Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 142 of 356
Found at i:45772929 original size:29 final size:29
Alignment explanation
Indices: 45772895--45772968 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
45772885 TAATCAACCG
*
45772895 CGCACACTTAGTGCCATGTACTTT-AAACT
1 CGCACACTTAGTGCCATGCA-TTTCAAACT
**
45772924 CGCACACTTAGTGCCATGCATTTCAAGTT
1 CGCACACTTAGTGCCATGCATTTCAAACT
*
45772953 CGCACACCTAGTGCCA
1 CGCACACTTAGTGCCA
45772969 ATCTCACAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 3 0.08
29 37 0.93
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAACT
Found at i:45774954 original size:47 final size:47
Alignment explanation
Indices: 45774876--45775114 Score: 361
Period size: 47 Copynumber: 5.1 Consensus size: 47
45774866 CCCTTCGGGA
* * * * * * *
45774876 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
***
45774923 CCCGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
45774970 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTACGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
45775017 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
45775064 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
45775111 CTTA
1 CTTA
45775115 CTATCATTTC
Statistics
Matches: 174, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 174 1.00
ACGTcount: A:0.28, C:0.32, G:0.09, T:0.31
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:45775308 original size:47 final size:47
Alignment explanation
Indices: 45775230--45775562 Score: 522
Period size: 47 Copynumber: 7.1 Consensus size: 47
45775220 CCCTTCGGGA
* * * * * * *
45775230 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
***
45775277 CCCGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
45775324 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
45775371 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
45775418 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
45775465 CTTATTACATATATACACTTTCGCATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
45775512 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
45775559 CTTA
1 CTTA
45775563 CTATCATTTC
Statistics
Matches: 262, Mismatches: 24, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 262 1.00
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:45779039 original size:40 final size:40
Alignment explanation
Indices: 45778984--45779164 Score: 161
Period size: 40 Copynumber: 4.5 Consensus size: 40
45778974 AGCATGATTA
* * *
45778984 CTCTTCGGGATTTAGCACGGATATATCACTAGCACGAATG
1 CTCTTCGGAACTTAGCCCGGATATATCACTAGCACGAATG
* *
45779024 CTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAATG
1 CTCTTCGGAACTTAGCCCGGATATATCACTAGCACGAATG
* * * * * *
45779064 CTCTTTGGGACTTAGCCCGGATTTAGTAACTCGCACCAATG
1 CTCTTCGGAACTTAGCCCGGATATA-TCACTAGCACGAATG
* * * *
45779105 C-CTTCGGATCTTAGTCCGGATATGGTCACTTAGCAC-AAAG
1 CTCTTCGGAACTTAGCCCGGATAT-ATCAC-TAGCACGAATG
* *
45779145 -ACTTCGGGACTTAGCCCGGA
1 CTCTTCGGAACTTAGCCCGGA
45779165 CATCATTCGA
Statistics
Matches: 112, Mismatches: 25, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
40 95 0.85
41 17 0.15
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.27
Consensus pattern (40 bp):
CTCTTCGGAACTTAGCCCGGATATATCACTAGCACGAATG
Found at i:45779079 original size:80 final size:80
Alignment explanation
Indices: 45778969--45779126 Score: 192
Period size: 80 Copynumber: 2.0 Consensus size: 80
45778959 CGAATACACG
* * * *
45778969 TCACCAGCATGATTACTCTTCGGGATTTAGCACGGATATA-TCACTAGCACGAATGCTCTTCGGA
1 TCACCAGCATGAATACTCTTCGGGACTTAGCACGGATATAGTAACTAGCACCAATGC-CTTCGGA
45779033 ACTTAGCCCGGATACA
65 ACTTAGCCCGGATACA
* * * * * * *
45779049 TCACTAGCATGAATGCTCTTTGGGACTTAGCCCGGATTTAGTAACTCGCACCAATGCCTTCGGAT
1 TCACCAGCATGAATACTCTTCGGGACTTAGCACGGATATAGTAACTAGCACCAATGCCTTCGGAA
*
45779114 CTTAGTCCGGATA
66 CTTAGCCCGGATA
45779127 TGGTCACTTA
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
80 52 0.80
81 13 0.20
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (80 bp):
TCACCAGCATGAATACTCTTCGGGACTTAGCACGGATATAGTAACTAGCACCAATGCCTTCGGAA
CTTAGCCCGGATACA
Found at i:45779501 original size:29 final size:29
Alignment explanation
Indices: 45779469--45779542 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
45779459 AATTCAACCA
* *
45779469 CGCACACTTAGTGCCATGTACTTT-AAAAT
1 CGCACACTTAGTGCCATGCA-TTTCAAAAC
**
45779498 CGCACACTTAGTGCCATGCATTTCAAGCC
1 CGCACACTTAGTGCCATGCATTTCAAAAC
45779527 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
45779543 ATCTCACAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 3 0.08
29 37 0.93
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.26
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAAAC
Found at i:45779585 original size:43 final size:43
Alignment explanation
Indices: 45779524--45779626 Score: 206
Period size: 43 Copynumber: 2.4 Consensus size: 43
45779514 TGCATTTCAA
45779524 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
45779567 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
45779610 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
45779627 TGAAAACCAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.26, C:0.36, G:0.16, T:0.22
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:45781718 original size:47 final size:47
Alignment explanation
Indices: 45781640--45781878 Score: 352
Period size: 47 Copynumber: 5.1 Consensus size: 47
45781630 CCCTTCGGGA
* * * * * * *
45781640 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
***
45781687 CCCGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
45781734 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTACGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
45781781 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
45781828 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
45781875 CTTA
1 CTTA
45781879 CTATCATTTC
Statistics
Matches: 172, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 172 1.00
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:45782072 original size:47 final size:47
Alignment explanation
Indices: 45781994--45782279 Score: 419
Period size: 47 Copynumber: 6.1 Consensus size: 47
45781984 CCCTTCGGGA
* * * * * * *
45781994 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
***
45782041 CCCGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
45782088 CTTAACACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
45782135 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
45782182 CTTATTACATATATACACTTTCGCATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
45782229 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
45782276 CTTA
1 CTTA
45782280 CTATCATTTC
Statistics
Matches: 217, Mismatches: 22, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 217 1.00
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:45788548 original size:38 final size:38
Alignment explanation
Indices: 45788506--45788581 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
45788496 TGAACTTTTT
*
45788506 GGCTAGTTTTCTTTTGGATTTTGACTTTCGTTTTAGTA
1 GGCTAGTTTTCTTTTGGATTTGGACTTTCGTTTTAGTA
45788544 GGCTAGTTTTCTTTTGGATTTGGACTTTCGTTTTAGTA
1 GGCTAGTTTTCTTTTGGATTTGGACTTTCGTTTTAGTA
45788582 CTTACTTTGC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.13, C:0.11, G:0.22, T:0.54
Consensus pattern (38 bp):
GGCTAGTTTTCTTTTGGATTTGGACTTTCGTTTTAGTA
Found at i:45788933 original size:16 final size:17
Alignment explanation
Indices: 45788901--45788935 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
45788891 TTTGGGCTTC
*
45788901 AAAATTGTGTTTTAAAT
1 AAAATTGTGTCTTAAAT
45788918 AAAATTGT-TCTTAAAT
1 AAAATTGTGTCTTAAAT
45788934 AA
1 AA
45788936 TTTGAACAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.43
Consensus pattern (17 bp):
AAAATTGTGTCTTAAAT
Found at i:45790852 original size:70 final size:70
Alignment explanation
Indices: 45790772--45791143 Score: 602
Period size: 70 Copynumber: 5.3 Consensus size: 70
45790762 TAGTTTATTA
*
45790772 CTAATTAATATGCTGCTGTTATACTGTAAATTATTGGCTGTCCAAATTTGGACAAATTCATGGTG
1 CTAATTAATATGCTGCTGTTATACTGTAAATTATTGGCTGTCCAAATTAGGACAAATTCATGGTG
45790837 CTTAG
66 CTTAG
* * * *
45790842 CTAATGAATATGCTGCTGTTATACTATAAATTATTAGCTGTCAAAATTAGGACAAATTCATGGTG
1 CTAATTAATATGCTGCTGTTATACTGTAAATTATTGGCTGTCCAAATTAGGACAAATTCATGGTG
45790907 CTTAG
66 CTTAG
*
45790912 CTAATTAATATACTGCTGTTATACTGTAAATTATTGGCTGTCCAAATTAGGACAAATTCATGGTG
1 CTAATTAATATGCTGCTGTTATACTGTAAATTATTGGCTGTCCAAATTAGGACAAATTCATGGTG
45790977 CTTAG
66 CTTAG
* * *
45790982 CTAATTAATATTCTGCTGTTATACTTTAAATTATTGGCTGTCCAAATTAGGAAAAATTCATGGTG
1 CTAATTAATATGCTGCTGTTATACTGTAAATTATTGGCTGTCCAAATTAGGACAAATTCATGGTG
45791047 CTTAG
66 CTTAG
* * *
45791052 CTAACTAATATGCTGCTGTAATATTGTAAATTATTGGCTGTCCAAATTAGGACAAATTCATGGTG
1 CTAATTAATATGCTGCTGTTATACTGTAAATTATTGGCTGTCCAAATTAGGACAAATTCATGGTG
*
45791117 TTTAG
66 CTTAG
* *
45791122 CTAATTAAAATG-TGTTGTTATA
1 CTAATTAATATGCTGCTGTTATA
45791144 GATCAAGGAA
Statistics
Matches: 278, Mismatches: 24, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
69 8 0.03
70 270 0.97
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (70 bp):
CTAATTAATATGCTGCTGTTATACTGTAAATTATTGGCTGTCCAAATTAGGACAAATTCATGGTG
CTTAG
Found at i:45791707 original size:48 final size:48
Alignment explanation
Indices: 45791541--45791717 Score: 187
Period size: 48 Copynumber: 3.7 Consensus size: 48
45791531 TATGTGTGCT
* * * * *
45791541 AGTGTAAGACCATGTTTGGAACATGGCATCAGCCAC-ATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGAACATGACATCGGCCTCGA-CATGAGAGCC
* * * * *
45791589 AGTGTAAGACCATGTCTGAAACATGACATCGGCATCGAGACGAGAGCT
1 AGTGTAAGACCATGTCTGGAACATGACATCGGCCTCGACATGAGAGCC
*
45791637 AGTGTAAGACCATGTCTAGG-ACATGACATCGGCCTCGACATGTGAGCC
1 AGTGTAAGACCATGTCT-GGAACATGACATCGGCCTCGACATGAGAGCC
* * * *
45791685 AATGTAAGACCATGTTTGGGACATGGCATCGGC
1 AGTGTAAGACCATGTCTGGAACATGACATCGGC
45791718 GGTTTACCCT
Statistics
Matches: 108, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
47 2 0.02
48 104 0.96
49 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.21
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGAACATGACATCGGCCTCGACATGAGAGCC
Found at i:45791709 original size:96 final size:96
Alignment explanation
Indices: 45791538--45791717 Score: 229
Period size: 96 Copynumber: 1.9 Consensus size: 96
45791528 TGATATGTGT
* * * *
45791538 GCTAGTGTAAGACCATGTTTGGAACATGGCATCAGCCACATTATGAGAGCCAGTGTAAGACCATG
1 GCTAGTGTAAGACCATGTTAGGAACATGACATCAGCCACATCATGAGAGCCAATGTAAGACCATG
45791603 TCTGAAACATGACATCGGCATCGAGACGAGA
66 TCTGAAACATGACATCGGCATCGAGACGAGA
* * *
45791634 GCTAGTGTAAGACCATGTCTAGG-ACATGACATCGGCCTCGA-CATGTGAGCCAATGTAAGACCA
1 GCTAGTGTAAGACCATGT-TAGGAACATGACATCAGCCAC-ATCATGAGAGCCAATGTAAGACCA
* ** *
45791697 TGTTTGGGACATGGCATCGGC
64 TGTCTGAAACATGACATCGGC
45791718 GGTTTACCCT
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
96 67 0.94
97 4 0.06
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (96 bp):
GCTAGTGTAAGACCATGTTAGGAACATGACATCAGCCACATCATGAGAGCCAATGTAAGACCATG
TCTGAAACATGACATCGGCATCGAGACGAGA
Found at i:45791943 original size:11 final size:11
Alignment explanation
Indices: 45791929--45791957 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
45791919 AGAAATGATT
45791929 TTGTGATGACC
1 TTGTGATGACC
45791940 TTGTGATGACC
1 TTGTGATGACC
45791951 TTGTGAT
1 TTGTGAT
45791958 TATGGATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.17, C:0.14, G:0.28, T:0.41
Consensus pattern (11 bp):
TTGTGATGACC
Found at i:45794825 original size:227 final size:227
Alignment explanation
Indices: 45794425--45794837 Score: 781
Period size: 227 Copynumber: 1.8 Consensus size: 227
45794415 GTGTCTCTCA
45794425 TACTCATTTTACCTTGTTTATTATAGTACCACTTATATATTTATACCAAGATTATCATCTTACAA
1 TACTCATTTTACCTTGTTTATTATAGTACCACTTATATATTTATACCAAGATTATCATCTTACAA
*
45794490 AATATCTTCAGCTTAATCATCAAGCATTCATATTTAAAACTAGATCATATCTTTATAAAATACGA
66 AATATCTTCAGCTTAATCATCAAGCATTCATATTTAAAACTAGATCATATCTTTATAAAATACCA
* *
45794555 CAATTCCGATACGTAAAATAACATGTTTGCCTGAAACATTTCAATTCAACTCCATATCTGTTATT
131 CAATTCAGATACGTAAAATAACATGTTTGCCTAAAACATTTCAATTCAACTCCATATCTGTTATT
45794620 CTTTAATATTCCATTAGCGACCAAGTAGTCCT
196 CTTTAATATTCCATTAGCGACCAAGTAGTCCT
* *
45794652 TACTTATTTTACCTTGTTTATTATAGTACCACTTATATATTTATACCAGGATTATCATCTTACAA
1 TACTCATTTTACCTTGTTTATTATAGTACCACTTATATATTTATACCAAGATTATCATCTTACAA
45794717 AATATCTTCAGCTTAATCATCAAGCATTCATATTTAAAACTAGATCATATCTTTATAAAATACCA
66 AATATCTTCAGCTTAATCATCAAGCATTCATATTTAAAACTAGATCATATCTTTATAAAATACCA
45794782 CAATTCAGATACGTAAAATAACATGTTTGCCTAAAACATTTCAATTCAACTCCATA
131 CAATTCAGATACGTAAAATAACATGTTTGCCTAAAACATTTCAATTCAACTCCATA
45794838 CCCAACAAGC
Statistics
Matches: 181, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
227 181 1.00
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.38
Consensus pattern (227 bp):
TACTCATTTTACCTTGTTTATTATAGTACCACTTATATATTTATACCAAGATTATCATCTTACAA
AATATCTTCAGCTTAATCATCAAGCATTCATATTTAAAACTAGATCATATCTTTATAAAATACCA
CAATTCAGATACGTAAAATAACATGTTTGCCTAAAACATTTCAATTCAACTCCATATCTGTTATT
CTTTAATATTCCATTAGCGACCAAGTAGTCCT
Found at i:45796129 original size:4 final size:4
Alignment explanation
Indices: 45796083--45796110 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
45796073 CATGCGATGC
45796083 AATG AATG AATG AATG AATG AATG AATG
1 AATG AATG AATG AATG AATG AATG AATG
45796111 CATAAATGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
AATG
Found at i:45799544 original size:3 final size:3
Alignment explanation
Indices: 45799536--45799569 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
45799526 ACTAATTTAA
45799536 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
45799570 CAAACCAACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:45800091 original size:16 final size:16
Alignment explanation
Indices: 45800051--45800090 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
45800041 CTTTTTTTTC
45800051 TTTTTTTTTGCTGGAA
1 TTTTTTTTTGCTGGAA
**
45800067 AATTTTTTTGCT-GAA
1 TTTTTTTTTGCTGGAA
45800082 TTTTTTTTT
1 TTTTTTTTT
45800091 TTGCTCTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.15, C:0.05, G:0.12, T:0.68
Consensus pattern (16 bp):
TTTTTTTTTGCTGGAA
Found at i:45800402 original size:30 final size:30
Alignment explanation
Indices: 45800317--45800433 Score: 103
Period size: 30 Copynumber: 3.9 Consensus size: 30
45800307 TGTAATTTTT
* * **
45800317 AGAAAATTT-AGGGTTAAAATGCAATTTAA
1 AGAAAGTTTAAGGGTCAAAATAAAATTTAA
* * * * * *
45800346 GGAAAGTTTAGGGGCCTAAGTGAAATTTAA
1 AGAAAGTTTAAGGGTCAAAATAAAATTTAA
45800376 AGAAAGTTTAAGGGTCAAAATAAAATTTAGA
1 AGAAAGTTTAAGGGTCAAAATAAAATTTA-A
* *
45800407 A-AAAGTTTAGGGGTCAAAATACAATTT
1 AGAAAGTTTAAGGGTCAAAATAAAATTT
45800434 TTATTTTTTG
Statistics
Matches: 70, Mismatches: 16, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
29 7 0.10
30 61 0.87
31 2 0.03
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.28
Consensus pattern (30 bp):
AGAAAGTTTAAGGGTCAAAATAAAATTTAA
Found at i:45800465 original size:24 final size:25
Alignment explanation
Indices: 45800430--45800476 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
45800420 TCAAAATACA
*
45800430 ATTTTTATTTTTTGAAAATTTTTTT
1 ATTTTTATTTTTTGAAAAATTTTTT
45800455 ATTTTTATTTTTT-AAAAATTTT
1 ATTTTTATTTTTTGAAAAATTTT
45800477 GAAAATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (25 bp):
ATTTTTATTTTTTGAAAAATTTTTT
Found at i:45806498 original size:40 final size:40
Alignment explanation
Indices: 45806184--45806484 Score: 416
Period size: 40 Copynumber: 7.6 Consensus size: 40
45806174 AATGCTGTCT
* *
45806184 GGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA-ATCC
* * *
45806223 GGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATTCC
1 GGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATCC
45806263 GGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCC
45806302 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCC
* *
45806342 GGGTTAAGTCTCGAAGGCATTTGTGCGAGTTACTAAATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCC
*
45806382 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCC
* * *
45806422 GGGTTAAGTCCCGAAGGCATTTGTACGAATTACTATAA-CC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCC
*
45806462 GGGCTATGTCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTG
45806485 AACGAGGAGC
Statistics
Matches: 240, Mismatches: 15, Indels: 13
0.90 0.06 0.05
Matches are distributed among these distances:
39 51 0.21
40 179 0.75
41 10 0.04
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCC
Found at i:45812014 original size:39 final size:39
Alignment explanation
Indices: 45811947--45812242 Score: 468
Period size: 39 Copynumber: 7.5 Consensus size: 39
45811937 ACAAAATATG
* * * *
45811947 CGGGACTTTAAGCCCGAATATAATACCAGCAC-AAAGCCTA
1 CGGGAC-TT-AGCCCGGATATAACACCAGCACGAATGCCTT
45811987 CGGGACTTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGAC-TTAGCCCGGATATAACACCAGCACGAATGCCTT
*
45812027 CGGGGCTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
45812066 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
45812105 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
* *
45812144 TGGGACTTAGCCCGGATATAACACTAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
*
45812183 CGAGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
1 CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
* *
45812222 CCGGACTTAGCCCTGATATAA
1 CGGGACTTAGCCCGGATATAA
45812243 TTCTTCATTA
Statistics
Matches: 241, Mismatches: 14, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
39 221 0.92
40 20 0.08
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.19
Consensus pattern (39 bp):
CGGGACTTAGCCCGGATATAACACCAGCACGAATGCCTT
Found at i:45815529 original size:18 final size:19
Alignment explanation
Indices: 45815508--45815558 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
45815498 ATTGGACTAG
45815508 TAATTTAATATAA-ATATA
1 TAATTTAATATAATATATA
* *
45815526 TAATTATTATTTAATATATA
1 TAATT-TAATATAATATATA
45815546 TAA-TTAATATAAT
1 TAATTTAATATAAT
45815559 TATTTTTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
18 12 0.44
19 7 0.26
20 8 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TAATTTAATATAATATATA
Found at i:45815553 original size:24 final size:26
Alignment explanation
Indices: 45815510--45815563 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
45815500 TGGACTAGTA
45815510 ATTTAATATAAATATATAAT-T-ATT
1 ATTTAATATAAATATATAATATAATT
*
45815534 ATTTAATATATATA-ATTAATATAATT
1 ATTTAATATAAATATA-TAATATAATT
45815560 ATTT
1 ATTT
45815564 TTATAACATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 1 0.04
24 17 0.65
25 1 0.04
26 7 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
ATTTAATATAAATATATAATATAATT
Found at i:45815574 original size:26 final size:29
Alignment explanation
Indices: 45815523--45815575 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
45815513 TAATATAAAT
*
45815523 ATATAATTATTATTTAATATATATAATTA
1 ATATAATTATTATTTAATATACATAATTA
45815552 ATATAATTATT-TTT-ATA-ACATAAT
1 ATATAATTATTATTTAATATACATAAT
45815576 ATATTCAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 6 0.26
27 3 0.13
28 3 0.13
29 11 0.48
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (29 bp):
ATATAATTATTATTTAATATACATAATTA
Found at i:45826150 original size:105 final size:101
Alignment explanation
Indices: 45825972--45826166 Score: 241
Period size: 105 Copynumber: 1.9 Consensus size: 101
45825962 AATTGACGGA
* *
45825972 TAAGACCATGGTTGGACCATGGCAATATTTAAATGTAAAACCATAGCTGGGCTATGGCATTTCAG
1 TAAGACCATGGTTGGACCATGGCAATATATAAATGTAAAACCATAGCTGGGCTATGGCATTTCAA
* *
45826037 TGAAAAGACTATAATTGGGTTATGGCACCGTGAACG
66 TGAAAAGACCATAAATGGGTTATGGCACCGTGAACG
*** * *
45826073 TAAGACCATGGTTGGACCATGGCAGTAAATATATGTGTGTAAGACCATAGCTGGGTTATGGCA-T
1 TAAGACCATGGTTGGACCATGGC----AATATATAAATGTAAAACCATAGCTGGGCTATGGCATT
45826137 TCTAAT-AGAAAGACCATAAATGGGTTATGG
62 TC-AATGA-AAAGACCATAAATGGGTTATGG
45826167 TGCTATGAGA
Statistics
Matches: 79, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
101 23 0.29
104 4 0.05
105 52 0.66
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (101 bp):
TAAGACCATGGTTGGACCATGGCAATATATAAATGTAAAACCATAGCTGGGCTATGGCATTTCAA
TGAAAAGACCATAAATGGGTTATGGCACCGTGAACG
Found at i:45826671 original size:2 final size:2
Alignment explanation
Indices: 45826664--45826690 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
45826654 ATTATGAATG
45826664 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
45826691 TATATATATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:45828536 original size:25 final size:26
Alignment explanation
Indices: 45828498--45828547 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
45828488 GGACCCACCA
45828498 CAACTCATATGAGCTTATCG-ATTTG
1 CAACTCATATGAGCTTATCGTATTTG
45828523 CAACTCATGA-GAGCTTATCGTATTT
1 CAACTCAT-ATGAGCTTATCGTATTT
45828548 TAGCTCGGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (26 bp):
CAACTCATATGAGCTTATCGTATTTG
Found at i:45833138 original size:54 final size:53
Alignment explanation
Indices: 45832972--45833262 Score: 241
Period size: 54 Copynumber: 5.2 Consensus size: 53
45832962 TACAAAAATC
*
45832972 CAGTATTTAAAAGAAAAATTTTGGTGCTGGCCTGTCAATGGCTAGCACCAGACT
1 CAGTATTTAAAA-AAAAAATTTGGTGCTGGCCTGTCAATGGCTAGCACCAGACT
* *
45833026 TAGTATTTAAAAAAAAAATCTTTTTTTTGTGCTGGCCTGTCAATGGCTAGCACCAGACT
1 CAGTATTTAAAAAAAAAA------TTTGGTGCTGGCCTGTCAATGGCTAGCACCAGACT
* * *
45833085 CAGTATTTTAAAAAAAAAATTTGGTGCTGGCCTGTCAATTG-TCGGCACTAGACT
1 CAGTA-TTTAAAAAAAAAATTTGGTGCTGGCCTGTCAATGGCT-AGCACCAGACT
* **
45833139 CAATATTTTAAAATATATATATATATTTTGGTTTTGGCCTGTCAATGG-TCAGCACCAGACT
1 CAGTA-TTTAAAA-A-A-A-A-A-A-TTTGGTGCTGGCCTGTCAATGGCT-AGCACCAGACT
* * **
45833200 ACCAGCATTT-AAAAAAAAA-TT-GTGTTGGCCTGTCAATGGCGGGCACCAGACT
1 --CAGTATTTAAAAAAAAAATTTGGTGCTGGCCTGTCAATGGCTAGCACCAGACT
*
45833252 CAATATTTAAA
1 CAGTATTTAAA
45833263 TTTTTCTTTT
Statistics
Matches: 197, Mismatches: 21, Indels: 41
0.76 0.08 0.16
Matches are distributed among these distances:
50 6 0.03
51 2 0.01
52 27 0.14
53 8 0.04
54 52 0.26
55 2 0.01
56 2 0.01
57 2 0.01
58 2 0.01
59 40 0.20
60 15 0.08
61 33 0.17
62 3 0.02
63 3 0.02
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (53 bp):
CAGTATTTAAAAAAAAAATTTGGTGCTGGCCTGTCAATGGCTAGCACCAGACT
Found at i:45833214 original size:113 final size:112
Alignment explanation
Indices: 45832971--45833331 Score: 313
Period size: 113 Copynumber: 3.2 Consensus size: 112
45832961 ATACAAAAAT
** * *
45832971 CCAGTA-TTTAAAAGAAAAATTTTGGTGCTGGCCTGTCAATGGCTAGCACCAGACTTAGTATTTA
1 CCAGTATTTTAAAA-AAAAA--TT-GTGCTGGCCTGTCAATGGCGGGCACCAGACTCAATATTTA
* * ** * * * **
45833035 AAAAAAAAATCT-TTTTTTTGTGCTGGCCTGTCAATGGCTAGCACCAGACT-
62 AATATATCATATATATTTTAGTTTTGGCCTGTCAATGGC-AGCACCAGACTA
* *
45833085 -CAGTATTTTAAAAAAAAAATTTGGTGCTGGCCTGTCAATTGTC-GGCACTAGACTCAATATTTT
1 CCAGTATTTT-AAAAAAAAA-TT-GTGCTGGCCTGTCAA-TGGCGGGCACCAGACTCAATA-TTT
*
45833148 AAAATATAT-ATATATATTTTGGTTTTGGCCTGTCAATGGTCAGCACCAGACTA
61 -AAATATATCATATATATTTTAGTTTTGGCCTGTCAATGG-CAGCACCAGACTA
* * *
45833201 CCAGCA-TTTAAAAAAAAATTGTGTTGGCCTGTCAATGGCGGGCACCAGACTCAATATTTAAATT
1 CCAGTATTTTAAAAAAAAATTGTGCTGGCCTGTCAATGGCGGGCACCAGACTCAATATTTAAATA
* * * * * * * *
45833265 TTTCTTTTTTTTTTTAGTTTTGGCCTATCAATGGCCGGCACTAGACTA
66 TATCATATATATTTTAGTTTTGGCCTGTCAATGG-CAGCACCAGACTA
45833313 CCAGTATTTTAAAAAAAAA
1 CCAGTATTTTAAAAAAAAA
45833332 ATCTTTTTGA
Statistics
Matches: 206, Mismatches: 29, Indels: 25
0.79 0.11 0.10
Matches are distributed among these distances:
111 6 0.03
112 46 0.22
113 77 0.37
114 19 0.09
115 50 0.24
116 4 0.02
117 4 0.02
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (112 bp):
CCAGTATTTTAAAAAAAAATTGTGCTGGCCTGTCAATGGCGGGCACCAGACTCAATATTTAAATA
TATCATATATATTTTAGTTTTGGCCTGTCAATGGCAGCACCAGACTA
Found at i:45833518 original size:54 final size:55
Alignment explanation
Indices: 45833403--45833588 Score: 150
Period size: 54 Copynumber: 3.4 Consensus size: 55
45833393 TTTTAAAAAA
** * ** * *
45833403 ACTGAGTCTGGTGCCAGCCATTGACAGGCCAGCA-CAAAAAA-A--ATTTAAAAT
1 ACTGAGTCTGGTGCTGGCCATTGACAAGTAAGCACCAAAAAAGATTTTTTTAAAT
* * * ***
45833454 ATTGAGTCTGGTGCTGGCCATTGAGAAGTCAGCACC-AAAATTTTTTTTTTAAAT
1 ACTGAGTCTGGTGCTGGCCATTGACAAGTAAGCACCAAAAAAGATTTTTTTAAAT
* *
45833508 ACTGAGTCTGGTG-TCGACCATTGACAGGTAAGCACCAAAAAAAAGATTTTTTTAAAT
1 ACTGAGTCTGGTGCT-GGCCATTGACAAGTAAGCACC--AAAAAAGATTTTTTTAAAT
* *
45833565 ACTGAGTCTAGTGCCGGCCATTGA
1 ACTGAGTCTGGTGCTGGCCATTGA
45833589 TAGGCCGACA
Statistics
Matches: 105, Mismatches: 21, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
51 32 0.30
52 1 0.01
53 1 0.01
54 36 0.34
57 35 0.33
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (55 bp):
ACTGAGTCTGGTGCTGGCCATTGACAAGTAAGCACCAAAAAAGATTTTTTTAAAT
Found at i:45834304 original size:24 final size:25
Alignment explanation
Indices: 45834264--45834311 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
45834254 CTCTTGAGAG
45834264 CTTACCGTATTTCAGCTCGAAAGAA
1 CTTACCGTATTTCAGCTCGAAAGAA
*
45834289 CTTACC-TATTAT-AGCTCGTAAGA
1 CTTACCGTATT-TCAGCTCGAAAGA
45834312 GCATACATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (25 bp):
CTTACCGTATTTCAGCTCGAAAGAA
Found at i:45836265 original size:27 final size:26
Alignment explanation
Indices: 45836214--45836265 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
45836204 GTTATAAAAT
*
45836214 AAAGAGAAATTGAGAGAATAAAGAAC
1 AAAGAGAAATTGAAAGAATAAAGAAC
*
45836240 AAAGA-AAATATGAAAGTAATAGAGAA
1 AAAGAGAAAT-TGAAAG-AATAAAGAA
45836266 TGTACTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 4 0.18
26 10 0.45
27 8 0.36
ACGTcount: A:0.63, C:0.02, G:0.21, T:0.13
Consensus pattern (26 bp):
AAAGAGAAATTGAAAGAATAAAGAAC
Found at i:45836603 original size:23 final size:23
Alignment explanation
Indices: 45836560--45836609 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
45836550 TAGTTTACTA
* * *
45836560 ATTTTTAATATTTTAATTAAATT
1 ATTTTTAATATTTAAAATAAAAT
45836583 ATTTTTAAT-TATTAAAATAAAAT
1 ATTTTTAATAT-TTAAAATAAAAT
45836606 ATTT
1 ATTT
45836610 GAAGGAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTTTTAATATTTAAAATAAAAT
Found at i:45837059 original size:13 final size:13
Alignment explanation
Indices: 45837041--45837079 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
45837031 AAATTTATCG
45837041 ATATTTAAAAATA
1 ATATTTAAAAATA
45837054 ATATTTAATAAAT-
1 ATATTTAA-AAATA
*
45837067 ATATATAAAAATA
1 ATATTTAAAAATA
45837080 TTTATAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
12 4 0.17
13 15 0.65
14 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATATTTAAAAATA
Found at i:45837079 original size:23 final size:25
Alignment explanation
Indices: 45837049--45837129 Score: 89
Period size: 25 Copynumber: 3.4 Consensus size: 25
45837039 CGATATTTAA
*
45837049 AAATAATATTTAATAAATA-TATAT
1 AAATAATATTTAATAAATATTACAT
45837073 AAA-AATATTT-AT-AATATTACAT
1 AAATAATATTTAATAAATATTACAT
* * *
45837095 AAATGATATTTAATAAATTTTAAAT
1 AAATAATATTTAATAAATATTACAT
*
45837120 ATATAATATT
1 AAATAATATT
45837130 CATCAATTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
21 4 0.09
22 9 0.19
23 13 0.28
24 5 0.11
25 16 0.34
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (25 bp):
AAATAATATTTAATAAATATTACAT
Found at i:45837087 original size:32 final size:33
Alignment explanation
Indices: 45837051--45837127 Score: 90
Period size: 32 Copynumber: 2.4 Consensus size: 33
45837041 ATATTTAAAA
45837051 ATAATATTTAATAAAT-ATATATAA-AAATATTT
1 ATAATATTTAATAAATGATATATAATAAAT-TTT
*
45837083 ATAATA-TTACATAAATGATATTTAATAAATTTT
1 ATAATATTTA-ATAAATGATATATAATAAATTTT
*
45837116 A-AATATATAATA
1 ATAATATTTAATA
45837128 TTCATCAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
31 3 0.08
32 19 0.49
33 13 0.33
34 4 0.10
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (33 bp):
ATAATATTTAATAAATGATATATAATAAATTTT
Found at i:45837110 original size:14 final size:14
Alignment explanation
Indices: 45837040--45837112 Score: 51
Period size: 13 Copynumber: 5.0 Consensus size: 14
45837030 TAAATTTATC
45837040 GATATTTAA-AAAT
1 GATATTTAATAAAT
*
45837053 AATATTTAATAAAT
1 GATATTTAATAAAT
* *
45837067 -ATATATAAAAATATT
1 GATATTTAATAA-A-T
*
45837082 TATAATATTACATAAAT
1 GAT-AT-TTA-ATAAAT
45837099 GATATTTAATAAAT
1 GATATTTAATAAAT
45837113 TTTAAATATA
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
13 17 0.36
14 11 0.23
15 4 0.09
16 4 0.09
17 5 0.11
18 3 0.06
19 3 0.06
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (14 bp):
GATATTTAATAAAT
Found at i:45837951 original size:14 final size:14
Alignment explanation
Indices: 45837934--45837963 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
45837924 TTTTTTAGTT
45837934 TATATAATATGAAA
1 TATATAATATGAAA
45837948 TATATAATATGAAA
1 TATATAATATGAAA
45837962 TA
1 TA
45837964 AAAACAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (14 bp):
TATATAATATGAAA
Found at i:45840962 original size:25 final size:24
Alignment explanation
Indices: 45840942--45841004 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 24
45840932 AGCCATAATT
*
45840942 GGGAAGTTCACAAAGAACCATATC
1 GGGAAGCTCACAAAGAACCATATC
* *
45840966 GGGAAGCTCACGAAGAGCC-TATC
1 GGGAAGCTCACAAAGAACCATATC
**
45840989 AAGAAGCTCACAAAGA
1 GGGAAGCTCACAAAGA
45841005 GCTATGTAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 17 0.52
24 16 0.48
ACGTcount: A:0.41, C:0.22, G:0.24, T:0.13
Consensus pattern (24 bp):
GGGAAGCTCACAAAGAACCATATC
Found at i:45843405 original size:43 final size:44
Alignment explanation
Indices: 45843305--45843443 Score: 119
Period size: 43 Copynumber: 3.2 Consensus size: 44
45843295 ACTGCTAATA
* * ** * *
45843305 TGTTGTGCATCCACAACCTAGTGGTAGCTTTTA-CAGAC-AATTA
1 TGTTGTGTATCCACAACCTAGTGGAAAATTTTATCTG-CGAATTT
* * *
45843348 TGTTGTGCATCCACAGTCC-AGTGGCAAATTTTATCTGCGAATTT
1 TGTTGTGTATCCACA-ACCTAGTGGAAAATTTTATCTGCGAATTT
*
45843392 TGTTGTGTA-CCACAACCTAGTGGAAAATTTTATTTGCG-ATTT
1 TGTTGTGTATCCACAACCTAGTGGAAAATTTTATCTGCGAATTT
45843434 T-TCTGTGTAT
1 TGT-TGTGTAT
45843444 TCATAGCTCA
Statistics
Matches: 80, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
41 1 0.01
42 13 0.16
43 50 0.62
44 16 0.20
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.38
Consensus pattern (44 bp):
TGTTGTGTATCCACAACCTAGTGGAAAATTTTATCTGCGAATTT
Found at i:45843509 original size:44 final size:44
Alignment explanation
Indices: 45843351--45843509 Score: 142
Period size: 43 Copynumber: 3.7 Consensus size: 44
45843341 ACAATTATGT
* * * *
45843351 TGTGCATCCACAGTCCAGTGGCAAATTTTATCTGCGAATTTTGT
1 TGTGTATCCACAGCCCAGTGGTAAATTTTATCTGCGAATTTTGC
* * * * *
45843395 TGTGTA-CCACAACCTAGTGGAAAATTTTATTTGCG-ATTTTTC
1 TGTGTATCCACAGCCCAGTGGTAAATTTTATCTGCGAATTTTGC
* * * * ** *
45843437 TGTGTATTCATAGCTCATTGGTTGATTTTATCTACGAATTTTGC
1 TGTGTATCCACAGCCCAGTGGTAAATTTTATCTGCGAATTTTGC
* *
45843481 TATGTATCCACAGCCCAGTGGTGAATTTT
1 TGTGTATCCACAGCCCAGTGGTAAATTTT
45843510 TTTACAAACC
Statistics
Matches: 86, Mismatches: 27, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
42 11 0.13
43 42 0.49
44 33 0.38
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (44 bp):
TGTGTATCCACAGCCCAGTGGTAAATTTTATCTGCGAATTTTGC
Found at i:45844060 original size:27 final size:27
Alignment explanation
Indices: 45844030--45844081 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
45844020 GTTTTTTTAA
*
45844030 ATGT-TAAAATATAGATTTTAATTAATT
1 ATGTGTAAAATAGAGATTTT-ATTAATT
*
45844057 ATGTGTTAAATAGAGATTTTATTAA
1 ATGTGTAAAATAGAGATTTTATTAA
45844082 AATTATGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (27 bp):
ATGTGTAAAATAGAGATTTTATTAATT
Found at i:45846400 original size:30 final size:29
Alignment explanation
Indices: 45846364--45846424 Score: 86
Period size: 30 Copynumber: 2.1 Consensus size: 29
45846354 TCCTTTTACT
** *
45846364 AATAGCTAATTATGGTCTTTGTTGTTTTCA
1 AATAGCTAATTATGCACTATGTTG-TTTCA
45846394 AATAGCTAATTATGCACTATGTTGTTTCA
1 AATAGCTAATTATGCACTATGTTGTTTCA
45846423 AA
1 AA
45846425 CATCAATCTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 7 0.25
30 21 0.75
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (29 bp):
AATAGCTAATTATGCACTATGTTGTTTCA
Found at i:45849041 original size:15 final size:15
Alignment explanation
Indices: 45849021--45849088 Score: 64
Period size: 15 Copynumber: 4.2 Consensus size: 15
45849011 TTAAATATAT
45849021 TTAAAAATATAAAAA
1 TTAAAAATATAAAAA
*
45849036 TTAAAAATAAAAAAA
1 TTAAAAATATAAAAA
*
45849051 TTATAAAAATAAATAAAAG
1 -T-TAAAAAT--ATAAAAA
*
45849070 TAAAAAATATATAAAA
1 TTAAAAATATA-AAAA
45849086 TTA
1 TTA
45849089 TATATATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
15 17 0.40
16 6 0.14
17 13 0.31
18 1 0.02
19 5 0.12
ACGTcount: A:0.72, C:0.00, G:0.01, T:0.26
Consensus pattern (15 bp):
TTAAAAATATAAAAA
Found at i:45849059 original size:17 final size:17
Alignment explanation
Indices: 45849022--45849090 Score: 72
Period size: 17 Copynumber: 4.1 Consensus size: 17
45849012 TAAATATATT
*
45849022 TAAAAATATAAAAA-T-
1 TAAAAATAAAAAAATTA
45849037 TAAAAATAAAAAAATTA
1 TAAAAATAAAAAAATTA
*
45849054 TAAAAATAAATAAAAGTA
1 TAAAAATAAA-AAAATTA
*
45849072 -AAAAATATATAAAATTA
1 TAAAAATA-AAAAAATTA
45849089 TA
1 TA
45849091 TATATAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
15 13 0.29
16 1 0.02
17 23 0.51
18 8 0.18
ACGTcount: A:0.72, C:0.00, G:0.01, T:0.26
Consensus pattern (17 bp):
TAAAAATAAAAAAATTA
Found at i:45849066 original size:10 final size:9
Alignment explanation
Indices: 45849022--45849085 Score: 50
Period size: 8 Copynumber: 7.6 Consensus size: 9
45849012 TAAATATATT
45849022 TAAAAAT-A
1 TAAAAATAA
45849030 TAAAAAT--
1 TAAAAATAA
45849037 TAAAAATAA
1 TAAAAATAA
*
45849046 -AAAAATTA
1 TAAAAATAA
45849054 TAAAAATAAA
1 TAAAAAT-AA
*
45849064 TAAAAGT-A
1 TAAAAATAA
45849072 -AAAAATATA
1 TAAAAATA-A
45849081 TAAAA
1 TAAAA
45849086 TTATATATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
7 12 0.27
8 15 0.33
9 7 0.16
10 11 0.24
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (9 bp):
TAAAAATAA
Found at i:45849099 original size:21 final size:21
Alignment explanation
Indices: 45849075--45849115 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
45849065 AAAAGTAAAA
45849075 AATATATAAAATTATATATAT
1 AATATATAAAATTATATATAT
* * *
45849096 AATATCTACAATTTTATATA
1 AATATATAAAATTATATATA
45849116 CTTCAGTTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (21 bp):
AATATATAAAATTATATATAT
Found at i:45849549 original size:23 final size:23
Alignment explanation
Indices: 45849523--45849585 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
45849513 ATATTTTACG
* *
45849523 GATGAATCGCCAGTAGATTTGCA
1 GATGAATCGCAAGTAGATATGCA
* * *
45849546 GATGAATTGCTAGTAGATATGCG
1 GATGAATCGCAAGTAGATATGCA
*
45849569 GATAAATCGCAAGTAGA
1 GATGAATCGCAAGTAGA
45849586 ACTTCCTCCT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.35, C:0.13, G:0.27, T:0.25
Consensus pattern (23 bp):
GATGAATCGCAAGTAGATATGCA
Found at i:45852821 original size:47 final size:47
Alignment explanation
Indices: 45852770--45852935 Score: 212
Period size: 47 Copynumber: 3.5 Consensus size: 47
45852760 GTGTATATGA
45852770 GATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGT
1 GATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGT
* *
45852817 GATAAGGCCGAATGGCCAATGTGATGAATATGAACATGCATATATGT
1 GATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGT
* * *
45852864 GATAAGGCCGAATGGCTAATGTGA-AATATGTATGAGATATGCATATGTG-
1 GATAAGGCCGAATGGCCAATGTGATGA-ATG--TGA-ACATGCATATGTGT
* *
45852913 G-TAAAGCCGAATGGTCAATGTGA
1 GATAAGGCCGAATGGCCAATGTGA
45852936 AATATATATA
Statistics
Matches: 105, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
46 1 0.01
47 70 0.67
48 19 0.18
49 4 0.04
50 11 0.10
ACGTcount: A:0.34, C:0.11, G:0.28, T:0.26
Consensus pattern (47 bp):
GATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATGTGT
Found at i:45852950 original size:50 final size:48
Alignment explanation
Indices: 45852857--45853041 Score: 264
Period size: 48 Copynumber: 3.8 Consensus size: 48
45852847 TGAACATGCA
* *
45852857 TATATGTGATAAGGCCGAATGGCTAATGTGAAATATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
* *
45852905 CATATGTGGTAAAGCCGAATGG-TCAATGTGAAATATATATATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCT-AATGTG-AA-ATATGTATGAGATATG
* * *
45852955 TATATGTTGTAAAGCCGAATGGCTAGTGTGAACTATGTATGAGATATG
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
*
45853003 TATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTA
1 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTA
45853042 GGCGATGTGC
Statistics
Matches: 122, Mismatches: 11, Indels: 8
0.87 0.08 0.06
Matches are distributed among these distances:
47 1 0.01
48 76 0.62
49 4 0.03
50 40 0.33
51 1 0.01
ACGTcount: A:0.35, C:0.08, G:0.26, T:0.31
Consensus pattern (48 bp):
TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
Found at i:45852977 original size:98 final size:98
Alignment explanation
Indices: 45852761--45853038 Score: 290
Period size: 98 Copynumber: 2.9 Consensus size: 98
45852751 TGTGATTGTG
* * * * *
45852761 TGTATATGAGATAAGGCCGAATGGCCAATGTGATGA-ATG--TGA-ACATGCATATGTGTGATAA
1 TGTATATGTGATAAAGCCGAATGGCTAATGTGA-AATATGTATGAGATATGCATATGTG-G-TAA
* * * *
45852822 GGCCGAATGGCCAATGTG--AT-GA-ATATGA-ACA
63 AGCCGAATGGCTAATGTGAAATATATATATGAGATA
*
45852853 TGCATATATGTGATAAGGCCGAATGGCTAATGTGAAATATGTATGAGATATGCATATGTGGTAAA
1 TG--TATATGTGATAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGCATATGTGGTAAA
45852918 GCCGAATGG-TCAATGTGAAATATATATATGAGATA
64 GCCGAATGGCT-AATGTGAAATATATATATGAGATA
* * *
45852953 TGTATATGTTG-TAAAGCCGAATGGCTAGTGTGAACTATGTATGAGATATGTATATGTGGTAAAG
1 TGTATATG-TGATAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGCATATGTGGTAAAG
*
45853017 CCGAATGGCTAGTGTGAAATAT
65 CCGAATGGCTAATGTGAAATAT
45853039 GTAGGCGATG
Statistics
Matches: 159, Mismatches: 13, Indels: 22
0.82 0.07 0.11
Matches are distributed among these distances:
92 2 0.01
93 1 0.01
94 32 0.20
95 18 0.11
96 4 0.03
97 14 0.09
98 75 0.47
99 9 0.06
100 4 0.03
ACGTcount: A:0.35, C:0.09, G:0.27, T:0.29
Consensus pattern (98 bp):
TGTATATGTGATAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGCATATGTGGTAAAGC
CGAATGGCTAATGTGAAATATATATATGAGATA
Found at i:45853232 original size:37 final size:37
Alignment explanation
Indices: 45853177--45853294 Score: 184
Period size: 37 Copynumber: 3.2 Consensus size: 37
45853167 ACATGAAACT
*
45853177 TGGAAATATATTCCGGGTAAGACCCGATGACTACGTG
1 TGGAGATATATTCCGGGTAAGACCCGATGACTACGTG
45853214 TGGAGATATATTCCGGGTAAGACCCGATGACTACGTG
1 TGGAGATATATTCCGGGTAAGACCCGATGACTACGTG
* * *
45853251 TGGAGAT-TTTGTCCGGGTAAGACCCGATAACTCCGTG
1 TGGAGATATAT-TCCGGGTAAGACCCGATGACTACGTG
45853288 TGGAGAT
1 TGGAGAT
45853295 TTTGTCTGAG
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
36 2 0.03
37 74 0.97
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
TGGAGATATATTCCGGGTAAGACCCGATGACTACGTG
Found at i:45855361 original size:21 final size:22
Alignment explanation
Indices: 45855336--45855377 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
45855326 CAAAAATACT
*
45855336 TCTCTCCCCT-TTATTTCTCCC
1 TCTCTCACCTCTTATTTCTCCC
45855357 TCTCTCACCTCTTATTTCTCC
1 TCTCTCACCTCTTATTTCTCC
45855378 ACAAAATAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.07, C:0.45, G:0.00, T:0.48
Consensus pattern (22 bp):
TCTCTCACCTCTTATTTCTCCC
Found at i:45861817 original size:29 final size:29
Alignment explanation
Indices: 45861781--45861885 Score: 158
Period size: 29 Copynumber: 3.6 Consensus size: 29
45861771 TAATCAACCG
45861781 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGTACTTTAAACT
* * **
45861810 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGTACTTT-AAACT
45861839 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGTACTTTAAACT
45861868 CGCACACTTAGTGCCATG
1 CGCACACTTAGTGCCATG
45861886 CATTTCAAGT
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.05
29 60 0.91
30 3 0.05
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.30
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGTACTTTAAACT
Found at i:45861849 original size:58 final size:58
Alignment explanation
Indices: 45861781--45861906 Score: 243
Period size: 58 Copynumber: 2.2 Consensus size: 58
45861771 TAATCAACCG
45861781 CGCACACTTAGTGCCATGTACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTT
1 CGCACACTTAGTGCCATGTACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTT
*
45861839 CGCACACTTAGTGCCATGTACTTTAAACTCGCACACTTAGTGCCATGCATTTCAAGTT
1 CGCACACTTAGTGCCATGTACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTT
45861897 CGCACACTTA
1 CGCACACTTA
45861907 CCTTTTCTGC
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
58 67 1.00
ACGTcount: A:0.27, C:0.29, G:0.14, T:0.30
Consensus pattern (58 bp):
CGCACACTTAGTGCCATGTACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTT
Found at i:45861899 original size:29 final size:29
Alignment explanation
Indices: 45861781--45861906 Score: 157
Period size: 29 Copynumber: 4.3 Consensus size: 29
45861771 TAATCAACCG
*
45861781 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
45861810 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
*
45861839 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
**
45861868 CGCACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
45861897 CGCACACTTA
1 CGCACACTTA
45861907 CCTTTTCTGC
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
28 6 0.07
29 74 0.89
30 3 0.04
ACGTcount: A:0.27, C:0.29, G:0.14, T:0.30
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:45863710 original size:29 final size:29
Alignment explanation
Indices: 45863674--45863778 Score: 158
Period size: 29 Copynumber: 3.6 Consensus size: 29
45863664 TAATCAACCG
45863674 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGTACTTTAAACT
* * **
45863703 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGTACTTT-AAACT
45863732 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGTACTTTAAACT
45863761 CGCACACTTAGTGCCATG
1 CGCACACTTAGTGCCATG
45863779 CATTTCAAGT
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.05
29 60 0.91
30 3 0.05
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.30
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGTACTTTAAACT
Found at i:45863742 original size:58 final size:58
Alignment explanation
Indices: 45863674--45863799 Score: 243
Period size: 58 Copynumber: 2.2 Consensus size: 58
45863664 TAATCAACCG
45863674 CGCACACTTAGTGCCATGTACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTT
1 CGCACACTTAGTGCCATGTACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTT
*
45863732 CGCACACTTAGTGCCATGTACTTTAAACTCGCACACTTAGTGCCATGCATTTCAAGTT
1 CGCACACTTAGTGCCATGTACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTT
45863790 CGCACACTTA
1 CGCACACTTA
45863800 CCTTTTCTGC
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
58 67 1.00
ACGTcount: A:0.27, C:0.29, G:0.14, T:0.30
Consensus pattern (58 bp):
CGCACACTTAGTGCCATGTACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTT
Found at i:45863792 original size:29 final size:29
Alignment explanation
Indices: 45863674--45863799 Score: 157
Period size: 29 Copynumber: 4.3 Consensus size: 29
45863664 TAATCAACCG
*
45863674 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
45863703 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
*
45863732 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
**
45863761 CGCACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
45863790 CGCACACTTA
1 CGCACACTTA
45863800 CCTTTTCTGC
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
28 6 0.07
29 74 0.89
30 3 0.04
ACGTcount: A:0.27, C:0.29, G:0.14, T:0.30
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:45863940 original size:29 final size:29
Alignment explanation
Indices: 45863901--45863977 Score: 104
Period size: 29 Copynumber: 2.6 Consensus size: 29
45863891 CTTAATAATC
45863901 AACCACGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCC-TGTACATTTA
*
45863931 AACTCGCACACTTAGTG-CTGTACAATTTA
1 AACCCGCACACTTAGTGCCTGTAC-ATTTA
45863960 AACCCGCACACTTAGTGC
1 AACCCGCACACTTAGTGC
45863978 ATATCTCATG
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.79
30 3 0.07
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.26
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCTGTACATTTA
Found at i:45871921 original size:29 final size:29
Alignment explanation
Indices: 45871885--45871989 Score: 158
Period size: 29 Copynumber: 3.6 Consensus size: 29
45871875 TAATCAACCG
45871885 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGTACTTTAAACT
* * **
45871914 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGTACTTT-AAACT
45871943 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGTACTTTAAACT
45871972 CGCACACTTAGTGCCATG
1 CGCACACTTAGTGCCATG
45871990 CATTTCAAGT
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.05
29 60 0.91
30 3 0.05
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.30
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGTACTTTAAACT
Found at i:45871953 original size:58 final size:58
Alignment explanation
Indices: 45871885--45872010 Score: 234
Period size: 58 Copynumber: 2.2 Consensus size: 58
45871875 TAATCAACCG
45871885 CGCACACTTAGTGCCATGTACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTT
1 CGCACACTTAGTGCCATGTACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTT
*
45871943 CGCACACTTAGTGCCATGTACTTTAAACTCGCACACTTAGTGCCATGCATTTCAAGTT
1 CGCACACTTAGTGCCATGTACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTT
*
45872001 CACACACTTA
1 CGCACACTTA
45872011 CCTTTTCTGC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 66 1.00
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.30
Consensus pattern (58 bp):
CGCACACTTAGTGCCATGTACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTT
Found at i:45872006 original size:29 final size:29
Alignment explanation
Indices: 45871887--45872010 Score: 144
Period size: 29 Copynumber: 4.3 Consensus size: 29
45871877 ATCAACCGCG
*
45871887 CACACTTAGTGCCATGTACTTTAAACTCA
1 CACACTTAGTGCCATGCACTTTAAACTCA
** *
45871916 CACACTTAGTGCCATGCA-TTTCAAGTTCG
1 CACACTTAGTGCCATGCACTTT-AAACTCA
* *
45871945 CACACTTAGTGCCATGTACTTTAAACTCG
1 CACACTTAGTGCCATGCACTTTAAACTCA
**
45871974 CACACTTAGTGCCATGCA-TTTCAAGTTCA
1 CACACTTAGTGCCATGCACTTT-AAACTCA
45872003 CACACTTA
1 CACACTTA
45872011 CCTTTTCTGC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
28 6 0.07
29 72 0.89
30 3 0.04
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.31
Consensus pattern (29 bp):
CACACTTAGTGCCATGCACTTTAAACTCA
Found at i:45872151 original size:29 final size:30
Alignment explanation
Indices: 45872112--45872190 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
45872102 CTTAATAATC
45872112 AACCACGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
45872142 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
45872171 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
45872191 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:45874895 original size:28 final size:27
Alignment explanation
Indices: 45874857--45875067 Score: 152
Period size: 28 Copynumber: 7.5 Consensus size: 27
45874847 AACCGATCTT
45874857 GCACACACAGTGCTCGGTTACAGAACTC
1 GCACACACAGTGCTCGGTTAC-GAACTC
**** *
45874885 GCACACACAGTGCCTCAACAACCGATCTC
1 GCACACACAGTG-CTCGGTTA-CGAACTC
* *
45874914 GCATACACAGTGCTTGGTTACGGAACTC
1 GCACACACAGTGCTCGGTTAC-GAACTC
**** *
45874942 GCACACACAGTGCCTCAACAACCGATCTC
1 GCACACACAGTG-CTCGGTTA-CGAACTC
*
45874971 GCACACACAATGCTCGGTTACGGAACTC
1 GCACACACAGTGCTCGGTTAC-GAACTC
* **** * *
45874999 GCACACACAATGCCTCAACAACCATCTC
1 GCACACACAGTG-CTCGGTTACGAACTC
45875027 GCACACACAGTGCTCGGTTACGAAACTC
1 GCACACACAGTGCTCGGTTACG-AACTC
*
45875055 ACACACACAGTGC
1 GCACACACAGTGC
45875068 CTATGTTCAC
Statistics
Matches: 136, Mismatches: 39, Indels: 16
0.71 0.20 0.08
Matches are distributed among these distances:
27 7 0.05
28 83 0.61
29 44 0.32
30 2 0.01
ACGTcount: A:0.30, C:0.36, G:0.18, T:0.17
Consensus pattern (27 bp):
GCACACACAGTGCTCGGTTACGAACTC
Found at i:45874904 original size:57 final size:57
Alignment explanation
Indices: 45874830--45875069 Score: 392
Period size: 57 Copynumber: 4.2 Consensus size: 57
45874820 TTACTTTGTT
* * *
45874830 ACACACAGTGCCCCAACAACCGATCTTGCACACACAGTGCTCGGTTACAGAACTCGC
1 ACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCGC
* *
45874887 ACACACAGTGCCTCAACAACCGATCTCGCATACACAGTGCTTGGTTACGGAACTCGC
1 ACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCGC
*
45874944 ACACACAGTGCCTCAACAACCGATCTCGCACACACAATGCTCGGTTACGGAACTCGC
1 ACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCGC
* * *
45875001 ACACACAATGCCTCAACAACC-ATCTCGCACACACAGTGCTCGGTTACGAAACTCAC
1 ACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCGC
45875057 ACACACAGTGCCT
1 ACACACAGTGCCT
45875070 ATGTTCACTT
Statistics
Matches: 170, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
56 44 0.26
57 126 0.74
ACGTcount: A:0.30, C:0.36, G:0.17, T:0.17
Consensus pattern (57 bp):
ACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCGC
Found at i:45876935 original size:26 final size:26
Alignment explanation
Indices: 45876906--45876965 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
45876896 TCCCTTTGAA
* * *
45876906 TCATTCGATATTTTGCACACTAAGTG
1 TCATTCAATATCTCGCACACTAAGTG
45876932 TCATTCTCAATATCTCGCACACTAAGTG
1 TCA-T-TCAATATCTCGCACACTAAGTG
*
45876960 CCATTC
1 TCATTC
45876966 TCAATATTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 5 0.18
27 2 0.07
28 21 0.75
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (26 bp):
TCATTCAATATCTCGCACACTAAGTG
Found at i:45876951 original size:28 final size:28
Alignment explanation
Indices: 45876920--45876981 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
45876910 TCGATATTTT
*
45876920 GCACACTAAGTGTCATTCTCAATATCTC
1 GCACACTAAGTGCCATTCTCAATATCTC
*
45876948 GCACACTAAGTGCCATTCTCAATATTTC
1 GCACACTAAGTGCCATTCTCAATATCTC
*
45876976 GTACAC
1 GCACAC
45876982 CGAGTACCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.29, C:0.29, G:0.11, T:0.31
Consensus pattern (28 bp):
GCACACTAAGTGCCATTCTCAATATCTC
Found at i:45876991 original size:28 final size:28
Alignment explanation
Indices: 45876933--45876991 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
45876923 CACTAAGTGT
* *
45876933 CATTCTCAATATCTCGCACACTAAGTGC
1 CATTCTCAATATCTCGCACACCAAGTAC
* * *
45876961 CATTCTCAATATTTCGTACACCGAGTAC
1 CATTCTCAATATCTCGCACACCAAGTAC
45876989 CAT
1 CAT
45876992 ATTTGATTGC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.29, C:0.31, G:0.10, T:0.31
Consensus pattern (28 bp):
CATTCTCAATATCTCGCACACCAAGTAC
Found at i:45880791 original size:130 final size:130
Alignment explanation
Indices: 45880558--45880817 Score: 403
Period size: 130 Copynumber: 2.0 Consensus size: 130
45880548 CACTCAAAAA
* * *
45880558 GACCACTTACCTCTGTGAAAACTGAAAGAATGAAACTACATCACTGAAGCAACATATAAGCAACA
1 GACCACTTACCTCTGTGAAAACTGAAAGAATAAAACTACATCACTGAAACAACATACAAGCAACA
* * * **
45880623 ATTACCGAGATGTAACTGGCAATAACAAGGGATGACAAAAGAGATGTAAGAAGAAGAACACCAGT
66 ATTACCAAGATGTAACTAGCAATAACAAGGGACGACAAAAGAGATAAAAGAAGAAGAACACCAGT
* * *
45880688 GACCACTTACCTTTGTGGAAACTGAAAGAATAAAACTACATCACTGAAACAACGTACAAGCAACA
1 GACCACTTACCTCTGTGAAAACTGAAAGAATAAAACTACATCACTGAAACAACATACAAGCAACA
* *
45880753 GTTACCAAGATGTAACTAGCAATGACAAGGGACGACAAAAGAGATAAAAGAAGAAGAACACCAGT
66 ATTACCAAGATGTAACTAGCAATAACAAGGGACGACAAAAGAGATAAAAGAAGAAGAACACCAGT
45880818 AGCAATTGCA
Statistics
Matches: 117, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
130 117 1.00
ACGTcount: A:0.46, C:0.19, G:0.19, T:0.16
Consensus pattern (130 bp):
GACCACTTACCTCTGTGAAAACTGAAAGAATAAAACTACATCACTGAAACAACATACAAGCAACA
ATTACCAAGATGTAACTAGCAATAACAAGGGACGACAAAAGAGATAAAAGAAGAAGAACACCAGT
Found at i:45880837 original size:130 final size:130
Alignment explanation
Indices: 45880576--45880852 Score: 358
Period size: 130 Copynumber: 2.1 Consensus size: 130
45880566 ACCTCTGTGA
* * * * *
45880576 AAACTGAAAGAATGAAACTACATCACTGAAGCAACATATAAGCAACAATTACCGAGATGTAACTG
1 AAACTGAAAGAATAAAACTACATCACTGAAACAACATACAAGCAACAATTACCAAGATGTAACTA
* ** * *** *
45880641 GCAATAACAAGGGATGACAAAAGAGATGTAAGAAGAAGAACACCAGTGACCACTTACCTTTGTGG
66 GCAATAACAAGGGACGACAAAAGAGATAAAAGAAGAAGAACACCAGTGACCAATTACAGCTATGG
* *
45880706 AAACTGAAAGAATAAAACTACATCACTGAAACAACGTACAAGCAACAGTTACCAAGATGTAACTA
1 AAACTGAAAGAATAAAACTACATCACTGAAACAACATACAAGCAACAATTACCAAGATGTAACTA
* * *
45880771 GCAATGACAAGGGACGACAAAAGAGATAAAAGAAGAAGAACACCAGT-AGCAATTGCAAGCTATG
66 GCAATAACAAGGGACGACAAAAGAGATAAAAGAAGAAGAACACCAGTGACCAATTAC-AGCTATG
45880835 G
130 G
* *
45880836 AAACCGAAAGAAAAAAA
1 AAACTGAAAGAATAAAA
45880853 AGAAAAAAAA
Statistics
Matches: 126, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
129 6 0.05
130 120 0.95
ACGTcount: A:0.49, C:0.17, G:0.19, T:0.15
Consensus pattern (130 bp):
AAACTGAAAGAATAAAACTACATCACTGAAACAACATACAAGCAACAATTACCAAGATGTAACTA
GCAATAACAAGGGACGACAAAAGAGATAAAAGAAGAAGAACACCAGTGACCAATTACAGCTATGG
Found at i:45884048 original size:13 final size:13
Alignment explanation
Indices: 45884005--45884057 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
45883995 CATGGAATGG
45884005 AAATTTTA-TTTT
1 AAATTTTAGTTTT
*
45884017 --ATTTTACTTATT
1 AAATTTTAGTT-TT
45884029 AAAATTTTAGTTTT
1 -AAATTTTAGTTTT
45884043 AAATTTTAGTTTT
1 AAATTTTAGTTTT
45884056 AA
1 AA
45884058 TAATTCACAA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
10 6 0.17
11 2 0.06
12 2 0.06
13 15 0.43
14 2 0.06
15 8 0.23
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (13 bp):
AAATTTTAGTTTT
Found at i:45884288 original size:13 final size:13
Alignment explanation
Indices: 45884270--45884322 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
45884260 CATAGAATTA
45884270 TTAAAACTAAAAT
1 TTAAAACTAAAAT
45884283 TTAAAACTAAAATT
1 TTAAAACTAAAA-T
*
45884297 TTAATAAGTAAAA-
1 TTAA-AACTAAAAT
45884310 -TAAAA-TAAAAT
1 TTAAAACTAAAAT
45884321 TT
1 TT
45884323 CCATTCCATG
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
10 5 0.14
11 2 0.06
12 4 0.11
13 12 0.34
14 5 0.14
15 7 0.20
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (13 bp):
TTAAAACTAAAAT
Found at i:45884310 original size:15 final size:14
Alignment explanation
Indices: 45884265--45884310 Score: 58
Period size: 13 Copynumber: 3.2 Consensus size: 14
45884255 ACAAGCATAG
45884265 AATTATTAAAACTAA
1 AATT-TTAAAACTAA
45884280 AA-TTTAAAACTAA
1 AATTTTAAAACTAA
*
45884293 AATTTTAATAAGTAA
1 AATTTTAA-AACTAA
45884308 AAT
1 AAT
45884311 AAAATAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 12 0.43
14 6 0.21
15 10 0.36
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (14 bp):
AATTTTAAAACTAA
Found at i:45893887 original size:93 final size:93
Alignment explanation
Indices: 45893759--45893929 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
45893749 GCCCCTAAGT
* *
45893759 GAACTCGGACTCAACTCAATGAGCTCAGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
45893824 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * *
45893852 GAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCATCCATAGGTGAACTCGGAGTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTCAGG-CATTCGCATCCATAAGTGAACTCGGACTCAACTCA
45893916 ACGAGTTCGGATGC
65 ACGAGTTCGGATGC
45893930 TCAACCATCC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 2 0.03
93 70 0.97
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCAGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:45893919 original size:46 final size:45
Alignment explanation
Indices: 45893756--45893926 Score: 172
Period size: 46 Copynumber: 3.7 Consensus size: 45
45893746 TCCGCCCCTA
* * *
45893756 AGTGAACTCGGACTCAACTCAATGAGCTCAGG-CGTTCGCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCATCCAT
*
45893801 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-T
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCAT
*
45893849 CA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT
*
45893894 AGGTGAACTCGGAGTCAACTCAACGAGTTCGGA
1 A-GTGAACTCGGACTCAACTCAACGAGTTCGGA
45893927 TGCTCAACCA
Statistics
Matches: 105, Mismatches: 9, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 3 0.03
45 3 0.03
46 55 0.52
47 29 0.28
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT
Found at i:45901373 original size:46 final size:47
Alignment explanation
Indices: 45901320--45901486 Score: 157
Period size: 46 Copynumber: 3.6 Consensus size: 47
45901310 AACCCGCCCC
*
45901320 TAAGTGAACTCAGACTCAACTCAACGAGCTCGAG-CGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGAGACGTTCGCATCCA
* * * *
45901366 TAAGTGAACTCGGACTCAACTCAACAAGGTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGCTC-GA-GAC--GTTCGCATCCA
* * * *
45901414 TCA-CGAACTCGGACTCAACTCAACGAGTTCG-GACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGAGACGTTCGCATCCA
* *
45901459 TAGGTGAACTCGGAGTCAACTCAACGAG
1 TAAGTGAACTCGGACTCAACTCAACGAG
45901487 TTCGGATGCT
Statistics
Matches: 97, Mismatches: 15, Indels: 18
0.75 0.12 0.14
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 3 0.03
45 1 0.01
46 51 0.53
47 26 0.27
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.20
Consensus pattern (47 bp):
TAAGTGAACTCGGACTCAACTCAACGAGCTCGAGACGTTCGCATCCA
Found at i:45901433 original size:93 final size:93
Alignment explanation
Indices: 45901325--45901495 Score: 263
Period size: 93 Copynumber: 1.8 Consensus size: 93
45901315 GCCCCTAAGT
*
45901325 GAACTCAGACTCAACTCAACGAGCTC-GAGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCAGACTCAACTCAACGAGCTCGGA-CATTCGCATCCATAAGTGAACTCGGACTCAACTCA
45901389 ACAAGGTCGGATGCCTAGTTACATCTCAC
65 ACAAGGTCGGATGCCTAGTTACATCTCAC
* * * *
45901418 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAGGTGAACTCGGAGTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
* *
45901483 CGAGTTCGGATGC
66 CAAGGTCGGATGC
45901496 TCAACCATCC
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
93 68 0.97
94 2 0.03
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CAAGGTCGGATGCCTAGTTACATCTCAC
Found at i:45901950 original size:30 final size:30
Alignment explanation
Indices: 45901916--45901975 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
45901906 ATTTAATACG
45901916 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
45901946 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
45901976 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:45907227 original size:71 final size:71
Alignment explanation
Indices: 45907143--45907287 Score: 290
Period size: 71 Copynumber: 2.0 Consensus size: 71
45907133 TTAAAACAAT
45907143 TTGCATATTTGTGTGTATTTTGTTAAAACGTTTCATTCGTTTTGAAAACTCGTTATCCCTACTAC
1 TTGCATATTTGTGTGTATTTTGTTAAAACGTTTCATTCGTTTTGAAAACTCGTTATCCCTACTAC
45907208 TAGCTG
66 TAGCTG
45907214 TTGCATATTTGTGTGTATTTTGTTAAAACGTTTCATTCGTTTTGAAAACTCGTTATCCCTACTAC
1 TTGCATATTTGTGTGTATTTTGTTAAAACGTTTCATTCGTTTTGAAAACTCGTTATCCCTACTAC
45907279 TAGCTG
66 TAGCTG
45907285 TTG
1 TTG
45907288 TAAATAAAAA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 74 1.00
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.46
Consensus pattern (71 bp):
TTGCATATTTGTGTGTATTTTGTTAAAACGTTTCATTCGTTTTGAAAACTCGTTATCCCTACTAC
TAGCTG
Found at i:45911866 original size:43 final size:43
Alignment explanation
Indices: 45911678--45911853 Score: 266
Period size: 43 Copynumber: 4.1 Consensus size: 43
45911668 GTTAAATCCC
* * *
45911678 GCAGGCTTCATGCTGGT-AT-TATATTCGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* *
45911719 GCAGGCTTCGTACCGGTGATGTGTATTCGGGCCTTTGTGCCTA
1 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
*
45911762 GCAGGCTTTGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* *
45911805 GAAGGCTTCGTGCCGGTGATATGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
45911848 GCAGGC
1 GCAGGC
45911854 ATAATGCCGG
Statistics
Matches: 121, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
41 14 0.12
42 2 0.02
43 105 0.87
ACGTcount: A:0.12, C:0.24, G:0.32, T:0.31
Consensus pattern (43 bp):
GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
Found at i:45917343 original size:40 final size:39
Alignment explanation
Indices: 45917299--45917532 Score: 344
Period size: 40 Copynumber: 5.9 Consensus size: 39
45917289 AGATATAGCT
* *
45917299 ACTCGCTCAAATGCCTTCGGGACATAGCCCGGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTT-TAGTA
* *
45917339 ACTCGCACCAATGCCTTCGGGACTTAGCCCGGATTTGGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-TTTAGTA
*
45917379 ACTCAG-ACAAATGCCTTCGGGACTTAGCCCGGATTTGGTA
1 ACTC-GCACAAATGCCTTCGGGACTTAGCCCGG-TTTAGTA
*
45917419 ACTCGCACAAATGCCTTCGGGACTTAGCCCAGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCC-GGTTTAGTA
45917459 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-TTTAGTA
*
45917499 ACTCGCGCAAATGCCTTCGGGACTTAGCCCGGTT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTT
45917533 ATCATCCGAA
Statistics
Matches: 180, Mismatches: 9, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
39 4 0.02
40 172 0.96
41 4 0.02
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.25
Consensus pattern (39 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTTAGTA
Found at i:45919194 original size:68 final size:68
Alignment explanation
Indices: 45919120--45919258 Score: 269
Period size: 68 Copynumber: 2.0 Consensus size: 68
45919110 ATTTACTAAA
*
45919120 TCGAAACTTAAAACTTTCACACATTCATAATCACCTATTTTAGACAATAAATATCATATTCAAAT
1 TCGAAACTTAAAACTTTCACACATTCATAATCACATATTTTAGACAATAAATATCATATTCAAAT
45919185 AAT
66 AAT
45919188 TCGAAACTTAAAACTTTCACACATTCATAATCACATATTTTAGACAATAAATATCATATTCAAAT
1 TCGAAACTTAAAACTTTCACACATTCATAATCACATATTTTAGACAATAAATATCATATTCAAAT
45919253 AAT
66 AAT
45919256 TCG
1 TCG
45919259 GTGACTCGGT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.34
Consensus pattern (68 bp):
TCGAAACTTAAAACTTTCACACATTCATAATCACATATTTTAGACAATAAATATCATATTCAAAT
AAT
Found at i:45921113 original size:25 final size:25
Alignment explanation
Indices: 45921085--45921132 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
45921075 GCAGTACAGT
*
45921085 CTATCTATAGCGGTTTCAGTTTATG
1 CTATCTATAGCAGTTTCAGTTTATG
45921110 CTATCTATAGCAGTTTCAGTTTA
1 CTATCTATAGCAGTTTCAGTTTA
45921133 AAACACATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.44
Consensus pattern (25 bp):
CTATCTATAGCAGTTTCAGTTTATG
Found at i:45926211 original size:16 final size:17
Alignment explanation
Indices: 45926179--45926213 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
45926169 TTAAGATAAG
*
45926179 TATTAAATTTAATTAAA
1 TATTAAATCTAATTAAA
45926196 TATTAAATCT-ATTAAA
1 TATTAAATCTAATTAAA
45926212 TA
1 TA
45926214 ATATTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
TATTAAATCTAATTAAA
Found at i:45929265 original size:41 final size:41
Alignment explanation
Indices: 45929208--45929289 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
45929198 AATGGATAAG
* *
45929208 AGTATGCGGGTAGACTTTAGCATGGCTACTGGAGAGAAGGT
1 AGTATGCGGATAGACTTTAGCATGGCTACTAGAGAGAAGGT
45929249 AGTATGCGGATAGACTTTAGCATGGCTACTAGAGAGAAGGT
1 AGTATGCGGATAGACTTTAGCATGGCTACTAGAGAGAAGGT
45929290 CTCATCGTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.29, C:0.12, G:0.34, T:0.24
Consensus pattern (41 bp):
AGTATGCGGATAGACTTTAGCATGGCTACTAGAGAGAAGGT
Found at i:45936386 original size:40 final size:40
Alignment explanation
Indices: 45936288--45936543 Score: 288
Period size: 40 Copynumber: 6.5 Consensus size: 40
45936278 AAGCCAAGTA
* * *
45936288 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTC-AATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* * *
45936326 CCTTCGGGACATAGCTCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
45936366 CCTTCCGGACTTAGCCCGGATATAGTAGCTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
45936406 CCTTCGAGACTTAGCCC-GATGTAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
45936445 CCTTCGGGACTTAGCCCAGATGTAATAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
45936485 CCTTCGGGACTTAGCCCAGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
45936525 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
45936544 TTATCATCCG
Statistics
Matches: 190, Mismatches: 23, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
38 12 0.06
39 51 0.27
40 127 0.67
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:45936434 original size:79 final size:78
Alignment explanation
Indices: 45936288--45936543 Score: 284
Period size: 79 Copynumber: 3.2 Consensus size: 78
45936278 AAGCCAAGTA
* * * * *
45936288 CCTTCGGGATTTA-ACCGGATATAGCTACTCGCTC-AATGCCTTCGGGACATAGCTCGGATATAG
1 CCTTCGGGACTTAGCCCGGATATAG-TACTCGCACAAATGCCTTCGGGACTTAGC-CCGATATAG
*
45936351 TAACTCGCACCAATG
64 TAACTCGCACAAATG
* * * *
45936366 CCTTCCGGACTTAGCCCGGATATAGTAGCTCGCACAAATGCCTTCGAGACTTAGCCCGATGTAAT
1 CCTTCGGGACTTAGCCCGGATATAGTA-CTCGCACAAATGCCTTCGGGACTTAGCCCGATATAGT
45936431 AACTCGCACAAATG
65 AACTCGCACAAATG
* * * *
45936445 CCTTCGGGACTTAGCCCAGATGTAATAACTTGCACAAATGCCTTCGGGACTTAGCCCAGA-ACTA
1 CCTTCGGGACTTAGCCCGGATATAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCC-GATA-TA
* * *
45936509 GTCACTAGCGCAAATG
63 GTAACTCGCACAAATG
45936525 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
45936544 TTATCATCCG
Statistics
Matches: 150, Mismatches: 22, Indels: 10
0.82 0.12 0.05
Matches are distributed among these distances:
78 13 0.09
79 85 0.57
80 52 0.35
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (78 bp):
CCTTCGGGACTTAGCCCGGATATAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGATATAGTA
ACTCGCACAAATG
Found at i:45936498 original size:119 final size:118
Alignment explanation
Indices: 45936314--45936542 Score: 300
Period size: 119 Copynumber: 1.9 Consensus size: 118
45936304 GGATATAGCT
* * * * *
45936314 ACTCGCTCAATGCCTTCGGGACATAGCTCGGATATAGTAACTCGCACCAATGCCTTCCGGACTTA
1 ACTCGCACAATGCCTTCGGGACATAGCCCAGATATAATAACTCGCACAAATGCCTTCCGGACTTA
* *
45936379 GCCCGGATA-TAGT-AGCTCGCACAAATGCCTTCGAGACTTAGCCCGATGTAATA
66 GCCCAGA-ACTAGTCA-CTAGCACAAATGCCTTCGAGACTTAGCCCGATGTAATA
* * * *
45936432 ACTCGCACAAATGCCTTCGGGACTTAGCCCAGATGTAATAACTTGCACAAATGCCTTCGGGACTT
1 ACTCGCAC-AATGCCTTCGGGACATAGCCCAGATATAATAACTCGCACAAATGCCTTCCGGACTT
* *
45936497 AGCCCAGAACTAGTCACTAGCGCAAATGCCTTCGGGACTTAGCCCG
65 AGCCCAGAACTAGTCACTAGCACAAATGCCTTCGAGACTTAGCCCG
45936543 GTTATCATCC
Statistics
Matches: 95, Mismatches: 13, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
118 8 0.08
119 86 0.91
120 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (118 bp):
ACTCGCACAATGCCTTCGGGACATAGCCCAGATATAATAACTCGCACAAATGCCTTCCGGACTTA
GCCCAGAACTAGTCACTAGCACAAATGCCTTCGAGACTTAGCCCGATGTAATA
Found at i:45941450 original size:26 final size:26
Alignment explanation
Indices: 45941414--45941523 Score: 157
Period size: 26 Copynumber: 4.2 Consensus size: 26
45941404 TGATACAAAT
*
45941414 TGATAATAGGTTAGGTAGATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
45941440 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* * * *
45941466 TTACAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
45941492 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
45941518 TGATAA
1 TGATAA
45941524 GAATTTCATG
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:45947205 original size:26 final size:26
Alignment explanation
Indices: 45947169--45947278 Score: 166
Period size: 26 Copynumber: 4.2 Consensus size: 26
45947159 TGATACAAAT
*
45947169 TGATAATAGGTTAGGTAGATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
45947195 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* * *
45947221 TGACAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
45947247 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
45947273 TGATAA
1 TGATAA
45947279 GAATTTCATG
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 79 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.35
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:45954862 original size:38 final size:38
Alignment explanation
Indices: 45954819--45954891 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
45954809 AATATTAGAG
45954819 TCAGATTAACAGAACATATATACCGAATCCTACCCCTA
1 TCAGATTAACAGAACATATATACCGAATCCTACCCCTA
*
45954857 TCAGATTAACAGAACATATATACTGAATCCTACCC
1 TCAGATTAACAGAACATATATACCGAATCCTACCC
45954892 TCATCCTCTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (38 bp):
TCAGATTAACAGAACATATATACCGAATCCTACCCCTA
Found at i:45957788 original size:14 final size:11
Alignment explanation
Indices: 45957752--45957791 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
45957742 ATTCTTGTCT
*
45957752 ATAAATATATA
1 ATAATTATATA
45957763 ATAATTATATA
1 ATAATTATATA
*
45957774 ATAATTATAAA
1 ATAATTATATA
45957785 ATAATTA
1 ATAATTA
45957792 AAATGTACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATAATTATATA
Found at i:45958722 original size:20 final size:18
Alignment explanation
Indices: 45958686--45958725 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 18
45958676 ACTTGTGATG
45958686 TTAATATGCTTAATTTAA
1 TTAATATGCTTAATTTAA
45958704 TTAATATGGCTTAAATTTAA
1 TTAATAT-GCTT-AATTTAA
45958724 TT
1 TT
45958726 CGTGTTAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.35
19 4 0.20
20 9 0.45
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (18 bp):
TTAATATGCTTAATTTAA
Found at i:45960489 original size:10 final size:10
Alignment explanation
Indices: 45960476--45960557 Score: 61
Period size: 9 Copynumber: 8.6 Consensus size: 10
45960466 TCGTAAAAAA
45960476 TATAAAATTT
1 TATAAAATTT
45960486 TAT-AAATTT
1 TATAAAATTT
*
45960495 TATAAAAATTG
1 TAT-AAAATTT
45960506 TA-AAAA-TT
1 TATAAAATTT
*
45960514 TATAAAA-TA
1 TATAAAATTT
45960523 TATAGAAA---
1 TATA-AAATTT
*
45960531 TATAAAATAAT
1 TATAAAAT-TT
45960542 TATAAAATTT
1 TATAAAATTT
45960552 TATAAA
1 TATAAA
45960558 TTCGTAAGAA
Statistics
Matches: 60, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
7 3 0.05
8 7 0.12
9 22 0.37
10 13 0.22
11 15 0.25
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (10 bp):
TATAAAATTT
Found at i:45960491 original size:19 final size:19
Alignment explanation
Indices: 45960489--45960557 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 19
45960479 AAAATTTTAT
* *
45960489 AAATTTTATAAAAATTGTA
1 AAATTTTATAAAAAATATA
* *
45960508 AAAATTTATAAAATATATA
1 AAATTTTATAAAAAATATA
45960527 GAAA---TATAAAATAATTATA
1 -AAATTTTATAAAA-AA-TATA
45960546 AAATTTTATAAA
1 AAATTTTATAAA
45960558 TTCGTAAGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
17 7 0.18
18 4 0.10
19 19 0.49
20 3 0.08
21 6 0.15
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
AAATTTTATAAAAAATATA
Found at i:45960500 original size:28 final size:28
Alignment explanation
Indices: 45960469--45960557 Score: 90
Period size: 28 Copynumber: 3.1 Consensus size: 28
45960459 ATAAAAATCG
45960469 TAAAAAATATAAAATTTTATAAATTTTA
1 TAAAAAATATAAAATTTTATAAATTTTA
* * * * *
45960497 TAAAAATTGTAAAAATTTATAAAATATA
1 TAAAAAATATAAAATTTTATAAATTTTA
* *
45960525 T-AGAAATATAAAATAATTATAAAATTTTA
1 TAAAAAATATAAAAT-TTTAT-AAATTTTA
45960554 TAAA
1 TAAA
45960558 TTCGTAAGAA
Statistics
Matches: 45, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
27 9 0.20
28 28 0.62
29 7 0.16
30 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (28 bp):
TAAAAAATATAAAATTTTATAAATTTTA
Found at i:45960520 original size:9 final size:9
Alignment explanation
Indices: 45960476--45960557 Score: 62
Period size: 10 Copynumber: 8.7 Consensus size: 9
45960466 TCGTAAAAAA
45960476 TATAAAATTT
1 TATAAAA-TT
*
45960486 TATAAATTT
1 TATAAAATT
45960495 TATAAAAATT
1 TAT-AAAATT
45960505 GTA-AAAATT
1 -TATAAAATT
*
45960514 TATAAAATA
1 TATAAAATT
45960523 TATAGAAA--
1 TATA-AAATT
45960531 TATAAAATAAT
1 TATAAAAT--T
45960542 TATAAAATTT
1 TATAAAA-TT
45960552 TATAAA
1 TATAAA
45960558 TTCGTAAGAA
Statistics
Matches: 60, Mismatches: 3, Indels: 18
0.74 0.04 0.22
Matches are distributed among these distances:
7 3 0.05
8 6 0.10
9 20 0.33
10 21 0.35
11 9 0.15
12 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (9 bp):
TATAAAATT
Found at i:45960578 original size:9 final size:9
Alignment explanation
Indices: 45960452--45960621 Score: 60
Period size: 9 Copynumber: 18.0 Consensus size: 9
45960442 AAATTAGAAA
*
45960452 AAAAAATAT
1 AAAAATTAT
**
45960461 AAAAATCGT
1 AAAAATTAT
*
45960470 AAAAAATAT
1 AAAAATTAT
*
45960479 AAAATTTTAT
1 AAAA-ATTAT
**
45960489 AAATTTTAT
1 AAAAATTAT
*
45960498 AAAAATTGT
1 AAAAATTAT
45960507 AAAAATT-T
1 AAAAATTAT
45960515 ATAAAATATAT
1 A-AAAAT-TAT
*
45960526 AGAAA-TAT
1 AAAAATTAT
45960534 AAAATAATTAT
1 -AAA-AATTAT
*
45960545 -AAAATTTT
1 AAAAATTAT
* *
45960553 ATAAATTCGT
1 AAAAATT-AT
45960563 AAGAAAATTAT
1 -A-AAAATTAT
45960574 AAAAAATT-T
1 -AAAAATTAT
*
45960583 AAAGAAATAT
1 AAA-AATTAT
** *
45960593 AAATTTCTTAA
1 AAA--AATTAT
45960604 AAAAATTAT
1 AAAAATTAT
45960613 AAAAATTAT
1 AAAAATTAT
45960622 TGTACCAAAA
Statistics
Matches: 119, Mismatches: 28, Indels: 28
0.68 0.16 0.16
Matches are distributed among these distances:
8 13 0.11
9 64 0.54
10 23 0.19
11 14 0.12
12 5 0.04
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (9 bp):
AAAAATTAT
Found at i:45960615 original size:20 final size:19
Alignment explanation
Indices: 45960551--45960615 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 19
45960541 TTATAAAATT
* *
45960551 TTATAAATTCGTAAGAAAA
1 TTATAAATTCTTAAAAAAA
* *
45960570 TTATAAAAAAT-TTAAAGAAA
1 TTAT--AAATTCTTAAAAAAA
45960590 -TATAAATTTCTTAAAAAAA
1 TTATAAA-TTCTTAAAAAAA
45960609 TTATAAA
1 TTATAAA
45960616 AATTATTGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 9
0.70 0.12 0.18
Matches are distributed among these distances:
17 3 0.09
18 1 0.03
19 15 0.43
20 12 0.34
21 4 0.11
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (19 bp):
TTATAAATTCTTAAAAAAA
Found at i:45965316 original size:34 final size:34
Alignment explanation
Indices: 45965278--45965354 Score: 86
Period size: 34 Copynumber: 2.3 Consensus size: 34
45965268 TGAACACTTA
* *
45965278 ATAAGCATGACT-TTTGCTACTGA-GTTGATCTATT
1 ATAAGCAT-ACTATTTACTACT-ATGTTGAACTATT
* *
45965312 ATAAGCATATTATTTACTACTATGTTGAACTGTT
1 ATAAGCATACTATTTACTACTATGTTGAACTATT
45965346 ATAAGCATA
1 ATAAGCATA
45965355 TTGATTGCTA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
33 3 0.08
34 34 0.92
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.40
Consensus pattern (34 bp):
ATAAGCATACTATTTACTACTATGTTGAACTATT
Found at i:45965366 original size:34 final size:34
Alignment explanation
Indices: 45965290--45965367 Score: 97
Period size: 34 Copynumber: 2.3 Consensus size: 34
45965280 AAGCATGACT
*
45965290 TTTGCTACTGAGTTGATCTATTATAAGCATATTA
1 TTTGCTACTGAGTTGAACTATTATAAGCATATTA
* *
45965324 TTTACTACT-ATGTTGAACTGTTATAAGCATATTGA
1 TTTGCTACTGA-GTTGAACTATTATAAGCATATT-A
45965359 -TTGCTACTG
1 TTTGCTACTG
45965368 TATTGTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
33 1 0.03
34 35 0.95
35 1 0.03
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (34 bp):
TTTGCTACTGAGTTGAACTATTATAAGCATATTA
Found at i:45966186 original size:5 final size:5
Alignment explanation
Indices: 45966176--45966204 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
45966166 CATGCATGAC
45966176 ATTTA ATTTA ATTTA ATTTA ATTTA ATTT
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTT
45966205 TAGGATACTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
ATTTA
Found at i:45966437 original size:23 final size:20
Alignment explanation
Indices: 45966399--45966448 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 20
45966389 TCCACTCAGG
45966399 ATTTTTTTAAAAATAAATTAA
1 ATTTTTTTAAAAATAAA-TAA
*
45966420 ATTTTCTTCTAAATATAAATAA
1 ATTTT-TT-TAAAAATAAATAA
45966442 ATATTTT
1 AT-TTTT
45966449 AAATTAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 5 0.20
22 8 0.32
23 12 0.48
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTTTTTAAAAATAAATAA
Found at i:45968685 original size:28 final size:27
Alignment explanation
Indices: 45968642--45968767 Score: 100
Period size: 28 Copynumber: 4.6 Consensus size: 27
45968632 TCGTGTGTAT
*
45968642 CCTATTTTTCAAATTTTATAGTCTTGC
1 CCTATTTTTCAAATTTTATAGTTTTGC
*
45968669 CACTATTTTTCAGATTTTATTA-TTTTGTC
1 C-CTATTTTTCAAATTTTA-TAGTTTTG-C
45968698 CCTAATTTTT-AAATTTTATAGTTTTG-
1 CCT-ATTTTTCAAATTTTATAGTTTTGC
* * * *
45968724 CCTTTATTTTCAGA-TTTACAGTTTTTCC
1 CCTAT-TTTTCAAATTTTATAG-TTTTGC
*
45968752 CCTATTTTAC-AATTTT
1 CCTATTTTTCAAATTTT
45968768 CATATTAGAC
Statistics
Matches: 79, Mismatches: 10, Indels: 20
0.72 0.09 0.18
Matches are distributed among these distances:
25 1 0.01
26 14 0.18
27 16 0.20
28 38 0.48
29 10 0.13
ACGTcount: A:0.22, C:0.16, G:0.06, T:0.56
Consensus pattern (27 bp):
CCTATTTTTCAAATTTTATAGTTTTGC
Found at i:45972282 original size:11 final size:11
Alignment explanation
Indices: 45972266--45972290 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
45972256 TGACTATGCC
45972266 ATTACAAGCCT
1 ATTACAAGCCT
45972277 ATTACAAGCCT
1 ATTACAAGCCT
45972288 ATT
1 ATT
45972291 CTACAGGTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (11 bp):
ATTACAAGCCT
Found at i:45974983 original size:15 final size:15
Alignment explanation
Indices: 45974963--45974996 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
45974953 GGTATTATAA
45974963 AATTAAGAAAAAATC
1 AATTAAGAAAAAATC
*
45974978 AATTAATAAAAAATC
1 AATTAAGAAAAAATC
45974993 AATT
1 AATT
45974997 GAACTGGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (15 bp):
AATTAAGAAAAAATC
Found at i:45975406 original size:25 final size:24
Alignment explanation
Indices: 45975356--45975402 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
45975346 AAACACTAAA
* *
45975356 AAAAAAGATAGAAATTATAGAAAT
1 AAAAAACATAGAAATTATAAAAAT
*
45975380 AAAAAACATATAAATTATAAAAA
1 AAAAAACATAGAAATTATAAAAA
45975403 ATAATAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.21
Consensus pattern (24 bp):
AAAAAACATAGAAATTATAAAAAT
Found at i:45975740 original size:17 final size:17
Alignment explanation
Indices: 45975711--45975743 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
45975701 AAAAACAATA
45975711 ATTATATTTTTATAAAT
1 ATTATATTTTTATAAAT
45975728 ATTAT-TTTATTATAAA
1 ATTATATTT-TTATAAA
45975744 ATTTAGACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTATATTTTTATAAAT
Found at i:45980050 original size:44 final size:46
Alignment explanation
Indices: 45979981--45980073 Score: 111
Period size: 44 Copynumber: 2.1 Consensus size: 46
45979971 TATAACATCT
* * *
45979981 ATTCCATTCGACCAAACACAAGAATT-CT-ATTATAGTTCTATTCC
1 ATTCCATTCAACCAAACACAAGAATTACTGATTACAGCTCTATTCC
* *
45980025 ATTCCATTCAACCAAACA-ATTGAATTATTGATTACAGCTCTATTCC
1 ATTCCATTCAACCAAACACA-AGAATTACTGATTACAGCTCTATTCC
45980071 ATT
1 ATT
45980074 ATAGTGAACC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
43 1 0.02
44 22 0.54
45 1 0.02
46 17 0.41
ACGTcount: A:0.34, C:0.24, G:0.06, T:0.35
Consensus pattern (46 bp):
ATTCCATTCAACCAAACACAAGAATTACTGATTACAGCTCTATTCC
Found at i:45983617 original size:40 final size:40
Alignment explanation
Indices: 45983556--45983740 Score: 232
Period size: 41 Copynumber: 4.6 Consensus size: 40
45983546 CTCGCACAAG
* * * * *
45983556 GCCTTCGGTCTTAACCCGGATATGGTCAC-TAGCATAAAT
1 GCCTTCGGACTTAGCCCGGATATAGTCGCTTAGCACAAAT
45983595 GCCTTCGGGACTTAGCCCGGATATAGTCGC-TAGCACAAAT
1 GCCTTC-GGACTTAGCCCGGATATAGTCGCTTAGCACAAAT
* * *
45983635 GCCTTCGGATCTTAGTCCGGATCTAGTCGCTTAGCACAAAA
1 GCCTTCGGA-CTTAGCCCGGATATAGTCGCTTAGCACAAAT
45983676 GCCTTCAGGACTTAGCCCGGATATAGTCGCTTAGCACCAAA-
1 GCCTTC-GGACTTAGCCCGGATATAGTCGCTTAGCA-CAAAT
45983717 GCCTTCGAGACTTAGCCCGGATAT
1 GCCTTCG-GACTTAGCCCGGATAT
45983741 CATTCGAGTA
Statistics
Matches: 130, Mismatches: 10, Indels: 10
0.87 0.07 0.07
Matches are distributed among these distances:
39 9 0.07
40 53 0.41
41 61 0.47
42 7 0.05
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
GCCTTCGGACTTAGCCCGGATATAGTCGCTTAGCACAAAT
Found at i:45983687 original size:81 final size:82
Alignment explanation
Indices: 45983585--45983738 Score: 233
Period size: 81 Copynumber: 1.9 Consensus size: 82
45983575 ATATGGTCAC
* * *
45983585 TAGCATAAATGCCTTCGGGACTTAGCCCGGATATAGTCGC-TAGCA-CAAATGCCTTCG-GATCT
1 TAGCACAAAAGCCTTCAGGACTTAGCCCGGATATAGTCGCTTAGCACCAAA-GCCTTCGAGA-CT
*
45983647 TAGTCCGGATCTAGTCGCT
64 TAGCCCGGATCTAGTCGCT
45983666 TAGCACAAAAGCCTTCAGGACTTAGCCCGGATATAGTCGCTTAGCACCAAAGCCTTCGAGACTTA
1 TAGCACAAAAGCCTTCAGGACTTAGCCCGGATATAGTCGCTTAGCACCAAAGCCTTCGAGACTTA
45983731 GCCCGGAT
66 GCCCGGAT
45983739 ATCATTCGAG
Statistics
Matches: 66, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
81 37 0.56
82 23 0.35
83 6 0.09
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (82 bp):
TAGCACAAAAGCCTTCAGGACTTAGCCCGGATATAGTCGCTTAGCACCAAAGCCTTCGAGACTTA
GCCCGGATCTAGTCGCT
Found at i:46003868 original size:40 final size:39
Alignment explanation
Indices: 46003796--46003931 Score: 197
Period size: 40 Copynumber: 3.5 Consensus size: 39
46003786 TCGATGATAA
46003796 CCGGGCTAAGT-CCGAAGGCATTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTACTATAT
46003834 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCA-TTGTGCGAGTTACTATAT
*
46003874 CCGGGCTAAGTCCCGAAGGCAGTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCA-TTGTGCGAGTTA-CTATAT
* *
46003914 CC-GGCTAAATCCCAAAGG
1 CCGGGCTAAGTCCCGAAGG
46003932 TACTTGGTTT
Statistics
Matches: 91, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
38 11 0.12
39 25 0.27
40 55 0.60
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.23
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTGTGCGAGTTACTATAT
Found at i:46011714 original size:40 final size:40
Alignment explanation
Indices: 46011659--46011836 Score: 288
Period size: 40 Copynumber: 4.5 Consensus size: 40
46011649 CGGATGATAA
46011659 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
46011699 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
46011739 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
46011779 CCGAGCTAAGTCCCGAAGGCAGTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
46011819 CC-GGCTAAATCCCAAAGG
1 CCGGGCTAAGTCCCGAAGG
46011837 TACTTGGTTT
Statistics
Matches: 131, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
39 15 0.11
40 116 0.89
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:46022595 original size:14 final size:15
Alignment explanation
Indices: 46022571--46022599 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
46022561 TCAGTAGACC
46022571 ACACATTCAAAAATA
1 ACACATTCAAAAATA
46022586 ACAC-TTCAAAAATA
1 ACACATTCAAAAATA
46022600 CTTTTCAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.59, C:0.21, G:0.00, T:0.21
Consensus pattern (15 bp):
ACACATTCAAAAATA
Found at i:46022751 original size:18 final size:20
Alignment explanation
Indices: 46022712--46022752 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
46022702 CATTGAAGTG
*
46022712 TATTTAGAAAAGTGTCGTTC
1 TATTTAGAAAAGTCTCGTTC
46022732 TATTT-GAAAAGTCT-GTTC
1 TATTTAGAAAAGTCTCGTTC
46022750 TAT
1 TAT
46022753 ATAAAAATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 7 0.35
19 8 0.40
20 5 0.25
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.44
Consensus pattern (20 bp):
TATTTAGAAAAGTCTCGTTC
Found at i:46023285 original size:34 final size:34
Alignment explanation
Indices: 46023242--46023325 Score: 159
Period size: 34 Copynumber: 2.5 Consensus size: 34
46023232 GGTCCAATAT
*
46023242 CAGTAATAGTAACAGAGTGTGCCTTAGCCCATTA
1 CAGTAATAGTAACAGAGTGTGCCATAGCCCATTA
46023276 CAGTAATAGTAACAGAGTGTGCCATAGCCCATTA
1 CAGTAATAGTAACAGAGTGTGCCATAGCCCATTA
46023310 CAGTAATAGTAACAGA
1 CAGTAATAGTAACAGA
46023326 AATGCAAACA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (34 bp):
CAGTAATAGTAACAGAGTGTGCCATAGCCCATTA
Found at i:46023646 original size:27 final size:27
Alignment explanation
Indices: 46023586--46023639 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
46023576 AAACATATCA
* *
46023586 TAGGGGTATAACAGTCATTTTACCTGT
1 TAGGGGTATAACAGTCATTTCACCAGT
* *
46023613 TAGGGGTATAATAGTCATTTCATCAGT
1 TAGGGGTATAACAGTCATTTCACCAGT
46023640 ATGGGGTCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (27 bp):
TAGGGGTATAACAGTCATTTCACCAGT
Done.