Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr10
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31
Warning! 2980117 characters in sequence are not A, C, G, or T
File 119 of 284
Found at i:39416156 original size:16 final size:16
Alignment explanation
Indices: 39416135--39416165 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
39416125 TTTCTTTTGT
39416135 TTCTTTATTTTATTTA
1 TTCTTTATTTTATTTA
39416151 TTCTTTATTTTATTT
1 TTCTTTATTTTATTT
39416166 TATTTACTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.77
Consensus pattern (16 bp):
TTCTTTATTTTATTTA
Found at i:39416297 original size:3 final size:3
Alignment explanation
Indices: 39416289--39416397 Score: 80
Period size: 3 Copynumber: 35.0 Consensus size: 3
39416279 TTATCTCAAT
* * * **
39416289 TAA TAA TAA AAA T-A TAA TAA TAA TAA TAA TAA GTAA TTA T-C TTT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
*
39416333 TACT TAA TAAA TAA GTAA -ATA TATA TAAA TAA TAA TAA TAA TAA TAA
1 TA-A TAA T-AA TAA -TAA TA-A TA-A T-AA TAA TAA TAA TAA TAA TAA
39416380 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
39416398 GTAAATATCT
Statistics
Matches: 90, Mismatches: 7, Indels: 18
0.78 0.06 0.16
Matches are distributed among these distances:
2 4 0.04
3 67 0.74
4 18 0.20
5 1 0.01
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:39416412 original size:77 final size:76
Alignment explanation
Indices: 39416289--39416437 Score: 271
Period size: 77 Copynumber: 1.9 Consensus size: 76
39416279 TTATCTCAAT
*
39416289 TAATAATAAAAATATAATAATAATAATAATAAGTAATTATCTTTTACTTAATAAATAAGTAAATA
1 TAATAATAAAAATATAATAATAATAATAATAAGTAAATATCTTTTACTTAATAAATAAGTAAATA
39416354 TATATAAATAA
66 TATATAAATAA
*
39416365 TAATAATAATAATAATAATAATAATAATAATAAGTAAATATCTTTTACTTAATAAATAAGTAAAT
1 TAATAATAAAAAT-ATAATAATAATAATAATAAGTAAATATCTTTTACTTAATAAATAAGTAAAT
39416430 ATATATAA
65 ATATATAA
39416438 CATACATTTG
Statistics
Matches: 70, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
76 12 0.17
77 58 0.83
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (76 bp):
TAATAATAAAAATATAATAATAATAATAATAAGTAAATATCTTTTACTTAATAAATAAGTAAATA
TATATAAATAA
Found at i:39418343 original size:49 final size:46
Alignment explanation
Indices: 39418192--39418356 Score: 152
Period size: 49 Copynumber: 3.5 Consensus size: 46
39418182 TATGTGAGCC
* * *
39418192 AGTGTAAGACATGTCTGGGACATGCATCAGCATT-AAGACAAGAGTT
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCTTGAATATAA-AGTT
* * * * * *
39418238 AGTGTAAGACATGTCTGGAACATGAATCGGCCTCGGGATATACAAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCT-TGAATATA-AAGTT
* *
39418286 AGTGTAAGACCTGTCTAGGACATGGCATCAGCCTTGATATATGAAAGTT
1 AGTGTAAGACATGTCTGGGACAT-GCATCAGCCTTGA-ATAT-AAAGTT
* *
39418335 AGTGTAAGACCTATCTGGGACA
1 AGTGTAAGACATGTCTGGGACA
39418357 CGACATCGAC
Statistics
Matches: 94, Mismatches: 19, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
46 29 0.31
48 27 0.29
49 37 0.39
50 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCTTGAATATAAAGTT
Found at i:39419610 original size:20 final size:21
Alignment explanation
Indices: 39419571--39419610 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
39419561 GTCAACAGAG
*
39419571 CCACACGGGCATGTTGCCCTT
1 CCACACAGGCATGTTGCCCTT
*
39419592 CCACACAGGCGTG-TGCCCT
1 CCACACAGGCATGTTGCCCT
39419611 GTTTTAAGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.15, C:0.40, G:0.25, T:0.20
Consensus pattern (21 bp):
CCACACAGGCATGTTGCCCTT
Found at i:39419958 original size:70 final size:70
Alignment explanation
Indices: 39419871--39420016 Score: 229
Period size: 70 Copynumber: 2.1 Consensus size: 70
39419861 TTTTGGTTAC
* * * *
39419871 ATAATTTTGACGAAAGAGTGTTTAATTAGATTACATGGGCTAAATTGCGTAGTCGAATAAAGTAG
1 ATAAATTTGACGAAAGAGTGTTTAATTAGAGTACATGGGCTAAATAGCGTAATCGAATAAAGTAG
39419936 GATTT
66 GATTT
* *
39419941 ATAAATTTGACGAAAGAGTGTTTAATTAGAGTATATGGGCTAAATAGCGTAATTGAATAAAGTAG
1 ATAAATTTGACGAAAGAGTGTTTAATTAGAGTACATGGGCTAAATAGCGTAATCGAATAAAGTAG
*
39420006 TATTT
66 GATTT
39420011 ATAAAT
1 ATAAAT
39420017 AGAATTAAAT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.39, C:0.05, G:0.21, T:0.34
Consensus pattern (70 bp):
ATAAATTTGACGAAAGAGTGTTTAATTAGAGTACATGGGCTAAATAGCGTAATCGAATAAAGTAG
GATTT
Found at i:39428299 original size:12 final size:12
Alignment explanation
Indices: 39428284--39428315 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
39428274 TATAGCATAA
39428284 GCTCTAGCAGGT
1 GCTCTAGCAGGT
39428296 GCTCTAGCAGGT
1 GCTCTAGCAGGT
39428308 GCTCTAGC
1 GCTCTAGC
39428316 TTCTGATCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.16, C:0.28, G:0.31, T:0.25
Consensus pattern (12 bp):
GCTCTAGCAGGT
Found at i:39431148 original size:68 final size:68
Alignment explanation
Indices: 39431001--39431156 Score: 149
Period size: 68 Copynumber: 2.2 Consensus size: 68
39430991 AGCCGATTTG
* * * * *
39431001 TCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATT
1 TCTCGTAGCTCTCTTGTCTACATGGTGTACATCAC-TCGAATCACACATGCGACCTAGCTACATA
*
39431066 TATC
65 TATA
* *
39431070 TCTCACGTAGCTCTCTTGTCTACATGG-GATACATC-C-CGTATCACACATGTGACCTAGCTACT
1 TCT--CGTAGCTCTCTTGTCTACATGGTG-TACATCACTCGAATCACACATGCGACCTAGCTAC-
39431132 ATATAGTA
62 ATATA-TA
39431140 TCTCGTAGC-CTTCTTGT
1 TCTCGTAGCTC-TCTTGT
39431157 ACACATGATG
Statistics
Matches: 73, Mismatches: 8, Indels: 13
0.78 0.09 0.14
Matches are distributed among these distances:
67 1 0.01
68 33 0.45
69 7 0.10
70 6 0.08
71 26 0.36
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.35
Consensus pattern (68 bp):
TCTCGTAGCTCTCTTGTCTACATGGTGTACATCACTCGAATCACACATGCGACCTAGCTACATAT
ATA
Found at i:39433909 original size:46 final size:46
Alignment explanation
Indices: 39433839--39434013 Score: 153
Period size: 46 Copynumber: 3.8 Consensus size: 46
39433829 TGTAACCCAC
* * *
39433839 CCATAAGCGAACTC-AGACCCAACTCAATGAGCTCGGGCATTCGCAT
1 CCATAAGTGAACTCGA-ACTCAACTCAACGAGCTCGGGCATTCGCAT
* * * *
39433885 CCATAAGTGCACTCGAACTCAACTCAACGACCTTGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGAACTCAACTCAACGAGCTCGG--G-C-A-TTCGCAT
* * * *
39433935 -C-TCA-CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
1 CCATAAGTGAACTCGAACTCAACTCAACGAGCTCGGGCATTCGCAT
*
39433978 CCATAAGTTAACTCGAACTCAACTCAACGAGCTCGG
1 CCATAAGTGAACTCGAACTCAACTCAACGAGCTCGG
39434014 ATGCCCAAAT
Statistics
Matches: 100, Mismatches: 19, Indels: 20
0.72 0.14 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 54 0.54
47 25 0.25
48 3 0.03
49 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGAACTCAACTCAACGAGCTCGGGCATTCGCAT
Found at i:39433964 original size:93 final size:93
Alignment explanation
Indices: 39433846--39434018 Score: 274
Period size: 93 Copynumber: 1.9 Consensus size: 93
39433836 CACCCATAAG
* * *
39433846 CGAACTCAGACCCAACTCAATGAGCTCGGGCATTCGCATCCATAAGTGCACTCGAACTCAACTCA
1 CGAACTCAGACCCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCA
*
39433911 ACGACCTTGGATGCCTAGTTACATCTCA
66 ACGACCTCGGATGCCTAGTTACATCTCA
* * *
39433939 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTTAACTCGAACTCAACTCA
1 CGAACTCAGACCCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCA
*
39434004 ACGAGCTCGGATGCC
66 ACGACCTCGGATGCC
39434019 CAAATATCCT
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.20
Consensus pattern (93 bp):
CGAACTCAGACCCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGAACTCAACTCA
ACGACCTCGGATGCCTAGTTACATCTCA
Found at i:39441476 original size:46 final size:46
Alignment explanation
Indices: 39441408--39441579 Score: 154
Period size: 46 Copynumber: 3.7 Consensus size: 46
39441398 TGAAACCCGC
** *
39441408 CCATAAGTTTACTCAGATTCAACTCAACGAGCTCGGGCTTTCGTAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCTTTCGTAT
* * * *
39441454 CCATAAGTGAACTCGGACTCAACTCAACAAACTCGGATGCCTAGTT-ATAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGG--G-CT--TTCGTAT
* * * * * *
39441504 -C-TCA-CGAACTCAAACTCAACTCAACGAGCTCGGACATTCGCAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCTTTCGTAT
39441547 CCATAAGTGAACTCAGACTCAACTCAACGAGCT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCT
39441580 TGGATGCCCA
Statistics
Matches: 97, Mismatches: 20, Indels: 18
0.72 0.15 0.13
Matches are distributed among these distances:
42 2 0.02
43 2 0.02
44 2 0.02
45 2 0.02
46 54 0.56
47 24 0.25
48 3 0.03
49 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (46 bp):
CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCTTTCGTAT
Found at i:39448294 original size:24 final size:24
Alignment explanation
Indices: 39448217--39448277 Score: 122
Period size: 24 Copynumber: 2.5 Consensus size: 24
39448207 GATCAAATTT
39448217 GCACACATAGTGCTCGTCACACTC
1 GCACACATAGTGCTCGTCACACTC
39448241 GCACACATAGTGCTCGTCACACTC
1 GCACACATAGTGCTCGTCACACTC
39448265 GCACACATAGTGC
1 GCACACATAGTGC
39448278 CATAGTACAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.26, C:0.36, G:0.18, T:0.20
Consensus pattern (24 bp):
GCACACATAGTGCTCGTCACACTC
Found at i:39452693 original size:43 final size:43
Alignment explanation
Indices: 39452640--39452726 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
39452630 TGAGGTATGT
* *
39452640 AGCATCCGAGCTCGTTGAGAGGTCCGAGTTCATTATGGATGCG
1 AGCATCCGAGCTCGTTGAGAGGTCCAAGTTCATGATGGATGCG
*
39452683 AGCATCCGAGCTCGTTGAGTGGTCCAAGTTCATGATGGATGCG
1 AGCATCCGAGCTCGTTGAGAGGTCCAAGTTCATGATGGATGCG
39452726 A
1 A
39452727 TTCATGTAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.22, C:0.21, G:0.32, T:0.25
Consensus pattern (43 bp):
AGCATCCGAGCTCGTTGAGAGGTCCAAGTTCATGATGGATGCG
Found at i:39455732 original size:42 final size:41
Alignment explanation
Indices: 39455664--39455810 Score: 117
Period size: 41 Copynumber: 3.6 Consensus size: 41
39455654 TTGGTCTCGA
*
39455664 AAGGGCTTTTGAGCCAGTGCTAATAACC-GAACTTAGTTTCG
1 AAGGGCTTTTGAGCCAGTGCTAATAACCAG-ACTTAGTTCCG
* *
39455705 AAGGGCTTTTTAGAGTCAGTG-TCATAACCAGACTTAGTTCCG
1 AAGGGC-TTTT-GAGCCAGTGCTAATAACCAGACTTAGTTCCG
* * *
39455747 AAGGGCCTTCGAGCCAGTAGTCTAAT--CC-GAGCTT-GGTCTCG
1 AAGGGCTTTTGAGCCAGT-G-CTAATAACCAGA-CTTAGTTC-CG
* *
39455788 AAGGGCTTTTGATCCGGTGCTAA
1 AAGGGCTTTTGAGCCAGTGCTAA
39455811 GAGTCGGGCT
Statistics
Matches: 86, Mismatches: 12, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
39 4 0.05
40 13 0.15
41 30 0.35
42 27 0.31
43 12 0.14
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.29
Consensus pattern (41 bp):
AAGGGCTTTTGAGCCAGTGCTAATAACCAGACTTAGTTCCG
Found at i:39455793 original size:41 final size:40
Alignment explanation
Indices: 39455645--39455796 Score: 123
Period size: 42 Copynumber: 3.7 Consensus size: 40
39455635 TCGGGGTTTA
* *
39455645 AATCCGAGCTTGGTCTCGAAAGGGCTTTTGAGCCAGTG-CT
1 AATCCGAGCTTAGTCTCG-AAGGGCTTTAGAGCCAGTGTCT
* * *
39455685 AATAACCGAACTTAGTTTCGAAGGGCTTTTTAGAGTCAGTGTCAT
1 AAT--CCGAGCTTAGTCTCGAAGGGC--TTTAGAGCCAGTGTC-T
* *
39455730 AA-CC-AGACTTAGT-TCCGAAGGGCCTTCGAGCCAGTAGTCT
1 AATCCGAG-CTTAGTCT-CGAAGGGCTTTAGAGCCAGT-GTCT
*
39455770 AATCCGAGCTTGGTCTCGAAGGGCTTT
1 AATCCGAGCTTAGTCTCGAAGGGCTTT
39455797 TGATCCGGTG
Statistics
Matches: 89, Mismatches: 11, Indels: 23
0.72 0.09 0.19
Matches are distributed among these distances:
40 15 0.17
41 28 0.31
42 31 0.35
43 11 0.12
44 1 0.01
45 3 0.03
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (40 bp):
AATCCGAGCTTAGTCTCGAAGGGCTTTAGAGCCAGTGTCT
Found at i:39464569 original size:25 final size:25
Alignment explanation
Indices: 39464541--39464619 Score: 65
Period size: 25 Copynumber: 3.3 Consensus size: 25
39464531 CTAATGGCCG
39464541 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
* *** ****
39464566 ATGTGAT-AAGGCCTAA-TG-GCCG
1 ATGTGATGAATGTGAAAGTGTATAT
39464588 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
39464613 ATGTGAT
1 ATGTGAT
39464620 AAGGCCTAAT
Statistics
Matches: 35, Mismatches: 16, Indels: 6
0.61 0.28 0.11
Matches are distributed among these distances:
22 7 0.20
23 7 0.20
24 7 0.20
25 14 0.40
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (25 bp):
ATGTGATGAATGTGAAAGTGTATAT
Found at i:39464680 original size:49 final size:49
Alignment explanation
Indices: 39464525--39464912 Score: 623
Period size: 49 Copynumber: 8.1 Consensus size: 49
39464515 GAAATGATAG
39464525 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
39464572 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
39464619 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
39464668 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
*
39464717 TAAGGCCCAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
*
39464766 TAAGGCCCAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
*
39464815 TAAGGCCCAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
* * * * * *
39464862 -CAGAGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A-ATGTGA
1 TAAG-GCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
39464909 TAAG
1 TAAG
39464913 TCCCGAAGGG
Statistics
Matches: 327, Mismatches: 8, Indels: 11
0.95 0.02 0.03
Matches are distributed among these distances:
46 2 0.01
47 127 0.39
48 3 0.01
49 195 0.60
ACGTcount: A:0.32, C:0.10, G:0.30, T:0.28
Consensus pattern (49 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
Found at i:39465087 original size:37 final size:37
Alignment explanation
Indices: 39465031--39465109 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
39465021 CCGAGCTCTA
* * *
39465031 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
39465068 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
39465105 AAGAC
1 AAGAC
39465110 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:39466590 original size:13 final size:13
Alignment explanation
Indices: 39466572--39466598 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39466562 GTTTAATTAG
39466572 TTAATTAGTTTAA
1 TTAATTAGTTTAA
39466585 TTAATTAGTTTAA
1 TTAATTAGTTTAA
39466598 T
1 T
39466599 AAACAACCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (13 bp):
TTAATTAGTTTAA
Found at i:39466598 original size:9 final size:9
Alignment explanation
Indices: 39466559--39466587 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
39466549 TCTCTTTGCT
39466559 TTAGTTTAA
1 TTAGTTTAA
39466568 TTAG-TTAA
1 TTAGTTTAA
39466576 TTAGTTTAA
1 TTAGTTTAA
39466585 TTA
1 TTA
39466588 ATTAGTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (9 bp):
TTAGTTTAA
Found at i:39470577 original size:40 final size:40
Alignment explanation
Indices: 39470517--39470740 Score: 301
Period size: 40 Copynumber: 5.5 Consensus size: 40
39470507 ACCCAAGTAT
* * *
39470517 CTTCGGGATTTAG-TCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGC
* **
39470556 CTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATGC
39470596 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATGC
*
39470636 CTTCGGGACTTAGCCCGGGTATAGCAACTACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGCAACTA---GCACAAATGC
* *
39470679 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGC
39470719 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
39470741 CATCCGAATA
Statistics
Matches: 166, Mismatches: 13, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
39 12 0.07
40 116 0.70
41 1 0.01
43 37 0.22
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGC
Found at i:39470713 original size:83 final size:80
Alignment explanation
Indices: 39470517--39470740 Score: 308
Period size: 83 Copynumber: 2.8 Consensus size: 80
39470507 ACCCAAGTAT
* * * * *
39470517 CTTCGGGATTTAG-TCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGT
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
**
39470581 CACTAGCATGAATGC
66 CACTAGCACAAATGC
* *
39470596 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGGTATAG-
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
39470660 CAACTACTCGCACAAATGC
66 C-ACTA---GCACAAATGC
*
39470679 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
39470741 CATCCGAATA
Statistics
Matches: 128, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
79 13 0.10
80 48 0.38
83 67 0.52
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
CACTAGCACAAATGC
Found at i:39472780 original size:48 final size:47
Alignment explanation
Indices: 39472576--39472896 Score: 260
Period size: 48 Copynumber: 6.7 Consensus size: 47
39472566 GGGTAGGATA
* * * *
39472576 CCGATGCCATGTCCCAGACATGGTCTTACACTAACTATCGTAATCGAGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAT-AT-TAGG
* * * *
39472625 CCGACGCCATGTCCCAGACTTGGTCTTACACTGGCTCTCATATATCCGTG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAT-T-AG-G
* *
39472675 CCGATGCCATGTCCTAGACATGGTCTTACACT-GACACATC-TCA-TA-G
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAG-CTC-TCAT-ATTAGG
* * *
39472721 CCGATGTCATGTCCCAGACATGCTCTTACACTAGCT-TACATCTTGAGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCT-CATATT-AGG
* * * * *
39472769 CCGATGTCATGTCCCAGACATGGTCTTAAACTAGCTCTCATCTCAATG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAT-TAGG
* * * * * *
39472817 CTGATACGATGTCCCAGACATGGTCTTACATTGGCTCTCATAATATGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATTA-GG
*
39472865 CCGATG-CATGTCCCAGACAT-GTCTTAGACTAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAG
39472897 TACACATATC
Statistics
Matches: 218, Mismatches: 40, Indels: 31
0.75 0.14 0.11
Matches are distributed among these distances:
44 1 0.00
45 1 0.00
46 42 0.19
47 16 0.07
48 83 0.38
49 39 0.18
50 33 0.15
51 3 0.01
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (47 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATTAGG
Found at i:39472811 original size:96 final size:94
Alignment explanation
Indices: 39472576--39472896 Score: 303
Period size: 96 Copynumber: 3.4 Consensus size: 94
39472566 GGGTAGGATA
* * * * * * *
39472576 CCGATGCCATGTCCCAGACATGGTCTTACACTAACTATCGTAATCGAGGCCGACGCCATGTCCCA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAT-CTC-AAGCCGATGACATGTCCCA
* *
39472641 GACTTGGTCTTACACTGGCTCTCATATATCCGTG
64 GACATGGTCTTACACTGGCTCTCATAT-T-AG-G
* * * *
39472675 CCGATGCCATGTCCTAGACATGGTCTTACACT-G-ACACATCTCATAGCCGATGTCATGTCCCAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCA-AGCCGATGACATGTCCCAG
* * *
39472738 ACATGCTCTTACACTAGCT-TACATCTTGAGG
65 ACATGGTCTTACACTGGCTCT-CATATT-AGG
* * *
39472769 CCGATGTCATGTCCCAGACATGGTCTTAAACTAGCTCTCATCTCAATGCTGAT-ACGATGTCCCA
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAA-GCCGATGAC-ATGTCCCA
* *
39472833 GACATGGTCTTACATTGGCTCTCATAATATGG
64 GACATGGTCTTACACTGGCTCTCATATTA-GG
*
39472865 CCGATG-CATGTCCCAGACAT-GTCTTAGACTAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAG
39472897 TACACATATC
Statistics
Matches: 185, Mismatches: 29, Indels: 21
0.79 0.12 0.09
Matches are distributed among these distances:
94 41 0.22
95 22 0.12
96 88 0.48
97 3 0.02
99 31 0.17
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (94 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATCTCAAGCCGATGACATGTCCCAGA
CATGGTCTTACACTGGCTCTCATATTAGG
Found at i:39472868 original size:144 final size:142
Alignment explanation
Indices: 39472576--39472896 Score: 344
Period size: 142 Copynumber: 2.2 Consensus size: 142
39472566 GGGTAGGATA
* *
39472576 CCGATGCCATGTCCCAGACATGGTCTTACACTAACTATCGTAATCGAGGCCGACGCCATGTCCCA
1 CCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTATCATAATCGAGGCCGACGCCATGTCCCA
* * * ** * *
39472641 GACTTGGTCTTACACTGGCTCTCATATATCCGTGCCGATGCCATGTCCTAGACATGGTCTTACAC
64 GACATGGTCTTAAACTAGCTCTCA-ATATCAATGCCGATACCATGTCCCAGACATGGTCTTACAC
*
39472706 TGACACATCTCATAG
128 TGACACATCTAATAG
* * * *
39472721 CCGATGTCATGTCCCAGACATGCTCTTACACTAGCT-TACAT-CTTGAGGCCGATGTCATGTCCC
1 CCGATG-CATGTCCCAGACATG-TCTTACACTAGCTAT-CATAATCGAGGCCGACGCCATGTCCC
* * * *
39472784 AGACATGGTCTTAAACTAGCTCTC-ATCTCAATGCTGATACGATGTCCCAGACATGGTCTTACAT
63 AGACATGGTCTTAAACTAGCTCTCAATATCAATGCCGATACCATGTCCCAGACATGGTCTTACAC
* *
39472848 TGGCTC-TCATAATATGG
128 TGACACATC-TAATA--G
*
39472865 CCGATGCATGTCCCAGACATGTCTTAGACTAG
1 CCGATGCATGTCCCAGACATGTCTTACACTAG
39472897 TACACATATC
Statistics
Matches: 149, Mismatches: 22, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
141 2 0.01
142 50 0.34
143 15 0.10
144 48 0.32
145 34 0.23
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (142 bp):
CCGATGCATGTCCCAGACATGTCTTACACTAGCTATCATAATCGAGGCCGACGCCATGTCCCAGA
CATGGTCTTAAACTAGCTCTCAATATCAATGCCGATACCATGTCCCAGACATGGTCTTACACTGA
CACATCTAATAG
Found at i:39479167 original size:49 final size:49
Alignment explanation
Indices: 39479110--39479231 Score: 185
Period size: 49 Copynumber: 2.5 Consensus size: 49
39479100 GTTGTGTGTT
*
39479110 AGTGTAAGACCTATCTAGGACATGGCATTGGCAC-CGATAGAT-AAGAGTC
1 AGTGTAAGACCTATCTGGGACATGGCATTGGC-CTCGATAGATGAA-AGTC
* *
39479159 AGTGTAAGACCTATCTGGGATATGGCATTGGCCTCGATATATGAAAGTC
1 AGTGTAAGACCTATCTGGGACATGGCATTGGCCTCGATAGATGAAAGTC
39479208 AGTGTAAGACCTATCTGGGACATG
1 AGTGTAAGACCTATCTGGGACATG
39479232 AAATCGACTT
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
48 1 0.01
49 64 0.96
50 2 0.03
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.25
Consensus pattern (49 bp):
AGTGTAAGACCTATCTGGGACATGGCATTGGCCTCGATAGATGAAAGTC
Found at i:39485768 original size:19 final size:19
Alignment explanation
Indices: 39485740--39485803 Score: 83
Period size: 19 Copynumber: 3.4 Consensus size: 19
39485730 TTCAAATGTC
*
39485740 CACACGGTCTGGGTTGTGA
1 CACACGGTCTGGGCTGTGA
* * *
39485759 CACACTGTCTGAGCTATGA
1 CACACGGTCTGGGCTGTGA
*
39485778 CACACGGTCTAGGCTGTGA
1 CACACGGTCTGGGCTGTGA
39485797 CACACGG
1 CACACGG
39485804 CTTGGTCACA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.22, C:0.27, G:0.30, T:0.22
Consensus pattern (19 bp):
CACACGGTCTGGGCTGTGA
Found at i:39488091 original size:22 final size:22
Alignment explanation
Indices: 39488063--39488108 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
39488053 AGATCCCAAC
39488063 TACTCCATCAATTTATAATATA
1 TACTCCATCAATTTATAATATA
39488085 TACTCCATCAATTTATAATATA
1 TACTCCATCAATTTATAATATA
39488107 TA
1 TA
39488109 TATCTTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (22 bp):
TACTCCATCAATTTATAATATA
Found at i:39497246 original size:12 final size:12
Alignment explanation
Indices: 39497231--39497258 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
39497221 GTGATGATTG
39497231 AGCTGATAATTC
1 AGCTGATAATTC
39497243 AGCTGATAATTC
1 AGCTGATAATTC
39497255 AGCT
1 AGCT
39497259 TATTGATGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (12 bp):
AGCTGATAATTC
Found at i:39506445 original size:11 final size:11
Alignment explanation
Indices: 39506429--39506471 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
39506419 AAGTGGAAAG
39506429 TGAATTTGAAT
1 TGAATTTGAAT
39506440 TGAATTGTG-AT
1 TGAATT-TGAAT
* *
39506451 TGAATTGGAAG
1 TGAATTTGAAT
39506462 TGAATTTGAA
1 TGAATTTGAA
39506472 ATAGAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 1 0.04
11 24 0.89
12 2 0.07
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.40
Consensus pattern (11 bp):
TGAATTTGAAT
Found at i:39506902 original size:24 final size:24
Alignment explanation
Indices: 39506869--39506933 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
39506859 CTTATTTTAT
* * *
39506869 TAAATAAAATATTTTAAAATATAA
1 TAAATCAAATATTTAAAAACATAA
39506893 TAAATCAAATACATTTAAAAACATAA
1 TAAATCAAAT--ATTTAAAAACATAA
39506919 -AAA-CAAATA-TTAAAA
1 TAAATCAAATATTTAAAA
39506934 CAAGAAACAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
21 6 0.17
22 1 0.03
24 14 0.39
25 3 0.08
26 12 0.33
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (24 bp):
TAAATCAAATATTTAAAAACATAA
Found at i:39506918 original size:26 final size:24
Alignment explanation
Indices: 39506879--39506927 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
39506869 TAAATAAAAT
* *
39506879 ATTTTAAAATATAATAAATCAAATAC
1 ATTTAAAAACATAA-AAA-CAAATAC
39506905 ATTTAAAAACATAAAAACAAATA
1 ATTTAAAAACATAAAAACAAATA
39506928 TTAAAACAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.29
25 3 0.14
26 12 0.57
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAC
Found at i:39510336 original size:48 final size:47
Alignment explanation
Indices: 39510275--39510796 Score: 755
Period size: 48 Copynumber: 11.0 Consensus size: 47
39510265 ATATACACAC
* *
39510275 ATCTCCTACATATTTCACATTAGCCATTCGGCTTTACCAAATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATA-AT
*
39510323 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATATAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATA-AT
* *
39510371 ATCTCATATATATTTCACATTAGCCATTTGGCTTTACCACATAT-AT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATAAT
* *
39510417 ATCCCATACATATTTCATATTAGCCATTCGGCTTTACCACATATATAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATA-AT
* *
39510465 ATCTCATATATATTTCACATTAGCCATTTGGCTTTACCACATAT-AT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATAAT
* *
39510511 ATCCCATACATATTTCATATTAGCCATTCGGCTTTACCACATATATAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATA-AT
* *
39510559 ATCTCATATATATTTCACATTAGCCATTTGGCTTTACCACATAT-AT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATAAT
* *
39510605 ATCCCATACATATTTCATATTAGCCATTCGGCTTTACCACATATATAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATA-AT
* *
39510653 ATCTCATATATATTTCACATTAGCCATTTGGCTTTACCACATAT-AT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATAAT
* * *
39510699 ATCCCATACATATTTCATATTAGCCATTCGGCTTTACCGCATATACAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATA-AT
* *
39510747 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACACATATAT
1 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATA-AT
39510795 AT
1 AT
39510797 ATTTGTCTTG
Statistics
Matches: 426, Mismatches: 40, Indels: 16
0.88 0.08 0.03
Matches are distributed among these distances:
46 167 0.39
48 259 0.61
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (47 bp):
ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATAAT
Found at i:39510460 original size:94 final size:94
Alignment explanation
Indices: 39510275--39510794 Score: 905
Period size: 94 Copynumber: 5.5 Consensus size: 94
39510265 ATATACACAC
* * * * * *
39510275 ATCTCCTACATATTTCACATTAGCCATTCGGCTTTACCAAATATACATATCTCATATATATTTCA
1 ATCTCATATATATTTCACATTAGCCATTTGGCTTTACCACATAT--ATATCCCATACATATTTCA
*
39510340 CATTAGCCATTCGGCTTTACCACATATATAT
64 TATTAGCCATTCGGCTTTACCACATATATAT
39510371 ATCTCATATATATTTCACATTAGCCATTTGGCTTTACCACATATATATCCCATACATATTTCATA
1 ATCTCATATATATTTCACATTAGCCATTTGGCTTTACCACATATATATCCCATACATATTTCATA
39510436 TTAGCCATTCGGCTTTACCACATATATAT
66 TTAGCCATTCGGCTTTACCACATATATAT
39510465 ATCTCATATATATTTCACATTAGCCATTTGGCTTTACCACATATATATCCCATACATATTTCATA
1 ATCTCATATATATTTCACATTAGCCATTTGGCTTTACCACATATATATCCCATACATATTTCATA
39510530 TTAGCCATTCGGCTTTACCACATATATAT
66 TTAGCCATTCGGCTTTACCACATATATAT
39510559 ATCTCATATATATTTCACATTAGCCATTTGGCTTTACCACATATATATCCCATACATATTTCATA
1 ATCTCATATATATTTCACATTAGCCATTTGGCTTTACCACATATATATCCCATACATATTTCATA
39510624 TTAGCCATTCGGCTTTACCACATATATAT
66 TTAGCCATTCGGCTTTACCACATATATAT
39510653 ATCTCATATATATTTCACATTAGCCATTTGGCTTTACCACATATATATCCCATACATATTTCATA
1 ATCTCATATATATTTCACATTAGCCATTTGGCTTTACCACATATATATCCCATACATATTTCATA
* *
39510718 TTAGCCATTCGGCTTTACCGCATATACAT
66 TTAGCCATTCGGCTTTACCACATATATAT
* * * *
39510747 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACACATATAT
1 ATCTCATATATATTTCACATTAGCCATTTGGCTTTACCACATATATAT
39510795 ATATTTGTCT
Statistics
Matches: 411, Mismatches: 13, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
94 371 0.90
96 40 0.10
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (94 bp):
ATCTCATATATATTTCACATTAGCCATTTGGCTTTACCACATATATATCCCATACATATTTCATA
TTAGCCATTCGGCTTTACCACATATATAT
Found at i:39516579 original size:3 final size:3
Alignment explanation
Indices: 39516573--39516626 Score: 74
Period size: 3 Copynumber: 18.0 Consensus size: 3
39516563 TTTTTCTTAC
*
39516573 TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT T-T TAT CTAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
*
39516618 TAT CAT TAT
1 TAT TAT TAT
39516627 CATTTACATT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 2 0.04
3 40 0.89
4 3 0.07
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:39524686 original size:89 final size:89
Alignment explanation
Indices: 39524505--39524695 Score: 204
Period size: 89 Copynumber: 2.1 Consensus size: 89
39524495 ATTATGATAG
* * * * * *
39524505 ATCTTATCTTCCTGAAGTTGCAGTGAAGCAGATTAAAGTCACCAACCTTGTCTCCTTGAAGTTGC
1 ATCTTATCTCCCTGAAGTAGCAGTAAAGCAGATTAAAGTCACAAACCTTATCTCCTTAAAGTTGC
*
39524570 AGCGGAGCAGACTGAAGACAGCAA
66 AGCGGAGCAGACTAAAGACAGCAA
* * *** *
39524594 ATCTCATCTCCCTGAAGTAGCAGTAAAGCAGATTGAAGTTGTAAATCTTATCTCCTTAAAGTTGC
1 ATCTTATCTCCCTGAAGTAGCAGTAAAGCAGATTAAAGTCACAAACCTTATCTCCTTAAAGTTGC
* * * *
39524659 AGTGGAGCTGA-TCAAAGATAGCGA
66 AGCGGAGCAGACT-AAAGACAGCAA
*
39524683 ATCTTATTTCCCT
1 ATCTTATCTCCCT
39524696 AACGTTGCAG
Statistics
Matches: 82, Mismatches: 19, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
88 1 0.01
89 81 0.99
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.28
Consensus pattern (89 bp):
ATCTTATCTCCCTGAAGTAGCAGTAAAGCAGATTAAAGTCACAAACCTTATCTCCTTAAAGTTGC
AGCGGAGCAGACTAAAGACAGCAA
Found at i:39524803 original size:44 final size:43
Alignment explanation
Indices: 39524739--39524855 Score: 155
Period size: 44 Copynumber: 2.7 Consensus size: 43
39524729 TATGGCAAAT
* *
39524739 CTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCATCA-GC
1 CTTATCTCCCTGAAG-TGCAGTGGAGCAGATTAAAGCCA-CAGGC
* *
39524783 CTTATCTCCCTAAAGATGCAGTGGAGCAAATTAAAGCCACAGGC
1 CTTATCTCCCTGAAG-TGCAGTGGAGCAGATTAAAGCCACAGGC
39524827 CTTATCTCCCTGAAGTGGCAGTGGAGCAG
1 CTTATCTCCCTGAAGT-GCAGTGGAGCAG
39524856 TAGAGCAGAT
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
43 3 0.05
44 61 0.95
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (43 bp):
CTTATCTCCCTGAAGTGCAGTGGAGCAGATTAAAGCCACAGGC
Found at i:39526329 original size:3 final size:3
Alignment explanation
Indices: 39526323--39526363 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
39526313 TGTTGTTTCT
39526323 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
39526364 ATTATTATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:39526368 original size:3 final size:3
Alignment explanation
Indices: 39526362--39526430 Score: 104
Period size: 3 Copynumber: 22.7 Consensus size: 3
39526352 CTTCTTCTTC
39526362 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TCTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
*
39526410 TTA TCA TTA TTA TTA TCTA TT
1 TTA TTA TTA TTA TTA T-TA TT
39526431 CATGCATTTT
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
2 2 0.03
3 53 0.87
4 6 0.10
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:39527733 original size:34 final size:34
Alignment explanation
Indices: 39527694--39527764 Score: 115
Period size: 34 Copynumber: 2.1 Consensus size: 34
39527684 TGCAATTTAG
39527694 TTCTTCCCTAATTAAACACACAATCAGTAAAATT
1 TTCTTCCCTAATTAAACACACAATCAGTAAAATT
* **
39527728 TTCTTCCCTAATTGAACACACAATTGGTAAAATT
1 TTCTTCCCTAATTAAACACACAATCAGTAAAATT
39527762 TTC
1 TTC
39527765 GTAACAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.35
Consensus pattern (34 bp):
TTCTTCCCTAATTAAACACACAATCAGTAAAATT
Found at i:39529683 original size:36 final size:36
Alignment explanation
Indices: 39529642--39529710 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
39529632 TACTACAGTG
*
39529642 TTGATCATAGGCTATTGGGGCTCCTATTTTTTTGTA
1 TTGATCATAGGCTATTGGAGCTCCTATTTTTTTGTA
*
39529678 TTGATCATAGGCTATTGGAGCTCCTTTTTTTTT
1 TTGATCATAGGCTATTGGAGCTCCTATTTTTTT
39529711 TTTTTTGTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.16, C:0.14, G:0.20, T:0.49
Consensus pattern (36 bp):
TTGATCATAGGCTATTGGAGCTCCTATTTTTTTGTA
Found at i:39540788 original size:75 final size:75
Alignment explanation
Indices: 39540588--39540897 Score: 414
Period size: 73 Copynumber: 4.2 Consensus size: 75
39540578 TGATGTTTTT
* *
39540588 ATTTCTG-TTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACACTGA
1 ATTTCTGCTTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCGGA
39540652 GGTAATTTCA
66 GGTAATTTCA
* * * ** *
39540662 ATTTATGCTTTT--TAAACATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGGCACGCGGA
1 ATTTCTGCTTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCGGA
*
39540725 GGTATTTTCA
66 GGTAATTTCA
* * *
39540735 ATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTTAGTTGAGCCTCAGGACACGCTGA
1 ATTTCTGCTTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCGGA
39540800 GGTAATTTCA
66 GGTAATTTCA
* * *
39540810 ATTTATGCTTTTC--AAAAATCAACTCATATTGTAAGAGATGAGTTGAGCCTCAGGACACGCGGA
1 ATTTCTGCTTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCGGA
*
39540873 GGTATTTTCA
66 GGTAATTTCA
* **
39540883 AATTCTATTTTTCAA
1 ATTTCTGCTTTTCAA
39540898 TTTATGTTTT
Statistics
Matches: 203, Mismatches: 28, Indels: 9
0.85 0.12 0.04
Matches are distributed among these distances:
73 127 0.63
74 6 0.03
75 70 0.34
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (75 bp):
ATTTCTGCTTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCGGA
GGTAATTTCA
Found at i:39540863 original size:148 final size:147
Alignment explanation
Indices: 39540588--39540893 Score: 513
Period size: 148 Copynumber: 2.1 Consensus size: 147
39540578 TGATGTTTTT
39540588 ATTTCTGTTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACACTGAG
1 ATTTCTGTTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACACTGAG
* * * * *
39540653 GTAATTTCAATTTATGCTTTTTAAACATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGGC
66 GTAATTTCAATTTATGCTTTTCAAAAATCAACTCATATTGTAAGAGATGAGTTGAGCCTCAGGAC
39540718 ACGCGGAGGTATTTTCA
131 ACGCGGAGGTATTTTCA
* * *
39540735 ATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTTAGTTGAGCCTCAGGACACGCTGA
1 ATTTCTG-TTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACACTGA
39540800 GGTAATTTCAATTTATGCTTTTCAAAAATCAACTCATATTGTAAGAGATGAGTTGAGCCTCAGGA
65 GGTAATTTCAATTTATGCTTTTCAAAAATCAACTCATATTGTAAGAGATGAGTTGAGCCTCAGGA
39540865 CACGCGGAGGTATTTTCA
130 CACGCGGAGGTATTTTCA
* *
39540883 AATTCTATTTT
1 ATTTCTGTTTT
39540894 TCAATTTATG
Statistics
Matches: 148, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
147 11 0.07
148 137 0.93
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Consensus pattern (147 bp):
ATTTCTGTTTTCAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACACTGAG
GTAATTTCAATTTATGCTTTTCAAAAATCAACTCATATTGTAAGAGATGAGTTGAGCCTCAGGAC
ACGCGGAGGTATTTTCA
Found at i:39540987 original size:14 final size:15
Alignment explanation
Indices: 39540968--39541003 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
39540958 TTTTGAGCTA
39540968 TTTTCAAATTT-TGT
1 TTTTCAAATTTATGT
39540982 TTTTC-AATTTATGT
1 TTTTCAAATTTATGT
39540996 TTTTCAAA
1 TTTTCAAA
39541004 AAAATCAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.25
14 13 0.65
15 2 0.10
ACGTcount: A:0.25, C:0.08, G:0.06, T:0.61
Consensus pattern (15 bp):
TTTTCAAATTTATGT
Found at i:39541064 original size:91 final size:91
Alignment explanation
Indices: 39540805--39541165 Score: 337
Period size: 91 Copynumber: 4.0 Consensus size: 91
39540795 GCTGAGGTAA
* *
39540805 TTTCAATTTATGCTTTTC--AAAAATCAACTCATATTGTAAGAGATGAGTTGAGCCTCAGG--AC
1 TTTCAATTTATGTTTTTCAAAAAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAGGTCAC
* * *
39540866 ACGCGGAGGTATTTTCAAATTCTATT
66 ATGCGGAGCTATTTTCAAATTCTGTT
* * * * * *
39540892 TTTCAATTTATGTTTTTCAAAAAAATCAATTCATATTGCGAGAGGTGAGTTGAGTCT-TGG-CTC
1 TTTCAATTTATGTTTTTCAAAAAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAGGTCAC
** *
39540955 ATGTTTTGAGCTATTTTCAAATTTTGTT
66 ATG--CGGAGCTATTTTCAAATTCTGTT
* * *
39540983 TTTCAATTTATGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
1 TTTCAATTTATGTTTTTCAAAAAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAGGTCAC
* * * * *
39541048 ATGTC-GAGGTACTTTCAAAATCGGCT
66 ATG-CGGAGCTATTTTCAAATTCTGTT
* * * * * *
39541074 TTTCAAATTAAG-TTTT-AAAAAAACCAATTCATATTGCAAGAAATGAGTTGAG-CTCAAGATCA
1 TTTCAATTTATGTTTTTCAAAAAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTC-AGGTCA
* * *
39541136 CATGCTGAGCTATTTTCAATTTTTGTT
65 CATGCGGAGCTATTTTCAAATTCTGTT
39541163 TTT
1 TTT
39541166 AATGTCTGTT
Statistics
Matches: 224, Mismatches: 41, Indels: 16
0.80 0.15 0.06
Matches are distributed among these distances:
87 17 0.08
88 6 0.03
89 91 0.41
90 4 0.02
91 98 0.44
92 3 0.01
93 5 0.02
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.38
Consensus pattern (91 bp):
TTTCAATTTATGTTTTTCAAAAAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAGGTCAC
ATGCGGAGCTATTTTCAAATTCTGTT
Found at i:39541137 original size:89 final size:87
Alignment explanation
Indices: 39540805--39541226 Score: 234
Period size: 91 Copynumber: 4.8 Consensus size: 87
39540795 GCTGAGGTAA
* * * ** * *
39540805 TTTCAATTTATGCTTTT-CAAAAATCAACTCATATTGTAAGAGATGAGTTGAGCCTCAGGA-CAC
1 TTTCAAATTATG-TTTTAAAAAAATCAATTCATATTGCGAGAAATGAGTTGAG-CTCAAGATCAC
* * * **
39540868 --GCGGAGGTATTTTCAAATTCTATT
64 ATGC-GAGCTACTTTCAAAATC-GGT
* ** ** * *
39540892 TTTCAATTTATGTTTTTCAAAAAAATCAATTCATATTGCGAGAGGTGAGTTGAG-TCTTG-GCTC
1 TTTCAAATTATG-TTTT-AAAAAAATCAATTCATATTGCGAGAAATGAGTTGAGCTCAAGATCAC
* * * * *
39540955 ATGTTTTGAGCTATTTTCAAATTTTGTT
64 ATG---CGAGCTACTTTCAAA-ATCGGT
* * ** * *
39540983 TTTCAATTTATGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGTCA
1 TTTCAAATTATG-TTTT-AAAAAAATCAATTCATATTGCGAGAAATGAGTTGAG-CTCAAGATCA
*
39541047 CATGTCGAGGTACTTTCAAAATCGGCT
63 CATG-CGAGCTACTTTCAAAATCGG-T
* * *
39541074 TTTCAAATTAAGTTTTAAAAAAACCAATTCATATTGCAAGAAATGAGTTGAGCTCAAGATCACAT
1 TTTCAAATTATGTTTTAAAAAAATCAATTCATATTGCGAGAAATGAGTTGAGCTCAAGATCACAT
* ** **
39541139 GCTGAGCTATTTTCAATTTTTGT
66 GC-GAGCTACTTTCAAAATCGGT
* * * *
39541162 TTT-TAATGTCTG-TTT-AAAGAGTCAATTCATATTGCGAGAAATGAGTTGAGCTCAAGATCACA
1 TTTCAAAT-TATGTTTTAAAAAAATCAATTCATATTGCGAGAAATGAGTTGAGCTCAAGATCACA
39541224 TGC
65 TGC
39541227 CGAGTAAAGA
Statistics
Matches: 274, Mismatches: 45, Indels: 33
0.78 0.13 0.09
Matches are distributed among these distances:
86 46 0.17
87 27 0.10
88 10 0.04
89 83 0.30
90 6 0.02
91 92 0.34
92 3 0.01
93 7 0.03
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (87 bp):
TTTCAAATTATGTTTTAAAAAAATCAATTCATATTGCGAGAAATGAGTTGAGCTCAAGATCACAT
GCGAGCTACTTTCAAAATCGGT
Found at i:39541147 original size:180 final size:177
Alignment explanation
Indices: 39540805--39541212 Score: 418
Period size: 180 Copynumber: 2.3 Consensus size: 177
39540795 GCTGAGGTAA
*
39540805 TTTCAATTTATGCTTTTCAAAAATCAACTCATATTGTAAGAGATGAGTTGAGCCTCAGGACACGC
1 TTTCAATTTATGCTTTTCAAAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAGGACACGC
* * * * * * * *
39540870 GGAGGTATTTTCAAATTCTATTTTTCAATTTATGTTTTTCAAAAAAATCAATTCATATTGCGAGA
66 GGAGGTACTTTCAAAATCGACTTTTCAAATTAAGTTTTTCAAAAAAACCAATTCATATTGCAAGA
** ** * *
39540935 GGTGAGTTGAGTCTTGGCTCATGTTTTGAGCTATTTTCAAATTTTGTT
131 AATGAGTTGAGTCAAGGCACATG-TCTGAGCTATTTTCAAATTTTGTT
* * * *
39540983 TTTCAATTTATGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
1 TTTCAATTTATGCTTTTC--AAAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAGG--AC
* *
39541048 ATGTC-GAGGTACTTTCAAAATCGGCTTTTCAAATTAAG-TTTT-AAAAAAACCAATTCATATTG
62 ACG-CGGAGGTACTTTCAAAATCGACTTTTCAAATTAAGTTTTTCAAAAAAACCAATTCATATTG
* *
39541110 CAAGAAATGAGTTGAGCTCAAGATCACATG-CTGAGCTATTTTCAATTTTTGTT
126 CAAGAAATGAGTTGAG-TCAAG-GCACATGTCTGAGCTATTTTCAAATTTTGTT
* * * * * *
39541163 TTT-AATGTCTG--TTT-AAAGAGTCAATTCATATTGCGAGAAATGAGTTGAGC
1 TTTCAATTTATGCTTTTCAAA-AATCAACTCATATTGCAAGAGATGAGTTGAGC
39541213 TCAAGATCAC
Statistics
Matches: 193, Mismatches: 29, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
174 3 0.02
175 28 0.15
177 3 0.02
178 17 0.09
179 6 0.03
180 93 0.48
181 7 0.04
182 35 0.18
183 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.38
Consensus pattern (177 bp):
TTTCAATTTATGCTTTTCAAAAATCAACTCATATTGCAAGAGATGAGTTGAGCCTCAGGACACGC
GGAGGTACTTTCAAAATCGACTTTTCAAATTAAGTTTTTCAAAAAAACCAATTCATATTGCAAGA
AATGAGTTGAGTCAAGGCACATGTCTGAGCTATTTTCAAATTTTGTT
Found at i:39542969 original size:3 final size:3
Alignment explanation
Indices: 39542961--39543000 Score: 71
Period size: 3 Copynumber: 13.0 Consensus size: 3
39542951 ATTTATTTAT
39542961 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TGTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
39543001 GAGTATACTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:39543134 original size:3 final size:3
Alignment explanation
Indices: 39543088--39543118 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
39543078 GTATCCCAAC
*
39543088 ATT ATT ATT ATT ATT ACT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
39543119 GTATATGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:39545393 original size:15 final size:15
Alignment explanation
Indices: 39545370--39545404 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
39545360 GTATTCTAAA
*
39545370 ATTAATTTATATATT
1 ATTAATTTACATATT
*
39545385 ATTATTTTACATATT
1 ATTAATTTACATATT
39545400 ATTAA
1 ATTAA
39545405 CTTTTGATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTAATTTACATATT
Found at i:39545738 original size:13 final size:13
Alignment explanation
Indices: 39545720--39545744 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39545710 TTTTTATCAT
39545720 TGTTATTTCATGA
1 TGTTATTTCATGA
39545733 TGTTATTTCATG
1 TGTTATTTCATG
39545745 CTCAATACTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.08, G:0.16, T:0.56
Consensus pattern (13 bp):
TGTTATTTCATGA
Found at i:39551000 original size:31 final size:31
Alignment explanation
Indices: 39550927--39551002 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 31
39550917 GAGACCTTAA
* *
39550927 AAAAATAAATAAAATATAAAAATAAAAAAAG
1 AAAAATAAAAAAAATATAAAAATAAAAAAAC
** *
39550958 AAAGAATAAAAAATAATATAAAAA-AATCAATC
1 AAA-AATAAAAAA-AATATAAAAATAAAAAAAC
39550990 AAAAATAAAAAAA
1 AAAAATAAAAAAA
39551003 TTATCAATCA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
30 1 0.03
31 12 0.32
32 15 0.39
33 10 0.26
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.16
Consensus pattern (31 bp):
AAAAATAAAAAAAATATAAAAATAAAAAAAC
Found at i:39551008 original size:22 final size:23
Alignment explanation
Indices: 39550983--39551025 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
39550973 ATATAAAAAA
*
39550983 ATCAATCAAAAATA-AAAAAATT
1 ATCAATCAAAAAAAGAAAAAATT
39551005 ATCAATCAAAAAAAGAAAAAA
1 ATCAATCAAAAAAAGAAAAAA
39551026 AAAGAAGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.72, C:0.09, G:0.02, T:0.16
Consensus pattern (23 bp):
ATCAATCAAAAAAAGAAAAAATT
Found at i:39552601 original size:44 final size:45
Alignment explanation
Indices: 39552521--39552622 Score: 125
Period size: 44 Copynumber: 2.3 Consensus size: 45
39552511 AGCAACCAGC
* * * * **
39552521 CTTATCTTCCTGAGGTAGCAAGGGATCAGGTCGAAGATTGTAG-T
1 CTTATCTTCCTAAGGTAGCAAGGAAACAGATCGAAGATCATAGAT
*
39552565 CTTATCTTCCTAAGGTAGCAAGGAAACAGATTGAAGATCATAGAT
1 CTTATCTTCCTAAGGTAGCAAGGAAACAGATCGAAGATCATAGAT
*
39552610 CTTATCTCCCTAA
1 CTTATCTTCCTAA
39552623 ACAATAGTGG
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 36 0.73
45 13 0.27
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (45 bp):
CTTATCTTCCTAAGGTAGCAAGGAAACAGATCGAAGATCATAGAT
Found at i:39552602 original size:177 final size:177
Alignment explanation
Indices: 39552280--39553236 Score: 1165
Period size: 177 Copynumber: 5.4 Consensus size: 177
39552270 GGTAGCAATA
* * * *
39552280 GAGCAGATCGAAGATGGCGAATCTTATCTTCCTGAAGTAGTA-GGGAACAGATTTTAGCCACCAG
1 GAGCAGATCGAAGATGGTGAATCTTATCTTCCCGAGGTAGCAGGGGAACAGATTTTAGCCACCAG
* * * *
39552344 CCTTATCTTTCTGATGTAGCAAG-GAGT-AGGTCGAAGATTGTAGTCTTATCTTCCTGAGGTAGC
66 CCTTATCTCTCTGAGGTAGCAAGAGA-TCAGGTTGAAGTTTGTAGTCTTATCTTCCTGAGGTAGC
** * * *
39552407 AAGGAAGCAGACTGAAGATCATAAATCTTATCTCCCTAAACAGTAGTA
130 AAGGAAGCAGACTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTG
* * * *
39552455 GAGTAGATCGAATATGATGAATCTTATCTTCCCGAGGTAGCAGGGGAACAGATTTTAGCAACCAG
1 GAGCAGATCGAAGATGGTGAATCTTATCTTCCCGAGGTAGCAGGGGAACAGATTTTAGCCACCAG
* * * *
39552520 CCTTATCT-TCCTGAGGTAGCAAGGGATCAGGTCGAAGATTGTAGTCTTATCTTCCTAAGGTAGC
66 CCTTATCTCT-CTGAGGTAGCAAGAGATCAGGTTGAAGTTTGTAGTCTTATCTTCCTGAGGTAGC
* * ** * *
39552584 AAGGAAACAGATTGAAGATCATAGATCTTATCTCCCTAAACAATAGTG
130 AAGGAAGCAGACTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTG
* ** *
39552632 GAGCAGGTCGAAGATGGCAAATCTTATCTTCCCGAGGTAGCAGGGGAGCAGATTTTAGCCACCAG
1 GAGCAGATCGAAGATGGTGAATCTTATCTTCCCGAGGTAGCAGGGGAACAGATTTTAGCCACCAG
* * * *
39552697 CCTTATCTCTCTAAGGTAGCAAGAGAGT-AGGTTGAAGTTTGTAGTCTTATTTTCCTGAGGAAGT
66 CCTTATCTCTCTGAGGTAGCAAGAGA-TCAGGTTGAAGTTTGTAGTCTTATCTTCCTGAGGTAGC
* * * * *
39552761 AAAGAAGCAAACTAAATATTGTAGACCTTATCTCCCTAAGCAGTAGTG
130 AAGGAAGCAGACTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTG
** * * * * *
39552809 GAGTGGA-CTGAAGATGATGAATCTTATCTTCCTGAGGTAGGATGGGAGCAGATTTTAGCCACCA
1 GAGCAGATC-GAAGATGGTGAATCTTATCTTCCCGAGGTAGCAGGGGAACAGATTTTAGCCACCA
* * * * * *
39552873 GCCTTATCCCTCTGAGGTAGCATGAGAGCAGGTTGAAGTTTGAAGTCTTATCTTCTTGAGATAGC
65 GCCTTATCTCTCTGAGGTAGCAAGAGATCAGGTTGAAGTTTGTAGTCTTATCTTCCTGAGGTAGC
* * * *
39552938 AAGGAAGCAGACTAAAGATTGTAGATATTATCTCCTTAAGTAGTAGTG
130 AAGGAAGCAGACTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTG
* * * *
39552986 GAGTAGATCGAAGATGGTGAATCTTATCTTCTCGAGGTAGCAGGGGAGCAGATTTTAGCCACTAG
1 GAGCAGATCGAAGATGGTGAATCTTATCTTCCCGAGGTAGCAGGGGAACAGATTTTAGCCACCAG
* *
39553051 TCC-TATCTCTCTGAGGTAGTAAGAGAGCAGGTTGAAGTTTGTAGTCTTATCTTCCTGAGGTAGC
66 -CCTTATCTCTCTGAGGTAGCAAGAGATCAGGTTGAAGTTTGTAGTCTTATCTTCCTGAGGTAGC
* * *
39553115 AAGGAAGCAAATTGAAGATTGTAGATTTTATCTCCCTAAGCAGTAGTG
130 AAGGAAGCAGACTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTG
* * * * *
39553163 GAGCAGATCGAAGAT-GTCGAATCTTATCTTTCCGGGGTAGCACGAGAACAGATTTTAGCCACTA
1 GAGCAGATCGAAGATGGT-GAATCTTATCTTCCCGAGGTAGCAGGGGAACAGATTTTAGCCACCA
39553227 GCCTTATCTC
65 GCCTTATCTC
39553237 CCTAAAGTTG
Statistics
Matches: 676, Mismatches: 94, Indels: 22
0.85 0.12 0.03
Matches are distributed among these distances:
175 36 0.05
176 47 0.07
177 588 0.87
178 5 0.01
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (177 bp):
GAGCAGATCGAAGATGGTGAATCTTATCTTCCCGAGGTAGCAGGGGAACAGATTTTAGCCACCAG
CCTTATCTCTCTGAGGTAGCAAGAGATCAGGTTGAAGTTTGTAGTCTTATCTTCCTGAGGTAGCA
AGGAAGCAGACTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTG
Found at i:39553130 original size:44 final size:45
Alignment explanation
Indices: 39552882--39553147 Score: 109
Period size: 44 Copynumber: 6.0 Consensus size: 45
39552872 AGCCTTATCC
* ** * *
39552882 CTCTGAGGTAGCATGAGAGCAGGTTGAAGTTTGAAGTCTTATCTT
1 CTCTGAGGTAGCAAGAGAGCAAATTGAAGATTGTAGTCTTATCTT
* * * * *
39552927 CT-TGAGATAGCAAG-GAAGCAGACTAAAGATTGTAGATATTATC-T
1 CTCTGAGGTAGCAAGAG-AGCAAATTGAAGATTGTAG-TCTTATCTT
* * * * * * * * *
39552971 C-CTTAAGTAG-TAGTGGAGTAGATCGAAGATGGTGAATCTTATCTT
1 CTCTGAGGTAGCAAG-AGAGCAAATTGAAGATTGT-AGTCTTATCTT
* * * ** **** *
39553016 CTC-GAGGTAGCAGGGGAGCAGATTTTAGCCACTAGTCCTATC-T
1 CTCTGAGGTAGCAAGAGAGCAAATTGAAGATTGTAGTCTTATCTT
* ** *
39553059 CTCTGAGGTAGTAAGAGAGCAGGTTGAAGTTTGTAGTCTTATCTT
1 CTCTGAGGTAGCAAGAGAGCAAATTGAAGATTGTAGTCTTATCTT
*
39553104 C-CTGAGGTAGCAAG-GAAGCAAATTGAAGATTGTAGATTTTATCT
1 CTCTGAGGTAGCAAGAG-AGCAAATTGAAGATTGTAG-TCTTATCT
39553148 CCCTAAGCAG
Statistics
Matches: 159, Mismatches: 49, Indels: 26
0.68 0.21 0.11
Matches are distributed among these distances:
43 8 0.05
44 112 0.70
45 37 0.23
46 2 0.01
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.31
Consensus pattern (45 bp):
CTCTGAGGTAGCAAGAGAGCAAATTGAAGATTGTAGTCTTATCTT
Found at i:39555764 original size:15 final size:15
Alignment explanation
Indices: 39555741--39555775 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
39555731 GTATTCTAAA
*
39555741 ATTAATTTATATATT
1 ATTAATTTACATATT
*
39555756 ATTATTTTACATATT
1 ATTAATTTACATATT
39555771 ATTAA
1 ATTAA
39555776 CTTTTGATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTAATTTACATATT
Found at i:39556108 original size:13 final size:13
Alignment explanation
Indices: 39556090--39556114 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39556080 TTTTTATCAT
39556090 TGTTATTTCATGA
1 TGTTATTTCATGA
39556103 TGTTATTTCATG
1 TGTTATTTCATG
39556115 CTCAATACTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.08, G:0.16, T:0.56
Consensus pattern (13 bp):
TGTTATTTCATGA
Found at i:39564209 original size:6 final size:6
Alignment explanation
Indices: 39564194--39564236 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
39564184 ACAATCATGG
*
39564194 ATATAT ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA A
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA A
39564237 ACAGTAAGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
ATATAA
Found at i:39566093 original size:13 final size:13
Alignment explanation
Indices: 39566075--39566104 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
39566065 TAATTTGATC
39566075 TATACACTTATTT
1 TATACACTTATTT
39566088 TATACACTTATTT
1 TATACACTTATTT
39566101 TATA
1 TATA
39566105 ACCCCTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.53
Consensus pattern (13 bp):
TATACACTTATTT
Found at i:39566832 original size:3 final size:3
Alignment explanation
Indices: 39566824--39566856 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
39566814 ATAAATCAAG
39566824 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
39566857 TTACTTGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:39567012 original size:31 final size:30
Alignment explanation
Indices: 39566954--39567012 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
39566944 TTGTTCTTAT
**
39566954 TATTATTATTACTATTATTATTCATTGTCA
1 TATTATTATTACTATTATTATAAATTGTCA
39566984 TATTATTTATGTACT-TTATTATAAATTGT
1 TATTA-TTAT-TACTATTATTATAAATTGT
39567013 ACTCCTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 5 0.20
31 16 0.64
32 4 0.16
ACGTcount: A:0.31, C:0.07, G:0.05, T:0.58
Consensus pattern (30 bp):
TATTATTATTACTATTATTATAAATTGTCA
Found at i:39567097 original size:13 final size:13
Alignment explanation
Indices: 39567081--39567105 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39567071 TTTTCTTTAA
39567081 TATTTATTTATTG
1 TATTTATTTATTG
39567094 TATTTATTTATT
1 TATTTATTTATT
39567106 TATCCCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (13 bp):
TATTTATTTATTG
Found at i:39573206 original size:53 final size:54
Alignment explanation
Indices: 39573033--39573239 Score: 229
Period size: 53 Copynumber: 3.8 Consensus size: 54
39573023 ATTAGGGTTT
* * * *
39573033 AAGGATACCAAGTAAGACCATGCCAAGGCATGACATTGGTAAGTTCTACAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGACAATGGTAAGTTCTATAAGGC
* * * * * * * *
39573087 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAACTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGACAATGGT-AAGTTCTATAAGGC
* * * *
39573142 AAAGATCCCATGTAAGACCATGCCAAGGCATGACAATGGTGAGTTC-ATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGACAATGGTAAGTTCTATAAGGC
*
39573195 AAGGATACCATGTAAGACCATGTCAAGACATGGA-AATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACAT-GACAATGGTAAGTT
39573240 TAAAAAGGAA
Statistics
Matches: 124, Mismatches: 27, Indels: 5
0.79 0.17 0.03
Matches are distributed among these distances:
53 44 0.35
54 38 0.31
55 42 0.34
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGACAATGGTAAGTTCTATAAGGC
Found at i:39574631 original size:33 final size:35
Alignment explanation
Indices: 39574583--39574657 Score: 100
Period size: 33 Copynumber: 2.2 Consensus size: 35
39574573 AAAACTAAAT
* * *
39574583 GACTGATACTGATACTGAGATGGGCTAAGG-CCAA
1 GACTGTTACTGATACTGAAAAGGGCTAAGGCCCAA
*
39574617 -ACTGTTACTGATACTGAAAAGGGCTTAGGCCCAA
1 GACTGTTACTGATACTGAAAAGGGCTAAGGCCCAA
39574651 GACTGTT
1 GACTGTT
39574658 TGACTGTGCA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
33 25 0.71
34 4 0.11
35 6 0.17
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.24
Consensus pattern (35 bp):
GACTGTTACTGATACTGAAAAGGGCTAAGGCCCAA
Found at i:39575883 original size:40 final size:40
Alignment explanation
Indices: 39575800--39576064 Score: 281
Period size: 40 Copynumber: 6.7 Consensus size: 40
39575790 TGAGCCTACA
* * * * *
39575800 GGTCTTT-AACCCGGATTCCATTCCAGCACGA-AGCCTGCA
1 GGTCTTTAAACCTGGATACAATTCCAGCA-TATAGCCTGCG
*
39575839 GGTCTTTAAACCTGGATACAATTCTAGCATATAGCCTGCG
1 GGTCTTTAAACCTGGATACAATTCCAGCATATAGCCTGCG
* * * *
39575879 GGTCTTTAAA-CTCGGATTCCATTCCAGAACGA-AGCCTGCG
1 GGTCTTTAAACCT-GGATACAATTCCAGCA-TATAGCCTGCG
*
39575919 GGTCTTTAAACTTGGATACAATTCCAGCATATAGCCTGCG
1 GGTCTTTAAACCTGGATACAATTCCAGCATATAGCCTGCG
* * *
39575959 GGTCTTTAAA-CTCGGATACCATTCTAGCACGA-AGCCTGCG
1 GGTCTTTAAACCT-GGATACAATTCCAGCA-TATAGCCTGCG
* *
39575999 GGTCTTTAAACCCGGATACAATTCCAGCATATAGCTTGCG
1 GGTCTTTAAACCTGGATACAATTCCAGCATATAGCCTGCG
* *
39576039 GGTCTTTAAACCCGGATACCATTCCA
1 GGTCTTTAAACCTGGATACAATTCCA
39576065 ATACTCATAT
Statistics
Matches: 190, Mismatches: 26, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
39 13 0.07
40 173 0.91
41 4 0.02
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (40 bp):
GGTCTTTAAACCTGGATACAATTCCAGCATATAGCCTGCG
Found at i:39575911 original size:80 final size:80
Alignment explanation
Indices: 39575800--39576064 Score: 424
Period size: 80 Copynumber: 3.3 Consensus size: 80
39575790 TGAGCCTACA
* * *
39575800 GGTCTTT-AACCCGGATTCCATTCCAGCACGAAGCCTGCAGGTCTTTAAACCTGGATACAATTCT
1 GGTCTTTAAACCCGGATACCATTCCAGCACGAAGCCTGCGGGTCTTTAAACCTGGATACAATTCC
39575864 AGCATATAGCCTGCG
66 AGCATATAGCCTGCG
* * * *
39575879 GGTCTTTAAACTCGGATTCCATTCCAGAACGAAGCCTGCGGGTCTTTAAACTTGGATACAATTCC
1 GGTCTTTAAACCCGGATACCATTCCAGCACGAAGCCTGCGGGTCTTTAAACCTGGATACAATTCC
39575944 AGCATATAGCCTGCG
66 AGCATATAGCCTGCG
* * *
39575959 GGTCTTTAAACTCGGATACCATTCTAGCACGAAGCCTGCGGGTCTTTAAACCCGGATACAATTCC
1 GGTCTTTAAACCCGGATACCATTCCAGCACGAAGCCTGCGGGTCTTTAAACCTGGATACAATTCC
*
39576024 AGCATATAGCTTGCG
66 AGCATATAGCCTGCG
39576039 GGTCTTTAAACCCGGATACCATTCCA
1 GGTCTTTAAACCCGGATACCATTCCA
39576065 ATACTCATAT
Statistics
Matches: 172, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
79 7 0.04
80 165 0.96
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (80 bp):
GGTCTTTAAACCCGGATACCATTCCAGCACGAAGCCTGCGGGTCTTTAAACCTGGATACAATTCC
AGCATATAGCCTGCG
Found at i:39575976 original size:120 final size:120
Alignment explanation
Indices: 39575800--39576064 Score: 324
Period size: 120 Copynumber: 2.2 Consensus size: 120
39575790 TGAGCCTACA
* * *
39575800 GGTCTTT-AACCCGGATTCCATTCCAGCACGA-AGCCTGCAGGTCTTTAAACCTGGATACAATTC
1 GGTCTTTAAACCCGGATACAATTCCAGCA-TATAGCCTGCAGGTCTTTAAACCTGGATACAATTC
* * * *
39575863 TAGCA-TATAGCCTGCGGGTCTTTAAACTCGGATTCCATTCCAGAACGA-AGCCTGCG
65 TAGCACGA-AGCCTGCGGGTCTTTAAACCCGGATACAATTCCAGAA-GATAGCCTGCG
** * *
39575919 GGTCTTTAAACTTGGATACAATTCCAGCATATAGCCTGCGGGTCTTTAAA-CTCGGATACCATTC
1 GGTCTTTAAACCCGGATACAATTCCAGCATATAGCCTGCAGGTCTTTAAACCT-GGATACAATTC
* * *
39575983 TAGCACGAAGCCTGCGGGTCTTTAAACCCGGATACAATTCCAGCATATAGCTTGCG
65 TAGCACGAAGCCTGCGGGTCTTTAAACCCGGATACAATTCCAGAAGATAGCCTGCG
*
39576039 GGTCTTTAAACCCGGATACCATTCCA
1 GGTCTTTAAACCCGGATACAATTCCA
39576065 ATACTCATAT
Statistics
Matches: 124, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
119 11 0.09
120 112 0.90
121 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (120 bp):
GGTCTTTAAACCCGGATACAATTCCAGCATATAGCCTGCAGGTCTTTAAACCTGGATACAATTCT
AGCACGAAGCCTGCGGGTCTTTAAACCCGGATACAATTCCAGAAGATAGCCTGCG
Found at i:39578749 original size:20 final size:20
Alignment explanation
Indices: 39578724--39578766 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
39578714 TTTTTCTCAT
39578724 GCGGCTTCAATTGCCTCGAC
1 GCGGCTTCAATTGCCTCGAC
39578744 GCGGCTTCAATTGCCTCGAC
1 GCGGCTTCAATTGCCTCGAC
39578764 GCG
1 GCG
39578767 TAAGCTACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.35, G:0.28, T:0.23
Consensus pattern (20 bp):
GCGGCTTCAATTGCCTCGAC
Found at i:39582660 original size:40 final size:40
Alignment explanation
Indices: 39582573--39582849 Score: 330
Period size: 40 Copynumber: 7.0 Consensus size: 40
39582563 ACATTTCTAA
* * * *
39582573 CACG-AGCCTACGGGTCTTT-AACCTGGATTCCATTCTAG
1 CACGAAGCCTGCGGGTCTTTAAACCCGGATACCATTCCAG
* *
39582611 CACGAAGCCTGCGGGTCTTTAAACCCGGATACAATTCTAG
1 CACGAAGCCTGCGGGTCTTTAAACCCGGATACCATTCCAG
* * * *
39582651 CA-TATAGCCTGCGGGTCTTTAAACCTGGATTCCATTCCAA
1 CACGA-AGCCTGCGGGTCTTTAAACCCGGATACCATTCCAG
* * *
39582691 CACGAAGCCTGCGGGTCTTTAAACCCGAACACAATTCCAG
1 CACGAAGCCTGCGGGTCTTTAAACCCGGATACCATTCCAG
* *
39582731 CA-TATAGCCTGCGAGTCTTTAAACCCGGATACCATTCCAG
1 CACGA-AGCCTGCGGGTCTTTAAACCCGGATACCATTCCAG
* *
39582771 CACGAAGCTTGCGGGTCTTTAAACCCGGATACAATTCCAG
1 CACGAAGCCTGCGGGTCTTTAAACCCGGATACCATTCCAG
*
39582811 CA-TATAGCCTGCGGGTCTTTAAACCCGGATACCATTCCA
1 CACGA-AGCCTGCGGGTCTTTAAACCCGGATACCATTCCA
39582850 ATACTCATAT
Statistics
Matches: 203, Mismatches: 29, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
38 4 0.02
39 17 0.08
40 180 0.89
41 2 0.01
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (40 bp):
CACGAAGCCTGCGGGTCTTTAAACCCGGATACCATTCCAG
Found at i:39582709 original size:80 final size:80
Alignment explanation
Indices: 39582577--39582850 Score: 424
Period size: 80 Copynumber: 3.4 Consensus size: 80
39582567 TTCTAACACG
* * * * *
39582577 AGCCTACGGGTCTTT-AACCTGGATTCCATTCTAGCACGAAGCCTGCGGGTCTTTAAACCCGGAT
1 AGCCTGCGGGTCTTTAAACCCGGATACCATTCCAACACGAAGCCTGCGGGTCTTTAAACCCGGAT
*
39582641 ACAATTCTAGCATAT
66 ACAATTCCAGCATAT
* * * *
39582656 AGCCTGCGGGTCTTTAAACCTGGATTCCATTCCAACACGAAGCCTGCGGGTCTTTAAACCCGAAC
1 AGCCTGCGGGTCTTTAAACCCGGATACCATTCCAACACGAAGCCTGCGGGTCTTTAAACCCGGAT
39582721 ACAATTCCAGCATAT
66 ACAATTCCAGCATAT
* * *
39582736 AGCCTGCGAGTCTTTAAACCCGGATACCATTCCAGCACGAAGCTTGCGGGTCTTTAAACCCGGAT
1 AGCCTGCGGGTCTTTAAACCCGGATACCATTCCAACACGAAGCCTGCGGGTCTTTAAACCCGGAT
39582801 ACAATTCCAGCATAT
66 ACAATTCCAGCATAT
39582816 AGCCTGCGGGTCTTTAAACCCGGATACCATTCCAA
1 AGCCTGCGGGTCTTTAAACCCGGATACCATTCCAA
39582851 TACTCATATT
Statistics
Matches: 179, Mismatches: 15, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
79 14 0.08
80 165 0.92
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.25
Consensus pattern (80 bp):
AGCCTGCGGGTCTTTAAACCCGGATACCATTCCAACACGAAGCCTGCGGGTCTTTAAACCCGGAT
ACAATTCCAGCATAT
Found at i:39591615 original size:27 final size:28
Alignment explanation
Indices: 39591531--39591626 Score: 140
Period size: 28 Copynumber: 3.4 Consensus size: 28
39591521 CATGAGATTG
* * *
39591531 GCACTAAGTGTGCGGGTTTAAATTGTATA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
39591560 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
39591588 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
39591615 GCACTGAGTGTG
1 GCACTAAGTGTG
39591627 TGGACTTAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
27 22 0.35
28 23 0.37
29 18 0.29
ACGTcount: A:0.27, C:0.11, G:0.28, T:0.33
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:39591639 original size:27 final size:27
Alignment explanation
Indices: 39591556--39591641 Score: 93
Period size: 27 Copynumber: 3.1 Consensus size: 27
39591546 GTTTAAATTG
* *
39591556 TATAGCACTAAGTGTGCGAGTTTGATTA
1 TATAGCACTAAGTGTGCGA-CTTGAATA
* *
39591584 TATAGCACTAAGTGTGCGAGTTGATTA
1 TATAGCACTAAGTGTGCGACTTGAATA
* *
39591611 TATAGCACTGAGTGTGTGGACTT-AATA
1 TATAGCACTAAGTGTG-CGACTTGAATA
39591638 TATA
1 TATA
39591642 TTTTTTAATC
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
27 29 0.56
28 23 0.44
ACGTcount: A:0.30, C:0.10, G:0.24, T:0.35
Consensus pattern (27 bp):
TATAGCACTAAGTGTGCGACTTGAATA
Found at i:39591641 original size:29 final size:27
Alignment explanation
Indices: 39591531--39591642 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
39591521 CATGAGATTG
** *
39591531 GCACTAAGTGTGCGGGTTTAAATTGTATA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
39591560 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
39591588 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
* *
39591615 GCACTGAGTGTGTGGACTTAATATATAT
1 GCACTAAGTGTG-CGACTTAAT-TATAT
39591643 TTTTTAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 22 0.31
28 29 0.40
29 21 0.29
ACGTcount: A:0.29, C:0.11, G:0.26, T:0.35
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:39593242 original size:217 final size:217
Alignment explanation
Indices: 39592867--39593290 Score: 525
Period size: 217 Copynumber: 2.0 Consensus size: 217
39592857 AGAAATATAA
* * *
39592867 GTCGTAATGCACAAGGGTCAGAGTAGTCGAACCCAGGAACAGGGACGACTTTAACTAATAAACTG
1 GTCGTAATGCACAAAGGTCAGAGTAGTCGAACCCAGCAAAAGGGACGACTTTAACTAATAAACTG
* ** * * *
39592932 TACCAATTTGCCCAACCAAAAATTCTACAAAAATTCTACCATATATATATATGAGTCTAGTTCCG
66 TACAAATTTGCCCAACCAAAAATTCTACAAAAATAATACCATAGATACACATGAGTCTAGTTCCG
* * * * **
39592997 GGGAAAATTTACGGAACTGGATTTCGAGTTTC-AGAACTCAAGATATGATTTTTAAAGTGACTAG
131 GGGAAAAATCACGAAACTGGATTTCGAGTTACGA-AACTCAAGATATGATTTTTAAAACGACTAG
*
39593061 TACGCAGATTGGGAGATATCCAT
195 TACACAGATTGGGAGATATCCAT
** * * * *
39593084 GTCGTAATGGGCAAAGGTCAGTGTAGTCGACCCCTGCAAAATGGGA-GACTTTGACTAATAAACT
1 GTCGTAATGCACAAAGGTCAGAGTAGTCGAACCCAGCAAAA-GGGACGACTTTAACTAATAAACT
* * *
39593148 GTACAAATTTGCCCGACCAAAAATTCTAGAAAAA-AATA-CATAGATGGGCACATGAGTCTAGTT
65 GTACAAATTTGCCCAACCAAAAATTCTACAAAAATAATACCATAGAT--ACACATGAGTCTAGTT
* *
39593211 TCTGGGAAAAATCACGAAACT-GATTTTCGAGTTACGAAACTCAAGATATGATTTTTAAAACGAC
128 CCGGGGAAAAATCACGAAACTGGA-TTTCGAGTTACGAAACTCAAGATATGATTTTTAAAACGAC
39593275 TAGTACACAGATTGGG
192 TAGTACACAGATTGGG
39593291 CAGTGTCTGG
Statistics
Matches: 175, Mismatches: 27, Indels: 10
0.83 0.13 0.05
Matches are distributed among these distances:
215 6 0.03
216 4 0.02
217 160 0.91
218 5 0.03
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (217 bp):
GTCGTAATGCACAAAGGTCAGAGTAGTCGAACCCAGCAAAAGGGACGACTTTAACTAATAAACTG
TACAAATTTGCCCAACCAAAAATTCTACAAAAATAATACCATAGATACACATGAGTCTAGTTCCG
GGGAAAAATCACGAAACTGGATTTCGAGTTACGAAACTCAAGATATGATTTTTAAAACGACTAGT
ACACAGATTGGGAGATATCCAT
Found at i:39593936 original size:38 final size:38
Alignment explanation
Indices: 39593888--39593960 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
39593878 ATCATTTTTC
39593888 ATTTATTTTGGCCGAAAATTCTAAGGAAGGAGGAATTA
1 ATTTATTTTGGCCGAAAATTCTAAGGAAGGAGGAATTA
*
39593926 ATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 ATTTATTTTGGCCGAAAATTCTAAGGAAGGAGGAA
39593961 GGAGTTCTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.30
Consensus pattern (38 bp):
ATTTATTTTGGCCGAAAATTCTAAGGAAGGAGGAATTA
Found at i:39595242 original size:40 final size:40
Alignment explanation
Indices: 39595148--39595292 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
39595138 TACTCGAATG
* *
39595148 ATATCCGGGCTAAGTCCCGAACGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
39595189 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
39595229 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* *
39595269 ATATCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
39595293 CTTGTGCGAG
Statistics
Matches: 91, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
39 1 0.01
40 62 0.68
41 27 0.30
42 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:39601988 original size:38 final size:38
Alignment explanation
Indices: 39601945--39602020 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
39601935 TTCATCCTTT
39601945 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
39601983 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
1 TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
39602021 GGAGTTCTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.32
Consensus pattern (38 bp):
TTCATTTCTTTTGGCCGAAAATTCTAAGGAAGGAGGAA
Found at i:39603301 original size:40 final size:40
Alignment explanation
Indices: 39603207--39603351 Score: 170
Period size: 40 Copynumber: 3.6 Consensus size: 40
39603197 TACTCGAATG
* *
39603207 ATATCCGGGCTAAGTCCCGAACGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
39603248 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* *
39603288 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGAGC-
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGA-CT
*
39603328 ATATCCGGGTTAAGAT-CCGAAGGC
1 ATATCCGGGCTAAG-TCCCGAAGGC
39603352 CTTGTACGAG
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
39 1 0.01
40 60 0.66
41 29 0.32
42 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:39605306 original size:40 final size:40
Alignment explanation
Indices: 39605205--39605402 Score: 303
Period size: 40 Copynumber: 5.0 Consensus size: 40
39605195 TGGATGATAA
* * * *
39605205 CCGGGCTAAGTCCTGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
39605245 CCGGGC-AAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
39605284 CCGGGCTAAGTCCCGAAGGCATTGGTGCAAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
39605324 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG-AGTTACTATAT
39605364 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
39605403 CATAGTTACA
Statistics
Matches: 146, Mismatches: 8, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
38 1 0.01
39 35 0.24
40 108 0.74
41 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:39606128 original size:40 final size:39
Alignment explanation
Indices: 39606030--39606292 Score: 278
Period size: 40 Copynumber: 6.6 Consensus size: 39
39606020 TCCTCGTTCA
* * * *
39606030 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
39606069 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
39606108 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
39606148 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
39606188 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
39606228 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
39606269 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
39606293 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 21, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
39 40 0.20
40 145 0.74
41 12 0.06
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:39606252 original size:120 final size:119
Alignment explanation
Indices: 39606030--39606292 Score: 307
Period size: 120 Copynumber: 2.2 Consensus size: 119
39606020 TCCTCGTTCA
* * *
39606030 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
* * *
39606095 TAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAAC-TCGCAC
66 TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
* * * * *
39606148 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGACATAACCCGG-
* * ** * *
39606213 ATTT-GTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
63 ATTTAATAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAATAACTTAGCAC
*
39606269 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
39606293 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 37 0.31
120 75 0.62
121 9 0.07
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
Found at i:39606301 original size:41 final size:41
Alignment explanation
Indices: 39606224--39606301 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
39606214 TTTGTATCTC
* * *
39606224 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
39606265 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
39606302 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:39612471 original size:40 final size:39
Alignment explanation
Indices: 39612373--39612555 Score: 188
Period size: 40 Copynumber: 4.6 Consensus size: 39
39612363 TCCTCGTTCA
* * *
39612373 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCACAC
* *
39612412 AATGCCTTCGGGACATAACCCGGATTTAATAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCACAC
* *
39612451 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCACAC
* * * * * *
39612491 AAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAACTCA-CAC
* *
39612532 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
39612556 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
39 39 0.32
40 76 0.63
41 6 0.05
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCACAC
Found at i:39621531 original size:40 final size:40
Alignment explanation
Indices: 39621430--39621765 Score: 470
Period size: 40 Copynumber: 8.5 Consensus size: 40
39621420 TTGATGATAA
* * * *
39621430 CCGGGCTAAGTCCCGGAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
39621470 CCGGGC-AAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
39621509 CCGGGCTAAGTCCCAAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
39621549 CCGGGCTAAGTCCCGAAGGCATTTGTGTGAAG-TACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG-AGTTACTATAT
*
39621589 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
39621629 CCGGGCTAAGTCCCGAAGGCATTTGTGTGAAG-TACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG-AGTTACTATAT
*
39621669 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
39621709 CCGGGCTAAGTCCCGAAGGCATTTGAGC-AG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
**
39621748 CC-GGCTAAACCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
39621766 TACTTGGTTG
Statistics
Matches: 270, Mismatches: 19, Indels: 16
0.89 0.06 0.05
Matches are distributed among these distances:
38 17 0.06
39 46 0.17
40 203 0.75
41 4 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:39639631 original size:22 final size:23
Alignment explanation
Indices: 39639588--39639631 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
39639578 CTCTCTCTAG
*
39639588 GGTTAAGGATTTTATTTTTTTAA
1 GGTTAAGGATTTTATTTATTTAA
* *
39639611 GGTTAGGGTTTTTA-TTATTTA
1 GGTTAAGGATTTTATTTATTTA
39639632 GGGTATTTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.23, C:0.00, G:0.20, T:0.57
Consensus pattern (23 bp):
GGTTAAGGATTTTATTTATTTAA
Found at i:39641498 original size:30 final size:30
Alignment explanation
Indices: 39641464--39641526 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
39641454 ATTTAACAAG
*
39641464 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAACAACAAAATTAA
* *
39641494 CAAATGCCTTTAAAATAACAATAAAATTAA
1 CAAATGCCTCTAAAATAACAACAAAATTAA
39641524 CAA
1 CAA
39641527 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.57, C:0.16, G:0.03, T:0.24
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAACAACAAAATTAA
Found at i:39641518 original size:11 final size:11
Alignment explanation
Indices: 39641504--39641534 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
39641494 CAAATGCCTT
39641504 TAAAATAACAA
1 TAAAATAACAA
39641515 TAAAATTAACAA
1 TAAAA-TAACAA
39641527 TAAAATAA
1 TAAAATAA
39641535 GTTTTATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (11 bp):
TAAAATAACAA
Found at i:39643048 original size:3 final size:3
Alignment explanation
Indices: 39643040--39643077 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
39643030 TTTTCTTTTG
39643040 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
39643078 CTCTCTCTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:39643082 original size:2 final size:2
Alignment explanation
Indices: 39643075--39643903 Score: 1644
Period size: 2 Copynumber: 415.5 Consensus size: 2
39643065 TTCTTCTTCT
39643075 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39643117 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39643159 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39643201 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39643243 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39643285 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39643327 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39643369 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39643411 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39643453 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39643495 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39643537 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39643579 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39643621 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39643663 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39643705 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39643747 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39643789 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39643831 TC TC TC TC TC TC TC TC TC TC TC TC TC T- TC T- TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
39643871 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
39643904 TATTTCATGA
Statistics
Matches: 825, Mismatches: 0, Indels: 4
1.00 0.00 0.00
Matches are distributed among these distances:
1 2 0.00
2 823 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:39644244 original size:21 final size:21
Alignment explanation
Indices: 39644220--39644259 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39644210 ATGCATGTCT
*
39644220 ATTTTTAAGGAAAAGACTAAA
1 ATTTTCAAGGAAAAGACTAAA
*
39644241 ATTTTCATGGAAAAGACTA
1 ATTTTCAAGGAAAAGACTA
39644260 CATAAGACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
ATTTTCAAGGAAAAGACTAAA
Found at i:39651577 original size:38 final size:38
Alignment explanation
Indices: 39651533--39651608 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
39651523 TTTGATTTCT
39651533 TTAAAGAAGATGATTGTGATTTGTTCATAAATCTTTTA
1 TTAAAGAAGATGATTGTGATTTGTTCATAAATCTTTTA
*
39651571 TTAAAGAAGATGATTGTGATTTGTTCATAAATGTTTTA
1 TTAAAGAAGATGATTGTGATTTGTTCATAAATCTTTTA
39651609 CCAGAAATTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.34, C:0.04, G:0.17, T:0.45
Consensus pattern (38 bp):
TTAAAGAAGATGATTGTGATTTGTTCATAAATCTTTTA
Found at i:39655760 original size:45 final size:46
Alignment explanation
Indices: 39655673--39655760 Score: 117
Period size: 45 Copynumber: 1.9 Consensus size: 46
39655663 TGAGCCATGT
*
39655673 ATCAAGAAGCTTATCGGGGCTAAACAGGAAACTCATAAGAGTTTTA
1 ATCAAGAAGCTTATCGGAGCTAAACAGGAAACTCATAAGAGTTTTA
* * *
39655719 ATCAAGAAGCTTAT-TGAGCTTAACAGGTAACTC-TAATGAGTT
1 ATCAAGAAGCTTATCGGAGCTAAACAGGAAACTCATAA-GAGTT
39655761 ATTATTAGGG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 3 0.08
45 20 0.54
46 14 0.38
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (46 bp):
ATCAAGAAGCTTATCGGAGCTAAACAGGAAACTCATAAGAGTTTTA
Found at i:39659141 original size:20 final size:20
Alignment explanation
Indices: 39659122--39659159 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39659112 AGTGTTAAAT
39659122 TAAATTAAT-TAAATGCAAA
1 TAAATTAATCTAAATGCAAA
*
39659141 TGAATTAATCTAAATGCAA
1 TAAATTAATCTAAATGCAA
39659160 TGAATGAAAT
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:0.08, G:0.08, T:0.32
Consensus pattern (20 bp):
TAAATTAATCTAAATGCAAA
Found at i:39659148 original size:19 final size:19
Alignment explanation
Indices: 39659124--39659164 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
39659114 TGTTAAATTA
39659124 AATTAAT-TAAATGCAAATG
1 AATTAATCTAAATGC-AATG
39659143 AATTAATCTAAATGCAATG
1 AATTAATCTAAATGCAATG
39659162 AAT
1 AAT
39659165 GAAATGAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.51, C:0.07, G:0.10, T:0.32
Consensus pattern (19 bp):
AATTAATCTAAATGCAATG
Found at i:39664495 original size:40 final size:40
Alignment explanation
Indices: 39664425--39664641 Score: 260
Period size: 40 Copynumber: 5.5 Consensus size: 40
39664415 AAGCCAAGTA
* * * *
39664425 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGAATATAG-TAACTCGCACGAATG
* *
39664464 CCTTCGGGACATAGCCCAAATATAGTAACTCGCACGAATG
1 CCTTCGGGACTTAGCCCGAATATAGTAACTCGCACGAATG
* *
39664504 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACGAATG
1 CCTTCGGGACTTAGCCCGAATATAGTAACTCGCACGAATG
* *
39664544 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGAATATAGTAACTCGCACGAATG
* * * * *
39664584 CCTTCGGGACTTAGCCCGGAA-CTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCC-GAATATAGTAACTCGCACGAATG
39664624 CCTTCGGGACTTAGCCCG
1 CCTTCGGGACTTAGCCCG
39664642 GTTATCATCC
Statistics
Matches: 158, Mismatches: 17, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
39 13 0.08
40 143 0.91
41 2 0.01
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGAATATAGTAACTCGCACGAATG
Found at i:39672605 original size:40 final size:40
Alignment explanation
Indices: 39672543--39672760 Score: 253
Period size: 40 Copynumber: 5.5 Consensus size: 40
39672533 AAGCCAAGTA
* * * *
39672543 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
39672582 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
39672622 CCTTCGGGACTTAGCCCGGATATAGTAACTCGTACGAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* ** *
39672662 CCTTCGGGATTTAGCCCATATATAGTAATTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * ** *
39672702 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGTGCAAATA
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
39672742 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
39672761 TTATCATCCA
Statistics
Matches: 153, Mismatches: 23, Indels: 5
0.85 0.13 0.03
Matches are distributed among these distances:
39 13 0.08
40 140 0.92
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:39680525 original size:27 final size:27
Alignment explanation
Indices: 39680495--39680547 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
39680485 CAATAACAGT
*
39680495 TGGGCCT-AGCCCTTTAATAGAATCAGG
1 TGGGCCTAAGCCCATT-ATAGAATCAGG
*
39680522 TGGGCCTAAGCCCATTATGGAATCAG
1 TGGGCCTAAGCCCATTATAGAATCAG
39680548 TATCAAATGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (27 bp):
TGGGCCTAAGCCCATTATAGAATCAGG
Found at i:39680604 original size:21 final size:22
Alignment explanation
Indices: 39680575--39680621 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
39680565 TAGATAGATA
39680575 ACCAGCCCAGT-CCAACCAACAC
1 ACCAGCCCA-TACCAACCAACAC
*
39680597 ACCA-CCCATACCAACCAGCAC
1 ACCAGCCCATACCAACCAACAC
39680618 ACCA
1 ACCA
39680622 TGTGGGGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 1 0.04
21 18 0.78
22 4 0.17
ACGTcount: A:0.38, C:0.51, G:0.06, T:0.04
Consensus pattern (22 bp):
ACCAGCCCATACCAACCAACAC
Found at i:39680728 original size:22 final size:22
Alignment explanation
Indices: 39680688--39680730 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
39680678 CACTAAGTCA
*
39680688 ACAGAACGACTCAACGCCGTAG
1 ACAGAACGACTAAACGCCGTAG
* *
39680710 ACAGAACGGCTAAAGGCCGTA
1 ACAGAACGACTAAACGCCGTA
39680731 AATATGGTAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.37, C:0.28, G:0.26, T:0.09
Consensus pattern (22 bp):
ACAGAACGACTAAACGCCGTAG
Found at i:39683601 original size:22 final size:22
Alignment explanation
Indices: 39683575--39683619 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
39683565 ATTATGTGTA
39683575 TTAATTCATAATATAA-TTAATT
1 TTAATTCAT-ATATAATTTAATT
* *
39683597 TTAATTTATATCTAATTTAATT
1 TTAATTCATATATAATTTAATT
39683619 T
1 T
39683620 GGGTTAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAATTCATATATAATTTAATT
Found at i:39686428 original size:44 final size:44
Alignment explanation
Indices: 39686378--39686551 Score: 242
Period size: 44 Copynumber: 4.0 Consensus size: 44
39686368 CTCGCTCNCC
39686378 GTATTGTCAGAGAGCAGATCAAAGATAGCAGATTTGGCATCTCT
1 GTATTGTCAGAGAGCAGATCAAAGATAGCAGATTTGGCATCTCT
* * * * ** *
39686422 GTATTGTCAGTGAACAAATCGAAGAT-GCAGATTTGGTGTTTCT
1 GTATTGTCAGAGAGCAGATCAAAGATAGCAGATTTGGCATCTCT
* *
39686465 GTATTGTCAGAGAGCAGATCGAAGGTAGCAGATTTGGCATCTCT
1 GTATTGTCAGAGAGCAGATCAAAGATAGCAGATTTGGCATCTCT
* *
39686509 GTATTGTCAGAGAGCAGATCAAAGATAACAGATTTGGCGTCTC
1 GTATTGTCAGAGAGCAGATCAAAGATAGCAGATTTGGCATCTC
39686552 AGTCAAGATA
Statistics
Matches: 111, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
43 36 0.32
44 75 0.68
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (44 bp):
GTATTGTCAGAGAGCAGATCAAAGATAGCAGATTTGGCATCTCT
Found at i:39686534 original size:87 final size:88
Alignment explanation
Indices: 39686378--39686545 Score: 266
Period size: 87 Copynumber: 1.9 Consensus size: 88
39686368 CTCGCTCNCC
* *
39686378 GTATTGTCAGAGAGCAGATCAAAGATAGCAGATTTGGCATCTCTGTATTGTCAGTGAACAAATCG
1 GTATTGTCAGAGAGCAGATCAAAGATAGCAGATTTGGCATCTCTGTATTGTCAGAGAACAAATCA
*
39686443 AAGAT-GCAGATTTGGTGTTTCT
66 AAGATAACAGATTTGGTGTTTCT
* * * *
39686465 GTATTGTCAGAGAGCAGATCGAAGGTAGCAGATTTGGCATCTCTGTATTGTCAGAGAGCAGATCA
1 GTATTGTCAGAGAGCAGATCAAAGATAGCAGATTTGGCATCTCTGTATTGTCAGAGAACAAATCA
39686530 AAGATAACAGATTTGG
66 AAGATAACAGATTTGG
39686546 CGTCTCAGTC
Statistics
Matches: 73, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
87 64 0.88
88 9 0.12
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.29
Consensus pattern (88 bp):
GTATTGTCAGAGAGCAGATCAAAGATAGCAGATTTGGCATCTCTGTATTGTCAGAGAACAAATCA
AAGATAACAGATTTGGTGTTTCT
Found at i:39686628 original size:44 final size:44
Alignment explanation
Indices: 39686556--39686781 Score: 326
Period size: 44 Copynumber: 5.1 Consensus size: 44
39686546 CGTCTCAGTC
* * *
39686556 AAGATAACAGATTTGGCGTCTCTGTATTGCCAGAGAGCAGATCG
1 AAGATAGCAGATTTGGCATCTCTGTATTGTCAGAGAGCAGATCG
* * * *
39686600 AAGGTAGCAGATTTGGCGTCTCTATATTGTCAGAGAGCAGATCA
1 AAGATAGCAGATTTGGCATCTCTGTATTGTCAGAGAGCAGATCG
* * *
39686644 AAGATAGCAGATTTGGTATCTCTGTATTGTCAAAGAGCAAATCG
1 AAGATAGCAGATTTGGCATCTCTGTATTGTCAGAGAGCAGATCG
* * *
39686688 AAGACAGCAGATTTGGTATCTCTGTATTGTCAGAGAGCAAATCG
1 AAGATAGCAGATTTGGCATCTCTGTATTGTCAGAGAGCAGATCG
*
39686732 AAGATAGCAGATTTGGCATCTTTGTATTGTCAGAGAGCAGATCG
1 AAGATAGCAGATTTGGCATCTCTGTATTGTCAGAGAGCAGATCG
39686776 AAGATA
1 AAGATA
39686782 TCAACATGGT
Statistics
Matches: 164, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 164 1.00
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (44 bp):
AAGATAGCAGATTTGGCATCTCTGTATTGTCAGAGAGCAGATCG
Found at i:39686649 original size:114 final size:114
Alignment explanation
Indices: 39686449--39686659 Score: 368
Period size: 114 Copynumber: 1.9 Consensus size: 114
39686439 ATCGAAGATG
* * * *
39686449 CAGATTTGGTGTTTCTGTATTGTCAGAGAGCAGATCGAAGGTAGCAGATTTGGCATCTCTGTATT
1 CAGATTTGGCGTCTCTGTATTGCCAGAGAGCAGATCGAAGGTAGCAGATTTGGCATCTCTATATT
39686514 GTCAGAGAGCAGATCAAAGATAACAGATTTGGCGTCTCAGTCAAGATAA
66 GTCAGAGAGCAGATCAAAGATAACAGATTTGGCGTCTCAGTCAAGATAA
*
39686563 CAGATTTGGCGTCTCTGTATTGCCAGAGAGCAGATCGAAGGTAGCAGATTTGGCGTCTCTATATT
1 CAGATTTGGCGTCTCTGTATTGCCAGAGAGCAGATCGAAGGTAGCAGATTTGGCATCTCTATATT
*
39686628 GTCAGAGAGCAGATCAAAGATAGCAGATTTGG
66 GTCAGAGAGCAGATCAAAGATAACAGATTTGG
39686660 TATCTCTGTA
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 91 1.00
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (114 bp):
CAGATTTGGCGTCTCTGTATTGCCAGAGAGCAGATCGAAGGTAGCAGATTTGGCATCTCTATATT
GTCAGAGAGCAGATCAAAGATAACAGATTTGGCGTCTCAGTCAAGATAA
Found at i:39686699 original size:158 final size:157
Alignment explanation
Indices: 39686399--39686703 Score: 439
Period size: 158 Copynumber: 1.9 Consensus size: 157
39686389 GAGCAGATCA
* * * * *
39686399 AAGATAGCAGATTTGGCATCTCTGTATTGTCAGTGAACAAATCGAAGATGCAGATTTGGTGTTTC
1 AAGATAACAGATTTGGCATCTCTGTATTGCCAGAGAACAAATCGAAGATGCAGATTTGGCGTCTC
* * * * *
39686464 TGTATTGTCAGAGAGCAGATCGAAGGTAGCAGATTTGGCATCTCTGTATTGTCAGAGAGCAGATC
66 TATATTGTCAGAGAGCAGATCAAAGATAGCAGATTTGGCATCTCTGTATTGTCAAAGAGCAAATC
*
39686529 AAAGATAACAGATTTGGCGTCTCAGTC
131 AAAGACAACAGATTTGGCGTCTCAGTC
* * * *
39686556 AAGATAACAGATTTGGCGTCTCTGTATTGCCAGAGAGCAGATCGAAGGTAGCAGATTTGGCGTCT
1 AAGATAACAGATTTGGCATCTCTGTATTGCCAGAGAACAAATCGAAGAT-GCAGATTTGGCGTCT
*
39686621 CTATATTGTCAGAGAGCAGATCAAAGATAGCAGATTTGGTATCTCTGTATTGTCAAAGAGCAAAT
65 CTATATTGTCAGAGAGCAGATCAAAGATAGCAGATTTGGCATCTCTGTATTGTCAAAGAGCAAAT
* *
39686686 CGAAGACAGCAGATTTGG
130 CAAAGACAACAGATTTGG
39686704 TATCTCTGTA
Statistics
Matches: 129, Mismatches: 18, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
157 42 0.33
158 87 0.67
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.28
Consensus pattern (157 bp):
AAGATAACAGATTTGGCATCTCTGTATTGCCAGAGAACAAATCGAAGATGCAGATTTGGCGTCTC
TATATTGTCAGAGAGCAGATCAAAGATAGCAGATTTGGCATCTCTGTATTGTCAAAGAGCAAATC
AAAGACAACAGATTTGGCGTCTCAGTC
Found at i:39688299 original size:21 final size:21
Alignment explanation
Indices: 39688254--39688312 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
39688244 TAAGTATTAT
*
39688254 ATATATTATTTTTTATATATAA
1 ATATA-TATTATTTATATATAA
39688276 ATAGTA-ATTATTTATATA-ATA
1 ATA-TATATTATTTATATATA-A
39688297 ATATATATTA-TTATAT
1 ATATATATTATTTATAT
39688313 GTCTTTATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
20 9 0.27
21 19 0.58
22 3 0.09
23 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
ATATATATTATTTATATATAA
Found at i:39688378 original size:20 final size:18
Alignment explanation
Indices: 39688324--39688419 Score: 71
Period size: 16 Copynumber: 5.4 Consensus size: 18
39688314 TCTTTATAAA
39688324 TTTTATTATATGTTATA-T
1 TTTTATTATAT-TTATATT
*
39688342 TTTTA--ATATATACTATT
1 TTTTATTATATTTA-TATT
39688359 TATTCTATTATATTTATA--
1 T-TT-TATTATATTTATATT
39688377 TTTTATTATATGTTATATAT
1 TTTTATTATAT-TTATAT-T
39688397 TTTTATTATA--TATATT
1 TTTTATTATATTTATATT
*
39688413 ATTTATT
1 TTTTATT
39688420 TTACCATATT
Statistics
Matches: 65, Mismatches: 3, Indels: 22
0.72 0.03 0.24
Matches are distributed among these distances:
15 2 0.03
16 21 0.32
17 14 0.22
18 8 0.12
19 2 0.03
20 12 0.18
21 6 0.09
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTTATTATATTTATATT
Found at i:39688395 original size:25 final size:25
Alignment explanation
Indices: 39688323--39688411 Score: 76
Period size: 25 Copynumber: 3.5 Consensus size: 25
39688313 GTCTTTATAA
*
39688323 ATTTTATTATATGTTATATTTTTAAT
1 ATTTTATTATATGTTATATATTT-AT
*
39688349 ATATACTATT-TAT-TCTATTATATTTAT
1 AT-T-TTATTATATGT-TA-TATATTTAT
*
39688376 ATTTTATTATATGTTATATATTTTT
1 ATTTTATTATATGTTATATATTTAT
*
39688401 ATTATA-TATAT
1 ATTTTATTATAT
39688412 TATTTATTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
24 5 0.10
25 17 0.33
26 9 0.17
27 11 0.21
28 10 0.19
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (25 bp):
ATTTTATTATATGTTATATATTTAT
Found at i:39688434 original size:41 final size:42
Alignment explanation
Indices: 39688348--39688435 Score: 99
Period size: 41 Copynumber: 2.1 Consensus size: 42
39688338 ATATTTTTAA
* **
39688348 TATATACTATTTATTCTATTATATTTATATTTTATTATATGT
1 TATATACTATTTATTATATTATATTTATATTTTACCATATGT
* * *
39688390 TATATA-TTTTTATTATA-TATATTATTTATTTTACCATATTT
1 TATATACTATTTATTATATTATATT-TATATTTTACCATATGT
39688431 TATAT
1 TATAT
39688436 GTAAAATTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
40 6 0.15
41 27 0.69
42 6 0.15
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (42 bp):
TATATACTATTTATTATATTATATTTATATTTTACCATATGT
Found at i:39690790 original size:88 final size:88
Alignment explanation
Indices: 39690641--39690815 Score: 323
Period size: 88 Copynumber: 2.0 Consensus size: 88
39690631 GGGAGACTTC
*
39690641 GACTTCAATAATCCCGAGTCCGATAGCTGACGAACCAAAATCTATAAAATAGAGATTCAAAGAAG
1 GACTTCAATAATCCCGAGTCCGATAGCTGACGAACCAAAATCTATAAAACAGAGATTCAAAGAAG
39690706 CGGAGTAAGAATTTAATGCTTAT
66 CGGAGTAAGAATTTAATGCTTAT
*
39690729 GACTTCAATAATCCCGATTCCGATAGCTGACGAACCAAAATCTATAAAACAGAGATTCAAAGAAG
1 GACTTCAATAATCCCGAGTCCGATAGCTGACGAACCAAAATCTATAAAACAGAGATTCAAAGAAG
*
39690794 CGGAGTAAGCATTTAATGCTTA
66 CGGAGTAAGAATTTAATGCTTA
39690816 GTAAGTTTTG
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
88 84 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (88 bp):
GACTTCAATAATCCCGAGTCCGATAGCTGACGAACCAAAATCTATAAAACAGAGATTCAAAGAAG
CGGAGTAAGAATTTAATGCTTAT
Found at i:39691314 original size:39 final size:40
Alignment explanation
Indices: 39691148--39691331 Score: 246
Period size: 40 Copynumber: 4.6 Consensus size: 40
39691138 GCTACTCGCT
* * *
39691148 CAAATGCCTTCGGGACATAGCCCGG-TTAGAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTAGCA
* *
39691188 CAATTGCCTTCGGGACTTAGCCCGGATTTAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTAGCA
*
39691228 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTAGCA
** * *
39691268 CAAATGCCTTCGGGACTT-GCCCGGAACTAGTCACTAGCG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTAGCA
*
39691307 CAGATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
39691332 TTATCATCCA
Statistics
Matches: 130, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
39 33 0.25
40 95 0.73
41 2 0.02
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTAGCA
Found at i:39692609 original size:27 final size:27
Alignment explanation
Indices: 39692578--39692631 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
39692568 CTTCCAAGCT
*
39692578 GAACATGAAGCAAGAGCTCCTTCCTTC
1 GAACATGAAGCAACAGCTCCTTCCTTC
39692605 GAACATGAAGCAACAGCTCCTTCCTTC
1 GAACATGAAGCAACAGCTCCTTCCTTC
39692632 TTCCTTAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.22
Consensus pattern (27 bp):
GAACATGAAGCAACAGCTCCTTCCTTC
Found at i:39699364 original size:39 final size:40
Alignment explanation
Indices: 39699191--39699381 Score: 242
Period size: 40 Copynumber: 4.8 Consensus size: 40
39699181 GGATATAGCT
* * *
39699191 ACTCGCTCAAATGCCTTCGGGACATAGCCCGG-TTAGAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT-TAGTA
*
39699231 ACTCGCACAATTGCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* *
39699271 ACTCGTACAAATGCCTTCGGGACTTAGTCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
** *
39699311 ACTCGCACAAATGCCTTCGGGACTT-GCCCGGAACTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * * *
39699350 ACTAGCGCAGATGCCTTCGGGACTTTGCCCGG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
39699382 TTATCATCCA
Statistics
Matches: 134, Mismatches: 15, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
39 32 0.24
40 100 0.75
41 2 0.01
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.25
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:39710404 original size:50 final size:50
Alignment explanation
Indices: 39710324--39710658 Score: 275
Period size: 50 Copynumber: 6.6 Consensus size: 50
39710314 AAGGTTACGT
* * * *
39710324 GAGCCAGTGTAAGACCATGT-TTGGAACATGGCATCGACCTCGAGAAATAA
1 GAGCTAGTGTAAGACCATGTCTAGG-ACATGGCATCGACCTCGAGATATGA
* *
39710374 GAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGGCCTCGAGGTATGA
1 GAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGACCTCGAGATATGA
* *
39710424 GAGCTAGTGTAAGACCATGTCTGGGACATGGCATATGGCATCGACCTTGAGATATGA
1 GAGCTAGTGTAAGACCATGTCT-----A-GG-ACATGGCATCGACCTCGAGATATGA
*** * *
39710481 GAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGGTATCGATAGATGA
1 GAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGACCTCGAGATATGA
* * * * * * ** * *
39710531 GAGCCAATGTAGGACCATGTCTGGGGCATGGCATCG-GCT-TTGATGTGT
1 GAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGACCTCGAGATATGA
* * * * ** * *
39710579 GAGCCAGTGTAAGATCATGTCTGGGACATGGCATCG-GCT-TTGATGTGT
1 GAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGACCTCGAGATATGA
*
39710627 GAGCTAGTGTAAGACCATGTCTGGGACATGGC
1 GAGCTAGTGTAAGACCATGTCTAGGACATGGC
39710659 GTCGGCACCT
Statistics
Matches: 241, Mismatches: 36, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
48 77 0.32
49 1 0.00
50 111 0.46
51 5 0.02
52 1 0.00
55 1 0.00
56 2 0.01
57 43 0.18
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.24
Consensus pattern (50 bp):
GAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGACCTCGAGATATGA
Found at i:39710480 original size:57 final size:57
Alignment explanation
Indices: 39710401--39710514 Score: 192
Period size: 57 Copynumber: 2.0 Consensus size: 57
39710391 TGTCTAGGAC
* * *
39710401 ATGGCATCGGCCTCGAGGTATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCAT
1 ATGGCATCGACCTCGAGATATGAGAGCTAGTGTAAGACCATGTCTAGGACATGGCAT
*
39710458 ATGGCATCGACCTTGAGATATGAGAGCTAGTGTAAGACCATGTCTAGGACATGGCAT
1 ATGGCATCGACCTCGAGATATGAGAGCTAGTGTAAGACCATGTCTAGGACATGGCAT
39710515 CGGTATCGAT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (57 bp):
ATGGCATCGACCTCGAGATATGAGAGCTAGTGTAAGACCATGTCTAGGACATGGCAT
Found at i:39710508 original size:107 final size:104
Alignment explanation
Indices: 39710350--39710658 Score: 339
Period size: 107 Copynumber: 3.0 Consensus size: 104
39710340 ATGTTTGGAA
* * * *
39710350 CATGGCATCGACCTCGAGAAATAAGAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGGCCTC
1 CATGGCATCGACCTTGAGATATGAGAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGGCATC
39710415 GAGGTATGAGAGCTAGTGTAAGACCATGTCTGGGACATGG
66 GA-GTATGAGAGCTAGTGTAAGACCATGTCTGGGACATGG
*
39710455 CATATGGCATCGACCTTGAGATATGAGAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGGTA
1 C--ATGGCATCGACCTTGAGATATGAGAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGGCA
* * *
39710520 TCGA-TAGATGAGAGCCAATGTAGGACCATGTCT-GG----GG
64 TCGAGT--ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGG
* * * * * * * * *
39710557 CATGGCATCG-GCTT-TGATGTGTGAGCCAGTGTAAGATCATGTCTGGGACATGGCATCGGCTTT
1 CATGGCATCGACCTTGAGATATGAGAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGGCATC
* *
39710620 GA-TGTGTGAGCTAGTGTAAGACCATGTCTGGGACATGG
66 GAGTATGAGAGCTAGTGTAAGACCATGTCTGGGACATGG
39710658 C
1 C
39710659 GTCGGCACCT
Statistics
Matches: 172, Mismatches: 23, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
96 21 0.12
97 2 0.01
98 43 0.25
99 3 0.02
100 9 0.05
101 3 0.02
102 3 0.02
105 2 0.01
106 2 0.01
107 84 0.49
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.24
Consensus pattern (104 bp):
CATGGCATCGACCTTGAGATATGAGAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGGCATC
GAGTATGAGAGCTAGTGTAAGACCATGTCTGGGACATGG
Found at i:39710602 original size:48 final size:48
Alignment explanation
Indices: 39710481--39710664 Score: 244
Period size: 48 Copynumber: 3.8 Consensus size: 48
39710471 TGAGATATGA
* * * *
39710481 GAGCTAGTGTAAGACCATGTCTAGGACATGGCATCGG-TATCGATAGATGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCT-TTGAT-G-TGT
* * *
39710531 GAGCCAATGTAGGACCATGTCTGGGGCATGGCATCGGCTTTGATGTGT
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTTGATGTGT
*
39710579 GAGCCAGTGTAAGATCATGTCTGGGACATGGCATCGGCTTTGATGTGT
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTTGATGTGT
* *
39710627 GAGCTAGTGTAAGACCATGTCTGGGACATGGCGTCGGC
1 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
39710665 ACCTTACCCT
Statistics
Matches: 119, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
48 81 0.68
49 1 0.01
50 36 0.30
51 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.34, T:0.26
Consensus pattern (48 bp):
GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTTGATGTGT
Found at i:39715639 original size:18 final size:19
Alignment explanation
Indices: 39715603--39715642 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
39715593 TTATAAAAAA
*
39715603 ATTAATTTGCATTTAAATT
1 ATTAATTTGAATTTAAATT
*
39715622 ATTAA-TTGAATTTTAATT
1 ATTAATTTGAATTTAAATT
39715640 ATT
1 ATT
39715643 GTTATAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (19 bp):
ATTAATTTGAATTTAAATT
Found at i:39720989 original size:5 final size:5
Alignment explanation
Indices: 39720979--39721229 Score: 493
Period size: 5 Copynumber: 50.0 Consensus size: 5
39720969 TTTGAGAAAG
39720979 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
39721029 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
39721079 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
39721129 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
39721179 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA AT-AAA ATAAA
39721230 GAACACATAA
Statistics
Matches: 245, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
5 240 0.98
6 5 0.02
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Done.