAATATA
769525 TATAT
1 TATAT
769530 AAATTCTTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 12 0.39
16 8 0.26
17 11 0.35
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (17 bp):
TATATGTGTGTAATATA
Found at i:769998 original size:76 final size:76
Alignment explanation
Indices: 769903--770100 Score: 192
Period size: 76 Copynumber: 2.6 Consensus size: 76
769893 GAAATTAGGG
* * *
769903 ATGTATAT-ATTAGATTCGAATATGTATGAGTATACAAGTATAAGTTCATGTTTTGATTATAAG-
1 ATGTATATGA-TAGATTCGAATATGTATGAGTATACATGTATAAGTTCATGTATTGA-AATAAGA
769966 TATGTA-ATTATAT
64 TATG-AGATTATAT
* * * * * *
769979 ATGTATATGATAGACTCGAATATATAT-ATATATACATGTATAAATTCTTGTATTGAAATTAGAT
1 ATGTATATGATAGATTCGAATATGTATGA-GTATACATGTATAAGTTCATGTATTGAAATAAGAT
*
770043 ATGAGTTTATAT
65 ATGAGATTATAT
* *
770055 ATGTATATG-TGAGGTTCGAATGTGTATG-GTTATACATGTATAAGTT
1 ATGTATATGAT-AGATTCGAATATGTATGAG-TATACATGTATAAGTT
770101 TTATATTGAA
Statistics
Matches: 99, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
75 7 0.07
76 91 0.92
77 1 0.01
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.42
Consensus pattern (76 bp):
ATGTATATGATAGATTCGAATATGTATGAGTATACATGTATAAGTTCATGTATTGAAATAAGATA
TGAGATTATAT
Found at i:770539 original size:41 final size:41
Alignment explanation
Indices: 770491--770711 Score: 343
Period size: 41 Copynumber: 5.4 Consensus size: 41
770481 CAGGCTTAGC
* * *
770491 GCCTAGCAGGCTAAGTGTCGGTGATCTGAATTAGGCTATAA
1 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAA
* *
770532 GCCTAGCAGGCTAAGTGCCGGTGAACTGAATTAGGTTATAA
1 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAA
* *
770573 GCCTAGCAGGCTAAGTGCCGGTGATCGGAATCAGGCTATAA
1 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAA
*
770614 GCCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGTTATAA
1 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAA
* *
770655 GCCTAGCAGGCTAAGTGCCAGTGATCTGAATCAGGTTATCA
1 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAA
*
770696 GCCTAGCAAGCTAAGT
1 GCCTAGCAGGCTAAGT
770712 ACAGGTGAAT
Statistics
Matches: 166, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 166 1.00
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (41 bp):
GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAA
Found at i:770943 original size:34 final size:37
Alignment explanation
Indices: 770905--770975 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
770895 TATGTATGTA
770905 TGCATTCGGCA-A-ATGTG-GATTATAAGTATATATG
1 TGCATTCGGCATATATGTGTGATTATAAGTATATATG
* *
770939 TGCATTCGGCATATCTTTGTGATTATAAGTATATATG
1 TGCATTCGGCATATATGTGTGATTATAAGTATATATG
770976 CTTTTGGCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
34 11 0.34
35 1 0.03
36 3 0.09
37 17 0.53
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (37 bp):
TGCATTCGGCATATATGTGTGATTATAAGTATATATG
Found at i:778245 original size:41 final size:41
Alignment explanation
Indices: 778200--778377 Score: 212
Period size: 41 Copynumber: 4.1 Consensus size: 41
778190 GGCTCGATGC
* *
778200 CTAGCAGGTTTAATGCCGGTGAATTATTTCAGATTTTATGT
1 CTAGCAGGCTTAATGCCGGTGAATTATTTCAGACTTTATGT
*
778241 CTAGCAGGTTTAATGCCGGTGAATTATTTCAGACTTTATGT
1 CTAGCAGGCTTAATGCCGGTGAATTATTTCAGACTTTATGT
* *
778282 CTAACAGGCTTATTGCCGGTGAATTATTTCAGACTTATTTCAGACTTTATGT
1 CTAGCAGGCTTAATGCCGGTG---------A-A-TTATTTCAGACTTTATGT
778334 CTAGCAGGCTTAATGCCGGTGAATTATTTCAGACTTTATGT
1 CTAGCAGGCTTAATGCCGGTGAATTATTTCAGACTTTATGT
778375 CTA
1 CTA
778378 NNNNNNNNNN
Statistics
Matches: 120, Mismatches: 6, Indels: 22
0.81 0.04 0.15
Matches are distributed among these distances:
41 79 0.66
42 1 0.01
43 1 0.01
50 1 0.01
51 1 0.01
52 37 0.31
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCGGTGAATTATTTCAGACTTTATGT
Found at i:778342 original size:52 final size:52
Alignment explanation
Indices: 778264--778369 Score: 194
Period size: 52 Copynumber: 2.0 Consensus size: 52
778254 TGCCGGTGAA
*
778264 TTATTTCAGACTTTATGTCTAACAGGCTTATTGCCGGTGAATTATTTCAGAC
1 TTATTTCAGACTTTATGTCTAACAGGCTTAATGCCGGTGAATTATTTCAGAC
*
778316 TTATTTCAGACTTTATGTCTAGCAGGCTTAATGCCGGTGAATTATTTCAGAC
1 TTATTTCAGACTTTATGTCTAACAGGCTTAATGCCGGTGAATTATTTCAGAC
778368 TT
1 TT
778370 TATGTCTANN
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.41
Consensus pattern (52 bp):
TTATTTCAGACTTTATGTCTAACAGGCTTAATGCCGGTGAATTATTTCAGAC
Found at i:779282 original size:82 final size:82
Alignment explanation
Indices: 779061--779289 Score: 323
Period size: 82 Copynumber: 2.8 Consensus size: 82
779051 AGGCTTAGCA
**
779061 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTACCGGTGAA
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGTCGGTGAA
* *
779126 TTGAATCAGGTTATAAG
66 CTGAATCAGATTATAAG
* ** *
779143 CCTAGCAGGCTAAGTGCCAGTGATCTGAATCAGGCTATAATTCTAGCAGGCTTAGTGTCGGTGAA
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGTCGGTGAA
*
779208 CTGAATCATATTATAAG
66 CTGAATCAGATTATAAG
* * * * * *
779225 CCTAGCAAGCTAAGTGTCGGTGATCTAAATCAAGTTATAAGCCTAGCAGGCTAAGTGTTGGTGAA
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGTCGGTGAA
779290 TTTGTTTAAA
Statistics
Matches: 128, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
82 128 1.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (82 bp):
CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGTCGGTGAA
CTGAATCAGATTATAAG
Found at i:779288 original size:41 final size:41
Alignment explanation
Indices: 779061--779281 Score: 291
Period size: 41 Copynumber: 5.4 Consensus size: 41
779051 AGGCTTAGCA
*
779061 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAG
*
779102 CCTAGCAGGCTAAGTACCGGTGAAT-TGAATCAGGTTATAAG
1 CCTAGCAGGCTAAGTGCCGGTG-ATCTGAATCAGGTTATAAG
* * *
779143 CCTAGCAGGCTAAGTGCCAGTGATCTGAATCAGGCTATAAT
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAG
* * * * **
779184 TCTAGCAGGCTTAGTGTCGGTGAACTGAATCATATTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAG
* * * *
779225 CCTAGCAAGCTAAGTGTCGGTGATCTAAATCAAGTTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAG
779266 CCTAGCAGGCTAAGTG
1 CCTAGCAGGCTAAGTG
779282 TTGGTGAATT
Statistics
Matches: 155, Mismatches: 23, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
40 2 0.01
41 151 0.97
42 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (41 bp):
CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAG
Found at i:785817 original size:27 final size:27
Alignment explanation
Indices: 785787--785840 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
785777 TTTATTTCTT
* * *
785787 AGATTTTCTTAACGTTAGAATCAAATA
1 AGATTTTATTAACATAAGAATCAAATA
785814 AGATTTTATTAACATAAGAATCAAATA
1 AGATTTTATTAACATAAGAATCAAATA
785841 TTTACCAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.35
Consensus pattern (27 bp):
AGATTTTATTAACATAAGAATCAAATA
Found at i:797164 original size:3 final size:3
Alignment explanation
Indices: 797156--797194 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
797146 CCAATCATAA
797156 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
797195 TGTTGTAACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:807558 original size:21 final size:21
Alignment explanation
Indices: 807534--807577 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
807524 TATTGATAAT
*
807534 CAATACACAATCTCAAGATAC
1 CAATACACAATCGCAAGATAC
807555 CAATACACAATCGCAAGATAC
1 CAATACACAATCGCAAGATAC
807576 CA
1 CA
807578 TCTTTCCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.48, C:0.30, G:0.07, T:0.16
Consensus pattern (21 bp):
CAATACACAATCGCAAGATAC
Found at i:810687 original size:16 final size:16
Alignment explanation
Indices: 810668--810701 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
810658 AGAAAGTGTG
*
810668 AAAAGAAAGAAATTAA
1 AAAAAAAAGAAATTAA
810684 AAAAAAAAGAAATTAA
1 AAAAAAAAGAAATTAA
810700 AA
1 AA
810702 CGTGAGGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (16 bp):
AAAAAAAAGAAATTAA
Found at i:814777 original size:10 final size:10
Alignment explanation
Indices: 814762--814811 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
814752 TTGCACTATG
814762 TTCTTTCTTT
1 TTCTTTCTTT
814772 TTCTTTCTTT
1 TTCTTTCTTT
*
814782 TTCTTGT-TCT
1 TTCTT-TCTTT
814792 TTC-TT-TTT
1 TTCTTTCTTT
814800 TTCTTTACTTT
1 TTCTTT-CTTT
814811 T
1 T
814812 GATATTTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
8 6 0.18
9 3 0.09
10 20 0.59
11 5 0.15
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (10 bp):
TTCTTTCTTT
Found at i:814786 original size:16 final size:16
Alignment explanation
Indices: 814765--814799 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
814755 CACTATGTTC
*
814765 TTTCTTTTTCTTTCTT
1 TTTCTTGTTCTTTCTT
814781 TTTCTTGTTCTTTCTT
1 TTTCTTGTTCTTTCTT
814797 TTT
1 TTT
814800 TTCTTTACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (16 bp):
TTTCTTGTTCTTTCTT
Found at i:816690 original size:35 final size:37
Alignment explanation
Indices: 816628--816705 Score: 142
Period size: 35 Copynumber: 2.2 Consensus size: 37
816618 AGAAATAGCA
816628 GAATTTAGGGACATTTTGAAAAATTTCTATTTTTCTC
1 GAATTTAGGGACATTTTGAAAAATTTCTATTTTTCTC
816665 GAATTT-GGGACATTTT-AAAAATTTCTATTTTTCTC
1 GAATTTAGGGACATTTTGAAAAATTTCTATTTTTCTC
816700 GAATTT
1 GAATTT
816706 CCACCCAATC
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
35 25 0.61
36 10 0.24
37 6 0.15
ACGTcount: A:0.29, C:0.10, G:0.13, T:0.47
Consensus pattern (37 bp):
GAATTTAGGGACATTTTGAAAAATTTCTATTTTTCTC
Found at i:832817 original size:18 final size:17
Alignment explanation
Indices: 832784--832821 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
832774 NNNTATAAAT
832784 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
832802 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
832819 TGT
1 TGT
832822 AGAAGGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.47
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:833075 original size:23 final size:23
Alignment explanation
Indices: 833048--833164 Score: 118
Period size: 23 Copynumber: 5.3 Consensus size: 23
833038 AGTGTTATTG
833048 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * * *
833071 TTCA---GT-GCTACGACTATAT
1 ATCAGTGGTAGCTTCGGCTACAT
833090 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * **
833113 -TTAGTGGTAGCTACGGCTATGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
833135 ATCAGTGGTAGCTTCAGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
833158 ATCAGTG
1 ATCAGTG
833165 TGGCACTTAT
Statistics
Matches: 72, Mismatches: 17, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
19 13 0.18
20 2 0.03
22 20 0.28
23 37 0.51
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:833141 original size:45 final size:42
Alignment explanation
Indices: 833048--833164 Score: 155
Period size: 45 Copynumber: 2.7 Consensus size: 42
833038 AGTGTTATTG
833048 ATCAGTGGTAGCTTCGGCTACATTTCAGTGCTACGACTATAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGCTACGACTATAT
* *
833090 ATCAGTGGTAGCTTCGGCTACATTT-AGTGGTAGCTACGGCTATGT
1 ATCAGTGGTAGCTTCGGCTACATTTCA---GT-GCTACGACTATAT
* *
833135 ATCAGTGGTAGCTTCAGCTACATATCAGTG
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTG
833165 TGGCACTTAT
Statistics
Matches: 66, Mismatches: 4, Indels: 10
0.82 0.05 0.12
Matches are distributed among these distances:
41 1 0.02
42 26 0.39
43 2 0.03
44 2 0.03
45 34 0.52
46 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (42 bp):
ATCAGTGGTAGCTTCGGCTACATTTCAGTGCTACGACTATAT
Found at i:835929 original size:54 final size:54
Alignment explanation
Indices: 835812--835929 Score: 157
Period size: 54 Copynumber: 2.2 Consensus size: 54
835802 GTATCATACA
* *
835812 GCCTAAGACACGACCGTGTGAATCAAGTCAGTGAGTTACACGGTCTAGCACACG
1 GCCTACGACACGACCGTGTGAATCAAGTCAGAGAGTTACACGGTCTAGCACACG
* * ** *
835866 GCTTGCGACACGGTCGTGTGACA-CAAGTCAGAGAGTTACACGGTCTAGCACATG
1 GCCTACGACACGACCGTGTGA-ATCAAGTCAGAGAGTTACACGGTCTAGCACACG
835920 GCCTACGACA
1 GCCTACGACA
835930 TGGCCATGTC
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
54 53 0.98
55 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.27, T:0.19
Consensus pattern (54 bp):
GCCTACGACACGACCGTGTGAATCAAGTCAGAGAGTTACACGGTCTAGCACACG
Found at i:835947 original size:54 final size:54
Alignment explanation
Indices: 835835--835960 Score: 162
Period size: 54 Copynumber: 2.3 Consensus size: 54
835825 CCGTGTGAAT
* * * * *
835835 CAAGTCAGTGAGTTACACGGTCTAGCACACGGCTTGCGACACGGTCGTGTGACA
1 CAAGTCAGTGAGTTACACGGTCTAGCACACGGCCTACGACACGGCCATGTCACA
* * * *
835889 CAAGTCAGAGAGTTACACGGTCTAGCACATGGCCTACGACATGGCCATGTCACC
1 CAAGTCAGTGAGTTACACGGTCTAGCACACGGCCTACGACACGGCCATGTCACA
*
835943 CAAGTTAGTGAGTTACAC
1 CAAGTCAGTGAGTTACAC
835961 AATTTAAGAC
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 61 1.00
ACGTcount: A:0.27, C:0.26, G:0.26, T:0.21
Consensus pattern (54 bp):
CAAGTCAGTGAGTTACACGGTCTAGCACACGGCCTACGACACGGCCATGTCACA
Found at i:848064 original size:25 final size:25
Alignment explanation
Indices: 848027--848078 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
848017 CTATTTTTAC
848027 ATAGAAAAATGTCACATCTTCACGG
1 ATAGAAAAATGTCACATCTTCACGG
*
848052 ATAGAAAAGTGTCACATCTTCACGG
1 ATAGAAAAATGTCACATCTTCACGG
848077 AT
1 AT
848079 CACAAAAGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.25
Consensus pattern (25 bp):
ATAGAAAAATGTCACATCTTCACGG
Found at i:850021 original size:22 final size:22
Alignment explanation
Indices: 849974--850023 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
849964 TTGAGTTCTA
*
849974 TTAGTTAAGTGGATTAAATAGTC
1 TTAG-TAAGTGGATTAAATAGAC
*
849997 TTAGTAAGATGGATT-AATGGAC
1 TTAGTAAG-TGGATTAAATAGAC
850019 TTAGT
1 TTAGT
850024 GAGTAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.38
Consensus pattern (22 bp):
TTAGTAAGTGGATTAAATAGAC
Found at i:852271 original size:54 final size:54
Alignment explanation
Indices: 852160--852273 Score: 122
Period size: 54 Copynumber: 2.1 Consensus size: 54
852150 ATACACGATC
* * * ** ** * *
852160 GTGTGAATCAAGTCAGTGAGTTACACGGTCTGGCACACGCCCTGGGACATGGTT
1 GTGTGAATCAAGTCAGAGAGTTACACGGCCTGACACACAACCTACGACACGGCT
*
852214 GTGTG-ATACAAGTCAGAGAGTTACACGGCCTGACACACAACCTACGAGACGGCT
1 GTGTGAAT-CAAGTCAGAGAGTTACACGGCCTGACACACAACCTACGACACGGCT
852268 GTGTGA
1 GTGTGA
852274 CCCAAGTTAG
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
53 2 0.04
54 46 0.96
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.21
Consensus pattern (54 bp):
GTGTGAATCAAGTCAGAGAGTTACACGGCCTGACACACAACCTACGACACGGCT
Found at i:853784 original size:390 final size:390
Alignment explanation
Indices: 852527--854085 Score: 2811
Period size: 390 Copynumber: 4.0 Consensus size: 390
852517 AATCAATTTT
852527 AGTTAATTAATATTAAATGACATTATTGTTTTGTTTTGAAGTTAATTGTTCTAATTTGTACAGTA
1 AGTTAATTAATATTAAATGACATTATTGTTTTGTTTTGAAGTTAATTGTTCTAATTTGTACAGTA
852592 ATGCTCCGTAACTCTAATTCGGCAACGGAGATGAGTTAGGGGTGTTACAAGAAAATACCAGGATA
66 ATGCTCCGTAACTCTAATTCGGCAACGGAGATGAGTTAGGGGTGTTACAAGAAAATACCAGGATA
* *
852657 TCATAAAAAAATAAGAATGTCTTCCTTAGTATGTGCTTAAAAAATGGAGTTCATCAGTCTTTGGA
131 TCATAAAAAAATAGGAATGTCTTCCTTAGTATGTGCTTAAAAAATGGAGTTCATCAGTCCTTGGA
852722 AGGTAGAGGGAGAATTGGTGAGGCCAAAAGGCATCACTAAAAACTCATAGTGACCTTCATGAGTT
196 AGGTAGAGGGAGAATTGGTGAGGCCAAAAGGCATCACTAAAAACTCATAGTGACCTTCATGAGTT
852787 TTGAAGGTTTTTCATGGAATGTCAGGCTCAATTATTCTGATCTATTGGTATCCAACCATGATACG
261 TTGAAGGTTTTTCATGGAATGTCAGGCTCAATTATTCTGATCTATTGGTATCCAACCATGATACG
**
852852 ATCCTGGCTTTGTCGAATGATCCGAGTCATTTATAAGTTCGATCGTCTAACAAGAAGTATCATTC
326 ATCCTGGCTCCGTCGAATGATCCGAGTCATTTATAAGTTCGATCGTCTAACAAGAAGTATCATTC
*
852917 AGTTAATTAATATTAAATGACATTATTGTTTTGTTTTGAAGTTAATTATTCTAATTTGTACAGTA
1 AGTTAATTAATATTAAATGACATTATTGTTTTGTTTTGAAGTTAATTGTTCTAATTTGTACAGTA
*
852982 ATGCTCCGTAACTCTAATTCGGCAACGGAAATGAGTTAGGGGTGTTACAAGAAAATACCAGGATA
66 ATGCTCCGTAACTCTAATTCGGCAACGGAGATGAGTTAGGGGTGTTACAAGAAAATACCAGGATA
853047 TCAT-AAAAAA-AGGAATGTCTTCCTTAGTATGTGCTTAAAAAATGGAGTTCATCAGTCCTTGGA
131 TCATAAAAAAATAGGAATGTCTTCCTTAGTATGTGCTTAAAAAATGGAGTTCATCAGTCCTTGGA
853110 AGGTAGAGGGAGAATTGGTGAGGCCAAAAGGCATCACTAAAAACTCATAGTGACCTTCATGAGTT
196 AGGTAGAGGGAGAATTGGTGAGGCCAAAAGGCATCACTAAAAACTCATAGTGACCTTCATGAGTT
* * *
853175 TTGAAGGTTTTTCATGGAATGTCAGGCTAAAATATCCTGATCTATTGGTATCCAACCATGATACG
261 TTGAAGGTTTTTCATGGAATGTCAGGCTCAATTATTCTGATCTATTGGTATCCAACCATGATACG
* * *
853240 ATCCTGGCTTCGTCGAATGATCCGAGTCATTTATAAGTTCGATCATCTAACAAGAAGTATTATTC
326 ATCCTGGCTCCGTCGAATGATCCGAGTCATTTATAAGTTCGATCGTCTAACAAGAAGTATCATTC
853305 AGTTAATTAATATTAAATGACATTATTGTTTTGTTTTGAAGTTAATTGTTCTAATTTGTACAGTA
1 AGTTAATTAATATTAAATGACATTATTGTTTTGTTTTGAAGTTAATTGTTCTAATTTGTACAGTA
*
853370 ATGCTCCGTAACTCTAATTCGGCAACGGAGATGAGTTAGGGTTGTTACAAGAAAATACCAGGATA
66 ATGCTCCGTAACTCTAATTCGGCAACGGAGATGAGTTAGGGGTGTTACAAGAAAATACCAGGATA
* * *
853435 TCATAAAAAAA-AGGAATGTCTTCATTAGTTTTTGCTTAAAAAATGGAGTTCATCAGTCCTTGGA
131 TCATAAAAAAATAGGAATGTCTTCCTTAGTATGTGCTTAAAAAATGGAGTTCATCAGTCCTTGGA
*
853499 AGGTAGAGGGAGAATTGGTGAGGCCAAAAGGCATCACAAAAAACTCATAGTGACCTTCATGAGTT
196 AGGTAGAGGGAGAATTGGTGAGGCCAAAAGGCATCACTAAAAACTCATAGTGACCTTCATGAGTT
***
853564 TTGAAGGTTTTTCATGGAATGTCAGGCTCAATTATTCTGATCTATTGGTATCTTGGCCATGATAC
261 TTGAAGGTTTTTCATGGAATGTCAGGCTCAATTATTCTGATCTATTGGTATC-CAACCATGATAC
*
853629 GATCCTGGCTCCGTTGAATGATCCGAGTCATTTATAAGTTCGATCGTCTAACAAGAAGTATCATT
325 GATCCTGGCTCCGTCGAATGATCCGAGTCATTTATAAGTTCGATCGTCTAACAAGAAGTATCATT
853694 C
390 C
853695 AGTTAATTAATATTAAATGACATTATTGTTTTGTTTTGAAGTTAATTGTTCTAATTTGTACAGTA
1 AGTTAATTAATATTAAATGACATTATTGTTTTGTTTTGAAGTTAATTGTTCTAATTTGTACAGTA
*
853760 ATGCTCCGTAACTCTAATTCGGCAACGAAGATGAGTTAGGGGTGTTACAAGAAAATACCAGGATA
66 ATGCTCCGTAACTCTAATTCGGCAACGGAGATGAGTTAGGGGTGTTACAAGAAAATACCAGGATA
853825 TCATAAAAAAATAGGAATGTCTTCCTTAGTATGTGCTTAAAAAATGGAGTTCATCAGTCCTTGGA
131 TCATAAAAAAATAGGAATGTCTTCCTTAGTATGTGCTTAAAAAATGGAGTTCATCAGTCCTTGGA
* * *
853890 AGGTAGAGGGTGAATTGGTGAGGCCGAAAGGCATCACCAAAAACTCATAGTGACCTTCATGAGTT
196 AGGTAGAGGGAGAATTGGTGAGGCCAAAAGGCATCACTAAAAACTCATAGTGACCTTCATGAGTT
* *
853955 TTGAAGGTTTTTCATGGAACGTCAGGCTCAATTATTCTGATCTATTGGTATCCTACCATGATACG
261 TTGAAGGTTTTTCATGGAATGTCAGGCTCAATTATTCTGATCTATTGGTATCCAACCATGATACG
* *
854020 AT-CTCGGCTCTGTCGAATGATCGGAGTCATTTATAAGTTCGATCGTCTAACAAGAAGTATCATT
326 ATCCT-GGCTCCGTCGAATGATCCGAGTCATTTATAAGTTCGATCGTCTAACAAGAAGTATCATT
854084 C
390 C
854085 A
1 A
854086 TTTACGTTGT
Statistics
Matches: 1123, Mismatches: 42, Indels: 8
0.96 0.04 0.01
Matches are distributed among these distances:
388 371 0.33
389 177 0.16
390 412 0.37
391 163 0.15
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.33
Consensus pattern (390 bp):
AGTTAATTAATATTAAATGACATTATTGTTTTGTTTTGAAGTTAATTGTTCTAATTTGTACAGTA
ATGCTCCGTAACTCTAATTCGGCAACGGAGATGAGTTAGGGGTGTTACAAGAAAATACCAGGATA
TCATAAAAAAATAGGAATGTCTTCCTTAGTATGTGCTTAAAAAATGGAGTTCATCAGTCCTTGGA
AGGTAGAGGGAGAATTGGTGAGGCCAAAAGGCATCACTAAAAACTCATAGTGACCTTCATGAGTT
TTGAAGGTTTTTCATGGAATGTCAGGCTCAATTATTCTGATCTATTGGTATCCAACCATGATACG
ATCCTGGCTCCGTCGAATGATCCGAGTCATTTATAAGTTCGATCGTCTAACAAGAAGTATCATTC
Found at i:854622 original size:143 final size:144
Alignment explanation
Indices: 854350--854639 Score: 555
Period size: 143 Copynumber: 2.0 Consensus size: 144
854340 CTAGAGGTAT
854350 AGTTTTTGGGTGAACGCCACACTTGATTTGAGTGATAAGTTCGAAGCAGACTAAGTTTGATGCCA
1 AGTTTTTGGGT--ACGCCACACTTGATTTGAGTGATAAGTTCGAAGCAGACTAAGTTTGATGCCA
854415 CTGACAACAGATAAGCCAAGCTAAGTCCTTGAACGAAATTTGAGAGTAGTATTCTCACAAAATAA
64 CTGACAACAGATAAGCCAAGCTAAGTCCTTGAACGAAATTTGAGAGTAGTATTCTCACAAAATAA
854480 CTCAAATAATATTCTG
129 CTCAAATAATATTCTG
854496 AGTTTTTGGGT-CGCCACACTTGATTTGAGTGATAAGTTCGAAGCAGACTAAGTTTGATGCCACT
1 AGTTTTTGGGTACGCCACACTTGATTTGAGTGATAAGTTCGAAGCAGACTAAGTTTGATGCCACT
854560 GACAACAGATAAGCCAAGCTAAGTCCTTGAACGAAATTTGAGAGTAGTATTCTCACAAAATAACT
66 GACAACAGATAAGCCAAGCTAAGTCCTTGAACGAAATTTGAGAGTAGTATTCTCACAAAATAACT
854625 CAAATAATATTCTG
131 CAAATAATATTCTG
854639 A
1 A
854640 TTGTCAAAAG
Statistics
Matches: 144, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
143 133 0.92
146 11 0.08
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (144 bp):
AGTTTTTGGGTACGCCACACTTGATTTGAGTGATAAGTTCGAAGCAGACTAAGTTTGATGCCACT
GACAACAGATAAGCCAAGCTAAGTCCTTGAACGAAATTTGAGAGTAGTATTCTCACAAAATAACT
CAAATAATATTCTG
Found at i:859686 original size:33 final size:33
Alignment explanation
Indices: 859622--859686 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
859612 AAATTATAAG
* * * *
859622 TATTATATGTACTCTAATACTTTATTTATTATT
1 TATTAGATGTAATCTAATACTTAATTAATTATT
859655 TATTAGATGTAATCTAATGA-TTAATTAATTAT
1 TATTAGATGTAATCTAAT-ACTTAATTAATTAT
859687 GATTATGATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 26 0.96
34 1 0.04
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.52
Consensus pattern (33 bp):
TATTAGATGTAATCTAATACTTAATTAATTATT
Found at i:859693 original size:6 final size:6
Alignment explanation
Indices: 859682--859710 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
859672 TGATTAATTA
859682 ATTATG ATTATG ATTATG ATTATG ATTAT
1 ATTATG ATTATG ATTATG ATTATG ATTAT
859711 AAGAGAAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (6 bp):
ATTATG
Found at i:867128 original size:38 final size:39
Alignment explanation
Indices: 867016--867128 Score: 140
Period size: 40 Copynumber: 2.9 Consensus size: 39
867006 GGCGTTTGTA
* *
867016 TAAAAAAAGCCGCTAAAAATCAAGCATTA-CTGGCGCTTT
1 TAAAAAAAGCCGCTAAAAATCGAGTATTAGC-GGCGCTTT
* *
867055 TAAAAAAACGCCACTAAAGATCGAGTATTAGCGGCGCTTT
1 TAAAAAAA-GCCGCTAAAAATCGAGTATTAGCGGCGCTTT
**
867095 TTGAAAAAGCCGCTAAAAAT-GAGTATTAGCGGCG
1 TAAAAAAAGCCGCTAAAAATCGAGTATTAGCGGCG
867129 TTTCCCAAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
38 14 0.22
39 18 0.28
40 31 0.48
41 1 0.02
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (39 bp):
TAAAAAAAGCCGCTAAAAATCGAGTATTAGCGGCGCTTT
Found at i:867151 original size:38 final size:38
Alignment explanation
Indices: 867019--867141 Score: 106
Period size: 40 Copynumber: 3.2 Consensus size: 38
867009 GTTTGTATAA
* * ***
867019 AAAAAGCCGCTAAAAATCAAGCATTA-CTGGCGCTTTTAA
1 AAAAAGCCGCTAAAAAT-GAGTATTAGC-GGCGCTTTCCC
* * ***
867058 AAAAACGCCACTAAAGATCGAGTATTAGCGGCGCTTTTTG
1 AAAAA-GCCGCTAAAAAT-GAGTATTAGCGGCGCTTTCCC
867098 AAAAAGCCGCTAAAAATGAGTATTAGCGGCG-TTTCCC
1 AAAAAGCCGCTAAAAATGAGTATTAGCGGCGCTTTCCC
867135 AAAAAGC
1 AAAAAGC
867142 GTCGCAAAAA
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
37 10 0.14
38 14 0.20
39 15 0.21
40 31 0.44
41 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (38 bp):
AAAAAGCCGCTAAAAATGAGTATTAGCGGCGCTTTCCC
Found at i:867444 original size:41 final size:41
Alignment explanation
Indices: 867176--867444 Score: 322
Period size: 41 Copynumber: 6.6 Consensus size: 41
867166 ATTTCGGGGA
* * * * * *
867176 TTTAGCGACGTTTCTGAAGAAGTGCCGCTAATGCTCGGGGC
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGTC
* * * * *
867217 TTTAGCGGCGTTTCTCAAGAAGCGCCGCTAATGCTCGGGGC
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGTC
* * **
867258 TTTAGCGGTGTTTTTGGAAATTCGCCGCTAATGCTCTGGTC
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGTC
*
867299 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGTC
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGTC
* * * *
867340 TTTAGCGACATTTTTGGAAAAGCGCCGCTAATGCTCTAGTC
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGTC
* *
867381 TTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCTAGTC
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGTC
**
867422 TTTAGCGGCACTTTTGAAAAAGC
1 TTTAGCGGCGTTTTTGAAAAAGC
867445 TCTGCAAAAA
Statistics
Matches: 203, Mismatches: 25, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 203 1.00
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.31
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCTGGTC
Found at i:867926 original size:14 final size:15
Alignment explanation
Indices: 867907--867940 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
867897 TAGGTTTTAA
867907 GGGTTTAAGGGTT-G
1 GGGTTTAAGGGTTAG
*
867921 GGGTTTAAGGTTTAG
1 GGGTTTAAGGGTTAG
867936 GGGTT
1 GGGTT
867941 AGTAGTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.15, C:0.00, G:0.47, T:0.38
Consensus pattern (15 bp):
GGGTTTAAGGGTTAG
Found at i:869462 original size:256 final size:257
Alignment explanation
Indices: 868996--869509 Score: 1021
Period size: 256 Copynumber: 2.0 Consensus size: 257
868986 CTATCGCTTC
868996 TCTCCTCCTGCTAAACGCCTTGTTCTTCTTGTTGGTAAACCCTCATTTCTTCTCTTTTTAGGGTT
1 TCTCCTCCTGCTAAACGCCTTGTTCTTCTTGTTGGTAAACCCTCATTTCTTCTCTTTTTAGGGTT
869061 CAACCCCCCTTGATTTTGTTGAAGAGGATTGATAGTGAAAAATGGCTTGTTGAGTTTGATGCAAA
66 CAACCCCCCTTGATTTTGTTGAAGAGGATTGATAGTGAAAAATGGCTTGTTGAGTTTGATGCAAA
869126 TCTGGCAATTCAGCTAAATAGAAACAAAGAACCTTTTGGGTATGTTAGTTATTTACTTATTTTAG
131 TCTGGCAATTCAGCTAAATAGAAACAAAGAACCTTTTGGGTATGTTAGTTATTTACTTATTTTAG
869191 CTTTATACTAAAAGGCTAAGTATTTTTTATATAATTGTTTCCTTTTTGAGTTTAGTTTTGAG
196 CTTTATACTAAAAGGCTAAGTATTTTTTATATAATTGTTTCCTTTTTGAGTTTAGTTTTGAG
869253 TCTCCTCCTG-TAAACGCCTTGTTCTTCTTGTTGGTAAACCCTCATTTCTTCTCTTTTTAGGGTT
1 TCTCCTCCTGCTAAACGCCTTGTTCTTCTTGTTGGTAAACCCTCATTTCTTCTCTTTTTAGGGTT
869317 CAACCCCCCTTGATTTTGTTGAAGAGGATTGATAGTGAAAAATGGCTTGTTGAGTTTGATGCAAA
66 CAACCCCCCTTGATTTTGTTGAAGAGGATTGATAGTGAAAAATGGCTTGTTGAGTTTGATGCAAA
869382 TCTGGCAATTCAGCTAAATAGAAACAAAGAACCTTTTGGGTATGTTAGTTATTTACTTATTTTAG
131 TCTGGCAATTCAGCTAAATAGAAACAAAGAACCTTTTGGGTATGTTAGTTATTTACTTATTTTAG
869447 CTTTATACTAAAAGGCTAAGTATTTTTTATATAATTGTTTCCTTTTTGAGTTTAGTTTTGAG
196 CTTTATACTAAAAGGCTAAGTATTTTTTATATAATTGTTTCCTTTTTGAGTTTAGTTTTGAG
869509 T
1 T
869510 TTAGCTTCTT
Statistics
Matches: 257, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
256 247 0.96
257 10 0.04
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.42
Consensus pattern (257 bp):
TCTCCTCCTGCTAAACGCCTTGTTCTTCTTGTTGGTAAACCCTCATTTCTTCTCTTTTTAGGGTT
CAACCCCCCTTGATTTTGTTGAAGAGGATTGATAGTGAAAAATGGCTTGTTGAGTTTGATGCAAA
TCTGGCAATTCAGCTAAATAGAAACAAAGAACCTTTTGGGTATGTTAGTTATTTACTTATTTTAG
CTTTATACTAAAAGGCTAAGTATTTTTTATATAATTGTTTCCTTTTTGAGTTTAGTTTTGAG
Found at i:872932 original size:20 final size:20
Alignment explanation
Indices: 872904--872951 Score: 71
Period size: 19 Copynumber: 2.4 Consensus size: 20
872894 TTTAAAAAGA
872904 AAAAGAAAAAGCAAAAAGCGC
1 AAAA-AAAAAGCAAAAAGCGC
*
872925 -AAAAAAAAGCAAAAAGCGT
1 AAAAAAAAAGCAAAAAGCGC
872944 AAAAAAAA
1 AAAAAAAA
872952 CCGCAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.73, C:0.10, G:0.15, T:0.02
Consensus pattern (20 bp):
AAAAAAAAAGCAAAAAGCGC
Found at i:896089 original size:45 final size:45
Alignment explanation
Indices: 896025--896152 Score: 166
Period size: 45 Copynumber: 2.8 Consensus size: 45
896015 TATACGCCTA
**
896025 AAATGAGTAAGACTGTAGCTGAAAGATGCTATGACATCATGACAG
1 AAATGAGTAAGACCATAGCTGAAAGATGCTATGACATCATGACAG
***
896070 AAATGAGTAAGACCATAGCTGAAAGATGCTATGACATCATGGTTG
1 AAATGAGTAAGACCATAGCTGAAAGATGCTATGACATCATGACAG
** * * *
896115 TTAGGACTAAGACCATAGCTGAAAGATGCTATGGCATC
1 AAATGAGTAAGACCATAGCTGAAAGATGCTATGACATC
896153 CTTTGATAGT
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 73 1.00
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (45 bp):
AAATGAGTAAGACCATAGCTGAAAGATGCTATGACATCATGACAG
Found at i:896321 original size:27 final size:27
Alignment explanation
Indices: 896238--896391 Score: 121
Period size: 27 Copynumber: 5.7 Consensus size: 27
896228 TAGTCCATCA
* * *
896238 GGACATCAAACACTGGATAGTTCGATG
1 GGACATTAAACACGGGATAGTCCGATG
** * * * *
896265 GGATGTTAAGCATGAGATAGTCCAATG
1 GGACATTAAACACGGGATAGTCCGATG
**
896292 GGACATTAAACACGGGATAGTCCGGCG
1 GGACATTAAACACGGGATAGTCCGATG
* * *
896319 GGACGTTAAACATGGTATAG-CCTGATG
1 GGACATTAAACACGGGATAGTCC-GATG
* ** *
896346 AGACGGTAAACACGAGATAGTCCGATG
1 GGACATTAAACACGGGATAGTCCGATG
*
896373 GGACATTAAACATGGGATA
1 GGACATTAAACACGGGATA
896392 CTCTATTAGG
Statistics
Matches: 93, Mismatches: 32, Indels: 4
0.72 0.25 0.03
Matches are distributed among these distances:
26 2 0.02
27 89 0.96
28 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.21
Consensus pattern (27 bp):
GGACATTAAACACGGGATAGTCCGATG
Found at i:902862 original size:27 final size:27
Alignment explanation
Indices: 902828--903008 Score: 197
Period size: 27 Copynumber: 6.7 Consensus size: 27
902818 ACACACCGGA
902828 GAAATGGAAGCCTTTGTGGCAATATAT
1 GAAATGGAAGCCTTTGTGGCAATATAT
* *
902855 GACATGGAAGCCTTTGTGGCAATCTAT
1 GAAATGGAAGCCTTTGTGGCAATATAT
* * *
902882 GAAATGGAAGCCTTTAT-G-ATGTATCT
1 GAAATGGAAGCCTTTGTGGCA-ATATAT
* * * *
902908 GAAATAGAAGCCTTTGTGAC-GTATCT
1 GAAATGGAAGCCTTTGTGGCAATATAT
*
902934 GAAATGGAAGCCTTTGTGGCAATCTAT
1 GAAATGGAAGCCTTTGTGGCAATATAT
* * *
902961 GAAACGGAAGCCTTTGTGGCGATCTAT
1 GAAATGGAAGCCTTTGTGGCAATATAT
*
902988 GAAAAGGAAGGCCTTTGTGGC
1 GAAATGGAA-GCCTTTGTGGC
903009 GTAGTCTAAA
Statistics
Matches: 131, Mismatches: 18, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
25 1 0.01
26 43 0.33
27 76 0.58
28 11 0.08
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (27 bp):
GAAATGGAAGCCTTTGTGGCAATATAT
Found at i:902917 original size:26 final size:26
Alignment explanation
Indices: 902828--902948 Score: 109
Period size: 26 Copynumber: 4.6 Consensus size: 26
902818 ACACACCGGA
* * * *
902828 GAAATGGAAGCCTTTGTGGCAATATAT
1 GAAATGGAAGCCTTTATGAC-GTATCT
* * * *
902855 GACATGGAAGCCTTTGTGGC-AATCTAT
1 GAAATGGAAGCCTTTATGACGTATC--T
*
902882 GAAATGGAAGCCTTTATGATGTATCT
1 GAAATGGAAGCCTTTATGACGTATCT
* *
902908 GAAATAGAAGCCTTTGTGACGTATCT
1 GAAATGGAAGCCTTTATGACGTATCT
902934 GAAATGGAAGCCTTT
1 GAAATGGAAGCCTTT
902949 GTGGCAATCT
Statistics
Matches: 79, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
25 2 0.03
26 38 0.48
27 36 0.46
28 3 0.04
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.31
Consensus pattern (26 bp):
GAAATGGAAGCCTTTATGACGTATCT
Found at i:902960 original size:79 final size:80
Alignment explanation
Indices: 902828--902975 Score: 235
Period size: 79 Copynumber: 1.9 Consensus size: 80
902818 ACACACCGGA
* * * *
902828 GAAATGGAAGCCTTTGTGGCAATATATGACATGGAAGCCTTTGTGGCAATCTATGAAATGGAAGC
1 GAAATAGAAGCCTTTGTGACAATATATGAAATGGAAGCCTTTGTGGCAATCTATGAAACGGAAGC
902893 CTTTATGATGTATCT
66 CTTTATGATGTATCT
* *
902908 GAAATAGAAGCCTTTGTGAC-GTATCTGAAATGGAAGCCTTTGTGGCAATCTATGAAACGGAAGC
1 GAAATAGAAGCCTTTGTGACAATATATGAAATGGAAGCCTTTGTGGCAATCTATGAAACGGAAGC
902972 CTTT
66 CTTT
902976 GTGGCGATCT
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
79 44 0.71
80 18 0.29
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (80 bp):
GAAATAGAAGCCTTTGTGACAATATATGAAATGGAAGCCTTTGTGGCAATCTATGAAACGGAAGC
CTTTATGATGTATCT
Found at i:903173 original size:27 final size:27
Alignment explanation
Indices: 903143--903362 Score: 142
Period size: 27 Copynumber: 8.2 Consensus size: 27
903133 GACTGGATGG
* *
903143 TATGGTAAATATTGAAGGAATAGTACA
1 TATGGAAAATACTGAAGGAATAGTACA
*
903170 TATGGAAAATACTAAAGGAATAGTACA
1 TATGGAAAATACTGAAGGAATAGTACA
* * * *
903197 TATGGTGAACT-CTGAAAGAATAGTACG
1 TATGG-AAAATACTGAAGGAATAGTACA
* * *
903224 TATGGAAAACACTAAAGGAATGGTACA
1 TATGGAAAATACTGAAGGAATAGTACA
** * *
903251 TATGGCGAACACTGAAGGAATAATACA
1 TATGGAAAATACTGAAGGAATAGTACA
* * * *
903278 TATAGTG-AACT-CTAAATGAATAGTACG
1 TAT-G-GAAAATACTGAAGGAATAGTACA
* * * *
903305 TATGCAAAA-ACTAAAAGAATGGTACA
1 TATGGAAAATACTGAAGGAATAGTACA
* ** * *
903331 TCTGGCGAACACTGAAGGAATAGTACG
1 TATGGAAAATACTGAAGGAATAGTACA
903358 TATGG
1 TATGG
903363 TGAAAATTGA
Statistics
Matches: 145, Mismatches: 41, Indels: 14
0.73 0.20 0.07
Matches are distributed among these distances:
26 23 0.16
27 116 0.80
28 5 0.03
29 1 0.01
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.23
Consensus pattern (27 bp):
TATGGAAAATACTGAAGGAATAGTACA
Found at i:903201 original size:54 final size:54
Alignment explanation
Indices: 903143--903363 Score: 185
Period size: 54 Copynumber: 4.1 Consensus size: 54
903133 GACTGGATGG
* *
903143 TATGGTAAATATTGAAGGAATAGTACATATGGAAAATACTAAAGGAATAGTACA
1 TATGGTAAATACTGAAGGAATAGTACATATGGAAAACACTAAAGGAATAGTACA
* * * *
903197 TATGGTGAACT-CTGAAAGAATAGTACGTATGGAAAACACTAAAGGAATGGTACA
1 TATGGT-AAATACTGAAGGAATAGTACATATGGAAAACACTAAAGGAATAGTACA
** * * * ** * * *
903251 TATGGCGAACACTGAAGGAATAATACATATAGTGAACTCTAAATGAATAGTACG
1 TATGGTAAATACTGAAGGAATAGTACATATGGAAAACACTAAAGGAATAGTACA
* * * * * * ** * *
903305 TAT-GCAAAAACTAAAAGAATGGTACATCTGGCGAACACTGAAGGAATAGTACG
1 TATGGTAAATACTGAAGGAATAGTACATATGGAAAACACTAAAGGAATAGTACA
903358 TATGGT
1 TATGGT
903364 GAAAATTGAG
Statistics
Matches: 131, Mismatches: 33, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
53 42 0.32
54 86 0.66
55 3 0.02
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.24
Consensus pattern (54 bp):
TATGGTAAATACTGAAGGAATAGTACATATGGAAAACACTAAAGGAATAGTACA
Found at i:903269 original size:81 final size:80
Alignment explanation
Indices: 903157--903366 Score: 296
Period size: 81 Copynumber: 2.6 Consensus size: 80
903147 GTAAATATTG
* ** * *
903157 AAGGAATAGTACATATGGAAAATACTAAAGGAATAGTACATATGGTGAACTCTGAAA-GAATAGT
1 AAGGAATGGTACATATGGCGAACACTGAAGGAATAGTACATATGGTGAACTCT-AAATGAATAGT
*
903221 ACGTATGGAAAACACTA
65 ACGTATGCAAAA-ACTA
* *
903238 AAGGAATGGTACATATGGCGAACACTGAAGGAATAATACATATAGTGAACTCTAAATGAATAGTA
1 AAGGAATGGTACATATGGCGAACACTGAAGGAATAGTACATATGGTGAACTCTAAATGAATAGTA
903303 CGTATGCAAAAACTA
66 CGTATGCAAAAACTA
* * *
903318 AAAGAATGGTACATCTGGCGAACACTGAAGGAATAGTACGTATGGTGAA
1 AAGGAATGGTACATATGGCGAACACTGAAGGAATAGTACATATGGTGAA
903367 AATTGAGAGA
Statistics
Matches: 115, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
80 51 0.44
81 64 0.56
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.22
Consensus pattern (80 bp):
AAGGAATGGTACATATGGCGAACACTGAAGGAATAGTACATATGGTGAACTCTAAATGAATAGTA
CGTATGCAAAAACTA
Found at i:907588 original size:15 final size:16
Alignment explanation
Indices: 907560--907589 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
907550 TTACTTATCT
907560 TTGTTCTCTTATTCTC
1 TTGTTCTCTTATTCTC
907576 TTGTTCT-TTATTCT
1 TTGTTCTCTTATTCT
907590 TTATTTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.07, C:0.20, G:0.07, T:0.67
Consensus pattern (16 bp):
TTGTTCTCTTATTCTC
Found at i:908337 original size:18 final size:18
Alignment explanation
Indices: 908297--908344 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
908287 TTGTAATTAA
*
908297 AATTTTTAAAATATAATT
1 AATTTTAAAAATATAATT
*
908315 AATTTTAAAAATATTTATT
1 AATTTTAAAAATA-TAATT
908334 -ATTTTAAAAAT
1 AATTTTAAAAAT
908345 TATCTTTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 23 0.85
19 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AATTTTAAAAATATAATT
Found at i:909758 original size:4 final size:4
Alignment explanation
Indices: 909749--909785 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
909739 ATCTGTTTCA
909749 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT T
909786 TACCAACCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (4 bp):
TAAT
Found at i:912155 original size:24 final size:24
Alignment explanation
Indices: 912123--912170 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
912113 TTGACCGAGA
912123 TAAATTATGATTTACTCAGTAAAC
1 TAAATTATGATTTACTCAGTAAAC
912147 TAAATTATGATTTACTCAGTAAAC
1 TAAATTATGATTTACTCAGTAAAC
912171 CTATCTCTTG
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:0.12, G:0.08, T:0.38
Consensus pattern (24 bp):
TAAATTATGATTTACTCAGTAAAC
Found at i:922332 original size:45 final size:45
Alignment explanation
Indices: 922253--922339 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
922243 ATGATGTTAG
* * * * *
922253 GTATTTAATATATTGTTGAAAACTGGAATGTTGTTAAATTATTAT
1 GTATTTAACATATTGTTAAAAAATGAAATATTGTTAAATTATTAT
*
922298 GTATTTAGCATATTGTTAAAAAATGAAATATTGTTAAATTAT
1 GTATTTAACATATTGTTAAAAAATGAAATATTGTTAAATTAT
922340 GAATTGAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.39, C:0.02, G:0.14, T:0.45
Consensus pattern (45 bp):
GTATTTAACATATTGTTAAAAAATGAAATATTGTTAAATTATTAT
Found at i:922547 original size:21 final size:21
Alignment explanation
Indices: 922522--922659 Score: 80
Period size: 21 Copynumber: 6.6 Consensus size: 21
922512 TGAGCTTCTG
*
922522 TTAACTCATATGAGTTTCAGT
1 TTAACTCTTATGAGTTTCAGT
* * *
922543 TTAACCCTTATGGGTTTCCGT
1 TTAACTCTTATGAGTTTCAGT
* * * *
922564 TCAGCTCTTTTGAGCTTCAGT
1 TTAACTCTTATGAGTTTCAGT
* *
922585 TTAACCCTTATGGGTTTCCA-T
1 TTAACTCTTATGAGTTT-CAGT
* * **
922606 TCAACTCTTACGAGTTTCCCT
1 TTAACTCTTATGAGTTTCAGT
* * * *
922627 TCAACCCTTATGGGTTTCTGT
1 TTAACTCTTATGAGTTTCAGT
* *
922648 TTAGCACTTATG
1 TTAACTCTTATG
922660 TGCTTTTGTG
Statistics
Matches: 85, Mismatches: 30, Indels: 4
0.71 0.25 0.03
Matches are distributed among these distances:
20 1 0.01
21 82 0.96
22 2 0.02
ACGTcount: A:0.19, C:0.23, G:0.16, T:0.42
Consensus pattern (21 bp):
TTAACTCTTATGAGTTTCAGT
Found at i:922584 original size:42 final size:42
Alignment explanation
Indices: 922524--922644 Score: 161
Period size: 42 Copynumber: 2.9 Consensus size: 42
922514 AGCTTCTGTT
* *
922524 AACTCATATGAGTTTCAGTTTAACCCTTATGGGTTTCCGTTC
1 AACTCTTATGAGTTTCAGTTTAACCCTTATGGGTTTCCATTC
* * *
922566 AGCTCTTTTGAGCTTCAGTTTAACCCTTATGGGTTTCCATTC
1 AACTCTTATGAGTTTCAGTTTAACCCTTATGGGTTTCCATTC
* ** *
922608 AACTCTTACGAGTTTCCCTTCAACCCTTATGGGTTTC
1 AACTCTTATGAGTTTCAGTTTAACCCTTATGGGTTTC
922645 TGTTTAGCAC
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 67 1.00
ACGTcount: A:0.19, C:0.25, G:0.16, T:0.40
Consensus pattern (42 bp):
AACTCTTATGAGTTTCAGTTTAACCCTTATGGGTTTCCATTC
Found at i:936019 original size:20 final size:20
Alignment explanation
Indices: 935994--936036 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
935984 GGAAATAGAA
935994 GATGATGCTTGACCGTATTG
1 GATGATGCTTGACCGTATTG
936014 GATGATGCTTGACCGTATTG
1 GATGATGCTTGACCGTATTG
936034 GAT
1 GAT
936037 ATTTTTCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.14, G:0.30, T:0.35
Consensus pattern (20 bp):
GATGATGCTTGACCGTATTG
Found at i:941510 original size:16 final size:16
Alignment explanation
Indices: 941489--941519 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
941479 AAATTAAAAT
*
941489 TAATTAATTAAATTTC
1 TAATTAAATAAATTTC
941505 TAATTAAATAAATTT
1 TAATTAAATAAATTT
941520 TCTCAACCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
TAATTAAATAAATTTC
Found at i:947426 original size:11 final size:11
Alignment explanation
Indices: 947381--947437 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
947371 TCGACGGCAG
*
947381 TATTAGGATAAA
1 TATTA-GATTAA
*
947393 TATTACATTAA
1 TATTAGATTAA
947404 TATTAGATATTAA
1 TATTAG--ATTAA
* *
947417 TGTTAGATTAC
1 TATTAGATTAA
947428 TATTAGATTA
1 TATTAGATTA
947438 GGGTTTACTT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
11 22 0.59
12 5 0.14
13 10 0.27
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.44
Consensus pattern (11 bp):
TATTAGATTAA
Found at i:950518 original size:36 final size:36
Alignment explanation
Indices: 950466--950534 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
950456 TTTAGGAATT
* *
950466 TGAGAATACCTAATATC-TTGTTTAGGAGCTTGGAAA
1 TGAGAAGACCTAATATCATT-TTCAGGAGCTTGGAAA
*
950502 TGAGAAGACCTGATATCATTTTCAGGAGCTTGG
1 TGAGAAGACCTAATATCATTTTCAGGAGCTTGG
950535 GAAGATCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
36 27 0.93
37 2 0.07
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (36 bp):
TGAGAAGACCTAATATCATTTTCAGGAGCTTGGAAA
Found at i:963732 original size:16 final size:16
Alignment explanation
Indices: 963711--963750 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
963701 AATAATTTGA
963711 TAATTTTACTAACAAT
1 TAATTTTACTAACAAT
*
963727 TAATTTTATTAACAAT
1 TAATTTTACTAACAAT
*
963743 TAGTTTTA
1 TAATTTTA
963751 ATTTTATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (16 bp):
TAATTTTACTAACAAT
Found at i:963772 original size:21 final size:21
Alignment explanation
Indices: 963726--963785 Score: 84
Period size: 22 Copynumber: 2.8 Consensus size: 21
963716 TTACTAACAA
* *
963726 TTAATTTTATTAACAATTAGTT
1 TTAATTTTATTAA-AAATAATT
963748 TTAATTTTATTAAAAATAATT
1 TTAATTTTATTAAAAATAATT
963769 TTAATTTTAATTAAAAA
1 TTAATTTT-ATTAAAAA
963786 CGGGCCGGGC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.40
22 21 0.60
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
TTAATTTTATTAAAAATAATT
Found at i:965042 original size:22 final size:22
Alignment explanation
Indices: 965000--965044 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
964990 TGTAACAAGA
**
965000 TTTTAATTTAACATGTTTAATT
1 TTTTAATTTAACATGAATAATT
*
965022 TTTTAATTTAACTTGAATAATT
1 TTTTAATTTAACATGAATAATT
965044 T
1 T
965045 CACTAGATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (22 bp):
TTTTAATTTAACATGAATAATT
Found at i:972880 original size:24 final size:22
Alignment explanation
Indices: 972845--972888 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
972835 TAGGTTAATA
972845 CTATGCACAAAGCACAACCTGG
1 CTATGCACAAAGCACAACCTGG
*
972867 CTATGACACCAAAGTACAACCT
1 CTATG-CA-CAAAGCACAACCT
972889 TTTCTCGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 2 0.11
24 12 0.63
ACGTcount: A:0.39, C:0.32, G:0.14, T:0.16
Consensus pattern (22 bp):
CTATGCACAAAGCACAACCTGG
Found at i:987034 original size:85 final size:85
Alignment explanation
Indices: 986921--987076 Score: 217
Period size: 85 Copynumber: 1.8 Consensus size: 85
986911 AACAGAATAG
* * **
986921 GAAAGCCTTTTTGGTGAACCTTTAAAAGGAAAGCCTTTTTGGCGAACCTCT-AGAAGGAAAGCCT
1 GAAAGCCTTTTTGATGAACCTTTAAAAGGAAAGCCTTTATGGAAAACCTCTGA-AAGGAAAGCCT
986985 TTGTGGCGAACTTCCAAAAAT
65 TTGTGGCGAACTTCCAAAAAT
* * *
987006 GAAAG-CTTTTGTGATGAACCTTTGAAAGGAAAGCCTTTATGGAAAACTTCTGAAAGGAGAGCCT
1 GAAAGCCTTTT-TGATGAACCTTTAAAAGGAAAGCCTTTATGGAAAACCTCTGAAAGGAAAGCCT
987070 TTGTGGC
65 TTGTGGC
987077 AACCTTCGAA
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
84 5 0.08
85 56 0.90
86 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (85 bp):
GAAAGCCTTTTTGATGAACCTTTAAAAGGAAAGCCTTTATGGAAAACCTCTGAAAGGAAAGCCTT
TGTGGCGAACTTCCAAAAAT
Found at i:987083 original size:28 final size:28
Alignment explanation
Indices: 986919--987104 Score: 130
Period size: 28 Copynumber: 6.6 Consensus size: 28
986909 CTAACAGAAT
* *
986919 AGGAAAGCCTTTTTGGTGAACCTT-TAAA
1 AGGAAAGCCTTTGTGG-CAACCTTCTAAA
* *
986947 AGGAAAGCCTTTTTGGCGAACC-TCTAGA
1 AGGAAAGCCTTTGTGGC-AACCTTCTAAA
*
986975 AGGAAAGCCTTTGTGGCGAA-CTTCCAAAA
1 AGGAAAGCCTTTGTGGC-AACCTT-CTAAA
* * *
987004 ATGAAAGCTTTTGTGATG-AACCTT-TGAA
1 AGGAAAGCCTTTGTG--GCAACCTTCTAAA
* * * *
987032 AGGAAAGCCTTTATGGAAAACTTCTGAA
1 AGGAAAGCCTTTGTGGCAACCTTCTAAA
* * *
987060 AGGAGAGCCTTTGTGGCAACCTTCGAAG
1 AGGAAAGCCTTTGTGGCAACCTTCTAAA
* *
987088 ATGAAAGTCTTTGTGGC
1 AGGAAAGCCTTTGTGGC
987105 GTATTAGGAA
Statistics
Matches: 126, Mismatches: 23, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
26 1 0.01
27 7 0.06
28 96 0.76
29 18 0.14
30 3 0.02
31 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (28 bp):
AGGAAAGCCTTTGTGGCAACCTTCTAAA
Found at i:987196 original size:27 final size:27
Alignment explanation
Indices: 987113--987197 Score: 73
Period size: 27 Copynumber: 3.1 Consensus size: 27
987103 GCGTATTAGG
* **
987113 AAAGAAAGCCCTTGTGGCAATCTCTAT
1 AAAGAAAGCCTTTGTGGCAATCTAAAT
* ** * **
987140 AATGGGAGCCTTTGTGGCTAA-CCACGT
1 AAAGAAAGCCTTTGTGGC-AATCTAAAT
987167 AAAGAAAGCCTTTGTGGCAATCTAAAT
1 AAAGAAAGCCTTTGTGGCAATCTAAAT
987194 AAAG
1 AAAG
987198 GAAGGTTTAT
Statistics
Matches: 42, Mismatches: 14, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
26 2 0.05
27 38 0.90
28 2 0.05
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (27 bp):
AAAGAAAGCCTTTGTGGCAATCTAAAT
Found at i:994121 original size:14 final size:14
Alignment explanation
Indices: 994104--994130 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
994094 ATTTTTATCT
994104 TTTAATTTTCTTAG
1 TTTAATTTTCTTAG
994118 TTTAATTTTCTTA
1 TTTAATTTTCTTA
994131 CTTAAAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.07, G:0.04, T:0.67
Consensus pattern (14 bp):
TTTAATTTTCTTAG
Found at i:1003595 original size:20 final size:20
Alignment explanation
Indices: 1003579--1003650 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
1003569 ACCAAAATTT
1003579 TATTTTAAAAATTAAAAAAG
1 TATTTTAAAAATTAAAAAAG
*
1003599 TATTTTAAAAATACTTAAAAA-
1 TATTTTAAAAAT--TAAAAAAG
*** *
1003620 T-TAAAAAAAATTTAAAAAG
1 TATTTTAAAAATTAAAAAAG
1003639 TATTTTAAAAAT
1 TATTTTAAAAAT
1003651 ATTTTCAAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
18 7 0.17
19 1 0.02
20 26 0.63
21 1 0.02
22 6 0.15
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (20 bp):
TATTTTAAAAATTAAAAAAG
Found at i:1003631 original size:40 final size:40
Alignment explanation
Indices: 1003585--1003683 Score: 137
Period size: 40 Copynumber: 2.5 Consensus size: 40
1003575 ATTTTATTTT
1003585 AAAAATTAAAAAAGTATTTTAAAAATACTTAAAAATTAAA
1 AAAAATTAAAAAAGTATTTTAAAAATACTTAAAAATTAAA
* * **
1003625 AAAAATTTAAAAAGTATTTTAAAAATATTTTCAAATTAAA
1 AAAAATTAAAAAAGTATTTTAAAAATACTTAAAAATTAAA
* *
1003665 AATAA-TAAAAAAATATTTT
1 AAAAATTAAAAAAGTATTTT
1003684 GAAGGCCCGG
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
39 12 0.23
40 40 0.77
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (40 bp):
AAAAATTAAAAAAGTATTTTAAAAATACTTAAAAATTAAA
Found at i:1003643 original size:11 final size:10
Alignment explanation
Indices: 1003579--1003654 Score: 50
Period size: 9 Copynumber: 7.5 Consensus size: 10
1003569 ACCAAAATTT
*
1003579 TATTTTAAAA
1 TATTTAAAAA
*
1003589 -ATTAAAAAA
1 TATTTAAAAA
1003598 GTATTTTAAAAA
1 -TA-TTTAAAAA
*
1003610 TACTT-AAAA
1 TATTTAAAAA
*
1003619 -ATTAAAAAA
1 TATTTAAAAA
*
1003628 AATTTAAAAA
1 TATTTAAAAA
1003638 GTATTTTAAAAA
1 -TA-TTTAAAAA
1003650 TATTT
1 TATTT
1003655 TCAAATTAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
8 2 0.04
9 15 0.29
10 13 0.25
11 6 0.12
12 15 0.29
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (10 bp):
TATTTAAAAA
Found at i:1007317 original size:18 final size:17
Alignment explanation
Indices: 1007274--1007322 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
1007264 AAGCTTTATA
* *
1007274 TGTGTTTATTTTTTTTCT
1 TGTGTTTA-TTTTATTCG
*
1007292 TGTTTTTATGTTTATTCG
1 TGTGTTTAT-TTTATTCG
1007310 TGTGTTTATTTTA
1 TGTGTTTATTTTA
1007323 GTTTTTATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 5 0.19
18 21 0.81
ACGTcount: A:0.10, C:0.04, G:0.14, T:0.71
Consensus pattern (17 bp):
TGTGTTTATTTTATTCG
Found at i:1009462 original size:45 final size:44
Alignment explanation
Indices: 1009393--1009551 Score: 153
Period size: 45 Copynumber: 3.6 Consensus size: 44
1009383 TACACGGTGG
* * *
1009393 ATCAGCACACAAC-ACCACCCTTATAGACAATAGTACTCGGTGAA
1 ATCAGCACATAACAACCACCTTTATA-ACAATGGTACTCGGTGAA
* *
1009437 ATCAGCACATAGCAACCACCTTTATACTCAATGGTAC-CGGGTGAA
1 ATCAGCACATAACAACCACCTTTATA-ACAATGGTACTC-GGTGAA
* * *
1009482 ATCAGCACATAACAACCACCTATATAACCATTGGTA-TCCGATGAA
1 ATCAGCACATAACAACCACCTTTATAA-CAATGGTACT-CGGTGAA
* * *
1009527 ATTAGCACATAGCATCCACCTTTAT
1 ATCAGCACATAACAACCACCTTTAT
1009552 TTTCATTAAT
Statistics
Matches: 95, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
44 12 0.13
45 82 0.86
46 1 0.01
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (44 bp):
ATCAGCACATAACAACCACCTTTATAACAATGGTACTCGGTGAA
Found at i:1012307 original size:26 final size:27
Alignment explanation
Indices: 1012232--1012309 Score: 81
Period size: 26 Copynumber: 2.9 Consensus size: 27
1012222 CATAAGGGTC
1012232 TTTCACTTCATGA-TATGCCAC-AAGGCT
1 TTTC-CTTCAT-ATTATGCCACAAAGGCT
* * *
1012259 TTTCCTTCATGTTACGCTACAAAGGC-
1 TTTCCTTCATATTATGCCACAAAGGCT
*
1012285 TTTCGTTCATATTATGCCACAAAGG
1 TTTCCTTCATATTATGCCACAAAGG
1012310 TTGTCCATTC
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
26 33 0.79
27 9 0.21
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (27 bp):
TTTCCTTCATATTATGCCACAAAGGCT
Found at i:1012426 original size:54 final size:53
Alignment explanation
Indices: 1012295--1012427 Score: 153
Period size: 53 Copynumber: 2.5 Consensus size: 53
1012285 TTTCGTTCAT
* * *
1012295 ATTATGCCACAAAGG-TTGTCCATTCAAGAATCACCACAGAGGTTTTTTTTCCC
1 ATTATGCCACAAAGGCTT-TCCATTTAAGAACCACCACAGAGGTTTTCTTTCCC
* * * *
1012348 ATTATGCCACAAAGTCATTT-CATTTAAGAACCGCCATAGAGGCTTTTCTTTCTC
1 ATTATGCCACAAAGGC-TTTCCATTTAAGAACCACCACAGAGG-TTTTCTTTCCC
*
1012402 ATTATGCCATAAAGGCTTTCCATTTA
1 ATTATGCCACAAAGGCTTTCCATTTA
1012428 CTAGAGTGTT
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
53 35 0.52
54 30 0.45
55 2 0.03
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.35
Consensus pattern (53 bp):
ATTATGCCACAAAGGCTTTCCATTTAAGAACCACCACAGAGGTTTTCTTTCCC
Found at i:1027365 original size:30 final size:29
Alignment explanation
Indices: 1027331--1027390 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 29
1027321 ATAAAATATT
1027331 ATCATATTTCATTTACT-TTTTAAAACTTAG
1 ATCATATTTCATTT-CTATTTTAAAA-TTAG
* *
1027361 ATCATTTTTCATTTGTATTTTAAAATTAG
1 ATCATATTTCATTTCTATTTTAAAATTAG
1027390 A
1 A
1027391 AACTTGGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.52
Consensus pattern (29 bp):
ATCATATTTCATTTCTATTTTAAAATTAG
Found at i:1029935 original size:14 final size:15
Alignment explanation
Indices: 1029918--1029947 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1029908 AATGTATGGT
1029918 TTGAAAT-TAAATAA
1 TTGAAATGTAAATAA
1029932 TTGAAATGTAAATAA
1 TTGAAATGTAAATAA
1029947 T
1 T
1029948 AAAGTGTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (15 bp):
TTGAAATGTAAATAA
Found at i:1035641 original size:125 final size:127
Alignment explanation
Indices: 1035325--1035845 Score: 660
Period size: 126 Copynumber: 4.1 Consensus size: 127
1035315 GGCCAAACAT
* * * * * * *
1035325 GAACTACTGTAGAAAAATAGCGTCGACATGGGAGCTTTTTTTCA-TCAATTTTGTTGACAGTTCA
1 GAACTACTGTAGAAAAAGAGCATCTACGTGGGAGCTTTTTTTAAGT-AATTTTGCTGACAGTGCA
* * * *
1035389 TCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAAATATTTTTTTAG
65 TCCTGCTTGAAGCGTTTTTCACACTATTTGTTCAGAAACATATTCTCAAAATTATTTTTTCAG
* * * *
1035452 GAACTACTATAGAAAAAGAGCAT-TCATGTGGGAG-TTTTTTTAAGTAATTTTGCTAATAGTGCA
1 GAACTACTGTAGAAAAAGAGCATCT-ACGTGGGAGCTTTTTTTAAGTAATTTTGCTGACAGTGCA
* * * * * * *
1035515 TCTTGCTTGAAGCGTTTTTAACATTATTTGCTCAGAAACATCTTTTC-AAATTATTTTTTCAA
65 TCCTGCTTGAAGCGTTTTTCACACTATTTGTTCAGAAACATATTCTCAAAATTATTTTTTCAG
* *
1035577 GAACTACTGTAGGAAAAGAGCATCTACGTGGGAGCTTTTTTT-AGTAATTTTGCCGACAGTGCAT
1 GAACTACTGTAGAAAAAGAGCATCTACGTGGGAGCTTTTTTTAAGTAATTTTGCTGACAGTGCAT
*
1035641 CCTGCTTGAAGCGTTTTTCACACTATTTGTTCAGAATCATATTCTCAAAATTATTTTTTCAG
66 CCTGCTTGAAGCGTTTTTCACACTATTTGTTCAGAAACATATTCTCAAAATTATTTTTTCAG
* * * * *
1035703 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGC-TTTTTTCAGTATTTTTACTGACAGTGCAT
1 GAACTACTGTAGAAAAAGAGCATCTACGTGGGAGCTTTTTTTAAGTAATTTTGCTGACAGTGCAT
* * *
1035767 CCTGGTTGAAGCGTTTTTCACATTATTTGTTCA-AAATCGTATTCTCAAAATTATTTTTTCAG
66 CCTGCTTGAAGCGTTTTTCACACTATTTGTTCAGAAA-CATATTCTCAAAATTATTTTTTCAG
*
1035829 GAATTACTGTAGAAAAA
1 GAACTACTGTAGAAAAA
1035846 AACAAAATCC
Statistics
Matches: 343, Mismatches: 44, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
125 107 0.31
126 208 0.61
127 28 0.08
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (127 bp):
GAACTACTGTAGAAAAAGAGCATCTACGTGGGAGCTTTTTTTAAGTAATTTTGCTGACAGTGCAT
CCTGCTTGAAGCGTTTTTCACACTATTTGTTCAGAAACATATTCTCAAAATTATTTTTTCAG
Found at i:1035778 original size:251 final size:253
Alignment explanation
Indices: 1035325--1035845 Score: 708
Period size: 251 Copynumber: 2.1 Consensus size: 253
1035315 GGCCAAACAT
* * ** *
1035325 GAACTACTGTAGAAAAATAGCGTCGACATGGGAGCTTTTTTTCATCAATTTTGTTGACAGTTCAT
1 GAACTACTGTAGAAAAAGAGCATCGACATGGGAGCTTTTTTTCATCAATTTTGCCGACAGTGCAT
* * *
1035390 CCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAAATATTTTTTTAGGAA
66 CCTGCTTGAAGCGTTTTTCACACTATTTGTTCAGAAACATATTCTCAAAAATATTTTTTCAGGAA
* * * * * *
1035455 CTACTATAGAAAAAGAGCATTCATGTGGGAGTTTTTTTAAGTAATTTTGCTAATAGTGCATCTTG
131 CTACTATAGAAAAAGAGCATCCACGTGGGAGCTTTTTTAAGTAATTTTACTAACAGTGCATCCTG
* *
1035520 CTTGAAGCGTTTTTAACATTATTTGCTCAGAAA-CATCTTTTC-AAATTATTTTTTCAA
196 CTTGAAGCGTTTTTAACATTATTTGCTCA-AAATCATATTCTCAAAATTATTTTTTCAA
* * *
1035577 GAACTACTGTAGGAAAAGAGCATCTACGTGGGAGCTTTTTTT-AGT-AATTTTGCCGACAGTGCA
1 GAACTACTGTAGAAAAAGAGCATCGACATGGGAGCTTTTTTTCA-TCAATTTTGCCGACAGTGCA
* *
1035640 TCCTGCTTGAAGCGTTTTTCACACTATTTGTTCAGAATCATATTCTCAAAATTATTTTTTCAGGA
65 TCCTGCTTGAAGCGTTTTTCACACTATTTGTTCAGAAACATATTCTCAAAAATATTTTTTCAGGA
* * * * *
1035705 ACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTATTTTTACTGACAGTGCATCCT
130 ACTACTATAGAAAAAGAGCATCCACGTGGGAGCTTTTTTAAGTAATTTTACTAACAGTGCATCCT
* * * * *
1035770 GGTTGAAGCGTTTTTCACATTATTTGTTCAAAATCGTATTCTCAAAATTATTTTTTCAG
195 GCTTGAAGCGTTTTTAACATTATTTGCTCAAAATCATATTCTCAAAATTATTTTTTCAA
*
1035829 GAATTACTGTAGAAAAA
1 GAACTACTGTAGAAAAA
1035846 AACAAAATCC
Statistics
Matches: 233, Mismatches: 33, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
250 3 0.01
251 163 0.70
252 67 0.29
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (253 bp):
GAACTACTGTAGAAAAAGAGCATCGACATGGGAGCTTTTTTTCATCAATTTTGCCGACAGTGCAT
CCTGCTTGAAGCGTTTTTCACACTATTTGTTCAGAAACATATTCTCAAAAATATTTTTTCAGGAA
CTACTATAGAAAAAGAGCATCCACGTGGGAGCTTTTTTAAGTAATTTTACTAACAGTGCATCCTG
CTTGAAGCGTTTTTAACATTATTTGCTCAAAATCATATTCTCAAAATTATTTTTTCAA
Found at i:1036026 original size:7 final size:7
Alignment explanation
Indices: 1036016--1036047 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
1036006 TAAAATTCCT
1036016 AAAACCC
1 AAAACCC
1036023 AAAACCC
1 AAAACCC
1036030 AAAACCC
1 AAAACCC
1036037 AAAACCC
1 AAAACCC
1036044 AAAA
1 AAAA
1036048 TTATTTTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.62, C:0.38, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAACCC
Found at i:1036640 original size:115 final size:110
Alignment explanation
Indices: 1036405--1036651 Score: 334
Period size: 110 Copynumber: 2.2 Consensus size: 110
1036395 TAGTCGGTTC
* *
1036405 ACTTATTATTTATTTGATTTTGTGATTTTAGAAGGAGAGAAGGCAACAATAAATTTTATTTTAAA
1 ACTTATTATTTGTTTGATTTTGTGATTTTAGAAGGAGAGAAGGCAACAACAAATTTTATTTTAAA
* * *
1036470 GGTAATTTTTTGTAATTGTTATTTATTTGTTTAGGGTTTTGTGGT
66 GGTAATTTTTTATAATTATTATTTATTTGTTTAGGATTTTGTGGT
* * * *
1036515 ACTTATTATTTGTTTAATTTTGTGATTTTGGAAGGAGAGGAGGCAACAACAAATTTTGTTTTAAA
1 ACTTATTATTTGTTTGATTTTGTGATTTTAGAAGGAGAGAAGGCAACAACAAATTTTATTTTAAA
1036580 GGTAATTTTTTTATTTATAATTATTATTTATTTGTTTAGGATTTTG-GGTT
66 GGTAA----TTT-TTTATAATTATTATTTATTTGTTTAGGATTTTGTGG-T
**
1036630 TGTTATTATTTGTTTGATTTTG
1 ACTTATTATTTGTTTGATTTTG
1036652 ACTTTTTTAC
Statistics
Matches: 119, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
110 64 0.54
114 5 0.04
115 50 0.42
ACGTcount: A:0.27, C:0.03, G:0.19, T:0.52
Consensus pattern (110 bp):
ACTTATTATTTGTTTGATTTTGTGATTTTAGAAGGAGAGAAGGCAACAACAAATTTTATTTTAAA
GGTAATTTTTTATAATTATTATTTATTTGTTTAGGATTTTGTGGT
Found at i:1040341 original size:24 final size:25
Alignment explanation
Indices: 1040240--1040416 Score: 96
Period size: 25 Copynumber: 7.2 Consensus size: 25
1040230 AAAATCTTCC
* **
1040240 GAGCCATATAA-CGAGAAGCTCATGT
1 GAGCCA-ATAATCGGGAAGCTCATAA
*
1040265 GAGCCATGTAA-CGGGAAGCTCATAA
1 GAGCCA-ATAATCGGGAAGCTCATAA
* ** **
1040290 GAGCC-ATATTCGATAAGCTCATGC
1 GAGCCAATAATCGGGAAGCTCATAA
* *
1040314 GAGCCAAT-ATCGGGTAGCT-TTCAA
1 GAGCCAATAATCGGGAAGCTCAT-AA
*
1040338 GAGCCATTAATCGGGAAGCTCATAA
1 GAGCCAATAATCGGGAAGCTCATAA
* * * ***
1040363 GAGCCAATTATCAGAAAGCTCCGGA
1 GAGCCAATAATCGGGAAGCTCATAA
* *
1040388 GAACCAATTATCGGGACA-CTCATAA
1 GAGCCAATAATCGGGA-AGCTCATAA
1040413 GAGC
1 GAGC
1040417 TGTGGTGTAT
Statistics
Matches: 112, Mismatches: 34, Indels: 12
0.71 0.22 0.08
Matches are distributed among these distances:
23 3 0.03
24 29 0.26
25 78 0.70
26 2 0.02
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (25 bp):
GAGCCAATAATCGGGAAGCTCATAA
Found at i:1040364 original size:25 final size:25
Alignment explanation
Indices: 1040240--1040368 Score: 97
Period size: 25 Copynumber: 5.2 Consensus size: 25
1040230 AAAATCTTCC
* **
1040240 GAGCCATATAA-CGAGAAGCTCATGT
1 GAGCCAT-TAATCGGGAAGCTCATAA
1040265 GAGCCATGTAA-CGGGAAGCTCATAA
1 GAGCCAT-TAATCGGGAAGCTCATAA
* ** **
1040290 GAGCCA-TATTCGATAAGCTCATGC
1 GAGCCATTAATCGGGAAGCTCATAA
* * *
1040314 GAGCCAAT-ATCGGGTAGCT-TTCAA
1 GAGCCATTAATCGGGAAGCTCAT-AA
1040338 GAGCCATTAATCGGGAAGCTCATAA
1 GAGCCATTAATCGGGAAGCTCATAA
1040363 GAGCCA
1 GAGCCA
1040369 ATTATCAGAA
Statistics
Matches: 80, Mismatches: 19, Indels: 10
0.73 0.17 0.09
Matches are distributed among these distances:
23 3 0.04
24 30 0.38
25 46 0.57
26 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.20
Consensus pattern (25 bp):
GAGCCATTAATCGGGAAGCTCATAA
Found at i:1047962 original size:25 final size:25
Alignment explanation
Indices: 1047934--1048129 Score: 127
Period size: 25 Copynumber: 7.8 Consensus size: 25
1047924 AAGCTCTTCC
*
1047934 GAGCCATATAACGGGAAGCTCATGT
1 GAGCCATATAACGGGAAGCTCATGA
* ** *
1047959 GAGCCATGTAACTAGAAGCTCATGC
1 GAGCCATATAACGGGAAGCTCATGA
* * *
1047984 GAGCCATAT-TCGAGAAGCTCATGC
1 GAGCCATATAACGGGAAGCTCATGA
* *
1048008 GAGCCAT-TAATTGGGAAGCTCATAA
1 GAGCCATATAA-CGGGAAGCTCATGA
* *
1048033 AAGCCAT-TAATCGGGAAGCTCATAA
1 GAGCCATATAA-CGGGAAGCTCATGA
* *
1048058 GAGCCA-ATTATCGGGAAGCTC-CGAA
1 GAGCCATA-TAACGGGAAGCTCATG-A
* *
1048083 GAGCCA-ATTATCGGGAATGCTCATAA
1 GAGCCATA-TAACGGGAA-GCTCATGA
*
1048109 GAGCACATA-AACGGAAAGCTC
1 GAGC-CATATAACGGGAAGCTC
1048130 TTTCAAGCCA
Statistics
Matches: 140, Mismatches: 22, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
23 1 0.01
24 20 0.14
25 99 0.71
26 17 0.12
27 2 0.01
28 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.19
Consensus pattern (25 bp):
GAGCCATATAACGGGAAGCTCATGA
Found at i:1048004 original size:24 final size:25
Alignment explanation
Indices: 1047924--1048014 Score: 112
Period size: 25 Copynumber: 3.7 Consensus size: 25
1047914 CATAAACGGA
* * *
1047924 AAGCTCTTCCGAGCCATATAACGGG
1 AAGCTCATGCGAGCCATATAACGAG
* * *
1047949 AAGCTCATGTGAGCCATGTAACTAG
1 AAGCTCATGCGAGCCATATAACGAG
*
1047974 AAGCTCATGCGAGCCATAT-TCGAG
1 AAGCTCATGCGAGCCATATAACGAG
1047998 AAGCTCATGCGAGCCAT
1 AAGCTCATGCGAGCCAT
1048015 TAATTGGGAA
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
24 20 0.36
25 36 0.64
ACGTcount: A:0.30, C:0.25, G:0.24, T:0.21
Consensus pattern (25 bp):
AAGCTCATGCGAGCCATATAACGAG
Found at i:1048063 original size:50 final size:50
Alignment explanation
Indices: 1047934--1048112 Score: 152
Period size: 50 Copynumber: 3.6 Consensus size: 50
1047924 AAGCTCTTCC
** * * **
1047934 GAGCCATATAA-CGGGAAGCTCATGTGAGCCATGTAACT-AGAAGCTCATGC
1 GAGCCAT-TAATCGGGAAGCTCATAAGAGCCAT-TAATTGGGAAGCTCATAA
* * **
1047984 GAGCCA-TATTCGAGAAGCTCATGCGAGCCATTAATTGGGAAGCTCATAA
1 GAGCCATTAATCGGGAAGCTCATAAGAGCCATTAATTGGGAAGCTCATAA
* * **
1048033 AAGCCATTAATCGGGAAGCTCATAAGAGCCAATT-ATCGGGAAGCTCCGAA
1 GAGCCATTAATCGGGAAGCTCATAAGAGCC-ATTAATTGGGAAGCTCATAA
1048083 GAGCCAATT-ATCGGGAATGCTCATAAGAGC
1 GAGCC-ATTAATCGGGAA-GCTCATAAGAGC
1048113 ACATAAACGG
Statistics
Matches: 107, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
48 6 0.06
49 33 0.31
50 50 0.47
51 18 0.17
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.20
Consensus pattern (50 bp):
GAGCCATTAATCGGGAAGCTCATAAGAGCCATTAATTGGGAAGCTCATAA
Found at i:1048128 original size:51 final size:50
Alignment explanation
Indices: 1048034--1048129 Score: 124
Period size: 51 Copynumber: 1.9 Consensus size: 50
1048024 AGCTCATAAA
* * *
1048034 AGCCATTAATCGGGAAGCTCATAAGAGCCAATTATCGGGAAGCTCCGAAG
1 AGCCATTAATCGGGAAGCTCATAAGAGCCAATAAACGGAAAGCTCCGAAG
1048084 AGCCAATT-ATCGGGAATGCTCATAAGAG-CACATAAACGGAAAGCTC
1 AGCC-ATTAATCGGGAA-GCTCATAAGAGCCA-ATAAACGGAAAGCTC
1048130 TTTCAAGCCA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
50 14 0.35
51 26 0.65
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (50 bp):
AGCCATTAATCGGGAAGCTCATAAGAGCCAATAAACGGAAAGCTCCGAAG
Found at i:1048265 original size:25 final size:24
Alignment explanation
Indices: 1048237--1048409 Score: 120
Period size: 25 Copynumber: 7.0 Consensus size: 24
1048227 CTCTTCCAAC
**
1048237 CCATATAACGGGAAGCTCATGTGAG
1 CCATAT-ACGGGAAGCTCATAAGAG
1048262 CCATGCA-ACGGGAAGCTCATAAGAG
1 CCAT--ATACGGGAAGCTCATAAGAG
*
1048287 CCATATTCGGGAAGCTCATAAGAG
1 CCATATACGGGAAGCTCATAAGAG
* **
1048311 CCATATTCGGGAAGCTCATGCGAG
1 CCATATACGGGAAGCTCATAAGAG
* ** ***
1048335 CTA-ATATCGGGTGGCTCCGGAGAG
1 CCATATA-CGGGAAGCTCATAAGAG
*
1048359 CCAT-TAATCGAGAAGCTCATAAGAG
1 CCATAT-A-CGGGAAGCTCATAAGAG
*
1048384 CCA-ATTATCGGGACGCTCATAAGAG
1 CCATA-TA-CGGGAAGCTCATAAGAG
1048409 C
1 C
1048410 TGTGGTGTAT
Statistics
Matches: 119, Mismatches: 21, Indels: 16
0.76 0.13 0.10
Matches are distributed among these distances:
23 3 0.03
24 56 0.47
25 58 0.49
26 1 0.01
27 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.27, T:0.19
Consensus pattern (24 bp):
CCATATACGGGAAGCTCATAAGAG
Found at i:1048302 original size:24 final size:24
Alignment explanation
Indices: 1048270--1048409 Score: 131
Period size: 24 Copynumber: 5.8 Consensus size: 24
1048260 AGCCATGCAA
1048270 CGGGAAGCTCATAAGAGCCATATT
1 CGGGAAGCTCATAAGAGCCATATT
1048294 CGGGAAGCTCATAAGAGCCATATT
1 CGGGAAGCTCATAAGAGCCATATT
** *
1048318 CGGGAAGCTCATGCGAGCTA-ATAT
1 CGGGAAGCTCATAAGAGCCATAT-T
** *** *
1048342 CGGGTGGCTCCGGAGAGCCATTAAT
1 CGGGAAGCTCATAAGAGCCA-TATT
*
1048367 CGAGAAGCTCATAAGAGCCA-ATTAT
1 CGGGAAGCTCATAAGAGCCATA-T-T
*
1048392 CGGGACGCTCATAAGAGC
1 CGGGAAGCTCATAAGAGC
1048410 TGTGGTGTAT
Statistics
Matches: 92, Mismatches: 19, Indels: 9
0.77 0.16 0.08
Matches are distributed among these distances:
23 3 0.03
24 56 0.61
25 32 0.35
26 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.28, T:0.19
Consensus pattern (24 bp):
CGGGAAGCTCATAAGAGCCATATT
Found at i:1048345 original size:48 final size:48
Alignment explanation
Indices: 1048245--1048409 Score: 145
Period size: 49 Copynumber: 3.4 Consensus size: 48
1048235 ACCCATATAA
** * *
1048245 CGGGAAGCTCATGTGAGCCATGCAA-CGGGAAGCTCATAAGAGCCATATT
1 CGGGAAGCTCATAAGAGCCAT-TAATCGGGAAGCTCATAAGAGCAATA-T
* **
1048294 CGGGAAGCTCATAAGAGCCA-TATTCGGGAAGCTCATGCGAGCTAATAT
1 CGGGAAGCTCATAAGAGCCATTAATCGGGAAGCTCATAAGAGC-AATAT
** *** *
1048342 CGGGTGGCTCCGGAGAGCCATTAATCGAGAAGCTCATAAGAGCCAATTAT
1 CGGGAAGCTCATAAGAGCCATTAATCGGGAAGCTCATAAGAG-CAA-TAT
*
1048392 CGGGACGCTCATAAGAGC
1 CGGGAAGCTCATAAGAGC
1048410 TGTGGTGTAT
Statistics
Matches: 90, Mismatches: 21, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
47 1 0.01
48 32 0.36
49 40 0.44
50 17 0.19
ACGTcount: A:0.30, C:0.22, G:0.28, T:0.19
Consensus pattern (48 bp):
CGGGAAGCTCATAAGAGCCATTAATCGGGAAGCTCATAAGAGCAATAT
Found at i:1048587 original size:24 final size:24
Alignment explanation
Indices: 1048449--1048589 Score: 99
Period size: 24 Copynumber: 5.8 Consensus size: 24
1048439 ACAACAAAAT
*
1048449 CGGGATGCTCATT-AGAGCTAGTAA
1 CGGGATGCTC-TTGAGAGCTAATAA
* * * * *
1048473 TGGGAAGCTCGTGAGAGCCATATAT
1 CGGGATGCTCTTGAGAGCTA-ATAA
* ** * *
1048498 CGAG-TAGCTCAAGAGAGCAAATAT
1 CGGGAT-GCTCTTGAGAGCTAATAA
* *
1048522 CGAGATGCTCATGAGAGCTAATAA
1 CGGGATGCTCTTGAGAGCTAATAA
1048546 CGGGATGCT-TATGAGAGCTAATAA
1 CGGGATGCTCT-TGAGAGCTAATAA
*
1048570 CGGGATGCTCTTGCGAGCTA
1 CGGGATGCTCTTGAGAGCTA
1048590 TGGTGTGTTT
Statistics
Matches: 93, Mismatches: 18, Indels: 12
0.76 0.15 0.10
Matches are distributed among these distances:
23 1 0.01
24 75 0.81
25 17 0.18
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (24 bp):
CGGGATGCTCTTGAGAGCTAATAA
Found at i:1049856 original size:16 final size:17
Alignment explanation
Indices: 1049835--1049867 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1049825 AAACACGATG
*
1049835 GAAAAATATCA-AAGAA
1 GAAAAAAATCAGAAGAA
1049851 GAAAAAAATCAGAAGAA
1 GAAAAAAATCAGAAGAA
1049868 AATTGTAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.70, C:0.06, G:0.15, T:0.09
Consensus pattern (17 bp):
GAAAAAAATCAGAAGAA
Found at i:1056330 original size:16 final size:15
Alignment explanation
Indices: 1056308--1056349 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
1056298 AGGGAGAGAA
1056308 TAGAAGAAAAAAATG
1 TAGAAGAAAAAAATG
*
1056323 T--AAGAAGAAAATTG
1 TAGAAGAA-AAAAATG
1056337 TAGAAGAAAAAAA
1 TAGAAGAAAAAAA
1056350 GAACATGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
13 5 0.23
14 7 0.32
15 5 0.23
16 5 0.23
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.14
Consensus pattern (15 bp):
TAGAAGAAAAAAATG
Found at i:1058227 original size:26 final size:26
Alignment explanation
Indices: 1058168--1058227 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
1058158 TTTTCTTTTC
** *
1058168 TTTTTCTTTTCATTTTTAGTTTAGGT
1 TTTTTCTTTTCATTTTTAGAGTAGAT
*
1058194 TTTCTCTTTTC-TTTTTAGAGTAGAT
1 TTTTTCTTTTCATTTTTAGAGTAGAT
1058219 TTTATTCTT
1 TTT-TTCTT
1058228 GTAGTTTTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
25 14 0.50
26 14 0.50
ACGTcount: A:0.13, C:0.10, G:0.10, T:0.67
Consensus pattern (26 bp):
TTTTTCTTTTCATTTTTAGAGTAGAT
Found at i:1058665 original size:42 final size:42
Alignment explanation
Indices: 1058597--1058699 Score: 154
Period size: 42 Copynumber: 2.5 Consensus size: 42
1058587 GTATATATGC
* *
1058597 CTAGG-TGAGACGGAGAGGTAACCTTAGGTGGTATCTTTTAGT
1 CTAGGATGAGACTGAGAGGT-ATCTTAGGTGGTATCTTTTAGT
* *
1058639 CTAGGATGAGGCTGGGAGGTATCTTAGGTGGTATCTTTTAGT
1 CTAGGATGAGACTGAGAGGTATCTTAGGTGGTATCTTTTAGT
1058681 CTAGGATGAGACTGAGAGG
1 CTAGGATGAGACTGAGAGG
1058700 AGGTTCCTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
42 43 0.80
43 11 0.20
ACGTcount: A:0.23, C:0.11, G:0.36, T:0.30
Consensus pattern (42 bp):
CTAGGATGAGACTGAGAGGTATCTTAGGTGGTATCTTTTAGT
Found at i:1090499 original size:31 final size:31
Alignment explanation
Indices: 1090461--1090519 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1090451 GTTACTGAAC
1090461 TATTCGAAAGTGTTCATTTAAGTCACTAAAT
1 TATTCGAAAGTGTTCATTTAAGTCACTAAAT
* * *
1090492 TATTCGAAAGTTTTTATTTAAGTTACTA
1 TATTCGAAAGTGTTCATTTAAGTCACTA
1090520 GGCTGTTAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (31 bp):
TATTCGAAAGTGTTCATTTAAGTCACTAAAT
Found at i:1090754 original size:6 final size:6
Alignment explanation
Indices: 1090743--1090768 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1090733 ATGAATTGTA
1090743 AAAGAG AAAGAG AAAGAG AAAGAG AA
1 AAAGAG AAAGAG AAAGAG AAAGAG AA
1090769 CTTTCGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (6 bp):
AAAGAG
Found at i:1092586 original size:39 final size:39
Alignment explanation
Indices: 1092503--1092594 Score: 109
Period size: 40 Copynumber: 2.3 Consensus size: 39
1092493 AGCAGCATTT
*
1092503 TTAGCGGCGTTTGGATAAAAAATGCCGCTAAAGATCGATCA
1 TTAGCGGCGTTT-GATAAAAAATGCCGCTAAAGATAGA-CA
1092544 TTAGCGGCGCTTT-ATAAAAAATGCCGCTGAAA-ATAAGA-A
1 TTAGCGGCG-TTTGATAAAAAATGCCGCT-AAAGAT-AGACA
1092583 TTAGCGGCGTTT
1 TTAGCGGCGTTT
1092595 TCCAAAAAGC
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
38 3 0.06
39 10 0.21
40 17 0.36
41 14 0.30
42 3 0.06
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (39 bp):
TTAGCGGCGTTTGATAAAAAATGCCGCTAAAGATAGACA
Found at i:1092786 original size:114 final size:113
Alignment explanation
Indices: 1092583--1092893 Score: 437
Period size: 114 Copynumber: 2.8 Consensus size: 113
1092573 AAAATAAGAA
*** * * *
1092583 TTAGCGGCGTTTTCCAAAAAGCGCCGC-AAAAAACTAAGCCCAATGGCGCCGTGTTCCAAGCTTT
1 TTAGCGGCGTTTTTGGAAAAGCGCCGCAAAAAAACTAAGCCCAACGGCGCCGTTTTCTAAGCTTT
* * *
1092647 CGGGGATTTAGTGGCGTTTTGAAGAAAGCGCCGCTAATGCTCAGGGCT
66 CGGGGATTTAGAGGCGTTTTTAAGAAAGCGCCGCTAATGCCCAGGGCT
* * *
1092695 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAAACTAAGCCCAACGGTGCCGTTTTCTAAGATT
1 TTAGCGGCGTTTTTGGAAAAGCGCCGC-AAAAAAACTAAGCCCAACGGCGCCGTTTTCTAAGCTT
* *
1092760 TCAGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCCCAGGGCT
65 TCGGGGATTTAGAGGCGTTTTTAAGAAAGCGCCGCTAATGCCCAGGGCT
* * * *
1092809 TTAGTGGCGTTTTTGGAAAAGCGCCGCAAAAAAACTATGCCCAACGGCGCTG-TTTCTGAGCTTT
1 TTAGCGGCGTTTTTGGAAAAGCGCCGCAAAAAAACTAAGCCCAACGGCGCCGTTTTCTAAGCTTT
1092873 CGGGGATTTAGAGGCGTTTTT
66 CGGGGATTTAGAGGCGTTTTT
1092894 GGGAAAGCTC
Statistics
Matches: 175, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
112 52 0.30
113 22 0.13
114 101 0.58
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (113 bp):
TTAGCGGCGTTTTTGGAAAAGCGCCGCAAAAAAACTAAGCCCAACGGCGCCGTTTTCTAAGCTTT
CGGGGATTTAGAGGCGTTTTTAAGAAAGCGCCGCTAATGCCCAGGGCT
Found at i:1092985 original size:73 final size:73
Alignment explanation
Indices: 1092808--1093053 Score: 352
Period size: 73 Copynumber: 3.4 Consensus size: 73
1092798 TGCCCAGGGC
* * * *
1092808 TTTAGTGGCGTTTTTGGAAAAGCGCCGC-AAAAAAACTATGCCCAACGGCGCTG-TTTCTGAGCT
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAAACTAAGCCCAACGGCGCCGTTTTCTGAGCT
1092871 TTCGGGGA
66 TTCGGGGA
* *
1092879 TTTAGAGGCGTTTTTGGGAAAGCTCCGCAAAAAAAAACTAAGCCCAACGGCGCCGTTTTCTGAGC
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGC-AAAAAAAACTAAGCCCAACGGCGCCGTTTTCTGAGC
*
1092944 TTTTGGGGA
65 TTTCGGGGA
* * *
1092953 TTTAGCGGTGTTTTTGGGAAAGCGCCGCAAAAAAAACTAAGCCCAACGGCGCCGTTTTCTAAGAT
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAAACTAAGCCCAACGGCGCCGTTTTCTGAGCT
*
1093018 TTCAGGGA
66 TTCGGGGA
**
1093026 TTTAGCGGCGTTTTTAAGAAAGCGCCGC
1 TTTAGCGGCGTTTTTGGGAAAGCGCCGC
1093054 TAATGCCCAG
Statistics
Matches: 156, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
71 25 0.16
73 89 0.57
74 42 0.27
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (73 bp):
TTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAAACTAAGCCCAACGGCGCCGTTTTCTGAGCT
TTCGGGGA
Found at i:1093471 original size:15 final size:14
Alignment explanation
Indices: 1093451--1093499 Score: 64
Period size: 15 Copynumber: 3.4 Consensus size: 14
1093441 CTATGCTTTA
1093451 AGGGTTAGGGGATTT
1 AGGGTTAGGGG-TTT
1093466 AGGGTTAGGGG-TT
1 AGGGTTAGGGGTTT
*
1093479 AGGGATTTGGGGTTT
1 AGGG-TTAGGGGTTT
1093494 AGGGTT
1 AGGGTT
1093500 TCAACAGTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
13 6 0.19
14 8 0.26
15 17 0.55
ACGTcount: A:0.16, C:0.00, G:0.49, T:0.35
Consensus pattern (14 bp):
AGGGTTAGGGGTTT
Found at i:1093478 original size:22 final size:22
Alignment explanation
Indices: 1093447--1093497 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
1093437 AGTGCTATGC
*
1093447 TTTAAGGGTTAGGGGATTTAGGG
1 TTTAGGGGTTA-GGGATTTAGGG
*
1093470 -TTAGGGGTTAGGGATTTGGGG
1 TTTAGGGGTTAGGGATTTAGGG
1093491 TTTAGGG
1 TTTAGGG
1093498 TTTCAACAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.18, C:0.00, G:0.47, T:0.35
Consensus pattern (22 bp):
TTTAGGGGTTAGGGATTTAGGG
Found at i:1093498 original size:21 final size:21
Alignment explanation
Indices: 1093451--1093499 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
1093441 CTATGCTTTA
1093451 AGGGTTAGGGGATTTAGGGTT
1 AGGGTTAGGGGATTTAGGGTT
*
1093472 AGGGGTTA-GGGATTTGGGGTTT
1 A-GGGTTAGGGGATTTAGGG-TT
1093494 AGGGTT
1 AGGGTT
1093500 TCAACAGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.16, C:0.00, G:0.49, T:0.35
Consensus pattern (21 bp):
AGGGTTAGGGGATTTAGGGTT
Found at i:1093898 original size:15 final size:17
Alignment explanation
Indices: 1093870--1093904 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
1093860 GGATAGGACC
1093870 AAAATATAAGAAAATAT
1 AAAATATAAGAAAATAT
1093887 AAAATA-AA-AAAATAT
1 AAAATATAAGAAAATAT
1093902 AAA
1 AAA
1093905 TGAAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.56
16 2 0.11
17 6 0.33
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (17 bp):
AAAATATAAGAAAATAT
Found at i:1094532 original size:2 final size:2
Alignment explanation
Indices: 1094527--1094559 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1094517 TTTTGACTTG
*
1094527 TA TA TA TA TA CA 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 TA T
1094560 GTTATATGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1095276 original size:194 final size:194
Alignment explanation
Indices: 1094966--1095362 Score: 494
Period size: 194 Copynumber: 2.0 Consensus size: 194
1094956 GTCTTTGAAA
* * * *
1094966 AATGGGAATACGGGTTTTGTTTAACTGTCTCAATTGCTTCTCGACAAAACCCAGTTTACAACATT
1 AATGGGAATACAGGTGTTGTTTAACTGTCTCAATTGCTTCTCAACAAAACCCAGTTTACAACATA
* * * *
1095031 TCTGACGTTATAAAATCTTGATTCCTTACTGATTCTGCTGAATTTGTGTTTATGGTTGTCGATAT
66 TCCGAAGCTATAAAATCTTGATTCCTTACTGATTCTGCTGAATTTGTGTTTATGATTGTCGATAT
* * * * *
1095096 ATGATGTTTGTTGTTGTATATTGCTTTTGAGTTTTACAAAAGTCGAAGAGAAA-CATTTTTAAG
131 ATGATATTTGTTGCTATATATTGCTTTTGAGTTTTACAAAAGTCGAAGAAAAATCACTTTTAAG
* * * * **
1095159 AATGGGAATTCAGGTGTTGTTTAACTGTC-CGAATTTCTTCTTAACAAAACCCCATTTTATGACA
1 AATGGGAATACAGGTGTTGTTTAACTGTCTC-AATTGCTTCTCAACAAAA-CCCAGTTTACAACA
* * * *
1095223 TATCCGAAGCTATGAAATCTTGATTCCTTGA-TGTTTCTGCTGGATTTGTGTTTATGATTGTTGA
64 TATCCGAAGCTATAAAATCTTGATTCCTT-ACTGATTCTGCTGAATTTGTGTTTATGATTGTCGA
* * * *
1095287 TATATGCTATTTGTTGCTATATATTGCTTTTGAGTTTTTCAAGAGTCGAAGAAAAATGACTTTTA
128 TATATGATATTTGTTGCTATATATTGCTTTTGAGTTTTACAAAAGTCGAAGAAAAATCACTTTTA
1095352 AG
193 AG
*
1095354 AACGGGAAT
1 AATGGGAAT
1095363 CTGTTTGTCG
Statistics
Matches: 172, Mismatches: 28, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
192 1 0.01
193 41 0.24
194 113 0.66
195 17 0.10
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (194 bp):
AATGGGAATACAGGTGTTGTTTAACTGTCTCAATTGCTTCTCAACAAAACCCAGTTTACAACATA
TCCGAAGCTATAAAATCTTGATTCCTTACTGATTCTGCTGAATTTGTGTTTATGATTGTCGATAT
ATGATATTTGTTGCTATATATTGCTTTTGAGTTTTACAAAAGTCGAAGAAAAATCACTTTTAAG
Found at i:1096969 original size:43 final size:43
Alignment explanation
Indices: 1096860--1097132 Score: 354
Period size: 43 Copynumber: 6.4 Consensus size: 43
1096850 TAAAAAGTCA
** * * * *
1096860 TGTT-TTTAGCGGCGTTTGT-CAAAAAGAGCCACTAAAAGTCT
1 TGTTCTTTAGCGGCGTTTGTGGTAGAAGCGCCGCTAAAGGTCT
* * * * *
1096901 TCTT-TATAGTGGCGTTTGTTGTAGAAGCGCCGCTAAAGGTCA
1 TGTTCTTTAGCGGCGTTTGTGGTAGAAGCGCCGCTAAAGGTCT
* * * *
1096943 TGATCTTTAGCGGCATTTGTGTTAGAAGCGCCGTTAAAGGTCT
1 TGTTCTTTAGCGGCGTTTGTGGTAGAAGCGCCGCTAAAGGTCT
* *
1096986 TGTTCTTTAGCGACGTTTGTGTTAGAAGCGCCGCTAAAGGTCT
1 TGTTCTTTAGCGGCGTTTGTGGTAGAAGCGCCGCTAAAGGTCT
*
1097029 TGTTCTTTAGCGGCGTTTGTGGTAGAAGAGCCGCTAAAGGTCT
1 TGTTCTTTAGCGGCGTTTGTGGTAGAAGCGCCGCTAAAGGTCT
*
1097072 TGTTCTTTAGCGGTGTTTGTGGTAGAAGCGCCGCTAAAGGTCT
1 TGTTCTTTAGCGGCGTTTGTGGTAGAAGCGCCGCTAAAGGTCT
1097115 TGTTCTTTAGCGGCGTTT
1 TGTTCTTTAGCGGCGTTT
1097133 ATTTTTAAAA
Statistics
Matches: 201, Mismatches: 29, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
41 16 0.08
42 17 0.08
43 168 0.84
ACGTcount: A:0.20, C:0.17, G:0.29, T:0.35
Consensus pattern (43 bp):
TGTTCTTTAGCGGCGTTTGTGGTAGAAGCGCCGCTAAAGGTCT
Found at i:1097214 original size:25 final size:25
Alignment explanation
Indices: 1097180--1097240 Score: 113
Period size: 25 Copynumber: 2.4 Consensus size: 25
1097170 ACAGTGGCAT
*
1097180 TTTTTGCGGCGCTTGCCGCAAATAC
1 TTTTAGCGGCGCTTGCCGCAAATAC
1097205 TTTTAGCGGCGCTTGCCGCAAATAC
1 TTTTAGCGGCGCTTGCCGCAAATAC
1097230 TTTTAGCGGCG
1 TTTTAGCGGCG
1097241 TTAAAAGCGC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.16, C:0.26, G:0.26, T:0.31
Consensus pattern (25 bp):
TTTTAGCGGCGCTTGCCGCAAATAC
Found at i:1097273 original size:22 final size:22
Alignment explanation
Indices: 1097243--1097285 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1097233 TAGCGGCGTT
* *
1097243 AAAAGCGCCACTAAAGGCCTAA
1 AAAAACGCCACTAAAAGCCTAA
1097265 AAAAACGCCACTAAAAGCCTA
1 AAAAACGCCACTAAAAGCCTA
1097286 TTTTGGTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.28, G:0.14, T:0.09
Consensus pattern (22 bp):
AAAAACGCCACTAAAAGCCTAA
Found at i:1098680 original size:18 final size:21
Alignment explanation
Indices: 1098640--1098685 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 21
1098630 AATTATAAAT
1098640 TTTTTTATATATTCTTTAGAA
1 TTTTTTATATATTCTTTAGAA
*
1098661 TTTTTTAT-T-TT-TTTATAA
1 TTTTTTATATATTCTTTAGAA
1098679 TTTTTTA
1 TTTTTTA
1098686 AAATATAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 13 0.54
19 2 0.08
20 1 0.04
21 8 0.33
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (21 bp):
TTTTTTATATATTCTTTAGAA
Found at i:1098685 original size:10 final size:10
Alignment explanation
Indices: 1098640--1098685 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
1098630 AATTATAAAT
1098640 TTTTTTATATA
1 TTTTTTATA-A
* *
1098651 TTCTTTAGAA
1 TTTTTTATAA
1098661 TTTTTTAT--
1 TTTTTTATAA
1098669 TTTTTTATAA
1 TTTTTTATAA
1098679 TTTTTTA
1 TTTTTTA
1098686 AAATATAAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
8 8 0.28
10 14 0.48
11 7 0.24
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:1098725 original size:19 final size:20
Alignment explanation
Indices: 1098701--1098745 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
1098691 TAAAGTTTAA
1098701 AATTTTTAAAAA-TATTTTG
1 AATTTTTAAAAATTATTTTG
1098720 AA-TTTTAAAAATTATTTTG
1 AATTTTTAAAAATTATTTTG
1098739 AATTTTT
1 AATTTTT
1098746 TAAATTTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.38
19 11 0.46
20 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (20 bp):
AATTTTTAAAAATTATTTTG
Found at i:1098750 original size:19 final size:19
Alignment explanation
Indices: 1098701--1098751 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
1098691 TAAAGTTTAA
*
1098701 AATTTTTAAAAATATTTTG
1 AATTTTTAAAATTATTTTG
*
1098720 AATTTTAAAAATTATTTTG
1 AATTTTTAAAATTATTTTG
*
1098739 AATTTTTTAAATT
1 AATTTTTAAAATT
1098752 TTTGTTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (19 bp):
AATTTTTAAAATTATTTTG
Found at i:1099525 original size:13 final size:13
Alignment explanation
Indices: 1099504--1099540 Score: 51
Period size: 11 Copynumber: 3.0 Consensus size: 13
1099494 TTAGAATGAA
1099504 GGAGAACACAAGT
1 GGAGAACACAAGT
*
1099517 GGTGAACACAA--
1 GGAGAACACAAGT
1099528 GGAGAACACAAGT
1 GGAGAACACAAGT
1099541 CGCAACCAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
11 10 0.50
13 10 0.50
ACGTcount: A:0.46, C:0.16, G:0.30, T:0.08
Consensus pattern (13 bp):
GGAGAACACAAGT
Found at i:1101234 original size:15 final size:15
Alignment explanation
Indices: 1101214--1101244 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1101204 CAACTCTAAG
1101214 TATCAAAACACCAAT
1 TATCAAAACACCAAT
*
1101229 TATCAAAACCCCAAT
1 TATCAAAACACCAAT
1101244 T
1 T
1101245 GACATACTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.23
Consensus pattern (15 bp):
TATCAAAACACCAAT
Found at i:1115101 original size:20 final size:20
Alignment explanation
Indices: 1115078--1115126 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1115068 AAGGCACTAG
1115078 AGTGCAAACAGAGACACCAA
1 AGTGCAAACAGAGACACCAA
* *
1115098 AGTGTGAAA-AGAGGCACCAA
1 AGTG-CAAACAGAGACACCAA
1115118 AGTGCAAAC
1 AGTGCAAAC
1115127 CCATACAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 3 0.12
20 18 0.75
21 3 0.12
ACGTcount: A:0.47, C:0.20, G:0.24, T:0.08
Consensus pattern (20 bp):
AGTGCAAACAGAGACACCAA
Found at i:1134279 original size:14 final size:15
Alignment explanation
Indices: 1134239--1134280 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
1134229 AGATTCTCAA
1134239 AAACACCATTGGAAAC
1 AAACA-CATTGGAAAC
*
1134255 AAACACA-TGGATAC
1 AAACACATTGGAAAC
1134269 AAACA-ATTGGAA
1 AAACACATTGGAA
1134281 TGGATCGTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 1 0.04
14 15 0.65
15 2 0.09
16 5 0.22
ACGTcount: A:0.52, C:0.19, G:0.14, T:0.14
Consensus pattern (15 bp):
AAACACATTGGAAAC
Found at i:1136068 original size:46 final size:46
Alignment explanation
Indices: 1135998--1136091 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
1135988 GGTTTAAAAG
1135998 ACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGA
* *
1136044 ACCTCGACCCACTATCAAGGATGATAGTAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGA
1136090 AC
1 AC
1136092 GCCACACTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (46 bp):
ACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGA
Found at i:1145273 original size:20 final size:20
Alignment explanation
Indices: 1145250--1145298 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1145240 CAATGTTTAT
*
1145250 ACAGAGTCACCGAA-GTGCAA
1 ACAGAGGCA-CGAATGTGCAA
1145270 ACAGAGGCACGAATGTGCAA
1 ACAGAGGCACGAATGTGCAA
*
1145290 TCAGAGGCA
1 ACAGAGGCA
1145299 TTAAAGTGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.39, C:0.22, G:0.29, T:0.10
Consensus pattern (20 bp):
ACAGAGGCACGAATGTGCAA
Done.