Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 168 of 318
Found at i:52162625 original size:79 final size:82
Alignment explanation
Indices: 52162514--52162698 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 82
52162504 GCTACTCGTT
*
52162514 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
52162577 GATTTAGTAAC-TCGCA
66 GATATAGTAACTTAGCA
* ** **
52162593 CAAATGCCTTC-GGATCTTAGTCCGGATT-TAGTAACTCGCATGAATGCCTTCGGATCTTAGTCC
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTATAGTAACTCGCACAAATGCCTTCGGATCTTAACCC
*
52162656 GGATATAGTCACTTAGCA
65 GGATATAGTAACTTAGCA
52162674 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
52162699 CATCATTCGA
Statistics
Matches: 91, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
78 3 0.03
79 43 0.47
80 34 0.37
81 11 0.12
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:52175521 original size:30 final size:30
Alignment explanation
Indices: 52175485--52175615 Score: 171
Period size: 30 Copynumber: 4.5 Consensus size: 30
52175475 GACAAGATTG
* * * * *
52175485 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
*
52175515 GCACTAAGTGTGCGAGTTTG---ATTATATA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
52175543 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
52175573 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
52175602 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
52175616 GATTCACTAT
Statistics
Matches: 92, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.24
29 20 0.22
30 46 0.50
31 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:52175576 original size:58 final size:58
Alignment explanation
Indices: 52175485--52175615 Score: 174
Period size: 58 Copynumber: 2.2 Consensus size: 58
52175475 GACAAGATTG
* * * * * *
52175485 GCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAGTTTG-ATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAG-CTGAAATATATA
*
52175543 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTG-AAATATATA
52175602 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
52175616 GATTCACTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
57 2 0.03
58 41 0.64
59 21 0.33
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (58 bp):
GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTGAAATATATA
Found at i:52183301 original size:30 final size:30
Alignment explanation
Indices: 52183265--52183395 Score: 171
Period size: 30 Copynumber: 4.5 Consensus size: 30
52183255 GACAAGATTG
* * * * *
52183265 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
*
52183295 GCACTAAGTGTGCGAGTTTG---ATTATATA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
52183323 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
52183353 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
52183382 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
52183396 GATTCACTAT
Statistics
Matches: 92, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.24
29 20 0.22
30 46 0.50
31 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:52183356 original size:58 final size:58
Alignment explanation
Indices: 52183265--52183395 Score: 174
Period size: 58 Copynumber: 2.2 Consensus size: 58
52183255 GACAAGATTG
* * * * * *
52183265 GCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAGTTTG-ATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAG-CTGAAATATATA
*
52183323 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTG-AAATATATA
52183382 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
52183396 GATTCACTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
57 2 0.03
58 41 0.64
59 21 0.33
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (58 bp):
GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTGAAATATATA
Found at i:52192560 original size:18 final size:18
Alignment explanation
Indices: 52192537--52192574 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
52192527 AACGGCATGA
52192537 CAAGAAATTCATAGTGGT
1 CAAGAAATTCATAGTGGT
52192555 CAAGAAATTCATAGTGGT
1 CAAGAAATTCATAGTGGT
52192573 CA
1 CA
52192575 TACCTCGTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.26
Consensus pattern (18 bp):
CAAGAAATTCATAGTGGT
Found at i:52198752 original size:260 final size:259
Alignment explanation
Indices: 52198286--52198801 Score: 811
Period size: 260 Copynumber: 2.0 Consensus size: 259
52198276 AAGTCAAGCT
* *
52198286 GACTTGGATTGATCAGATTCGAGATAAGCAAATAGTGGATGATTATTTTATTCTTCGATTTTAAG
1 GACTTGGATTGATCAGATTCAAGATAAGCAAATAGTGGATGATTATTTTATTCTTCGATTTTAAA
* * * * *
52198351 AGGTTGAAGAGGGTAGGACTTCTGATTTGGGGCTAAATAGTAAGGGTGTTTTGTGTTTTAGAGGT
66 AGGTTGAAGAGGATAGGAATTCTGATTTGGGGCTAAATAGTAAGGGTGTTCTATGTTTCAGAGGT
*
52198416 CAGGTTTTTGTGCCTAATAATACTGAGTTGAGGCAATCCATATTACAGGAAGTGCATAGTAGCCC
131 CAGGTTTTTGTGCCTAATAATACTGAGTTGAGGCAATCCATATTACAGGAAATGCATAGTAGCCC
*
52198481 TTATGTTATGCATCCC-GATGGAAATAAGATGTATCAAGATCTCTGAGAGTTATACTGGTGGCTT
196 TTATGTTATGCATCCCAG-TGGAAATAAGATGTATCAAGATCTCTAAGAGTTATACT-GTGGCTT
52198545 A
259 A
* *
52198546 GACTTGGATTGATCATATTCAAGATAAGCAGATAGTGGATGATT-TTTTGATTCTTCGATTTTAA
1 GACTTGGATTGATCAGATTCAAGATAAGCAAATAGTGGATGATTATTTT-ATTCTTCGATTTTAA
* *
52198610 AAGGTTTAAGAGGATAGGAATTCTGATTTTGGGCTAAATAGTAAGGGTGTTCTATGTTTCAGAGG
65 AAGGTTGAAGAGGATAGGAATTCTGATTTGGGGCTAAATAGTAAGGGTGTTCTATGTTTCAGAGG
* ** *
52198675 TTAGGTTTTTGTGCCTAATAATGTTGGGTTGAGGCAATCCATATTACAGGAAATGCATAGTAGCC
130 TCAGGTTTTTGTGCCTAATAATACTGAGTTGAGGCAATCCATATTACAGGAAATGCATAGTAGCC
* **
52198740 CTTATTTTATGCATCCCAGTGGAAATAAGATGTATCGTGATCTCTAAGAGTTATACTGTGGC
195 CTTATGTTATGCATCCCAGTGGAAATAAGATGTATCAAGATCTCTAAGAGTTATACTGTGGC
52198802 CCAATTTGAA
Statistics
Matches: 234, Mismatches: 20, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
259 9 0.04
260 224 0.96
261 1 0.00
ACGTcount: A:0.28, C:0.11, G:0.25, T:0.35
Consensus pattern (259 bp):
GACTTGGATTGATCAGATTCAAGATAAGCAAATAGTGGATGATTATTTTATTCTTCGATTTTAAA
AGGTTGAAGAGGATAGGAATTCTGATTTGGGGCTAAATAGTAAGGGTGTTCTATGTTTCAGAGGT
CAGGTTTTTGTGCCTAATAATACTGAGTTGAGGCAATCCATATTACAGGAAATGCATAGTAGCCC
TTATGTTATGCATCCCAGTGGAAATAAGATGTATCAAGATCTCTAAGAGTTATACTGTGGCTTA
Found at i:52204938 original size:24 final size:24
Alignment explanation
Indices: 52204906--52204966 Score: 122
Period size: 24 Copynumber: 2.5 Consensus size: 24
52204896 AATCTCAAAT
52204906 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATG
52204930 GCACTATGTGTGCGATTTACTATG
1 GCACTATGTGTGCGATTTACTATG
52204954 GCACTATGTGTGC
1 GCACTATGTGTGC
52204967 AAACATAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (24 bp):
GCACTATGTGTGCGATTTACTATG
Found at i:52210149 original size:34 final size:34
Alignment explanation
Indices: 52210052--52210123 Score: 103
Period size: 34 Copynumber: 2.1 Consensus size: 34
52210042 TATGCATTTT
*
52210052 TGATACTG-TACT-AAATTGGGCTAAGGCCCACAC
1 TGATACTGTTACTGTAA-TGGGCTAAGGCCCACAC
*
52210085 TGATACTGTTACTGTAATGGGCTAAGGCCCACAT
1 TGATACTGTTACTGTAATGGGCTAAGGCCCACAC
52210119 TGATA
1 TGATA
52210124 TTTCCACTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
33 8 0.23
34 25 0.71
35 2 0.06
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (34 bp):
TGATACTGTTACTGTAATGGGCTAAGGCCCACAC
Found at i:52212007 original size:58 final size:56
Alignment explanation
Indices: 52211866--52212021 Score: 165
Period size: 57 Copynumber: 2.7 Consensus size: 56
52211856 CCACATGTCA
*
52211866 TATAACAGGATTACCAGTCCAGGCTAAATCCTTATTATAACGTATGCTCACAAGAGT
1 TATATCAGGATTACCAGTCCAGGCTAAATCCTTA-TATAACGTATGCTCACAAGAGT
** * * * *
52211923 TCGATTAGGGTTACCAGTCCAGGCTAAA-CCTTAATCATAACGTATGCTCGAGAGGTA-T
1 TATATCAGGATTACCAGTCCAGGCTAAATCCTT-AT-ATAACGTATGCTC-ACAAG-AGT
52211981 TATATCAGGATTACCCA-TCCAGGCTAAATCCTTTATATAAC
1 TATATCAGGATTA-CCAGTCCAGGCTAAATCC-TTATATAAC
52212022 AAGGTCATTG
Statistics
Matches: 81, Mismatches: 11, Indels: 13
0.77 0.10 0.12
Matches are distributed among these distances:
56 5 0.06
57 37 0.46
58 29 0.36
59 8 0.10
60 2 0.02
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.29
Consensus pattern (56 bp):
TATATCAGGATTACCAGTCCAGGCTAAATCCTTATATAACGTATGCTCACAAGAGT
Found at i:52215417 original size:29 final size:27
Alignment explanation
Indices: 52215383--52215485 Score: 98
Period size: 29 Copynumber: 3.6 Consensus size: 27
52215373 TACTCAATCA
*
52215383 CGCACACTTAGTGCCATGTGATTCAAGCC
1 CGCACACTTAGTGCCAT-T-ATTCAAGCT
* * *
52215412 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCAT-TA-TTCAAGCT
*
52215441 CGCACACTTAGTGCCATACATTACAAGCT
1 CGCACACTTAGTGCCAT-TATT-CAAGCT
*
52215470 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
52215486 ATCTCGTCAC
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 2 0.03
29 60 0.97
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (27 bp):
CGCACACTTAGTGCCATTATTCAAGCT
Found at i:52221300 original size:64 final size:63
Alignment explanation
Indices: 52221149--52221403 Score: 196
Period size: 68 Copynumber: 3.9 Consensus size: 63
52221139 TGATACACAT
* ** * * *
52221149 GATAA-GTAGCTAGGTCACATGTATGGTGCTGA-GTGCACATCATGT-GTACAAGAGAGCTACGA
1 GATAATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGCTACGA
* *
52221211 GACATTATGATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGATAAGAGAGCTA
1 G--A-TA--ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTA
52221276 C-A
61 CGA
* * * * *
52221278 GGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTA
1 -GATA-ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTA
52221343 CGA
61 CGA
** * * *
52221346 GATAAACTAGCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 GATAATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAG-ACAAGAGAGC
52221404 CGAACTATAT
Statistics
Matches: 153, Mismatches: 26, Indels: 27
0.74 0.13 0.13
Matches are distributed among these distances:
62 2 0.01
63 19 0.12
64 26 0.17
65 4 0.03
66 25 0.16
67 31 0.20
68 45 0.29
69 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (63 bp):
GATAATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGA
Found at i:52226790 original size:2 final size:2
Alignment explanation
Indices: 52226783--52226818 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
52226773 TAACATTAAC
52226783 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52226819 TAAGTTTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52229617 original size:2 final size:2
Alignment explanation
Indices: 52229610--52229636 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
52229600 CTTAGTGGAT
52229610 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
52229637 GTGAAAGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52232914 original size:2 final size:2
Alignment explanation
Indices: 52232907--52232939 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
52232897 AGTATTTGTC
52232907 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
52232940 ATTTTATTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52235975 original size:27 final size:27
Alignment explanation
Indices: 52235937--52235994 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
52235927 CAACCAAGCT
52235937 GAGTAAGAGGAAGGTTAGTATGATTAA
1 GAGTAAGAGGAAGGTTAGTATGATTAA
52235964 GAGTAAGAGGAAGGTTAGTATGATTAA
1 GAGTAAGAGGAAGGTTAGTATGATTAA
52235991 GAGT
1 GAGT
52235995 GGTATTGCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.40, C:0.00, G:0.34, T:0.26
Consensus pattern (27 bp):
GAGTAAGAGGAAGGTTAGTATGATTAA
Found at i:52249541 original size:14 final size:15
Alignment explanation
Indices: 52249515--52249544 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
52249505 AGTTGCATGC
52249515 AAAATTTTAAAATAA
1 AAAATTTTAAAATAA
52249530 AAAATTTT-AAATAA
1 AAAATTTTAAAATAA
52249544 A
1 A
52249545 CATTGAATTA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAATTTTAAAATAA
Found at i:52251603 original size:2 final size:2
Alignment explanation
Indices: 52251586--52251621 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
52251576 TAAATTGAAT
*
52251586 TA TA TA T- TA TA AA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
52251622 GTGTGTGTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:52251626 original size:2 final size:2
Alignment explanation
Indices: 52251621--52251674 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
52251611 TATATATATA
52251621 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
52251663 TG TG TC TG TG TG
1 TG TG TG TG TG TG
52251675 AATGAGATAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.02, G:0.48, T:0.50
Consensus pattern (2 bp):
TG
Found at i:52251848 original size:15 final size:15
Alignment explanation
Indices: 52251830--52251886 Score: 80
Period size: 15 Copynumber: 3.9 Consensus size: 15
52251820 TATCTGTTTT
*
52251830 ATTGAATTTATATTG
1 ATTGAAATTATATTG
*
52251845 ATTGAAATTATTTTG
1 ATTGAAATTATATTG
*
52251860 ATTGAATTTATATTG
1 ATTGAAATTATATTG
52251875 ATT-AAATTATAT
1 ATTGAAATTATAT
52251887 AATATATATG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
14 8 0.22
15 29 0.78
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (15 bp):
ATTGAAATTATATTG
Found at i:52251865 original size:30 final size:28
Alignment explanation
Indices: 52251826--52251884 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 28
52251816 TGAATATCTG
52251826 TTTTATTGAATTTATATTGATTGAAATTA
1 TTTTATTGAATTTATATTGATT-AAATTA
52251855 TTTTGATTGAATTTATATTGATTAAATTA
1 TTTT-ATTGAATTTATATTGATTAAATTA
52251884 T
1 T
52251885 ATAATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 18 0.62
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (28 bp):
TTTTATTGAATTTATATTGATTAAATTA
Found at i:52252307 original size:21 final size:21
Alignment explanation
Indices: 52252260--52252344 Score: 89
Period size: 21 Copynumber: 4.0 Consensus size: 21
52252250 TTTACCAATT
* *
52252260 AGGCACTTTATGTGTCGTATTTC
1 AGGCACCTCATGTGTCGTA--TC
52252283 AGGCACCTCATGTGTCGTATC
1 AGGCACCTCATGTGTCGTATC
* * *
52252304 AGGCACCTCGTGTGTCGTTTT
1 AGGCACCTCATGTGTCGTATC
* *
52252325 AGGCACTTTATGTGTCGTAT
1 AGGCACCTCATGTGTCGTAT
52252345 ACTGATCAGG
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
21 36 0.68
23 17 0.32
ACGTcount: A:0.16, C:0.21, G:0.25, T:0.38
Consensus pattern (21 bp):
AGGCACCTCATGTGTCGTATC
Found at i:52255142 original size:46 final size:45
Alignment explanation
Indices: 52255082--52255257 Score: 167
Period size: 46 Copynumber: 3.8 Consensus size: 45
52255072 TATTTGGGCA
*
52255082 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *** * *
52255128 TTCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
* *
52255175 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTGTGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * * *
52255221 CCCGAGCTCGTTGAGTTGAGTCTGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
52255258 GCGGGTTACA
Statistics
Matches: 104, Mismatches: 19, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 63 0.61
47 31 0.30
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:52255237 original size:93 final size:93
Alignment explanation
Indices: 52255078--52255250 Score: 274
Period size: 93 Copynumber: 1.9 Consensus size: 93
52255068 AGGATATTTG
* **
52255078 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAG
1 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
52255143 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * * *
52255171 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTGTGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
*
52255236 TTGAGTCTGAGTTCG
66 TTGAGTCCGAGTTCG
52255251 CTTATGGGCG
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:52261016 original size:2 final size:2
Alignment explanation
Indices: 52260999--52261036 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
52260989 TAAATTGAAT
*
52260999 TA TA TA T- TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
52261037 GTGTGTGTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:52261041 original size:2 final size:2
Alignment explanation
Indices: 52261036--52261091 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
52261026 TATATATATA
52261036 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
52261078 TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG
52261092 AACGAGATAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:52261265 original size:15 final size:15
Alignment explanation
Indices: 52261247--52261303 Score: 80
Period size: 15 Copynumber: 3.9 Consensus size: 15
52261237 TATCTGTTTT
*
52261247 ATTGAATTTATATTG
1 ATTGAAATTATATTG
*
52261262 ATTGAAATTATTTTG
1 ATTGAAATTATATTG
*
52261277 ATTGAATTTATATTG
1 ATTGAAATTATATTG
52261292 ATT-AAATTATAT
1 ATTGAAATTATAT
52261304 AATATATATG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
14 8 0.22
15 29 0.78
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (15 bp):
ATTGAAATTATATTG
Found at i:52261282 original size:30 final size:28
Alignment explanation
Indices: 52261243--52261301 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 28
52261233 TGAATATCTG
52261243 TTTTATTGAATTTATATTGATTGAAATTA
1 TTTTATTGAATTTATATTGATT-AAATTA
52261272 TTTTGATTGAATTTATATTGATTAAATTA
1 TTTT-ATTGAATTTATATTGATTAAATTA
52261301 T
1 T
52261302 ATAATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 18 0.62
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (28 bp):
TTTTATTGAATTTATATTGATTAAATTA
Found at i:52261713 original size:23 final size:23
Alignment explanation
Indices: 52261687--52261761 Score: 77
Period size: 21 Copynumber: 3.4 Consensus size: 23
52261677 AGGCACTTTA
*
52261687 TGTGTTGTATTTCAGGCACCTCG
1 TGTGTCGTATTTCAGGCACCTCG
*
52261710 TGTGTCGTA--TCAAGCACCTCG
1 TGTGTCGTATTTCAGGCACCTCG
* **
52261731 TGTGTCGT-TTT-AGGCACTTTA
1 TGTGTCGTATTTCAGGCACCTCG
52261752 TGTGTCGTAT
1 TGTGTCGTAT
52261762 ACTGATCAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
21 33 0.77
22 2 0.05
23 8 0.19
ACGTcount: A:0.15, C:0.20, G:0.25, T:0.40
Consensus pattern (23 bp):
TGTGTCGTATTTCAGGCACCTCG
Found at i:52263361 original size:14 final size:14
Alignment explanation
Indices: 52263342--52263382 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
52263332 GAACTCTCAC
52263342 ATGTGGATTCATAA
1 ATGTGGATTCATAA
*
52263356 ATGTGGATTCATAT
1 ATGTGGATTCATAA
* *
52263370 ATGCGAATTCATA
1 ATGTGGATTCATA
52263383 GATACGAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.37
Consensus pattern (14 bp):
ATGTGGATTCATAA
Found at i:52263463 original size:14 final size:14
Alignment explanation
Indices: 52263418--52263465 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
52263408 ATAGATGTAG
52263418 ATTTATACATGCAA
1 ATTTATACATGCAA
* * * **
52263432 AATTATATACGCGG
1 ATTTATACATGCAA
52263446 ATTTATACATGCAA
1 ATTTATACATGCAA
52263460 ATTTAT
1 ATTTAT
52263466 CGATGTGGAT
Statistics
Matches: 24, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (14 bp):
ATTTATACATGCAA
Found at i:52263475 original size:28 final size:28
Alignment explanation
Indices: 52263408--52263497 Score: 99
Period size: 28 Copynumber: 3.2 Consensus size: 28
52263398 GTGTGGATTC
* *
52263408 ATAGATGTAGATTTATACATGCAAAATT
1 ATAGATGTGGATTTATACATGCAAATTT
* * *
52263436 ATATACGCGGATTTATACATGCAAATTT
1 ATAGATGTGGATTTATACATGCAAATTT
* * * *
52263464 ATCGATGTGGATTTATAGATGCGAATTC
1 ATAGATGTGGATTTATACATGCAAATTT
52263492 ATAGAT
1 ATAGAT
52263498 ACGGATTCAT
Statistics
Matches: 49, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 49 1.00
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.36
Consensus pattern (28 bp):
ATAGATGTGGATTTATACATGCAAATTT
Found at i:52263495 original size:14 final size:14
Alignment explanation
Indices: 52263467--52263525 Score: 73
Period size: 14 Copynumber: 4.2 Consensus size: 14
52263457 CAAATTTATC
* *
52263467 GATGTGGATTTATA
1 GATGCGGATTCATA
*
52263481 GATGCGAATTCATA
1 GATGCGGATTCATA
*
52263495 GATACGGATTCATA
1 GATGCGGATTCATA
*
52263509 GATGTGGATTCATA
1 GATGCGGATTCATA
52263523 GAT
1 GAT
52263526 ACAAAATGTC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 38 1.00
ACGTcount: A:0.32, C:0.08, G:0.25, T:0.34
Consensus pattern (14 bp):
GATGCGGATTCATA
Found at i:52263503 original size:28 final size:28
Alignment explanation
Indices: 52263360--52263527 Score: 97
Period size: 28 Copynumber: 6.0 Consensus size: 28
52263350 TCATAAATGT
* *
52263360 GGATTCATATATGCGAATTCATAGATAC
1 GGATTTATAGATGCGAATTCATAGATAC
* * * * **
52263388 GAATCTATACG-TGTGGATTCATAGATGT
1 GGATTTATA-GATGCGAATTCATAGATAC
* * * * **
52263416 AGATTTATACATGCAAAATT-ATATACGC
1 GGATTTATAGATGC-GAATTCATAGATAC
* * * * **
52263444 GGATTTATACATGCAAATTTATCGATGT
1 GGATTTATAGATGCGAATTCATAGATAC
52263472 GGATTTATAGATGCGAATTCATAGATAC
1 GGATTTATAGATGCGAATTCATAGATAC
* * *
52263500 GGATTCATAGATGTGGATTCATAGATAC
1 GGATTTATAGATGCGAATTCATAGATAC
52263528 AAAATGTCTC
Statistics
Matches: 104, Mismatches: 32, Indels: 8
0.72 0.22 0.06
Matches are distributed among these distances:
27 5 0.05
28 96 0.92
29 3 0.03
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.34
Consensus pattern (28 bp):
GGATTTATAGATGCGAATTCATAGATAC
Found at i:52265622 original size:17 final size:17
Alignment explanation
Indices: 52265597--52265631 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
52265587 TTCATCGTGG
*
52265597 CGTCTCATGTTTGATGT
1 CGTCCCATGTTTGATGT
52265614 CGTCCCATGTTTGATGT
1 CGTCCCATGTTTGATGT
52265631 C
1 C
52265632 ACTACATCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.43
Consensus pattern (17 bp):
CGTCCCATGTTTGATGT
Found at i:52266603 original size:17 final size:17
Alignment explanation
Indices: 52266581--52266621 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
52266571 AAAAATGTTT
52266581 TTAAAAATT-TAAAATTA
1 TTAAAAATTATAAAA-TA
52266598 TT-AAAATTATAAAATA
1 TTAAAAATTATAAAATA
*
52266614 TAAAAAAT
1 TTAAAAAT
52266622 AGTTTTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TTAAAAATTATAAAATA
Found at i:52266619 original size:16 final size:16
Alignment explanation
Indices: 52266582--52266619 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
52266572 AAAATGTTTT
52266582 TAAAAATTTAAAATTA
1 TAAAAATTTAAAATTA
*
52266598 TTAAAATTATAAAA-TA
1 TAAAAATT-TAAAATTA
52266614 TAAAAA
1 TAAAAA
52266620 ATAGTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TAAAAATTTAAAATTA
Found at i:52269883 original size:25 final size:26
Alignment explanation
Indices: 52269854--52269904 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
52269844 CTTATTTCAT
*
52269854 TAAATAAAAAAT-TTTAAAAATATAA
1 TAAATAAAAAATATTTAAAAACATAA
* *
52269879 TAAATCAAATATATTTAAAAACATAA
1 TAAATAAAAAATATTTAAAAACATAA
52269905 AAACAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (26 bp):
TAAATAAAAAATATTTAAAAACATAA
Found at i:52269896 original size:26 final size:24
Alignment explanation
Indices: 52269866--52269914 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
52269856 AATAAAAAAT
*
52269866 TTTAAAAATATAATAAATCAAATATA
1 TTTAAAAACATAA-AAA-CAAATATA
52269892 TTTAAAAACATAAAAACAAATAT
1 TTTAAAAACATAAAAACAAATAT
52269915 TAAGACAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 3 0.14
26 12 0.55
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (24 bp):
TTTAAAAACATAAAAACAAATATA
Found at i:52269934 original size:21 final size:22
Alignment explanation
Indices: 52269901--52269943 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
52269891 ATTTAAAAAC
* *
52269901 ATAAAAACAAATATTAAGACAA
1 ATAAAAACAAATACTAAAACAA
*
52269923 ATAAAAA-TAATACTAAAACAA
1 ATAAAAACAAATACTAAAACAA
52269944 TTCTTAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.70, C:0.09, G:0.02, T:0.19
Consensus pattern (22 bp):
ATAAAAACAAATACTAAAACAA
Found at i:52274200 original size:20 final size:20
Alignment explanation
Indices: 52274177--52274224 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
52274167 AGCTCCGTCC
52274177 AGCTCAACTCAGCTCATTTG
1 AGCTCAACTCAGCTCATTTG
*** *
52274197 AGCTCGTTTCAGCTCGTTTG
1 AGCTCAACTCAGCTCATTTG
52274217 AGCTCAAC
1 AGCTCAAC
52274225 CGAGCTTACT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (20 bp):
AGCTCAACTCAGCTCATTTG
Found at i:52275542 original size:54 final size:54
Alignment explanation
Indices: 52275483--52275591 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
52275473 CAAACCGAGC
52275483 CTTCTATCCTTCATCCATCTTTGCTACCCATAGTCAAACCTATTACTAAACTTA
1 CTTCTATCCTTCATCCATCTTTGCTACCCATAGTCAAACCTATTACTAAACTTA
52275537 CTTCTATCCTTCATCCATCTTTGCTACCCATAGTCAAACCTATTACTAAACTTA
1 CTTCTATCCTTCATCCATCTTTGCTACCCATAGTCAAACCTATTACTAAACTTA
52275591 C
1 C
52275592 CCTTCTTGAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.28, C:0.32, G:0.04, T:0.37
Consensus pattern (54 bp):
CTTCTATCCTTCATCCATCTTTGCTACCCATAGTCAAACCTATTACTAAACTTA
Found at i:52276855 original size:6 final size:6
Alignment explanation
Indices: 52276830--52276877 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
52276820 AGTGTGAAAG
** * *
52276830 AAAGCAA AAAGAA AGTGAA AAAGAA AAAGAG AAGGAA AAAGAA AAAGA
1 AAAG-AA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGA
52276878 GATCGAGAGT
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
6 29 0.88
7 4 0.12
ACGTcount: A:0.73, C:0.02, G:0.23, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:52276858 original size:18 final size:18
Alignment explanation
Indices: 52276830--52276927 Score: 76
Period size: 18 Copynumber: 5.4 Consensus size: 18
52276820 AGTGTGAAAG
52276830 AAAGCAAAAAGAAAGTGAA
1 AAAG-AAAAAGAAAGTGAA
52276849 AAAGAAAAAGAGAAG-GAA
1 AAAGAAAAAGA-AAGTGAA
* *
52276867 AAAGAAAAAGAGA-TCGAG
1 AAAGAAAAAGAAAGT-GAA
** *
52276885 AGTGAAAAAGAATGTG-A
1 AAAGAAAAAGAAAGTGAA
* *
52276902 GAAGAAAAAGAAAATTGAA
1 AAAGAAAAAG-AAAGTGAA
52276921 AAAGAAA
1 AAAGAAA
52276928 TTGAGTCTGA
Statistics
Matches: 60, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
17 8 0.13
18 37 0.62
19 15 0.25
ACGTcount: A:0.66, C:0.02, G:0.24, T:0.07
Consensus pattern (18 bp):
AAAGAAAAAGAAAGTGAA
Found at i:52280152 original size:29 final size:29
Alignment explanation
Indices: 52280062--52280279 Score: 278
Period size: 29 Copynumber: 7.5 Consensus size: 29
52280052 ACTCGATTTC
* * **
52280062 GCACACTTAGTGCCATGTGATTT-AAGCCC
1 GCACACTTAGTGCCATAT-ATTTCCAGCAT
* *** *
52280091 GCACACATAGTGCCATACCCTTCGAGC-T
1 GCACACTTAGTGCCATATATTTCCAGCAT
** * *
52280119 CGCACACCCAGTGCCGTATATTTCCAGTAT
1 -GCACACTTAGTGCCATATATTTCCAGCAT
*
52280149 GCACACTTAGTACCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
52280178 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
52280207 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
52280236 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
52280265 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
52280280 ATCTCGTCAC
Statistics
Matches: 165, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
28 2 0.01
29 162 0.98
30 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.28
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:52283418 original size:29 final size:29
Alignment explanation
Indices: 52283328--52283516 Score: 229
Period size: 29 Copynumber: 6.5 Consensus size: 29
52283318 ACTCGATTTC
* * **
52283328 GCACACTTAGTGCCATGTGATTT-AAGCCC
1 GCACACTTAGTGCCATAT-ATTTCCAGCAT
* *** *
52283357 GCACACATAGTGCCATACCCTTCGAGC-T
1 GCACACTTAGTGCCATATATTTCCAGCAT
** *
52283385 CGCACACCCAGTGCCGTATATTTCCAGCAT
1 -GCACACTTAGTGCCATATATTTCCAGCAT
*
52283415 GCACACTTAGTACCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
52283444 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
52283473 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
52283502 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
52283517 ATCTCGTCAC
Statistics
Matches: 138, Mismatches: 19, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
28 2 0.01
29 135 0.98
30 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:52285264 original size:20 final size:20
Alignment explanation
Indices: 52285241--52285288 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
52285231 AGCTCCGTCC
52285241 AGCTCAACTCAGCTCATTTG
1 AGCTCAACTCAGCTCATTTG
*** * *
52285261 AGCTCGTTTTAGCTCGTTTG
1 AGCTCAACTCAGCTCATTTG
52285281 AGCTCAAC
1 AGCTCAAC
52285289 CGATCTTACT
Statistics
Matches: 20, Mismatches: 8, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (20 bp):
AGCTCAACTCAGCTCATTTG
Found at i:52289101 original size:10 final size:10
Alignment explanation
Indices: 52289082--52289131 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
52289072 TGAAATTCTA
52289082 AAAGATAAAT
1 AAAGATAAAT
52289092 ACAA-ATAAAT
1 A-AAGATAAAT
*
52289102 AAAGATAATT
1 AAAGATAAAT
52289112 AAAGATAAAT
1 AAAGATAAAT
52289122 GAAA-ATAAAT
1 -AAAGATAAAT
52289132 CCTAAAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 2 0.06
10 28 0.80
11 5 0.14
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:52289927 original size:95 final size:97
Alignment explanation
Indices: 52289795--52289975 Score: 269
Period size: 95 Copynumber: 1.9 Consensus size: 97
52289785 ATTTTATTTA
* * * *
52289795 TTTATTTTTACTTAGGAATATATTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACC-CA
1 TTTATTTTTACTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATAACAGCCAAGCACCTCA
52289859 -CCCTAGTTACTCAGCCCAACATACTCCTAATT
66 CCCCT-GTTACTCAGCCCAACATACTCCTAATT
* * *
52289891 TTTATTTTT-CTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATAATATCTAAGCACCTCA
1 TTTATTTTTACTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATAACAGCCAAGCACCTCA
52289955 CCCCTGTTACTCAGCCCAACA
66 CCCCTGTTACTCAGCCCAACA
52289976 CATCTTTAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
95 45 0.59
96 27 0.36
97 4 0.05
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.29
Consensus pattern (97 bp):
TTTATTTTTACTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATAACAGCCAAGCACCTCA
CCCCTGTTACTCAGCCCAACATACTCCTAATT
Found at i:52290792 original size:15 final size:17
Alignment explanation
Indices: 52290772--52290824 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 17
52290762 TTAATATCTG
52290772 AAAATAATAA-AT-AAT
1 AAAATAATAAGATAAAT
52290787 AAAATAATAAGATAAAAT
1 AAAATAATAAGAT-AAAT
* *
52290805 AAAATAA-AACAAAAAT
1 AAAATAATAAGATAAAT
52290821 AAAA
1 AAAA
52290825 ATTAGGTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
15 10 0.30
16 10 0.30
17 3 0.09
18 10 0.30
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (17 bp):
AAAATAATAAGATAAAT
Found at i:52293815 original size:17 final size:18
Alignment explanation
Indices: 52293795--52293828 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
52293785 AAGTGAATTG
52293795 AAATTGC-GAAATTAAAT
1 AAATTGCAGAAATTAAAT
52293812 AAATTGCAGAAATTAAA
1 AAATTGCAGAAATTAAA
52293829 ATGGAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (18 bp):
AAATTGCAGAAATTAAAT
Found at i:52294560 original size:20 final size:20
Alignment explanation
Indices: 52294537--52294576 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
52294527 TGAAATTCTA
52294537 AAAGATAAAT-ACAAATAAAT
1 AAAGATAAATGA-AAATAAAT
52294557 AAAGATAAATGAAAATAAAT
1 AAAGATAAATGAAAATAAAT
52294577 CCTAAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.70, C:0.03, G:0.07, T:0.20
Consensus pattern (20 bp):
AAAGATAAATGAAAATAAAT
Found at i:52294588 original size:23 final size:26
Alignment explanation
Indices: 52294562--52294612 Score: 63
Period size: 23 Copynumber: 2.1 Consensus size: 26
52294552 TAAATAAAGA
*
52294562 TAAATGAAAAT-AAATCC-TAA-AAT
1 TAAATCAAAATAAAATCCTTAATAAT
*
52294585 TAAATCTAAATAAAATCCTTAATAAT
1 TAAATCAAAATAAAATCCTTAATAAT
52294611 TA
1 TA
52294613 CCCTAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 9 0.39
24 6 0.26
25 3 0.13
26 5 0.22
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (26 bp):
TAAATCAAAATAAAATCCTTAATAAT
Found at i:52311330 original size:25 final size:25
Alignment explanation
Indices: 52311282--52311329 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
52311272 ATTATGGAAA
*
52311282 TATACTAACTACACCTTAAAAAAAG
1 TATACTAAATACACCTTAAAAAAAG
*
52311307 TATACTAAATACA-TTTAAAAAAA
1 TATACTAAATACACCTTAAAAAAA
52311330 AAGAGTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.56, C:0.15, G:0.02, T:0.27
Consensus pattern (25 bp):
TATACTAAATACACCTTAAAAAAAG
Found at i:52319463 original size:44 final size:45
Alignment explanation
Indices: 52319398--52319497 Score: 107
Period size: 44 Copynumber: 2.2 Consensus size: 45
52319388 TGCTACCTTG
* * * * *
52319398 GGGAGATAAGATTCGCCATCTTC-GATCTGCTCCGCTACCACTT-A
1 GGGAGATAAGATTCACAATCTTCAG-TCTACTCCACTACAACTTCA
*
52319442 GGGAGATAAGA-TCTACAATCTTCAGTCTACTCCACTGCAACTTCA
1 GGGAGATAAGATTC-ACAATCTTCAGTCTACTCCACTACAACTTCA
52319487 GGGAGATAAGA
1 GGGAGATAAGA
52319498 CTTGCTTTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
43 2 0.04
44 32 0.68
45 13 0.28
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (45 bp):
GGGAGATAAGATTCACAATCTTCAGTCTACTCCACTACAACTTCA
Found at i:52319519 original size:41 final size:41
Alignment explanation
Indices: 52319467--52319579 Score: 163
Period size: 41 Copynumber: 2.8 Consensus size: 41
52319457 CAATCTTCAG
52319467 TCTACTCCACTGCAACTTCAGGGAGATAAGACTTGCTTTAA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGACTTGCTTTAA
* * *
52319508 TCTACTCCACTGCCACTTTAGGGAGATAAGACTTGCTTTGA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGACTTGCTTTAA
* * * *
52319549 TCTGCTCCATTGCAACCTCAAGGAGATAAGA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGA
52319580 TCTACCATAT
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (41 bp):
TCTACTCCACTGCAACTTCAGGGAGATAAGACTTGCTTTAA
Found at i:52319753 original size:88 final size:88
Alignment explanation
Indices: 52319654--52319930 Score: 215
Period size: 88 Copynumber: 3.1 Consensus size: 88
52319644 CTCTTGCTAC
*
52319654 CTTAGAGAGATAAGGCTGGTGGCTAAAATTTTCTCCCCTGCTACCTCGAGAAGATAAAATTTGCC
1 CTTAGAGAGATAAGGCTGGTGGCTAAAATTTGCTCCCCTGCTACCTCGAGAAGATAAAATTTGCC
52319719 ATCTTTGATCCGCTCCACTACTA
66 ATCTTTGATCCGCTCCACTACTA
* * ** * * * * * * *
52319742 ATTAGGGAGAT-AGGATCTACAAT-CCT-CAGTCTGCTTCCTTGCTACCTC-AGGAAGATAAGA-
1 CTTAGAGAGATAAGG--CT--GGTGGCTAAAATTTGCTCCCCTGCTACCTCGA-GAAGATAAAAT
* * * * ** * * *
52319802 CTACAATCTTTAATCTACTCTC-TTGCCA
61 TTGCCATCTTTGATCCGCTC-CACTACTA
* * *
52319830 CCTTAGAGAGATAAGGCTGGTGGCTAAGATTTGCTCCCCTGCTACCTCGGGAAGATAAAATTCGC
1 -CTTAGAGAGATAAGGCTGGTGGCTAAAATTTGCTCCCCTGCTACCTCGAGAAGATAAAATTTGC
*
52319895 CATCTTCGATCCGCTCCACTACTA
65 CATCTTTGATCCGCTCCACTACTA
*
52319919 CTTAGGGAGATA
1 CTTAGAGAGATA
52319931 GGATCTACAA
Statistics
Matches: 130, Mismatches: 46, Indels: 26
0.64 0.23 0.13
Matches are distributed among these distances:
86 1 0.01
87 5 0.04
88 66 0.51
89 52 0.40
90 5 0.04
91 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (88 bp):
CTTAGAGAGATAAGGCTGGTGGCTAAAATTTGCTCCCCTGCTACCTCGAGAAGATAAAATTTGCC
ATCTTTGATCCGCTCCACTACTA
Found at i:52319786 original size:177 final size:177
Alignment explanation
Indices: 52319596--52320119 Score: 780
Period size: 177 Copynumber: 3.0 Consensus size: 177
52319586 ATATTGAGTT
* * *
52319596 TGCTTCATTGCTACCTCAGGAGGATAAGACTACAATCTTCAACCTAATCTCTTGCTACCTTAGAG
1 TGCTTCCTTGCTACCTCAGGAAGATAAGACTACAATCTTCAACCTACTCTCTTGCTACCTTAGAG
* * *
52319661 AGATAAGGCTGGTGGCTAAAATTTTCTCCCCTGCTACCTCGAGAAGATAAAATTTGCCATCTTTG
66 AGATAAGGCTGGTGGCTAAAATTTGCTCCCCTGCTACCTCGGGAAGATAAAATTTGCCATCTTCG
*
52319726 ATCCGCTCCACTACTAATTAGGGAGATAGGATCTACAATCCTCAGTC
131 ATCCGCTCCACTACTACTTAGGGAGATAGGATCTACAATCCTCAGTC
* * *
52319773 TGCTTCCTTGCTACCTCAGGAAGATAAGACTACAATCTTTAATCTACTCTCTTGCCACCTTAGAG
1 TGCTTCCTTGCTACCTCAGGAAGATAAGACTACAATCTTCAACCTACTCTCTTGCTACCTTAGAG
* *
52319838 AGATAAGGCTGGTGGCTAAGATTTGCTCCCCTGCTACCTCGGGAAGATAAAATTCGCCATCTTCG
66 AGATAAGGCTGGTGGCTAAAATTTGCTCCCCTGCTACCTCGGGAAGATAAAATTTGCCATCTTCG
52319903 ATCCGCTCCACTACTACTTAGGGAGATAGGATCTACAATCCTCAGTC
131 ATCCGCTCCACTACTACTTAGGGAGATAGGATCTACAATCCTCAGTC
* * * * *
52319950 TGCATCCTTGCTACCTCAGGAAAATAAGACTTCAATCTTCAACCTGCTCTCTTGCTACCTCAGAG
1 TGCTTCCTTGCTACCTCAGGAAGATAAGACTACAATCTTCAACCTACTCTCTTGCTACCTTAGAG
* * * * *
52320015 AGATAAGGCTTGTGGCTAAAATATGCTCCTCC-GCTATCTCGGGAAGATAAGATTTGCCATCTGC
66 AGATAAGGCTGGTGGCTAAAATTTGCTCC-CCTGCTACCTCGGGAAGATAAAATTTGCCATCTTC
* * * * * *
52320079 GATCTGCTCTACTACTGCTTAGGGAGACAAGATCTTCAATC
130 GATCCGCTCCACTACTACTTAGGGAGATAGGATCTACAATC
52320120 TTCAATCTAA
Statistics
Matches: 313, Mismatches: 33, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
177 311 0.99
178 2 0.01
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (177 bp):
TGCTTCCTTGCTACCTCAGGAAGATAAGACTACAATCTTCAACCTACTCTCTTGCTACCTTAGAG
AGATAAGGCTGGTGGCTAAAATTTGCTCCCCTGCTACCTCGGGAAGATAAAATTTGCCATCTTCG
ATCCGCTCCACTACTACTTAGGGAGATAGGATCTACAATCCTCAGTC
Found at i:52319988 original size:88 final size:87
Alignment explanation
Indices: 52319692--52319989 Score: 223
Period size: 89 Copynumber: 3.4 Consensus size: 87
52319682 TTTTCTCCCC
* * * * *
52319692 TGCTACCTC-GAGAAGATAAAATTTGCCATCTTTGATCCGCTCCACTACTAATTAGGGAGATAGG
1 TGCTACCTCAG-GAAGATAAGACTT-CAATCTTCGATCCGCTCCACTACTACTTAGGGAGATAGG
52319756 ATCTACAATCCTCAGTCTGCTTCCT
64 ATCTACAATCCTCAGTCTGC-TCCT
* ** ** * * * *
52319781 TGCTACCTCAGGAAGATAAGACTACAATCTTTAATCTACTCTC-TTGCCACCTTAGAGAGATAAG
1 TGCTACCTCAGGAAGATAAGACTTCAATCTTCGATCCGCTC-CACTACTA-CTTAGGGAGAT-AG
** * * * *
52319845 G--CT--GGTGGCTAAGATTTGCTCCCC
63 GATCTACAAT-CCTCAG-TCTGCT-CCT
* * *
52319869 TGCTACCTCGGGAAGATAA-AATTCGCCATCTTCGATCCGCTCCACTACTACTTAGGGAGATAGG
1 TGCTACCTCAGGAAGATAAGACTT--CAATCTTCGATCCGCTCCACTACTACTTAGGGAGATAGG
52319933 ATCTACAATCCTCAGTCTGCATCCT
64 ATCTACAATCCTCAGTCTGC-TCCT
*
52319958 TGCTACCTCAGGAAAATAAGACTTCAATCTTC
1 TGCTACCTCAGGAAGATAAGACTTCAATCTTC
52319990 AACCTGCTCT
Statistics
Matches: 153, Mismatches: 40, Indels: 33
0.68 0.18 0.15
Matches are distributed among these distances:
86 1 0.01
87 10 0.07
88 60 0.39
89 69 0.45
90 12 0.08
91 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.29
Consensus pattern (87 bp):
TGCTACCTCAGGAAGATAAGACTTCAATCTTCGATCCGCTCCACTACTACTTAGGGAGATAGGAT
CTACAATCCTCAGTCTGCTCCT
Found at i:52322254 original size:29 final size:29
Alignment explanation
Indices: 52322220--52322294 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
52322210 TACTCGATTT
*
52322220 CGCACACTTAGTGCCATGCGATTTAG-GCC
1 CGCACACTTAGTGCCATGC-ACTTAGAGCC
** * * *
52322249 CGCACACACAGTGCCATGCCCTTCGAGCT
1 CGCACACTTAGTGCCATGCACTTAGAGCC
52322278 CGCACACTTAGTGCCAT
1 CGCACACTTAGTGCCAT
52322295 ATATTTCCAG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
28 3 0.08
29 34 0.92
ACGTcount: A:0.21, C:0.36, G:0.21, T:0.21
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTAGAGCC
Found at i:52322311 original size:29 final size:29
Alignment explanation
Indices: 52322278--52322351 Score: 139
Period size: 29 Copynumber: 2.6 Consensus size: 29
52322268 CCTTCGAGCT
52322278 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
52322307 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
52322336 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
52322352 ATCTCGTCAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:52330166 original size:29 final size:28
Alignment explanation
Indices: 52330096--52330170 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
52330086 ATACTCGATT
* *
52330096 TCGCACACTTAGTGCCATGCGATTTAGC
1 TCGCACACTTAGTGCCATGCCATTGAGC
* ** *
52330124 CCGCACACACAGTGCCATGCCCTTCGAGC
1 TCGCACACTTAGTGCCATGCCATT-GAGC
52330153 TCGCACACTTAGTGCCAT
1 TCGCACACTTAGTGCCAT
52330171 ATATTTCCAG
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
28 19 0.51
29 18 0.49
ACGTcount: A:0.21, C:0.36, G:0.20, T:0.23
Consensus pattern (28 bp):
TCGCACACTTAGTGCCATGCCATTGAGC
Found at i:52330187 original size:29 final size:29
Alignment explanation
Indices: 52330154--52330227 Score: 139
Period size: 29 Copynumber: 2.6 Consensus size: 29
52330144 CCTTCGAGCT
52330154 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
52330183 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
52330212 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
52330228 ATCTCGTCAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:52336846 original size:46 final size:44
Alignment explanation
Indices: 52336742--52336849 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
52336732 TGTCTTTGAC
** * * *
52336742 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
52336786 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
52336832 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
52336850 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:52342981 original size:46 final size:44
Alignment explanation
Indices: 52342877--52342984 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
52342867 TGTCTTTGAC
** * * *
52342877 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
52342921 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
52342967 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
52342985 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:52348171 original size:19 final size:19
Alignment explanation
Indices: 52348147--52348186 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
52348137 AACAAGAATT
52348147 CTAACCATATAAATTATAC
1 CTAACCATATAAATTATAC
52348166 CTAACCATATAAATTATAC
1 CTAACCATATAAATTATAC
52348185 CT
1 CT
52348187 TCTAATTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.33
Consensus pattern (19 bp):
CTAACCATATAAATTATAC
Found at i:52349132 original size:46 final size:44
Alignment explanation
Indices: 52349028--52349135 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
52349018 TGTCTTTGAC
** * * *
52349028 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
52349072 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
52349118 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
52349136 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:52351766 original size:53 final size:53
Alignment explanation
Indices: 52351685--52351835 Score: 196
Period size: 53 Copynumber: 2.8 Consensus size: 53
52351675 CTTACACGGT
* * *
52351685 TCACATATCATACCGAAGCTATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAACCCAG-CTATGGTCTTATACGGAATCACATTA
* *
52351740 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAACCCAGCTATGGTCTTATACGGAATCACATTA
** *
52351793 TCACATTGCACCGATGCCATAACCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAACCCAGCTATGGTCTTATACGG
52351836 GCGCACTTAT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
52 1 0.01
53 79 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAACCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:52355837 original size:46 final size:44
Alignment explanation
Indices: 52355733--52355840 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
52355723 TGTCTTTGAC
** * * *
52355733 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
52355777 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
52355823 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
52355841 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:52361972 original size:46 final size:44
Alignment explanation
Indices: 52361868--52361975 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
52361858 TGTCTTTGAC
** * * *
52361868 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
52361912 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
52361958 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
52361976 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:52368106 original size:46 final size:44
Alignment explanation
Indices: 52368002--52368109 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
52367992 TGTCTTTGAC
** * * *
52368002 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
52368046 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
52368092 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
52368110 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:52374243 original size:46 final size:44
Alignment explanation
Indices: 52374139--52374246 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
52374129 TGTCTTTGAC
** * * *
52374139 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
52374183 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
52374229 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
52374247 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:52385157 original size:13 final size:13
Alignment explanation
Indices: 52385139--52385165 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
52385129 CTGTCCGTTG
52385139 GCATTTATCGCAA
1 GCATTTATCGCAA
52385152 GCATTTATCGCAA
1 GCATTTATCGCAA
52385165 G
1 G
52385166 TAGCAACATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (13 bp):
GCATTTATCGCAA
Found at i:52388604 original size:30 final size:30
Alignment explanation
Indices: 52388568--52388627 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
52388558 CCTCATCACT
52388568 GGATGTACCTGAGTAGAACCATATAAACTA
1 GGATGTACCTGAGTAGAACCATATAAACTA
52388598 GGATGTACCTGAGTAGAACCATATAAACTA
1 GGATGTACCTGAGTAGAACCATATAAACTA
52388628 TCGGTCTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (30 bp):
GGATGTACCTGAGTAGAACCATATAAACTA
Found at i:52394190 original size:41 final size:41
Alignment explanation
Indices: 52394143--52394255 Score: 163
Period size: 41 Copynumber: 2.8 Consensus size: 41
52394133 CAATCTTCAG
52394143 TCTACTCCACTGCAACTTCAGGGAGATAAGACTTGCTTTAA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGACTTGCTTTAA
* * * *
52394184 TCTACTCCACTGCCACTTTAGGGAGATAAGGCTTGCTTTGA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGACTTGCTTTAA
* * *
52394225 TCTGCTCCATTGCAACTTCAAGGAGATAAGA
1 TCTACTCCACTGCAACTTCAGGGAGATAAGA
52394256 TCTACCATAT
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.29
Consensus pattern (41 bp):
TCTACTCCACTGCAACTTCAGGGAGATAAGACTTGCTTTAA
Found at i:52394474 original size:177 final size:177
Alignment explanation
Indices: 52394281--52394604 Score: 452
Period size: 177 Copynumber: 1.8 Consensus size: 177
52394271 CTGTTTCATT
* * *
52394281 GCTACCTCAAGAAGATAAGACTACAATCTTCAACCTACTCTCTTGCTACCTTAGAGAGATAAGGC
1 GCTACCTCAAGAAGATAAAACTACAATCTTCAACCTACTCTCTTACTACCTTAGAGAGATAAGAC
* ** * ** *
52394346 TGGTGGCTAAAATTTTCTCCCCTGCTACCTCGGGAAGATAA-ATTTTTCCATCTTCGATCCGCTC
66 TGGTGGCTAAAATCTGATCCCCCGCTACCTCGGGAAGATAAGA-TTCGCCATCTGCGATCCGCTC
*
52394410 CAGTACTACTTAGGGAGATAGGATCTACAATCCTCAGTCTGCTTCCTA
130 CACTACTACTTAGGGAGATAGGATCTACAATCCTCAGTCTGCTTCCTA
* * * * *
52394458 GCTACCTCAGGAAGATAAAACTTCAATCTTCAATCTGCTCTCTTACTACCTTAGAGAGATAAGAT
1 GCTACCTCAAGAAGATAAAACTACAATCTTCAACCTACTCTCTTACTACCTTAGAGAGATAAGAC
* *
52394523 TGGTGGCTAAAATCTGATCCCCCGCTATCTCGGGAAGATAAGATTCGCCATCTGCGATCTGCTCC
66 TGGTGGCTAAAATCTGATCCCCCGCTACCTCGGGAAGATAAGATTCGCCATCTGCGATCCGCTCC
* *
52394588 ACTATTGCTTAGGGAGA
131 ACTACTACTTAGGGAGA
52394605 CAAGATCTTC
Statistics
Matches: 126, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
177 125 0.99
178 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (177 bp):
GCTACCTCAAGAAGATAAAACTACAATCTTCAACCTACTCTCTTACTACCTTAGAGAGATAAGAC
TGGTGGCTAAAATCTGATCCCCCGCTACCTCGGGAAGATAAGATTCGCCATCTGCGATCCGCTCC
ACTACTACTTAGGGAGATAGGATCTACAATCCTCAGTCTGCTTCCTA
Found at i:52394563 original size:88 final size:88
Alignment explanation
Indices: 52394281--52394563 Score: 214
Period size: 88 Copynumber: 3.2 Consensus size: 88
52394271 CTGTTTCATT
** * * * * * **
52394281 GCTACCTCAAGAAGATAAGACTACAATCTTCAACCTACTCTCTTGCTACCTTAGAGAGATAAGGC
1 GCTACCTCGGGAAGATAAAACTTCAATCTTCAATCTGCTCTCTTACTACCTTAGAGAGATAAGAT
* * *
52394346 TGGTGGCTAAAATTTTCTCCCCT
66 TGGTGGCTAAAATCTGCTCCCCA
** * * * * * *
52394369 GCTACCTCGGGAAGATAAATTTTTCCATCTTCGATCCGCTC-CAGTACTA-CTTAGGGAGATAGG
1 GCTACCTCGGGAAGATAAA-ACTTCAATCTTCAATCTGCTCTC-TTACTACCTTAGAGAGATAAG
** * * * * *
52394432 ATCTACAAT-CCT-CAGTCTGCTTCCTA
64 AT-T--GGTGGCTAAAATCTGCTCCCCA
*
52394458 GCTACCTCAGGAAGATAAAACTTCAATCTTCAATCTGCTCTCTTACTACCTTAGAGAGATAAGAT
1 GCTACCTCGGGAAGATAAAACTTCAATCTTCAATCTGCTCTCTTACTACCTTAGAGAGATAAGAT
* *
52394523 TGGTGGCTAAAATCTGATCCCCC
66 TGGTGGCTAAAATCTGCTCCCCA
*
52394546 GCTATCTCGGGAAGATAA
1 GCTACCTCGGGAAGATAA
52394564 GATTCGCCAT
Statistics
Matches: 139, Mismatches: 47, Indels: 18
0.68 0.23 0.09
Matches are distributed among these distances:
86 1 0.01
87 2 0.01
88 75 0.54
89 58 0.42
90 2 0.01
91 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (88 bp):
GCTACCTCGGGAAGATAAAACTTCAATCTTCAATCTGCTCTCTTACTACCTTAGAGAGATAAGAT
TGGTGGCTAAAATCTGCTCCCCA
Found at i:52403033 original size:24 final size:24
Alignment explanation
Indices: 52403006--52403056 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
52402996 TAGCTAGCTA
* *
52403006 CTCTTGCATCTGCGCTTGCATTTG
1 CTCTTGCATATCCGCTTGCATTTG
**
52403030 CTCTTGCATATCCTTTTGCATTTG
1 CTCTTGCATATCCGCTTGCATTTG
52403054 CTC
1 CTC
52403057 CAATTTTTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.10, C:0.29, G:0.16, T:0.45
Consensus pattern (24 bp):
CTCTTGCATATCCGCTTGCATTTG
Found at i:52408169 original size:10 final size:10
Alignment explanation
Indices: 52408154--52408197 Score: 52
Period size: 10 Copynumber: 4.1 Consensus size: 10
52408144 AGTAAGTTAA
52408154 AAAGATAAAT
1 AAAGATAAAT
52408164 AAAGATAAAAAT
1 AAAGAT--AAAT
*
52408176 AAAAATAAAT
1 AAAGATAAAT
52408186 AAAAGATAAAT
1 -AAAGATAAAT
52408197 A
1 A
52408198 GTAGGGGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
10 11 0.38
11 9 0.31
12 9 0.31
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:52418256 original size:41 final size:41
Alignment explanation
Indices: 52418198--52418297 Score: 146
Period size: 41 Copynumber: 2.4 Consensus size: 41
52418188 ATTCTGCTGT
52418198 AACTTCAGGGAGATAAGACTTACTTTAATCTGCTCCAGTGC
1 AACTTCAGGGAGATAAGACTTACTTTAATCTGCTCCAGTGC
* * * *
52418239 CACTTCAGGGAGATAAGACTTGCTTTGATCTGCTCCATTGC
1 AACTTCAGGGAGATAAGACTTACTTTAATCTGCTCCAGTGC
* *
52418280 AACCTCAAGGAGATAAGA
1 AACTTCAGGGAGATAAGA
52418298 TCTACCATAT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (41 bp):
AACTTCAGGGAGATAAGACTTACTTTAATCTGCTCCAGTGC
Found at i:52418464 original size:88 final size:88
Alignment explanation
Indices: 52418372--52418648 Score: 217
Period size: 88 Copynumber: 3.1 Consensus size: 88
52418362 CTCTTGTTAC
*
52418372 CTTAGAGAGATAAGGTTGGTGGCTAAAATTTGCTCCCCTGCTACCTCGGGAAGATAAAATTCGCC
1 CTTAGAGAGATAAGGTTGGTGGCTAAAATCTGCTCCCCTGCTACCTCGGGAAGATAAAATTCGCC
*
52418437 ATCTTTGATCGGCTCCACTACTA
66 ATCTTCGATCGGCTCCACTACTA
* * * * * * * * *
52418460 CTTAGGGAGAT-AGGATCTACAGT-CCT-CAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACT
1 CTTAGAGAGATAAGG-T-T--GGTGGCTAAAATCTGCTCCCCTGCTACCTCGGGAAGATAA-AAT
* * * * *
52418522 T--CAATCTTCAACCGGCTCTC-TTGCTA
61 TCGCCATCTTCGATCGGCTC-CACTACTA
* * * * *
52418548 TCTTAGAGAGATAAGGCTGGTGGCTAAAATCTACTCCCCTACTATCTCGGGAAGATAAGATTCGC
1 -CTTAGAGAGATAAGGTTGGTGGCTAAAATCTGCTCCCCTGCTACCTCGGGAAGATAAAATTCGC
* * *
52418613 CATCTGCGATCTGCTCCACTACTG
65 CATCTTCGATCGGCTCCACTACTA
52418637 CTTA-AGGAGATA
1 CTTAGA-GAGATA
52418649 GGATCTTCAA
Statistics
Matches: 137, Mismatches: 38, Indels: 28
0.67 0.19 0.14
Matches are distributed among these distances:
86 2 0.01
87 8 0.06
88 64 0.47
89 53 0.39
90 8 0.06
91 2 0.01
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (88 bp):
CTTAGAGAGATAAGGTTGGTGGCTAAAATCTGCTCCCCTGCTACCTCGGGAAGATAAAATTCGCC
ATCTTCGATCGGCTCCACTACTA
Found at i:52418491 original size:177 final size:177
Alignment explanation
Indices: 52418286--52418654 Score: 551
Period size: 177 Copynumber: 2.1 Consensus size: 177
52418276 TTGCAACCTC
* **
52418286 AAGGAGATAAGATCTACCA-TATTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTACAAT
1 AAGGAGATAGGATCTA-CAGTCCTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTACAAT
* * * * * *
52418350 CTTCAACCTACTCTCTTGTTACCTTAGAGAGATAAGGTTGGTGGCTAAAATTTGCTCCCCTGCTA
65 CTTCAACCGACTCTCTTGCTACCTTAGAGAGATAAGGCTGGTGGCTAAAATCTACTCCCCTACTA
**
52418415 CCTCGGGAAGATAAAATTCGCCATCTTTGATCGGCTCCACTACTACTT
130 CCTCGGGAAGATAAAATTCGCCATCTGCGATCGGCTCCACTACTACTT
* *
52418463 AGGGAGATAGGATCTACAGTCCTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTTCAATC
1 AAGGAGATAGGATCTACAGTCCTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTACAATC
* * *
52418528 TTCAACCGGCTCTCTTGCTATCTTAGAGAGATAAGGCTGGTGGCTAAAATCTACTCCCCTACTAT
66 TTCAACCGACTCTCTTGCTACCTTAGAGAGATAAGGCTGGTGGCTAAAATCTACTCCCCTACTAC
* * *
52418593 CTCGGGAAGATAAGATTCGCCATCTGCGATCTGCTCCACTACTGCTT
131 CTCGGGAAGATAAAATTCGCCATCTGCGATCGGCTCCACTACTACTT
52418640 AAGGAGATAGGATCT
1 AAGGAGATAGGATCT
52418655 TCAATCTTCA
Statistics
Matches: 171, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
176 2 0.01
177 169 0.99
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.29
Consensus pattern (177 bp):
AAGGAGATAGGATCTACAGTCCTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTACAATC
TTCAACCGACTCTCTTGCTACCTTAGAGAGATAAGGCTGGTGGCTAAAATCTACTCCCCTACTAC
CTCGGGAAGATAAAATTCGCCATCTGCGATCGGCTCCACTACTACTT
Found at i:52418695 original size:177 final size:177
Alignment explanation
Indices: 52418286--52418699 Score: 508
Period size: 177 Copynumber: 2.3 Consensus size: 177
52418276 TTGCAACCTC
* * ** * * * * *
52418286 AAGGAGATAAGATCTACCATATTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTACAATC
1 AAGGAGATAGGATCTACAATCCTCAATCTACTTCCTTACAACCTCAGGAAGATAAGACTTCAATC
* * * * * *
52418351 TTCAACCTACTCTCTTGTTACCTTAGAGAGATAAGGTTGGTGGCTAAAATTTGCTCCCCTGCTAC
66 TTCAACCGACTCTCTTGCTACCTTAGAGAGATAAGGCTGGTGGCTAAAATCTACTCCCCTACTAC
**
52418416 CTCGGGAAGATAAAATTCGCCATCTTTGATCGGCTCCACTACTACTT
131 CTCGGGAAGATAAAATTCGCCATCTGCGATCGGCTCCACTACTACTT
* * * * * *
52418463 AGGGAGATAGGATCTACAGTCCTCAGTCTGCTTCCTTGCTACCTCAGGAAGATAAGACTTCAATC
1 AAGGAGATAGGATCTACAATCCTCAATCTACTTCCTTACAACCTCAGGAAGATAAGACTTCAATC
* * *
52418528 TTCAACCGGCTCTCTTGCTATCTTAGAGAGATAAGGCTGGTGGCTAAAATCTACTCCCCTACTAT
66 TTCAACCGACTCTCTTGCTACCTTAGAGAGATAAGGCTGGTGGCTAAAATCTACTCCCCTACTAC
* * *
52418593 CTCGGGAAGATAAGATTCGCCATCTGCGATCTGCTCCACTACTGCTT
131 CTCGGGAAGATAAAATTCGCCATCTGCGATCGGCTCCACTACTACTT
* * *
52418640 AAGGAGATAGGATCTTCAATCTTCAATCTACTT-CTCTACAACTTCAAGG-AGATAAGACTT
1 AAGGAGATAGGATCTACAATCCTCAATCTACTTCCT-TACAACCTC-AGGAAGATAAGACTT
52418700 GTTTTGATCT
Statistics
Matches: 205, Mismatches: 30, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
176 2 0.01
177 200 0.98
178 3 0.01
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (177 bp):
AAGGAGATAGGATCTACAATCCTCAATCTACTTCCTTACAACCTCAGGAAGATAAGACTTCAATC
TTCAACCGACTCTCTTGCTACCTTAGAGAGATAAGGCTGGTGGCTAAAATCTACTCCCCTACTAC
CTCGGGAAGATAAAATTCGCCATCTGCGATCGGCTCCACTACTACTT
Found at i:52420474 original size:34 final size:34
Alignment explanation
Indices: 52420433--52420501 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
52420423 GTAAGCATAG
52420433 AGAGCGAATGGTAACTTCTCATGCCAATCTCTAT
1 AGAGCGAATGGTAACTTCTCATGCCAATCTCTAT
52420467 AGAGCGAATGGTAACTTCTCATGCCAATCTCTAT
1 AGAGCGAATGGTAACTTCTCATGCCAATCTCTAT
52420501 A
1 A
52420502 AGTTTCGGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.29
Consensus pattern (34 bp):
AGAGCGAATGGTAACTTCTCATGCCAATCTCTAT
Found at i:52420623 original size:17 final size:17
Alignment explanation
Indices: 52420603--52420635 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
52420593 TAAACTATAT
52420603 TTTATTT-TTTTATTTGG
1 TTTATTTATTTT-TTTGG
52420620 TTTATTTATTTTTTTG
1 TTTATTTATTTTTTTG
52420636 TAAATAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.79
Consensus pattern (17 bp):
TTTATTTATTTTTTTGG
Found at i:52423126 original size:28 final size:28
Alignment explanation
Indices: 52423094--52423152 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
52423084 AGAACTAGAA
52423094 GATTATTGAATTCAAAGATTTCTCTTGT
1 GATTATTGAATTCAAAGATTTCTCTTGT
52423122 GATTATTGAATTCAAAGATTTCTCTTGT
1 GATTATTGAATTCAAAGATTTCTCTTGT
52423150 GAT
1 GAT
52423153 GCTCGTTCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.29, C:0.10, G:0.15, T:0.46
Consensus pattern (28 bp):
GATTATTGAATTCAAAGATTTCTCTTGT
Found at i:52425356 original size:49 final size:49
Alignment explanation
Indices: 52425277--52425517 Score: 261
Period size: 49 Copynumber: 4.9 Consensus size: 49
52425267 TCTATTGTGA
*
52425277 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGAAAAGT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGAAAAGT
** * *
52425326 GGTCGTATGTGTAGTACTAAGTGCAGGCTACTATGCGTACC-GAATAACTT
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGAA-AA-GT
* * * ** * **
52425376 CGATCACGTGTGTAGTACTAAGTGTAGGCTACTACATGTATCAG-ATGGTT
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGAAAAG-T
* * * *
52425426 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGGATAATT
1 -GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGAAAAGT
*
52425476 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCA
1 GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCA
52425518 AATAGCCTTG
Statistics
Matches: 155, Mismatches: 31, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
48 3 0.02
49 78 0.50
50 40 0.26
51 33 0.21
52 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (49 bp):
GGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGAAAAGT
Found at i:52425360 original size:26 final size:26
Alignment explanation
Indices: 52425284--52425360 Score: 65
Period size: 26 Copynumber: 3.1 Consensus size: 26
52425274 TGAGGTCACG
52425284 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
** **
52425310 TGTGTACCAGAAAAGT---GG-T-CGTA
1 TGTGTAGTA-CTAAGTGCAGGCTAC-TA
52425333 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
52425359 TG
1 TG
52425361 CGTACCGAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 14
0.62 0.14 0.24
Matches are distributed among these distances:
22 5 0.14
23 10 0.28
24 2 0.06
25 2 0.06
26 12 0.33
27 5 0.14
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (26 bp):
TGTGTAGTACTAAGTGCAGGCTACTA
Found at i:52425467 original size:101 final size:98
Alignment explanation
Indices: 52425279--52425508 Score: 300
Period size: 101 Copynumber: 2.3 Consensus size: 98
52425269 TATTGTGAGG
** **
52425279 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGAAAAGTGGTCGTATGTGTAGTACT
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGAAAAGTGGTCACATGTGTAGTACT
52425344 AAGTGCAGGCTACTATGCGTACCGAATAACTTCGA
66 AAGTGCAGGCTACTATGCGTACCGAATAA-TT-GA
* * ** *
52425379 TCACGTGTGTAGTACTAAGTGTAGGCTACTACATGTATCAG-ATGGTTAGGTCACGTGTGTAGTA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGAAAAG-T-GGTCACATGTGTAGTA
* * *
52425443 CTAAGTGCAGGCTACTATGTGTACCGGATAATTGG
64 CTAAGTGCAGGCTACTATGCGTACCGAATAATTGA
*
52425478 TCACATGTGTAGTACTAAGTGCAGGCTACTA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTA
52425509 TGCGTACCAA
Statistics
Matches: 114, Mismatches: 14, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
99 32 0.28
100 40 0.35
101 42 0.37
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.30
Consensus pattern (98 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGAAAAGTGGTCACATGTGTAGTACT
AAGTGCAGGCTACTATGCGTACCGAATAATTGA
Found at i:52431515 original size:6 final size:6
Alignment explanation
Indices: 52431504--52431547 Score: 52
Period size: 6 Copynumber: 6.8 Consensus size: 6
52431494 AATTTGTGTG
*
52431504 TTTTTA TTTTTA TTTTTTTA TTTTTA TTTTTT TATTTTA TTTTT
1 TTTTTA TTTTTA --TTTTTA TTTTTA TTTTTA T-TTTTA TTTTT
52431548 CACACTGTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 22 0.67
7 5 0.15
8 6 0.18
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:52431523 original size:8 final size:8
Alignment explanation
Indices: 52431510--52431541 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
52431500 TGTGTTTTTA
52431510 TTTTTATT
1 TTTTTATT
52431518 TTTTTA--
1 TTTTTATT
52431524 TTTTTATT
1 TTTTTATT
52431532 TTTTTATT
1 TTTTTATT
52431540 TT
1 TT
52431542 ATTTTTCACA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 6 0.27
8 16 0.73
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTATT
Found at i:52431527 original size:13 final size:14
Alignment explanation
Indices: 52431504--52431547 Score: 81
Period size: 14 Copynumber: 3.2 Consensus size: 14
52431494 AATTTGTGTG
52431504 TTTTTATTTTTATT
1 TTTTTATTTTTATT
52431518 TTTTTATTTTTATT
1 TTTTTATTTTTATT
52431532 TTTTTA-TTTTATT
1 TTTTTATTTTTATT
52431545 TTT
1 TTT
52431548 CACACTGTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 10 0.33
14 20 0.67
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTATTTTTATT
Found at i:52433214 original size:33 final size:33
Alignment explanation
Indices: 52433177--52433245 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
52433167 CAAACATACG
52433177 AAGTAATAATTAAATAATGCATGATATACAAAA
1 AAGTAATAATTAAATAATGCATGATATACAAAA
52433210 AAGTAATAATTAAATAATGCATGATATACAAAA
1 AAGTAATAATTAAATAATGCATGATATACAAAA
52433243 AAG
1 AAG
52433246 AGTAATACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.58, C:0.06, G:0.10, T:0.26
Consensus pattern (33 bp):
AAGTAATAATTAAATAATGCATGATATACAAAA
Found at i:52433587 original size:19 final size:19
Alignment explanation
Indices: 52433528--52433587 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 19
52433518 AAAAGAATTT
* *
52433528 ATAAAATAACACATAATAT
1 ATAAAATAATACATAATAA
**
52433547 A-AAAAT-AT-CATTTTAA
1 ATAAAATAATACATAATAA
52433563 AGTAAAATAATACATAATAA
1 A-TAAAATAATACATAATAA
52433583 ATAAA
1 ATAAA
52433588 TTATTAATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
16 6 0.19
17 1 0.03
18 10 0.32
19 7 0.23
20 7 0.23
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (19 bp):
ATAAAATAATACATAATAA
Found at i:52436115 original size:205 final size:200
Alignment explanation
Indices: 52435664--52436162 Score: 782
Period size: 205 Copynumber: 2.5 Consensus size: 200
52435654 AAATCTGCTT
* * *
52435664 CTTCGATTTGTTCTCTAACAATACAGAGATGACAAATCATCTTAGATTTGCTTCAGCGTAAGCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCAC
* * *
52435729 GCGAAAACCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGAATGCCAAACCATCTT
*
52435794 GGATCTGCTTCAGTCATCTGAAGGTTAGATCTGCTATATATCTGCTCTCCGTCGAAATAGAGATG
131 GGATCTGCTTCAGTCATCTGAAGGTTAGATCTGCTATATATCTACTCTCCGTCGAAATAGAGATG
*
52435859 CCAGA
196 CCAAA
* * * * * *
52435864 CTTTGATTTGTTCTCTGTCAATACAGAGATACCAAATCATCTTAGATTAGCTTCATCGTAAGCTC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCAC
52435929 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGAATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGAATGCCAAACCATCTT
* * *
52435994 GGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTACTCTCCGTTGAAATGG
131 GGATCTGCTTCAG--T---CATCTGAAGGTTAGATCTGCTATATATCTACTCTCCGTCGAAATAG
52436059 AGATGCCAAA
191 AGATGCCAAA
* *
52436069 CTTCGATTTGTTCTCTGACAATACAGAGATGCCCAATCATCTTAGATTTGCTTCAACGTAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCAC
52436134 GTGAAAGCCAAATCAGCTATGTCTTCGAT
66 GTGAAAGCCAAATCAGCTATGTCTTCGAT
52436163 CTGCTCTCTG
Statistics
Matches: 270, Mismatches: 24, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
200 132 0.49
202 1 0.00
205 137 0.51
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (200 bp):
CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAGCAC
GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGAATGCCAAACCATCTT
GGATCTGCTTCAGTCATCTGAAGGTTAGATCTGCTATATATCTACTCTCCGTCGAAATAGAGATG
CCAAA
Found at i:52439990 original size:40 final size:40
Alignment explanation
Indices: 52439882--52440091 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
52439872 CGGGATTTAA
* * * * *
52439882 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
52439922 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
52439962 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
52440002 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
52440042 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
52440082 CCGGATATAT
1 CCGGATATAT
52440092 TTCCAATGTT
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 152 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:52447637 original size:14 final size:14
Alignment explanation
Indices: 52447614--52447643 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
52447604 ATTCTGGTTC
52447614 AACTTCATTTAGAA
1 AACTTCATTTAGAA
*
52447628 AACTTTATTTAGAA
1 AACTTCATTTAGAA
52447642 AA
1 AA
52447644 AGAATATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.37
Consensus pattern (14 bp):
AACTTCATTTAGAA
Found at i:52451515 original size:19 final size:19
Alignment explanation
Indices: 52451456--52451515 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 19
52451446 AAAAGAATTT
* *
52451456 ATAAAATAACACATAATAT
1 ATAAAATAATACATAATAA
**
52451475 A-AAAAT-AT-CATTTTAA
1 ATAAAATAATACATAATAA
52451491 AGTAAAATAATACATAATAA
1 A-TAAAATAATACATAATAA
52451511 ATAAA
1 ATAAA
52451516 TTATTAATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
16 6 0.19
17 1 0.03
18 10 0.32
19 7 0.23
20 7 0.23
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (19 bp):
ATAAAATAATACATAATAA
Found at i:52451847 original size:11 final size:11
Alignment explanation
Indices: 52451796--52451877 Score: 51
Period size: 11 Copynumber: 6.9 Consensus size: 11
52451786 AACAATATAT
52451796 ATATAAATAATTA
1 ATAT-AATAA-TA
52451809 ATA-AATATATA
1 ATATAATA-ATA
* *
52451820 ATACAAGTAAAA
1 ATATAA-TAATA
52451832 ATATAATAATA
1 ATATAATAATA
*
52451843 ATATAAAAATA
1 ATATAATAATA
52451854 ATGACGTAA-AATA
1 AT-A--TAATAATA
52451867 ATAATAATAAT
1 AT-ATAATAAT
52451878 TTGTGAAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
11 28 0.49
12 14 0.25
13 12 0.21
14 3 0.05
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.30
Consensus pattern (11 bp):
ATATAATAATA
Found at i:52454589 original size:94 final size:94
Alignment explanation
Indices: 52454414--52454590 Score: 273
Period size: 94 Copynumber: 1.9 Consensus size: 94
52454404 AACTAAAAAT
* *
52454414 AAATAAGAATGGTTTTGGTGGCCGTAGAGCCTCCCCTATTCACATCTATCTATATGTATATTAAA
1 AAATAAGAATGGTTTTGGTGGCCGTAGAGCCTCCCCTATTCACATCTATCTACATATATATTAAA
** *
52454479 AATAGAAGGTAGAAGAAAGCGTATGTTAA
66 AATAGAACCTAAAAGAAAGCGTATGTTAA
** * *
52454508 AAATAAGAATGGTTTTGGTGGTTGTAGTGCCTCCCCTATTCACATCTATCTACATATTTATTAAA
1 AAATAAGAATGGTTTTGGTGGCCGTAGAGCCTCCCCTATTCACATCTATCTACATATATATTAAA
52454573 AATAGAACCTAAAAGAAA
66 AATAGAACCTAAAAGAAA
52454591 TCAGCCCCGC
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
94 74 1.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.31
Consensus pattern (94 bp):
AAATAAGAATGGTTTTGGTGGCCGTAGAGCCTCCCCTATTCACATCTATCTACATATATATTAAA
AATAGAACCTAAAAGAAAGCGTATGTTAA
Found at i:52462232 original size:15 final size:15
Alignment explanation
Indices: 52462214--52462243 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52462204 GTTCAGTTCA
52462214 GTTCAGTTCTACTCT
1 GTTCAGTTCTACTCT
*
52462229 GTTCCGTTCTACTCT
1 GTTCAGTTCTACTCT
52462244 ATTATGTTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.30, G:0.13, T:0.47
Consensus pattern (15 bp):
GTTCAGTTCTACTCT
Found at i:52462244 original size:20 final size:20
Alignment explanation
Indices: 52462221--52462271 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
52462211 TCAGTTCAGT
52462221 TCTACTCTGTTCCGTTCTAC
1 TCTACTCTGTTCCGTTCTAC
* * * *
52462241 TCTATTATGTTCTGTTCTGC
1 TCTACTCTGTTCCGTTCTAC
*
52462261 TTTACTCTGTT
1 TCTACTCTGTT
52462272 TTGTTCTGTC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.10, C:0.25, G:0.12, T:0.53
Consensus pattern (20 bp):
TCTACTCTGTTCCGTTCTAC
Found at i:52462254 original size:25 final size:25
Alignment explanation
Indices: 52462226--52462280 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
52462216 TCAGTTCTAC
52462226 TCTGTTCCG-TTCTACTCTATTATGT
1 TCTGTTCCGCTT-TACTCTATTATGT
* * *
52462251 TCTGTTCTGCTTTACTCTGTTTTGT
1 TCTGTTCCGCTTTACTCTATTATGT
52462276 TCTGT
1 TCTGT
52462281 CATATTCTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 24 0.92
26 2 0.08
ACGTcount: A:0.07, C:0.22, G:0.15, T:0.56
Consensus pattern (25 bp):
TCTGTTCCGCTTTACTCTATTATGT
Found at i:52468265 original size:21 final size:20
Alignment explanation
Indices: 52468239--52468291 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
52468229 TCATACACTT
52468239 TTCTTTTCTTTCGTTCATTAA
1 TTCTTTTCTTT-GTTCATTAA
*
52468260 TTCTTTTCGTTTGTTCTTTAA
1 TTCTTTTC-TTTGTTCATTAA
52468281 TT-TATTTCTTT
1 TTCT-TTTCTTT
52468292 TACTCCAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 4 0.14
21 22 0.76
22 3 0.10
ACGTcount: A:0.11, C:0.15, G:0.06, T:0.68
Consensus pattern (20 bp):
TTCTTTTCTTTGTTCATTAA
Found at i:52471692 original size:18 final size:19
Alignment explanation
Indices: 52471669--52471711 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
52471659 CAAACTTTTG
52471669 TTTTTATATTT-TTAT-ACA
1 TTTTTAT-TTTATTATCACA
52471687 TTTTTATTTTATTATGCACA
1 TTTTTATTTTATTAT-CACA
52471707 TTTTT
1 TTTTT
52471712 TTATCAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.14
18 11 0.50
20 8 0.36
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTTATTTTATTATCACA
Found at i:52473823 original size:40 final size:40
Alignment explanation
Indices: 52473777--52473860 Score: 150
Period size: 40 Copynumber: 2.1 Consensus size: 40
52473767 TAAGTTTCGT
*
52473777 GTAAGTATGGTGTTTTTCTTTTTGAGAAGGATGTTTTTAG
1 GTAAGTATGGTGTTTGTCTTTTTGAGAAGGATGTTTTTAG
*
52473817 GTAAGTATGGTGTTTGTCTTTTTGATAAGGATGTTTTTAG
1 GTAAGTATGGTGTTTGTCTTTTTGAGAAGGATGTTTTTAG
52473857 GTAA
1 GTAA
52473861 TCTTATTTGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.21, C:0.02, G:0.27, T:0.49
Consensus pattern (40 bp):
GTAAGTATGGTGTTTGTCTTTTTGAGAAGGATGTTTTTAG
Found at i:52475442 original size:22 final size:21
Alignment explanation
Indices: 52475389--52475512 Score: 63
Period size: 22 Copynumber: 5.4 Consensus size: 21
52475379 TCAATTTGTA
* *
52475389 AGAGCTTACTATTCCCAACTCGT
1 AGAGCTTACTATT--CACCTCTT
52475412 ATGAGCTTACTATTCACCTCTT
1 A-GAGCTTACTATTCACCTCTT
*
52475434 CAGAGCTTACCGT-TTCAGCT-TAAT
1 -AGAGCTTA-C-TATTCACCTCT--T
* * *
52475458 AGAGCTTACTGTTCTCAACTCAT
1 AGAGCTTACT-AT-TCACCTCTT
*
52475481 ATGAGCTTACTATTCACCTTTT
1 A-GAGCTTACTATTCACCTCTT
52475503 CAGAGCTTAC
1 -AGAGCTTAC
52475513 CGTTTCAGCT
Statistics
Matches: 80, Mismatches: 9, Indels: 25
0.70 0.08 0.22
Matches are distributed among these distances:
21 1 0.01
22 29 0.36
23 22 0.28
24 28 0.35
ACGTcount: A:0.25, C:0.27, G:0.13, T:0.35
Consensus pattern (21 bp):
AGAGCTTACTATTCACCTCTT
Found at i:52475461 original size:23 final size:23
Alignment explanation
Indices: 52475435--52475535 Score: 84
Period size: 23 Copynumber: 4.4 Consensus size: 23
52475425 TCACCTCTTC
52475435 AGAGCTTACCGTTTCAGCTTAAT
1 AGAGCTTACCGTTTCAGCTTAAT
* * *
52475458 AGAGCTTACTGTTCTCAAC-TCAT
1 AGAGCTTACCGTT-TCAGCTTAAT
* *
52475481 ATGAGCTTA-C-TATTCACCTT-TT
1 A-GAGCTTACCGT-TTCAGCTTAAT
*
52475503 CAGAGCTTACCGTTTCAGCTCAAT
1 -AGAGCTTACCGTTTCAGCTTAAT
52475527 AGAGCTTAC
1 AGAGCTTAC
52475536 TGTTCATCAA
Statistics
Matches: 61, Mismatches: 9, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
22 13 0.21
23 35 0.57
24 13 0.21
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.35
Consensus pattern (23 bp):
AGAGCTTACCGTTTCAGCTTAAT
Found at i:52475491 original size:24 final size:23
Alignment explanation
Indices: 52475390--52475539 Score: 69
Period size: 23 Copynumber: 6.5 Consensus size: 23
52475380 CAATTTGTAA
* * *
52475390 GAGCTTACTATTCCCAACTCGTAT
1 GAGCTTACTGTT-TCAACTCATAT
* * *
52475414 GAGCTTACT-ATTCACCTCTTCA-
1 GAGCTTACTGTTTCAACTCAT-AT
* * *
52475436 GAGCTTACCGTTTCAGCTTA-AT
1 GAGCTTACTGTTTCAACTCATAT
52475458 AGAGCTTACTGTTCTCAACTCATAT
1 -GAGCTTACTGTT-TCAACTCATAT
* * **
52475483 GAGCTTACT-ATTCACCTTTTCA-
1 GAGCTTACTGTTTCAACTCAT-AT
* *
52475505 GAGCTTACCGTTTCAGCTCA-AT
1 GAGCTTACTGTTTCAACTCATAT
52475527 AGAGCTTACTGTT
1 -GAGCTTACTGTT
52475540 CATCAACACA
Statistics
Matches: 94, Mismatches: 22, Indels: 21
0.69 0.16 0.15
Matches are distributed among these distances:
21 2 0.02
22 28 0.30
23 38 0.40
24 24 0.26
25 2 0.02
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.36
Consensus pattern (23 bp):
GAGCTTACTGTTTCAACTCATAT
Found at i:52475505 original size:69 final size:69
Alignment explanation
Indices: 52475389--52475546 Score: 262
Period size: 69 Copynumber: 2.3 Consensus size: 69
52475379 TCAATTTGTA
* * *
52475389 AGAGCTTACTATTCCCAACTCGTATGAGCTTACTATTCACCTCTTCAGAGCTTACCGTTTCAGCT
1 AGAGCTTACTGTTCTCAACTCATATGAGCTTACTATTCACCTCTTCAGAGCTTACCGTTTCAGCT
*
52475454 TAAT
66 CAAT
*
52475458 AGAGCTTACTGTTCTCAACTCATATGAGCTTACTATTCACCTTTTCAGAGCTTACCGTTTCAGCT
1 AGAGCTTACTGTTCTCAACTCATATGAGCTTACTATTCACCTCTTCAGAGCTTACCGTTTCAGCT
52475523 CAAT
66 CAAT
52475527 AGAGCTTACTGTTCATCAAC
1 AGAGCTTACTGTTC-TCAAC
52475547 ACAGGAGGAG
Statistics
Matches: 83, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
69 78 0.94
70 5 0.06
ACGTcount: A:0.25, C:0.27, G:0.13, T:0.35
Consensus pattern (69 bp):
AGAGCTTACTGTTCTCAACTCATATGAGCTTACTATTCACCTCTTCAGAGCTTACCGTTTCAGCT
CAAT
Found at i:52479287 original size:66 final size:65
Alignment explanation
Indices: 52479160--52479287 Score: 168
Period size: 66 Copynumber: 1.9 Consensus size: 65
52479150 TACTATGTGT
* * * *
52479160 ACACCATGTAGACAAGAGAGCTACGGGATATATGTAGTAGGTCGCATGCGTGGTTCCAAGTGAAG
1 ACACCATGTAGACAAGAGAGCTACGAGATAAATG-AGTAGGTCACATGCGTGGTACCAAGTGAAG
52479225 G
65 G
* *
52479226 ACACCATGTAGACAAGAGAGCTACGAGATAAACTG-GCTAGGTCACATGGGTGGTACTAAGTG
1 ACACCATGTAGACAAGAGAGCTACGAGATAAA-TGAG-TAGGTCACATGCGTGGTACCAAGTG
52479288 TTCACCATGT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
65 1 0.02
66 51 0.94
67 2 0.04
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.20
Consensus pattern (65 bp):
ACACCATGTAGACAAGAGAGCTACGAGATAAATGAGTAGGTCACATGCGTGGTACCAAGTGAAGG
Found at i:52482723 original size:26 final size:25
Alignment explanation
Indices: 52482672--52482730 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
52482662 CAACTCTTAT
* *
52482672 GAGCTTACCGTTATTCATCTCAGAG
1 GAGCTTACCATTATTCAGCTCAGAG
**
52482697 GAGCTTACCATTATTTCAGCTTGGAG
1 GAGCTTACCATTA-TTCAGCTCAGAG
52482723 GAGCTTAC
1 GAGCTTAC
52482731 TGTTTACAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 12 0.41
26 17 0.59
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (25 bp):
GAGCTTACCATTATTCAGCTCAGAG
Found at i:52483215 original size:17 final size:17
Alignment explanation
Indices: 52483188--52483233 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
52483178 GCTTTATAAT
52483188 GGTTCGGAAGCTCGTTCA
1 GGTT-GGAAGCTCGTTCA
**
52483206 GGTTGGAAGCTCGTTTG
1 GGTTGGAAGCTCGTTCA
52483223 GGTTGGAAGCT
1 GGTTGGAAGCT
52483234 TGTCGGAGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 22 0.85
18 4 0.15
ACGTcount: A:0.15, C:0.15, G:0.39, T:0.30
Consensus pattern (17 bp):
GGTTGGAAGCTCGTTCA
Found at i:52483399 original size:2 final size:2
Alignment explanation
Indices: 52483392--52483429 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
52483382 TATACTTTGC
52483392 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52483430 AATGGCCTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:52487869 original size:18 final size:18
Alignment explanation
Indices: 52487845--52487880 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
52487835 TAATTTTTAA
*
52487845 TAAAAATTTTATAA-TTT
1 TAAAAAATTTATAACTTT
52487862 TAAAAAATTTATAACTTT
1 TAAAAAATTTATAACTTT
52487880 T
1 T
52487881 TTTGTAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
TAAAAAATTTATAACTTT
Found at i:52491955 original size:21 final size:21
Alignment explanation
Indices: 52491929--52491970 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
52491919 AGTCATGCCT
52491929 AAAGTGGTAAACATTCTTGAC
1 AAAGTGGTAAACATTCTTGAC
52491950 AAAGTGGTAAACATTCTTGAC
1 AAAGTGGTAAACATTCTTGAC
52491971 CATCAGGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (21 bp):
AAAGTGGTAAACATTCTTGAC
Found at i:52493480 original size:16 final size:16
Alignment explanation
Indices: 52493449--52493485 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
52493439 ATGTGAATAA
52493449 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
52493465 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
52493481 TATTA
1 TATTA
52493486 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:52505596 original size:95 final size:97
Alignment explanation
Indices: 52505497--52505671 Score: 209
Period size: 100 Copynumber: 1.8 Consensus size: 97
52505487 TTATATTCAT
**
52505497 ATATGT-AAAATA-TTTGT-TACA-T-TATTAT-TATACATATTTCATATTATATTTTATTATAT
1 ATATGTCAAAATATTTTGTATACATTATATTATATATACAT-TTTCATATTATATAAT-TTATA-
*
52505556 TTATTTATGTATTTTTATTACATATTATATTTTACC
63 TTA-TTATATATTTTTATTACATATTATATTTTACC
* * * *
52505592 ATATGTCATAATATTTTTTATATATTATATTATATATACATTTTTATATTATATAATTTATATTA
1 ATATGTCAAAATATTTTGTATACATTATATTATATATACATTTTCATATTATATAATTTATATTA
52505657 TTATATATTTTTATT
66 TTATATATTTTTATT
52505672 TGTAAATTAT
Statistics
Matches: 67, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
95 6 0.09
96 5 0.07
97 18 0.27
98 6 0.09
99 6 0.09
100 19 0.28
101 7 0.10
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (97 bp):
ATATGTCAAAATATTTTGTATACATTATATTATATATACATTTTCATATTATATAATTTATATTA
TTATATATTTTTATTACATATTATATTTTACC
Found at i:52505646 original size:17 final size:17
Alignment explanation
Indices: 52505616--52505663 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
52505606 TTTTTATATA
52505616 TTATATTA-TATATACAT
1 TTATATTATTATATA-AT
*
52505633 TTTTA-TATTATATAAT
1 TTATATTATTATATAAT
52505649 TTATATTATTATATA
1 TTATATTATTATATA
52505664 TTTTTATTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 8 0.30
17 19 0.70
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (17 bp):
TTATATTATTATATAAT
Found at i:52505653 original size:24 final size:25
Alignment explanation
Indices: 52505607--52505665 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
52505597 TCATAATATT
*
52505607 TTTTATATATTATATTATATATACA
1 TTTTATATATTATATAATATATACA
*
52505632 TTTT-TATATTATATAAT-T-TATA
1 TTTTATATATTATATAATATATACA
52505654 TTATTATATATT
1 TT-TTATATATT
52505666 TTTATTTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 5 0.17
23 3 0.10
24 18 0.60
25 4 0.13
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (25 bp):
TTTTATATATTATATAATATATACA
Done.