Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 138 of 325
Found at i:42084431 original size:46 final size:46
Alignment explanation
Indices: 42084265--42084483 Score: 248
Period size: 46 Copynumber: 4.7 Consensus size: 46
42084255 TGTAACCCGC
* * * * *
42084265 CCATAAGCGAACTTGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* * * *
42084311 CAACAAGTGAACTCGGACTCAACTCAACAAGCTT-GG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAG-TTCGGACATTCGC-A--T
* ***
42084357 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
42084404 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
42084450 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC
42084484 AGATGCCCAA
Statistics
Matches: 144, Mismatches: 20, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.02
46 105 0.73
47 30 0.21
49 4 0.03
50 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:42086433 original size:45 final size:49
Alignment explanation
Indices: 42086374--42086467 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 49
42086364 AAAACGCCGC
*
42086374 TAAAGGTCATAAAAAT-TAAAAAAA-TAAAA-T-ATTAT-AAAATATTG
1 TAAAAGTCATAAAAATATAAAAAAATTAAAATTCATTATCAAAATATTG
42086418 TAAAAGTCATGAAAAATATAAAAAAATTAAAATTCATTATCAAAATATTG
1 TAAAAGTCAT-AAAAATATAAAAAAATTAAAATTCATTATCAAAATATTG
42086468 AGAAGAAGAA
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
44 9 0.21
45 6 0.14
46 8 0.19
47 5 0.12
48 1 0.02
49 5 0.12
50 9 0.21
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.30
Consensus pattern (49 bp):
TAAAAGTCATAAAAATATAAAAAAATTAAAATTCATTATCAAAATATTG
Found at i:42087330 original size:21 final size:22
Alignment explanation
Indices: 42087293--42087350 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
42087283 AATCACAACT
42087293 TTTAGACACCATAAA-TTGCAGCA
1 TTTA-ACACC-TAAATTTGCAGCA
* *
42087316 TTTAACACCTAAATTTTCAGTA
1 TTTAACACCTAAATTTGCAGCA
*
42087338 TTTAACACATAAA
1 TTTAACACCTAAA
42087351 ATGGTTTTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.13
22 23 0.74
23 4 0.13
ACGTcount: A:0.41, C:0.19, G:0.07, T:0.33
Consensus pattern (22 bp):
TTTAACACCTAAATTTGCAGCA
Found at i:42092582 original size:7 final size:7
Alignment explanation
Indices: 42092557--42092602 Score: 78
Period size: 7 Copynumber: 6.9 Consensus size: 7
42092547 ATTCAATTAT
42092557 TATTTTA
1 TATTTTA
42092564 -ATTTTA
1 TATTTTA
42092570 -ATTTTA
1 TATTTTA
42092576 TATTTTA
1 TATTTTA
42092583 TATTTTA
1 TATTTTA
42092590 TATTTTA
1 TATTTTA
42092597 TATTTT
1 TATTTT
42092603 TTTAGTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 12 0.32
7 26 0.68
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TATTTTA
Found at i:42092842 original size:47 final size:47
Alignment explanation
Indices: 42092748--42092842 Score: 113
Period size: 47 Copynumber: 2.0 Consensus size: 47
42092738 TAGACGGATT
* * * *
42092748 TATCTCAATCTTTTTTAAAGGTTGTCTTAGACAAGATTTATCCCAAC
1 TATCTAAACCTTTTTTAAAAGTTGTCTTAGACAAGATCTATCCCAAC
*
42092795 TATCTAAACCTTTTTTAAAAGTTG-CATTAGACAATG-TCTATCTCAAC
1 TATCTAAACCTTTTTTAAAAGTTGTC-TTAGACAA-GATCTATCCCAAC
42092842 T
1 T
42092843 TTGCTTTAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
46 1 0.02
47 39 0.95
48 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (47 bp):
TATCTAAACCTTTTTTAAAAGTTGTCTTAGACAAGATCTATCCCAAC
Found at i:42092900 original size:37 final size:37
Alignment explanation
Indices: 42092859--42093245 Score: 301
Period size: 37 Copynumber: 10.6 Consensus size: 37
42092849 TAGACGGGTT
* * *
42092859 TATCCCAACCTTTTTAAAAGTTGTCTTAGATAAGGTA
1 TATCCCAACCTTTTTAAAGGTTGCCTTAGATAAGGTC
** * * *
42092896 TATCCCAACCTTTTT-AAGGTTGTATTAGATGA-CTT
1 TATCCCAACCTTTTTAAAGGTTGCCTTAGATAAGGTC
** * * *
42092931 TATCTTAACTTTTTTAAAGGTTGCCTTAAACAAGGTC
1 TATCCCAACCTTTTTAAAGGTTGCCTTAGATAAGGTC
* * * **
42092968 TATCCTAACCTTTTT-AGGGTTGCTTTAGACGA-GTC
1 TATCCCAACCTTTTTAAAGGTTGCCTTAGATAAGGTC
* * * *
42093003 TATTCCAACTTTTTTTAAGGGTTGCCTTAGAGAAGGTC
1 TATCCCAAC-CTTTTTAAAGGTTGCCTTAGATAAGGTC
* * *
42093041 TATCCCAACCTTTTT-AAGGTTACCTTAAACAA-GTC
1 TATCCCAACCTTTTTAAAGGTTGCCTTAGATAAGGTC
* * * *
42093076 TATCCTAACATTTTTTAAGGGTTGCCTTAGACAAGGTC
1 TATCCCAAC-CTTTTTAAAGGTTGCCTTAGATAAGGTC
** * *
42093114 TATCCCAACC-TTTTAAAGGTTATCTTAAATGA-GTC
1 TATCCCAACCTTTTTAAAGGTTGCCTTAGATAAGGTC
* * *
42093149 TATCCCAACCTTTTTTAAGTGTTACCTTAGAT-TGGTC
1 TATCCCAACCTTTTTAAAG-GTTGCCTTAGATAAGGTC
*
42093186 TATCCTAACCTTTTTCAAAGGTTGGCCTT-GACT-AGGTC
1 TATCCCAACCTTTTT-AAAGGTT-GCCTTAGA-TAAGGTC
42093224 TATCCCAACCTTTTTTAAAGGT
1 TATCCCAACC-TTTTTAAAGGT
42093246 CGGCATTGAC
Statistics
Matches: 280, Mismatches: 55, Indels: 29
0.77 0.15 0.08
Matches are distributed among these distances:
35 47 0.17
36 85 0.30
37 94 0.34
38 49 0.17
39 5 0.02
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (37 bp):
TATCCCAACCTTTTTAAAGGTTGCCTTAGATAAGGTC
Found at i:42093045 original size:73 final size:72
Alignment explanation
Indices: 42092843--42093241 Score: 333
Period size: 73 Copynumber: 5.5 Consensus size: 72
42092833 TATCTCAACT
* * * * ** * * *
42092843 TTGCTTTAGACGGGTTTATCCCAACCTTTTTAAAAGTTGTCTTAGATAAGGTATATCCCAACCTT
1 TTGCTTTAGACGAGTCTATTCCAACTTTTTTAAGGGTTGCCTTAGACAAGGTCTATCCCAACCTT
42092908 TTTAAGG
66 TTTAAGG
* * * * * * *
42092915 TTG-TATTAGATGACTTTA-TCTTAACTTTTTTAAAGGTTGCCTTAAACAAGGTCTATCCTAACC
1 TTGCT-TTAGACGAGTCTATTC-CAACTTTTTTAAGGGTTGCCTTAGACAAGGTCTATCCCAACC
*
42092978 TTTTTAGGG
64 TTTTTAAGG
*
42092987 TTGCTTTAGACGAGTCTATTCCAACTTTTTTTAAGGGTTGCCTTAGAGAAGGTCTATCCCAACCT
1 TTGCTTTAGACGAGTCTATTCCAAC-TTTTTTAAGGGTTGCCTTAGACAAGGTCTATCCCAACCT
42093052 TTTTAAGG
65 TTTTAAGG
* * * *
42093060 TTACCTTAAACAAGTCTA-TCCTAACATTTTTTAAGGGTTGCCTTAGACAAGGTCTATCCCAACC
1 TTGCTTTAGACGAGTCTATTCC-AAC-TTTTTTAAGGGTTGCCTTAGACAAGGTCTATCCCAACC
*
42093124 TTTTAAAGG
64 TTTTTAAGG
* * * * * * ** *
42093133 TT-ATCTTAAATGAGTCTATCCCAACCTTTTTTAAGTGTTACCTTAGA-TTGGTCTATCCTAACC
1 TTGCT-TTAGACGAGTCTATTCCAA-CTTTTTTAAGGGTTGCCTTAGACAAGGTCTATCCCAACC
42093196 TTTTTCAAAGG
64 TTTTT--AAGG
* * *
42093207 TTGGCCTT-GACTAGGTCTATCCCAACCTTTTTTAA
1 TT-GCTTTAGACGA-GTCTATTCCAA-CTTTTTTAA
42093242 AGGTCGGCAT
Statistics
Matches: 268, Mismatches: 45, Indels: 25
0.79 0.13 0.07
Matches are distributed among these distances:
71 2 0.01
72 91 0.34
73 141 0.53
74 11 0.04
75 23 0.09
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (72 bp):
TTGCTTTAGACGAGTCTATTCCAACTTTTTTAAGGGTTGCCTTAGACAAGGTCTATCCCAACCTT
TTTAAGG
Found at i:42093192 original size:110 final size:108
Alignment explanation
Indices: 42092859--42093237 Score: 349
Period size: 110 Copynumber: 3.5 Consensus size: 108
42092849 TAGACGGGTT
* * * * * * * *
42092859 TATCCCAACCTTTTTAAAAGTTGTCTTAGATAAGGTATATCCCAACCTTTTTAAGGTTGTATTAG
1 TATCCTAACTTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTAAAGGTTGTCTTAG
* * ** *
42092924 ATGACTTTATCTTAA-CTTTTTTAAAGGTTGCCTTAAACAAGGTC
66 ATGAGTCTATCCCAACCTTTTTT-AAGGTTACCTTAAA-AAGGTC
* * * * * * * *
42092968 TATCCTAACCTTTTT-AGGGTTGCTTTAGACGA-GTCTATTCCAACTTTTTTTAAGGGTTGCCTT
1 TATCCTAACTTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCCAAC--CTTTTAAAGGTTGTCTT
42093031 AGA-GAAGGTCTATCCCAACC-TTTTTAAGGTTACCTTAAACAA-GTC
64 AGATG-A-GTCTATCCCAACCTTTTTTAAGGTTACCTTAAA-AAGGTC
* *
42093076 TATCCTAACATTTTTTAAGGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTAAAGGTTATCTTA
1 TATCCTAAC-TTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTAAAGGTTGTCTTA
* * **
42093141 AATGAGTCTATCCCAACCTTTTTTAAGTGTTACCTTAGATTGGTC
65 GATGAGTCTATCCCAACCTTTTTTAAG-GTTACCTTAAAAAGGTC
* *
42093186 TATCCTAACCTTTTTCAAAGGTTGGCCTT-GACTAGGTCTATCCCAACCTTTT
1 TATCCTAA-CTTTTTTAAAGGTT-GCCTTAGACAAGGTCTATCCCAACCTTTT
42093238 TTAAAGGTCG
Statistics
Matches: 222, Mismatches: 34, Indels: 27
0.78 0.12 0.10
Matches are distributed among these distances:
107 10 0.05
108 37 0.17
109 75 0.34
110 82 0.37
111 18 0.08
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (108 bp):
TATCCTAACTTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTAAAGGTTGTCTTAG
ATGAGTCTATCCCAACCTTTTTTAAGGTTACCTTAAAAAGGTC
Found at i:42093271 original size:38 final size:38
Alignment explanation
Indices: 42093192--42093271 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 38
42093182 GGTCTATCCT
* * * *
42093192 AACCTTTTTCAAAGGTTGGCCTTGACTAGGTCTATCCC
1 AACCTTTTTCAAAGGTCGGCATTGACTAGGCCTATCAC
* * *
42093230 AACCTTTTTTAAAGGTCGGCATTGACTGGGCCTTTCAC
1 AACCTTTTTCAAAGGTCGGCATTGACTAGGCCTATCAC
42093268 AACC
1 AACC
42093272 CTTCAATAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.33
Consensus pattern (38 bp):
AACCTTTTTCAAAGGTCGGCATTGACTAGGCCTATCAC
Found at i:42095232 original size:74 final size:75
Alignment explanation
Indices: 42095136--42095286 Score: 198
Period size: 74 Copynumber: 2.0 Consensus size: 75
42095126 AGTACGATGT
* * * *
42095136 ACATGCTGACGTCATAAATAGAGAGTTACACAGCTTGAGGACACGGGCG-GTCCCTATGTCCACA
1 ACATGCTAACGTCATAAATAGAGAGTTACACAGCCTGAAGACACGAGCGTGTCCCTATGTCCACA
42095200 CGA-GCGTGTG
66 -GAGGCGTGTG
* * * * *
42095210 ACATGCTAATGTCATAAGTAGAGAGTTACACGGCCTGAAGACACGAGCGTGTCCCTATTTCCATA
1 ACATGCTAACGTCATAAATAGAGAGTTACACAGCCTGAAGACACGAGCGTGTCCCTATGTCCACA
42095275 GAGGCGTGTG
66 GAGGCGTGTG
42095285 AC
1 AC
42095287 CCTGTTTCAT
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
74 44 0.67
75 22 0.33
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.22
Consensus pattern (75 bp):
ACATGCTAACGTCATAAATAGAGAGTTACACAGCCTGAAGACACGAGCGTGTCCCTATGTCCACA
GAGGCGTGTG
Found at i:42095552 original size:26 final size:26
Alignment explanation
Indices: 42095523--42095574 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
42095513 GGGTAAGGGG
42095523 TGTTACATTTAGTGGTATCAAAGCAT
1 TGTTACATTTAGTGGTATCAAAGCAT
42095549 TGTTACATTTAGTGGTATCAAAGCAT
1 TGTTACATTTAGTGGTATCAAAGCAT
42095575 GGTTTAGTCG
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:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (26 bp):
TGTTACATTTAGTGGTATCAAAGCAT
Found at i:42097061 original size:15 final size:15
Alignment explanation
Indices: 42097028--42097082 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
42097018 GGTATTGTGA
*
42097028 TTGGATTTTCTTGT-T
1 TTGGA-TTTCTTATAT
42097043 TTGGATTTCTT-TAT
1 TTGGATTTCTTATAT
42097057 GTTGGATTT-TTATAT
1 -TTGGATTTCTTATAT
42097072 TCTGGATTTCT
1 T-TGGATTTCT
42097083 CCGTTATGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
13 1 0.03
14 10 0.29
15 23 0.66
16 1 0.03
ACGTcount: A:0.13, C:0.07, G:0.18, T:0.62
Consensus pattern (15 bp):
TTGGATTTCTTATAT
Found at i:42099682 original size:46 final size:46
Alignment explanation
Indices: 42099570--42099689 Score: 140
Period size: 46 Copynumber: 2.6 Consensus size: 46
42099560 TTCGGTTGCT
*
42099570 AGTGTAAGACATGTCTGGGACATGCATCGGCCGCATTATGAAATGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGG-CACATTATGAAATGCC
* *
42099617 AGTGTAAGAAATGTATGGGACATGCATC-G-ACATTGA-GACGAGA-GCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCACATT-ATGA--A-ATGCC
42099663 AGTGTAAGACATGTCTGGGACATGCAT
1 AGTGTAAGACATGTCTGGGACATGCAT
42099690 TGGCTACAAG
Statistics
Matches: 64, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
44 6 0.09
45 1 0.02
46 30 0.47
47 27 0.42
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCACATTATGAAATGCC
Found at i:42105773 original size:40 final size:39
Alignment explanation
Indices: 42105608--42105791 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
42105598 GAAATTGATG
* * *
42105608 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
42105648 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
42105688 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
42105728 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
42105767 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
42105792 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:42105816 original size:80 final size:81
Alignment explanation
Indices: 42105648--42105836 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
42105638 GCTGGAAATT
* * * *
42105648 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
42105713 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
42105729 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
42105792 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
42105808 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
42105837 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:42116138 original size:28 final size:28
Alignment explanation
Indices: 42116098--42116190 Score: 150
Period size: 28 Copynumber: 3.3 Consensus size: 28
42116088 ATGCACTATT
42116098 ATACCCCTATGTATGCAAAATTACCATA
1 ATACCCCTATGTATGCAAAATTACCATA
*
42116126 ATACCCCTATGTATGCAAAATTGCCATA
1 ATACCCCTATGTATGCAAAATTACCATA
* * *
42116154 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATTACCATA
42116182 ATACCCCTA
1 ATACCCCTA
42116191 GGGTTAATTT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 60 1.00
ACGTcount: A:0.35, C:0.27, G:0.09, T:0.29
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATTACCATA
Found at i:42116354 original size:27 final size:27
Alignment explanation
Indices: 42116296--42116385 Score: 119
Period size: 28 Copynumber: 3.2 Consensus size: 27
42116286 AGGAAGCGTC
42116296 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* *
42116324 CTGGTGGCCCTGCCACATATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
42116351 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
42116380 CTGGTG
1 CTGGTG
42116386 ACTCTATCAC
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 23 0.42
28 25 0.45
29 7 0.13
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.32
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:42116396 original size:29 final size:28
Alignment explanation
Indices: 42116308--42116396 Score: 81
Period size: 27 Copynumber: 3.2 Consensus size: 28
42116298 GGTGGCTATG
* * * *
42116308 CCACAAATTATCTGTTCTGGTGGCCCTG
1 CCACAAAATATCTGTTCTGGTGACACTA
* * *
42116336 CCAC-ATATATCTGTTCTGGTGGCACTG
1 CCACAAAATATCTGTTCTGGTGACACTA
*
42116363 CCACAAAATATCTGTATCTGGTGACTCTA
1 CCACAAAATATCTGT-TCTGGTGACACTA
*
42116392 TCACA
1 CCACA
42116397 TTTTCTGTAT
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
27 24 0.47
28 13 0.25
29 14 0.27
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (28 bp):
CCACAAAATATCTGTTCTGGTGACACTA
Found at i:42116404 original size:55 final size:56
Alignment explanation
Indices: 42116296--42116410 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 56
42116286 AGGAAGCGTC
* * *
42116296 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACATATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTACCACATATATCTGTAT
* * *
42116351 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTATCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTACCACATATATCTGTAT
42116407 CTGG
1 CTGG
42116411 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
54 1 0.02
55 30 0.59
56 20 0.39
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTACCACATATATCTGTAT
Found at i:42122751 original size:23 final size:23
Alignment explanation
Indices: 42122725--42122792 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
42122715 TCTAATGATC
42122725 TAAAACGATAAGCTCTTTTGAGT
1 TAAAACGATAAGCTCTTTTGAGT
* *
42122748 TAAAAC-AGTAAGCTCTATCGAGT
1 TAAAACGA-TAAGCTCTTTTGAGT
* * *
42122771 TGAAATGGTAAGCTCTTTTGAG
1 TAAAACGATAAGCTCTTTTGAG
42122793 CTGAAACAGT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
22 1 0.03
23 35 0.97
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (23 bp):
TAAAACGATAAGCTCTTTTGAGT
Found at i:42122764 original size:46 final size:46
Alignment explanation
Indices: 42122698--42122841 Score: 141
Period size: 46 Copynumber: 3.1 Consensus size: 46
42122688 GCTCCTACTA
*
42122698 AGCTAATAACAATAAGCTCTAATGATCTAAAACGATAAGCTCTTTTG
1 AGCTAA-AACAGTAAGCTCTAATGATCTAAAACGATAAGCTCTTTTG
* * * *
42122745 AGTTAAAACAGTAAGCTCT-ATCGAGT-TGAAATGGTAAGCTCTTTTG
1 AGCTAAAACAGTAAGCTCTAAT-GA-TCTAAAACGATAAGCTCTTTTG
* * * *
42122791 AGCTGAAACAGTAAGCTCCAATGAGCTGAAAAC-AGTAAGCTCTTATG
1 AGCTAAAACAGTAAGCTCTAATGATCT-AAAACGA-TAAGCTCTTTTG
42122838 AGCT
1 AGCT
42122842 GATATATCGA
Statistics
Matches: 78, Mismatches: 13, Indels: 12
0.76 0.13 0.12
Matches are distributed among these distances:
45 2 0.03
46 50 0.64
47 26 0.33
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.28
Consensus pattern (46 bp):
AGCTAAAACAGTAAGCTCTAATGATCTAAAACGATAAGCTCTTTTG
Found at i:42122797 original size:23 final size:23
Alignment explanation
Indices: 42122733--42122843 Score: 114
Period size: 23 Copynumber: 4.8 Consensus size: 23
42122723 TCTAAAACGA
* *
42122733 TAAGCTCTTTTGAGTTAAAACAG
1 TAAGCTCTTTTGAGCTGAAACAG
* * * **
42122756 TAAGCTCTATCGAGTTGAAATGG
1 TAAGCTCTTTTGAGCTGAAACAG
42122779 TAAGCTCTTTTGAGCTGAAACAG
1 TAAGCTCTTTTGAGCTGAAACAG
***
42122802 TAAGCTCCAATGAGCTGAAAACAG
1 TAAGCTCTTTTGAGCTG-AAACAG
*
42122826 TAAGCTCTTATGAGCTGA
1 TAAGCTCTTTTGAGCTGA
42122844 TATATCGATA
Statistics
Matches: 72, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
23 51 0.71
24 21 0.29
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (23 bp):
TAAGCTCTTTTGAGCTGAAACAG
Found at i:42122828 original size:24 final size:24
Alignment explanation
Indices: 42122789--42122843 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
42122779 TAAGCTCTTT
42122789 TGAGCTG-AAACAGTAAGCTCCAA
1 TGAGCTGAAAACAGTAAGCTCCAA
**
42122812 TGAGCTGAAAACAGTAAGCTCTTA
1 TGAGCTGAAAACAGTAAGCTCCAA
42122836 TGAGCTGA
1 TGAGCTGA
42122844 TATATCGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 7 0.24
24 22 0.76
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (24 bp):
TGAGCTGAAAACAGTAAGCTCCAA
Found at i:42128001 original size:42 final size:42
Alignment explanation
Indices: 42127928--42128024 Score: 131
Period size: 42 Copynumber: 2.3 Consensus size: 42
42127918 TGTGGCCTGA
* * **
42127928 CACAAGGGTGTGTATATCGGTCGTGTGTGGCACACGGGCAGG
1 CACATGGGCGTGTATATCGGTCGTGTGTGGCACACAAGCAGG
* * *
42127970 CACATGGGCGTGTCTATCGGTCGTGTTTGGCACACAAGCTGG
1 CACATGGGCGTGTATATCGGTCGTGTGTGGCACACAAGCAGG
42128012 CACATGGGCGTGT
1 CACATGGGCGTGT
42128025 GGTCAGCCGT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.18, C:0.22, G:0.37, T:0.24
Consensus pattern (42 bp):
CACATGGGCGTGTATATCGGTCGTGTGTGGCACACAAGCAGG
Found at i:42131223 original size:23 final size:23
Alignment explanation
Indices: 42131197--42131309 Score: 88
Period size: 23 Copynumber: 4.8 Consensus size: 23
42131187 AGCTCGTAAA
*
42131197 AGCTTACTGTTTCAGCTCATTAG
1 AGCTTACTGTTTCAGCTCAATAG
* * *
42131220 AGCTTACCGATTCAGATCGAA-AG
1 AGCTTACTGTTTCAGCTC-AATAG
* * *
42131243 AGCTTACCGTTT-AGCTTAATAA
1 AGCTTACTGTTTCAGCTCAATAG
*
42131265 AGCTTACCAT-TTTCAGCGCAATAG
1 AGCTTA-C-TGTTTCAGCTCAATAG
42131289 AGCTTACTGTTTATCAGCTCA
1 AGCTTACTG-TT-TCAGCTCA
42131310 GGAAGAGCCT
Statistics
Matches: 69, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
21 2 0.03
22 11 0.16
23 33 0.48
24 16 0.23
25 7 0.10
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (23 bp):
AGCTTACTGTTTCAGCTCAATAG
Found at i:42133051 original size:96 final size:96
Alignment explanation
Indices: 42132882--42133104 Score: 293
Period size: 96 Copynumber: 2.3 Consensus size: 96
42132872 GGGTGTTACA
* * * * * * *
42132882 GGCCACATTATGAGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCGTTGATATGTGTGC
1 GGCCACATTATGAGAGCCAGTGTAAGACCATGCTCGGGACATGGCATCGGCATTGAGACGAGAGC
* *
42132947 TAGTGTAAGACCATGTCTAGGACATGGCATT
66 TAGCGTAAGACCATGTCTAGGACATGGCATC
* *
42132978 GGCCACATTATGAGAGCCAGTGTAAGATCATGCTCGGGACATGGTATCGGCATTGAGACGAGAGC
1 GGCCACATTATGAGAGCCAGTGTAAGACCATGCTCGGGACATGGCATCGGCATTGAGACGAGAGC
*
42133043 TAGCGTAAGACCATGTCTGGGACATGGCATC
66 TAGCGTAAGACCATGTCTAGGACATGGCATC
* * ** *
42133074 GTCCTCAACATGTGAGCCAGTGTAAGACCAT
1 GGCCACATTATGAGAGCCAGTGTAAGACCAT
42133105 TTATGGATAT
Statistics
Matches: 109, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
96 109 1.00
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (96 bp):
GGCCACATTATGAGAGCCAGTGTAAGACCATGCTCGGGACATGGCATCGGCATTGAGACGAGAGC
TAGCGTAAGACCATGTCTAGGACATGGCATC
Found at i:42133099 original size:48 final size:48
Alignment explanation
Indices: 42132890--42133104 Score: 207
Period size: 48 Copynumber: 4.5 Consensus size: 48
42132880 CAGGCCACAT
* * **
42132890 TATGAGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCGTTGA
1 TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCAA
* * * * * * *
42132938 TATGTGTGCTAGTGTAAGACCATGTCTAGGACATGGCATTGGCCACAT
1 TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCAA
* * * **
42132986 TATGAGAGCCAGTGTAAGATCATG-CTCGGGACATGGTATCGGCATTGA
1 TATGAGAGCCAGTGTAAGACCATGTCT-GGGACATGGCATCGGCCTCAA
* * * * *
42133034 GACGAGAGCTAGCGTAAGACCATGTCTGGGACATGGCATCGTCCTCAA
1 TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCAA
* *
42133082 CATGTGAGCCAGTGTAAGACCAT
1 TATGAGAGCCAGTGTAAGACCAT
42133105 TTATGGATAT
Statistics
Matches: 127, Mismatches: 38, Indels: 4
0.75 0.22 0.02
Matches are distributed among these distances:
47 2 0.02
48 123 0.97
49 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.24
Consensus pattern (48 bp):
TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCAA
Found at i:42137751 original size:37 final size:37
Alignment explanation
Indices: 42137692--42137800 Score: 164
Period size: 37 Copynumber: 2.9 Consensus size: 37
42137682 AGCTCAGACG
* * *
42137692 AAATCTCCACACGAAGTTATCGGGTCTCACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
42137729 AAATCTCCACACGTAGTCATCGGGTCTTACCTGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* *
42137766 TAATCTCCACACATAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
42137801 ATATATTTCC
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 65 1.00
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:42137916 original size:48 final size:48
Alignment explanation
Indices: 42137845--42138087 Score: 378
Period size: 48 Copynumber: 5.1 Consensus size: 48
42137835 TGTTACAACA
* * * *
42137845 TTCACATTAGCCATTCGGCTTTACCACATATTCATATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
*
42137893 TTCACATTCGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
42137941 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* *
42137989 TTCATATTAGCTATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* * * * *
42138037 TTCATATTGGCCCTTCGGCTTTACCACATATACATGTCACACTTATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
42138085 TTC
1 TTC
42138088 TTTATCTTGT
Statistics
Matches: 182, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 182 1.00
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.36
Consensus pattern (48 bp):
TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
Found at i:42140723 original size:45 final size:45
Alignment explanation
Indices: 42140647--42140815 Score: 171
Period size: 45 Copynumber: 3.8 Consensus size: 45
42140637 ATGTATTGTC
* * * *
42140647 ATGGTATCTTTCAACTATGGTCTTAT-ACATTTCTGGTATAGTGCC
1 ATGGTATCTTTCAACTATGATCTT-TCTCATTTCTGGTATAATGCA
* * *
42140692 ATAGTGTCTTTCAACTATGATCTTTCTCATTTCGGGTATAATGCA
1 ATGGTATCTTTCAACTATGATCTTTCTCATTTCTGGTATAATGCA
* * * * * **
42140737 ATGGTATCTTTCAACCATGGTCTTTTTCGTTTCTGGTACAATGTT
1 ATGGTATCTTTCAACTATGATCTTTCTCATTTCTGGTATAATGCA
*
42140782 ATGGTATCTTTCAACTAT-AGTCTTTCTTATTTCT
1 ATGGTATCTTTCAACTATGA-TCTTTCTCATTTCT
42140816 CAATCCAAAA
Statistics
Matches: 100, Mismatches: 22, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
44 1 0.01
45 99 0.99
ACGTcount: A:0.21, C:0.18, G:0.15, T:0.46
Consensus pattern (45 bp):
ATGGTATCTTTCAACTATGATCTTTCTCATTTCTGGTATAATGCA
Found at i:42140792 original size:90 final size:90
Alignment explanation
Indices: 42140558--42140814 Score: 227
Period size: 90 Copynumber: 2.9 Consensus size: 90
42140548 GAGGATGCCG
* ** * * *
42140558 TGGTATCTTTCAACCATGGTCTTATACGTTTCCAAAGT--GATGCTATAGTATCTTTCAACTGTA
1 TGGTATCTTTCAACCATGGTCTTATACATTT-C-TGGTACAATGCCATAGTATCTTTCAACTATA
* * * * * *
42140621 GTCATAT-TCATTGCTGATGTATTGTC-A
64 GTC-TTTCTCATTTCGGGTATAATG-CAA
* * * *
42140648 TGGTATCTTTCAACTATGGTCTTATACATTTCTGGTATAGTGCCATAGTGTCTTTCAACTAT-GA
1 TGGTATCTTTCAACCATGGTCTTATACATTTCTGGTACAATGCCATAGTATCTTTCAACTATAG-
42140712 TCTTTCTCATTTCGGGTATAATGCAA
65 TCTTTCTCATTTCGGGTATAATGCAA
* * * ** *
42140738 TGGTATCTTTCAACCATGGTCTTTTTCGTTTCTGGTACAATGTTATGGTATCTTTCAACTATAGT
1 TGGTATCTTTCAACCATGGTCTTATACATTTCTGGTACAATGCCATAGTATCTTTCAACTATAGT
*
42140803 CTTTCTTATTTC
66 CTTTCTCATTTC
42140815 TCAATCCAAA
Statistics
Matches: 135, Mismatches: 26, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
88 2 0.01
89 5 0.04
90 127 0.94
91 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.16, T:0.44
Consensus pattern (90 bp):
TGGTATCTTTCAACCATGGTCTTATACATTTCTGGTACAATGCCATAGTATCTTTCAACTATAGT
CTTTCTCATTTCGGGTATAATGCAA
Found at i:42143585 original size:47 final size:46
Alignment explanation
Indices: 42143512--42143735 Score: 168
Period size: 46 Copynumber: 4.8 Consensus size: 46
42143502 TGGGTAAGGT
* * *
42143512 GCCGATGCCATGTCCCAAACACGGTCTTACACTAGCTCACATCTCAA
1 GCCGATGCCATGTCCCAGACA-TGTCTTACACTAGCTCATATCTCAA
* * * *
42143559 GTCGATGCCACGTCCCAGACATGGTCTTACACT-GAC-AATATCTTATA
1 GCCGATGCCATGTCCCAGACAT-GTCTTACACTAG-CTCATATCTCA-A
* * * * *
42143606 GCCAATG-CATGTCCCAGACATGTTTTACACTAGCTTATGTCTCGAG
1 GCCGATGCCATGTCCCAGACATGTCTTACACTAGCTCATATCTC-AA
* * * *
42143652 GCCGATG-TATGTCCCAGACATGTCTTACACTAGCACTTGTCTCAA
1 GCCGATGCCATGTCCCAGACATGTCTTACACTAGCTCATATCTCAA
* ** * *
42143697 TTCCGATGCCACATCCCAGACACCGTCTTACACTGGCTC
1 -GCCGATGCCATGTCCCAGACA-TGTCTTACACTAGCTC
42143736 TCATAATGTG
Statistics
Matches: 139, Mismatches: 29, Indels: 17
0.75 0.16 0.09
Matches are distributed among these distances:
45 11 0.08
46 69 0.50
47 46 0.33
48 13 0.09
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.26
Consensus pattern (46 bp):
GCCGATGCCATGTCCCAGACATGTCTTACACTAGCTCATATCTCAA
Found at i:42144144 original size:30 final size:30
Alignment explanation
Indices: 42144117--42144197 Score: 144
Period size: 30 Copynumber: 2.7 Consensus size: 30
42144107 CATCTTTGGT
* *
42144117 AAAATGACCATTTTTCCCCTAGACTTTGAC
1 AAAATGACCATTTTACCCCTAAACTTTGAC
42144147 AAAATGACCATTTTACCCCTAAACTTTGAC
1 AAAATGACCATTTTACCCCTAAACTTTGAC
42144177 AAAATGACCATTTTACCCCTA
1 AAAATGACCATTTTACCCCTA
42144198 TGGTTGAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.35, C:0.27, G:0.07, T:0.31
Consensus pattern (30 bp):
AAAATGACCATTTTACCCCTAAACTTTGAC
Found at i:42150332 original size:30 final size:30
Alignment explanation
Indices: 42150298--42150358 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
42150288 TTCCCGAGCC
42150298 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
* * *
42150328 TAGGGGCAAAATTGTAATTTTGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
42150358 T
1 T
42150359 GAGTTAAGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATGCAAAAGTT
Found at i:42163373 original size:45 final size:45
Alignment explanation
Indices: 42163303--42163393 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 45
42163293 AATTAAATTA
**
42163303 ACCATTATTAGCAAGTTTAGTTTCATTTAAGTCATA-CATATATAT
1 ACCATTATTAGCAAGTTTAACTTCATTTAAGTCA-AGCATATATAT
*
42163348 ACCATTATTAGCAGGTTTAACTTCATTTAAGTCAAGCATATATAT
1 ACCATTATTAGCAAGTTTAACTTCATTTAAGTCAAGCATATATAT
42163393 A
1 A
42163394 TTAAGGCATA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
44 1 0.02
45 41 0.98
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (45 bp):
ACCATTATTAGCAAGTTTAACTTCATTTAAGTCAAGCATATATAT
Found at i:42163431 original size:36 final size:36
Alignment explanation
Indices: 42163391--42163462 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
42163381 AAGCATATAT
* * *
42163391 ATATTAAGGCATATGTATATTGTTTAGCTTCATTTA
1 ATATTAAGACATATATATAATGTTTAGCTTCATTTA
* * *
42163427 ATATTAATACATATATTTAATGTTTTGCTTCATTTA
1 ATATTAAGACATATATATAATGTTTAGCTTCATTTA
42163463 GGTCATGCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.32, C:0.08, G:0.10, T:0.50
Consensus pattern (36 bp):
ATATTAAGACATATATATAATGTTTAGCTTCATTTA
Found at i:42165200 original size:40 final size:40
Alignment explanation
Indices: 42165143--42165338 Score: 274
Period size: 40 Copynumber: 5.0 Consensus size: 40
42165133 TCGAATGATG
* * * *
42165143 TCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGACTAAGAT-CCGAAGGCATTTGTGC-GAGTTACTAAA
*
42165183 TCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
42165223 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
42165263 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
** *
42165303 TCCGGGTTAAG-T-CGAAGGCATTTGTGTGAGTTACTA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTA
42165339 TAACCGGGCT
Statistics
Matches: 145, Mismatches: 9, Indels: 6
0.91 0.06 0.04
Matches are distributed among these distances:
38 23 0.16
39 1 0.01
40 114 0.79
41 7 0.05
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:42165397 original size:78 final size:79
Alignment explanation
Indices: 42165156--42165398 Score: 239
Period size: 80 Copynumber: 3.1 Consensus size: 79
42165146 GGGCTAAGTC
* * * * **
42165156 CCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATTCGTGCGAGTTACT
1 CCGAAGGCATTTGTGC-GAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTTACT
** *
42165220 AAATCCGGACTAAGAT
65 AAATCCGGGTTAA-CT
**
42165236 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTA
1 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTTACTA
*
42165301 AATCCGGGTTAAGT
66 AATCCGGGTTAACT
* * *
42165315 -CGAAGGCATTTGTGTGAGTTACTATAA-CCGGGCT-A-TTCCCGAAGGCATTTGAACGAG-TAG
1 CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGACTAAGAT-CCGAAGGCATTTGAACGAGTTA-
*
42165375 CTATATCC-GGTTAAACT
63 CTAAATCCGGGTT-AACT
42165392 CCGAAGG
1 CCGAAGG
42165399 TACGTGATTC
Statistics
Matches: 143, Mismatches: 14, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
76 7 0.05
77 28 0.20
78 35 0.24
79 3 0.02
80 63 0.44
81 7 0.05
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTTACTA
AATCCGGGTTAACT
Found at i:42168844 original size:39 final size:40
Alignment explanation
Indices: 42168744--42168925 Score: 176
Period size: 40 Copynumber: 4.6 Consensus size: 40
42168734 TCGAATGATG
* * *
42168744 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGC-AAGTTACTAAA
* * * *
42168784 TCCGGACTAGGAT-CCGAAGGCATTCGTGCGAGTTAATAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTCGTGCAAGTTACTAAA
42168824 TCCGGGCTAAG-CCCGAAGGCATT-GTGCAAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAA
* * * **
42168862 CCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCGCTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTA-AA
**
42168903 -CCGGGCTTCGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
42168926 TGAGCGAGTC
Statistics
Matches: 117, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
38 22 0.19
39 23 0.20
40 63 0.54
41 9 0.08
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.23
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAA
Found at i:42168889 original size:78 final size:80
Alignment explanation
Indices: 42168744--42168925 Score: 210
Period size: 78 Copynumber: 2.3 Consensus size: 80
42168734 TCGAATGATG
* * * *
42168744 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGGCATTC
1 TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTC
42168809 GTGCGAGTTAATAAA
66 GTGCGAGTTAATAAA
* **
42168824 TCCGGGCTAAG-CCCGAAGGCATTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGGCATT
***
42168886 CGTGCGAGTCGCTATAA
65 CGTGCGAGTTAATA-AA
**
42168903 -CCGGGCTTCGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
42168926 TGAGCGAGTC
Statistics
Matches: 87, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
77 1 0.01
78 46 0.53
79 29 0.33
80 11 0.13
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.23
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTC
GTGCGAGTTAATAAA
Found at i:42177556 original size:24 final size:24
Alignment explanation
Indices: 42177529--42177759 Score: 372
Period size: 24 Copynumber: 9.6 Consensus size: 24
42177519 CTTATTATGT
* * *
42177529 TCGCACACATAGAGCTATAGCAAA
1 TCGCACACATAGTGCCATAGTAAA
* *
42177553 TCGCACACATAGTGCTATAGCAAA
1 TCGCACACATAGTGCCATAGTAAA
*
42177577 TCGCACACATAGTGCTATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
42177601 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
42177625 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
*
42177649 TCGCACACATAGTGCCATAGTGAA
1 TCGCACACATAGTGCCATAGTAAA
*
42177673 TCGCACACATAGTGCCATAGTGAA
1 TCGCACACATAGTGCCATAGTAAA
*
42177697 TCGCACACATAGTGCCATAGTGAA
1 TCGCACACATAGTGCCATAGTAAA
*
42177721 TCGCAAACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
42177745 TCGCACACATAGTGC
1 TCGCACACATAGTGC
42177760 ATTTGAGATA
Statistics
Matches: 200, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 200 1.00
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (24 bp):
TCGCACACATAGTGCCATAGTAAA
Found at i:42184755 original size:24 final size:24
Alignment explanation
Indices: 42184728--42184934 Score: 342
Period size: 24 Copynumber: 8.6 Consensus size: 24
42184718 CTTATTATGT
* * *
42184728 TCGCACACATAGAGCTATAGCAAA
1 TCGCACACATAGTGCCATAGTAAA
* *
42184752 TCGCACACATAGTGCTATAGCAAA
1 TCGCACACATAGTGCCATAGTAAA
*
42184776 TCGCACACATAGTGCTATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
42184800 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
42184824 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
*
42184848 TCGCACACATAGTGCCATAGTGAA
1 TCGCACACATAGTGCCATAGTAAA
*
42184872 TCGCACACATAGTGCCATAGTGAA
1 TCGCACACATAGTGCCATAGTAAA
42184896 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
42184920 TCGCACACATAGTGC
1 TCGCACACATAGTGC
42184935 ATTTGAGATA
Statistics
Matches: 178, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 178 1.00
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (24 bp):
TCGCACACATAGTGCCATAGTAAA
Found at i:42186226 original size:40 final size:40
Alignment explanation
Indices: 42186001--42186198 Score: 260
Period size: 40 Copynumber: 5.0 Consensus size: 40
42185991 TCGAATGATG
* * * *
42186001 TCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGACTAAGAT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* *
42186041 TCCGGACTAAGATCGGAAGGCATTCGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
*
42186081 TCCGGACTAAGATCCGAAGGCATTTGTGTGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
42186121 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
*
42186161 TCCGTG-TTAAG-TCCCGAAGGCATTTGTGCGAGTTACTA
1 TCCG-GACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA
42186199 TAACCGGGCT
Statistics
Matches: 143, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
39 1 0.01
40 134 0.94
41 8 0.06
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (40 bp):
TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:42187760 original size:2 final size:2
Alignment explanation
Indices: 42187753--42187782 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
42187743 TAAGTCAGGC
42187753 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42187783 TATTAAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42189979 original size:25 final size:25
Alignment explanation
Indices: 42189933--42189980 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
42189923 TTATAATATG
* * * *
42189933 AAAATGACCGTTTTGCCTCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
42189958 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
42189981 GTTTATGTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:42190049 original size:20 final size:20
Alignment explanation
Indices: 42190024--42190082 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
42190014 TAAATATGGT
42190024 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
*
42190044 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAA
42190064 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
42190083 GGTAATCATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:42190064 original size:11 final size:11
Alignment explanation
Indices: 42190028--42190082 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
42190018 TATGGTATGT
42190028 ATGATATGCAC
1 ATGATATGCAC
* *
42190039 ATGAAATG--T
1 ATGATATGCAC
42190048 ATGATATGCAC
1 ATGATATGCAC
*
42190059 ATGATATG--T
1 ATGATATGCAC
42190068 ATGATATGCAC
1 ATGATATGCAC
42190079 ATGA
1 ATGA
42190083 GGTAATCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:42190162 original size:24 final size:24
Alignment explanation
Indices: 42190134--42190180 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
42190124 AGGAAGTGAA
42190134 AAAGGGCTTATGCCCCAGTTATTG
1 AAAGGGCTTATGCCCCAGTTATTG
*
42190158 AAAGGGCTTTTGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
42190181 AAAACAGGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.32
Consensus pattern (24 bp):
AAAGGGCTTATGCCCCAGTTATTG
Found at i:42190431 original size:31 final size:31
Alignment explanation
Indices: 42190396--42190490 Score: 181
Period size: 31 Copynumber: 3.1 Consensus size: 31
42190386 CGTTTATAGT
42190396 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
42190427 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
42190458 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
42190489 AA
1 AA
42190491 TATGAAAAGG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:42194201 original size:21 final size:22
Alignment explanation
Indices: 42194177--42194219 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
42194167 TTACATGTAA
* *
42194177 TTATTTAG-TAAATTATATTGT
1 TTATGTAGTTAAATAATATTGT
42194198 TTATGTAGTTAAATAATATTGT
1 TTATGTAGTTAAATAATATTGT
42194220 ACTTCCTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (22 bp):
TTATGTAGTTAAATAATATTGT
Found at i:42198152 original size:233 final size:235
Alignment explanation
Indices: 42197783--42198213 Score: 677
Period size: 233 Copynumber: 1.8 Consensus size: 235
42197773 TTAGGATTTT
** *
42197783 ATGTGATGGATGTGAATGTGTATACATGAGCTAAGGCCGAATGGCAAATGTGATGAATGTGAACA
1 ATGTGATGGATGTGAACATGTATACATGAGATAAGGCCGAATGGCAAATGTGATGAATGTGAACA
* * * * * *
42197848 TGCATTTGTGTGCTAAGGCCGAATGGCAAATGTGATGAACGTGAACATGCATTTGTGTGATAAGA
66 TGCATATGTGTGATAAGGCCGAATGGCAAATGTGAAGAACATGAACATGCATATATGTGATAAGA
* * ** *
42197913 CCGAATGGCCAATGTGATGAATGTGAACATGTATATGTGTGATAAGGCCGAATGGCCAATGTGAT
131 CCGAATGGCCAATGTGATAAATGTGAACATGCATACATGTGATAAGGCAGAATGGCCAATGTGAT
42197978 GAATATGAACATGCATATATGTGATAAGGCCGAATGGCCA
196 GAATATGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
42198018 ATGTGAT-GATGTGAACATGTATATATGTGATAAGGCCGAATGGC-AATGTGATGAATGTGAACA
1 ATGTGATGGATGTGAACATGTATACATGAGATAAGGCCGAATGGCAAATGTGATGAATGTGAACA
* * *
42198081 TGCATATGTGTGATAAGGCCGAATGGCCAATGTGAAGAATATGAACATGCATATATGTGATAAGG
66 TGCATATGTGTGATAAGGCCGAATGGCAAATGTGAAGAACATGAACATGCATATATGTGATAAGA
42198146 CCGAATGGCCAATGTGATAAATGTGAACATGCATACATGTGATAAGGCAGAATGGCCAATGTGAT
131 CCGAATGGCCAATGTGATAAATGTGAACATGCATACATGTGATAAGGCAGAATGGCCAATGTGAT
42198211 GAA
196 GAA
42198214 CGTGGATGTG
Statistics
Matches: 177, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
233 138 0.78
234 32 0.18
235 7 0.04
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.26
Consensus pattern (235 bp):
ATGTGATGGATGTGAACATGTATACATGAGATAAGGCCGAATGGCAAATGTGATGAATGTGAACA
TGCATATGTGTGATAAGGCCGAATGGCAAATGTGAAGAACATGAACATGCATATATGTGATAAGA
CCGAATGGCCAATGTGATAAATGTGAACATGCATACATGTGATAAGGCAGAATGGCCAATGTGAT
GAATATGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:42198210 original size:22 final size:22
Alignment explanation
Indices: 42198135--42198210 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 22
42198125 ACATGCATAT
*
42198135 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCAGAATGGCCA
*
42198157 ATGTGATAAATGTG-A-ACAT-GCATA
1 ATGTGAT-AA-G-GCAGA-ATGGC-CA
42198181 CATGTGATAAGGCAGAATGGCCA
1 -ATGTGATAAGGCAGAATGGCCA
42198204 ATGTGAT
1 ATGTGAT
42198211 GAACGTGGAT
Statistics
Matches: 42, Mismatches: 3, Indels: 18
0.67 0.05 0.29
Matches are distributed among these distances:
22 15 0.36
23 10 0.24
24 9 0.21
25 8 0.19
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.24
Consensus pattern (22 bp):
ATGTGATAAGGCAGAATGGCCA
Found at i:42198247 original size:47 final size:47
Alignment explanation
Indices: 42197814--42198213 Score: 615
Period size: 47 Copynumber: 8.6 Consensus size: 47
42197804 ATACATGAGC
* * * *
42197814 TAAGGCCGAATGGCAAATGTGATGAATGTGAACATGCATTTGTGTGC
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGA
* * * *
42197861 TAAGGCCGAATGGCAAATGTGATGAACGTGAACATGCATTTGTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGA
* * *
42197908 TAAGACCGAATGGCCAATGTGATGAATGTGAACATGTATATGTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGA
*
42197955 TAAGGCCGAATGGCCAATGTGATGAATATGAACATGCATATATGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGA
*
42198002 TAAGGCCGAATGGCCAATGTGATG-ATGTGAACATGTATATATGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGA
*
42198048 TAAGGCCGAATGG-CAATGTGATGAATGTGAACATGCATATGTGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGA
* *
42198094 TAAGGCCGAATGGCCAATGTGAAGAATATGAACATGCATATATGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGA
* *
42198141 TAAGGCCGAATGGCCAATGTGATAAATGTGAACATGCATACATGTGA
1 TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGA
*
42198188 TAAGGCAGAATGGCCAATGTGATGAA
1 TAAGGCCGAATGGCCAATGTGATGAA
42198214 CGTGGATGTG
Statistics
Matches: 327, Mismatches: 24, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
45 10 0.03
46 66 0.20
47 251 0.77
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.26
Consensus pattern (47 bp):
TAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGA
Found at i:42198279 original size:233 final size:233
Alignment explanation
Indices: 42197814--42198302 Score: 624
Period size: 233 Copynumber: 2.1 Consensus size: 233
42197804 ATACATGAGC
* *
42197814 TAAGGCCGAATGGCAAATGTGATGAATGTGAACATGCATTTGTGTGCTAAGGCCGAATGGCAAAT
1 TAAGGCCGAATGGCAAATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCAAAT
* * * * *
42197879 GTGATGAACGTGAACATGCATTTGTGTGATAAGACCGAATGGCCAATGTGATGAATGTGAACATG
66 GTGAAGAACATGAACATGCATATATGTGATAAGACCGAATGGCCAATGTGATAAATGTGAACATG
* ** * * * *
42197944 TATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATATGAACATGCATATATGTGATAAGGCC
131 CATACATGTGATAAGGCAGAATGGCCAATGTGATGAACATGAACATGCATATATGTGAGAAAGCC
* * *
42198009 GAATGGCCAATGTGATGATGTGAACATGTATATATGTGA
196 GAATGGCCAATGCGATAATGTGAACATG-AGATATGTGA
*
42198048 TAAGGCCGAATGGC-AATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAAT
1 TAAGGCCGAATGGCAAATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCAAAT
* *
42198112 GTGAAGAATATGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATAAATGTGAACATG
66 GTGAAGAACATGAACATGCATATATGTGATAAGACCGAATGGCCAATGTGATAAATGTGAACATG
* * ** * *
42198177 CATACATGTGATAAGGCAGAATGGCCAATGTGATGAACGTGGATGTGTATATATGTGGGAAAGCC
131 CATACATGTGATAAGGCAGAATGGCCAATGTGATGAACATGAACATGCATATATGTGAGAAAGCC
** * *
42198242 GAATGGTTAATGCGA-AATGTGTATGAGATG-GATATGTGG
196 GAATGGCCAATGCGATAATGTG-A--ACATGAGATATGTGA
* * *
42198281 TAAAGCCAAATGGCTAATGTGA
1 TAAGGCCGAATGGCAAATGTGA
42198303 GATATGTATG
Statistics
Matches: 219, Mismatches: 32, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
232 5 0.02
233 189 0.86
234 21 0.10
235 4 0.02
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.26
Consensus pattern (233 bp):
TAAGGCCGAATGGCAAATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCAAAT
GTGAAGAACATGAACATGCATATATGTGATAAGACCGAATGGCCAATGTGATAAATGTGAACATG
CATACATGTGATAAGGCAGAATGGCCAATGTGATGAACATGAACATGCATATATGTGAGAAAGCC
GAATGGCCAATGCGATAATGTGAACATGAGATATGTGA
Found at i:42198280 original size:46 final size:46
Alignment explanation
Indices: 42198227--42198317 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
42198217 GGATGTGTAT
* * *
42198227 ATATGTGGGAAAGCCGAATGGTTAATGCGAAATGTGTATGAGATGG
1 ATATGTGGGAAAGCCAAATGGCTAATGCGAAATATGTATGAGATGG
* * *
42198273 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGTGGGAAAGCCAAATGGCTAATGCGAAATATGTATGAGATG
42198318 TGTATATATA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.34, C:0.07, G:0.32, T:0.27
Consensus pattern (46 bp):
ATATGTGGGAAAGCCAAATGGCTAATGCGAAATATGTATGAGATGG
Found at i:42201118 original size:38 final size:38
Alignment explanation
Indices: 42201068--42201163 Score: 111
Period size: 40 Copynumber: 2.5 Consensus size: 38
42201058 CCAACTCCTT
* * *
42201068 CCAACCCAACACACCATGTGGAGATAAAATCGACCCAC
1 CCAACCCTACACACCATATGGAGATAAAATCAACCCAC
* * * *
42201106 CCATCCTTACACACCAAATATGGGGATAAAATCAACCCAT
1 CCAACCCTACACACC--ATATGGAGATAAAATCAACCCAC
42201146 CCAACCCTACACACCATA
1 CCAACCCTACACACCATA
42201164 GAGTACTGTA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
38 15 0.32
40 32 0.68
ACGTcount: A:0.40, C:0.36, G:0.09, T:0.15
Consensus pattern (38 bp):
CCAACCCTACACACCATATGGAGATAAAATCAACCCAC
Found at i:42206320 original size:29 final size:29
Alignment explanation
Indices: 42206287--42206418 Score: 210
Period size: 29 Copynumber: 4.6 Consensus size: 29
42206277 CCTTCGAGCT
** * *
42206287 CGCACACCCAGTGCCGTATTTTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
* *
42206316 TGCACACTTAGTGTCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
42206345 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
42206374 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
42206403 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
42206419 ATCTCGTCAC
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 95 1.00
ACGTcount: A:0.26, C:0.32, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:42206321 original size:58 final size:58
Alignment explanation
Indices: 42206258--42206418 Score: 178
Period size: 58 Copynumber: 2.8 Consensus size: 58
42206248 AATTTAAGCC
* * * * * *
42206258 CGCACACATAGTGCCATACCCTTCGAGCTCGCACACCCAGTGCCGTATTTTTCCAGCA
1 CGCACACTTAGTGCCATACACTTCCAGCACGCACACCCAGTGCCATATATTTCCAGCA
* * * * **
42206316 TGCACACTTAGTGTCATATATTTCCAGCACGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATACACTTCCAGCACGCACACCCAGTGCCATATATTTCCAGCA
* * **
42206374 CGCACACTTAGTGCCATATATTTCCAGCACGCACACTTAGTGCCA
1 CGCACACTTAGTGCCATACACTTCCAGCACGCACACCCAGTGCCA
42206419 ATCTCGTCAC
Statistics
Matches: 89, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
58 89 1.00
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.26
Consensus pattern (58 bp):
CGCACACTTAGTGCCATACACTTCCAGCACGCACACCCAGTGCCATATATTTCCAGCA
Found at i:42215626 original size:18 final size:17
Alignment explanation
Indices: 42215603--42215636 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
42215593 TAGCTGTGCC
42215603 GTTTTCTCTTCTGTATTA
1 GTTTTCTCTTCT-TATTA
42215621 GTTTTCTCTTCTTATT
1 GTTTTCTCTTCTTATT
42215637 TTCTTCCCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.09, C:0.18, G:0.09, T:0.65
Consensus pattern (17 bp):
GTTTTCTCTTCTTATTA
Found at i:42216787 original size:25 final size:25
Alignment explanation
Indices: 42216755--42216802 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
42216745 CTATAACATG
* * *
42216755 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
42216780 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
42216803 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:42216886 original size:11 final size:11
Alignment explanation
Indices: 42216850--42216905 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
42216840 CATGGTATGT
42216850 ATGATATGCAC
1 ATGATATGCAC
* *
42216861 ATGACATG--T
1 ATGATATGCAC
42216870 ATGATATGCAC
1 ATGATATGCAC
*
42216881 ATGATATG--T
1 ATGATATGCAC
42216890 ATGATATGCAC
1 ATGATATGCAC
42216901 ATGAT
1 ATGAT
42216906 GTAATCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:42216905 original size:20 final size:20
Alignment explanation
Indices: 42216839--42216905 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
42216829 ATTTTGATAA
*
42216839 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
42216859 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
42216879 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
42216899 ACATGAT
1 ACATGAT
42216906 GTAATCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:42216985 original size:23 final size:23
Alignment explanation
Indices: 42216955--42217121 Score: 262
Period size: 23 Copynumber: 7.1 Consensus size: 23
42216945 AGGAAGTGAA
42216955 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
42216978 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
42217001 AAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
*
42217025 AAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-T
*
42217049 AAAGGGCTTATGCCCCTGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
42217072 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
* *
42217095 AAAAGGGCTTTTGCCCTAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
42217119 AAA
1 AAA
42217122 AGAGGCTAGG
Statistics
Matches: 136, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
23 70 0.51
24 66 0.49
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.30
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:42217033 original size:24 final size:23
Alignment explanation
Indices: 42216954--42217128 Score: 251
Period size: 24 Copynumber: 7.4 Consensus size: 23
42216944 GAGGAAGTGA
42216954 AAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
42216977 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
42217000 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
42217023 CAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
*
42217047 CAAAAGGGCTTATGCCCCTGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
*
42217071 TAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTA-T
* *
42217095 AAAAGGGCTTTTGCCCTAGTTATT
1 AAAAGGGCTTATGCCCCAGTTA-T
42217119 AAAAGAGGCT
1 AAAAG-GGCT
42217129 AGGCCTCCAA
Statistics
Matches: 141, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
23 65 0.46
24 72 0.51
25 4 0.03
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (23 bp):
AAAAGGGCTTATGCCCCAGTTAT
Found at i:42217046 original size:47 final size:46
Alignment explanation
Indices: 42216955--42217128 Score: 249
Period size: 47 Copynumber: 3.7 Consensus size: 46
42216945 AGGAAGTGAA
*
42216955 AAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
*
42217001 AAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTAT-T
* *
42217049 AAAGGGCTTATGCCCCTGTTATTAAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
* *
42217095 AAAAGGGCTTTTGCCCTAGTTATTAAAAGAGGCT
1 -AAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCT
42217129 AGGCCTCCAA
Statistics
Matches: 114, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
46 22 0.19
47 62 0.54
48 26 0.23
49 4 0.04
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (46 bp):
AAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATT
Found at i:42217370 original size:31 final size:30
Alignment explanation
Indices: 42217335--42217398 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 30
42217325 CGTTTACAGT
42217335 AAAGGCTTCGGCCCAGTAATATGAAATATAG
1 AAAGGCTTCGGCCCAGTAATATGAAATAT-G
* **
42217366 AAAGGCTTCGGCCTAGTGTTATGAAATATG
1 AAAGGCTTCGGCCCAGTAATATGAAATATG
42217396 AAA
1 AAA
42217399 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.25
Consensus pattern (30 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATG
Found at i:42223690 original size:40 final size:40
Alignment explanation
Indices: 42223616--42223836 Score: 288
Period size: 40 Copynumber: 5.6 Consensus size: 40
42223606 AACCCAAGTA
* * *
42223616 CCTTCGGGATTTAG-CCAGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* * *
42223655 CCTTCAGGTCTTAGCCCGGATATAGTCACTAGCACAAAAG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* * *
42223695 CCTTCGGGACTTAGCCCAGATATAG-CGACTCGCACAAACG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* *
42223735 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAACTG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
42223775 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCAC-CATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
42223814 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
42223837 CATCCGAATA
Statistics
Matches: 159, Mismatches: 19, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
39 37 0.23
40 120 0.75
41 2 0.01
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:42226894 original size:40 final size:40
Alignment explanation
Indices: 42226706--42226887 Score: 231
Period size: 40 Copynumber: 4.5 Consensus size: 40
42226696 TGAATGATAC
* ** *
42226706 CCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTG-TTATAT
42226746 CCGGGCTAAAGACCCGAAGGCATTCGTGCAAGTTGTTATAT
1 CCGGGCT-AAGACCCGAAGGCATTCGTGCAAGTTGTTATAT
*
42226787 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTATAT
* *** *
42226827 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTATAT
* *
42226867 TCGGGTTAAGACCCGAAGGCA
1 CCGGGCTAAGACCCGAAGGCA
42226888 ATTGTGCTGC
Statistics
Matches: 127, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
40 92 0.72
41 33 0.26
42 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTATAT
Found at i:42234344 original size:29 final size:29
Alignment explanation
Indices: 42234310--42234384 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
42234300 TACTCGATTT
*
42234310 CGCACACTTAGTGCCATGCGATTTAG-GCC
1 CGCACACTTAGTGCCATGC-ACTTAGAGCC
** * * *
42234339 CGCACACACAGTGCCATGCCCTTCGAGCT
1 CGCACACTTAGTGCCATGCACTTAGAGCC
42234368 CGCACACTTAGTGCCAT
1 CGCACACTTAGTGCCAT
42234385 ATATTTCCAG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
28 3 0.08
29 34 0.92
ACGTcount: A:0.21, C:0.36, G:0.21, T:0.21
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTAGAGCC
Found at i:42234401 original size:29 final size:29
Alignment explanation
Indices: 42234368--42234441 Score: 139
Period size: 29 Copynumber: 2.6 Consensus size: 29
42234358 CCTTCGAGCT
42234368 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
42234397 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
42234426 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
42234442 ATCTCGTCAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:42235607 original size:14 final size:16
Alignment explanation
Indices: 42235588--42235619 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
42235578 GCATCCATGC
42235588 TCATTT-TTT-TTTTT
1 TCATTTCTTTATTTTT
42235602 TCATTTCTTTATTTTT
1 TCATTTCTTTATTTTT
42235618 TC
1 TC
42235620 TACATAATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 3 0.19
16 7 0.44
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.78
Consensus pattern (16 bp):
TCATTTCTTTATTTTT
Found at i:42241770 original size:56 final size:55
Alignment explanation
Indices: 42241704--42241851 Score: 181
Period size: 56 Copynumber: 2.7 Consensus size: 55
42241694 AATATAGCTT
* *
42241704 GCCTCTCAACAGGGCTACATAAGAGCACCTGGACCTAGCATGCATCACATAACTAC-
1 GCCTCTCAACAGGGCTACAT-A-AGCTCCTGGACCTAGCATGCACCACATAACTACA
* * * * *
42241760 GCCTCTCAACAAGGCTACATAAGCTCCCGGACCTAGCGTGTACCACATAATTACA
1 GCCTCTCAACAGGGCTACATAAGCTCCTGGACCTAGCATGCACCACATAACTACA
* *
42241815 TGCCTCTCAATAGGGCTACACAAGCTCCTGGACCTAG
1 -GCCTCTCAACAGGGCTACATAAGCTCCTGGACCTAG
42241852 GATGTATTAT
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
54 27 0.34
55 1 0.01
56 51 0.65
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.20
Consensus pattern (55 bp):
GCCTCTCAACAGGGCTACATAAGCTCCTGGACCTAGCATGCACCACATAACTACA
Found at i:42244926 original size:21 final size:18
Alignment explanation
Indices: 42244892--42244946 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 18
42244882 TAGGAAGAAT
*
42244892 AAAGAAATGAA-AAAAAA
1 AAAGAAAAGAAGAAAAAA
* * *
42244909 AGAGAATATGAAGAAAAAC
1 AAAGAA-AAGAAGAAAAAA
42244928 AAAGAAAAGAA-AAAAAA
1 AAAGAAAAGAAGAAAAAA
42244945 AA
1 AA
42244947 GTGTTCATTC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
17 12 0.39
18 9 0.29
19 10 0.32
ACGTcount: A:0.78, C:0.02, G:0.15, T:0.05
Consensus pattern (18 bp):
AAAGAAAAGAAGAAAAAA
Found at i:42246138 original size:29 final size:29
Alignment explanation
Indices: 42246105--42246197 Score: 123
Period size: 29 Copynumber: 3.2 Consensus size: 29
42246095 TGACGAGATT
* *
42246105 GGCACTAAGTGTGCGTGCTGGAAATATAA
1 GGCACTAAGTGTGCATGCTGGAAAAATAA
*
42246134 GGCACTAAGTGTGCATGCTGGAAAAATAT
1 GGCACTAAGTGTGCATGCTGGAAAAATAA
* * * *
42246163 GACACTATGTGTGCAAGCTGGAAAAATAC
1 GGCACTAAGTGTGCATGCTGGAAAAATAA
42246192 GGCACT
1 GGCACT
42246198 GGGTGTGCGA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (29 bp):
GGCACTAAGTGTGCATGCTGGAAAAATAA
Found at i:42246210 original size:29 final size:29
Alignment explanation
Indices: 42246105--42246210 Score: 115
Period size: 29 Copynumber: 3.7 Consensus size: 29
42246095 TGACGAGATT
* *
42246105 GGCACTAAGTGTGCGTGCTGGAAATATAA
1 GGCACTAAGTGTGCGAGCTGGAAAAATAA
*
42246134 GGCACTAAGTGTGC-ATGCTGGAAAAATAT
1 GGCACTAAGTGTGCGA-GCTGGAAAAATAA
* * * *
42246163 GACACTATGTGTGCAAGCTGGAAAAATAC
1 GGCACTAAGTGTGCGAGCTGGAAAAATAA
**
42246192 GGCACTGGGTGTGCGAGCT
1 GGCACTAAGTGTGCGAGCT
42246211 CGGAGGGTAT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
29 64 0.98
30 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.31, T:0.23
Consensus pattern (29 bp):
GGCACTAAGTGTGCGAGCTGGAAAAATAA
Found at i:42252821 original size:21 final size:18
Alignment explanation
Indices: 42252783--42252835 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
42252773 GGAAGAATAA
42252783 AGAAATGAAAAAAAAAAG
1 AGAAATGAAAAAAAAAAG
42252801 AGAATATGAAGAAAAACAAAG
1 AGAA-ATGAA-AAAAA-AAAG
42252822 A-AAA-GAAAAAAAAA
1 AGAAATGAAAAAAAAA
42252836 GTGTTCATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
16 2 0.06
17 5 0.16
18 7 0.22
19 6 0.19
20 7 0.22
21 5 0.16
ACGTcount: A:0.77, C:0.02, G:0.15, T:0.06
Consensus pattern (18 bp):
AGAAATGAAAAAAAAAAG
Found at i:42254023 original size:27 final size:27
Alignment explanation
Indices: 42253991--42254149 Score: 108
Period size: 29 Copynumber: 5.6 Consensus size: 27
42253981 GTGACGAGAT
*
42253991 TGGCACTAAGTGTGCGTGCTGGAAATA
1 TGGCACTAAGTGTGCGAGCTGGAAATA
42254018 TGGCACTAAGTGTGC-ATGCTGGAAAAATA
1 TGGCACTAAGTGTGCGA-GCTGG--AAATA
* * *
42254047 TGACACTATGTGTGCAAGCTGGAAAAATA
1 TGGCACTAAGTGTGCGAGCTGG--AAATA
* * **
42254076 CGGCACT-GGTGTGCGAGCTCGGAGGGTA
1 TGGCACTAAGTGTGCGAGCT-GGA-AATA
* * *
42254104 TGGCACTATGTGTGCGGGCT-TAAATTA
1 TGGCACTAAGTGTGCGAGCTGGAAA-TA
42254131 CGTGGCACTAAGTGTGCGA
1 --TGGCACTAAGTGTGCGA
42254150 AATCGAGTAG
Statistics
Matches: 105, Mismatches: 17, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
27 24 0.23
28 18 0.17
29 62 0.59
30 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.33, T:0.25
Consensus pattern (27 bp):
TGGCACTAAGTGTGCGAGCTGGAAATA
Found at i:42254082 original size:29 final size:29
Alignment explanation
Indices: 42253991--42254082 Score: 125
Period size: 29 Copynumber: 3.2 Consensus size: 29
42253981 GTGACGAGAT
*
42253991 TGGCACTAAGTGTGCGTGCTGG--AAATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
42254018 TGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
* * *
42254047 TGACACTATGTGTGCAAGCTGGAAAAATA
1 TGGCACTAAGTGTGCATGCTGGAAAAATA
*
42254076 CGGCACT
1 TGGCACT
42254083 GGTGTGCGAG
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
27 21 0.37
29 36 0.63
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.24
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAAAATA
Found at i:42258858 original size:40 final size:40
Alignment explanation
Indices: 42258792--42258958 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
42258782 AAATTGAATG
* * *
42258792 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
42258831 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
42258871 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
42258911 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
42258951 ATATCCGG
1 ATATCCGG
42258959 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:42259483 original size:28 final size:28
Alignment explanation
Indices: 42259443--42259499 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
42259433 TGATGTATAT
42259443 ATGTACGGCCATGCGAAAATGGCTCGTA
1 ATGTACGGCCATGCGAAAATGGCTCGTA
42259471 ATGTACGGCCATGCGAAAATGGCTCGTA
1 ATGTACGGCCATGCGAAAATGGCTCGTA
42259499 A
1 A
42259500 AGTGAAGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.21
Consensus pattern (28 bp):
ATGTACGGCCATGCGAAAATGGCTCGTA
Found at i:42266896 original size:40 final size:40
Alignment explanation
Indices: 42266811--42266961 Score: 141
Period size: 40 Copynumber: 3.8 Consensus size: 40
42266801 AATTGAATGA
* * * *
42266811 TATCCGGGCTAAGCCCCGAAGACAATTATGCTG-GAAATTA-
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC-GAGACA-TAC
* * *
42266851 TATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC--GAGACATAC
*
42266892 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGACATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGACATAC
*
42266931 TATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
42266962 ACGTGGTTAT
Statistics
Matches: 92, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
38 3 0.03
39 5 0.05
40 80 0.87
41 3 0.03
42 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.22
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGACATAC
Found at i:42266975 original size:40 final size:40
Alignment explanation
Indices: 42266848--42266977 Score: 154
Period size: 40 Copynumber: 3.2 Consensus size: 40
42266838 ATGCTGGAAA
* * *
42266848 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* * * ***
42266888 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGACA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
*
42266928 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGG
42266968 TTATATCCGG
1 TTATATCCGG
42266978 TTATATTCCG
Statistics
Matches: 72, Mismatches: 17, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
39 1 0.01
40 71 0.99
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
Found at i:42266976 original size:80 final size:80
Alignment explanation
Indices: 42266810--42266977 Score: 207
Period size: 80 Copynumber: 2.1 Consensus size: 80
42266800 AAATTGAATG
* *
42266810 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATTATATCCGGGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTGGAAATTATATCCGGGCTAAGACCCGAAGGCA
42266875 ATTGTGCTAGTGGCT
66 ATTGTGCTAGTGGCT
* * * * *
42266890 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGACATTCTATCCGGGCTAAGACCCGAAGG
1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTG-GAAATTATATCCGGGCTAAGACCCGAAGG
* *
42266953 CATTTGTGC-ACGTGGTT
64 CAATTGTGCTA-GTGGCT
42266970 ATATCCGG
1 ATATCCGG
42266978 TTATATTCCG
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
79 5 0.07
80 70 0.93
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTGGAAATTATATCCGGGCTAAGACCCGAAGGCA
ATTGTGCTAGTGGCT
Found at i:42273225 original size:47 final size:45
Alignment explanation
Indices: 42273153--42273470 Score: 202
Period size: 47 Copynumber: 6.8 Consensus size: 45
42273143 GTTATGTGAG
* *
42273153 AGCTAGTATAAGACCATGTCTGGGACATGGCATCGGTATTGAGA-GTA
1 AGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATTGAGATG-A
* *
42273200 AGGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACATTAAGAT--
1 A-GCTAGTGTAAGACATGTCTGGGACATGCATC-G--GCATTGAGATGA
* * * *
42273247 AGCCAGTGTAAGACCATGTTTGAGACATGGCATCGG-AGTAGAGATGA
1 AGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCA-TTGAGATGA
* * *
42273294 CTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGATGATGA
1 -AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCATTGA-GATGA
* * * *
42273341 TAGCCAGTGTAAGACGTGTCTGGGACATGCATCGGC--TCAGTTTTG-
1 -AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAG--ATGA
* * * * *
42273386 TGCTAGTGTAAGACATGTCTGGGATATGCATCAGCACGTAT-ACACGA
1 AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCA--T-TGAGATGA
*
42273433 GAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGGC
1 -AGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
42273471 CTCGATAGAG
Statistics
Matches: 212, Mismatches: 35, Indels: 45
0.73 0.12 0.15
Matches are distributed among these distances:
44 32 0.15
45 6 0.03
46 29 0.14
47 79 0.37
48 40 0.19
49 19 0.09
50 7 0.03
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.25
Consensus pattern (45 bp):
AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGATGA
Found at i:42273300 original size:94 final size:92
Alignment explanation
Indices: 42273161--42273469 Score: 322
Period size: 94 Copynumber: 3.3 Consensus size: 92
42273151 AGAGCTAGTA
* * * *
42273161 TAAGACCATGTCTGGGACATGGCATCGGTATTGAGAGTAAGGCTAGTGTAAGACATGTCTGGGAC
1 TAAGACCATGTCTGAGACATGGCATCGG-ATAGAGA-TGATGCTAGTGTAAGACATGTCTGGGAC
42273226 ATGCATCAGCCACATTAAGATAGCCAGTG
64 ATGCATCAGCCACATTAAGATAGCCAGTG
*
42273255 TAAGACCATGTTTGAGACATGGCATCGGAGTAGAGATGACTGCTAGTGTAAGACATGTCTGGGAC
1 TAAGACCATGTCTGAGACATGGCATCGGA-TAGAGATGA-TGCTAGTGTAAGACATGTCTGGGAC
* * * *
42273320 ATGCATCGGCCTCGATGATGATAGCCAGTG
64 ATGCATCAGCCAC-ATTAAGATAGCCAGTG
* * * *** *
42273350 TAAGA-CGTGTCTGGGACAT-GCATCGGCTCAGTTTTG-TGCTAGTGTAAGACATGTCTGGGATA
1 TAAGACCATGTCTGAGACATGGCATCGGAT-AGAGATGATGCTAGTGTAAGACATGTCTGGGACA
* * *
42273412 TGCATCAG-CACGTATACACGAGAGCTAGTG
65 TGCATCAGCCACAT-TA-A-GATAGCCAGTG
42273442 TAAGACCATGTCT-AGGACATGGCATCGG
1 TAAGACCATGTCTGA-GACATGGCATCGG
42273470 CCTCGATAGA
Statistics
Matches: 179, Mismatches: 26, Indels: 20
0.80 0.12 0.09
Matches are distributed among these distances:
89 1 0.01
90 3 0.02
91 32 0.18
92 15 0.08
93 25 0.14
94 84 0.47
95 19 0.11
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (92 bp):
TAAGACCATGTCTGAGACATGGCATCGGATAGAGATGATGCTAGTGTAAGACATGTCTGGGACAT
GCATCAGCCACATTAAGATAGCCAGTG
Found at i:42273775 original size:2 final size:2
Alignment explanation
Indices: 42273768--42273804 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
42273758 GTTGTTGTTG
42273768 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42273805 GCAACTTACT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:42277034 original size:40 final size:40
Alignment explanation
Indices: 42276985--42277150 Score: 174
Period size: 40 Copynumber: 4.2 Consensus size: 40
42276975 TCTTCGGAAT
* *
42276985 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATATAACCACTAGCACAAATGCCTTCGGGTC
* **** * *
42277024 TTAACCCGGAT-TTGGTAGCTTGCACAAATGCCTTTGGGTC
1 TTAGCCCGGATATAACCA-CTAGCACAAATGCCTTCGGGTC
* * *
42277064 TTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTC
1 TTAGCCCGGATATAACCACTAGCACAAATGCCTTCGGGTC
* * *
42277104 TTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATATAACCACTAGCACAAATGCCTTCGGGTC
42277144 TTAGCCC
1 TTAGCCC
42277151 AGGTATCATT
Statistics
Matches: 101, Mismatches: 23, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
39 5 0.05
40 94 0.93
41 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
TTAGCCCGGATATAACCACTAGCACAAATGCCTTCGGGTC
Found at i:42277133 original size:80 final size:80
Alignment explanation
Indices: 42276976--42277150 Score: 194
Period size: 80 Copynumber: 2.2 Consensus size: 80
42276966 AACCGAGCTT
* * * * **
42276976 CTTCGGAATTTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGATTTGGT
1 CTTCGGGACTTAGCCCGGATATAACAACAAGCACAATTGCCTTCGGGTCTTAACCCGGATATAAT
*
42277040 AGCTTGCACAAATGC
66 AGCTAGCACAAATGC
* * ** *
42277055 CTTTGGGTCTTAGCCCGGATATAACAACTCGCACGAA-TGCCTTCGGGTCTTAGCCCGGATATAA
1 CTTCGGGACTTAGCCCGGATATAACAACAAGCAC-AATTGCCTTCGGGTCTTAACCCGGATATAA
*
42277119 TCA-CTAGCATAAATGC
65 T-AGCTAGCACAAATGC
42277135 CTTCGGGACTTAGCCC
1 CTTCGGGACTTAGCCC
42277151 AGGTATCATT
Statistics
Matches: 78, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
79 9 0.12
80 66 0.85
81 3 0.04
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAACAACAAGCACAATTGCCTTCGGGTCTTAACCCGGATATAAT
AGCTAGCACAAATGC
Found at i:42284265 original size:94 final size:93
Alignment explanation
Indices: 42284104--42284417 Score: 352
Period size: 94 Copynumber: 3.4 Consensus size: 93
42284094 GTTATATGAG
* * * * *
42284104 AGCCAGTATAAGACCATGTCTAGGACATGGCATCGACATTGAGAGGAGGGCTAGTGTAAGACATG
1 AGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGC-TAGAGATGAGTGCTAGTGTAAGACATG
42284169 TCTGGGACATGCATCAGCCACATTAAGAT
65 TCTGGGACATGCATCAGCCACATTAAGAT
* *
42284198 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTAGAGATGAGTGCCAGTGTAAGACATG
1 AGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGC-TAGAGATGAGTGCTAGTGTAAGACATG
* * * *
42284263 TCTGGGACATGCATCGGCCTCGATGATGAT
65 TCTGGGACATGCATCAGCCAC-ATTAAGAT
* * * *
42284293 AGCCAATGTAAGA-CGTGTCTAGGACAT-G-ATCGGCTA-AG-TGTTGTTCTAGTGTAAGACATG
1 AGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCTAGAGATG-AGTGCTAGTGTAAGACATG
* * *
42284353 TTTGGGACATGCATCAG-CACGTATACATGAG
65 TCTGGGACATGCATCAGCCACAT-TA-A-GAT
*
42284384 AGCTAGTGTAAGACCATGTCTAGGACATGGCATC
1 AGCCAGTGTAAGACCATGTCTAGGACATGGCATC
42284418 TGCCTCGATG
Statistics
Matches: 184, Mismatches: 28, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
88 1 0.01
89 5 0.03
90 33 0.18
91 15 0.08
92 19 0.10
93 2 0.01
94 91 0.49
95 18 0.10
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.24
Consensus pattern (93 bp):
AGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCTAGAGATGAGTGCTAGTGTAAGACATGT
CTGGGACATGCATCAGCCACATTAAGAT
Found at i:42284291 original size:47 final size:48
Alignment explanation
Indices: 42284099--42284457 Score: 221
Period size: 47 Copynumber: 7.6 Consensus size: 48
42284089 ATTGGGTTAT
* * * * * *
42284099 ATGAGAGCCAGTATAAGACCATGTCTAGGACATGGCATCGACATTGA-G
1 ATGAGTGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGCCTCGATG
* * * * * *
42284147 AGGAGGGCTAGTGTAAGA-CATGTCTGGGACATGCATCAGCCAC-ATT
1 ATGAGTGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCCTCGATG
* * *
42284193 AAGA-TAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCGTAGA-G
1 ATGAGT-GCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGCCTCGATG
42284241 ATGAGTGCCAGTGTAAGA-CATGTCTGGGACATGCATCGGCCTCGATG
1 ATGAGTGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCCTCGATG
* * * *
42284288 ATGA-TAGCCAATGTAAGA-CGTGTCTAGGACATG-ATCGG-CT--AAG
1 ATGAGT-GCCAGTGTAAGACCATGTCTGGGACATGCATCGGCCTCGATG
* * * * * * *
42284331 -TGTTGTTCTAGTGTAAGA-CATGTTTGGGACATGCATCAG-CACGTATAC
1 ATG-AGTGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCCTCG-AT-G
* * * *
42284379 ATGAGAGCTAGTGTAAGACCATGTCTAGGACATGGCATCTGCCTCGATG
1 ATGAGTGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGCCTCGATG
**
42284428 --GAGATAGCCAACGTAAGACCATGTCTGGGA
1 ATGAG-T-GCCAGTGTAAGACCATGTCTGGGA
42284458 TATGGCAGCA
Statistics
Matches: 240, Mismatches: 50, Indels: 41
0.73 0.15 0.12
Matches are distributed among these distances:
42 2 0.01
43 23 0.10
44 6 0.03
45 3 0.01
46 37 0.15
47 74 0.31
48 48 0.20
49 36 0.15
50 8 0.03
51 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (48 bp):
ATGAGTGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCCTCGATG
Found at i:42284725 original size:2 final size:2
Alignment explanation
Indices: 42284718--42284752 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
42284708 GTTGTTGTTG
* *
42284718 TA TA TA TA AA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42284753 GCAACTTACT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:42285873 original size:48 final size:47
Alignment explanation
Indices: 42285741--42285884 Score: 171
Period size: 50 Copynumber: 2.9 Consensus size: 47
42285731 GAGAGGGGTG
42285741 TTACAGATGCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCA
1 TTACA-ATGCCGATG-CATGTCCCAAACATGGTCTTACACTAGCTCTCA
** * *
42285790 TATATCGGTGTCGATGCTATGTCCCAGACATGGTCTTACACTAGCTCTCA
1 T-TA-CAATGCCGATGC-ATGTCCCAAACATGGTCTTACACTAGCTCTCA
* * *
42285840 TTACAATACCGATGTCATGTTCCAAACATGGTCTTACACTGGCTC
1 TTACAATGCCGATG-CATGTCCCAAACATGGTCTTACACTAGCTC
42285885 ACATATTACC
Statistics
Matches: 80, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
48 33 0.41
49 5 0.06
50 41 0.51
51 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (47 bp):
TTACAATGCCGATGCATGTCCCAAACATGGTCTTACACTAGCTCTCA
Found at i:42286020 original size:19 final size:20
Alignment explanation
Indices: 42285993--42286030 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
42285983 AAAATCACAC
*
42285993 ATTCCATAC-AATAACAATT
1 ATTCAATACAAATAACAATT
42286012 ATTCAATACAAATAACAAT
1 ATTCAATACAAATAACAAT
42286031 AGAATGGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (20 bp):
ATTCAATACAAATAACAATT
Found at i:42293041 original size:3 final size:3
Alignment explanation
Indices: 42292748--42293022 Score: 113
Period size: 3 Copynumber: 93.0 Consensus size: 3
42292738 TATTATTCAA
* ** * *
42292748 ATT ATT ACT ATT ATT ATT ATT ATT CCT ATGT -GT ATT ATT ACT ACTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT A-TT
* * *
42292794 A-T ATG ATT GTT ATT -TCT ACT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * *
42292838 ATT ATT ATT ATT ATT ATT ATT ATG AAT A-T ATC AGT ATT ATC AAT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * * * * *
42292884 ATT GTT ATT ATT AGT ATT -TT GTC AGT GTC AGT ATT ATT -TT CGTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT
* * * *
42292928 ACCTT TTT ATT TTT ATT TTT ATT ATT -TCT ATT ATT GTT ATT ATT -TT
1 A--TT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT
* * * * * *
42292974 -TT ATT ACT ATT ATT GTT A-T ATT ATC GTT ATT ATT CTT ACT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
42293020 ATT
1 ATT
42293023 GTTAATGCAA
Statistics
Matches: 193, Mismatches: 62, Indels: 34
0.67 0.21 0.12
Matches are distributed among these distances:
2 19 0.10
3 166 0.86
4 6 0.03
5 2 0.01
ACGTcount: A:0.27, C:0.07, G:0.06, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:42293338 original size:17 final size:18
Alignment explanation
Indices: 42293308--42293344 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
42293298 GTATTTCTAG
42293308 TACTATATTACA-TTTAT
1 TACTATATTACATTTTAT
42293325 TACT-TATTAGCATTTTAT
1 TACTATATTA-CATTTTAT
42293343 TA
1 TA
42293345 TTACTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.28
17 6 0.33
18 7 0.39
ACGTcount: A:0.32, C:0.11, G:0.03, T:0.54
Consensus pattern (18 bp):
TACTATATTACATTTTAT
Found at i:42295363 original size:28 final size:28
Alignment explanation
Indices: 42295323--42295401 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
42295313 GCAATCAAAT
* * *
42295323 ATGGTACTCAGTGTACGAAATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
*
42295351 ATGGCACTTAGTGTGCGAGATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
* *
42295379 ATGACACTTAGTGTGCAAAATAT
1 ATGGCACTTAGTGTGCGAAATAT
42295402 CAAATGATTC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.29
Consensus pattern (28 bp):
ATGGCACTTAGTGTGCGAAATATTGAGA
Found at i:42295620 original size:43 final size:44
Alignment explanation
Indices: 42295512--42295623 Score: 131
Period size: 44 Copynumber: 2.5 Consensus size: 44
42295502 TTTATAATGG
* * *
42295512 TGATATTCGGGCTTTGAGCCTAGCAAGCTTTAAGCTGGTGAATAA
1 TGATA-TCGGGCTTCGAGCCTAGCAAGCTATAAGCCGGTGAATAA
*
42295557 T-ATTATCGGGCTTCGGGCCTAGCAAGCTATAATGCCGGT-AA-AA
1 TGA-TATCGGGCTTCGAGCCTAGCAAGCTATAA-GCCGGTGAATAA
*
42295600 TGATATCGGGCTTCAAGCCTAGCA
1 TGATATCGGGCTTCGAGCCTAGCA
42295624 GGAAAAATGT
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
43 22 0.38
44 28 0.48
45 8 0.14
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.28
Consensus pattern (44 bp):
TGATATCGGGCTTCGAGCCTAGCAAGCTATAAGCCGGTGAATAA
Found at i:42300259 original size:46 final size:45
Alignment explanation
Indices: 42300166--42300251 Score: 120
Period size: 46 Copynumber: 1.9 Consensus size: 45
42300156 TACATCTCTC
* * **
42300166 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGA-ATGCCCAAACATAAGT
42300212 GAACTCGGACTCAACTCAACGAGTTCGG-ATGCCCAAACAT
1 GAACTCGGACTCAACTCAACGAGTTCGGAATGCCCAAACAT
42300252 CCTAGTGACA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
44 8 0.22
46 28 0.78
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.20
Consensus pattern (45 bp):
GAACTCGGACTCAACTCAACGAGTTCGGAATGCCCAAACATAAGT
Found at i:42314824 original size:15 final size:15
Alignment explanation
Indices: 42314804--42314833 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
42314794 TTGAAGACAC
42314804 AGTTGAAGACTGAAT
1 AGTTGAAGACTGAAT
42314819 AGTTGAAGACTGAAT
1 AGTTGAAGACTGAAT
42314834 CTCTAACTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.27, T:0.27
Consensus pattern (15 bp):
AGTTGAAGACTGAAT
Found at i:42320959 original size:9 final size:9
Alignment explanation
Indices: 42320945--42320974 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
42320935 TGAGTACGAT
42320945 TATTTGGAA
1 TATTTGGAA
42320954 TATTTGGAA
1 TATTTGGAA
42320963 TATTTGGAA
1 TATTTGGAA
42320972 TAT
1 TAT
42320975 CCATAACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (9 bp):
TATTTGGAA
Found at i:42324859 original size:78 final size:78
Alignment explanation
Indices: 42324730--42324885 Score: 294
Period size: 78 Copynumber: 2.0 Consensus size: 78
42324720 CACGCCCGTG
* *
42324730 TGTAGCAATTTCCTAGCCTCATTTGTCACCAAAACTTACCATTTTCCTGCACTAAAACTCACAAA
1 TGTAGCAATTTCCTAGCCTCATTTGCCACCAAAACTTACCATTTTCCTGCACCAAAACTCACAAA
42324795 CATATATCCACCA
66 CATATATCCACCA
42324808 TGTAGCAATTTCCTAGCCTCATTTGCCACCAAAACTTACCATTTTCCTGCACCAAAACTCACAAA
1 TGTAGCAATTTCCTAGCCTCATTTGCCACCAAAACTTACCATTTTCCTGCACCAAAACTCACAAA
42324873 CATATATCCACCA
66 CATATATCCACCA
42324886 ATCCAATATC
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 76 1.00
ACGTcount: A:0.33, C:0.32, G:0.06, T:0.28
Consensus pattern (78 bp):
TGTAGCAATTTCCTAGCCTCATTTGCCACCAAAACTTACCATTTTCCTGCACCAAAACTCACAAA
CATATATCCACCA
Found at i:42327272 original size:26 final size:25
Alignment explanation
Indices: 42327243--42327322 Score: 87
Period size: 24 Copynumber: 3.3 Consensus size: 25
42327233 ATCTTGGTCG
*
42327243 GTAAGCTCCTCCTGAGCTGAAAAACA
1 GTAAGCTCCTACTGAGCTG-AAAACA
* *
42327269 GTAAGCT-CTATTGAGCTGAAAACG
1 GTAAGCTCCTACTGAGCTGAAAACA
*
42327293 GTAAGCT-CTATTGAGCTG--AACA
1 GTAAGCTCCTACTGAGCTGAAAACA
42327315 GTAAGCTC
1 GTAAGCTC
42327323 TTTCAAGATG
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
22 10 0.20
24 23 0.47
25 9 0.18
26 7 0.14
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.24
Consensus pattern (25 bp):
GTAAGCTCCTACTGAGCTGAAAACA
Found at i:42327296 original size:24 final size:24
Alignment explanation
Indices: 42327241--42327312 Score: 99
Period size: 24 Copynumber: 2.9 Consensus size: 24
42327231 GAATCTTGGT
**
42327241 CGGTAAGCTCCTCCTGAGCTGAAAAA
1 CGGTAAGCT-CTATTGAGCTG-AAAA
*
42327267 CAGTAAGCTCTATTGAGCTGAAAA
1 CGGTAAGCTCTATTGAGCTGAAAA
42327291 CGGTAAGCTCTATTGAGCTGAA
1 CGGTAAGCTCTATTGAGCTGAA
42327313 CAGTAAGCTC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 25 0.60
25 9 0.21
26 8 0.19
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (24 bp):
CGGTAAGCTCTATTGAGCTGAAAA
Found at i:42327321 original size:22 final size:23
Alignment explanation
Indices: 42327255--42327323 Score: 95
Period size: 24 Copynumber: 2.9 Consensus size: 23
42327245 AAGCTCCTCC
42327255 TGAGCTGAAAAACAGTAAGCTCTAT
1 TGAGCTG--AAACAGTAAGCTCTAT
*
42327280 TGAGCTGAAAACGGTAAGCTCTAT
1 TGAGCTG-AAACAGTAAGCTCTAT
42327304 TGAGCTG-AACAGTAAGCTCT
1 TGAGCTGAAACAGTAAGCTCT
42327324 TTCAAGATGA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
22 12 0.29
24 23 0.55
25 7 0.17
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (23 bp):
TGAGCTGAAACAGTAAGCTCTAT
Found at i:42333219 original size:26 final size:26
Alignment explanation
Indices: 42333190--42333297 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
42333180 TGAAATGCCC
* *
42333190 ATCATGGAAAATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
42333216 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
42333242 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
42333268 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
42333294 ATCA
1 ATCA
42333298 ATTTGTACCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.37, C:0.23, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:42336232 original size:48 final size:48
Alignment explanation
Indices: 42336161--42336254 Score: 161
Period size: 48 Copynumber: 2.0 Consensus size: 48
42336151 AAGACATTTG
*
42336161 GTTGATATGTGTGCTAGTGTAAGACCATATCTAGGATATGGCATCGAT
1 GTTGATATGTGTGCTAGTGTAAGACCATATCTAGGACATGGCATCGAT
* *
42336209 GTTGATATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCG
1 GTTGATATGTGTGCTAGTGTAAGACCATATCTAGGACATGGCATCG
42336255 GCCACATTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.24, C:0.14, G:0.30, T:0.32
Consensus pattern (48 bp):
GTTGATATGTGTGCTAGTGTAAGACCATATCTAGGACATGGCATCGAT
Found at i:42336276 original size:48 final size:48
Alignment explanation
Indices: 42336224--42336447 Score: 204
Period size: 48 Copynumber: 4.6 Consensus size: 48
42336214 TATGTGTGCT
*
42336224 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-CACATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-CATTATGATAGCC
*
42336272 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-CTCAATATGCA-AGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-CATTATG-ATAGCC
* * * * * * *** *
42336320 AATGTAAGACCATGTTTGGAACATGGTATCAGTATTGTTAT-ATATGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACCATTATGATA-GCC
* * * *
42336368 AGTGTAAGACTATGTTTGGGACATGGCATTGGCACCGATGTATAATAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACC-AT-TATGATAGCC
* *
42336418 AATGTAAGACCATGTCTGGTACATGGCATC
1 AGTGTAAGACCATGTCTGGGACATGGCATC
42336448 AGCATTTTAT
Statistics
Matches: 140, Mismatches: 29, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
46 1 0.01
47 1 0.01
48 103 0.74
49 2 0.01
50 30 0.21
51 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.27
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCACCATTATGATAGCC
Found at i:42336597 original size:20 final size:20
Alignment explanation
Indices: 42336572--42336612 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
42336562 TGGTACGGGT
*
42336572 ATGTGTGCAAAACTCATGAG
1 ATGTGTACAAAACTCATGAG
42336592 ATGTGTACAAAACTCATGAG
1 ATGTGTACAAAACTCATGAG
42336612 A
1 A
42336613 AATGATCTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (20 bp):
ATGTGTACAAAACTCATGAG
Found at i:42339501 original size:63 final size:63
Alignment explanation
Indices: 42339322--42339572 Score: 213
Period size: 63 Copynumber: 3.8 Consensus size: 63
42339312 TATAGTTCGA
* * * *
42339322 CTCTCTTGTAC-ACATGGTGAACACTCAGTACCACCCATGTGACCTAGCCA-ATTTATCTCGTAG
1 CTCTCTTGT-CTACATGGTGTACACT-AGTACCACCCATGTGACCTAGCTACATATATCCCGTAG
* * * *
42339385 CTCTCTTGTCTACATGGTGTCCTTCACCTGGAACCACGCATGTGACCTAGCTACATATATCCCGT
1 CTCTCTTGTCTACATGGTG---TACA-CTAGTACCACCCATGTGACCTAGCTACATATATCCCGT
42339450 AG
62 AG
* **
42339452 CTCTCTT-TCTACATGGTGTACACATAGTATCACCCATGTGACCTAGCTACATCATAATGTCTTG
1 CTCTCTTGTCTACATGGTGTACAC-TAGTACCACCCATGTGACCTAGCTACAT-AT-A--TCCCG
42339516 TAG
61 TAG
* * * **
42339519 CTCTCTTGTAC-ACATGATGTGCACTCAGCACCATACATGTGACCTAGCTACATA
1 CTCTCTTGT-CTACATGGTGTACACT-AGTACCACCCATGTGACCTAGCTACATA
42339573 CTATATGTAT
Statistics
Matches: 153, Mismatches: 21, Indels: 24
0.77 0.11 0.12
Matches are distributed among these distances:
62 2 0.01
63 44 0.29
64 2 0.01
65 1 0.01
66 33 0.22
67 35 0.23
68 35 0.23
69 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.30
Consensus pattern (63 bp):
CTCTCTTGTCTACATGGTGTACACTAGTACCACCCATGTGACCTAGCTACATATATCCCGTAG
Found at i:42340272 original size:30 final size:30
Alignment explanation
Indices: 42340238--42340298 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
42340228 TCCTTAACTC
42340238 AAACTTTGGCAAAATTACAATTTTGCCCCT
1 AAACTTTGGCAAAATTACAATTTTGCCCCT
* * * *
42340268 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGCAAAATTACAATTTTGCCCCT
42340298 A
1 A
42340299 GGCTCGGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGCAAAATTACAATTTTGCCCCT
Found at i:42343636 original size:12 final size:14
Alignment explanation
Indices: 42343619--42343650 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
42343609 ATGAGAACAC
42343619 ATGTGTA-G-TACT
1 ATGTGTAGGCTACT
42343631 ATGTGTAGGCTACT
1 ATGTGTAGGCTACT
42343645 ATGTGT
1 ATGTGT
42343651 TTAAGATGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 1 0.06
14 10 0.56
ACGTcount: A:0.22, C:0.09, G:0.28, T:0.41
Consensus pattern (14 bp):
ATGTGTAGGCTACT
Found at i:42346348 original size:29 final size:29
Alignment explanation
Indices: 42346314--42346401 Score: 142
Period size: 29 Copynumber: 3.1 Consensus size: 29
42346304 ATTATATCAC
42346314 ATGGCCCATTAGGCCCAAATCACATTTAT
1 ATGGCCCATTAGGCCCAAATCACATTTAT
* *
42346343 ATGGCCCTTTAGGCCCAAATCACATCTAT
1 ATGGCCCATTAGGCCCAAATCACATTTAT
*
42346372 GTGGCCCATTAGGCCCAAATCACA-TTAT
1 ATGGCCCATTAGGCCCAAATCACATTTAT
42346400 AT
1 AT
42346402 TCATGCTCAC
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 4 0.08
29 49 0.92
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (29 bp):
ATGGCCCATTAGGCCCAAATCACATTTAT
Found at i:42348442 original size:39 final size:39
Alignment explanation
Indices: 42348276--42348456 Score: 231
Period size: 39 Copynumber: 4.6 Consensus size: 39
42348266 TCGTTCAAAC
* * ** * **
42348276 GCCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAAG
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
* * * *
42348316 GCCTTCGGGACTTAACCCGGATATCACAATTTGCACAATT
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
42348356 GCCTTCGGGCTTAGCCCGGATATCATAACTC-C-CAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
42348393 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
42348432 GCCTTCGGGCTTAGCCCGGATATCA
1 GCCTTCGGGCTTAGCCCGGATATCA
42348457 CTCGAACATT
Statistics
Matches: 124, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
37 36 0.29
38 2 0.02
39 48 0.39
40 38 0.31
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.24
Consensus pattern (39 bp):
GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
Found at i:42355823 original size:39 final size:39
Alignment explanation
Indices: 42355705--42355887 Score: 240
Period size: 39 Copynumber: 4.6 Consensus size: 39
42355695 TCGTTCAAAC
* * ** * **
42355705 GCCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAAG
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
* * * *
42355745 GCCTTCGGGACTTAACCCGGATATCACAATTTGCACAATT
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
*
42355785 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCCCAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
42355824 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
42355863 GCCTTCGGGCTTAGCCCGGATATCA
1 GCCTTCGGGCTTAGCCCGGATATCA
42355888 CTCGAACATT
Statistics
Matches: 126, Mismatches: 17, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
39 88 0.70
40 38 0.30
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24
Consensus pattern (39 bp):
GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
Found at i:42358706 original size:50 final size:50
Alignment explanation
Indices: 42358652--42358967 Score: 307
Period size: 50 Copynumber: 6.3 Consensus size: 50
42358642 CTGGTACGAA
* * *
42358652 TAGTAGCCTACACTTAGTATTAGACATGCGACCTATCAATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACG
* * * * *
42358702 TAGTAGCCTGTACTTAGTACTACACACGTGACTTATCCATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACG
* ** * ** *
42358752 TAGTAGCCTACACTTAGTACTGCACACATGATCGAAGT-T-AA-CGGGTATGCA
1 TAGTAGCCTGCACTTAGTACT--ACACATG--CGACCTATCAATCTGGTACACG
* * * * *
42358803 TAGTAGTCTGAAGTTAGTACTACACATGCGACCTATCAATTTGGTTCACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACG
* * * * *
42358853 TAGTAACCTGCACTTAGTACTACACA-CCTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGC-GACCTATCAATCTGGTACACG
* * *
42358903 TAGTAGCTTGCACTTAGTACTACACATGCGACCTAACAATCTAGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACG
42358953 TAGTAGCCTGCACTT
1 TAGTAGCCTGCACTT
42358968 TATACTATAC
Statistics
Matches: 209, Mismatches: 48, Indels: 18
0.76 0.17 0.07
Matches are distributed among these distances:
47 4 0.02
48 1 0.00
49 10 0.05
50 159 0.76
51 24 0.11
52 7 0.03
53 1 0.00
54 3 0.01
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACG
Found at i:42360392 original size:49 final size:50
Alignment explanation
Indices: 42360278--42360394 Score: 175
Period size: 49 Copynumber: 2.4 Consensus size: 50
42360268 CGTTTGTCGC
*
42360278 ACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACGTGTGTAGT
1 ACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACATGTGTAGT
* * *
42360328 ACTAAGTGCAGGCTACTACGTGTA-CTGGATTGTT-GGTCGCATGTGTAGT
1 ACTAAGTGCAGGCTACTACGTGTATC-AGATGGTTAGGTCACATGTGTAGT
42360377 ACTAAGTGCAGGCTACTA
1 ACTAAGTGCAGGCTACTA
42360395 TGCATACCAG
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
49 32 0.52
50 30 0.48
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (50 bp):
ACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACATGTGTAGT
Found at i:42360627 original size:16 final size:15
Alignment explanation
Indices: 42360606--42360635 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
42360596 GAATGGAGTA
42360606 AGTGAAATTATGTAAG
1 AGTGAAATT-TGTAAG
42360622 AGTGAAATTTGTAA
1 AGTGAAATTTGTAA
42360636 TAAAACAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.33
Consensus pattern (15 bp):
AGTGAAATTTGTAAG
Found at i:42361530 original size:16 final size:15
Alignment explanation
Indices: 42361509--42361540 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
42361499 AGCCACGAGA
42361509 TGTGGCTTGTAATGCT
1 TGTGGCTTGTAA-GCT
42361525 TGTGGCTTGTAAGCT
1 TGTGGCTTGTAAGCT
42361540 T
1 T
42361541 AATTATCCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.12, C:0.12, G:0.31, T:0.44
Consensus pattern (15 bp):
TGTGGCTTGTAAGCT
Found at i:42363719 original size:78 final size:81
Alignment explanation
Indices: 42363599--42363780 Score: 257
Period size: 78 Copynumber: 2.3 Consensus size: 81
42363589 TACTCGTTCA
* *
42363599 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
*
42363662 ATTTAGTAAC-TCGCAC
65 ATTTAGTAACTTAGCAC
**
42363678 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
*
42363741 TTTAGTCACTTAGCAC
66 TTTAGTAACTTAGCAC
*
42363757 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
42363781 CATCATTCGA
Statistics
Matches: 92, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
77 3 0.03
78 49 0.53
79 29 0.32
80 11 0.12
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TTTAGTAACTTAGCAC
Found at i:42363780 original size:40 final size:40
Alignment explanation
Indices: 42363597--42363780 Score: 252
Period size: 40 Copynumber: 4.7 Consensus size: 40
42363587 GCTACTCGTT
*
42363597 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
42363637 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
42363677 C-AATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
42363715 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
42363756 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
42363781 CATCATTCGA
Statistics
Matches: 129, Mismatches: 9, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
38 26 0.20
39 21 0.16
40 69 0.53
41 13 0.10
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Done.