Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 91 of 143
Found at i:28387636 original size:27 final size:27
Alignment explanation
Indices: 28387590--28387665 Score: 116
Period size: 27 Copynumber: 2.8 Consensus size: 27
28387580 TTTTTCGAAA
*
28387590 AAAGTCAACGGTCAACGGTCAACGGTC
1 AAAGTCAACGGTCAATGGTCAACGGTC
* *
28387617 AATGTCAACGGTCAGTGGTCAACGGTC
1 AAAGTCAACGGTCAATGGTCAACGGTC
*
28387644 AAAGTCAACGGTTAATGGTCAA
1 AAAGTCAACGGTCAATGGTCAA
28387666 AGTCAACGGT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.20
Consensus pattern (27 bp):
AAAGTCAACGGTCAATGGTCAACGGTC
Found at i:28387765 original size:15 final size:14
Alignment explanation
Indices: 28387721--28387768 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
28387711 TGGGTTGGAC
28387721 TTGGTTCAATTGGT
1 TTGGTTCAATTGGT
*
28387735 TTGGTTCAAATGGGT
1 TTGGTTC-AATTGGT
*
28387750 TTGGTTCACCTTGGT
1 TTGGTTCA-ATTGGT
28387765 TTGG
1 TTGG
28387769 GCTTAATGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
14 8 0.28
15 21 0.72
ACGTcount: A:0.12, C:0.10, G:0.31, T:0.46
Consensus pattern (14 bp):
TTGGTTCAATTGGT
Found at i:28388797 original size:29 final size:30
Alignment explanation
Indices: 28388765--28388821 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
28388755 TGTACTTTTC
*
28388765 AAAATTATATTTTTA-CCCTCAAACTTTAA
1 AAAATTACATTTTTACCCCTCAAACTTTAA
28388794 AAAATTACATTTTTACCCCTCAAACTTT
1 AAAATTACATTTTTACCCCTCAAACTTT
28388822 CTAAAAATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.40
Consensus pattern (30 bp):
AAAATTACATTTTTACCCCTCAAACTTTAA
Found at i:28388882 original size:30 final size:29
Alignment explanation
Indices: 28388758--28388880 Score: 120
Period size: 30 Copynumber: 4.1 Consensus size: 29
28388748 AGGTCCCTGT
* * *
28388758 ACTTTTCAAAATTATATTTTTACCCTCAA
1 ACTTTTAAAAATTACATTTTAACCCTCAA
* *
28388787 ACTTTAAAAAATTACATTTTTACCCCTCAA
1 ACTTTTAAAAATTACA-TTTTAACCCTCAA
* * **
28388817 ACTTTCTAAAAATCACGTTTTAACCCTTGA
1 ACTTT-TAAAAATTACATTTTAACCCTCAA
* *
28388847 ACTTCTTCAAGATTACATTTTAACCCTCAA
1 ACTT-TTAAAAATTACATTTTAACCCTCAA
28388877 ACTT
1 ACTT
28388881 CTCCAAAATC
Statistics
Matches: 74, Mismatches: 17, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
29 13 0.18
30 52 0.70
31 9 0.12
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.39
Consensus pattern (29 bp):
ACTTTTAAAAATTACATTTTAACCCTCAA
Found at i:28388896 original size:30 final size:29
Alignment explanation
Indices: 28388758--28388918 Score: 108
Period size: 30 Copynumber: 5.4 Consensus size: 29
28388748 AGGTCCCTGT
* * * *
28388758 ACTTTTCAAAATTATATTTTTACCCTCAA
1 ACTTTCCAAAATCACATTTTAACCCTCAA
** * *
28388787 ACTTTAAAAAATTACATTTTTACCCCTCAA
1 ACTTTCCAAAATCACA-TTTTAACCCTCAA
* * **
28388817 ACTTTCTAAAAATCACGTTTTAACCCTTGA
1 ACTTTC-CAAAATCACATTTTAACCCTCAA
* * *
28388847 ACTTCTTCAAGATTACATTTTAACCCTCAA
1 ACTT-TCCAAAATCACATTTTAACCCTCAA
* * *
28388877 ACTTCTCCAAAATCCCATTTT-GCCCCCAA
1 ACTT-TCCAAAATCACATTTTAACCCTCAA
28388906 ACTTATCCAAAAT
1 ACTT-TCCAAAAT
28388919 TATGATTTTA
Statistics
Matches: 104, Mismatches: 25, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
29 31 0.30
30 64 0.62
31 9 0.09
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.36
Consensus pattern (29 bp):
ACTTTCCAAAATCACATTTTAACCCTCAA
Found at i:28388946 original size:29 final size:29
Alignment explanation
Indices: 28388909--28389049 Score: 171
Period size: 29 Copynumber: 4.9 Consensus size: 29
28388899 CCCCCAAACT
** *
28388909 TATCC-AAAATTATGATTTTACCCTTGAA
1 TATCCAAAAATTACCATTTTACCCTCGAA
28388937 TATCCAAAAATTACCATTTTACCCTCGAA
1 TATCCAAAAATTACCATTTTACCCTCGAA
*
28388966 CATCCAAAAATTACCATTTTACCC-CGAA
1 TATCCAAAAATTACCATTTTACCCTCGAA
28388994 TATCCAAAAAATTACCATTTTACCC-CTGAA
1 TATCC-AAAAATTACCATTTTACCCTC-GAA
* * *
28389024 CATCCAAAAATTTCAATTTTAACCCT
1 TATCCAAAAATTACCATTTT-ACCCT
28389050 AAATTCCTCG
Statistics
Matches: 100, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
28 13 0.13
29 76 0.76
30 11 0.11
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.32
Consensus pattern (29 bp):
TATCCAAAAATTACCATTTTACCCTCGAA
Found at i:28388985 original size:58 final size:59
Alignment explanation
Indices: 28388910--28389049 Score: 189
Period size: 58 Copynumber: 2.4 Consensus size: 59
28388900 CCCCAAACTT
** *
28388910 ATCC-AAAATTATGATTTTACCCTTGAATATCC-AAAAATTACCATTTTA-CCCTCGAAC
1 ATCCAAAAATTACAATTTTACCCTCGAATATCCAAAAAATTACCATTTTACCCCT-GAAC
*
28388967 ATCCAAAAATTACCATTTTACCC-CGAATATCCAAAAAATTACCATTTTACCCCTGAAC
1 ATCCAAAAATTACAATTTTACCCTCGAATATCCAAAAAATTACCATTTTACCCCTGAAC
*
28389025 ATCCAAAAATTTCAATTTTAACCCT
1 ATCCAAAAATTACAATTTT-ACCCT
28389050 AAATTCCTCG
Statistics
Matches: 73, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
57 12 0.16
58 53 0.73
59 8 0.11
ACGTcount: A:0.39, C:0.26, G:0.04, T:0.31
Consensus pattern (59 bp):
ATCCAAAAATTACAATTTTACCCTCGAATATCCAAAAAATTACCATTTTACCCCTGAAC
Found at i:28391303 original size:10 final size:10
Alignment explanation
Indices: 28391288--28391337 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
28391278 CTATGTTGTT
*
28391288 TCCGAAGTAA
1 TCCGAAGCAA
28391298 TCCGAAGCAA
1 TCCGAAGCAA
28391308 TCCGAAGCTAA
1 TCCGAAGC-AA
*
28391319 --GGAATGCAA
1 TCCGAA-GCAA
28391328 TCCGAAGCAA
1 TCCGAAGCAA
28391338 AAAAATTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
9 5 0.15
10 23 0.70
11 5 0.15
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.14
Consensus pattern (10 bp):
TCCGAAGCAA
Found at i:28397610 original size:39 final size:39
Alignment explanation
Indices: 28397562--28398096 Score: 308
Period size: 39 Copynumber: 13.7 Consensus size: 39
28397552 CAGCCATTCG
*
28397562 ATCTTTTACCCCGAGCTTAGGGCAGATCACCATCAGCCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
* * * * * ***
28397601 ATCTCTTACCCCGAGCTTGGGACAAATTACAATCATTTA
1 ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
* * *
28397640 ATCTTTTACCTCGAGCCTGGGGCAGATCACTATCAGCCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
* ** *
28397679 ATCTCTTACCCCGAGCTCAGGGCAGATTGTAGCCATTC-G---
1 ATCTTTTACCCCGAGCTTGGGGCAGA-T-CA-CCA-TCAGCCA
*
28397718 ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAACCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
* * * ** * * ** *
28397757 ATCTCTTACCCTGAGC-TGGGGTAGATTGCAACCATTCG
1 ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
* * * * *
28397795 ATCTTTTACACTGAGCCTGGGGCAAATCACCATTAGCCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
* * *
28397834 TTCGATCTTTTACCCTGAGCCTAGGGCAGATTCTAGCCATTC-G---
1 ----ATCTTTTACCCCGAGCTTGGGGCAGA-TC-A-CCA-TCAGCCA
* ** * *
28397877 ATCTTTTACCCTGAGCTTAAGGCATATCACCATCAGTCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
* *
28397916 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCTG---
1 ATCTTTTACCCCGAGCTTGGGGCAGA-T-CA-CCATCAGCCA
* *
28397955 -TCTTTTACCCCGAGCCT-GGGTAGATCACCATCAGCCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
* * * ** * * * *
28397992 ATCTCTTACCTCGAGCTCGGGGCAGAT-TGCAGCCGTTCG
1 ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAG-CCA
* *
28398031 ATCTTTTACCTCGAGCTTGGGGCAGATCACCATCAGCGA
1 ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
* *
28398070 ATCTCTCACCCCGAGCTTGGGGCAGAT
1 ATCTTTTACCCCGAGCTTGGGGCAGAT
28398097 TGCAACCATC
Statistics
Matches: 372, Mismatches: 93, Indels: 62
0.71 0.18 0.12
Matches are distributed among these distances:
34 6 0.02
35 6 0.02
36 8 0.02
37 8 0.02
38 63 0.17
39 230 0.62
40 6 0.02
41 3 0.01
42 9 0.02
43 25 0.07
44 2 0.01
45 1 0.00
46 4 0.01
47 1 0.00
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.27
Consensus pattern (39 bp):
ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCA
Found at i:28397836 original size:43 final size:39
Alignment explanation
Indices: 28397788--28397892 Score: 138
Period size: 43 Copynumber: 2.6 Consensus size: 39
28397778 TAGATTGCAA
* *
28397788 CCATTCGATCTTTTACACTGAGCCTGGGGCAAATCACCATTAG
1 CCATTCGATCTTTTACCCTGAGCCTAGGGCAAAT--CC--TAG
* *
28397831 CCATTCGATCTTTTACCCTGAGCCTAGGGCAGATTCTAG
1 CCATTCGATCTTTTACCCTGAGCCTAGGGCAAATCCTAG
28397870 CCATTCGATCTTTTACCCTGAGC
1 CCATTCGATCTTTTACCCTGAGC
28397893 TTAAGGCATA
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
39 26 0.45
41 1 0.02
43 31 0.53
ACGTcount: A:0.22, C:0.30, G:0.18, T:0.30
Consensus pattern (39 bp):
CCATTCGATCTTTTACCCTGAGCCTAGGGCAAATCCTAG
Found at i:28398118 original size:78 final size:78
Alignment explanation
Indices: 28397523--28398105 Score: 681
Period size: 78 Copynumber: 7.5 Consensus size: 78
28397513 GAAGATTTCG
* * * *
28397523 ATCTCTTACCCTGAGCTTGGAGTAGATTGCAGCCATTCGATCTTTTACCCCGAGCTTAGGGCAGA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATTCGATCTTTTACCCCGAGCTTGGGGCAGA
28397588 TCACCATCAGCCA
66 TCACCATCAGCCA
* * * ** ** * *
28397601 ATCTCTTACCCCGAGCTTGGGACAAATTACAATCATTTAATCTTTTACCTCGAGCCTGGGGCAGA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATTCGATCTTTTACCCCGAGCTTGGGGCAGA
*
28397666 TCACTATCAGCCA
66 TCACCATCAGCCA
** *
28397679 ATCTCTTACCCCGAGCTCAGGGCAGATTGTAGCCATTCGATCTTTTACCCCGAGCTTGGGGCAGA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATTCGATCTTTTACCCCGAGCTTGGGGCAGA
*
28397744 TCACCATCAACCA
66 TCACCATCAGCCA
* * * * * * *
28397757 ATCTCTTACCCTGAGC-TGGGGTAGATTGCAACCATTCGATCTTTTACACTGAGCCTGGGGCAAA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATTCGATCTTTTACCCCGAGCTTGGGGCAGA
*
28397821 TCACCATTAGCCA
66 TCACCATCAGCCA
* * * * * **
28397834 TTCGATCTTTTACCCTGAGCCTAGGGCAGATT-CTAGCCATTCGATCTTTTACCCTGAGCTTAAG
1 ----ATCTCTTACCCCGAGCTTGGGGCAGATTGC-AGCCATTCGATCTTTTACCCCGAGCTTGGG
* *
28397898 GCATATCACCATCAGTCA
61 GCAGATCACCATCAGCCA
* *
28397916 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCA-TCTG-TCTTTTACCCCGAGCCT-GGGTAG
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATTC-GATCTTTTACCCCGAGCTTGGGGCAG
28397978 ATCACCATCAGCCA
65 ATCACCATCAGCCA
* * * *
28397992 ATCTCTTACCTCGAGCTCGGGGCAGATTGCAGCCGTTCGATCTTTTACCTCGAGCTTGGGGCAGA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATTCGATCTTTTACCCCGAGCTTGGGGCAGA
*
28398057 TCACCATCAGCGA
66 TCACCATCAGCCA
* *
28398070 ATCTCTCACCCCGAGCTTGGGGCAGATTGCAACCAT
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCAT
28398106 CCAATATCTT
Statistics
Matches: 421, Mismatches: 73, Indels: 22
0.82 0.14 0.04
Matches are distributed among these distances:
76 49 0.12
77 84 0.20
78 222 0.53
79 1 0.00
81 16 0.04
82 49 0.12
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.27
Consensus pattern (78 bp):
ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATTCGATCTTTTACCCCGAGCTTGGGGCAGA
TCACCATCAGCCA
Found at i:28400271 original size:29 final size:29
Alignment explanation
Indices: 28400229--28400488 Score: 138
Period size: 29 Copynumber: 8.9 Consensus size: 29
28400219 CAAAAGGTCA
*
28400229 CTAAACTTTCTAAAATTACATTTTTGCCC
1 CTAAACTTTTTAAAATTACATTTTTGCCC
* *
28400258 CTAAACTTTTTAAAACTACATTTTTACCC
1 CTAAACTTTTTAAAATTACATTTTTGCCC
* ** * *
28400287 TTAAACTTTCCAAAAATA-ATGTTTTGACC
1 CTAAACTTTTTAAAATTACAT-TTTTGCCC
*
28400316 CTAAACTTTTCTAAAATTACA--TTTGAACC
1 CTAAACTTTT-TAAAATTACATTTTTG-CCC
* * * **
28400345 CTAAAATTTTCCAAAATCACATTTTAACCC
1 CTAAACTTTT-TAAAATTACATTTTTGCCC
* * *
28400375 TTAAACATTTCTAAAATTATA-TTTTGACCC
1 CTAAAC-TTTTTAAAATTACATTTTTG-CCC
* * * **
28400405 TTAAAC-TTTCAAAATCACATTTTAACCC
1 CTAAACTTTTTAAAATTACATTTTTGCCC
* *
28400433 TTAAA-TTTCTCTAAGATTACA-TTTTGACCC
1 CTAAACTTT-T-TAAAATTACATTTTTG-CCC
* **
28400463 CTAAACTTCTCTAAAATCCCATTTTT
1 CTAAACTT-TTTAAAATTACATTTTT
28400489 CGATGTTCGT
Statistics
Matches: 172, Mismatches: 43, Indels: 30
0.70 0.18 0.12
Matches are distributed among these distances:
28 25 0.15
29 85 0.49
30 49 0.28
31 12 0.07
32 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.40
Consensus pattern (29 bp):
CTAAACTTTTTAAAATTACATTTTTGCCC
Found at i:28400377 original size:88 final size:86
Alignment explanation
Indices: 28400229--28400479 Score: 258
Period size: 88 Copynumber: 2.9 Consensus size: 86
28400219 CAAAAGGTCA
* * *
28400229 CTAAACTTTCTAAAATTACATTTTTG-CCCCTAAACTTTT-TAAAA-CTACATTTTTACCCTTAA
1 CTAAACTTTCTAAAATTACA--TTTGAACCCTAAAATTTTCTAAAATC-ACATTTTAACCCTTAA
*
28400291 ACTTTCCAAAAATAATGTTTTGACC
63 ACTTT-CAAAAATAATATTTTGACC
*
28400316 CTAAACTTTTCTAAAATTACATTTGAACCCTAAAATTTTCCAAAATCACATTTTAACCCTTAAAC
1 CTAAAC-TTTCTAAAATTACATTTGAACCCTAAAATTTTCTAAAATCACATTTTAACCCTTAAAC
* *
28400381 ATTTCTAAAATTATATTTTGACC
65 -TTTCAAAAATAATATTTTGACC
* * * * * * *
28400404 CTTAAACTTTC-AAAATCACATTTTAACCCTTAAATTTCTCTAAGATTACATTTTGACCCCTAAA
1 C-TAAACTTTCTAAAATTACATTTGAACCCTAAAATTT-TCTAAAATCACATTTTAACCCTTAAA
*
28400468 CTTCTCTAAAAT
64 CTT-TCAAAAAT
28400480 CCCATTTTTC
Statistics
Matches: 141, Mismatches: 15, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
86 4 0.03
87 42 0.30
88 86 0.61
89 9 0.06
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (86 bp):
CTAAACTTTCTAAAATTACATTTGAACCCTAAAATTTTCTAAAATCACATTTTAACCCTTAAACT
TTCAAAAATAATATTTTGACC
Found at i:28400426 original size:58 final size:59
Alignment explanation
Indices: 28400230--28400487 Score: 274
Period size: 58 Copynumber: 4.4 Consensus size: 59
28400220 AAAAGGTCAC
* ** * * *
28400230 TAAACTTTCTAAAATTACATTTTTGCCCCTAAACTTTT-TAAAACTACATTTTTACCCT
1 TAAACTTTCTAAAATCACATTTTAACCCTTAAACTTTTCTAAAATTACATTTTGACCCT
* * ** *
28400288 TAAACTTTCCAAAAATAATGTTTTGACCC-TAAACTTTTCTAAAATTACA-TTTGAACCCT
1 TAAACTTT-CTAAAATCACATTTTAACCCTTAAACTTTTCTAAAATTACATTTTG-ACCCT
* * * * *
28400347 AAAATTTTCCAAAATCACATTTTAACCCTTAAACATTTCTAAAATTATATTTTGACCCT
1 TAAACTTTCTAAAATCACATTTTAACCCTTAAACTTTTCTAAAATTACATTTTGACCCT
* *
28400406 TAAACTTTC-AAAATCACATTTTAACCCTTAAA-TTTCTCTAAGATTACATTTTGACCCC
1 TAAACTTTCTAAAATCACATTTTAACCCTTAAACTTT-TCTAAAATTACATTTTGACCCT
*
28400464 TAAACTTCTCTAAAATCCCATTTT
1 TAAACTT-TCTAAAATCACATTTT
28400488 TCGATGTTCG
Statistics
Matches: 168, Mismatches: 24, Indels: 14
0.82 0.12 0.07
Matches are distributed among these distances:
57 2 0.01
58 84 0.50
59 66 0.39
60 16 0.10
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.40
Consensus pattern (59 bp):
TAAACTTTCTAAAATCACATTTTAACCCTTAAACTTTTCTAAAATTACATTTTGACCCT
Found at i:28400486 original size:30 final size:29
Alignment explanation
Indices: 28400229--28400487 Score: 204
Period size: 30 Copynumber: 8.8 Consensus size: 29
28400219 CAAAAGGTCA
*
28400229 CTAAACTTTCTAAAATTACATTTTTG-CCC
1 CTAAACTTTCTAAAATCACA-TTTTGACCC
* *
28400258 CTAAACTTTTTAAAA-CTACATTTTTACCC
1 CTAAACTTTCTAAAATC-ACATTTTGACCC
* * * **
28400287 TTAAACTTTCCAAAAATAATGTTTTGA-CC
1 CTAAACTTT-CTAAAATCACATTTTGACCC
* *
28400316 CTAAACTTTTCTAAAATTACA-TTTGAACC
1 CTAAAC-TTTCTAAAATCACATTTTGACCC
* * *
28400345 CTAAAATTTTCCAAAATCACATTTTAACCC
1 CT-AAACTTTCTAAAATCACATTTTGACCC
* * *
28400375 TTAAACATTTCTAAAATTATATTTTGACCC
1 CTAAAC-TTTCTAAAATCACATTTTGACCC
* *
28400405 TTAAACTTTC-AAAATCACATTTTAACCC
1 CTAAACTTTCTAAAATCACATTTTGACCC
* * * *
28400433 TTAAATTTCTCTAAGATTACATTTTGACCC
1 CTAAACTT-TCTAAAATCACATTTTGACCC
*
28400463 CTAAACTTCTCTAAAATCCCATTTT
1 CTAAACTT-TCTAAAATCACATTTT
28400488 TCGATGTTCG
Statistics
Matches: 181, Mismatches: 38, Indels: 21
0.75 0.16 0.09
Matches are distributed among these distances:
28 31 0.17
29 67 0.37
30 83 0.46
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (29 bp):
CTAAACTTTCTAAAATCACATTTTGACCC
Found at i:28403910 original size:29 final size:30
Alignment explanation
Indices: 28403862--28404247 Score: 135
Period size: 29 Copynumber: 13.1 Consensus size: 30
28403852 TAAAACATAA
* *
28403862 TTTTGGAAAGTTTTAGGGGTAAAAATGTCAT
1 TTTTGGAAA-ATTTAGGGGTAAAAATGTAAT
* * * *
28403893 TTTAGGAAAATTTA-GGGTAAAATTATGAT
1 TTTTGGAAAATTTAGGGGTAAAAATGTAAT
* *
28403922 TTTTGG-AAGTTTAGGGGTGAAAATGTAAT
1 TTTTGGAAAATTTAGGGGTAAAAATGTAAT
* * * * *
28403951 TTTTGG--AAGTTCGAGAGCAAAAATATAAT
1 TTTTGGAAAATTTAG-GGGTAAAAATGTAAT
* * *
28403980 TTTT-GAGAAGTTT-GAGGGCAAAAATGTGAT
1 TTTTGGA-AAATTTAG-GGGTAAAAATGTAAT
* *
28404010 TTTTGG-AAGTTTAGGGGCAAAAATGTAAT
1 TTTTGGAAAATTTAGGGGTAAAAATGTAAT
* * * *
28404039 TTTT-GAGAAGTTCGGGGT-AAAATGTGAT
1 TTTTGGAAAATTTAGGGGTAAAAATGTAAT
* ** * *
28404067 TTTT-GAGAAGTTT-GGTACTCAAAATGTTAT
1 TTTTGGA-AAATTTAGG-GGTAAAAATGTAAT
** * *
28404097 TTTTGG-ATTTTTAAGGG-CAAAATGTAAT
1 TTTTGGAAAATTTAGGGGTAAAAATGTAAT
* * *
28404125 TTTT--AAGAAGTTCAAGGGTAAAAAAAGTAAT
1 TTTTGGAA-AA-TTTAGGGGT-AAAAATGTAAT
* * * * * *
28404156 TTTT-GACAAGTTCGAGGCTTAAAATGTGA-
1 TTTTGGAAAATTTAG-GGGTAAAAATGTAAT
* * *
28404185 TTTTAGAAAAGTTTAAGGGTTAAAATGTAA-
1 TTTTGGAAAA-TTTAGGGGTAAAAATGTAAT
*
28404215 TTTTGGAAAAGTTTAAGGGT-AAAATGTAAT
1 TTTTGGAAAA-TTTAGGGGTAAAAATGTAAT
28404245 TTT
1 TTT
28404248 AAAAAAGTTT
Statistics
Matches: 269, Mismatches: 63, Indels: 47
0.71 0.17 0.12
Matches are distributed among these distances:
27 1 0.00
28 43 0.16
29 108 0.40
30 83 0.31
31 33 0.12
32 1 0.00
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (30 bp):
TTTTGGAAAATTTAGGGGTAAAAATGTAAT
Found at i:28403951 original size:88 final size:88
Alignment explanation
Indices: 28403842--28404052 Score: 207
Period size: 88 Copynumber: 2.4 Consensus size: 88
28403832 AGTTTTGAAG
* ** * * * *
28403842 AGTTTAGGGTTAAAACA--TAATTTTGGAAAGTTTTAGGGGTAAAAATGTCATTTTAGGA-AAAT
1 AGTTTAGGGGTAAAA-ATGTAATTTTGGAAAGTTCGA-GAGCAAAAATATAATTTT-GGAGAAAT
* *
28403904 TT-AGGGTAAAATTATGATTTTTGGA
63 TTGAGGGCAAAAATATGATTTTTGGA
* * *
28403929 AGTTTAGGGGTGAAAATGTAATTTTTGG-AAGTTCGAGAGCAAAAATATAATTTTTGAGAAGTTT
1 AGTTTAGGGGTAAAAATGTAA-TTTTGGAAAGTTCGAGAGCAAAAATATAATTTTGGAGAAATTT
*
28403993 GAGGGCAAAAATGTGATTTTTGGA
65 GAGGGCAAAAATATGATTTTTGGA
* *
28404017 AGTTTAGGGGCAAAAATGTAATTTTTGAGAAGTTCG
1 AGTTTAGGGGTAAAAATGTAATTTTGGA-AAGTTCG
28404053 GGGTAAAATG
Statistics
Matches: 101, Mismatches: 16, Indels: 12
0.78 0.12 0.09
Matches are distributed among these distances:
86 3 0.03
87 37 0.37
88 48 0.48
89 13 0.13
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.36
Consensus pattern (88 bp):
AGTTTAGGGGTAAAAATGTAATTTTGGAAAGTTCGAGAGCAAAAATATAATTTTGGAGAAATTTG
AGGGCAAAAATATGATTTTTGGA
Found at i:28404001 original size:30 final size:30
Alignment explanation
Indices: 28403920--28404247 Score: 221
Period size: 30 Copynumber: 11.2 Consensus size: 30
28403910 TAAAATTATG
**
28403920 ATTTTTG-GAAGTTT-AGGGGTGAAAATGTA
1 ATTTTTGAGAAGTTTGA-GGGCAAAAATGTA
* * *
28403949 ATTTTTG-GAAGTTCGAGAGCAAAAATATA
1 ATTTTTGAGAAGTTTGAGGGCAAAAATGTA
*
28403978 ATTTTTGAGAAGTTTGAGGGCAAAAATGTG
1 ATTTTTGAGAAGTTTGAGGGCAAAAATGTA
28404008 ATTTTTG-GAAGTTT-AGGGGCAAAAATGTA
1 ATTTTTGAGAAGTTTGA-GGGCAAAAATGTA
* * *
28404037 ATTTTTGAGAAGTTCG-GGG-TAAAATGTG
1 ATTTTTGAGAAGTTTGAGGGCAAAAATGTA
** * *
28404065 ATTTTTGAGAAGTTTG-GTACTCAAAATGTT
1 ATTTTTGAGAAGTTTGAGGGC-AAAAATGTA
** *
28404095 ATTTTTG-GATTTTTAAGGGC-AAAATGTA
1 ATTTTTGAGAAGTTTGAGGGCAAAAATGTA
* ** * *
28404123 ATTTTTAAGAAGTTCAAGGGTAAAAAAAGTA
1 ATTTTTGAGAAGTTTGAGGG-CAAAAATGTA
* * * *
28404154 ATTTTTGACAAGTTCGA-GGCTTAAAATGTG
1 ATTTTTGAGAAGTTTGAGGGC-AAAAATGTA
* * * **
28404184 ATTTTAGAAAAGTTTAAGGGTTAAAATGTA
1 ATTTTTGAGAAGTTTGAGGGCAAAAATGTA
* * * *
28404214 ATTTTGGAAAAGTTTAAGGG-TAAAATGTA
1 ATTTTTGAGAAGTTTGAGGGCAAAAATGTA
28404243 ATTTT
1 ATTTT
28404248 AAAAAAGTTT
Statistics
Matches: 242, Mismatches: 44, Indels: 26
0.78 0.14 0.08
Matches are distributed among these distances:
28 37 0.15
29 86 0.36
30 96 0.40
31 23 0.10
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.37
Consensus pattern (30 bp):
ATTTTTGAGAAGTTTGAGGGCAAAAATGTA
Found at i:28404090 original size:59 final size:56
Alignment explanation
Indices: 28403920--28404081 Score: 191
Period size: 59 Copynumber: 2.8 Consensus size: 56
28403910 TAAAATTATG
* * *
28403920 ATTTTTG-GAAGTTTAGGGGTGAAAATGTAATTTTTGGAAGTTCGAGAGCAAAAATATA
1 ATTTTTGAGAAG-TTAGGGGT-AAAATGTGATTTTTGGAAGTTTG-GAGCAAAAATGTA
** *
28403978 ATTTTTGAGAAGTTTGAGGGCAAAAATGTGATTTTTGGAAGTTTAGGGGCAAAAATGTA
1 ATTTTTGAGAAG-TT-AGGGGTAAAATGTGATTTTTGGAAGTTT-GGAGCAAAAATGTA
*
28404037 ATTTTTGAGAAGTTCGGGGTAAAATGTGATTTTTGAGAAGTTTGG
1 ATTTTTGAGAAGTTAGGGGTAAAATGTGATTTTTG-GAAGTTTGG
28404082 TACTCAAAAT
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
57 20 0.22
58 16 0.18
59 50 0.55
60 5 0.05
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.36
Consensus pattern (56 bp):
ATTTTTGAGAAGTTAGGGGTAAAATGTGATTTTTGGAAGTTTGGAGCAAAAATGTA
Found at i:28404091 original size:117 final size:117
Alignment explanation
Indices: 28403853--28404247 Score: 297
Period size: 117 Copynumber: 3.4 Consensus size: 117
28403843 GTTTAGGGTT
* * * * * * * * *
28403853 AAAACATAATTTTGGA-AAGTTTTAGGGGTAAAAATGTCATTTTAGGAAAATTTAGGGTAAAATT
1 AAAATATAATTTTTGAGAAG-TTTAAGGGCAAAAATGTAATTTTTGG-AAGTTTAGGGGAAAA-A
* * *
28403917 ATG--ATTTTTG-GAAGTTTAGGGGTGAAAATGTAATTTTTG-GAAGTTCGAGAGCA
63 ATGTAATTTTTGAGAAG-TTCGGGGT-AAAATGTGATTTTTGAGAAGTTTGAGAGCA
* * *
28403970 AAAATATAATTTTTGAGAAGTTTGAGGGCAAAAATGTGATTTTTGGAAGTTTAGGGGCAAAAATG
1 AAAATATAATTTTTGAGAAGTTTAAGGGCAAAAATGTAATTTTTGGAAGTTTAGGGGAAAAAATG
*
28404035 TAATTTTTGAGAAGTTCGGGGTAAAATGTGATTTTTGAGAAGTTTG-GTA-CTC
66 TAATTTTTGAGAAGTTCGGGGTAAAATGTGATTTTTGAGAAGTTTGAG-AGC-A
* * ** * * *
28404087 AAAATGTTATTTTTG-GATTTTTAAGGGC-AAAATGTAATTTTTAAGAAGTTCAAGGGTAAAAAA
1 AAAATATAATTTTTGAGAAGTTTAAGGGCAAAAATGTAATTTTT-GGAAGTT-TAGGGGAAAAAA
* * * * * * * **
28404150 AGTAATTTTTGACAAGTTCGAGGCTTAAAATGTGATTTTAGAAAAGTTTAAGGGTT
64 TGTAATTTTTGAGAAGTTCG-GG-GTAAAATGTGATTTTTGAGAAGTTTGAGAGCA
* * * *
28404206 AAAATGTAATTTTGGAAAAGTTTAAGGG-TAAAATGTAATTTT
1 AAAATATAATTTTTGAGAAGTTTAAGGGCAAAAATGTAATTTT
28404248 AAAAAAGTTT
Statistics
Matches: 224, Mismatches: 39, Indels: 27
0.77 0.13 0.09
Matches are distributed among these distances:
115 16 0.07
116 44 0.20
117 97 0.43
118 9 0.04
119 35 0.16
120 23 0.10
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.36
Consensus pattern (117 bp):
AAAATATAATTTTTGAGAAGTTTAAGGGCAAAAATGTAATTTTTGGAAGTTTAGGGGAAAAAATG
TAATTTTTGAGAAGTTCGGGGTAAAATGTGATTTTTGAGAAGTTTGAGAGCA
Found at i:28404247 original size:59 final size:57
Alignment explanation
Indices: 28403834--28404257 Score: 188
Period size: 59 Copynumber: 7.2 Consensus size: 57
28403824 GAAAATACAG
* ** * *
28403834 TTTT-GAAGAGTTTAGGGTTAAAACATAATTTTGGAAAGTTTTAGGGGTAAAAATGTCA
1 TTTTAGAAAAGTTTAGGGTTAAAATGTAATTTTGGAAAG-TTTAAGGGT-AAAATGTAA
*
28403892 TTTTAGGAAAA-TTTAGGG-TAAAAT-TATGATTTTTGG-AAGTTTAGGGGTGAAAATGTAA
1 TTTTA-GAAAAGTTTAGGGTTAAAATGTA--A-TTTTGGAAAGTTTAAGGGT-AAAATGTAA
* * * * ** * * * * *
28403950 TTTTTG-GAAGTTCGAGAGCAAAAATATAATTTTTGAGAAGTTTGAGGGCAAAAATGTGA
1 TTTTAGAAAAGTT-TAGGGTTAAAATGTAATTTTGGA-AAGTTTAAGGG-TAAAATGTAA
* * ** * ** *
28404009 TTTTTG-GAAGTTTAGGGGCAAAAATGTAATTTTTGAGAAG-TTCGGGGTAAAATGTGA
1 TTTTAGAAAAGTTTA-GGGTTAAAATGTAATTTTGGA-AAGTTTAAGGGTAAAATGTAA
* * * ** *
28404066 TTTTTGAGAAGTTT--GGTACTCAAAATGTTATTTTTGG-ATTTTTAAGGGCAAAATGTAA
1 TTTTAGAAAAGTTTAGGGT--T-AAAATG-TAATTTTGGAAAGTTTAAGGGTAAAATGTAA
* * * * * ** * *
28404124 TTTTTA-AGAAGTTCAAGGGTAAAAAAAGTAATTTTTGACAAGTTCGAGGCTTAAAATGTGA
1 -TTTTAGAAAAGTT-TAGGGT-TAAAATGTAATTTTGGA-AAGTTTAAGG-GTAAAATGTAA
28404185 TTTTAGAAAAGTTTAAGGGTTAAAATGTAATTTTGGAAAAGTTTAAGGGTAAAATGTAA
1 TTTTAGAAAAGTTT-AGGGTTAAAATGTAATTTTGG-AAAGTTTAAGGGTAAAATGTAA
*
28404244 TTTTAAAAAAGTTT
1 TTTTAGAAAAGTTT
28404258 GGGGGGTCAA
Statistics
Matches: 283, Mismatches: 54, Indels: 57
0.72 0.14 0.14
Matches are distributed among these distances:
55 2 0.01
56 2 0.01
57 26 0.09
58 80 0.28
59 106 0.37
60 44 0.16
61 23 0.08
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.37
Consensus pattern (57 bp):
TTTTAGAAAAGTTTAGGGTTAAAATGTAATTTTGGAAAGTTTAAGGGTAAAATGTAA
Found at i:28406560 original size:78 final size:78
Alignment explanation
Indices: 28406469--28406914 Score: 504
Period size: 78 Copynumber: 5.7 Consensus size: 78
28406459 ATTTGCACCT
* ** * * *
28406469 AGCTCGGGGTAAGATATTGATTGATGGTGATCAGCCCTAGGCTCGGGGTAAAATATCGGATGACT
1 AGCTCGGGGTAAGAGATTGGCTGATGGTGATCAGCCCTAGGCTCGGGGTAAAAGATCGAATGGCT
28406534 GTAATCTG-CCCA
66 GTAATCTGCCCCA
** * *
28406546 AGGCTCGGGGTAAGAGATTGGCTGATGGTGATTTGCTCTAGGCTCGGGGTAAAAGATCAAATGGC
1 A-GCTCGGGGTAAGAGATTGGCTGATGGTGATCAGCCCTAGGCTCGGGGTAAAAGATCGAATGGC
*
28406611 TATAATCTGCCCCA
65 TGTAATCTGCCCCA
* * *
28406625 AGCTTGGGGTAAGAGATTGGCTGATGATGATCTGCCCTAGGCTCGGGGTAAAAGATCGAATGGCT
1 AGCTCGGGGTAAGAGATTGGCTGATGGTGATCAGCCCTAGGCTCGGGGTAAAAGATCGAATGGCT
*
28406690 GCAATCTGCCCCA
66 GTAATCTGCCCCA
* * * * * * *
28406703 AGCTTGGAGTAAGAGATTGGCTGATGGTTATCTA-CCCCAAGCTCGGAGTAAAAGA-CAAAATGG
1 AGCTCGGGGTAAGAGATTGGCTGATGGTGATC-AGCCCTAGGCTCGGGGTAAAAGATC-GAATGG
* *
28406766 CTGCAATCTGCCTCA
64 CTGTAATCTGCCCCA
* * * ** * * **
28406781 GGCTCGGTGTAAGAGATTGACTGACAGTGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGATT
1 AGCTCGGGGTAAGAGATTGGCTGATGGTGATCAGCCCTAGGCTCGGGGTAAAAGATCGAATGGCT
28406846 GTAATCTGCCCCA
66 GTAATCTGCCCCA
* * *
28406859 AGCTCGAGGTAAGAGATTGGCTGATGGTGATCTA-CCCTAAGCTCGGGGTAAGAGAT
1 AGCTCGGGGTAAGAGATTGGCTGATGGTGATC-AGCCCTAGGCTCGGGGTAAAAGAT
28406915 TGGATCTATA
Statistics
Matches: 310, Mismatches: 52, Indels: 13
0.83 0.14 0.03
Matches are distributed among these distances:
77 2 0.01
78 302 0.97
79 6 0.02
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.24
Consensus pattern (78 bp):
AGCTCGGGGTAAGAGATTGGCTGATGGTGATCAGCCCTAGGCTCGGGGTAAAAGATCGAATGGCT
GTAATCTGCCCCA
Found at i:28406764 original size:156 final size:156
Alignment explanation
Indices: 28406450--28406914 Score: 569
Period size: 156 Copynumber: 3.0 Consensus size: 156
28406440 TTTTTTTTGG
* * * * * * * *
28406450 ATGGTTACAATTTGCACCTAGCTCGGGGTAAGATATTGATTGATGGTGATCAGCCCTAGGCTCGG
1 ATGGCTACAATCTGCCCCAAGCTCGGGGTAAGAGATTGACTGATGATGATCTGCCCTAGGCTCGG
* * * * *
28406515 GGTAAAATATCGGATGACTGTAATCTG-CCCAAGGCTCGGGGTAAGAGATTGGCTGATGGTGATT
66 GGTAAAAGATCGAATGACTGTAATCTGCCCCAA-GCTTGGAGTAAGAGATTGGCTGATGGTGATC
* * *
28406579 TGCTCTAGGCTCGGGGTAAAAGATCAA
130 TACCCTAAGCTCGGGGTAAAAGATCAA
* * *
28406606 ATGGCTATAATCTGCCCCAAGCTTGGGGTAAGAGATTGGCTGATGATGATCTGCCCTAGGCTCGG
1 ATGGCTACAATCTGCCCCAAGCTCGGGGTAAGAGATTGACTGATGATGATCTGCCCTAGGCTCGG
* * *
28406671 GGTAAAAGATCGAATGGCTGCAATCTGCCCCAAGCTTGGAGTAAGAGATTGGCTGATGGTTATCT
66 GGTAAAAGATCGAATGACTGTAATCTGCCCCAAGCTTGGAGTAAGAGATTGGCTGATGGTGATCT
* *
28406736 ACCCCAAGCTCGGAGTAAAAGA-CAAA
131 ACCCTAAGCTCGGGGTAAAAGATC-AA
* * * * * *
28406762 ATGGCTGCAATCTGCCTCAGGCTCGGTGTAAGAGATTGACTGA-CAGTGATCTGCCCCAGGCTCG
1 ATGGCTACAATCTGCCCCAAGCTCGGGGTAAGAGATTGACTGATGA-TGATCTGCCCTAGGCTCG
* *
28406826 GGGTAAAAGATCGAATGATTGTAATCTGCCCCAAGC-TCGAGGTAAGAGATTGGCTGATGGTGAT
65 GGGTAAAAGATCGAATGACTGTAATCTGCCCCAAGCTTGGA-GTAAGAGATTGGCTGATGGTGAT
*
28406890 CTACCCTAAGCTCGGGGTAAGAGAT
129 CTACCCTAAGCTCGGGGTAAAAGAT
28406915 TGGATCTATA
Statistics
Matches: 263, Mismatches: 41, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
155 5 0.02
156 253 0.96
157 5 0.02
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (156 bp):
ATGGCTACAATCTGCCCCAAGCTCGGGGTAAGAGATTGACTGATGATGATCTGCCCTAGGCTCGG
GGTAAAAGATCGAATGACTGTAATCTGCCCCAAGCTTGGAGTAAGAGATTGGCTGATGGTGATCT
ACCCTAAGCTCGGGGTAAAAGATCAA
Found at i:28406917 original size:39 final size:39
Alignment explanation
Indices: 28406469--28406917 Score: 260
Period size: 39 Copynumber: 11.5 Consensus size: 39
28406459 ATTTGCACCT
* ** * *
28406469 AGCTCGGGGTAAGATATTGATTGATGGTGATCAGCCCTA
1 AGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCA
* * * * * *
28406508 GGCTCGGGGTAAAATATCGGATGACT-GTAATCTG-CCCA
1 AGCTCGGGGTAAGAGATTGGCTGA-TGGTGATCTGCCCCA
* * *
28406546 AGGCTCGGGGTAAGAGATTGGCTGATGGTGATTTGCTCTA
1 A-GCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCA
* * *
28406586 GGCTCGGGGTAAAAGATCAAATGGCT-A---TAATCTGCCCCA
1 AGCTCGGGGTAAGAGAT----TGGCTGATGGTGATCTGCCCCA
* * *
28406625 AGCTTGGGGTAAGAGATTGGCTGATGATGATCTGCCCTA
1 AGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCA
* *
28406664 GGCTCGGGGTAAAAGA-T--C-GAATGGCTGCAATCTGCCCCA
1 AGCTCGGGGTAAGAGATTGGCTG-ATGG-TG--ATCTGCCCCA
* * * *
28406703 AGCTTGGAGTAAGAGATTGGCTGATGGTTATCTACCCCA
1 AGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCA
* * ** *
28406742 AGCTCGGAGTAA-A-A--GACAAAATGGCTGCAATCTGCCTCA
1 AGCTCGGGGTAAGAGATTGGC-TGATGG-TG--ATCTGCCCCA
* * * **
28406781 GGCTCGGTGTAAGAGATTGACTGACAGTGATCTGCCCCA
1 AGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCA
* * * ** * *
28406820 GGCTCGGGGTAAAAGATCGAATGATTGTAATCTGCCCCA
1 AGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCA
* * *
28406859 AGCTCGAGGTAAGAGATTGGCTGATGGTGATCTACCCTA
1 AGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCA
28406898 AGCTCGGGGTAAGAGATTGG
1 AGCTCGGGGTAAGAGATTGG
28406918 ATCTATAATC
Statistics
Matches: 311, Mismatches: 71, Indels: 56
0.71 0.16 0.13
Matches are distributed among these distances:
35 8 0.03
36 9 0.03
37 4 0.01
38 6 0.02
39 258 0.83
40 5 0.02
41 4 0.01
42 8 0.03
43 9 0.03
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (39 bp):
AGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCA
Found at i:28418547 original size:58 final size:58
Alignment explanation
Indices: 28418474--28418870 Score: 321
Period size: 58 Copynumber: 6.8 Consensus size: 58
28418464 AAAGGGGTTG
* * *
28418474 AAAATG-AAGTTTTGGAGAGTTTAGGGTTAAAACGTAATTTTAGAAAATTTTAAGGGTA
1 AAAATGTAA-TTTTGGAAAGTTTAGGGTTAAAATGTAATTTTAGAAAAGTTTAAGGGTA
* * * * * * *
28418532 AAAATGTCATTTTGGAAAG-TTCGAGGTAAAAATGTGATTTTA-AGAAGTTT-GGCGGTC
1 AAAATGTAATTTTGGAAAGTTTAG-GGTTAAAATGTAATTTTAGAAAAGTTTAAG-GGTA
* ** * * * * * *
28418589 AAAATGTGATTTTTTAAAAGTTCGAGGGTCAAAATGTGATTTTTG-GAAGTTTAGGGGTA
1 AAAATGT-AATTTTGGAAAGTT-TAGGGTTAAAATGTAATTTTAGAAAAGTTTAAGGGTA
** * * * *
28418648 AAAATGTAATTTTTTAGAAG-TTCGAGGCTAAAATGTTATTTTTG-AAAGTTT-AGGGTA
1 AAAATGTAATTTTGGA-AAGTTTAG-GGTTAAAATGTAATTTTAGAAAAGTTTAAGGGTA
* * *
28418705 AAAATGTAATTTTTGAGAAGTTTGAGGG-TAAAATGTAATTTTTGAGAAGTTTAAGGGTA
1 AAAATGTAATTTTGGA-AAGTTT-AGGGTTAAAATGTAATTTTAGAAAAGTTTAAGGGTA
* *
28418764 AAAATGTAATTTT-GATAAGTTTGAGGGTTAAAATGTAATTTT-GAAAAGTTTAAAGGTT
1 AAAATGTAATTTTGGA-AAGTTT-AGGGTTAAAATGTAATTTTAGAAAAGTTTAAGGGTA
*
28418822 AAAATGTAATTTTGGAAAAGTTTAGGGGTAAAAATGTAATTTTAGAAAA
1 AAAATGTAATTTTGG-AAAGTTTA-GGGTTAAAATGTAATTTTAGAAAA
28418871 AATTTAGGGG
Statistics
Matches: 283, Mismatches: 37, Indels: 36
0.79 0.10 0.10
Matches are distributed among these distances:
56 1 0.00
57 59 0.21
58 118 0.42
59 96 0.34
60 9 0.03
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.37
Consensus pattern (58 bp):
AAAATGTAATTTTGGAAAGTTTAGGGTTAAAATGTAATTTTAGAAAAGTTTAAGGGTA
Found at i:28418598 original size:29 final size:28
Alignment explanation
Indices: 28418491--28418865 Score: 215
Period size: 29 Copynumber: 12.9 Consensus size: 28
28418481 AGTTTTGGAG
* * * *
28418491 AGTTTAGGGTTAAAACGTAATTTTAGAAA
1 AGTTTGGGGTAAAAATGTAATTTTA-AGA
* * * *
28418520 ATTTTAAGGGTAAAAATGTCATTTT-GGAA
1 AGTTT-GGGGTAAAAATGTAATTTTAAG-A
* * *
28418549 AGTTCGAGGTAAAAATGTGATTTTAAGA
1 AGTTTGGGGTAAAAATGTAATTTTAAGA
* *
28418577 AGTTTGGCGGTCAAAATGTGATTTTTTAA-A
1 AGTTTGG-GGTAAAAATGT-A-ATTTTAAGA
* * * **
28418607 AGTTCGAGGGTCAAAATGTGATTTTTGGA
1 AGTTTG-GGGTAAAAATGTAATTTTAAGA
*
28418636 AGTTTAGGGGTAAAAATGTAATTTTTTAGA
1 AGTTT-GGGGTAAAAATGTAA-TTTTAAGA
* * * *
28418666 AGTTCGAGGCT-AAAATGTTATTTT-TGAA
1 AGTTTG-GGGTAAAAATGTAATTTTAAG-A
* *
28418694 AGTTTAGGGTAAAAATGTAATTTTTGAGA
1 AGTTTGGGGTAAAAATGTAA-TTTTAAGA
*
28418723 AGTTTGAGGGT-AAAATGTAATTTTTGAGA
1 AGTTTG-GGGTAAAAATGTAA-TTTTAAGA
* * *
28418752 AGTTTAAGGGTAAAAATGTAATTTTGATA
1 AGTTT-GGGGTAAAAATGTAATTTTAAGA
*
28418781 AGTTTGAGGGTTAAAATGTAATTTTGAA-A
1 AGTTTG-GGGTAAAAATGTAATTTT-AAGA
** *
28418810 AGTTTAAAGGTTAAAATGTAATTTTGGAA-A
1 AGTTT-GGGGTAAAAATGTAATTTT--AAGA
28418840 AGTTTAGGGGTAAAAATGTAATTTTA
1 AGTTT-GGGGTAAAAATGTAATTTTA
28418866 GAAAAAATTT
Statistics
Matches: 278, Mismatches: 46, Indels: 45
0.75 0.12 0.12
Matches are distributed among these distances:
27 4 0.01
28 44 0.16
29 134 0.48
30 89 0.32
31 7 0.03
ACGTcount: A:0.37, C:0.02, G:0.23, T:0.37
Consensus pattern (28 bp):
AGTTTGGGGTAAAAATGTAATTTTAAGA
Found at i:28418631 original size:59 final size:58
Alignment explanation
Indices: 28418496--28418865 Score: 333
Period size: 59 Copynumber: 6.3 Consensus size: 58
28418486 TGGAGAGTTT
* * * * *
28418496 AGGGTTAAAACGTAATTTTAGAAAATTTTAAGGGTAAAAATGTCA-TTTTGGAAAGTTCG
1 AGGG-TAAAATGTAATTTTA-AGAAGTTTAAGGGTAAAAATGTAATTTTTGAAAAGTTCG
* * * * *
28418555 A-GGTAAAAATGTGATTTTAAGAAGTTT-GGCGGTCAAAATGTGATTTTTTAAAAGTTCG
1 AGGGT-AAAATGTAATTTTAAGAAGTTTAAG-GGTAAAAATGTAATTTTTGAAAAGTTCG
* ** * * *
28418613 AGGGTCAAAATGTGATTTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTTAGAAGTTCG
1 AGGGT-AAAATGTAATTTTAAGAAGTTTAAGGGTAAAAATGTAATTTTTGAAAAGTTCG
* * * * *
28418672 AGGCTAAAATGTTATTTT-TGAAAGTTT-AGGGTAAAAATGTAATTTTTGAGAAGTTTG
1 AGGGTAAAATGTAATTTTAAG-AAGTTTAAGGGTAAAAATGTAATTTTTGAAAAGTTCG
* * *
28418729 AGGGTAAAATGTAATTTTTGAGAAGTTTAAGGGTAAAAATGTAA-TTTTGATAAGTTTG
1 AGGGTAAAATGTAA-TTTTAAGAAGTTTAAGGGTAAAAATGTAATTTTTGAAAAGTTCG
* * * *
28418787 AGGGTTAAAATGTAATTTTGAA-AAGTTTAAAGGTTAAAATGTAATTTTGGAAAAGTT-T
1 AGGG-TAAAATGTAATTTT-AAGAAGTTTAAGGGTAAAAATGTAATTTTTGAAAAGTTCG
28418845 AGGGGTAAAAATGTAATTTTA
1 A-GGGT-AAAATGTAATTTTA
28418866 GAAAAAATTT
Statistics
Matches: 266, Mismatches: 31, Indels: 29
0.82 0.10 0.09
Matches are distributed among these distances:
56 1 0.00
57 58 0.22
58 99 0.37
59 106 0.40
60 2 0.01
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (58 bp):
AGGGTAAAATGTAATTTTAAGAAGTTTAAGGGTAAAAATGTAATTTTTGAAAAGTTCG
Found at i:28419508 original size:190 final size:190
Alignment explanation
Indices: 28419185--28419565 Score: 753
Period size: 190 Copynumber: 2.0 Consensus size: 190
28419175 TTAAAATTAA
28419185 TCAAAAGTTCAAAAGGGATAAGATTGTAAGTTTAAAAAAAAGCGGAAGGACCAATTGTATAAATA
1 TCAAAAGTTCAAAAGGGATAAGATTGTAAGTTTAAAAAAAAGCGGAAGGACCAATTGTATAAATA
*
28419250 GATCATTTAATGAAAACACATGGATCCTAAGTTGGGTCGGGTCGGAGCTCCTGGAACGACGTGTT
66 GACCATTTAATGAAAACACATGGATCCTAAGTTGGGTCGGGTCGGAGCTCCTGGAACGACGTGTT
28419315 TCATCCTTAAAAAATCCAAGCCGAAACGACAACGTTTTGTAGGCCTATAAAAGGCCAAAT
131 TCATCCTTAAAAAATCCAAGCCGAAACGACAACGTTTTGTAGGCCTATAAAAGGCCAAAT
28419375 TCAAAAGTTCAAAAGGGATAAGATTGTAAGTTTAAAAAAAAGCGGAAGGACCAATTGTATAAATA
1 TCAAAAGTTCAAAAGGGATAAGATTGTAAGTTTAAAAAAAAGCGGAAGGACCAATTGTATAAATA
28419440 GACCATTTAATGAAAACACATGGATCCTAAGTTGGGTCGGGTCGGAGCTCCTGGAACGACGTGTT
66 GACCATTTAATGAAAACACATGGATCCTAAGTTGGGTCGGGTCGGAGCTCCTGGAACGACGTGTT
28419505 TCATCCTTAAAAAATCCAAGCCGAAACGACAACGTTTTGTAGGCCTATAAAAGGCCAAAT
131 TCATCCTTAAAAAATCCAAGCCGAAACGACAACGTTTTGTAGGCCTATAAAAGGCCAAAT
28419565 T
1 T
28419566 TCTGAAATAA
Statistics
Matches: 190, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
190 190 1.00
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.24
Consensus pattern (190 bp):
TCAAAAGTTCAAAAGGGATAAGATTGTAAGTTTAAAAAAAAGCGGAAGGACCAATTGTATAAATA
GACCATTTAATGAAAACACATGGATCCTAAGTTGGGTCGGGTCGGAGCTCCTGGAACGACGTGTT
TCATCCTTAAAAAATCCAAGCCGAAACGACAACGTTTTGTAGGCCTATAAAAGGCCAAAT
Found at i:28420833 original size:6 final size:6
Alignment explanation
Indices: 28420816--28420897 Score: 62
Period size: 6 Copynumber: 13.8 Consensus size: 6
28420806 GGACTTTTAA
* * *
28420816 TTAAATT TTAAAT TTAAAT TCAAA- ATAAAT TTAAAT TTAAA- ATAAAT
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* * * *
28420863 TTAAAC TCAAA- ATAAAT TAAAAT TTAAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TT-AAAT TTAAA
28420898 ATTAGGTTCA
Statistics
Matches: 58, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
5 10 0.17
6 37 0.64
7 11 0.19
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (6 bp):
TTAAAT
Found at i:28420844 original size:17 final size:17
Alignment explanation
Indices: 28420824--28420892 Score: 102
Period size: 17 Copynumber: 4.1 Consensus size: 17
28420814 AATTAAATTT
28420824 TAAATTTAAATTCAAAA
1 TAAATTTAAATTCAAAA
*
28420841 TAAATTTAAATTTAAAA
1 TAAATTTAAATTCAAAA
*
28420858 TAAATTTAAACTCAAAA
1 TAAATTTAAATTCAAAA
* *
28420875 TAAATTAAAATTTAAAA
1 TAAATTTAAATTCAAAA
28420892 T
1 T
28420893 TTAAAATTAG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 46 1.00
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAATTTAAATTCAAAA
Found at i:28420849 original size:34 final size:34
Alignment explanation
Indices: 28420824--28420892 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
28420814 AATTAAATTT
*
28420824 TAAATTTAAATTCAAAATAAATTTAAATTTAAAA
1 TAAATTTAAACTCAAAATAAATTTAAATTTAAAA
*
28420858 TAAATTTAAACTCAAAATAAATTAAAATTTAAAA
1 TAAATTTAAACTCAAAATAAATTTAAATTTAAAA
28420892 T
1 T
28420893 TTAAAATTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.36
Consensus pattern (34 bp):
TAAATTTAAACTCAAAATAAATTTAAATTTAAAA
Found at i:28423423 original size:45 final size:45
Alignment explanation
Indices: 28423359--28423449 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
28423349 TTTATTATTA
28423359 TAAAAATATACAATTTAATTTCGATCCCTCAAAAATAATTTTCTG
1 TAAAAATATACAATTTAATTTCGATCCCTCAAAAATAATTTTCTG
*
28423404 TAAAAATATATAATTTAATTTCGATCCCTCAAAAATAATTTTCTG
1 TAAAAATATACAATTTAATTTCGATCCCTCAAAAATAATTTTCTG
28423449 T
1 T
28423450 CTCCGCTGTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.42, C:0.14, G:0.04, T:0.40
Consensus pattern (45 bp):
TAAAAATATACAATTTAATTTCGATCCCTCAAAAATAATTTTCTG
Found at i:28425284 original size:10 final size:10
Alignment explanation
Indices: 28425241--28425329 Score: 63
Period size: 10 Copynumber: 8.8 Consensus size: 10
28425231 ATCATTATTT
*
28425241 ATTTTTTTTA
1 ATTTTTTATA
*
28425251 CTTTTTTATA
1 ATTTTTTATA
**
28425261 ATTTCCTATA
1 ATTTTTTATA
*
28425271 ATTTTTTATG
1 ATTTTTTATA
*
28425281 ATTTTGTATTA
1 ATTTTTTA-TA
* *
28425292 AATTTTAATA
1 ATTTTTTATA
*
28425302 ATCTTTTTATT
1 AT-TTTTTATA
*
28425313 ATTTTCTAT-
1 ATTTTTTATA
28425322 ATTTTTTA
1 ATTTTTTA
28425330 AAAATCTATT
Statistics
Matches: 59, Mismatches: 18, Indels: 5
0.72 0.22 0.06
Matches are distributed among these distances:
9 7 0.12
10 38 0.64
11 14 0.24
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.66
Consensus pattern (10 bp):
ATTTTTTATA
Found at i:28427938 original size:132 final size:132
Alignment explanation
Indices: 28427753--28428017 Score: 406
Period size: 132 Copynumber: 2.0 Consensus size: 132
28427743 GAATTCGGGA
**
28427753 ATTACATGTTATATGGGCGCTGGTCTTAGATGTCCTACCGATGAGTGAGATCCGGCATATGTTAC
1 ATTACATGTTATATGGGCGCTAATCTTAGATGTCCTACCGATGAGTGAGATCCGGCATATGTTAC
* * *
28427818 AGATTCTCCACAGCTTATGTGAGCAGCATTGTGTAGCTTAACATCTCGACCCAGAGCTCGTGTGA
66 AGATTCTCCACAGCTCATGTGAGCAGCATCGTGTAGCTTAACATCTCGACCCACAGCTCGTGTGA
28427883 GC
131 GC
* * * *
28427885 ATTACATGTTATATGGGTGTTAATCTTAGATGTCCTACCGATG-GCTGAGATCCGGTATATGTTG
1 ATTACATGTTATATGGGCGCTAATCTTAGATGTCCTACCGATGAG-TGAGATCCGGCATATGTTA
* * *
28427949 CGGATTCTCCACATCTCGTGTGAGCAGCATCGTGTAGCTTAACATCTCGACCCACAGCTCGTGTG
65 CAGATTCTCCACAGCTCATGTGAGCAGCATCGTGTAGCTTAACATCTCGACCCACAGCTCGTGTG
28428014 AGC
130 AGC
28428017 A
1 A
28428018 GCTCCATTTC
Statistics
Matches: 120, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
131 1 0.01
132 119 0.99
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (132 bp):
ATTACATGTTATATGGGCGCTAATCTTAGATGTCCTACCGATGAGTGAGATCCGGCATATGTTAC
AGATTCTCCACAGCTCATGTGAGCAGCATCGTGTAGCTTAACATCTCGACCCACAGCTCGTGTGA
GC
Found at i:28433243 original size:42 final size:42
Alignment explanation
Indices: 28433184--28433267 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
28433174 CAAATATTTT
* *
28433184 TAAACTCAAATATAATTTCATTCGTCAAA-AACACTCATAAAC
1 TAAACCCAAATATAATTTCATTCCT-AAATAACACTCATAAAC
*
28433226 TAAACCCAAATATAATTTTATTCCTAAATAACACTCATAAAC
1 TAAACCCAAATATAATTTCATTCCTAAATAACACTCATAAAC
28433268 AACTCCTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 3 0.08
42 35 0.92
ACGTcount: A:0.48, C:0.21, G:0.01, T:0.30
Consensus pattern (42 bp):
TAAACCCAAATATAATTTCATTCCTAAATAACACTCATAAAC
Found at i:28435411 original size:21 final size:21
Alignment explanation
Indices: 28435365--28435412 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
28435355 CAAGCAACTT
28435365 AATAT-ATATTTCAATAATTA
1 AATATAATATTTCAATAATTA
* *
28435385 ATTATAATATTT-AATATTATA
1 AATATAATATTTCAATAAT-TA
28435406 AATATAA
1 AATATAA
28435413 AATAATTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
AATATAATATTTCAATAATTA
Found at i:28435890 original size:37 final size:38
Alignment explanation
Indices: 28435841--28435920 Score: 110
Period size: 37 Copynumber: 2.1 Consensus size: 38
28435831 ATTTTAAACA
*
28435841 AATTTTATTTTTTTTCAAGATT-TTTT-ACTATTCTTTT
1 AATTTTAATTTTTTTCAA-ATTATTTTAACTATTCTTTT
* *
28435878 AATTTTAATTTTTTTCAAATTATTTTAATTATTTTTTT
1 AATTTTAATTTTTTTCAAATTATTTTAACTATTCTTTT
28435916 AATTT
1 AATTT
28435921 ACGTCCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 3 0.08
37 21 0.55
38 14 0.37
ACGTcount: A:0.26, C:0.05, G:0.01, T:0.68
Consensus pattern (38 bp):
AATTTTAATTTTTTTCAAATTATTTTAACTATTCTTTT
Found at i:28454300 original size:860 final size:859
Alignment explanation
Indices: 28452221--28454770 Score: 4012
Period size: 859 Copynumber: 3.0 Consensus size: 859
28452211 TTAGTTGTCT
* * *
28452221 AGGGTAAATTCTCTCTA-CTTGAATCCTATAAACATTTTATTACCATAAATGCACCGGATAAGAT
1 AGGGTAAATTCTCTCTATC-TGAATCCTATAAACATTTGATTACCATAAATGCACCAGATAGGAT
* *
28452285 TGCAAGTGATGAGCTTACTTGGAGAATAAGGGCACCGCAGAGGGTTCGAGTGTTCTTCTAGTTAT
65 TGCAAGTGATGAGCTTACTTGGAGAATAAGGGCACC-CAAAGGGTTCGAGTGTTCTTCTGGTTAT
* * * * * *
28452350 TGGCTCGATATAAACTCTTGACAAACGAGGAACAAACCA-AGTGAGGCATGACTTCATTTCCTTT
129 TGGCTCGAGATAGACTCTTGACAAACGAGGAACAGACTAGA-TGAGGTATGACTTCGTTTCCTTT
* * ** * *
28452414 CTATGATCGATGTGGACTGGACATAGAGTCTATAATGCATGTTGTTAGGGAGTGTGGGTTTTCTA
193 CTATGATCAATGTGGATTGGATGTAGAGTCTATAATGCATGTTGTTAGGGACTATGGGTTTTCTA
* * * *
28452479 ATTTAGTTTGAAAATCTGTTGTACTGAGAAGTGCGTGGAATGTCTTTTTTAACTTATTGCATGTT
258 ATTTAGTTTGAAAATCTATTGTACCGAGAAGTGCGTGGAATGTCTTTTTTAGCTTATTGCTTGTT
*
28452544 CGATGGAAAATTTGGAATATTGGGAATGAAGGTAATATAAAGTCTCAATATGGTGAATGACCTAC
323 CGATGGAATATTTGGAATATTGGGAATGAAGGTAATATAAAGTCTCAATATGGTGAATGACCTAC
* * * *
28452609 TTTCTTTTCTATTATTACTTGGTTTCTTTAGAAGAGTTGGAATGAATTCATCTTCACTGGGGTAA
388 TTTTTTTTCTATTATTACTTGGTTTCTTTAGAAGAGTTGAAATGAATTCATCTTCACTGCGGTGA
* * * *
28452674 GTAATAACAGCCATTCTCTCTTAGCTTTAGTTGGTGCTTAGACAAGGTCTTTATATACTAAAGGA
453 GTAACAACAGTCATGCTCTCTTAACTTTAGTTGGTGCTTAGACAAGGTCTTTATATACTAAAGGA
* *
28452739 GTGTCTGGAAATTGAGCTTGTAGATTCATGACTAAGGATTTGTGGAAATTTCCTATTCATGGATG
518 GTGTCTAGAAATTGAGCTTGTAGATTCATGACTAAGGGTTTGTGGAAATTTCCTATTCATGGATG
* * *
28452804 GGTTAAGGTGAATGTTGATGGCTCGATATCAAATTCTAGACCAAGAGCGACCATAGGTGGAGTGG
583 GGTTAAGGTGAACGTTGATGGCTCGGTATCGAATTCTAGACCAAGAGCGACCATAGGTGGAGTGG
* * * * *
28452869 TGAGAGGGCTGAATGAAAGTTGTATTAGGGGTTTTAAAATGGTGGTAGGATTGTCAAATATTTTT
648 TGAGAAGGCTGAATGGAAGTTGGA-TGGGGGTTTTGAAATGGTGGTAGGATTGTCAAATATTTTT
* * *
28452934 CATGTTGAAGCTTGAGCATTACTTGAAGGTTTGAAGTATGCTTGGGCACAAAAGTACTGTCAAGT
712 CAGGTTGAAGCTCGAGCATTACTTGAAGGTTTGAAGTATGCTTGGGCACAAAGGTACTGTCAAGT
* * * * * *
28452999 GAAGATTAAAAGTGATAATTCTCTGCTGATTATCGTTACATAAAATGGGTTAGCAGTAGCTAATA
777 GGAGATTAAAAGTGATAATTCTCTGCTGATTATCGTTATACAAAATGGGTTAGCAGCAACCAATA
28453064 AATACAAATGGTTGTTCG
842 AATACAAATGGTTGTTCG
* * * *
28453082 AGGGTAAATTCTCTATATTTGAATCTTATAAACATTTGATTATCATAAATGCACCAGATAGGATT
1 AGGGTAAATTCTCTCTATCTGAATCCTATAAACATTTGATTACCATAAATGCACCAGATAGGATT
* *
28453147 GTAAGTGATGAGCTTACTTGGAGAATAAGGGCA-CCAAAGGGTTCGAGAGTTCTTCTGGTTATTG
66 GCAAGTGATGAGCTTACTTGGAGAATAAGGGCACCCAAAGGGTTCGAGTGTTCTTCTGGTTATTG
** *
28453211 GCTCGAGATAGACTCTTGACAAACGAGGAATGGACTAGATGAGGTATGACTTCGTTTTCTTTCTA
131 GCTCGAGATAGACTCTTGACAAACGAGGAACAGACTAGATGAGGTATGACTTCGTTTCCTTTCTA
28453276 TGATCAATGTGGATTGGATGTAGAGTCTATAATGCATGTTGTTAGGGACTATGGGTTTTCTAATT
196 TGATCAATGTGGATTGGATGTAGAGTCTATAATGCATGTTGTTAGGGACTATGGGTTTTCTAATT
* *
28453341 TAGTTTGAAAATCTATTGTACCGAGAAGTGCGTGGAATGTCTTTTTTAGCTTATTGCTTATTCAA
261 TAGTTTGAAAATCTATTGTACCGAGAAGTGCGTGGAATGTCTTTTTTAGCTTATTGCTTGTTCGA
* * * *
28453406 TGGAATATTGGGAATATTGGGAATGAAGGTAATATAGAGTCTCAATATGATGAATGGCCTACTTT
326 TGGAATATTTGGAATATTGGGAATGAAGGTAATATAAAGTCTCAATATGGTGAATGACCTACTTT
* * *
28453471 TTTTTCTATTATTACTTAGTTTCTTTTGAAGAGTTGAAATGAATTCATCTTTACTGCGGTGAGTA
391 TTTTTCTATTATTACTTGGTTTCTTTAGAAGAGTTGAAATGAATTCATCTTCACTGCGGTGAGTA
* *
28453536 ACAACAATCATGCTCTCTTAACTTTAGTTGGTGCTTAGACAAGGTCTTTATATACTAAAGGGGTG
456 ACAACAGTCATGCTCTCTTAACTTTAGTTGGTGCTTAGACAAGGTCTTTATATACTAAAGGAGTG
* *
28453601 TCTAGAAATTGAGCTTGTAGATTTATGACTAAGGGTTTGTGGAAATTTCTTATTCATGGATGGGT
521 TCTAGAAATTGAGCTTGTAGATTCATGACTAAGGGTTTGTGGAAATTTCCTATTCATGGATGGGT
*
28453666 TAAGGTGAACGTTGATGGCTCGGTATCGAATTCTAGACCAAGAGCGACCATAAGTGGAGTGGTGA
586 TAAGGTGAACGTTGATGGCTCGGTATCGAATTCTAGACCAAGAGCGACCATAGGTGGAGTGGTGA
* *
28453731 GAAGGCCGAATGGAAGTTGGATGGGGGCTTTGAAATGGTGGTAGGATTGTCAAATATTTTTCAGG
651 GAAGGCTGAATGGAAGTTGGATGGGGGTTTTGAAATGGTGGTAGGATTGTCAAATATTTTTCAGG
28453796 TTGAAGCTCGAGCATTACTTGAAGGTTTGAAGTATGCTTGGGCACAAAGGTACTGTCAAGTGGAG
716 TTGAAGCTCGAGCATTACTTGAAGGTTTGAAGTATGCTTGGGCACAAAGGTACTGTCAAGTGGAG
*
28453861 ATTAAAAGTGATAATTCTCTGCTGATTATCGTTATACAAAATGGGTTAGCAGCAACCAATAATTA
781 ATTAAAAGTGATAATTCTCTGCTGATTATCGTTATACAAAATGGGTTAGCAGCAACCAATAAATA
28453926 CAAATGGTTGTTCG
846 CAAATGGTTGTTCG
* *
28453940 GGGGTAAATTCTCTCTATCTGAATCCTATAAACATTTGATTACCACAAATGCACCAGATAGGATT
1 AGGGTAAATTCTCTCTATCTGAATCCTATAAACATTTGATTACCATAAATGCACCAGATAGGATT
* *
28454005 GCAAGTGATTAGCTTACTTGGAGAATAAGGGCACCACAAAGGGTTCGAGTGTTTTTCTGGTTATT
66 GCAAGTGATGAGCTTACTTGGAGAATAAGGGCACC-CAAAGGGTTCGAGTGTTCTTCTGGTTATT
*
28454070 GGCTCGAGATAGACTCTTGATAAACGAGGAACAGACTAGATGAGGTATGACTTCGTTTCCTTTCT
130 GGCTCGAGATAGACTCTTGACAAACGAGGAACAGACTAGATGAGGTATGACTTCGTTTCCTTTCT
28454135 ATGATCAATGTGGATTGGATGTAGAGTCTATAATGCATGTTGTTAGGGACTATGGGTTTTCTAAT
195 ATGATCAATGTGGATTGGATGTAGAGTCTATAATGCATGTTGTTAGGGACTATGGGTTTTCTAAT
*
28454200 TTAGTTTGAAAATATATTGTACCGAGAAGTGCGTGGAATGTCTTTTTTAGCTTATTGCTTGTTCG
260 TTAGTTTGAAAATCTATTGTACCGAGAAGTGCGTGGAATGTCTTTTTTAGCTTATTGCTTGTTCG
**
28454265 ATGGAATATTTGGAATATTGGGAATGAAGGTAATATAAAGTCTCAATATGGCAAATGACCTAC-T
325 ATGGAATATTTGGAATATTGGGAATGAAGGTAATATAAAGTCTCAATATGGTGAATGACCTACTT
* * *
28454329 TTTTTTCTATTATTACTTGGTTTCTTTGGAAGAGTTGCAATGAAATCATCTTCACTGCGGTGAGT
390 TTTTTTCTATTATTACTTGGTTTCTTTAGAAGAGTTGAAATGAATTCATCTTCACTGCGGTGAGT
*
28454394 AACAACAGTCATGCT-TACTTAACTTTAGTTGGAGCTTAGACAAGGTCTTTATATACTAAAGGAG
455 AACAACAGTCATGCTCT-CTTAACTTTAGTTGGTGCTTAGACAAGGTCTTTATATACTAAAGGAG
* * *
28454458 TGTCTATAAATTGAGCTTGTAGATTCATGACTAAGGGTTTGCGAAAATTTCCTATTCATGGATGG
519 TGTCTAGAAATTGAGCTTGTAGATTCATGACTAAGGGTTTGTGGAAATTTCCTATTCATGGATGG
* *
28454523 GTTAAGGTGAACGTTGATGGCTCGGTAACGAATTCTAGACCAAGAGCGGCCATAGGTGGAGTGGT
584 GTTAAGGTGAACGTTGATGGCTCGGTATCGAATTCTAGACCAAGAGCGACCATAGGTGGAGTGGT
* * * * * *
28454588 GAAAATGCTGAATGGAAGTTGGATGGGGGTTTTGAAATAGTGGTAAGATTGTCAAAAAATTTTCA
649 GAGAAGGCTGAATGGAAGTTGGATGGGGGTTTTGAAATGGTGGTAGGATTGTCAAATATTTTTCA
* * ** * * * * *
28454653 GGTTAAAGCTCGGGCATTTTTTGAAGGTTTAAAGTATGCTTGGGAACAAGGGTACCGTTAAGTGG
714 GGTTGAAGCTCGAGCATTACTTGAAGGTTTGAAGTATGCTTGGGCACAAAGGTACTGTCAAGTGG
* * * *
28454718 AGATTGAGAGTGATAATTCTCTGCTGATTGTCATTATACAAAATGGGTTAGCA
779 AGATTAAAAGTGATAATTCTCTGCTGATTATCGTTATACAAAATGGGTTAGCA
28454771 ACTGATACGA
Statistics
Matches: 1549, Mismatches: 135, Indels: 12
0.91 0.08 0.01
Matches are distributed among these distances:
858 266 0.17
859 920 0.59
860 274 0.18
861 89 0.06
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (859 bp):
AGGGTAAATTCTCTCTATCTGAATCCTATAAACATTTGATTACCATAAATGCACCAGATAGGATT
GCAAGTGATGAGCTTACTTGGAGAATAAGGGCACCCAAAGGGTTCGAGTGTTCTTCTGGTTATTG
GCTCGAGATAGACTCTTGACAAACGAGGAACAGACTAGATGAGGTATGACTTCGTTTCCTTTCTA
TGATCAATGTGGATTGGATGTAGAGTCTATAATGCATGTTGTTAGGGACTATGGGTTTTCTAATT
TAGTTTGAAAATCTATTGTACCGAGAAGTGCGTGGAATGTCTTTTTTAGCTTATTGCTTGTTCGA
TGGAATATTTGGAATATTGGGAATGAAGGTAATATAAAGTCTCAATATGGTGAATGACCTACTTT
TTTTTCTATTATTACTTGGTTTCTTTAGAAGAGTTGAAATGAATTCATCTTCACTGCGGTGAGTA
ACAACAGTCATGCTCTCTTAACTTTAGTTGGTGCTTAGACAAGGTCTTTATATACTAAAGGAGTG
TCTAGAAATTGAGCTTGTAGATTCATGACTAAGGGTTTGTGGAAATTTCCTATTCATGGATGGGT
TAAGGTGAACGTTGATGGCTCGGTATCGAATTCTAGACCAAGAGCGACCATAGGTGGAGTGGTGA
GAAGGCTGAATGGAAGTTGGATGGGGGTTTTGAAATGGTGGTAGGATTGTCAAATATTTTTCAGG
TTGAAGCTCGAGCATTACTTGAAGGTTTGAAGTATGCTTGGGCACAAAGGTACTGTCAAGTGGAG
ATTAAAAGTGATAATTCTCTGCTGATTATCGTTATACAAAATGGGTTAGCAGCAACCAATAAATA
CAAATGGTTGTTCG
Found at i:28461194 original size:26 final size:25
Alignment explanation
Indices: 28461161--28461213 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 25
28461151 AATTAATTAC
28461161 AAATTTAAA-TAATAAATAATATATT
1 AAATTTAAACTAATAAA-AATATATT
28461186 AAATATTAAATCCTAATAAAAATATATT
1 AAAT-TTAAA--CTAATAAAAATATATT
28461214 TTAAAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 4 0.17
26 5 0.21
28 8 0.33
29 7 0.29
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (25 bp):
AAATTTAAACTAATAAAAATATATT
Found at i:28461830 original size:107 final size:107
Alignment explanation
Indices: 28461644--28461857 Score: 410
Period size: 107 Copynumber: 2.0 Consensus size: 107
28461634 AAACACACAA
28461644 CAATTAAATCATCTTGAATTATTTCATGAGTTAGATAATTTACTAAACTTACCAAGACACCTATT
1 CAATTAAATCATCTTGAATTATTTCATGAGTTAGATAATTTACTAAACTTACCAAGACACCTATT
*
28461709 TGTTCACCCTTGTCTCCAAATTTATTTCTCTTCCTTTTATTT
66 TGTTCACCCTTGTCTCCAAATTTAGTTCTCTTCCTTTTATTT
*
28461751 CAATTAAATCATCTTGAATTATTTCATGAGTTAGATAATTTACTAAACTTATCAAGACACCTATT
1 CAATTAAATCATCTTGAATTATTTCATGAGTTAGATAATTTACTAAACTTACCAAGACACCTATT
28461816 TGTTCACCCTTGTCTCCAAATTTAGTTCTCTTCCTTTTATTT
66 TGTTCACCCTTGTCTCCAAATTTAGTTCTCTTCCTTTTATTT
28461858 TGTCAATCTT
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
107 105 1.00
ACGTcount: A:0.29, C:0.20, G:0.07, T:0.44
Consensus pattern (107 bp):
CAATTAAATCATCTTGAATTATTTCATGAGTTAGATAATTTACTAAACTTACCAAGACACCTATT
TGTTCACCCTTGTCTCCAAATTTAGTTCTCTTCCTTTTATTT
Found at i:28462093 original size:114 final size:114
Alignment explanation
Indices: 28461895--28462102 Score: 255
Period size: 114 Copynumber: 1.8 Consensus size: 114
28461885 ATACATTGGA
* * * *
28461895 CCTTTTGACGCGAGATGAAATGACACCCAAGCACTCTCTCCCGATTACTCAACCCAACATGCTCT
1 CCTTTTGACGCGAGATGAAATGACAACCAAGCACTCTCACCCCATTACTCAACCCAACATACTCT
* *
28461960 CAATTTTTTTTCTTGTTTTTGTTTT-TTTCTTTGTTTAGAATATGTTAGC
66 CAATTTTTTATCTTCTTTTT-TTTTATTTCTTTGTTTAGAATATGTTAGC
** *
28462009 CCTTTTGACGCGA-AGTGAAATGACAACCAAGCACTC-CACCCCAGTTACTCAGTCTAACATACT
1 CCTTTTGACGCGAGA-TGAAATGACAACCAAGCACTCTCACCCCA-TTACTCAACCCAACATACT
28462072 C-CGAATTTATTTAT-TTCTTTTTTTTTATTTC
64 CTC-AATTT-TTTATCTTCTTTTTTTTTATTTC
28462103 CGGTTAGCAG
Statistics
Matches: 80, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
113 11 0.14
114 65 0.81
115 4 0.05
ACGTcount: A:0.24, C:0.25, G:0.12, T:0.39
Consensus pattern (114 bp):
CCTTTTGACGCGAGATGAAATGACAACCAAGCACTCTCACCCCATTACTCAACCCAACATACTCT
CAATTTTTTATCTTCTTTTTTTTTATTTCTTTGTTTAGAATATGTTAGC
Found at i:28462866 original size:20 final size:20
Alignment explanation
Indices: 28462836--28462873 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
28462826 TTTCCTAGAC
28462836 AAATAAGAAAATAAATAAATA
1 AAATAAGAAAA-AAATAAATA
28462857 AAAT-AGAAAAAAATAAA
1 AAATAAGAAAAAAATAAA
28462874 AATAATTGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 6 0.35
21 4 0.24
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (20 bp):
AAATAAGAAAAAAATAAATA
Found at i:28466930 original size:21 final size:21
Alignment explanation
Indices: 28466888--28466931 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
28466878 CCTCAGTTTT
*
28466888 CTTTTGAAAATCTACAGTTTG
1 CTTTTGAAAATCTACAGATTG
* *
28466909 CTTTTGAAAATTTATAGATTG
1 CTTTTGAAAATCTACAGATTG
28466930 CT
1 CT
28466932 GCTGAAATTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (21 bp):
CTTTTGAAAATCTACAGATTG
Found at i:28469745 original size:15 final size:16
Alignment explanation
Indices: 28469727--28469759 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
28469717 GAAGCATAAG
28469727 AGAATG-GAAAAAAAA
1 AGAATGTGAAAAAAAA
28469742 AGAATGTTGAAAAAAAA
1 AGAATG-TGAAAAAAAA
28469759 A
1 A
28469760 TTGCTCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
17 10 0.62
ACGTcount: A:0.70, C:0.00, G:0.18, T:0.12
Consensus pattern (16 bp):
AGAATGTGAAAAAAAA
Found at i:28470076 original size:21 final size:21
Alignment explanation
Indices: 28470052--28470091 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
28470042 TAAAAACCCT
*
28470052 AAACAATAACTCTAAAAAATA
1 AAACAATAACCCTAAAAAATA
**
28470073 AAACCCTAACCCTAAAAAA
1 AAACAATAACCCTAAAAAA
28470092 CACAAGAGGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (21 bp):
AAACAATAACCCTAAAAAATA
Found at i:28474673 original size:6 final size:6
Alignment explanation
Indices: 28474662--28474686 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
28474652 CTCTTTCTTT
28474662 TGCTTA TGCTTA TGCTTA TGCTTA T
1 TGCTTA TGCTTA TGCTTA TGCTTA T
28474687 AAGTTTATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (6 bp):
TGCTTA
Found at i:28475646 original size:20 final size:21
Alignment explanation
Indices: 28475603--28475647 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
28475593 ATATGTAACT
*
28475603 TTTGTAAAATTTGTATTTGAA
1 TTTGTAAAATTTGTATTTAAA
28475624 TTTGT-AAATTTGT-TTTAAGA
1 TTTGTAAAATTTGTATTTAA-A
28475644 TTTG
1 TTTG
28475648 AATCCATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 4 0.18
20 13 0.59
21 5 0.23
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.56
Consensus pattern (21 bp):
TTTGTAAAATTTGTATTTAAA
Found at i:28479109 original size:26 final size:26
Alignment explanation
Indices: 28479063--28479113 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
28479053 AAATTTTAAG
*
28479063 ATTTTTATAAAAAATTTAAAATTTAT
1 ATTTTTATAAAAAATTAAAAATTTAT
*
28479089 ATTTTTA-AAAATATATAAAAATTTA
1 ATTTTTATAAAAAAT-TAAAAATTTA
28479114 AAAATTTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
ATTTTTATAAAAAATTAAAAATTTAT
Found at i:28479237 original size:18 final size:16
Alignment explanation
Indices: 28479204--28479236 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
28479194 ATTTTTAAAA
28479204 AATTTCAAATATATAT
1 AATTTCAAATATATAT
*
28479220 AATTTCAAATTTATAT
1 AATTTCAAATATATAT
28479236 A
1 A
28479237 TTCTATCATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTTCAAATATATAT
Found at i:28482022 original size:18 final size:21
Alignment explanation
Indices: 28481966--28482015 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
28481956 TATTGACAGT
28481966 TATTGTGTTGTATAAATACAC
1 TATTGTGTTGTATAAATACAC
28481987 TATTGTGTTGTATAAATACAC
1 TATTGTGTTGTATAAATACAC
28482008 TATTGTGT
1 TATTGTGT
28482016 ATCAATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.46
Consensus pattern (21 bp):
TATTGTGTTGTATAAATACAC
Found at i:28482025 original size:21 final size:21
Alignment explanation
Indices: 28481966--28482023 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
28481956 TATTGACAGT
**
28481966 TATTGTGTTGTATAAATACAC
1 TATTGTGTTCAATAAATACAC
**
28481987 TATTGTGTTGTATAAATACAC
1 TATTGTGTTCAATAAATACAC
28482008 TATTGTGTATCAATAA
1 TATTGTGT-TCAATAA
28482024 TAAAGATCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
21 29 0.85
22 5 0.15
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (21 bp):
TATTGTGTTCAATAAATACAC
Found at i:28483897 original size:3 final size:3
Alignment explanation
Indices: 28483889--28483946 Score: 53
Period size: 3 Copynumber: 19.3 Consensus size: 3
28483879 GTATTCAGGT
* * * * * * *
28483889 TTA TTA TTA TTA TTA TTG TTG TTA TTG TTG TTG TTA TTA CTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28483937 TTA TTA TTA T
1 TTA TTA TTA T
28483947 CATCATCATC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.24, C:0.03, G:0.09, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:28493372 original size:21 final size:20
Alignment explanation
Indices: 28493331--28493437 Score: 72
Period size: 20 Copynumber: 5.1 Consensus size: 20
28493321 AAAAATTATA
*
28493331 TTATTGTTTTGGTGCTTTTT
1 TTATTGTTTTGGTGCTGTTT
*
28493351 TTATTGTTTTGATTGCTGTTT
1 TTATTGTTTTG-GTGCTGTTT
* * * * *
28493372 TTACTCTTTT-TTACTTTTTT
1 TTATTGTTTTGGTGC-TGTTT
28493392 TTATTGCTATTTTGGTGCTGTTTT
1 TTATTG---TTTTGGTGCTG-TTT
* *
28493416 TTATTGTTTTAGTGTTGTTT
1 TTATTGTTTTGGTGCTGTTT
28493436 TT
1 TT
28493438 GCTATTATTT
Statistics
Matches: 67, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
19 3 0.04
20 24 0.36
21 24 0.36
23 5 0.07
24 11 0.16
ACGTcount: A:0.08, C:0.07, G:0.16, T:0.69
Consensus pattern (20 bp):
TTATTGTTTTGGTGCTGTTT
Found at i:28493372 original size:32 final size:33
Alignment explanation
Indices: 28493335--28493425 Score: 107
Period size: 32 Copynumber: 2.8 Consensus size: 33
28493325 ATTATATTAT
28493335 TGTTTTGGTGCT-TTTTTTATTGTTTTGATTGC
1 TGTTTTGGTGCTCTTTTTTATTGTTTTGATTGC
* * *
28493367 TGTTTT--TACTCTTTTTTACTTTTTTTTATTGC
1 TGTTTTGGTGCTCTTTTTTA-TTGTTTTGATTGC
* *
28493399 TATTTTGGTGCTGTTTTTTATTGTTTT
1 TGTTTTGGTGCTCTTTTTTATTGTTTT
28493426 AGTGTTGTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
30 3 0.06
31 7 0.15
32 22 0.46
33 6 0.12
34 10 0.21
ACGTcount: A:0.08, C:0.08, G:0.15, T:0.69
Consensus pattern (33 bp):
TGTTTTGGTGCTCTTTTTTATTGTTTTGATTGC
Found at i:28493448 original size:23 final size:22
Alignment explanation
Indices: 28493399--28493471 Score: 62
Period size: 21 Copynumber: 3.3 Consensus size: 22
28493389 TTTTTATTGC
*
28493399 TATTTTGGTGCTGTTTTT--TAT
1 TATTTT-GTGTTGTTTTTGCTAT
*
28493420 TGTTTTAGTGTTGTTTTTGCTAT
1 TATTTT-GTGTTGTTTTTGCTAT
*
28493443 TATTTT-TGTTGTTGTCTTGCTGT
1 TATTTTGTGTTGTT-T-TTGCTAT
28493466 TATTTT
1 TATTTT
28493472 TTTTGCTATT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
21 22 0.51
22 1 0.02
23 20 0.47
ACGTcount: A:0.08, C:0.05, G:0.19, T:0.67
Consensus pattern (22 bp):
TATTTTGTGTTGTTTTTGCTAT
Found at i:28493463 original size:64 final size:63
Alignment explanation
Indices: 28493337--28493463 Score: 141
Period size: 64 Copynumber: 2.0 Consensus size: 63
28493327 TATATTATTG
* * * *
28493337 TTTTGGTGCTTTTTTTATTGTTTTGATTGCTGTTTTTACTCTTTTTTACTTTTTTTTATTGCTA
1 TTTTGGTGCTTTTTTTATTGTTTTGAGTGCTGTTTTTACTATTTTTTA-TTTGTTGTATTGCTA
* * *
28493401 TTTTGGTGCTGTTTTTTATTGTTTT-AGTGTTGTTTTTGCTATTATTTT-TGTTGTTGTCTTGCT
1 TTTTGGTGCT-TTTTTTATTGTTTTGAGTGCTGTTTTTACTATT-TTTTAT-TTGTTGTATTGCT
28493464 GTTATTTTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
63 1 0.02
64 34 0.64
65 18 0.34
ACGTcount: A:0.08, C:0.08, G:0.17, T:0.68
Consensus pattern (63 bp):
TTTTGGTGCTTTTTTTATTGTTTTGAGTGCTGTTTTTACTATTTTTTATTTGTTGTATTGCTA
Found at i:28493493 original size:12 final size:12
Alignment explanation
Indices: 28493428--28493502 Score: 62
Period size: 12 Copynumber: 6.3 Consensus size: 12
28493418 ATTGTTTTAG
* *
28493428 TGTTGTTTTTGC
1 TGTTATTTTTGT
*
28493440 TATTATTTTTGT
1 TGTTATTTTTGT
* * *
28493452 TGTT-GTCTTGC
1 TGTTATTTTTGT
*
28493463 TGTTATTTTTTT
1 TGTTATTTTTGT
* *
28493475 TGCTATTTTGGT
1 TGTTATTTTTGT
28493487 TGTTATTTTTGT
1 TGTTATTTTTGT
28493499 TGTT
1 TGTT
28493503 TGGATTTTAT
Statistics
Matches: 46, Mismatches: 16, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
11 8 0.17
12 38 0.83
ACGTcount: A:0.07, C:0.05, G:0.19, T:0.69
Consensus pattern (12 bp):
TGTTATTTTTGT
Found at i:28499212 original size:18 final size:20
Alignment explanation
Indices: 28499177--28499214 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
28499167 TTGCACTTTT
*
28499177 TATATTATGTTATTTTTATA
1 TATATTATGTTATATTTATA
28499197 TATATTATG-TA-ATTTATA
1 TATATTATGTTATATTTATA
28499215 ACACATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
20 9 0.53
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
TATATTATGTTATATTTATA
Found at i:28499322 original size:8 final size:8
Alignment explanation
Indices: 28499309--28499337 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
28499299 TAATAAATAA
28499309 AAATTATT
1 AAATTATT
28499317 AAATTATT
1 AAATTATT
28499325 AAA-TATT
1 AAATTATT
28499332 AAATTA
1 AAATTA
28499338 AAATAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (8 bp):
AAATTATT
Found at i:28502010 original size:105 final size:105
Alignment explanation
Indices: 28501824--28502663 Score: 886
Period size: 105 Copynumber: 8.0 Consensus size: 105
28501814 CAGGCTACCC
* * * * ** * *
28501824 CTTTTCGGTAGTCCGGACAATCTACGTAAGCTAGAGTGTGGTTCAATAGTTTGTCTGCTAATATT
1 CTTTTCGATAGTCTGGACGATCTAGGTAAGCTAGAGTGCCGTTCAGTAGTTTGTCTGCTAAAATT
* * * *
28501889 TCTTGCAGCATCTGGGGTACTTTCTTTCATTGAAAGGACA
66 TCTTACAGCATTTTGGGTACTTTCTTTCATTGAAGGGACA
* * * * *
28501929 CTTTTCGATAGTCTGGATGATATAGGTAAGCTAGAGTGCCGTTTAGTATTTTGTCTGGTAAAATT
1 CTTTTCGATAGTCTGGACGATCTAGGTAAGCTAGAGTGCCGTTCAGTAGTTTGTCTGCTAAAATT
* *
28501994 TCTTACAGCATTTGGGGTACTTTCTTTCATTGAAGGGACG
66 TCTTACAGCATTTTGGGTACTTTCTTTCATTGAAGGGACA
* * * * * * * * *
28502034 CTTCTCAAAAGTTTGGACGATCTAGGTAAGCTATAGTGCCTTTCAGTAGTTTGTCTACTCATATT
1 CTTTTCGATAGTCTGGACGATCTAGGTAAGCTAGAGTGCCGTTCAGTAGTTTGTCTGCTAAAATT
*
28502099 TCTTACAGCATTTTGGGTACTCTCTTTCATTGAAGGGACA
66 TCTTACAGCATTTTGGGTACTTTCTTTCATTGAAGGGACA
* * * * * * * *
28502139 TTTTTCAATAGTTTGGACGATCTAGGTAAGATAAAGTGCCTTTCAGTAGTTTGTCTGCTCATATT
1 CTTTTCGATAGTCTGGACGATCTAGGTAAGCTAGAGTGCCGTTCAGTAGTTTGTCTGCTAAAATT
*
28502204 TCTTACAGCATTTTGGGTACTTTCTTTAATTGAAGGGACA
66 TCTTACAGCATTTTGGGTACTTTCTTTCATTGAAGGGACA
* *
28502244 CTTTTC-AGTAGTTTGGACGATCTAGGTAAGCTAGAGTGCCATTCAGTAGTTTGTCTGC-AAATA
1 CTTTTCGA-TAGTCTGGACGATCTAGGTAAGCTAGAGTGCCGTTCAGTAGTTTGTCTGCTAAA-A
* **
28502307 TTTCTTACAGCATTTGGGGTACTTTCTTTCATTGAACAGACA
64 TTTCTTACAGCATTTTGGGTACTTTCTTTCATTGAAGGGACA
* * ** * * * *
28502349 GTTTTCCATAGTCCAGACAATCTAGGTAAGCTAGAGCGCGGTTCGGTAGTTTGTCTGC-AAATAT
1 CTTTTCGATAGTCTGGACGATCTAGGTAAGCTAGAGTGCCGTTCAGTAGTTTGTCTGCTAAA-AT
* ** * * *
28502413 CTCGAACAGCTTTTTGGGTACTTTCTTTCGTTGAAGGGACG
65 TTCTTACAGCATTTTGGGTACTTTCTTTCATTGAAGGGACA
** * * * *
28502454 CTTTTCGATAGTCCAGA-TAGTCTAGGTAAGCTA-TGTG--GTTTAATAGTTTGTCTGCTAAAAT
1 CTTTTCGATAGTCTGGACGA-TCTAGGTAAGCTAGAGTGCCGTTCAGTAGTTTGTCTGCTAAAAT
* * * * *
28502515 TTCTTTCAGCATTTTGGGCACTTCCTTCCATTGAGGGGACA
65 TTCTTACAGCATTTTGGGTACTTTCTTTCATTGAAGGGACA
* * ** *
28502556 CTTTTTGATAGTCTGGACAATCTAGGTAA-CTTAGAGTGTGGTTCAGTAGTTTGTCTGCTAATAT
1 CTTTTCGATAGTCTGGACGATCTAGGTAAGC-TAGAGTGCCGTTCAGTAGTTTGTCTGCTAAAAT
* * * *
28502620 TTCTTACTGCATTTCGGGTACTTTCTTTCGTTGAAGGGTCA
65 TTCTTACAGCATTTTGGGTACTTTCTTTCATTGAAGGGACA
28502661 CTT
1 CTT
28502664 CTATTGACCT
Statistics
Matches: 619, Mismatches: 106, Indels: 20
0.83 0.14 0.03
Matches are distributed among these distances:
101 1 0.00
102 72 0.12
103 7 0.01
104 5 0.01
105 533 0.86
106 1 0.00
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (105 bp):
CTTTTCGATAGTCTGGACGATCTAGGTAAGCTAGAGTGCCGTTCAGTAGTTTGTCTGCTAAAATT
TCTTACAGCATTTTGGGTACTTTCTTTCATTGAAGGGACA
Found at i:28503524 original size:7 final size:7
Alignment explanation
Indices: 28503512--28503548 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
28503502 CCGCTGCATT
28503512 CTTCATG
1 CTTCATG
*
28503519 CTTCATT
1 CTTCATG
28503526 CTTCATG
1 CTTCATG
28503533 CTTCATG
1 CTTCATG
28503540 CTTCATG
1 CTTCATG
28503547 CT
1 CT
28503549 ATTTACATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.14, C:0.30, G:0.11, T:0.46
Consensus pattern (7 bp):
CTTCATG
Found at i:28503527 original size:14 final size:14
Alignment explanation
Indices: 28503508--28503548 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
28503498 TTTCCCGCTG
28503508 CATTCTTCATGCTT
1 CATTCTTCATGCTT
28503522 CATTCTTCATGCTT
1 CATTCTTCATGCTT
*
28503536 CATGCTTCATGCT
1 CATTCTTCATGCT
28503549 ATTTACATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.15, C:0.29, G:0.10, T:0.46
Consensus pattern (14 bp):
CATTCTTCATGCTT
Found at i:28513008 original size:38 final size:38
Alignment explanation
Indices: 28512966--28513249 Score: 192
Period size: 38 Copynumber: 7.6 Consensus size: 38
28512956 GTCAAGGCCG
*
28512966 ACCTTTAAAAAAGGTTGAAATAGGTATTGTCTAAGGCA
1 ACCTTTAAAAAAGGTTGAAATAGATATTGTCTAAGGCA
* * *** *
28513004 ACCTTTTAAAAAAGATTGGAATAGAT-CCATATAAGGCA
1 ACC-TTTAAAAAAGGTTGAAATAGATATTGTCTAAGGCA
*
28513042 ACC-TT-AAAAAGGTTGGAATAGACT-TTGTCTAAGGCA
1 ACCTTTAAAAAAGGTTGAAATAGA-TATTGTCTAAGGCA
* * ** *
28513078 ACCTTTAAAAAAAGTTGAAATAAACCTTGTCTAAGGAA
1 ACCTTTAAAAAAGGTTGAAATAGATATTGTCTAAGGCA
* * * *
28513116 ACC-TT-AAAAAGATT-AAGATATATTTTGTCTAAGGGA
1 ACCTTTAAAAAAGGTTGAA-ATAGATATTGTCTAAGGCA
* * * * * *
28513152 ACCTTTAAAAAAGATTGAGATAAACA-TCTCTAACGCA
1 ACCTTTAAAAAAGGTTGAAATAGATATTGTCTAAGGCA
* * **
28513189 ACCTTT--AAAAGGTTGAGATAGATCTAATCTAAGGCAA
1 ACCTTTAAAAAAGGTTGAAATAGATATTGTCTAAGGC-A
* * *
28513226 ACTTTTAAAAAAAGTTGAGATAGA
1 ACCTTTAAAAAAGGTTGAAATAGA
28513250 GCTGTCTAAA
Statistics
Matches: 194, Mismatches: 39, Indels: 25
0.75 0.15 0.10
Matches are distributed among these distances:
35 32 0.16
36 46 0.24
37 26 0.13
38 55 0.28
39 35 0.18
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (38 bp):
ACCTTTAAAAAAGGTTGAAATAGATATTGTCTAAGGCA
Found at i:28513070 original size:74 final size:73
Alignment explanation
Indices: 28512973--28513497 Score: 285
Period size: 74 Copynumber: 7.2 Consensus size: 73
28512963 CCGACCTTTA
* * *
28512973 AAAAAGGTTGAAATAG-GTATTGTCTAAGGCAACCTTTTAAAAAAGATTGGAATAGATCCATATA
1 AAAAAGGTTGGAATAGACT-TTGTCTAAGGCAACCTTTTAAAAAAGATTGGAATAGA-CCATCTA
*
28513037 AGGCAACCTT
64 AAGCAACCTT
* * * *
28513047 AAAAAGGTTGGAATAGACTTTGTCTAAGGCAACCTTTAAAAAAAG-TTGAAATAAACCTTGTCTA
1 AAAAAGGTTGGAATAGACTTTGTCTAAGGCAACCTTTTAAAAAAGATTGGAATAGACC--ATCTA
* *
28513111 AGGAAACCTT
64 AAGCAACCTT
* * * * * *
28513121 AAAAAGATT-AAGATATATTTTGTCTAAGGGAACC-TTTAAAAAAGATT-GAGATA-AACATCTC
1 AAAAAGGTTGGA-ATAGACTTTGTCTAAGGCAACCTTTTAAAAAAGATTGGA-ATAGACCA--TC
*
28513182 TAACGCAACCTT
62 TAAAGCAACCTT
* ** * **
28513194 TAAAAGGTT-GAGATAGA-TCTAATCTAAGGCAAACTTTTAAAAAA-AGTT-GAGATAGAGCTGT
1 AAAAAGGTTGGA-ATAGACT-TTGTCTAAGGCAACCTTTTAAAAAAGA-TTGGA-ATAGA-CCAT
*
28513255 CTAAAACAACCTT
61 CTAAAGCAACCTT
* * *
28513268 AAAAAGGTTGGGAA-AGAC-----C---GACAATCTTTTAAAAAA-ATTAGG-ATAGAGCCGTCT
1 AAAAAGGTT-GGAATAGACTTTGTCTAAGGCAACCTTTTAAAAAAGATT-GGAATAGA-CCATCT
*
28513322 AAAGCAATCTTTT
63 AAAGCAA-C-CTT
* * *
28513335 AAAAAGGTTGAAATAGAC-TTGTCTAAGGCAACCTTTAAAAAAAG-TTGAAATAGACCAATCTAA
1 AAAAAGGTTGGAATAGACTTTGTCTAAGGCAACCTTTTAAAAAAGATTGGAATAGACC-ATCTAA
*
28513398 AACAACCTT
65 AGCAACCTT
* * * ** * * *
28513407 AAAATGATTGGGATAGA-TCTAATCTAAGACAACC-TTTAAAAAAGGTTTGG-ATA-AACATGTC
1 AAAAAGGTTGGAATAGACT-TTGTCTAAGGCAACCTTTTAAAAAA-GATTGGAATAGACCA--TC
*
28513468 TAAAACAACCTT
62 TAAAGCAACCTT
28513480 AAAAAGGTTGGAATAGAC
1 AAAAAGGTTGGAATAGAC
28513498 ACATGTAAAA
Statistics
Matches: 354, Mismatches: 59, Indels: 76
0.72 0.12 0.16
Matches are distributed among these distances:
65 19 0.05
66 20 0.06
67 16 0.05
69 1 0.00
71 2 0.01
72 28 0.08
73 106 0.30
74 157 0.44
75 3 0.01
76 2 0.01
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.26
Consensus pattern (73 bp):
AAAAAGGTTGGAATAGACTTTGTCTAAGGCAACCTTTTAAAAAAGATTGGAATAGACCATCTAAA
GCAACCTT
Found at i:28513256 original size:147 final size:148
Alignment explanation
Indices: 28512992--28513497 Score: 356
Period size: 147 Copynumber: 3.5 Consensus size: 148
28512982 GAAATAGGTA
* * *
28512992 TTGTCTAAGGCAACCTTTTAAAAAAGATTGGAATAGATCCATATAAGGCAACCTTAAAAAGGTTG
1 TTGTCTAAGGCAACCTTTTAAAAAAGATTGGAAAACATCCATATAACGCAACCTTAAAAAGGTTG
** *
28513057 GAATAGACTTTGTCTAAGGCAACCTTTAAAAAAAGTTGAAATAAACCTTGTCTAAGGA-AACCTT
66 GAATAGACTTAATCTAAGGCAACCTTTAAAAAAAGTTGAAATAAACCTTGTCTAA-AACAACCTT
28513121 AAAAAGATTAAGATATATT
130 AAAAAGATTAAGATATATT
* * *
28513140 TTGTCTAAGGGAACC-TTTAAAAAAGATTGAGATAAACAT-C-TCTAACGCAACCTTTAAAAGGT
1 TTGTCTAAGGCAACCTTTTAAAAAAGATTG-GA-AAACATCCATATAACGCAACCTTAAAAAGGT
* * * *
28513202 T-GAGATAGA-TCTAATCTAAGGCAAACTTTTAAAAAAAGTTGAGATAGAGC-TGTCTAAAACAA
64 TGGA-ATAGACT-TAATCTAAGGC-AACCTTTAAAAAAAGTTGAAATAAACCTTGTCTAAAACAA
* **
28513264 CCTTAAAAAGGTTGGGA-A-A--
126 CCTTAAAAAGATTAAGATATATT
* * * * * * * * * * *
28513283 --GAC--CGACAATCTTTTAAAAAA-ATTAGG-ATAGAGCCGTCTAAAGCAATCTTTTAAAAAGG
1 TTGTCTAAGGCAACCTTTTAAAAAAGATT-GGAAAACATCCATATAACGCAA-C-CTTAAAAAGG
* * * **
28513342 TTGAAATAGACTT-GTCTAAGGCAACCTTTAAAAAAAGTTGAAATAGACC-AATCTAAAACAACC
63 TTGGAATAGACTTAATCTAAGGCAACCTTTAAAAAAAGTTGAAATAAACCTTGTCTAAAACAACC
* ** * *
28513405 TTAAAATGATTGGGATAGATC
128 TTAAAAAGATTAAGATATATT
** * * * *
28513426 TAATCTAAGACAACC-TTTAAAAAAGGTTTGGATAAACATGTC-TA-AA-ACAACCTTAAAAAGG
1 TTGTCTAAGGCAACCTTTTAAAAAA-GATTGGA-AAACAT-CCATATAACGCAACCTTAAAAAGG
28513487 TTGGAATAGAC
63 TTGGAATAGAC
28513498 ACATGTAAAA
Statistics
Matches: 282, Mismatches: 49, Indels: 57
0.73 0.13 0.15
Matches are distributed among these distances:
137 3 0.01
138 1 0.00
139 66 0.23
140 20 0.07
141 19 0.07
142 2 0.01
145 21 0.07
146 15 0.05
147 82 0.29
148 44 0.16
149 8 0.03
150 1 0.00
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (148 bp):
TTGTCTAAGGCAACCTTTTAAAAAAGATTGGAAAACATCCATATAACGCAACCTTAAAAAGGTTG
GAATAGACTTAATCTAAGGCAACCTTTAAAAAAAGTTGAAATAAACCTTGTCTAAAACAACCTTA
AAAAGATTAAGATATATT
Found at i:28513496 original size:73 final size:72
Alignment explanation
Indices: 28513333--28513497 Score: 190
Period size: 73 Copynumber: 2.3 Consensus size: 72
28513323 AAGCAATCTT
* ** * *
28513333 TTAAAAAGGTTGAAATAGACTTGTCTAAGGCAACCTTTAAAAAAAGTTGAAATAGACCAATCTAA
1 TTAAAAAGGTTGGAATAGACTAATCTAAGACAACCTTTAAAAAAAGTTGAAATAGAACAATCTAA
28513398 AACAACC
66 AACAACC
* * * * * *
28513405 TTAAAATGATTGGGATAGATCTAATCTAAGACAACCTTTAAAAAAGGTTTG-GATA-AACATGTC
1 TTAAAAAGGTTGGAATAGA-CTAATCTAAGACAACCTTTAAAAAAAG-TTGAAATAGAACA-ATC
28513468 TAAAACAACC
63 TAAAACAACC
28513478 TTAAAAAGGTTGGAATAGAC
1 TTAAAAAGGTTGGAATAGAC
28513498 ACATGTAAAA
Statistics
Matches: 76, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
72 19 0.25
73 54 0.71
74 3 0.04
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.25
Consensus pattern (72 bp):
TTAAAAAGGTTGGAATAGACTAATCTAAGACAACCTTTAAAAAAAGTTGAAATAGAACAATCTAA
AACAACC
Found at i:28513507 original size:35 final size:37
Alignment explanation
Indices: 28513319--28513510 Score: 128
Period size: 37 Copynumber: 5.3 Consensus size: 37
28513309 GATAGAGCCG
* * * * ***
28513319 TCTAAAGCAATCTTTTAAAAAGGTTGAAATAGACTTG
1 TCTAAAACAACCTTTAAAAAAGGTTGGAATAGACACA
** * *
28513356 TCTAAGGCAACCTTTAAAAAAAGTTGAAATAGAC-CAA
1 TCTAAAACAACCTTTAAAAAAGGTTGGAATAGACAC-A
* * *
28513393 TCTAAAACAACC-TT-AAAATGATTGGGATAGATCTA-A
1 TCTAAAACAACCTTTAAAAAAGGTTGGAATAGA-C-ACA
* * **
28513429 TCTAAGACAACCTTTAAAAAAGGTTTGG-ATAAACATG
1 TCTAAAACAACCTTTAAAAAAGG-TTGGAATAGACACA
28513466 TCTAAAACAACC-TT-AAAAAGGTTGGAATAGACACA
1 TCTAAAACAACCTTTAAAAAAGGTTGGAATAGACACA
*
28513501 TGTAAAACAA
1 TCTAAAACAA
28513511 TTTTTTTATT
Statistics
Matches: 123, Mismatches: 23, Indels: 20
0.74 0.14 0.12
Matches are distributed among these distances:
34 4 0.03
35 34 0.28
36 18 0.15
37 54 0.44
38 9 0.07
39 4 0.03
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.26
Consensus pattern (37 bp):
TCTAAAACAACCTTTAAAAAAGGTTGGAATAGACACA
Found at i:28517496 original size:398 final size:403
Alignment explanation
Indices: 28516825--28517616 Score: 1102
Period size: 398 Copynumber: 2.0 Consensus size: 403
28516815 AATTAATGTG
* * * **
28516825 AACCTTAAATCTCGAACATCAAGGTTTAAGGTTTGGAGTCAAAATATAAAATTCAGGGTTTGAGA
1 AACCTTAAATCTCAAACATCAAGATTCAAGGTTTGGAGTCAAAATATAAAATTCAAAGTTTGAGA
* * *
28516890 TTTAAGATTTAATGTTTATTTTTAGCATTTAAAGATTTGAGATAATGAGTTATGAATTTGGGGTT
66 TTCAAGATTTAATGTTCATATTTAGCATTTAAAGATTTGAGATAATGAGTTATGAATTTGGGGTT
* * * *
28516955 TAGTGATTATAATTTTAGAGTTTGGGGTTTAAAGATATCACTTTTTTATTTAAACTTAAAATTAA
131 TAATGATTATAATTTTAAAGTTTGGGGATTAAAGATATCACTTTTTTATTTAAACCTAAAATTAA
28517020 GTTAGATTATCACACATGATATTGTAAATGAGAGAAAATTTTATTTATTAAAAAATTATTGGTTG
196 GTTAGATTATCACACATGATATTGTAAATGAGAGAAAATTTTATTTATTAAAAAATTATTGGTTG
*
28517085 CTCAATTTATTTTTTATTTTTTATTTAAATATTTTATATAAAAATATTGTAATAATATTTATTAT
261 CTCAATTTATTTTTAATTTTTTATTTAAATATTTTATATAAAAATATTGTAATAATATTTATTAT
* * * *
28517150 CATTAAAAAACTT-T-AAG-TTTTTTCAATTAAATAATGCTTTTTATTTCACA-TAATTAATATG
326 CATTAAAAAAATTCTAAAGTTTTTTTCAATCAAATAATGCGTTTTATTT-AAAGTAATTAATATG
28517211 AACCCTAAATTTTA
390 AACCCTAAATTTTA
* * * *
28517225 AACCTTAAATCTCAAACATCAAGATTCACGGTTT-GAGATCGAGATATAAGATTCAAAGTTTGAG
1 AACCTTAAATCTCAAACATCAAGATTCAAGGTTTGGAG-TCAAAATATAAAATTCAAAGTTTGAG
** *
28517289 ATTCAAGATTTAATGTTCATATTTAGGGTTTAAAGATTT-AGAGTTATGAGTTAT-AAGTTTGGG
65 ATTCAAGATTTAATGTTCATATTTAGCATTTAAAGATTTGAGA-TAATGAGTTATGAA-TTTGGG
* * * * *
28517352 GTTTAATG-TCTATGATTTTAAAGTTT-GGGATTAAGGATATC-GTTTTTTATTTGATCCTAAAA
128 GTTTAATGAT-TATAATTTTAAAGTTTGGGGATTAAAGATATCACTTTTTTATTTAAACCTAAAA
* * * * *
28517414 TTAAGTTAGATTATCACACGTGATATTGTAGATTATAGAAAATTTTATTTATTAAAAAATTGTTG
192 TTAAGTTAGATTATCACACATGATATTGTAAATGAGAGAAAATTTTATTTATTAAAAAATTATTG
*
28517479 GTTGTTCAGA-TTATTTTTAATTTTTTATTTAAATATTTTATATAAAAATATTGTAATAATATTT
257 GTTGCTCA-ATTTATTTTTAATTTTTTATTTAAATATTTTATATAAAAATATTGTAATAATATTT
*
28517543 ATTATCATTAAAAAAATTCTAAAGTTTTTTTTTTCAATCAAATAATGCGTTTTATTTAAAGTAGT
321 ATTATCATTAAAAAAATTCTAAAG---TTTTTTTCAATCAAATAATGCGTTTTATTTAAAGTAAT
28517608 TAATATGAA
383 TAATATGAA
28517617 ATATTATTTA
Statistics
Matches: 344, Mismatches: 36, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
398 154 0.45
399 24 0.07
400 125 0.36
403 2 0.01
404 39 0.11
ACGTcount: A:0.36, C:0.06, G:0.13, T:0.44
Consensus pattern (403 bp):
AACCTTAAATCTCAAACATCAAGATTCAAGGTTTGGAGTCAAAATATAAAATTCAAAGTTTGAGA
TTCAAGATTTAATGTTCATATTTAGCATTTAAAGATTTGAGATAATGAGTTATGAATTTGGGGTT
TAATGATTATAATTTTAAAGTTTGGGGATTAAAGATATCACTTTTTTATTTAAACCTAAAATTAA
GTTAGATTATCACACATGATATTGTAAATGAGAGAAAATTTTATTTATTAAAAAATTATTGGTTG
CTCAATTTATTTTTAATTTTTTATTTAAATATTTTATATAAAAATATTGTAATAATATTTATTAT
CATTAAAAAAATTCTAAAGTTTTTTTCAATCAAATAATGCGTTTTATTTAAAGTAATTAATATGA
ACCCTAAATTTTA
Found at i:28518400 original size:109 final size:109
Alignment explanation
Indices: 28518212--28518752 Score: 483
Period size: 109 Copynumber: 4.9 Consensus size: 109
28518202 TAGGATAGAT
* * * *
28518212 TTGTCTAA-AGCAACTTTAAAAAGGTTAGGG-TA-AGCCTTGTCTAAGGTAACATTTAAAAAAAG
1 TTGTCTAAGA-CAACCTTAAAAAGGTT-GGGATAGA-CCTTGTCTAAGGCAAC-CTTAAAAAAGG
* *
28518274 TTGGGATAGAC-CTATCTAAGGCAATATTTAAAAAAGGTTGGGATAGACC
62 TTGGGATAGACTC-ATCTAAGGCAATCTTT-AAAAAGGTTGGGATAAACC
* * *
28518323 TTGTTTAAGACAACCTTAAAAAAGTTGGGATAGACCTTATCTAAGGCAACCTT-AAAAAGGTTGG
1 TTGTCTAAGACAACCTTAAAAAGGTTGGGATAGACCTTGTCTAAGGCAACCTTAAAAAAGGTTGG
* * *
28518387 GATAGACTCATCTAAGGCAA-CCTTAAAAAGGTTGAGATAGACC
66 GATAGACTCATCTAAGGCAATCTTTAAAAAGGTTGGGATAAACC
** *
28518430 TTGTCTAAGGTAACCTTAAAAAGGTT-GGACTACG-CCTTGTCTAAGGCAACATTTAAAAAAGGT
1 TTGTCTAAGACAACCTTAAAAAGGTTGGGA-TA-GACCTTGTCTAAGGCAAC-CTTAAAAAAGGT
* * * * *
28518493 TGGGATAGACCCGTTTAAGGTAAT-TTTAAAAAGGTTGGGATAAATC
63 TGGGATAGACTCATCTAAGGCAATCTTTAAAAAGGTTGGGATAAACC
* * * * * * * * *
28518539 ATGTCTAAGATAATCTTAAAAAGGTTAGAATAGACCTTGTTTGAGGGAACCTTTAAAAAAAGTTG
1 TTGTCTAAGACAACCTTAAAAAGGTTGGGATAGACCTTGTCTAAGGCAACC-TTAAAAAAGGTTG
** * * * * *
28518604 GGATAGACCTTGTTTAAGGTAACCTTTAAAAAAAGTTGGGATAAATC
65 GGATAGA-CTCATCTAAGGCAATCTTT-AAAAAGGTTGGGATAAACC
* ** *
28518651 TTGTCTAAGGCAACCTTTTAAAAAGGTTGGGATAGACCTTGTCTAAAACAACCTT-AAAAAGATT
1 TTGTCTAAGACAACC--TTAAAAAGGTTGGGATAGACCTTGTCTAAGGCAACCTTAAAAAAGGTT
** *
28518715 GGGATAGACCTTTTCTAAGGCAA-CCTTAAAAAGGTTGG
64 GGGATAGA-CTCATCTAAGGCAATCTTTAAAAAGGTTGG
28518753 CATAGTGTTA
Statistics
Matches: 358, Mismatches: 55, Indels: 35
0.80 0.12 0.08
Matches are distributed among these distances:
106 3 0.01
107 57 0.16
108 6 0.02
109 130 0.36
110 30 0.08
111 43 0.12
112 58 0.16
113 2 0.01
114 29 0.08
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.28
Consensus pattern (109 bp):
TTGTCTAAGACAACCTTAAAAAGGTTGGGATAGACCTTGTCTAAGGCAACCTTAAAAAAGGTTGG
GATAGACTCATCTAAGGCAATCTTTAAAAAGGTTGGGATAAACC
Found at i:28518610 original size:38 final size:38
Alignment explanation
Indices: 28518199--28518757 Score: 504
Period size: 36 Copynumber: 15.3 Consensus size: 38
28518189 TTTATTGAAG
* * *
28518199 GGTTAGGATAGA-TTTGTCTAAAGCAA-CTTT-AAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAA
* *
28518234 GGTTAGGG-TA-AGCCTTGTCTAAGGTAACATTTAAAAAA
1 GGTT-GGGATAGA-CCTTGTCTAAGGCAACCTTTAAAAAA
* * **
28518272 AGTTGGGATAGACC-TATCTAAGGCAATATTTAAAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAA
* *
28518309 GGTTGGGATAGACCTTGTTTAAGACAACC-TTAAAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAA
*
28518346 -GTTGGGATAGACCTTATCTAAGGCAACC-TT-AAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAA
**
28518381 GGTTGGGATAGA-CTCATCTAAGGCAACC-TT-AAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAA
* *
28518416 GGTTGAGATAGACCTTGTCTAAGGTAACC-TT-AAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAA
*
28518452 GGTT-GGACTACG-CCTTGTCTAAGGCAACATTTAAAAAA
1 GGTTGGGA-TA-GACCTTGTCTAAGGCAACCTTTAAAAAA
* * * *
28518490 GGTTGGGATAGACC-CGTTTAAGGTAA--TTTTAAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAA
* * * ** *
28518525 GGTTGGGATAAATCATGTCTAAGATAATC-TT-AAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAA
* * * * *
28518561 GGTTAGAATAGACCTTGTTTGAGGGAACCTTTAAAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAA
* * *
28518599 AGTTGGGATAGACCTTGTTTAAGGTAACCTTTAAAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAA
* * * *
28518637 AGTTGGGATAAATCTTGTCTAAGGCAACCTTTTAAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAA
**
28518675 GGTTGGGATAGACCTTGTCTAAAACAACC-TT-AAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAA
* *
28518711 GATTGGGATAGACCTTTTCTAAGGCAACC-TT-AAAAA
1 GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAA
*
28518747 GGTTGGCATAG
1 GGTTGGGATAG
28518758 TGTTAGACAA
Statistics
Matches: 437, Mismatches: 66, Indels: 41
0.80 0.12 0.08
Matches are distributed among these distances:
34 1 0.00
35 66 0.15
36 171 0.39
37 66 0.15
38 129 0.30
39 4 0.01
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (38 bp):
GGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAA
Found at i:28519049 original size:141 final size:140
Alignment explanation
Indices: 28518743--28519171 Score: 569
Period size: 140 Copynumber: 3.1 Consensus size: 140
28518733 GGCAACCTTA
* * *
28518743 AAAAG-GTTGGCATAGTGTTAGACAAAGCCAACTCTTATTTAAGTGTTGCCTTAGGCATGCATAT
1 AAAAGTGTCGGCATAGTGTTGGACAAAGCCAACTCTTATTTAAGCGTTGCCTTAGGCATGCATAT
* * * *
28518807 CCCAACCCTTATATAAAGAGTTGGCCAAAGCATATGCCAGCAAGTCTAT-CCTACACTTAGGAAA
66 CCCAACCCTTATACAAAGAGTTGGCCAAAGCGTATGTCAGCAAGTCTATCCCAACACTTAGGAAA
* *
28518871 GTATTGGCGC
131 GTATTGCCCC
* * *
28518881 AAAAGTGTCGCCATAGTGTTGGACAAAGCCGACTCTTAGTTT-AGCATTGCCTTAGGCATGCATA
1 AAAAGTGTCGGCATAGTGTTGGACAAAGCCAACTCTTA-TTTAAGCGTTGCCTTAGGCATGCATA
** * * *
28518945 TCTTAACCTTTATACAAAAGAGTTGGCAAAAGCGTATGTCGGCAAGTCTATCCCAACACTTAGGA
65 TCCCAACCCTTATAC-AAAGAGTTGGCCAAAGCGTATGTCAGCAAGTCTATCCCAACACTTAGGA
*
28519010 AAGT-TTCGTCCC
129 AAGTATT-GCCCC
* * * *
28519022 AAAAGTGTCGGCATAGTGTTGGCCAAAGGCAACTTTTATTTAAGCGTTGTCTTAGGCATGCATAT
1 AAAAGTGTCGGCATAGTGTTGGACAAAGCCAACTCTTATTTAAGCGTTGCCTTAGGCATGCATAT
* *
28519087 CCCAACCCTTATACAAAGAGTTGGCCAAAGCGTATGTTAGCAAGTCTATCCCAACACTTAGAAAA
66 CCCAACCCTTATACAAAGAGTTGGCCAAAGCGTATGTCAGCAAGTCTATCCCAACACTTAGGAAA
* *
28519152 ATGTTGCCCC
131 GTATTGCCCC
28519162 AAAAGTGTCG
1 AAAAGTGTCG
28519172 TCTTAGAACT
Statistics
Matches: 251, Mismatches: 33, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
138 5 0.02
139 59 0.24
140 101 0.40
141 86 0.34
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (140 bp):
AAAAGTGTCGGCATAGTGTTGGACAAAGCCAACTCTTATTTAAGCGTTGCCTTAGGCATGCATAT
CCCAACCCTTATACAAAGAGTTGGCCAAAGCGTATGTCAGCAAGTCTATCCCAACACTTAGGAAA
GTATTGCCCC
Found at i:28519987 original size:24 final size:25
Alignment explanation
Indices: 28519951--28520002 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
28519941 TTAGTTCTTC
* *
28519951 AAAAACAACATTTTTGAT-ATTTTTT
1 AAAAACAAAATTTAT-ATAATTTTTT
28519976 AAAAA-AAAATTTATATAATTTTTT
1 AAAAACAAAATTTATATAATTTTTT
28520000 AAA
1 AAA
28520003 TAATTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 2 0.08
24 17 0.71
25 5 0.21
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (25 bp):
AAAAACAAAATTTATATAATTTTTT
Found at i:28533621 original size:2 final size:2
Alignment explanation
Indices: 28533614--28533642 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
28533604 ATACACAATT
28533614 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
28533643 TCATGGGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:28534246 original size:60 final size:60
Alignment explanation
Indices: 28534168--28534638 Score: 468
Period size: 61 Copynumber: 7.8 Consensus size: 60
28534158 CCACCAGTAT
* * * *
28534168 TTTTTTGTCAGATAAAAAATTTAAATTTTTTGGTGTTGGCCATTGCATGGCCGACACTCCC
1 TTTTTTATCTGATAAAAAATTCAAATTTTTTGGTGTTGACCATTGCATGGCCGACAC-CCC
* * *
28534229 TTTTTTATCTGGTAAAAAAATCAATTTTTTTTGGTGTTGACCATTGCATGGCCGACACTCCC
1 TTTTTTATCTGATAAAAAATTCAA-ATTTTTTGGTGTTGACCATTGCATGGCCGACAC-CCC
* * * *
28534291 -TTTTTGTCAGATAAAAAATTCAAATTTTTTGGTATTGACCATTGCATGGCCGACACCTAC
1 TTTTTTATCTGATAAAAAATTCAAATTTTTTGGTGTTGACCATTGCATGGCCGACACC-CC
* * * * * * *
28534351 TTTTTTATCTGGTAAAAAAAAATC-ATTTTTTTAGTATTGGCCATTGCATGACCGACACTCCC
1 TTTTTTATCT-G-ATAAAAAATTCAAATTTTTTGGTGTTGACCATTGCATGGCCGACAC-CCC
* * * * **
28534413 -TTTTTGTCAGATAAAAAATTCAAATTTTTTGGTGCTGACTATTGCATGGCTAACACCCCC
1 TTTTTTATCTGATAAAAAATTCAAATTTTTTGGTGTTGACCATTGCATGGCCGACA-CCCC
* * * * * *
28534473 ATTTTTATCTGGTAAAAAA-TC-AATTTTTTTGTATTGGCCATTGCATGACCGACACCCC
1 TTTTTTATCTGATAAAAAATTCAAATTTTTTGGTGTTGACCATTGCATGGCCGACACCCC
* * * *
28534531 CTTTTTGTCTGATAAAAAATTTAAATTTTTTGGTGTTGACCATTGCATGACCGACACCACC
1 TTTTTTATCTGATAAAAAATTCAAATTTTTTGGTGTTGACCATTGCATGGCCGACACC-CC
* * * * *
28534592 TTTTTAATCTGATAAAAAAATCAATTTTTTTGATGTTGGCCA-TGCAT
1 TTTTTTATCTGATAAAAAATTCAAATTTTTTGGTGTTGACCATTGCAT
28534639 TGGCTAACGC
Statistics
Matches: 336, Mismatches: 62, Indels: 25
0.79 0.15 0.06
Matches are distributed among these distances:
58 20 0.06
59 36 0.11
60 99 0.29
61 104 0.31
62 67 0.20
63 10 0.03
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (60 bp):
TTTTTTATCTGATAAAAAATTCAAATTTTTTGGTGTTGACCATTGCATGGCCGACACCCC
Found at i:28534260 original size:122 final size:121
Alignment explanation
Indices: 28534169--28534622 Score: 625
Period size: 122 Copynumber: 3.8 Consensus size: 121
28534159 CACCAGTATT
* *
28534169 TTTTTGTCAGATAAAAAATTTAAATTTTTTGGTGTTGGCCATTGCATGGCCGACACTC-CCTTTT
1 TTTTTGTCAGATAAAAAATTCAAATTTTTTGGTGTTGACCATTGCATGGCCGACAC-CACCTTTT
* * * *
28534233 TTATCTGGTAAAAAAATCAATTTTTTTTGGTGTTGACCATTGCATGGCCGACACTCCC
65 TTATCTGGTAAAAAAATCAATTTTTTTTAGTATTGGCCATTGCA-GACCGACACTCCC
*
28534291 TTTTTGTCAGATAAAAAATTCAAATTTTTTGGTATTGACCATTGCATGGCCGACACCTA-CTTTT
1 TTTTTGTCAGATAAAAAATTCAAATTTTTTGGTGTTGACCATTGCATGGCCGACACC-ACCTTTT
28534355 TTATCTGGTAAAAAAA--AATCATTTTTTTAGTATTGGCCATTGCATGACCGACACTCCC
65 TTATCTGGTAAAAAAATCAAT--TTTTTTTAGTATTGGCCATTGCA-GACCGACACTCCC
* * ** * *
28534413 TTTTTGTCAGATAAAAAATTCAAATTTTTTGGTGCTGACTATTGCATGGCTAACACCCCCATTTT
1 TTTTTGTCAGATAAAAAATTCAAATTTTTTGGTGTTGACCATTGCATGGCCGACACCACCTTTTT
*
28534478 TATCTGGT-AAAAAATCAA-TTTTTTT-GTATTGGCCATTGCATGACCGACACCCCC
66 TATCTGGTAAAAAAATCAATTTTTTTTAGTATTGGCCATTGCA-GACCGACACTCCC
* * *
28534532 TTTTTGTCTGATAAAAAATTTAAATTTTTTGGTGTTGACCATTGCATGACCGACACCACCTTTTT
1 TTTTTGTCAGATAAAAAATTCAAATTTTTTGGTGTTGACCATTGCATGGCCGACACCACCTTTTT
* *
28534597 AATCTGATAAAAAAATCAATTTTTTT
66 TATCTGGTAAAAAAATCAATTTTTTT
28534623 GATGTTGGCC
Statistics
Matches: 297, Mismatches: 26, Indels: 19
0.87 0.08 0.06
Matches are distributed among these distances:
119 90 0.30
120 20 0.07
121 13 0.04
122 172 0.58
123 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (121 bp):
TTTTTGTCAGATAAAAAATTCAAATTTTTTGGTGTTGACCATTGCATGGCCGACACCACCTTTTT
TATCTGGTAAAAAAATCAATTTTTTTTAGTATTGGCCATTGCAGACCGACACTCCC
Found at i:28538719 original size:22 final size:23
Alignment explanation
Indices: 28538665--28538721 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 23
28538655 ATAACATTAG
*
28538665 ACCACCCAAATTTCAGCTCACCT
1 ACCACCCAAATTCCAGCTCACCT
* *
28538688 A-AACCGAAATTCCAGCTCACC-
1 ACCACCCAAATTCCAGCTCACCT
28538709 ACCACCCAAATTC
1 ACCACCCAAATTC
28538722 TGTCGTTGAC
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 1 0.04
22 26 0.93
23 1 0.04
ACGTcount: A:0.35, C:0.42, G:0.05, T:0.18
Consensus pattern (23 bp):
ACCACCCAAATTCCAGCTCACCT
Found at i:28539956 original size:22 final size:21
Alignment explanation
Indices: 28539943--28539988 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
28539933 TTTATAATAT
*
28539943 TTTTTTTCTATTTTTGAAATG
1 TTTTTTTATATTTTTGAAATG
28539964 TTTTTTTATATTTTTG-AAT-
1 TTTTTTTATATTTTTGAAATG
28539983 TTTTTT
1 TTTTTT
28539989 AAAAAATGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 6 0.25
20 3 0.12
21 15 0.62
ACGTcount: A:0.17, C:0.02, G:0.07, T:0.74
Consensus pattern (21 bp):
TTTTTTTATATTTTTGAAATG
Found at i:28540049 original size:169 final size:168
Alignment explanation
Indices: 28539751--28540100 Score: 508
Period size: 169 Copynumber: 2.1 Consensus size: 168
28539741 GAGATGATAT
28539751 ATTTTCGAATTTTTTATAATATTTTTTTCTATTTTCGAAATGTTTTTATATTTTCGAATTTTTAA
1 ATTTTCGAATTTTTTATAATATTTTTTTCTATTTTCGAAATGTTTTTATATTTTCGAATTTTT-A
* *
28539816 AAAATCAAAATCTGATATTTTTTACACATTTTTTTACATTTTTTGAAATATAAAGAATACATTTT
65 AAAA-CAAAATCTGATATTTTTTACAAATTTTTTTACATTTTTTGAAATATAAAAAATACATTTT
28539881 CGAAATATTTTTTTACAAATAAAAAATCTGATATTTTTAC
129 CGAAATATTTTTTTACAAATAAAAAATCTGATATTTTTAC
* * *
28539921 ATTTTTGAATTTTTTATAATATTTTTTTTCTATTTTTGAAATGTTTTTTTATATTTTTGAATTTT
1 ATTTTCGAATTTTTTATAATA-TTTTTTTCTATTTTCGAAATG--TTTTTATATTTTCGAATTTT
** * *
28539986 T-TTAA-AAAATGTGATATTTTTTGCAAATATTTTTTACA-TTTTTGAAATATAAAAAATACATT
63 TAAAAACAAAATCTGATATTTTTTACAAAT-TTTTTTACATTTTTTGAAATATAAAAAATACATT
* * *
28540048 TTCGGAATATTTTTTTACAAATTAAAAATCTGATTTTTTTAC
127 TTCGAAATATTTTTTTACAAATAAAAAATCTGATATTTTTAC
*
28540090 ATTTTCAAATT
1 ATTTTCGAATT
28540101 AAGTTGGGGC
Statistics
Matches: 162, Mismatches: 14, Indels: 9
0.88 0.08 0.05
Matches are distributed among these distances:
169 91 0.56
170 29 0.18
171 22 0.14
173 20 0.12
ACGTcount: A:0.34, C:0.07, G:0.06, T:0.54
Consensus pattern (168 bp):
ATTTTCGAATTTTTTATAATATTTTTTTCTATTTTCGAAATGTTTTTATATTTTCGAATTTTTAA
AAACAAAATCTGATATTTTTTACAAATTTTTTTACATTTTTTGAAATATAAAAAATACATTTTCG
AAATATTTTTTTACAAATAAAAAATCTGATATTTTTAC
Found at i:28541409 original size:20 final size:20
Alignment explanation
Indices: 28541384--28541431 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
28541374 GCTTAGTGAC
28541384 TCAACTTTCAAAACAATCA-T
1 TCAACTTT-AAAACAATCACT
*
28541404 TCAACTGTTAAAATAATCACT
1 TCAACT-TTAAAACAATCACT
28541425 T-AACTTT
1 TCAACTTT
28541432 TGAAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 19 0.76
21 4 0.16
ACGTcount: A:0.42, C:0.21, G:0.02, T:0.35
Consensus pattern (20 bp):
TCAACTTTAAAACAATCACT
Found at i:28542129 original size:39 final size:36
Alignment explanation
Indices: 28542086--28542167 Score: 92
Period size: 39 Copynumber: 2.2 Consensus size: 36
28542076 GACCCTAAGT
*
28542086 TATCACAAGAATCTTCTAATTTTTGCTTTGCTTCTGAGA
1 TATCACAAGAATCTTCTAATTTCT--TTTGCTT-TGAGA
* * * *
28542125 TATCAGATGAATCTTCTGATTTCTTTTGCTTTGAGT
1 TATCACAAGAATCTTCTAATTTCTTTTGCTTTGAGA
28542161 TATCACA
1 TATCACA
28542168 GGCATCAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
36 10 0.27
37 7 0.19
39 20 0.54
ACGTcount: A:0.24, C:0.17, G:0.13, T:0.45
Consensus pattern (36 bp):
TATCACAAGAATCTTCTAATTTCTTTTGCTTTGAGA
Found at i:28542654 original size:20 final size:20
Alignment explanation
Indices: 28542629--28542666 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
28542619 ATTTTTCGAA
*
28542629 AGTTAAGTGATTATTTTAAC
1 AGTTAAGTAATTATTTTAAC
28542649 AGTTAAGTAATTATTTTA
1 AGTTAAGTAATTATTTTA
28542667 TCTTCAGATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47
Consensus pattern (20 bp):
AGTTAAGTAATTATTTTAAC
Found at i:28543009 original size:19 final size:18
Alignment explanation
Indices: 28542976--28543014 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
28542966 AAGATTATAG
*
28542976 ATTATATTTTTTATATTA
1 ATTATATTATTTATATTA
28542994 ATTATATTAATTTATATTA
1 ATTATATT-ATTTATATTA
28543013 AT
1 AT
28543015 CTTTTTTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTATATTATTTATATTA
Found at i:28543010 original size:10 final size:10
Alignment explanation
Indices: 28542985--28543014 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
28542975 GATTATATTT
28542985 TTTATATTAA
1 TTTATATTAA
28542995 -TTATATTAA
1 TTTATATTAA
28543004 TTTATATTAA
1 TTTATATTAA
28543014 T
1 T
28543015 CTTTTTTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TTTATATTAA
Found at i:28543429 original size:26 final size:26
Alignment explanation
Indices: 28543393--28543444 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
28543383 AGGTTAGTGG
28543393 GATTAGGTGAAATAAGTGGATGATAA
1 GATTAGGTGAAATAAGTGGATGATAA
28543419 GATTAGGTGAAATAAGTGGATGATAA
1 GATTAGGTGAAATAAGTGGATGATAA
28543445 AAGGAAGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.31, T:0.27
Consensus pattern (26 bp):
GATTAGGTGAAATAAGTGGATGATAA
Found at i:28546269 original size:51 final size:51
Alignment explanation
Indices: 28546208--28546531 Score: 400
Period size: 51 Copynumber: 6.3 Consensus size: 51
28546198 CTATAAACGA
* * *
28546208 AAAGGTCCGATGACTAAGTGTCATCGTGAGGAAGTGAATCCTATACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
*
28546259 AAAGGCCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
*
28546310 AAAGGTTCGATGA-TGAAGTGTCATCGTGAG-ACAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACT-AAGTGTCATCGTGAGTA-AATGAATCCTTTACGGATT
* * * *
28546361 AAAGGTCCGATGATTAAGTATAATCGTGAGTAAATGAATCCTTTATGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * *
28546412 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* ** * ** * * **
28546463 AAGGGTCCGATGACTTTGTGTCATTGTGAGTGTATGAATTCTTATATGGAAC
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTT-TACGGATT
28546515 AAGAGGTCCGATGACTA
1 AA-AGGTCCGATGACTA
28546532 TATTTCATTG
Statistics
Matches: 239, Mismatches: 28, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
50 2 0.01
51 216 0.90
52 9 0.04
53 12 0.05
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.29
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:28549460 original size:52 final size:52
Alignment explanation
Indices: 28549382--28549629 Score: 293
Period size: 52 Copynumber: 4.8 Consensus size: 52
28549372 GCCATAAACG
* * * *
28549382 AAGAGGTCCAATGATTAAGTGTCATCGTGAGTATTTAAATCCTTTACGGATT
1 AAGAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
* * *
28549434 AAGAGGTCTGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTATGGACT
1 AAGAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
28549486 AAGAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
1 AAGAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
* * * * * *
28549538 AAGAAGTCCGATGACTCTA-TGTAATCGTGAGTATATGAATCCCTTGCGAATT
1 AAGAGGTCCGATGACT-AAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
* * * * * *
28549590 ATA-AGGTTCGGTGGCTATGTGTCATTGCGAGTATATGAAT
1 A-AGAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAAT
28549630 GACGTGAAAT
Statistics
Matches: 168, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
52 166 0.99
53 2 0.01
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (52 bp):
AAGAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
Found at i:28550384 original size:21 final size:21
Alignment explanation
Indices: 28550344--28550384 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
28550334 ATGCATGACA
*
28550344 TGTATCGGTAGAAATTACACT
1 TGTATCGGTAGAAATAACACT
* *
28550365 TGTATTGGTAGAACTAACAC
1 TGTATCGGTAGAAATAACAC
28550385 AGATACCGGT
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:0.34, C:0.15, G:0.20, T:0.32
Consensus pattern (21 bp):
TGTATCGGTAGAAATAACACT
Found at i:28553758 original size:52 final size:52
Alignment explanation
Indices: 28553604--28553787 Score: 217
Period size: 52 Copynumber: 3.5 Consensus size: 52
28553594 GCCATAAATG
* *
28553604 AAGAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGAATT
1 AAGAGGTCCGATGACTAAGTGTTATCGTGAGTATATGAATCCTTTACGGATT
* * *
28553656 AAGAAGTCCGATGACTAAGTGTTATCATGAGTATATGAATCCTTTTCGGATT
1 AAGAGGTCCGATGACTAAGTGTTATCGTGAGTATATGAATCCTTTACGGATT
* ** * * *
28553708 AAGAGGTTCGATGACTTTGTGTTTTCGTGAGTATATGAATCCCTTGCGGATT
1 AAGAGGTCCGATGACTAAGTGTTATCGTGAGTATATGAATCCTTTACGGATT
* * * *
28553760 ATA-AGGTCCGGTGGCTATGTGTCATCGT
1 A-AGAGGTCCGATGACTAAGTGTTATCGT
28553788 ATGTAACAGC
Statistics
Matches: 112, Mismatches: 19, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
52 111 0.99
53 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (52 bp):
AAGAGGTCCGATGACTAAGTGTTATCGTGAGTATATGAATCCTTTACGGATT
Found at i:28555037 original size:51 final size:51
Alignment explanation
Indices: 28554977--28555214 Score: 291
Period size: 51 Copynumber: 4.6 Consensus size: 51
28554967 CTATAAACGA
* *
28554977 AAAGGTCCGATGACTAAATGTCATCGTGAGGAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
*
28555028 AAAGGTCCGATGACTAAGTGTCATCGTGCGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * *
28555079 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* ** * * * **
28555130 -AAGGATTCGATGACTTTGTGTCATCGTGAGTATATGAATTCCTATATGGAAC
1 AAAGG-TCCGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTACGGATT
*
28555182 AAGAGATCCGATGACTATA-TGTCATCGTGAGTA
1 AA-AGGTCCGATGACTA-AGTGTCATCGTGAGTA
28555215 TGAAATGAAA
Statistics
Matches: 162, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
50 4 0.02
51 124 0.77
52 8 0.05
53 24 0.15
54 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:28556315 original size:129 final size:129
Alignment explanation
Indices: 28556085--28556342 Score: 516
Period size: 129 Copynumber: 2.0 Consensus size: 129
28556075 AAAATTATGT
28556085 AACATTTAGGTATTGTTTTAAATTGTGAGAAATGATTTTTGAATTGAATAAAGATGTAAATAGTC
1 AACATTTAGGTATTGTTTTAAATTGTGAGAAATGATTTTTGAATTGAATAAAGATGTAAATAGTC
28556150 GGATATGTTTAAAGGATAAACAGTATAAAATGAATAGAAAACACCGGAATCCAAACCAGTGATG
66 GGATATGTTTAAAGGATAAACAGTATAAAATGAATAGAAAACACCGGAATCCAAACCAGTGATG
28556214 AACATTTAGGTATTGTTTTAAATTGTGAGAAATGATTTTTGAATTGAATAAAGATGTAAATAGTC
1 AACATTTAGGTATTGTTTTAAATTGTGAGAAATGATTTTTGAATTGAATAAAGATGTAAATAGTC
28556279 GGATATGTTTAAAGGATAAACAGTATAAAATGAATAGAAAACACCGGAATCCAAACCAGTGATG
66 GGATATGTTTAAAGGATAAACAGTATAAAATGAATAGAAAACACCGGAATCCAAACCAGTGATG
28556343 GTACTCCCCC
Statistics
Matches: 129, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
129 129 1.00
ACGTcount: A:0.43, C:0.08, G:0.19, T:0.30
Consensus pattern (129 bp):
AACATTTAGGTATTGTTTTAAATTGTGAGAAATGATTTTTGAATTGAATAAAGATGTAAATAGTC
GGATATGTTTAAAGGATAAACAGTATAAAATGAATAGAAAACACCGGAATCCAAACCAGTGATG
Found at i:28561420 original size:26 final size:26
Alignment explanation
Indices: 28561391--28561445 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
28561381 GTGTCATCGT
28561391 GAGTATATGAATCCTTTACGGATTAA
1 GAGTATATGAATCCTTTACGGATTAA
*
28561417 GAGTATATGAATCCTTTATGGATTAA
1 GAGTATATGAATCCTTTACGGATTAA
28561443 GAG
1 GAG
28561446 GTCTGATGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.35
Consensus pattern (26 bp):
GAGTATATGAATCCTTTACGGATTAA
Found at i:28561545 original size:52 final size:52
Alignment explanation
Indices: 28561417--28561545 Score: 159
Period size: 52 Copynumber: 2.5 Consensus size: 52
28561407 TACGGATTAA
* * ** *
28561417 GAGTATATGAATCCTTTATGGATTAAGAGGTCTGATGACTAAGTCTTATCGT
1 GAGTATATGAATCCTTTACGGATTAAGAAGTCCAATGACTAAGTCTAATCGT
* ** *
28561469 GAGTATATGAATCCTTTACAGATTAAGAAGTCCAATGACTCTGTGTAATCGT
1 GAGTATATGAATCCTTTACGGATTAAGAAGTCCAATGACTAAGTCTAATCGT
* *
28561521 GAGTATATGAATCCCTTGCGGATTA
1 GAGTATATGAATCCTTTACGGATTA
28561546 TAAGGTCCGG
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (52 bp):
GAGTATATGAATCCTTTACGGATTAAGAAGTCCAATGACTAAGTCTAATCGT
Found at i:28561566 original size:52 final size:52
Alignment explanation
Indices: 28561417--28561584 Score: 149
Period size: 52 Copynumber: 3.2 Consensus size: 52
28561407 TACGGATTAA
* ** * ** * * *
28561417 GAGTATATGAATCCTTTATGGATTAAGAGGTCTGATGACTAAGTCTTATCGT
1 GAGTATATGAATCCCTTACAGATTAAGAAGTCCAATGACTATGTGTAATCGT
* *
28561469 GAGTATATGAATCCTTTACAGATTAAGAAGTCCAATGACTCTGTGTAATCGT
1 GAGTATATGAATCCCTTACAGATTAAGAAGTCCAATGACTATGTGTAATCGT
* * * ** * * *
28561521 GAGTATATGAATCCCTTGCGGATTATA-AGGTCCGGTGGCTATGTGTCATCGC
1 GAGTATATGAATCCCTTACAGATTA-AGAAGTCCAATGACTATGTGTAATCGT
28561573 GAGTATATGAAT
1 GAGTATATGAAT
28561585 GACGTGAAAT
Statistics
Matches: 96, Mismatches: 19, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
52 95 0.99
53 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (52 bp):
GAGTATATGAATCCCTTACAGATTAAGAAGTCCAATGACTATGTGTAATCGT
Found at i:28565534 original size:52 final size:52
Alignment explanation
Indices: 28565456--28565651 Score: 295
Period size: 52 Copynumber: 3.8 Consensus size: 52
28565446 GCCATAAACG
28565456 AAGAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
1 AAGAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
* *
28565508 AAGAGGTCCGATGACTAAGTGTCATCGTGACTATATGAATCCTTTACGCATT
1 AAGAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
** *
28565560 AAGAGGTCCGATGACTCTGTGTCATCGTGAGTATATGAATCCCTTACGGATT
1 AAGAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
* * * *
28565612 ATA-AGGTCCGGTGGCTATGTGTCATCTTGAGTATATGAAT
1 A-AGAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAAT
28565652 GATGTGAAAT
Statistics
Matches: 132, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
52 131 0.99
53 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (52 bp):
AAGAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
Found at i:28572732 original size:37 final size:37
Alignment explanation
Indices: 28572689--28572835 Score: 231
Period size: 37 Copynumber: 4.0 Consensus size: 37
28572679 CTTACACAAA
* * *
28572689 TTCAGGCTTTGTGCTTAGTAGGCTCTGTGCTGGTGTT
1 TTCAGGCTTTGTGCCTAGTAGGCTCTATGCCGGTGTT
28572726 TTCAGGCTTTGTGCCTAGTAGGCTCTATGCCGGTGTT
1 TTCAGGCTTTGTGCCTAGTAGGCTCTATGCCGGTGTT
*
28572763 TTCAAGCTTTGTGCCTAGTAGGCTCTATGCCGGTGTT
1 TTCAGGCTTTGTGCCTAGTAGGCTCTATGCCGGTGTT
* * *
28572800 TTCAGGCTTTGTGCTTAGTAGGCTCTGTGTCGGTGT
1 TTCAGGCTTTGTGCCTAGTAGGCTCTATGCCGGTGT
28572836 AATTGGGCTA
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 102 1.00
ACGTcount: A:0.10, C:0.19, G:0.31, T:0.40
Consensus pattern (37 bp):
TTCAGGCTTTGTGCCTAGTAGGCTCTATGCCGGTGTT
Found at i:28572852 original size:74 final size:74
Alignment explanation
Indices: 28572704--28572854 Score: 196
Period size: 74 Copynumber: 2.0 Consensus size: 74
28572694 GCTTTGTGCT
* * *
28572704 TAGTAGGCTCTGTGCTGGTGTTTTCAGGCTTTGTGCCTAGTAGGCTCTATGCCGGTGTTTTCAAG
1 TAGTAGGCTCTATGCCGGTGTTTTCAGGCTTTGTGCCTAGTAGGCTCTATGCCGGTGTATTCAAG
* *
28572769 CTTTGTGCC
66 CTATATGCC
* * * **
28572778 TAGTAGGCTCTATGCCGGTGTTTTCAGGCTTTGTGCTTAGTAGGCTCTGTGTCGGTGTAATT-GG
1 TAGTAGGCTCTATGCCGGTGTTTTCAGGCTTTGTGCCTAGTAGGCTCTATGCCGGTGT-ATTCAA
28572842 GCTATATGCC
65 GCTATATGCC
28572852 TAG
1 TAG
28572855 CAGGTTTTGT
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
74 64 0.97
75 2 0.03
ACGTcount: A:0.13, C:0.19, G:0.30, T:0.38
Consensus pattern (74 bp):
TAGTAGGCTCTATGCCGGTGTTTTCAGGCTTTGTGCCTAGTAGGCTCTATGCCGGTGTATTCAAG
CTATATGCC
Found at i:28582370 original size:33 final size:33
Alignment explanation
Indices: 28582291--28582373 Score: 89
Period size: 32 Copynumber: 2.5 Consensus size: 33
28582281 GGGATTTTGG
* * *
28582291 TTTAGGTTTAAAAA-ATGTGGGATATTTCGGGT
1 TTTAGGTTTAAAAATTTTTGGGATATTTCGGGA
* * *
28582323 TTTAGATTTCAAAATTTTTGGGA-ATTTGGGGA
1 TTTAGGTTTAAAAATTTTTGGGATATTTCGGGA
28582355 TTTAGGTTTTAAAAATTTT
1 TTTAGG-TTTAAAAATTTT
28582374 ATGATTTTCG
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
32 24 0.59
33 17 0.41
ACGTcount: A:0.29, C:0.02, G:0.23, T:0.46
Consensus pattern (33 bp):
TTTAGGTTTAAAAATTTTTGGGATATTTCGGGA
Found at i:28582462 original size:62 final size:62
Alignment explanation
Indices: 28582376--28582494 Score: 159
Period size: 62 Copynumber: 1.9 Consensus size: 62
28582366 AAAATTTTAT
* * *
28582376 GATTTTCGAGATTTTTAGGGTTGTTGGGTTTGGGAAATTTGGTTTAGGTTTAAGAAATATGGA
1 GATTTTCGAGATTTTTAGGGTTGTTAGGATTGGGAAATTTGGTTTAAGTTTAA-AAATATGGA
* * * *
28582439 GATTTT-GGGATTTTTTGGGTTGTTAGGATTGGGGATTTTGGTTTAAGTTTAAAAAT
1 GATTTTCGAGATTTTTAGGGTTGTTAGGATTGGGAAATTTGGTTTAAGTTTAAAAAT
28582495 TTAGGGATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
61 4 0.08
62 39 0.80
63 6 0.12
ACGTcount: A:0.23, C:0.01, G:0.31, T:0.45
Consensus pattern (62 bp):
GATTTTCGAGATTTTTAGGGTTGTTAGGATTGGGAAATTTGGTTTAAGTTTAAAAATATGGA
Found at i:28590557 original size:2 final size:2
Alignment explanation
Indices: 28590550--28590586 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
28590540 CAGGTACATT
28590550 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
28590587 TATCATCATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:28592361 original size:15 final size:16
Alignment explanation
Indices: 28592341--28592379 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
28592331 AATTATTTAA
28592341 AAATTATAAAAATA-T
1 AAATTATAAAAATATT
* *
28592356 AAATTATTAAATTATT
1 AAATTATAAAAATATT
28592372 AAATTATA
1 AAATTATA
28592380 TTTTTACTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATTATAAAAATATT
Found at i:28598916 original size:16 final size:17
Alignment explanation
Indices: 28598897--28598930 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
28598887 AAATACAAAT
28598897 ATTAAATAT-TAAATAA
1 ATTAAATATATAAATAA
*
28598913 ATTAATTATATAAATAA
1 ATTAAATATATAAATAA
28598930 A
1 A
28598931 AATAAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTAAATATATAAATAA
Found at i:28601572 original size:27 final size:27
Alignment explanation
Indices: 28601542--28601597 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
28601532 ACTCTAGGAT
*
28601542 AAGGATACCTTAATCGTCTATGCCATA
1 AAGGATACCTTAATAGTCTATGCCATA
*
28601569 AAGGATGCCTTAATAGTCTATGCCATA
1 AAGGATACCTTAATAGTCTATGCCATA
28601596 AA
1 AA
28601598 TCCATAGTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.29
Consensus pattern (27 bp):
AAGGATACCTTAATAGTCTATGCCATA
Found at i:28604859 original size:20 final size:20
Alignment explanation
Indices: 28604834--28604878 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
28604824 CATGATTTGT
*
28604834 ATTAAGAGTAAATAG-GCTTA
1 ATTAAGAGTAAA-AGAGATTA
*
28604854 ATTAAGATTAAAAGAGATTA
1 ATTAAGAGTAAAAGAGATTA
28604874 ATTAA
1 ATTAA
28604879 AGCTTAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.51, C:0.02, G:0.16, T:0.31
Consensus pattern (20 bp):
ATTAAGAGTAAAAGAGATTA
Found at i:28607743 original size:5 final size:5
Alignment explanation
Indices: 28607733--28607759 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
28607723 AGTATGTGTT
28607733 ATGTG ATGTG ATGTG ATGTG ATGTG AT
1 ATGTG ATGTG ATGTG ATGTG ATGTG AT
28607760 TATTGTGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.37, T:0.41
Consensus pattern (5 bp):
ATGTG
Found at i:28611790 original size:102 final size:102
Alignment explanation
Indices: 28611664--28611918 Score: 474
Period size: 102 Copynumber: 2.5 Consensus size: 102
28611654 GATCAAAATT
*
28611664 ACAATGGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATT
1 ACAATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATT
28611729 CCTATCCTCTTGAAGTTGCAGTAAACTTGGATTAAAA
66 CCTATCCTCTTGAAGTTGCAGTAAACTTGGATTAAAA
*
28611766 ACAATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCATGATGAAGCTTCAAACATCAATT
1 ACAATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATT
*
28611831 CCTATCCTCTTGAAGTTGCAGTAAAGTTGGATTAAAA
66 CCTATCCTCTTGAAGTTGCAGTAAACTTGGATTAAAA
*
28611868 ATAATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGC
1 ACAATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGC
28611919 CTCGACATCA
Statistics
Matches: 148, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 148 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (102 bp):
ACAATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATT
CCTATCCTCTTGAAGTTGCAGTAAACTTGGATTAAAA
Found at i:28611802 original size:50 final size:50
Alignment explanation
Indices: 28611735--28611904 Score: 150
Period size: 50 Copynumber: 3.4 Consensus size: 50
28611725 AATTCCTATC
28611735 CTCT-TGAAGTTGCAGTAAACTTGGATTAAAAACAATAGCAAGTCTTTAT
1 CTCTCTGAAGTTGCAGTAAACTTGGATTAAAAACAATAGCAAGTCTTTAT
* * * *** * * * *
28611784 CTCTCTGAAGTTGTAGTAAGAGCAT-GATGAAGCTTCAAACATCAATTC-CTAT
1 CTCTCTGAAGTTGCAGTAA-A-CTTGGATTAA-AAAC-AATAGCAAGTCTTTAT
* *
28611836 C-CTCTTGAAGTTGCAGTAAAGTTGGATTAAAAATAATAGCAAGTCTTTAT
1 CTCTC-TGAAGTTGCAGTAAACTTGGATTAAAAACAATAGCAAGTCTTTAT
*
28611886 CTCTCTGAAGTTGTAGTAA
1 CTCTCTGAAGTTGCAGTAA
28611905 GAGCAAGATG
Statistics
Matches: 89, Mismatches: 23, Indels: 17
0.69 0.18 0.13
Matches are distributed among these distances:
49 12 0.13
50 31 0.35
51 18 0.20
52 20 0.22
53 8 0.09
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (50 bp):
CTCTCTGAAGTTGCAGTAAACTTGGATTAAAAACAATAGCAAGTCTTTAT
Found at i:28611854 original size:52 final size:53
Alignment explanation
Indices: 28611682--28611854 Score: 171
Period size: 52 Copynumber: 3.4 Consensus size: 53
28611672 AAGTCTTTAT
* *
28611682 CTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATC
1 CTCTCTGAAGTTGCAGTAAGAGCATGATGAAGCTTCAAACATCAATTCCTATC
* * *** * * * *
28611735 CTCT-TGAAGTTGCAGTAA-A-CTTGGATTAA-AAAC-AATAGCAAGTCTTTAT-
1 CTCTCTGAAGTTGCAGTAAGAGCAT-GATGAAGCTTCAAACATCAATTC-CTATC
*
28611784 CTCTCTGAAGTTGTAGTAAGAGCATGATGAAGCTTCAAACATCAATTCCTATC
1 CTCTCTGAAGTTGCAGTAAGAGCATGATGAAGCTTCAAACATCAATTCCTATC
28611837 CTCT-TGAAGTTGCAGTAA
1 CTCTCTGAAGTTGCAGTAA
28611855 AGTTGGATTA
Statistics
Matches: 90, Mismatches: 22, Indels: 17
0.70 0.17 0.13
Matches are distributed among these distances:
49 12 0.13
50 18 0.20
51 12 0.13
52 32 0.36
53 16 0.18
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (53 bp):
CTCTCTGAAGTTGCAGTAAGAGCATGATGAAGCTTCAAACATCAATTCCTATC
Found at i:28612225 original size:6 final size:6
Alignment explanation
Indices: 28612216--28612332 Score: 64
Period size: 6 Copynumber: 20.0 Consensus size: 6
28612206 GATTTATTTC
** * * **
28612216 TAAATT TAAATT T-ACCT TAAATT TAAATT TTAATT CATTTT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
** * * *
28612263 TAAATT T-GTTT TAAATT TAAATA T-AGTT TAAATT TGAAA-- TAATTT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT T-AAATT TAAATT
* *
28612308 TAAACT TAAACTT TAAAAT TAAATT
1 TAAATT TAAA-TT TAAATT TAAATT
28612333 CAAAGTCCAT
Statistics
Matches: 78, Mismatches: 26, Indels: 14
0.66 0.22 0.12
Matches are distributed among these distances:
4 2 0.03
5 10 0.13
6 58 0.74
7 8 0.10
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.50
Consensus pattern (6 bp):
TAAATT
Found at i:28612262 original size:41 final size:42
Alignment explanation
Indices: 28612201--28612284 Score: 116
Period size: 41 Copynumber: 2.0 Consensus size: 42
28612191 TTTAGATTAG
*
28612201 TTTTAGATTTATTTCTAAATTTAAATTTACCTTAAATTTAAA
1 TTTTAGATTCATTTCTAAATTTAAATTTACCTTAAATTTAAA
* ***
28612243 TTTTA-ATTCATTTTTAAATTTAAATTTGTTTTAAATTTAAA
1 TTTTAGATTCATTTCTAAATTTAAATTTACCTTAAATTTAAA
28612284 T
1 T
28612285 ATAGTTTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 32 0.86
42 5 0.14
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (42 bp):
TTTTAGATTCATTTCTAAATTTAAATTTACCTTAAATTTAAA
Found at i:28612283 original size:17 final size:18
Alignment explanation
Indices: 28612254--28612317 Score: 73
Period size: 17 Copynumber: 3.7 Consensus size: 18
28612244 TTTAATTCAT
*
28612254 TTTTAAATTTAAAT-TTG
1 TTTTAAATTTAAATATAG
28612271 TTTTAAATTTAAATATAG
1 TTTTAAATTTAAATATAG
28612289 -TTTAAATTTGAAATA-A-
1 TTTTAAATTT-AAATATAG
*
28612305 TTTTAAACTTAAA
1 TTTTAAATTTAAA
28612318 CTTTAAAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
16 3 0.07
17 32 0.76
18 7 0.17
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (18 bp):
TTTTAAATTTAAATATAG
Found at i:28612997 original size:12 final size:12
Alignment explanation
Indices: 28612972--28613034 Score: 63
Period size: 12 Copynumber: 4.9 Consensus size: 12
28612962 AGTTATAACA
*
28612972 TAATAAATATTAT
1 TAAT-AATAATAT
28612985 TAATAATAATAT
1 TAATAATAATAT
* *
28612997 TAATAATAACAG
1 TAATAATAATAT
28613009 TAATAATGAATTTAT
1 TAATAAT-AA--TAT
28613024 TAATAATAATA
1 TAATAATAATA
28613035 AATAAATATT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
12 26 0.62
13 6 0.14
14 2 0.05
15 8 0.19
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.40
Consensus pattern (12 bp):
TAATAATAATAT
Found at i:28613045 original size:24 final size:24
Alignment explanation
Indices: 28613018--28613066 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
28613008 GTAATAATGA
* *
28613018 ATTTATTAATAATAATAAATAAAT
1 ATTTATTAATAAAAATAAAAAAAT
*
28613042 ATTTATTATTAAAAATAAAAAAAT
1 ATTTATTAATAAAAATAAAAAAAT
28613066 A
1 A
28613067 GAAAACGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
ATTTATTAATAAAAATAAAAAAAT
Found at i:28614113 original size:30 final size:29
Alignment explanation
Indices: 28614070--28614331 Score: 130
Period size: 29 Copynumber: 8.9 Consensus size: 29
28614060 CCCCAGAGGT
*
28614070 CCAAACTTCCCAAAAATTTCATTTTTAACC
1 CCAAACTT-CCAAAAATTCCATTTTTAACC
*
28614100 CCAAAACTTCCAAAAATTATCA-TTTT-ACC
1 CC-AAACTTCCAAAAATT-CCATTTTTAACC
*
28614129 CTCAAACTTCTAAAAATTCCA-TTTTAACC
1 C-CAAACTTCCAAAAATTCCATTTTTAACC
* ***
28614158 CTGATTTTTCCAAAAATTACC-TTTTT-ACC
1 C-CAAACTTCCAAAAATT-CCATTTTTAACC
**
28614187 TCCTGACTTCCAAAAATTCCATTTTTAACC
1 -CCAAACTTCCAAAAATTCCATTTTTAACC
* ** *
28614217 TCGATTCTTCCTAAAATTACCA-TTTT-ACC
1 -CCAAACTTCCAAAAATT-CCATTTTTAACC
* *
28614246 CTCGAACTTTCCTAAAATTCCA-TTTTAACC
1 C-CAAAC-TTCCAAAAATTCCATTTTTAACC
* *** *
28614276 CTGATTTTTCCCTAAAATTACCA-TTTT-ACC
1 C-CAAACTT-CCAAAAATT-CCATTTTTAACC
*
28614306 CTCAAACTTCCAAAAATTTCATTTTT
1 C-CAAACTTCCAAAAATTCCATTTTT
28614332 GATCCCCATT
Statistics
Matches: 184, Mismatches: 32, Indels: 33
0.74 0.13 0.13
Matches are distributed among these distances:
28 11 0.06
29 78 0.42
30 76 0.41
31 19 0.10
ACGTcount: A:0.32, C:0.27, G:0.02, T:0.38
Consensus pattern (29 bp):
CCAAACTTCCAAAAATTCCATTTTTAACC
Found at i:28614243 original size:59 final size:58
Alignment explanation
Indices: 28614074--28614446 Score: 321
Period size: 59 Copynumber: 6.3 Consensus size: 58
28614064 AGAGGTCCAA
* ** *** * *
28614074 ACTTCCCAAAAATTTCATTTTTAACCCCAAAACTTCCAAAAATTATCATTTTACCCTCAA
1 ACTT-CCAAAAATTCCATTTTTAACCCTGATTTTTCCAAAAATTACCATTTTACCC-CAG
* * *
28614134 ACTTCTAAAAATTCCA-TTTTAACCCTGATTTTTCCAAAAATTACCTTTTTACCTCCTG
1 ACTTCCAAAAATTCCATTTTTAACCCTGATTTTTCCAAAAATTACCATTTTACC-CCAG
* *
28614192 ACTTCCAAAAATTCCATTTTTAA-CCTCGATTCTTCCTAAAATTACCATTTTACCCTC-G
1 ACTTCCAAAAATTCCATTTTTAACCCT-GATTTTTCCAAAAATTACCATTTTACCC-CAG
* * *
28614250 AACTTTCCTAAAATTCCA-TTTTAACCCTGATTTTTCCCTAAAATTACCATTTTACCCTCAA
1 -AC-TTCCAAAAATTCCATTTTTAACCCTGATTTTT-CCAAAAATTACCATTTTACCC-CAG
* * * * *
28614311 ACTTCCAAAAATTTCATTTTTGATCCC-CATTTTTTCAAAAATTACCATTTTACCCCCG
1 ACTTCCAAAAATTCCATTTTT-AACCCTGATTTTTCCAAAAATTACCATTTTACCCCAG
* * * * * *
28614369 AATAT-CAAAAATTCC-GTTTTAACTCTGAATTTTCCCAAAATTACCATTTTGCCCC-G
1 ACT-TCCAAAAATTCCATTTTTAACCCTGATTTTTCCAAAAATTACCATTTTACCCCAG
*
28614425 AGCGTCCAAAAATTACCATTTT
1 A-CTTCCAAAAATT-CCATTTT
28614447 GCCTCCGAGT
Statistics
Matches: 257, Mismatches: 39, Indels: 35
0.78 0.12 0.11
Matches are distributed among these distances:
56 6 0.02
57 36 0.14
58 65 0.25
59 91 0.35
60 55 0.21
61 4 0.02
ACGTcount: A:0.32, C:0.27, G:0.03, T:0.38
Consensus pattern (58 bp):
ACTTCCAAAAATTCCATTTTTAACCCTGATTTTTCCAAAAATTACCATTTTACCCCAG
Found at i:28614331 original size:29 final size:29
Alignment explanation
Indices: 28614071--28614331 Score: 174
Period size: 30 Copynumber: 8.8 Consensus size: 29
28614061 CCCAGAGGTC
*
28614071 CAAACTTCCCAAAAATTTCATTTTTAACCC-
1 CAAACTT-CCAAAAATTCCATTTTT-ACCCT
*
28614101 CAAAACTTCCAAAAATTATCA-TTTTACCCT
1 C-AAACTTCCAAAAATT-CCATTTTTACCCT
* *
28614131 CAAACTTCTAAAAATTCCATTTTAACCCT
1 CAAACTTCCAAAAATTCCATTTTTACCCT
* ***
28614160 GATTTTTCCAAAAATTACC-TTTTTA-CCT
1 CAAACTTCCAAAAATT-CCATTTTTACCCT
** *
28614188 CCTGACTTCCAAAAATTCCATTTTTAACCT
1 -CAAACTTCCAAAAATTCCATTTTTACCCT
** *
28614218 CGATTCTTCCTAAAATTACCA-TTTTACCCT
1 C-AAACTTCCAAAAATT-CCATTTTTACCCT
* * *
28614248 CGAACTTTCCTAAAATTCCATTTTAACCCT
1 CAAAC-TTCCAAAAATTCCATTTTTACCCT
* *** *
28614278 GATTTTTCCCTAAAATTACCA-TTTTACCCT
1 CAAACTT-CCAAAAATT-CCATTTTTACCCT
*
28614308 CAAACTTCCAAAAATTTCATTTTT
1 CAAACTTCCAAAAATTCCATTTTT
28614332 GATCCCCATT
Statistics
Matches: 181, Mismatches: 35, Indels: 31
0.73 0.14 0.13
Matches are distributed among these distances:
28 9 0.05
29 78 0.43
30 79 0.44
31 15 0.08
ACGTcount: A:0.33, C:0.27, G:0.02, T:0.38
Consensus pattern (29 bp):
CAAACTTCCAAAAATTCCATTTTTACCCT
Found at i:28614376 original size:28 final size:28
Alignment explanation
Indices: 28614345--28614474 Score: 77
Period size: 28 Copynumber: 4.6 Consensus size: 28
28614335 CCCCATTTTT
28614345 TCAAAAATTACCATTTTACCCCCGAATA
1 TCAAAAATTACCATTTTACCCCCGAATA
* * * * *
28614373 TCAAAAATT-CCGTTTTAACTCTGAATTT
1 TCAAAAATTACCATTTTACCCCCGAA-TA
* * ***
28614401 TCCCAAAATTACCATTTT-GCCCCGAGCG
1 T-CAAAAATTACCATTTTACCCCCGAATA
* * *
28614429 TCCAAAAATTACCATTTTGCCTCCGAGTA
1 T-CAAAAATTACCATTTTACCCCCGAATA
*
28614458 TCTAAAAATCA-CATTTT
1 TC-AAAAATTACCATTTT
28614475 CAAATCCCGA
Statistics
Matches: 78, Mismatches: 19, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
27 12 0.15
28 35 0.45
29 25 0.32
30 6 0.08
ACGTcount: A:0.33, C:0.26, G:0.08, T:0.33
Consensus pattern (28 bp):
TCAAAAATTACCATTTTACCCCCGAATA
Found at i:28614464 original size:29 final size:28
Alignment explanation
Indices: 28614405--28614474 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
28614395 GAATTTTCCC
*
28614405 AAAATTACCATTTTGCCCCGAGCGTCCA
1 AAAATTACCATTTTGCCCCGAGCATCCA
* *
28614433 AAAATTACCATTTTGCCTCCGAGTATCTA
1 AAAATTACCATTTTGCC-CCGAGCATCCA
*
28614462 AAAATCA-CATTTT
1 AAAATTACCATTTT
28614475 CAAATCCCGA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 23 0.62
29 14 0.38
ACGTcount: A:0.33, C:0.26, G:0.10, T:0.31
Consensus pattern (28 bp):
AAAATTACCATTTTGCCCCGAGCATCCA
Found at i:28617698 original size:29 final size:29
Alignment explanation
Indices: 28617665--28617768 Score: 131
Period size: 29 Copynumber: 3.6 Consensus size: 29
28617655 ATAAAAAAAC
*
28617665 AATAAAAGTTATAAAAAATATTAAATTTT
1 AATAAAAATTATAAAAAATATTAAATTTT
28617694 AATAAAAATTAT-AAAAATATTTAAATTTT
1 AATAAAAATTATAAAAAATA-TTAAATTTT
* * * *
28617723 ATTAAAAATTATAAAAATTATAAAATTCGT
1 AATAAAAATTATAAAAAATATTAAATT-TT
28617753 AA-AAAAATTATAAAAA
1 AATAAAAATTATAAAAA
28617769 TTATCGTACT
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
28 7 0.11
29 51 0.77
30 8 0.12
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.36
Consensus pattern (29 bp):
AATAAAAATTATAAAAAATATTAAATTTT
Found at i:28617709 original size:9 final size:9
Alignment explanation
Indices: 28617666--28617772 Score: 79
Period size: 9 Copynumber: 11.2 Consensus size: 9
28617656 TAAAAAAACA
*
28617666 ATAAAAGTT
1 ATAAAAATT
*
28617675 ATAAAAAAT
1 ATAAAAATT
**
28617684 ATTAAATTTT
1 A-TAAAAATT
28617694 AATAAAAATT
1 -ATAAAAATT
28617704 ATAAAAATAT
1 ATAAAAAT-T
* **
28617714 TTAAATTTT
1 ATAAAAATT
28617723 ATTAAAAATT
1 A-TAAAAATT
28617733 ATAAAAATT
1 ATAAAAATT
*
28617742 ATAAAATTCGT
1 ATAAAAAT--T
*
28617753 AAAAAAATT
1 ATAAAAATT
28617762 ATAAAAATT
1 ATAAAAATT
28617771 AT
1 AT
28617773 CGTACTAAAA
Statistics
Matches: 75, Mismatches: 17, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
9 43 0.57
10 24 0.32
11 8 0.11
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (9 bp):
ATAAAAATT
Found at i:28617993 original size:10 final size:10
Alignment explanation
Indices: 28617950--28618053 Score: 104
Period size: 10 Copynumber: 10.3 Consensus size: 10
28617940 TTTTATTCAA
28617950 TTTATAATATT
1 TTTATAAT-TT
28617961 TTTATAA-TT
1 TTTATAATTT
***
28617970 TTTATAAAAG
1 TTTATAATTT
*
28617980 TTTACAATTT
1 TTTATAATTT
28617990 TTTATAATTT
1 TTTATAATTT
**
28618000 TTTACGATTT
1 TTTATAATTT
28618010 TTTATAATTT
1 TTTATAATTT
28618020 TTTATAATTT
1 TTTATAATTT
28618030 TTT-TAAATTTT
1 TTTAT-AA-TTT
*
28618041 TTTATAGTTT
1 TTTATAATTT
28618051 TTT
1 TTT
28618054 GTCACAGGTC
Statistics
Matches: 77, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
9 10 0.13
10 52 0.68
11 14 0.18
12 1 0.01
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (10 bp):
TTTATAATTT
Done.