Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr10
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: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31
Warning! 2980117 characters in sequence are not A, C, G, or T
File 118 of 284
Found at i:39038571 original size:29 final size:29
Alignment explanation
Indices: 39038499--39038573 Score: 114
Period size: 29 Copynumber: 2.6 Consensus size: 29
39038489 GGTCGTCACC
*
39038499 ATCCCTTTTCATAATCAATAGCCAAAGCT
1 ATCCCTTTTCATATTCAATAGCCAAAGCT
* *
39038528 ATCGCTTTTCATATTCGATAGCCAAAGCT
1 ATCCCTTTTCATATTCAATAGCCAAAGCT
*
39038557 ATCCCTTTTCGTATTCA
1 ATCCCTTTTCATATTCA
39038574 TTGATCGCCG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.28, C:0.27, G:0.09, T:0.36
Consensus pattern (29 bp):
ATCCCTTTTCATATTCAATAGCCAAAGCT
Found at i:39042739 original size:20 final size:21
Alignment explanation
Indices: 39042697--39042739 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
39042687 ATTTTAGTGA
** *
39042697 TTGATGATAGATTATGGATGT
1 TTGATGATAGATTATACAAGT
39042718 TTGATGATAG-TTATACAAGT
1 TTGATGATAGATTATACAAGT
39042738 TT
1 TT
39042740 TGTTAAGTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.30, C:0.02, G:0.23, T:0.44
Consensus pattern (21 bp):
TTGATGATAGATTATACAAGT
Found at i:39043324 original size:52 final size:50
Alignment explanation
Indices: 39043246--39043350 Score: 174
Period size: 52 Copynumber: 2.1 Consensus size: 50
39043236 AAATCCCAGT
* *
39043246 TGAACGTTAGGAATAGATTAGGATACAAATGACATGTCACTAGGGGTTATTA
1 TGAACCTTAGGAATAGATTACGATACAAATGAC--GTCACTAGGGGTTATTA
39043298 TGAACCTTAGGAATAGATTACGATACAAATGACGTCACTAGGGGTTATTA
1 TGAACCTTAGGAATAGATTACGATACAAATGACGTCACTAGGGGTTATTA
39043348 TGA
1 TGA
39043351 TTATGTGATC
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
50 20 0.39
52 31 0.61
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (50 bp):
TGAACCTTAGGAATAGATTACGATACAAATGACGTCACTAGGGGTTATTA
Found at i:39045271 original size:15 final size:16
Alignment explanation
Indices: 39045244--39045273 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
39045234 GATAACAATT
39045244 AATATATATTATATAA
1 AATATATATTATATAA
39045260 AATATA-ATTATATA
1 AATATATATTATATA
39045274 TAGTTTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATATATATTATATAA
Found at i:39048231 original size:43 final size:43
Alignment explanation
Indices: 39048115--39048273 Score: 146
Period size: 43 Copynumber: 3.7 Consensus size: 43
39048105 CGTACAATGC
* * *
39048115 CAATGTCCCAGACGTGGTCTTACA-TTTAATCAAATATCGATGT
1 CAATGTCCCAGACATGGTCTTACACGTAAATCAAATA-CGATGT
* * *
39048158 CACTATCCCAGACAGGGTCTT--ACGTGAAATCAAATACGATGT
1 CAATGTCCCAGACATGGTCTTACACGT-AAATCAAATACGATGT
* * ** *
39048200 CAATGTCCTAGACATGGTCTTAGACGTAAATCATAAGCCGATGC
1 CAATGTCCCAGACATGGTCTTACACGTAAATCA-AATACGATGT
* *
39048244 CAACGTCCCAGACGTGGTCTTACACG-AAAT
1 CAATGTCCCAGACATGGTCTTACACGTAAAT
39048274 TACATATCGG
Statistics
Matches: 94, Mismatches: 17, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
41 1 0.01
42 24 0.26
43 36 0.38
44 33 0.35
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (43 bp):
CAATGTCCCAGACATGGTCTTACACGTAAATCAAATACGATGT
Found at i:39055392 original size:43 final size:43
Alignment explanation
Indices: 39055345--39055497 Score: 129
Period size: 43 Copynumber: 3.6 Consensus size: 43
39055335 TCCTAGATGT
*
39055345 GGTCTTACATGTAATCAAATATCGATGCCACTGTCCCAGACAG
1 GGTCTTACACGTAATCAAATATCGATGCCACTGTCCCAGACAG
* * * * *
39055388 GGTCTTACACGAAATCAAATA-CGATGTCGA-TAT-CTAGACAT
1 GGTCTTACACGTAATCAAATATCGATG-CCACTGTCCCAGACAG
*
39055429 GGTCTTACACGTAAATCATAA-GTCGATGCCAAC-GTCCCAGAC-G
1 GGTCTTACACGT-AATCA-AATATCGATGCC-ACTGTCCCAGACAG
* * *
39055472 TGGTCTTACACGAAATTACATATCGA
1 -GGTCTTACACGTAATCAAATATCGA
39055498 ATCTTACATC
Statistics
Matches: 85, Mismatches: 16, Indels: 18
0.71 0.13 0.15
Matches are distributed among these distances:
41 17 0.20
42 14 0.16
43 38 0.45
44 16 0.19
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (43 bp):
GGTCTTACACGTAATCAAATATCGATGCCACTGTCCCAGACAG
Found at i:39055795 original size:15 final size:18
Alignment explanation
Indices: 39055775--39055814 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 18
39055765 ATCTATATAA
39055775 ATTCAAATTTA-AC-TT-
1 ATTCAAATTTACACATTC
39055790 ATTC-AATTTACACATTC
1 ATTCAAATTTACACATTC
39055807 ATTCAAAT
1 ATTCAAAT
39055815 CAATCCATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 6 0.29
15 6 0.29
16 2 0.10
17 4 0.19
18 3 0.14
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTCAAATTTACACATTC
Found at i:39056610 original size:13 final size:13
Alignment explanation
Indices: 39056594--39056618 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39056584 CACACAAACG
39056594 ATTAAATTTTCAT
1 ATTAAATTTTCAT
39056607 ATTAAATTTTCA
1 ATTAAATTTTCA
39056619 CACATACTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTAAATTTTCAT
Found at i:39062523 original size:47 final size:47
Alignment explanation
Indices: 39062460--39063694 Score: 1831
Period size: 47 Copynumber: 26.3 Consensus size: 47
39062450 CCCTTCGGGA
* *
39062460 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * * * *
39062507 CTTATCACATATATACACCTTCACATCCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
39062554 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTCAGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
39062601 CTTATCACATATATACACTTTCACATTCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * **
39062648 CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACCCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
39062695 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * **
39062742 CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACCCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
39062789 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * **
39062836 CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACCCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
39062883 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * **
39062930 CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACCCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
39062977 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * **
39063024 CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACCCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
39063071 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * **
39063118 CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACCCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
39063165 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * **
39063212 CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACCCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
39063259 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * **
39063306 CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACCCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
39063353 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * **
39063400 CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACCCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
39063447 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
39063494 CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
39063541 CTTATCACATATGTACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
39063588 CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
39063635 CTTATCACATATATACACTTTCACATTCATCACATTTGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
39063682 CTTATCACATATA
1 CTTATCACATATA
39063695 CATATCTTGT
Statistics
Matches: 1055, Mismatches: 133, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 1055 1.00
ACGTcount: A:0.28, C:0.32, G:0.09, T:0.31
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:39062624 original size:94 final size:94
Alignment explanation
Indices: 39062460--39063696 Score: 2213
Period size: 94 Copynumber: 13.2 Consensus size: 94
39062450 CCCTTCGGGA
* * * * **
39062460 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGCCTTATCACATATATACAC
1 CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACCCGGCCTTATCACATATATACAC
* * *
39062525 CTTCACATCCATCACATCGGCCATTAGGT
66 TTTCACATTCATCACATCGGCCATTAGGC
* * * ** *
39062554 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTCAGCCTTATCACATATATACAC
1 CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACCCGGCCTTATCACATATATACAC
* * * *
39062619 TTTCACATTCATCACGTTGGCCACTCGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
39062648 CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACCCGGCCTTATCACATATATACAC
1 CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACCCGGCCTTATCACATATATACAC
39062713 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
39062742 CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACCCGGCCTTATCACATATATACAC
1 CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACCCGGCCTTATCACATATATACAC
39062807 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
39062836 CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACCCGGCCTTATCACATATATACAC
1 CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACCCGGCCTTATCACATATATACAC
39062901 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
39062930 CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACCCGGCCTTATCACATATATACAC
1 CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACCCGGCCTTATCACATATATACAC
39062995 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
39063024 CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACCCGGCCTTATCACATATATACAC
1 CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACCCGGCCTTATCACATATATACAC
39063089 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
39063118 CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACCCGGCCTTATCACATATATACAC
1 CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACCCGGCCTTATCACATATATACAC
39063183 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
39063212 CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACCCGGCCTTATCACATATATACAC
1 CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACCCGGCCTTATCACATATATACAC
39063277 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
39063306 CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACCCGGCCTTATCACATATATACAC
1 CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACCCGGCCTTATCACATATATACAC
39063371 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
39063400 CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACCCGGCCTTATCACATATATACAC
1 CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACCCGGCCTTATCACATATATACAC
* *
39063465 TTTCACATTCATCACATTGGCCATTCGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
* * * *
39063494 CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGCCTTATCACATATGTACAC
1 CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACCCGGCCTTATCACATATATACAC
39063559 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
*
39063588 CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACTCGGCCTTATCACATATATACAC
1 CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACCCGGCCTTATCACATATATACAC
** *
39063653 TTTCACATTCATCACATTTGCCATTCGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
39063682 CTTATCACATATACA
1 CTTATCACATATACA
39063697 TATCTTGTAC
Statistics
Matches: 1108, Mismatches: 35, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
94 1108 1.00
ACGTcount: A:0.28, C:0.32, G:0.09, T:0.31
Consensus pattern (94 bp):
CTTATCACATATACACACTTTCACATTCATCACGTTGGCCACCCGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGC
Found at i:39063572 original size:25 final size:25
Alignment explanation
Indices: 39063450--39063575 Score: 88
Period size: 25 Copynumber: 5.3 Consensus size: 25
39063440 ACCCGGCCTT
*
39063450 ATCACATATATACACTTTCACATTC
1 ATCACATATGTACACTTTCACATTC
* * * *
39063475 ATCACAT-TG-GC-CATTCGGCCTT-
1 ATCACATATGTACACTTTC-ACATTC
*
39063497 ATCACATATATACACTTTCACATTC
1 ATCACATATGTACACTTTCACATTC
** * *
39063522 ATCACAT-TGGCCAC--TCGGCCTT-
1 ATCACATATGTACACTTTC-ACATTC
39063544 ATCACATATGTACACTTTCACATTC
1 ATCACATATGTACACTTTCACATTC
39063569 ATCACAT
1 ATCACAT
39063576 CGGCCATTAG
Statistics
Matches: 72, Mismatches: 19, Indels: 20
0.65 0.17 0.18
Matches are distributed among these distances:
22 20 0.28
23 13 0.18
24 12 0.17
25 27 0.38
ACGTcount: A:0.29, C:0.30, G:0.07, T:0.33
Consensus pattern (25 bp):
ATCACATATGTACACTTTCACATTC
Found at i:39066249 original size:42 final size:43
Alignment explanation
Indices: 39066189--39066274 Score: 129
Period size: 42 Copynumber: 2.0 Consensus size: 43
39066179 TGTGTTTCAT
* *
39066189 AATCATGAACTTAAACCACAATTC-ATGAGTTCAAATCACATA
1 AATCATGAACTCAAACCACAACTCAATGAGTTCAAATCACATA
* *
39066231 AATCATGAACTCAGACCACAACTCAATGAGTTCAGATCACATA
1 AATCATGAACTCAAACCACAACTCAATGAGTTCAAATCACATA
39066274 A
1 A
39066275 TTCCTAATGA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 21 0.54
43 18 0.46
ACGTcount: A:0.44, C:0.23, G:0.09, T:0.23
Consensus pattern (43 bp):
AATCATGAACTCAAACCACAACTCAATGAGTTCAAATCACATA
Found at i:39079063 original size:20 final size:20
Alignment explanation
Indices: 39079038--39079102 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
39079028 TGTTTCATAA
39079038 TCATGAACTCAGACCACAAC
1 TCATGAACTCAGACCACAAC
** * * *
39079058 TCATGAGTTCAAATCACATAAA
1 TCATGAACTCAGA-C-CACAAC
39079080 TCATGAACTCAGACCACAAC
1 TCATGAACTCAGACCACAAC
39079100 TCA
1 TCA
39079103 ATGAGTTTAG
Statistics
Matches: 33, Mismatches: 10, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
20 17 0.52
21 2 0.06
22 14 0.42
ACGTcount: A:0.42, C:0.29, G:0.09, T:0.20
Consensus pattern (20 bp):
TCATGAACTCAGACCACAAC
Found at i:39079091 original size:42 final size:43
Alignment explanation
Indices: 39079036--39079121 Score: 147
Period size: 42 Copynumber: 2.0 Consensus size: 43
39079026 TGTGTTTCAT
39079036 AATCATGAACTCAGACCACAACTC-ATGAGTTCAAATCACATA
1 AATCATGAACTCAGACCACAACTCAATGAGTTCAAATCACATA
* *
39079078 AATCATGAACTCAGACCACAACTCAATGAGTTTAGATCACATA
1 AATCATGAACTCAGACCACAACTCAATGAGTTCAAATCACATA
39079121 A
1 A
39079122 TTCCTAATGA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 24 0.59
43 17 0.41
ACGTcount: A:0.43, C:0.24, G:0.10, T:0.22
Consensus pattern (43 bp):
AATCATGAACTCAGACCACAACTCAATGAGTTCAAATCACATA
Found at i:39079097 original size:22 final size:21
Alignment explanation
Indices: 39079036--39079098 Score: 65
Period size: 22 Copynumber: 3.0 Consensus size: 21
39079026 TGTGTTTCAT
39079036 AATCATGAACTCAGACCAC-A
1 AATCATGAACTCAGACCACAA
* ** * *
39079056 ACTCATGAGTTCAAATCACATA
1 AATCATGAACTCAGACCACA-A
39079078 AATCATGAACTCAGACCACAA
1 AATCATGAACTCAGACCACAA
39079099 CTCAATGAGT
Statistics
Matches: 31, Mismatches: 10, Indels: 3
0.70 0.23 0.07
Matches are distributed among these distances:
20 14 0.45
21 1 0.03
22 16 0.52
ACGTcount: A:0.44, C:0.27, G:0.10, T:0.19
Consensus pattern (21 bp):
AATCATGAACTCAGACCACAA
Found at i:39083751 original size:29 final size:28
Alignment explanation
Indices: 39083713--39083789 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 28
39083703 TTTTCACATG
*
39083713 GCCTGGCACATGCCCGTGTCCCTCACACA
1 GCCTGACACA-GCCCGTGTCCCTCACACA
* *
39083742 GCCTGACACACACCCGTGTCCCTCACACG
1 GCCTGACACA-GCCCGTGTCCCTCACACA
39083771 GCCATGACAC-GCCCGTGTC
1 GCC-TGACACAGCCCGTGTC
39083790 TAAAACCCTT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
28 8 0.19
29 28 0.67
30 6 0.14
ACGTcount: A:0.18, C:0.45, G:0.21, T:0.16
Consensus pattern (28 bp):
GCCTGACACAGCCCGTGTCCCTCACACA
Found at i:39096026 original size:105 final size:105
Alignment explanation
Indices: 39095840--39096051 Score: 397
Period size: 105 Copynumber: 2.0 Consensus size: 105
39095830 CATCGAACAC
39095840 CCGAATGGTATTATCAAGCCAGAACTCGGCCCTTTCAGCATCATCAGTTACTATGGCCTTGAACT
1 CCGAATGGTATTATCAAGCCAGAACTCGGCCCTTTCAGCATCATCAGTTACTATGGCCTTGAACT
*
39095905 CCTCGGCCCCAGGCTTCCTAATCAAGTCTACAGGTGGCTT
66 CCTCGGCCCCACGCTTCCTAATCAAGTCTACAGGTGGCTT
* *
39095945 CCGAATGGTATTATCAAGCCAGAACTCGGCCCTTTCGGCATCATCAGTTACTATGGTCTTGAACT
1 CCGAATGGTATTATCAAGCCAGAACTCGGCCCTTTCAGCATCATCAGTTACTATGGCCTTGAACT
39096010 CCTCGGCCCCACGCTTCCTAATCAAGTCTACAGGTGGCTT
66 CCTCGGCCCCACGCTTCCTAATCAAGTCTACAGGTGGCTT
39096050 CC
1 CC
39096052 TCAGCCTCAC
Statistics
Matches: 104, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
105 104 1.00
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.27
Consensus pattern (105 bp):
CCGAATGGTATTATCAAGCCAGAACTCGGCCCTTTCAGCATCATCAGTTACTATGGCCTTGAACT
CCTCGGCCCCACGCTTCCTAATCAAGTCTACAGGTGGCTT
Found at i:39099109 original size:84 final size:84
Alignment explanation
Indices: 39098968--39099134 Score: 316
Period size: 84 Copynumber: 2.0 Consensus size: 84
39098958 TATGAATCGA
* *
39098968 TTCTTCTTCTTAGCTCATATCAGCCTGAATTTCAACCTCCGACGGACTAATTATGTGCGAAGGAT
1 TTCTTCTTCATAGCTCATATCAGCCTGAATTTCAACCTCCAACGGACTAATTATGTGCGAAGGAT
39099033 CAGATCTATAGCGCCGAAG
66 CAGATCTATAGCGCCGAAG
39099052 TTCTTCTTCATAGCTCATATCAGCCTGAATTTCAACCTCCAACGGACTAATTATGTGCGAAGGAT
1 TTCTTCTTCATAGCTCATATCAGCCTGAATTTCAACCTCCAACGGACTAATTATGTGCGAAGGAT
39099117 CAGATCTATAGCGCCGAA
66 CAGATCTATAGCGCCGAA
39099135 AAGGAGTGTA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 81 1.00
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (84 bp):
TTCTTCTTCATAGCTCATATCAGCCTGAATTTCAACCTCCAACGGACTAATTATGTGCGAAGGAT
CAGATCTATAGCGCCGAAG
Found at i:39103842 original size:34 final size:34
Alignment explanation
Indices: 39103789--39103870 Score: 130
Period size: 34 Copynumber: 2.4 Consensus size: 34
39103779 CCCATTTCAG
* *
39103789 TTACAAT-CCAGTATCAGTGTGGGCTTTAGCCCA
1 TTACAATAACAGTATAAGTGTGGGCTTTAGCCCA
39103822 TTACAATAACAGTATAAGTGTGGGCTTTAGCCCA
1 TTACAATAACAGTATAAGTGTGGGCTTTAGCCCA
*
39103856 TTACAATAATAGTAT
1 TTACAATAACAGTAT
39103871 CAGAAAATGC
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 7 0.16
34 38 0.84
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (34 bp):
TTACAATAACAGTATAAGTGTGGGCTTTAGCCCA
Found at i:39111594 original size:25 final size:25
Alignment explanation
Indices: 39111566--39111615 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
39111556 TACAATAACA
39111566 GTATCAGTGTGGGCTTTAGCCCATT
1 GTATCAGTGTGGGCTTTAGCCCATT
* *
39111591 GTATTAGTGTGGGCTTTAGTCCATT
1 GTATCAGTGTGGGCTTTAGCCCATT
39111616 ACAATAACAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.28, T:0.40
Consensus pattern (25 bp):
GTATCAGTGTGGGCTTTAGCCCATT
Found at i:39122324 original size:12 final size:12
Alignment explanation
Indices: 39122307--39122338 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
39122297 GAGTTATAAT
39122307 GAATAAAAGAAA
1 GAATAAAAGAAA
39122319 GAATAAAAGAAA
1 GAATAAAAGAAA
39122331 -AA-AAAAGA
1 GAATAAAAGA
39122339 GGTAATGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 6 0.30
11 2 0.10
12 12 0.60
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (12 bp):
GAATAAAAGAAA
Found at i:39124243 original size:42 final size:40
Alignment explanation
Indices: 39124144--39124332 Score: 297
Period size: 40 Copynumber: 4.7 Consensus size: 40
39124134 GAGCATTGGA
39124144 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
* *
39124184 ATATATCCGGGCTAAGACCAGCAGGCATTTGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
39124224 ATATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
1 --ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
*
39124266 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
* ** *
39124306 CTATGCCCGGGTTAAGACCCGAAGGCA
1 ATATATCCGGGCTAAGACCCGAAGGCA
39124333 ATTGAGCTTG
Statistics
Matches: 138, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
40 100 0.72
42 38 0.28
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.23
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
Found at i:39124281 original size:82 final size:80
Alignment explanation
Indices: 39124144--39124332 Score: 297
Period size: 82 Copynumber: 2.3 Consensus size: 80
39124134 GAGCATTGGA
*
39124144 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATATATCCGGGCTAAGACCAGCAGG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATATATCCGGGCTAAGACCAGAAGG
*
39124209 CATTTGTGCGAGTTG
66 CATTCGTGCGAGTTG
*
39124224 ATATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATATATCCGGGCTAAGACCCGAA
1 --ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATATATCCGGGCTAAGACCAGAA
39124289 GGCATTCGTGCGAGTTG
64 GGCATTCGTGCGAGTTG
* ** *
39124306 CTATGCCCGGGTTAAGACCCGAAGGCA
1 ATATATCCGGGCTAAGACCCGAAGGCA
39124333 ATTGAGCTTG
Statistics
Matches: 100, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
80 23 0.23
82 77 0.77
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.23
Consensus pattern (80 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATATATCCGGGCTAAGACCAGAAGG
CATTCGTGCGAGTTG
Found at i:39132482 original size:28 final size:29
Alignment explanation
Indices: 39132451--39132510 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
39132441 GATTTTTAGT
*
39132451 AAAAATGCATATT-AGGGATTAAATTGAG
1 AAAAATGCAAATTGAGGGATTAAATTGAG
* * * *
39132479 AAAAGTGTAAATTGAGGGGTTAAATTGTG
1 AAAAATGCAAATTGAGGGATTAAATTGAG
39132508 AAA
1 AAA
39132511 TAAATGAAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 10 0.38
29 16 0.62
ACGTcount: A:0.45, C:0.02, G:0.25, T:0.28
Consensus pattern (29 bp):
AAAAATGCAAATTGAGGGATTAAATTGAG
Found at i:39132969 original size:29 final size:29
Alignment explanation
Indices: 39132937--39133009 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
39132927 AGTGCGCATT
* * *
39132937 TTGAGATAGCTTCGGACTTAGTGTGCGAA
1 TTGAAATAGCTTCAGAATTAGTGTGCGAA
39132966 TTGAAATAGCTTCAGAATTAGTGTGCGAA
1 TTGAAATAGCTTCAGAATTAGTGTGCGAA
39132995 TTGAAATAGCTTCAG
1 TTGAAATAGCTTCAG
39133010 CTTTATGTGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.32
Consensus pattern (29 bp):
TTGAAATAGCTTCAGAATTAGTGTGCGAA
Found at i:39140721 original size:13 final size:13
Alignment explanation
Indices: 39140689--39140722 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
39140679 CCTGTGACAC
*
39140689 GGTCGTATCTGGT
1 GGTCGTGTCTGGT
39140702 GGTCGTGTCTGGT
1 GGTCGTGTCTGGT
39140715 GGTCGTGT
1 GGTCGTGT
39140723 GAGGCACACG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.03, C:0.15, G:0.44, T:0.38
Consensus pattern (13 bp):
GGTCGTGTCTGGT
Found at i:39141326 original size:2 final size:2
Alignment explanation
Indices: 39141319--39141343 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39141309 AACATTGGCT
39141319 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
39141344 TATTAAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39146238 original size:27 final size:29
Alignment explanation
Indices: 39146204--39146272 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 29
39146194 ATGCCTTATT
*
39146204 GGTGTGTTTGGGAGGA-TATATTATACC-
1 GGTGTGTTTGGGAGGATTATAATATACCG
*
39146231 GGTGTGTTAT-GGAGGATTTATAATATTCCG
1 GGTGTGTT-TGGGAGGA-TTATAATATACCG
39146261 GGTGTGTTTGGG
1 GGTGTGTTTGGG
39146273 TTTGATATTC
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
27 14 0.40
28 1 0.03
29 10 0.29
30 10 0.29
ACGTcount: A:0.19, C:0.06, G:0.36, T:0.39
Consensus pattern (29 bp):
GGTGTGTTTGGGAGGATTATAATATACCG
Found at i:39152231 original size:5 final size:5
Alignment explanation
Indices: 39152221--39152248 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
39152211 AATAATTAAG
39152221 TATAT TATAT TATAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TAT
39152249 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:39158066 original size:62 final size:62
Alignment explanation
Indices: 39157990--39158113 Score: 239
Period size: 62 Copynumber: 2.0 Consensus size: 62
39157980 GCAGAAAAGC
39157990 TGTAATTGAATTAAGGGCAATGTTTGCACGACTTAGTATCACTGATGATGGGAGTCTTTTGG
1 TGTAATTGAATTAAGGGCAATGTTTGCACGACTTAGTATCACTGATGATGGGAGTCTTTTGG
*
39158052 TGTAATTGAATTAAGGGCAATGTTTGCACGACTTAGTATCACTGTTGATGGGAGTCTTTTGG
1 TGTAATTGAATTAAGGGCAATGTTTGCACGACTTAGTATCACTGATGATGGGAGTCTTTTGG
39158114 CTGAATTAAG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.25, C:0.11, G:0.27, T:0.36
Consensus pattern (62 bp):
TGTAATTGAATTAAGGGCAATGTTTGCACGACTTAGTATCACTGATGATGGGAGTCTTTTGG
Found at i:39158643 original size:64 final size:64
Alignment explanation
Indices: 39158564--39158691 Score: 238
Period size: 64 Copynumber: 2.0 Consensus size: 64
39158554 GCAAGTAAGA
*
39158564 AAAATGCTATATGGGTAATAGTTGATCGACTCACAAAATCGGCTCATTTTATAACTGTCAGAAT
1 AAAATGCTATATGGGTAATAGTTGATCGACTCACAAAATCAGCTCATTTTATAACTGTCAGAAT
*
39158628 AAAATGCTATATGGGTAATAGTTGATCGACTCACAAAATCAGCTCATTTTATAGCTGTCAGAAT
1 AAAATGCTATATGGGTAATAGTTGATCGACTCACAAAATCAGCTCATTTTATAACTGTCAGAAT
39158692 GGATTGGTCA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (64 bp):
AAAATGCTATATGGGTAATAGTTGATCGACTCACAAAATCAGCTCATTTTATAACTGTCAGAAT
Found at i:39160003 original size:5 final size:5
Alignment explanation
Indices: 39159993--39160020 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
39159983 AATAATTAAG
39159993 TATAT TATAT TATAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TAT
39160021 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:39163744 original size:43 final size:43
Alignment explanation
Indices: 39163685--39164738 Score: 1921
Period size: 43 Copynumber: 24.5 Consensus size: 43
39163675 CCAGCATCAT
* * * *
39163685 AGCCTGCTAGGTACGAAGGCCCGAATACACATCATCGGCACGA
1 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
* **
39163728 AGCCTACTAGGCACGAAGGCCCGAATACACATCACCGGTGCGA
1 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
* *
39163771 AGCCTGCTAGACACGAAGGCCCGAATACACATCACCGGCAAGA
1 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
39163814 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
1 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
39163857 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
1 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
39163900 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
1 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
39163943 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
1 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
39163986 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
1 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
39164029 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
1 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
39164072 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
1 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
39164115 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
1 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
39164158 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
1 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
39164201 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
1 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
39164244 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
1 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
39164287 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
1 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
39164330 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
1 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
39164373 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
1 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
39164416 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
1 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
* *
39164459 AGCCTGCTAGGCACGAAGGCTCGAATACACATCACCGGCAAGA
1 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
* *
39164502 AGCCTGCTAGGCACGAAGGCCCGAATTCACATCACCGGCAAGA
1 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
39164545 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
1 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
* *
39164588 AGCCTGCTAGGCACGAAGGCCCGAATTCACATCACCGGCAAGA
1 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
* *
39164631 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGA
1 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
* *
39164674 AGCCTGCTAGGAACGAAGGCCCGAATACACATCACCGGCACA-A
1 AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTA-AGA
39164717 AGCCTGCTAGGCACGAAGGCCC
1 AGCCTGCTAGGCACGAAGGCCC
39164739 AATTATAATA
Statistics
Matches: 985, Mismatches: 25, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
43 985 1.00
ACGTcount: A:0.32, C:0.31, G:0.26, T:0.11
Consensus pattern (43 bp):
AGCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGA
Found at i:39176145 original size:85 final size:85
Alignment explanation
Indices: 39176002--39176170 Score: 329
Period size: 85 Copynumber: 2.0 Consensus size: 85
39175992 TTTGGTAATA
39176002 ATCTGTTTGGGGACAGCAGCAGTAAGGTGAATTTGGAAAATCGCCATAATTTGTAGGAGTTGAAT
1 ATCTGTTTGGGGACAGCAGCAGTAAGGTGAATTTGGAAAATCGCCATAATTTGTAGGAGTTGAAT
39176067 TAGAAGCTGAGTGAATTATG
66 TAGAAGCTGAGTGAATTATG
*
39176087 ATCTGTTTGGGGACAGCAGCAGTAAGGTGATTTTGGAAAATCGCCATAATTTGTAGGAGTTGAAT
1 ATCTGTTTGGGGACAGCAGCAGTAAGGTGAATTTGGAAAATCGCCATAATTTGTAGGAGTTGAAT
39176152 TAGAAGCTGAGTGAATTAT
66 TAGAAGCTGAGTGAATTAT
39176171 TTCATTAAAG
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 83 1.00
ACGTcount: A:0.31, C:0.09, G:0.29, T:0.30
Consensus pattern (85 bp):
ATCTGTTTGGGGACAGCAGCAGTAAGGTGAATTTGGAAAATCGCCATAATTTGTAGGAGTTGAAT
TAGAAGCTGAGTGAATTATG
Found at i:39177196 original size:40 final size:40
Alignment explanation
Indices: 39177141--39177368 Score: 402
Period size: 40 Copynumber: 5.7 Consensus size: 40
39177131 GAGCATTGGA
39177141 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
39177181 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
39177221 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
39177261 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
39177301 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
39177341 ATATGTCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
39177369 ATGTGTTTGC
Statistics
Matches: 181, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 181 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:39183487 original size:42 final size:42
Alignment explanation
Indices: 39183405--39183549 Score: 159
Period size: 42 Copynumber: 3.4 Consensus size: 42
39183395 CCCAAACGTC
* * * *
39183405 GTCTTACATGTAATCAAATATCAATGCCACTGTCCCAGACAGG
1 GTCTTACACGAAATCAAATA-CGATGCCAATGTCCCAGACAGG
* **
39183448 GTCTTACACGGAATCAAATACGATGCCAATGTCCCAGACATA
1 GTCTTACACGAAATCAAATACGATGCCAATGTCCCAGACAGG
*
39183490 GTCTTACACGTAAATCTCAAAT-CGATGCCAACGTCCCAGAC-GTG
1 GTCTTACACG-AAA--TCAAATACGATGCCAATGTCCCAGACAG-G
39183534 GTCTTACACGAAATCA
1 GTCTTACACGAAATCA
39183550 CATATCGAAA
Statistics
Matches: 88, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
41 3 0.03
42 28 0.32
43 23 0.26
44 28 0.32
45 6 0.07
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (42 bp):
GTCTTACACGAAATCAAATACGATGCCAATGTCCCAGACAGG
Found at i:39183538 original size:86 final size:85
Alignment explanation
Indices: 39183385--39183549 Score: 201
Period size: 86 Copynumber: 1.9 Consensus size: 85
39183375 AGCTTGTACA
* * *
39183385 ATGCCAACGTCCCAAACGTCGTCTTACATGTAATCAAATATCAATGCCACTGTCCCAGACAGGGT
1 ATGCCAACGTCCCAAACATAGTCTTACACGTAATCAAATATCAATGCCACTGTCCCAGACAGGGT
*
39183450 CTTACACGGAATCAAATACG
66 CTTACACGAAATCAAATACG
* * * *
39183470 ATGCCAATGTCCCAGACATAGTCTTACACGTAAATCTCAA-ATCGATGCCAAC-GTCCCAGAC-G
1 ATGCCAACGTCCCAAACATAGTCTTACACGT-AATC-AAATATCAATGCC-ACTGTCCCAGACAG
39183532 TGGTCTTACACGAAATCA
63 -GGTCTTACACGAAATCA
39183550 CATATCGAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
85 27 0.40
86 37 0.54
87 4 0.06
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.22
Consensus pattern (85 bp):
ATGCCAACGTCCCAAACATAGTCTTACACGTAATCAAATATCAATGCCACTGTCCCAGACAGGGT
CTTACACGAAATCAAATACG
Found at i:39190040 original size:2 final size:2
Alignment explanation
Indices: 39190033--39190065 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
39190023 ACAAGGAAAT
*
39190033 GA GA GA GA GA GA GA GA GA GA GA GA GG GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
39190066 GGGGTCGGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (2 bp):
GA
Found at i:39201273 original size:55 final size:54
Alignment explanation
Indices: 39201133--39201286 Score: 168
Period size: 55 Copynumber: 2.8 Consensus size: 54
39201123 TAAATTGTAC
* * *
39201133 AGCACTAAGTGTGCGATTCGACTT-TGTTGCACTAAGTGTGCGA-AATGAATATG
1 AGCACTAAGTGTGCGATTTGA-TTATGTGGCACTAAGTGTGCGAGTATGAATATG
* ** * * *
39201186 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTCTGACTATG
1 A-GCACTAAGTGTGCGATTTGATTATGTGGCACTAAGTGTGCGAGTATGAATATG
* *
39201241 TAGCACTAAGTGTACGATTTGATTACGTGGCACTAAGTGTGCGAGT
1 -AGCACTAAGTGTGCGATTTGATTATGTGGCACTAAGTGTGCGAGT
39201287 TGATTATATA
Statistics
Matches: 82, Mismatches: 15, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
53 1 0.01
54 35 0.43
55 45 0.55
56 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.29
Consensus pattern (54 bp):
AGCACTAAGTGTGCGATTTGATTATGTGGCACTAAGTGTGCGAGTATGAATATG
Found at i:39201274 original size:82 final size:81
Alignment explanation
Indices: 39201134--39201289 Score: 206
Period size: 82 Copynumber: 1.9 Consensus size: 81
39201124 AAATTGTACA
* * * * *
39201134 GCACTAAGTGTGCGATTCGACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTACGAAATGAATACGATGCACTAAGTGT
39201199 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
** *
39201215 GCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTACGATTTGATTACG-TGGCACTAAGT
1 GCACTAAGTGTGCGAGTC-GACTATGTAGCACTAAGTGTACGAAATGAATACGAT-GCACTAAGT
*
39201279 GTGCGAGTTGA
64 GTGCGAATTGA
39201290 TTATATAACG
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
81 18 0.28
82 46 0.72
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTACGAAATGAATACGATGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:39201290 original size:27 final size:27
Alignment explanation
Indices: 39201134--39201293 Score: 146
Period size: 27 Copynumber: 5.9 Consensus size: 27
39201124 AAATTGTACA
*
39201134 GCACTAAGTGTGCG-ATTCGACTT-TGTT
1 GCACTAAGTGTGCGAATT-GA-TTATGTG
* *
39201161 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGAATTGATTATG-TG
** *
39201188 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGATTATGTG
* * *
39201215 GCACTAAGTGTGCGAGTCTGACTATGTA
1 GCACTAAGTGTGCGAAT-TGATTATGTG
* * *
39201243 GCACTAAGTGTACGATTTGATTACGTG
1 GCACTAAGTGTGCGAATTGATTATGTG
*
39201270 GCACTAAGTGTGCGAGTTGATTAT
1 GCACTAAGTGTGCGAATTGATTAT
39201294 ATAACGCTGA
Statistics
Matches: 110, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
26 1 0.01
27 84 0.76
28 25 0.23
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (27 bp):
GCACTAAGTGTGCGAATTGATTATGTG
Found at i:39217264 original size:21 final size:21
Alignment explanation
Indices: 39217238--39217278 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
39217228 AGACGAGCAA
* *
39217238 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
39217259 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
39217279 TTGAGTAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:39221284 original size:7 final size:7
Alignment explanation
Indices: 39221221--39221363 Score: 51
Period size: 7 Copynumber: 19.9 Consensus size: 7
39221211 ACTAATTTAT
39221221 CTAAACC
1 CTAAACC
*
39221228 CTAATCC
1 CTAAACC
**
39221235 TCTAATTC
1 -CTAAACC
*
39221243 CTAACCC
1 CTAAACC
*
39221250 CTAAAATC
1 CT-AAACC
39221258 CTAAACC
1 CTAAACC
**
39221265 CTTCA-C
1 CTAAACC
*
39221271 ATAAACC
1 CTAAACC
39221278 CTAAACC
1 CTAAACC
* *
39221285 CCAGACC
1 CTAAACC
39221292 CGT-AACC
1 C-TAAACC
39221299 C-ATAACC
1 CTA-AACC
* *
39221306 ATTAACC
1 CTAAACC
39221313 ACATAAACC
1 -C-TAAACC
39221322 CTAAACCC
1 CTAAA-CC
*
39221330 CTAACCC
1 CTAAACC
39221337 CT-AACC
1 CTAAACC
*
39221343 CTTAACCC
1 C-TAAACC
39221351 CTAAACC
1 CTAAACC
*
39221358 TTAAAC
1 CTAAAC
39221364 ACCAGCCCTT
Statistics
Matches: 98, Mismatches: 26, Indels: 24
0.66 0.18 0.16
Matches are distributed among these distances:
6 7 0.07
7 64 0.65
8 22 0.22
9 5 0.05
ACGTcount: A:0.38, C:0.41, G:0.01, T:0.20
Consensus pattern (7 bp):
CTAAACC
Found at i:39221321 original size:37 final size:36
Alignment explanation
Indices: 39221274--39221357 Score: 98
Period size: 37 Copynumber: 2.3 Consensus size: 36
39221264 CCTTCACATA
* *
39221274 AACCC-TAAACCCCAGACCCGTAACCCATAACCATT
1 AACCCATAAACCCCAAACCCCTAACCCATAACCATT
* * *
39221309 AACCACATAAACCCTAAACCCCTAACCCCTAACCCTT
1 AACC-CATAAACCCCAAACCCCTAACCCATAACCATT
*
39221346 AACCCCTAAACC
1 AACCCATAAACC
39221358 TTAAACACCA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
35 4 0.10
36 8 0.20
37 29 0.71
ACGTcount: A:0.38, C:0.45, G:0.02, T:0.14
Consensus pattern (36 bp):
AACCCATAAACCCCAAACCCCTAACCCATAACCATT
Found at i:39221359 original size:14 final size:14
Alignment explanation
Indices: 39221320--39221361 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
39221310 ACCACATAAA
*
39221320 CCCTAAACCCCTAAC
1 CCCTAAA-CCTTAAC
*
39221335 CCCTAACCCTTAAC
1 CCCTAAACCTTAAC
39221349 CCCTAAACCTTAA
1 CCCTAAACCTTAA
39221362 ACACCAGCCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 18 0.75
15 6 0.25
ACGTcount: A:0.33, C:0.48, G:0.00, T:0.19
Consensus pattern (14 bp):
CCCTAAACCTTAAC
Found at i:39221574 original size:7 final size:7
Alignment explanation
Indices: 39221564--39221590 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
39221554 AACCCTAAAC
39221564 CCATAAT
1 CCATAAT
39221571 CCATAAT
1 CCATAAT
39221578 CCATAAT
1 CCATAAT
39221585 CCATAA
1 CCATAA
39221591 ACCCTGAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.30, G:0.00, T:0.26
Consensus pattern (7 bp):
CCATAAT
Found at i:39221652 original size:14 final size:15
Alignment explanation
Indices: 39221633--39221671 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
39221623 CTAACCCCTG
39221633 ATCCTTAAA-CCATA
1 ATCCTTAAACCCATA
39221647 ATCCTTAAACCCCATA
1 ATCCTTAAA-CCCATA
*
39221663 ATCCCTAAA
1 ATCCTTAAA
39221672 ACTTAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.41
16 13 0.59
ACGTcount: A:0.41, C:0.33, G:0.00, T:0.26
Consensus pattern (15 bp):
ATCCTTAAACCCATA
Found at i:39226672 original size:28 final size:28
Alignment explanation
Indices: 39226640--39226697 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
39226630 AAAATGAATG
39226640 TTAGCCATCATTAAAGGTTTAATACAAA
1 TTAGCCATCATTAAAGGTTTAATACAAA
39226668 TTAGCCATCATTAAAGGTTTAATACAAA
1 TTAGCCATCATTAAAGGTTTAATACAAA
39226696 TT
1 TT
39226698 GAAGGGTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.34
Consensus pattern (28 bp):
TTAGCCATCATTAAAGGTTTAATACAAA
Found at i:39227262 original size:47 final size:49
Alignment explanation
Indices: 39227190--39227417 Score: 192
Period size: 47 Copynumber: 4.9 Consensus size: 49
39227180 GGGTAAGGTG
* *
39227190 CTGATGCCATATCCCAGACATGGTCTTACACTGGCTCAT-ATCTTAAGT
1 CTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCAAGT
* * * **
39227238 C-AATGCCATGTCCCAGACATGGTCTTACACCGACT-ATCATCTTGTAG-
1 CTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATC-TCAAGT
* * * * * * *
39227285 CGGATG-CATGTCCCAAACAT-GTCTTACACTGGCTTA-CGTCCCGAGG
1 CTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCAAGT
* * *
39227331 CTGATG-CATGTCCCAGACAT-GTCCTACACTAGCTC-TCGTCTCAA-T
1 CTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCAAGT
*
39227376 GCTGATGCCATGTCCTAGACATGGTCTTACACTGGCTC-TCAT
1 -CTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCAT
39227418 AATGTGGCCA
Statistics
Matches: 145, Mismatches: 26, Indels: 18
0.77 0.14 0.10
Matches are distributed among these distances:
45 2 0.01
46 59 0.41
47 61 0.42
48 23 0.16
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.29
Consensus pattern (49 bp):
CTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCAAGT
Found at i:39227337 original size:46 final size:46
Alignment explanation
Indices: 39227287--39227459 Score: 168
Period size: 46 Copynumber: 3.7 Consensus size: 46
39227277 TCTTGTAGCG
*
39227287 GATGCATGTCCCAAACATGTCTTACACTGGCT-TACGTCCCGAGGCT
1 GATGCATGTCCCAAACATGTCTTACACTGGCTCT-CGTCACGAGGCT
* * * * * *
39227333 GATGCATGTCCCAGACATGTCCTACACTAGCTCTCGTCTCAATGCT
1 GATGCATGTCCCAAACATGTCTTACACTGGCTCTCGTCACGAGGCT
* * * * * * *
39227379 GATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATAATGTGGCC
1 GATG-CATGTCCCAAACAT-GTCTTACACTGGCTCTCGTCACGAGGCT
* *
39227427 AATGCATGTCCCAAACATGTCTTACACTAGCTC
1 GATGCATGTCCCAAACATGTCTTACACTGGCTC
39227460 ACAAACAAAT
Statistics
Matches: 103, Mismatches: 21, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
46 56 0.54
47 26 0.25
48 21 0.20
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (46 bp):
GATGCATGTCCCAAACATGTCTTACACTGGCTCTCGTCACGAGGCT
Found at i:39232224 original size:13 final size:13
Alignment explanation
Indices: 39232208--39232260 Score: 56
Period size: 13 Copynumber: 4.1 Consensus size: 13
39232198 AATGGGTTAG
39232208 GTAAATGTTCCAT
1 GTAAATGTTCCAT
39232221 GTAAATGTTCCAT
1 GTAAATGTTCCAT
* *
39232234 G-ATAATGGTT-TAG
1 GTA-AAT-GTTCCAT
39232247 GTAAATGTTCCAT
1 GTAAATGTTCCAT
39232260 G
1 G
39232261 ATGGGCATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
12 4 0.12
13 24 0.75
14 4 0.12
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (13 bp):
GTAAATGTTCCAT
Found at i:39232227 original size:26 final size:26
Alignment explanation
Indices: 39232142--39232221 Score: 142
Period size: 26 Copynumber: 3.1 Consensus size: 26
39232132 TGGTACAAAT
39232142 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
39232168 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
39232194 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
39232220 TG
1 TG
39232222 TAAATGTTCC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 50 1.00
ACGTcount: A:0.33, C:0.07, G:0.25, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:39232236 original size:39 final size:39
Alignment explanation
Indices: 39232182--39232260 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
39232172 AATGGATTAG
39232182 GTAAATATTCCATGATAATGGGTTAGGTAAATGTTCCAT
1 GTAAATATTCCATGATAATGGGTTAGGTAAATGTTCCAT
* *
39232221 GTAAATGTTCCATGATAATGGTTTAGGTAAATGTTCCAT
1 GTAAATATTCCATGATAATGGGTTAGGTAAATGTTCCAT
39232260 G
1 G
39232261 ATGGGCATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.37
Consensus pattern (39 bp):
GTAAATATTCCATGATAATGGGTTAGGTAAATGTTCCAT
Found at i:39233957 original size:27 final size:27
Alignment explanation
Indices: 39233860--39233964 Score: 135
Period size: 27 Copynumber: 3.9 Consensus size: 27
39233850 AGGAAGCGTC
*
39233860 CTGGTGGCTATGCCACAATTATCTG-AT
1 CTGGTGGCTCTGCCACAA-TATCTGTAT
39233887 CTGGTGGCTCTGCCACATATATCTGT-T
1 CTGGTGGCTCTGCCACA-ATATCTGTAT
39233914 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGGCTCTGCCACAATATCTGTAT
* *
39233941 CTGGTGACT-TCGTCACAATATCTG
1 CTGGTGGCTCT-GCCACAATATCTG
39233965 GCAGCCTCGC
Statistics
Matches: 71, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
26 9 0.13
27 61 0.86
28 1 0.01
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATATCTGTAT
Found at i:39235484 original size:27 final size:27
Alignment explanation
Indices: 39235422--39235478 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
39235412 TATTTTTTAT
39235422 GATTGATTTACTATTAATATTGAATTG
1 GATTGATTTACTATTAATATTGAATTG
39235449 GATTGATTTACTATTAATATTGAATTG
1 GATTGATTTACTATTAATATTGAATTG
39235476 GAT
1 GAT
39235479 ATATTTTAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (27 bp):
GATTGATTTACTATTAATATTGAATTG
Found at i:39244134 original size:20 final size:20
Alignment explanation
Indices: 39244109--39244149 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
39244099 CTTTGGAGGA
*
39244109 ATGAGGACTGCTGCCAAAGT
1 ATGAGGACTACTGCCAAAGT
39244129 ATGAGGACTACTGCCAAAGT
1 ATGAGGACTACTGCCAAAGT
39244149 A
1 A
39244150 CTTCAGCTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.27, T:0.20
Consensus pattern (20 bp):
ATGAGGACTACTGCCAAAGT
Found at i:39249544 original size:42 final size:43
Alignment explanation
Indices: 39249474--39249557 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 43
39249464 TCCTACATGT
*
39249474 AATCAAATATCGATGCCACTGTCCCAGACAGGGTCTTACACGA
1 AATCAAATATCGATGCCAATGTCCCAGACAGGGTCTTACACGA
* *
39249517 AATCAAATA-CGATGCCAATGTCTCAGACATGGTCTTACACG
1 AATCAAATATCGATGCCAATGTCCCAGACAGGGTCTTACACG
39249558 TATGATGTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
42 29 0.76
43 9 0.24
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (43 bp):
AATCAAATATCGATGCCAATGTCCCAGACAGGGTCTTACACGA
Found at i:39254482 original size:50 final size:49
Alignment explanation
Indices: 39254375--39254507 Score: 160
Period size: 50 Copynumber: 2.7 Consensus size: 49
39254365 CTGGTACGCA
* * ** *
39254375 TAGTAGCCTGCACA-TAGTACTACACATGCGACCAATTATCTGGTACACG
1 TAGTAGCCTGCA-ATTAGTACTACACACGTGACCAACCATCTGATACACG
* *
39254424 TAGCAGCCTACAATTAGTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCAATTAGTACTACACACGTGACC-AACCATCTGATACACG
**
39254474 TAGTAGCCTGCTCTTAGTACTACACACGTGACCA
1 TAGTAGCCTGCAATTAGTACTACACACGTGACCA
39254508 CAGTTTTCGG
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
48 1 0.01
49 28 0.39
50 42 0.59
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.24
Consensus pattern (49 bp):
TAGTAGCCTGCAATTAGTACTACACACGTGACCAACCATCTGATACACG
Found at i:39255014 original size:50 final size:50
Alignment explanation
Indices: 39254934--39255032 Score: 180
Period size: 50 Copynumber: 2.0 Consensus size: 50
39254924 TCTTTCATGA
* *
39254934 CATATTTCCACATCATAAATACCATTCCATCAACTTTTCCAATATATTAT
1 CATACTTCCACATCATAAACACCATTCCATCAACTTTTCCAATATATTAT
39254984 CATACTTCCACATCATAAACACCATTCCATCAACTTTTCCAATATATTA
1 CATACTTCCACATCATAAACACCATTCCATCAACTTTTCCAATATATTA
39255033 AATCATAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.36, C:0.28, G:0.00, T:0.35
Consensus pattern (50 bp):
CATACTTCCACATCATAAACACCATTCCATCAACTTTTCCAATATATTAT
Found at i:39256881 original size:224 final size:224
Alignment explanation
Indices: 39256491--39256942 Score: 904
Period size: 224 Copynumber: 2.0 Consensus size: 224
39256481 AATATCTCAA
39256491 TTGAAAACATTAACTATAATTGACTTACTTGAGAGAAGTAATCCACCATACCGATTGAAACTCGC
1 TTGAAAACATTAACTATAATTGACTTACTTGAGAGAAGTAATCCACCATACCGATTGAAACTCGC
39256556 ACTTTTATCACTTATACCTTTACTGTTGTCAAACCTTACACGAAAATTAGAAAAATCCGAATACT
66 ACTTTTATCACTTATACCTTTACTGTTGTCAAACCTTACACGAAAATTAGAAAAATCCGAATACT
39256621 GAAATCACCACATCACCCAAATCAAATCAGAAGTATAGCTATACTTGACATGATTATCACGAGCT
131 GAAATCACCACATCACCCAAATCAAATCAGAAGTATAGCTATACTTGACATGATTATCACGAGCT
39256686 GAAGAATGCACTCCGAACATGAGTCATAG
196 GAAGAATGCACTCCGAACATGAGTCATAG
39256715 TTGAAAACATTAACTATAATTGACTTACTTGAGAGAAGTAATCCACCATACCGATTGAAACTCGC
1 TTGAAAACATTAACTATAATTGACTTACTTGAGAGAAGTAATCCACCATACCGATTGAAACTCGC
39256780 ACTTTTATCACTTATACCTTTACTGTTGTCAAACCTTACACGAAAATTAGAAAAATCCGAATACT
66 ACTTTTATCACTTATACCTTTACTGTTGTCAAACCTTACACGAAAATTAGAAAAATCCGAATACT
39256845 GAAATCACCACATCACCCAAATCAAATCAGAAGTATAGCTATACTTGACATGATTATCACGAGCT
131 GAAATCACCACATCACCCAAATCAAATCAGAAGTATAGCTATACTTGACATGATTATCACGAGCT
39256910 GAAGAATGCACTCCGAACATGAGTCATAG
196 GAAGAATGCACTCCGAACATGAGTCATAG
39256939 TTGA
1 TTGA
39256943 CAAATTACGG
Statistics
Matches: 228, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
224 228 1.00
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (224 bp):
TTGAAAACATTAACTATAATTGACTTACTTGAGAGAAGTAATCCACCATACCGATTGAAACTCGC
ACTTTTATCACTTATACCTTTACTGTTGTCAAACCTTACACGAAAATTAGAAAAATCCGAATACT
GAAATCACCACATCACCCAAATCAAATCAGAAGTATAGCTATACTTGACATGATTATCACGAGCT
GAAGAATGCACTCCGAACATGAGTCATAG
Found at i:39257010 original size:30 final size:30
Alignment explanation
Indices: 39256957--39257014 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
39256947 TTACGGAATA
39256957 AAGATAGCAAGAAAACCGAATAAAGAAATCC
1 AAGATAG-AAGAAAACCGAATAAAGAAATCC
*
39256988 AAGATAG-AGAAACCCAGAATAAAGAAA
1 AAGATAGAAGAAAACC-GAATAAAGAAA
39257015 CCCAGAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 7 0.28
30 11 0.44
31 7 0.28
ACGTcount: A:0.60, C:0.14, G:0.17, T:0.09
Consensus pattern (30 bp):
AAGATAGAAGAAAACCGAATAAAGAAATCC
Found at i:39257013 original size:15 final size:15
Alignment explanation
Indices: 39256965--39257033 Score: 70
Period size: 15 Copynumber: 4.7 Consensus size: 15
39256955 TAAAGATAGC
*
39256965 AAGAAAACC-GAATA
1 AAGAAACCCAGAATA
*
39256979 AAGAAATCCA-AGATA
1 AAGAAACCCAGA-ATA
*
39256994 GAGAAACCCAGAATA
1 AAGAAACCCAGAATA
*
39257009 AAGAAACCCAGAGTA
1 AAGAAACCCAGAATA
*
39257024 AAGACACCCA
1 AAGAAACCCA
39257034 AGATACGATA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
14 9 0.20
15 36 0.78
16 1 0.02
ACGTcount: A:0.57, C:0.20, G:0.16, T:0.07
Consensus pattern (15 bp):
AAGAAACCCAGAATA
Found at i:39257033 original size:30 final size:30
Alignment explanation
Indices: 39256965--39257033 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
39256955 TAAAGATAGC
* *
39256965 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAACCCAGAATAAAGAAACCCAAGATA
*
39256994 GAGAAACCCAGAATAAAGAAACCC-AGAGTA
1 AAGAAACCCAGAATAAAGAAACCCAAGA-TA
*
39257024 AAGACACCCA
1 AAGAAACCCA
39257034 AGATACGATA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 10 0.30
30 23 0.70
ACGTcount: A:0.57, C:0.20, G:0.16, T:0.07
Consensus pattern (30 bp):
AAGAAACCCAGAATAAAGAAACCCAAGATA
Found at i:39262804 original size:22 final size:21
Alignment explanation
Indices: 39262765--39262810 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
39262755 AGGGCGGTGG
*
39262765 CAATGGTGGTGCAAGGTGGTAA
1 CAATGGTGATGCAAGGTGG-AA
* *
39262787 CAATGGTGATGTATGGTGGAA
1 CAATGGTGATGCAAGGTGGAA
39262808 CAA
1 CAA
39262811 AATGGGCAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.30, C:0.09, G:0.37, T:0.24
Consensus pattern (21 bp):
CAATGGTGATGCAAGGTGGAA
Found at i:39266009 original size:5 final size:5
Alignment explanation
Indices: 39265999--39266036 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
39265989 TTTGTGTGTT
39265999 TTTTA TTTTA TTTTA TTTTA -TTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
39266037 CACAAATTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:39266024 original size:14 final size:14
Alignment explanation
Indices: 39265999--39266035 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
39265989 TTTGTGTGTT
39265999 TTTTATTTTATTTTA
1 TTTTA-TTTATTTTA
39266014 TTTTATTTATTTTA
1 TTTTATTTATTTTA
39266028 TTTTATTT
1 TTTTATTT
39266036 TCACAAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTATTTATTTTA
Found at i:39266024 original size:19 final size:19
Alignment explanation
Indices: 39266000--39266036 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
39265990 TTGTGTGTTT
39266000 TTTATTTTATTTTATTTTA
1 TTTATTTTATTTTATTTTA
39266019 TTTATTTTATTTTATTTT
1 TTTATTTTATTTTATTTT
39266037 CACAAATTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTATTTTATTTTATTTTA
Found at i:39269176 original size:27 final size:27
Alignment explanation
Indices: 39269146--39269323 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
39269136 ATATTGACTC
* * * *
39269146 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
39269173 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
39269200 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
39269228 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
39269255 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
39269282 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
39269309 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
39269324 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:39269285 original size:82 final size:81
Alignment explanation
Indices: 39269167--39269322 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
39269157 TGCTATATAA
* *
39269167 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
39269232 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
39269249 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
39269313 CACTTAGTGC
65 CACTTAGTGC
39269323 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:39269820 original size:12 final size:12
Alignment explanation
Indices: 39269803--39269829 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
39269793 ATGGCATACT
39269803 TATGTATATATA
1 TATGTATATATA
39269815 TATGTATATATA
1 TATGTATATATA
39269827 TAT
1 TAT
39269830 ACTTCGGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TATGTATATATA
Found at i:39273121 original size:49 final size:49
Alignment explanation
Indices: 39273062--39273257 Score: 248
Period size: 50 Copynumber: 3.9 Consensus size: 49
39273052 TAGCCAAAGC
* *
39273062 TATCTGGTACACATAGTAGCCTGCACATAGTACTACACATGCGACCAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCAAT
* * *
39273111 TATCTGGTACACGTAGTAGCCTACACTTAGTACTACACATGTGACCTAAC
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACC-AAT
* * * *
39273161 CATCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCACAGT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCA-A-T
* * * *
39273212 TTTCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGAGACC
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACC
39273258 TCACAATAGA
Statistics
Matches: 126, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
49 43 0.34
50 45 0.36
51 38 0.30
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.26
Consensus pattern (49 bp):
TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACCAAT
Found at i:39283811 original size:27 final size:27
Alignment explanation
Indices: 39283781--39283958 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
39283771 ATATTGAGTC
* * * *
39283781 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
39283808 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
39283835 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
39283863 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
39283890 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
39283917 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
39283944 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
39283959 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:39283920 original size:82 final size:81
Alignment explanation
Indices: 39283802--39283957 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
39283792 TGCTATATAA
* *
39283802 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
39283867 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
39283884 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
39283948 CACTTAGTGC
65 CACTTAGTGC
39283958 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:39287013 original size:46 final size:46
Alignment explanation
Indices: 39286944--39287034 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
39286934 ATCATCGGTA
** * *
39286944 ATAACCGGTGAGCCCTAGAAAGCTCCGGACTTCGGTAACATTTCTC
1 ATAACCGGCAAGCCCCAGAAAGCTCCGAACTTCGGTAACATTTCTC
* *
39286990 ATAACCGGCAAGCCCCAGGAAGCTCCGAACTTCGGTAATATTTCT
1 ATAACCGGCAAGCCCCAGAAAGCTCCGAACTTCGGTAACATTTCT
39287035 TGGAGGCTTC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (46 bp):
ATAACCGGCAAGCCCCAGAAAGCTCCGAACTTCGGTAACATTTCTC
Found at i:39297949 original size:40 final size:40
Alignment explanation
Indices: 39297868--39298128 Score: 366
Period size: 40 Copynumber: 6.6 Consensus size: 40
39297858 AAACCAAGTA
** * *
39297868 CCTTCGGGGTTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGTTATAG-TAACTCGCACAAATG
*
39297907 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
39297947 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
** *
39297987 CCTTTAGGACTTGGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
39298027 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
* * *
39298067 CCTTCGGGACTTAGCCCAGATATAGTAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
39298107 CCTTCGGG-CTTAGCCTGGTTAT
1 CCTTCGGGACTTAGCCCGGTTAT
39298129 CAATCCGAAT
Statistics
Matches: 202, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
39 24 0.12
40 178 0.88
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.27
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
Found at i:39306112 original size:40 final size:40
Alignment explanation
Indices: 39306031--39306291 Score: 393
Period size: 40 Copynumber: 6.6 Consensus size: 40
39306021 AAACCAAGTA
** * *
39306031 CCTTCGGGGTTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGTTATAG-TAACTCGCACAAATG
*
39306070 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
39306110 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
39306150 CCTTCGGGACTTGGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
39306190 CCTTCGGGACTTGGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
* * *
39306230 CCTTCGGCACTTATCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
39306270 CCTTCGGG-CTTAGCCCGGTTAT
1 CCTTCGGGACTTAGCCCGGTTAT
39306292 CAATCCGAAT
Statistics
Matches: 206, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
39 25 0.12
40 181 0.88
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.27
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
Found at i:39313974 original size:15 final size:14
Alignment explanation
Indices: 39313948--39313990 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
39313938 TGTGATTATG
*
39313948 GTTTCATTAATTAA
1 GTTTAATTAATTAA
39313962 GTTTAATTAAATTAA
1 GTTTAATT-AATTAA
* *
39313977 TTTTGATTAATTAA
1 GTTTAATTAATTAA
39313991 AGTTAAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (14 bp):
GTTTAATTAATTAA
Found at i:39315610 original size:20 final size:19
Alignment explanation
Indices: 39315584--39315641 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 19
39315574 ATTGGTGATC
39315584 AGAGGCATCAAAGTGCAAAA
1 AGAGGCA-CAAAGTGCAAAA
* * *
39315604 AGGGGCACTGAAGTGCAAAT
1 AGAGGCAC-AAAGTGCAAAA
*
39315624 AGAGGCACCAAATTGCAA
1 AGAGGCA-CAAAGTGCAA
39315642 GCCCCATACA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
19 1 0.03
20 28 0.93
21 1 0.03
ACGTcount: A:0.43, C:0.17, G:0.28, T:0.12
Consensus pattern (19 bp):
AGAGGCACAAAGTGCAAAA
Found at i:39320367 original size:13 final size:13
Alignment explanation
Indices: 39320349--39320373 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39320339 GGTTGTTTAT
39320349 TAAACTAATTAAC
1 TAAACTAATTAAC
39320362 TAAACTAATTAA
1 TAAACTAATTAA
39320374 TTAATTAAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:39320376 original size:17 final size:17
Alignment explanation
Indices: 39320354--39320386 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
39320344 TTTATTAAAC
39320354 TAATTAACTAAACTAAT
1 TAATTAACTAAACTAAT
*
39320371 TAATTAATTAAACTAA
1 TAATTAACTAAACTAA
39320387 AGTAAAGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (17 bp):
TAATTAACTAAACTAAT
Found at i:39323303 original size:6 final size:6
Alignment explanation
Indices: 39323294--39323350 Score: 87
Period size: 6 Copynumber: 9.5 Consensus size: 6
39323284 AATAAAATTG
* * *
39323294 AAATGA AAATAA AAATAA AAGTAC AAATAA AAATAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
39323342 AAATAA AAA
1 AAATAA AAA
39323351 GATAGGAGGA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.79, C:0.02, G:0.04, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:39323309 original size:12 final size:11
Alignment explanation
Indices: 39323284--39323349 Score: 69
Period size: 12 Copynumber: 5.6 Consensus size: 11
39323274 AAAAGAAAAT
**
39323284 AATAAAATTGA
1 AATAAAATAAA
39323295 AATGAAAATAAA
1 AAT-AAAATAAA
*
39323307 AATAAAAGTACA
1 AATAAAA-TAAA
39323319 AATAAAAATAAA
1 AAT-AAAATAAA
39323331 AATAAAAATAAA
1 AAT-AAAATAAA
39323343 AATAAAA
1 AATAAAA
39323350 AGATAGGAGG
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
11 11 0.23
12 33 0.69
13 4 0.08
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.18
Consensus pattern (11 bp):
AATAAAATAAA
Found at i:39328758 original size:13 final size:13
Alignment explanation
Indices: 39328740--39328764 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39328730 GGTTGTTTAT
39328740 TAAACTAATTAAC
1 TAAACTAATTAAC
39328753 TAAACTAATTAA
1 TAAACTAATTAA
39328765 TTAGTTAAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:39332620 original size:48 final size:47
Alignment explanation
Indices: 39332414--39332628 Score: 163
Period size: 46 Copynumber: 4.6 Consensus size: 47
39332404 TGATATGTGT
* * * * * *
39332414 GCTAATGTAAGACATGTCTGGGACATGCATCAGCCAC-AG-TATGAGA
1 GCTAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATA-CAAA
* * * *
39332460 GCCAATGTAAGACATGTCTAGGACATGCAACGGCCTCGAGATATTTAAA
1 GCTAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATA--CAAA
* * * * *
39332509 -CCAGTGTTAGACATGTCTGGGACATGCATCGGCATTGAG--ACGAAA
1 GCTAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATAC-AAA
* * *
39332554 GCTGGTGTAAGCCATGTCTAGGACATGCATCGGCCTCGCGATACACAA
1 GCTAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATACA-AA
*
39332602 GCTAGTGTAAGACCTGTCT-GGTACATG
1 GCTAGTGTAAGACATGTCTAGG-ACATG
39332629 GCGTCATCTT
Statistics
Matches: 135, Mismatches: 25, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
45 3 0.02
46 64 0.47
47 5 0.04
48 60 0.44
49 3 0.02
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (47 bp):
GCTAGTGTAAGACATGTCTAGGACATGCATCGGCCTCGAGATACAAA
Found at i:39332703 original size:49 final size:49
Alignment explanation
Indices: 39332648--39332773 Score: 146
Period size: 49 Copynumber: 2.6 Consensus size: 49
39332638 TGTAGTGTGT
* * * *
39332648 CAGTGTAAGACCCGTCTAGGACATGGCATCGACAC-CGATAGATGAGAGC
1 CAGTGTAAGACCTGTCTGGGACATGGCACCGAC-CTCGATAGATGAAAGC
* * * * *
39332697 CAGTGTAAGACCTGTCTGGGACACGACACCGACCTTGCTATATGAAAGC
1 CAGTGTAAGACCTGTCTGGGACATGGCACCGACCTCGATAGATGAAAGC
39332746 CAGTGTAAGACCATGTCTGGGACATGGC
1 CAGTGTAAGACC-TGTCTGGGACATGGC
39332774 GTCGGCATCT
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
48 1 0.02
49 50 0.78
50 13 0.20
ACGTcount: A:0.29, C:0.25, G:0.28, T:0.19
Consensus pattern (49 bp):
CAGTGTAAGACCTGTCTGGGACATGGCACCGACCTCGATAGATGAAAGC
Found at i:39335299 original size:21 final size:21
Alignment explanation
Indices: 39335275--39335344 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
39335265 CACATACATT
39335275 ATGAACTCAGACCACAACTCA
1 ATGAACTCAGACCACAACTCA
* * * *
39335296 ATGAGCTCTGATGTCACATATATC-
1 ATGAACTCAGA--CCACA-A-CTCA
*
39335320 ATGAACTCAGACTACAACTCA
1 ATGAACTCAGACCACAACTCA
39335341 ATGA
1 ATGA
39335345 GATCAGATCA
Statistics
Matches: 35, Mismatches: 9, Indels: 10
0.65 0.17 0.19
Matches are distributed among these distances:
20 2 0.06
21 14 0.40
22 3 0.09
23 4 0.11
24 10 0.29
25 2 0.06
ACGTcount: A:0.39, C:0.26, G:0.13, T:0.23
Consensus pattern (21 bp):
ATGAACTCAGACCACAACTCA
Found at i:39339104 original size:24 final size:24
Alignment explanation
Indices: 39339077--39339126 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
39339067 AATTGTTATA
39339077 TAGCATGAATATGCCTATTGAGTC
1 TAGCATGAATATGCCTATTGAGTC
*
39339101 TAGCATGAGTATGCCTATTGAGTC
1 TAGCATGAATATGCCTATTGAGTC
39339125 TA
1 TA
39339127 TGGACTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (24 bp):
TAGCATGAATATGCCTATTGAGTC
Found at i:39342801 original size:12 final size:12
Alignment explanation
Indices: 39342784--39342808 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39342774 TGATCTATCG
39342784 ATTTCTAGCCAT
1 ATTTCTAGCCAT
39342796 ATTTCTAGCCAT
1 ATTTCTAGCCAT
39342808 A
1 A
39342809 CTTTGAGCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.40
Consensus pattern (12 bp):
ATTTCTAGCCAT
Found at i:39345920 original size:31 final size:29
Alignment explanation
Indices: 39345851--39345920 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 29
39345841 ATGCATATGA
*
39345851 CCCTTAACTTTTCATTAATTACACATTTT
1 CCCTAAACTTTTCATTAATTACACATTTT
* *
39345880 CTCTAAACTTTTACATTTATTACA-ATTTAAT
1 CCCTAAACTTTT-CATTAATTACACATTT--T
39345911 CCCTAAACTT
1 CCCTAAACTT
39345921 AAAATTCCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
29 14 0.41
30 10 0.29
31 10 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (29 bp):
CCCTAAACTTTTCATTAATTACACATTTT
Found at i:39352410 original size:38 final size:38
Alignment explanation
Indices: 39352359--39352567 Score: 157
Period size: 38 Copynumber: 5.0 Consensus size: 38
39352349 ATGAAAAAAA
* * *
39352359 AACGTGGGGCTAAGTGGATATTCCACGGTTATACGTGT
1 AACGTGGTGCTAAGTGGATATACCACGGTTATACATGT
*
39352397 AACGTGGTGCTAAGTGGATATACCACGATTACACATATTGGTACATGT
1 AACGTGGTGCTAAGTGGATATACCACG-GT-----TA----TACATGT
* *
39352445 AACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATT
1 AACGTGGTGCTAAGTGGATATACCACGGTT--ATACA-TG------T
* *
39352492 AACGTGGTGCTAAGTGCATATACCACGGTTAAACATGT
1 AACGTGGTGCTAAGTGGATATACCACGGTTATACATGT
* *
39352530 AACGTGGTGCTAAGTGGATATGCCACAGTTATACATGT
1 AACGTGGTGCTAAGTGGATATACCACGGTTATACATGT
39352568 TAATTTGAAA
Statistics
Matches: 137, Mismatches: 15, Indels: 38
0.72 0.08 0.20
Matches are distributed among these distances:
38 60 0.44
39 1 0.01
40 3 0.02
41 2 0.01
42 1 0.01
44 5 0.04
45 3 0.02
47 30 0.22
48 32 0.23
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (38 bp):
AACGTGGTGCTAAGTGGATATACCACGGTTATACATGT
Found at i:39352518 original size:47 final size:48
Alignment explanation
Indices: 39352389--39352527 Score: 199
Period size: 48 Copynumber: 2.9 Consensus size: 48
39352379 TTCCACGGTT
* *
39352389 ATACGTGTAACGTGGTGCTAAGTGGATATACCACGATTACACATATTG
1 ATACATGTAACGTGGTGCTAAGTGGATATACCACGGTTACACATATTG
* * *
39352437 GTACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTG
1 ATACATGTAACGTGGTGCTAAGTGGATATACCACGGTTACACATATTG
* * *
39352485 ATTCAT-TAACGTGGTGCTAAGTGCATATACCACGGTTAAACAT
1 ATACATGTAACGTGGTGCTAAGTGGATATACCACGGTTACACAT
39352528 GTAACGTGGT
Statistics
Matches: 80, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
47 33 0.41
48 47 0.59
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (48 bp):
ATACATGTAACGTGGTGCTAAGTGGATATACCACGGTTACACATATTG
Found at i:39354203 original size:52 final size:50
Alignment explanation
Indices: 39354125--39354405 Score: 162
Period size: 49 Copynumber: 5.6 Consensus size: 50
39354115 ATTGTGAGAA
* * * * ** *
39354125 CACATGTGTTGTACTATGTGTAGGCTACTATGTGTTTAAGATGGTTTTAGGT
1 CACATGTGTAGTACAAAGTGTAGGCTACTACGTGTACAAGATAG--TTAGGT
** *
39354177 CATGTGTGTAGTACAAAGTGTAGGCTACTACGTGTACCAGATAGTTAGGT
1 CACATGTGTAGTACAAAGTGTAGGCTACTACGTGTACAAGATAGTTAGGT
* * * * * *
39354227 CGCATGTGTAGTACTAAGTGTAGGCTACT-CTGCGTACCCA-ACAGCTTCA-AT
1 CACATGTGTAGTACAAAGTGTAGGCTACTAC-GTGTA-CAAGATAG-TT-AGGT
** * *
39354278 CATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATC-AGATAGTTAGGT
1 CACATGTGTAGTACAAAGTGTAGGCTACTACGTGTA-CAAGATAGTTAGGT
* * * ** *
39354328 CAC--GCTGTAGTACTAAGCGCAGGCTACTACGTGTACCGGATTGTTA-GT
1 CACATG-TGTAGTACAAAGTGTAGGCTACTACGTGTACAAGATAGTTAGGT
** * * *
39354376 CGTATGTGTTGTACTAAGTGCAGGCTACTA
1 CACATGTGTAGTACAAAGTGTAGGCTACTA
39354406 TGCATACCAG
Statistics
Matches: 185, Mismatches: 33, Indels: 25
0.76 0.14 0.10
Matches are distributed among these distances:
48 5 0.03
49 60 0.32
50 45 0.24
51 39 0.21
52 36 0.19
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (50 bp):
CACATGTGTAGTACAAAGTGTAGGCTACTACGTGTACAAGATAGTTAGGT
Found at i:39354312 original size:26 final size:26
Alignment explanation
Indices: 39354283--39354362 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
39354273 TCAATCATGT
39354283 GTGTAGTACTAAGTGCAGGCTACTAC
1 GTGTAGTACTAAGTGCAGGCTACTAC
* *
39354309 GTGTA-T-CAGATAGT-TAGG-T-C-AC
1 GTGTAGTAC-TA-AGTGCAGGCTACTAC
*
39354331 GCTGTAGTACTAAGCGCAGGCTACTAC
1 G-TGTAGTACTAAGTGCAGGCTACTAC
39354358 GTGTA
1 GTGTA
39354363 CCGGATTGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 18
0.63 0.08 0.29
Matches are distributed among these distances:
22 3 0.08
23 7 0.17
24 7 0.17
25 7 0.17
26 13 0.32
27 3 0.08
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.28
Consensus pattern (26 bp):
GTGTAGTACTAAGTGCAGGCTACTAC
Found at i:39354350 original size:49 final size:48
Alignment explanation
Indices: 39354182--39354419 Score: 196
Period size: 49 Copynumber: 4.8 Consensus size: 48
39354172 TAGGTCATGT
* * *
39354182 GTGTAGTACAAAGTGTAGGCTACTACGTGTACCAGATAGTTAGGTCGCAT
1 GTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTA-GTCG-AC
* * * * *
39354232 GTGTAGTACTAAGTGTAGGCTACT-CTGCGTACCCA-ACAGCTTCAATC-ATGT
1 GTGTAGTACTAAGTGCAGGCTACTAC-GTGTA-CCAGATAG-TT-AGTCGA--C
*
39354283 GTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATAGTTAGGTC-AC
1 GTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTA-GTCGAC
* * * *
39354331 GCTGTAGTACTAAGCGCAGGCTACTACGTGTACCGGATTGTTAGTCGTAT
1 G-TGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGTCG-AC
* * **
39354381 GTGTTGTACTAAGTGCAGGCTACTATGCATACCAGATAG
1 GTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
39354420 CTTCGGTTAC
Statistics
Matches: 154, Mismatches: 22, Indels: 25
0.77 0.11 0.12
Matches are distributed among these distances:
48 4 0.03
49 71 0.46
50 39 0.25
51 38 0.25
52 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (48 bp):
GTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGTCGAC
Found at i:39354445 original size:149 final size:150
Alignment explanation
Indices: 39354183--39354456 Score: 349
Period size: 149 Copynumber: 1.8 Consensus size: 150
39354173 AGGTCATGTG
* * *
39354183 TGTAGTACAAAGTGTAGGCTACTACGTGTACCAGATAGTTAGGTCGCATGTGTAGTACTAAGTGT
1 TGTAGTACAAAGCGCAGGCTACTACGTGTACCAGATAGTTAGGTCGCATGTGTAGTACTAAGTGC
* * * *
39354248 AGGCTACTCTGCGTACCCAACAGCTTCAATCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGT
66 AGGCTACTATGCATACCCAACAGCTTCAATCAAGTGTGTAGTAATAAGTGCAGGCTACTACGTGT
39354313 ATCAGATAGTTAGGTCACGC
131 ATCAGATAGTTAGGTCACGC
* * * * *
39354333 TGTAGTACTAAGCGCAGGCTACTACGTGTACCGGATTGTTA-GTCGTATGTGTTGTACTAAGTGC
1 TGTAGTACAAAGCGCAGGCTACTACGTGTACCAGATAGTTAGGTCGCATGTGTAGTACTAAGTGC
* ** *
39354397 AGGCTACTATGCATA-CCAGATAGCTTCGGTTACAAG-G-GTGGTAATAAGTGCAGGCTACTA
66 AGGCTACTATGCATACCCA-ACAGCTTC-AAT-CAAGTGTGTAGTAATAAGTGCAGGCTACTA
39354457 TGCATACGAA
Statistics
Matches: 105, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
148 3 0.03
149 61 0.58
150 38 0.36
151 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (150 bp):
TGTAGTACAAAGCGCAGGCTACTACGTGTACCAGATAGTTAGGTCGCATGTGTAGTACTAAGTGC
AGGCTACTATGCATACCCAACAGCTTCAATCAAGTGTGTAGTAATAAGTGCAGGCTACTACGTGT
ATCAGATAGTTAGGTCACGC
Found at i:39354649 original size:16 final size:15
Alignment explanation
Indices: 39354628--39354657 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
39354618 GAACGTAGCA
39354628 AGTGAAATTATGTAAG
1 AGTGAAATT-TGTAAG
39354644 AGTGAAATTTGTAA
1 AGTGAAATTTGTAA
39354658 TAAAACAGTT
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:0.43, C:0.00, G:0.23, T:0.33
Consensus pattern (15 bp):
AGTGAAATTTGTAAG
Found at i:39356175 original size:18 final size:18
Alignment explanation
Indices: 39356152--39356250 Score: 155
Period size: 18 Copynumber: 5.5 Consensus size: 18
39356142 GCGTGTCCCA
*
39356152 AGCCACATGGGCGTGTGT
1 AGCCACACGGGCGTGTGT
*
39356170 AGCCACACGAGCGTGTGT
1 AGCCACACGGGCGTGTGT
39356188 AGCCACACGGGCGTGTGT
1 AGCCACACGGGCGTGTGT
39356206 AGCCACACGGGCGTGTGT
1 AGCCACACGGGCGTGTGT
*
39356224 AGCCACACAGGCGTGTGT
1 AGCCACACGGGCGTGTGT
39356242 -GACCACACG
1 AG-CCACACG
39356251 ATTCAACACA
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
17 1 0.01
18 74 0.99
ACGTcount: A:0.20, C:0.28, G:0.35, T:0.16
Consensus pattern (18 bp):
AGCCACACGGGCGTGTGT
Found at i:39357350 original size:337 final size:336
Alignment explanation
Indices: 39356673--39357351 Score: 918
Period size: 337 Copynumber: 2.0 Consensus size: 336
39356663 CTCCCTAAAT
* * * * *
39356673 TTCTAAGGGATATCTTCTATAGATTTTATTTACATATACAGATTTCCCTAAGGGACTAAGTACAA
1 TTCTAAGGGACATCTTCTATAAATTTTATTTACATACACAAATTGCCCTAAGGGACTAAGTACAA
* * *
39356738 TTATATCACTTATAGTGTCTTCTACTATAACTCTCAGTTTAACAGACATAGAGCAAGAAACATAT
66 TTATATCACTTACAGTGTCTTCTACTATAACTCTCAGTTAAACAAACATAGAGCAAGAAACATAT
* **
39356803 GAATGAGTAGAACCTACATCTATCAAAGAAAGAACTGTACAGAATTAATTGTAAAAGTACATTTG
131 GAATGAGTAGAACCTACATCTATAAAAGAAAGAACTGTACAGAATTAATTGTAAAAGTACATACG
* *
39356868 ATGACATTAGATGCATCATGGTCCTCTCTGCGCCTCACAGCATAAACCAAGGCAAGCTATCTAGC
196 ATGACATCAGATGCATCATGGTCCTCTCTACGCCTCACAGCATAAACCAAGGCAAGCTATCTAGC
* * * * *
39356933 ATCAATGCAATTCACACTATGACCAGTTGCTCTCTGTGCAGTATTACCAGCTCTATTACTACCAT
261 ATCAATGCAATTCACACTATGACCAGTTGCTCTCTATCCAGTATTACCAACTATATTACTACCAC
39356998 GTGCCCTTTGA
326 GTGCCCTTTGA
* *
39357009 TTCTAAGGGACATCTTCTATAAATTTTATTTACATACACAAATTGCCCTAGGGGACTAAGTACAG
1 TTCTAAGGGACATCTTCTATAAATTTTATTTACATACACAAATTGCCCTAAGGGACTAAGTACAA
**
39357074 TTATATCAC-TAGCAGTGTCTTCTACTATAACTCTCAGTTAAACAAACATAGAGCAAGCCACATA
66 TTATATCACTTA-CAGTGTCTTCTACTATAACTCTCAGTTAAACAAACATAGAGCAAGAAACATA
* * * * *
39357138 TGAATGAGTAGAACCTACATCTGTAAAAGCAAAGTACTGTATATAATTAATTGTAAAAGTACCTA
130 TGAATGAGTAGAACCTACATCTATAAAAG-AAAGAACTGTACAGAATTAATTGTAAAAGTACATA
** * * *** *
39357203 CGATGACATCA-ACTGCATCATGGTCCTCTCTACGCCTCATTGCATAAACTATGGTGTGCTGTCT
194 CGATGACATCAGA-TGCATCATGGTCCTCTCTACGCCTCACAGCATAAACCAAGGCAAGCTATCT
* *
39357267 AGCATCAATGCGATTCACACCCTA-G-CTAGTTGCTCTCTATCCAGTATTACCAACTATATTACT
258 AGCATCAATGCAATTCACA--CTATGACCAGTTGCTCTCTATCCAGTATTACCAACTATATTACT
**
39357330 ACGGCGT-CCCTTTTGA
321 ACCACGTGCCC-TTTGA
39357346 TTCTAA
1 TTCTAA
39357352 TTTCATTGGG
Statistics
Matches: 298, Mismatches: 39, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
335 2 0.01
336 145 0.49
337 147 0.49
338 1 0.00
339 3 0.01
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.31
Consensus pattern (336 bp):
TTCTAAGGGACATCTTCTATAAATTTTATTTACATACACAAATTGCCCTAAGGGACTAAGTACAA
TTATATCACTTACAGTGTCTTCTACTATAACTCTCAGTTAAACAAACATAGAGCAAGAAACATAT
GAATGAGTAGAACCTACATCTATAAAAGAAAGAACTGTACAGAATTAATTGTAAAAGTACATACG
ATGACATCAGATGCATCATGGTCCTCTCTACGCCTCACAGCATAAACCAAGGCAAGCTATCTAGC
ATCAATGCAATTCACACTATGACCAGTTGCTCTCTATCCAGTATTACCAACTATATTACTACCAC
GTGCCCTTTGA
Found at i:39362690 original size:52 final size:52
Alignment explanation
Indices: 39362612--39362712 Score: 193
Period size: 52 Copynumber: 1.9 Consensus size: 52
39362602 CAACCCAAGT
39362612 TAACCTGAAAACCCTACGGAACATGGGTAAGAAAGGGGGGTAAGCTTTATGC
1 TAACCTGAAAACCCTACGGAACATGGGTAAGAAAGGGGGGTAAGCTTTATGC
*
39362664 TAACCTGAAAACCCTACGGTACATGGGTAAGAAAGGGGGGTAAGCTTTA
1 TAACCTGAAAACCCTACGGAACATGGGTAAGAAAGGGGGGTAAGCTTTA
39362713 CGCTTAGTAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.35, C:0.17, G:0.29, T:0.20
Consensus pattern (52 bp):
TAACCTGAAAACCCTACGGAACATGGGTAAGAAAGGGGGGTAAGCTTTATGC
Found at i:39366855 original size:22 final size:22
Alignment explanation
Indices: 39366830--39366873 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
39366820 TATCTAAAAC
39366830 AGTCAAGCAAATTATAATTATT
1 AGTCAAGCAAATTATAATTATT
*
39366852 AGTCAAGTAAATTATAATTATT
1 AGTCAAGCAAATTATAATTATT
39366874 GATGAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (22 bp):
AGTCAAGCAAATTATAATTATT
Found at i:39369018 original size:33 final size:33
Alignment explanation
Indices: 39368976--39369141 Score: 105
Period size: 33 Copynumber: 5.3 Consensus size: 33
39368966 ATCAATGGAT
* * * * *
39368976 ATTTCCTTTTCCAGTAGTACACTCAAGGTGTAC
1 ATTTCCTTTTCAAATAGTACACACAAAGTATAC
*
39369009 ATTTCCTTTTCAAATGGTACACACAAAGTATAC
1 ATTTCCTTTTCAAATAGTACACACAAAGTATAC
* *
39369042 CTTTCCTTTTCAAATGGTACA-A-AAAG--T--
1 ATTTCCTTTTCAAATAGTACACACAAAGTATAC
* * * * *
39369069 ATGT-CGTTTCAAGT-GTACGCACAAAGTGTAC
1 ATTTCCTTTTCAAATAGTACACACAAAGTATAC
** ** *
39369100 ATAGCCTTTTCATGTAGTATACACAAAGTATAC
1 ATTTCCTTTTCAAATAGTACACACAAAGTATAC
*
39369133 TTTTCCTTT
1 ATTTCCTTT
39369142 CCACATTCGA
Statistics
Matches: 103, Mismatches: 22, Indels: 16
0.73 0.16 0.11
Matches are distributed among these distances:
25 4 0.04
26 9 0.09
27 6 0.06
29 2 0.02
31 6 0.06
32 9 0.09
33 67 0.65
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.36
Consensus pattern (33 bp):
ATTTCCTTTTCAAATAGTACACACAAAGTATAC
Found at i:39370204 original size:63 final size:63
Alignment explanation
Indices: 39370104--39370223 Score: 213
Period size: 63 Copynumber: 1.9 Consensus size: 63
39370094 CCCTATCATA
*
39370104 AAAATATGAAAATCATTAAAAACGAGACATAGGACTTACCTAATTTGGCCATGAAAGCTTTCT
1 AAAATATGAAAATCATTAAAAACGAGACATAGAACTTACCTAATTTGGCCATGAAAGCTTTCT
* *
39370167 AAAATATGAAAATCATTAAAAACGGGACATAGAACTTACCTAATTTGTCCATGAAAG
1 AAAATATGAAAATCATTAAAAACGAGACATAGAACTTACCTAATTTGGCCATGAAAG
39370224 TTTTTTTCTC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 54 1.00
ACGTcount: A:0.45, C:0.15, G:0.14, T:0.26
Consensus pattern (63 bp):
AAAATATGAAAATCATTAAAAACGAGACATAGAACTTACCTAATTTGGCCATGAAAGCTTTCT
Found at i:39372798 original size:80 final size:80
Alignment explanation
Indices: 39372684--39373512 Score: 1452
Period size: 80 Copynumber: 10.4 Consensus size: 80
39372674 GCTACTTGCT
* * **
39372684 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACCTAACCCG-
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCTTGA
* * *
39372748 GATATAGTAACTCGCA
66 AAT-TAGTCACTAGCA
* * **
39372764 CAAATGCCTTCGGGACCTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCTTGA
39372829 AATTAGTCACTAGCA
66 AATTAGTCACTAGCA
* * *
39372844 CAAATGCCTTCGGGACTTAGCCCGGTTATCA-T--C-CGGATATTCATTGCCTTCGGGACTTAGC
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT-AGTAACTCGCACA---AATGCCTTCGGGACTTAGC
39372905 TTGAAATTAGTCACTAGCA
62 TTGAAATTAGTCACTAGCA
39372924 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCTTGA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCTTGA
39372989 AATTAGTCACTAGCA
66 AATTAGTCACTAGCA
39373004 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCTTGA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCTTGA
39373069 AATTAGTCACTAGCA
66 AATTAGTCACTAGCA
39373084 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCTTGA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCTTGA
39373149 AATTAGTCACTAGCA
66 AATTAGTCACTAGCA
39373164 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCTTGA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCTTGA
39373229 AATTAGTCACTAGCA
66 AATTAGTCACTAGCA
39373244 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCTTGA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCTTGA
39373309 AATTAGTCACTAGCA
66 AATTAGTCACTAGCA
39373324 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCTTGA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCTTGA
39373389 AATTAGTCACTAGCA
66 AATTAGTCACTAGCA
39373404 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCTTGA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCTTGA
39373469 AATTAGTCACTAGCA
66 AATTAGTCACTAGCA
39373484 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
39373513 CATCCGGATA
Statistics
Matches: 723, Mismatches: 17, Indels: 18
0.95 0.02 0.02
Matches are distributed among these distances:
77 4 0.01
78 1 0.00
79 1 0.00
80 709 0.98
81 3 0.00
82 1 0.00
83 4 0.01
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCTTGA
AATTAGTCACTAGCA
Found at i:39380607 original size:40 final size:40
Alignment explanation
Indices: 39380530--39380684 Score: 190
Period size: 40 Copynumber: 3.9 Consensus size: 40
39380520 AAACCAAGTA
* * *
39380530 CCTTCGGGATTTAG-CCAGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
39380569 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
39380609 CCTTCGAGACTTAGCCC-GAAATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
*
39380649 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACA
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
39380685 GAAATTAGTA
Statistics
Matches: 98, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
39 16 0.16
40 80 0.82
41 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:39380718 original size:59 final size:59
Alignment explanation
Indices: 39380626--39380743 Score: 209
Period size: 59 Copynumber: 2.0 Consensus size: 59
39380616 GACTTAGCCC
* *
39380626 GAAATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACA
1 GAAATTAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
*
39380685 GAAATTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
1 GAAATTAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
39380744 AATGCCTTCG
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.23
Consensus pattern (59 bp):
GAAATTAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
Found at i:39380745 original size:40 final size:41
Alignment explanation
Indices: 39380685--39380806 Score: 194
Period size: 40 Copynumber: 3.0 Consensus size: 41
39380675 AACTCGCACA
39380685 GAAATTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
1 GAAATTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
* *
39380726 GATA-TAGTAACTCGCACAAATGCCTTCGAGACTTAGCCC-
1 GAAATTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
* *
39380765 GAAATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCG
1 GAAATTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
39380806 G
1 G
39380807 TTATCATCCG
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
39 3 0.04
40 66 0.90
41 4 0.05
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (41 bp):
GAAATTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
Found at i:39380783 original size:99 final size:99
Alignment explanation
Indices: 39380591--39380783 Score: 273
Period size: 99 Copynumber: 1.9 Consensus size: 99
39380581 AGCCCGGTTA
* *
39380591 TAGTAACTCGCACAAATGCCTTCGAGACTTAGCCCGAAATTAGTCACTAGCACAAATGCCTTCGG
1 TAGTAACTCGCACAAATGCCTTCGAGACTTAGCCCGAAATTAGTAACTAGCACAAATGCCTTCGA
** *
39380656 GACTTAGCCCGGTTATAGTAACTCGCACAGAAAT
66 GACTTAGCCCGAATATAGTAACTAGCACAGAAAT
* * *
39380690 TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG-GATATAGTAACTCGCACAAATGCCTTCG
1 TAGTAACTCGCACAAATGCCTTCGAGACTTAGCCCGAAAT-TAGTAACTAGCACAAATGCCTTCG
*
39380754 AGACTTAGCCCGAA-ATTAGTCACTAGCACA
65 AGACTTAGCCCGAATA-TAGTAACTAGCACA
39380784 AATGCCTTCG
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
98 3 0.04
99 80 0.96
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (99 bp):
TAGTAACTCGCACAAATGCCTTCGAGACTTAGCCCGAAATTAGTAACTAGCACAAATGCCTTCGA
GACTTAGCCCGAATATAGTAACTAGCACAGAAAT
Found at i:39380806 original size:139 final size:139
Alignment explanation
Indices: 39380556--39380810 Score: 492
Period size: 139 Copynumber: 1.8 Consensus size: 139
39380546 AGATATAGCT
* *
39380556 ACTCGCTCAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGAGACTT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGAGACTT
39380621 AGCCCGAAATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAG
66 AGCCCGAAATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAG
39380686 AAATTAGTA
131 AAATTAGTA
39380695 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGAGACTT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGAGACTT
39380760 AGCCCGAAATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
66 AGCCCGAAATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
39380811 CATCCGGATA
Statistics
Matches: 114, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
139 114 1.00
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.24
Consensus pattern (139 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGAGACTT
AGCCCGAAATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAG
AAATTAGTA
Found at i:39386570 original size:33 final size:33
Alignment explanation
Indices: 39386547--39386682 Score: 108
Period size: 33 Copynumber: 4.4 Consensus size: 33
39386537 ACTCGAGGTG
39386547 TACATTTCCTTTTCAAATGGTACACACAAAGTA
1 TACATTTCCTTTTCAAATGGTACACACAAAGTA
*
39386580 TACCTTTCCTTTTCAAATGGTACA-A-AAAG--
1 TACATTTCCTTTTCAAATGGTACACACAAAGTA
* * * *
39386609 T--ATGT-CGTTTCAAGT-GTACACACAAAGTG
1 TACATTTCCTTTTCAAATGGTACACACAAAGTA
** ** * *
39386638 TACATAGCCTTTTCATGTAGTATACACAAAGTA
1 TACATTTCCTTTTCAAATGGTACACACAAAGTA
*
39386671 TACTTTTCCTTT
1 TACATTTCCTTT
39386683 CCACATTCGA
Statistics
Matches: 81, Mismatches: 14, Indels: 16
0.73 0.13 0.14
Matches are distributed among these distances:
25 5 0.06
26 9 0.11
27 6 0.07
29 2 0.02
31 6 0.07
32 9 0.11
33 44 0.54
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (33 bp):
TACATTTCCTTTTCAAATGGTACACACAAAGTA
Found at i:39388337 original size:103 final size:104
Alignment explanation
Indices: 39388093--39388358 Score: 419
Period size: 103 Copynumber: 2.6 Consensus size: 104
39388083 GTTGTACATA
** *
39388093 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCGATATCCACCGTATCT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
* **
39388158 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
66 CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
*
39388197 GAGGGGTTGCTAAGTGCTGATTCCCC-AGTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAAGTGCGATATCCACCGTATC
39388261 TCTGAAAT-AAAAAGGGGGTTGCTATGTGCTGATTCCCCC
65 TCTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
* * *
39388300 AAGGGGTTGCTAAGTGCTGATTCCCCGATTAAGTGGTGGTGCTAAGTGCGAGATCCACC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACC
39388359 AATAACGGTT
Statistics
Matches: 149, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
103 83 0.56
104 66 0.44
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.30
Consensus pattern (104 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
Found at i:39395820 original size:103 final size:104
Alignment explanation
Indices: 39395585--39395850 Score: 435
Period size: 103 Copynumber: 2.6 Consensus size: 104
39395575 GTTGTACATA
** *
39395585 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCGATATCCACCGTATCT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
* **
39395650 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
66 CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
*
39395689 GAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
39395754 CTGAAAT-AAAAAGGGGGTTGCTATGTGCTGATTCCCCC
66 CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
* * *
39395792 AAGGGGTTGCTAAGTGCTGATTCCCCGATTAAGTGGTGGTGCTAAGTGCGAGATCCACC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACC
39395851 AATAACGGTT
Statistics
Matches: 151, Mismatches: 11, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
103 84 0.56
104 67 0.44
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.30
Consensus pattern (104 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
Found at i:39397698 original size:20 final size:21
Alignment explanation
Indices: 39397658--39397698 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
39397648 GTGATTTCTC
*
39397658 TATTCTCTATCAATAACCTTT
1 TATTCTCTATCAATAAACTTT
*
39397679 TATTTTCTATC-ATAAACTTT
1 TATTCTCTATCAATAAACTTT
39397699 CAATTTACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.29, C:0.20, G:0.00, T:0.51
Consensus pattern (21 bp):
TATTCTCTATCAATAAACTTT
Found at i:39397704 original size:21 final size:21
Alignment explanation
Indices: 39397663--39397704 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
39397653 TTCTCTATTC
* *
39397663 TCTATCAATAACCTTTTATTT
1 TCTATCAATAAACTTTAATTT
39397684 TCTATC-ATAAACTTTCAATTT
1 TCTATCAATAAACTTT-AATTT
39397705 ACAACATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (21 bp):
TCTATCAATAAACTTTAATTT
Found at i:39399032 original size:10 final size:10
Alignment explanation
Indices: 39399005--39399054 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
39398995 TTAAATTCTA
*
39399005 AAAGATAAGT
1 AAAGATAAAT
39399015 ACAA-ATAAAT
1 A-AAGATAAAT
*
39399025 AAAGATAATT
1 AAAGATAAAT
39399035 AAAGATAAAT
1 AAAGATAAAT
39399045 GAAA-ATAAAT
1 -AAAGATAAAT
39399055 CCTAAAATGA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
9 2 0.06
10 27 0.79
11 5 0.15
ACGTcount: A:0.66, C:0.02, G:0.10, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:39408334 original size:29 final size:27
Alignment explanation
Indices: 39408316--39408378 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
39408306 ATATTAAGTC
*
39408316 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTACTATATAATCAACT
*
39408343 CGCACACTTAGTACTATATAATCAAACT
1 CGCACACTCAGTACTATATAATC-AACT
39408371 CGCACACT
1 CGCACACT
39408379 TAGTGCTGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
27 21 0.64
28 12 0.36
ACGTcount: A:0.35, C:0.30, G:0.10, T:0.25
Consensus pattern (27 bp):
CGCACACTCAGTACTATATAATCAACT
Found at i:39408378 original size:28 final size:28
Alignment explanation
Indices: 39408316--39408413 Score: 126
Period size: 28 Copynumber: 3.5 Consensus size: 28
39408306 ATATTAAGTC
*
39408316 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
39408343 CGCACACTTAGTACTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
39408371 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
39408400 CGCACACTTAGTGC
1 CGCACACTTAGTGC
39408414 CAATCTCATG
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
27 21 0.34
28 22 0.35
29 19 0.31
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:39411550 original size:18 final size:16
Alignment explanation
Indices: 39411515--39411545 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39411505 AGCAAAGCAA
*
39411515 AAAGTAGCAGAGAAAG
1 AAAGGAGCAGAGAAAG
39411531 AAAGGAGCAGAGAAA
1 AAAGGAGCAGAGAAA
39411546 AAGAAGAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.06, G:0.32, T:0.03
Consensus pattern (16 bp):
AAAGGAGCAGAGAAAG
Found at i:39414050 original size:20 final size:20
Alignment explanation
Indices: 39414025--39414121 Score: 135
Period size: 20 Copynumber: 4.8 Consensus size: 20
39414015 GAATAGGGGC
39414025 ACATGCCCGTGTGGCCT-GA
1 ACATGCCCGTGTGGCCTGGA
39414044 GACATGCCCGTGTGGCCTGGA
1 -ACATGCCCGTGTGGCCTGGA
* *
39414065 ACATGCCCATGTGGCCT-AA
1 ACATGCCCGTGTGGCCTGGA
39414084 GACATGCCCGTGTGGCCTGGA
1 -ACATGCCCGTGTGGCCTGGA
*
39414105 ACATGCCTGTGTGGCCT
1 ACATGCCCGTGTGGCCT
39414122 ACCCTTGGGC
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
19 1 0.01
20 65 0.94
21 3 0.04
ACGTcount: A:0.16, C:0.30, G:0.32, T:0.22
Consensus pattern (20 bp):
ACATGCCCGTGTGGCCTGGA
Found at i:39414080 original size:40 final size:40
Alignment explanation
Indices: 39414025--39414122 Score: 169
Period size: 40 Copynumber: 2.5 Consensus size: 40
39414015 GAATAGGGGC
*
39414025 ACATGCCCGTGTGGCCTGAGACATGCCCGTGTGGCCTGGA
1 ACATGCCCGTGTGGCCTAAGACATGCCCGTGTGGCCTGGA
*
39414065 ACATGCCCATGTGGCCTAAGACATGCCCGTGTGGCCTGGA
1 ACATGCCCGTGTGGCCTAAGACATGCCCGTGTGGCCTGGA
*
39414105 ACATGCCTGTGTGGCCTA
1 ACATGCCCGTGTGGCCTA
39414123 CCCTTGGGCA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.17, C:0.30, G:0.32, T:0.21
Consensus pattern (40 bp):
ACATGCCCGTGTGGCCTAAGACATGCCCGTGTGGCCTGGA
Found at i:39415103 original size:37 final size:39
Alignment explanation
Indices: 39415016--39415112 Score: 119
Period size: 40 Copynumber: 2.5 Consensus size: 39
39415006 CACACCAGAA
*
39415016 TGGCGACCAACGCCTCATCGGATAGTTCGAAGCAAATAAG
1 TGGCGACCAACGCCTCATCGGATAGTCCGAAGC-AATAAG
* * *
39415056 TGACGACCAACGTCTCATCGGCTAAG-CCGAAGC-A-AAG
1 TGGCGACCAACGCCTCATCGGAT-AGTCCGAAGCAATAAG
39415093 TGGCGACCAACGCCTCATCG
1 TGGCGACCAACGCCTCATCG
39415113 AATCTATATG
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
37 21 0.42
38 1 0.02
40 26 0.52
41 2 0.04
ACGTcount: A:0.30, C:0.30, G:0.25, T:0.15
Consensus pattern (39 bp):
TGGCGACCAACGCCTCATCGGATAGTCCGAAGCAATAAG
Done.