Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 165 of 214
Found at i:48818887 original size:9 final size:9
Alignment explanation
Indices: 48818873--48818900 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
48818863 TTTTGTTACA
48818873 ACAATTAAT
1 ACAATTAAT
48818882 ACAATTAAT
1 ACAATTAAT
48818891 ACAATTAAT
1 ACAATTAAT
48818900 A
1 A
48818901 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:48818921 original size:68 final size:68
Alignment explanation
Indices: 48818843--48819052 Score: 388
Period size: 68 Copynumber: 3.1 Consensus size: 68
48818833 TCAAGTTTAT
*
48818843 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
48818908 AAA
66 AAA
48818911 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
48818976 AAA
66 AAA
48818979 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
48819042 AAT
66 AAA
48819045 TTTACTAA
1 TTTACTAA
48819053 CAATTAGTTT
Statistics
Matches: 140, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
66 27 0.19
67 1 0.01
68 112 0.80
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:48818953 original size:9 final size:9
Alignment explanation
Indices: 48818941--48818968 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
48818931 TTTTATTACA
48818941 ACAATTAAT
1 ACAATTAAT
48818950 ACAATTAAT
1 ACAATTAAT
48818959 ACAATTAAT
1 ACAATTAAT
48818968 A
1 A
48818969 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:48819196 original size:5 final size:5
Alignment explanation
Indices: 48819186--48819216 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
48819176 GCCCGTATCT
*
48819186 CGGGC CGGGC CGGAC CGGGC CGGGC CGGGC C
1 CGGGC CGGGC CGGGC CGGGC CGGGC CGGGC C
48819217 TAGTAAACGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.03, C:0.42, G:0.55, T:0.00
Consensus pattern (5 bp):
CGGGC
Found at i:48827117 original size:21 final size:23
Alignment explanation
Indices: 48827091--48827133 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
48827081 ATAGATTTTG
48827091 TTTTATAAA-TTTTAAA-TATTA
1 TTTTATAAAGTTTTAAAGTATTA
48827112 TTTTATAAAGTTTTAAAGTATT
1 TTTTATAAAGTTTTAAAGTATT
48827134 TTGTAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 9 0.45
22 7 0.35
23 4 0.20
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (23 bp):
TTTTATAAAGTTTTAAAGTATTA
Found at i:48827135 original size:20 final size:21
Alignment explanation
Indices: 48827091--48827141 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
48827081 ATAGATTTTG
*
48827091 TTTTATAAATTTTAAATATTA
1 TTTTATAAATTTTAAATAGTA
48827112 TTTTATAAAGTTTT-AA-AGTA
1 TTTTATAAA-TTTTAAATAGTA
*
48827132 TTTTGTAAAT
1 TTTTATAAAT
48827142 ATTTCTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 1 0.04
20 11 0.41
21 11 0.41
22 4 0.15
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (21 bp):
TTTTATAAATTTTAAATAGTA
Found at i:48831124 original size:41 final size:41
Alignment explanation
Indices: 48831064--48831214 Score: 257
Period size: 41 Copynumber: 3.7 Consensus size: 41
48831054 AGACTATACG
48831064 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAA
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAA
*
48831105 CCTAGCAGGCTAAGCGCCGGTGATCTGAATCAGGTTATAAA
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAA
* *
48831146 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAA
*
48831187 CCTAGCAAGCTAAGTGCCGGTGAATCTG
1 CCTAGCAGGCTAAGTGCCGGTG-ATCTG
48831215 TTAAATTAAG
Statistics
Matches: 104, Mismatches: 5, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
41 99 0.95
42 5 0.05
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.23
Consensus pattern (41 bp):
CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAA
Found at i:48832629 original size:45 final size:45
Alignment explanation
Indices: 48832578--48832669 Score: 166
Period size: 45 Copynumber: 2.0 Consensus size: 45
48832568 AATAATTTAA
*
48832578 GTAAATATTTTCCATTAAAATTTGTCACTTTAGAATTTTGATTAT
1 GTAAATATTTTCCATTAAAATTTATCACTTTAGAATTTTGATTAT
*
48832623 GTAAATATTTTCCATTAAAATTTATCACTTTATAATTTTGATTAT
1 GTAAATATTTTCCATTAAAATTTATCACTTTAGAATTTTGATTAT
48832668 GT
1 GT
48832670 TGTTCCCATA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.34, C:0.09, G:0.08, T:0.50
Consensus pattern (45 bp):
GTAAATATTTTCCATTAAAATTTATCACTTTAGAATTTTGATTAT
Found at i:48833165 original size:31 final size:30
Alignment explanation
Indices: 48833096--48833165 Score: 70
Period size: 31 Copynumber: 2.3 Consensus size: 30
48833086 AAGTTAACCT
* *
48833096 CTGAACTTGAAAATTGTTCTCATATTGGGA
1 CTGAACTTGAAAATTGATCCCATATTGGGA
* *
48833126 CATAAACTTGGAAATTGATCCCA-ATTTGGGGA
1 C-TGAACTTGAAAATTGATCCCATA-TT-GGGA
48833158 CTGAACTT
1 CTGAACTT
48833166 TAGGGTTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
30 2 0.06
31 25 0.78
32 5 0.16
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (30 bp):
CTGAACTTGAAAATTGATCCCATATTGGGA
Found at i:48833286 original size:59 final size:63
Alignment explanation
Indices: 48833189--48833329 Score: 136
Period size: 59 Copynumber: 2.3 Consensus size: 63
48833179 AAAAATTAGG
*
48833189 GACTAACTT-GAACAAAAAAAAGGTTCTAAGTCCCAATGT-AGGAACAAATGCCAAGTTTA-AT
1 GACTAACTTGGAACAAAAAAAAGGTTCTAAGTCCCAATGTGA-GAACAAATGCAAAGTTTAGAT
* * * *
48833250 GACTAACTTGGAA-AAAACAAA-GTTC-ATA-TCCTAATGTGAGAACAATTTCAAAGTTTAGAT
1 GACTAACTTGGAACAAAAAAAAGGTTCTA-AGTCCCAATGTGAGAACAAATGCAAAGTTTAGAT
* **
48833310 -ACTAACATGGATGAAAAAAA
1 GACTAACTTGGAACAAAAAAA
48833330 CATTTAGACC
Statistics
Matches: 67, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
59 34 0.51
60 14 0.21
61 16 0.24
62 3 0.04
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.24
Consensus pattern (63 bp):
GACTAACTTGGAACAAAAAAAAGGTTCTAAGTCCCAATGTGAGAACAAATGCAAAGTTTAGAT
Found at i:48836719 original size:26 final size:26
Alignment explanation
Indices: 48836648--48836720 Score: 101
Period size: 26 Copynumber: 2.8 Consensus size: 26
48836638 TATTTTCTTG
48836648 AAATTTTACTAGAGGTAAAATCGTCA
1 AAATTTTACTAGAGGTAAAATCGTCA
* * * *
48836674 AAATTTTACCATAGGCAAAATCTTCA
1 AAATTTTACTAGAGGTAAAATCGTCA
*
48836700 AAATTTTACTAGGGGTAAAAT
1 AAATTTTACTAGAGGTAAAAT
48836721 AGGGATGAGA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (26 bp):
AAATTTTACTAGAGGTAAAATCGTCA
Found at i:48838782 original size:18 final size:18
Alignment explanation
Indices: 48838759--48838794 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
48838749 ATACGAGTAC
48838759 ACAGATCAGGACAAATTT
1 ACAGATCAGGACAAATTT
48838777 ACAGATCAGGACAAATTT
1 ACAGATCAGGACAAATTT
48838795 GCTTCTAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.22
Consensus pattern (18 bp):
ACAGATCAGGACAAATTT
Found at i:48842599 original size:6 final size:6
Alignment explanation
Indices: 48842590--48842630 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
48842580 AAAATAATAA
48842590 TTGGGT TTGGGT TTGGGT TTGGGT TTGGGT TTGGGT TTGGG
1 TTGGGT TTGGGT TTGGGT TTGGGT TTGGGT TTGGGT TTGGG
48842631 GTTTAAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (6 bp):
TTGGGT
Found at i:48846487 original size:16 final size:14
Alignment explanation
Indices: 48846466--48846503 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 14
48846456 AAAAGAAAAT
48846466 AAAGTAAAGAAATGAA
1 AAAGTAAA-AAAT-AA
48846482 AAAGTAAAAAATAA
1 AAAGTAAAAAATAA
48846496 AAA-TAAAA
1 AAAGTAAAA
48846504 CAAAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.23
14 5 0.23
15 4 0.18
16 8 0.36
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.13
Consensus pattern (14 bp):
AAAGTAAAAAATAA
Found at i:48846498 original size:15 final size:16
Alignment explanation
Indices: 48846466--48846498 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
48846456 AAAAGAAAAT
*
48846466 AAAGTAAAGAAATGAA
1 AAAGTAAAGAAATAAA
48846482 AAAGTAAA-AAATAAA
1 AAAGTAAAGAAATAAA
48846497 AA
1 AA
48846499 TAAAACAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (16 bp):
AAAGTAAAGAAATAAA
Found at i:48864455 original size:41 final size:41
Alignment explanation
Indices: 48864410--48864487 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
48864400 AATCCAAATA
** *
48864410 TGATACACTGGCACGAAGCCTGCTAGGCATAAAGCCTGATC
1 TGATACACCAGCACAAAGCCTGCTAGGCATAAAGCCTGATC
*
48864451 TGATACACCAGCATAAAGCCTGCTAGGCATAAAGCCT
1 TGATACACCAGCACAAAGCCTGCTAGGCATAAAGCCT
48864488 ACTAGGCACA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.32, C:0.27, G:0.22, T:0.19
Consensus pattern (41 bp):
TGATACACCAGCACAAAGCCTGCTAGGCATAAAGCCTGATC
Found at i:48864482 original size:16 final size:16
Alignment explanation
Indices: 48864461--48864504 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
48864451 TGATACACCA
48864461 GCATAAAGCCTGCTAG
1 GCATAAAGCCTGCTAG
*
48864477 GCATAAAGCCTACTAG
1 GCATAAAGCCTGCTAG
*
48864493 GCACAAAGCCTG
1 GCATAAAGCCTG
48864505 AATATAAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.34, C:0.27, G:0.23, T:0.16
Consensus pattern (16 bp):
GCATAAAGCCTGCTAG
Found at i:48866639 original size:28 final size:28
Alignment explanation
Indices: 48866600--48866653 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
48866590 CGACCAGTTT
* *
48866600 AAAAAAATATTAAAATAAAGATGTTTAA
1 AAAAAAACATTAAAATAAAAATGTTTAA
**
48866628 AAAAAAACATTACTATAAAAATGTTT
1 AAAAAAACATTAAAATAAAAATGTTT
48866654 TTATTTTTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.61, C:0.04, G:0.06, T:0.30
Consensus pattern (28 bp):
AAAAAAACATTAAAATAAAAATGTTTAA
Found at i:48873372 original size:21 final size:22
Alignment explanation
Indices: 48873333--48873373 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
48873323 GAATAACAAT
*
48873333 AGAAAGAAAGAAGAGAAAATGG
1 AGAAAGAAAGAAGAAAAAATGG
*
48873355 AGAAGGAAA-AAGAAAAAAT
1 AGAAAGAAAGAAGAAAAAAT
48873374 TAGAAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.68, C:0.00, G:0.27, T:0.05
Consensus pattern (22 bp):
AGAAAGAAAGAAGAAAAAATGG
Found at i:48877386 original size:50 final size:50
Alignment explanation
Indices: 48877262--48877510 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
48877252 GATAATAACA
* * ** * *
48877262 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
48877313 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
48877363 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
48877413 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
48877468 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
48877511 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:48877440 original size:100 final size:104
Alignment explanation
Indices: 48877261--48877510 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
48877251 TGATAATAAC
**
48877261 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
48877326 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
48877363 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
48877426 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
48877468 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
48877511 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:48877626 original size:13 final size:13
Alignment explanation
Indices: 48877605--48877636 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
48877595 GCTTGGATCA
*
48877605 TCATCAAATAAAT
1 TCATAAAATAAAT
48877618 TCATAAAATAAAT
1 TCATAAAATAAAT
48877631 TCATAA
1 TCATAA
48877637 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:48877883 original size:30 final size:30
Alignment explanation
Indices: 48877848--48877905 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
48877838 CCTCGACTCT
*
48877848 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
48877878 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
48877906 AAGGCTCAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:48882551 original size:3 final size:3
Alignment explanation
Indices: 48882543--48882628 Score: 145
Period size: 3 Copynumber: 28.7 Consensus size: 3
48882533 TTATCTACAA
* * *
48882543 TAC TAC TAC TAC TAC TAC CAC TAC TAC TAC TAC TAT TAC TAC TAG TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
48882591 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
48882629 TGGAGCACTC
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.34, C:0.31, G:0.01, T:0.34
Consensus pattern (3 bp):
TAC
Found at i:48885442 original size:118 final size:120
Alignment explanation
Indices: 48885232--48885468 Score: 433
Period size: 118 Copynumber: 2.0 Consensus size: 120
48885222 GGAGTCATGA
* *
48885232 ATTCCGAACATAAACCATACAACGGACATGAAGAATGCAAAAAAAAAAAACCCTTTAACTTCGTT
1 ATTCCGAACATAAACCATACAACGAACATGAAAAATGCAAAAAAAAAAAACCCTTTAACTTCGTT
48885297 ATTTCAATCAAAATTTCATTTTAATTTTATAGACTTTTAATAAATATATGAGTTG
66 ATTTCAATCAAAATTTCATTTTAATTTTATAGACTTTTAATAAATATATGAGTTG
48885352 ATTCCGAACATAAACCATACAACGAACATGAAAAATGC-AAAAAAAAAAA-CCTTTAACTTCGTT
1 ATTCCGAACATAAACCATACAACGAACATGAAAAATGCAAAAAAAAAAAACCCTTTAACTTCGTT
*
48885415 ATTTCAATCAAAATTTCATTTTAATTTTATAGACTTTTAATAAATATATTAGTT
66 ATTTCAATCAAAATTTCATTTTAATTTTATAGACTTTTAATAAATATATGAGTT
48885469 ACCTCTTTCA
Statistics
Matches: 114, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
118 67 0.59
119 11 0.10
120 36 0.32
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (120 bp):
ATTCCGAACATAAACCATACAACGAACATGAAAAATGCAAAAAAAAAAAACCCTTTAACTTCGTT
ATTTCAATCAAAATTTCATTTTAATTTTATAGACTTTTAATAAATATATGAGTTG
Found at i:48889345 original size:45 final size:44
Alignment explanation
Indices: 48889281--48889391 Score: 134
Period size: 45 Copynumber: 2.5 Consensus size: 44
48889271 TAATCTATAG
*
48889281 CTTCAATCTGTTCCACTGCAACTTCAG-GAAAATAAGATCCGCTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGAG-AAATAAGATCCG-TAT
* * * **
48889326 CTTCAGTCTGCTCCACTGCAACTTCAGAGAGATAAGGTTTGTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGAGAAATAAGATCCGTAT
*
48889370 CTTCAATCTGCCCCACTGCAAC
1 CTTCAATCTGCTCCACTGCAAC
48889392 CTCAAGGGAT
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
44 23 0.40
45 33 0.58
46 1 0.02
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (44 bp):
CTTCAATCTGCTCCACTGCAACTTCAGAGAAATAAGATCCGTAT
Found at i:48889386 original size:44 final size:45
Alignment explanation
Indices: 48889149--48889405 Score: 142
Period size: 41 Copynumber: 5.8 Consensus size: 45
48889139 GGATTAATAG
* * * * *
48889149 CTTCAATCTGCTCCACTGCAACTTTAGGGAGATAATAT-TG--GT
1 CTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATCCGCTAT
* * * **
48889191 -TT-AACCTACTCCACTGCAACTTCAGAGAGATAAGGTTTG--AT
1 CTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATCCGCTAT
* * * * **
48889232 -AT-GATCTGCTCTACTGTAACTTCAGAGAGATAAGATCTATAATCTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATC----CGCTAT
* *
48889279 AGCTTCAATCTGTTCCACTGCAACTTCAG-GAAAATAAGATCCGCTAT
1 --CTTCAATCTGCTCCACTGCAACTTCAGAG-AGATAAGATCCGCTAT
* * **
48889326 CTTCAGTCTGCTCCACTGCAACTTCAGAGAGATAAGGTTTG-TAT
1 CTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATCCGCTAT
* * *
48889370 CTTCAATCTGCCCCACTGCAACCTCA-AGGGATAAGA
1 CTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGA
48889406 CTTGTGGCTC
Statistics
Matches: 166, Mismatches: 36, Indels: 25
0.73 0.16 0.11
Matches are distributed among these distances:
40 28 0.17
41 34 0.20
43 8 0.05
44 26 0.16
45 33 0.20
46 1 0.01
47 6 0.04
50 2 0.01
51 28 0.17
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (45 bp):
CTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAGATCCGCTAT
Found at i:48890233 original size:24 final size:24
Alignment explanation
Indices: 48890181--48890233 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
48890171 TGCCCCTACT
**
48890181 GTAATCTTCAAAGTTCAATCTGCC
1 GTAATCTTCAAAGTTCAATCCACC
* * *
48890205 ATAATCTTCAAGGTTCAGTCCACC
1 GTAATCTTCAAAGTTCAATCCACC
48890229 GTAAT
1 GTAAT
48890234 TTTGGGACAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (24 bp):
GTAATCTTCAAAGTTCAATCCACC
Found at i:48890895 original size:108 final size:108
Alignment explanation
Indices: 48890703--48890899 Score: 295
Period size: 108 Copynumber: 1.8 Consensus size: 108
48890693 GAAAAATGCT
* *
48890703 TGAAAAAGATTATCATAATGGACAAGATCAAATTTTATTGAGAGCAAAGCTCTAAACAAATAAAT
1 TGAAAAAGATTATCACAATGGACAAGATCAAATTTTATTGAGAGCAAAGCTCGAAACAAATAAAT
* *
48890768 TAATCAGGATAGCAAATTTTGCTAAAATTCAAAGTGAATAAGA
66 TAATCAAGATAACAAATTTTGCTAAAATTCAAAGTGAATAAGA
** * * * *
48890811 TGAAAAAGATTATCACAATGGACAAGATGGAATTTTGTTGAGAGCAAAGCTCGAGACGAATAGAT
1 TGAAAAAGATTATCACAATGGACAAGATCAAATTTTATTGAGAGCAAAGCTCGAAACAAATAAAT
*
48890876 TAATCAAGATAACATATTTTGCTA
66 TAATCAAGATAACAAATTTTGCTA
48890900 GAATAAAAAA
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
108 78 1.00
ACGTcount: A:0.45, C:0.11, G:0.17, T:0.27
Consensus pattern (108 bp):
TGAAAAAGATTATCACAATGGACAAGATCAAATTTTATTGAGAGCAAAGCTCGAAACAAATAAAT
TAATCAAGATAACAAATTTTGCTAAAATTCAAAGTGAATAAGA
Found at i:48902627 original size:19 final size:19
Alignment explanation
Indices: 48902603--48902639 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
48902593 TAAATGAACA
*
48902603 AATAATAGCAATAATAATT
1 AATAATAACAATAATAATT
*
48902622 AATAATAACAGTAATAAT
1 AATAATAACAATAATAAT
48902640 ATCAAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.30
Consensus pattern (19 bp):
AATAATAACAATAATAATT
Found at i:48904347 original size:23 final size:23
Alignment explanation
Indices: 48904316--48904360 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
48904306 TACAATCAAT
48904316 ATTACACATATC-AACAAGCCATA
1 ATTACACAT-TCAAACAAGCCATA
*
48904339 ATTAGACATTCAAAACAAGCCA
1 ATTACACATTC-AAACAAGCCA
48904361 AAATAAGTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 2 0.11
23 8 0.42
24 9 0.47
ACGTcount: A:0.49, C:0.24, G:0.07, T:0.20
Consensus pattern (23 bp):
ATTACACATTCAAACAAGCCATA
Found at i:48910947 original size:33 final size:33
Alignment explanation
Indices: 48910910--48910979 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
48910900 GGTCTTACGT
*
48910910 TCATAGTGCAATAACCCAGT-TATGGTCTTATCA
1 TCATAATGCAATAACCCA-TCTATGGTCTTATCA
* *
48910943 TCATAATGCCATAGCCCATCTATGGTCTTA-CA
1 TCATAATGCAATAACCCATCTATGGTCTTATCA
48910975 T-ATAA
1 TCATAA
48910980 ACACTGCCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 4 0.12
32 4 0.12
33 25 0.76
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (33 bp):
TCATAATGCAATAACCCATCTATGGTCTTATCA
Found at i:48910990 original size:101 final size:101
Alignment explanation
Indices: 48910803--48911042 Score: 399
Period size: 101 Copynumber: 2.4 Consensus size: 101
48910793 AATTCATCCT
* * *
48910803 TTACATTCATAGTGCCATAACCCAATTATGGTCTTGTCATCAGAATGCCATAGCCCAGCTATGGT
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGCTATGGT
48910868 CTTACATATAAACAATACCATGGTCCAACCATGGTC
66 CTTACATATAAACAATACCATGGTCCAACCATGGTC
* * *
48910904 TTACGTTCATAGTGCAATAACCCAGTTATGGTCTTATCATCATAATGCCATAGCCCATCTATGGT
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGCTATGGT
* *
48910969 CTTACATATAAACACTGCCATGGTCCAACCATGGTC
66 CTTACATATAAACAATACCATGGTCCAACCATGGTC
*
48911005 TTACGTTCATTGTGCCATAACCCAGTTATGGTCTTATC
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATC
48911043 CGGCAATTCA
Statistics
Matches: 129, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
101 129 1.00
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.31
Consensus pattern (101 bp):
TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGCTATGGT
CTTACATATAAACAATACCATGGTCCAACCATGGTC
Found at i:48917681 original size:3 final size:3
Alignment explanation
Indices: 48917673--48917699 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
48917663 AAGCATAAAC
48917673 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
48917700 CATTGGAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:48918481 original size:12 final size:11
Alignment explanation
Indices: 48918458--48918491 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
48918448 GAAAGGTAAA
48918458 TTTTTTTATTT
1 TTTTTTTATTT
*
48918469 TATTTTTATTT
1 TTTTTTTATTT
48918480 TTTTTGTTATTT
1 TTTTT-TTATTT
48918492 ATTCTTGGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.12, C:0.00, G:0.03, T:0.85
Consensus pattern (11 bp):
TTTTTTTATTT
Found at i:48919646 original size:88 final size:88
Alignment explanation
Indices: 48919514--48919703 Score: 362
Period size: 88 Copynumber: 2.2 Consensus size: 88
48919504 ATCTATTCCA
48919514 CTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAA
1 CTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAA
48919579 TCTGCCATCTTCGATCTGCTTCG
66 TCTGCCATCTTCGATCTGCTTCG
* *
48919602 CTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTGAAA
1 CTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAA
48919667 TCTGCCATCTTCGATCTGCTTCG
66 TCTGCCATCTTCGATCTGCTTCG
48919690 CTGCCAAATACAGG
1 CTGCCAAATACAGG
48919704 AAGGCAAGAT
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 100 1.00
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (88 bp):
CTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAA
TCTGCCATCTTCGATCTGCTTCG
Found at i:48919757 original size:44 final size:44
Alignment explanation
Indices: 48919666--48920105 Score: 325
Period size: 44 Copynumber: 10.2 Consensus size: 44
48919656 GGGAGGTGAA
* * *
48919666 ATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAG
1 ATCTGCTATCTTCGATCTACTTC-CTGCC-AATACAGGAAGACAAG
* * * *
48919712 ATTTG-TAATCTTCGATCTACTTCATGCCAATACATGAAGATAAG
1 ATCTGCT-ATCTTCGATCTACTTCCTGCCAATACAGGAAGACAAG
* ** * **
48919756 ATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTC-CTGCCAATACAGGAAGACAAG
* * * * *
48919801 ATCTGC-ATCTTCGATCCACTTCCTACCAATATAGGAAGATAGG
1 ATCTGCTATCTTCGATCTACTTCCTGCCAATACAGGAAGACAAG
* *
48919844 ATCTGCTACCTTCGATCTACTTCAC-GCCAATACATGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTC-CTGCCAATACAGGAAGACAAG
* * ** **
48919888 ATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTC-CTGCCAATACAGGAAGACAAG
* * * * *
48919933 ATCTGC-ATCTTCGATCCACTTCCTACCAATATAGGAAGATAGG
1 ATCTGCTATCTTCGATCTACTTCCTGCCAATACAGGAAGACAAG
* *
48919976 ATCTGCTACCTTCGATCTACTTCAC-GCCAATACATGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTC-CTGCCAATACAGGAAGACAAG
* * * **
48920020 ATC-G--ATC-T--A-CTTC-GCC-ACCAATATGGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTCCTGCCAATACAGGAAGACAAG
* * * * *
48920055 ATCTGC-ATCTTCGATCCACTTCCTACCAATATAGGAAGATAGG
1 ATCTGCTATCTTCGATCTACTTCCTGCCAATACAGGAAGACAAG
48920098 ATCTGCTA
1 ATCTGCTA
48920106 CCGCCTAGTG
Statistics
Matches: 311, Mismatches: 66, Indels: 36
0.75 0.16 0.09
Matches are distributed among these distances:
35 19 0.06
36 2 0.01
37 6 0.02
38 2 0.01
40 2 0.01
41 4 0.01
42 2 0.01
43 68 0.22
44 140 0.45
45 47 0.15
46 19 0.06
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (44 bp):
ATCTGCTATCTTCGATCTACTTCCTGCCAATACAGGAAGACAAG
Found at i:48919857 original size:132 final size:132
Alignment explanation
Indices: 48919721--48920107 Score: 668
Period size: 132 Copynumber: 3.0 Consensus size: 132
48919711 GATTTGTAAT
* *
48919721 CTTCGATCTACTTCATGCCAATACATGAAGATAAGATCTGCTTTCTTCGATCTACTTCGCCACCA
1 CTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCA
*
48919786 GTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCT
66 ATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCT
48919851 AC
131 AC
*
48919853 CTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCA
1 CTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCA
48919918 ATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCT
66 ATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCT
48919983 AC
131 AC
48919985 CTTCGATCTACTTCACGCCAATACATGAAGACAAGA----------TCGATCTACTTCGCCACCA
1 CTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCA
48920040 ATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCT
66 ATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCT
48920105 AC
131 AC
48920107 C
1 C
48920108 GCCTAGTGTT
Statistics
Matches: 250, Mismatches: 5, Indels: 10
0.94 0.02 0.04
Matches are distributed among these distances:
122 86 0.34
132 164 0.66
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.27
Consensus pattern (132 bp):
CTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCA
ATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCT
AC
Found at i:48920093 original size:78 final size:78
Alignment explanation
Indices: 48919943--48920093 Score: 180
Period size: 78 Copynumber: 1.9 Consensus size: 78
48919933 ATCTGCATCT
* * * * *
48919943 TCGATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATA
1 TCGATCCACTTCCCACCAATATAGGAAGACAAGATCTGCTACCTTCGATCCACTTCACACCAATA
*
48920008 CATGAAGACAAGA
66 CAGGAAGACAAGA
* * *
48920021 TCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTACCAA
1 TCGATCCACTTC-CCACCAATATAGGAAGACAAGATCTGCTACCTTCGATCCACTTCAC-ACCAA
*
48920084 TATAGGAAGA
64 TACAGGAAGA
48920094 TAGGATCTGC
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
77 1 0.02
78 37 0.61
79 23 0.38
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (78 bp):
TCGATCCACTTCCCACCAATATAGGAAGACAAGATCTGCTACCTTCGATCCACTTCACACCAATA
CAGGAAGACAAGA
Found at i:48932449 original size:23 final size:22
Alignment explanation
Indices: 48932416--48932483 Score: 61
Period size: 23 Copynumber: 3.1 Consensus size: 22
48932406 TAAGCTCTTC
*
48932416 TTGTTTTATTGGATTATTTTTTA
1 TTGTTTAATTGGATTA-TTTTTA
48932439 TTGTTTAATTGG-TTGATTTTTA
1 TTGTTTAATTGGATT-ATTTTTA
* *
48932461 --GTTTAATTAGATTAATTTATA
1 TTGTTTAATTGGATT-ATTTTTA
48932482 TT
1 TT
48932484 AATTTGATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 9 0.24
21 8 0.22
22 8 0.22
23 12 0.32
ACGTcount: A:0.24, C:0.00, G:0.13, T:0.63
Consensus pattern (22 bp):
TTGTTTAATTGGATTATTTTTA
Found at i:48947509 original size:28 final size:30
Alignment explanation
Indices: 48947464--48947521 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 30
48947454 TTTTTTTTCC
48947464 TTCCTTTCCTTTTAATTTTT-CTT-ATTCT
1 TTCCTTTCCTTTTAATTTTTCCTTCATTCT
*
48947492 TTCCTTT-CTTTATCATTTTTCCTTCATTCT
1 TTCCTTTCCTTT-TAATTTTTCCTTCATTCT
48947522 CTTCTCTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 4 0.15
28 14 0.54
29 3 0.12
30 5 0.19
ACGTcount: A:0.10, C:0.24, G:0.00, T:0.66
Consensus pattern (30 bp):
TTCCTTTCCTTTTAATTTTTCCTTCATTCT
Found at i:48952153 original size:71 final size:71
Alignment explanation
Indices: 48952072--48952269 Score: 236
Period size: 71 Copynumber: 2.8 Consensus size: 71
48952062 GAATTAATTT
* * * *
48952072 GATGGCTGAGATCTAACATGTGTTGCGGATTCTCAACAGCTTGAGTGAGTATCATCAAATCATTT
1 GATGGTTGAGATCTAACATGTGTTGCGGATTCTCAACAGCTTGAGTGAGCAGCATCAAATCATTC
48952137 TTTATC
66 TTTATC
* * ** * * * *
48952143 GATGGTTGAGATTTAGCACATGTTGCGAATTCTCGATAGCTTGAGTGAGCAGCATCGAATCATTC
1 GATGGTTGAGATCTAACATGTGTTGCGGATTCTCAACAGCTTGAGTGAGCAGCATCAAATCATTC
48952208 TTTATC
66 TTTATC
* * * *
48952214 AATGGTTGAGATCCAACATAG-GTTGCAGATCCTCAACAGCTTGAGTGAGCAGCATC
1 GATGGTTGAGATCTAACAT-GTGTTGCGGATTCTCAACAGCTTGAGTGAGCAGCATC
48952270 GAATAAAACT
Statistics
Matches: 103, Mismatches: 23, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
71 103 1.00
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.31
Consensus pattern (71 bp):
GATGGTTGAGATCTAACATGTGTTGCGGATTCTCAACAGCTTGAGTGAGCAGCATCAAATCATTC
TTTATC
Found at i:48954840 original size:23 final size:23
Alignment explanation
Indices: 48954814--48954866 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
48954804 ATAAGTGCCA
*
48954814 CACTGATATGTAG-CTAAAGCTAC
1 CACTGATATGTAGCCGAAA-CTAC
*
48954837 CACTGAAATGTAGCCGAAACTAC
1 CACTGATATGTAGCCGAAACTAC
48954860 CACTGAT
1 CACTGAT
48954867 CAATAACACT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAACTAC
Found at i:48955118 original size:18 final size:17
Alignment explanation
Indices: 48955092--48955130 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
48955082 ATTTTCCTTC
48955092 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
48955109 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
48955127 CACA
1 CACA
48955131 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:48956056 original size:11 final size:11
Alignment explanation
Indices: 48956040--48956065 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
48956030 TCGGCCAAGT
48956040 TTTGTGCTTTA
1 TTTGTGCTTTA
48956051 TTTGTGCTTTA
1 TTTGTGCTTTA
48956062 TTTG
1 TTTG
48956066 GTGAGTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.08, G:0.19, T:0.65
Consensus pattern (11 bp):
TTTGTGCTTTA
Found at i:48956859 original size:42 final size:42
Alignment explanation
Indices: 48956783--48956933 Score: 187
Period size: 42 Copynumber: 3.6 Consensus size: 42
48956773 TTAGGATACT
**
48956783 GATATGTGATTACGTGTAAGACCATGTCTAGGACATTGGCTTC
1 GATATGTGATT-CGTGTAAGACCATGTCTAGGACATTGGCACC
* * * *
48956826 -ATCATGTGATTCATGTAAGGCCATATCTGGGACATTGGCACC
1 GAT-ATGTGATTCGTGTAAGACCATGTCTAGGACATTGGCACC
* *
48956868 GATATGAGATTCGTGTAAGACCATGTCTAGGACATTGGCATC
1 GATATGTGATTCGTGTAAGACCATGTCTAGGACATTGGCACC
* *
48956910 GATATGAGAATCGTGTAAGACCAT
1 GATATGTGATTCGTGTAAGACCAT
48956934 AGCTAACTGT
Statistics
Matches: 93, Mismatches: 13, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
42 83 0.89
43 10 0.11
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.29
Consensus pattern (42 bp):
GATATGTGATTCGTGTAAGACCATGTCTAGGACATTGGCACC
Found at i:48958074 original size:17 final size:17
Alignment explanation
Indices: 48958052--48958102 Score: 93
Period size: 17 Copynumber: 3.0 Consensus size: 17
48958042 GACTAATCCC
*
48958052 TATACATCACTTAGGTA
1 TATACATTACTTAGGTA
48958069 TATACATTACTTAGGTA
1 TATACATTACTTAGGTA
48958086 TATACATTACTTAGGTA
1 TATACATTACTTAGGTA
48958103 CATGCCACAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (17 bp):
TATACATTACTTAGGTA
Found at i:48958874 original size:23 final size:23
Alignment explanation
Indices: 48958804--48958888 Score: 108
Period size: 21 Copynumber: 3.9 Consensus size: 23
48958794 CCTGATCAGT
48958804 ATACGACACAT-AAGTGCCTGA-
1 ATACGACACATAAAGTGCCTGAG
** *
48958825 A-ACGACACACGAGGTGCCT--G
1 ATACGACACATAAAGTGCCTGAG
48958845 ATACGACACATAAAGTGCCTGAG
1 ATACGACACATAAAGTGCCTGAG
48958868 ATACGACACATAAAGTGCCTG
1 ATACGACACATAAAGTGCCTG
48958889 GTCGGCAAAG
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
20 9 0.17
21 23 0.43
23 22 0.41
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.16
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAG
Found at i:48958886 original size:44 final size:41
Alignment explanation
Indices: 48958804--48958888 Score: 116
Period size: 44 Copynumber: 2.0 Consensus size: 41
48958794 CCTGATCAGT
* *
48958804 ATACGACACATAAGTGCCTGAAACGACACACGAGGTGCCTG
1 ATACGACACATAAGTGCCTGAAACGACACACAAAGTGCCTG
*
48958845 ATACGACACATAAAGTGCCTGAGATACGACACATAAAGTGCCTG
1 ATACGACACAT-AAGTGCCTGA-A-ACGACACACAAAGTGCCTG
48958889 GTCGGCAAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 11 0.29
42 10 0.26
43 1 0.03
44 16 0.42
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.16
Consensus pattern (41 bp):
ATACGACACATAAGTGCCTGAAACGACACACAAAGTGCCTG
Found at i:48959959 original size:16 final size:15
Alignment explanation
Indices: 48959933--48959962 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
48959923 TTGCTCTCTG
48959933 TTTCTTTCTTTCTTA
1 TTTCTTTCTTTCTTA
48959948 TTTCTATTCTTTCTT
1 TTTCT-TTCTTTCTT
48959963 TTGTTATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTCTTTCTTTCTTA
Found at i:48959984 original size:5 final size:5
Alignment explanation
Indices: 48959968--48960003 Score: 63
Period size: 5 Copynumber: 7.0 Consensus size: 5
48959958 TTCTTTTGTT
48959968 ATATA TATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA -ATATA ATATA ATATA ATATA ATATA ATATA
48960004 TTAATAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:48959994 original size:15 final size:16
Alignment explanation
Indices: 48959968--48960043 Score: 68
Period size: 15 Copynumber: 4.6 Consensus size: 16
48959958 TTCTTTTGTT
48959968 ATATATATATAATATA
1 ATATATATATAATATA
48959984 ATATA-ATATAATATA
1 ATATATATATAATATA
*
48959999 ATATAT-TAATAATAATC
1 ATATATAT-ATAAT-ATA
*
48960016 AT-TACTTACATATATATA
1 ATATA--TATATA-ATATA
48960034 ATATATATAT
1 ATATATATAT
48960044 TAACTAGAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
15 16 0.33
16 12 0.25
17 8 0.17
18 8 0.17
19 4 0.08
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATATATATAATATA
Found at i:48970175 original size:23 final size:23
Alignment explanation
Indices: 48970131--48970175 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
48970121 TTATCAGTAT
* * *
48970131 CCACCACCACCATGGTACTACCC
1 CCACCACCACCAAGGCAATACCC
*
48970154 CCACCTCCACCAAGGCAATACC
1 CCACCACCACCAAGGCAATACC
48970176 AACACTAGTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.29, C:0.51, G:0.09, T:0.11
Consensus pattern (23 bp):
CCACCACCACCAAGGCAATACCC
Found at i:48978441 original size:30 final size:30
Alignment explanation
Indices: 48978407--48978467 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
48978397 CACTATTTTG
*
48978407 TATGAGTCATAAAAGTAAGTTTGTTTGTTA
1 TATGAGTCATAAAAGTAAGTTTATTTGTTA
48978437 TATGAGTCATAAAAGTAAGTTTATTTGTTA
1 TATGAGTCATAAAAGTAAGTTTATTTGTTA
48978467 T
1 T
48978468 GTAAAGGAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.34, C:0.03, G:0.18, T:0.44
Consensus pattern (30 bp):
TATGAGTCATAAAAGTAAGTTTATTTGTTA
Found at i:48978826 original size:38 final size:38
Alignment explanation
Indices: 48978783--48978891 Score: 141
Period size: 38 Copynumber: 2.9 Consensus size: 38
48978773 TTCACTATTT
**
48978783 TGTATGAGTCATAAAAATAAAATTGTTTGTTATGCAAAA
1 TGTATGAGTCATAAAAATAAGTTTGTTTGTTATG-AAAA
*
48978822 -GTATGAGTCATAAAAGTAAGTTTGTTTGTTATGAAAA
1 TGTATGAGTCATAAAAATAAGTTTGTTTGTTATGAAAA
* *
48978859 TGTATGAAT-AAAAAAAGTAAGTTTGTTTGTTAT
1 TGTATGAGTCATAAAAA-TAAGTTTGTTTGTTAT
48978892 ATGAGTCATA
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
37 9 0.15
38 53 0.85
ACGTcount: A:0.40, C:0.03, G:0.18, T:0.39
Consensus pattern (38 bp):
TGTATGAGTCATAAAAATAAGTTTGTTTGTTATGAAAA
Found at i:48979027 original size:28 final size:28
Alignment explanation
Indices: 48978986--48979044 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
48978976 TTAATGGTCA
48978986 CAAGACTATCCATGGTTTTCTAACAGTG
1 CAAGACTATCCATGGTTTTCTAACAGTG
*
48979014 CAAGACTATTCATGGTTTTCTAACAGTG
1 CAAGACTATCCATGGTTTTCTAACAGTG
48979042 CAA
1 CAA
48979045 TAAATCCAGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (28 bp):
CAAGACTATCCATGGTTTTCTAACAGTG
Found at i:48981391 original size:93 final size:92
Alignment explanation
Indices: 48981189--48981440 Score: 319
Period size: 93 Copynumber: 2.7 Consensus size: 92
48981179 GTATGTATGT
* * * * * * *
48981189 TTTCATAAAATTTTAATGTCGTATTTGTATTTTGAAAATGCCCAATGTGGTCCTTGAACTATCAA
1 TTTCATAAAATTCTAATGTGGTACTTGAACTTTGAAAATGTCCAATGTGGTACTTGAACTATCAA
48981254 T-TTGTATTTTATTATGGTACATGTAC
66 TATTGTATTTTATTATGGTACATGTAC
* * * *
48981280 TATCATAAAATATCTAATGTGGTACTTGAACTTTGAAAATATCCAATTTGGTGCTTGAACTATCA
1 TTTCATAAAAT-TCTAATGTGGTACTTGAACTTTGAAAATGTCCAATGTGGTACTTGAACTATCA
* *
48981345 ATATGTGT-TTTTATTATGTTACTTGTAC
65 ATAT-TGTATTTTATTATGGTACATGTAC
* * *
48981373 TTTCATAAAATGTCTAATGTGGTGCTTGCACCTTGAAAATGTCCAATGTGGTACTTGAACTATCA
1 TTTCATAAAAT-TCTAATGTGGTACTTGAACTTTGAAAATGTCCAATGTGGTACTTGAACTATCA
48981438 ATA
65 ATA
48981441 CTTTCAAAAA
Statistics
Matches: 138, Mismatches: 20, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
91 10 0.07
92 46 0.33
93 79 0.57
94 3 0.02
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (92 bp):
TTTCATAAAATTCTAATGTGGTACTTGAACTTTGAAAATGTCCAATGTGGTACTTGAACTATCAA
TATTGTATTTTATTATGGTACATGTAC
Found at i:48986231 original size:114 final size:114
Alignment explanation
Indices: 48986010--48986445 Score: 369
Period size: 114 Copynumber: 3.8 Consensus size: 114
48986000 CCAACTCTAT
* * * * * *
48986010 GAATCCTGTAACTAATCCTATGGCTAAAGTTGCATCC-C-GGGAGCACGGTGGTACTACCATTCC
1 GAATCCTGTAACTTATCCCATGGCTAAAGTAGCATCCTCAGAGA-CA-AGT-GT--TACAATTCC
* * * * * * * * *
48986073 AGTAGAGACCAACTTAGACCATGTAAAGGATGAAGATTTGTCCAACAACCCCAA
61 AGTAAATACGAATTTAGAACATGTAAAAGATAAAGGTTTATCCAACAACCCCAA
* * * * *
48986127 GAATCTTGTAACTTATCCCAAGGCTGAAGTAGCATCCTCAGAGACAAGTGTTACCATTCCGGTAA
1 GAATCCTGTAACTTATCCCATGGCTAAAGTAGCATCCTCAGAGACAAGTGTTACAATTCCAGTAA
* *
48986192 ATACGAATTTAGAATATGTAAAAGGTAAAGGTTTATCCAACAACCCCAA
66 ATACGAATTTAGAACATGTAAAAGATAAAGGTTTATCCAACAACCCCAA
* * * *
48986241 GAATCCTGTAAGTTATCCCATGGCTAAAGTTGAAT-CTGCAGAGACGAGTGTTACAATTCCAGTA
1 GAATCCTGTAACTTATCCCATGGCTAAAGTAGCATCCT-CAGAGACAAGTGTTACAATTCCAGTA
* * * * ** * *
48986305 GATACGAATTTAGACCATGTAACAGATAACGGTTTGCCCAATAGCCCCAA
65 AATACGAATTTAGAACATGTAAAAGATAAAGGTTTATCCAACAACCCCAA
* * ** ** *
48986355 GAATCCTGTAACTTCTCCTATGGCTAAAGTTA-CATCCTCAGAGAGGAGCATTACCATTCCAGTA
1 GAATCCTGTAACTTATCCCATGGCTAAAG-TAGCATCCTCAGAGACAAGTGTTACAATTCCAGTA
* * *
48986419 GATATGAACTTT-GACCATGTAAAAGAT
65 AATACGAA-TTTAGAACATGTAAAAGAT
48986446 TCCCATGCCA
Statistics
Matches: 263, Mismatches: 50, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
113 2 0.01
114 214 0.81
115 6 0.02
116 2 0.01
117 33 0.13
118 3 0.01
119 3 0.01
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (114 bp):
GAATCCTGTAACTTATCCCATGGCTAAAGTAGCATCCTCAGAGACAAGTGTTACAATTCCAGTAA
ATACGAATTTAGAACATGTAAAAGATAAAGGTTTATCCAACAACCCCAA
Found at i:48991042 original size:12 final size:12
Alignment explanation
Indices: 48991024--48991096 Score: 67
Period size: 12 Copynumber: 5.9 Consensus size: 12
48991014 CTTTTTAAGC
48991024 TTTTCATCAAGT
1 TTTTCATCAAGT
*
48991036 CTTTCATCAAGTGT
1 TTTTCATCAA--GT
48991050 TTTTCATCAAGT
1 TTTTCATCAAGT
* *
48991062 TTTTAAGCAAAG-
1 TTTTCATC-AAGT
*
48991074 TTTCCATCAAGT
1 TTTTCATCAAGT
*
48991086 TTTTAATCAAG
1 TTTTCATCAAG
48991097 CCTTTATCTT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
11 3 0.06
12 31 0.65
13 3 0.06
14 11 0.23
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44
Consensus pattern (12 bp):
TTTTCATCAAGT
Found at i:48991056 original size:14 final size:14
Alignment explanation
Indices: 48991024--48991065 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
48991014 CTTTTTAAGC
48991024 TTTTCATCAA--GT
1 TTTTCATCAAGTGT
*
48991036 CTTTCATCAAGTGT
1 TTTTCATCAAGTGT
48991050 TTTTCATCAAGT-T
1 TTTTCATCAAGTGT
48991063 TTT
1 TTT
48991066 AAGCAAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 9 0.35
13 4 0.15
14 13 0.50
ACGTcount: A:0.21, C:0.17, G:0.10, T:0.52
Consensus pattern (14 bp):
TTTTCATCAAGTGT
Found at i:48992026 original size:286 final size:286
Alignment explanation
Indices: 48991514--48992088 Score: 1141
Period size: 286 Copynumber: 2.0 Consensus size: 286
48991504 CCGAAAGGAT
48991514 AGATTGTCTAATCGATTTTCCGTGAACACATTTCAGGTTCCAGGTTCCATGAACCTAAAACCTAT
1 AGATTGTCTAATCGATTTTCCGTGAACACATTTCAGGTTCCAGGTTCCATGAACCTAAAACCTAT
48991579 GGAACCTGGAACCTGGAACCTCGAAAAAACCCGTGCCTAAAGCTGAGCTTAGTTTAATTAATTTT
66 GGAACCTGGAACCTGGAACCTCGAAAAAACCCGTGCCTAAAGCTGAGCTTAGTTTAATTAATTTT
48991644 TCTTCAGATTTATTTAACTGTTTTTATTATTTTATTTTCAGCTTTTACTTTTCACGCATTTTTTT
131 TCTTCAGATTTATTTAACTGTTTTTATTATTTTATTTTCAGCTTTTACTTTTCACGCATTTTTTT
48991709 CCTGTTTATTTCAGGTTTCAGGTTTTCAATTTTATCCTCTCCCCAAATTTTTTGGGCACGACAAC
196 CCTGTTTATTTCAGGTTTCAGGTTTTCAATTTTATCCTCTCCCCAAATTTTTTGGGCACGACAAC
48991774 TGCCCAAACACAAATCTAGTCGAGAA
261 TGCCCAAACACAAATCTAGTCGAGAA
48991800 AGATTGTCTAATCGATTTTCCGTGAACACATTTCAGGTTCCAGGTTCCATGAACCTAAAACCTAT
1 AGATTGTCTAATCGATTTTCCGTGAACACATTTCAGGTTCCAGGTTCCATGAACCTAAAACCTAT
48991865 GGAACCTGGAACCTGGAACCTCGAAAAAACCCGTGCCTAAAGCTGAGCTTAGTTTAATTAATTTT
66 GGAACCTGGAACCTGGAACCTCGAAAAAACCCGTGCCTAAAGCTGAGCTTAGTTTAATTAATTTT
48991930 TCTTCAGATTTATTTAACTGTTTTTATTATTTTATTTTCAGCTTTTACTTTTCACGCATTTTTTT
131 TCTTCAGATTTATTTAACTGTTTTTATTATTTTATTTTCAGCTTTTACTTTTCACGCATTTTTTT
48991995 CCTGTTTATTTCAGGTTTCAGGTTTTCAATTTTATCCTCTCCCCAAATTTTTTGGGCACGACAAC
196 CCTGTTTATTTCAGGTTTCAGGTTTTCAATTTTATCCTCTCCCCAAATTTTTTGGGCACGACAAC
*
48992060 TGCCCAGACACAAATCTAGTCGAGAA
261 TGCCCAAACACAAATCTAGTCGAGAA
48992086 AGA
1 AGA
48992089 GAAACAATTT
Statistics
Matches: 288, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
286 288 1.00
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (286 bp):
AGATTGTCTAATCGATTTTCCGTGAACACATTTCAGGTTCCAGGTTCCATGAACCTAAAACCTAT
GGAACCTGGAACCTGGAACCTCGAAAAAACCCGTGCCTAAAGCTGAGCTTAGTTTAATTAATTTT
TCTTCAGATTTATTTAACTGTTTTTATTATTTTATTTTCAGCTTTTACTTTTCACGCATTTTTTT
CCTGTTTATTTCAGGTTTCAGGTTTTCAATTTTATCCTCTCCCCAAATTTTTTGGGCACGACAAC
TGCCCAAACACAAATCTAGTCGAGAA
Found at i:48995497 original size:25 final size:24
Alignment explanation
Indices: 48995456--48995517 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
48995446 TCATTTCAAT
*
48995456 TTGGTTTTTAAAATTTAATGGGTA
1 TTGGGTTTTAAAATTTAATGGGTA
* *
48995480 TTGGGTTTTAAAGTTTTAATGGGTT
1 TTGGGTTTTAAA-ATTTAATGGGTA
**
48995505 TTGACTTTTAAAA
1 TTGGGTTTTAAAA
48995518 GTATTGAGTA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
24 11 0.35
25 20 0.65
ACGTcount: A:0.27, C:0.02, G:0.21, T:0.50
Consensus pattern (24 bp):
TTGGGTTTTAAAATTTAATGGGTA
Found at i:49000068 original size:17 final size:17
Alignment explanation
Indices: 49000046--49000083 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
49000036 CGAAATACAT
*
49000046 AATATACAATAATTTAA
1 AATATAAAATAATTTAA
*
49000063 AATATAAAATAATTTGA
1 AATATAAAATAATTTAA
49000080 AATA
1 AATA
49000084 AATATATAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (17 bp):
AATATAAAATAATTTAA
Found at i:49002060 original size:17 final size:17
Alignment explanation
Indices: 49002038--49002075 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
49002028 CGAAATACAT
*
49002038 AATATACAATAATTTAA
1 AATATAAAATAATTTAA
*
49002055 AATATAAAATAATTTGA
1 AATATAAAATAATTTAA
49002072 AATA
1 AATA
49002076 AATATATAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (17 bp):
AATATAAAATAATTTAA
Found at i:49008380 original size:3 final size:3
Alignment explanation
Indices: 49008372--49008428 Score: 64
Period size: 3 Copynumber: 19.3 Consensus size: 3
49008362 ATCATTTTAA
* * *
49008372 TAT TAT TAT TAC TAT TA- TAT TA- TAT CAT TAT TAC TAT TAT TAT TATT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
49008419 TAT TAT TAT T
1 TAT TAT TAT T
49008429 TACTTATTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
2 4 0.09
3 38 0.84
4 3 0.07
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:49008401 original size:22 final size:23
Alignment explanation
Indices: 49008371--49008426 Score: 89
Period size: 22 Copynumber: 2.5 Consensus size: 23
49008361 GATCATTTTA
49008371 ATATTATTATTACTATTA-TATT
1 ATATTATTATTACTATTATTATT
*
49008393 ATATCATTATTACTATTATTATT
1 ATATTATTATTACTATTATTATT
49008416 AT-TTATTATTA
1 ATATTATTATTA
49008427 TTTACTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 25 0.81
23 6 0.19
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (23 bp):
ATATTATTATTACTATTATTATT
Found at i:49008439 original size:22 final size:22
Alignment explanation
Indices: 49008371--49008439 Score: 61
Period size: 22 Copynumber: 3.0 Consensus size: 22
49008361 GATCATTTTA
49008371 ATATTATTATTAC-TATTATATT
1 ATATTATTATTACTTATT-TATT
*
49008393 ATATCATTATTAC-TATTATTATT
1 ATATTATTATTACTTA-T-TTATT
49008416 ATTTATTATTATTTACTTATTTAT
1 A--TATTATTA-TTACTTATTTAT
49008440 AATTTATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
22 14 0.36
23 6 0.15
24 1 0.03
25 11 0.28
26 5 0.13
27 2 0.05
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (22 bp):
ATATTATTATTACTTATTTATT
Found at i:49008439 original size:25 final size:24
Alignment explanation
Indices: 49008372--49008446 Score: 75
Period size: 25 Copynumber: 3.1 Consensus size: 24
49008362 ATCATTTTAA
49008372 TATTATTATTAC-TATTATATTATAT
1 TATTATTATTACTTATT-TATTAT-T
* *
49008397 CATTATTACTA-TTA-TTATTATT
1 TATTATTATTACTTATTTATTATT
*
49008419 TATTATTATTTACTTATTTATAATT
1 TATTATTA-TTACTTATTTATTATT
49008444 TAT
1 TAT
49008447 ATACACATGC
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
22 8 0.20
23 8 0.20
24 4 0.10
25 21 0.51
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.61
Consensus pattern (24 bp):
TATTATTATTACTTATTTATTATT
Found at i:49008467 original size:22 final size:22
Alignment explanation
Indices: 49008442--49008494 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
49008432 TTATTTATAA
*
49008442 TTTAT-ATACACATGCATATATT
1 TTTATAATACACATACAT-TATT
*
49008464 TTTATAATATACATACATTATT
1 TTTATAATACACATACATTATT
*
49008486 TTTACAATA
1 TTTATAATA
49008495 TATATACGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 17 0.63
23 10 0.37
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (22 bp):
TTTATAATACACATACATTATT
Found at i:49008511 original size:24 final size:22
Alignment explanation
Indices: 49008451--49008509 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
49008441 ATTTATATAC
* *
49008451 ACATGCATATATTTTTATAATAT
1 ACATACAT-TATTTTTACAATAT
49008474 ACATACATTATTTTTACAATAT
1 ACATACATTATTTTTACAATAT
* *
49008496 ATATAC-GTATTTTT
1 ACATACATTATTTTT
49008510 TTATATTCTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 7 0.22
22 18 0.56
23 7 0.22
ACGTcount: A:0.37, C:0.10, G:0.03, T:0.49
Consensus pattern (22 bp):
ACATACATTATTTTTACAATAT
Found at i:49008674 original size:25 final size:25
Alignment explanation
Indices: 49008621--49008674 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
49008611 ATCTTATAAA
* *
49008621 ATATATATTTGCATATAATTATATT
1 ATATATATTTGCATATAATTAAATC
49008646 ATATATATTT-C-TATAATTTAAATAC
1 ATATATATTTGCATATAA-TTAAAT-C
49008671 ATAT
1 ATAT
49008675 CCATATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 5 0.20
24 6 0.24
25 14 0.56
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.50
Consensus pattern (25 bp):
ATATATATTTGCATATAATTAAATC
Found at i:49015016 original size:13 final size:12
Alignment explanation
Indices: 49014998--49015045 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
49014988 TCTTCATTGT
49014998 TTTTGAAAAGTAC
1 TTTTGAAAAGT-C
*
49015011 TTTTGAAAAGTG
1 TTTTGAAAAGTC
*
49015023 TTGTGGAAAAGTTC
1 TT-TTGAAAAG-TC
49015037 TTTTGAAAA
1 TTTTGAAAA
49015046 ATTTGAGTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 2 0.07
13 24 0.83
14 3 0.10
ACGTcount: A:0.35, C:0.04, G:0.21, T:0.40
Consensus pattern (12 bp):
TTTTGAAAAGTC
Found at i:49015250 original size:24 final size:24
Alignment explanation
Indices: 49015223--49015278 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
49015213 AATATTTTAA
*
49015223 TATATAAT-ATTAATTTTAAATATT
1 TATA-AATAATTAATATTAAATATT
* *
49015247 TATAAGTAATTAATATTAATTATT
1 TATAAATAATTAATATTAAATATT
49015271 TATTAAAT
1 TA-TAAAT
49015279 TTAATTAGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 2 0.08
24 20 0.77
25 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TATAAATAATTAATATTAAATATT
Found at i:49025117 original size:20 final size:21
Alignment explanation
Indices: 49025078--49025140 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 21
49025068 GCTGAACCAA
*
49025078 TATTTTAATCATTTAATTTTAT
1 TATTTTAATCA-TAAATTTTAT
49025100 TATTTTAATCA-AAATTTTAT
1 TATTTTAATCATAAATTTTAT
*
49025120 TAAATTTTTAT-ATAAATTTTA
1 T--ATTTTAATCATAAATTTTA
49025141 ATAATATATG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
20 9 0.25
21 1 0.03
22 26 0.72
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTTTAATCATAAATTTTAT
Found at i:49029240 original size:31 final size:32
Alignment explanation
Indices: 49029200--49029263 Score: 112
Period size: 31 Copynumber: 2.0 Consensus size: 32
49029190 TTTGAGAAGA
49029200 AAAATCTAGTACTCAGATTTTATGTTTTTAGG
1 AAAATCTAGTACTCAGATTTTATGTTTTTAGG
*
49029232 AAAA-CTAGTACTCGGATTTTATGTTTTTAGG
1 AAAATCTAGTACTCAGATTTTATGTTTTTAGG
49029263 A
1 A
49029264 CAATAAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 27 0.87
32 4 0.13
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.42
Consensus pattern (32 bp):
AAAATCTAGTACTCAGATTTTATGTTTTTAGG
Found at i:49037942 original size:13 final size:13
Alignment explanation
Indices: 49037924--49037949 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
49037914 ATGTGTTTCA
49037924 TGATTGTTTTGGT
1 TGATTGTTTTGGT
49037937 TGATTGTTTTGGT
1 TGATTGTTTTGGT
49037950 ACGGATCCAA
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:0.00, G:0.31, T:0.62
Consensus pattern (13 bp):
TGATTGTTTTGGT
Found at i:49039920 original size:70 final size:70
Alignment explanation
Indices: 49039846--49039976 Score: 235
Period size: 70 Copynumber: 1.9 Consensus size: 70
49039836 TAAGCTCATG
* *
49039846 TTATTACATCAAATAATATCAAAATAACTCAAAAAAAATTCTATTTTATTACATCAAATAAACTT
1 TTATTACATCAAATAATATCAAAATAACTCAAAAAAAATTATATTTTATTACATAAAATAAACTT
49039911 CTATT
66 CTATT
*
49039916 TTATTACATCAAATAATATCAAAATAACTCAAAAAAATTTATATTTTATTACATAAAATAA
1 TTATTACATCAAATAATATCAAAATAACTCAAAAAAAATTATATTTTATTACATAAAATAA
49039977 TATCAAAATA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 58 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (70 bp):
TTATTACATCAAATAATATCAAAATAACTCAAAAAAAATTATATTTTATTACATAAAATAAACTT
CTATT
Found at i:49039929 original size:25 final size:25
Alignment explanation
Indices: 49039874--49039931 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
49039864 TCAAAATAAC
*
49039874 TCAAAAAAAATTCTATTTTATTACA
1 TCAAATAAAATTCTATTTTATTACA
*
49039899 TCAAATAAACTTCTATTTTATTACA
1 TCAAATAAAATTCTATTTTATTACA
49039924 TCAAATAA
1 TCAAATAA
49039932 TATCAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (25 bp):
TCAAATAAAATTCTATTTTATTACA
Found at i:49039948 original size:45 final size:45
Alignment explanation
Indices: 49039899--49039986 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 45
49039889 TTTTATTACA
* * *
49039899 TCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAAC
1 TCAAAAAAACTTATATTTTATTACATAAAATAATATCAAAATAAC
*
49039944 TCAAAAAAATTTATATTTTATTACATAAAATAATATCAAAATA
1 TCAAAAAAACTTATATTTTATTACATAAAATAATATCAAAATA
49039987 TTCAAAATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.36
Consensus pattern (45 bp):
TCAAAAAAACTTATATTTTATTACATAAAATAATATCAAAATAAC
Found at i:49041329 original size:20 final size:20
Alignment explanation
Indices: 49041292--49041329 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
49041282 TTTATTTTTA
*
49041292 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
49041312 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
49041330 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:49042141 original size:22 final size:21
Alignment explanation
Indices: 49042105--49042164 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
49042095 GGCTCGGCTC
*
49042105 ATTT-TTTTAATAAATACCAAAA
1 ATTTATTTTAA-AAATA-AAAAA
49042127 ATTTATTTTAAAAATTAAAAAA
1 ATTTATTTTAAAAA-TAAAAAA
**
49042149 AAATATTTTAAAAATA
1 ATTTATTTTAAAAATA
49042165 TTTTAAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 2 0.06
22 23 0.70
23 8 0.24
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTTATTTTAAAAATAAAAAA
Found at i:49042161 original size:11 final size:11
Alignment explanation
Indices: 49042147--49042252 Score: 81
Period size: 11 Copynumber: 10.4 Consensus size: 11
49042137 AAAATTAAAA
49042147 AAAAATATTTT
1 AAAAATATTTT
49042158 AAAAATATTTT
1 AAAAATATTTT
49042169 --AAA-A--TT
1 AAAAATATTTT
*
49042175 AAAAAAATTTT
1 AAAAATATTTT
49042186 AAAAATTATTTT
1 AAAAA-TATTTT
49042198 AAAAATATTTT
1 AAAAATATTTT
49042209 --AAA-A--TT
1 AAAAATATTTT
**
49042215 AAAAA-ATAAT
1 AAAAATATTTT
49042225 AAAATAGTATTTT
1 AAAA-A-TATTTT
49042238 AAAAATATTTT
1 AAAAATATTTT
49042249 AAAA
1 AAAA
49042253 TAAAAAAAAT
Statistics
Matches: 78, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
6 4 0.05
8 9 0.12
9 7 0.09
10 5 0.06
11 35 0.45
12 11 0.14
13 7 0.09
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:49042196 original size:40 final size:40
Alignment explanation
Indices: 49042136--49042269 Score: 182
Period size: 40 Copynumber: 3.4 Consensus size: 40
49042126 AATTTATTTT
*
49042136 AAAAATTAAAAAAAAATATTTTAAAAATATTTTAAAATTAA
1 AAAAATT-ATAAAAAATATTTTAAAAATATTTTAAAATTAA
* *
49042177 AAAAATTTTAAAAATTATTTTAAAAATATTTTAAAATT-A
1 AAAAATTATAAAAAATATTTTAAAAATATTTTAAAATTAA
* * *
49042216 AAAAATAATAAAATAGTATTTTAAAAATATTTTAAAATAAA
1 AAAAATTATAAAA-AATATTTTAAAAATATTTTAAAATTAA
49042257 AAAAATTA-AAAAA
1 AAAAATTATAAAAA
49042270 TAAATATATT
Statistics
Matches: 83, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
39 13 0.16
40 55 0.66
41 15 0.18
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (40 bp):
AAAAATTATAAAAAATATTTTAAAAATATTTTAAAATTAA
Found at i:49042857 original size:51 final size:51
Alignment explanation
Indices: 49042796--49042893 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 51
49042786 AAATTATTTA
49042796 AAATAGGGATTTAAGAGAAATTTAAGAA-GAACTTGAGAGCAAATTGAAATT
1 AAATAGGGATTTAAGAGAAATTT-AGAAGGAACTTGAGAGCAAATTGAAATT
* * *
49042847 AAATATGGATTTAAGAGAAATTTTGAAGGAATTTGAGAGCAAATTGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAACTTGAGAGCAAATTGA
49042894 GAGGAAATTG
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 3 0.07
51 40 0.93
ACGTcount: A:0.47, C:0.03, G:0.22, T:0.28
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAACTTGAGAGCAAATTGAAATT
Found at i:49042893 original size:11 final size:11
Alignment explanation
Indices: 49042869--49042930 Score: 90
Period size: 11 Copynumber: 5.6 Consensus size: 11
49042859 AAGAGAAATT
*
49042869 TTGA-AGGAAT
1 TTGAGAGGAAA
*
49042879 TTGAGAGCAAA
1 TTGAGAGGAAA
49042890 TTGAGAGGAAA
1 TTGAGAGGAAA
49042901 TTGAGAGGAAA
1 TTGAGAGGAAA
49042912 TTGAGAGGAAA
1 TTGAGAGGAAA
49042923 TTTGAGAG
1 -TTGAGAG
49042931 AGGATTAGTT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
10 4 0.09
11 36 0.77
12 7 0.15
ACGTcount: A:0.42, C:0.02, G:0.34, T:0.23
Consensus pattern (11 bp):
TTGAGAGGAAA
Found at i:49044669 original size:41 final size:41
Alignment explanation
Indices: 49044624--49044756 Score: 176
Period size: 41 Copynumber: 3.1 Consensus size: 41
49044614 ATGTTAAGGG
49044624 TTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAATTTAATTA
1 TTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAATTT-A--A
* * *
49044668 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTCAACTTAA
1 --TTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAATTTAA
* *
49044711 TTAGGGTTTACAACTTAATTAGGTTAGGGTTTTTAATTTAA
1 TTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAATTTAA
49044752 TTAGG
1 TTAGG
49044757 TTAGGGTTTT
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
41 41 0.52
43 1 0.01
45 1 0.01
46 36 0.46
ACGTcount: A:0.27, C:0.05, G:0.21, T:0.47
Consensus pattern (41 bp):
TTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAATTTAA
Found at i:49044731 original size:64 final size:67
Alignment explanation
Indices: 49044622--49044769 Score: 239
Period size: 64 Copynumber: 2.2 Consensus size: 67
49044612 GAATGTTAAG
* *
49044622 GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAATTTAATTAGGTTAGGGTTTTTAATTTA
1 GGTTAGGGTTTTCAACTTAA-TA-GTTAGGGTTTACAACTTAATTAGGTTAGGGTTTTTAATTTA
49044687 ATTA
64 ATTA
49044691 GGTTAGGGTTTTCAACTT-A-A-TTAGGGTTTACAACTTAATTAGGTTAGGGTTTTTAATTTAAT
1 GGTTAGGGTTTTCAACTTAATAGTTAGGGTTTACAACTTAATTAGGTTAGGGTTTTTAATTTAAT
49044753 TA
66 TA
49044755 GGTTAGGGTTTTCAA
1 GGTTAGGGTTTTCAA
49044770 TTTTTATCAC
Statistics
Matches: 77, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
64 57 0.74
66 1 0.01
68 1 0.01
69 18 0.23
ACGTcount: A:0.26, C:0.05, G:0.22, T:0.46
Consensus pattern (67 bp):
GGTTAGGGTTTTCAACTTAATAGTTAGGGTTTACAACTTAATTAGGTTAGGGTTTTTAATTTAAT
TA
Found at i:49044771 original size:23 final size:23
Alignment explanation
Indices: 49044622--49044772 Score: 213
Period size: 23 Copynumber: 6.8 Consensus size: 23
49044612 GAATGTTAAG
*
49044622 GGTTAGGGTTTTCAACTTAATTA
1 GGTTAGGGTTTTCAATTTAATTA
49044645 GGTTAGGGTTTTCAATTTAATTA
1 GGTTAGGGTTTTCAATTTAATTA
*
49044668 GGTTAGGGTTTTTAATTTAATTA
1 GGTTAGGGTTTTCAATTTAATTA
*
49044691 GGTTAGGGTTTTCAACTT-A--A
1 GGTTAGGGTTTTCAATTTAATTA
* *
49044711 --TTAGGGTTTACAACTTAATTA
1 GGTTAGGGTTTTCAATTTAATTA
*
49044732 GGTTAGGGTTTTTAATTTAATTA
1 GGTTAGGGTTTTCAATTTAATTA
49044755 GGTTAGGGTTTTCAATTT
1 GGTTAGGGTTTTCAATTT
49044773 TTATCACATC
Statistics
Matches: 114, Mismatches: 9, Indels: 10
0.86 0.07 0.08
Matches are distributed among these distances:
18 15 0.13
19 1 0.01
20 1 0.01
21 1 0.01
22 1 0.01
23 95 0.83
ACGTcount: A:0.26, C:0.05, G:0.22, T:0.47
Consensus pattern (23 bp):
GGTTAGGGTTTTCAATTTAATTA
Found at i:49044799 original size:25 final size:25
Alignment explanation
Indices: 49044771--49045131 Score: 280
Period size: 25 Copynumber: 14.9 Consensus size: 25
49044761 GGTTTTCAAT
*
49044771 TTTTATCACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
49044796 TTTTATTACATCAAAT-AA----TA
1 TTTTATTACATCAAATAAACTTCTA
** * * *
49044816 --TTAAAACAACTCAAAAAAATTTCAA
1 TTTTATTAC-A-TCAAATAAACTTCTA
49044841 TTTTTATTACATC-AATAAAACTTCTA
1 -TTTTATTACATCAAAT-AAACTTCTA
*
49044867 TTTTATTACATCATATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
49044892 TTTTATTACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
49044917 TTTTATTACATCAAAT-AA-TATC-A
1 TTTTATTACATCAAATAAACT-TCTA
** * * * *
49044940 --AAATAAC-TCAAAAAAATTTCAA
1 TTTTATTACATCAAATAAACTTCTA
49044962 TTTTTATTACATC-AATAAAACTTCTA
1 -TTTTATTACATCAAAT-AAACTTCTA
* *
49044988 TTTTATTACATCATATAAACTTTTA
1 TTTTATTACATCAAATAAACTTCTA
49045013 TTTTATTACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
49045038 TTTTATTACATCAAAT-AA-TATC-A
1 TTTTATTACATCAAATAAACT-TCTA
** * * * *
49045061 --AAATAAC-TCAAAAAAATTTCAA
1 TTTTATTACATCAAATAAACTTCTA
49045083 TTTTTATTACATC-AATAAAACTTCTA
1 -TTTTATTACATCAAAT-AAACTTCTA
*
49045109 TTTTATTACATCAAACAAACTTC
1 TTTTATTACATCAAATAAACTTC
49045132 AAAATATTCA
Statistics
Matches: 267, Mismatches: 37, Indels: 64
0.73 0.10 0.17
Matches are distributed among these distances:
18 5 0.02
19 1 0.00
20 17 0.06
21 18 0.07
22 4 0.01
23 4 0.01
24 10 0.04
25 169 0.63
26 33 0.12
27 1 0.00
28 5 0.02
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (25 bp):
TTTTATTACATCAAATAAACTTCTA
Found at i:49044985 original size:121 final size:121
Alignment explanation
Indices: 49044771--49045131 Score: 668
Period size: 121 Copynumber: 3.0 Consensus size: 121
49044761 GGTTTTCAAT
* * *
49044771 TTTTATCACATCAAATAAACTTCTATTTTATTACATCAAATAATATTAAAACAACTCAAAAAAAT
1 TTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAAAT
49044836 TTCAATTTTTATTACATCAATAAAACTTCTATTTTATTACATCATATAAACTTCTA
66 TTCAATTTTTATTACATCAATAAAACTTCTATTTTATTACATCATATAAACTTCTA
49044892 TTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAAAT
1 TTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAAAT
*
49044957 TTCAATTTTTATTACATCAATAAAACTTCTATTTTATTACATCATATAAACTTTTA
66 TTCAATTTTTATTACATCAATAAAACTTCTATTTTATTACATCATATAAACTTCTA
49045013 TTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAAAT
1 TTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAAAT
* *
49045078 TTCAATTTTTATTACATCAATAAAACTTCTATTTTATTACATCAAACAAACTTC
66 TTCAATTTTTATTACATCAATAAAACTTCTATTTTATTACATCATATAAACTTC
49045132 AAAATATTCA
Statistics
Matches: 233, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
121 233 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (121 bp):
TTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAAAAAT
TTCAATTTTTATTACATCAATAAAACTTCTATTTTATTACATCATATAAACTTCTA
Found at i:49046256 original size:7 final size:7
Alignment explanation
Indices: 49046246--49046277 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
49046236 TTATATACAT
49046246 AATACTA
1 AATACTA
49046253 AATACTA
1 AATACTA
49046260 AATACTA
1 AATACTA
*
49046267 AATACAA
1 AATACTA
49046274 AATA
1 AATA
49046278 TCTATTTGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.25
Consensus pattern (7 bp):
AATACTA
Found at i:49046263 original size:14 final size:14
Alignment explanation
Indices: 49046240--49046277 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
49046230 TATTAGTTAT
*
49046240 ATACATAATACTAA
1 ATACAAAATACTAA
*
49046254 ATACTAAATACTAA
1 ATACAAAATACTAA
49046268 ATACAAAATA
1 ATACAAAATA
49046278 TCTATTTGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.61, C:0.13, G:0.00, T:0.26
Consensus pattern (14 bp):
ATACAAAATACTAA
Found at i:49047524 original size:51 final size:51
Alignment explanation
Indices: 49047390--49047513 Score: 187
Period size: 51 Copynumber: 2.4 Consensus size: 51
49047380 TATTTTAAAA
* * *
49047390 AAGGAAATTGAGAGCAAATTGAAATTAAATATGGGTTTGAGAGATTTTTGG
1 AAGGAAATTGAGAGAAAATTGAAATTAAATATGGATTTGAGAGAATTTTGG
* *
49047441 AATGAAATTGAGAGGAAATTGAAATTAAATATGGATTT-ATGAGAATTTTGG
1 AAGGAAATTGAGAGAAAATTGAAATTAAATATGGATTTGA-GAGAATTTTGG
49047492 AAGGAAATTGAGAGAAAATTGA
1 AAGGAAATTGAGAGAAAATTGA
49047514 GAGGAAATAT
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
50 1 0.02
51 65 0.98
ACGTcount: A:0.44, C:0.01, G:0.26, T:0.30
Consensus pattern (51 bp):
AAGGAAATTGAGAGAAAATTGAAATTAAATATGGATTTGAGAGAATTTTGG
Found at i:49047526 original size:12 final size:11
Alignment explanation
Indices: 49047493--49047528 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
49047483 GAATTTTGGA
49047493 AGGAAATTGAG
1 AGGAAATTGAG
*
49047504 AGAAAATTGAG
1 AGGAAATTGAG
49047515 AGGAAATATGAG
1 AGGAAAT-TGAG
49047527 AG
1 AG
49047529 AGGATTTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 16 0.73
12 6 0.27
ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:49048210 original size:15 final size:15
Alignment explanation
Indices: 49048190--49048218 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
49048180 GTGTGATAAA
49048190 TTAAATAGAATTTTC
1 TTAAATAGAATTTTC
49048205 TTAAATAGAATTTT
1 TTAAATAGAATTTT
49048219 GAATTGTAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.48
Consensus pattern (15 bp):
TTAAATAGAATTTTC
Found at i:49056712 original size:10 final size:10
Alignment explanation
Indices: 49056699--49056740 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
49056689 TAAAAAAACA
*
49056699 AAAAATCATT
1 AAAAATTATT
49056709 AAAAATTA-T
1 AAAAATTATT
*
49056718 AATAATTATT
1 AAAAATTATT
*
49056728 AAAAATTAAT
1 AAAAATTATT
49056738 AAA
1 AAA
49056741 GAAAAATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 8 0.30
10 19 0.70
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAAATTATT
Found at i:49056840 original size:6 final size:6
Alignment explanation
Indices: 49056829--49056861 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
49056819 AGTGTAGTAA
49056829 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAA
49056862 TAAGTATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:49056864 original size:16 final size:16
Alignment explanation
Indices: 49056829--49056879 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
49056819 AGTGTAGTAA
49056829 AAAAATAAAAATAAAAAT
1 AAAAATAAAAAT--AAAT
49056847 AAAAATAAAAATAAAT
1 AAAAATAAAAATAAAT
** *
49056863 AAGTATATAAATAAAT
1 AAAAATAAAAATAAAT
49056879 A
1 A
49056880 TGACACTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
16 18 0.60
18 12 0.40
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (16 bp):
AAAAATAAAAATAAAT
Found at i:49056977 original size:16 final size:15
Alignment explanation
Indices: 49056956--49057016 Score: 61
Period size: 15 Copynumber: 3.9 Consensus size: 15
49056946 AAAATTTTAT
49056956 ATAATTTATAAAGAAA
1 ATAATTTATAAA-AAA
49056972 ATAATTTATTAAAAATA
1 ATAATTTA-TAAAAA-A
** *
49056989 A-AAAATAGAAAAAA
1 ATAATTTATAAAAAA
49057003 ATAATTTATAAAAA
1 ATAATTTATAAAAA
49057017 TATTTAGAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
14 2 0.06
15 14 0.39
16 14 0.39
17 6 0.17
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (15 bp):
ATAATTTATAAAAAA
Found at i:49057016 original size:14 final size:16
Alignment explanation
Indices: 49056956--49057014 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
49056946 AAAATTTTAT
49056956 ATAATTTATAAAGAAA
1 ATAATTTATAAAGAAA
49056972 ATAATTTATTAAA-AATA
1 ATAATTTA-TAAAGAA-A
** *
49056989 A-AAAATAGAAA-AAA
1 ATAATTTATAAAGAAA
49057003 ATAATTTATAAA
1 ATAATTTATAAA
49057015 AATATTTAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
14 2 0.06
15 12 0.35
16 14 0.41
17 6 0.18
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
ATAATTTATAAAGAAA
Found at i:49057299 original size:19 final size:19
Alignment explanation
Indices: 49057277--49057322 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
49057267 TTTCTAATAA
49057277 TTTTTATAAATTTTA--AT
1 TTTTTATAAATTTTATGAT
*
49057294 TTTTTTTATAATTTTATGAT
1 TTTTTATA-AATTTTATGAT
49057314 TTTTTATAA
1 TTTTTATAA
49057323 TTCTAGAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 7 0.29
18 7 0.29
19 1 0.04
20 9 0.38
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTTATAAATTTTATGAT
Found at i:49057306 original size:18 final size:18
Alignment explanation
Indices: 49057277--49057324 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
49057267 TTTCTAATAA
*
49057277 TTTTTATAAATTTTAAT-TT
1 TTTTTAT-AATTTT-ATGAT
49057296 TTTTTATAATTTTATGAT
1 TTTTTATAATTTTATGAT
49057314 TTTTTATAATT
1 TTTTTATAATT
49057325 CTAGAATGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 2 0.07
18 18 0.67
19 7 0.26
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTTTATAATTTTATGAT
Found at i:49057550 original size:32 final size:32
Alignment explanation
Indices: 49057514--49057584 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
49057504 ATCAATCATA
* *
49057514 ACATGGTACCACTACATCAACCATTAATGATG
1 ACATGGTACCACTACATCAACAAATAATGATG
* * * * *
49057546 ACATGGCACTACTACGTCAACAAATATTGCTG
1 ACATGGTACCACTACATCAACAAATAATGATG
49057578 ACATGGT
1 ACATGGT
49057585 GTATGTTAAC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.25
Consensus pattern (32 bp):
ACATGGTACCACTACATCAACAAATAATGATG
Found at i:49059746 original size:19 final size:19
Alignment explanation
Indices: 49059722--49059760 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
49059712 GTTTGCAACC
49059722 TAAATAAATAA-ATAAATAA
1 TAAAT-AATAATATAAATAA
*
49059741 TAAATAATAATATTAATAA
1 TAAATAATAATATAAATAA
49059760 T
1 T
49059761 CTCTAGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAATAATAATATAAATAA
Found at i:49061034 original size:21 final size:21
Alignment explanation
Indices: 49061002--49061046 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
49060992 TATTAGTTTA
49061002 ACCCAAGGTAATTTTAACTTG
1 ACCCAAGGTAATTTTAACTTG
*
49061023 ACCC-AGGATAATTTTGACTTG
1 ACCCAAGG-TAATTTTAACTTG
49061044 ACC
1 ACC
49061047 TGTAATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (21 bp):
ACCCAAGGTAATTTTAACTTG
Found at i:49062634 original size:17 final size:18
Alignment explanation
Indices: 49062605--49062640 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
49062595 ATTATAAATC
*
49062605 TAAAAAATAAATGTTAAA
1 TAAAAAATAAATGTGAAA
49062623 TAAAAAAT-AATGTGAAA
1 TAAAAAATAAATGTGAAA
49062640 T
1 T
49062641 TCGAGTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (18 bp):
TAAAAAATAAATGTGAAA
Found at i:49079766 original size:12 final size:13
Alignment explanation
Indices: 49079731--49079772 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
49079721 AAAAGTTTTG
49079731 CTTTCTTTTCCCT
1 CTTTCTTTTCCCT
* *
49079744 ATTTATTTTCCC-
1 CTTTCTTTTCCCT
*
49079756 CTTTCTTTTCCAT
1 CTTTCTTTTCCCT
49079769 CTTT
1 CTTT
49079773 TTCTTTGCAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.07, C:0.31, G:0.00, T:0.62
Consensus pattern (13 bp):
CTTTCTTTTCCCT
Found at i:49081057 original size:91 final size:88
Alignment explanation
Indices: 49080885--49081089 Score: 225
Period size: 91 Copynumber: 2.3 Consensus size: 88
49080875 TTTAACTACA
* * *
49080885 AACACTCGTGGTTTATCCACAAATTACTAGCAGCTTTAATCTGCAAACCCGTTGTGTATTCACAA
1 AACACTCGTAGTTTATCCACAAATTACTAGCAGCTTTAATCTACAAACCCGTTGTGTATTCAAAA
* * * *
49080950 CTACTTGTAGCATATTAACTTGC
66 CCACTGGCAGCATATTAACCTGC
* *
49080973 AAGCACTCGTAGTTTATCCACAACTTA-TACTGACAGCTATT-ATCTACAAACCTGTTGTGTATT
1 AA-CACTCGTAGTTTATCCACAAATTACTA--G-CAGCT-TTAATCTACAAACCCGTTGTGTATT
** *
49081036 CAAAACCACTGGCAGTGTATTAACCTGT
61 CAAAACCACTGGCAGCATATTAACCTGC
* *
49081064 AACACTAGCAGTTTATCCACAAATTA
1 AACACTCGTAGTTTATCCACAAATTA
49081090 GAGTTACTGT
Statistics
Matches: 97, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
88 4 0.04
89 22 0.23
90 22 0.23
91 47 0.48
92 2 0.02
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (88 bp):
AACACTCGTAGTTTATCCACAAATTACTAGCAGCTTTAATCTACAAACCCGTTGTGTATTCAAAA
CCACTGGCAGCATATTAACCTGC
Found at i:49082809 original size:29 final size:27
Alignment explanation
Indices: 49082744--49082809 Score: 62
Period size: 29 Copynumber: 2.3 Consensus size: 27
49082734 GTCTTCATAC
49082744 ATTTAAAATTTAGTTTCTATATTTTTA
1 ATTTAAAATTTAGTTTCTATATTTTTA
* *
49082771 TTTTAAAAAATTTAGTCCTTTTAT-TTTTTGA
1 ATTT--AAAATTTAGT--TTCTATATTTTT-A
49082802 ATTTAAAA
1 ATTTAAAA
49082810 ATTCAAACCT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
27 3 0.10
29 14 0.45
30 5 0.16
31 9 0.29
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.56
Consensus pattern (27 bp):
ATTTAAAATTTAGTTTCTATATTTTTA
Found at i:49082810 original size:31 final size:29
Alignment explanation
Indices: 49082748--49082810 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 29
49082738 TCATACATTT
*
49082748 AAAATTTAGTTTCTATATTTTTATTTTAA
1 AAAATTTAGTTTCTATATTTTTAATTTAA
*
49082777 AAAATTTAGTCCTTTTAT-TTTTTGAATTTAA
1 AAAATTTAGT--TTCTATATTTTT-AATTTAA
49082808 AAA
1 AAA
49082811 TTCAAACCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 10 0.34
30 5 0.17
31 14 0.48
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.54
Consensus pattern (29 bp):
AAAATTTAGTTTCTATATTTTTAATTTAA
Found at i:49084012 original size:41 final size:41
Alignment explanation
Indices: 49083735--49083997 Score: 438
Period size: 41 Copynumber: 6.4 Consensus size: 41
49083725 TTTCGGGGGC
* *
49083735 TTTAGTGGCGTTTTTATGTAAGCGCCGCTAATGTTCTGGGC
1 TTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGTTCTGGGA
*
49083776 TTTCGCGGCGTTTTTATGTAAGCGCCGCTAATGTTCTGGGA
1 TTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGTTCTGGGA
*
49083817 TTTAGCGGCGTTTTTATGTAAGCACCGCTAATGTTCTGGGA
1 TTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGTTCTGGGA
49083858 TTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGTTCTGGGA
1 TTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGTTCTGGGA
* *
49083899 TTTAGCAGCGTTTTTATTTAAGCGCCGCTAATGTTCTGGGA
1 TTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGTTCTGGGA
* *
49083940 TTTAGTGGCGTTTTTAAT-TAAGCGCCGCTAATGTTCTGGGC
1 TTTAGCGGCGTTTTT-ATGTAAGCGCCGCTAATGTTCTGGGA
49083981 TTTAGCGGCGTTTTTAT
1 TTTAGCGGCGTTTTTAT
49083998 CGATGTGCCA
Statistics
Matches: 209, Mismatches: 12, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
40 2 0.01
41 205 0.98
42 2 0.01
ACGTcount: A:0.17, C:0.17, G:0.27, T:0.39
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGTTCTGGGA
Found at i:49084026 original size:123 final size:123
Alignment explanation
Indices: 49083735--49084027 Score: 369
Period size: 123 Copynumber: 2.4 Consensus size: 123
49083725 TTTCGGGGGC
* * * * * *
49083735 TTTAGTGGCGTTTTTATGTAAGCGCCGCTAATGTTCTGGGC-TTTCGCGGCGTTTTTATGTAAGC
1 TTTAGCGGCGTTTTTATGTAAGCGCCACTAATGTGC-AGGCATTTAGCAGCGTTTTTATGTAAGC
49083799 GCCGCTAATGTTCTGGGATTTAGCGGCGTTTTTATGTAAGCACCGCTAATGTTCTGGGA
65 GCCGCTAATGTTCTGGGATTTAGCGGCGTTTTTATGTAAGCACCGCTAATGTTCTGGGA
* * * * *
49083858 TTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGTTCTGGGATTTAGCAGCGTTTTTATTTAAGCG
1 TTTAGCGGCGTTTTTATGTAAGCGCCACTAATGTGCAGGCATTTAGCAGCGTTTTTATGTAAGCG
* * *
49083923 CCGCTAATGTTCTGGGATTTAGTGGCGTTTTTAAT-TAAGCGCCGCTAATGTTCTGGGC
66 CCGCTAATGTTCTGGGATTTAGCGGCGTTTTT-ATGTAAGCACCGCTAATGTTCTGGGA
* * *
49083981 TTTAGCGGCGTTTTTATCG-ATGTGCCACTAAT-TCGCAGGCCTTTAGC
1 TTTAGCGGCGTTTTTAT-GTAAGCGCCACTAATGT-GCAGGCATTTAGC
49084028 GGCACTTTTT
Statistics
Matches: 150, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
122 3 0.02
123 144 0.96
124 3 0.02
ACGTcount: A:0.17, C:0.18, G:0.27, T:0.38
Consensus pattern (123 bp):
TTTAGCGGCGTTTTTATGTAAGCGCCACTAATGTGCAGGCATTTAGCAGCGTTTTTATGTAAGCG
CCGCTAATGTTCTGGGATTTAGCGGCGTTTTTATGTAAGCACCGCTAATGTTCTGGGA
Found at i:49084066 original size:123 final size:123
Alignment explanation
Indices: 49083735--49084077 Score: 338
Period size: 123 Copynumber: 2.8 Consensus size: 123
49083725 TTTCGGGGGC
* * * * * * ** *
49083735 TTTAGTGGCGTTTTTATGTAAGCGCCGCTAATGTTCTGGGC-TTTCGCGGCGTTTTTATGTAAGC
1 TTTAGCGGCGTTTTTATGTAAGCGCCACTAATGTGC-AGGCATTTAGCAGCGTTTTTATAAAAAC
*
49083799 GCCGCTAATGTTCTGGGATTTAGCGGCGTTTTTATGTAAGCACCGCTAATGTTCTGGGA
65 GCCGCTAATGTTCTGGGATTTAGTGGCGTTTTTATGTAAGCACCGCTAATGTTCTGGGA
* * * * ** *
49083858 TTTAGCGGCGTTTTTATGTAAGCGCCGCTAATGTTCTGGGATTTAGCAGCGTTTTTATTTAAGCG
1 TTTAGCGGCGTTTTTATGTAAGCGCCACTAATGTGCAGGCATTTAGCAGCGTTTTTATAAAAACG
* *
49083923 CCGCTAATGTTCTGGGATTTAGTGGCGTTTTTAAT-TAAGCGCCGCTAATGTTCTGGGC
66 CCGCTAATGTTCTGGGATTTAGTGGCGTTTTT-ATGTAAGCACCGCTAATGTTCTGGGA
* * * * *
49083981 TTTAGCGGCGTTTTTATCG-ATGTGCCACTAAT-TCGCAGGCCTTTAGCGGCACTTTTT-TAAAA
1 TTTAGCGGCGTTTTTAT-GTAAGCGCCACTAATGT-GCAGGCATTTAGCAGC-GTTTTTAT-AAA
* ** *
49084043 AACGCCGCTAATGCTCT-TCATTTAGTGGCATTTTT
62 AACGCCGCTAATGTTCTGGGATTTAGTGGCGTTTTT
49084078 GGAAAGCGCC
Statistics
Matches: 189, Mismatches: 25, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
122 3 0.02
123 162 0.86
124 24 0.13
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (123 bp):
TTTAGCGGCGTTTTTATGTAAGCGCCACTAATGTGCAGGCATTTAGCAGCGTTTTTATAAAAACG
CCGCTAATGTTCTGGGATTTAGTGGCGTTTTTATGTAAGCACCGCTAATGTTCTGGGA
Found at i:49084470 original size:16 final size:16
Alignment explanation
Indices: 49084437--49084518 Score: 57
Period size: 16 Copynumber: 5.3 Consensus size: 16
49084427 TGGTTTAAGG
*
49084437 GTTT-AGGG-TTTGTA
1 GTTTAAGGGTTTTATA
49084451 GTTTAAGGGTTTTATA
1 GTTTAAGGGTTTTATA
*
49084467 GTTTAA-GGTTTAAT-
1 GTTTAAGGGTTTTATA
** * *
49084481 GTTTACTATAG-TATGTA
1 GTTTA--AGGGTTTTATA
49084498 GTTTAAGGGTTTTATA
1 GTTTAAGGGTTTTATA
49084514 GTTTA
1 GTTTA
49084519 TGGTTTAGGG
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
14 9 0.18
15 13 0.25
16 23 0.45
17 6 0.12
ACGTcount: A:0.24, C:0.01, G:0.24, T:0.50
Consensus pattern (16 bp):
GTTTAAGGGTTTTATA
Found at i:49084567 original size:22 final size:21
Alignment explanation
Indices: 49084542--49084582 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
49084532 GTTATATTGG
49084542 GTTTGTGA-TTTAGTGTTTTAAA
1 GTTTG-GAGTTTAGT-TTTTAAA
49084564 GTTTGGAGTTTAGTTTTTA
1 GTTTGGAGTTTAGTTTTTA
49084583 TAGTCAGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.20, C:0.00, G:0.24, T:0.56
Consensus pattern (21 bp):
GTTTGGAGTTTAGTTTTTAAA
Found at i:49088820 original size:9 final size:9
Alignment explanation
Indices: 49088789--49088845 Score: 57
Period size: 9 Copynumber: 6.7 Consensus size: 9
49088779 TTAAAGTTCA
49088789 AATTT-CAT
1 AATTTACAT
* *
49088797 AACTTACGT
1 AATTTACAT
*
49088806 ATTTTACAT
1 AATTTACAT
49088815 AATTTACAT
1 AATTTACAT
49088824 AA-TT-CAT
1 AATTTACAT
*
49088831 AATTTACAA
1 AATTTACAT
49088840 AATTTA
1 AATTTA
49088846 AATATATAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
7 5 0.13
8 8 0.21
9 26 0.67
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.44
Consensus pattern (9 bp):
AATTTACAT
Found at i:49088833 original size:16 final size:16
Alignment explanation
Indices: 49088812--49088843 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
49088802 ACGTATTTTA
*
49088812 CATAATTTACATAATT
1 CATAATTTACAAAATT
49088828 CATAATTTACAAAATT
1 CATAATTTACAAAATT
49088844 TAAATATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (16 bp):
CATAATTTACAAAATT
Found at i:49088970 original size:12 final size:12
Alignment explanation
Indices: 49088955--49089007 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
49088945 CATAGTATTG
49088955 TACATAATAACT
1 TACATAATAACT
49088967 TACA-AA-AACT
1 TACATAATAACT
*
49088977 TACATAATAACC
1 TACATAATAACT
49088989 TACATAATAACT
1 TACATAATAACT
*
49089001 TATATAA
1 TACATAA
49089008 CAATACATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
10 8 0.22
11 4 0.11
12 24 0.67
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (12 bp):
TACATAATAACT
Found at i:49088983 original size:22 final size:24
Alignment explanation
Indices: 49088955--49089007 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 24
49088945 CATAGTATTG
*
49088955 TACATAATAACTTACA-AA-AACT
1 TACATAATAACCTACATAATAACT
49088977 TACATAATAACCTACATAATAACT
1 TACATAATAACCTACATAATAACT
*
49089001 TATATAA
1 TACATAA
49089008 CAATACATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 15 0.56
23 2 0.07
24 10 0.37
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (24 bp):
TACATAATAACCTACATAATAACT
Found at i:49089075 original size:9 final size:9
Alignment explanation
Indices: 49089061--49089488 Score: 432
Period size: 9 Copynumber: 47.1 Consensus size: 9
49089051 CACAAAAACA
49089061 ATAACTTAC
1 ATAACTTAC
49089070 ATAACTTAC
1 ATAACTTAC
*
49089079 ATAAACTTGC
1 AT-AACTTAC
* *
49089089 ATAAATTAA
1 ATAACTTAC
**
49089098 ATAACTTGT
1 ATAACTTAC
* *
49089107 ATAAATTAA
1 ATAACTTAC
*
49089116 ATAACTTAT
1 ATAACTTAC
49089125 ATAACTTAC
1 ATAACTTAC
*
49089134 ATAACCTAC
1 ATAACTTAC
49089143 ATAACTTAC
1 ATAACTTAC
*
49089152 ATAAATTA-
1 ATAACTTAC
49089160 AGTAACTTTAC
1 A-TAAC-TTAC
**
49089171 GGAACTTAC
1 ATAACTTAC
49089180 ATAACTTAC
1 ATAACTTAC
*
49089189 ATAACCTAC
1 ATAACTTAC
*
49089198 ATAACGTAC
1 ATAACTTAC
* *
49089207 GTAAATTA-
1 ATAACTTAC
49089215 AGTAACTTAC
1 A-TAACTTAC
49089225 ATAACTTAC
1 ATAACTTAC
*
49089234 ATAACCTAC
1 ATAACTTAC
* * *
49089243 ATAAATAAA
1 ATAACTTAC
49089252 ATAACTTAC
1 ATAACTTAC
49089261 ATAACTTAC
1 ATAACTTAC
*
49089270 ATAACCTAC
1 ATAACTTAC
49089279 ATAACTTAC
1 ATAACTTAC
49089288 ATAACTTAC
1 ATAACTTAC
*
49089297 ATAAACTTGC
1 AT-AACTTAC
* *
49089307 ATAAATTAA
1 ATAACTTAC
49089316 ATAACTTAC
1 ATAACTTAC
49089325 ATAACTTAC
1 ATAACTTAC
*
49089334 ATAACGTAC
1 ATAACTTAC
* *
49089343 ATAAATTAA
1 ATAACTTAC
49089352 ATAACTTAC
1 ATAACTTAC
49089361 ATAACTTAC
1 ATAACTTAC
*
49089370 ATAAATTA-
1 ATAACTTAC
49089378 AGTAACTTAC
1 A-TAACTTAC
*
49089388 ATAACTCAC
1 ATAACTTAC
*
49089397 ATAAACTTGC
1 AT-AACTTAC
* *
49089407 ATAAATTAA
1 ATAACTTAC
49089416 ATAACTTAC
1 ATAACTTAC
49089425 ATAACTTAC
1 ATAACTTAC
*
49089434 ATAACGTAC
1 ATAACTTAC
* *
49089443 ATAAATTAA
1 ATAACTTAC
49089452 ATAACTTAC
1 ATAACTTAC
49089461 ATAACTTAC
1 ATAACTTAC
*
49089470 ATAAATTA-
1 ATAACTTAC
49089478 AGTAACTTAC
1 A-TAACTTAC
49089488 A
1 A
49089489 AGATTTAGGC
Statistics
Matches: 339, Mismatches: 68, Indels: 23
0.79 0.16 0.05
Matches are distributed among these distances:
8 3 0.01
9 304 0.90
10 32 0.09
ACGTcount: A:0.48, C:0.18, G:0.03, T:0.31
Consensus pattern (9 bp):
ATAACTTAC
Done.