Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 131 of 213
Found at i:38335651 original size:44 final size:44
Alignment explanation
Indices: 38335554--38335652 Score: 108
Period size: 44 Copynumber: 2.2 Consensus size: 44
38335544 CGAAGAAGTA
* * * * ** *
38335554 AATCTTATCTCCCTGAGGTTGTAGTGGAGCAGATTGAAGTCGAT
1 AATCTTATCTCCCTGAAGTTGTAATGGAGCAGATTAAACTAAAG
* *
38335598 AATCCTATCTCCCTGAAGTTGTAATGGAGCGGATTAAACTAAAG
1 AATCTTATCTCCCTGAAGTTGTAATGGAGCAGATTAAACTAAAG
*
38335642 GATCTTATCTC
1 AATCTTATCTC
38335653 TCTAAAATTA
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.31
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGTAATGGAGCAGATTAAACTAAAG
Found at i:38335809 original size:44 final size:44
Alignment explanation
Indices: 38335743--38335943 Score: 153
Period size: 44 Copynumber: 4.6 Consensus size: 44
38335733 GAAAATGGTG
* *
38335743 AATCTTATCTCCCTAAGGTTACAGTGGAGCAGATTGAAGCCAGA
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGA
* *
38335787 AATCTTATCTCCCTGAGATTACAGTTGAGCTGATTGAAGCC-GA
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGA
* * ** *** *
38335830 TAATCCTATCTCCCTGA-AGTTATAGTGGAGTGGATT-AAAATAAA
1 -AATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGCCAGA
* * * * * * *
38335874 AGATCTTATCTCTCTGAAATTACAGTAGAGTAGATCGCA-TCAG-
1 A-ATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGA
*
38335917 -GTCTTATCTCCCTGAGATTACAGTGGA
1 AATCTTATCTCCCTGAGATTACAGTGGA
38335944 ATAGACCGAA
Statistics
Matches: 124, Mismatches: 27, Indels: 15
0.75 0.16 0.09
Matches are distributed among these distances:
41 23 0.19
43 6 0.05
44 93 0.75
45 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (44 bp):
AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGA
Found at i:38335919 original size:233 final size:233
Alignment explanation
Indices: 38335553--38336047 Score: 812
Period size: 233 Copynumber: 2.1 Consensus size: 233
38335543 CCGAAGAAGT
* ** *
38335553 AAATCTTATCTCCCTGAGGTTGTAGTGGAGCAGATTGAAGTCGATAATCCTATCTCCCTGAAGTT
1 AAATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTT
* * *
38335618 GTAATGGAGCGGATTAAACTAAAGGATCTTATCTCTCTAAAATTACAGTAGAGTAGATCGCATCA
66 ATAATGGAGCGGATTAAAATAAAAGATCTTATCTCTCTAAAATTACAGTAGAGTAGATCGCATCA
* * *
38335683 GGTCTTATCTCCCTGAGATTACAGTGGAATAGACTAAAGAATTCCTAATCGAAAATGGTGAATCT
131 GGTCTTATCTCCCTGAGATTACAGTGGAATAGACCAAAGAACTCCTAATCAAAAATGGTGAATCT
38335748 TATCTCCCTAAGGTTACAGTGGAGCAGATTGAAGCCAG
196 TATCTCCCTAAGGTTACAGTGGAGCAGATTGAAGCCAG
* *
38335786 AAATCTTATCTCCCTGAGATTACAGTTGAGCTGATTGAAGCCGATAATCCTATCTCCCTGAAGTT
1 AAATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTT
* * *
38335851 ATAGTGGAGTGGATTAAAATAAAAGATCTTATCTCTCTGAAATTACAGTAGAGTAGATCGCATCA
66 ATAATGGAGCGGATTAAAATAAAAGATCTTATCTCTCTAAAATTACAGTAGAGTAGATCGCATCA
* *
38335916 GGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAACTCTTAATCAAAAATGGTGAATCT
131 GGTCTTATCTCCCTGAGATTACAGTGGAATAGACCAAAGAACTCCTAATCAAAAATGGTGAATCT
38335981 TATCTCCCTAAGGTTACAGTGGAGCAGATTGAAGCCAG
196 TATCTCCCTAAGGTTACAGTGGAGCAGATTGAAGCCAG
* *
38336019 AAATCTTATCTCCCTGCG-GTACAGTGGAG
1 AAATCTTATCTCCCTGAGATTACAGTGGAG
38336048 AAGGTCAAAG
Statistics
Matches: 242, Mismatches: 20, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
232 9 0.04
233 233 0.96
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.29
Consensus pattern (233 bp):
AAATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTT
ATAATGGAGCGGATTAAAATAAAAGATCTTATCTCTCTAAAATTACAGTAGAGTAGATCGCATCA
GGTCTTATCTCCCTGAGATTACAGTGGAATAGACCAAAGAACTCCTAATCAAAAATGGTGAATCT
TATCTCCCTAAGGTTACAGTGGAGCAGATTGAAGCCAG
Found at i:38338789 original size:27 final size:27
Alignment explanation
Indices: 38338759--38338935 Score: 135
Period size: 27 Copynumber: 6.6 Consensus size: 27
38338749 ATATTGAGCC
* *
38338759 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
38338786 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
38338813 CGCACACTTAGTGCTACATAGTCAAACC
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
38338841 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
38338868 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
38338895 CGCACACTTAGTGCAACA-AGT-AGAAT
1 CGCACACTTAGTGCTACATAATCA-ACT
38338921 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
38338936 GTACAATTTA
Statistics
Matches: 121, Mismatches: 25, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
25 1 0.01
26 17 0.14
27 80 0.66
28 23 0.19
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:38338871 original size:55 final size:54
Alignment explanation
Indices: 38338759--38338935 Score: 162
Period size: 55 Copynumber: 3.3 Consensus size: 54
38338749 ATATTGAGCC
* * * * *
38338759 CGCACACTCAGTGCTATATAATCAACTCGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
* * ** *
38338813 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACCCGCACACTTAGTGCCACATAATCAAAT
* *** * *
38338868 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACA-AGT-AGAAT
1 CGCACACTTAGTGCTA-CATAATCAACCCGCACACTTAGTGCCACATAATCA-AAT
38338921 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
38338936 GTACAATTTA
Statistics
Matches: 101, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
52 1 0.01
53 18 0.18
54 38 0.38
55 44 0.44
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
Found at i:38346708 original size:27 final size:27
Alignment explanation
Indices: 38346678--38346853 Score: 176
Period size: 27 Copynumber: 6.5 Consensus size: 27
38346668 TTGAGCCCGT
* * *
38346678 ACACTCAGTGCTATATAATCAACTCGC
1 ACACTTAGTGCTACATAGTCAACTCGC
* * **
38346705 ACACTTAGTGCTACGTAATCAAAACGC
1 ACACTTAGTGCTACATAGTCAACTCGC
38346732 ACACTTAGTGCTACATAGTCAAACTCGC
1 ACACTTAGTGCTACATAGTC-AACTCGC
** * *
38346760 ACACTTAGTGCCGCATGGTCAATTCGC
1 ACACTTAGTGCTACATAGTCAACTCGC
* **
38346787 ACACTTAGTGC-ATCATATTCATTTCGC
1 ACACTTAGTGCTA-CATAGTCAACTCGC
*
38346814 ACACTTAGTGCAACATAGTCATA-TCGC
1 ACACTTAGTGCTACATAGTCA-ACTCGC
38346841 ACACTTAGTGCTA
1 ACACTTAGTGCTA
38346854 TACAATTTAA
Statistics
Matches: 125, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
27 102 0.82
28 23 0.18
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (27 bp):
ACACTTAGTGCTACATAGTCAACTCGC
Found at i:38347419 original size:13 final size:13
Alignment explanation
Indices: 38347401--38347425 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38347391 TACTAAATTT
38347401 TCATGGATTCAAG
1 TCATGGATTCAAG
38347414 TCATGGATTCAA
1 TCATGGATTCAA
38347426 TATACCATTA
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:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TCATGGATTCAAG
Found at i:38360955 original size:40 final size:40
Alignment explanation
Indices: 38360901--38361444 Score: 894
Period size: 40 Copynumber: 13.6 Consensus size: 40
38360891 CATTTGAATG
38360901 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
38360941 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
38360981 ATATCCGGGTTAAGA-CCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
38361020 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
38361060 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
38361100 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
38361140 ATATCCGGGCTAAGACCCGAAGGCATTTGTGTGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
38361180 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
38361220 ATATCCGGGCTAAGACCTGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
38361260 ATATCCGGGATAAGACCCGAAGGCATTTGTGCGAACTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* * *
38361300 ATATCCGGGATAAGACCCGACGGCGTTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
38361340 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC-AAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAA-TTGAT
** * *
38361380 ATATCCGGGCTAAGACCCGAAGGCATTCATGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
38361420 ATACCCGGGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCA
38361445 ATTGAGCTTG
Statistics
Matches: 475, Mismatches: 26, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
39 40 0.08
40 434 0.91
41 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
Found at i:38368582 original size:40 final size:40
Alignment explanation
Indices: 38368528--38369831 Score: 1663
Period size: 40 Copynumber: 32.6 Consensus size: 40
38368518 CATTTGAATG
38368528 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
38368568 ATATCCGGGTTAAGACCCAAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
38368608 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
38368648 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
38368688 ATATCTGGGTTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
38368728 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
**
38368768 ATATCCGGGCTAAGACCTAAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
38368808 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
38368848 ATATCCGGGCTAAGACCTGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
38368888 ATATCCGGGATAAGACCCGAAGGCATTTGTGCGAACTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* * *
38368928 ATATCCGGGATAAGACCCGACGGCGTTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
38368968 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC-AAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAA-TTGAT
* * *
38369008 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* * * * *** * *
38369048 ATACCCGGGTTAAGACCCGAAGGCAATTGAGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* ** * *** * *
38369088 ATATCC-GGCTAA-ATTCCGAAGAAAGGTT-TAATAAATGCTTT
1 ATATCCGGGCTAAGA-CCCGAAGGCA-TTTGTGCGAATTG--AT
* * ** * * * ** *
38369129 GTGTTTGAGCCTTAGTA-ACGAAAGTG-AAATATG-G-ATGTG-T
1 ATATCCG-GGCTAAG-ACCCG-AAG-GCATTTGTGCGAAT-TGAT
* * * * * * * *
38369169 CATGAT-TGTTGAT-ATA--TG-TGTGCA--TGAGC-ATTTGAAT
1 -AT-ATCCG-GGCTAAGACCCGAAG-GCATTTGTGCGAATTG-AT
38369206 GATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 -ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
38369247 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
38369287 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
38369327 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
38369367 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
38369407 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
38369447 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
38369487 ATATCCGGGGTAAGACCTGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
38369527 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
38369567 ATATCCGGGCTAAGACCTGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
38369607 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
38369647 ATATCCGGGATAAGACCCGAAGGCATTTGTGCGAACTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
* *
38369687 ATATCCGGGCTAAGACCCGACGGCGTTTGTGCGAATTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
*
38369727 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC-AAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAA-TTGAT
* * *
38369767 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
** *
38369807 ATGCCCGGGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCA
38369832 ATTGAGCTTG
Statistics
Matches: 1122, Mismatches: 111, Indels: 62
0.87 0.09 0.05
Matches are distributed among these distances:
35 4 0.00
36 8 0.01
37 7 0.01
38 2 0.00
39 23 0.02
40 1041 0.93
41 16 0.01
42 6 0.01
43 9 0.01
44 5 0.00
45 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAATTGAT
Found at i:38375920 original size:35 final size:34
Alignment explanation
Indices: 38375901--38375995 Score: 154
Period size: 35 Copynumber: 2.7 Consensus size: 34
38375891 TCAGTTGCAC
*
38375901 TAGCTCTTATGAGCATTGGTGTGTTTTGATGGGAT
1 TAGCTCTTATGAGCATTGGTGTGTTTAG-TGGGAT
*
38375936 TAGCTCTTATGAGCATTGGTGTGTTTTAGAGGGAT
1 TAGCTCTTATGAGCATTGGTGTG-TTTAGTGGGAT
38375971 TAGCTCTTATGAGCATTGGTGTGTT
1 TAGCTCTTATGAGCATTGGTGTGTT
38375996 GTAACACTTA
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
34 2 0.04
35 51 0.89
36 4 0.07
ACGTcount: A:0.18, C:0.09, G:0.31, T:0.42
Consensus pattern (34 bp):
TAGCTCTTATGAGCATTGGTGTGTTTAGTGGGAT
Found at i:38382048 original size:24 final size:25
Alignment explanation
Indices: 38381988--38382042 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
38381978 CCAATATTTG
* *
38381988 GCTCTCACGAGCTTCCCGTTATATG
1 GCTCTTACGAGCTTCCCGTTATATA
*
38382013 GTTCTTACGAGCTTCCCGTTA-ATA
1 GCTCTTACGAGCTTCCCGTTATATA
38382037 GCTCTT
1 GCTCTT
38382043 TGGAGCATCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.16, C:0.29, G:0.18, T:0.36
Consensus pattern (25 bp):
GCTCTTACGAGCTTCCCGTTATATA
Found at i:38382145 original size:25 final size:25
Alignment explanation
Indices: 38382117--38382186 Score: 77
Period size: 27 Copynumber: 2.7 Consensus size: 25
38382107 CTCGATATAT
**
38382117 GGCTCTTTGGAGCTTCCTGATTAAA
1 GGCTCTTTGGAGCTTCCCAATTAAA
* *
38382142 GGCTCTTTCATGAGCTTCCCAATTAAT
1 GGCTCTTT--GGAGCTTCCCAATTAAA
*
38382169 GGCTCTCTGGAGCTTCCC
1 GGCTCTTTGGAGCTTCCC
38382187 GATATTGGCT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
25 17 0.46
27 20 0.54
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.34
Consensus pattern (25 bp):
GGCTCTTTGGAGCTTCCCAATTAAA
Found at i:38382279 original size:25 final size:25
Alignment explanation
Indices: 38382225--38382317 Score: 82
Period size: 25 Copynumber: 3.7 Consensus size: 25
38382215 ATTAGCTCGT
*
38382225 ATGAGCTTCCCGTTA-ATGGCTC-T
1 ATGAGCTTCCCGTTACATGGCTCAA
* *
38382248 CTAGAGCTTCCCGTTACATGGCTCAG
1 AT-GAGCTTCCCGTTACATGGCTCAA
* **
38382274 ATGAGCTTCTCGTTTTATGGCTCAA
1 ATGAGCTTCCCGTTACATGGCTCAA
* *
38382299 AAGAGCTTCCTGTTTACAT
1 ATGAGCTTCCCG-TTACAT
38382318 TTCTGCATAA
Statistics
Matches: 54, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
23 1 0.02
24 13 0.24
25 35 0.65
26 5 0.09
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.34
Consensus pattern (25 bp):
ATGAGCTTCCCGTTACATGGCTCAA
Found at i:38384735 original size:11 final size:10
Alignment explanation
Indices: 38384709--38384737 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
38384699 AAGAACAAGA
38384709 AGAAAAATAC
1 AGAAAAATAC
38384719 AGAAAAATAC
1 AGAAAAATAC
38384729 AGAAAAATA
1 AGAAAAATA
38384738 AATACTACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.72, C:0.07, G:0.10, T:0.10
Consensus pattern (10 bp):
AGAAAAATAC
Found at i:38389076 original size:6 final size:6
Alignment explanation
Indices: 38389065--38389089 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
38389055 ATCAATAATC
38389065 AAATAA AAATAA AAATAA AAATAA A
1 AAATAA AAATAA AAATAA AAATAA A
38389090 TTTCACTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:38390347 original size:17 final size:18
Alignment explanation
Indices: 38390321--38390357 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
38390311 ACACAAGGTC
38390321 CACCACCTTCT-GAATAT
1 CACCACCTTCTGGAATAT
*
38390338 CACCAGCTTCTGGAATAT
1 CACCACCTTCTGGAATAT
38390356 CA
1 CA
38390358 GATGTTGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.30, C:0.32, G:0.11, T:0.27
Consensus pattern (18 bp):
CACCACCTTCTGGAATAT
Found at i:38394352 original size:14 final size:14
Alignment explanation
Indices: 38394335--38394361 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38394325 CCTTGGACCC
38394335 TGGACCCTAAACCA
1 TGGACCCTAAACCA
38394349 TGGACCCTAAACC
1 TGGACCCTAAACC
38394362 CAGACCTTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.37, G:0.15, T:0.15
Consensus pattern (14 bp):
TGGACCCTAAACCA
Found at i:38396150 original size:19 final size:20
Alignment explanation
Indices: 38396113--38396150 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
38396103 ATTTAAAAAC
**
38396113 TTAATTATTACTTTGATATT
1 TTAATTATTACTTACATATT
38396133 TTAATTA-TACTTACATAT
1 TTAATTATTACTTACATAT
38396151 ATGCAAATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.34, C:0.08, G:0.03, T:0.55
Consensus pattern (20 bp):
TTAATTATTACTTACATATT
Found at i:38396542 original size:36 final size:36
Alignment explanation
Indices: 38396502--38396577 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 36
38396492 TGACATTATG
38396502 GAATA-AATTAATGA-ATGATTAATAGATAATTGAAGT
1 GAATATAA-TAATGAGATGATTAATAGATAA-TGAAGT
* * *
38396538 GAATATGATATTGAGTTGATTAATAGATAATGAAGT
1 GAATATAATAATGAGATGATTAATAGATAATGAAGT
38396574 GAAT
1 GAAT
38396578 GTGATATTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 20 0.57
37 15 0.43
ACGTcount: A:0.46, C:0.00, G:0.20, T:0.34
Consensus pattern (36 bp):
GAATATAATAATGAGATGATTAATAGATAATGAAGT
Found at i:38396550 original size:17 final size:17
Alignment explanation
Indices: 38396530--38396587 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
38396520 TTAATAGATA
38396530 ATTGAAGTGAATATGAT
1 ATTGAAGTGAATATGAT
*
38396547 ATTG-AGTTGATTAATAGAT
1 ATTGAAG-TGAAT-AT-GAT
* *
38396566 AATGAAGTGAATGTGAT
1 ATTGAAGTGAATATGAT
38396583 ATTGA
1 ATTGA
38396588 GTTATGAAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
16 2 0.06
17 15 0.47
18 3 0.09
19 10 0.31
20 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.24, T:0.36
Consensus pattern (17 bp):
ATTGAAGTGAATATGAT
Found at i:38396583 original size:36 final size:37
Alignment explanation
Indices: 38396517--38396590 Score: 132
Period size: 36 Copynumber: 2.0 Consensus size: 37
38396507 AATTAATGAA
38396517 TGATTAATAGATAATTGAAGTGAATATGATATTGAGT
1 TGATTAATAGATAATTGAAGTGAATATGATATTGAGT
*
38396554 TGATTAATAGATAA-TGAAGTGAATGTGATATTGAGT
1 TGATTAATAGATAATTGAAGTGAATATGATATTGAGT
38396590 T
1 T
38396591 ATGAAACGTG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 22 0.61
37 14 0.39
ACGTcount: A:0.39, C:0.00, G:0.23, T:0.38
Consensus pattern (37 bp):
TGATTAATAGATAATTGAAGTGAATATGATATTGAGT
Found at i:38396603 original size:20 final size:21
Alignment explanation
Indices: 38396578--38396617 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
38396568 TGAAGTGAAT
38396578 GTGATATTGAG-TTATGAAAC
1 GTGATATTGAGATTATGAAAC
38396598 GTGATATTGAGATTATGAAA
1 GTGATATTGAGATTATGAAA
38396618 TATGATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.35
Consensus pattern (21 bp):
GTGATATTGAGATTATGAAAC
Found at i:38396623 original size:21 final size:20
Alignment explanation
Indices: 38396579--38396623 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
38396569 GAAGTGAATG
*
38396579 TGATATTGAGTTATGAAACG
1 TGATATTGAGTTATGAAACA
*
38396599 TGATATTGAGATTATGAAATA
1 TGATATTGAG-TTATGAAACA
38396620 TGAT
1 TGAT
38396624 TTTATGGACT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.38
Consensus pattern (20 bp):
TGATATTGAGTTATGAAACA
Found at i:38396747 original size:40 final size:40
Alignment explanation
Indices: 38396687--38396815 Score: 117
Period size: 40 Copynumber: 3.4 Consensus size: 40
38396677 GGGCACAATC
* *
38396687 ATCGTTGGTTCATCCAACTAGAGCTTGGCTCACTATTTAT
1 ATCGTCGGTTTATCCAACTAGAGCTTGGCTCACTATTTAT
* * * *
38396727 ATCGTCGGTTTATTCGACTAGCG-TTGGGCGCA--A---AT
1 ATCGTCGGTTTATCCAACTAGAGCTT-GGCTCACTATTTAT
* * *
38396762 ATCGTTGGTTTATCCAACTAGATCTGGGCTCACTATTTAT
1 ATCGTCGGTTTATCCAACTAGAGCTTGGCTCACTATTTAT
*
38396802 ATCGTCAGTTTATC
1 ATCGTCGGTTTATC
38396816 TGAATAGCGC
Statistics
Matches: 67, Mismatches: 15, Indels: 14
0.70 0.16 0.15
Matches are distributed among these distances:
35 25 0.37
36 1 0.01
37 1 0.01
38 1 0.01
39 2 0.03
40 37 0.55
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (40 bp):
ATCGTCGGTTTATCCAACTAGAGCTTGGCTCACTATTTAT
Found at i:38396778 original size:75 final size:75
Alignment explanation
Indices: 38396650--38396864 Score: 308
Period size: 75 Copynumber: 2.9 Consensus size: 75
38396640 TGAGTAATTG
* * * * * *
38396650 ATATTGTCGGTTCATTCGACTAGTGCTGGGCAC-AATCATCGTTGGTTCATCCAACTAGAGCTTG
1 ATATCGTCGGTTTATTCGACTAGCGCTGGGCGCAAAT-ATCGTTGGTTTATCCAACTAGAGCTGG
38396714 GCTCACTATTT
65 GCTCACTATTT
* *
38396725 ATATCGTCGGTTTATTCGACTAGCGTTGGGCGCAAATATCGTTGGTTTATCCAACTAGATCTGGG
1 ATATCGTCGGTTTATTCGACTAGCGCTGGGCGCAAATATCGTTGGTTTATCCAACTAGAGCTGGG
38396790 CTCACTATTT
66 CTCACTATTT
* *
38396800 ATATCGTCAGTTTA-TCTGAATAGCGCTGGGCGCAAATATCGTTGGTTTATCCAACTAGAGCTGG
1 ATATCGTCGGTTTATTC-GACTAGCGCTGGGCGCAAATATCGTTGGTTTATCCAACTAGAGCTGG
38396864 G
65 G
38396865 ATAACTGATT
Statistics
Matches: 126, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
74 2 0.02
75 121 0.96
76 3 0.02
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.34
Consensus pattern (75 bp):
ATATCGTCGGTTTATTCGACTAGCGCTGGGCGCAAATATCGTTGGTTTATCCAACTAGAGCTGGG
CTCACTATTT
Found at i:38396863 original size:35 final size:35
Alignment explanation
Indices: 38396668--38396864 Score: 128
Period size: 35 Copynumber: 5.3 Consensus size: 35
38396658 GGTTCATTCG
* * *
38396668 ACTAGTGCTGGGCAC-AATCATCGTTGGTTCATCCA
1 ACTAGAGCTGGGCGCAAAT-ATCGTTGGTTTATCCA
* * * * *
38396703 ACTAGAGCTTGGCTCACTATTTATATCGTCGGTTTATTCG
1 ACTAGAGCTGGGCGCA--A---ATATCGTTGGTTTATCCA
* *
38396743 ACTAGCGTTGGGCGCAAATATCGTTGGTTTATCCA
1 ACTAGAGCTGGGCGCAAATATCGTTGGTTTATCCA
* * ** *
38396778 ACTAGATCTGGGCTCACTATTTATATCGTCAGTTTATCTGA
1 ACTAGAGCTGGGCGCA--A---ATATCGTTGGTTTATC-CA
*
38396819 A-TAGCGCTGGGCGCAAATATCGTTGGTTTATCCA
1 ACTAGAGCTGGGCGCAAATATCGTTGGTTTATCCA
38396853 ACTAGAGCTGGG
1 ACTAGAGCTGGG
38396865 ATAACTGATT
Statistics
Matches: 121, Mismatches: 28, Indels: 26
0.69 0.16 0.15
Matches are distributed among these distances:
34 2 0.02
35 62 0.51
37 1 0.01
38 3 0.02
40 49 0.40
41 4 0.03
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (35 bp):
ACTAGAGCTGGGCGCAAATATCGTTGGTTTATCCA
Found at i:38409698 original size:47 final size:47
Alignment explanation
Indices: 38409647--38409807 Score: 243
Period size: 47 Copynumber: 3.4 Consensus size: 47
38409637 TTAGGATTCT
* * *
38409647 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
**
38409694 ATGTGATGAATGCAAAAGTGTATATACATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATAT--ATGTGATAAGGCCTAATGGCCG
38409743 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
38409790 ATGTGATGAATGTGAAAG
1 ATGTGATGAATGTGAAAG
38409808 GGCCGAGTGG
Statistics
Matches: 104, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
46 1 0.01
47 59 0.57
49 44 0.42
ACGTcount: A:0.34, C:0.10, G:0.29, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:38409737 original size:49 final size:47
Alignment explanation
Indices: 38409668--38409801 Score: 223
Period size: 49 Copynumber: 2.8 Consensus size: 47
38409658 GTGAACATGC
*
38409668 ATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGCAAAAGTGT
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGCAAAAGTGT
**
38409715 ATATACATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
1 ATAT--ATGTGATAAGGCCTAATGGCCGATGTGATGAATGCAAAAGTGT
38409764 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATG
1 ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATG
38409802 TGAAAGGGCC
Statistics
Matches: 82, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
47 38 0.46
49 44 0.54
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.28
Consensus pattern (47 bp):
ATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGCAAAAGTGT
Found at i:38410030 original size:37 final size:37
Alignment explanation
Indices: 38409974--38410052 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
38409964 CCGAGCTCTA
* * * *
38409974 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCAGGT
*
38410011 AAGACCCGATAACTTCGTGTGGAGATTATGTCCAGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCAGGT
38410048 AAGAC
1 AAGAC
38410053 TTCGTAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCAGGT
Found at i:38411978 original size:43 final size:43
Alignment explanation
Indices: 38411917--38412019 Score: 197
Period size: 43 Copynumber: 2.4 Consensus size: 43
38411907 TTGGTTTTCA
38411917 GCACTAAGTGTGCGGGCAATAAGTGTTCACGATTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGATTGTGAGATTG
*
38411960 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGATTGTGAGATTG
38412003 GCACTAAGTGTGCGGGC
1 GCACTAAGTGTGCGGGC
38412020 TTGAAATGCA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.23, C:0.16, G:0.35, T:0.26
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGATTGTGAGATTG
Found at i:38412039 original size:29 final size:29
Alignment explanation
Indices: 38412001--38412074 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
38411991 GTTGTGAGAT
* *
38412001 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
* *
38412030 TGGCAATAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
38412059 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
38412075 TGGTTGATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
28 5 0.13
29 34 0.87
ACGTcount: A:0.27, C:0.15, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:38412619 original size:40 final size:40
Alignment explanation
Indices: 38412422--38412607 Score: 257
Period size: 40 Copynumber: 4.7 Consensus size: 40
38412412 CTAAGTGACC
38412422 ATATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGAT
1 ATATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGAT
* *
38412462 GTATCCGGACTATGTTCCGAAGAGCATTCGTGCTAGTGAT
1 ATATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGAT
*
38412502 GTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGAT
1 ATATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGAT
*** * *
38412542 ATATCCGTG-CTAAACCCCGAAGAGCATTCGTGCTGGTGTT
1 ATATCCG-GACTAAGTTCCGAAGAGCATTCGTGCTAGTGAT
* * *
38412582 ATATCCGGGCTAGGTCCCGAAGAGCA
1 ATATCCGGACTAAGTTCCGAAGAGCA
38412608 ATCATGCTGG
Statistics
Matches: 132, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
39 1 0.01
40 130 0.98
41 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGAT
Found at i:38416021 original size:47 final size:47
Alignment explanation
Indices: 38415970--38416241 Score: 393
Period size: 47 Copynumber: 5.7 Consensus size: 47
38415960 TTAGGATTCT
* * *
38415970 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
* *
38416017 ATGTGATGAATGCGAAAGTGTATATACATGTGACAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATAT--ATGTGATAAGGCCTAATGGCCG
38416066 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
38416113 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
38416160 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
38416207 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
38416242 TCCCGAAGGG
Statistics
Matches: 205, Mismatches: 17, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
46 1 0.00
47 160 0.78
49 44 0.21
ACGTcount: A:0.32, C:0.10, G:0.31, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:38416410 original size:37 final size:37
Alignment explanation
Indices: 38416360--38416475 Score: 196
Period size: 37 Copynumber: 3.1 Consensus size: 37
38416350 CCGAGCTCTA
38416360 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
38416397 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
* * * *
38416434 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
38416471 AAGAC
1 AAGAC
38416476 TTCGTAATAA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 75 1.00
ACGTcount: A:0.22, C:0.19, G:0.33, T:0.26
Consensus pattern (37 bp):
AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
Found at i:38419604 original size:64 final size:63
Alignment explanation
Indices: 38419529--38419665 Score: 175
Period size: 63 Copynumber: 2.2 Consensus size: 63
38419519 AGACATGTGT
* * * *
38419529 TAATGCGGTACAAACGAAGACACCATTAATAGACTTAAAACAACTAAAACAATTACACATGTAA
1 TAATGCTGTACAAACCAAGACACAATTAATAGACTT-AAACAACTAAAACAATCACACATGTAA
* * * * *
38419593 TAATGCTGTACAAACCATGACACAATTAATAGGCTTAAACAACTAAGATAATCAGACATGTAA
1 TAATGCTGTACAAACCAAGACACAATTAATAGACTTAAACAACTAAAACAATCACACATGTAA
*
38419656 TAATGTTGTA
1 TAATGCTGTA
38419666 TGAAATCAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
63 32 0.51
64 31 0.49
ACGTcount: A:0.47, C:0.17, G:0.12, T:0.24
Consensus pattern (63 bp):
TAATGCTGTACAAACCAAGACACAATTAATAGACTTAAACAACTAAAACAATCACACATGTAA
Found at i:38438813 original size:40 final size:40
Alignment explanation
Indices: 38438715--38439017 Score: 396
Period size: 40 Copynumber: 7.6 Consensus size: 40
38438705 TCCTCGTTCA
* * * * *
38438715 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
38438754 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
38438794 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
38438834 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
38438874 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
38438914 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
38438954 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
38438994 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
38439018 CAGCATTCAA
Statistics
Matches: 240, Mismatches: 20, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
39 37 0.15
40 195 0.81
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:38445555 original size:40 final size:40
Alignment explanation
Indices: 38445457--38445759 Score: 396
Period size: 40 Copynumber: 7.6 Consensus size: 40
38445447 TCCTCGTTCA
* * * * *
38445457 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
38445496 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
38445536 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
38445576 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
38445616 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
38445656 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
38445696 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
38445736 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
38445760 CAGCATTCAA
Statistics
Matches: 240, Mismatches: 20, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
39 37 0.15
40 195 0.81
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:38448965 original size:88 final size:88
Alignment explanation
Indices: 38448467--38448953 Score: 659
Period size: 88 Copynumber: 5.5 Consensus size: 88
38448457 AAGATAACAA
* * ** * * ** *
38448467 ATCTTGCCTTCCTGTACTGACAGTAAAGTAGATCGAAGACACTAGCCTTGCCTCCCTCAGTGGCA
1 ATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCA
*
38448532 GCGGAGCAGGCTAAAAATAGCAT
66 GCGGAGCAGGCTAAAAATAGCAG
* *
38448555 ATCTTGCCTTCCTGCACCGACAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTTGCA
1 ATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCA
* * * *
38448620 GCAGAGCGGGCTGAAAATAGTAG
66 GCGGAGCAGGCTAAAAATAGCAG
* * *
38448643 ATCTTGCCTTCCTGCACCGACAACGAAGCAGATCGAAGTCACCAGCCTTGCCTCCCTGGGTTGTA
1 ATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCA
*
38448708 GTGGAGCAGGCTAAAAATAGCAG
66 GCGGAGCAGGCTAAAAATAGCAG
* * * * *
38448731 ATCTTACCTTCCTTCACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCTTGGGTTGTA
1 ATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCA
* * *
38448796 GCAGAGCAGACTAAAAATAACAG
66 GCGGAGCAGGCTAAAAATAGCAG
38448819 ATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCA
1 ATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCA
* *
38448884 GTGGAGCAGGTTAAAAATAGCAG
66 GCGGAGCAGGCTAAAAATAGCAG
* * * * *
38448907 ATCTTGCCTTCTTGCACTGACAGCGAAGCAGATTGATGACCCCAGCC
1 ATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCC
38448954 CTATCTCCCT
Statistics
Matches: 351, Mismatches: 48, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
88 351 1.00
ACGTcount: A:0.27, C:0.28, G:0.24, T:0.21
Consensus pattern (88 bp):
ATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCA
GCGGAGCAGGCTAAAAATAGCAG
Found at i:38449019 original size:44 final size:44
Alignment explanation
Indices: 38448953--38449329 Score: 374
Period size: 44 Copynumber: 8.7 Consensus size: 44
38448943 TGACCCCAGC
** * *
38448953 CCTATCTCCCTGGTTAGTAGTGGAATAGGTTAAAGATTGTGAAC
1 CCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAAT
* *
38448997 CCTATCTTCTTGGACAGCAGTGGAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAAT
* * * *
38449041 CCTATCTCCCTGGTCAGCAGTGGAAGAGGTTGAAGATTGAGAAT
1 CCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAAT
* * **
38449085 TCTATCTCCCTGGGCAGCAGTGGAATAAATT--A-A---TGAAT
1 CCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAAT
* * *
38449123 CTTATCTCCCTGGATAGTAGTGGAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAAT
** * * *
38449167 CCTATCTCCCTGGTTAGCAGTGGAATATGTTGAAATATTGAGAAT
1 CCTATCTCCCTGGACAGCAGTGGAATAGGTT-AAAGATTGTGAAT
* * * * * *
38449212 TCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGGTTGT-AGGT
1 CCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGA-AT
* * * *
38449256 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATCGTGAAC
1 CCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAAT
*
38449300 CCTATCTCCCT-GAGCAGCAGTGGAGTAGGT
1 CCTATCTCCCTGGA-CAGCAGTGGAATAGGT
38449330 GGAAAATAGC
Statistics
Matches: 273, Mismatches: 50, Indels: 20
0.80 0.15 0.06
Matches are distributed among these distances:
38 28 0.10
40 1 0.00
41 2 0.01
42 1 0.00
43 2 0.01
44 201 0.74
45 38 0.14
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.29
Consensus pattern (44 bp):
CCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAAT
Found at i:38450183 original size:17 final size:17
Alignment explanation
Indices: 38450161--38450212 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 17
38450151 ATGGAAACAT
* *
38450161 AATCTTCGAGGATATGC
1 AATCTTAGAAGATATGC
38450178 AATCTTAGATATGATATGC
1 AATCTTAGA-A-GATATGC
38450197 AATCTTAGAAGATATG
1 AATCTTAGAAGATATG
38450213 ATTTTGTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 14 0.45
18 1 0.03
19 16 0.52
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.33
Consensus pattern (17 bp):
AATCTTAGAAGATATGC
Found at i:38450227 original size:23 final size:22
Alignment explanation
Indices: 38450171--38450228 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 22
38450161 AATCTTCGAG
38450171 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
38450190 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
38450212 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
38450229 TATTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.39
22 8 0.24
23 12 0.36
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:38452859 original size:50 final size:50
Alignment explanation
Indices: 38452568--38452859 Score: 374
Period size: 50 Copynumber: 5.9 Consensus size: 50
38452558 GATAATAACA
* * * * * *
38452568 TGCCAAAGCCATGTCCCAAACATGGTCGTACATGGGATGCT-TTTTGTAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTTATCT-CGG
* * * * ** * *
38452617 TGCCAATGTCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
* * * *
38452667 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
*
38452717 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
38452767 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
38452817 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTT
38452860 TACCCAAATG
Statistics
Matches: 216, Mismatches: 24, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
48 3 0.01
49 34 0.16
50 179 0.83
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
Found at i:38453228 original size:29 final size:29
Alignment explanation
Indices: 38453195--38453254 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
38453185 CCTTGACTCG
38453195 AACTTTGGAAAAATTACAATTTTGCCCCA
1 AACTTTGGAAAAATTACAATTTTGCCCCA
* * * *
38453224 AACTTTTGCATAATTACACTTTTGCCCCA
1 AACTTTGGAAAAATTACAATTTTGCCCCA
38453253 AA
1 AA
38453255 GCTCGGAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.33
Consensus pattern (29 bp):
AACTTTGGAAAAATTACAATTTTGCCCCA
Found at i:38457326 original size:45 final size:44
Alignment explanation
Indices: 38457142--38457349 Score: 170
Period size: 45 Copynumber: 4.6 Consensus size: 44
38457132 CGAAATGAGA
* * * *
38457142 AAGACCATAATTGAAAGATACTATGGCACTAAACCGACAATGTGT
1 AAGACCATAGTTGAAAGATACTATGGCACTAAATCGAGAATG-AT
* * * ** *
38457187 AAAACCATAGTTGAAAGATATTGTGGCGTTAAATCCA-ATATGAAT
1 AAGACCATAGTTGAAAGATACTATGGCACTAAATCGAGA-ATG-AT
* * *
38457232 AAGACAATAGTTGAAAGATACTATGACA-TCACATCG-GTAATGAT
1 AAGACCATAGTTGAAAGATACTATGGCACT-AAATCGAG-AATGAT
**
38457276 CAAGACCATAGTTGAAAGATACTATGGCACTACTTCGAGAATGCAT
1 -AAGACCATAGTTGAAAGATACTATGGCACTAAATCGAGAATG-AT
* * *
38457322 AAGACCATGGTTGGAAGATACCATGGCA
1 AAGACCATAGTTGAAAGATACTATGGCA
38457350 TCCTTTGAAA
Statistics
Matches: 131, Mismatches: 24, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
44 4 0.03
45 122 0.93
46 5 0.04
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (44 bp):
AAGACCATAGTTGAAAGATACTATGGCACTAAATCGAGAATGAT
Found at i:38459173 original size:34 final size:34
Alignment explanation
Indices: 38459134--38459201 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
38459124 CCATCCAAGA
38459134 CATAACTTTTGAGTAGGTGATATTGGCTTCAAAC
1 CATAACTTTTGAGTAGGTGATATTGGCTTCAAAC
38459168 CATAACTTTTGAGTAGGTGATATTGGCTTCAAAC
1 CATAACTTTTGAGTAGGTGATATTGGCTTCAAAC
38459202 TATGAACAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (34 bp):
CATAACTTTTGAGTAGGTGATATTGGCTTCAAAC
Found at i:38462326 original size:79 final size:81
Alignment explanation
Indices: 38462190--38462374 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 81
38462180 TTGAATGATG
* *
38462190 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
38462254 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
38462269 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
38462331 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* * *
38462349 ACTGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
38462375 AACGAGTAGC
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 1 0.01
79 56 0.62
80 33 0.37
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:38462381 original size:40 final size:40
Alignment explanation
Indices: 38462190--38462374 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
38462180 TTGAATGATG
* * * *
38462190 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
38462230 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
38462270 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
38462309 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
38462350 -CTGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
38462375 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:38462396 original size:79 final size:79
Alignment explanation
Indices: 38462243--38462407 Score: 192
Period size: 79 Copynumber: 2.1 Consensus size: 79
38462233 GGACTAAGAT
* * **
38462243 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
38462308 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * *
38462322 CCGAAGGCAATTGTGCGAGTTACT-ATAACTGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
38462385 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
38462401 CCGAAGG
1 CCGAAGG
38462408 TACGTGATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
78 2 0.03
79 46 0.63
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:38479571 original size:22 final size:22
Alignment explanation
Indices: 38479546--38479589 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
38479536 AGCTTCCAAC
38479546 CCGATCAAGCTTTTGATAATCT
1 CCGATCAAGCTTTTGATAATCT
38479568 CCGATCAAGCTTTTGATAATCT
1 CCGATCAAGCTTTTGATAATCT
38479590 ATAAAGTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (22 bp):
CCGATCAAGCTTTTGATAATCT
Found at i:38483049 original size:78 final size:80
Alignment explanation
Indices: 38482873--38483175 Score: 363
Period size: 78 Copynumber: 3.8 Consensus size: 80
38482863 GCTCCTCGTT
* * *
38482873 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCACAAATGCCTTCGGGACTTAACCC
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAATCTCGCACAAATGCCTTCGGGACTTAGCCC
*
38482936 GGATTTAGTAACTCGCA
64 GGATTTAGTATCTCGCA
38482953 CAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTAATCTCGCACAAATGCCTTCGGGACTTAGCCCGG
* *
38483016 AATTAGTATCTCGTA
66 ATTTAGTATCTCGCA
* * *
38483031 CAAATGCCTTCGGGCTTAGCCTGGAATTAGT-ATCTCTCACAAATGCCTTC-GGATCTTAGTCCG
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTAATCTCGCACAAATGCCTTCGGGA-CTTAGCCCG
38483094 GATTTAGTATCTCGCA
65 GATTTAGTATCTCGCA
* * * * *
38483110 CAAATGCCTTCGGATCTTGGTCCGGATATT-GTCA-CTTAGCACAAA-GCCTTCGGGACTTAGCC
1 CAAATGCCTTCGG-GCTTAGCCCGGA-ATTAGTAATC-TCGCACAAATGCCTTCGGGACTTAGCC
38483172 CGGA
63 CGGA
38483176 CATCATTCAA
Statistics
Matches: 196, Mismatches: 18, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
77 2 0.01
78 71 0.36
79 67 0.34
80 42 0.21
81 14 0.07
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.27
Consensus pattern (80 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTAATCTCGCACAAATGCCTTCGGGACTTAGCCCGG
ATTTAGTATCTCGCA
Found at i:38483175 original size:40 final size:41
Alignment explanation
Indices: 38482873--38483175 Score: 357
Period size: 40 Copynumber: 7.6 Consensus size: 41
38482863 GCTCCTCGTT
* *
38482873 CAAATGCCTTCGGGACATAGCCCGGTTA-TAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATTAGT-ATCTCGCA
* *
38482913 CAAATGCCTTCGGGACTTAACCCGGAT-TTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATTAGTATCTCGCA
38482953 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATTAGTATCTCGCA
*
38482992 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGATATTAGTATCTCGCA
* *
38483031 CAAATGCCTTCGGG-CTTAGCCTGGA-ATTAGTATCTCTCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATTAGTATCTCGCA
*
38483070 CAAATGCCTTC-GGATCTTAGTCCGGAT-TTAGTATCTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATTAGTATCTCGCA
* * *
38483110 CAAATGCCTTC-GGATCTTGGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATTAGT-ATC-TCGCA
38483151 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
38483176 CATCATTCAA
Statistics
Matches: 236, Mismatches: 17, Indels: 20
0.86 0.06 0.07
Matches are distributed among these distances:
38 2 0.01
39 108 0.46
40 112 0.47
41 14 0.06
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.27
Consensus pattern (41 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATTAGTATCTCGCA
Found at i:38490987 original size:39 final size:39
Alignment explanation
Indices: 38490870--38491119 Score: 360
Period size: 39 Copynumber: 6.3 Consensus size: 39
38490860 GCTCCTCGTT
* *
38490870 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
38490910 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
*
38490950 CAAATTCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
38490989 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
38491028 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
* * *
38491067 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGG-GCTTAGCCCGGAATTAGTATCTCGCA
38491107 CAAATGCCTTCGG
1 CAAATGCCTTCGG
38491120 ATCTTGGTCC
Statistics
Matches: 196, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
39 113 0.58
40 81 0.41
41 2 0.01
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
Found at i:38491120 original size:40 final size:40
Alignment explanation
Indices: 38490870--38491172 Score: 340
Period size: 39 Copynumber: 7.7 Consensus size: 40
38490860 GCTCCTCGTT
*
38490870 CAAATGCCTTCGG-GACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGAG-CTTAGCCCGGATT-TAGT-ATCTCGCA
* *
38490910 CAAATGCCTTCGG-GACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGAG-CTTAGCCCGGATTTAGTATCTCGCA
* *
38490950 CAAATTCCTTCGG-GCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGAGCTTAGCCCGGATTTAGTATCTCGCA
*
38490989 CAAATGCCTTCGG-GCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGAGCTTAGCCCGGATTTAGTATCTCGCA
*
38491028 CAAATGCCTTCGG-GCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGAGCTTAGCCCGGATTTAGTATCTCGCA
* *
38491067 CAAATGCCTTCGGATCTTAGTCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGAGCTTAGCCCGGATTTAGTATCTCGCA
* * * *
38491107 CAAATGCCTTCGGATCTTGGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGAGCTTAGCCCGGAT-TTAGT-ATC-TCGCA
38491148 CAAA-GCCTTC-GAGACTTAGCCCGGA
1 CAAATGCCTTCGGAG-CTTAGCCCGGA
38491173 CATCATTCAA
Statistics
Matches: 240, Mismatches: 16, Indels: 14
0.89 0.06 0.05
Matches are distributed among these distances:
39 115 0.48
40 112 0.47
41 13 0.05
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (40 bp):
CAAATGCCTTCGGAGCTTAGCCCGGATTTAGTATCTCGCA
Found at i:38493913 original size:40 final size:40
Alignment explanation
Indices: 38493869--38493949 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
38493859 GTGGACATAG
**
38493869 CTCACGACCTTGTCCCTGCGAGCCTTACGCGAACTCTCCT
1 CTCACGACCTCATCCCTGCGAGCCTTACGCGAACTCTCCT
* * * *
38493909 CTCACGACCTCATTCCTGCGAGGCTTACGTGAGCTCTCCT
1 CTCACGACCTCATCCCTGCGAGCCTTACGCGAACTCTCCT
38493949 C
1 C
38493950 GCGGGCTTCT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.15, C:0.41, G:0.19, T:0.26
Consensus pattern (40 bp):
CTCACGACCTCATCCCTGCGAGCCTTACGCGAACTCTCCT
Found at i:38500570 original size:16 final size:16
Alignment explanation
Indices: 38500549--38500580 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
38500539 GTTTTGTTGC
*
38500549 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
38500565 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
38500581 CTTTTAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:38500865 original size:51 final size:51
Alignment explanation
Indices: 38500806--38500996 Score: 207
Period size: 51 Copynumber: 3.8 Consensus size: 51
38500796 CCGGTTCACA
*
38500806 TAGTAGCCTGAACATAGTACTACATATGTGACCATCACTATCCGATACACG
1 TAGTAGCCTGAACATAGTACTACACATGTGACCATCACTATCCGATACACG
* * ** *
38500857 TAGTAGCCTGCACATAGTACTACACACGTGATGGA--AGCTATCCAGTATGCA--
1 TAGTAGCCTGAACATAGTACTACACATGTGA-CCATCA-CTATCC-G-ATACACG
* *
38500908 TAGTAGCCTGTACATAGTACTACACATGCGACCTATCA-T-TCCGATACACG
1 TAGTAGCCTGAACATAGTACTACACATGTGACC-ATCACTATCCGATACACG
38500958 TAGTAGCCT-ACACATAGTACTACACATGTGACCATCACT
1 TAGTAGCCTGA-ACATAGTACTACACATGTGACCATCACT
38500997 TTCACTTTCA
Statistics
Matches: 115, Mismatches: 14, Indels: 23
0.76 0.09 0.15
Matches are distributed among these distances:
48 4 0.03
49 5 0.04
50 35 0.30
51 64 0.56
52 2 0.02
53 5 0.04
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (51 bp):
TAGTAGCCTGAACATAGTACTACACATGTGACCATCACTATCCGATACACG
Found at i:38500963 original size:101 final size:102
Alignment explanation
Indices: 38500804--38500988 Score: 302
Period size: 101 Copynumber: 1.8 Consensus size: 102
38500794 TACCGGTTCA
* * *
38500804 CATAGTAGCCTGAACATAGTACTACATATGTGACCATCACTATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGAACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTACA
38500869 CATAGTACTACACACGTGATGGAAGCTATCCAGTATG
66 CATAGTACTACACACGTGATGGAAGCTATCCAGTATG
*
38500906 CATAGTAGCCTGTACATAGTACTACACATGCGACCTATCA-T-TCCGATACACGTAGTAGCCTAC
1 CATAGTAGCCTGAACATAGTACTACACATGCGACC-ATCACTATCCGATACACGTAGTAGCCTAC
*
38500969 ACATAGTACTACACATGTGA
65 ACATAGTACTACACACGTGA
38500989 CCATCACTTT
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
101 40 0.52
102 33 0.43
103 4 0.05
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.25
Consensus pattern (102 bp):
CATAGTAGCCTGAACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTACA
CATAGTACTACACACGTGATGGAAGCTATCCAGTATG
Found at i:38501011 original size:101 final size:103
Alignment explanation
Indices: 38500800--38501017 Score: 259
Period size: 101 Copynumber: 2.1 Consensus size: 103
38500790 ATGATACCGG
* *
38500800 TTCACATAGTAGCCTGAACATAGTACTACATATGTGACCATCACTATCCGATACACGTAGTAGCC
1 TTCACATAGTAGCCTGAACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCC
* ** *
38500865 TGCACATAGTACTACACACGTGATGGAAGCTATCCAGT
66 TACACATAGTACTACACACGTGATCCAAGCTATCCACT
* * *
38500903 AT-GCATAGTAGCCTGTACATAGTACTACACATGCGACCTATCA-T-TCCGATACACGTAGTAGC
1 TTCACATAGTAGCCTGAACATAGTACTACACATGCGACC-ATCACTATCCGATACACGTAGTAGC
* *
38500965 CTACACATAGTACTACACATGTGA-CCATCA-CT-TTCACT
65 CTACACATAGTACTACACACGTGATCCA--AGCTATCCACT
*
38501003 TTCACATAGTGGCCT
1 TTCACATAGTAGCCT
38501018 ACACACAGTC
Statistics
Matches: 97, Mismatches: 14, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
100 6 0.06
101 52 0.54
102 34 0.35
103 5 0.05
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.27
Consensus pattern (103 bp):
TTCACATAGTAGCCTGAACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCC
TACACATAGTACTACACACGTGATCCAAGCTATCCACT
Found at i:38503761 original size:20 final size:19
Alignment explanation
Indices: 38503714--38503762 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
38503704 TTTATTGAAA
*
38503714 ATGAATCAATATATATGTT
1 ATGAAACAATATATATGTT
*
38503733 AT-AATACAATTTATCATGTT
1 ATGAA-ACAATATAT-ATGTT
38503753 ATGAAACAAT
1 ATGAAACAAT
38503763 GTAAATCCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 2 0.08
19 9 0.36
20 12 0.48
21 2 0.08
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (19 bp):
ATGAAACAATATATATGTT
Found at i:38504609 original size:31 final size:31
Alignment explanation
Indices: 38504571--38504632 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
38504561 TCGTAACATC
38504571 GACACATGAAATACATTATGTATTTTATCTA
1 GACACATGAAATACATTATGTATTTTATCTA
*
38504602 GACACATGAAATACATTATGTATTTTCTCTA
1 GACACATGAAATACATTATGTATTTTATCTA
38504633 ACTCAGACGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.39
Consensus pattern (31 bp):
GACACATGAAATACATTATGTATTTTATCTA
Found at i:38508994 original size:42 final size:41
Alignment explanation
Indices: 38508933--38509127 Score: 204
Period size: 42 Copynumber: 4.7 Consensus size: 41
38508923 AACTCACACA
* *
38508933 ATGCCATAT-CCCAGATATGGTCTTACATGCTATCAT-ATATCG
1 ATGCCA-ATGCCCAGACATGGTCTTACATG-AATC-TCATATCG
* *
38508975 ATGCCAATAG-CCAG-CTATGGTCTTACAAGAATCTCATATTG
1 ATGCCAAT-GCCCAGAC-ATGGTCTTACATGAATCTCATATCG
*
38509016 ATGCCAATGTCCCAGACATGGTCTTACACGAATCTCATATCG
1 ATGCCAATG-CCCAGACATGGTCTTACATGAATCTCATATCG
*
38509058 ATGCCAATGTCCCAGACATGGTCTTACATGAATCAT-ATAACG
1 ATGCCAATG-CCCAGACATGGTCTTACATGAATC-TCATATCG
38509100 AT-CACAATGTCCCAGACATGGTCTTACA
1 ATGC-CAATG-CCCAGACATGGTCTTACA
38509128 CGTAATCACA
Statistics
Matches: 136, Mismatches: 8, Indels: 18
0.84 0.05 0.11
Matches are distributed among these distances:
40 2 0.01
41 19 0.14
42 113 0.83
43 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (41 bp):
ATGCCAATGCCCAGACATGGTCTTACATGAATCTCATATCG
Found at i:38509040 original size:84 final size:83
Alignment explanation
Indices: 38508933--38509134 Score: 227
Period size: 84 Copynumber: 2.4 Consensus size: 83
38508923 AACTCACACA
* * * *
38508933 ATGCC-ATATCCCAGATATGGTCTTACATGCTATCAT-ATATCGATGCCAATAG-CCAG-CTATG
1 ATGCCAATGTCCCAGACATGGTCTTACACG-AATC-TCATATCGATGCCAAT-GCCCAGAC-ATG
**
38508994 GTCTTACAAGAATC-TCATATTG
62 GTCTTACAAGAATCAT-ATAACG
38509016 ATGCCAATGTCCCAGACATGGTCTTACACGAATCTCATATCGATGCCAATGTCCCAGACATGGTC
1 ATGCCAATGTCCCAGACATGGTCTTACACGAATCTCATATCGATGCCAATG-CCCAGACATGGTC
*
38509081 TTACATGAATCATATAACG
65 TTACAAGAATCATATAACG
38509100 AT-CACAATGTCCCAGACATGGTCTTACACGTAATC
1 ATGC-CAATGTCCCAGACATGGTCTTACACG-AATC
38509135 ACATCTCAGT
Statistics
Matches: 104, Mismatches: 7, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
82 2 0.02
83 23 0.22
84 73 0.70
85 6 0.06
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (83 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGAATCTCATATCGATGCCAATGCCCAGACATGGTCT
TACAAGAATCATATAACG
Found at i:38533152 original size:17 final size:18
Alignment explanation
Indices: 38533120--38533155 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
38533110 TACTTTAATC
*
38533120 TCTTTTTCAATTTTCTTT
1 TCTTTTTCAATATTCTTT
38533138 TCTTTTTCAA-ATTCTTT
1 TCTTTTTCAATATTCTTT
38533155 T
1 T
38533156 TCACTCTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (18 bp):
TCTTTTTCAATATTCTTT
Found at i:38533237 original size:22 final size:22
Alignment explanation
Indices: 38533199--38533243 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
38533189 TCTTTCGCTT
*
38533199 TTTCAATTTCTTGTTTTTTTTC
1 TTTCAATTTCTTGTTTTGTTTC
*
38533221 TTTC-ATTTCTTTTTTTTGTTTC
1 TTTCAATTTC-TTGTTTTGTTTC
38533243 T
1 T
38533244 AGATTTCATT
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:0.07, C:0.13, G:0.04, T:0.76
Consensus pattern (22 bp):
TTTCAATTTCTTGTTTTGTTTC
Found at i:38534299 original size:12 final size:12
Alignment explanation
Indices: 38534279--38534329 Score: 61
Period size: 13 Copynumber: 4.2 Consensus size: 12
38534269 TACACCACAA
38534279 AAATTTTTTTTC
1 AAATTTTTTTTC
38534291 -AA-TTTTTTTC
1 AAATTTTTTTTC
*
38534301 GAATTTTTTTTC
1 AAATTTTTTTTC
38534313 AAAATTTTTTTTGC
1 -AAATTTTTTTT-C
38534327 AAA
1 AAA
38534330 CTTACTCCGG
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
10 8 0.24
11 4 0.12
12 8 0.24
13 13 0.38
14 1 0.03
ACGTcount: A:0.27, C:0.08, G:0.04, T:0.61
Consensus pattern (12 bp):
AAATTTTTTTTC
Found at i:38534308 original size:22 final size:23
Alignment explanation
Indices: 38534280--38534323 Score: 72
Period size: 22 Copynumber: 1.9 Consensus size: 23
38534270 ACACCACAAA
38534280 AATTTTTTTTC-AATTTTTTTCG
1 AATTTTTTTTCAAATTTTTTTCG
38534302 AATTTTTTTTCAAAATTTTTTT
1 AATTTTTTTTC-AAATTTTTTT
38534324 TGCAAACTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 11 0.55
24 9 0.45
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.68
Consensus pattern (23 bp):
AATTTTTTTTCAAATTTTTTTCG
Found at i:38538568 original size:23 final size:23
Alignment explanation
Indices: 38538534--38538592 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
38538524 CTACCATGCT
* *
38538534 ATAAAAGTAGACATAATTGTGCT
1 ATAAAAGCAGACATAATTGTGCC
38538557 ATAGAAA-CAGACATAATTGTGCC
1 ATA-AAAGCAGACATAATTGTGCC
38538580 ATAAAAGCAGACA
1 ATAAAAGCAGACA
38538593 AAACCATTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 3 0.09
23 26 0.81
24 3 0.09
ACGTcount: A:0.47, C:0.14, G:0.17, T:0.22
Consensus pattern (23 bp):
ATAAAAGCAGACATAATTGTGCC
Found at i:38542949 original size:11 final size:12
Alignment explanation
Indices: 38542929--38542968 Score: 55
Period size: 11 Copynumber: 3.3 Consensus size: 12
38542919 TAAATGGTTC
38542929 ATTTATATATTT
1 ATTTATATATTT
*
38542941 -TTTAAATATTT
1 ATTTATATATTT
38542952 ATTTATATATTAT
1 ATTTATATATT-T
38542965 ATTT
1 ATTT
38542969 TTAGCTCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 10 0.42
12 9 0.38
13 5 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATTTATATATTT
Found at i:38554006 original size:20 final size:20
Alignment explanation
Indices: 38553968--38554007 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
38553958 AATATTTTCT
* *
38553968 AGTAAATTATTTTATAGAAA
1 AGTAAAATATTTTACAGAAA
*
38553988 AGTAAAATATTTTCCAGAAA
1 AGTAAAATATTTTACAGAAA
38554008 TTATTTTACG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (20 bp):
AGTAAAATATTTTACAGAAA
Found at i:38554022 original size:34 final size:35
Alignment explanation
Indices: 38553956--38554022 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
38553946 CAAACAGCAG
* *
38553956 AAAATATTTTCTAGTAAATTATTTTATAGAAAAGT
1 AAAATATTTTCCAGTAAATTATTTTACAGAAAAGT
*
38553991 AAAATATTTTCCAG-AAATTATTTTACGGAAAA
1 AAAATATTTTCCAGTAAATTATTTTACAGAAAA
38554023 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.39
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATTATTTTACAGAAAAGT
Found at i:38555053 original size:17 final size:17
Alignment explanation
Indices: 38555031--38555063 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
38555021 AAACACTGTT
*
38555031 GACAAGTATGTAGACCC
1 GACAAGTATGCAGACCC
38555048 GACAAGTATGCAGACC
1 GACAAGTATGCAGACC
38555064 AAGCTGTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.15
Consensus pattern (17 bp):
GACAAGTATGCAGACCC
Found at i:38556706 original size:13 final size:13
Alignment explanation
Indices: 38556690--38556714 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38556680 AAATATATTT
38556690 TAAAAATAAAAAA
1 TAAAAATAAAAAA
38556703 TAAAAATAAAAA
1 TAAAAATAAAAA
38556715 TATTTTTAAA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:38558152 original size:34 final size:36
Alignment explanation
Indices: 38558082--38558156 Score: 118
Period size: 37 Copynumber: 2.1 Consensus size: 36
38558072 TTATTACCAA
*
38558082 TTTAAGGTTTAGTTAGTATTTTTATCAAAAAAAAAGG
1 TTTAAGGTTTAGTCAGTATTTTTAT-AAAAAAAAAGG
38558119 TTTAAGGTTTAGTCAGTA-TTTTAT-AAAAAAAAGG
1 TTTAAGGTTTAGTCAGTATTTTTATAAAAAAAAAGG
38558153 TTTA
1 TTTA
38558157 GGCAGTAGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
34 14 0.38
36 6 0.16
37 17 0.46
ACGTcount: A:0.40, C:0.03, G:0.16, T:0.41
Consensus pattern (36 bp):
TTTAAGGTTTAGTCAGTATTTTTATAAAAAAAAAGG
Found at i:38558169 original size:3 final size:3
Alignment explanation
Indices: 38558163--38558201 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
38558153 TTTAGGCAGT
*
38558163 AGA AGA AGAA AGA AAA AGA AG- AGA AGA AGA AGA AGA AGA
1 AGA AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
38558202 GAAAAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:38558198 original size:17 final size:18
Alignment explanation
Indices: 38558166--38558204 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
38558156 AGGCAGTAGA
38558166 AGAAGAAAGAAAAAGAAG
1 AGAAGAAAGAAAAAGAAG
*
38558184 AGAAG-AAGAAGAAGAAG
1 AGAAGAAAGAAAAAGAAG
38558201 AGAA
1 AGAA
38558205 AAAAATAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (18 bp):
AGAAGAAAGAAAAAGAAG
Found at i:38558946 original size:26 final size:26
Alignment explanation
Indices: 38558910--38558961 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
38558900 CAAATTGTAG
38558910 ATGAAAAATACCAATTGGTTTCTAAC
1 ATGAAAAATACCAATTGGTTTCTAAC
38558936 ATGAAAAATACCAATTGGTTTCTAAC
1 ATGAAAAATACCAATTGGTTTCTAAC
38558962 CCTTAACCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (26 bp):
ATGAAAAATACCAATTGGTTTCTAAC
Found at i:38559960 original size:27 final size:26
Alignment explanation
Indices: 38559901--38559960 Score: 61
Period size: 27 Copynumber: 2.2 Consensus size: 26
38559891 ATTTAAAAAA
*
38559901 ATAAAAAATCATAAAATTTATTAAAT
1 ATAAAAAATCATAAAATTGATTAAAT
38559927 ATGAAAAAAT-A-AAAATTGATATAAACTT
1 AT-AAAAAATCATAAAATTGAT-TAAA--T
38559955 ATAAAA
1 ATAAAA
38559961 TTTATAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
25 8 0.28
26 7 0.24
27 11 0.38
28 3 0.10
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.30
Consensus pattern (26 bp):
ATAAAAAATCATAAAATTGATTAAAT
Found at i:38559991 original size:17 final size:17
Alignment explanation
Indices: 38559904--38559993 Score: 53
Period size: 17 Copynumber: 5.1 Consensus size: 17
38559894 TAAAAAAATA
38559904 AAAAATCATAAAATTTAT
1 AAAAAT-ATAAAATTTAT
* *
38559922 -TAAATATGAAAA--AAT
1 AAAAATAT-AAAATTTAT
*
38559937 AAAAATTGATATAAACTTAT
1 AAAAA-T-ATA-AAATTTAT
*
38559957 -AAAATTTATAAATATTAT
1 AAAAATATA-AAAT-TTAT
38559975 AAAAATATAAAATTTAT
1 AAAAATATAAAATTTAT
38559992 AA
1 AA
38559994 TGAATTATAA
Statistics
Matches: 56, Mismatches: 7, Indels: 19
0.68 0.09 0.23
Matches are distributed among these distances:
15 2 0.04
16 5 0.09
17 22 0.39
18 14 0.25
19 11 0.20
20 2 0.04
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (17 bp):
AAAAATATAAAATTTAT
Found at i:38560002 original size:45 final size:44
Alignment explanation
Indices: 38559911--38560006 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 44
38559901 ATAAAAAATC
38559911 ATAAAATTTATTAAATATGAAAAAATAAAAATTGATATAAACTT
1 ATAAAATTTATTAAATATGAAAAAATAAAAATTGATATAAACTT
* * *
38559955 ATAAAATTTA-TAAATATTATAAAAATATAAAATTTATAATGAA-TT
1 ATAAAATTTATTAAATATGA-AAAAATA-AAAATTGAT-ATAAACTT
38560000 ATAAAAT
1 ATAAAAT
38560007 CAATAAAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
43 8 0.17
44 17 0.37
45 17 0.37
46 4 0.09
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.36
Consensus pattern (44 bp):
ATAAAATTTATTAAATATGAAAAAATAAAAATTGATATAAACTT
Found at i:38560013 original size:45 final size:43
Alignment explanation
Indices: 38559922--38560013 Score: 105
Period size: 45 Copynumber: 2.1 Consensus size: 43
38559912 TAAAATTTAT
**
38559922 TAAATATGAAAAAATAAAAATTGATATAAACTTATAAAATTTA
1 TAAATATGAAAAAATAAAAATTGATATAAACTTATAAAATCAA
* * *
38559965 TAAATATTATAAAAATATAAAATTTATAATGAA-TTATAAAATCAA
1 TAAATATGA-AAAAATA-AAAATTGAT-ATAAACTTATAAAATCAA
38560010 TAAA
1 TAAA
38560014 AAATATTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
43 8 0.20
44 7 0.17
45 22 0.54
46 4 0.10
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (43 bp):
TAAATATGAAAAAATAAAAATTGATATAAACTTATAAAATCAA
Found at i:38560598 original size:8 final size:9
Alignment explanation
Indices: 38560549--38560793 Score: 79
Period size: 10 Copynumber: 25.8 Consensus size: 9
38560539 TTTATGATTT
38560549 TTTTTATAA
1 TTTTTATAA
38560558 TTTTTATAA
1 TTTTTATAA
*
38560567 GTTTATATCAA
1 -TTTTTAT-AA
*
38560578 TTTTAAT-A
1 TTTTTATAA
38560586 TTTTTAT-A
1 TTTTTATAA
*
38560594 TTTTTTTACCA
1 TTTTTATA--A
*
38560605 TTTTTATTAT
1 TTTTTA-TAA
*
38560615 TTTTTAAGAA
1 TTTTT-ATAA
* * *
38560625 TTCTAATACG
1 TTTTTATA-A
*
38560635 TTTTTTTAA
1 TTTTTATAA
*
38560644 TATTTAAAATAA
1 T-TTT--TATAA
*
38560656 GTTTTATTAA
1 TTTTTA-TAA
**
38560666 TTTCATTATTT
1 TTT--TTATAA
38560677 TTTTTATAA
1 TTTTTATAA
*
38560686 TTTATTAGAA
1 TTT-TTATAA
*
38560696 CTTATTT-GAA
1 -TT-TTTATAA
38560706 TTTTTAT-A
1 TTTTTATAA
*
38560714 TTTTTATTA
1 TTTTTATAA
*
38560723 TATTTATAA
1 TTTTTATAA
38560732 TATTTTAT-A
1 T-TTTTATAA
38560741 TTTTTATAA
1 TTTTTATAA
*
38560750 TATTTTATCA
1 T-TTTTATAA
*
38560760 TTTTAATAA
1 TTTTTATAA
* *
38560769 GGTTATATAA
1 -TTTTTATAA
*
38560779 TTTTAAT-A
1 TTTTTATAA
38560787 TTTTTAT
1 TTTTTAT
38560794 TTTTATTTTT
Statistics
Matches: 172, Mismatches: 41, Indels: 47
0.66 0.16 0.18
Matches are distributed among these distances:
8 38 0.22
9 45 0.26
10 60 0.35
11 20 0.12
12 9 0.05
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:38560600 original size:19 final size:20
Alignment explanation
Indices: 38560578--38560619 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
38560568 TTTATATCAA
*
38560578 TTTTAATATTTTTA-TATTT
1 TTTTAACATTTTTATTATTT
*
38560597 TTTTACCATTTTTATTATTT
1 TTTTAACATTTTTATTATTT
38560617 TTT
1 TTT
38560620 AAGAATTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTAACATTTTTATTATTT
Found at i:38560741 original size:16 final size:16
Alignment explanation
Indices: 38560720--38560767 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 16
38560710 TATATTTTTA
38560720 TTATATTTATAATATT
1 TTATATTTATAATATT
38560736 TTATATTTTTATAATATT
1 TTATA--TTTATAATATT
38560754 TTATCATTT-TAATA
1 TTAT-ATTTATAATA
38560768 AGGTTATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 10 0.34
17 3 0.10
18 15 0.52
19 1 0.03
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (16 bp):
TTATATTTATAATATT
Found at i:38560742 original size:27 final size:26
Alignment explanation
Indices: 38560698--38560800 Score: 97
Period size: 27 Copynumber: 4.0 Consensus size: 26
38560688 TATTAGAACT
*
38560698 TATTTGAAT-TTTTATATTTTTATTA
1 TATTTTAATATTTTATATTTTTATTA
*
38560723 TATTTATAATATTTTATATTTTTATAA
1 TATTT-TAATATTTTATATTTTTATTA
***
38560750 TATTTT-ATCATTTTAATAAGGTTA-TA
1 TATTTTAAT-ATTTT-ATATTTTTATTA
38560776 TAATTTTAATATTTT-TATTTTTATT
1 T-ATTTTAATATTTTATATTTTTATT
38560801 TTTAATATTT
Statistics
Matches: 62, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
25 12 0.19
26 12 0.19
27 36 0.58
28 2 0.03
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (26 bp):
TATTTTAATATTTTATATTTTTATTA
Found at i:38560793 original size:19 final size:19
Alignment explanation
Indices: 38560704--38560793 Score: 57
Period size: 19 Copynumber: 4.9 Consensus size: 19
38560694 AACTTATTTG
*
38560704 AATTTTTATATTTTTAT-T
1 AATTTTAATATTTTTATAT
38560722 ATATTTATAATA-TTTTATAT
1 A-ATTT-TAATATTTTTATAT
*
38560742 --TTTT-ATAATATTT-TAT
1 AATTTTAAT-ATTTTTATAT
* ***
38560758 CATTTTAATAAGGTTATAT
1 AATTTTAATATTTTTATAT
38560777 AATTTTAATATTTTTAT
1 AATTTTAATATTTTTAT
38560794 TTTTATTTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 17
0.68 0.11 0.21
Matches are distributed among these distances:
15 2 0.04
16 5 0.09
17 6 0.11
18 8 0.15
19 28 0.52
20 5 0.09
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.62
Consensus pattern (19 bp):
AATTTTAATATTTTTATAT
Found at i:38560823 original size:21 final size:21
Alignment explanation
Indices: 38560779--38560824 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
38560769 GGTTATATAA
*
38560779 TTTTAATATTTTTATTTTTAT
1 TTTTAATATTTTAATTTTTAT
38560800 TTTTAATA-TTTAATTTATT-T
1 TTTTAATATTTTAATTT-TTAT
38560820 TTTTA
1 TTTTA
38560825 TTTTTTTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTAATATTTTAATTTTTAT
Found at i:38562049 original size:19 final size:19
Alignment explanation
Indices: 38562025--38562064 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
38562015 TGAATGAAGT
38562025 TATGCTAAAATTGACTGAG
1 TATGCTAAAATTGACTGAG
*
38562044 TATGCTAAAATTGATTGAG
1 TATGCTAAAATTGACTGAG
38562063 TA
1 TA
38562065 CATGAATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (19 bp):
TATGCTAAAATTGACTGAG
Found at i:38562398 original size:27 final size:27
Alignment explanation
Indices: 38562360--38562417 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
38562350 TTCCATGACA
* * **
38562360 TACTTTGAATGGATCGCCTTTGTGGCG
1 TACTCTGAATGGATCACCTTAATGGCG
*
38562387 TACTCTGAATGGTTCACCTTAATGGCG
1 TACTCTGAATGGATCACCTTAATGGCG
38562414 TACT
1 TACT
38562418 TTGTATGATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (27 bp):
TACTCTGAATGGATCACCTTAATGGCG
Found at i:38573210 original size:12 final size:12
Alignment explanation
Indices: 38573193--38573217 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38573183 GGTGTTCATT
38573193 CGGTTAACCGAC
1 CGGTTAACCGAC
38573205 CGGTTAACCGAC
1 CGGTTAACCGAC
38573217 C
1 C
38573218 TAAAATAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:38573373 original size:9 final size:9
Alignment explanation
Indices: 38573351--38573435 Score: 98
Period size: 9 Copynumber: 9.4 Consensus size: 9
38573341 TTTGGTTAAA
*
38573351 AATTAACCG
1 AATTACCCG
* *
38573360 CATTACCTG
1 AATTACCCG
*
38573369 AATTACCCA
1 AATTACCCG
*
38573378 AATTACTCG
1 AATTACCCG
38573387 AATTACCCG
1 AATTACCCG
*
38573396 AATTAACCG
1 AATTACCCG
*
38573405 AATTACTCG
1 AATTACCCG
38573414 AATTACCCG
1 AATTACCCG
*
38573423 AATTAACCG
1 AATTACCCG
38573432 AATT
1 AATT
38573436 GAATCACTAC
Statistics
Matches: 62, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 62 1.00
ACGTcount: A:0.38, C:0.26, G:0.09, T:0.27
Consensus pattern (9 bp):
AATTACCCG
Found at i:38573391 original size:27 final size:27
Alignment explanation
Indices: 38573361--38573435 Score: 114
Period size: 27 Copynumber: 2.8 Consensus size: 27
38573351 AATTAACCGC
* *
38573361 ATTACCTGAATTACCCAAATTACTCGA
1 ATTACCCGAATTAACCAAATTACTCGA
*
38573388 ATTACCCGAATTAACCGAATTACTCGA
1 ATTACCCGAATTAACCAAATTACTCGA
*
38573415 ATTACCCGAATTAACCGAATT
1 ATTACCCGAATTAACCAAATT
38573436 GAATCACTAC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.37, C:0.25, G:0.09, T:0.28
Consensus pattern (27 bp):
ATTACCCGAATTAACCAAATTACTCGA
Found at i:38573478 original size:6 final size:6
Alignment explanation
Indices: 38573467--38573495 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
38573457 ATTTTTAGAC
38573467 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
1 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
38573496 AATTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (6 bp):
TTTAGT
Found at i:38575039 original size:31 final size:29
Alignment explanation
Indices: 38574972--38575041 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 29
38574962 ACCTCAGATT
*
38574972 ACATTTTAGTCACTTATATTTGAAATGTT
1 ACATTTTAGTCACTTATATTTGAAATGTA
* *
38575001 ACATTTTAGTCACTT-TCATTATCGTATTGTA
1 ACATTTTAGTCACTTAT-ATT-T-GAAATGTA
38575032 ACATTTTAGT
1 ACATTTTAGT
38575042 TACTGAGCCG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 1 0.03
29 18 0.51
30 1 0.03
31 15 0.43
ACGTcount: A:0.29, C:0.13, G:0.10, T:0.49
Consensus pattern (29 bp):
ACATTTTAGTCACTTATATTTGAAATGTA
Found at i:38575273 original size:203 final size:204
Alignment explanation
Indices: 38575034--38575446 Score: 774
Period size: 203 Copynumber: 2.0 Consensus size: 204
38575024 GTATTGTAAC
*
38575034 ATTTTAGTTACTGAGCCGTTAATTGCCGTTAACAGTATAACAGTAAGCTGACGTGGCATGTTAAA
1 ATTTTAGTCACTGAGCCGTTAATTGCCGTTAACAGTATAACAGTAAGCTGACGTGGCATGTTAAA
38575099 TCATCATTTTAAATGAAAATTTTAGATTAAATTATACAATTGATCCCTATATTTTTTTCGTTTTG
66 TCATCATTTTAAATGAAAATTTTAGATTAAATTATACAATTGATCCCTATATTTTTTTCGTTTTG
*
38575164 AGCAATTTAATTTTTTCTTTTATGTTTTTCAAC-TTTTTTTTCTTATTTTCCATTCTCTTTTGTT
131 AGCAATTTAATTTTTTCTTTTATGTTTTTCAACTTTTTTTTTCTTATTCTCCATTCTCTTTTGTT
38575228 TCTCCCTCT
196 TCTCCCTCT
*
38575237 ATTTTAGTCACTGAGCCGTTAATTGCCGTTAACAGTATAACGGTAAGCTGACGTGGCATGTTAAA
1 ATTTTAGTCACTGAGCCGTTAATTGCCGTTAACAGTATAACAGTAAGCTGACGTGGCATGTTAAA
38575302 TCATCATTTTAAATGAAAATTTTAGATTAAATTATACAATTGATCCCTATATTTTTTTCGTTTTG
66 TCATCATTTTAAATGAAAATTTTAGATTAAATTATACAATTGATCCCTATATTTTTTTCGTTTTG
*
38575367 AGCAATTTAATTTTTTCTTTTATGTTTTTTAACTTTTTTTTTTCTTATTCTCCATTCTCTTTTGT
131 AGCAATTTAATTTTTTCTTTTATGTTTTTCAAC-TTTTTTTTTCTTATTCTCCATTCTCTTTTGT
38575432 TTCTCCCTCT
195 TTCTCCCTCT
38575442 ATTTT
1 ATTTT
38575447 CCTCCCTTTT
Statistics
Matches: 204, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
203 160 0.78
205 44 0.22
ACGTcount: A:0.25, C:0.15, G:0.11, T:0.49
Consensus pattern (204 bp):
ATTTTAGTCACTGAGCCGTTAATTGCCGTTAACAGTATAACAGTAAGCTGACGTGGCATGTTAAA
TCATCATTTTAAATGAAAATTTTAGATTAAATTATACAATTGATCCCTATATTTTTTTCGTTTTG
AGCAATTTAATTTTTTCTTTTATGTTTTTCAACTTTTTTTTTCTTATTCTCCATTCTCTTTTGTT
TCTCCCTCT
Found at i:38581931 original size:20 final size:20
Alignment explanation
Indices: 38581894--38581932 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
38581884 AATGACTTGG
*
38581894 AAAATTTTAATTTCGAGACC
1 AAAATTTTAAATTCGAGACC
38581914 AAAATTTTTAAATT-GAGAC
1 AAAA-TTTTAAATTCGAGAC
38581933 GTTTCGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (20 bp):
AAAATTTTAAATTCGAGACC
Found at i:38585475 original size:39 final size:40
Alignment explanation
Indices: 38585354--38585538 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 40
38585344 GCTACTCGTT
*
38585354 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* * *
38585394 CAATTGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
38585434 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
38585473 CAAATGCCTTC-GGATCTTAGTCTGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
38585514 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
38585539 CATCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 10
0.81 0.13 0.07
Matches are distributed among these distances:
38 2 0.02
39 32 0.26
40 74 0.61
41 13 0.11
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:38590930 original size:27 final size:27
Alignment explanation
Indices: 38590891--38590955 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
38590881 ATATAGAGTA
*
38590891 CGCCACCAAGGCATTCCATTCAGAATT
1 CGCCACAAAGGCATTCCATTCAGAATT
* * *
38590918 TGCCACAAAGGCATTCCTTTCAGAGTT
1 CGCCACAAAGGCATTCCATTCAGAATT
*
38590945 CGCTACAAAGG
1 CGCCACAAAGG
38590956 TTATTCTTAC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.23
Consensus pattern (27 bp):
CGCCACAAAGGCATTCCATTCAGAATT
Found at i:38596413 original size:14 final size:14
Alignment explanation
Indices: 38596391--38596429 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
38596381 ATAACAGTGA
38596391 TAATAATAATAAAT
1 TAATAATAATAAAT
* *
38596405 TAATTATAATAGAT
1 TAATAATAATAAAT
38596419 TAATAATAATA
1 TAATAATAATA
38596430 TTACTGAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (14 bp):
TAATAATAATAAAT
Found at i:38609279 original size:36 final size:36
Alignment explanation
Indices: 38609230--38609298 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
38609220 TTCTTTCTTC
* *
38609230 TTGATTTTTCAGCTCCTGTCCAGCAGCCAAACATTT
1 TTGATTTTCCAGCTCCTGTCCAACAGCCAAACATTT
38609266 TTGATTTTCCAGCTCCTGTCCAACAGCCAAACA
1 TTGATTTTCCAGCTCCTGTCCAACAGCCAAACA
38609299 CTCAGTCATT
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:0.25, C:0.30, G:0.13, T:0.32
Consensus pattern (36 bp):
TTGATTTTCCAGCTCCTGTCCAACAGCCAAACATTT
Found at i:38619442 original size:11 final size:13
Alignment explanation
Indices: 38619426--38619457 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
38619416 ATTTCAATGA
38619426 AAAATTTCG-T-G
1 AAAATTTCGTTCG
38619437 AAAATTTCGTTCG
1 AAAATTTCGTTCG
38619450 AAAATTTC
1 AAAATTTC
38619458 AACGTTTGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 9 0.47
12 1 0.05
13 9 0.47
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (13 bp):
AAAATTTCGTTCG
Found at i:38620822 original size:50 final size:50
Alignment explanation
Indices: 38620654--38621041 Score: 458
Period size: 51 Copynumber: 7.7 Consensus size: 50
38620644 TATCGATGAA
* * ***
38620654 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGGT
* ** * *
38620705 CACATGTGTAGTACTAAACT-AAGGCTACTATGTGTACCG-AAAAGCTTTGGT
1 CACGTGTGTAGTACT-ATGTGAAGGCTACTACGTGAACCGTAAAA-C-TTGGT
* * *
38620756 CACGTGTGTAGTACTATGTGAAGGCTACTACATGAATCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGGT
* * ***
38620806 CACGTGTGTAATACTATGTGAAGGCTACTACGTGTACCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGGT
* * * *
38620857 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCG-AAAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAA-C-TTGGT
* *
38620908 CACGTGTGTAGTACTATGTGAAGGCTACTACATGAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGGT
* *
38620958 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACTGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGGT
38621008 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
38621042 TATCGAATGA
Statistics
Matches: 287, Mismatches: 41, Indels: 19
0.83 0.12 0.05
Matches are distributed among these distances:
49 6 0.02
50 127 0.44
51 145 0.51
52 9 0.03
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGGT
Found at i:38620890 original size:26 final size:26
Alignment explanation
Indices: 38620810--38620892 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
38620800 CTTGATCACG
* *
38620810 TGTGTAATACTATGTGAAGGCTACTA
1 TGTGTAGTACTAAGTGAAGGCTACTA
* * *
38620836 CGTGTACCG-A-TAAATGATGG-TCAC-A
1 TGTGTA--GTACTAAGTGAAGGCT-ACTA
38620861 TGTGTAGTACTAAGTGAAGGCTACTA
1 TGTGTAGTACTAAGTGAAGGCTACTA
38620887 TGTGTA
1 TGTGTA
38620893 CCGAAAAGCT
Statistics
Matches: 42, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
23 1 0.02
24 1 0.02
25 17 0.40
26 22 0.52
27 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.31
Consensus pattern (26 bp):
TGTGTAGTACTAAGTGAAGGCTACTA
Found at i:38620930 original size:152 final size:152
Alignment explanation
Indices: 38620654--38621048 Score: 632
Period size: 152 Copynumber: 2.6 Consensus size: 152
38620644 TATCGATGAA
* *
38620654 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATGATGGTCACATGTGTAGTAC
*
38620719 TAAACT-AAGGCTACTATGTGTACCGAAAAGCTTTGGTCACGTGTGTAGTACTATGTGAAGGCTA
66 T-AAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGTCACGTGTGTAGTACTATGTGAAGGCTA
*
38620783 CTACATGAATCGTAAAACTTGAT
130 CTACATGAACCGTAAAACTTGAT
* *
38620806 CACGTGTGTAATACTATGTGAAGGCTACTACGTGTACCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATGATGGTCACATGTGTAGTAC
38620871 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGTCACGTGTGTAGTACTATGTGAAGGCTAC
66 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGTCACGTGTGTAGTACTATGTGAAGGCTAC
38620936 TACATGAACCGTAAAACTTGAT
131 TACATGAACCGTAAAACTTGAT
* *** * *
38620958 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACTG-TAAAACTTGATCACGTGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATGATGGTCACATGTGTAGTAC
* * *
38621022 TATGTGAAGGCTACTACGTGTATCGAA
66 TAAGTGAAGGCTACTATGTGTACCGAA
38621049 TGATAAAAGT
Statistics
Matches: 225, Mismatches: 17, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
151 47 0.21
152 178 0.79
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (152 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATGATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGTCACGTGTGTAGTACTATGTGAAGGCTAC
TACATGAACCGTAAAACTTGAT
Found at i:38626206 original size:55 final size:55
Alignment explanation
Indices: 38626122--38626236 Score: 203
Period size: 55 Copynumber: 2.1 Consensus size: 55
38626112 AATTATCTAC
* *
38626122 AAATATGATTGTGTGTATTGTGATGTATGCATGAATATGTATGTATTGACTTTGT
1 AAATATGATTGTGTGTATTGTGATGTATGCATGAATATATATGTATTGACTCTGT
*
38626177 AAATATGATTGTGTGTATTGTGATGTATGCTTGAATATATATGTATTGACTCTGT
1 AAATATGATTGTGTGTATTGTGATGTATGCATGAATATATATGTATTGACTCTGT
38626232 AAATA
1 AAATA
38626237 AACTATTGAT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.30, C:0.04, G:0.22, T:0.44
Consensus pattern (55 bp):
AAATATGATTGTGTGTATTGTGATGTATGCATGAATATATATGTATTGACTCTGT
Found at i:38627680 original size:50 final size:50
Alignment explanation
Indices: 38627622--38627758 Score: 166
Period size: 50 Copynumber: 2.7 Consensus size: 50
38627612 TATTGAGGTT
* * *
38627622 ATGAGAGGTCCCACGTAAGACCATATCTATGACATGGAATTGGCACCGAG
1 ATGAGAGGTCCCACGTAAGACCATGTCTGTGACATGGAATGGGCACCGAG
* * * * * *
38627672 ATGAGAGGTCCCCCATAAGACCATGTCTGGGACATAGCATGGGCACCGAT
1 ATGAGAGGTCCCACGTAAGACCATGTCTGTGACATGGAATGGGCACCGAG
** *
38627722 ATGAGAACTCCCATGTAAGACCATGTCTGTGACATGG
1 ATGAGAGGTCCCACGTAAGACCATGTCTGTGACATGG
38627759 CTTTGGCATG
Statistics
Matches: 71, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 71 1.00
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.20
Consensus pattern (50 bp):
ATGAGAGGTCCCACGTAAGACCATGTCTGTGACATGGAATGGGCACCGAG
Found at i:38627992 original size:20 final size:20
Alignment explanation
Indices: 38627967--38628016 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
38627957 ATGAGTTATT
38627967 TAAGTAAGCAAGTAAGTAAA
1 TAAGTAAGCAAGTAAGTAAA
38627987 TAAGTAAG-AGAGTAAGTAAA
1 TAAGTAAGCA-AGTAAGTAAA
*
38628007 AAAG-AAGCAA
1 TAAGTAAGCAA
38628017 ATACCGTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 5 0.19
20 22 0.81
ACGTcount: A:0.58, C:0.04, G:0.22, T:0.16
Consensus pattern (20 bp):
TAAGTAAGCAAGTAAGTAAA
Found at i:38630827 original size:36 final size:36
Alignment explanation
Indices: 38630782--38630852 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
38630772 GTAAAGCACC
38630782 TCAGTCAGAATAGATCCGAAAGGCTGCTAAACTGAG
1 TCAGTCAGAATAGATCCGAAAGGCTGCTAAACTGAG
* *
38630818 TCAGTCAGAATAGATCCGAAAGGCTGTTGAACTGA
1 TCAGTCAGAATAGATCCGAAAGGCTGCTAAACTGA
38630853 ATAGAGTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.21
Consensus pattern (36 bp):
TCAGTCAGAATAGATCCGAAAGGCTGCTAAACTGAG
Found at i:38635951 original size:20 final size:20
Alignment explanation
Indices: 38635926--38635967 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
38635916 TATGTCGAGG
* *
38635926 TTGGAGCTGAATGAGGTGAC
1 TTGGAGCTAAATGAGGTAAC
38635946 TTGGAGCTAAATGAGGTAAC
1 TTGGAGCTAAATGAGGTAAC
38635966 TT
1 TT
38635968 CTTCACTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.10, G:0.33, T:0.29
Consensus pattern (20 bp):
TTGGAGCTAAATGAGGTAAC
Found at i:38638677 original size:25 final size:25
Alignment explanation
Indices: 38638649--38638696 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
38638639 TTTAAAGGGG
*
38638649 GTAAGGCATTTCGCATGAATTTTTA
1 GTAAGGCATTTCGCATAAATTTTTA
38638674 GTAAGGCATTTCGCATAAATTTT
1 GTAAGGCATTTCGCATAAATTTT
38638697 AAAGTATGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (25 bp):
GTAAGGCATTTCGCATAAATTTTTA
Found at i:38642425 original size:7 final size:6
Alignment explanation
Indices: 38642409--38642450 Score: 57
Period size: 6 Copynumber: 6.7 Consensus size: 6
38642399 TCACATATTT
*
38642409 AAAAAG AAAAAG AAAAAG AAAAAG AATAAAG AGCAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AA-AAAG A-AAAAG AAAA
38642451 GTTTAATCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 22 0.69
7 10 0.31
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:38650152 original size:51 final size:50
Alignment explanation
Indices: 38650021--38650208 Score: 189
Period size: 51 Copynumber: 3.7 Consensus size: 50
38650011 TATCATTCGA
* * * * * *
38650021 TACACGTATTAGACTTCACATAGTACTACACACGTGATCAAACTTTCTGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAACCTTCCGG
* * * *
38650071 TTCATGTAGTAGGCTACACATAGTACTACACACGTGACCAAAGCCTTCCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAA-CCTTCCGG
* * * * *
38650122 TACACATAGTAGCCTGCACATAGTACTACACATGTGACCATTATC-TCTCGA
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA-AACCTTC-CGG
* *
38650173 TACACGTAGTAGCCTGCACTTAGTATTACACACGTG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTG
38650209 GTTATAGGCA
Statistics
Matches: 114, Mismatches: 21, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
50 38 0.33
51 75 0.66
52 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (50 bp):
TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAACCTTCCGG
Found at i:38664316 original size:19 final size:19
Alignment explanation
Indices: 38664247--38664373 Score: 94
Period size: 19 Copynumber: 6.7 Consensus size: 19
38664237 ACATACTAGA
* *
38664247 ACATAAAGTGCATGCTAGC
1 ACATAAAGTGCATACTGGC
* *
38664266 ACA-AATAGTGCACACGGGC
1 ACATAA-AGTGCATACTGGC
* *
38664285 ACAGAATGTGCATACTGGC
1 ACATAAAGTGCATACTGGC
* *
38664304 ACATAAAGTGCATATTGAC
1 ACATAAAGTGCATACTGGC
* ** *
38664323 ACACATTGTGTATACTGGC
1 ACATAAAGTGCATACTGGC
* *
38664342 ACATATAGTGCATATTGGC
1 ACATAAAGTGCATACTGGC
* *
38664361 ACACATAGTGCAT
1 ACATAAAGTGCAT
38664374 CATCGGATAA
Statistics
Matches: 84, Mismatches: 22, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
18 2 0.02
19 80 0.95
20 2 0.02
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (19 bp):
ACATAAAGTGCATACTGGC
Found at i:38664338 original size:38 final size:38
Alignment explanation
Indices: 38664291--38664373 Score: 130
Period size: 38 Copynumber: 2.2 Consensus size: 38
38664281 GGGCACAGAA
38664291 TGTGCATACTGGCACATAAAGTGCATATTGACACACAT
1 TGTGCATACTGGCACATAAAGTGCATATTGACACACAT
* * *
38664329 TGTGTATACTGGCACATATAGTGCATATTGGCACACAT
1 TGTGCATACTGGCACATAAAGTGCATATTGACACACAT
*
38664367 AGTGCAT
1 TGTGCAT
38664374 CATCGGATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.29
Consensus pattern (38 bp):
TGTGCATACTGGCACATAAAGTGCATATTGACACACAT
Found at i:38686210 original size:20 final size:20
Alignment explanation
Indices: 38686185--38686250 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 20
38686175 ATCAGGAAGC
*
38686185 TTTGGTAACTTGTCTGCAAT
1 TTTGGTAACTTGTCTACAAT
**
38686205 TTTGGTGGCTTGTCTACAAT
1 TTTGGTAACTTGTCTACAAT
** * *
38686225 ACTGGCAATTTGTCTACAAT
1 TTTGGTAACTTGTCTACAAT
*
38686245 TCTGGT
1 TTTGGT
38686251 GGCTTGTTGA
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.42
Consensus pattern (20 bp):
TTTGGTAACTTGTCTACAAT
Found at i:38686257 original size:20 final size:20
Alignment explanation
Indices: 38686193--38686257 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
38686183 GCTTTGGTAA
* *
38686193 CTTGTCTGCAATTTTGGTGG
1 CTTGTCTACAATTCTGGTGG
* ***
38686213 CTTGTCTACAATACTGGCAA
1 CTTGTCTACAATTCTGGTGG
*
38686233 TTTGTCTACAATTCTGGTGG
1 CTTGTCTACAATTCTGGTGG
38686253 CTTGT
1 CTTGT
38686258 TGATCTACCA
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.17, C:0.18, G:0.23, T:0.42
Consensus pattern (20 bp):
CTTGTCTACAATTCTGGTGG
Found at i:38690441 original size:27 final size:26
Alignment explanation
Indices: 38690397--38690533 Score: 123
Period size: 27 Copynumber: 5.1 Consensus size: 26
38690387 AACACGTTAG
* * *
38690397 GAAAGAAACTCCTTTGTGATAAACTTT
1 GAAAGAAA-ACCTTTGTGGTGAACTTT
*
38690424 GAAAGAAAACCTTCTGTGGCGAACTTT
1 GAAAGAAAACCTT-TGTGGTGAACTTT
* *
38690451 GAAAGAAAGCCTTTGTGGTGAACTCT
1 GAAAGAAAACCTTTGTGGTGAACTTT
*
38690477 AAAAGAAAACCCTTT-TCGGTGAACTTT
1 GAAAGAAAA-CCTTTGT-GGTGAACTTT
* * * *
38690504 CAAAAAAAACCCTTTGTGGCGAACTCT
1 GAAAGAAAA-CCTTTGTGGTGAACTTT
38690531 GAA
1 GAA
38690534 TGGACTATCC
Statistics
Matches: 91, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
26 23 0.25
27 67 0.74
28 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (26 bp):
GAAAGAAAACCTTTGTGGTGAACTTT
Found at i:38698972 original size:264 final size:264
Alignment explanation
Indices: 38698502--38699039 Score: 1040
Period size: 264 Copynumber: 2.0 Consensus size: 264
38698492 CAGGTAGAAG
38698502 GTGTTAAAACTGCTTAAATTGATATTTTTATGTGTTTATGCAAAAAAACTCAGTTTTTAAATAAA
1 GTGTTAAAACTGCTTAAATTGATATTTTTATGTGTTTATGCAAAAAAACTCAGTTTTTAAATAAA
38698567 ATCTATCAACATCACACTTTTTCACTTCAATATTGAAAAACAAGTTTTTAATAAAATCCAAATTA
66 ATCTATCAACATCACACTTTTTCACTTCAATATTGAAAAACAAGTTTTTAATAAAATCCAAATTA
* *
38698632 GTTTTGAATAATGATTACATTTTTACAAATGAAATACTAAATCTATTAATTTCTAAAATTATCAT
131 ATTTTGAATAATGATTACATTTTTACAAATGAAATACTAAATCTATCAATTTCTAAAATTATCAT
38698697 GTTTTTGAGAAATTAAGATTAACATTCGATTTTACTTATTTTGAATAGATAAACCAATGTTTTTA
196 GTTTTTGAGAAATTAAGATTAACATTCGATTTTACTTATTTTGAATAGATAAACCAATGTTTTTA
38698762 AAAT
261 AAAT
38698766 GTGTTAAAACTGCTTAAATTGATATTTTTATGTGTTTATGCAAAAAAACTCAGTTTTTAAATAAA
1 GTGTTAAAACTGCTTAAATTGATATTTTTATGTGTTTATGCAAAAAAACTCAGTTTTTAAATAAA
*
38698831 ATCTGTCAACATCACACTTTTTCACTTCAATATTGAAAAACAAGTTTTTAATAAAATCCAAATTA
66 ATCTATCAACATCACACTTTTTCACTTCAATATTGAAAAACAAGTTTTTAATAAAATCCAAATTA
38698896 ATTTTGAATAATGATTACATTTTTACAAATGAAATACTAAATCTATCAATTTCTAAAATTATCAT
131 ATTTTGAATAATGATTACATTTTTACAAATGAAATACTAAATCTATCAATTTCTAAAATTATCAT
38698961 GTTTTTGAGAAATTAAGATTAACATTCGATTTTACTTATTTTGAATAGATAAACCAATGTTTTTA
196 GTTTTTGAGAAATTAAGATTAACATTCGATTTTACTTATTTTGAATAGATAAACCAATGTTTTTA
38699026 AAAT
261 AAAT
38699030 GTGTTCAAAA
1 GTGTT-AAAA
38699040 TTATGAAATT
Statistics
Matches: 270, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
264 266 0.99
265 4 0.01
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.41
Consensus pattern (264 bp):
GTGTTAAAACTGCTTAAATTGATATTTTTATGTGTTTATGCAAAAAAACTCAGTTTTTAAATAAA
ATCTATCAACATCACACTTTTTCACTTCAATATTGAAAAACAAGTTTTTAATAAAATCCAAATTA
ATTTTGAATAATGATTACATTTTTACAAATGAAATACTAAATCTATCAATTTCTAAAATTATCAT
GTTTTTGAGAAATTAAGATTAACATTCGATTTTACTTATTTTGAATAGATAAACCAATGTTTTTA
AAAT
Found at i:38700334 original size:29 final size:29
Alignment explanation
Indices: 38700292--38700384 Score: 125
Period size: 29 Copynumber: 3.2 Consensus size: 29
38700282 ATGGAGGAGT
38700292 TCAAGTATCCACCAAGTAAATTTCGCAAG
1 TCAAGTATCCACCAAGTAAATTTCGCAAG
38700321 TCAAGTATCCACCAAGTAAAGTTT-GCAAG
1 TCAAGTATCCACCAAGTAAA-TTTCGCAAG
** * * *
38700350 TCAAGTATCTGCCAAGTAAAGTTCCCAAA
1 TCAAGTATCCACCAAGTAAATTTCGCAAG
38700379 TCAAGT
1 TCAAGT
38700385 GTTCGCCAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
28 2 0.04
29 52 0.91
30 3 0.05
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (29 bp):
TCAAGTATCCACCAAGTAAATTTCGCAAG
Found at i:38700342 original size:16 final size:16
Alignment explanation
Indices: 38700294--38700342 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
38700284 GGAGGAGTTC
38700294 AAGTATCCACCAAGTA
1 AAGTATCCACCAAGTA
* * *
38700310 AA-T-TTC-GCAAGTC
1 AAGTATCCACCAAGTA
38700323 AAGTATCCACCAAGTA
1 AAGTATCCACCAAGTA
38700339 AAGT
1 AAGT
38700343 TTGCAAGTCA
Statistics
Matches: 24, Mismatches: 6, Indels: 6
0.67 0.17 0.17
Matches are distributed among these distances:
13 7 0.29
14 3 0.12
15 3 0.12
16 11 0.46
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.22
Consensus pattern (16 bp):
AAGTATCCACCAAGTA
Found at i:38700371 original size:16 final size:16
Alignment explanation
Indices: 38700317--38700371 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
38700307 GTAAATTTCG
* **
38700317 CAAGTCAAGTATCCAC
1 CAAGTAAAGTATCTGC
38700333 CAAGTAAAGT-T-TG-
1 CAAGTAAAGTATCTGC
*
38700346 CAAGTCAAGTATCTGC
1 CAAGTAAAGTATCTGC
38700362 CAAGTAAAGT
1 CAAGTAAAGT
38700372 TCCCAAATCA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
13 9 0.29
14 1 0.03
15 3 0.10
16 18 0.58
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (16 bp):
CAAGTAAAGTATCTGC
Done.